Michael Snyder - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
 Molecular, Cellular and Developmental Biology Yale University, New Haven, CT 
Area:
genomics, proteomics
Website:
http://snyderlab.stanford.edu/

500 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Monte E, Furihata T, Wang G, Perea-Gil I, Wei E, Chaib H, Nair R, Guevara JV, Mares R, Cheng X, Zhuge Y, Black K, Serrano R, Dagan-Rosenfeld O, Maguire P, ... ... Snyder MP, et al. Personalized transcriptome signatures in a cardiomyopathy stem cell biobank. Biorxiv : the Preprint Server For Biology. PMID 38798547 DOI: 10.1101/2024.05.10.593618  0.741
2024 Zhang S, Shu H, Zhou J, Rubin-Sigler J, Yang X, Liu Y, Cooper-Knock J, Monte E, Zhu C, Tu S, Li H, Tong M, Ecker J, Ichida J, Shen Y, ... ... Snyder M, et al. Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases. Biorxiv : the Preprint Server For Biology. PMID 38798507 DOI: 10.1101/2024.05.14.594252  0.796
2024 Li Y, Tan M, Akkari-Henić A, Zhang L, Kip M, Sun S, Sepers JJ, Xu N, Ariyurek Y, Kloet SL, Davis RP, Mikkers H, Gruber JJ, Snyder MP, Li X, et al. Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs. Nature Biomedical Engineering. PMID 38778183 DOI: 10.1038/s41551-024-01204-8  0.81
2024 Shankar V, Wilhelmy J, Curtis EJ, Michael B, Cervantes L, Mallajosyula VA, Davis RW, Snyder M, Younis S, Robinson WH, Shankar S, Mischel PS, Bonilla H, Davis MM. Oxidative Stress is a shared characteristic of ME/CFS and Long COVID. Biorxiv : the Preprint Server For Biology. PMID 38746454 DOI: 10.1101/2024.05.04.592477  0.497
2024 Jahanbani F, Sing JC, Maynard RD, Jahanbani S, Dafoe J, Dafoe W, Jones N, Wallace KJ, Rastan A, Maecker HT, Röst HL, Snyder MP, Davis RW. Longitudinal cytokine and multi-modal health data of an extremely severe ME/CFS patient with HSD reveals insights into immunopathology, and disease severity. Frontiers in Immunology. 15: 1369295. PMID 38650940 DOI: 10.3389/fimmu.2024.1369295  0.502
2024 Zhang S, Moll T, Rubin-Sigler J, Tu S, Li S, Yuan E, Liu M, Butt A, Harvey C, Gornall S, Alhalthli E, Shaw A, Souza CDS, Ferraiuolo L, Hornstein E, ... ... Snyder MP, et al. Deep learning modeling of rare noncoding genetic variants in human motor neurons defines as a therapeutic target for ALS. Medrxiv : the Preprint Server For Health Sciences. PMID 38633814 DOI: 10.1101/2024.03.30.24305115  0.685
2024 Wei X, Tsai MS, Liang L, Jiang L, Hung CJ, Jelliffe-Pawlowski L, Rand L, Snyder M, Jiang C. Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process. Cell Reports. 43: 114078. PMID 38598334 DOI: 10.1016/j.celrep.2024.114078  0.35
2024 Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, ... ... Snyder MP, et al. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host & Microbe. PMID 38479397 DOI: 10.1016/j.chom.2024.02.012  0.781
2024 Nshanian M, Geller BS, Gruber JJ, Chleilat F, Camarillo JM, Kelleher NL, Zhao Y, Snyder MP. Short-chain fatty acids propionate and butyrate control growth and differentiation linked to cellular metabolism. Research Square. PMID 38410440 DOI: 10.21203/rs.3.rs-3935562/v1  0.664
2024 Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, ... ... Snyder MP, et al. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Biorxiv : the Preprint Server For Biology. PMID 38352363 DOI: 10.1101/2024.02.01.577565  0.781
2024 Harvey C, Weinreich M, Lee JAK, Shaw AC, Ferraiuolo L, Mortiboys H, Zhang S, Hop PJ, Zwamborn RAJ, van Eijk K, Julian TH, Moll T, Iacoangeli A, Al Khleifat A, Quinn JP, ... ... Snyder MP, et al. Rare and common genetic determinants of mitochondrial function determine severity but not risk of amyotrophic lateral sclerosis. Heliyon. 10: e24975. PMID 38317984 DOI: 10.1016/j.heliyon.2024.e24975  0.396
2024 Nshanian M, Geller BS, Gruber JJ, Chleilat F, Camarillo JM, Kelleher NL, Zhao Y, Snyder MP. Short-chain fatty acids propionate and butyrate control growth and differentiation linked to cellular metabolism. Biorxiv : the Preprint Server For Biology. PMID 38293216 DOI: 10.1101/2024.01.11.575111  0.664
2023 Isobe S, Nair RV, Kang HY, Wang L, Moonen JR, Shinohara T, Cao A, Taylor S, Otsuki S, Marciano DP, Harper RL, Adil MS, Zhang C, Lago-Docampo M, Körbelin J, ... ... Snyder MP, et al. Reduced FOXF1 links unrepaired DNA damage to pulmonary arterial hypertension. Nature Communications. 14: 7578. PMID 37989727 DOI: 10.1038/s41467-023-43039-y  0.593
2023 Yu M, Nie Y, Yang J, Yang S, Li R, Rao V, Hu X, Fang C, Li S, Song D, Guo F, Snyder MP, Chang HY, Kuo CJ, Xu J, et al. Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer's disease. Cell Reports. 42: 113392. PMID 37925638 DOI: 10.1016/j.celrep.2023.113392  0.737
2023 Hornburg D, Wu S, Moqri M, Zhou X, Contrepois K, Bararpour N, Traber GM, Su B, Metwally AA, Avina M, Zhou W, Ubellacker JM, Mishra T, Schüssler-Fiorenza Rose SM, Kavathas PB, ... ... Snyder MP, et al. Dynamic lipidome alterations associated with human health, disease and ageing. Nature Metabolism. PMID 37697054 DOI: 10.1038/s42255-023-00880-1  0.47
2023 Mengelkoch S, Lautman Z, Alley JC, Roos LG, Ehlert B, Moriarity DP, Lancaster S, Miryam Schüssler-Fiorenza Rose S, Snyder MP, Slavich GM. Multi-omics approaches in psychoneuroimmunology and health research: Conceptual considerations and methodological recommendations. Brain, Behavior, and Immunity. PMID 37543247 DOI: 10.1016/j.bbi.2023.07.022  0.784
2023 Hickey JW, Becker WR, Nevins SA, Horning A, Perez AE, Zhu C, Zhu B, Wei B, Chiu R, Chen DC, Cotter DL, Esplin ED, Weimer AK, Caraccio C, Venkataraaman V, ... ... Snyder M, et al. Organization of the human intestine at single-cell resolution. Nature. 619: 572-584. PMID 37468586 DOI: 10.1038/s41586-023-05915-x  0.782
2023 Jain Y, Godwin LL, Ju Y, Sood N, Quardokus EM, Bueckle A, Longacre T, Horning A, Lin Y, Esplin ED, Hickey JW, Snyder MP, Patterson NH, Spraggins JM, Börner K. Segmentation of human functional tissue units in support of a Human Reference Atlas. Communications Biology. 6: 717. PMID 37468557 DOI: 10.1038/s42003-023-04848-5  0.756
2023 Wei W, Riley NM, Lyu X, Shen X, Guo J, Raun SH, Zhao M, Moya-Garzon MD, Basu H, Sheng-Hwa Tung A, Li VL, Huang W, Wiggenhorn AL, Svensson KJ, Snyder MP, et al. Organism-wide, cell-type-specific secretome mapping of exercise training in mice. Cell Metabolism. PMID 37141889 DOI: 10.1016/j.cmet.2023.04.011  0.675
2023 Gaddameedi JD, Chou T, Geller BS, Rangarajan A, Swaminathan TA, Dixon D, Long K, Golder CJ, Vuong VA, Banuelos S, Greenhouse R, Snyder MP, Lipchik AM, Gruber JJ. Acetyl-Click Screening Platform Identifies Small-Molecule Inhibitors of Histone Acetyltransferase 1 (HAT1). Journal of Medicinal Chemistry. PMID 37027002 DOI: 10.1021/acs.jmedchem.3c00039  0.778
2023 Pyke RM, Mellacheruvu D, Dea S, Abbott CW, Zhang SV, Phillips NA, Harris J, Bartha G, Desai S, McClory R, West J, Snyder MP, Chen R, Boyle SM. Withdrawal of 'Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation'. Molecular & Cellular Proteomics : McP. 22: 100511. PMID 37019059 DOI: 10.1016/j.mcpro.2023.100511  0.709
2023 Pyke RM, Mellacheruvu D, Dea S, Abbott C, Zhang SV, Phillips NA, Harris J, Bartha G, Desai S, McClory R, West J, Snyder MP, Chen R, Boyle SM. Precision neoantigen discovery using large-scale immunopeptidomes and composite modeling of MHC peptide presentation. Molecular & Cellular Proteomics : McP. 100506. PMID 36796642 DOI: 10.1016/j.mcpro.2023.100506  0.738
2023 Shen X, Kellogg R, Panyard DJ, Bararpour N, Castillo KE, Lee-McMullen B, Delfarah A, Ubellacker J, Ahadi S, Rosenberg-Hasson Y, Ganz A, Contrepois K, Michael B, Simms I, Wang C, ... ... Snyder MP, et al. Multi-omics microsampling for the profiling of lifestyle-associated changes in health. Nature Biomedical Engineering. PMID 36658343 DOI: 10.1038/s41551-022-00999-8  0.689
2022 Jiang P, Gao F, Liu S, Zhang S, Zhang X, Xia Z, Zhang W, Jiang T, Zhu JL, Zhang Z, Shu Q, Snyder M, Li J. Longitudinally tracking personal physiomes for precision management of childhood epilepsy. Plos Digital Health. 1: e0000161. PMID 36812648 DOI: 10.1371/journal.pdig.0000161  0.388
2022 Erwin GS, Gürsoy G, Al-Abri R, Suriyaprakash A, Dolzhenko E, Zhu K, Hoerner CR, White SM, Ramirez L, Vadlakonda A, Vadlakonda A, von Kraut K, Park J, Brannon CM, Sumano DA, ... ... Snyder MP, et al. Recurrent repeat expansions in human cancer genomes. Nature. 613: 96-102. PMID 36517591 DOI: 10.1038/s41586-022-05515-1  0.794
2022 Pang B, van Weerd JH, Hamoen FL, Snyder MP. Identification of non-coding silencer elements and their regulation of gene expression. Nature Reviews. Molecular Cell Biology. PMID 36344659 DOI: 10.1038/s41580-022-00549-9  0.796
2022 Moll T, Odon V, Harvey C, Collins MO, Peden A, Franklin J, Graves E, Marshall JN, Dos Santos Souza C, Zhang S, Castelli L, Hautbergue G, Azzouz M, Gordon D, Krogan N, ... ... Snyder MP, et al. Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication. Life Science Alliance. 6. PMID 36241425 DOI: 10.26508/lsa.202201449  0.468
2022 Wang YJ, Zhang X, Lam CK, Guo H, Wang C, Zhang S, Wu JC, Snyder M, Li J. Systems analysis of de novo mutations in congenital heart diseases identified a protein network in the hypoplastic left heart syndrome. Cell Systems. PMID 36167075 DOI: 10.1016/j.cels.2022.09.001  0.414
2022 Roodgar M, Suchy FP, Nguyen LH, Bajpai VK, Sinha R, Vilches-Moure JG, Van Bortle K, Bhadury J, Metwally A, Jiang L, Jian R, Chiang R, Oikonomopoulos A, Wu JC, Weissman IL, ... ... Snyder MP, et al. Chimpanzee and pig-tailed macaque iPSCs: Improved culture and generation of primate cross-species embryos. Cell Reports. 40: 111264. PMID 36044843 DOI: 10.1016/j.celrep.2022.111264  0.782
2022 Moonen JR, Chappell J, Shi M, Shinohara T, Li D, Mumbach MR, Zhang F, Nair RV, Nasser J, Mai DH, Taylor S, Wang L, Metzger RJ, Chang HY, Engreitz JM, ... Snyder MP, et al. KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress. Nature Communications. 13: 4941. PMID 35999210 DOI: 10.1038/s41467-022-32566-9  0.613
2022 Shen X, Shao W, Wang C, Liang L, Chen S, Zhang S, Rusu M, Snyder MP. Deep learning-based pseudo-mass spectrometry imaging analysis for precision medicine. Briefings in Bioinformatics. PMID 35947990 DOI: 10.1093/bib/bbac331  0.716
2022 Shen X, Wang C, Snyder MP. massDatabase: utilities for the operation of the public compound and pathway database. Bioinformatics (Oxford, England). PMID 35944213 DOI: 10.1093/bioinformatics/btac546  0.684
2022 Jahanbani F, Maynard RD, Sing JC, Jahanbani S, Perrino JJ, Spacek DV, Davis RW, Snyder MP. Phenotypic characteristics of peripheral immune cells of Myalgic encephalomyelitis/chronic fatigue syndrome via transmission electron microscopy: A pilot study. Plos One. 17: e0272703. PMID 35943990 DOI: 10.1371/journal.pone.0272703  0.768
2022 Shen X, Yan H, Wang C, Gao P, Johnson CH, Snyder MP. TidyMass an object-oriented reproducible analysis framework for LC-MS data. Nature Communications. 13: 4365. PMID 35902589 DOI: 10.1038/s41467-022-32155-w  0.695
2022 Metwally AA, Zhang T, Wu S, Kellogg R, Zhou W, Contrepois K, Tang H, Snyder M. Robust Identification of Temporal Biomarkers in Longitudinal Omics Studies. Bioinformatics (Oxford, England). PMID 35762936 DOI: 10.1093/bioinformatics/btac403  0.417
2022 Perea-Gil I, Seeger T, Bruyneel AAN, Termglinchan V, Monte E, Lim EW, Vadgama N, Furihata T, Gavidia AA, Arthur Ataam J, Bharucha N, Martinez-Amador N, Ameen M, Nair P, Serrano R, ... ... Snyder MP, et al. Serine biosynthesis as a novel therapeutic target for dilated cardiomyopathy. European Heart Journal. PMID 35728000 DOI: 10.1093/eurheartj/ehac305  0.73
2022 Becker WR, Nevins SA, Chen DC, Chiu R, Horning AM, Guha TK, Laquindanum R, Mills M, Chaib H, Ladabaum U, Longacre T, Shen J, Esplin ED, Kundaje A, Ford JM, ... ... Snyder MP, et al. Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer. Nature Genetics. PMID 35726067 DOI: 10.1038/s41588-022-01088-x  0.777
2022 Taylor S, Isobe S, Cao A, Contrepois K, Benayoun BA, Jiang L, Wang L, Melemenidis S, Ozen MO, Otsuki S, Shinohara T, Sweatt AJ, Kaplan J, Moonen JR, Marciano DP, ... ... Snyder MP, et al. Endogenous Retroviral Elements Generate Pathologic Neutrophils in Pulmonary Arterial Hypertension. American Journal of Respiratory and Critical Care Medicine. PMID 35696338 DOI: 10.1164/rccm.202102-0446OC  0.567
2022 Zhang S, Cooper-Knock J, Weimer AK, Shi M, Kozhaya L, Unutmaz D, Harvey C, Julian TH, Furini S, Frullanti E, Fava F, Renieri A, Gao P, Shen X, Timpanaro IS, ... ... Snyder MP, et al. Multiomic analysis reveals cell-type-specific molecular determinants of COVID-19 severity. Cell Systems. PMID 35690068 DOI: 10.1016/j.cels.2022.05.007  0.768
2022 Gao P, Shen X, Zhang X, Jiang C, Zhang S, Zhou X, Schüssler-Fiorenza Rose SM, Snyder M. Precision environmental health monitoring by longitudinal exposome and multi-omics profiling. Genome Research. PMID 35667843 DOI: 10.1101/gr.276521.121  0.775
2022 Van Bortle K, Marciano DP, Liu Q, Chou T, Lipchik AM, Gollapudi S, Geller BS, Monte E, Kamakaka RT, Snyder MP. A cancer-associated RNA polymerase III identity drives robust transcription and expression of snaR-A noncoding RNA. Nature Communications. 13: 3007. PMID 35637192 DOI: 10.1038/s41467-022-30323-6  0.799
2022 Lancaster SM, Lee-McMullen B, Abbott CW, Quijada JV, Hornburg D, Park H, Perelman D, Peterson DJ, Tang M, Robinson A, Ahadi S, Contrepois K, Hung CJ, Ashland M, McLaughlin T, ... ... Snyder MP, et al. Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans. Cell Host & Microbe. PMID 35483363 DOI: 10.1016/j.chom.2022.03.036  0.751
2022 Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, et al. Author Correction: Perspectives on ENCODE. Nature. PMID 35474002 DOI: 10.1038/s41586-021-04213-8  0.4
2022 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, ... ... Snyder MP, et al. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. PMID 35474001 DOI: 10.1038/s41586-021-04226-3  0.752
2022 Boddy S, Islam M, Moll T, Kurz J, Burrows D, McGown A, Bhargava A, Julian TH, Harvey C, Marshall JN, Hall BP, Allen SP, Kenna KP, Sanderson E, Zhang S, ... ... Snyder MP, et al. Unbiased metabolome screen leads to personalized medicine strategy for amyotrophic lateral sclerosis. Brain Communications. 4: fcac069. PMID 35441136 DOI: 10.1093/braincomms/fcac069  0.424
2022 Pyke RM, Mellacheruvu D, Dea S, Abbott CW, McDaniel L, Bhave DP, Zhang SV, Levy E, Bartha G, West J, Snyder MP, Chen RO, Boyle SM. A machine learning algorithm with subclonal sensitivity reveals widespread pan-cancer human leukocyte antigen loss of heterozygosity. Nature Communications. 13: 1925. PMID 35414054 DOI: 10.1038/s41467-022-29203-w  0.739
2022 Moll T, Odon V, Harvey C, Collins MO, Peden A, Franklin J, Graves E, Marshall JNG, Dos Santos Souza C, Zhang S, Azzouz M, Gordon D, Krogan N, Ferraiuolo L, Snyder MP, et al. Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication. Biorxiv : the Preprint Server For Biology. PMID 35291294 DOI: 10.1101/2022.03.06.483172  0.471
