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Raymond K. Auerbach, Ph.D. - Publications

Affiliations: 
Computational Biology and Bioinformatics Yale University, New Haven, CT 
Area:
Computational Biology and Bioinformatics
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22 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 Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, ... ... Auerbach R, et al. Comparative analysis of the transcriptome across distant species. Nature. 512: 445-8. PMID 25164755 DOI: 10.1038/Nature13424  0.573
2014 Ehmer U, Zmoos AF, Auerbach RK, Vaka D, Butte AJ, Kay MA, Sage J. Organ size control is dominant over Rb family inactivation to restrict proliferation in vivo. Cell Reports. 8: 371-81. PMID 25017070 DOI: 10.1016/J.Celrep.2014.06.025  0.328
2013 Auerbach RK, Chen B, Butte AJ. Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. Bioinformatics (Oxford, England). 29: 1922-4. PMID 23732275 DOI: 10.1093/Bioinformatics/Btt316  0.463
2013 Lefrançois P, Auerbach RK, Yellman CM, Roeder GS, Snyder M. Centromere-like regions in the budding yeast genome. Plos Genetics. 9: e1003209. PMID 23349633 DOI: 10.1371/Journal.Pgen.1003209  0.457
2012 Euskirchen G, Auerbach RK, Snyder M. SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions. The Journal of Biological Chemistry. 287: 30897-905. PMID 22952240 DOI: 10.1074/Jbc.R111.309302  0.411
2012 Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 148: 84-98. PMID 22265404 DOI: 10.1016/J.Cell.2011.12.014  0.56
2011 Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB. The real cost of sequencing: higher than you think! Genome Biology. 12: 125. PMID 21867570 DOI: 10.1186/Gb-2011-12-8-125  0.61
2011 Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, Bhardwaj N, Gerstein MB, Snyder M. Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. Plos Genetics. 7: e1002008. PMID 21408204 DOI: 10.1371/Journal.Pgen.1002008  0.7
2011 Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, et al. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Research. 21: 276-85. PMID 21177971 DOI: 10.1101/Gr.110189.110  0.667
2011 Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, et al. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data (Genome Research (2011) 21, (276-285)) Genome Research. 21: 811.  0.622
2010 Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 330: 1775-87. PMID 21177976 DOI: 10.1126/Science.1196914  0.711
2010 Cheung KH, Samwald M, Auerbach RK, Gerstein MB. Structured digital tables on the Semantic Web: toward a structured digital literature. Molecular Systems Biology. 6: 403. PMID 20739925 DOI: 10.1038/Msb.2010.45  0.412
2010 Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, et al. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. Plos Genetics. 6: e1000848. PMID 20174564 DOI: 10.1371/Journal.Pgen.1000848  0.665
2009 Pearson T, Giffard P, Beckstrom-Sternberg S, Auerbach R, Hornstra H, Tuanyok A, Price EP, Glass MB, Leadem B, Beckstrom-Sternberg JS, Allan GJ, Foster JT, Wagner DM, Okinaka RT, Sim SH, et al. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. Bmc Biology. 7: 78. PMID 19922616 DOI: 10.1186/1741-7007-7-78  0.353
2009 Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M. Mapping accessible chromatin regions using Sono-Seq. Proceedings of the National Academy of Sciences of the United States of America. 106: 14926-31. PMID 19706456 DOI: 10.1073/Pnas.0905443106  0.537
2009 Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M. Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. Bmc Genomics. 10: 37. PMID 19159457 DOI: 10.1186/1471-2164-10-37  0.588
2009 Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nature Biotechnology. 27: 66-75. PMID 19122651 DOI: 10.1038/Nbt.1518  0.591
2008 Tuanyok A, Leadem BR, Auerbach RK, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS, Mayo M, Wuthiekanun V, Brettin TS, Nierman WC, Peacock SJ, Currie BJ, Wagner DM, Keim P. Genomic islands from five strains of Burkholderia pseudomallei. Bmc Genomics. 9: 566. PMID 19038032 DOI: 10.1186/1471-2164-9-566  0.397
2007 Tuanyok A, Auerbach RK, Brettin TS, Bruce DC, Munk AC, Detter JC, Pearson T, Hornstra H, Sermswan RW, Wuthiekanun V, Peacock SJ, Currie BJ, Keim P, Wagner DM. A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. Journal of Bacteriology. 189: 9044-9. PMID 17933898 DOI: 10.1128/Jb.01264-07  0.347
2007 Beckstrom-Sternberg SM, Auerbach RK, Godbole S, Pearson JV, Beckstrom-Sternberg JS, Deng Z, Munk C, Kubota K, Zhou Y, Bruce D, Noronha J, Scheuermann RH, Wang A, Wei X, Wang J, et al. Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. Plos One. 2: e947. PMID 17895988 DOI: 10.1371/Journal.Pone.0000947  0.441
2007 Auerbach RK, Tuanyok A, Probert WS, Kenefic L, Vogler AJ, Bruce DC, Munk C, Brettin TS, Eppinger M, Ravel J, Wagner DM, Keim P. Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America. Plos One. 2: e770. PMID 17712418 DOI: 10.1371/Journal.Pone.0000770  0.372
2007 Touchman JW, Wagner DM, Hao J, Mastrian SD, Shah MK, Vogler AJ, Allender CJ, Clark EA, Benitez DS, Youngkin DJ, Girard JM, Auerbach RK, Beckstrom-Sternberg SM, Keim P. A North American Yersinia pestis draft genome sequence: SNPs and phylogenetic analysis. Plos One. 2: e220. PMID 17311096 DOI: 10.1371/Journal.Pone.0000220  0.331
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