John A. Stamatoyannopoulos - Publications

Affiliations: 
Genome Sciences University of Washington, Seattle, Seattle, WA 
Area:
Genetics, Molecular Biology

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

Year Citation  Score
2024 Paquette A, Ahuna K, Hwang YM, Pearl J, Liao H, Shannon P, Kadam L, Lapehn S, Bucher M, Roper R, Funk C, MacDonald J, Bammler T, Baloni P, Brockway H, ... ... Stamatoyannopoulos J, et al. A genome scale transcriptional regulatory model of the human placenta. Science Advances. 10: eadf3411. PMID 38941464 DOI: 10.1126/sciadv.adf3411  0.323
2024 Breeze CE, Haugen E, Gutierrez-Arcelus M, Yao X, Teschendorff A, Beck S, Dunham I, Stamatoyannopoulos J, Franceschini N, Machiela MJ, Berndt SI. FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases. Genome Biology. 25: 3. PMID 38167104 DOI: 10.1186/s13059-023-03126-1  0.332
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, ... ... Stamatoyannopoulos JA, 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  0.332
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, ... ... Stamatoyannopoulos JA, 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  0.354
2021 Georgolopoulos G, Psatha N, Iwata M, Nishida A, Som T, Yiangou M, Stamatoyannopoulos JA, Vierstra J. Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation. Nature Communications. 12: 6790. PMID 34815405 DOI: 10.1038/s41467-021-27159-x  0.314
2021 Halow JM, Byron R, Hogan MS, Ordoñez R, Groudine M, Bender MA, Stamatoyannopoulos JA, Maurano MT. Tissue context determines the penetrance of regulatory DNA variation. Nature Communications. 12: 2850. PMID 33990600 DOI: 10.1038/s41467-021-23139-3  0.758
2020 Vierstra J, Lazar J, Sandstrom R, Halow J, Lee K, Bates D, Diegel M, Dunn D, Neri F, Haugen E, Rynes E, Reynolds A, Nelson J, Johnson A, Frerker M, ... ... Stamatoyannopoulos JA, et al. Global reference mapping of human transcription factor footprints. Nature. 583: 729-736. PMID 32728250 DOI: 10.1038/S41586-020-2528-X  0.549
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, ... ... Stamatoyannopoulos JA, 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  0.507
2020 Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, et al. Perspectives on ENCODE. Nature. 583: 693-698. PMID 32728248 DOI: 10.1038/S41586-020-2449-8  0.492
2020 Meuleman W, Muratov A, Rynes E, Halow J, Lee K, Bates D, Diegel M, Dunn D, Neri F, Teodosiadis A, Reynolds A, Haugen E, Nelson J, Johnson A, Frerker M, ... ... Stamatoyannopoulos J, et al. Index and biological spectrum of human DNase I hypersensitive sites. Nature. PMID 32728217 DOI: 10.1038/S41586-020-2559-3  0.515
2020 Stergachis AB, Debo BM, Haugen E, Churchman LS, Stamatoyannopoulos JA. Single-molecule regulatory architectures captured by chromatin fiber sequencing. Science (New York, N.Y.). 368: 1449-1454. PMID 32587015 DOI: 10.1126/Science.Aaz1646  0.364
2020 Lazar JE, Stehling-Sun S, Nandakumar V, Wang H, Chee DR, Howard NP, Acosta R, Dunn D, Diegel M, Neri F, Castillo A, Ibarrientos S, Lee K, Lescano N, Van Biber B, ... ... Stamatoyannopoulos JA, et al. Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling. Cell Reports. 31: 107676. PMID 32460018 DOI: 10.1016/J.Celrep.2020.107676  0.532
2020 Federation AJ, Nandakumar V, Searle BC, Stergachis A, Wang H, Pino LK, Merrihew G, Ting YS, Howard N, Kutyavin T, MacCoss MJ, Stamatoyannopoulos JA. Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins. Cell Reports. 30: 2463-2471.e5. PMID 32101728 DOI: 10.1016/J.Celrep.2020.01.096  0.44
2019 Sullivan AM, Arsovski AA, Thompson A, Sandstrom R, Thurman RE, Neph S, Johnson AK, Sullivan ST, Sabo PJ, Neri FV, Weaver M, Diegel M, Nemhauser JL, Stamatoyannopoulos JA, Bubb KL, et al. Mapping and Dynamics of Regulatory DNA in Maturing Siliques. Frontiers in Plant Science. 10: 1434. PMID 31798605 DOI: 10.3389/Fpls.2019.01434  0.431
2019 Morton EA, Hall AN, Kwan E, Mok C, Queitsch K, Nandakumar V, Stamatoyannopoulos J, Brewer BJ, Waterston R, Queitsch C. Challenges and Approaches to Genotyping Repetitive DNA. G3 (Bethesda, Md.). PMID 31757929 DOI: 10.1534/G3.119.400771  0.41
2019 Breeze CE, Reynolds AP, van Dongen J, Dunham I, Lazar J, Neph S, Vierstra J, Bourque G, Teschendorff AE, Stamatoyannopoulos JA, Beck S. eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data. Bioinformatics (Oxford, England). PMID 31161210 DOI: 10.1093/Bioinformatics/Btz456  0.355
2019 Rouhanifard SH, Mellis IA, Dunagin M, Bayatpour S, Jiang CL, Dardani I, Symmons O, Emert B, Torre E, Cote A, Sullivan A, Stamatoyannopoulos JA, Raj A. Amendments: Author Correction: ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. Nature Biotechnology. 37: 102. PMID 30605160 DOI: 10.1038/Nbt0119-102B  0.32
