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Year Citation  Score
2018 Richter DJ, Fozouni P, Eisen M, King N. Gene family innovation, conservation and loss on the animal stem lineage. Elife. 7. PMID 29848444 DOI: 10.7554/eLife.34226  0.4
2015 Paris M, Villalta JE, Eisen MB, Lott SE. Sex Bias and Maternal Contribution to Gene Expression Divergence in Drosophila Blastoderm Embryos. Plos Genetics. 11: e1005592. PMID 26485701 DOI: 10.1371/journal.pgen.1005592  1
2015 Harrison MM, Eisen MB. Transcriptional Activation of the Zygotic Genome in Drosophila. Current Topics in Developmental Biology. 113: 85-112. PMID 26358871 DOI: 10.1016/bs.ctdb.2015.07.028  1
2015 Bourne PE, Brenner SE, Eisen MB. Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation. Plos Computational Biology. 11: e1004317. PMID 26107720 DOI: 10.1371/journal.pcbi.1004317  1
2015 Combs PA, Eisen MB. Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols. Peerj. 3: e869. PMID 25834775 DOI: 10.7717/peerj.869  1
2014 Schiabor KM, Quan AS, Eisen MB. Saccharomyces cerevisiae mitochondria are required for optimal attractiveness to Drosophila melanogaster. Plos One. 9: e113899. PMID 25462617 DOI: 10.1371/journal.pone.0113899  1
2014 MacManes MD, Eisen MB. Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus. Peerj. 2: e642. PMID 25374784 DOI: 10.7717/peerj.642  1
2014 Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, ... ... Eisen MB, et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research. 24: 1209-23. PMID 24985915 DOI: 10.1101/gr.159384.113  0.76
2014 Wong VL, Ellison CE, Eisen MB, Pachter L, Brem RB. Structural variation among wild and industrial strains of Penicillium chrysogenum. Plos One. 9: e96784. PMID 24824901 DOI: 10.1371/journal.pone.0096784  1
2014 Kuntz SG, Eisen MB. Drosophila embryogenesis scales uniformly across temperature in developmentally diverse species. Plos Genetics. 10: e1004293. PMID 24762628 DOI: 10.1371/journal.pgen.1004293  1
2014 Lott SE, Villalta JE, Zhou Q, Bachtrog D, Eisen MB. Sex-specific embryonic gene expression in species with newly evolved sex chromosomes. Plos Genetics. 10: e1004159. PMID 24550743 DOI: 10.1371/journal.pgen.1004159  1
2013 Paris M, Kaplan T, Li XY, Villalta JE, Lott SE, Eisen MB. Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. Plos Genetics. 9: e1003748. PMID 24068946 DOI: 10.1371/journal.pgen.1003748  1
2013 Ingram WM, Goodrich LM, Robey EA, Eisen MB. Mice infected with low-virulence strains of Toxoplasma gondii lose their innate aversion to cat urine, even after extensive parasite clearance. Plos One. 8: e75246. PMID 24058668 DOI: 10.1371/journal.pone.0075246  1
2013 Combs PA, Eisen MB. Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression. Plos One. 8: e71820. PMID 23951250 DOI: 10.1371/journal.pone.0071820  1
2013 Macmanes MD, Eisen MB. Improving transcriptome assembly through error correction of high-throughput sequence reads. Peerj. 1: e113. PMID 23904992 DOI: 10.7717/peerj.113  1
2013 Ali-Murthy Z, Lott SE, Eisen MB, Kornberg TB. An essential role for zygotic expression in the pre-cellular Drosophila embryo. Plos Genetics. 9: e1003428. PMID 23593026 DOI: 10.1371/journal.pgen.1003428  1
2013 Rands CM, Darling A, Fujita M, Kong L, Webster MT, Clabaut C, Emes RD, Heger A, Meader S, Hawkins MB, Eisen MB, Teiling C, Affourtit J, Boese B, Grant PR, et al. Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. Bmc Genomics. 14: 95. PMID 23402223 DOI: 10.1186/1471-2164-14-95  1
2013 Zhou H, Kaplan T, Li Y, Grubisic I, Zhang Z, Wang PJ, Eisen MB, Tjian R. Dual functions of TAF7L in adipocyte differentiation. Elife. 2: e00170. PMID 23326641 DOI: 10.7554/eLife.00170  1
2013 Lusk RW, Eisen MB. Spatial promoter recognition signatures may enhance transcription factor specificity in yeast. Plos One. 8: e53778. PMID 23320104 DOI: 10.1371/journal.pone.0053778  1
2013 Hu TT, Eisen MB, Thornton KR, Andolfatto P. A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Research. 23: 89-98. PMID 22936249 DOI: 10.1101/gr.141689.112  1
