MacArthur, Stewart, Li, Xiao-Yong, Li, Jingyi, Brown, James B, Chu, Hou Cheng, Zeng, Lucy, ...
Abstract Background We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of...
Jans, Judith, Gladden, John M., Ralston, Edward J., Pickle, Catherine S., Michel, Agnès H., Pferdehirt, Rebecca R., ...
In many species, a dosage compensation complex (DCC) is targeted to X chromosomes of one sex to equalize levels of X-gene products between males (1X) and females (2X). Here we identify cis-acting...
PointCloudXplore: A Visualization Tool for 3D Gene Expression Data (2008)
Oliver Rübel, Gunther H. Weber, Charless C. Fowlkes, Lisa Simirenko, ...
a suite of methods that support quantitative, computational analysis of threedimensional (3D) gene expression patterns with cellular resolution in early Drosophila embryos, aiming at a more in-depth...
Hanchuan Peng, Fuhui Long, Jie Zhou, Garmay Leung, Michael B Eisen
Automatic image analysis for gene expression patterns of fly embryos
Shultzaberger, Ryan K., Chiang, Derek Y., Moses, Alan M., Eisen, Michael B.
Eukaryotic gene expression is often under the control of cooperatively acting transcription factors whose binding is limited by structural constraints. By determining these structural constraints, we...
Li, Xiao-Yong, MacArthur, Stewart, Bourgon, Richard, Nix, David, Pollard, Daniel A., Iyer, Venky N., ...
Design of a combinatorial dna microarray for protein-dna interaction studies (2008)
Mintseris, Julian, Eisen, Michael B.
Background: Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Recently,...
Aging and Gene Expression in the Primate (2008)
Hunter B. Fraser, Joshua B. Plotkin, Svante Pääbo, Michael B. Eisen
It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes...
¶ To whom correspondence should be addressed. E-mail: (2008)
P. Wall, Aaron E. Hirsh, Hunter B. Fraser, Guri Giaever, Michael B. Eisen, Marcus W. Feldman
Running head: yeast functional genomics and evolutionary rate Background Statistical noise and inaccuracy in functional genomic estimates of protein dispensability and evolutionary rate present...
Xiao-yong Li, Stewart MacArthur, Richard Bourgon, David Nix, Daniel A. Pollard, Venky N. Iyer, ...
Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to...
Charless C. Fowlkes, Gunther H. Weber, Oliver Rübel, Min-yu Huang, ...
To fully understand animal transcription networks, it is essential to accurately measure the spatial and temporal expression patterns of transcription factors and their targets. We describe a...
Trevor Hastie, Robert Tibshirani, Michael B Eisen, Ash Alizadeh, Ronald Levy, Louis Staudt, ...
shaving ’ as a method for identifying distinct sets of genes
BIOINFORMATICS Vol. 18 no. 9 2002 (2007)
Identification of regulatory elements using a feature selection method Sund uz Keles
Audrey P Gasch, Michael B Eisen
the conditional coregulation of yeast gene expression
Derek Y. Chiang, Patrick O. Brown, Michael B. Eisen
Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles
Noise Minimization in Eukaryotic Gene Expression (2007)
Hunter B. Fraser, Aaron E. Hirsh, Guri Giaever, Jochen Kumm, Michael B. Eisen
All organisms have elaborate mechanisms to control rates of protein production. However, protein production is also subject to stochastic fluctuations, or ‘‘noise.’ ’ Several recent studies...
Daniel A Pollard, Jens Stoye, Susan E Celniker, Michael B Eisen, Open Access
© 2004 Pollard et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this...
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007)
Lin, Michael F, Kheradpour, Pouya, Pedersen, Jakob S, Parts, Leopold, Carlson, Joseph W, ...
Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12...
Automatic image analysis for gene expression patterns of fly embryos (2007)
Peng, Hanchuan, Long, Fuhui, Zhou, Jie, Leung, Garmay, Eisen, Michael B, Myers, Eugene W
Abstract Background Staining the m RNA of a gene via in situ hybridization (ISH) during the development of a D. melanogaster embryo delivers the detailed spatio-temporal pattern of expression of the...
Luengo Hendriks, Cris L, Keränen, Soile VE, Fowlkes, Charless C, Simirenko, Lisa, Weber, Gunther H, DePace, Angela H, ...
Abstract Background To model and thoroughly understand animal transcription networks, it is essential to derive accurate spatial and temporal descriptions of developing gene expression patterns with...
Design of a combinatorial DNA microarray for protein-DNA interaction studies (2006)
Mintseris, Julian, Eisen, Michael B
Abstract Background Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Recently,...
PointCloudXplore: a visualization tool for 3D gene expression data (2006)
Rubel, Oliver, Weber, Gunther H., Keranen, Soile V.E., Fowlkes, Charles C., Luengo Hendriks, Cristian L., Simirenko, Lisa, ...
Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila (2006)
Alan M. Moses, Daniel A. Pollard, David A. Nix, Venky N. Iyer, Xiao-Yong Li, Mark D. Biggin, ...
The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Daniel A. Pollard, Venky N. Iyer, Alan M. Moses, Michael B. Eisen
The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three...
Insights into social insects from the genome of the honeybee Apis mellifera (2006)
Robinson, Gene E, Gibbs, Richard A, Worley, Kim C, Evans, Jay D, Maleszka, Ryszard, ...
Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes,...
