Michael Eisen, Ph.D.

Lab Head from 2000

Ph.D. in 1996 in Biophysics with Don Wiley


Elya C, Zhang V, Ludington W, Eisen MB (2016). Stable host gene expression in the gut of adult Drosophila melanogaster with different bacterial mono-associations.
Preprint  

Combs PA, Eisen MB (2016). Genome-wide measurement of spatial expression in patterning mutants of Drosophila melanogaster.
Preprint  

Kuntz SG, Eisen MB (2015). Oxygen changes drive non-uniform scaling in Drosophila melanogaster embryogenesis.
Journal  Preprint  Data:Figshare  

Paris M, Villalta JE, Eisen MB, Lott SE (2015). Sex Bias and Maternal Contribution to Gene Expression Divergence in Drosophila Blastoderm Embryos.
Journal  PubMed  PMC  Data:GEO  

Harrison MM, Eisen MB (2015). Transcriptional Activation of the Zygotic Genome in Drosophila.
Journal  PubMed  

Bourne PE, Brenner SE, Eisen MB (2015). Ten Years of PLoS Computational Biology: A Decade of Appreciation and Innovation.
Journal  PubMed  PMC  

Combs PA, Eisen MB (2015). Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols.
Journal  PubMed  PMC  Web  Data:GEO  

Schiabor KM, Quan AS, Eisen MB (2014). Saccharomyces cerevisiae mitochondria are required for optimal attractiveness to Drosophila melanogaster.
Journal  PubMed  PMC  Preprint  

MacManes MD, Eisen MB (2014). Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus.
Journal  PubMed  PMC  Preprint  Data:SRA  Data:DRYAD  

Li XY, Harrison MM, Villalta JE, Kaplan T, Eisen MB (2014). Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition.
Journal  PubMed  PMC  Preprint  Data:GEO  

Chen ZX, Sturgill D, Qu J, Jiang H, Park S et al. (2014). Comparative validation of the D. melanogaster modENCODE transcriptome annotation.
Journal  PubMed  PMC  

Wong VL, Ellison CE, Eisen MB, Pachter L, Brem RB (2014). Structural variation among wild and industrial strains of Penicillium chrysogenum.
Journal  PubMed  PMC  

Kuntz SG, Eisen MB (2014). Drosophila embryogenesis scales uniformly across temperature in developmentally diverse species.
Journal  PubMed  PMC  Preprint  Data:DRYAD  

Lott SE, Villalta JE, Zhou Q, Bachtrog D, Eisen MB (2014). Sex-specific embryonic gene expression in species with newly evolved sex chromosomes.
Journal  PubMed  PMC  Data:GEO  

Paris M, Kaplan T, Li XY, Villalta JE, Lott SE et al. (2013). Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression.
Journal  PubMed  PMC  Web  Data:GEO  

Ingram WM, Goodrich LM, Robey EA, Eisen MB (2013). Mice infected with low-virulence strains of Toxoplasma gondii lose their innate aversion to cat urine, even after extensive parasite clearance.
Journal  PubMed  PMC  

Combs PA, Eisen MB (2013). Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.
Journal  PubMed  PMC  Web  Data:GEO  

MacManes MD, Eisen MB (2013). Improving transcriptome assembly through error correction of high-throughput sequence reads.
Journal  PubMed  PMC  Data:DRYAD  Software:SCRIPTS  

Ali-Murthy Z, Lott SE, Eisen MB, Kornberg TB (2013). An essential role for zygotic expression in the pre-cellular Drosophila embryo.
Journal  PubMed  PMC  Web  

Rands CM, Darling A, Fujita M, Kong L, Webster MT et al. (2013). Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence.
Journal  PubMed  PMC  

Zhou H, Kaplan T, Li Y, Grubisic I, Zhang Z et al. (2013). Dual functions of TAF7L in adipocyte differentiation.
Journal  PubMed  PMC  Web  

Lusk RW, Eisen MB (2013). Spatial promoter recognition signatures may enhance transcription factor specificity in yeast.
Journal  PubMed  PMC  

