| Year |
Citation |
Score |
| 2024 |
Sumida TS, Lincoln MR, He L, Park Y, Ota M, Oguchi A, Son R, Yi A, Stillwell HA, Leissa GA, Fujio K, Murakawa Y, Kulminski AM, Epstein CB, Bernstein BE, ... Kellis M, et al. An autoimmune transcriptional circuit drives FOXP3 regulatory T cell dysfunction. Science Translational Medicine. 16: eadp1720. PMID 39196959 DOI: 10.1126/scitranslmed.adp1720 |
0.666 |
|
| 2024 |
Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, ... ... Kellis M, et al. Complete sequencing of ape genomes. Biorxiv : the Preprint Server For Biology. PMID 39131277 DOI: 10.1101/2024.07.31.605654 |
0.565 |
|
| 2024 |
Mathys H, Boix CA, Akay LA, Xia Z, Davila-Velderrain J, Ng AP, Jiang X, Abdelhady G, Galani K, Mantero J, Band N, James BT, Babu S, Galiana-Melendez F, Louderback K, ... ... Kellis M, et al. Single-cell multiregion dissection of Alzheimer's disease. Nature. PMID 39048816 DOI: 10.1038/s41586-024-07606-7 |
0.668 |
|
| 2024 |
Whited AM, Jungreis I, Allen J, Cleveland CL, Mudge JM, Kellis M, Rinn JL, Hough LE. Biophysical characterization of high-confidence, small human proteins. Biophysical Reports. 100167. PMID 38909903 DOI: 10.1016/j.bpr.2024.100167 |
0.754 |
|
| 2024 |
Ruzicka WB, Mohammadi S, Fullard JF, Davila-Velderrain J, Subburaju S, Tso DR, Hourihan M, Jiang S, Lee HC, Bendl J, Voloudakis G, Haroutunian V, Hoffman GE, Roussos P, Kellis M. Single-cell multi-cohort dissection of the schizophrenia transcriptome. Science (New York, N.Y.). 384: eadg5136. PMID 38781388 DOI: 10.1126/science.adg5136 |
0.66 |
|
| 2024 |
Whited AM, Jungreis I, Allen J, Cleveland C, Mudge JM, Kellis M, Rinn J, Hough LE. Biophysical characterization of high-confidence, small human proteins. Biorxiv : the Preprint Server For Biology. PMID 38659920 DOI: 10.1101/2024.04.12.589296 |
0.754 |
|
| 2024 |
Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz DW, Bandaru R, Zheng H, Fu H, ... ... Kellis M, et al. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Nature Communications. 15: 2790. PMID 38555308 DOI: 10.1038/s41467-024-47196-6 |
0.46 |
|
| 2024 |
Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz D, Bandaru R, Zheng H, Fu H, ... ... Kellis M, et al. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Biorxiv : the Preprint Server For Biology. PMID 38260558 DOI: 10.1101/2024.01.02.573710 |
0.47 |
|
| 2023 |
Shi J, Jia Z, Sun J, Wang X, Zhao X, Zhao C, Liang F, Song X, Guan J, Jia X, Yang J, Chen Q, Yu K, Jia Q, Wu J, ... ... Kellis M, et al. Structural variants involved in high-altitude adaptation detected using single-molecule long-read sequencing. Nature Communications. 14: 8282. PMID 38092772 DOI: 10.1038/s41467-023-44034-z |
0.317 |
|
| 2023 |
Gschwind AR, Mualim KS, Karbalayghareh A, Sheth MU, Dey KK, Jagoda E, Nurtdinov RN, Xi W, Tan AS, Jones H, Ma XR, Yao D, Nasser J, Avsec Ž, James BT, ... ... Kellis M, et al. An encyclopedia of enhancer-gene regulatory interactions in the human genome. Biorxiv : the Preprint Server For Biology. PMID 38014075 DOI: 10.1101/2023.11.09.563812 |
0.632 |
|
| 2023 |
Sun N, Akay LA, Murdock MH, Park Y, Galiana-Melendez F, Bubnys A, Galani K, Mathys H, Jiang X, Ng AP, Bennett DA, Tsai LH, Kellis M. Author Correction: Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer's disease. Nature Neuroscience. PMID 37907809 DOI: 10.1038/s41593-023-01507-0 |
0.495 |
|
| 2023 |
Xiong X, James BT, Boix CA, Park YP, Galani K, Victor MB, Sun N, Hou L, Ho LL, Mantero J, Scannail AN, Dileep V, Dong W, Mathys H, Bennett DA, ... ... Kellis M, et al. Epigenomic dissection of Alzheimer's disease pinpoints causal variants and reveals epigenome erosion. Cell. 186: 4422-4437.e21. PMID 37774680 DOI: 10.1016/j.cell.2023.08.040 |
0.558 |
|
| 2023 |
Sun N, Victor MB, Park YP, Xiong X, Scannail AN, Leary N, Prosper S, Viswanathan S, Luna X, Boix CA, James BT, Tanigawa Y, Galani K, Mathys H, Jiang X, ... ... Kellis M, et al. Human microglial state dynamics in Alzheimer's disease progression. Cell. 186: 4386-4403.e29. PMID 37774678 DOI: 10.1016/j.cell.2023.08.037 |
0.559 |
|
| 2023 |
Hou L, Xiong X, Park Y, Boix C, James B, Sun N, He L, Patel A, Zhang Z, Molinie B, Van Wittenberghe N, Steelman S, Nusbaum C, Aguet F, Ardlie KG, ... Kellis M, et al. Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease. Nature Genetics. PMID 37770633 DOI: 10.1038/s41588-023-01509-5 |
0.811 |
|
| 2023 |
Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, ... ... Kellis M, et al. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. PMID 37738970 DOI: 10.1016/j.cell.2023.08.026 |
0.664 |
|
| 2023 |
Sun N, Akay LA, Murdock MH, Park Y, Galiana-Melendez F, Bubnys A, Galani K, Mathys H, Jiang X, Ng AP, Bennett DA, Tsai LH, Kellis M. Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer's disease. Nature Neuroscience. PMID 37264161 DOI: 10.1038/s41593-023-01334-3 |
0.54 |
|
| 2023 |
Huang WC, Peng Z, Murdock MH, Liu L, Mathys H, Davila-Velderrain J, Jiang X, Chen M, Ng AP, Kim T, Abdurrob F, Gao F, Bennett DA, Kellis M, Tsai LH. Lateral mammillary body neurons in mouse brain are disproportionately vulnerable in Alzheimer's disease. Science Translational Medicine. 15: eabq1019. PMID 37075128 DOI: 10.1126/scitranslmed.abq1019 |
0.631 |
|
| 2023 |
Schreiber J, Boix C, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, ... ... Kellis M, et al. The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles. Genome Biology. 24: 79. PMID 37072822 DOI: 10.1186/s13059-023-02915-y |
0.658 |
|
| 2022 |
Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, ... ... Kellis M, et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Research. PMID 36420896 DOI: 10.1093/nar/gkac1071 |
0.803 |
|
| 2022 |
Blanchard JW, Akay LA, Davila-Velderrain J, von Maydell D, Mathys H, Davidson SM, Effenberger A, Chen CY, Maner-Smith K, Hajjar I, Ortlund EA, Bula M, Agbas E, Ng A, Jiang X, ... ... Kellis M, et al. APOE4 impairs myelination via cholesterol dysregulation in oligodendrocytes. Nature. PMID 36385529 DOI: 10.1038/s41586-022-05439-w |
0.665 |
|
| 2022 |
Welch GM, Boix CA, Schmauch E, Davila-Velderrain J, Victor MB, Dileep V, Bozzelli PL, Su Q, Cheng JD, Lee A, Leary NS, Pfenning AR, Kellis M, Tsai LH. Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration. Science Advances. 8: eabo4662. PMID 36170369 DOI: 10.1126/sciadv.abo4662 |
0.767 |
|
| 2022 |
Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, ... ... Kellis M, et al. Standardized annotation of translated open reading frames. Nature Biotechnology. PMID 35831657 DOI: 10.1038/s41587-022-01369-0 |
0.643 |
|
| 2022 |
Singh N, Benoit MR, Zhou J, Das B, Davila-Velderrain J, Kellis M, Tsai LH, Hu X, Yan R. BACE-1 inhibition facilitates the transition from homeostatic microglia to DAM-1. Science Advances. 8: eabo1286. PMID 35714196 DOI: 10.1126/sciadv.abo1286 |
0.644 |
|
| 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, ... ... Kellis M, 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 |
0.76 |
|
| 2022 |
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, ... ... Kellis M, et al. Publisher Correction: Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. PMID 35332335 DOI: 10.1038/s41586-022-04653-w |
0.617 |
|
| 2021 |
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, ... ... Kellis M, et al. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. PMID 34942634 DOI: 10.1038/s41586-021-04352-y |
0.659 |
|
| 2021 |
Barker SJ, Raju RM, Milman NEP, Wang J, Davila-Velderrain J, Gunter-Rahman F, Parro CC, Bozzelli PL, Abdurrob F, Abdelaal K, Bennett DA, Kellis M, Tsai LH. MEF2 is a key regulator of cognitive potential and confers resilience to neurodegeneration. Science Translational Medicine. 13: eabd7695. PMID 34731014 DOI: 10.1126/scitranslmed.abd7695 |
0.627 |
|
| 2021 |
Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, ... ... Kellis M, et al. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nature Biotechnology. PMID 34663921 DOI: 10.1038/s41587-021-01021-3 |
0.651 |
|
| 2021 |