Pollard, Daniel A., Iyer, Venky N., Moses, Alan M., Eisen, Michael B.
The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three...
Pollard, Daniel A, Moses, Alan M, Iyer, Venky N, Eisen, Michael B
Abstract Background Molecular evolutionary studies of noncoding sequences rely on multiple alignments. Yet how multiple alignment accuracy varies across sequence types, tree topologies, divergences...
Pollard, Daniel A., Moses, Alan M., Iyer, Venky N., Eisen, Michael B.
Background: Molecular evolutionary studies of noncoding sequences rely on multiple alignments. Yet how multiple alignment accuracy varies across sequence types, tree topologies, divergences and...
Primate-specific evolution of an LDLR enhancer (2006)
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M, Chanan, Sumita, Brown, Myles, ...
Background 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. Results In this...
Large-scale turnover of functional transcription factor binding sites in Drosophila (2006)
Alan M. Moses, Daniel Pollard, David A Nix, Venky N. Iyer, Xiao-Yong Li, Mark D Biggin, ...
The gain and loss of functional transcription-factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Daniel Pollard, Venky N. Iyer, Alan M. Moses, Michael B. Eisen
Understanding the basis for incongruence of phylogenies constructed from different genes or loci and how to properly handle such disaccord is an important challenge to evolutionary biology. To...
Large-scale turnover of functional transcription factor binding sites in Drosophila (2006)
Moses, Alan M., Pollard, Daniel A., Nix, David A., Iyer, Venky N., Li, Xiao-Yong, Biggin, Mark D., ...
The gain and loss of functional transcription-factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Primate-Specific Evolution of an LDLR Enhancer (2006)
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M., Chanan, Sumita, Brown, Myles, ...
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. In this study, we...
Flexible promoter architecture requirements for coactivator recruitment (2006)
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
Abstract Background The spatial organization of transcription factor binding sites in regulatory DNA, and the composition of intersite sequences, influences the assembly of the multiprotein complexes...
In Vivo Enhancer Analysis Chromosome 16 Conserved Noncoding Sequences (2006)
Pennacchio, Len A., Ahituv, Nadav, Moses, Alan M., Nobrega, Marcelo, Prabhakar, Shyam, Shoukry, Malak, ...
The identification of enhancers with predicted specificities in vertebrate genomes remains a significant challenge that is hampered by a lack of experimentally validated training sets. In this study,...
Soile Ve Keränen, Charless C Fowlkes, Lisa Simirenko, Gunther H Weber, Angela H Depace, ...
Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline
Bmc Bioinformatics, Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen, Michael B Eisen
Research article Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
Large-scale turnover of functional transcription factor binding sites in Drosophila (2006)
Alan M. Moses, Daniel A. Pollard, David A. Nix, Venky N. Iyer, Xiao-yong Li, Mark D. Biggin, ...
The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Article type Methodology article (2006)
Bmc Bioinformatics, Michael B Eisen, Julian Mintseris, Michael B. Eisen
This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fully formatted PDF and full text (HTML) versions will be made available soon. Design of a combinatorial...
Derek Y Chiang, David A Nix, Ryan K Shultzaberger, Audrey P Gasch, Michael B Eisen, Derek Y Chiang, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available shortly after the date of publication, from the URL listed below....
Rapid quantitative profiling of complex microbial populations (2006)
Palmer, Chana, Bik, Elisabeth M., Eisen, Michael B., Eckburg, Paul B., Sana, Theodore R., Wolber, Paul K., ...
Diverse and complex microbial ecosystems are found in virtually every environment on earth, yet we know very little about their composition and ecology. Comprehensive identification and...
Bmc Bioinformatics, Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen, Michael B Eisen
Research article Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
Primate-specific evolution of an LDLR enhancer (2005)
Wang, Qian-Fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M., Chanan, Sumita, Brown, Myles, ...
Aging and Gene Expression in the Primate Brain (2005)
Hunter B. Fraser, Philipp Khaitovich, Joshua B. Plotkin, Svante Pääbo, Michael B. Eisen
Transcriptional profiles in human and chimpanzee reveal a diversity of aging patterns present within the human brain, as well as how rapidly genome-wide patterns of aging can evolve between species.
Aging and Gene Expression in the Primate Brain (2005)
Hunter B. Fraser, Philipp Khaitovich, Joshua B. Plotkin, Svante Pääbo, Michael B. Eisen
It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes...
Correction: Serendipitous discovery of Wolbachiagenomes in multiple Drosophilaspecies (2005)
Salzberg, Steven L, Dunning Hotopp, Julie, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
No abstract available.
Abstract The identification of transcription factor binding sites in genome sequences is an important problem in contemporary sequence analysis, and a plethora of approaches to the problem have been...
Serendipitous discovery of Wolbachiagenomes in multiple Drosophilaspecies (2005)
Salzberg, Steven L, Hotopp, Julie, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
Abstract Background The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of...
Aging and Gene Expression in the Primate Brain (2005)
Fraser, Hunter B., Khaitovich, Philipp, Plotkin, Joshua B., Paabo, Svante, Eisen, Michael B.
It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes...
GATA: a graphic alignment tool for comparative sequence analysis (2005)
Nix, David A, Eisen, Michael B
Abstract Background Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence...
Estimating Motifs Under Order Restrictions (2005)
Van Zwet, Erik W, Kechris, Katherina J, Bickel, Peter J, Eisen , Michael B.
