My Bibliography

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Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y, Lacadie MC, Meza J, Khandpekar M, Ganna M, Choudhury E, Swofford R, Phan H, Ramirez CC, Campbell M, Likhite M, Farrell NP, Weimer AK, Pampari A, Ramalingam V, Reese F, Borsari B, Yu X, Wattenberg E, Ruiz-Romero M, Razavi-Mohseni M, Xu J, Galeev T, Colubri A, Beer MA, Guigó R, Gerstein MB, Engreitz JM, Ljungman M, Reddy TE, Snyder MP, Epstein CB, Gaskell E, Bernstein BE, Dickel DE, Visel A, Pennacchio LA, Mortazavi A, Kundaje A, Weng Z. An expanded registry of candidate cis-regulatory elements. Nature. 2026 Jan 7;. doi: 10.1038/s41586-025-09909-9. [Epub ahead of print] PubMed PMID: 41501460.

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Gryzunov N, Penzar D, Kamenets V, Vyaltsev V, Kozin I, Eliseeva IA, Nozdrin V, Vorontsov IE, Bushuev S, Strekalovskikh V, Zinkevich A, Andrews G, Bedarew M, Blass I, Frolov D, Lariushina I, Moore J, Orenstein Y, Roev G, Salimov D, Shimshoviz N, Tziony I, Weng Z, Bucher P, Deplancke B, Fornes O, Grau J, Grosse I, Jolma A, Kolpakov FA, Makeev VJ, Hughes TR, Kulakovskiy IV. Inferring binding specificities of human transcription factors with the wisdom of crowds. bioRxiv. 2025 Nov 17;. doi: 10.1101/2025.11.16.688692. PubMed PMID: 41332515; PubMed Central PMCID: PMC12667932.

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Dawood M, Heavner B, Wheeler MM, Ungar RA, LoTempio J, Wiel L, Berger S, Bernstein JA, Chong JX, Délot EC, Eichler EE, Lupski JR, Shojaie A, Talkowski ME, Wagner AH, Wei CL, Wellington C, Wheeler MT, Carvalho CMB, Gibbs RA, Gifford CA, May S, Miller DE, Rehm HL, Samocha KE, Sedlazeck FJ, Vilain E, O'Donnell-Luria A, Posey JE, Chadwick LH, Bamshad MJ, Montgomery SB. GREGoR: accelerating genomics for rare diseases. Nature. 2025 Nov;647(8089):331-342. doi: 10.1038/s41586-025-09613-8. Epub 2025 Nov 12. PubMed PMID: 41224980.

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Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y, Lacadie MC, Meza J, Ganna M, Choudhury E, Swofford R, Farrell NP, Pampari A, Ramalingam V, Reese F, Borsari B, Yu M, Wattenberg E, Ruiz-Romero M, Razavi-Mohseni M, Xu J, Galeev T, Beer MA, Guigó R, Gerstein M, Engreitz J, Ljungman M, Reddy TE, Snyder MP, Epstein CB, Gaskell E, Bernstein BE, Dickel DE, Visel A, Pennacchio LA, Mortazavi A, Kundaje A, Weng Z. An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation. bioRxiv. 2024 Dec 26;. doi: 10.1101/2024.12.26.629296. PubMed PMID: 39763870; PubMed Central PMCID: PMC11703161.

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Deciphering the impact of genomic variation on function. Nature. 2024 Sep;633(8028):47-57. doi: 10.1038/s41586-024-07510-0. Epub 2024 Sep 4. Review. PubMed PMID: 39232149; PubMed Central PMCID: PMC11973978.

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Pratt HE, Andrews G, Shedd N, Phalke N, Li T, Pampari A, Jensen M, Wen C, Consortium P, Gandal MJ, Geschwind DH, Gerstein M, Moore J, Kundaje A, Colubri A, Weng Z. Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. Sci Adv. 2024 May 24;10(21):eadj4452. doi: 10.1126/sciadv.adj4452. Epub 2024 May 23. PubMed PMID: 38781344; PubMed Central PMCID: PMC11114231.

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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, Shamim MS, Durand NC, Rao SSP, Mahajan R, Doughty BR, Andreeva K, Ulirsch JC, Fan K, Perez EM, Nguyen TC, Kelley DR, Finucane HK, Moore JE, Weng Z, Kellis M, Bassik MC, Price AL, Beer MA, Guigó R, Stamatoyannopoulos JA, Lieberman Aiden E, Greenleaf WJ, Leslie CS, Steinmetz LM, Kundaje A, Engreitz JM. An encyclopedia of enhancer-gene regulatory interactions in the human genome. bioRxiv. 2023 Nov 13;. doi: 10.1101/2023.11.09.563812. PubMed PMID: 38014075; PubMed Central PMCID: PMC10680627.

