Manolis Kellis - Publications

CSAIL Massachusetts Institute of Technology, Cambridge, MA, United States 

202 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
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/  0.88
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  0.64
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  0.88
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  0.64
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  0.76
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  0.88
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  0.64
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  0.88
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  0.64
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  0.44
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  0.72
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  0.92
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  0.88
2020 Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, ... ... Kellis M, et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 578: 102-111. PMID 32025015 DOI: 10.1038/s41586-020-1965-x  0.72
2020 Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS, Johnson R. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Communications Biology. 3: 56. PMID 32024996 DOI: 10.1038/s42003-019-0741-7  0.56
2020 Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, Reimand J. Integrative pathway enrichment analysis of multivariate omics data. Nature Communications. 11: 735. PMID 32024846 DOI: 10.1038/s41467-019-13983-9  0.44
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  0.88
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  0.84
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  0.64
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  0.64
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  0.88
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  0.92
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  0.64
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  0.64
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  0.36
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  0.88
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  0.64
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  0.6
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  0.64
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  0.88
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  0.64
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  0.68
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  0.76
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  0.88
2018 Wang J, Pejaver VR, Dann GP, Wolf MY, Kellis M, Huang Y, Garcia BA, Radivojac P, Kashina A. Target site specificity and in vivo complexity of the mammalian arginylome. Scientific Reports. 8: 16177. PMID 30385798 DOI: 10.1038/s41598-018-34639-6  0.68
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  0.88
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  0.36
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  0.92
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  0.92
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  0.64
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  0.44
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  0.92
2018 Juul M, Madsen T, Guo Q, Bertl J, Hobolth A, Kellis M, Pedersen JS. ncdDetect2: Improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation. Bioinformatics (Oxford, England). PMID 29945188 DOI: 10.1093/bioinformatics/bty511  0.48
2018 Wang Y, Li Y, Yue M, Wang J, Kumar S, Wechsler-Reya RJ, Zhang Z, Ogawa Y, Kellis M, Duester G, Zhao JC. Publisher Correction: N-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications. Nature Neuroscience. PMID 29880878 DOI: 10.1038/s41593-018-0169-2  0.72
2018 Barbeira AN, Dickinson SP, Bonazzola R, Zheng J, Wheeler HE, Torres JM, Torstenson ES, Shah KP, Garcia T, Edwards TL, Stahl EA, Huckins LM, Nicolae DL, Cox NJ, et al. Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. Nature Communications. 9: 1825. PMID 29739930 DOI: 10.1038/s41467-018-03621-1  0.4
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  1
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  0.84
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  0.48
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  0.72
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  0.92
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  0.96
2017 Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD, et al. The impact of rare variation on gene expression across tissues. Nature. 550: 239-243. PMID 29022581 DOI: 10.1038/nature24267  0.52
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  0.68
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  0.52
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  0.96
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  0.92
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  0.88
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  0.92
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  0.44
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  0.88
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  0.88
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  0.88
2016 Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, Zhao Y, Mobbs CV, Schadt EE, Zhu J, Tu Z. Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. Scientific Reports. 6: 19384. PMID 26795431 DOI: 10.1038/srep19384  0.64
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  0.68
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  0.96
2015 Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, Zhao Y, Mobbs CV, Schadt EE, Zhu J, Tu Z. Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. Scientific Reports. 5: 15145. PMID 26477495 DOI: 10.1038/srep15145  0.88
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  0.96
2015 Park Y, Kellis M. Deep learning for regulatory genomics. Nature Biotechnology. 33: 825-6. PMID 26252139 DOI: 10.1038/nbt.3313  0.44
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  0.6
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  0.88
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  0.88
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  0.88
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  0.48
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  0.88
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  0.92
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  0.88
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  0.88
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  0.88
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  0.88
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  0.56
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  0.88
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  0.88
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  0.56
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  0.92
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  0.88
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  0.88
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  0.88
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  0.48
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.96
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  1
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  0.88
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  0.88
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  0.88
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  0.92
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.96
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  0.88
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  0.88
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  0.92
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  0.88
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  0.88
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  0.96
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  0.88
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  0.88
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  0.88
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  0.68
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  1
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  0.88
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  0.88
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  0.96
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  0.88
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  0.88
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  0.96
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
2012 Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nature Methods. 9: 215-6. PMID 22373907 DOI: 10.1038/nmeth.1906  0.92
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  0.88
2012 Califano A, Kellis M, Stolovitzky G. Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 special issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 101. PMID 22300312 DOI: 10.1089/cmb.2012.010p  0.88
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  0.88
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  1
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  0.96
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  1
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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: 10.1093/bioinformatics/btr209  0.92
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  0.88
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  0.88
2011 . A user's guide to the encyclopedia of DNA elements (ENCODE). Plos Biology. 9: e1001046. PMID 21526222 DOI: 10.1371/journal.pbio.1001046  0.88
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  0.88
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  0.88
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  0.88
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  1
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  0.92
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  0.64
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  0.88
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  1
2011 Organ CL, Rasmussen MD, Baldwin MW, Kellis M, Edwards SV. Phylogenomic Approach to the Evolutionary Dynamics of Gene Duplication in Birds Evolution After Gene Duplication. 253-268. DOI: 10.1002/9780470619902.ch14  0.88
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  0.32
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  0.88
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  0.88
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  0.88
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  0.92
2010 Kellis M, Rinn JL. Sequences to systems. Genome Biology. 11: 303. PMID 20500907 DOI: 10.1186/gb-2010-11-5-303  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  1
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  1
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  0.88
2007 Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Research. 17: 1850-64. PMID 17989254 DOI: 10.1101/gr.6597907  0.88
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  0.88
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  0.96
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  0.76
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  0.88
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  0.88
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  0.88
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  0.68
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  0.64
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  0.88
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  0.88
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  0.64
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  0.64
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  0.88
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  0.88
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  0.64
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