2022 Zhang S, Cooper-Knock J, Weimer AK, Shi M, Moll T, Marshall JNG, Harvey C, Nezhad HG, Franklin J, Souza CDS, Ning K, Wang C, Li J, Dilliott AA, Farhan S, ... ... Snyder MP, et al. Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis. Neuron. PMID 35045337 DOI: 10.1016/j.neuron.2021.12.019  0.463
2021 Cefalu WT, Andersen DK, Arreaza-Rubín G, Pin CL, Sato S, Verchere CB, Woo M, Rosenblum ND, Rosenblum N, Cefalu W, Andersen DK, Arreaza-Rubín G, Dhara C, James SP, ... ... Snyder M, et al. Heterogeneity of Diabetes: β-Cells, Phenotypes, and Precision Medicine: Proceedings of an International Symposium of the Canadian Institutes of Health Research's Institute of Nutrition, Metabolism and Diabetes and the U.S. National Institutes of Health's National Institute of Diabetes and Digestive and Kidney Diseases. Diabetes. PMID 34957490 DOI: 10.2337/db21-0777  0.374
2021 Rauscher B, Mueller WF, Clauder-Münster S, Jakob P, Islam MS, Sun H, Ghidelli-Disse S, Boesche M, Bantscheff M, Pflaumer H, Collier P, Haase B, Chen S, Hoffman R, Wang G, ... ... Snyder M, et al. Patient-derived gene and protein expression signatures of NGLY1 deficiency. Journal of Biochemistry. PMID 34878535 DOI: 10.1093/jb/mvab131  0.542
2021 Julian TH, Boddy S, Islam M, Kurz J, Whittaker KJ, Moll T, Harvey C, Zhang S, Snyder MP, McDermott C, Cooper-Knock J, Shaw PJ. A review of Mendelian randomization in amyotrophic lateral sclerosis. Brain : a Journal of Neurology. PMID 34791088 DOI: 10.1093/brain/awab420  0.409
2021 Kim DS, Risca VI, Reynolds DL, Chappell J, Rubin AJ, Jung N, Donohue LKH, Lopez-Pajares V, Kathiria A, Shi M, Zhao Z, Deep H, Sharmin M, Rao D, Lin S, ... ... Snyder MP, et al. The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation. Nature Genetics. PMID 34650237 DOI: 10.1038/s41588-021-00947-3  0.616
2021 Bahmani A, Alavi A, Buergel T, Upadhyayula S, Wang Q, Ananthakrishnan SK, Alavi A, Celis D, Gillespie D, Young G, Xing Z, Nguyen MHH, Haque A, Mathur A, Payne J, ... ... Snyder MP, et al. A scalable, secure, and interoperable platform for deep data-driven health management. Nature Communications. 12: 5757. PMID 34599181 DOI: 10.1038/s41467-021-26040-1  0.476
2021 Sanghi A, Gruber JJ, Metwally A, Jiang L, Reynolds W, Sunwoo J, Orloff L, Chang HY, Kasowski M, Snyder MP. Chromatin accessibility associates with protein-RNA correlation in human cancer. Nature Communications. 12: 5732. PMID 34593797 DOI: 10.1038/s41467-021-25872-1  0.808
2021 Zhang X, Gao P, Snyder MP. The Exposome in the Era of the Quantified Self. Annual Review of Biomedical Data Science. 4: 255-277. PMID 34465170 DOI: 10.1146/annurev-biodatasci-012721-122807  0.312
2021 Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK, Chang HY. Structured elements drive extensive circular RNA translation. Molecular Cell. PMID 34437836 DOI: 10.1016/j.molcel.2021.07.042  0.455
2021 Shen X, Wu S, Liang L, Chen S, Contrepois K, Zhu ZJ, Snyder M. metID: a R package for automatable compound annotation for LC-MS-based data. Bioinformatics (Oxford, England). PMID 34432001 DOI: 10.1093/bioinformatics/btab583  0.674
2021 Abbott CW, Boyle SM, Pyke RM, McDaniel LD, Levy E, Navarro FCP, Mellacheruvu D, Zhang SV, Tan M, Santiago R, Rusan ZM, Milani P, Bartha G, Harris J, McClory R, ... Snyder MP, et al. Prediction of Immunotherapy Response in Melanoma through Combined Modeling of Neoantigen Burden and Immune-Related Resistance Mechanisms. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 27: 4265-4276. PMID 34341053 DOI: 10.1158/1078-0432.CCR-20-4314  0.718
2021 Roodgar M, Good BH, Garud NR, Martis S, Avula M, Zhou W, Lancaster SM, Lee H, Babveyh A, Nesamoney S, Pollard KS, Snyder MP. Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. Genome Research. 31: 1433-1446. PMID 34301627 DOI: 10.1101/gr.265058.120  0.779
2021 Zhang S, Cooper-Knock J, Weimer AK, Harvey C, Julian TH, Wang C, Li J, Furini S, Frullanti E, Fava F, Renieri A, Pan C, Song J, Billing-Ross P, Gao P, ... ... Snyder MP, et al. Common and rare variant analyses combined with single-cell multiomics reveal cell-type-specific molecular mechanisms of COVID-19 severity. Medrxiv : the Preprint Server For Health Sciences. PMID 34189540 DOI: 10.1101/2021.06.15.21258703  0.773
2021 Pyke RM, Mellacheruvu D, Dea S, Abbott C, Zhang SV, Phillips NA, Harris J, Bartha G, Desai S, McClory R, West J, Snyder MP, Chen R, Boyle SM. Precision neoantigen discovery using large-scale immunopeptidomes and composite modeling of MHC peptide presentation. Molecular & Cellular Proteomics : McP. 100111. PMID 34126241 DOI: 10.1016/j.mcpro.2021.100111  0.738
2021 Julian TH, Glascow N, Barry ADF, Moll T, Harvey C, Klimentidis YC, Newell M, Zhang S, Snyder MP, Cooper-Knock J, Shaw PJ. Physical exercise is a risk factor for amyotrophic lateral sclerosis: Convergent evidence from Mendelian randomisation, transcriptomics and risk genotypes. Ebiomedicine. 68: 103397. PMID 34051439 DOI: 10.1016/j.ebiom.2021.103397  0.368
2021 Dunn J, Kidzinski L, Runge R, Witt D, Hicks JL, Schüssler-Fiorenza Rose SM, Li X, Bahmani A, Delp SL, Hastie T, Snyder MP. Wearable sensors enable personalized predictions of clinical laboratory measurements. Nature Medicine. PMID 34031607 DOI: 10.1038/s41591-021-01339-0  0.534
2021 Arif M, Zhang C, Li X, Güngör C, Çakmak B, Arslantürk M, Tebani A, Özcan B, Subaş O, Zhou W, Piening B, Turkez H, Fagerberg L, Price N, Hood L, ... Snyder M, et al. iNetModels 2.0: an interactive visualization and database of multi-omics data. Nucleic Acids Research. PMID 33849075 DOI: 10.1093/nar/gkab254  0.45
2021 Li Y, Zhang S, Snyder MP, Meador KJ. Precision medicine in women with epilepsy: The challenge, systematic review, and future direction. Epilepsy & Behavior : E&B. 118: 107928. PMID 33774354 DOI: 10.1016/j.yebeh.2021.107928  0.368
2021 Li D, Shao NY, Moonen JR, Zhao Z, Shi M, Otsuki S, Wang L, Nguyen T, Yan E, Marciano DP, Contrepois K, Li CG, Wu JC, Snyder MP, Rabinovitch M. ALDH1A3 Coordinates Metabolism with Gene Regulation in Pulmonary Arterial Hypertension. Circulation. PMID 33764154 DOI: 10.1161/CIRCULATIONAHA.120.048845  0.642
2021 Cooper-Knock J, Zhang S, Kenna KP, Moll T, Franklin JP, Allen S, Nezhad HG, Iacoangeli A, Yacovzada NY, Eitan C, Hornstein E, Elhaik E, Celadova P, Bose D, Farhan S, ... ... Snyder MP, et al. Rare variant burden analysis within enhancers identifies CAV1 as an ALS risk gene. Cell Reports. 34: 108730. PMID 33535055 DOI: 10.1016/j.celrep.2021.108730  0.411
2021 Yang Y, Li X, Ma Z, Wang C, Yang Q, Byrne-Steele M, Hong R, Min Q, Zhou G, Cheng Y, Qin G, Youngyunpipatkul JV, Wing JB, Sakaguchi S, Toonstra C, ... ... Snyder MP, et al. CTLA-4 expression by B-1a B cells is essential for immune tolerance. Nature Communications. 12: 525. PMID 33483505 DOI: 10.1038/s41467-020-20874-x  0.404
2021 Jiang C, Zhang X, Gao P, Chen Q, Snyder M. Decoding personal biotic and abiotic airborne exposome. Nature Protocols. PMID 33437065 DOI: 10.1038/s41596-020-00451-8  0.426
2020 Bezdan D, Grigorev K, Meydan C, Pelissier Vatter FA, Cioffi M, Rao V, MacKay M, Nakahira K, Burnham P, Afshinnekoo E, Westover C, Butler D, Mozsary C, Donahoe T, Foox J, ... ... Snyder MP, et al. Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers. Iscience. 23: 101844. PMID 33376973 DOI: 10.1016/j.isci.2020.101844  0.699
2020 Hennigs JK, Cao A, Li CG, Shi M, Mienert J, Miyagawa K, Körbelin J, Marciano DP, Chen PI, Roughley M, Elliott MV, Harper RL, Bill MA, Chappell J, Moonen JR, ... ... Snyder MP, et al. PPARγ-p53-Mediated Vasculoregenerative Program to Reverse Pulmonary Hypertension. Circulation Research. PMID 33322916 DOI: 10.1161/CIRCRESAHA.119.316339  0.708
2020 Cooper-Knock J, Zhang S, Kenna KP, Moll T, Franklin JP, Allen S, Nezhad HG, Iacoangeli A, Yacovzada NY, Eitan C, Hornstein E, Ehilak E, Celadova P, Bose D, Farhan S, ... ... Snyder MP, et al. Rare Variant Burden Analysis within Enhancers Identifies CAV1 as an ALS Risk Gene. Cell Reports. 33: 108456. PMID 33264630 DOI: 10.1016/j.celrep.2020.108456  0.456
2020 Lancaster SM, Sanghi A, Wu S, Snyder MP. A Customizable Analysis Flow in Integrative Multi-Omics. Biomolecules. 10. PMID 33260881 DOI: 10.3390/biom10121606  0.776
2020 Sailani MR, Metwally AA, Zhou W, Rose SMS, Ahadi S, Contrepois K, Mishra T, Zhang MJ, Kidziński Ł, Chu TJ, Snyder MP. Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California. Nature Communications. 11: 4933. PMID 33004787 DOI: 10.1038/s41467-020-18758-1  0.414
2020 Sailani MR, Jahanbani F, Abbott CW, Lee H, Zia A, Rego S, Winkelmann J, Hopfner F, Khan TN, Katsanis N, Müller SH, Berg D, Lyman KM, Mychajliw C, Deuschl G, ... ... Snyder MP, et al. Candidate variants in TUB are associated with familial tremor. Plos Genetics. 16: e1009010. PMID 32956375 DOI: 10.1371/Journal.Pgen.1009010  0.781
2020 Jiang L, Wang M, Lin S, Jian R, Li X, Chan J, Dong G, Fang H, Robinson AE, Snyder MP. A Quantitative Proteome Map of the Human Body. Cell. PMID 32916130 DOI: 10.1016/J.Cell.2020.08.036  0.309
2020 Briganti F, Sun H, Wei W, Wu J, Zhu C, Liss M, Karakikes I, Rego S, Cipriano A, Snyder M, Meder B, Xu Z, Millat G, Gotthardt M, Mercola M, et al. iPSC Modeling of RBM20-Deficient DCM Identifies Upregulation of RBM20 as a Therapeutic Strategy. Cell Reports. 32: 108117. PMID 32905764 DOI: 10.1016/J.Celrep.2020.108117  0.577
2020 Tombácz D, Prazsák I, Csabai Z, Moldován N, Dénes B, Snyder M, Boldogkői Z. Long-read assays shed new light on the transcriptome complexity of a viral pathogen. Scientific Reports. 10: 13822. PMID 32796917 DOI: 10.1038/S41598-020-70794-5  0.37
2020 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, ... ... Snyder MP, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4  0.784
2020 Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, et al. Perspectives on ENCODE. Nature. 583: 693-698. PMID 32728248 DOI: 10.1038/S41586-020-2449-8  0.533
2020 Grubert F, Srivas R, Spacek DV, Kasowski M, Ruiz-Velasco M, Sinnott-Armstrong N, Greenside P, Narasimha A, Liu Q, Geller B, Sanghi A, Kulik M, Sa S, Rabinovitch M, Kundaje A, ... ... Snyder M, et al. Landscape of cohesin-mediated chromatin loops in the human genome. Nature. 583: 737-743. PMID 32728247 DOI: 10.1038/S41586-020-2151-X  0.791
2020 Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, ... ... Snyder M, et al. An integrative ENCODE resource for cancer genomics. Nature Communications. 11: 3696. PMID 32728046 DOI: 10.1038/S41467-020-14743-W  0.577
2020 Cao W, Lee H, Wu W, Zaman A, McCorkle S, Yan M, Chen J, Xing Q, Sinnott-Armstrong N, Xu H, Sailani MR, Tang W, Cui Y, Liu J, Guan H, ... ... Snyder M, et al. Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma. Nature Communications. 11: 3675. PMID 32699215 DOI: 10.1038/S41467-020-17227-Z  0.805
2020 Leng Y, Jiang C, Xing X, Tsai MS, Snyder M, Zhai A, Yao G. Prevention of Severe Intestinal Barrier Dysfunction Through a Single-Species Probiotics Is Associated With the Activation of Microbiome-Mediated Glutamate-Glutamine Biosynthesis. Shock (Augusta, Ga.). PMID 32694391 DOI: 10.1097/Shk.0000000000001593  0.386
2020 Roodgar M, Babveyh A, Nguyen LH, Zhou W, Sinha R, Lee H, Hanks JB, Avula M, Jiang L, Jian R, Lee H, Song G, Chaib H, Weissman IL, Batzoglou S, ... ... Snyder MP, et al. Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding. Gigascience. 9. PMID 32649757 DOI: 10.1093/Gigascience/Giaa069  0.797
2020 Tombácz D, Torma G, Gulyás G, Moldován N, Snyder M, Boldogkői Z. Meta-analytic approach for transcriptome profiling of herpes simplex virus type 1. Scientific Data. 7: 223. PMID 32647284 DOI: 10.1038/S41597-020-0558-8  0.341
2020 Liang L, Rasmussen MH, Piening B, Shen X, Chen S, Röst H, Snyder JK, Tibshirani R, Skotte L, Lee NC, Contrepois K, Feenstra B, Zackriah H, Snyder M, Melbye M. Metabolic Dynamics and Prediction of Gestational Age and Time to Delivery in Pregnant Women. Cell. 181: 1680-1692.e15. PMID 32589958 DOI: 10.1016/J.Cell.2020.05.002  0.689
2020 Contrepois K, Wu S, Moneghetti KJ, Hornburg D, Ahadi S, Tsai MS, Metwally AA, Wei E, Lee-McMullen B, Quijada JV, Chen S, Christle JW, Ellenberger M, Balliu B, Taylor S, ... ... Snyder MP, et al. Molecular Choreography of Acute Exercise. Cell. 181: 1112-1130.e16. PMID 32470399 DOI: 10.1016/J.Cell.2020.04.043  0.404
2020 Zhou X, Johnson JS, Spakowicz D, Zhou W, Zhou Y, Sodergren E, Snyder M, Weinstock GM. Longitudinal Analysis of Serum Cytokine Levels and Gut Microbial Abundance Links IL-17/IL-22 with and Insulin Sensitivity in Humans. Diabetes. PMID 32366680 DOI: 10.2337/Db19-0592  0.601
2020 Reyes-Palomares A, Gu M, Grubert F, Berest I, Sa S, Kasowski M, Arnold C, Shuai M, Srivas R, Miao S, Li D, Snyder MP, Rabinovitch M, Zaugg JB. Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension. Nature Communications. 11: 1673. PMID 32245974 DOI: 10.1038/S41467-020-15463-X  0.786
2020 Cissé OH, Ma L, Jiang C, Snyder M, Kovacs JA. Humans Are Selectively Exposed to Pneumocystis jirovecii. Mbio. 11. PMID 32156824 DOI: 10.1128/Mbio.03138-19  0.416
2020 Pang B, Snyder MP. Systematic identification of silencers in human cells. Nature Genetics. PMID 32094911 DOI: 10.1038/S41588-020-0578-5  0.798
2020 Ahadi S, Zhou W, Schüssler-Fiorenza Rose SM, Sailani MR, Contrepois K, Avina M, Ashland M, Brunet A, Snyder M. Personal aging markers and ageotypes revealed by deep longitudinal profiling. Nature Medicine. 26: 83-90. PMID 31932806 DOI: 10.1038/S41591-019-0719-5  0.471
2020 Sanghi A, Orloff L, Snyder M. SAT-LB25 A Multi-Omics Analysis of Advanced Papillary Thyroid Cancer Journal of the Endocrine Society. 4. DOI: 10.1210/Jendso/Bvaa046.2154  0.763
2019 Li L, Fu K, Zhou W, Snyder M. Applying circulating tumor DNA methylation in the diagnosis of lung cancer. Precision Clinical Medicine. 2: 45-56. PMID 35694699 DOI: 10.1093/pcmedi/pbz003  0.41
2019 Snyder M, Zhou W. Big data and health. The Lancet. Digital Health. 1: e252-e254. PMID 33323249 DOI: 10.1016/S2589-7500(19)30109-8  0.363
2019 Witt D, Kellogg R, Snyder M, Dunn J. Windows Into Human Health Through Wearables Data Analytics. Current Opinion in Biomedical Engineering. 9: 28-46. PMID 31832566 DOI: 10.1016/j.cobme.2019.01.001  0.508
2019 Tombácz D, Moldován N, Balázs Z, Gulyás G, Csabai Z, Boldogkői M, Snyder M, Boldogkői Z. Multiple Long-Read Sequencing Survey of Herpes Simplex Virus Dynamic Transcriptome. Frontiers in Genetics. 10: 834. PMID 31608102 DOI: 10.3389/Fgene.2019.00834  0.388
2019 Tycko J, Wainberg M, Marinov GK, Ursu O, Hess GT, Ego BK, Aradhana, Li A, Truong A, Trevino AE, Spees K, Yao D, Kaplow IM, Greenside PG, Morgens DW, ... ... Snyder MP, et al. Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements. Nature Communications. 10: 4063. PMID 31492858 DOI: 10.1038/S41467-019-11955-7  0.67
2019 Tian W, Jiang X, Sung YK, Shuffle E, Wu TH, Kao PN, Tu AB, Dorfmüller P, Cao A, Wang L, Peng G, Kim Y, Zhang P, Chappell J, Pasupneti S, ... ... Snyder MP, et al. Phenotypically-Silent Bone Morphogenetic Protein Receptor 2 (Bmpr2) Mutations Predispose Rats to Inflammation-Induced Pulmonary Arterial Hypertension by Enhancing The Risk for Neointimal Transformation. Circulation. PMID 31462075 DOI: 10.1161/Circulationaha.119.040629  0.457
