Harrisson MM, Li X-Y, Kaplan T, Botchan MR, Eisen MB. (2011) Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition. PLoS Genet 7(10): e1002266. doi:10.1371/journal.pgen.1002266

Fowlkes, C.C., Eckenrode, K.B., Bragdon, M.D., Meyer, M., Wunderlich, Z., Simirenko, L., Luengo Hendriks, C.L., Keränen, S.V.E., Henriquez, C., Knowles, D.W., Biggin, M.D., Eisen, M.B., DePace, A.H.. (2011) A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. PLoS Genetics, 7(10): e1002346. doi:10.1371/journal.pgen.1002346

Harrison, M.M., Li, X.-Y., Kaplan, T., Botchan M.R., and Eisen M.B.. (2011) Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition. PLoS Genet 7(10): e1002266. doi:10.1371/journal.pgen.1002266

Kaplan T, Li X-Y, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB. (2011) Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development. PLoS Genet 7(2): e1001290. doi:10.1371/journal.pgen.1001290

Lott SE, Villalta JE, Schroth GP, Luo S, Tonkin LA, Eisen MB. (2011) Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq. PLoS Biol 9(2): e1000590. doi:10.1371/journal.pbio.100059

Li, X-Y, Thomas, S., Sabo, P.J., Eisen, M.B., Stamatoyannopoulos. J.A., and Biggin, M.D.. (2011) The Role of Chromatin Accessibility in Directing the Widespread, Overlapping Patterns of Drosophila Transcription Factor Binding. Genome Biology 12, R34

Thomas, S., Li, X.-Y., Sabo, P.J., Sandstrom, R., Thurman, R., Canfield, T.K, Giste, E., Fisher, W., Hammonds, A., Celniker, S.E., Eisen, M.B., Biggin, M.D., and Stamatoyannopoulos, J.A.. (2011) Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biology 12, R43

Liu Z,Scannell DR, Eisen MB, Tjian R. (2011) Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3. Cell. 2011 Sep 2;146(5):720-31

Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB. (2010) Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol. 2010 Mar 23;8(3):e1000343

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. (2010) Integrating data clustering and visualization for the analysis of 3D gene expression data. IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar;7(1):64-79

Lusk RW, Eisen MB. (2010) Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers. PLoS Genet. 2010 Jan 22;6(1):e1000829

Shultzaberger RK, Malashock DS, Kirsch JF, Eisen MB. (2010) The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts. PLoS Genet. 2010 July; 6(7): e1001042

Levin TC, Glazer AM, Pachter L, Brem RB, Eisen MB. (2010) Exploring the genetic basis of variation in gene predictions with a synthetic association study. PLoS One. 2010 Jul 29;5(7):e11645

Leung G, Eisen MB. (2009) Identifying cis-regulatory sequences by word profile similarity. PLoS One. 2009 Sep 4;4(9):e6901

Rosenblum EB, Poorten TJ, Settles M, Murdoch GK, Robert J, Maddox N, Eisen MB. (2009) Genome-wide transcriptional response of Silurana (Xenopus) tropicalis to infection with the deadly chytrid fungus. PLoS One. 2009 Aug 4;4(8):e6494

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. (2009) Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol. 2009;10(7):R80. Epub 2009 Jul 23

Teytelman L, Özaydin B, Zill O, Lefrançois P, Snyder M, Rine J, Eisen MB. (2009) Impact of chromatin structures on DNA processing for genomic analyses. PLoS One. 2009 Aug 20;4(8):e6700

Jans J, Gladden JM, Ralston EJ, Pickle CS, Michel AH, Pferdehirt RR, Eisen MB, Meyer BJ. (2009) A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome. Genes Dev. 2009 Mar 1;23(5):602-18

Peterson BK, Hare EE, Iyer VN, Storage S, Conner L, Papaj DR, Kurashima R, Jang E, Eisen MB. (2009) Big Genomes Facilitate the Comparative Identification of Regulatory Elements. PLoS ONE 4(3): e4688. doi:10.1371/journal.pone.0004688

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, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 2008 Feb;6(2):e27

Lusk RW, Eisen MB. (2008) Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast. Pac Symp Biocomput. 2008;:489-500

Rosenblum EB, Stajich JE, Maddox N, Eisen MB. (2008) Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. Proc Natl Acad Sci U S A. 2008 Oct 13

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, Celniker SE, Rubin GM. (2008) Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9715-20. Epub 2008 Jul 9

Fowlkes CC, Hendriks CL, Ker&aumel;nen SV, Weber GH, R&uumel;bel O, Huang MY, Chatoor S, DePace AH, Simirenko L, Henriquez C, Beaton A, Weiszmann R, Celniker S, Hamann B, Knowles DW, Biggin MD, Eisen MB, Malik J. (2008) A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 2008 Apr 18;133(2):364-74

Hare EE, Peterson BK, Eisen MB. (2008) A careful look at binding site reorganization in the even-skipped enhancers of Drosophila and sepsids.. PLoS Genet. 2008 November; 4(11): e1000268.