2012 Teytelman L, Osborne Nishimura EA, Özaydin B, Eisen MB, Rine J. The enigmatic conservation of a Rap1 binding site in the Saccharomyces cerevisiae HMR-E silencer. G3 (Bethesda, Md.). 2: 1555-62. PMID 23275878 DOI: 10.1534/g3.112.004077  1
2012 Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin MD, Celniker SE. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 109: 21330-5. PMID 23236164 DOI: 10.1073/pnas.1209589110  1
2012 Shultzaberger RK, Maerkl SJ, Kirsch JF, Eisen MB. Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain. Plos Genetics. 8: e1002614. PMID 22496663 DOI: 10.1371/journal.pgen.1002614  1
2012 Atherton J, Boley N, Brown B, Ogawa N, Davidson SM, Eisen MB, Biggin MD, Bickel P. A model for sequential evolution of ligands by exponential enrichment (SELEX) data Annals of Applied Statistics. 6: 928-949. DOI: 10.1214/12-AOAS537  1
2011 Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT. The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda, Md.). 1: 11-25. PMID 22384314 DOI: 10.1534/g3.111.000273  1
2011 Fowlkes CC, Eckenrode KB, Bragdon MD, Meyer M, Wunderlich Z, Simirenko L, Luengo Hendriks CL, Keränen SV, Henriquez C, Knowles DW, Biggin MD, Eisen MB, DePace AH. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. Plos Genetics. 7: e1002346. PMID 22046143 DOI: 10.1371/journal.pgen.1002346  1
2011 Harrison MM, Li XY, Kaplan T, Botchan MR, Eisen MB. Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition. Plos Genetics. 7: e1002266. PMID 22028662 DOI: 10.1371/journal.pgen.1002266  1
2011 Liu Z, Scannell DR, Eisen MB, Tjian R. Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell. 146: 720-31. PMID 21884934 DOI: 10.1016/j.cell.2011.08.005  1
2011 Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biology. 12: R34. PMID 21473766 DOI: 10.1186/gb-2011-12-4-r34  1
2011 Lott SE, Villalta JE, Schroth GP, Luo S, Tonkin LA, Eisen MB. Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. Plos Biology. 9: e1000590. PMID 21346796 DOI: 10.1371/journal.pbio.1000590  1
2011 Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. Plos Genetics. 7: e1001290. PMID 21304941 DOI: 10.1371/journal.pgen.1001290  1
2011 Head AJ, Eisen MB. How college students use the web to conduct everyday life research First Monday. 16.  1
2010 Rübel O, Ahern S, Bethel EW, Biggin MD, Childs H, Cormier-Michel E, Depace A, Eisen MB, Fowlkes CC, Geddes CG, Hagen H, Hamann B, Huang MY, Keränen SV, Knowles DW, et al. Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data. Procedia Computer Science. 1: 1757-1764. PMID 23762211 DOI: 10.1016/j.procs.2010.04.197  1
2010 Eisen M. DNA dealt wrong hand on cover. Nature. 467: 401. PMID 20864983 DOI: 10.1038/467401d  1
2010 Shultzaberger RK, Malashock DS, Kirsch JF, Eisen MB. The fitness landscapes of cis-acting binding sites in different promoter and environmental contexts. Plos Genetics. 6: e1001042. PMID 20686658 DOI: 10.1371/journal.pgen.1001042  1
2010 Levin TC, Glazer AM, Pachter L, Brem RB, Eisen MB. Exploring the genetic basis of variation in gene predictions with a synthetic association study. Plos One. 5: e11645. PMID 20686598 DOI: 10.1371/journal.pone.0011645  1
2010 Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. Plos Biology. 8: e1000343. PMID 20351773 DOI: 10.1371/journal.pbio.1000343  1
2010 Rübel O, Weber GH, Huang MY, Bethel EW, Biggin MD, Fowlkes CC, Luengo Hendriks CL, Keränen SV, Eisen MB, Knowles DW, Malik J, Hagen H, Hamann B. Integrating data clustering and visualization for the analysis of 3D gene expression data. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 7: 64-79. PMID 20150669 DOI: 10.1109/TCBB.2008.49  1
2010 Lusk RW, Eisen MB. Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers. Plos Genetics. 6: e1000829. PMID 20107516 DOI: 10.1371/journal.pgen.1000829  1
2009 Leung G, Eisen MB. Identifying cis-regulatory sequences by word profile similarity. Plos One. 4: e6901. PMID 19730735 DOI: 10.1371/journal.pone.0006901  1
2009 Rosenblum EB, Poorten TJ, Settles M, Murdoch GK, Robert J, Maddox N, Eisen MB. Genome-wide transcriptional response of Silurana (Xenopus) tropicalis to infection with the deadly chytrid fungus. Plos One. 4: e6494. PMID 19701481 DOI: 10.1371/journal.pone.0006494  1