Transcription factors and many other DNA-binding proteins recognize more than one specific sequence. Among sequences recognized by a given DNA-binding protein, different positions exhibit varying...
Estimating Motifs Under Order Restrictions (2005)
Van Zwet, Erik W, Kechris, Katherina J, Bickel, Peter J, Eisen , Michael B.
Transcription factors and many other DNA-binding proteins recognize more than one specific sequence. Among sequences recognized by a given DNA-binding protein, different positions exhibit varying...
Estimating Motifs Under Order Restrictions (2005)
Van Zwet, Erik W, Kechris, Katherina J, Bickel, Peter J, Eisen , Michael B.
Transcription factors and many other DNA-binding proteins recognize more than one specific sequence. Among sequences recognized by a given DNA-binding protein, different positions exhibit varying...
Estimating Motifs Under Order Restrictions (2005)
Van Zwet, Erik W, Kechris, Katherina J, Bickel, Peter J, Eisen , Michael B.
Transcription factors and many other DNA-binding proteins recognize more than one specific sequence. Among sequences recognized by a given DNA-binding protein, different positions exhibit varying...
GATA: A graphic alignment tool for comparative sequence analysis (2005)
Nix, David A., Eisen, Michael B.
Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear....
Aging and Gene Expression in the Primate Brain (2005)
Fraser, Hunter B., Khaitovich, Philipp, Plotkin, Joshua B., Pääbo, Svante, Eisen, Michael B.
It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes...
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species (2005)
Salzberg, Steven L., Dunning Hotopp, Julie C., Delcher, Arthur L., Pop, Mihai, Smith, Douglas R, Eisen, Michael B., ...
Background: The Trace Archive is a repository for the raw, unanalyzed data generated by largescale genome sequencing projects. The existence of this data offers scientists the possibility of...
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species (2005)
Salzberg, Steven L., Dunning Hotopp, Julie C., Delcher, Arthur L., Pop, Mihai, Smith, Douglas R, Eisen, Michael B., ...
Background: The Trace Archive is a repository for the raw, unanalyzed data generated by largescale genome sequencing projects. The existence of this data offers scientists the possibility of...
Rapid quantitative profiling of complex microbial populations (2005)
Chana Palmer, Elisabeth M. Bik, Michael B. Eisen, Paul B. Eckburg, Theodore R. Sana, Paul K. Wolber, ...
Diverse and complex microbial ecosystems are found in virtually every environment on earth, yet we know very little about their composition and ecology. Comprehensive identification and...
the Inference of Sequence Specificity (2005)
Michael B Eisen, Michael B. Eisen, Michael B. Eisen
This information has not been peer-reviewed. Responsibility for the findings rests solely with the author(s).
GATA: a graphic alignment tool for comparative sequence analysis (2005)
Bmc Bioinformatics, David A Nix, Michael B Eisen, Open Access, David A Nix, Michael B Eisen
Software
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
A systematic examination of the gene regulatory elements in ascomycete fungi reveals striking conservation along with some examples of the ways in which regulatory systems can evolve.
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Moses, Alan M, Chiang, Derek Y, Pollard, Daniel A, Iyer, Venky N, Eisen, Michael B
Abstract We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding-site...
PLoS Medicine—A Medical Journal for the Internet Age (2004)
Michael B. Eisen, Patrick O. Brown, Harold E. Varmus
A message from the founders of the Public Library of Science.
Berman, Benjamin P, Pfeiffer, Barret D, Laverty, Todd R, Salzberg, Steven L, Rubin, Gerald M, Eisen, Michael B, ...
Abstract Background The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of...
Berman, Benjamin P., Pfeiffer, Barret D., Laverty, Todd R., Salzberg, Steven L., Rubin, Gerald M., Eisen, Michael B., ...
Detecting DNA regulatory motifs by incorporating positional trends in information content (2004)
Kechris, Katherina J, Van Zwet, Erik, Bickel, Peter J, Eisen, Michael B
Abstract On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, we propose a simple extension to the model-based motif discovery...
Noise Minimization in Eukaryotic Gene Expression (2004)
Hunter B. Fraser, Aaron E. Hirsh, Guri Giaever, Jochen Kumm, Michael B. Eisen
Analysis of gene expression data for nearly every gene in yeast provides evidence that random variation in the production rate of proteins could significantly affect the fitness of an organism.
Noise Minimization in Eukaryotic Gene Expression (2004)
Hunter B. Fraser, Aaron E. Hirsh, Guri Giaever, Jochen Kumm, Michael B. Eisen
All organisms have elaborate mechanisms to control rates of protein production. However, protein production is also subject to stochastic fluctuations, or “noise.” Several recent studies in...
Detecting DNA regulatory motifs by incorporating positional trends in information content (2004)
Kechris, Katherina J., Van Zwet, Erik, Bickel, Peter J., Eisen, Michael B.
On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, we propose a simple extension to the model-based motif discovery methods....
Fay, Justin C, McCullough, Heather L, Sniegowski, Paul D, Eisen, Michael B
Abstract Background The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated...
Coevolution of gene expression among interacting proteins (2004)
Fraser, Hunter B., Hirsh, Aaron E., Wall, Dennis P., Eisen, Michael B.
Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well...
Fay, Justin C., McCullough, Heather L., Sniegowski, Paul D., Eisen, Michael B.
Background: The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with...
