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Page 1
Topologically associating domain boundaries are required for normal genome function.
Rajderkar S, Barozzi I, Zhu Y, Hu R, Zhang Y, Li B, Alcaina Caro A, Fukuda-Yuzawa Y, Kelman G, Akeza A, Blow MJ, Pham Q, Harrington AN, Godoy J, Meky EM, von Maydell K, Hunter RD, Akiyama JA, Novak CS, Plajzer-Frick I, Afzal V, Tran S, Lopez-Rios J, Talkowski ME, Lloyd KCK, Ren B, Dickel DE, Visel A, Pennacchio LA. Rajderkar S, et al. Among authors: novak cs. Commun Biol. 2023 Apr 20;6(1):435. doi: 10.1038/s42003-023-04819-w. Commun Biol. 2023. PMID: 37081156 Free PMC article.
Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants.
Kvon EZ, Zhu Y, Kelman G, Novak CS, Plajzer-Frick I, Kato M, Garvin TH, Pham Q, Harrington AN, Hunter RD, Godoy J, Meky EM, Akiyama JA, Afzal V, Tran S, Escande F, Gilbert-Dussardier B, Jean-Marçais N, Hudaiberdiev S, Ovcharenko I, Dobbs MB, Gurnett CA, Manouvrier-Hanu S, Petit F, Visel A, Dickel DE, Pennacchio LA. Kvon EZ, et al. Among authors: novak cs. Cell. 2020 Mar 19;180(6):1262-1271.e15. doi: 10.1016/j.cell.2020.02.031. Epub 2020 Mar 12. Cell. 2020. PMID: 32169219 Free PMC article.
An atlas of dynamic chromatin landscapes in mouse fetal development.
Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. Gorkin DU, et al. Among authors: novak cs. Nature. 2020 Jul;583(7818):744-751. doi: 10.1038/s41586-020-2093-3. Epub 2020 Jul 29. Nature. 2020. PMID: 32728240 Free PMC article.
Perspectives on ENCODE.
ENCODE Project Consortium; 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. ENCODE Project Consortium, et al. Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29. Nature. 2020. PMID: 32728248 Free PMC article.
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
ENCODE Project Consortium; 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. ENCODE Project Consortium, et al. Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29. Nature. 2020. PMID: 32728249 Free PMC article.
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation.
Sethi A, Gu M, Gumusgoz E, Chan L, Yan KK, Rozowsky J, Barozzi I, Afzal V, Akiyama JA, Plajzer-Frick I, Yan C, Novak CS, Kato M, Garvin TH, Pham Q, Harrington A, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, Visel A, Dickel DE, Yip KY, Sutton R, Pennacchio LA, Gerstein M. Sethi A, et al. Among authors: novak cs. Nat Methods. 2020 Aug;17(8):807-814. doi: 10.1038/s41592-020-0907-8. Epub 2020 Jul 29. Nat Methods. 2020. PMID: 32737473 Free PMC article.
Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development.
Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. Gorkin DU, et al. Among authors: novak cs. Nature. 2020 Oct;586(7831):E31. doi: 10.1038/s41586-020-2841-4. Nature. 2020. PMID: 33037424 Free PMC article.
Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development.
Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. Gorkin DU, et al. Among authors: novak cs. Nature. 2021 Jan;589(7842):E4. doi: 10.1038/s41586-020-03089-4. Nature. 2021. PMID: 33398137 Free PMC article. No abstract available.
Ultraconserved enhancer function does not require perfect sequence conservation.
Snetkova V, Ypsilanti AR, Akiyama JA, Mannion BJ, Plajzer-Frick I, Novak CS, Harrington AN, Pham QT, Kato M, Zhu Y, Godoy J, Meky E, Hunter RD, Shi M, Kvon EZ, Afzal V, Tran S, Rubenstein JLR, Visel A, Pennacchio LA, Dickel DE. Snetkova V, et al. Among authors: novak cs. Nat Genet. 2021 Apr;53(4):521-528. doi: 10.1038/s41588-021-00812-3. Epub 2021 Mar 29. Nat Genet. 2021. PMID: 33782603 Free PMC article.
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