2018 Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, ... ... Stamatoyannopoulos JA, et al. Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics. PMID 30202056 DOI: 10.1038/S41588-018-0195-8  0.451
2018 Woo J, Stehling-Sun S, Deeg HJ, Papayannopoulou T, Urnov FD, Stamatoyannopoulos JA. Regulatory Reprogramming of Erythropoiesis By DNMT3A Mutation Blood. 132: 4343-4343. DOI: 10.1182/Blood-2018-99-120110  0.397
2018 Pearl J, Urnov FD, Stamatoyannopoulos JA. Potent and Timed Epigenetic Repression of PD-1 in Human T Cells Blood. 132: 3493-3493. DOI: 10.1182/Blood-2018-99-119011  0.356
2017 Cremer M, Schmid VJ, Kraus F, Markaki Y, Hellmann I, Maiser A, Leonhardt H, John S, Stamatoyannopoulos J, Cremer T. Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters. Epigenetics & Chromatin. 10: 39. PMID 28784182 DOI: 10.1186/S13072-017-0146-0  0.36
2017 Lazaridis I, Mittnik A, Patterson N, Mallick S, Rohland N, Pfrengle S, Furtwängler A, Peltzer A, Posth C, Vasilakis A, McGeorge PJP, Konsolaki-Yannopoulou E, Korres G, Martlew H, Michalodimitrakis M, ... ... Stamatoyannopoulos JA, et al. Genetic origins of the Minoans and Mycenaeans. Nature. PMID 28783727 DOI: 10.1038/Nature23310  0.311
2017 Stamatoyannopoulos J. Connecting the regulatory genome. Nature Genetics. 48: 479-80. PMID 27120444 DOI: 10.1038/Ng.3553  0.456
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, ... ... Stamatoyannopoulos JA, 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  0.63
2016 Zrazhevskiy P, Akilesh S, Tai W, Queitsch K, True LD, Fromm J, Wu D, Nelson P, Stamatoyannopoulos JA, Gao X. Cross-Platform DNA Encoding for Single-Cell Imaging of Gene Expression. Angewandte Chemie (International Ed. in English). PMID 27273345 DOI: 10.1002/Anie.201603945  0.305
2016 Neph S, Reynolds AP, Kuehn MS, Stamatoyannopoulos JA. Operating on Genomic Ranges Using BEDOPS. Methods in Molecular Biology (Clifton, N.J.). 1418: 267-81. PMID 27008020 DOI: 10.1007/978-1-4939-3578-9_14  0.363
2016 Vierstra J, Stamatoyannopoulos JA. Genomic footprinting. Nature Methods. 13: 213-21. PMID 26914205 DOI: 10.1038/nmeth.3768  0.43
2016 Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA. Erratum: Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo. Nature Genetics. 48: 101. PMID 26711113 DOI: 10.1038/ng0116-101c  0.702
2015 Maurano MT, Stamatoyannopoulos JA. Taking Stock of Regulatory Variation. Cell Systems. 1: 18-21. PMID 27135686 DOI: 10.1016/J.Cels.2015.07.011  0.695
2015 Turner TN, Hormozdiari F, Duyzend MH, McClymont SA, Hook PW, Iossifov I, Raja A, Baker C, Hoekzema K, Stessman HA, Zody MC, Nelson BJ, Huddleston J, Sandstrom R, Smith JD, ... ... Stamatoyannopoulos J, et al. Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. American Journal of Human Genetics. PMID 26749308 DOI: 10.1016/J.Ajhg.2015.11.023  0.443
2015 Geeven G, Zhu Y, Kim BJ, Bartholdy BA, Yang SM, Macfarlan TS, Gifford WD, Pfaff SL, Verstegen MJ, Pinto H, Vermunt MW, Creyghton MP, Wijchers PJ, Stamatoyannopoulos JA, Skoultchi AI, et al. Local compartment changes and regulatory landscape alterations in histone H1-depleted cells. Genome Biology. 16: 289. PMID 26700097 DOI: 10.1186/S13059-015-0857-0  0.428
2015 Letourneau A, Santoni FA, Bonilla X, Reza Sailani M, Gonzalez D, Kind J, Chevalier C, Thurman R, Sandstrom RS, Hibaoui Y, Garieri M, Popadin K, Falconnet E, Gagnebin M, Gehrig C, ... ... Stamatoyannopoulos JA, et al. Corrigendum: Domains of genome-wide gene expression dysregulation in Down's syndrome. Nature. PMID 26633627 DOI: 10.1038/Nature16135  0.343
2015 Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, Sunyaev SR. APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions. Cell Reports. PMID 26527001 DOI: 10.1016/J.Celrep.2015.09.077  0.332
2015 He X, Tillo D, Vierstra J, Syed KS, Deng C, Ray JG, Stamatoyannopoulos J, Fitzgerald PC, Vinson C. Methylated cytosines mutate to transcription factor binding sites that drive tetrapod evolution. Genome Biology and Evolution. PMID 26507798 DOI: 10.1093/Gbe/Evv205  0.484
2015 Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA. Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo. Nature Genetics. PMID 26502339 DOI: 10.1038/Ng.3432  0.779
2015 Hochner H, Allard C, Granot-Hershkovitz E, Chen J, Sitlani CM, Sazdovska S, Lumley T, McKnight B, Rice K, Enquobahrie DA, Meigs JB, Kwok P, Hivert MF, Borecki IB, Gomez F, ... ... Stamatoyannopoulos J, et al. Parent-of-Origin Effects of the APOB Gene on Adiposity in Young Adults. Plos Genetics. 11: e1005573. PMID 26451733 DOI: 10.1371/Journal.Pgen.1005573  0.331
