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Recent Papers
Discordance of gene and species trees in Drosophila
Large-scale turnover of functional transcription-factor binding sites in Drosophila

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

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.

Pollard DA, Moses AM, Iyer VN and Eisen MB. Detecting the limits of regulatory element conservation and divergence estimation using multiple pairwise and multiple alignments. BMC Bioinformatic 7(1):376.

Mintseris J, Eisen MB (2006). Design of a combinatorial DNA microarray for protein-DNA interaction studies. BMC Bioinformatics 7(1):429.

Chiang DY, Nix DA, Shultzaberger RK, Gasch AP, Eisen MB (2006). Flexible promoter architecture requirements for coactivator recruitment. BMC Molecular Biology 7(1):16.

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 Research 34(1):e5.

Fraser HB, Khaitovich P, Plotkin JB, Paabo S and Eisen MB (2005). Aging and Gene Expression in the Primate Brain. PLoS Biology 3(9):e274.

Levy O, Ptacin JL, Pease PJ, Gore J, Eisen MB, Bustamante C, Cozzarellu NR (2005). Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FstK translocase. PNAS102(49):17618-23.

Moses AM (2005). Molecular evolution of transcriptional regulation. Ph.D. Thesis. University of California, Berkeley.

Chiang DY (2005). Computational and Experimental Analyses of Promoter Architecture in Yeasts. Ph.D. Thesis. University of California, Berkeley.

Fraser HB (2005). Studies of evolution from a genomic perspective. Ph.D. Thesis. University of California, Berkeley.

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.

Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, Feldman MW (2005). Functional genomic analysis of the rates of protein evolution. PNAS 102(15):5483-5488.

Salzberg SL, Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB and Nelson WC. Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology 6(3):R23.

Nix DA and Eisen MB. GATA: a graphic alignment tool for comparative sequence analysis. BMC Bioinformatics 5(12):R98.

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

Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M and Eisen MB (2004). Conservation and evolution of cis-regulatory systems in Ascomycete fungi. PLoS Biology 2(12):e398.

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

Kechris KJ, van Zwet E, Bickel PJ and Eisen MB (2004). Detecting DNA regulatory motifs by incorperating positional trends in information content. Genome Biology 5(7):R50.

Fraser HB, Hirsh AE, Wall DP and Eisen MB (2004). Coevolution of gene expression among interacting protein. PNAS 101(24):9033-38.

Fraser HB, Hirsh AE, Giaever G, Kumm J and Eisen MB (2004). Noise minimization in eukaryotic gene expression. PLoS Biology 6(2):1-5.

Fay JC, McCullough HL, Sniegowski PD and Eisen MB (2004). Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biology 2004, 5:R26.

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

Moses AM, Chiang DY, Eisen MB (2004). Phylogenetic Motif Detection by Expectation Maximization of Evolutionary Mixtures. Pacific Symposium on Biocomputing.

Moses AM, Chiang DY, Kellis M, Lander ES and Eisen MB (2003). Position specific variation in the rate of evolution in transcription factor binding sites BMC Evolutionary Biology 3(19).

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

Keles S, van der Laan MJ, Dudoit S, Xing B and Eisen MB (2003). Supervised Detection of Regulatory Motifs in DNA Sequences Statistical Applications in Genetics and Molecular Biology 2(1):5.

Gasch AP and Eisen MB (2002). Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biology 3(11), 1-22.

Berman BP, Nubu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM and 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 99, 757-62.

Keles S, van der Laan M and Eisen MB (2002). Identification of regulatory elements using a feature selection method. Bioinformatics 18, 1167-75.

Sorlie 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, Lonning PE, Borresen-Dale AL. (2001). Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 98, 10869-10874.

Chiang DY, Brown PO, and Eisen MB. (2001). Visualizing Association Between Genome Sequences and Gene Expression Data Using Genome-Mean Expression Profiles. Bioinformatics S1, 49-55.

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, Brown PO, Muramatsu M, Shimada H, Okazaki Y, Hayashizaki Y. (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 98, 2199-2204.

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 and Cherry JM. (2001). The Stanford Microarray Database. Nucleic Acids Res 29, 152-5.

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, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Staudt LM (2000). Distinct Types of Diffuse Large B-Cell Lymphoma Identified by Gene Expression Profiling. Nature 403, 503-11.

Lossos IS, Alizadeh AA, Eisen MB, Chan WC, Brown PO, Botstein D, Staudt LM and 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 97, 10209-13.

Perou CM, Sorlie 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, Lonning PE, Borresen-Dale AL, Brown PO and Botstein D. (2000). Molecular Portraits of Human Breast Tumours. Nature 406, 747-52.

Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D and Brown PO. (2000). Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes. Mol Biol Cell 11, 4241-57.

Belenkiy R, Haefele A, Eisen MB and 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 Proteins. Biochim Biophys Acta 1467, 207-18.

Diehn M, Eisen MB, Botstein D and Brown PO. (2000). Large-Scale Identification of Secreted and Membrane-Associated Gene Products Using DNA Microarrays. Nat Genet 25, 58-62.

Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, Chan WC, Botstein D and Brown P. (2000). 'Gene Shaving' as a Method for Identifying Distinct Sets of Genes with Similar Expression Patterns. GenomeBiology.com 1,

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 and Brown PO. (2000). Systematic Variation in Gene Expression Patterns in Human Cancer Cell Lines. Nat Genet 24, 227-35.

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 and Weinstein JN. (2000). A Gene Expression Database for the Molecular Pharmacology of Cancer. Nat Genet 24, 236-44.

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 and Brown PO. (1999). The Transcriptional Program in the Response of Human Fibroblasts to Serum. Science 283, 83-7.

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 and Botstein D. (1999). Distinctive Gene Expression Patterns in Human Mammary Epithelial Cells and Breast Cancers. Proc Natl Acad Sci U S A 96, 9212-7.

Johannes G, Carter MS, Eisen MB, Brown PO and 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 96, 13118-23.

Eisen MB and Brown PO. (1999). DNA Arrays for Analysis of Gene Expression. Methods Enzymol 303, 179-205.

Bassett DE, Eisen MB and Boguski MS. (1999). Gene Expression Informatics--It's All in Your Mine. Nat Genet 21, 51-5.

Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D and Brown PO. (1999). Genome-Wide Analysis of DNA Copy-Number Changes Using cDNA Microarrays. Nat Genet 23, 41-6.

Eisen MB, Spellman PT, Brown PO and Botstein D. (1998). Cluster Analysis and Display of Genome-Wide Expression Patterns. Proc Natl Acad Sci U S A 95, 14863-8.

Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D and Futcher B. (1998). Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces Cerevisiae by Microarray Hybridization. Mol Biol Cell 9, 3273-97.

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

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

Eisen MB, Sabesan S, Skehel JJ and 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 232, 19-31.

Eisen MB, Wiley DC, Karplus M and Hubbard RE. (1994). HOOK: A Program for Finding Novel Molecular Architectures That Satisfy the Chemical and Steric Requirements of a Macromolecule Binding Site. Proteins 19, 199-221.

Sauter NK, Glick GD, Crowther RL, Park SJ, Eisen MB, Skehel JJ, Knowles JR and Wiley DC. (1992). Crystallographic Detection of a Second Ligand Binding Site in Influenza Virus Hemagglutinin. Proc Natl Acad Sci U S A 89, 324-8.

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