2009 Teytelman L, Ozaydin B, Zill O, Lefrançois P, Snyder M, Rine J, Eisen MB. Impact of chromatin structures on DNA processing for genomic analyses. Plos One. 4: e6700. PMID 19693276 DOI: 10.1371/journal.pone.0006700  1
2009 MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keränen SV, Knowles DW, Stapleton M, Bickel P, Biggin MD, Eisen MB. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biology. 10: R80. PMID 19627575 DOI: 10.1186/gb-2009-10-7-r80  1
2009 Eisen M, Salzberg S. Open access: the sooner the better. Science (New York, N.Y.). 325: 266; author reply 26. PMID 19608896 DOI: 10.1126/science.325_266c  1
2009 Jans J, Gladden JM, Ralston EJ, Pickle CS, Michel AH, Pferdehirt RR, Eisen MB, Meyer BJ. A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome. Genes & Development. 23: 602-18. PMID 19270160 DOI: 10.1101/gad.1751109  1
2009 Peterson BK, Hare EE, Iyer VN, Storage S, Conner L, Papaj DR, Kurashima R, Jang E, Eisen MB. Big genomes facilitate the comparative identification of regulatory elements. Plos One. 4: e4688. PMID 19259274 DOI: 10.1371/journal.pone.0004688  1
2009 Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Molecular Cell. 33: 438-49. PMID 19250905 DOI: 10.1016/j.molcel.2009.01.022  1
2009 Garnett AT, Han TM, Gilchrist MJ, Smith JC, Eisen MB, Wardle FC, Amacher SL. Identification of direct T-box target genes in the developing zebrafish mesoderm. Development (Cambridge, England). 136: 749-60. PMID 19158186 DOI: 10.1242/dev.024703  1
2008 Hare EE, Peterson BK, Eisen MB. A careful look at binding site reorganization in the even-skipped enhancers of Drosophila and sepsids. Plos Genetics. 4: e1000268. PMID 19043550 DOI: 10.1371/journal.pgen.1000268  1
2008 Teytelman L, Eisen MB, Rine J. Silent but not static: accelerated base-pair substitution in silenced chromatin of budding yeasts. Plos Genetics. 4: e1000247. PMID 18989454 DOI: 10.1371/journal.pgen.1000247  1
2008 Rosenblum EB, Stajich JE, Maddox N, Eisen MB. Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. Proceedings of the National Academy of Sciences of the United States of America. 105: 17034-9. PMID 18852473 DOI: 10.1073/pnas.0804173105  1
2008 Pfeiffer BD, Jenett A, Hammonds AS, Ngo TT, Misra S, Murphy C, Scully A, Carlson JW, Wan KH, Laverty TR, Mungall C, Svirskas R, Kadonaga JT, Doe CQ, Eisen MB, et al. Tools for neuroanatomy and neurogenetics in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 105: 9715-20. PMID 18621688 DOI: 10.1073/pnas.0803697105  1
2008 Hare EE, Peterson BK, Iyer VN, Meier R, Eisen MB. Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. Plos Genetics. 4: e1000106. PMID 18584029 DOI: 10.1371/journal.pgen.1000106  1
2008 Fowlkes CC, Hendriks CL, Keränen SV, Weber GH, Rübel O, Huang MY, Chatoor S, DePace AH, Simirenko L, Henriquez C, Beaton A, Weiszmann R, Celniker S, Hamann B, Knowles DW, ... ... Eisen MB, et al. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 133: 364-74. PMID 18423206 DOI: 10.1016/j.cell.2008.01.053  1
2008 Lee C, Li X, Hechmer A, Eisen M, Biggin MD, Venters BJ, Jiang C, Li J, Pugh BF, Gilmour DS. NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Molecular and Cellular Biology. 28: 3290-300. PMID 18332113 DOI: 10.1128/MCB.02224-07  1
2008 Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, ... ... Eisen MB, et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. Plos Biology. 6: e27. PMID 18271625 DOI: 10.1371/journal.pbio.0060027  1
2008 Misulovin Z, Schwartz YB, Li XY, Kahn TG, Gause M, MacArthur S, Fay JC, Eisen MB, Pirrotta V, Biggin MD, Dorsett D. Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma. 117: 89-102. PMID 17965872 DOI: 10.1007/s00412-007-0129-1  1
2008 Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Hou CC, Ogawa N, Inwood W, Sementchenko V, Beaton A, ... ... Eisen MB, et al. Correction: Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm (PLoS Biology (2008) 6,2 (e27) DOI: 10.1371/journal.pbio.0060027) Plos Biology. 6: 1600. DOI: 10.1371/journal.pbio.0060190  1
