Derek Yung-Ho Chiang - Publications

Affiliations: 
2005 University of California, Berkeley, Berkeley, CA 

45 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
2014 Jeck WR, Parker J, Carson CC, Shields JM, Sambade MJ, Peters EC, Burd CE, Thomas NE, Chiang DY, Liu W, Eberhard DA, Ollila D, Grilley-Olson J, Moschos S, Neil Hayes D, et al. Targeted next generation sequencing identifies clinically actionable mutations in patients with melanoma. Pigment Cell & Melanoma Research. 27: 653-63. PMID 24628946 DOI: 10.1111/pcmr.12238  1
2014 Grassian AR, Pagliarini R, Chiang DY. Mutations of isocitrate dehydrogenase 1 and 2 in intrahepatic cholangiocarcinoma. Current Opinion in Gastroenterology. 30: 295-302. PMID 24569570 DOI: 10.1097/MOG.0000000000000050  1
2013 Cleary SP, Jeck WR, Zhao X, Chen K, Selitsky SR, Savich GL, Tan TX, Wu MC, Getz G, Lawrence MS, Parker JS, Li J, Powers S, Kim H, Fischer S, ... ... Chiang DY, et al. Identification of driver genes in hepatocellular carcinoma by exome sequencing. Hepatology (Baltimore, Md.). 58: 1693-702. PMID 23728943 DOI: 10.1002/hep.26540  1
2013 Huang Y, Hu Y, Jones CD, MacLeod JN, Chiang DY, Liu Y, Prins JF, Liu J. A robust method for transcript quantification with RNA-seq data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 167-87. PMID 23461570 DOI: 10.1089/cmb.2012.0230  1
2013 Mezlini AM, Smith EJ, Fiume M, Buske O, Savich GL, Shah S, Aparicio S, Chiang DY, Goldenberg A, Brudno M. iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Research. 23: 519-29. PMID 23204306 DOI: 10.1101/gr.142232.112  1
2013 Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, et al. DiffSplice: the genome-wide detection of differential splicing events with RNA-seq. Nucleic Acids Research. 41: e39. PMID 23155066 DOI: 10.1093/nar/gks1026  1
2013 Wang P, Dong Q, Zhang C, Kuan PF, Liu Y, Jeck WR, Andersen JB, Jiang W, Savich GL, Tan TX, Auman JT, Hoskins JM, Misher AD, Moser CD, Yourstone SM, ... ... Chiang DY, et al. Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas. Oncogene. 32: 3091-100. PMID 22824796 DOI: 10.1038/onc.2012.315  1
2012 Kuan PF, Chiang DY. Integrating prior knowledge in multiple testing under dependence with applications to detecting differential DNA methylation. Biometrics. 68: 774-83. PMID 22260651 DOI: 10.1111/j.1541-0420.2011.01730.x  1
2011 Cho J, Pastorino S, Zeng Q, Xu X, Johnson W, Vandenberg S, Verhaak R, Cherniack AD, Watanabe H, Dutt A, Kwon J, Chao YS, Onofrio RC, Chiang D, Yuza Y, et al. Glioblastoma-derived epidermal growth factor receptor carboxyl-terminal deletion mutants are transforming and are sensitive to EGFR-directed therapies. Cancer Research. 71: 7587-96. PMID 22001862 DOI: 10.1158/0008-5472.CAN-11-0821  1
2011 Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K, Sougnez C, Voet D, Saksena G, Sivachenko A, Jing R, Parkin M, Pugh T, Verhaak RG, Stransky N, ... ... Chiang DY, et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nature Genetics. 43: 964-8. PMID 21892161 DOI: 10.1038/ng.936  1
2011 Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, Chiang DY, Liu J, Prins JF. FDM: a graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics (Oxford, England). 27: 2633-40. PMID 21824971 DOI: 10.1093/bioinformatics/btr458  1
2011 Dooley AL, Winslow MM, Chiang DY, Banerji S, Stransky N, Dayton TL, Snyder EL, Senna S, Whittaker CA, Bronson RT, Crowley D, Barretina J, Garraway L, Meyerson M, Jacks T. Nuclear factor I/B is an oncogene in small cell lung cancer. Genes & Development. 25: 1470-5. PMID 21764851 DOI: 10.1101/gad.2046711  1
2011 Winslow MM, Dayton TL, Verhaak RG, Kim-Kiselak C, Snyder EL, Feldser DM, Hubbard DD, DuPage MJ, Whittaker CA, Hoersch S, Yoon S, Crowley D, Bronson RT, Chiang DY, Meyerson M, et al. Suppression of lung adenocarcinoma progression by Nkx2-1. Nature. 473: 101-4. PMID 21471965 DOI: 10.1038/nature09881  1