Teytelman L, Osborne Nishimura EA, Ozaydin B, Eisen MB, Rine J (2012). The enigmatic conservation of a Rap1 binding site in the Saccharomyces cerevisiae HMR-E silencer.
Journal  PubMed  PMC  

Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD et al. (2012). DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila.
Journal  PubMed  PMC  

Hu TT, Eisen MB, Thornton KR, Andolfatto P (2012). A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.
Journal  PubMed  PMC  

Shultzaberger RK, Maerkl SJ, Kirsch JF, Eisen MB (2012). Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain.
Journal  PubMed  PMC  

Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ et al. (2011). The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus.
Journal  PubMed  PMC  

Fowlkes CC, Eckenrode KB, Bragdon MD, Meyer M, Wunderlich Z et al. (2011). A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.
Journal  PubMed  PMC  

Harrison MM, Li XY, 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.
Journal  PubMed  PMC  

Liu Z, Scannell DR, Eisen MB, Tjian R (2011). Control of embryonic stem cell lineage commitment by core promoter factor, TAF3.
Journal  PubMed  PMC  

Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA et al. (2011). The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding.
Journal  PubMed  PMC  

Lott SE, Villalta JE, Schroth GP, Luo S, Tonkin LA et al. (2011). Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq.
Journal  PubMed  PMC  Web  

Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA et al. (2011). Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development.
Journal  PubMed  PMC  

Shultzaberger RK, Malashock DS, Kirsch JF, Eisen MB (2010). The fitness landscapes of cis-acting binding sites in different promoter and environmental contexts.
Journal  PubMed  PMC  

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.
Journal  PubMed  PMC  

Rubel O, Ahern S, Bethel EW, Biggin MD, Childs H et al. (2013). Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data.
Journal  PubMed  PMC  

Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L et al. (2010). Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.
Journal  PubMed  PMC  Web  

Rubel O, Weber GH, Huang MY, Bethel EW, Biggin MD et al. (2010). Integrating data clustering and visualization for the analysis of 3D gene expression data.
Journal  PubMed  

Lusk RW, Eisen MB (2010). Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers.
Journal  PubMed  PMC  

Leung G, Eisen MB (2009). Identifying cis-regulatory sequences by word profile similarity.
Journal  PubMed  PMC  

Rosenblum EB, Poorten TJ, Settles M, Murdoch GK, Robert J et al. (2009). Genome-wide transcriptional response of Silurana (Xenopus) tropicalis to infection with the deadly chytrid fungus.
Journal  PubMed  PMC  

Teytelman L, Ozaydin B, Zill O, Lefrancois P, Snyder M et al. (2009). Impact of chromatin structures on DNA processing for genomic analyses.
Journal  PubMed  PMC  

MacArthur S, Li XY, Li J, Brown JB, Chu HC et al. (2009). Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions.
Journal  PubMed  PMC  

Jans J, Gladden JM, Ralston EJ, Pickle CS, Michel AH et al. (2009). A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome.
Journal  PubMed  PMC  

Peterson BK, Hare EE, Iyer VN, Storage S, Conner L et al. (2009). Big genomes facilitate the comparative identification of regulatory elements.
Journal  PubMed  PMC  

Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE et al. (2009). Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members.
Journal  PubMed  PMC  

Garnett AT, Han TM, Gilchrist MJ, Smith JC, Eisen MB et al. (2009). Identification of direct T-box target genes in the developing zebrafish mesoderm.
Journal  PubMed  PMC  

Hare EE, Peterson BK, Eisen MB (2008). A careful look at binding site reorganization in the even-skipped enhancers of Drosophila and sepsids.
Journal  PubMed  PMC  

Teytelman L, Eisen MB, Rine J (2008). Silent but not static: accelerated base-pair substitution in silenced chromatin of budding yeasts.
Journal  PubMed  PMC  

Rosenblum EB, Stajich JE, Maddox N, Eisen MB (2008). Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis.
Journal  PubMed  PMC  

Pfeiffer BD, Jenett A, Hammonds AS, Ngo TT, Misra S et al. (2008). Tools for neuroanatomy and neurogenetics in Drosophila.
Journal  PubMed  PMC  