Park YP, Kellis M. CoCoA-diff: counterfactual inference for single-cell gene expression analysis. Genome Biology. 22: 228. PMID 34404460 DOI: 10.1186/s13059-021-02438-4 |
0.601 |
|
| 2021 |
Cao J, Novoa EM, Zhang Z, Chen WCW, Liu D, Choi GCG, Wong ASL, Wehrspaun C, Kellis M, Lu TK. High-throughput 5' UTR engineering for enhanced protein production in non-viral gene therapies. Nature Communications. 12: 4138. PMID 34230498 DOI: 10.1038/s41467-021-24436-7 |
0.801 |
|
| 2021 |
Xiong X, Hou L, Park YP, Molinie B, Gregory RI, Kellis M. Genetic drivers of mA methylation in human brain, lung, heart and muscle. Nature Genetics. PMID 34211177 DOI: 10.1038/s41588-021-00890-3 |
0.555 |
|
| 2021 |
He L, Davila-Velderrain J, Sumida TS, Hafler DA, Kellis M, Kulminski AM. NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data. Communications Biology. 4: 629. PMID 34040149 DOI: 10.1038/s42003-021-02146-6 |
0.675 |
|
| 2021 |
Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, et al. Erratum to: Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution. PMID 34015138 DOI: 10.1093/molbev/msab100 |
0.771 |
|
| 2021 |
Jungreis I, Sealfon R, Kellis M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Nature Communications. 12: 2642. PMID 33976134 DOI: 10.1038/s41467-021-22905-7 |
0.81 |
|
| 2021 |
Jungreis I, Nelson CW, Ardern Z, Finkel Y, Krogan NJ, Sato K, Ziebuhr J, Stern-Ginossar N, Pavesi A, Firth AE, Gorbalenya AE, Kellis M. Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution. Virology. 558: 145-151. PMID 33774510 DOI: 10.1016/j.virol.2021.02.013 |
0.697 |
|
| 2021 |
He L, Loika Y, Park Y, Bennett DA, Kellis M, Kulminski AM. Exome-wide age-of-onset analysis reveals exonic variants in ERN1 and SPPL2C associated with Alzheimer's disease. Translational Psychiatry. 11: 146. PMID 33637690 DOI: 10.1038/s41398-021-01263-4 |
0.561 |
|
| 2021 |
Boix CA, James BT, Park YP, Meuleman W, Kellis M. Regulatory genomic circuitry of human disease loci by integrative epigenomics. Nature. PMID 33536621 DOI: 10.1038/s41586-020-03145-z |
0.818 |
|
| 2021 |
Blanchard JW, Bula M, Davila-Velderrain J, Akay LA, Zhu L, Frank A, Victor MB, Bonner JM, Mathys H, Lin YT, Ko T, Bennett DA, Cam HP, Kellis M, Tsai LH. Author Correction: Reconstruction of the human blood-brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes. Nature Medicine. PMID 33514950 DOI: 10.1038/s41591-021-01250-8 |
0.639 |
|
| 2020 |
Iserman C, Roden CA, Boerneke MA, Sealfon RSG, McLaughlin GA, Jungreis I, Fritch EJ, Hou YJ, Ekena J, Weidmann CA, Theesfeld CL, Kellis M, Troyanskaya OG, Baric RS, Sheahan TP, et al. Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid. Molecular Cell. PMID 33290746 DOI: 10.1016/j.molcel.2020.11.041 |
0.804 |
|
| 2020 |
Shim WJ, Sinniah E, Xu J, Vitrinel B, Alexanian M, Andreoletti G, Shen S, Sun Y, Balderson B, Boix C, Peng G, Jing N, Wang Y, Kellis M, Tam PPL, et al. Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity. Cell Systems. PMID 33278344 DOI: 10.1016/j.cels.2020.11.001 |
0.334 |
|
| 2020 |
Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, ... ... Kellis M, et al. GENCODE 2021. Nucleic Acids Research. PMID 33270111 DOI: 10.1093/nar/gkaa1087 |
0.739 |
|
| 2020 |
Mohammadi S, Davila-Velderrain J, Kellis M. A multiresolution framework to characterize single-cell state landscapes. Nature Communications. 11: 5399. PMID 33106496 DOI: 10.1038/s41467-020-18416-6 |
0.675 |
|
| 2020 |
Kousi M, Söylemez O, Ozanturk A, Mourtzi N, Akle S, Jungreis I, Muller J, Cassa CA, Brand H, Mokry JA, Wolf MY, Sadeghpour A, McFadden K, Lewis RA, Talkowski ME, ... ... Kellis M, et al. Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy. Nature Genetics. PMID 33046855 DOI: 10.1038/s41588-020-0707-1 |
0.687 |
|
| 2020 |
Jungreis I, Sealfon R, Kellis M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Research Square. PMID 33024961 DOI: 10.21203/rs.3.rs-80345/v1 |
0.815 |
|
| 2020 |
Marco A, Meharena HS, Dileep V, Raju RM, Davila-Velderrain J, Zhang AL, Adaikkan C, Young JZ, Gao F, Kellis M, Tsai LH. Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble. Nature Neuroscience. PMID 33020654 DOI: 10.1038/s41593-020-00717-0 |
0.681 |
|
| 2020 |
Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, et al. Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution. PMID 32946576 DOI: 10.1093/Molbev/Msaa240 |
0.801 |
|
| 2020 |
Berger E, Yorukoglu D, Zhang L, Nyquist SK, Shalek AK, Kellis M, Numanagić I, Berger B. Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets. Nature Communications. 11: 4662. PMID 32938926 DOI: 10.1038/S41467-020-18320-Z |
0.6 |
|
| 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, ... ... Kellis M, 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 |
0.805 |
|
| 2020 |
Eisenberg AR, Higdon AL, Hollerer I, Fields AP, Jungreis I, Diamond PD, Kellis M, Jovanovic M, Brar GA. Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast. Cell Systems. PMID 32710835 DOI: 10.1016/J.Cels.2020.06.011 |
0.737 |
|
| 2020 |
Lee H, Fenster RJ, Pineda SS, Gibbs WS, Mohammadi S, Davila-Velderrain J, Garcia FJ, Therrien M, Novis HS, Gao F, Wilkinson H, Vogt T, Kellis M, LaVoie MJ, Heiman M. Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation. Neuron. PMID 32681824 DOI: 10.1016/J.Neuron.2020.06.021 |
0.696 |
|
| 2020 |
Jungreis I, Sealfon R, Kellis M. Sarbecovirus comparative genomics elucidates gene content of SARS-CoV-2 and functional impact of COVID-19 pandemic mutations. Biorxiv : the Preprint Server For Biology. PMID 32577641 DOI: 10.1101/2020.06.02.130955 |
0.81 |
|
| 2020 |
Blanchard JW, Bula M, Davila-Velderrain J, Akay LA, Zhu L, Frank A, Victor MB, Bonner JM, Mathys H, Lin YT, Ko T, Bennett DA, Cam HP, Kellis M, Tsai LH. Reconstruction of the human blood-brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes. Nature Medicine. PMID 32514169 DOI: 10.1038/S41591-020-0886-4 |
0.682 |
|
| 2020 |
Huckins LM, Chatzinakos C, Breen MS, Hartmann J, Klengel T, da Silva Almeida AC, Dobbyn A, Girdhar K, Hoffman GE, Klengel C, Logue MW, Lori A, Maihofer AX, Morrison FG, Nguyen HT, ... ... Kellis M, et al. Analysis of Genetically Regulated Gene Expression Identifies a Prefrontal PTSD Gene, SNRNP35, Specific to Military Cohorts. Cell Reports. 31: 107716. PMID 32492425 DOI: 10.1016/J.Celrep.2020.107716 |
0.614 |
|
| 2020 |
Li Y, Nair P, Lu XH, Wen Z, Wang Y, Dehaghi AAK, Miao Y, Liu W, Ordog T, Biernacka JM, Ryu E, Olson JE, Frye MA, Liu A, Guo L, ... ... Kellis M, et al. Inferring multimodal latent topics from electronic health records. Nature Communications. 11: 2536. PMID 32439869 DOI: 10.1038/S41467-020-16378-3 |
0.677 |
|
| 2020 |
Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, ... ... Kellis M, et al. Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries. Nature Communications. 11: 1715. PMID 32238811 DOI: 10.1038/S41467-020-15236-6 |
0.674 |
|
| 2020 |
Khan YA, Jungreis I, Wright JC, Mudge JM, Choudhary JS, Firth AE, Kellis M. Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon. Bmc Genetics. 21: 25. PMID 32138667 DOI: 10.1186/S12863-020-0828-7 |
0.699 |
|
| 2020 |
Wertz MH, Mitchem MR, Pineda SS, Hachigian LJ, Lee H, Lau V, Powers A, Kulicke R, Madan GK, Colic M, Therrien M, Vernon A, Beja-Glasser VF, Hegde M, Gao F, ... Kellis M, et al. Genome-wide In Vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT Toxicity. Neuron. PMID 32004439 DOI: 10.1016/J.Neuron.2020.01.004 |
0.385 |
|
| 2020 |
Martinez-Gomez L, Abascal F, Jungreis I, Pozo F, Kellis M, Mudge JM, Tress ML. Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation. Nar Genomics and Bioinformatics. 2: lqz023. PMID 31886458 DOI: 10.1093/nargab/lqz023 |
0.718 |
|
| 2020 |
Feizi S, Quon G, Recamonde-Mendoza M, Medard M, Kellis M, Jadbabaie A. Spectral Alignment of Graphs Ieee Transactions On Network Science and Engineering. 7: 1182-1197. DOI: 10.1109/Tnse.2019.2913233 |
0.746 |
|
| 2019 |
Chen D, Sun N, Hou L, Kim R, Faith J, Aslanyan M, Tao Y, Zheng Y, Fu J, Liu W, Kellis M, Clark A. Human Primordial Germ Cells Are Specified from Lineage-Primed Progenitors. Cell Reports. 29: 4568-4582.e5. PMID 31875561 DOI: 10.1016/J.Celrep.2019.11.083 |