2015 Vierstra J, Reik A, Chang KH, Stehling-Sun S, Zhou Y, Hinkley SJ, Paschon DE, Zhang L, Psatha N, Bendana YR, O'Neil CM, Song AH, Mich AK, Liu PQ, Lee G, ... ... Stamatoyannopoulos JA, et al. Functional footprinting of regulatory DNA. Nature Methods. PMID 26322838 DOI: 10.1038/Nmeth.3554  0.481
2015 Maurano MT, Wang H, John S, Shafer A, Canfield T, Lee K, Stamatoyannopoulos JA. Role of DNA Methylation in Modulating Transcription Factor Occupancy. Cell Reports. PMID 26257180 DOI: 10.1016/J.Celrep.2015.07.024  0.738
2015 Funnell AP, Prontera P, Ottaviani V, Piccione M, Giambona A, Maggio A, Ciaffoni F, Stehling-Sun S, Marra M, Masiello F, Varricchio L, Stamatoyannopoulos JA, Migliaccio AR, Papayannopoulou T. 2p15-p16.1 microdeletions encompassing and proximal to BCL11A are associated with elevated HbF in addition to neurologic impairment. Blood. 126: 89-93. PMID 26019277 DOI: 10.1182/Blood-2015-04-638528  0.364
2015 Wilken MS, Brzezinski JA, La Torre A, Siebenthall K, Thurman R, Sabo P, Sandstrom RS, Vierstra J, Canfield TK, Hansen RS, Bender MA, Stamatoyannopoulos J, Reh TA. DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements. Epigenetics & Chromatin. 8: 8. PMID 25972927 DOI: 10.1186/1756-8935-8-8  0.406
2015 Mayer A, di Iulio J, Maleri S, Eser U, Vierstra J, Reynolds A, Sandstrom R, Stamatoyannopoulos JA, Churchman LS. Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell. 161: 541-54. PMID 25910208 DOI: 10.1016/J.Cell.2015.03.010  0.435
2015 Polak P, Karli? R, Koren A, Thurman R, Sandstrom R, Lawrence MS, Reynolds A, Rynes E, Vlahovi?ek K, Stamatoyannopoulos JA, Sunyaev SR. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature. 518: 360-4. PMID 25693567 DOI: 10.1038/Nature14221  0.354
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, ... ... Stamatoyannopoulos JA, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248  0.491
2015 Stavreva DA, Coulon A, Baek S, Sung MH, John S, Stixova L, Tesikova M, Hakim O, Miranda T, Hawkins M, Stamatoyannopoulos JA, Chow CC, Hager GL. Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing. Genome Research. 25: 845-57. PMID 25677181 DOI: 10.1101/Gr.184168.114  0.368
2015 Liu M, Maurano MT, Wang H, Qi H, Song CZ, Navas PA, Emery DW, Stamatoyannopoulos JA, Stamatoyannopoulos G. Genomic discovery of potent chromatin insulators for human gene therapy. Nature Biotechnology. 33: 198-203. PMID 25580597 DOI: 10.1038/Nbt.3062  0.737
2015 Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin JM, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE. Resolving the complexity of the human genome using single-molecule sequencing. Nature. 517: 608-11. PMID 25383537 DOI: 10.1038/Nature13907  0.469
2015 Urnov FD, Reik A, Vierstra J, Chang K, Zhou Y, Mich A, Adrian J, Fox L, Psatha N, Tan S, Yannaki E, Craig S, Rebar EJ, Stamatoyannopoulos J, Papayannopoulou T, et al. Clinical-Scale Genome Editing of the Human BCL11A Erythroid Enhancer for Treatment of the Hemoglobinopathies Blood. 126: 204-204. DOI: 10.1182/Blood.V126.23.204.204  0.369
2015 Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA. Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo Nature Genetics. DOI: 10.1038/ng.3432  0.316
2015 Reik A, Chang K, Vierstra J, Psatha N, Stehling-Sun S, Zhou Y, O'Neil CM, Mich A, Miller JC, Lee G, Tan S, Jiang H, Stamatoyannopoulos G, Papayannopoulou T, Rebar EJ, ... ... Stamatoyannopoulos JA, et al. 53. From GWAS To the Clinic: Genome-Editing the Human BCL11A Erythroid Enhancer for Fetal Globin Elevation in the Hemoglobinopathies Molecular Therapy. 23: S23-S24. DOI: 10.1016/S1525-0016(16)33658-9  0.477
2015 Sullivan AM, Bubb KL, Sandstrom R, Stamatoyannopoulos JA, Queitsch C. DNase I hypersensitivity mapping, genomic footprinting, and transcription factor networks in plants Current Plant Biology. 3: 40-47. DOI: 10.1016/J.Cpb.2015.10.001  0.43
2014 Vierstra J, Rynes E, Sandstrom R, Zhang M, Canfield T, Hansen RS, Stehling-Sun S, Sabo PJ, Byron R, Humbert R, Thurman RE, Johnson AK, Vong S, Lee K, Bates D, ... ... Stamatoyannopoulos JA, et al. Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. Science (New York, N.Y.). 346: 1007-12. PMID 25411453 DOI: 10.1126/Science.1246426  0.506
2014 Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, ... Stamatoyannopoulos JA, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. 515: 402-5. PMID 25409831 DOI: 10.1038/Nature13986  0.361
2014 Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, ... ... Stamatoyannopoulos JA, et al. Conservation of trans-acting circuitry during mammalian regulatory evolution. Nature. 515: 365-70. PMID 25409825 DOI: 10.1038/Nature13972  0.504