2019 Gruber JJ, Chen J, Geller B, Jäger N, Lipchik AM, Wang G, Kurian AW, Ford JM, Snyder MP. Chromatin Remodeling in Response to BRCA2-Crisis. Cell Reports. 28: 2182-2193.e6. PMID 31433991 DOI: 10.1016/J.Celrep.2019.07.057  0.79
2019 Han CM, Catoe D, Munro SA, Khnouf R, Snyder MP, Santiago JG, Salit ML, Cenik C. Simultaneous RNA purification and size selection using on-chip isotachophoresis with an ionic spacer. Lab On a Chip. PMID 31328753 DOI: 10.1039/C9Lc00311H  0.671
2019 Lee J, Termglinchan V, Diecke S, Itzhaki I, Lam CK, Garg P, Lau E, Greenhaw M, Seeger T, Wu H, Zhang JZ, Chen X, Gil IP, Ameen M, Sallam K, ... ... Snyder MP, et al. Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy. Nature. PMID 31316208 DOI: 10.1038/S41586-019-1406-X  0.382
2019 Stowers RS, Shcherbina A, Israeli J, Gruber JJ, Chang J, Nam S, Rabiee A, Teruel MN, Snyder MP, Kundaje A, Chaudhuri O. Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility. Nature Biomedical Engineering. PMID 31285581 DOI: 10.1038/S41551-019-0420-5  0.627
2019 Gruber JJ, Geller B, Lipchik AM, Chen J, Salahudeen AA, Ram AN, Ford JM, Kuo CJ, Snyder MP. HAT1 Coordinates Histone Production and Acetylation via H4 Promoter Binding. Molecular Cell. PMID 31278053 DOI: 10.1016/J.Molcel.2019.05.034  0.787
2019 Landegren N, Rosen LB, Freyhult E, Eriksson D, Fall T, Smith G, Ferre EMN, Brodin P, Sharon D, Snyder M, Lionakis M, Anderson M, Kämpe O. Comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'. Elife. 8. PMID 31244471 DOI: 10.7554/Elife.43578  0.743
2019 Huang M, Tailor J, Zhen Q, Gillmor AH, Miller ML, Weishaupt H, Chen J, Zheng T, Nash EK, McHenry LK, An Z, Ye F, Takashima Y, Clarke J, Ayetey H, ... ... Snyder MP, et al. Engineering Genetic Predisposition in Human Neuroepithelial Stem Cells Recapitulates Medulloblastoma Tumorigenesis. Cell Stem Cell. PMID 31204176 DOI: 10.1016/J.Stem.2019.05.013  0.652
2019 Chen J, Haanpää MK, Gruber JJ, Jäger N, Ford JM, Snyder MP. High-Resolution Bisulfite-Sequencing of Peripheral Blood DNA Methylation in Early-Onset and Familial Risk Breast Cancer Patients. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 31175093 DOI: 10.1158/1078-0432.Ccr-18-2423  0.776
2019 Zhou W, Sailani MR, Contrepois K, Zhou Y, Ahadi S, Leopold SR, Zhang MJ, Rao V, Avina M, Mishra T, Johnson J, Lee-McMullen B, Chen S, Metwally AA, Tran TDB, ... ... Snyder M, et al. Longitudinal multi-omics of host-microbe dynamics in prediabetes. Nature. 569: 663-671. PMID 31142858 DOI: 10.1038/S41586-019-1236-X  0.779
2019 Marciano DP, Snyder MP. Personalized Metabolomics. Methods in Molecular Biology (Clifton, N.J.). 1978: 447-456. PMID 31119679 DOI: 10.1007/978-1-4939-9236-2_27  0.606
2019 Csabai Z, Tombácz D, Deim Z, Snyder M, Boldogkői Z. Analysis of the Complete Genome Sequence of a Novel, Pseudorabies Virus Strain Isolated in Southeast Europe. The Canadian Journal of Infectious Diseases & Medical Microbiology = Journal Canadien Des Maladies Infectieuses Et De La Microbiologie Medicale. 2019: 1806842. PMID 31093307 DOI: 10.1155/2019/1806842  0.301
2019 Schüssler-Fiorenza Rose SM, Contrepois K, Moneghetti KJ, Zhou W, Mishra T, Mataraso S, Dagan-Rosenfeld O, Ganz AB, Dunn J, Hornburg D, Rego S, Perelman D, Ahadi S, Sailani MR, Zhou Y, ... ... Snyder MP, et al. A longitudinal big data approach for precision health. Nature Medicine. 25: 792-804. PMID 31068711 DOI: 10.1038/S41591-019-0414-6  0.702
2019 Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, ... ... Snyder MP, et al. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science (New York, N.Y.). 364. PMID 30975860 DOI: 10.1126/Science.Aau8650  0.717
2019 Li J, Li X, Zhang S, Snyder M. Gene-Environment Interaction in the Era of Precision Medicine. Cell. 177: 38-44. PMID 30901546 DOI: 10.1016/J.Cell.2019.03.004  0.559
2019 Sailani MR, Halling JF, Møller HD, Lee H, Plomgaard P, Pilegaard H, Snyder MP, Regenberg B. Lifelong physical activity is associated with promoter hypomethylation of genes involved in metabolism, myogenesis, contractile properties and oxidative stress resistance in aged human skeletal muscle. Scientific Reports. 9: 3272. PMID 30824849 DOI: 10.1038/S41598-018-37895-8  0.705
2019 Boldogkői Z, Moldován N, Balázs Z, Snyder M, Tombácz D. Long-Read Sequencing - A Powerful Tool in Viral Transcriptome Research. Trends in Microbiology. PMID 30824172 DOI: 10.1016/J.Tim.2019.01.010  0.372
2019 Landegren N, Rosen LB, Freyhult E, Eriksson D, Fall T, Smith G, Ferre EMN, Brodin P, Sharon D, Snyder M, Lionakis M, Anderson M, Kämpe O. Author response: Comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies' Elife. DOI: 10.7554/Elife.43578.018  0.729
2019 Gruber J, Chen J, Geller B, Jager N, Lipchik A, Snyder M. Abstract P3-05-02: Not presented Cancer Research. 79. DOI: 10.1158/1538-7445.Sabcs18-P3-05-02  0.737
2019 Li L, Fu K, Zhou W, Snyder M. Applying circulating tumor DNA methylation in the diagnosis of lung cancer Precision Clinical Medicine. 2: 45-56. DOI: 10.1093/Pcmedi/Pbz003  0.455
2019 Urban A, Zhu X, Zhou B, Sloan S, Pattni R, Fiston-Lavier A, Snyder M, Petrov D, Abyzov A, Vaccarino F, Barres B, Vogel H, Tamminga C, Levinson D. Sa94Machine Learning Analysis Of Ultra-Deep Whole-Genome Sequencing In Human Brain Reveals Somatic Genomic Retrotransposition In Glia As Well As In Neurons European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2018.08.316  0.569
2019 Liang L, Dunn JP, Chen S, Tsai M, Hornburg D, Newmann S, Chung P, Avina M, Leng Y, Holman R, Lee TH, Berrios S, Qureshi SA, Baer R, Etemadi M, ... ... Snyder M, et al. 1009: Smart Diaphragm Study: Multi-omics profiling and cervical device measurements during pregnancy American Journal of Obstetrics and Gynecology. 220: S649. DOI: 10.1016/J.Ajog.2018.11.1033  0.532
2018 Rego S, Dagan-Rosenfeld O, Zhou W, Sailani MR, Limcaoco P, Colbert E, Avina M, Wheeler J, Craig C, Salins D, Röst HL, Dunn J, McLaughlin T, Steinmetz LM, Bernstein JA, ... Snyder MP, et al. High-frequency actionable pathogenic exome variants in an average-risk cohort. Cold Spring Harbor Molecular Case Studies. 4. PMID 30487145 DOI: 10.1101/mcs.a003178  0.737
2018 Boldogkői Z, Szűcs A, Balázs Z, Sharon D, Snyder M, Tombácz D. Transcriptomic study of Herpes simplex virus type-1 using full-length sequencing techniques. Scientific Data. 5: 180266. PMID 30480662 DOI: 10.1038/Sdata.2018.266  0.774
2018 Minhas PS, Liu L, Moon PK, Joshi AU, Dove C, Mhatre S, Contrepois K, Wang Q, Lee BA, Coronado M, Bernstein D, Snyder MP, Migaud M, Majeti R, Mochly-Rosen D, et al. Macrophage de novo NAD synthesis specifies immune function in aging and inflammation. Nature Immunology. PMID 30478397 DOI: 10.1038/S41590-018-0255-3  0.652
2018 Tombácz D, Prazsák I, Szucs A, Dénes B, Snyder M, Boldogkoi Z. Dynamic transcriptome profiling dataset of vaccinia virus obtained from long-read sequencing techniques. Gigascience. 7. PMID 30476066 DOI: 10.1093/Gigascience/Giy139  0.305
2018 Chen R, Xia L, Tu K, Duan M, Kukurba K, Li-Pook-Than J, Xie D, Snyder M. Longitudinal personal DNA methylome dynamics in a human with a chronic condition. Nature Medicine. PMID 30397358 DOI: 10.1038/S41591-018-0237-X  0.439
2018 Haney MS, Bohlen CJ, Morgens DW, Ousey JA, Barkal AA, Tsui CK, Ego BK, Levin R, Kamber RA, Collins H, Tucker A, Li A, Vorselen D, Labitigan L, Crane E, ... ... Snyder MP, et al. Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. Nature Genetics. PMID 30397336 DOI: 10.1038/S41588-018-0254-1  0.41
2018 Maróti Z, Boldogkői Z, Tombácz D, Snyder M, Kalmár T. Evaluation of whole exome sequencing as an alternative to BeadChip and whole genome sequencing in human population genetic analysis. Bmc Genomics. 19: 778. PMID 30373510 DOI: 10.1186/S12864-018-5168-X  0.382
2018 Balázs Z, Tombácz D, Szűcs A, Snyder M, Boldogkői Z. Dual Platform Long-Read RNA-Sequencing Dataset of the Human Cytomegalovirus Lytic Transcriptome. Frontiers in Genetics. 9: 432. PMID 30319694 DOI: 10.3389/Fgene.2018.00432  0.316
2018 Dunn J, Runge R, Snyder M. Wearables and the medical revolution. Personalized Medicine. 15: 429-448. PMID 30259801 DOI: 10.2217/Pme-2018-0044  0.548
2018 Jiang C, Wang X, Li X, Inlora J, Wang T, Liu Q, Snyder M. Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring. Cell. 175: 277-291.e31. PMID 30241608 DOI: 10.1016/J.Cell.2018.08.060  0.485
2018 Li J, Pan C, Zhang S, Spin JM, Deng A, Leung LLK, Dalman RL, Tsao PS, Snyder M. Decoding the Genomics of Abdominal Aortic Aneurysm. Cell. 174: 1361-1372.e10. PMID 30193110 DOI: 10.1016/J.Cell.2018.07.021  0.527
2018 Liu Q, Van Bortle K, Zhang Y, Zhao MT, Zhang JZ, Geller BS, Gruber JJ, Jiang C, Wu JC, Snyder MP. Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid. Scientific Reports. 8: 12960. PMID 30154523 DOI: 10.1038/S41598-018-31192-0  0.709
2018 Tombácz D, Balázs Z, Csabai Z, Snyder M, Boldogkői Z. Long-Read Sequencing Revealed an Extensive Transcript Complexity in Herpesviruses. Frontiers in Genetics. 9: 259. PMID 30065753 DOI: 10.3389/Fgene.2018.00259  0.345
2018 Li J, Hong X, Mesiano S, Muglia LJ, Wang X, Snyder M, Stevenson DK, Shaw GM. Natural Selection Has Differentiated the Progesterone Receptor among Human Populations. American Journal of Human Genetics. PMID 29937092 DOI: 10.1016/J.Ajhg.2018.05.009  0.312
2018 Tombácz D, Sharon D, Szűcs A, Moldován N, Snyder M, Boldogkői Z. Transcriptome-wide survey of pseudorabies virus using next- and third-generation sequencing platforms. Scientific Data. 5: 180119. PMID 29917014 DOI: 10.1038/Sdata.2018.119  0.771
2018 You Y, Cuevas-Diaz Duran R, Jiang L, Dong X, Zong S, Snyder M, Wu JQ. An integrated global regulatory network of hematopoietic precursor cell self-renewal and differentiation. Integrative Biology : Quantitative Biosciences From Nano to Macro. PMID 29892750 DOI: 10.1039/C8Ib00059J  0.337
2018 Kellogg RA, Dunn J, Snyder MP. Personal Omics for Precision Health. Circulation Research. 122: 1169-1171. PMID 29700064 DOI: 10.1161/CIRCRESAHA.117.310909  0.492
2018 Im H, Rao V, Sridhar K, Bentley J, Mishra T, Chen R, Hall J, Graber A, Zhang Y, Li X, Mias GI, Snyder MP, Greenberg PL. Distinct transcriptomic and exomic abnormalities within myelodysplastic syndrome marrow cells. Leukemia & Lymphoma. 1-11. PMID 29616851 DOI: 10.1080/10428194.2018.1452210  0.808
2018 Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, et al. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nature Genetics. PMID 29610481 DOI: 10.1038/S41588-018-0091-2  0.539
2018 Yu KH, Lee TL, Wang CS, Chen YJ, Ré C, Kou SC, Chiang JH, Kohane IS, Snyder M. Systematic Protein Prioritization for Targeted Proteomics Studies through Literature Mining. Journal of Proteome Research. PMID 29505266 DOI: 10.1021/Acs.Jproteome.7B00772  0.309
2018 Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, ... ... Snyder MP, et al. Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. Cell Systems. PMID 29361466 DOI: 10.1016/J.Cels.2017.12.013  0.784
2018 Moldován N, Szucs A, Tombácz D, Balázs Z, Csabai Z, Snyder M, Boldogkoi Z. Multi-platform Next-generation Sequencing Identifies Novel RNA Molecules and Transcript Isoforms of the Endogenous Retrovirus Isolated from Cultured Cells. Fems Microbiology Letters. PMID 29361122 DOI: 10.1093/Femsle/Fny013  0.374
2018 Rappoport N, Toung J, Hadley D, Wong RJ, Fujioka K, Reuter J, Abbott CW, Oh S, Hu D, Eng C, Huntsman S, Bodian DL, Niederhuber JE, Hong X, Zhang G, ... ... Snyder MP, et al. A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth. Scientific Reports. 8: 226. PMID 29317701 DOI: 10.1038/S41598-017-18246-5  0.789
2018 Kim D, Risca V, Chappell J, Shi M, Zhao Z, Jung N, Chang H, Snyder M, Greenleaf W, Kundaje A, Khavari P. 795 Decoding regulatory sequence across skin differentiation with deep learning Journal of Investigative Dermatology. 138: S135. DOI: 10.1016/J.Jid.2018.03.805  0.603
2017 Theodorou E, Scanga R, Twardowski M, Snyder MP, Brouzes E. A Droplet Microfluidics Based Platform for Mining Metagenomic Libraries for Natural Compounds. Micromachines. 8. PMID 30400422 DOI: 10.3390/Mi8080230  0.544
2017 Moldován N, Tombácz D, Szűcs A, Csabai Z, Snyder M, Boldogkői Z. Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus. Frontiers in Microbiology. 8: 2708. PMID 29403453 DOI: 10.3389/Fmicb.2017.02708  0.393
2017 Balázs Z, Tombácz D, Szűcs A, Snyder M, Boldogkői Z. Long-read sequencing of the human cytomegalovirus transcriptome with the Pacific Biosciences RSII platform. Scientific Data. 4: 170194. PMID 29257134 DOI: 10.1038/Sdata.2017.194  0.372
2017 Carter AC, Chang HY, Church G, Dombkowski A, Ecker JR, Gil E, Giresi PG, Greely H, Greenleaf WJ, Hacohen N, He C, Hill D, Ko J, Kohane I, Kundaje A, ... ... Snyder MP, et al. Challenges and recommendations for epigenomics in precision health. Nature Biotechnology. 35: 1128-1132. PMID 29220033 DOI: 10.1038/Nbt.4030  0.505
2017 Balázs Z, Tombácz D, Szűcs A, Csabai Z, Megyeri K, Petrov AN, Snyder M, Boldogkői Z. Long-Read Sequencing of Human Cytomegalovirus Transcriptome Reveals RNA Isoforms Carrying Distinct Coding Potentials. Scientific Reports. 7: 15989. PMID 29167532 DOI: 10.1038/S41598-017-16262-Z  0.395
2017 Yu KH, Berry GJ, Rubin DL, Ré C, Altman RB, Snyder M. Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma. Cell Systems. PMID 29153840 DOI: 10.1016/J.Cels.2017.10.014  0.326
2017 Sailani MR, Chappell J, Inlora J, Lynch L, Narasimha A, Mazroui S, Zia A, Bernstein J, Aryani O, Snyder MP. WISP3 mutation associated with Pseudorheumatoid Dysplasia. Cold Spring Harbor Molecular Case Studies. PMID 29092958 DOI: 10.1101/mcs.a001990  0.785
2017 Szűcs A, Moldován N, Tombácz D, Csabai Z, Snyder M, Boldogkői Z. Long-Read Sequencing Reveals a GC Pressure during the Evolution of Porcine Endogenous Retrovirus. Genome Announcements. 5. PMID 28982996 DOI: 10.1128/Genomea.01040-17  0.336
2017 Yu KH, Fitzpatrick MR, Pappas L, Chan W, Kung J, Snyder M. Omics AnalySIs System for PRecision Oncology (OASISPRO): A Web-based Omics Analysis Tool for Clinical Phenotype Prediction. Bioinformatics (Oxford, England). PMID 28968749 DOI: 10.1093/Bioinformatics/Btx572  0.302
2017 Pan C, McInnes G, Deflaux N, Snyder M, Bingham J, Datta S, Tsao PS. Cloud-based Interactive Analytics for Terabytes of Genomic Variants Data. Bioinformatics (Oxford, England). PMID 28961771 DOI: 10.1093/Bioinformatics/Btx468  0.364
2017 Van Bortle K, Phanstiel DH, Snyder MP. Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation. Genome Biology. 18: 180. PMID 28931413 DOI: 10.1186/S13059-017-1310-3  0.706
2017 Phanstiel DH, Van Bortle K, Spacek D, Hess GT, Shamim MS, Machol I, Love MI, Aiden EL, Bassik MC, Snyder MP. Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. Molecular Cell. PMID 28890333 DOI: 10.1016/J.Molcel.2017.08.006  0.799
2017 Cenik B, Cenik C, Snyder MP, Brown ES. Plasma sterols and depressive symptom severity in a population-based cohort. Plos One. 12: e0184382. PMID 28886149 DOI: 10.1371/Journal.Pone.0184382  0.641