0.317 |
|
| 2019 |
Mohammadi S, Davila-Velderrain J, Kellis M. Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution. Cell Systems. PMID 31786210 DOI: 10.1016/J.Cels.2019.10.007 |
0.704 |
|
| 2019 |
Menon M, Mohammadi S, Davila-Velderrain J, Goods BA, Cadwell TD, Xing Y, Stemmer-Rachamimov A, Shalek AK, Love JC, Kellis M, Hafler BP. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nature Communications. 10: 4902. PMID 31653841 DOI: 10.1038/S41467-019-12780-8 |
0.725 |
|
| 2019 |
Mudge JM, Jungreis I, Hunt T, Gonzalez JM, Wright JC, Kay M, Davidson C, Fitzgerald S, Seal R, Tweedie S, He L, Waterhouse RM, Li Y, Bruford E, Choudhary JS, ... ... Kellis M, et al. Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. Genome Research. PMID 31537640 DOI: 10.1101/Gr.246462.118 |
0.814 |
|
| 2019 |
Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, Kellis M, Ren B. Joint profiling of DNA methylation and chromatin architecture in single cells. Nature Methods. PMID 31384045 DOI: 10.1038/S41592-019-0502-Z |
0.493 |
|
| 2019 |
Liu D, Davila-Velderrain J, Zhang Z, Kellis M. Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization. Nucleic Acids Research. PMID 31265076 DOI: 10.1093/Nar/Gkz538 |
0.809 |
|
| 2019 |
Wu MR, Nissim L, Stupp D, Pery E, Binder-Nissim A, Weisinger K, Enghuus C, Palacios SR, Humphrey M, Zhang Z, Maria Novoa E, Kellis M, Weiss R, Rabkin SD, Tabach Y, et al. A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS). Nature Communications. 10: 2880. PMID 31253799 DOI: 10.1038/S41467-019-10912-8 |
0.766 |
|
| 2019 |
Currall BB, Chen M, Sallari RC, Cotter M, Wong KE, Robertson NG, Penney KL, Lunardi A, Reschke M, Hickox AE, Yin Y, Wong GT, Fung J, Brown KK, Williamson RE, ... ... Kellis M, et al. Corrigendum: Loss of LDAH associated with prostate cancer and hearing loss. Human Molecular Genetics. 28: 1753-1754. PMID 31222336 DOI: 10.1093/Hmg/Ddz036 |
0.754 |
|
| 2019 |
Novoa EM, Jungreis I, Jaillon O, Kellis M. Elucidation of Codon Usage Signatures across the Domains of Life. Molecular Biology and Evolution. PMID 31220870 DOI: 10.1093/Molbev/Msz124 |
0.796 |
|
| 2019 |
Mathys H, Davila-Velderrain J, Peng Z, Gao F, Mohammadi S, Young JZ, Menon M, He L, Abdurrob F, Jiang X, Martorell AJ, Ransohoff RM, Hafler BP, Bennett DA, Kellis M, et al. Author Correction: Single-cell transcriptomic analysis of Alzheimer's disease. Nature. PMID 31209304 DOI: 10.1038/S41586-019-1329-6 |
0.663 |
|
| 2019 |
Glorioso CA, Pfenning AR, Lee SS, Bennett DA, Sibille EL, Kellis M, Guarente LP. Rate of brain aging and are synergistic risk factors for Alzheimer's disease. Life Science Alliance. 2. PMID 31133613 DOI: 10.26508/lsa.201900303 |
0.619 |
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| 2019 |
Mathys H, Davila-Velderrain J, Peng Z, Gao F, Mohammadi S, Young JZ, Menon M, He L, Abdurrob F, Jiang X, Martorell AJ, Ransohoff RM, Hafler BP, Bennett DA, Kellis M, et al. Single-cell transcriptomic analysis of Alzheimer's disease. Nature. PMID 31042697 DOI: 10.1038/S41586-019-1195-2 |
0.688 |
|
| 2019 |
McCorkindale AL, Wahle P, Werner S, Jungreis I, Menzel P, Shukla CJ, Abreu RLP, Irizarry RA, Meyer IM, Kellis M, Zinzen RP. A gene expression atlas of embryonic neurogenesis in reveals complex spatiotemporal regulation of lncRNAs. Development (Cambridge, England). 146. PMID 30923056 DOI: 10.1242/Dev.175265 |
0.73 |
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| 2019 |
Liu M, Jiang Y, Wedow R, Li Y, Brazel DM, Chen F, Datta G, Davila-Velderrain J, McGuire D, Tian C, Zhan X, Choquet H, Docherty AR, ... ... Kellis M, et al. Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use. Nature Genetics. PMID 30643251 DOI: 10.1038/S41588-018-0307-5 |
0.671 |
|
| 2019 |
Zhang Z, Chng K, Lingadahalli S, Chen Z, Liu MH, Do HH, Cai S, Rinaldi N, Poh HM, Li G, Sung Y, Heng CL, Core LJ, Tan SK, Ruan XA, ... ... Kellis M, et al. An AR-ERG transcriptional signature defined by long range chromatin interactomes in prostate cancer cells. Genome Research. PMID 30606742 DOI: 10.1101/Gr.230243.117 |
0.774 |
|
| 2019 |
Feizi S, Medard M, Quon G, Kellis M, Duffy K. Network Infusion to Infer Information Sources in Networks Ieee Transactions On Network Science and Engineering. 6: 402-417. DOI: 10.1109/Tnse.2018.2854218 |
0.767 |
|
| 2018 |
Wang X, He L, Goggin SM, Saadat A, Wang L, Sinnott-Armstrong N, Claussnitzer M, Kellis M. High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human. Nature Communications. 9: 5380. PMID 30568279 DOI: 10.1038/S41467-018-07746-1 |
0.777 |
|
| 2018 |
Abascal F, Juan D, Jungreis I, Kellis M, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML. Loose ends: almost one in five human genes still have unresolved coding status. Nucleic Acids Research. PMID 30395326 DOI: 10.1093/Nar/Gky1146 |
0.706 |
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| 2018 |
Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, ... ... Kellis M, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. PMID 30357393 DOI: 10.1093/Nar/Gky955 |
0.754 |
|
| 2018 |
Currall BB, Chen M, Sallari RC, Cotter M, Wong KE, Robertson NG, Penney KL, Lunardi A, Reschke M, Hickox AE, Yin Y, Wong GT, Fung J, Brown KK, Williamson RE, ... ... Kellis M, et al. Loss of LDAH associated with prostate cancer and hearing loss. Human Molecular Genetics. PMID 30169630 DOI: 10.1093/Hmg/Ddy310 |
0.807 |
|
| 2018 |
Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, ... ... Kellis M, et al. Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries. Nature Communications. 9: 3493. PMID 30140049 DOI: 10.1038/s41467-018-05975-y |
0.63 |
|
| 2018 |
Natarajan P, Peloso GM, Zekavat SM, Montasser M, Ganna A, Chaffin M, Khera AV, Zhou W, Bloom JM, Engreitz JM, Ernst J, O'Connell JR, Ruotsalainen SE, Alver M, Manichaikul A, ... ... Kellis M, et al. Deep-coverage whole genome sequences and blood lipids among 16,324 individuals. Nature Communications. 9: 3391. PMID 30140000 DOI: 10.1038/S41467-018-05747-8 |
0.686 |
|
| 2018 |
Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, ... ... Kellis M, et al. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science (New York, N.Y.). PMID 30139913 DOI: 10.1126/Science.Aar3146 |
0.811 |
|
| 2018 |
Beaudoin JD, Novoa EM, Vejnar CE, Yartseva V, Takacs CM, Kellis M, Giraldez AJ. Analyses of mRNA structure dynamics identify embryonic gene regulatory programs. Nature Structural & Molecular Biology. 25: 677-686. PMID 30061596 DOI: 10.1038/S41594-018-0091-Z |
0.669 |
|
| 2018 |
Miyamoto K, Nguyen KT, Allen GE, Jullien J, Kumar D, Otani T, Bradshaw CR, Livesey FJ, Kellis M, Gurdon JB. Chromatin Accessibility Impacts Transcriptional Reprogramming in Oocytes. Cell Reports. 24: 304-311. PMID 29996092 DOI: 10.1016/J.Celrep.2018.06.030 |
0.492 |
|
| 2018 |
Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, ... ... Kellis M, et al. Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries. Nature Communications. 9: 2606. PMID 29973585 DOI: 10.1038/S41467-018-04668-W |
0.671 |
|
| 2018 |
Gamazon ER, Segrè AV, van de Bunt M, Wen X, Xi HS, Hormozdiari F, Ongen H, Konkashbaev A, Derks EM, Aguet F, Quan J, Nicolae DL, Eskin E, Kellis M, et al. Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation. Nature Genetics. PMID 29955180 DOI: 10.1038/S41588-018-0154-4 |
0.394 |
|
| 2018 |
Bansal MS, Kellis M, Kordi M, Kundu S. RANGER-DTL 2.0: Rigorous Reconstruction of Gene-Family Evolution by Duplication, Transfer, and Loss. Bioinformatics (Oxford, England). PMID 29688310 DOI: 10.1093/Bioinformatics/Bty314 |
0.689 |
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| 2018 |
Loughran G, Jungreis I, Tzani I, Power M, Dmitriev RI, Ivanov IP, Kellis M, Atkins JF. Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. The Journal of Biological Chemistry. PMID 29386352 DOI: 10.1074/Jbc.M117.818526 |
0.713 |
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| 2018 |