Benchmarking tools for the alignment of functional noncoding DNA (2004)
Pollard, Daniel A, Bergman, Casey M, Stoye, Jens, Celniker, Susan E, Eisen, Michael B
Abstract Background Numerous tools have been developed to align genomic sequences. However, their relative performance in specific applications remains poorly characterized. Alignments of...
Benchmarking tools for the alignment of functional noncoding DNA (2004)
Daniel A. Pollard, Jens Stoye, E. Celniker, Michael B. Eisen, Cb Eh
* corresponding author. Background Numerous tools have been developed to align genomic sequences. However, their relative performance in specific applications remains poorly characterized. Alignments...
clusters in Drosophila melanogaster and Drosophila (2004)
Benjamin P Berman, Barret D Pfeiffer, Todd R Laverty, Steven L Salzberg, Gerald M Rubin, Michael B Eisen, ...
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site
Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer, Michael B Eisen
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
Conservation and evolution of cis-regulatory systems in ascomycete fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Katherina J Kechris, Erik Van Zwet, Peter J Bickel, Michael B Eisen
The electronic version of this article is the complete one and can be found online at
Why PLoS Became a Publisher (2003)
Patrick O. Brown, Michael B. Eisen, Harold E. Varmus
Public Library of Science has grown from a grassroots movement to a nonprofit publisher, in order to catalyze change towards open-access publishing of the scientific literature.
Position specific variation in the rate of evolution in transcription factor binding sites (2003)
Moses, Alan M., Chiang, Derek Y., Kellis, Manolis, Lander, Eric S., Eisen, Michael B.
Background: The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental...
Position specific variation in the rate of evolution in transcription factor binding sites (2003)
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Abstract Background The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of...
Supervised Detection of Regulatory Motifs in DNA Sequences (2003)
Keles, Sunduz, Van Der Laan, Mark J., Dudoit, Sandrine, Xing, Biao, Eisen , Michael B.
Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural...
Supervised Detection of Regulatory Motifs in DNA Sequences (2003)
Keles, Sunduz, Van Der Laan, Mark J., Dudoit, Sandrine, Xing, Biao, Eisen , Michael B.
Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural...
Supervised Detection of Regulatory Motifs in DNA Sequences (2003)
Keles, Sunduz, Van Der Laan, Mark J., Dudoit, Sandrine, Xing, Biao, Eisen , Michael B.
Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural...
Supervised Detection of Regulatory Motifs in DNA Sequences (2003)
Keles, Sunduz, Van Der Laan, Mark J., Dudoit, Sandrine, Xing, Biao, Eisen , Michael B.
Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural...
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Abstract Background Transcriptional regulation in eukaryotes often involves multiple transcription factors binding to the same transcription control region, and to understand the regulatory content...
Supervised Detection of Regulatory Motifs in DNA Sequences (2003)
Keles, Sunduz, Van Der Laan, Mark J., Dudoit, Sandrine, Xing, Biao, Eisen, Michael B.
Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural...
Supervised Detection of Regulatory Motifs in DNA Sequences (2003)
Keles, Sunduz, Van Der Laan, Mark J., Dudoit, Sandrine, Xing, Biao, Eisen, Michael B.
Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural...
Supervised Detection of Regulatory Motifs in DNA Sequences (2003)
Keles, Sunduz, Van Der Laan, Mark J., Dudoit, Sandrine, Xing, Biao, Eisen, Michael B.
Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural...
Supervised Detection of Regulatory Motifs in DNA Sequences (2003)
Keles, Sunduz, Van Der Laan, Mark J., Dudoit, Sandrine, Xing, Biao, Eisen, Michael B.
Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural...
Supervised detection of regulatory motifs in DNA sequences (2003)
Sunduz Keles, Rine Dudoit, Rine Dudoit, Biao Xing, Biao Xing, ...
Copyright c○2003 by the authors. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic,...
Supervised detection of regulatory motifs in DNA sequences (2003)
Rine Dudoit, Biao Xing, Michael B. Eisen
Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural...
BMC Evolutionary Biology BioMed Central (2003)
Alan M Moses, Derek Y Chiang, Manolis Kellis, Eric S L, Michael B Eisen, Eric S Lander, ...
Research article Position specific variation in the rate of evolution in transcription factor binding sites
2003 Chiang et Volume al. 4, Issue 7, Article R43 Open Access (2003)
Derek Y Chiang, Alan M Moses, Manolis Kellis, Eric S L, Michael B Eisen
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
lymphoma identified by gene expression profiling. Nature, 403:503–511, February 2000. (2003)
Mark L. Adams, Markus Enzelberger, Stephen Quake, Thomas J. Albert, Jason Norton, ...
gration on detector arrays for absorption and fluorescence micro-spectrometers. Sensors and
BMC Evolutionary Biology BioMed Central (2003)
Alan M Moses, Derek Y Chiang, Manolis Kellis, Eric S L, Michael B Eisen, Eric S Lander, ...
Research article Position specific variation in the rate of evolution in transcription factor binding sites
Gasch, Audrey P, Eisen, Michael B
Abstract Background Organisms simplify the orchestration of gene expression by coregulating genes whose products function together in the cell. Many proteins serve different roles depending on the...
Identification of regulatory elements using a feature selection method (2002)
Keles, Sündüz, Van Der Laan, Mark, Eisen, Michael B.
Motivation: Many methods have been described to identify regulatory motifs in the transcription control regions of genes that exhibit similar patterns of gene expression across a variety of...