2017 Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, ... Snyder M, et al. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nature Genetics. PMID 28805829 DOI: 10.1038/Ng.3935  0.506
2017 Ma S, Snyder M, Dinesh-Kumar SP. Discovery of Novel Human Gene Regulatory Modules from Gene Co-expression and Promoter Motif Analysis. Scientific Reports. 7: 5557. PMID 28717181 DOI: 10.1038/S41598-017-05705-2  0.362
2017 Tombácz D, Csabai Z, Szűcs A, Balázs Z, Moldován N, Sharon D, Snyder M, Boldogkői Z. Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1. Frontiers in Microbiology. 8: 1079. PMID 28676792 DOI: 10.3389/Fmicb.2017.01079  0.781
2017 Liu Q, Jiang C, Xu J, Zhao M, Van Bortle K, Cheng X, Wang G, Chang HY, Wu JC, Snyder MP. Genome-Wide Temporal Profiling of Transcriptome and Open-Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs. Circulation Research. PMID 28663367 DOI: 10.1161/Circresaha.116.310456  0.577
2017 Csabai Z, Takács IF, Snyder M, Boldogkői Z, Tombácz D. Evaluation of the impact of ul54 gene-deletion on the global transcription and DNA replication of pseudorabies virus. Archives of Virology. PMID 28577213 DOI: 10.1007/S00705-017-3420-3  0.352
2017 Moldován N, Balázs Z, Tombácz D, Csabai Z, Szűcs A, Snyder M, Boldogkői Z. Multi-platform analysis reveals a complex transcriptome architecture of a circovirus. Virus Research. 237: 37-46. PMID 28549855 DOI: 10.1016/J.Virusres.2017.05.010  0.37
2017 Morgens DW, Wainberg M, Boyle EA, Ursu O, Araya CL, Tsui CK, Haney MS, Hess GT, Han K, Jeng EE, Li A, Snyder MP, Greenleaf WJ, Kundaje A, Bassik MC. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. Nature Communications. 8: 15178. PMID 28474669 DOI: 10.1038/Ncomms15178  0.708
2017 Yan KS, Janda CY, Chang J, Zheng GXY, Larkin KA, Luca VC, Chia LA, Mah AT, Han A, Terry JM, Ootani A, Roelf K, Lee M, Yuan J, Li X, ... ... Snyder MP, et al. Non-equivalence of Wnt and R-spondin ligands during Lgr5(+) intestinal stem-cell self-renewal. Nature. PMID 28467820 DOI: 10.1038/Nature22313  0.392
2017 Li J, Oehlert J, Snyder M, Stevenson DK, Shaw GM. Fetal de novo mutations and preterm birth. Plos Genetics. 13: e1006689. PMID 28388617 DOI: 10.1371/Journal.Pgen.1006689  0.365
2017 Chang J, Mancuso MR, Maier C, Liang X, Yuki K, Yang L, Kwong JW, Wang J, Rao V, Vallon M, Kosinski C, Zhang JJ, Mah AT, Xu L, Li L, ... ... Snyder M, et al. Gpr124 is essential for blood-brain barrier integrity in central nervous system disease. Nature Medicine. PMID 28288111 DOI: 10.1038/Nm.4309  0.73
2017 Tombácz D, Balázs Z, Csabai Z, Moldován N, Szűcs A, Sharon D, Snyder M, Boldogkői Z. Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing. Scientific Reports. 7: 43751. PMID 28256586 DOI: 10.1038/Srep43751  0.781
2017 Tombácz D, Moldován N, Balázs Z, Csabai Z, Snyder M, Boldogkői Z. Genetic Adaptation of Porcine Circovirus Type 1 to Cultured Porcine Kidney Cells Revealed by Single-Molecule Long-Read Sequencing Technology. Genome Announcements. 5. PMID 28153895 DOI: 10.1128/Genomea.01539-16  0.333
2017 Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, et al. Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic Acids Research. PMID 28126923 DOI: 10.1093/Nar/Gkx026  0.336
2017 Takahashi S, Andreoletti G, Chen R, Munehira Y, Batra A, Afzal NA, Beattie RM, Bernstein JA, Ennis S, Snyder M. De novo and rare mutations in the HSPA1L heat shock gene associated with inflammatory bowel disease. Genome Medicine. 9: 8. PMID 28126021 DOI: 10.1186/S13073-016-0394-9  0.343
2017 Li X, Dunn J, Salins D, Zhou G, Zhou W, Schüssler-Fiorenza Rose SM, Perelman D, Colbert E, Runge R, Rego S, Sonecha R, Datta S, McLaughlin T, Snyder MP. Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information. Plos Biology. 15: e2001402. PMID 28081144 DOI: 10.1371/Journal.Pbio.2001402  0.655
2017 Tevlin R, Seo EY, Marecic O, McArdle A, Tong X, Zimdahl B, Malkovskiy A, Sinha R, Gulati G, Li X, Wearda T, Morganti R, Lopez M, Ransom RC, Duldulao CR, ... ... Snyder M, et al. Pharmacological rescue of diabetic skeletal stem cell niches. Science Translational Medicine. 9. PMID 28077677 DOI: 10.1126/Scitranslmed.Aag2809  0.406
2017 Reza Sailani M, Jahanbani F, Nasiri J, Behnam M, Salehi M, Sedghi M, Hoseinzadeh M, Takahashi S, Zia A, Gruber J, Lynch JL, Lam D, Winkelmann J, Amirkiai S, Pang B, ... ... Snyder MP, et al. Association of AHSG with alopecia and mental retardation (APMR) syndrome. Human Genetics. PMID 28054173 DOI: 10.1007/S00439-016-1756-5  0.788
2017 Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ, Roth FP. A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N(1)-methyladenosine modification. Rna (New York, N.Y.). 23: 270-283. PMID 27994090 DOI: 10.1261/Rna.059105.116  0.7
2017 Gruber J, Snyder M. Abstract P6-05-01: Low BRCA2 levels cause epigenetic activation of growth adaptive pathways without inducing recurrent genomic mutations Cancer Research. 77. DOI: 10.1158/1538-7445.Sabcs16-P6-05-01  0.685
2017 Lopez-Pajares V, Rubin A, Barajas B, Furlan-Magaril M, Mumbach M, Greenleaf W, Kundaje A, Snyder M, Chang H, Fraser P, Khavari P. 464 Dynamic and stable enhancer-promoter contacts regulate epidermal terminal differentiation Journal of Investigative Dermatology. 137: S80. DOI: 10.1016/J.Jid.2017.02.483  0.439
2016 Gu M, Shao NY, Sa S, Li D, Termglinchan V, Ameen M, Karakikes I, Sosa G, Grubert F, Lee J, Cao A, Taylor S, Ma Y, Zhao Z, Chappell J, ... ... Snyder MP, et al. Patient-Specific iPSC-Derived Endothelial Cells Uncover Pathways that Protect against Pulmonary Hypertension in BMPR2 Mutation Carriers. Cell Stem Cell. PMID 28017794 DOI: 10.1016/J.Stem.2016.08.019  0.769
2016 Ang YS, Rivas RN, Ribeiro AJ, Srivas R, Rivera J, Stone NR, Pratt K, Mohamed TM, Fu JD, Spencer CI, Tippens ND, Li M, Narasimha A, Radzinsky E, Moon-Grady AJ, ... ... Snyder MP, et al. Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis. Cell. 167: 1734-1749.e22. PMID 27984724 DOI: 10.1016/J.Cell.2016.11.033  0.785
2016 Yu KH, Hart SN, Goldfeder R, Zhang QC, Parker SC, Snyder M. HARNESSING BIG DATA FOR PRECISION MEDICINE: INFRASTRUCTURES AND APPLICATIONS. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 22: 635-639. PMID 27897013 DOI: 10.1142/9789813207813_0058  0.481
2016 Sa S, Gu M, Chappell J, Shao NY, Ameen M, Elliott KA, Li D, Grubert F, Li CG, Taylor S, Cao A, Ma Y, Fong R, Nguyen L, Wu JC, ... Snyder MP, et al. iPSC Model of Pulmonary Arterial Hypertension Reveals Novel Gene Expression and Patient Specificity. American Journal of Respiratory and Critical Care Medicine. PMID 27779452 DOI: 10.1164/Rccm.201606-1200Oc  0.748
2016 Lefrançois P, Rockmill B, Xie P, Roeder GS, Snyder M. Multiple Pairwise Analysis of Non-homologous Centromere Coupling Reveals Preferential Chromosome Size-Dependent Interactions and a Role for Bouquet Formation in Establishing the Interaction Pattern. Plos Genetics. 12: e1006347. PMID 27768699 DOI: 10.1371/Journal.Pgen.1006347  0.651
2016 Reuter JA, Spacek DV, Pai RK, Snyder MP. Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling. Nature Methods. PMID 27723755 DOI: 10.1038/nmeth.4028  0.816
2016 Tombácz D, Csabai Z, Oláh P, Balázs Z, Likó I, Zsigmond L, Sharon D, Snyder M, Boldogkői Z. Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus. Plos One. 11: e0162868. PMID 27685795 DOI: 10.1371/Journal.Pone.0162868  0.792
2016 Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nature Genetics. PMID 27526324 DOI: 10.1038/Ng.3646  0.453
2016 Snyder M, Mias G, Stanberry L, Kolker E. Metadata Checklist for the Integrated Personal Omics Study: Proteomics and Metabolomics Experiments. Big Data. 1: 202-6. PMID 27447252 DOI: 10.1089/big.2013.0040  0.679
2016 Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, ... ... Snyder MP, et al. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell. PMID 27372738 DOI: 10.1016/J.Cell.2016.05.069  0.378
2016 Arda HE, Li L, Tsai J, Torre EA, Rosli Y, Peiris H, Spitale RC, Dai C, Gu X, Qu K, Wang P, Wang J, Grompe M, Scharfmann R, Snyder MS, et al. Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function. Cell Metabolism. PMID 27133132 DOI: 10.1016/J.Cmet.2016.04.002  0.423
2016 Yu KH, Snyder M. Omics profiling in precision oncology. Molecular & Cellular Proteomics : McP. PMID 27099341 DOI: 10.1074/Mcp.O116.059253  0.312
2016 Contrepois K, Liang L, Snyder M. Can Metabolic Profiles Be Used as a Phenotypic Readout of the Genome to Enhance Precision Medicine? Clinical Chemistry. PMID 26960666 DOI: 10.1373/Clinchem.2015.251181  0.347
2016 Landegren N, Sharon D, Freyhult E, Hallgren Å, Eriksson D, Edqvist PH, Bensing S, Wahlberg J, Nelson LM, Gustafsson J, Husebye ES, Anderson MS, Snyder M, Kämpe O. Proteome-wide survey of the autoimmune target repertoire in autoimmune polyendocrine syndrome type 1. Scientific Reports. 6: 20104. PMID 26830021 DOI: 10.1038/Srep20104  0.76
2016 Bray MS, Loos RJ, McCaffery JM, Ling C, Franks PW, Weinstock GM, Snyder MP, Vassy JL, Agurs-Collins T. NIH working group report-using genomic information to guide weight management: From universal to precision treatment. Obesity (Silver Spring, Md.). 24: 14-22. PMID 26692578 DOI: 10.1002/Oby.21381  0.433
2016 Alla R, Luo S, Helman E, Boyle SM, Clark MJ, Scott K, Sripakdeevong P, Karbelashvili M, Church DM, Snyder M, West J, Chen R. Abstract 3616: Fix the fixation: effect of formalin fixation on targeted sequencing, variant calling and gene expression Cancer Research. 76: 3616-3616. DOI: 10.1158/1538-7445.Am2016-3616  0.318
2015 Li J, Ma Z, Shi M, Malty RH, Aoki H, Minic Z, Phanse S, Jin K, Wall DP, Zhang Z, Urban AE, Hallmayer J, Babu M, Snyder M. Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders. Cell Systems. 1: 361-374. PMID 26949739 DOI: 10.1016/J.Cels.2015.11.002  0.311
2015 Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf WJ. Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nature Genetics. PMID 26691984 DOI: 10.1038/Ng.3471  0.79
2015 Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nature Biotechnology. PMID 26655498 DOI: 10.1038/Nbt.3416  0.593
2015 Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, ... ... Snyder M, et al. Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. PMID 26560031 DOI: 10.1038/Nature16075  0.785
2015 Dewey FE, Grove ME, Priest JR, Waggott D, Batra P, Miller CL, Wheeler M, Zia A, Pan C, Karzcewski KJ, Miyake C, Whirl-Carrillo M, Klein TE, Datta S, Altman RB, Snyder M, et al. Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data. Plos Genetics. 11: e1005496. PMID 26448358 DOI: 10.1371/Journal.Pgen.1005496  0.381
2015 Yan JF, Kim H, Jeong SK, Lee HJ, Sethi MK, Lee LY, Beavis RC, Im H, Snyder MP, Hofree M, Ideker T, Wu SL, Paik YK, Fanayan S, Hancock WS. Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. Journal of Proteome Research. PMID 26435392 DOI: 10.1021/Acs.Jproteome.5B00827  0.477
2015 Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, ... ... Snyder M, et al. Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell. PMID 26300125 DOI: 10.1016/J.Cell.2015.07.048  0.802
2015 Cenik C, Sarinay Cenik E, Byeon GW, Grubert F, Candille SI, Spacek D, Alsallakh B, Tilgner H, Araya CL, Tang H, Ricci E, Snyder MP. Integrative analysis of RNA, translation and protein levels reveals distinct regulatory variation across humans. Genome Research. PMID 26297486 DOI: 10.1101/Gr.193342.115  0.803
2015 Patwardhan A, Harris J, Leng N, Bartha G, Church DM, Luo S, Haudenschild C, Pratt M, Zook J, Salit M, Tirch J, Morra M, Chervitz S, Li M, Clark M, ... ... Snyder M, et al. Achieving high-sensitivity for clinical applications using augmented exome sequencing. Genome Medicine. 7: 71. PMID 26269718 DOI: 10.1186/S13073-015-0197-4  0.374
2015 Ungewickell A, Bhaduri A, Rios E, Reuter J, Lee CS, Mah A, Zehnder A, Ohgami R, Kulkarni S, Armstrong R, Weng WK, Gratzinger D, Tavallaee M, Rook A, Snyder M, et al. Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2. Nature Genetics. PMID 26258847 DOI: 10.1038/Ng.3370  0.754
2015 Tyler-Smith C, Yang H, Landweber LF, Dunham I, Knoppers BM, Donnelly P, Mardis ER, Snyder M, McVean G. Where Next for Genetics and Genomics? Plos Biology. 13: e1002216. PMID 26225775 DOI: 10.1371/Journal.Pbio.1002216  0.303
2015 Lambrus BG, Uetake Y, Clutario KM, Daggubati V, Snyder M, Sluder G, Holland AJ. p53 protects against genome instability following centriole duplication failure. The Journal of Cell Biology. 210: 63-77. PMID 26150389 DOI: 10.1083/Jcb.201502089  0.323
2015 Marcobal A, Yusufaly T, Higginbottom S, Snyder M, Sonnenburg JL, Mias GI. Metabolome progression during early gut microbial colonization of gnotobiotic mice. Scientific Reports. 5: 11589. PMID 26118551 DOI: 10.1038/Srep11589  0.677
2015 Landegren N, Sharon D, Shum AK, Khan IS, Fasano KJ, Hallgren Å, Kampf C, Freyhult E, Ardesjö-Lundgren B, Alimohammadi M, Rathsman S, Ludvigsson JF, Lundh D, Motrich R, Rivero V, ... ... Snyder M, et al. Transglutaminase 4 as a prostate autoantigen in male subfertility. Science Translational Medicine. 7: 292ra101. PMID 26084804 DOI: 10.1126/Scitranslmed.Aaa9186  0.729
2015 Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 523: 486-90. PMID 26083756 DOI: 10.1038/Nature14590  0.467
2015 Melton C, Reuter JA, Spacek DV, Snyder M. Recurrent somatic mutations in regulatory regions of human cancer genomes. Nature Genetics. PMID 26053494 DOI: 10.1038/Ng.3332  0.798
2015 Phanstiel DH, Boyle AP, Heidari N, Snyder MP. Mango: A bias correcting ChIA-PET analysis pipeline. Bioinformatics (Oxford, England). PMID 26034063 DOI: 10.1093/Bioinformatics/Btv336  0.768
2015 Li J, Yu KH, Oehlert J, Jeliffe-Pawlowski LL, Gould JB, Stevenson DK, Snyder M, Shaw GM, O'Brodovich HM. Exome Sequencing of Neonatal Blood Spots Identifies Genes Implicated in Bronchopulmonary Dysplasia. American Journal of Respiratory and Critical Care Medicine. PMID 26030808 DOI: 10.1164/Rccm.201501-0168Oc  0.334
2015 Song G, Dickins BJ, Demeter J, Engel S, Gallagher J, Choe K, Dunn B, Snyder M, Cherry JM. Correction: AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. Plos One. 10: e0129184. PMID 26017550 DOI: 10.1371/Journal.Pone.0129184  0.34
2015 Tombácz D, Csabai Z, Oláh P, Havelda Z, Sharon D, Snyder M, Boldogk?i Z. Characterization of novel transcripts in pseudorabies virus. Viruses. 7: 2727-44. PMID 26008709 DOI: 10.3390/V7052727  0.775
2015 Reuter JA, Spacek DV, Snyder MP. High-Throughput Sequencing Technologies. Molecular Cell. 58: 586-597. PMID 26000844 DOI: 10.1016/j.molcel.2015.05.004  0.794
2015 Chen R, Im H, Snyder M. Whole-Exome Enrichment with the Roche NimbleGen SeqCap EZ Exome Library SR Platform. Cold Spring Harbor Protocols. 2015: pdb.prot084855. PMID 25762419 DOI: 10.1101/Pdb.Prot084855  0.404
2015 Chen R, Im H, Snyder M. Whole-Exome Enrichment with the Illumina TruSeq Exome Enrichment Platform. Cold Spring Harbor Protocols. 2015: pdb.prot084863. PMID 25762418 DOI: 10.1101/Pdb.Prot084863  0.419
2015 Chen R, Im H, Snyder M. Whole-Exome Enrichment with the Agilent SureSelect Human All Exon Platform. Cold Spring Harbor Protocols. 2015: pdb.prot083659. PMID 25762417 DOI: 10.1101/Pdb.Prot083659  0.42