2008 Rübel O, Weber GH, Huang MY, Bethel EW, Keränen SVE, Fowlkes CC, Hendriks CLL, DePace AH, Simirenko L, Eisen MB, Biggin MD, Hagen H, Malik J, Knowles DW, Hamann B. PointCloudXplore 2: Visual exploration of 3D gene expression Lecture Notes in Informatics (Lni), Proceedings - Series of the Gesellschaft Fur Informatik (Gi). 125-137.  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 Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, ... ... Eisen MB, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/nature06340  1
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/nature06341  1
2007 Peng H, Long F, Zhou J, Leung G, Eisen MB, Myers EW. Automatic image analysis for gene expression patterns of fly embryos. Bmc Cell Biology. 8: S7. PMID 17634097 DOI: 10.1186/1471-2121-8-S1-S7  1
2006 Keränen SV, Fowlkes CC, Luengo Hendriks CL, Sudar D, Knowles DW, Malik J, Biggin MD. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics. Genome Biology. 7: R124. PMID 17184547 DOI: 10.1186/gb-2006-7-12-r124  1
2006 Luengo Hendriks CL, Keränen SV, Fowlkes CC, Simirenko L, Weber GH, DePace AH, Henriquez C, Kaszuba DW, Hamann B, Eisen MB, Malik J, Sudar D, Biggin MD, Knowles DW. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biology. 7: R123. PMID 17184546 DOI: 10.1186/gb-2006-7-12-r123  1
2006 Pollard DA, Iyer VN, Moses AM, Eisen MB. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. Plos Genetics. 2: e173. PMID 17132051 DOI: 10.1371/journal.pgen.0020173  1
2006 Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, ... ... Eisen MB, et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature. 444: 499-502. PMID 17086198 DOI: 10.1038/nature05295  1
2006 Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB. Large-scale turnover of functional transcription factor binding sites in Drosophila. Plos Computational Biology. 2: e130. PMID 17040121 DOI: 10.1371/journal.pcbi.0020130  1
2006 Mintseris J, Eisen MB. Design of a combinatorial DNA microarray for protein-DNA interaction studies. Bmc Bioinformatics. 7: 429. PMID 17018151 DOI: 10.1186/1471-2105-7-429  1
2006 Pollard DA, Moses AM, Iyer VN, Eisen MB. Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. Bmc Bioinformatics. 7: 376. PMID 16904011 DOI: 10.1186/1471-2105-7-376  1
2006 Wang QF, Prabhakar S, Wang Q, Moses AM, Chanan S, Brown M, Eisen MB, Cheng JF, Rubin EM, Boffelli D. Primate-specific evolution of an LDLR enhancer. Genome Biology. 7: R68. PMID 16884525 DOI: 10.1186/gb-2006-7-8-R68  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
2006 Palmer C, Bik EM, Eisen MB, Eckburg PB, Sana TR, Wolber PK, Relman DA, Brown PO. Rapid quantitative profiling of complex microbial populations. Nucleic Acids Research. 34: e5. PMID 16407321 DOI: 10.1093/nar/gnj007  1
2006 Peng H, Long F, Eisen MB, Myers EW. Clustering gene expression patterns of fly embryos 2006 3rd Ieee International Symposium On Biomedical Imaging: From Nano to Macro - Proceedings. 2006: 1144-1147.  1
2005 Levy O, Ptacin JL, Pease PJ, Gore J, Eisen MB, Bustamante C, Cozzarelli NR. Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proceedings of the National Academy of Sciences of the United States of America. 102: 17618-23. PMID 16301526 DOI: 10.1073/pnas.0508932102  1
2005 Bourne PE, Brenner SE, Eisen MB. PLoS Computational Biology: a new community journal. Plos Computational Biology. 1: e4. PMID 16103905 DOI: 10.1371/journal.pcbi.0010004  1
2005 Fraser HB, Khaitovich P, Plotkin JB, Pääbo S, Eisen MB. Aging and gene expression in the primate brain. Plos Biology. 3: e274. PMID 16048372 DOI: 10.1371/journal.pbio.0030274  1
2005 Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC. Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology. 6: 402. PMID 15998463 DOI: 10.1186/gb-2005-6-7-402  1
2005 Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, Feldman MW. Functional genomic analysis of the rates of protein evolution. Proceedings of the National Academy of Sciences of the United States of America. 102: 5483-8. PMID 15800036 DOI: 10.1073/pnas.0501761102  1