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Reese F, Williams B, Balderrama-Gutierrez G, Wyman D, Çelik MH, Rebboah E, Rezaie N, Trout D, Razavi-Mohseni M, Jiang Y, Borsari B, Morabito S, Liang HY, McGill CJ, Rahmanian S, Sakr J, Jiang S, Zeng W, Carvalho K, Weimer AK, Dionne LA, McShane A, Bedi K, Elhajjajy SI, Upchurch S, Jou J, Youngworth I, Gabdank I, Sud P, Jolanki O, Strattan JS, Kagda MS, Snyder MP, Hitz BC, Moore JE, Weng Z, Bennett D, Reinholdt L, Ljungman M, Beer MA, Gerstein MB, Pachter L, Guigó R, Wold BJ, Mortazavi A. The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRxiv. 2023 May 16;. doi: 10.1101/2023.05.15.540865. PubMed PMID: 37292896; PubMed Central PMCID: PMC10245583.

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Andrews G, Fan K, Pratt HE, Phalke N, Karlsson EK, Lindblad-Toh K, Gazal S, Moore JE, Weng Z. Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science. 2023 Apr 28;380(6643):eabn7930. doi: 10.1126/science.abn7930. Epub 2023 Apr 28. PubMed PMID: 37104580.

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Zhou H, Arapoglou T, Li X, Li Z, Zheng X, Moore J, Asok A, Kumar S, Blue EE, Buyske S, Cox N, Felsenfeld A, Gerstein M, Kenny E, Li B, Matise T, Philippakis A, Rehm HL, Sofia HJ, Snyder G, Weng Z, Neale B, Sunyaev SR, Lin X. FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Res. 2023 Jan 6;51(D1):D1300-D1311. doi: 10.1093/nar/gkac966. PubMed PMID: 36350676; PubMed Central PMCID: PMC9825437.

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Pratt HE, Andrews GR, Phalke N, Huey JD, Purcaro MJ, van der Velde A, Moore JE, Weng Z. Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. Nucleic Acids Res. 2022 Jan 7;50(D1):D141-D149. doi: 10.1093/nar/gkab1039. PubMed PMID: 34755879; PubMed Central PMCID: PMC8728199.

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Moore JE, Zhang XO, Elhajjajy SI, Fan K, Pratt HE, Reese F, Mortazavi A, Weng Z. Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types. Genome Res. 2022 Feb;32(2):389-402. doi: 10.1101/gr.275723.121. Epub 2021 Dec 23. PubMed PMID: 34949670; PubMed Central PMCID: PMC8805725.

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Fan K, Moore JE, Zhang XO, Weng Z. Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes. Nucleic Acids Res. 2021 Jun 4;49(10):5705-5725. doi: 10.1093/nar/gkab345. PubMed PMID: 33978759; PubMed Central PMCID: PMC8191798.

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van der Velde A, Fan K, Tsuji J, Moore JE, Purcaro MJ, Pratt HE, Weng Z. Annotation of chromatin states in 66 complete mouse epigenomes during development. Commun Biol. 2021 Feb 22;4(1):239. doi: 10.1038/s42003-021-01756-4. PubMed PMID: 33619351; PubMed Central PMCID: PMC7900196.

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Li X, Li Z, Zhou H, Gaynor SM, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Aslibekyan S, Ballantyne CM, Bielak LF, Blangero J, Boerwinkle E, Bowden DW, Broome JG, Conomos MP, Correa A, Cupples LA, Curran JE, Freedman BI, Guo X, Hindy G, Irvin MR, Kardia SLR, Kathiresan S, Khan AT, Kooperberg CL, Laurie CC, Liu XS, Mahaney MC, Manichaikul AW, Martin LW, Mathias RA, McGarvey ST, Mitchell BD, Montasser ME, Moore JE, Morrison AC, O'Connell JR, Palmer ND, Pampana A, Peralta JM, Peyser PA, Psaty BM, Redline S, Rice KM, Rich SS, Smith JA, Tiwari HK, Tsai MY, Vasan RS, Wang FF, Weeks DE, Weng Z, Wilson JG, Yanek LR, Neale BM, Sunyaev SR, Abecasis GR, Rotter JI, Willer CJ, Peloso GM, Natarajan P, Lin X. Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nat Genet. 2020 Sep;52(9):969-983. doi: 10.1038/s41588-020-0676-4. Epub 2020 Aug 24. PubMed PMID: 32839606; PubMed Central PMCID: PMC7483769.

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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, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29. PubMed PMID: 32728249; PubMed Central PMCID: PMC7410828.

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Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. Perspectives on ENCODE. Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29. PubMed PMID: 32728248; PubMed Central PMCID: PMC7410827.

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Moore JE, Pratt HE, Purcaro MJ, Weng Z. A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods. Genome Biol. 2020 Jan 22;21(1):17. doi: 10.1186/s13059-019-1924-8. PubMed PMID: 31969180; PubMed Central PMCID: PMC6977301.

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Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, Yan C, Rhie SK, Manakongtreecheep K, Zhou H, Nathan A, Peters M, Mattei E, Fitzgerald D, Brunetti T, Moore J, Jiang Y, Girdhar K, Hoffman GE, Kalayci S, Gümüş ZH, Crawford GE, Roussos P, Akbarian S, Jaffe AE, White KP, Weng Z, Sestan N, Geschwind DH, Knowles JA, Gerstein MB. Comprehensive functional genomic resource and integrative model for the human brain. Science. 2018 Dec 14;362(6420). doi: 10.1126/science.aat8464. PubMed PMID: 30545857; PubMed Central PMCID: PMC6413328.