Teytelman L, Eisen MB, Rine J. (2008) Silent but not static: accelerated base-pair substitution in silenced chromatin of budding yeasts.. PLoS Genet. 2008 Nov;4(11):e1000247.

Rosenblum EB, Stajich JE, Maddox N, Eisen MB. (2008) Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis.. Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17034-9.

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, Celniker SE, Rubin GM. (2008) Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9715-20.

Hare EE, Peterson BK, Iyer VN, Meier R, Eisen MB. (2008) Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation. PLoS Genet 4(6): e1000106. doi:10.1371/journal.pgen.1000106

Shultzaberger RK, Chiang DY, Moses AM, Eisen MB. (2007) Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. PLoS ONE. 2007 Nov 21;2(11):e1199

Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maede. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007 Nov 8;450(7167):219-32

Drosophila 12 Genomes Consortium, et. al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18

Misulovin Z, Schwartz YB, Li XY, Kahn TG, Gause M, MacArthur S, Fay JC, Eisen MB, Pirrotta V, Biggin MD, Dorsett D. (2007) Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma. 2008 Feb;117(1):89-102. Epub 2007 Oct 27

Peng H, Long F, Zhou J, Leung G, Eisen MB, Myers EW. (2007) Automatic image analysis for gene expression patterns of fly embryos. BMC Cell Biol. 2007 Jul 10;8 Suppl 1:S7

Pollard DA, Iyer VN, Moses AM, Eisen MB. (2006) Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genetics

Palmer C, Bik EM, Eisen MB, Eckburg PB, Sana TR, Wolber PK, Relman DA, Brown PO. (2006) Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res. 2006 Jan 10;34(1):e5

Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB. (2006) Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Computational Biology 2(10):e130

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. (2006) Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol. 2006;7(12):R123

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, Couronne O, Eisen MB, Visel A, Rubin EM. (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006 Nov 23;444(7118):499-502. Epub 2006 Nov 5

Mintseris J, Eisen MB. (2006) Design of a combinatorial DNA microarray for protein-DNA interaction studies. BMC Bioinformatics. 2006 Oct 3;7:429

Pollard DA, Moses AM, Iyer VN, Eisen MB. (2006) Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. BMC Bioinformatics. 2006 Aug 14;7:376

Wang QF, Prabhakar S, Wang Q, Moses AM, Chanan S, Brown M, Eisen MB, Cheng JF, Rubin EM, Boffelli D. (2006) Primate-specific evolution of an LDLR enhancer. Genome Biol. 2006;7(8):R68. Epub 2006 Aug 2

Chiang DY, Nix DA, Shultzaberger RK, Gasch AP, Eisen MB. (2006) Flexible promoter architecture requirements for coactivator recruitment. BMC Mol Biol. 2006 Apr 28;7:16

van Zwet EW, Kechris KJ, Bickel PJ, Eisen MB. (2005) Estimating motifs under order restrictions. Stat Appl Genet Mol Biol. 2005;4:Article1. Epub 2005 Jan 10

Levy O, Ptacin JL, Pease PJ, Gore J, Eisen MB, Bustamante C, Cozzarelli NR. (2005) Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17618-23. Epub 2005 Nov 21

Bourne PE, Brenner SE, Eisen MB. (2005) PLoS Computational Biology: a new community journal. PLoS Comput Biol. 2005 Jun;1(1):e4

Fraser HB, Khaitovich P, Plotkin JB, Pääbo S, Eisen MB. (2005) Aging and gene expression in the primate brain. PLoS Biol. 2005 Sep;3(9):e274. Epub 2005 Aug 2

Eisen MB. (2005) All motifs are not created equal: structural properties of transcription factor - dna interactions and the inference of sequence specificity. Genome Biology 6:P7

Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC. (2005) Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.. Genome Biol. 2005;6(7):402. Epub 2005 Jun 24

Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, Feldman MW. (2005) Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5483-8. Epub 2005 Mar 30

Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC. (2005) Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol. 2005;6(3):R23. Epub 2005 Feb 22

Nix DA, Eisen MB. (2005) GATA: a graphic alignment tool for comparative sequence analysis. BMC Bioinformatics. 2005 Jan 17;6:9

Fraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB. (2004) Noise minimization in eukaryotic gene expression. PLoS Biol. 2004 Jun;2(6):e137. Epub 2004 Apr 27

Fay JC, McCullough HL, Sniegowski PD, Eisen MB. (2004) Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biol. 2004;5(4):R26. Epub 2004 Mar 24

Moses AM, Chiang DY, Eisen MB. (2004) Phylogenetic motif detection by expectation-maximization on evolutionary mixtures. Pac Symp Biocomput. 2004;:324-35

Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. (2004) Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics. 2004 Jan 21;5:6

Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB. (2004) MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. enome Biol. 2004;5(12):R98. Epub 2004 Nov 30

Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB. (2004) Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol. 2004 Dec;2(12):e398. Epub 2004 Nov 9

Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE. (2004) Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol. 2004;5(9):R61. Epub 2004 Aug 20