Hornshøj H, Nielsen MM, Sinnott-Armstrong NA, Świtnicki MP, Juul M, Madsen T, Sallari R, Kellis M, Ørntoft T, Hobolth A, Pedersen JS. Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival. Npj Genomic Medicine. 3: 1. PMID 29354286 DOI: 10.1038/S41525-017-0040-5 |
0.797 |
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| 2018 |
Wang Y, Li Y, Yue M, Wang J, Kumar S, Wechsler-Reya RJ, Zhang Z, Ogawa Y, Kellis M, Duester G, Zhao JC. N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications. Nature Neuroscience. PMID 29335608 DOI: 10.1038/S41593-017-0057-1 |
0.367 |
|
| 2017 |
Ernst J, Kellis M. Chromatin-state discovery and genome annotation with ChromHMM. Nature Protocols. 12: 2478-2492. PMID 29120462 DOI: 10.1038/Nprot.2017.124 |
0.679 |
|
| 2017 |
Liu Y, Sarkar A, Kheradpour P, Ernst J, Kellis M. Evidence of reduced recombination rate in human regulatory domains. Genome Biology. 18: 193. PMID 29058599 DOI: 10.1186/S13059-017-1308-X |
0.795 |
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| 2017 |
Day FR, Thompson DJ, Helgason H, Chasman DI, Finucane H, Sulem P, Ruth KS, Whalen S, Sarkar AK, Albrecht E, Altmaier E, Amini M, Barbieri CM, Boutin T, Campbell A, ... ... Kellis M, et al. Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk. Nature Genetics. PMID 28436984 DOI: 10.1038/Ng.3841 |
0.71 |
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| 2017 |
Marco E, Meuleman W, Huang J, Glass K, Pinello L, Wang J, Kellis M, Yuan GC. Multi-scale chromatin state annotation using a hierarchical hidden Markov model. Nature Communications. 8: 15011. PMID 28387224 DOI: 10.1038/Ncomms15011 |
0.791 |
|
| 2017 |
Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Goke J, Mueller NS, ... Kellis M, et al. Predicting gene expression in massively parallel reporter assays: a comparative study. Human Mutation. PMID 28220625 DOI: 10.1002/Humu.23197 |
0.661 |
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| 2017 |
Shi AH, Li Y, Murugadoss K, Kellis M. Abstract A15: Deconvolution of diverse cell types in the tumor microenvironment by jointly modeling transcriptomic and epigenomic information Cancer Immunology Research. 5. DOI: 10.1158/2326-6074.Tumimm16-A15 |
0.315 |
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| 2017 |
Murugadoss K, Rasmussen M, Shi A, Kellis M. Abstract A14: Convergence analysis of regulatory mutations into immuno-modulatory pathways across 14 tumor types Cancer Immunology Research. 5. DOI: 10.1158/2326-6074.Tumimm16-A14 |
0.359 |
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| 2017 |
Murugadoss K, Kellis M. Abstract B20: Discovery of combination therapies in a pan-cancer context through functional complementarity and convergence analysis of oncogenic drivers Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-B20 |
0.378 |
|
| 2017 |
Liu Y, Reed S, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Adalsteinsson V, Kellis M. Abstract 5689: Identify tissue-of-origin in cancer cfDNA by whole genome sequencing Cancer Research. 77: 5689-5689. DOI: 10.1158/1538-7445.Am2017-5689 |
0.498 |
|
| 2017 |
Feizi S, Makhdoumi A, Duffy K, Kellis M, Medard M. Network Maximal Correlation Ieee Transactions On Network Science and Engineering. 4: 229-247. DOI: 10.1109/Tnse.2017.2716966 |
0.762 |
|
| 2016 |
Le Gros MA, Clowney EJ, Magklara A, Yen A, Markenscoff-Papadimitriou E, Colquitt B, Myllys M, Kellis M, Lomvardas S, Larabell CA. Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo. Cell Reports. 17: 2125-2136. PMID 27851973 DOI: 10.1016/J.Celrep.2016.10.060 |
0.788 |
|
| 2016 |
Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen TS, Kellis M. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Nature Biotechnology. PMID 27701403 DOI: 10.1038/nbt.3678 |
0.64 |
|
| 2016 |
van der Harst P, van Setten J, Verweij N, Vogler G, Franke L, Maurano MT, Wang X, Mateo Leach I, Eijgelsheim M, Sotoodehnia N, Hayward C, Sorice R, Meirelles O, Lyytikäinen LP, Polašek O, ... ... Kellis M, et al. 52 Genetic Loci Influencing Myocardial Mass. Journal of the American College of Cardiology. 68: 1435-48. PMID 27659466 DOI: 10.1016/J.Jacc.2016.07.729 |
0.683 |
|
| 2016 |
Jungreis I, Chan CS, Waterhouse RM, Fields G, Lin MF, Kellis M. Evolutionary dynamics of abundant stop codon readthrough. Molecular Biology and Evolution. PMID 27604222 DOI: 10.1093/Molbev/Msw189 |
0.814 |
|
| 2016 |
Li Y, Kellis M. Joint Bayesian inference of risk variants and tissue-specific epigenomic enrichments across multiple complex human diseases. Nucleic Acids Research. PMID 27407109 DOI: 10.1093/Nar/Gkw627 |
0.406 |
|
| 2016 |
Barsacchi M, Novoa EM, Kellis M, Bechini A. SwiSpot: Modeling Riboswitches by Spotting Out Switching Sequences. Bioinformatics (Oxford, England). PMID 27378291 DOI: 10.1093/Bioinformatics/Btw401 |
0.674 |
|
| 2016 |
Wang X, Tucker NR, Rizki G, Mills R, Krijger PH, de Wit E, Subramanian V, Bartell E, Nguyen XX, Ye J, Leyton-Mange J, Dolmatova EV, van der Harst P, de Laat W, Ellinor PT, ... ... Kellis M, et al. Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures. Elife. 5. PMID 27162171 DOI: 10.7554/Elife.10557 |
0.762 |
|
| 2016 |
Smith JG, Felix JF, Morrison AC, Kalogeropoulos A, Trompet S, Wilk JB, Gidlöf O, Wang X, Morley M, Mendelson M, Joehanes R, Ligthart S, Shan X, Bis JC, Wang YA, ... ... Kellis M, et al. Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure. Plos Genetics. 12: e1006034. PMID 27149122 DOI: 10.1371/Journal.Pgen.1006034 |
0.757 |
|
| 2016 |
Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân R, Sahni N, Cotsapas C, ... ... Kellis M, et al. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science (New York, N.Y.). 351: 1450-4. PMID 27013732 DOI: 10.1126/Science.Aad2257 |
0.698 |
|
| 2016 |
Ma J, Diedrich JK, Jungreis I, Donaldson C, Vaughan J, Kellis M, Yates JR, Saghatelian A. Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides. Analytical Chemistry. PMID 27010111 DOI: 10.1021/Acs.Analchem.6B00191 |
0.717 |
|
| 2016 |
Marbach D, Lamparter D, Quon G, Kellis M, Kutalik Z, Bergmann S. Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases. Nature Methods. PMID 26950747 DOI: 10.1038/Nmeth.3799 |
0.831 |
|
| 2016 |
Bekelis K, Kerley-Hamilton JS, Teegarden A, Tomlinson CR, Kuintzle R, Simmons N, Singer RJ, Roberts DW, Kellis M, Hendrix DA. MicroRNA and gene expression changes in unruptured human cerebral aneurysms. Journal of Neurosurgery. 1-10. PMID 26918470 DOI: 10.3171/2015.11.Jns151841 |
0.632 |
|
| 2016 |
Claussnitzer M, Hui CC, Kellis M. FTO Obesity Variant and Adipocyte Browning in Humans. The New England Journal of Medicine. 374: 192-3. PMID 26760096 DOI: 10.1056/NEJMc1513316 |
0.6 |
|
| 2016 |
Ward LD, Kellis M. HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. Nucleic Acids Research. 44: D877-81. PMID 26657631 DOI: 10.1093/Nar/Gkv1340 |
0.755 |
|
| 2016 |
Wang X, Tucker NR, Rizki G, Mills R, Krijger PH, Wit Ed, Subramanian V, Bartell E, Nguyen X, Ye J, Leyton-Mange J, Dolmatova EV, Harst Pvd, Laat Wd, Ellinor PT, ... ... Kellis M, et al. Author response: Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures Elife. DOI: 10.7554/Elife.10557.031 |
0.742 |
|
| 2015 |
Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, Shao Z, Xie H, Xu J, De Los Angeles A, Zhang Y, ... ... Kellis M, et al. PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. Cell Reports. 12: 1456-1470. PMID 26299972 DOI: 10.1016/J.Celrep.2015.07.053 |
0.671 |
|
| 2015 |
Claussnitzer M, Dankel SN, Kim KH, Quon G, Meuleman W, Haugen C, Glunk V, Sousa IS, Beaudry JL, Puviindran V, Abdennur NA, Liu J, Svensson PA, Hsu YH, Drucker DJ, ... ... Kellis M, et al. FTO Obesity Variant Circuitry and Adipocyte Browning in Humans. The New England Journal of Medicine. 373: 895-907. PMID 26287746 DOI: 10.1056/Nejmoa1502214 |
0.789 |
|
| 2015 |
Yen A, Kellis M. Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type. Nature Communications. 6: 7973. PMID 26282110 DOI: 10.1038/Ncomms8973 |
0.81 |
|
| 2015 |
Park Y, Kellis M. Deep learning for regulatory genomics. Nature Biotechnology. 33: 825-6. PMID 26252139 DOI: 10.1038/Nbt.3313 |