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Revealing the brain's molecular architecture. Science. 2018 Dec 14;362(6420):1262-1263. doi: 10.1126/science.362.6420.1262. PubMed PMID: 30545881.

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Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, Moran Losada P, Khan Z, Mleczko J, Xia Y, Dai R, Wang D, Yang YT, Xu M, Fish K, Hof PR, Warrell J, Fitzgerald D, White K, Jaffe AE, Peters MA, Gerstein M, Liu C, Iakoucheva LM, Pinto D, Geschwind DH. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science. 2018 Dec 14;362(6420). doi: 10.1126/science.aat8127. PubMed PMID: 30545856; PubMed Central PMCID: PMC6443102.

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Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti-Rodríguez P, Won H, de Leeuw CA, Pardiñas AF, Hu M, Jin F, Li Y, Owen MJ, O'Donovan MC, Walters JTR, Posthuma D, Reimers MA, Levitt P, Weinberger DR, Hyde TM, Kleinman JE, Geschwind DH, Hawrylycz MJ, State MW, Sanders SJ, Sullivan PF, Gerstein MB, Lein ES, Knowles JA, Sestan N. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science. 2018 Dec 14;362(6420). doi: 10.1126/science.aat7615. PubMed PMID: 30545854; PubMed Central PMCID: PMC6413317.

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Amiri A, Coppola G, Scuderi S, Wu F, Roychowdhury T, Liu F, Pochareddy S, Shin Y, Safi A, Song L, Zhu Y, Sousa AMM, Gerstein M, Crawford GE, Sestan N, Abyzov A, Vaccarino FM. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science. 2018 Dec 14;362(6420). doi: 10.1126/science.aat6720. PubMed PMID: 30545853; PubMed Central PMCID: PMC6426303.

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Fu S, Wang Q, Moore JE, Purcaro MJ, Pratt HE, Fan K, Gu C, Jiang C, Zhu R, Kundaje A, Lu A, Weng Z. Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers. Nucleic Acids Res. 2018 Nov 30;46(21):11184-11201. doi: 10.1093/nar/gky753. PubMed PMID: 30137428; PubMed Central PMCID: PMC6265487.

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Chen W, Moore J, Ozadam H, Shulha HP, Rhind N, Weng Z, Moore MJ. Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling. Cell. 2018 May 3;173(4):1031-1044.e13. doi: 10.1016/j.cell.2018.03.062. PubMed PMID: 29727662; PubMed Central PMCID: PMC6090549.

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Mou H, Smith JL, Peng L, Yin H, Moore J, Zhang XO, Song CQ, Sheel A, Wu Q, Ozata DM, Li Y, Anderson DG, Emerson CP, Sontheimer EJ, Moore MJ, Weng Z, Xue W. CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion. Genome Biol. 2017 Jun 14;18(1):108. doi: 10.1186/s13059-017-1237-8. PubMed PMID: 28615073; PubMed Central PMCID: PMC5470253.

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Mou H, Moore J, Malonia SK, Li Y, Ozata DM, Hough S, Song CQ, Smith JL, Fischer A, Weng Z, Green MR, Xue W. Genetic disruption of oncogenic Kras sensitizes lung cancer cells to Fas receptor-mediated apoptosis. Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):3648-3653. doi: 10.1073/pnas.1620861114. Epub 2017 Mar 20. PubMed PMID: 28320962; PubMed Central PMCID: PMC5389295.

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Song CQ, Li Y, Mou H, Moore J, Park A, Pomyen Y, Hough S, Kennedy Z, Fischer A, Yin H, Anderson DG, Conte D Jr, Zender L, Wang XW, Thorgeirsson S, Weng Z, Xue W. Genome-Wide CRISPR Screen Identifies Regulators of Mitogen-Activated Protein Kinase as Suppressors of Liver Tumors in Mice. Gastroenterology. 2017 Apr;152(5):1161-1173.e1. doi: 10.1053/j.gastro.2016.12.002. Epub 2016 Dec 10. PubMed PMID: 27956228; PubMed Central PMCID: PMC6204228.

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Tran H, Almeida S, Moore J, Gendron TF, Chalasani U, Lu Y, Du X, Nickerson JA, Petrucelli L, Weng Z, Gao FB. Differential Toxicity of Nuclear RNA Foci versus Dipeptide Repeat Proteins in a Drosophila Model of C9ORF72 FTD/ALS. Neuron. 2015 Sep 23;87(6):1207-1214. doi: 10.1016/j.neuron.2015.09.015. PubMed PMID: 26402604; PubMed Central PMCID: PMC4589299.

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Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. doi: 10.1093/nar/gks1221. Epub 2012 Nov 29. PubMed PMID: 23203885; PubMed Central PMCID: PMC3531197.