Audrey P Gasch, Michael B Eisen
the conditional coregulation of yeast gene expression
Identification of Regulatory Elements Using A Feature Selection Method (2001)
Keles, Sunduz, Van Der Laan, Mark J., Eisen, Michael B.
Many methods have been described to identify regulatory motifs in the transcription control regions of genes that exhibit similar patterns of gene expression across a variety of experimental...
Identification of Regulatory Elements Using A Feature Selection Method (2001)
Keles, Sunduz, Van Der Laan, Mark J., Eisen, Michael B.
Many methods have been described to identify regulatory motifs in the transcription control regions of genes that exhibit similar patterns of gene expression across a variety of experimental...
Identification of Regulatory Elements Using A Feature Selection Method (2001)
Keles, Sunduz, Van Der Laan, Mark J., Eisen, Michael B.
Many methods have been described to identify regulatory motifs in the transcription control regions of genes that exhibit similar patterns of gene expression across a variety of experimental...
Identification of Regulatory Elements Using A Feature Selection Method (2001)
Keles, Sunduz, Van Der Laan, Mark J., Eisen, Michael B.
Many methods have been described to identify regulatory motifs in the transcription control regions of genes that exhibit similar patterns of gene expression across a variety of experimental...
The Stanford Microarray Database (2001)
Sherlock, Gavin, Hernandez-Boussard, Tina, Kasarskis, Andrew, Binkley, Gail, Matese, John C., Dwight, Selina S., ...
The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two...
Chiang, Derek Y., Brown, Patrick O., Eisen, Michael B.
The combination of genome-wide expression patterns and full genome sequences offers a great opportunity to further our understanding of the mechanisms and logic of transcriptional regulation. Many...
Hastie, Trevor, Tibshirani, Robert, Eisen, Michael B, Alizadeh, Ash, Levy, Ronald, Staudt, Louis, ...
Abstract Background Large gene expression studies, such as those conducted using DNA arrays, often provide millions of different pieces of data. To address the problem of analyzing such data, we...
Genomic expression programs in the response of yeast cells to environmental changes (2000)
Audrey P. Gasch, Paul T. Spellman, Camilla M. Kao, Orna Carmel-harel, Michael B. Eisen, Gisela Storz, ...
We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over...
Comment Review Reports Deposited Research Interactions Information Refereed (2000)
Research Gene Shaving', Trevor Hastie, Robert Tibshirani, Michael B Eisen, Ash Alizadeh, Ronald Levy, ...
Background: Large gene expression studies, such as those conducted using DNA arrays, often provide millions of different pieces of data. To address the problem of analyzing such data, we describe a...
Microarray Hybridization □d, Paul T. Spellman, Gavin Sherlock, Michael Q. Zhang, Vishwanath R, Kirk Anders, ...
this article is available at www.molbiolcell.org.
Michael B. Eisen, Subramaniam Sabesan, John J. Skehel, Don C. Wiley
The structures of five complexes of the X-31 influenza A (H3N2) virus hemagglutinin with sialyloligosaccharide receptor analogs have been determined from 2.5 to 2.8 A ˚ resolution by X-ray...
'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns
Hastie, Trevor, Tibshirani, Robert, Eisen, Michael B, Alizadeh, Ash, Levy, Ronald, Staudt, Louis, ...
Genomic Expression Programs in the Response of Yeast Cells to Environmental ChangesD⃞
Gasch, Audrey P., Spellman, Paul T., Kao, Camilla M., Carmel-Harel, Orna, Eisen, Michael B., Storz, Gisela, ...
We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over...
Distinctive gene expression patterns in human mammary epithelial cells and breast cancers
Perou, Charles M., Jeffrey, Stefanie S., Van De Rijn, Matt, Rees, Christian A., Eisen, Michael B., Ross, Douglas T., ...
cDNA microarrays and a clustering algorithm were used to identify patterns of gene expression in human mammary epithelial cells growing in culture and in primary human breast tumors. Clusters of...
Johannes, Gregg, Carter, Mark S., Eisen, Michael B., Brown, Patrick O., Sarnow, Peter
Although most eukaryotic mRNAs need a functional cap binding complex eIF4F for efficient 5′ end- dependent scanning to initiate translation, picornaviral, hepatitis C viral, and a few cellular RNAs...
Cluster analysis and display of genome-wide expression patterns
Eisen, Michael B., Spellman, Paul T., Brown, Patrick O., Botstein, David
A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in...
Spellman, Paul T., Sherlock, Gavin, Zhang, Michael Q., Iyer, Vishwanath R., Anders, Kirk, Eisen, Michael B., ...
We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures...
Lossos, Izidore S., Alizadeh, Ash A., Eisen, Michael B., Chan, Wing C., Brown, Patrick O., Botstein, David, ...
B cell diffuse large cell lymphoma (B-DLCL) is a heterogeneous group of tumors, based on significant variations in morphology, clinical presentation, and response to treatment. Gene expression...
The Stanford Microarray Database
Sherlock, Gavin, Hernandez-Boussard, Tina, Kasarskis, Andrew, Binkley, Gail, Matese, John C., Dwight, Selina S., ...
The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two...
Miki, Rika, Kadota, Koji, Bono, Hidemasa, Mizuno, Yosuke, Tomaru, Yasuhiro, Carninci, Piero, ...