0.59 |
|
| 2015 |
Chibnik LB, Yu L, Eaton ML, Srivastava G, Schneider JA, Kellis M, Bennett DA, De Jager PL. Alzheimer's loci: epigenetic associations and interaction with genetic factors. Annals of Clinical and Translational Neurology. 2: 636-47. PMID 26125039 DOI: 10.1002/Acn3.201 |
0.316 |
|
| 2015 |
Rogers JM, Barrera LA, Reyon D, Sander JD, Kellis M, Joung JK, Bulyk ML. Context influences on TALE-DNA binding revealed by quantitative profiling. Nature Communications. 6: 7440. PMID 26067805 DOI: 10.1038/Ncomms8440 |
0.62 |
|
| 2015 |
Madabhushi R, Gao F, Pfenning AR, Pan L, Yamakawa S, Seo J, Rueda R, Phan TX, Yamakawa H, Pao PC, Stott RT, Gjoneska E, Nott A, Cho S, Kellis M, et al. Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes. Cell. 161: 1592-605. PMID 26052046 DOI: 10.1016/J.Cell.2015.05.032 |
0.694 |
|
| 2015 |
Sealfon RS, Lin MF, Jungreis I, Wolf MY, Kellis M, Sabeti PC. FRESCo: finding regions of excess synonymous constraint in diverse viruses. Genome Biology. 16: 38. PMID 25853568 DOI: 10.1186/S13059-015-0603-7 |
0.811 |
|
| 2015 |
Feizi S, Marbach D, Médard M, Kellis M. Corrigendum: Network deconvolution as a general method to distinguish direct dependencies in networks. Nature Biotechnology. 33: 424. PMID 25850062 DOI: 10.1038/Nbt0415-424 |
0.763 |
|
| 2015 |
Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E, Achuthan P, Guo H, Fortune MD, Stevens H, Walker NM, ... ... Kellis M, et al. Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nature Genetics. 47: 381-6. PMID 25751624 DOI: 10.1038/Ng.3245 |
0.793 |
|
| 2015 |
Hatchi E, Skourti-Stathaki K, Ventz S, Pinello L, Yen A, Kamieniarz-Gdula K, Dimitrov S, Pathania S, McKinney KM, Eaton ML, Kellis M, Hill SJ, Parmigiani G, Proudfoot NJ, Livingston DM. BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Molecular Cell. 57: 636-47. PMID 25699710 DOI: 10.1016/J.Molcel.2015.01.011 |
0.795 |
|
| 2015 |
Gjoneska E, Pfenning AR, Mathys H, Quon G, Kundaje A, Tsai LH, Kellis M. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature. 518: 365-9. PMID 25693568 DOI: 10.1038/Nature14252 |
0.804 |
|
| 2015 |
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, ... ... Kellis M, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248 |
0.781 |
|
| 2015 |
Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, ... ... Kellis M, et al. Intermediate DNA methylation is a conserved signature of genome regulation. Nature Communications. 6: 6363. PMID 25691127 DOI: 10.1038/Ncomms7363 |
0.387 |
|
| 2015 |
Ernst J, Kellis M. Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. Nature Biotechnology. 33: 364-76. PMID 25690853 DOI: 10.1038/Nbt.3157 |
0.651 |
|
| 2015 |
Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, ... ... Kellis M, et al. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science (New York, N.Y.). 347: 1258522. PMID 25554792 DOI: 10.1126/Science.1258522 |
0.826 |
|
| 2015 |
Bansal MS, Wu YC, Alm EJ, Kellis M. Improved gene tree error correction in the presence of horizontal gene transfer. Bioinformatics (Oxford, England). 31: 1211-8. PMID 25481006 DOI: 10.1093/Bioinformatics/Btu806 |
0.689 |
|
| 2015 |
Ardlie KG, DeLuca DS, Segrè AV, Sullivan TJ, Young TR, Gelfand ET, Trowbridge CA, Maller JB, Tukiainen T, Lek M, Ward LD, Kheradpour P, Iriarte B, Meng Y, Palmer CD, ... ... Kellis M, et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans Science. 348: 648-660. DOI: 10.1126/science.1262110 |
0.8 |
|
| 2014 |
Whitney O, Pfenning AR, Howard JT, Blatti CA, Liu F, Ward JM, Wang R, Audet JN, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED. Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science (New York, N.Y.). 346: 1256780. PMID 25504732 DOI: 10.1126/Science.1256780 |
0.788 |
|
| 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, ... ... Kellis M, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992 |
0.843 |
|
| 2014 |
Sugathan A, Biagioli M, Golzio C, Erdin S, Blumenthal I, Manavalan P, Ragavendran A, Brand H, Lucente D, Miles J, Sheridan SD, Stortchevoi A, Kellis M, Haggarty SJ, Katsanis N, et al. CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors. Proceedings of the National Academy of Sciences of the United States of America. 111: E4468-77. PMID 25294932 DOI: 10.1073/Pnas.1405266111 |
0.442 |
|
| 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 |
0.807 |
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| 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, ... ... Kellis M, et al. Comparative analysis of regulatory information and circuits across distant species. Nature. 512: 453-6. PMID 25164757 DOI: 10.1038/Nature13668 |
0.817 |
|
| 2014 |
Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, ... ... Kellis M, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/Nature13415 |
0.732 |
|
| 2014 |
Zhao B, Barrera LA, Ersing I, Willox B, Schmidt SC, Greenfeld H, Zhou H, Mollo SB, Shi TT, Takasaki K, Jiang S, Cahir-McFarland E, Kellis M, Bulyk ML, Kieff E, et al. The NF-κB genomic landscape in lymphoblastoid B cells. Cell Reports. 8: 1595-606. PMID 25159142 DOI: 10.1016/J.Celrep.2014.07.037 |
0.593 |
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| 2014 |
De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML, Keenan BT, Ernst J, McCabe C, Tang A, Raj T, Replogle J, Brodeur W, Gabriel S, ... ... Kellis M, et al. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nature Neuroscience. 17: 1156-63. PMID 25129075 DOI: 10.1038/Nn.3786 |
0.71 |
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| 2014 |
Rajagopal N, Ernst J, Ray P, Wu J, Zhang M, Kellis M, Ren B. Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies. G3 (Bethesda, Md.). 4: 2051-63. PMID 25122670 DOI: 10.1534/G3.114.013565 |
0.645 |
|
| 2014 |
Loughran G, Chou MY, Ivanov IP, Jungreis I, Kellis M, Kiran AM, Baranov PV, Atkins JF. Evidence of efficient stop codon readthrough in four mammalian genes. Nucleic Acids Research. 42: 8928-38. PMID 25013167 DOI: 10.1093/Nar/Gku608 |
0.744 |
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| 2014 |
Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, ... ... Kellis M, et al. Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Research. 24: 1224-35. PMID 24985916 DOI: 10.1101/Gr.168807.113 |
0.811 |
|
| 2014 |
Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, ... ... Kellis M, et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research. 24: 1209-23. PMID 24985915 DOI: 10.1101/Gr.159384.113 |
0.46 |
|
| 2014 |
Arking DE, Pulit SL, Crotti L, van der Harst P, Munroe PB, Koopmann TT, Sotoodehnia N, Rossin EJ, Morley M, Wang X, Johnson AD, Lundby A, Gudbjartsson DF, Noseworthy PA, Eijgelsheim M, ... ... Kellis M, et al. Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. Nature Genetics. 46: 826-36. PMID 24952745 DOI: 10.1038/Ng.3014 |
0.801 |
|
| 2014 |
Libeskind-Hadas R, Wu YC, Bansal MS, Kellis M. Pareto-optimal phylogenetic tree reconciliation. Bioinformatics (Oxford, England). 30: i87-95. PMID 24932009 DOI: 10.1093/Bioinformatics/Btu289 |
0.652 |
|
| 2014 |
Califano A, Kellis M, Stolovitzky G. RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2013 special issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 21: 371-2. PMID 24784777 DOI: 10.1089/Cmb.2014.009P |
0.35 |
|
| 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 |
0.842 |
|
| 2014 |
Washietl S, Bernhart SH, Kellis M. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments. Methods in Molecular Biology (Clifton, N.J.). 1097: 125-41. PMID 24639158 DOI: 10.1007/978-1-62703-709-9_7 |
0.705 |
|
| 2014 |
Lee MN, Ye C, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, ... ... Kellis M, et al. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science (New York, N.Y.). 343: 1246980. PMID 24604203 DOI: 10.1126/Science.1246980 |
0.707 |
|
| 2014 |
Ma J, Ward CC, Jungreis I, Slavoff SA, Schwaid AG, Neveu J, Budnik BA, Kellis M, Saghatelian A. Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue. Journal of Proteome Research. 13: 1757-65. PMID 24490786 DOI: 10.1021/Pr401280W |