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.
Journal  PubMed  PMC  

Fowlkes CC, Hendriks CL, Keranen SV, Weber GH, Rubel O et al. (2008). A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm.
Journal  PubMed  

Li XY, MacArthur S, Bourgon R, Nix DA, Pollard DA et al. (2008). Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.
Journal  PubMed  PMC  

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.
PubMed  

Shultzaberger RK, Chiang DY, Moses AM, Eisen MB (2007). Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis.
Journal  PubMed  PMC  

Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L et al. (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Journal  PubMed  PMC  

Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B et al. (2007). Evolution of genes and genomes on the Drosophila phylogeny.
Journal  PubMed  Data:FLYBASE  Data:WORKING  

Misulovin Z, Schwartz YB, Li XY, Kahn TG, Gause M et al. (2007). Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome.
Journal  PubMed  PMC  

Peng H, Long F, Zhou J, Leung G, Eisen MB et al. (2007). Automatic image analysis for gene expression patterns of fly embryos.
Journal  PubMed  PMC  

Luengo Hendriks CL, Keranen SV, Fowlkes CC, Simirenko L, Weber GH et al. (2007). Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline.
Journal  PubMed  PMC  

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

Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA et al. (2006). In vivo enhancer analysis of human conserved non-coding sequences.
Journal  PubMed  

Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY et al. (2006). Large-scale turnover of functional transcription factor binding sites in Drosophila.
Journal  PubMed  PMC  Software:CisEvolver  

Mintseris J, Eisen MB (2006). Design of a combinatorial DNA microarray for protein-DNA interaction studies.
Journal  PubMed  PMC  

Pollard DA, Moses AM, Iyer VN, Eisen MB (2006). Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments.
Journal  PubMed  PMC  Software:CisEvolver  

Wang QF, Prabhakar S, Wang Q, Moses AM, Chanan S et al. (2006). Primate-specific evolution of an LDLR enhancer.
Journal  PubMed  PMC  

Chiang DY, Nix DA, Shultzaberger RK, Gasch AP, Eisen MB (2006). Flexible promoter architecture requirements for coactivator recruitment.
Journal  PubMed  PMC  

van Zwet EW, Kechris KJ, Bickel PJ, Eisen MB (2005). Estimating motifs under order restrictions.
Journal  PubMed  

Keles S, van der Laan MJ, Dudoit S, Xing B, Eisen MB (2003). Supervised detection of regulatory motifs in DNA sequences.
Journal  PubMed  

Palmer C, Bik EM, Eisen MB, Eckburg PB, Sana TR et al. (2006). Rapid quantitative profiling of complex microbial populations.
Journal  PubMed  PMC  

Levy O, Ptacin JL, Pease PJ, Gore J, Eisen MB et al. (2005). Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase.
Journal  PubMed  PMC  

Bourne PE, Brenner SE, Eisen MB (2005). PLoS Computational Biology: a new community journal.
Journal  PubMed  PMC  

Fraser HB, Khaitovich P, Plotkin JB, Paabo S, Eisen MB (2005). Aging and gene expression in the primate brain.
Journal  PubMed  PMC  

Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR et al. (2005). Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.
Journal  PubMed  PMC  

Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G et al. (2005). Functional genomic analysis of the rates of protein evolution.
Journal  PubMed  PMC  

Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR et al. (2005). Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.
Journal  PubMed  PMC  

Nix DA, Eisen MB (2005). GATA: a graphic alignment tool for comparative sequence analysis.
Journal  PubMed  PMC  

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.
Journal  PubMed  PMC  Web  Software:MONKEY  

Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M et al. (2004). Conservation and evolution of cis-regulatory systems in ascomycete fungi.
Journal  PubMed  PMC  

Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM et al. (2004). Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.
Journal  PubMed  PMC  Web  

Kechris KJ, van Zwet E, Bickel PJ, Eisen MB (2004). Detecting DNA regulatory motifs by incorporating positional trends in information content.
Journal  PubMed  PMC  

Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB (2004). Correction: Benchmarking tools for the alignment of functional noncoding DNA.
Journal  PubMed  PMC  