2015 Lardenois A, Stuparevic I, Liu Y, Law MJ, Becker E, Smagulova F, Waern K, Guilleux MH, Horecka J, Chu A, Kervarrec C, Strich R, Snyder M, Davis RW, Steinmetz LM, et al. The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. Nucleic Acids Research. 43: 115-28. PMID 25477386 DOI: 10.1093/Nar/Gku1185  0.803
2015 Araya CL, Cenik C, Reuter J, Snyder M, Greenleaf W. Abstract B2-42: Systematic dissection of multi-scale mutational hotspots across 21 cancer types reveals a rich landscape of functionally targeted oncogenic disruptions Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B2-42  0.802
2014 Li J, Shi M, Ma Z, Zhao S, Euskirchen G, Ziskin J, Urban A, Hallmayer J, Snyder M. Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. Molecular Systems Biology. 10: 774. PMID 25549968 DOI: 10.15252/Msb.20145487  0.4
2014 Haraksingh RR, Jahanbani F, Rodriguez-Paris J, Gelernter J, Nadeau KC, Oghalai JS, Schrijver I, Snyder MP. Exome sequencing and genome-wide copy number variant mapping reveal novel associations with sensorineural hereditary hearing loss. Bmc Genomics. 15: 1155. PMID 25528277 DOI: 10.1186/1471-2164-15-1155  0.762
2014 Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP. Comparison of the transcriptional landscapes between human and mouse tissues. Proceedings of the National Academy of Sciences of the United States of America. 111: 17224-9. PMID 25413365 DOI: 10.1073/Pnas.1413624111  0.493
2014 Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. 515: 402-5. PMID 25409831 DOI: 10.1038/Nature13986  0.565
2014 Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, ... Snyder MP, et al. Principles of regulatory information conservation between mouse and human. Nature. 515: 371-5. PMID 25409826 DOI: 10.1038/Nature13985  0.765
2014 Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, ... Snyder MP, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992  0.773
2014 Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Research. 24: 1963-76. PMID 25319995 DOI: 10.1101/Gr.168872.113  0.424
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/Pnas.1410434111  0.709
2014 Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP. Genome-wide map of regulatory interactions in the human genome. Genome Research. 24: 1905-17. PMID 25228660 DOI: 10.1101/Gr.176586.114  0.824
2014 Lefrançois P, Gallagher JE, Snyder M. Global analysis of transcription factor-binding sites in yeast using ChIP-Seq. Methods in Molecular Biology (Clifton, N.J.). 1205: 231-55. PMID 25213249 DOI: 10.1007/978-1-4939-1363-3_15  0.689
2014 Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, ... ... Snyder M, et al. Comparative analysis of regulatory information and circuits across distant species. Nature. 512: 453-6. PMID 25164757 DOI: 10.1038/Nature13668  0.814
2014 Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, ... ... Snyder M, et al. Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. 512: 400-5. PMID 25164749 DOI: 10.1038/Nature13497  0.816
2014 Martin AR, Costa HA, Lappalainen T, Henn BM, Kidd JM, Yee MC, Grubert F, Cann HM, Snyder M, Montgomery SB, Bustamante CD. Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture. Plos Genetics. 10: e1004549. PMID 25121757 DOI: 10.1371/Journal.Pgen.1004549  0.755
2014 Tombácz D, Sharon D, Oláh P, Csabai Z, Snyder M, Boldogk?i Z. Strain Kaplan of Pseudorabies Virus Genome Sequenced by PacBio Single-Molecule Real-Time Sequencing Technology. Genome Announcements. 2. PMID 25035325 DOI: 10.1128/Genomea.00628-14  0.757
2014 Sharon D, Snyder M. Serum profiling using protein microarrays to identify disease related antigens. Methods in Molecular Biology (Clifton, N.J.). 1176: 169-78. PMID 25030927 DOI: 10.1007/978-1-4939-0992-6_14  0.732
2014 Tilgner H, Grubert F, Sharon D, Snyder MP. Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proceedings of the National Academy of Sciences of the United States of America. 111: 9869-74. PMID 24961374 DOI: 10.1073/Pnas.1400447111  0.807
2014 Phanstiel DH, Boyle AP, Araya CL, Snyder MP. Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures. Bioinformatics (Oxford, England). 30: 2808-10. PMID 24903420 DOI: 10.1093/Bioinformatics/Btu379  0.782
2014 Kukurba KR, Zhang R, Li X, Smith KS, Knowles DA, How Tan M, Piskol R, Lek M, Snyder M, Macarthur DG, Li JB, Montgomery SB. Allelic expression of deleterious protein-coding variants across human tissues. Plos Genetics. 10: e1004304. PMID 24786518 DOI: 10.1371/Journal.Pgen.1004304  0.372
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/Pnas.1318948111  0.754
2014 Buenrostro JD, Araya CL, Chircus LM, Layton CJ, Chang HY, Snyder MP, Greenleaf WJ. Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nature Biotechnology. 32: 562-8. PMID 24727714 DOI: 10.1038/Nbt.2880  0.76
2014 Enns GM, Shashi V, Bainbridge M, Gambello MJ, Zahir FR, Bast T, Crimian R, Schoch K, Platt J, Cox R, Bernstein JA, Scavina M, Walter RS, Bibb A, Jones M, ... ... Snyder M, et al. Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 16: 751-8. PMID 24651605 DOI: 10.1038/Gim.2014.22  0.752
2014 Dewey FE, Grove ME, Pan C, Goldstein BA, Bernstein JA, Chaib H, Merker JD, Goldfeder RL, Enns GM, David SP, Pakdaman N, Ormond KE, Caleshu C, Kingham K, Klein TE, ... ... Snyder M, et al. Clinical interpretation and implications of whole-genome sequencing. Jama. 311: 1035-45. PMID 24618965 DOI: 10.1001/Jama.2014.1717  0.32
2014 Brdlik CM, Niu W, Snyder M. Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans. Methods in Enzymology. 539: 89-111. PMID 24581441 DOI: 10.1016/B978-0-12-420120-0.00007-4  0.375
2014 Kuleshov V, Xie D, Chen R, Pushkarev D, Ma Z, Blauwkamp T, Kertesz M, Snyder M. Whole-genome haplotyping using long reads and statistical methods. Nature Biotechnology. 32: 261-6. PMID 24561555 DOI: 10.1038/Nbt.2833  0.459
2014 Tragante V, Barnes MR, Ganesh SK, Lanktree MB, Guo W, Franceschini N, Smith EN, Johnson T, Holmes MV, Padmanabhan S, Karczewski KJ, Almoguera B, Barnard J, Baumert J, Chang YP, ... ... Snyder M, et al. Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci. American Journal of Human Genetics. 94: 349-60. PMID 24560520 DOI: 10.1016/J.Ajhg.2013.12.016  0.337
2014 Karczewski KJ, Snyder M, Altman RB, Tatonetti NP. Coherent Functional Modules Improve Transcription Factor Target Identification, Cooperativity Prediction, and Disease Association Plos Genetics. 10. PMID 24516403 DOI: 10.1371/Journal.Pgen.1004122  0.33
2014 Kanai T, Seki S, Jenks JA, Kohli A, Kawli T, Martin DP, Snyder M, Bacchetta R, Nadeau KC. Identification of STAT5A and STAT5B target genes in human T cells. Plos One. 9: e86790. PMID 24497979 DOI: 10.1371/Journal.Pone.0086790  0.372
2014 Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY. Landscape and variation of RNA secondary structure across the human transcriptome. Nature. 505: 706-9. PMID 24476892 DOI: 10.1038/Nature12946  0.609
2014 Snyder M, Mias G, Stanberry L, Kolker E. Metadata checklist for the integrated personal OMICS study: proteomics and metabolomics experiments. Omics : a Journal of Integrative Biology. 18: 81-5. PMID 24456466 DOI: 10.1089/Omi.2013.0148  0.666
2014 Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, ... ... Snyder M, et al. Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. Omics : a Journal of Integrative Biology. 18: 10-4. PMID 24456465 DOI: 10.1089/Omi.2013.0149  0.71
2014 Karczewski KJ, Fernald GH, Martin AR, Snyder M, Tatonetti NP, Dudley JT. STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud. Plos One. 9: e84860. PMID 24454756 DOI: 10.1371/Journal.Pone.0084860  0.338
2014 Menon R, Im H, Zhang EY, Wu SL, Chen R, Snyder M, Hancock WS, Omenn GS. Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes. Journal of Proteome Research. 13: 212-27. PMID 24111759 DOI: 10.1021/Pr400773V  0.425
2014 Heffelfinger C, Pakstis AJ, Speed WC, Clark AP, Haigh E, Fang R, Furtado MR, Kidd KK, Snyder MP. Haplotype structure and positive selection at TLR1. European Journal of Human Genetics : Ejhg. 22: 551-7. PMID 24002163 DOI: 10.1038/Ejhg.2013.194  0.726
2014 Sharon D, Tilgner H, Grubert F, Snyder M. Erratum: A single-molecule long-read survey of the human transcriptome Nature Biotechnology. 32: 291-291. DOI: 10.1038/Nbt0314-291B  0.763
2013 Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, ... ... Snyder M, et al. Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. Big Data. 1: 196-201. PMID 27447251 DOI: 10.1089/big.2013.0039  0.689
2013 Mias GI, Snyder M. Personal genomes, quantitative dynamic omics and personalized medicine. Quantitative Biology. 1: 71-90. PMID 25798291 DOI: 10.1007/s40484-013-0005-3  0.696
2013 Stanberry L, Mias GI, Haynes W, Higdon R, Snyder M, Kolker E. Integrative analysis of longitudinal metabolomics data from a personal multi-omics profile. Metabolites. 3: 741-60. PMID 24958148 DOI: 10.3390/Metabo3030741  0.708
2013 Mias GI, Chen R, Zhang Y, Sridhar K, Sharon D, Xiao L, Im H, Snyder MP, Greenberg PL. Specific plasma autoantibody reactivity in myelodysplastic syndromes. Scientific Reports. 3: 3311. PMID 24264604 DOI: 10.1038/Srep03311  0.771
2013 Xie D, Boyle AP, Wu L, Zhai J, Kawli T, Snyder M. Dynamic trans-acting factor colocalization in human cells. Cell. 155: 713-24. PMID 24243024 DOI: 10.1016/J.Cell.2013.09.043  0.648
2013 Hardee J, Ouyang Z, Zhang Y, Kundaje A, Lacroute P, Snyder M. STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma. G3 (Bethesda, Md.). 3: 2173-85. PMID 24142927 DOI: 10.1534/G3.113.007674  0.786
2013 Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, ... ... Snyder M, et al. Extensive variation in chromatin states across humans. Science (New York, N.Y.). 342: 750-2. PMID 24136358 DOI: 10.1126/Science.1242510  0.799
2013 Sharon D, Tilgner H, Grubert F, Snyder M. A single-molecule long-read survey of the human transcriptome. Nature Biotechnology. 31: 1009-14. PMID 24108091 DOI: 10.1038/Nbt.2705  0.794
2013 Ma S, Shah S, Bohnert HJ, Snyder M, Dinesh-Kumar SP. Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways. Plos Genetics. 9: e1003840. PMID 24098147 DOI: 10.1371/Journal.Pgen.1003840  0.343
2013 Franceschini N, Fox E, Zhang Z, Edwards TL, Nalls MA, Sung YJ, Tayo BO, Sun YV, Gottesman O, Adeyemo A, Johnson AD, Young JH, Rice K, Duan Q, Chen F, ... ... Snyder M, et al. Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations. American Journal of Human Genetics. 93: 545-54. PMID 23972371 DOI: 10.1016/J.Ajhg.2013.07.010  0.339
2013 Qian F, Chung L, Zheng W, Bruno V, Alexander RP, Wang Z, Wang X, Kurscheid S, Zhao H, Fikrig E, Gerstein M, Snyder M, Montgomery RR. Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis. Viruses. 5: 1664-81. PMID 23881275 DOI: 10.3390/V5071664  0.33
2013 Merker JD, Roskin KM, Ng D, Pan C, Fisk DG, King JJ, Hoh R, Stadler M, Okumoto LM, Abidi P, Hewitt R, Jones CD, Gojenola L, Clark MJ, Zhang B, ... ... Snyder M, et al. Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes. Haematologica. 98: 1689-96. PMID 23872309 DOI: 10.3324/Haematol.2013.092379  0.381
2013 Haraksingh RR, Snyder MP. Impacts of variation in the human genome on gene regulation. Journal of Molecular Biology. 425: 3970-7. PMID 23871684 DOI: 10.1016/J.Jmb.2013.07.015  0.792
2013 Chen R, Giliani S, Lanzi G, Mias GI, Lonardi S, Dobbs K, Manis J, Im H, Gallagher JE, Phanstiel DH, Euskirchen G, Lacroute P, Bettinger K, Moratto D, Weinacht K, ... ... Snyder M, et al. Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias. The Journal of Allergy and Clinical Immunology. 132: 656-664.e17. PMID 23830146 DOI: 10.1016/J.Jaci.2013.06.013  0.776
2013 Wellensiek BP, Larsen AC, Stephens B, Kukurba K, Waern K, Briones N, Liu L, Snyder M, Jacobs BL, Kumar S, Chaput JC. Genome-wide profiling of human cap-independent translation-enhancing elements. Nature Methods. 10: 747-50. PMID 23770754 DOI: 10.1038/Nmeth.2522  0.811
2013 Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ, Montgomery SB, Snyder M. Systematic functional regulatory assessment of disease-associated variants. Proceedings of the National Academy of Sciences of the United States of America. 110: 9607-12. PMID 23690573 DOI: 10.1073/Pnas.1219099110  0.373
2013 Wu L, Candille SI, Choi Y, Xie D, Jiang L, Li-Pook-Than J, Tang H, Snyder M. Variation and genetic control of protein abundance in humans. Nature. 499: 79-82. PMID 23676674 DOI: 10.1038/Nature12223  0.368
2013 Zhang EY, Cristofanilli M, Robertson F, Reuben JM, Mu Z, Beavis RC, Im H, Snyder M, Hofree M, Ideker T, Omenn GS, Fanayan S, Jeong SK, Paik YK, Zhang AF, et al. Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer. Journal of Proteome Research. 12: 2805-17. PMID 23647160 DOI: 10.1021/Pr4001527  0.543
2013 Clark MJ, Chen R, Snyder M. Exome sequencing by targeted enrichment. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit7.12. PMID 23547016 DOI: 10.1002/0471142727.Mb0712S102  0.436
2013 Won KJ, Zhang X, Wang T, Ding B, Raha D, Snyder M, Ren B, Wang W. Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Research. 41: 4423-32. PMID 23482391 DOI: 10.1093/Nar/Gkt143  0.349
2013 Fanayan S, Smith JT, Lee LY, Yan F, Snyder M, Hancock WS, Nice E. Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405. Journal of Proteome Research. 12: 1732-42. PMID 23458625 DOI: 10.1021/Pr3010869  0.367
2013 Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M. Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda, Md.). 3: 387-97. PMID 23450794 DOI: 10.1534/G3.112.004812  0.394
2013 Huang XA, Yin H, Sweeney S, Raha D, Snyder M, Lin H. A major epigenetic programming mechanism guided by piRNAs. Developmental Cell. 24: 502-16. PMID 23434410 DOI: 10.1016/J.Devcel.2013.01.023  0.376
2013 Waern K, Snyder M. Extensive transcript diversity and novel upstream open reading frame regulation in yeast. G3 (Bethesda, Md.). 3: 343-52. PMID 23390610 DOI: 10.1534/G3.112.003640  0.811
2013 Lefrançois P, Auerbach RK, Yellman CM, Roeder GS, Snyder M. Centromere-like regions in the budding yeast genome. Plos Genetics. 9: e1003209. PMID 23349633 DOI: 10.1371/Journal.Pgen.1003209  0.691
2013 Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology. 14: R5. PMID 23347407 DOI: 10.1186/Gb-2013-14-1-R5  0.368
2013 Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, Dalton S, Fenyo D, Fanayan S, Gates C, Gaudet P, Hincapie M, Hanash S, Kim H, Jeong SK, ... ... Snyder M, et al. A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. Journal of Proteome Research. 12: 45-57. PMID 23259914 DOI: 10.1021/Pr300985J  0.744
2013 O'Huallachain M, Weissman SM, Snyder MP. The variable somatic genome. Cell Cycle (Georgetown, Tex.). 12: 5-6. PMID 23255102 DOI: 10.4161/cc.23069  0.789
2013 Li X, Wang X, Snyder M. Systematic investigation of protein-small molecule interactions. Iubmb Life. 65: 2-8. PMID 23225626 DOI: 10.1002/Iub.1111  0.301
2013 Mias GI, Snyder M. Multimodal dynamic profiling of healthy and diseased states for future personalized health care. Clinical Pharmacology and Therapeutics. 93: 29-32. PMID 23187877 DOI: 10.1038/Clpt.2012.204  0.69