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, ... ... Stamatoyannopoulos JA, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992  0.553
2014 Deyle DR, Hansen RS, Cornea AM, Li LB, Burt AA, Alexander IE, Sandstrom RS, Stamatoyannopoulos JA, Wei CL, Russell DW. A genome-wide map of adeno-associated virus-mediated human gene targeting. Nature Structural & Molecular Biology. 21: 969-75. PMID 25282150 DOI: 10.1038/Nsmb.2895  0.444
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, ... ... Stamatoyannopoulos J, 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  0.431
2014 Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, ... ... Stamatoyannopoulos JA, et al. Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Reports. 8: 2015-30. PMID 25220462 DOI: 10.1016/J.Celrep.2014.08.019  0.458
2014 Paschou P, Drineas P, Yannaki E, Razou A, Kanaki K, Tsetsos F, Padmanabhuni SS, Michalodimitrakis M, Renda MC, Pavlovic S, Anagnostopoulos A, Stamatoyannopoulos JA, Kidd KK, Stamatoyannopoulos G. Maritime route of colonization of Europe. Proceedings of the National Academy of Sciences of the United States of America. 111: 9211-6. PMID 24927591 DOI: 10.1073/Pnas.1320811111  0.323
2014 MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, ... ... Stamatoyannopoulos JA, et al. Guidelines for investigating causality of sequence variants in human disease. Nature. 508: 469-76. PMID 24759409 DOI: 10.1038/Nature13127  0.424
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, ... ... Stamatoyannopoulos JA, 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  0.564
2014 Letourneau A, Santoni FA, Bonilla X, Sailani MR, Gonzalez D, Kind J, Chevalier C, Thurman R, Sandstrom RS, Hibaoui Y, Garieri M, Popadin K, Falconnet E, Gagnebin M, Gehrig C, ... ... Stamatoyannopoulos JA, et al. Domains of genome-wide gene expression dysregulation in Down's syndrome. Nature. 508: 345-50. PMID 24740065 DOI: 10.1038/Nature13200  0.364
2014 Arvey A, van der Veeken J, Samstein RM, Feng Y, Stamatoyannopoulos JA, Rudensky AY. Inflammation-induced repression of chromatin bound by the transcription factor Foxp3 in regulatory T cells. Nature Immunology. 15: 580-7. PMID 24728351 DOI: 10.1038/Ni.2868  0.448
2014 Polak P, Lawrence MS, Haugen E, Stoletzki N, Stojanov P, Thurman RE, Garraway LA, Mirkin S, Getz G, Stamatoyannopoulos JA, Sunyaev SR. Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair. Nature Biotechnology. 32: 71-5. PMID 24336318 DOI: 10.1038/Nbt.2778  0.384
2014 Vierstra J, Wang H, John S, Sandstrom R, Stamatoyannopoulos JA. Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH. Nature Methods. 11: 66-72. PMID 24185839 DOI: 10.1038/Nmeth.2713  0.488
2013 Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM, Stamatoyannopoulos JA. Exonic transcription factor binding directs codon choice and affects protein evolution. Science (New York, N.Y.). 342: 1367-72. PMID 24337295 DOI: 10.1126/Science.1243490  0.47
2013 Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan GC, Porteus MH, ... Stamatoyannopoulos JA, et al. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science (New York, N.Y.). 342: 253-7. PMID 24115442 DOI: 10.1126/Science.1242088  0.508
2013 Shao J, He K, Wang H, Ho WS, Ren X, An X, Wong MK, Yan B, Xie D, Stamatoyannopoulos J, Zhao Z. Collaborative regulation of development but independent control of metabolism by two epidermis-specific transcription factors in Caenorhabditis elegans. The Journal of Biological Chemistry. 288: 33411-26. PMID 24097988 DOI: 10.1074/Jbc.M113.487975  0.446
2013 Chang KH, Huang A, Han H, Jiang Y, Fang X, Song CZ, Padilla S, Wang H, Qu H, Stamatoyannopoulos J, Li Q, Papayannopoulou T. Transcriptional environment and chromatin architecture interplay dictates globin expression patterns of heterospecific hybrids derived from undifferentiated human embryonic stem cells or from their erythroid progeny. Experimental Hematology. 41: 967-979.e6. PMID 23993951 DOI: 10.1016/J.Exphem.2013.08.005  0.361
2013 Xiong Q, Zhang Z, Chang KH, Qu H, Wang H, Qi H, Li Y, Ruan X, Yang Y, Yang Y, Li Y, Sandstrom R, Sabo PJ, Li Q, Stamatoyannopoulos G, ... Stamatoyannopoulos JA, et al. Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors. Bmc Genomics. 14: 587. PMID 23985037 DOI: 10.1186/1471-2164-14-587  0.519
2013 Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, Haugen E, Heimfeld S, Murry CE, Akey JM, Stamatoyannopoulos JA. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell. 154: 888-903. PMID 23953118 DOI: 10.1016/J.Cell.2013.07.020  0.407
