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Page 1
The YH database: the first Asian diploid genome database.
Li G, Ma L, Song C, Yang Z, Wang X, Huang H, Li Y, Li R, Zhang X, Yang H, Wang J, Wang J. Li G, et al. Among authors: ma l. Nucleic Acids Res. 2009 Jan;37(Database issue):D1025-8. doi: 10.1093/nar/gkn966. Nucleic Acids Res. 2009. PMID: 19073702 Free PMC article.
The diploid genome sequence of an Asian individual.
Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, Li G, Yang Z, Zhang G, Yang B, Yu C, Liang F, Li W, Li S, Li D, Ni P, Ruan J, Li Q, Zhu H, Liu D, Lu Z, Li N, Guo G, Zhang J, Ye J, Fang L, Hao Q, Chen Q, Liang Y, Su Y, San A, Ping C, Yang S, Chen F, Li L, Zhou K, Zheng H, Ren Y, Yang L, Gao Y, Yang G, Li Z, Feng X, Kristiansen K, Wong GK, Nielsen R, Durbin R, Bolund L, Zhang X, Li S, Yang H, Wang J. Wang J, et al. Among authors: ma l. Nature. 2008 Nov 6;456(7218):60-5. doi: 10.1038/nature07484. Nature. 2008. PMID: 18987735 Free PMC article.
The sequence and de novo assembly of the giant panda genome.
Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner CC, Lam TT, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam TW, Yiu SM, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong GK, Olson M, Zhang X, Li S, Yang H, Wang J, Wang J. Li R, et al. Among authors: ma l. Nature. 2010 Jan 21;463(7279):311-7. doi: 10.1038/nature08696. Epub 2009 Dec 13. Nature. 2010. PMID: 20010809 Free PMC article.
Snap: an integrated SNP annotation platform.
Li S, Ma L, Li H, Vang S, Hu Y, Bolund L, Wang J. Li S, et al. Among authors: ma l. Nucleic Acids Res. 2007 Jan;35(Database issue):D707-10. doi: 10.1093/nar/gkl969. Epub 2006 Nov 29. Nucleic Acids Res. 2007. PMID: 17135198 Free PMC article.
The genome of the cucumber, Cucumis sativus L.
Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J, Lin K, Jin W, Fei Z, Li G, Staub J, Kilian A, van der Vossen EA, Wu Y, Guo J, He J, Jia Z, Ren Y, Tian G, Lu Y, Ruan J, Qian W, Wang M, Huang Q, Li B, Xuan Z, Cao J, Asan, Wu Z, Zhang J, Cai Q, Bai Y, Zhao B, Han Y, Li Y, Li X, Wang S, Shi Q, Liu S, Cho WK, Kim JY, Xu Y, Heller-Uszynska K, Miao H, Cheng Z, Zhang S, Wu J, Yang Y, Kang H, Li M, Liang H, Ren X, Shi Z, Wen M, Jian M, Yang H, Zhang G, Yang Z, Chen R, Liu S, Li J, Ma L, Liu H, Zhou Y, Zhao J, Fang X, Li G, Fang L, Li Y, Liu D, Zheng H, Zhang Y, Qin N, Li Z, Yang G, Yang S, Bolund L, Kristiansen K, Zheng H, Li S, Zhang X, Yang H, Wang J, Sun R, Zhang B, Jiang S, Wang J, Du Y, Li S. Huang S, et al. Among authors: ma l. Nat Genet. 2009 Dec;41(12):1275-81. doi: 10.1038/ng.475. Epub 2009 Nov 1. Nat Genet. 2009. PMID: 19881527
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.
Single base-resolution methylome of the silkworm reveals a sparse epigenomic map.
Xiang H, Zhu J, Chen Q, Dai F, Li X, Li M, Zhang H, Zhang G, Li D, Dong Y, Zhao L, Lin Y, Cheng D, Yu J, Sun J, Zhou X, Ma K, He Y, Zhao Y, Guo S, Ye M, Guo G, Li Y, Li R, Zhang X, Ma L, Kristiansen K, Guo Q, Jiang J, Beck S, Xia Q, Wang W, Wang J. Xiang H, et al. Among authors: ma l, ma k. Nat Biotechnol. 2010 May;28(5):516-20. doi: 10.1038/nbt.1626. Epub 2010 May 2. Nat Biotechnol. 2010. PMID: 20436463
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.
Author Correction: 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. 2022 May;605(7909):E3. doi: 10.1038/s41586-021-04226-3. Nature. 2022. PMID: 35474001 Free PMC article. No abstract available.
Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster.
Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, Gao W, Moran JR, Rehm EJ, Grossman RL, Kellis M, White KP. Slattery M, et al. Among authors: ma l. Genome Res. 2014 Jul;24(7):1224-35. doi: 10.1101/gr.168807.113. Genome Res. 2014. PMID: 24985916 Free PMC article.
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