0.731 |
|
| 2014 |
Washietl S, Kellis M, Garber M. Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Research. 24: 616-28. PMID 24429298 DOI: 10.1101/Gr.165035.113 |
0.753 |
|
| 2014 |
Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature. 505: 701-5. PMID 24336214 DOI: 10.1038/Nature12894 |
0.71 |
|
| 2014 |
Kheradpour P, Kellis M. Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Research. 42: 2976-87. PMID 24335146 DOI: 10.1093/Nar/Gkt1249 |
0.736 |
|
| 2014 |
Wu YC, Rasmussen MD, Bansal MS, Kellis M. Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees. Genome Research. 24: 475-86. PMID 24310000 DOI: 10.1101/Gr.161968.113 |
0.795 |
|
| 2013 |
Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M, Liapis SC, Mallard W, Morse M, Swerdel MR, D'Ecclessis MF, ... ... Kellis M, et al. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife. 2: e01749. PMID 24381249 DOI: 10.7554/Elife.01749 |
0.71 |
|
| 2013 |
Hammonds AS, Bristow CA, Fisher WW, Weiszmann R, Wu S, Hartenstein V, Kellis M, Yu B, Frise E, Celniker SE. Spatial expression of transcription factors in Drosophila embryonic organ development. Genome Biology. 14: R140. PMID 24359758 DOI: 10.1186/Gb-2013-14-12-R140 |
0.672 |
|
| 2013 |
Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers RM, Wold BJ. Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps. Genome Research. 23: 2136-48. PMID 24170599 DOI: 10.1101/Gr.158261.113 |
0.664 |
|
| 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, ... Kellis 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 |
0.691 |
|
| 2013 |
Bansal MS, Alm EJ, Kellis M. Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 738-54. PMID 24033262 DOI: 10.1089/Cmb.2013.0073 |
0.692 |
|
| 2013 |
Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EG, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémy RM, Bast J, Bazykin GA, Chabrol O, ... ... Kellis M, et al. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature. 500: 453-7. PMID 23873043 DOI: 10.1038/Nature12326 |
0.395 |
|
| 2013 |
Feizi S, Marbach D, Médard M, Kellis M. Network deconvolution as a general method to distinguish direct dependencies in networks. Nature Biotechnology. 31: 726-33. PMID 23851448 DOI: 10.1038/Nbt.2635 |
0.774 |
|
| 2013 |
Thompson DA, Roy S, Chan M, Styczynski MP, Pfiffner J, French C, Socha A, Thielke A, Napolitano S, Muller P, Kellis M, Konieczka JH, Wapinski I, Regev A. Correction: Evolutionary principles of modular gene regulation in yeasts. Elife. 2: e01114. PMID 23840936 DOI: 10.7554/Elife.01114 |
0.613 |
|
| 2013 |
Thompson DA, Roy S, Chan M, Styczynsky MP, Pfiffner J, French C, Socha A, Thielke A, Napolitano S, Muller P, Kellis M, Konieczka JH, Wapinski I, Regev A. Evolutionary principles of modular gene regulation in yeasts. Elife. 2: e00603. PMID 23795289 DOI: 10.7554/Elife.00603 |
0.645 |
|
| 2013 |
Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, Hasz R, Walters G, Garcia F, Young N, Foster B, Moser M, Karasik E, Gillard B, Ramsey K, ... ... Kellis M, et al. The Genotype-Tissue Expression (GTEx) project Nature Genetics. 45: 580-585. PMID 23715323 DOI: 10.1038/Ng.2653 |
0.382 |
|
| 2013 |
Ward LD, Kellis M. Response to comment on "Evidence of abundant purifying selection in humans for recently acquired regulatory functions". Science (New York, N.Y.). 340: 682. PMID 23661743 DOI: 10.1126/Science.1233366 |
0.698 |
|
| 2013 |
Califano A, Kellis M, Stolovitzky G. Preface: RECOMB systems biology, regulatory genomics, and DREAM 2012 special issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 373-4. PMID 23641866 DOI: 10.1089/Cmb.2013.008P |
0.35 |
|
| 2013 |
Roy S, Wapinski I, Pfiffner J, French C, Socha A, Konieczka J, Habib N, Kellis M, Thompson D, Regev A. Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules. Genome Research. 23: 1039-50. PMID 23640720 DOI: 10.1101/Gr.146233.112 |
0.635 |
|
| 2013 |
Ernst J, Kellis M. Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. Genome Research. 23: 1142-54. PMID 23595227 DOI: 10.1101/Gr.144840.112 |
0.669 |
|
| 2013 |
Chan CS, Jungreis I, Kellis M. Heterologous stop codon readthrough of metazoan readthrough candidates in yeast. Plos One. 8: e59450. PMID 23544069 DOI: 10.1371/Journal.Pone.0059450 |
0.744 |
|
| 2013 |
Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B. RFECS: a random-forest based algorithm for enhancer identification from chromatin state. Plos Computational Biology. 9: e1002968. PMID 23526891 DOI: 10.1371/Journal.Pcbi.1002968 |
0.665 |
|
| 2013 |
Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J, Mikkelsen TS, Kellis M. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Research. 23: 800-11. PMID 23512712 DOI: 10.1101/Gr.144899.112 |
0.819 |
|
| 2013 |
Sun L, Goff LA, Trapnell C, Alexander R, Lo KA, Hacisuleyman E, Sauvageau M, Tazon-Vega B, Kelley DR, Hendrickson DG, Yuan B, Kellis M, Lodish HF, Rinn JL. Long noncoding RNAs regulate adipogenesis. Proceedings of the National Academy of Sciences of the United States of America. 110: 3387-92. PMID 23401553 DOI: 10.1073/Pnas.1222643110 |
0.741 |
|
| 2013 |
Grote P, Wittler L, Hendrix D, Koch F, Währisch S, Beisaw A, Macura K, Bläss G, Kellis M, Werber M, Herrmann BG. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Developmental Cell. 24: 206-14. PMID 23369715 DOI: 10.1016/J.Devcel.2012.12.012 |
0.673 |
|
| 2013 |
Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Research. 41: 827-41. PMID 23221638 DOI: 10.1093/Nar/Gks1284 |
0.776 |
|
| 2013 |
Meuleman W, Peric-Hupkes D, Kind J, Beaudry JB, Pagie L, Kellis M, Reinders M, Wessels L, van Steensel B. Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence. Genome Research. 23: 270-80. PMID 23124521 DOI: 10.1101/Gr.141028.112 |
0.774 |
|
| 2013 |
Wu YC, Rasmussen MD, Bansal MS, Kellis M. TreeFix: statistically informed gene tree error correction using species trees. Systematic Biology. 62: 110-20. PMID 22949484 DOI: 10.1093/Sysbio/Sys076 |
0.806 |
|
| 2013 |
Thompson DA, Roy S, Chan M, Styczynsky MP, Pfiffner J, French C, Socha A, Thielke A, Napolitano S, Muller P, Kellis M, Konieczka JH, Wapinski I, Regev A. Author response: Evolutionary principles of modular gene regulation in yeasts Elife. DOI: 10.7554/Elife.00603.031 |
0.626 |
|
| 2012 |
Talkowski ME, Maussion G, Crapper L, Rosenfeld JA, Blumenthal I, Hanscom C, Chiang C, Lindgren A, Pereira S, Ruderfer D, Diallo AB, Lopez JP, Turecki G, Chen ES, Gigek C, ... ... Kellis M, et al. Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities. American Journal of Human Genetics. 91: 1128-34. PMID 23217328 DOI: 10.1016/J.Ajhg.2012.10.016 |
0.355 |
|
| 2012 |
Jin B, Ernst J, Tiedemann RL, Xu H, Sureshchandra S, Kellis M, Dalton S, Liu C, Choi JH, Robertson KD. Linking DNA methyltransferases to epigenetic marks and nucleosome structure genome-wide in human tumor cells. Cell Reports. 2: 1411-24. PMID 23177624 DOI: 10.1016/J.Celrep.2012.10.017 |
0.629 |
|
| 2012 |
Ward LD, Kellis M. Interpreting noncoding genetic variation in complex traits and human disease. Nature Biotechnology. 30: 1095-106. PMID 23138309 DOI: 10.1038/Nbt.2422 |
0.75 |
|
| 2012 |
Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M. Computational analysis of noncoding RNAs. Wiley Interdisciplinary Reviews. Rna. 3: 759-78. PMID 22991327 DOI: 10.1002/Wrna.1134 |
0.787 |
|
| 2012 |
Sealfon R, Gire S, Ellis C, Calderwood S, Qadri F, Hensley L, Kellis M, Ryan ET, LaRocque RC, Harris JB, Sabeti PC. High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic. Bmc Genomics. 13: 468. PMID 22963323 DOI: 10.1186/1471-2164-13-468 |
0.725 |
|
| 2012 |
Ward LD, Kellis M. Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science (New York, N.Y.). 337: 1675-8. PMID 22956687 DOI: 10.1126/Science.1225057 |
0.743 |
|
| 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, ... ... Kellis 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 |
0.803 |
|
| 2012 |