2013 John S, Sabo PJ, Canfield TK, Lee K, Vong S, Weaver M, Wang H, Vierstra J, Reynolds AP, Thurman RE, Stamatoyannopoulos JA. Genome-scale mapping of DNase I hypersensitivity. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.27. PMID 23821440 DOI: 10.1002/0471142727.Mb2127S103  0.451
2013 He X, Chatterjee R, John S, Bravo H, Sathyanarayana BK, Biddie SC, FitzGerald PC, Stamatoyannopoulos JA, Hager GL, Vinson C. Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding. Bmc Genomics. 14: 428. PMID 23805837 DOI: 10.1186/1471-2164-14-428  0.45
2013 Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen LK, Mattick JS, Stamatoyannopoulos JA. DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nature Genetics. 45: 852-9. PMID 23793028 DOI: 10.1038/Ng.2677  0.528
2013 Lazarovici A, Zhou T, Shafer A, Dantas Machado AC, Riley TR, Sandstrom R, Sabo PJ, Lu Y, Rohs R, Stamatoyannopoulos JA, Bussemaker HJ. Probing DNA shape and methylation state on a genomic scale with DNase I. Proceedings of the National Academy of Sciences of the United States of America. 110: 6376-81. PMID 23576721 DOI: 10.1073/Pnas.1216822110  0.478
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  0.439
2013 Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS. Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Research. 23: 777-88. PMID 23482648 DOI: 10.1101/Gr.152140.112  0.454
2013 Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE, Absher DM, Wold BJ, Myers RM. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Research. 23: 555-67. PMID 23325432 DOI: 10.1101/Gr.147942.112  0.443
2013 Chang KH, Fang X, Wang H, Huang A, Cao H, Yang Y, Bonig H, Stamatoyannopoulos JA, Papayannopoulou T. Epigenetic modifications and chromosome conformations of the beta globin locus throughout development. Stem Cell Reviews. 9: 397-407. PMID 22374078 DOI: 10.1007/S12015-012-9355-X  0.375
2013 Maurano MT, Wang H, Shafer A, John S, Stamatoyannopoulos JA. DNA methylation alone does not cause most cell-type selective transcription factor binding Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P103  0.757
2013 Stamatoyannopoulos J. Gene Regulation: A Genomic Perspective Blood. 122: SCI-10-SCI-10. DOI: 10.1182/Blood.V122.21.Sci-10.Sci-10  0.555
2013 Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan G, Porteus MH, ... Stamatoyannopoulos J, et al. Fine-Mapping and Genome Editing Reveal An Essential Erythroid Enhancer At The HbF-Associated BCL11A Locus Blood. 122: 437-437. DOI: 10.1182/Blood.V122.21.437.437  0.562
2013 Lazarovici A, Zhou T, Shafer A, Machado ACD, Sandstrom R, Sabo PJ, Lu Y, Rohs R, Stamatoyannopoulos JA, Bussemaker HJ. 103 Probing DNA shape and methylation state on a genomic scale with DNase I Journal of Biomolecular Structure and Dynamics. 31: 65-65. DOI: 10.1080/07391102.2013.786345  0.492
2012 Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin MD, Celniker SE. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 109: 21330-5. PMID 23236164 DOI: 10.1073/Pnas.1209589110  0.511
2012 Xu J, Shao Z, Glass K, Bauer DE, Pinello L, Van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HK, Yuan GC, Orkin SH. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Developmental Cell. 23: 796-811. PMID 23041383 DOI: 10.1016/J.Devcel.2012.09.003  0.375
2012 Samstein RM, Arvey A, Josefowicz SZ, Peng X, Reynolds A, Sandstrom R, Neph S, Sabo P, Kim JM, Liao W, Li MO, Leslie C, Stamatoyannopoulos JA, Rudensky AY. Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Cell. 151: 153-66. PMID 23021222 DOI: 10.1016/J.Cell.2012.06.053  0.355
2012 Paige SL, Thomas S, Stoick-Cooper CL, Wang H, Maves L, Sandstrom R, Pabon L, Reinecke H, Pratt G, Keller G, Moon RT, Stamatoyannopoulos J, Murry CE. A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development. Cell. 151: 221-32. PMID 22981225 DOI: 10.1016/J.Cell.2012.08.027  0.378
2012 Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA. Circuitry and dynamics of human transcription factor regulatory networks. Cell. 150: 1274-86. PMID 22959076 DOI: 10.1016/J.Cell.2012.04.040  0.4
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, ... ... Stamatoyannopoulos JA, 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  0.402
2012 Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM. Personal and population genomics of human regulatory variation. Genome Research. 22: 1689-97. PMID 22955981 DOI: 10.1101/Gr.134890.111  0.777
2012 Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, Stamatoyannopoulos JA. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Research. 22: 1680-8. PMID 22955980 DOI: 10.1101/Gr.136101.111  0.777