2011 Toffanin S, Hoshida Y, Lachenmayer A, Villanueva A, Cabellos L, Minguez B, Savic R, Ward SC, Thung S, Chiang DY, Alsinet C, Tovar V, Roayaie S, Schwartz M, Bruix J, et al. MicroRNA-based classification of hepatocellular carcinoma and oncogenic role of miR-517a. Gastroenterology. 140: 1618-28.e16. PMID 21324318 DOI: 10.1053/j.gastro.2011.02.009  1
2010 Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Research. 38: e178. PMID 20802226 DOI: 10.1093/nar/gkq622  1
2010 Barretina J, Taylor BS, Banerji S, Ramos AH, Lagos-Quintana M, Decarolis PL, Shah K, Socci ND, Weir BA, Ho A, Chiang DY, Reva B, Mermel CH, Getz G, Antipin Y, et al. Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nature Genetics. 42: 715-21. PMID 20601955 DOI: 10.1038/ng.619  1
2010 Hu Y, Wang K, He X, Chiang DY, Prins JF, Liu J. A probabilistic framework for aligning paired-end RNA-seq data. Bioinformatics (Oxford, England). 26: 1950-7. PMID 20576625 DOI: 10.1093/bioinformatics/btq336  1
2010 Zender L, Villanueva A, Tovar V, Sia D, Chiang DY, Llovet JM. Cancer gene discovery in hepatocellular carcinoma. Journal of Hepatology. 52: 921-9. PMID 20385424 DOI: 10.1016/j.jhep.2009.12.034  1
2010 Tovar V, Alsinet C, Villanueva A, Hoshida Y, Chiang DY, Solé M, Thung S, Moyano S, Toffanin S, Mínguez B, Cabellos L, Peix J, Schwartz M, Mazzaferro V, Bruix J, et al. IGF activation in a molecular subclass of hepatocellular carcinoma and pre-clinical efficacy of IGF-1R blockage. Journal of Hepatology. 52: 550-9. PMID 20206398 DOI: 10.1016/j.jhep.2010.01.015  1
2010 Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, ... ... Chiang DY, et al. The landscape of somatic copy-number alteration across human cancers. Nature. 463: 899-905. PMID 20164920 DOI: 10.1038/nature08822  1
2009 Chiang DY, McCarroll SA. Mapping duplicated sequences. Nature Biotechnology. 27: 1001-2. PMID 19898454 DOI: 10.1038/nbt1109-1001  1
2009 Hoshida Y, Nijman SM, Kobayashi M, Chan JA, Brunet JP, Chiang DY, Villanueva A, Newell P, Ikeda K, Hashimoto M, Watanabe G, Gabriel S, Friedman SL, Kumada H, Llovet JM, et al. Integrative transcriptome analysis reveals common molecular subclasses of human hepatocellular carcinoma. Cancer Research. 69: 7385-92. PMID 19723656 DOI: 10.1158/0008-5472.CAN-09-1089  1
2009 Newell P, Toffanin S, Villanueva A, Chiang DY, Minguez B, Cabellos L, Savic R, Hoshida Y, Lim KH, Melgar-Lesmes P, Yea S, Peix J, Deniz K, Fiel MI, Thung S, et al. Ras pathway activation in hepatocellular carcinoma and anti-tumoral effect of combined sorafenib and rapamycin in vivo. Journal of Hepatology. 51: 725-33. PMID 19665249 DOI: 10.1016/j.jhep.2009.03.028  1
2009 Sos ML, Michel K, Zander T, Weiss J, Frommolt P, Peifer M, Li D, Ullrich R, Koker M, Fischer F, Shimamura T, Rauh D, Mermel C, Fischer S, Stückrath I, ... ... Chiang D, et al. Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. The Journal of Clinical Investigation. 119: 1727-40. PMID 19451690 DOI: 10.1172/JCI37127  1
2009 Mínguez B, Tovar V, Chiang D, Villanueva A, Llovet JM. Pathogenesis of hepatocellular carcinoma and molecular therapies. Current Opinion in Gastroenterology. 25: 186-94. PMID 19387255 DOI: 10.1097/MOG.0b013e32832962a1  1
2009 Keng VW, Villanueva A, Chiang DY, Dupuy AJ, Ryan BJ, Matise I, Silverstein KA, Sarver A, Starr TK, Akagi K, Tessarollo L, Collier LS, Powers S, Lowe SW, Jenkins NA, et al. A conditional transposon-based insertional mutagenesis screen for genes associated with mouse hepatocellular carcinoma. Nature Biotechnology. 27: 264-74. PMID 19234449 DOI: 10.1038/nbt.1526  1
2009 Yoo BK, Emdad L, Su ZZ, Villanueva A, Chiang DY, Mukhopadhyay ND, Mills AS, Waxman S, Fisher RA, Llovet JM, Fisher PB, Sarkar D. Astrocyte elevated gene-1 regulates hepatocellular carcinoma development and progression. The Journal of Clinical Investigation. 119: 465-77. PMID 19221438 DOI: 10.1172/JCI36460  1
2009 Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nature Methods. 6: 99-103. PMID 19043412 DOI: 10.1038/nmeth.1276  1
