R. David Hawkins - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 

27 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
2016 Celik S, Logsdon BA, Battle S, Drescher CW, Rendi M, Hawkins RD, Lee SI. Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer. Genome Medicine. 8: 66. PMID 27287041 DOI: 10.1186/S13073-016-0319-7  1
2016 Konki M, Pasumarthy K, Malonzo M, Sainio A, Valensisi C, Söderström M, Emani MR, Stubb A, Närvä E, Ghimire B, Laiho A, Järveläinen H, Lahesmaa R, Lähdesmäki H, Hawkins RD, et al. Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells Scientific Reports. 6. DOI: 10.1038/srep22190  1
2015 Kanduri K, Tripathi S, Larjo A, Mannerström H, Ullah U, Lund R, Hawkins RD, Ren B, Lähdesmäki H, Lahesmaa R. Identification of global regulators of T-helper cell lineage specification. Genome Medicine. 7: 122. PMID 26589177 DOI: 10.1186/S13073-015-0237-0  1
2015 Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins DR, Akey JM. Comprehensive identification and analysis of human accelerated regulatory DNA. Genome Research. PMID 26104583 DOI: 10.1101/Gr.192591.115  1
2014 Ware CB, Nelson AM, Mecham B, Hesson J, Zhou W, Jonlin EC, Jimenez-Caliani AJ, Deng X, Cavanaugh C, Cook S, Tesar PJ, Okada J, Margaretha L, Sperber H, Choi M, ... ... Hawkins RD, et al. Derivation of naive human embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America. 111: 4484-9. PMID 24623855 DOI: 10.1073/Pnas.1319738111  1
2014 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells Nature. 514: 126. DOI: 10.1038/Nature13843  1
2013 Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R. Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity. 38: 1271-84. PMID 23791644 DOI: 10.1016/J.Immuni.2013.05.011  1
2013 Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 153: 1134-48. PMID 23664764 DOI: 10.1016/J.Cell.2013.04.022  1
2012 Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Research. 22: 246-58. PMID 22156296 DOI: 10.1101/Gr.125872.111  1
2012 Elo LL, Kallio A, Laajala TD, Hawkins RD, Korpelainen E, Aittokallio T. Optimized detection of transcription factor-binding sites in ChIP-seq experiments Nucleic Acids Research. 40: e1. PMID 22009681 DOI: 10.1093/nar/gkr839  1
2011 Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z, Kuan S, Yu P, Liu H, Zhang X, Green RD, et al. Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Research. 21: 1393-409. PMID 21876557 DOI: 10.1038/Cr.2011.146  1
2011 Alvarado DM, Hawkins RD, Bashiardes S, Veile RA, Ku YC, Powder KE, Spriggs MK, Speck JD, Warchol ME, Lovett M. An RNA interference-based screen of transcription factor genes identifies pathways necessary for sensory regeneration in the avian inner ear. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 31: 4535-43. PMID 21430154 DOI: 10.1523/Jneurosci.5456-10.2011  1
2011 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 471: 68-73. PMID 21289626 DOI: 10.1038/Nature09798  1
2011 Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, ... ... Hawkins RD, et al. An assessment of histone-modification antibody quality. Nature Structural & Molecular Biology. 18: 91-3. PMID 21131980 DOI: 10.1038/Nsmb.1972  1
2010 Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, ... ... Hawkins RD, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/Nbt.1682  1
2010 Elo LL, Järvenpää H, Tuomela S, Raghav S, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Orešič M, Lähdesmäki H, Rasool O, Rao KV, Aittokallio T, et al. Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming Immunity. 32: 852-862. PMID 20620947 DOI: 10.1016/J.Immuni.2010.06.011  1
2010 Hawkins RD, Hon GC, Ren B. Next-generation genomics: An integrative approach Nature Reviews Genetics. 11: 476-486. PMID 20531367 DOI: 10.1038/Nrg2795  1
2010 Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 6: 479-91. PMID 20452322 DOI: 10.1016/J.Stem.2010.03.018  1
2009 Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462: 315-22. PMID 19829295 DOI: 10.1038/Nature08514  1
2009 Hon GC, Hawkins RD, Ren B. Predictive chromatin signatures in the mammalian genome Human Molecular Genetics. 18: R195-R201. PMID 19808796 DOI: 10.1093/Hmg/Ddp409  1
2009 Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 459: 108-12. PMID 19295514 DOI: 10.1038/Nature07829  1
2007 Hawkins RD, Bashiardes S, Powder KE, Sajan SA, Bhonagiri V, Alvarado DM, Speck J, Warchol ME, Lovett M. Large scale gene expression profiles of regenerating inner ear sensory epithelia. Plos One. 2: e525. PMID 17565378 DOI: 10.1371/Journal.Pone.0000525  1
2007 Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nature Genetics. 39: 311-318. PMID 17277777 DOI: 10.1038/Ng1966  1
2006 Hawkins RD, Ren B. Genome-wide location analysis: insights on transcriptional regulation. Human Molecular Genetics. 15: R1-7. PMID 16651365 DOI: 10.1093/Hmg/Ddl043  1
2006 Hawkins RD, Helms CA, Winston JB, Warchol ME, Lovett M. Applying genomics to the avian inner ear: development of subtractive cDNA resources for exploring sensory function and hair cell regeneration. Genomics. 87: 801-8. PMID 16516437 DOI: 10.1016/J.Ygeno.2005.12.014  1
2004 Hawkins RD, Lovett M. The developmental genetics of auditory hair cells. Human Molecular Genetics. 13: R289-96. PMID 15358736 DOI: 10.1093/Hmg/Ddh249  1
2003 Hawkins RD, Bashiardes S, Helms CA, Hu L, Saccone NL, Warchol ME, Lovett M. Gene expression differences in quiescent versus regenerating hair cells of avian sensory epithelia: implications for human hearing and balance disorders. Human Molecular Genetics. 12: 1261-72. PMID 12761041 DOI: 10.1093/Hmg/Ddg150  1
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