2012 Stamatoyannopoulos JA. What does our genome encode? Genome Research. 22: 1602-11. PMID 22955972 DOI: 10.1101/Gr.146506.112  0.473
2012 Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, ... ... Stamatoyannopoulos JA, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science (New York, N.Y.). 337: 1190-5. PMID 22955828 DOI: 10.1126/Science.1222794  0.738
2012 Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, ... ... Stamatoyannopoulos JA, et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature. 489: 83-90. PMID 22955618 DOI: 10.1038/Nature11212  0.789
2012 Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, ... ... Stamatoyannopoulos JA, et al. The accessible chromatin landscape of the human genome. Nature. 489: 75-82. PMID 22955617 DOI: 10.1038/Nature11232  0.774
2012 Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418  0.469
2012 Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R, Humbert R, Stamatoyannopoulos JA. BEDOPS: high-performance genomic feature operations. Bioinformatics (Oxford, England). 28: 1919-20. PMID 22576172 DOI: 10.1093/Bioinformatics/Bts277  0.695
2012 Ganis JJ, Hsia N, Trompouki E, de Jong JL, DiBiase A, Lambert JS, Jia Z, Sabo PJ, Weaver M, Sandstrom R, Stamatoyannopoulos JA, Zhou Y, Zon LI. Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR. Developmental Biology. 366: 185-94. PMID 22537494 DOI: 10.1016/J.Ydbio.2012.03.021  0.436
2012 Maurano MT, Wang H, Kutyavin T, Stamatoyannopoulos JA. Widespread site-dependent buffering of human regulatory polymorphism. Plos Genetics. 8: e1002599. PMID 22457641 DOI: 10.1371/Journal.Pgen.1002599  0.767
2012 Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, ... ... Stamatoyannopoulos J, et al. Evidence for transcript networks composed of chimeric RNAs in human cells. Plos One. 7: e28213. PMID 22238572 DOI: 10.1371/Journal.Pone.0028213  0.385
2012 Liu M, Li CL, Stamatoyannopoulos G, Dorschner MO, Humbert R, Stamatoyannopoulos JA, Emery DW. Gammaretroviral vector integration occurs overwhelmingly within and near DNase hypersensitive sites. Human Gene Therapy. 23: 231-7. PMID 21981728 DOI: 10.1089/Hum.2010.177  0.424
2012 Bauer DE, Kamran SC, Xu J, Lin C, Shao Z, Fujiwara Y, Voit RA, Porteus MH, Stamatoyannopoulos JA, Orkin SH. HbF-Associated Genetic Variation Marks an Erythroid Regulatory Element Essential for BCL11A Transcription and Subsequent Stage-Specific Globin Expression Blood. 120: 828-828. DOI: 10.1182/Blood.V120.21.828.828  0.478
2012 Wang H, Yang Y, QU H, Ruan X, Zhang Z, Xiong Q, Qi H, Stamatoyannopoulos G, Stamatoyannopoulos JA, Fang X. Functional Analysis of FOXO3A Involved in Erythroid Differentiation Blood. 120: 4731-4731. DOI: 10.1182/Blood.V120.21.4731.4731  0.423
2012 Xiong Q, Zhang Z, Qu H, Ruan X, Wang H, Zhang Q, Qi H, Li Y, Sun H, Chang K, Stamatoyannopoulos G, Stamatoyannopoulos JA, Fang X. Deciphering the Cis- and Trans-regulatory Roles of KLF6 in Primitive Hematopoiesis Blood. 120: 4730-4730. DOI: 10.1182/Blood.V120.21.4730.4730  0.449
2012 Zhaojun Z, Qian X, Shaobin W, Hai W, Qian Z, Heyuan Q, Yanming L, Hongying S, Kai-Hsin C, Stamatoyannopoulos G, Stamatoyannopoulos JA, Xiangdong F. Comprehensive Investigation of the Molecular Mechanism of Primitive Hematopoiesis Regulating by KLF3 Blood. 120: 4729-4729. DOI: 10.1182/Blood.V120.21.4729.4729  0.408
2012 Xu J, Shao Z, Glass K, Bauer DE, Pinello L, Van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HKA, Yuan G, Orkin SH. Genomic Determinants of Human Fetal and Adult Erythroid Gene Expression Blood. 120: 1227-1227. DOI: 10.1182/Blood.V120.21.1227.1227  0.427
2011 Suzuki M, Oda M, Ramos MP, Pascual M, Lau K, Stasiek E, Agyiri F, Thompson RF, Glass JL, Jing Q, Sandstrom R, Fazzari MJ, Hansen RS, Stamatoyannopoulos JA, McLellan AS, et al. Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. Genome Research. 21: 1833-40. PMID 21957152 DOI: 10.1101/Gr.116509.110  0.495
2011 Mercer TR, Neph S, Dinger ME, Crawford J, Smith MA, Shearwood AM, Haugen E, Bracken CP, Rackham O, Stamatoyannopoulos JA, Filipovska A, Mattick JS. The human mitochondrial transcriptome. Cell. 146: 645-58. PMID 21854988 DOI: 10.1016/J.Cell.2011.06.051  0.377
2011 Voss TC, Schiltz RL, Sung MH, Yen PM, Stamatoyannopoulos JA, Biddie SC, Johnson TA, Miranda TB, John S, Hager GL. Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism. Cell. 146: 544-54. PMID 21835447 DOI: 10.1016/J.Cell.2011.07.006  0.43
2011 Biddie SC, John S, Sabo PJ, Thurman RE, Johnson TA, Schiltz RL, Miranda TB, Sung MH, Trump S, Lightman SL, Vinson C, Stamatoyannopoulos JA, Hager GL. Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding. Molecular Cell. 43: 145-55. PMID 21726817 DOI: 10.1016/J.Molcel.2011.06.016  0.436