We have systematically characterized gene expression patterns in 49 adult and embryonic mouse tissues by using cDNA microarrays with 18,816 mouse cDNAs. Cluster analysis defined sets of genes that...
Sørlie, Therese, Perou, Charles M., Tibshirani, Robert, Aas, Turid, Geisler, Stephanie, Johnsen, Hilde, ...
The purpose of this study was to classify breast carcinomas based on variations in gene expression patterns derived from cDNA microarrays and to correlate tumor characteristics to clinical outcome. A...
Berman, Benjamin P., Nibu, Yutaka, Pfeiffer, Barret D., Tomancak, Pavel, Celniker, Susan E., Levine, Michael, ...
A major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. The first step in this process is...
Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
Gasch, Audrey P, Eisen, Michael B
A heuristically modified version of fuzzy k-means clustering has been used to identify overlapping clusters of yeast genes based on published gene-expression data following the response of yeast...
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
The determination of conserved sequences has identified individual transcription factor binding sites. The incorporation of both joint conservation and spacing constraints of sequence pairs predicts...
Position specific variation in the rate of evolution in transcription factor binding sites
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Brown, Patrick O, Eisen, Michael B, Varmus, Harold E
Public Library of Science has grown from a grassroots movement to a nonprofit publisher, in order to catalyze change towards open-access publishing of the scientific literature
Benchmarking tools for the alignment of functional noncoding DNA
Pollard, Daniel A, Bergman, Casey M, Stoye, Jens, Celniker, Susan E, Eisen, Michael B
Fay, Justin C, McCullough, Heather L, Sniegowski, Paul D, Eisen, Michael B
This study compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown in the presence or absence of copper sulfate. Insights were gained into the molecular basis...
Noise Minimization in Eukaryotic Gene Expression
Fraser, Hunter B, Hirsh, Aaron E, Giaever, Guri, Kumm, Jochen, Eisen, Michael B
All organisms have elaborate mechanisms to control rates of protein production. However, protein production is also subject to stochastic fluctuations, or “noise.” Several recent studies in...
Coevolution of gene expression among interacting proteins
Fraser, Hunter B., Hirsh, Aaron E., Wall, Dennis P., Eisen, Michael B.
Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well...
Detecting DNA regulatory motifs by incorporating positional trends in information content
Kechris, Katherina J, Van Zwet, Erik, Bickel, Peter J, Eisen, Michael B
On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, a simple extension to the model-based motif discovery method is proposed....
Berman, Benjamin P, Pfeiffer, Barret D, Laverty, Todd R, Salzberg, Steven L, Rubin, Gerald M, Eisen, Michael B, ...
27 predicted gene-regulatory regions in the Drosophila melanogaster genome were analyzed in vivo, confirming 15 active enhancer regions. A comparison with Drosophila pseudoobscura sequences revealed...
PLoS Medicine— A Medical Journal for the Internet Age
Eisen, Michael B, Brown, Patrick O, Varmus, Harold E
A message from the founders of the Public Library of Science
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi
Gasch, Audrey P, Moses, Alan M, Chiang, Derek Y, Fraser, Hunter B, Berardini, Mark, Eisen, Michael B
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Moses, Alan M, Chiang, Derek Y, Pollard, Daniel A, Iyer, Venky N, Eisen, Michael B
MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments.
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Hotopp, Julie C Dunning, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly:...
Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Dunning Hotopp, Julie C, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
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...
Aging and Gene Expression in the Primate Brain
Fraser, Hunter B, Khaitovich, Philipp, Plotkin, Joshua B, Pääbo, Svante, Eisen, Michael B
It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes...
Rapid quantitative profiling of complex microbial populations
Palmer, Chana, Bik, Elisabeth M., Eisen, Michael B., Eckburg, Paul B., Sana, Theodore R., Wolber, Paul K., ...
Diverse and complex microbial ecosystems are found in virtually every environment on earth, yet we know very little about their composition and ecology. Comprehensive identification and...
Levy, Oren, Ptacin, Jerod L., Pease, Paul J., Gore, Jeff, Eisen, Michael B., Bustamante, Carlos, ...
FtsK from Escherichia coli is a fast and sequence-directed DNA translocase with roles in chromosome dimer resolution, segregation, and decatenation. From the movement of single FtsK particles on...
Flexible promoter architecture requirements for coactivator recruitment
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
Moses, Alan M, Pollard, Daniel A, Nix, David A, Iyer, Venky N, Li, Xiao-Yong, Biggin, Mark D, ...
The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Pollard, Daniel A, Iyer, Venky N, Moses, Alan M, Eisen, Michael B
The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three...
'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns
Hastie, Trevor, Tibshirani, Robert, Eisen, Michael B, Alizadeh, Ash, Levy, Ronald, Staudt, Louis, ...
Genomic Expression Programs in the Response of Yeast Cells to Environmental ChangesD⃞
Gasch, Audrey P., Spellman, Paul T., Kao, Camilla M., Carmel-Harel, Orna, Eisen, Michael B., Storz, Gisela, ...
We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over...
Distinctive gene expression patterns in human mammary epithelial cells and breast cancers
Perou, Charles M., Jeffrey, Stefanie S., Van De Rijn, Matt, Rees, Christian A., Eisen, Michael B., Ross, Douglas T., ...
cDNA microarrays and a clustering algorithm were used to identify patterns of gene expression in human mammary epithelial cells growing in culture and in primary human breast tumors. Clusters of...