2005 Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC. Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology. 6: R23. PMID 15774024 DOI: 10.1186/gb-2005-6-3-r23  1
2005 Nix DA, Eisen MB. GATA: a graphic alignment tool for comparative sequence analysis. Bmc Bioinformatics. 6: 9. PMID 15655071 DOI: 10.1186/1471-2105-6-9  1
2005 Van Zwet EW, Kechris KJ, Bickel PJ, Eisen MB. Estimating motifs under order restrictions Statistical Applications in Genetics and Molecular Biology. 4: 16P.  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 Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biology. 5: R61. PMID 15345045 DOI: 10.1186/gb-2004-5-9-r61  1
2004 Kechris KJ, van Zwet E, Bickel PJ, Eisen MB. Detecting DNA regulatory motifs by incorporating positional trends in information content. Genome Biology. 5: R50. PMID 15239835 DOI: 10.1186/gb-2004-5-7-r50  1
2004 Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Correction: Benchmarking tools for the alignment of functional noncoding DNA. Bmc Bioinformatics. 5: 73. PMID 15186509 DOI: 10.1186/1471-2105-5-73  1
2004 Fraser HB, Hirsh AE, Wall DP, Eisen MB. Coevolution of gene expression among interacting proteins. Proceedings of the National Academy of Sciences of the United States of America. 101: 9033-8. PMID 15175431 DOI: 10.1073/pnas.0402591101  1
2004 Fraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB. Noise minimization in eukaryotic gene expression. Plos Biology. 2: e137. PMID 15124029 DOI: 10.1371/journal.pbio.0020137  1
2004 Fay JC, McCullough HL, Sniegowski PD, Eisen MB. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biology. 5: R26. PMID 15059259 DOI: 10.1186/gb-2004-5-4-r26  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
2004 Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Benchmarking tools for the alignment of functional noncoding DNA. Bmc Bioinformatics. 5: 6. PMID 14736341 DOI: 10.1186/1471-2105-5-6  1
2004 Eisen MB, Brown PO, Varmus HE. PLoS Medicine - A medical journal for the internet age Plos Medicine. 1: 002-003. DOI: 10.1371/journal.pmed.0010031  1
2003 Brown PO, Eisen MB, Varmus HE. Why PLoS became a publisher. Plos Biology. 1: E36. PMID 14551926 DOI: 10.1371/journal.pbio.0000036  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
2002 Gasch AP, Eisen MB. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biology. 3: RESEARCH0059. PMID 12429058  1
2002 Eisen MB, Brown PO, Varmus HE. Public-access group supports PubMed Central. Nature. 419: 111. PMID 12226637 DOI: 10.1038/419111c  1
2002 Kele? S, van der Laan M, Eisen MB. Identification of regulatory elements using a feature selection method. Bioinformatics (Oxford, England). 18: 1167-75. PMID 12217908  1
2002 Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proceedings of the National Academy of Sciences of the United States of America. 99: 757-62. PMID 11805330 DOI: 10.1073/pnas.231608898  1
2001 Sørlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proceedings of the National Academy of Sciences of the United States of America. 98: 10869-74. PMID 11553815 DOI: 10.1073/pnas.191367098  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
2001 Roberts RJ, Varmus HE, Ashburner M, Brown PO, Eisen MB, Khosla C, Kirschner M, Nusse R, Scott M, Wold B. Information access. Building a "GenBank" of the published literature. Science (New York, N.Y.). 291: 2318-9. PMID 11269300  1
2001 Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Sato K, Tokusumi Y, Kikuchi N, Ishii Y, ... ... Eisen MB, et al. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proceedings of the National Academy of Sciences of the United States of America. 98: 2199-204. PMID 11226216 DOI: 10.1073/pnas.041605498  1
2001 Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM. The Stanford Microarray Database. Nucleic Acids Research. 29: 152-5. PMID 11125075  1
2000 Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, Chan WC, Botstein D, Brown P. 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome Biology. 1: RESEARCH0003. PMID 11178228 DOI: 10.1186/gb-2000-1-2-research0003  1
2000 Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell. 11: 4241-57. PMID 11102521  1
