| Year |
Citation |
Score |
| 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 |
0.355 |
|
| 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 |
0.762 |
|
| 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 |
0.55 |
|
| 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 |
0.508 |
|
| 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 |
0.516 |
|
| 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 |
0.636 |
|
| 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 |
0.431 |
|
| 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 |
0.707 |
|
| 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 |
0.7 |
|
| 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 |
0.429 |
|
| 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 |
0.485 |
|
| 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 |
0.782 |
|
| 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 |
0.332 |
|
| 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 |
0.482 |
|
| 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 |
0.742 |
|
| 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 |
0.405 |
|
| 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 |
0.355 |
|
| 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 |
0.367 |
|
| 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 |
0.741 |
|
| 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 |
0.47 |
|
| 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 |
0.37 |
|
| 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 |
0.317 |
|
| 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 |
0.554 |
|
| 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 |
0.445 |
|
| 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 |
0.432 |
|
| 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 |
0.425 |
|
| 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 |
0.565 |
|
| 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 |
0.489 |
|
| 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 |
0.471 |
|
| 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 |
0.509 |
|
| 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 |
0.451 |
|
| 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 |
0.479 |
|
| 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 |
0.761 |
|
| 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 |
0.563 |
|
| 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 |
0.493 |
|
| 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 |
0.403 |
|
| 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 |
0.781 |
|
| 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 |
0.781 |
|
| 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 |
0.743 |
|
| 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 |
0.793 |
|
| 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 |
0.777 |
|
| 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 |
0.47 |
|
| 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 |
0.7 |
|
| 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 |
0.771 |
|
| 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 |
0.407 |
|
| 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 |
0.426 |
|
| 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 |
0.463 |
|
| 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 |
0.503 |
|
| 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 |
0.472 |
|
| 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 |
0.373 |
|
| 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 |
0.337 |
|
| 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 |
0.538 |
|
| 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 |
0.403 |
|
| 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 |
0.47 |
|
| 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 |
0.464 |
|
| 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 |
0.482 |
|
| 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 |
0.445 |
|
| 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 |
0.399 |
|
| 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 |
0.308 |
|
| 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 |
0.543 |
|
| 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 |
0.508 |
|
| 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 |
0.531 |
|
| 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 |
0.388 |
|
| 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 |
0.527 |
|
| 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 |
|
| Show low-probability matches. |