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.

Read our latest in Open Access Journals:


 Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. Paris M, Kaplan T, Li XY, Villalta JE, Lott SE, Eisen MB. (2013) PLoS Genet. 9(9):e1003748. doi: 10.1371/journal.pgen.1003748.



 Mice Infected with Low-Virulence Strains of Toxoplasma gondii Lose Their Innate Aversion to Cat Urine, Even after Extensive Parasite Clearance. Ingram WM, Goodrich LM, Robey EA, Eisen MB. (2013) PLoS One. 8(9):e75246. doi: 10.1371/journal.pone.0075246.



 Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression. Combs PA, Eisen MB. (2013) PLoS One. 8(8):e71820. doi: 10.1371/journal.pone.0071820.



 Improving transcriptome assembly through error correction of high-throughput sequence reads. Macmanes MD, Eisen MB. (2013) PeerJ. 1:e113. doi: 10.7717/peerj.113.



 Spatial promoter recognition signatures may enhance transcription factor specificity in yeast. Lusk RW, Eisen MB. (2013) PLoS One. 8(1):e53778. doi: 10.1371/journal.pone.0053778.



 Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain. Shultzaberger RK, Maerkl SJ, Kirsch JF, Eisen MB. (2012) PLoS Genet. 8(3):e1002614. doi: 10.1371/journal.pgen.1002614.



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



 Non-Canonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq
Lott SE, Villalta JE, Schroth GP, Luo S, Tonkin LA, Eisen MB. (2011) PLoS Biol 9(2):e1000590. doi: 10.1371/journal.pbio.1000590




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