Research Topics
| MICHAEL BRUCE EISENSummaryAffiliation: Lawrence Berkeley National Laboratory Country: USA Publications
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Detail Information
Publications
Conservation and evolution of cis-regulatory systems in ascomycete fungiAudrey 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...- Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeastsDerek Y Chiang
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
Genome Biol 4:R43. 2003..Our work suggests that positional information, especially the relative spacing between transcription factor binding sites, may represent a common organizing principle of transcription control regions... - Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscuraBenjamin 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... - Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clusteringAudrey P Gasch
Department of Genome Science, Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Genome Biol 3:RESEARCH0059. 2002..Our analysis presented here suggests that a prevalent theme in the regulation of yeast gene expression is the condition-specific coregulation of overlapping sets of genes... - Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipelineCris 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... - Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regionsStewart MacArthur
Genomics Division, Lawrence Berkeley National Laboratory, Cyclotron Road MS 84 181, Berkeley, CA 94720, USA
Genome Biol 10:R80. 2009.... - Detecting DNA regulatory motifs by incorporating positional trends in information contentKatherina 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... - MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary modelAlan 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... - Primate-specific evolution of an LDLR enhancerQian 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... - Serendipitous discovery of Wolbachia genomes in multiple Drosophila speciesSteven L Salzberg
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Genome Biol 6:R23. 2005.... - Flexible promoter architecture requirements for coactivator recruitmentDerek 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... - Position specific variation in the rate of evolution in transcription factor binding sitesAlan 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... - Automatic image analysis for gene expression patterns of fly embryosHanchuan 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... - Design of a combinatorial DNA microarray for protein-DNA interaction studiesJulian 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... - Correction: Benchmarking tools for the alignment of functional noncoding DNAD A Pollard
University of California, Berkeley, CA 94720, USA
BMC Bioinformatics 5:73. 2004 - Benchmarking tools for the alignment of functional noncoding DNADaniel 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... - GATA: a graphic alignment tool for comparative sequence analysisDavid 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... 
In vivo enhancer analysis of human conserved non-coding sequencesLen A Pennacchio
US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
Nature 444:499-502. 2006....
Integrating data clustering and visualization for the analysis of 3D gene expression dataOliver 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...- Transcription factors bind thousands of active and inactive regions in the Drosophila blastodermXiao Yong Li
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
PLoS Biol 6:e27. 2008.... - Determining physical constraints in transcriptional initiation complexes using DNA sequence analysisRyan 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... - Evolution of genes and genomes on the Drosophila phylogenyAndrew 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... - Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservationEmily 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... - Discovery of functional elements in 12 Drosophila genomes using evolutionary signaturesAlexander 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... - Large-scale turnover of functional transcription factor binding sites in DrosophilaAlan 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... - Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sortingDaniel 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... - Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignmentsDaniel 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... - Identification of regulatory elements using a feature selection methodSunduz 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))... - Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiaeJustin 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.... - Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genomeBenjamin 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... - Coevolution of gene expression among interacting proteinsHunter 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... - Functional genomic analysis of the rates of protein evolutionDennis 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.... - Noise minimization in eukaryotic gene expressionHunter 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... - Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila speciesSteven 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... - Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genomeZiva 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... - Aging and gene expression in the primate brainHunter B Fraser
Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
PLoS Biol 3:e274. 2005.... - Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocaseOren 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... - Rapid quantitative profiling of complex microbial populationsChana 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... - PLoS Computational Biology: a new community journalPhilip E Bourne
PLoS Comput Biol 1:e4. 2005