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, ... ... Kellis M, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Research. 22: 1760-74. PMID 22955987 DOI: 10.1101/Gr.135350.111 |
0.451 |
|
| 2012 |
Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biology. 13: R49. PMID 22950968 DOI: 10.1186/Gb-2012-13-9-R49 |
0.761 |
|
| 2012 |
Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, Kellis M, Collins JJ, Stolovitzky G. Wisdom of crowds for robust gene network inference. Nature Methods. 9: 796-804. PMID 22796662 DOI: 10.1038/Nmeth.2016 |
0.73 |
|
| 2012 |
Bansal MS, Alm EJ, Kellis M. Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics (Oxford, England). 28: i283-91. PMID 22689773 DOI: 10.1093/Bioinformatics/Bts225 |
0.698 |
|
| 2012 |
Wiggs JL, Yaspan BL, Hauser MA, Kang JH, Allingham RR, Olson LM, Abdrabou W, Fan BJ, Wang DY, Brodeur W, Budenz DL, Caprioli J, Crenshaw A, Crooks K, Delbono E, ... ... Kellis M, et al. Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. Plos Genetics. 8: e1002654. PMID 22570617 DOI: 10.1371/Journal.Pgen.1002654 |
0.649 |
|
| 2012 |
Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M. Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Research. 22: 1334-49. PMID 22456606 DOI: 10.1101/Gr.127191.111 |
0.811 |
|
| 2012 |
Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nature Methods. 9: 215-6. PMID 22373907 DOI: 10.1038/Nmeth.1906 |
0.643 |
|
| 2012 |
Melnikov A, Murugan A, Zhang X, Tesileanu T, Wang L, Rogov P, Feizi S, Gnirke A, Callan CG, Kinney JB, Kellis M, Lander ES, Mikkelsen TS. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nature Biotechnology. 30: 271-7. PMID 22371084 DOI: 10.1038/Nbt.2137 |
0.817 |
|
| 2012 |
Washietl S, Hofacker IL, Stadler PF, Kellis M. RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Research. 40: 4261-72. PMID 22287623 DOI: 10.1093/Nar/Gks009 |
0.692 |
|
| 2012 |
Rasmussen MD, Kellis M. Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Research. 22: 755-65. PMID 22271778 DOI: 10.1101/Gr.123901.111 |
0.717 |
|
| 2012 |
Ward LD, Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Research. 40: D930-4. PMID 22064851 DOI: 10.1093/Nar/Gkr917 |
0.743 |
|
| 2012 |
Wu YC, Rasmussen MD, Kellis M. Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny. Molecular Biology and Evolution. 29: 689-705. PMID 21900599 DOI: 10.1093/Molbev/Msr222 |
0.71 |
|
| 2012 |
De Jager P, Srivastava G, Eaton M, Chibnik L, Kellis M, Bennett D. Genome-Wide Exploration of DNA Methylation in the Aging Brain and Its Relation to Alzheimer's Disease (P05.070) Neurology. 78: P05.070-P05.070. DOI: 10.1212/Wnl.78.1_Meetingabstracts.P05.070 |
0.334 |
|
| 2012 |
Jager PD, Srivastava G, Eaton M, Chibnik L, Keenan B, Zou F, Song H, Younkin C, Younkin S, Ertekin-Taner N, Bernstein B, Meissner A, Kellis M, Bennett D. Genome-wide exploration of DNA methylation in the aging brain and its relation to Alzheimer's disease Alzheimers & Dementia. 8. DOI: 10.1016/J.Jalz.2012.05.1829 |
0.328 |
|
| 2012 |
Keenan B, Srivastava G, Eaton M, Schneider J, Chibnik L, Meissner A, Kellis M, Bennett D, Jager PD. The role of DNA methylation in Alzheimer's susceptibility genes with Alzheimer's disease phenotypes Alzheimers & Dementia. 8. DOI: 10.1016/J.Jalz.2012.05.1203 |
0.302 |
|
| 2011 |
Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 147: 1628-39. PMID 22196736 DOI: 10.1016/J.Cell.2011.09.057 |
0.734 |
|
| 2011 |
Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, Pedersen JS. New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Research. 21: 1929-43. PMID 21994249 DOI: 10.1101/Gr.112516.110 |
0.752 |
|
| 2011 |
Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Research. 21: 1916-28. PMID 21994248 DOI: 10.1101/Gr.108753.110 |
0.829 |
|
| 2011 |
Jungreis I, Lin MF, Spokony R, Chan CS, Negre N, Victorsen A, White KP, Kellis M. Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Research. 21: 2096-113. PMID 21994247 DOI: 10.1101/Gr.119974.110 |
0.755 |
|
| 2011 |
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, ... ... Kellis M, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530 |
0.819 |
|
| 2011 |
Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. Three periods of regulatory innovation during vertebrate evolution. Science (New York, N.Y.). 333: 1019-24. PMID 21852499 DOI: 10.1126/Science.1202702 |
0.682 |
|
| 2011 |
Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, ... ... Kellis M, et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Research. 21: 1659-71. PMID 21795386 DOI: 10.1101/Gr.125088.111 |
0.661 |
|
| 2011 |
Lin MF, Jungreis I, Kellis M. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics (Oxford, England). 27: i275-82. PMID 21685081 DOI: 10.1038/Npre.2010.4784.1 |
0.727 |
|
| 2011 |
Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P, Wang Y, Kong B, Langerød A, Børresen-Dale AL, Kim SK, ... ... Kellis M, et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nature Genetics. 43: 621-9. PMID 21642992 DOI: 10.1038/Ng.848 |
0.403 |
|
| 2011 |
Magklara A, Yen A, Colquitt BM, Clowney EJ, Allen W, Markenscoff-Papadimitriou E, Evans ZA, Kheradpour P, Mountoufaris G, Carey C, Barnea G, Kellis M, Lomvardas S. An epigenetic signature for monoallelic olfactory receptor expression. Cell. 145: 555-70. PMID 21529909 DOI: 10.1016/J.Cell.2011.03.040 |
0.79 |
|
| 2011 |
Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, ... ... Kellis M, et al. Comparative functional genomics of the fission yeasts. Science (New York, N.Y.). 332: 930-6. PMID 21511999 DOI: 10.1126/Science.1203357 |
0.683 |
|
| 2011 |
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 473: 43-9. PMID 21441907 DOI: 10.1038/Nature09906 |
0.832 |
|
| 2011 |
Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, ... ... Kellis M, et al. A cis-regulatory map of the Drosophila genome. Nature. 471: 527-31. PMID 21430782 DOI: 10.1038/Nature09990 |
0.826 |
|
| 2011 |
Ay F, Kellis M, Kahveci T. SubMAP: aligning metabolic pathways with subnetwork mappings. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 219-35. PMID 21385030 DOI: 10.1089/Cmb.2010.0280 |
0.716 |
|
| 2011 |
Hubisz MJ, Lin MF, Kellis M, Siepel A. Error and error mitigation in low-coverage genome assemblies. Plos One. 6: e17034. PMID 21340033 DOI: 10.1371/Journal.Pone.0017034 |
0.594 |
|
| 2011 |
Kellis M, Califano A, Bar-Joseph Z. Preface: RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges 2010 special issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 131. PMID 21314452 DOI: 10.1089/Cmb.2010.005P |
0.604 |
|
| 2011 |
Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, ... ... Kellis M, et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 471: 480-5. PMID 21179089 DOI: 10.1038/Nature09725 |
0.701 |
|
| 2011 |
Rasmussen MD, Kellis M. A Bayesian approach for fast and accurate gene tree reconstruction. Molecular Biology and Evolution. 28: 273-90. PMID 20660489 DOI: 10.1093/Molbev/Msq189 |
0.721 |
|
| 2010 |
Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, ... ... Kellis M, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374 |
0.82 |
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| 2010 |
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nature Biotechnology. 28: 1045-8. PMID 20944595 DOI: 10.1038/Nbt1010-1045 |
0.616 |
|
| 2010 |
Müller SA, Kohajda T, Findeiss S, Stadler PF, Washietl S, Kellis M, von Bergen M, Kalkhof S. Optimization of parameters for coverage of low molecular weight proteins. Analytical and Bioanalytical Chemistry. 398: 2867-81. PMID 20803007 DOI: 10.1007/S00216-010-4093-X |
0.698 |
|
| 2010 |
Syed Z, Stultz C, Kellis M, Indyk P, Guttag J. Motif Discovery in Physiological Datasets: A Methodology for Inferring Predictive Elements. Acm Transactions On Knowledge Discovery From Data. 4: 2. PMID 20730037 DOI: 10.1145/1644873.1644875 |
0.362 |
|
| 2010 |
Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature Biotechnology. 28: 817-25. PMID 20657582 DOI: 10.1038/Nbt.1662 |
0.707 |
|
| 2010 |
Kellis M, Rinn JL. Sequences to systems. Genome Biology. 11: 303. PMID 20500907 DOI: 10.1186/Gb-2010-11-5-303 |
0.572 |