Fraser HB, Hirsh AE, Wall DP, Eisen MB (2004). Coevolution of gene expression among interacting proteins.
Journal  PubMed  PMC  

Fraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB (2004). Noise minimization in eukaryotic gene expression.
Journal  PubMed  PMC  

Fay JC, McCullough HL, Sniegowski PD, Eisen MB (2004). Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae.
Journal  PubMed  PMC  

Moses AM, Chiang DY, Eisen MB (2004). Phylogenetic motif detection by expectation-maximization on evolutionary mixtures.
PubMed  Software:EMnEM  

Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB (2004). Benchmarking tools for the alignment of functional noncoding DNA.
Journal  PubMed  PMC  Web  

Brown PO, Eisen MB, Varmus HE (2003). Why PLoS became a publisher.
Journal  PubMed  PMC  

Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB (2003). Position specific variation in the rate of evolution in transcription factor binding sites.
Journal  PubMed  PMC  

Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB (2003). Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts.
Journal  PubMed  PMC  

Gasch AP, Eisen MB (2002). Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering.
PubMed  PMC  Web  Software:FuzzyK  

Eisen MB, Brown PO, Varmus HE (2002). Public-access group supports PubMed Central.
Journal  PubMed  

Keles S, van der Laan M, Eisen MB (2002). Identification of regulatory elements using a feature selection method.
PubMed  

Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE et al. (2002). Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.
Journal  PubMed  PMC  Web  

Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S et al. (2001). Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications.
Journal  PubMed  PMC  

Chiang DY, Brown PO, Eisen MB (2001). Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles.
PubMed  

Roberts RJ, Varmus HE, Ashburner M, Brown PO, Eisen MB et al. (2001). Information access. Building a "GenBank" of the published literature.
PubMed  

Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y 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.
Journal  PubMed  PMC  

Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R et al. (2000). 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns.
Journal  PubMed  PMC  

Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB et al. (2000). Genomic expression programs in the response of yeast cells to environmental changes.
PubMed  PMC  

Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS et al. (2000). Molecular portraits of human breast tumours.
Journal  PubMed  

Lossos IS, Alizadeh AA, Eisen MB, Chan WC, Brown PO et al. (2000). Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas.
Journal  PubMed  PMC  

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.
PubMed  

Diehn M, Eisen MB, Botstein D, Brown PO (2000). Large-scale identification of secreted and membrane-associated gene products using DNA microarrays.
Journal  PubMed  

Scherf U, Ross DT, Waltham M, Smith LH, Lee JK et al. (2000). A gene expression database for the molecular pharmacology of cancer.
Journal  PubMed  

Ross DT, Scherf U, Eisen MB, Perou CM, Rees C et al. (2000). Systematic variation in gene expression patterns in human cancer cell lines.
Journal  PubMed  

Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS et al. (2000). Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.
Journal  PubMed  

Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC et al. (2001). The Stanford Microarray Database.
PubMed  PMC  

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.
PubMed  PMC  

Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC et al. (2001). The Stanford Microarray Database.
PubMed  PMC  

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.
PubMed  PMC  

Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A et al. (1999). Genome-wide analysis of DNA copy-number changes using cDNA microarrays.
Journal  PubMed  

Perou CM, Jeffrey SS, van de Rijn M, Rees CA, Eisen MB et al. (1999). Distinctive gene expression patterns in human mammary epithelial cells and breast cancers.
PubMed  PMC  

Eisen MB, Brown PO (1999). DNA arrays for analysis of gene expression.
PubMed  

Bassett DE, Eisen MB, Boguski MS (1999). Gene expression informatics--it's all in your mine.
Journal  PubMed  

Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T et al. (1999). The transcriptional program in the response of human fibroblasts to serum.
PubMed  

Eisen MB, Spellman PT, Brown PO, Botstein D (1999). Cluster analysis and display of genome-wide expression patterns.
PubMed  PMC  

Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K et al. (1999). Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
PubMed  PMC  

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.
Journal  PubMed  

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.
Journal  PubMed  

Sauter NK, Glick GD, Crowther RL, Park SJ, Eisen MB et al. (1992). Crystallographic detection of a second ligand binding site in influenza virus hemagglutinin.
PubMed  PMC