2011 Wiench M, John S, Baek S, Johnson TA, Sung MH, Escobar T, Simmons CA, Pearce KH, Biddie SC, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, Hager GL. DNA methylation status predicts cell type-specific enhancer activity. The Embo Journal. 30: 3028-39. PMID 21701563 DOI: 10.1038/Emboj.2011.210  0.462
2011 Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biology. 12: R43. PMID 21569360 DOI: 10.1186/Gb-2011-12-5-R43  0.444
2011 Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biology. 12: R34. PMID 21473766 DOI: 10.1186/Gb-2011-12-4-R34  0.502
2011 Hakim O, Sung MH, Voss TC, Splinter E, John S, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, de Laat W, Hager GL. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Research. 21: 697-706. PMID 21471403 DOI: 10.1101/Gr.111153.110  0.47
2011 Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. Plos Genetics. 7: e1001290. PMID 21304941 DOI: 10.1371/Journal.Pgen.1001290  0.471
2011 John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nature Genetics. 43: 264-8. PMID 21258342 DOI: 10.1038/Ng.759  0.372
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, ... ... Stamatoyannopoulos JA, et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 471: 480-5. PMID 21179089 DOI: 10.1038/Nature09725  0.501
2011 Bauer DE, Xu J, Fujiwara Y, Stamatoyannopoulos JA, Orkin SH. Functional Evaluation of HbF-Associated Region of BCL11A Locus Blood. 118: 2148-2148. DOI: 10.1182/Blood.V118.21.2148.2148  0.491
2010 Stamatoyannopoulos JA. Illuminating eukaryotic transcription start sites. Nature Methods. 7: 501-3. PMID 20588267 DOI: 10.1038/Nmeth0710-501  0.386
2010 Miller BG, Stamatoyannopoulos JA. Integrative meta-analysis of differential gene expression in acute myeloid leukemia Plos One. 5. PMID 20209125 DOI: 10.1371/Journal.Pone.0009466  0.338
2010 Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proceedings of the National Academy of Sciences of the United States of America. 107: 139-44. PMID 19966280 DOI: 10.1073/Pnas.0912402107  0.521
2009 Sekimata M, Pérez-Melgosa M, Miller SA, Weinmann AS, Sabo PJ, Sandstrom R, Dorschner MO, Stamatoyannopoulos JA, Wilson CB. CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus. Immunity. 31: 551-64. PMID 19818655 DOI: 10.1016/J.Immuni.2009.08.021  0.406
2009 Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, ... Stamatoyannopoulos J, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (New York, N.Y.). 326: 289-93. PMID 19815776 DOI: 10.1126/Science.1181369  0.417
2009 Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nature Methods. 6: 283-9. PMID 19305407 DOI: 10.1038/Nmeth.1313  0.537
2009 Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR. Human mutation rate associated with DNA replication timing. Nature Genetics. 41: 393-5. PMID 19287383 DOI: 10.1038/Ng.363  0.402
2009 Kryukov GV, Shpunt A, Stamatoyannopoulos JA, Sunyaev SR. Power of deep, all-exon resequencing for discovery of human trait genes. Proceedings of the National Academy of Sciences of the United States of America. 106: 3871-6. PMID 19202052 DOI: 10.1073/Pnas.0812824106  0.423
2009 Fang X, Chang K, Bates D, Diegel M, Sandstrom R, Weaver M, Dorschner MO, Sabo PJ, Papayannopoulou T, Stamatoyannopoulos G, Stamatoyannopoulos J. Chromatin Profiling of the Globin Loci of Human ES Cells and ES-Derived Erythroid Cells. Blood. 114: 2535-2535. DOI: 10.1182/Blood.V114.22.2535.2535  0.391
2008 Stamatoyannopoulos JA, Dunham I. Epigenomics at the tipping point. Foreword. Pharmacogenomics. 9: 1781-3. PMID 19072634 DOI: 10.2217/14622416.9.12.1781  0.409
2008 Attanasio C, Reymond A, Humbert R, Lyle R, Kuehn MS, Neph S, Sabo PJ, Goldy J, Weaver M, Haydock A, Lee K, Dorschner M, Dermitzakis ET, Antonarakis SE, Stamatoyannopoulos JA. Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells. Genome Biology. 9: R168. PMID 19055709 DOI: 10.1186/Gb-2008-9-12-R168  0.469
2008 Gupta S, Dennis J, Thurman RE, Kingston R, Stamatoyannopoulos JA, Noble WS. Predicting human nucleosome occupancy from primary sequence. Plos Computational Biology. 4: e1000134. PMID 18725940 DOI: 10.1371/Journal.Pcbi.1000134  0.421
2008 Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, ... ... Stamatoyannopoulos J, et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 453: 56-64. PMID 18451855 DOI: 10.1038/Nature06862  0.463
2008 John S, Sabo PJ, Johnson TA, Sung MH, Biddie SC, Lightman SL, Voss TC, Davis SR, Meltzer PS, Stamatoyannopoulos JA, Hager GL. Interaction of the glucocorticoid receptor with the chromatin landscape. Molecular Cell. 29: 611-24. PMID 18342607 DOI: 10.1016/J.Molcel.2008.02.010  0.391
