Welcome to Michael Eisen’s lab in the Howard Hughes Medical Institute (HHMI) at  University of California at Berkeley (UCB). We are part of the  Department of Molecular and Cell Biology, the Department of Integrative Biology, the Museum of Vertebrate Zoology, and the California Institute for Quantitative Biosciences.

Our lab applies computational and experimental genomic approaches to study how genome sequences specify organismal form and function. We are particularly interested in the regulation of gene expression, and focus on how the information that specifies when and where genes are expressed is encoded in genome sequences, the role that regulated gene expression plays in animal development and the response of microbes to their environments, and how variation in and evolution of gene expression contributes to phenotypic variation and the remarkable diversity of life on Earth. This site contains a more detailed description of our research projects, an introduction to members of the lab, reprints of all of our publications, free downloadable and web-based software for the analysis of genome sequences and DNA microarray data, and other useful links and information.

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

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

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

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

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

MacManes MD, Eisen MB (2014) Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus.   DOI  PubMed  PMC

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

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

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

Kuntz SG, Eisen MB (2014) Drosophila embryogenesis scales uniformly across temperature in developmentally diverse species.   DOI  PubMed  PMC

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