2008 Villanueva A, Chiang DY, Newell P, Peix J, Thung S, Alsinet C, Tovar V, Roayaie S, Minguez B, Sole M, Battiston C, Van Laarhoven S, Fiel MI, Di Feo A, Hoshida Y, et al. Pivotal role of mTOR signaling in hepatocellular carcinoma. Gastroenterology. 135: 1972-83, 1983.e1-11. PMID 18929564 DOI: 10.1053/j.gastro.2008.08.008  1
2008 Hoshida Y, Villanueva A, Kobayashi M, Peix J, Chiang DY, Camargo A, Gupta S, Moore J, Wrobel MJ, Lerner J, Reich M, Chan JA, Glickman JN, Ikeda K, Hashimoto M, et al. Gene expression in fixed tissues and outcome in hepatocellular carcinoma. The New England Journal of Medicine. 359: 1995-2004. PMID 18923165 DOI: 10.1056/NEJMoa0804525  1
2008 Chiang DY, Villanueva A, Hoshida Y, Peix J, Newell P, Minguez B, LeBlanc AC, Donovan DJ, Thung SN, Solé M, Tovar V, Alsinet C, Ramos AH, Barretina J, Roayaie S, et al. Focal gains of VEGFA and molecular classification of hepatocellular carcinoma. Cancer Research. 68: 6779-88. PMID 18701503 DOI: 10.1158/0008-5472.CAN-08-0742  1
2008 Koivunen JP, Mermel C, Zejnullahu K, Murphy C, Lifshits E, Holmes AJ, Choi HG, Kim J, Chiang D, Thomas R, Lee J, Richards WG, Sugarbaker DJ, Ducko C, Lindeman N, et al. EML4-ALK fusion gene and efficacy of an ALK kinase inhibitor in lung cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 14: 4275-83. PMID 18594010 DOI: 10.1158/1078-0432.CCR-08-0168  1
2008 Kulke MH, Freed E, Chiang DY, Philips J, Zahrieh D, Glickman JN, Shivdasani RA. High-resolution analysis of genetic alterations in small bowel carcinoid tumors reveals areas of recurrent amplification and loss. Genes, Chromosomes & Cancer. 47: 591-603. PMID 18383209 DOI: 10.1002/gcc.20561  1
2007 Shultzaberger RK, Chiang DY, Moses AM, Eisen MB. Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. Plos One. 2: e1199. PMID 18030333 DOI: 10.1371/journal.pone.0001199  1
2007 Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, Shah K, Sato M, Thomas RK, Barletta JA, Borecki IB, ... ... Chiang DY, et al. Characterizing the cancer genome in lung adenocarcinoma. Nature. 450: 893-8. PMID 17982442 DOI: 10.1038/nature06358  1
2007 Villanueva A, Newell P, Chiang DY, Friedman SL, Llovet JM. Genomics and signaling pathways in hepatocellular carcinoma. Seminars in Liver Disease. 27: 55-76. PMID 17295177 DOI: 10.1055/s-2006-960171  1
2006 Chiang DY, Nix DA, Shultzaberger RK, Gasch AP, Eisen MB. Flexible promoter architecture requirements for coactivator recruitment. Bmc Molecular Biology. 7: 16. PMID 16646957 DOI: 10.1186/1471-2199-7-16  1
2004 Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB. MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biology. 5: R98. PMID 15575972 DOI: 10.1186/gb-2004-5-12-r98  1
2004 Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB. Conservation and evolution of cis-regulatory systems in ascomycete fungi. Plos Biology. 2: e398. PMID 15534694 DOI: 10.1371/journal.pbio.0020398  1
2004 Moses AM, Chiang DY, Eisen MB. Phylogenetic motif detection by expectation-maximization on evolutionary mixtures. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 324-35. PMID 14992514  1
2003 Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB. Position specific variation in the rate of evolution in transcription factor binding sites. Bmc Evolutionary Biology. 3: 19. PMID 12946282 DOI: 10.1186/1471-2148-3-19  1
2003 Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB. Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biology. 4: R43. PMID 12844359 DOI: 10.1186/gb-2003-4-7-r43  1
2003 Chiang DY, Moses AM, Kamvysselis M, Lander ES, Eisen MB. Phylogenetically and spatially conserved word pairs associated with gene expression changes in yeasts Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 84-93.  1
2001 Chiang DY, Brown PO, Eisen MB. Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics (Oxford, England). 17: S49-55. PMID 11472992  1
2000 Abe K, Rossman KL, Liu B, Ritola KD, Chiang D, Campbell SL, Burridge K, Der CJ. Vav2 is an activator of Cdc42, Rac1, and RhoA. The Journal of Biological Chemistry. 275: 10141-9. PMID 10744696 DOI: 10.1074/jbc.275.14.10141  1
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