2008 Levasseur DN, Wang J, Dorschner MO, Stamatoyannopoulos JA, Orkin SH. Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells. Genes & Development. 22: 575-80. PMID 18283123 DOI: 10.1101/Gad.1606308  0.429
2008 Thurman RE, Noble WS, Stamatoyannopoulos JA. Multi-scale correlations in continuous genomic data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 201-15. PMID 18229687 DOI: 10.1142/9789812776136_0021  0.35
2007 Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S. Analysis of sequence conservation at nucleotide resolution Plos Computational Biology. 3: e254. PMID 18166073 DOI: 10.1371/Journal.Pcbi.0030254  0.456
2007 Asthana S, Noble WS, Kryukov G, Grant CE, Sunyaev S, Stamatoyannopoulos JA. Widely distributed noncoding purifying selection in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 104: 12410-5. PMID 17640883 DOI: 10.1073/Pnas.0705140104  0.481
2007 Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z. Nucleosome positioning signals in genomic DNA. Genome Research. 17: 1170-7. PMID 17620451 DOI: 10.1101/Gr.6101007  0.444
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.535
2007 Thurman RE, Day N, Noble WS, Stamatoyannopoulos JA. Identification of higher-order functional domains in the human ENCODE regions. Genome Research. 17: 917-27. PMID 17568007 DOI: 10.1101/Gr.6081407  0.43
2007 Schoenborn JR, Dorschner MO, Sekimata M, Santer DM, Shnyreva M, Fitzpatrick DR, Stamatoyannopoulos JA, Stamatoyonnapoulos JA, Wilson CB. Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing transcription of the gene encoding interferon-gamma. Nature Immunology. 8: 732-42. PMID 17546033 DOI: 10.1038/Ni1474  0.402
2007 Day N, Hemmaplardh A, Thurman RE, Stamatoyannopoulos JA, Noble WS. Unsupervised segmentation of continuous genomic data. Bioinformatics (Oxford, England). 23: 1424-6. PMID 17384021 DOI: 10.1093/Bioinformatics/Btm096  0.398
2007 Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS. Quantifying similarity between motifs. Genome Biology. 8: R24. PMID 17324271 DOI: 10.1186/Gb-2007-8-2-R24  0.307
2006 Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, ... ... Stamatoyannopoulos JA, et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature Methods. 3: 511-8. PMID 16791208 DOI: 10.1038/Nmeth890  0.542
2005 Noble WS, Kuehn S, Thurman R, Yu M, Stamatoyannopoulos J. Predicting the in vivo signature of human gene regulatory sequences. Bioinformatics (Oxford, England). 21: i338-43. PMID 15961476 DOI: 10.1093/bioinformatics/bti1047  0.472
2004 Dorschner MO, Hawrylycz M, Humbert R, Wallace JC, Shafer A, Kawamoto J, Mack J, Hall R, Goldy J, Sabo PJ, Kohli A, Li Q, McArthur M, Stamatoyannopoulos JA. High-throughput localization of functional elements by quantitative chromatin profiling. Nature Methods. 1: 219-25. PMID 15782197 DOI: 10.1038/Nmeth721  0.507
2004 Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO, McArthur M, Stamatoyannopoulos JA. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proceedings of the National Academy of Sciences of the United States of America. 101: 16837-42. PMID 15550541 DOI: 10.1073/Pnas.0407387101  0.53
2004 Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Stamatoyannopoulos JA, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/Science.1105136  0.453
2004 Stamatoyannopoulos JA. The genomics of gene expression. Genomics. 84: 449-57. PMID 15498452 DOI: 10.1016/j.ygeno.2004.05.002  0.387
2004 Sabo PJ, Humbert R, Hawrylycz M, Wallace JC, Dorschner MO, McArthur M, Stamatoyannopoulos JA. Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proceedings of the National Academy of Sciences of the United States of America. 101: 4537-42. PMID 15070753 DOI: 10.1073/Pnas.0400678101  0.536
2004 Stamatoyannopoulos JA, Humbert R, Hawrylycz M, Wallace J, Dorschner MO, Kohli A, Li Q, McArthur M, Sabo PJ. Genome-Scale Analysis of Hematopoietic Regulatory Sequences by Digital Analysis of Chromatin Structure. Blood. 104: 4163-4163. DOI: 10.1182/Blood.V104.11.4163.4163  0.526
1997 Stamatoyannopoulos JA, Clegg CH, Li Q. Sheltering of gamma-globin expression from position effects requires both an upstream locus control region and a regulatory element 3' to the A gamma-globin gene. Molecular and Cellular Biology. 17: 240-7. PMID 8972204 DOI: 10.1128/Mcb.17.1.240  0.369
1994 Li Q, Stamatoyannopoulos JA. Position independence and proper developmental control of gamma-globin gene expression require both a 5' locus control region and a downstream sequence element. Molecular and Cellular Biology. 14: 6087-96. PMID 8065342 DOI: 10.1128/Mcb.14.9.6087  0.356
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