Kechris KJ, van Zwet E, Bickel PJ, Eisen MB. (2004) Detecting DNA regulatory motifs by incorporating positional trends in information content. Genome Biol. 2004;5(7):R50. Epub 2004 Jun 24

Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. (2004) Correction: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics. 2004 Jun 8;5:73

Fraser HB, Hirsh AE, Wall DP, Eisen MB. (2004) Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9033-8. Epub 2004 Jun 2

Keles S, van der Laan MJ, Dudoit S, Xing B, Eisen MB. (2003) Supervised detection of regulatory motifs in DNA sequences. 2003;2:Article5. Epub 2003 Aug 25

Brown PO, Eisen MB, Varmus HE. (2003) Why PLoS became a publisher. PLoS Biol. 2003 Oct;1(1):E36. Epub 2003 Oct 13

Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB. (2003) Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol. 2003 Aug 28;3:19. Epub 2003 Aug 28

Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB. (2003) Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol. 2003;4(7):R43. Epub 2003 Jun 26

Gasch AP, Eisen MB. (2002) Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol. 2002 Oct 10;3(11)

Keleş S, van der Laan M, Eisen MB. (2002) Identification of regulatory elements using a feature selection method. Bioinformatics. 2002 Sep;18(9):1167-75

Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB. (2002) Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):757-62

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. (2001) The Stanford Microarray Database. Nucleic Acids Res. 2001 Jan 1;29(1):152-5

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, Eystein Lønning P, Børresen-Dale AL. (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10869-74

Chiang DY, Brown PO, Eisen MB. (2001) Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics. 2001;17 Suppl 1:S49-55

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, Hamaguchi Y, Nishizuka I, Goto H, Nitanda H, Satomi S, Yoshiki A, Kusakabe M, DeRisi JL, Eisen MB, Iyer VR, . (2001) Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2199-204

Lossos IS, Alizadeh AA, Eisen MB, Chan WC, Brown PO, Botstein D, Staudt LM, Levy R. (2000) Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10209-13

Belenkiy R, Haefele A, Eisen MB, Wohlrab H. (2000) 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. Biochim Biophys Acta. 2000 Jul 31;1467(1):207-18

Diehn M, Eisen MB, Botstein D, Brown PO. (2000) Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nat Genet. 2000 May;25(1):58-62

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, Brown PO, Weinstein JN. (2000) A gene expression database for the molecular pharmacology of cancer. Nat Genet. 2000 Mar;24(3):236-44

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, Weinstein JN, Botstein D, Brown PO. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 2000 Mar;24(3):227-35

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 Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Le. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000 Feb 3;403(6769):503-11

Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, Chan WC, Botstein D, Brown P. (2000) ‘Gene Shaving’ as a method for identifying distinct sets of genes with similar expression patterns. Genome Biol. 2000;1(2)

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, Børresen-Dale AL, Brown PO, Botstein D. (2000) Molecular portraits of human breast tumours. Nature. 2000 Aug 17;406(6797):747-52

Johannes G, Carter MS, Eisen MB, Brown PO, Sarnow P. (1999) Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13118-23

Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO. (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet. 1999 Sep;23(1):41-6

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. (1999) Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9212-7

Eisen MB, Brown PO. (1999) DNA arrays for analysis of gene expression. Methods Enzymol. 1999;303:179-205

Bassett DE Jr, Eisen MB, Boguski MS. (1999) Gene expression informatics–it’s all in your mine. Nat Genet. 1999 Jan;21(1 Suppl):51-5

Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JC, Trent JM, Staudt LM, Hudson J Jr, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO. (1999) The transcriptional program in the response of human fibroblasts to serum. Science. 1999 Jan 1;283(5398):83-7

Alizadeh A, Eisen M, Botstein D, Brown PO, Staudt LM. (1998) Probing Lymphocyte Biology by Genomic-Scale Gene Expression Analysis. J Clin Immunol 18, 373-9

Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. (1998) The Transcriptional Program of Sporulation in Budding Yeast. Science 282, 699-705

Eisen MB, Spellman PT, Brown PO, Botstein D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8

Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 1998 Dec;9(12):3273-97

Eisen MB, Sabesan S, Skehel JJ, Wiley DC. (1997) Binding of the influenza A virus to cell-surface receptors: structures of five hemagglutinin-sialyloligosaccharide complexes determined by X-ray crystallography. Virology. 1997 May 26;232(1):19-31

Eisen MB, Wiley DC, Karplus M, Hubbard RE. (1994) HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site. Proteins. 1994 Jul;19(3):199-221

Sauter NK, Glick GD, Crowther RL, Park SJ, Eisen MB, Skehel JJ, Knowles JR, Wiley DC. (1992) Crystallographic detection of a second ligand binding site in influenza virus hemagglutinin. Proc Natl Acad Sci U S A. 1992 Jan 1;89(1):324-8

Kimmel AR, Eisen MB. (1988) Regulation of Gene Expression by the Intracellular Second Messengers Ip3 and Diacylglycerol. Dev Genet 9, 351-8