Michael Eisen Publications

Eisen Lab Research Publications

• Rosenblum EB, Stajich JE, Maddox N and Eisen MB (2008). Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. PNAS in press.
• Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, et al. (2008). Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 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. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing:489-500.
• 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.
• Fowlkes CC, Hendriks CL, Keränen SV, Weber GH, Rübel O, Huang MY, Chatoor S, DePace AH, Simirenko L, Henriquez C, Beaton A, et al. (2008). A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell 133(2):364-74.
• 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 8 Suppl 1:S7.
• Drosophila 12 Genomes Consortium: Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, et al. (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature 450(7167):203-18.
• Shultzaberger RK, Chiang DY, Moses AM, Eisen MB (2007). Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. PLoS ONE 2(11):e1199.
• Mintseris J, Eisen MB (2006). Design of a combinatorial DNA microarray for protein-DNA interaction studies. BMC Bioinformatics 7:429.
• Chiang DY, Nix DA, Shultzaberger RK, Gasch AP, Eisen MB (2006). Flexible promoter architecture requirements for coactivator recruitment. BMC Mol Biol 7:16.
• 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 7:376.
• Luengo Hendriks CL, Keränen SV, Fowlkes CC, Simirenko L, Weber GH, DePace AH, Henriquez C, Kaszuba DW, Hamann B, Eisen MB, Malik J, et al. (2006). Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol 7(12):R123.
• 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 Comput Biol 2(10):e130.
• 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 Genet 2(10):e173.
• Nix DA, Eisen MB (2005). GATA: a graphic alignment tool for comparative sequence analysis. BMC Bioinformatics 6:9.
• van Zwet EW, Kechris KJ, Bickel PJ, Eisen MB (2005). Estimating motifs under order restrictions. Statistical applications in genetics and molecular biology 4:Article1.
• Fraser HB, Khaitovich P, Plotkin JB, Pääbo S, Eisen MB (2005). Aging and gene expression in the primate brain. PLoS Biol 3(9):e274.
• Kechris KJ, van Zwet E, Bickel PJ, Eisen MB (2004). Detecting DNA regulatory motifs by incorporating positional trends in information content. Genome Biol 5(7):R50.
• 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 5(4):R26.
• Fraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB (2004). Noise minimization in eukaryotic gene expression. PLoS Biol 2(6):e137.
• 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. Genome Biol 5(12):R98.
• Fraser HB, Hirsh AE, Wall DP, Eisen MB (2004). Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci USA 101(24):9033-8.
• Moses AM, Chiang DY, Eisen MB (2004). Phylogenetic motif detection by expectation-maximization on evolutionary mixtures. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing:324-35.
• 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 2(12):e398.
• Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB (2004). Correction: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 5:73.
• Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB (2004). Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 5:6.
• 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 5(9):R61.
• 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 3:19.
• 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 4(7):R43.
• Keles S, van der Laan MJ, Dudoit S, Xing B, Eisen MB (2003). Supervised detection of regulatory motifs in DNA sequences. Statistical applications in genetics and molecular biology 2:Article5.
• Keleş S, van der Laan M, Eisen MB (2002). Identification of regulatory elements using a feature selection method. Bioinformatics 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 USA 99(2):757-62.
• Gasch AP, Eisen MB (2002). Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol 3(11):RESEARCH0059.
• Chiang DY, Brown PO, Eisen MB (2001). Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics 17 Suppl 1:S49-55.

Eisen Lab Collaborations

• Misulovin Z, Schwartz YB, Li XY, Kahn TG, Gause M, MacArthur S, Fay JC, Eisen MB, Pirrotta V, Biggin MD, Dorsett D (2008). Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma 117(1):89-102.
• Pfeiffer BD, Jenett A, Hammonds AS, Ngo TT, Misra S, Murphy C, Scully A, Carlson JW, Wan KH, Laverty TR, Mungall C, et al. (2008). Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci USA 105(28):9715-20.
• Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, et al. (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450(7167):219-32.
• 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 34(1):e5.
• Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, et al. (2006). In vivo enhancer analysis of human conserved non-coding sequences. Nature 444(7118):499-502.
• 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 7(8):R68.
• Salzberg SL, Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC (2005). Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol 6(3):R23.
• 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 USA 102(49):17618-23.
• 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 USA 102(15):5483-8.
• 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 6(7):402.

Michael Eisen Postdoctoral Work (w/Patrick O. Brown and David Botstein at Stanford)

• Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, et al. (2001). The Stanford Microarray Database. Nucleic Acids Res 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, et al. (2001). Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 98(19):10869-74.
• Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, et al. (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 USA 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 USA 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 proteins. Biochim Biophys Acta 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 25(1):58-62.
• Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, et al. (2000). Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403(6769):503-11.
• Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, et al. (2000). A gene expression database for the molecular pharmacology of cancer. Nat Genet 24(3):236-44.
• 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 1(2):RESEARCH0003.
• Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, et al. (2000). Molecular portraits of human breast tumours. Nature 406(6797):747-52.
• Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, van de Rijn M, Waltham M, Pergamenschikov A, et al. (2000). Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 24(3):227-35.
• Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000). Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11(12):4241-57.
• Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JC, Trent JM, Staudt LM, Hudson J, Boguski MS, Lashkari D, et al. (1999). The transcriptional program in the response of human fibroblasts to serum. Science 283(5398):83-7.
• 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 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, et al. (1999). Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA 96(16):9212-7.
• 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 USA 96(23):13118-23.
• 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 9(12):3273-97.
• Eisen MB, Spellman PT, Brown PO, Botstein D (1998). Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95(25):14863-8.

Michael Eisen Graduate Work (w/Don C. Wiley at Harvard)

• 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 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 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 USA 89(1):324-8.

Michael Eisen Essays and Reviews

• Bourne PE, Brenner SE, Eisen MB (2005). PLoS Computational Biology: a new community journal. PLoS Comput Biol 1(1):e4.
• Brown PO, Eisen MB, Varmus HE (2003). Why PLoS became a publisher. PLoS Biol 1(1):E36.
• Eisen MB, Brown PO, Varmus HE (2002). Public-access group supports PubMed Central. Nature 419(6903):111.
• Roberts RJ, Varmus HE, Ashburner M, Brown PO, Eisen MB, Khosla C, Kirschner M, Nusse R, Scott M, Wold B (2001). Information access. Building a "GenBank" of the published literature. Science 291(5512):2318-9.
• Bassett DE, Eisen MB, Boguski MS (1999). Gene expression informatics--it's all in your mine. Nat Genet 21(1 Suppl):51-5.
• Eisen MB, Brown PO (1999). DNA arrays for analysis of gene expression. Meth Enzymol 303:179-205.