MICHAEL BRUCE EISEN

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc Conservation and evolution of cis-regulatory systems in ascomycete fungi
    Audrey P Gasch
    Genome Sciences Department, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS Biol 2:e398. 2004
  2. pmc Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
    Derek Y Chiang
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Genome Biol 4:R43. 2003
  3. pmc Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
    Benjamin P Berman
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Genome Biol 5:R61. 2004
  4. pmc Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
    Audrey P Gasch
    Department of Genome Science, Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 3:RESEARCH0059. 2002
  5. pmc Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline
    Cris L Luengo Hendriks
    Berkeley Drosophila Transcription Network Project, Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
    Genome Biol 7:R123. 2006
  6. pmc Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
    Stewart MacArthur
    Genomics Division, Lawrence Berkeley National Laboratory, Cyclotron Road MS 84 181, Berkeley, CA 94720, USA
    Genome Biol 10:R80. 2009
  7. pmc Detecting DNA regulatory motifs by incorporating positional trends in information content
    Katherina J Kechris
    Department of Statistics, University of California, Berkeley, CA 94720, USA
    Genome Biol 5:R50. 2004
  8. pmc MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
    Alan M Moses
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    Genome Biol 5:R98. 2004
  9. pmc Primate-specific evolution of an LDLR enhancer
    Qian Fei Wang
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Biol 7:R68. 2006
  10. pmc Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
    Steven L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 6:R23. 2005