|
| 2010 |
Nègre N, Brown CD, Shah PK, Kheradpour P, Morrison CA, Henikoff JG, Feng X, Ahmad K, Russell S, White RA, Stein L, Henikoff S, Kellis M, White KP. A comprehensive map of insulator elements for the Drosophila genome. Plos Genetics. 6: e1000814. PMID 20084099 DOI: 10.1371/Journal.Pgen.1000814 |
0.77 |
|
| 2010 |
Murchison EP, Tovar C, Hsu A, Bender HS, Kheradpour P, Rebbeck CA, Obendorf D, Conlan C, Bahlo M, Blizzard CA, Pyecroft S, Kreiss A, Kellis M, Stark A, Harkins TT, et al. The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science (New York, N.Y.). 327: 84-7. PMID 20044575 DOI: 10.1126/Science.1180616 |
0.742 |
|
| 2010 |
Searle S, Frankish A, Bignell A, Aken B, Derrien T, Diekhans M, Harte R, Howald C, Kokocinski F, Lin M, Tress M, Van Baren M, Barnes I, Hunt T, Carvalho-Silva D, ... ... Kellis M, et al. The GENCODE human gene set Genome Biology. 11: P36. DOI: 10.1186/Gb-2010-11-S1-P36 |
0.441 |
|
| 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 |
0.393 |
|
| 2009 |
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, ... ... Kellis M, et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Research. 19: 1316-23. PMID 19498102 DOI: 10.1101/Gr.080531.108 |
0.454 |
|
| 2009 |
Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, ... ... Kellis M, et al. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature. 459: 657-62. PMID 19465905 DOI: 10.1038/Nature08064 |
0.732 |
|
| 2009 |
Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, ... ... Kellis M, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 459: 108-12. PMID 19295514 DOI: 10.1038/Nature07829 |
0.773 |
|
| 2009 |
Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, ... ... Kellis M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 458: 223-7. PMID 19182780 DOI: 10.1038/Nature07672 |
0.773 |
|
| 2009 |
Bignell A, Frankish A, Aken B, Diekhans M, Kokocinski F, Lin M, Tress M, Baren JV, Barnes I, Hunt T, Carvalho-Silva D, Davidson C, Donaldson S, Gilbert J, Hart E, ... ... Kellis M, et al. GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome Nature Precedings. 4: 1-1. DOI: 10.1038/Npre.2009.3155.1 |
0.393 |
|
| 2008 |
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, ... ... Kellis M, et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 453: 175-83. PMID 18464734 DOI: 10.1038/Nature06936 |
0.771 |
|
| 2008 |
Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel JA, Sachidanandam R, Hannon GJ, Brennecke J. An endogenous small interfering RNA pathway in Drosophila. Nature. 453: 798-802. PMID 18463631 DOI: 10.1038/Nature07007 |
0.323 |
|
| 2008 |
Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z, Kellis M, Grützner F, Stark A, Hannon GJ. Conservation of small RNA pathways in platypus. Genome Research. 18: 995-1004. PMID 18463306 DOI: 10.1101/Gr.073056.107 |
0.729 |
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| 2008 |
Lin MF, Deoras AN, Rasmussen MD, Kellis M. Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes. Plos Computational Biology. 4: e1000067. PMID 18421375 DOI: 10.1371/Journal.Pcbi.1000067 |
0.734 |
|
| 2008 |
Presser A, Elowitz MB, Kellis M, Kishony R. The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication. Proceedings of the National Academy of Sciences of the United States of America. 105: 950-4. PMID 18199840 DOI: 10.1073/Pnas.0707293105 |
0.311 |
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| 2008 |
Stark A, Bushati N, Jan CH, Kheradpour P, Hodges E, Brennecke J, Bartel DP, Cohen SM, Kellis M. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes & Development. 22: 8-13. PMID 18172160 DOI: 10.1101/Gad.1613108 |
0.708 |
|
| 2008 |
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, ... ... Kellis M, et al. Genome analysis of the platypus reveals unique signatures of evolution (Nature (2008) 453, (175-183)) Nature. 455: 256. DOI: 10.1038/Nature07253 |
0.714 |
|
| 2007 |
Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES. Distinguishing protein-coding and noncoding genes in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 104: 19428-33. PMID 18040051 DOI: 10.1073/Pnas.0709013104 |
0.578 |
|
| 2007 |
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, ... ... Kellis M, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/Nature06340 |
0.834 |
|
| 2007 |
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341 |
0.831 |
|
| 2007 |
Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, Adelman K, Levine M, Young RA. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature Genetics. 39: 1512-6. PMID 17994019 DOI: 10.1038/Ng.2007.26 |
0.484 |
|
| 2007 |
Rasmussen MD, Kellis M. Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. Genome Research. 17: 1932-42. PMID 17989260 DOI: 10.1101/Gr.7105007 |
0.755 |
|
| 2007 |
Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Research. 17: 1865-79. PMID 17989255 DOI: 10.1101/Gr.6593807 |
0.718 |
|
| 2007 |
Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL, Kulathinal RJ, Zhang P, Myrick KV, ... ... Kellis M, et al. Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Research. 17: 1823-36. PMID 17989253 DOI: 10.1101/Gr.6679507 |
0.482 |
|
| 2007 |
Kheradpour P, Stark A, Roy S, Kellis M. Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Research. 17: 1919-31. PMID 17989251 DOI: 10.1101/Gr.7090407 |
0.821 |
|
| 2007 |
Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M, Lander ES. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proceedings of the National Academy of Sciences of the United States of America. 104: 7145-50. PMID 17442748 DOI: 10.1073/Pnas.0701811104 |
0.613 |
|
| 2007 |
Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell. 128: 1089-103. PMID 17346786 DOI: 10.1016/J.Cell.2007.01.043 |
0.38 |
|
| 2007 |
Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, Young RA, Levine M. Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes & Development. 21: 385-90. PMID 17322397 DOI: 10.1101/Gad.1509607 |
0.56 |
|
| 2005 |
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, ... ... Kellis M, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 438: 803-19. PMID 16341006 DOI: 10.1038/Nature04338 |
0.655 |
|
| 2005 |
Bernstein BE, Kellis M. Large-scale discovery and validation of functional elements in the human genome. Genome Biology. 6: 312. PMID 15774039 DOI: 10.1186/Gb-2005-6-3-312 |
0.615 |
|
| 2005 |
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature. 434: 338-45. PMID 15735639 DOI: 10.1038/Nature03441 |
0.693 |
|
| 2004 |
Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, ... ... Kellis M, et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 431: 946-57. PMID 15496914 DOI: 10.1038/Nature03025 |
0.567 |
|
| 2004 |
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, et al. Transcriptional regulatory code of a eukaryotic genome. Nature. 431: 99-104. PMID 15343339 DOI: 10.1038/Nature02800 |
0.591 |
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| 2004 |
Kellis M, Patterson N, Birren B, Berger B, Lander ES. Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 319-55. PMID 15285895 DOI: 10.1089/1066527041410319 |
0.716 |
|
| 2004 |
Kellis M. The changing face of genomics. Genome Biology. 5: 324. PMID 15128443 DOI: 10.1186/Gb-2004-5-5-324 |
0.365 |
|
| 2004 |
Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 428: 617-24. PMID 15004568 DOI: 10.1038/Nature02424 |
0.585 |
|
| 2003 |
Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB. Position specific variation in the rate of evolution in transcription factor binding sites. Bmc Evolutionary Biology. 3: 19. PMID 12946282 DOI: 10.1186/1471-2148-3-19 |
0.52 |
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| 2003 |
Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB. Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biology. 4: R43. PMID 12844359 DOI: 10.1186/Gb-2003-4-7-R43 |
0.575 |
|
| 2003 |
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 423: 241-54. PMID 12748633 DOI: 10.1038/Nature01644 |
0.617 |
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