Johannes, Gregg, Carter, Mark S., Eisen, Michael B., Brown, Patrick O., Sarnow, Peter
Although most eukaryotic mRNAs need a functional cap binding complex eIF4F for efficient 5′ end- dependent scanning to initiate translation, picornaviral, hepatitis C viral, and a few cellular RNAs...
Cluster analysis and display of genome-wide expression patterns
Eisen, Michael B., Spellman, Paul T., Brown, Patrick O., Botstein, David
A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in...
Spellman, Paul T., Sherlock, Gavin, Zhang, Michael Q., Iyer, Vishwanath R., Anders, Kirk, Eisen, Michael B., ...
We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures...
Lossos, Izidore S., Alizadeh, Ash A., Eisen, Michael B., Chan, Wing C., Brown, Patrick O., Botstein, David, ...
B cell diffuse large cell lymphoma (B-DLCL) is a heterogeneous group of tumors, based on significant variations in morphology, clinical presentation, and response to treatment. Gene expression...
The Stanford Microarray Database
Sherlock, Gavin, Hernandez-Boussard, Tina, Kasarskis, Andrew, Binkley, Gail, Matese, John C., Dwight, Selina S., ...
The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two...
Miki, Rika, Kadota, Koji, Bono, Hidemasa, Mizuno, Yosuke, Tomaru, Yasuhiro, Carninci, Piero, ...
We have systematically characterized gene expression patterns in 49 adult and embryonic mouse tissues by using cDNA microarrays with 18,816 mouse cDNAs. Cluster analysis defined sets of genes that...
Sørlie, Therese, Perou, Charles M., Tibshirani, Robert, Aas, Turid, Geisler, Stephanie, Johnsen, Hilde, ...
The purpose of this study was to classify breast carcinomas based on variations in gene expression patterns derived from cDNA microarrays and to correlate tumor characteristics to clinical outcome. A...
Berman, Benjamin P., Nibu, Yutaka, Pfeiffer, Barret D., Tomancak, Pavel, Celniker, Susan E., Levine, Michael, ...
A major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. The first step in this process is...
Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
Gasch, Audrey P, Eisen, Michael B
A heuristically modified version of fuzzy k-means clustering has been used to identify overlapping clusters of yeast genes based on published gene-expression data following the response of yeast...
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
The determination of conserved sequences has identified individual transcription factor binding sites. The incorporation of both joint conservation and spacing constraints of sequence pairs predicts...
Position specific variation in the rate of evolution in transcription factor binding sites
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Brown, Patrick O, Eisen, Michael B, Varmus, Harold E
Public Library of Science has grown from a grassroots movement to a nonprofit publisher, in order to catalyze change towards open-access publishing of the scientific literature
Benchmarking tools for the alignment of functional noncoding DNA
Pollard, Daniel A, Bergman, Casey M, Stoye, Jens, Celniker, Susan E, Eisen, Michael B
Fay, Justin C, McCullough, Heather L, Sniegowski, Paul D, Eisen, Michael B
This study compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown in the presence or absence of copper sulfate. Insights were gained into the molecular basis...
Noise Minimization in Eukaryotic Gene Expression
Fraser, Hunter B, Hirsh, Aaron E, Giaever, Guri, Kumm, Jochen, Eisen, Michael B
All organisms have elaborate mechanisms to control rates of protein production. However, protein production is also subject to stochastic fluctuations, or “noise.” Several recent studies in...
Coevolution of gene expression among interacting proteins
Fraser, Hunter B., Hirsh, Aaron E., Wall, Dennis P., Eisen, Michael B.
Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well...
Detecting DNA regulatory motifs by incorporating positional trends in information content
Kechris, Katherina J, Van Zwet, Erik, Bickel, Peter J, Eisen, Michael B
On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, a simple extension to the model-based motif discovery method is proposed....
Berman, Benjamin P, Pfeiffer, Barret D, Laverty, Todd R, Salzberg, Steven L, Rubin, Gerald M, Eisen, Michael B, ...
27 predicted gene-regulatory regions in the Drosophila melanogaster genome were analyzed in vivo, confirming 15 active enhancer regions. A comparison with Drosophila pseudoobscura sequences revealed...
PLoS Medicine— A Medical Journal for the Internet Age
Eisen, Michael B, Brown, Patrick O, Varmus, Harold E
A message from the founders of the Public Library of Science
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi
Gasch, Audrey P, Moses, Alan M, Chiang, Derek Y, Fraser, Hunter B, Berardini, Mark, Eisen, Michael B
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Moses, Alan M, Chiang, Derek Y, Pollard, Daniel A, Iyer, Venky N, Eisen, Michael B
MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments.
Functional genomic analysis of the rates of protein evolution
Wall, Dennis P., Hirsh, Aaron E., Fraser, Hunter B., Kumm, Jochen, Giaever, Guri, Eisen, Michael B., ...
The evolutionary rates of proteins vary over several orders of magnitude. Recent work suggests that analysis of large data sets of evolutionary rates in conjunction with the results from...
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Hotopp, Julie C Dunning, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly:...
Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Dunning Hotopp, Julie C, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
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...
Aging and Gene Expression in the Primate Brain
Fraser, Hunter B, Khaitovich, Philipp, Plotkin, Joshua B, Pääbo, Svante, Eisen, Michael B
It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes...