2013 Chen R, Snyder M. Promise of personalized omics to precision medicine. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 5: 73-82. PMID 23184638 DOI: 10.1002/Wsbm.1198  0.388
2013 Ouyang Z, Snyder MP, Chang HY. SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. Genome Research. 23: 377-87. PMID 23064747 DOI: 10.1101/Gr.138545.112  0.41
2013 Menon R, Im H, Snyder M, Zhang E(, Chen R, Wu S, Hancock WS, Omenn GS. Abstract B38: Splice variants in aggressive human breast cancer subtypes Cancer Research. 73. DOI: 10.1158/1538-7445.Fbcr13-B38  0.409
2013 Jahaniani F, Rao V, Nevins S, Spacek D, Bharadwaj N, Reuter J, Snyder M. Emerging technologies to study long non-coding RNAs Molecular Biology of Long Non-Coding Rnas. 163-195. DOI: 10.1007/978-1-4614-8621-3_7  0.782
2012 Wu J, Grzeda KR, Stewart C, Grubert F, Urban AE, Snyder MP, Marth GT. Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data. Bmc Bioinformatics. 13: 305. PMID 23157288 DOI: 10.1186/1471-2105-13-305  0.75
2012 O'Huallachain M, Karczewski KJ, Weissman SM, Urban AE, Snyder MP. Extensive genetic variation in somatic human tissues. Proceedings of the National Academy of Sciences of the United States of America. 109: 18018-23. PMID 23043118 DOI: 10.1073/Pnas.1213736109  0.807
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, ... ... Snyder M, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111  0.517
2012 Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Research. 22: 1798-812. PMID 22955990 DOI: 10.1101/Gr.139105.112  0.519
2012 Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M. Annotation of functional variation in personal genomes using RegulomeDB. Genome Research. 22: 1790-7. PMID 22955989 DOI: 10.1101/Gr.137323.112  0.733
2012 Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Research. 22: 1748-59. PMID 22955986 DOI: 10.1101/gr.136127.111  0.6
2012 Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Research. 22: 1735-47. PMID 22955985 DOI: 10.1101/Gr.136366.111  0.338
2012 Charos AE, Reed BD, Raha D, Szekely AM, Weissman SM, Snyder M. A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells. Genome Research. 22: 1668-79. PMID 22955979 DOI: 10.1101/Gr.127761.111  0.816
2012 Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, ... ... Snyder M, et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research. 22: 1658-67. PMID 22955978 DOI: 10.1101/Gr.136838.111  0.343
2012 Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigó R. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Research. 22: 1616-25. PMID 22955974 DOI: 10.1101/Gr.134445.111  0.328
2012 Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, ... ... Snyder M, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 489: 91-100. PMID 22955619 DOI: 10.1038/Nature11245  0.803
2012 Euskirchen G, Auerbach RK, Snyder M. SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions. The Journal of Biological Chemistry. 287: 30897-905. PMID 22952240 DOI: 10.1074/Jbc.R111.309302  0.365
2012 Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biology. 13: R48. PMID 22950945 DOI: 10.1186/Gb-2012-13-9-R48  0.378
2012 Ma S, Bachan S, Porto M, Bohnert HJ, Snyder M, Dinesh-Kumar SP. Discovery of stress responsive DNA regulatory motifs in Arabidopsis. Plos One. 7: e43198. PMID 22912824 DOI: 10.1371/Journal.Pone.0043198  0.39
2012 Sarov M, Murray JI, Schanze K, Pozniakovski A, Niu W, Angermann K, Hasse S, Rupprecht M, Vinis E, Tinney M, Preston E, Zinke A, Enst S, Teichgraber T, Janette J, ... ... Snyder M, et al. A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell. 150: 855-66. PMID 22901814 DOI: 10.1016/J.Cell.2012.08.001  0.374
2012 Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418  0.729
2012 Chen R, Snyder M. Systems biology: personalized medicine for the future? Current Opinion in Pharmacology. 12: 623-8. PMID 22858243 DOI: 10.1016/J.Coph.2012.07.011  0.38
2012 Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics (Oxford, England). 28: 2267-9. PMID 22743228 DOI: 10.1093/Bioinformatics/Bts368  0.376
2012 Maston GA, Landt SG, Snyder M, Green MR. Characterization of enhancer function from genome-wide analyses. Annual Review of Genomics and Human Genetics. 13: 29-57. PMID 22703170 DOI: 10.1146/Annurev-Genom-090711-163723  0.402
2012 Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, ... ... Snyder M, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 148: 1293-307. PMID 22424236 DOI: 10.1016/J.Cell.2012.02.009  0.786
2012 Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M, Gerstein MB, Kidd JM, Bustamante CD, Snyder M. Detecting and annotating genetic variations using the HugeSeq pipeline. Nature Biotechnology. 30: 226-9. PMID 22398614 DOI: 10.1038/Nbt.2134  0.766
2012 Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F, Zhang F, Zhang Y, Snyder M, Cheng Y, Chen R, et al. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nature Biotechnology. 30: 221-3. PMID 22398612 DOI: 10.1038/Nbt.2152  0.526
2012 Heffelfinger C, Ouyang Z, Engberg A, Leffell DJ, Hanlon AM, Gordon PB, Zheng W, Zhao H, Snyder MP, Bale AE. Correlation of Global MicroRNA Expression With Basal Cell Carcinoma Subtype. G3 (Bethesda, Md.). 2: 279-86. PMID 22384406 DOI: 10.1534/G3.111.001115  0.718
2012 Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, ... ... Snyder M, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 148: 84-98. PMID 22265404 DOI: 10.1016/J.Cell.2011.12.014  0.373
2012 Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Performance comparison of whole-genome sequencing platforms. Nature Biotechnology. 30: 78-82. PMID 22178993 DOI: 10.1038/Nbt.2065  0.805
2012 Kaganovich M, Snyder M. Phosphorylation of yeast transcription factors correlates with the evolution of novel sequence and function Journal of Proteome Research. 11: 261-268. PMID 22141333 DOI: 10.1021/Pr201065K  0.386
2012 Szekely A, Zhang Y, Reed B, Schulz V, Wang Z, Euskirchen G, Snyder M, Ivanova N, Weissman S. Pooled Short Hairpin (shRNA) Library Screen Coupled with Next-Generation Sequencing Efficiently Uncover Transcriptional Network in Neural Lineage Development of Human Embryonic Stem Cells (IN8-1.009) Neurology. 78: IN8-1.009-IN8-1.009. DOI: 10.1212/Wnl.78.1_Meetingabstracts.In8-1.009  0.377
2012 Merker JD, Roskin K, Ng D, Pan C, Fisk DG, Jones CD, Gojenola L, Clark MJ, Zhang B, Cherry M, Snyder M, Boyd SD, Zehnder JL, Fire AZ, Gotlib J. Whole Genome Sequence Analysis of Primary Myelofibrosis. Blood. 120: 2863-2863. DOI: 10.1182/Blood.V120.21.2863.2863  0.356
2012 Lam HYK, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Erratum: Corrigendum: Performance comparison of whole-genome sequencing platforms Nature Biotechnology. 30: 562-562. DOI: 10.1038/Nbt0612-562E  0.777
2012 Waern K, Snyder M. RNA-Seq transcriptomics Access Science. DOI: 10.1036/1097-8542.Yb120237  0.776
2011 Yin H, Sweeney S, Raha D, Snyder M, Lin H. A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster. Plos Genetics. 7: e1002380. PMID 22194694 DOI: 10.1371/Journal.Pgen.1002380  0.397
2011 Haraksingh RR, Abyzov A, Gerstein M, Urban AE, Snyder M. Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms. Plos One. 6: e27859. PMID 22140474 DOI: 10.1371/Journal.Pone.0027859  0.773
2011 Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M. Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. Plos Computational Biology. 7: e1002190. PMID 22125477 DOI: 10.1371/Journal.Pcbi.1002190  0.322
2011 Mok J, Zhu X, Snyder M. Dissecting phosphorylation networks: lessons learned from yeast. Expert Review of Proteomics. 8: 775-86. PMID 22087660 DOI: 10.1586/Epr.11.64  0.78
2011 Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. Performance comparison of exome DNA sequencing technologies. Nature Biotechnology. 29: 908-14. PMID 21947028 DOI: 10.1038/Nbt.1975  0.447
2011 Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, ... ... Snyder M, et al. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. Plos Genetics. 7: e1002280. PMID 21935354 DOI: 10.1371/Journal.Pgen.1002280  0.359
2011 Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, ... Snyder MP, et al. A comprehensive map of mobile element insertion polymorphisms in humans. Plos Genetics. 7: e1002236. PMID 21876680 DOI: 10.1371/Journal.Pgen.1002236  0.739
2011 Waern K, Nagalakshmi U, Snyder M. RNA sequencing. Methods in Molecular Biology (Clifton, N.J.). 759: 125-32. PMID 21863485 DOI: 10.1007/978-1-61779-173-4_8  0.787
2011 Karczewski KJ, Tatonetti NP, Landt SG, Yang X, Slifer T, Altman RB, Snyder M. Cooperative transcription factor associations discovered using regulatory variation. Proceedings of the National Academy of Sciences of the United States of America. 108: 13353-8. PMID 21828005 DOI: 10.1073/Pnas.1103105108  0.339
2011 Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Molecular Systems Biology. 7: 522. PMID 21811232 DOI: 10.1038/Msb.2011.54  0.402
2011 Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M. Identification of genomic indels and structural variations using split reads. Bmc Genomics. 12: 375. PMID 21787423 DOI: 10.1186/1471-2164-12-375  0.369
2011 Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers CH, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, ... ... Snyder M, et al. The human proteome project: current state and future direction. Molecular & Cellular Proteomics : McP. 10: M111.009993. PMID 21742803 DOI: 10.1074/Mcp.M111.009993  0.328
2011 Zheng W, Gianoulis TA, Karczewski KJ, Zhao H, Snyder M. Regulatory variation within and between species. Annual Review of Genomics and Human Genetics. 12: 327-46. PMID 21721942 DOI: 10.1146/Annurev-Genom-082908-150139  0.377
2011 Wontakal SN, Guo X, Will B, Shi M, Raha D, Mahajan MC, Weissman S, Snyder M, Steidl U, Zheng D, Skoultchi AI. A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1. Plos Genetics. 7: e1001392. PMID 21695229 DOI: 10.1371/Journal.Pgen.1001392  0.34
2011 Li X, Snyder M. Metabolites as global regulators: a new view of protein regulation: systematic investigation of metabolite-protein interactions may help bridge the gap between genome-wide association studies and small molecule screening studies. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 33: 485-9. PMID 21495048 DOI: 10.1002/Bies.201100026  0.345
2011 Fasolo J, Sboner A, Sun MG, Yu H, Chen R, Sharon D, Kim PM, Gerstein M, Snyder M. Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes & Development. 25: 767-78. PMID 21460040 DOI: 10.1101/Gad.1998811  0.771
2011 Gianoulis TA, Agarwal A, Snyder M, Gerstein MB. The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics. Genome Biology. 12: R32. PMID 21453526 DOI: 10.1186/Gb-2011-12-3-R32  0.333
2011 Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, Bhardwaj N, Gerstein MB, Snyder M. Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. Plos Genetics. 7: e1002008. PMID 21408204 DOI: 10.1371/Journal.Pgen.1002008  0.408
2011 Smith MG, Ptacek J, Snyder M. Kinase substrate interactions. Methods in Molecular Biology (Clifton, N.J.). 723: 201-12. PMID 21370067 DOI: 10.1007/978-1-61779-043-0_13  0.626
2011 Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Research. 21: 974-84. PMID 21324876 DOI: 10.1101/Gr.114876.110  0.357
2011 Pérez-Lluch S, Blanco E, Carbonell A, Raha D, Snyder M, Serras F, Corominas M. Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing. Nucleic Acids Research. 39: 4628-39. PMID 21310711 DOI: 10.1093/Nar/Gkq1322  0.381
2011 Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, ... ... Snyder M, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 470: 59-65. PMID 21293372 DOI: 10.1038/Nature09708  0.767
2011 Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, et al. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Research. 21: 276-85. PMID 21177971 DOI: 10.1101/Gr.110189.110  0.383
2011 Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, ... ... Snyder M, et al. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Research. 21: 245-54. PMID 21177963 DOI: 10.1101/Gr.114587.110  0.373
2011 Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, Snyder M, Gerstein M. RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics (Oxford, England). 27: 281-3. PMID 21134889 DOI: 10.1093/Bioinformatics/Btq643  0.374
2011 Bloom J, Cristea IM, Procko AL, Lubkov V, Chait BT, Snyder M, Cross FR. Global analysis of Cdc14 phosphatase reveals diverse roles in mitotic processes. The Journal of Biological Chemistry. 286: 5434-45. PMID 21127052 DOI: 10.1074/Jbc.M110.205054  0.317
2011 Choe K, Gallagher J, Li E, Snyder M. Towards the full understanding of yeast transcription factor binding sites in genomic level F1000research. 2. DOI: 10.7490/F1000Research.1950.1  0.344
2010 Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, ... ... Snyder M, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 330: 1775-87. PMID 21177976 DOI: 10.1126/Science.1196914  0.406
2010 Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. Bmc Genomics. 11: 663. PMID 21106091 DOI: 10.1186/1471-2164-11-663  0.347
2010 Li X, Gianoulis TA, Yip KY, Gerstein M, Snyder M. Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses. Cell. 143: 639-50. PMID 21035178 DOI: 10.1016/J.Cell.2010.09.048  0.303
2010 Lefrançois P, Zheng W, Snyder M. ChIP-Seq using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites. Methods in Enzymology. 470: 77-104. PMID 20946807 DOI: 10.1016/S0076-6879(10)70004-5  0.706
2010 Bruno VM, Wang Z, Marjani SL, Euskirchen GM, Martin J, Sherlock G, Snyder M. Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Research. 20: 1451-8. PMID 20810668 DOI: 10.1101/Gr.109553.110  0.377
2010 Chen R, Snyder M. Yeast proteomics and protein microarrays. Journal of Proteomics. 73: 2147-57. PMID 20728591 DOI: 10.1016/J.Jprot.2010.08.003  0.429
2010 Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.". Nature Structural & Molecular Biology. 17: 920-3. PMID 20683474 DOI: 10.1038/Nsmb0810-920  0.54
2010 Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB. Annotating non-coding regions of the genome. Nature Reviews. Genetics. 11: 559-71. PMID 20628352 DOI: 10.1038/Nrg2814  0.374
2010 Raha D, Hong M, Snyder M. ChIP-Seq: a method for global identification of regulatory elements in the genome. Current Protocols in Molecular Biology. Unit 21.19.1-14. PMID 20583098 DOI: 10.1002/0471142727.Mb2119S91  0.363
2010 Sharon D, Chen R, Snyder M. Systems biology approaches to disease marker discovery. Disease Markers. 28: 209-24. PMID 20534906 DOI: 10.3233/Dma-2010-0707  0.78
2010 Talarek N, Cameroni E, Jaquenoud M, Luo X, Bontron S, Lippman S, Devgan G, Snyder M, Broach JR, De Virgilio C. Initiation of the TORC1-regulated G0 program requires Igo1/2, which license specific mRNAs to evade degradation via the 5'-3' mRNA decay pathway. Molecular Cell. 38: 345-55. PMID 20471941 DOI: 10.1016/J.Molcel.2010.02.039  0.752
2010 Lam HY, Kim PM, Mok J, Tonikian R, Sidhu SS, Turk BE, Snyder M, Gerstein MB. MOTIPS: automated motif analysis for predicting targets of modular protein domains. Bmc Bioinformatics. 11: 243. PMID 20459839 DOI: 10.1186/1471-2105-11-243  0.762