2000 Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lønning PE, et al. Molecular portraits of human breast tumours. Nature. 406: 747-52. PMID 10963602 DOI: 10.1038/35021093  1
2000 Lossos IS, Alizadeh AA, Eisen MB, Chan WC, Brown PO, Botstein D, Staudt LM, Levy R. Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas. Proceedings of the National Academy of Sciences of the United States of America. 97: 10209-13. PMID 10954754 DOI: 10.1073/pnas.180316097  1
2000 Belenkiy R, Haefele A, Eisen MB, Wohlrab H. The yeast mitochondrial transport proteins: new sequences and consensus residues, lack of direct relation between consensus residues and transmembrane helices, expression patterns of the transport protein genes, and protein-protein interactions with other proteins. Biochimica Et Biophysica Acta. 1467: 207-18. PMID 10930523 DOI: 10.1016/S0005-2736(00)00222-4  1
2000 Diehn M, Eisen MB, Botstein D, Brown PO. Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nature Genetics. 25: 58-62. PMID 10802657 DOI: 10.1038/75603  1
2000 Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, et al. A gene expression database for the molecular pharmacology of cancer. Nature Genetics. 24: 236-44. PMID 10700175 DOI: 10.1038/73439  1
2000 Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, et al. Systematic variation in gene expression patterns in human cancer cell lines. Nature Genetics. 24: 227-35. PMID 10700174 DOI: 10.1038/73432  1
2000 Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 403: 503-11. PMID 10676951 DOI: 10.1038/35000501  1
2000 Post DG, Eisen MB. How long is the coastline of the law? Thoughts on the fractal nature of legal systems Journal of Legal Studies. 29: 545.  1
1999 Johannes G, Carter MS, Eisen MB, Brown PO, Sarnow P. Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proceedings of the National Academy of Sciences of the United States of America. 96: 13118-23. PMID 10557283 DOI: 10.1073/pnas.96.23.13118  1
1999 Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nature Genetics. 23: 41-6. PMID 10471496 DOI: 10.1038/12640  1
1999 Perou CM, Jeffrey SS, van de Rijn M, Rees CA, Eisen MB, Ross DT, Pergamenschikov A, Williams CF, Zhu SX, Lee JC, Lashkari D, Shalon D, Brown PO, Botstein D. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proceedings of the National Academy of Sciences of the United States of America. 96: 9212-7. PMID 10430922 DOI: 10.1073/pnas.96.16.9212  1
1999 Eisen MB, Brown PO. DNA arrays for analysis of gene expression. Methods in Enzymology. 303: 179-205. PMID 10349646 DOI: 10.1016/S0076-6879(99)03014-1  1
1999 Bassett DE, Eisen MB, Boguski MS. Gene expression informatics--it's all in your mine. Nature Genetics. 21: 51-5. PMID 9915502 DOI: 10.1038/4478  1
1999 Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JC, Trent JM, Staudt LM, Hudson J, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO. The transcriptional program in the response of human fibroblasts to serum. Science (New York, N.Y.). 283: 83-7. PMID 9872747 DOI: 10.1126/science.283.5398.83  1
1998 Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America. 95: 14863-8. PMID 9843981 DOI: 10.1073/pnas.95.25.14863  1
1998 Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell. 9: 3273-97. PMID 9843569  1
1997 Eisen MB, Sabesan S, Skehel JJ, Wiley DC. Binding of the influenza A virus to cell-surface receptors: structures of five hemagglutinin-sialyloligosaccharide complexes determined by X-ray crystallography. Virology. 232: 19-31. PMID 9185585 DOI: 10.1006/viro.1997.8526  1
1994 Eisen MB, Wiley DC, Karplus M, Hubbard RE. HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site. Proteins. 19: 199-221. PMID 7937734 DOI: 10.1002/prot.340190305  1
1992 Sauter NK, Glick GD, Crowther RL, Park SJ, Eisen MB, Skehel JJ, Knowles JR, Wiley DC. Crystallographic detection of a second ligand binding site in influenza virus hemagglutinin. Proceedings of the National Academy of Sciences of the United States of America. 89: 324-8. PMID 1729702  1
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