Levy, Oren, Ptacin, Jerod L., Pease, Paul J., Gore, Jeff, Eisen, Michael B., Bustamante, Carlos, ...
FtsK from Escherichia coli is a fast and sequence-directed DNA translocase with roles in chromosome dimer resolution, segregation, and decatenation. From the movement of single FtsK particles on...
Rapid quantitative profiling of complex microbial populations
Palmer, Chana, Bik, Elisabeth M., Eisen, Michael B., Eckburg, Paul B., Sana, Theodore R., Wolber, Paul K., ...
Diverse and complex microbial ecosystems are found in virtually every environment on earth, yet we know very little about their composition and ecology. Comprehensive identification and...
Flexible promoter architecture requirements for coactivator recruitment
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
Moses, Alan M, Pollard, Daniel A, Nix, David A, Iyer, Venky N, Li, Xiao-Yong, Biggin, Mark D, ...
The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Pollard, Daniel A, Iyer, Venky N, Moses, Alan M, Eisen, Michael B
The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three...
Primate-specific evolution of an LDLR enhancer
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M, Chanan, Sumita, Brown, Myles, ...
Analysis of primate-specific evolution of the LDL receptor enhancer demonstrates a molecular mechanism by which ancestral mammalian regulatory elements can evolve to perform new functions.
Luengo Hendriks, Cris L, Keränen, Soile VE, Fowlkes, Charless C, Simirenko, Lisa, Weber, Gunther H, DePace, Angela H, ...
A suite of methods that provide the first quantitative three-dimensional description of gene expression and morphology with cellular resolution in whole Drosophila embryos is described.
Automatic image analysis for gene expression patterns of fly embryos
Peng, Hanchuan, Long, Fuhui, Zhou, Jie, Leung, Garmay, Eisen, Michael B, Myers, Eugene W
Determining Physical Constraints in Transcriptional Initiation Complexes Using DNA Sequence Analysis
Shultzaberger, Ryan K., Chiang, Derek Y., Moses, Alan M., Eisen, Michael B.
Eukaryotic gene expression is often under the control of cooperatively acting transcription factors whose binding is limited by structural constraints. By determining these structural constraints, we...
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
Li, Xiao-yong, MacArthur, Stewart, Bourgon, Richard, Nix, David, Pollard, Daniel A, Iyer, Venky N, ...
Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to...
Li, Xiao-yong, MacArthur, Stewart, Bourgon, Richard, Nix, David, Pollard, Daniel A, Iyer, Venky N, ...
Hare, Emily E., Peterson, Brant K., Iyer, Venky N., Meier, Rudolf, Eisen, Michael B.
The gene expression pattern specified by an animal regulatory sequence is generally viewed as arising from the particular arrangement of transcription factor binding sites it contains. However, we...
Silent but Not Static: Accelerated Base-Pair Substitution in Silenced Chromatin of Budding Yeasts
Teytelman, Leonid, Eisen, Michael B., Rine, Jasper
Subtelomeric DNA in budding yeasts, like metazoan heterochromatin, is gene poor, repetitive, transiently silenced, and highly dynamic. The rapid evolution of subtelomeric regions is commonly thought...
Tools for neuroanatomy and neurogenetics in Drosophila
Pfeiffer, Barret D., Jenett, Arnim, Hammonds, Ann S., Ngo, Teri-T B., Misra, Sima, Murphy, Christine, ...
We demonstrate the feasibility of generating thousands of transgenic Drosophila melanogaster lines in which the expression of an exogenous gene is reproducibly directed to distinct small subsets of...
Big Genomes Facilitate the Comparative Identification of Regulatory Elements
Peterson, Brant K., Hare, Emily E., Iyer, Venky N., Storage, Steven, Conner, Laura, Papaj, Daniel R., ...
The identification of regulatory sequences in animal genomes remains a significant challenge. Comparative genomic methods that use patterns of evolutionary conservation to identify non-coding...
Rosenblum, Erica Bree, Stajich, Jason E., Maddox, Nicole, Eisen, Michael B.
Amphibians around the world are being threatened by an emerging pathogen, the chytrid fungus Batrachochytrium dendrobatidis (Bd). Despite intensive ecological study in the decade since Bd was...
MacArthur, Stewart, Li, Xiao-Yong, Li, Jingyi, Brown, James B, Chu, Hou Cheng, Zeng, Lucy, ...
Distinct developmental fates in Drosophila melanogaster are specified by quantitative differences in transcription factor occupancy on a common set of bound regions.
Impact of Chromatin Structures on DNA Processing for Genomic Analyses
Teytelman, Leonid, Özaydın, Bilge, Zill, Oliver, Lefrançois, Philippe, Snyder, Michael, Rine, Jasper, ...
Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results...
Rosenblum, Erica Bree, Poorten, Thomas J., Settles, Matthew, Murdoch, Gordon K., Robert, Jacques, Maddox, Nicole, ...
Emerging infectious diseases are of great concern for both wildlife and humans. Several highly virulent fungal pathogens have recently been discovered in natural populations, highlighting the need...
Jans, Judith, Gladden, John M., Ralston, Edward J., Pickle, Catherine S., Michel, Agnès H., Pferdehirt, Rebecca R., ...
In many species, a dosage compensation complex (DCC) is targeted to X chromosomes of one sex to equalize levels of X-gene products between males (1X) and females (2X). Here we identify cis-acting...