2010 Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nature Structural & Molecular Biology. 17: 635-40. PMID 20418883 DOI: 10.1038/Nsmb.1794  0.582
2010 Camarena L, Bruno V, Euskirchen G, Poggio S, Snyder M. Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. Plos Pathogens. 6. PMID 20368969 DOI: 10.1371/Journal.Ppat.1000834  0.307
2010 Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, ... ... Snyder M, et al. Variation in transcription factor binding among humans. Science (New York, N.Y.). 328: 232-5. PMID 20299548 DOI: 10.1126/science.1183621  0.81
2010 Zheng W, Zhao H, Mancera E, Steinmetz LM, Snyder M. Genetic analysis of variation in transcription factor binding in yeast. Nature. 464: 1187-91. PMID 20237471 DOI: 10.1038/Nature08934  0.604
2010 Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S, Cui W, Gerstein M, Snyder M. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proceedings of the National Academy of Sciences of the United States of America. 107: 5254-9. PMID 20194744 DOI: 10.1073/Pnas.0914114107  0.303
2010 Snyder M, Du J, Gerstein M. Personal genome sequencing: Current approaches and challenges Genes and Development. 24: 423-431. PMID 20194435 DOI: 10.1101/Gad.1864110  0.363
2010 Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, ... ... Snyder M, et al. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. Plos Genetics. 6: e1000848. PMID 20174564 DOI: 10.1371/Journal.Pgen.1000848  0.357
2010 Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JL, ... ... Snyder M, et al. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Science Signaling. 3: ra12. PMID 20159853 DOI: 10.1126/Scisignal.2000482  0.771
2010 Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, Snyder M. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proceedings of the National Academy of Sciences of the United States of America. 107: 3639-44. PMID 20139302 DOI: 10.1073/Pnas.0911315106  0.552
2010 Nagalakshmi U, Waern K, Snyder M. RNA-Seq: a method for comprehensive transcriptome analysis. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 4.11.1-13. PMID 20069539 DOI: 10.1002/0471142727.Mb0411S89  0.801
2010 Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nature Biotechnology. 28: 47-55. PMID 20037582 DOI: 10.1038/Nbt.1600  0.392
2010 Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. Reply to Evidence against a genomic code for nucleosome positioning Nature Structural and Molecular Biology. 17: 920-923. DOI: 10.1038/nsmb0810-920  0.46
2009 Canaan A, Haviv I, Urban AE, Schulz VP, Hartman S, Zhang Z, Palejev D, Deisseroth AB, Lacy J, Snyder M, Gerstein M, Weissman SM. EBNA1 regulates cellular gene expression by binding cellular promoters. Proceedings of the National Academy of Sciences of the United States of America. 106: 22421-6. PMID 20080792 DOI: 10.1073/Pnas.0911676106  0.38
2009 Mok J, Im H, Snyder M. Global identification of protein kinase substrates by protein microarray analysis. Nature Protocols. 4: 1820-7. PMID 20010933 DOI: 10.1038/Nprot.2009.194  0.761
2009 Snyder M, Gallagher JE. Systems biology from a yeast omics perspective. Febs Letters. 583: 3895-9. PMID 19903479 DOI: 10.1016/J.Febslet.2009.11.011  0.328
2009 Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M. Mapping accessible chromatin regions using Sono-Seq. Proceedings of the National Academy of Sciences of the United States of America. 106: 14926-31. PMID 19706456 DOI: 10.1073/Pnas.0905443106  0.731
2009 Teytelman L, Ozaydin B, Zill O, Lefrançois P, Snyder M, Rine J, Eisen MB. Impact of chromatin structures on DNA processing for genomic analyses. Plos One. 4: e6700. PMID 19693276 DOI: 10.1371/Journal.Pone.0006700  0.36
2009 Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nature Structural & Molecular Biology. 16: 847-52. PMID 19620965 DOI: 10.1038/Nsmb.1636  0.536
2009 Korbel JO, Tirosh-Wagner T, Urban AE, Chen XN, Kasowski M, Dai L, Grubert F, Erdman C, Gao MC, Lange K, Sobel EM, Barlow GM, Aylsworth AS, Carpenter NJ, Clark RD, ... ... Snyder M, et al. The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proceedings of the National Academy of Sciences of the United States of America. 106: 12031-6. PMID 19597142 DOI: 10.1073/Pnas.0813248106  0.751
2009 Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants. Plos Computational Biology. 5: e1000432. PMID 19593373 DOI: 10.1371/Journal.Pcbi.1000432  0.348
2009 Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, et al. Unlocking the secrets of the genome. Nature. 459: 927-30. PMID 19536255 DOI: 10.1038/459927A  0.528
2009 Ni L, Bruce C, Hart C, Leigh-Bell J, Gelperin D, Umansky L, Gerstein MB, Snyder M. Dynamic and complex transcription factor binding during an inducible response in yeast. Genes & Development. 23: 1351-63. PMID 19487574 DOI: 10.1101/Gad.1781909  0.33
2009 Snyder M, Weissman S, Gerstein M. Personal phenotypes to go with personal genomes. Molecular Systems Biology. 5: 273. PMID 19455137 DOI: 10.1038/Msb.2009.32  0.367
2009 Theodorou E, Dalembert G, Heffelfinger C, White E, Weissman S, Corcoran L, Snyder M. A high throughput embryonic stem cell screen identifies Oct-2 as a bifunctional regulator of neuronal differentiation. Genes & Development. 23: 575-88. PMID 19270158 DOI: 10.1101/Gad.1772509  0.772
2009 Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biology. 10: R23. PMID 19236709 DOI: 10.1186/Gb-2009-10-2-R23  0.342
2009 Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M. Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. Bmc Genomics. 10: 37. PMID 19159457 DOI: 10.1186/1471-2164-10-37  0.702
2009 Demichelis F, Setlur SR, Beroukhim R, Perner S, Korbel JO, Lafargue CJ, Pflueger D, Pina C, Hofer MD, Sboner A, Svensson MA, Rickman DS, Urban A, Snyder M, Meyerson M, et al. Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes, Chromosomes & Cancer. 48: 366-80. PMID 19156837 DOI: 10.1002/Gcc.20647  0.312
2009 Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR, Kapranov P, Weissman SM, Newburger PE. A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood. 113: 2526-34. PMID 19144990 DOI: 10.1182/Blood-2008-06-162164  0.346
2009 Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nature Biotechnology. 27: 66-75. PMID 19122651 DOI: 10.1038/Nbt.1518  0.382
2009 Popescu SC, Popescu GV, Bachan S, Zhang Z, Gerstein M, Snyder M, Dinesh-Kumar SP. MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes & Development. 23: 80-92. PMID 19095804 DOI: 10.1101/Gad.1740009  0.301
2009 Wang LY, Abyzov A, Korbel JO, Snyder M, Gerstein M. MSB: a mean-shift-based approach for the analysis of structural variation in the genome. Genome Research. 19: 106-17. PMID 19037015 DOI: 10.1101/Gr.080069.108  0.312
2009 Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews. Genetics. 10: 57-63. PMID 19015660 DOI: 10.1038/Nrg2484  0.311
2008 Gong W, He K, Covington M, Dinesh-Kumar SP, Snyder M, Harmer SL, Zhu YX, Deng XW. The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Molecular Plant. 1: 27-41. PMID 19802365 DOI: 10.1093/Mp/Ssm009  0.339
2008 Seringhaus M, Rozowsky J, Royce T, Nagalakshmi U, Jee J, Snyder M, Gerstein M. Mismatch oligonucleotides in human and yeast: Guidelines for probe design on tiling microarrays Bmc Genomics. 9. PMID 19117516 DOI: 10.1186/1471-2164-9-635  0.306
2008 Hasin Y, Olender T, Khen M, Gonzaga-Jauregui C, Kim PM, Urban AE, Snyder M, Gerstein MB, Lancet D, Korbel JO. High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. Plos Genetics. 4: e1000249. PMID 18989455 DOI: 10.1371/Journal.Pgen.1000249  0.393
2008 Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB. Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Research. 18: 1865-74. PMID 18842824 DOI: 10.1101/Gr.081422.108  0.766
2008 Pan X, Urban AE, Palejev D, Schulz V, Grubert F, Hu Y, Snyder M, Weissman SM. A procedure for highly specific, sensitive, and unbiased whole-genome amplification. Proceedings of the National Academy of Sciences of the United States of America. 105: 15499-504. PMID 18832167 DOI: 10.1073/Pnas.0808028105  0.742
2008 Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, et al. Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding Genome Research. 18: 1906-1917. PMID 18787082 DOI: 10.1101/Gr.078519.108  0.333
2008 Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M. Modeling ChIP sequencing in silico with applications. Plos Computational Biology. 4: e1000158. PMID 18725927 DOI: 10.1371/Journal.Pcbi.1000158  0.364
2008 Reed BD, Charos AE, Szekely AM, Weissman SM, Snyder M. Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. Plos Genetics. 4: e1000133. PMID 18654640 DOI: 10.1371/Journal.Pgen.1000133  0.809
2008 Korbel JO, Kim PM, Chen X, Urban AE, Weissman S, Snyder M, Gerstein MB. The current excitement about copy-number variation: how it relates to gene duplications and protein families. Current Opinion in Structural Biology. 18: 366-74. PMID 18511261 DOI: 10.1016/J.Sbi.2008.02.005  0.36
2008 Lian Z, Karpikov A, Lian J, Mahajan MC, Hartman S, Gerstein M, Snyder M, Weissman SM. A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. Genome Research. 18: 1224-37. PMID 18487515 DOI: 10.1101/Gr.075804.107  0.675
2008 Wu JQ, Snyder M. RNA polymerase II stalling: Loading at the start prepares genes for a sprint Genome Biology. 9. PMID 18466645 DOI: 10.1186/Gb-2008-9-5-220  0.339
2008 Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (New York, N.Y.). 320: 1344-9. PMID 18451266 DOI: 10.1126/Science.1158441  0.814
2008 Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, ... ... Snyder M, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research. 18: 393-403. PMID 18258921 DOI: 10.1101/Gr.7080508  0.543
2008 Chang W, Zaarour RF, Reck-Peterson S, Rinn J, Singer RH, Snyder M, Novick P, Mooseker MS. Myo2p, a class V myosin in budding yeast, associates with a large ribonucleic acid-protein complex that contains mRNAs and subunits of the RNA-processing body. Rna (New York, N.Y.). 14: 491-502. PMID 18218704 DOI: 10.1261/Rna.665008  0.544
2008 Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M. Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biology. 9: R3. PMID 18173853 DOI: 10.1186/Gb-2008-9-1-R3  0.424
2007 Popescu SC, Snyder M, Dinesh-Kumar S. Arabidopsis protein microarrays for the high-throughput identification of protein-protein interactions. Plant Signaling & Behavior. 2: 416-20. PMID 19704619 DOI: 10.4161/Psb.2.5.4416  0.308
2007 Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, ... ... Snyder M, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science (New York, N.Y.). 318: 420-6. PMID 17901297 DOI: 10.1126/Science.1149504  0.767
2007 Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. Divergence of transcription factor binding sites across related yeast species. Science (New York, N.Y.). 317: 815-9. PMID 17690298 DOI: 10.1126/Science.1140748  0.334
2007 Borneman AR, Zhang ZD, Rozowsky J, Seringhaus MR, Gerstein M, Snyder M. Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Functional & Integrative Genomics. 7: 335-45. PMID 17638031 DOI: 10.1007/S10142-007-0054-7  0.305
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.823
2007 Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Research. 17: 910-6. PMID 17568006 DOI: 10.1101/Gr.5574907  0.394
2007 Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Research. 17: 898-909. PMID 17568005 DOI: 10.1101/Gr.5583007  0.667
2007 Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, ... ... Snyder M, et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Research. 17: 852-64. PMID 17568003 DOI: 10.1101/Gr.5650707  0.352
2007 Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Research. 17: 839-51. PMID 17568002 DOI: 10.1101/Gr.5586307  0.425
2007 Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Research. 17: 787-97. PMID 17567997 DOI: 10.1101/Gr.5573107  0.368
2007 Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Research. 17: 732-45. PMID 17567993 DOI: 10.1101/Gr.5696007  0.387
2007 Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Research. 17: 720-31. PMID 17567992 DOI: 10.1101/Gr.5716607  0.389
2007 Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. What is a gene, post-ENCODE? History and updated definition. Genome Research. 17: 669-81. PMID 17567988 DOI: 10.1101/Gr.6339607  0.382
2007 Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing Nature Methods. 4: 651-657. PMID 17558387 DOI: 10.1038/Nmeth1068  0.378
2007 Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS, Weissman SM, Snyder M, Gerstein MB. Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 104: 10110-5. PMID 17551006 DOI: 10.1073/Pnas.0703834104  0.764
2007 Zhu X, Gerstein M, Snyder M. Getting connected: analysis and principles of biological networks. Genes & Development. 21: 1010-24. PMID 17473168 DOI: 10.1101/Gad.1528707  0.531
2007 Popescu SC, Popescu GV, Bachan S, Zhang Z, Seay M, Gerstein M, Snyder M, Dinesh-Kumar SP. Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proceedings of the National Academy of Sciences of the United States of America. 104: 4730-5. PMID 17360592 DOI: 10.1073/Pnas.0611615104  0.319
2007 Yu H, Nguyen K, Royce T, Qian J, Nelson K, Snyder M, Gerstein M. Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool. Nucleic Acids Research. 35: e8. PMID 17158151 DOI: 10.1093/Nar/Gkl871  0.308
2007 Hall DA, Ptacek J, Snyder M. Protein microarray technology. Mechanisms of Ageing and Development. 128: 161-7. PMID 17126887 DOI: 10.1016/J.Mad.2006.11.021  0.707
2007 Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M, Gerstein MB. Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Research. 17: 886-97. PMID 17119069 DOI: 10.1101/Gr.5014606  0.392
2007 Ptacek J, Snyder M. 14 Yeast Protein Microarrays Methods in Microbiology. 36: 303-329,704-705. DOI: 10.1016/S0580-9517(06)36014-X  0.626
2006 Smith MG, Snyder M. Yeast as a model for human disease. Current Protocols in Human Genetics / Editorial Board, Jonathan L. Haines ... [Et Al.]. Unit 15.6. PMID 18428391 DOI: 10.1002/0471142905.Hg1506S48  0.392
2006 Rozowsky J, Wu J, Lian Z, Nagalakshmi U, Korbel JO, Kapranov P, Zheng D, Dyke S, Newburger P, Miller P, Gingeras TR, Weissman S, Gerstein M, Snyder M. Novel transcribed regions in the human genome. Cold Spring Harbor Symposia On Quantitative Biology. 71: 111-6. PMID 17381286 DOI: 10.1101/Sqb.2006.71.054  0.36
2006 Hudson ME, Snyder M. High-throughput methods of regulatory element discovery. Biotechniques. 41: 673, 675, 677 passim. PMID 17191608 DOI: 10.2144/000112322  0.382
2006 Zhu X, Gerstein M, Snyder M. ProCAT: a data analysis approach for protein microarrays. Genome Biology. 7: R110. PMID 17109749 DOI: 10.1186/Gb-2006-7-11-R110  0.552
2006 Dewan A, Liu M, Hartman S, Zhang SS, Liu DT, Zhao C, Tam PO, Chan WM, Lam DS, Snyder M, Barnstable C, Pang CP, Hoh J. HTRA1 promoter polymorphism in wet age-related macular degeneration. Science (New York, N.Y.). 314: 989-92. PMID 17053108 DOI: 10.1126/Science.1133807  0.646
2006 Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M. A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Bioinformatics (Oxford, England). 22: 3016-24. PMID 17038339 DOI: 10.1093/Bioinformatics/Btl515  0.325