Detail Information

Publications39

  1. pmc Conservation and evolution of cis-regulatory systems in ascomycete fungi
    Audrey P Gasch
    Genome Sciences Department, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    PLoS Biol 2:e398. 2004
    ..Our results suggest that the DNA binding specificity of these proteins has coevolved with the sequences found upstream of the Rpn4p target genes and suggest that Rpn4p has a different function in N. crassa...
  2. pmc Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
    Derek Y Chiang
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Genome Biol 4:R43. 2003
    ..We extend this concept of functional conservation to higher-order features of transcription control regions...
  3. pmc Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
    Benjamin P Berman
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Genome Biol 5:R61. 2004
    ..Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters...
  4. pmc Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
    Audrey P Gasch
    Department of Genome Science, Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 3:RESEARCH0059. 2002
    ..Because most commonly used analytical methods cannot appropriately represent these relationships, the connections between conditionally coregulated genes are often missed...
  5. pmc Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline
    Cris L Luengo Hendriks
    Berkeley Drosophila Transcription Network Project, Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
    Genome Biol 7:R123. 2006
    ..To model and thoroughly understand animal transcription networks, it is essential to derive accurate spatial and temporal descriptions of developing gene expression patterns with cellular resolution...
  6. pmc Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
    Stewart MacArthur
    Genomics Division, Lawrence Berkeley National Laboratory, Cyclotron Road MS 84 181, Berkeley, CA 94720, USA
    Genome Biol 10:R80. 2009
    ....
  7. pmc Detecting DNA regulatory motifs by incorporating positional trends in information content
    Katherina J Kechris
    Department of Statistics, University of California, Berkeley, CA 94720, USA
    Genome Biol 5:R50. 2004
    ..Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif...
  8. pmc MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
    Alan M Moses
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    Genome Biol 5:R98. 2004
    ..Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function...
  9. pmc Primate-specific evolution of an LDLR enhancer
    Qian Fei Wang
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Biol 7:R68. 2006
    ..Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain...
  10. pmc Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
    Steven L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 6:R23. 2005
    ....
  11. pmc Flexible promoter architecture requirements for coactivator recruitment
    Derek Y Chiang
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    BMC Mol Biol 7:16. 2006
    ..We characterized the components of promoter architecture that govern the yeast transcription factors Cbf1 and Met31/32, which bind independently, but collaboratively recruit the coactivator Met4...
  12. pmc Position specific variation in the rate of evolution in transcription factor binding sites
    Alan M Moses
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    BMC Evol Biol 3:19. 2003
    ..Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution...
  13. pmc Automatic image analysis for gene expression patterns of fly embryos
    Hanchuan Peng
    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
    BMC Cell Biol 8:S7. 2007
    ..The increasing availability of ISH image data motivates the development of automated computational approaches to the analysis of gene expression patterns...
  14. pmc Design of a combinatorial DNA microarray for protein-DNA interaction studies
    Julian Mintseris
    Boston University, Bioinformatics Program, Boston, MA, USA
    BMC Bioinformatics 7:429. 2006
    ..Recently, double-stranded protein-binding microarrays were developed as a potentially scalable approach to tackle transcription factor binding site identification...
  15. pmc Correction: Benchmarking tools for the alignment of functional noncoding DNA
    D A Pollard
    University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 5:73. 2004
  16. pmc Benchmarking tools for the alignment of functional noncoding DNA
    Daniel A Pollard
    Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 5:6. 2004
    ..For noncoding sequences, where such independent validation is lacking, simulation provides an effective means to generate "correct" alignments with which to benchmark alignment tools...
  17. pmc GATA: a graphic alignment tool for comparative sequence analysis
    David A Nix
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 6:9. 2005
    ..Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments...
  18. ncbi request reprint In vivo enhancer analysis of human conserved non-coding sequences
    Len A Pennacchio
    US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 444:499-502. 2006
    ....
  19. doi request reprint Integrating data clustering and visualization for the analysis of 3D gene expression data
    Oliver Rübel
    Lawrence Berkeley National Laboratory, 1 CyclotronRoad, Berkeley, CA 94720, USA
    IEEE/ACM Trans Comput Biol Bioinform 7:64-79. 2010
    ..We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors...
  20. pmc Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
    Xiao Yong Li
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS Biol 6:e27. 2008
    ....
  21. pmc Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis
    Ryan K Shultzaberger
    Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
    PLoS ONE 2:e1199. 2007
    ..Interestingly, we found that the major determinant of Met4 regulation was the sum of the strength of the Cbf1 and Met31 binding sites and that the energetic costs associated with spacing appeared to be minimal...
  22. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  23. pmc Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation
    Emily E Hare
    Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
    PLoS Genet 4:e1000106. 2008
    ..Together, these observations suggest that the local arrangement of binding sites relative to each other is more important than their overall arrangement into larger units of cis-regulatory function...
  24. pmc Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Alexander Stark
    The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
    Nature 450:219-32. 2007
    ..We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies...
  25. pmc Large-scale turnover of functional transcription factor binding sites in Drosophila
    Alan M Moses
    Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America
    PLoS Comput Biol 2:e130. 2006
    ..Finally, we show that binding-site gains and losses are asymmetrically distributed with respect to D. melanogaster, consistent with lineage-specific acquisition and loss of Zeste-responsive regulatory elements...
  26. pmc Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting
    Daniel A Pollard
    Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, USA
    PLoS Genet 2:e173. 2006
    ..Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this information will be valuable advancements for the field of comparative genomics...
  27. pmc Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
    Daniel A Pollard
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 7:376. 2006
    ..Yet how multiple alignment accuracy varies across sequence types, tree topologies, divergences and tools, and further how this variation impacts specific inferences, remains unclear...
  28. ncbi request reprint Identification of regulatory elements using a feature selection method
    Sunduz Keles
    Division of Biostatistics, U of California, Berkeley, CA 94720, USA
    Bioinformatics 18:1167-75. 2002
    ..We apply this method to a publicly available dataset of the yeast Saccharomyces cerevisiae, focussing on the 800 basepairs immediately upstream of each gene's translation start site (the upstream control region (UCR))...
  29. pmc Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae
    Justin C Fay
    Department of Genome Sciences, Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley, CA 94720, USA
    Genome Biol 5:R26. 2004
    ....
  30. pmc Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    Benjamin P Berman
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:757-62. 2002
    ..We tested one of the newly identified clusters, mapping upstream of the gap gene giant (gt), and show that it acts as an enhancer that recapitulates the posterior expression pattern of gt...
  31. pmc Coevolution of gene expression among interacting proteins
    Hunter B Fraser
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 101:9033-8. 2004
    ..Our results also suggest that expression coevolution can be used for computational prediction of protein-protein interactions...
  32. pmc Functional genomic analysis of the rates of protein evolution
    Dennis P Wall
    Department of Biological Sciences, and Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:5483-8. 2005
    ....
  33. pmc Noise minimization in eukaryotic gene expression
    Hunter B Fraser
    Department of Molecular and Cell Biology, University of California, Berkeley, USA
    PLoS Biol 2:e137. 2004
    ..Our results support the hypothesis that noise in gene expression is a biologically important variable, is generally detrimental to organismal fitness, and is subject to natural selection...
  34. pmc Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
    Steven L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 6:402. 2005
    ..A correction to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen and WC Nelson. Genome Biology 2005, 6:R23...
  35. pmc Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome
    Ziva Misulovin
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
    Chromosoma 117:89-102. 2008
    ..These mechanisms are likely involved in the etiology of Cornelia de Lange syndrome, in which mutation of one copy of the NIPBL gene encoding the human Nipped-B ortholog causes diverse structural and mental birth defects...
  36. pmc Aging and gene expression in the primate brain
    Hunter B Fraser
    Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
    PLoS Biol 3:e274. 2005
    ....
  37. pmc Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase
    Oren Levy
    Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:17618-23. 2005
    ..Finally, we show that the FtsK translocase is a powerful motor that is able to displace a triplex-forming oligo from a DNA substrate...
  38. pmc Rapid quantitative profiling of complex microbial populations
    Chana Palmer
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
    Nucleic Acids Res 34:e5. 2006
    ..This simple, rapid microarray procedure can be used to explore and systematically characterize complex microbial communities, such as those found within the human body...
  39. pmc PLoS Computational Biology: a new community journal
    Philip E Bourne
    PLoS Comput Biol 1:e4. 2005

Research Grants10

  1. Modeling the Evolution and Function of Drosophila cis-Regulatory Modules
    MICHAEL BRUCE EISEN; Fiscal Year: 2010
    ....
  2. Computational Analysis of Developmental cis-Regulation
    Michael Eisen; Fiscal Year: 2009
    ..Although we will focus our efforts on the Drosophila embryo, we believe the approaches and tools we develop will be of general use in the annotation of animal genomes. ..
  3. Modeling the Evolution and Function of Drosophila cis-Regulatory Modules
    Michael Eisen; Fiscal Year: 2009
    ....