2006 Royce TE, Rozowsky JS, Luscombe NM, Emanuelsson O, Yu H, Zhu X, Snyder M, Gerstein MB. Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies. Methods in Enzymology. 411: 282-311. PMID 16939796 DOI: 10.1016/S0076-6879(06)11015-0  0.552
2006 Ptacek J, Snyder M. Charging it up: global analysis of protein phosphorylation. Trends in Genetics : Tig. 22: 545-54. PMID 16908088 DOI: 10.1016/J.Tig.2006.08.005  0.624
2006 Seringhaus M, Paccanaro A, Borneman A, Snyder M, Gerstein M. Predicting essential genes in fungal genomes. Genome Research. 16: 1126-35. PMID 16899653 DOI: 10.1101/Gr.5144106  0.332
2006 Ho SW, Jona G, Chen CT, Johnston M, Snyder M. Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proceedings of the National Academy of Sciences of the United States of America. 103: 9940-5. PMID 16785442 DOI: 10.1073/Pnas.0509185103  0.377
2006 Seringhaus M, Kumar A, Hartigan J, Snyder M, Gerstein M. Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae. Nucleic Acids Research. 34: e57. PMID 16648358 DOI: 10.1093/Nar/Gkl184  0.347
2006 Zhu H, Hu S, Jona G, Zhu X, Kreiswirth N, Willey BM, Mazzulli T, Liu G, Song Q, Chen P, Cameron M, Tyler A, Wang J, Wen J, Chen W, ... ... Snyder M, et al. Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray. Proceedings of the National Academy of Sciences of the United States of America. 103: 4011-6. PMID 16537477 DOI: 10.1073/Pnas.0510921103  0.524
2006 Urban AE, Korbel JO, Selzer R, Richmond T, Hacker A, Popescu GV, Cubells JF, Green R, Emanuel BS, Gerstein MB, Weissman SM, Snyder M. High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proceedings of the National Academy of Sciences of the United States of America. 103: 4534-9. PMID 16537408 DOI: 10.1073/Pnas.0511340103  0.333
2006 Kastenmayer JP, Ni L, Chu A, Kitchen LE, Au WC, Yang H, Carter CD, Wheeler D, Davis RW, Boeke JD, Snyder MA, Basrai MA. Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Research. 16: 365-73. PMID 16510898 DOI: 10.1101/Gr.4355406  0.574
2006 Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, Snyder M, Oliver SG, Cyert M, Hughes TR, Boone C, Andrews B. Mapping pathways and phenotypes by systematic gene overexpression. Molecular Cell. 21: 319-30. PMID 16455487 DOI: 10.1016/J.Molcel.2005.12.011  0.384
2006 Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M. Target hub proteins serve as master regulators of development in yeast. Genes & Development. 20: 435-48. PMID 16449570 DOI: 10.1101/Gad.1389306  0.635
2006 Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao MY, Snyder M, Gerstein M. Design optimization methods for genomic DNA tiling arrays. Genome Research. 16: 271-81. PMID 16365382 DOI: 10.1101/Gr.4452906  0.638
2005 Gelperin DM, White MA, Wilkinson ML, Kon Y, Kung LA, Wise KJ, Lopez-Hoyo N, Jiang L, Piccirillo S, Yu H, Gerstein M, Dumont ME, Phizicky EM, Snyder M, Grayhack EJ. Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes & Development. 19: 2816-26. PMID 16322557 DOI: 10.1101/Gad.1362105  0.386
2005 Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, ... ... Snyder M, et al. Global analysis of protein phosphorylation in yeast. Nature. 438: 679-84. PMID 16319894 DOI: 10.1038/Nature04187  0.776
2005 Hartman SE, Bertone P, Nath AK, Royce TE, Gerstein M, Weissman S, Snyder M. Global changes in STAT target selection and transcription regulation upon interferon treatments. Genes & Development. 19: 2953-68. PMID 16319195 DOI: 10.1101/Gad.1371305  0.76
2005 Bertone P, Snyder M. Advances in functional protein microarray technology. The Febs Journal. 272: 5400-11. PMID 16262682 DOI: 10.1111/J.1742-4658.2005.04970.X  0.611
2005 Mah AS, Elia AE, Devgan G, Ptacek J, Schutkowski M, Snyder M, Yaffe MB, Deshaies RJ. Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening. Bmc Biochemistry. 6: 22. PMID 16242037 DOI: 10.1186/1471-2091-6-22  0.776
2005 Stolc V, Li L, Wang X, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder M, Gerstein M, Wang J, Deng XW. A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. Plant Molecular Biology. 59: 137-49. PMID 16217608 DOI: 10.1007/S11103-005-6164-5  0.415
2005 Pot I, Knockleby J, Aneliunas V, Nguyen T, Ah-Kye S, Liszt G, Snyder M, Hieter P, Vogel J. Spindle checkpoint maintenance requires Ame1 and Okp1. Cell Cycle (Georgetown, Tex.). 4: 1448-56. PMID 16177574 DOI: 10.4161/Cc.4.10.2106  0.546
2005 Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends in Genetics : Tig. 21: 466-75. PMID 15979196 DOI: 10.1016/J.Tig.2005.06.007  0.653
2005 Bertone P, Snyder M. Prospects and challenges in proteomics. Plant Physiology. 138: 560-2. PMID 15955915 DOI: 10.1104/Pp.104.900154  0.623
2005 Bertone P, Gerstein M, Snyder M. Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 13: 259-74. PMID 15868420 DOI: 10.1007/S10577-005-2165-0  0.676
2005 Rinn JL, Snyder M. Sexual dimorphism in mammalian gene expression. Trends in Genetics : Tig. 21: 298-305. PMID 15851067 DOI: 10.1016/J.Tig.2005.03.005  0.564
2005 Smith MG, Jona G, Ptacek J, Devgan G, Zhu H, Zhu X, Snyder M. Global analysis of protein function using protein microarrays. Mechanisms of Ageing and Development. 126: 171-5. PMID 15610776 DOI: 10.1016/J.Mad.2004.09.019  0.777
2004 White EJ, Emanuelsson O, Scalzo D, Royce T, Kosak S, Oakeley EJ, Weissman S, Gerstein M, Groudine M, Snyder M, Schübeler D. DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proceedings of the National Academy of Sciences of the United States of America. 101: 17771-6. PMID 15591350 DOI: 10.1073/Pnas.0408170101  0.384
2004 Berman P, Bertone P, Dasgupta B, Gerstein M, Kao MY, Snyder M. Fast optimal genome tiling with applications to microarray design and homology search. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 766-85. PMID 15579244 DOI: 10.1089/Cmb.2004.11.766  0.602
2004 Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nature Genetics. 36: 1331-9. PMID 15543148 DOI: 10.1038/Ng1473  0.513
2004 Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Global identification of human transcribed sequences with genome tiling arrays. Science (New York, N.Y.). 306: 2242-6. PMID 15539566 DOI: 10.1126/Science.1103388  0.797
2004 Huang J, Zhu H, Haggarty SJ, Spring DR, Hwang H, Jin F, Snyder M, Schreiber SL. Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proceedings of the National Academy of Sciences of the United States of America. 101: 16594-9. PMID 15539461 DOI: 10.1073/Pnas.0407117101  0.331
2004 Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Snyder M, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/Science.1105136  0.557
2004 Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M. Regulation of gene expression by a metabolic enzyme. Science (New York, N.Y.). 306: 482-4. PMID 15486299 DOI: 10.1126/Science.1096773  0.691
2004 Kumar A, Seringhaus M, Biery MC, Sarnovsky RJ, Umansky L, Piccirillo S, Heidtman M, Cheung KH, Dobry CJ, Gerstein MB, Craig NL, Snyder M. Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Research. 14: 1975-86. PMID 15466296 DOI: 10.1101/Gr.2875304  0.408
2004 Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 431: 308-12. PMID 15372033 DOI: 10.1038/Nature02782  0.326
2004 Rinn JL, Rozowsky JS, Laurenzi IJ, Petersen PH, Zou K, Zhong W, Gerstein M, Snyder M. Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. Developmental Cell. 6: 791-800. PMID 15177028 DOI: 10.1016/J.Devcel.2004.05.005  0.538
2004 Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. CREB binds to multiple loci on human chromosome 22. Molecular and Cellular Biology. 24: 3804-14. PMID 15082775 DOI: 10.1128/Mcb.24.9.3804-3814.2004  0.803
2004 Euskirchen G, Snyder M. A plethora of sites Nature Genetics. 36: 325-326. PMID 15054485 DOI: 10.1038/Ng0404-325  0.346
2004 Bidlingmaier S, Snyder M. Regulation of polarized growth initiation and termination cycles by the polarisome and Cdc42 regulators. The Journal of Cell Biology. 164: 207-18. PMID 14734532 DOI: 10.1083/Jcb.200307065  0.687
2004 Yates J, Snyder M. Proteomics and genomics Current Opinion in Chemical Biology. 8: 1-2. DOI: 10.1016/J.Cbpa.2003.12.011  0.335
2003 Lian Z, Euskirchen G, Rinn J, Martone R, Bertone P, Hartman S, Royce T, Nelson K, Sayward F, Luscombe N, Yang J, Li JL, Miller P, Urban AE, Gerstein M, ... ... Snyder M, et al. Identification of novel functional elements in the human genome. Cold Spring Harbor Symposia On Quantitative Biology. 68: 317-22. PMID 15338632 DOI: 10.1101/Sqb.2003.68.317  0.792
2003 Schweitzer B, Predki P, Snyder M. Microarrays to characterize protein interactions on a whole-proteome scale. Proteomics. 3: 2190-2199. PMID 14595818 DOI: 10.1002/Pmic.200300610  0.313
2003 Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (New York, N.Y.). 302: 449-53. PMID 14564010 DOI: 10.1126/Science.1087361  0.314
2003 Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. Distribution of NF-kappaB-binding sites across human chromosome 22. Proceedings of the National Academy of Sciences of the United States of America. 100: 12247-52. PMID 14527995 DOI: 10.1073/Pnas.2135255100  0.788
2003 Hanrahan J, Snyder M. Cytoskeletal activation of a checkpoint kinase. Molecular Cell. 12: 663-73. PMID 14527412 DOI: 10.1016/J.Molcel.2003.08.006  0.577
2003 Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M. ExpressYourself: A modular platform for processing and visualizing microarray data. Nucleic Acids Research. 31: 3477-82. PMID 12824348 DOI: 10.1093/Nar/Gkg628  0.753
2003 Snyder M, Gerstein M. Genomics. Defining genes in the genomics era. Science (New York, N.Y.). 300: 258-60. PMID 12690176 DOI: 10.1126/Science.1084354  0.374
2003 Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M, Armstrong CM, Li S, Jacotot L, Bertin N, Janky R, Moore T, Hudson JR, Hartley JL, Brasch MA, Vandenhaute J, ... ... Snyder M, et al. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nature Genetics. 34: 35-41. PMID 12679813 DOI: 10.1038/Ng1140  0.673
2003 Phizicky E, Bastiaens PIH, Zhu H, Snyder M, Fields S. Protein analysis on a proteomic scale Nature. 422: 208-215. PMID 12634794 DOI: 10.1038/Nature01512  0.556
2003 Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. The transcriptional activity of human Chromosome 22. Genes & Development. 17: 529-40. PMID 12600945 DOI: 10.1101/Gad.1055203  0.805
2003 Zhu H, Bilgin M, Ptacek J, Hall D, Casamayor A, Bertone P, Lopez N, Lan N, Jansen R, Bidlingmaier S, Devgan G, Miller P, Gerstein M, Snyder M. Workshop I – Global Analysis of Protein Activities Using Protein Chips Biophysical Journal. 84: 3488. DOI: 10.1016/S0006-3495(03)70069-1  0.788
2002 Cheung KH, Hager J, Nelson K, White K, Li Y, Snyder M, Williams K, Miller P. A dynamic approach to mapping coordinates between microplates and microarrays. Journal of Biomedical Informatics. 35: 306-12. PMID 12968779 DOI: 10.1016/S1532-0464(03)00033-9  0.479
2002 Michaud GA, Snyder M. Proteomic approaches for the global analysis of proteins Biotechniques. 33: 1308-1316. PMID 12503317 DOI: 10.2144/02336Pt04  0.354
2002 Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes & Development. 16: 3017-33. PMID 12464632 DOI: 10.1101/Gad.1039602  0.753
2002 Cheung KH, White K, Hager J, Gerstein M, Reinke V, Nelson K, Masiar P, Srivastava R, Li Y, Li J, Zhao H, Li J, Allison DB, Snyder M, Miller P, et al. YMD: a microarray database for large-scale gene expression analysis. Proceedings / Amia ... Annual Symposium. Amia Symposium. 140-4. PMID 12463803  0.441
2002 Coelho PS, Bryan AC, Kumar A, Shadel GS, Snyder M. A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA. Genes & Development. 16: 2755-60. PMID 12414727 DOI: 10.1101/Gad.1035002  0.369
2002 Snyder M, Kumar A. Yeast genomics: past, present, and future promise. Functional & Integrative Genomics. 2: 135-7. PMID 12243128 DOI: 10.1007/S10142-002-0064-4  0.325
2002 Horak CE, Snyder M. Global analysis of gene expression in yeast. Functional & Integrative Genomics. 2: 171-80. PMID 12192590 DOI: 10.1007/S10142-002-0065-3  0.653
2002 Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, ... ... Snyder M, et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418: 387-91. PMID 12140549 DOI: 10.1038/Nature00935  0.811
2002 Horak CE, Snyder M. ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods in Enzymology. 350: 469-83. PMID 12073330 DOI: 10.1016/S0076-6879(02)50979-4  0.676
2002 Kumar A, Vidan S, Snyder M. Insertional mutagenesis: transposon-insertion libraries as mutagens in yeast. Methods in Enzymology. 350: 219-29. PMID 12073314 DOI: 10.1016/S0076-6879(02)50965-4  0.336
2002 Bidlingmaier S, Snyder M. Carbohydrate analysis prepares to enter the "Omics" era. Chemistry & Biology. 9: 400-1. PMID 11983329 DOI: 10.1016/S1074-5521(02)00133-3  0.682
2002 Bidlingmaier S, Snyder M. Large-scale identification of genes important for apical growth in Saccharomyces cerevisiae by directed allele replacement technology (DART) screening. Functional & Integrative Genomics. 1: 345-56. PMID 11957109 DOI: 10.1007/S10142-001-0043-1  0.71
2002 Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y, Cheung KH, Miller P, Gerstein M, Roeder GS, Snyder M. Subcellular localization of the yeast proteome. Genes & Development. 16: 707-19. PMID 11914276 DOI: 10.1101/Gad.970902  0.319
2002 Zhu H, Snyder M. Omic" approaches for unraveling signaling networks. Current Opinion in Cell Biology. 14: 173-179. PMID 11891116 DOI: 10.1016/S0955-0674(02)00315-0  0.351
2002 Horak CE, Mahajan MC, Luscombe NM, Gerstein M, Weissman SM, Snyder M. GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proceedings of the National Academy of Sciences of the United States of America. 99: 2924-9. PMID 11867748 DOI: 10.1073/Pnas.052706999  0.651
2002 Harrison P, Kumar A, Lan N, Echols N, Snyder M, Gerstein M. A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution. Journal of Molecular Biology. 316: 409-19. PMID 11866506 DOI: 10.1006/Jmbi.2001.5343  0.384
2002 Harrison PM, Kumar A, Lang N, Snyder M, Gerstein M. A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Research. 30: 1083-90. PMID 11861898 DOI: 10.1093/Nar/30.5.1083  0.399
2002 Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, Bertone P, Miller P, Gerstein MB, Snyder M. An integrated approach for finding overlooked genes in yeast. Nature Biotechnology. 20: 58-63. PMID 11753363 DOI: 10.1038/Nbt0102-58  0.657
2002 Kumar A, Cheung KH, Tosches N, Masiar P, Liu Y, Miller P, Snyder M. The TRIPLES database: a community resource for yeast molecular biology. Nucleic Acids Research. 30: 73-5. PMID 11752258 DOI: 10.1093/Nar/30.1.73  0.329
2001 Kumar A, Snyder M. Genome-wide transposon mutagenesis in yeast. Current Protocols in Molecular Biology. 51. PMID 18265099 DOI: 10.1002/0471142727.Mb1303S51  0.353
2001 Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M. Global analysis of protein activities using proteome chips. Science (New York, N.Y.). 293: 2101-5. PMID 11474067 DOI: 10.1126/science.1062191  0.764
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