Ruvkun, Gary, Zuber, Maria T., Gilbert, Walter, Church, George M., Finney, Michael, Johnson, Sarah Stewart, ...
Snitkin, Evan S, Dudley, Aimée M, Janse, Daniel M, Wong, Kaisheen, Church, George M, Segrè, Daniel
Abstract Background Understanding the response of complex biochemical networks to genetic perturbations and environmental variability is a fundamental challenge in biology. Integration of...
Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus (2007)
Gregory C. Kettler, Adam C. Martiny, Katherine Huang, Jeremy Zucker, Maureen L. Coleman, Sebastien Rodrigue, ...
Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolates from diverse areas of the world's oceans...
Identifying metabolic enzymes with multiple types of association evidence (2006)
Kharchenko, Peter, Chen, Lifeng, Freund, Yoav, Vitkup, Dennis, Church, George M
Abstract Background Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational...
Beatriz Estrada, Sung E. Choe, Stephen S. Gisselbrecht, Sebastien Michaud, Lakshmi Raj, Brian W. Busser, ...
An important but largely unmet challenge in understanding the mechanisms that govern the formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the...
Molecular weight assessment of proteins in total proteome profiles using 1D-PAGE and LC/MS/MS (2005)
Ahmad, Q Rushdy, Nguyen, Dat H, Wingerd, Mark A, Church, George M, Steffen, Martin A
Abstract Background The observed molecular weight of a protein on a 1D polyacrylamide gel can provide meaningful insight into its biological function. Differences between a protein's observed...
Choe, Sung E, Boutros, Michael, Michelson, Alan M, Church, George M, Halfon, Marc S
Abstract Background As more methods are developed to analyze RNA-profiling data, assessing their performance using control datasets becomes increasingly important. Results We present a 'spike-in'...
The amino-acid mutational spectrum of human genetic disease (2003)
Vitkup, Dennis, Sander, Chris, Church, George M
Abstract Background Nonsynonymous mutations in the coding regions of human genes are responsible for phenotypic differences between humans and for susceptibility to genetic disease. Computational...
Nobuhisa Masuda, George M. Church
ed with TolC and contributes to multidrug resistance. Bacteria have developed sophisticated signaling systems for adaptive responses to a variety of environments. One of the major mechanisms of...
Christophe H. Schilling, Markus W. Covert, Iman Famili, George M. Church, Jeremy S. Edwards, Bernhard O. Palsson
this article cannot proceed without the signature of the person who read and corrected the proof on behalf of all the authors: signature date Fn* AQ: A can be learned from the genome of...
Martha L. Bulyk, George M. Church
We can determine the effects of many possible sequence variations in transcription factor binding sites using microarray binding experiments. Analysis of wild-type and mutant Zif268 (Egr1) zinc...
Kevin J. Cheung, George M. Church
tionof its abundance and degradation. We discuss the applicationof subgenic resolution DNA microarray analysis to study global mechanismsof RNA transcription and processing. Gene regulatiB i adynami...
Genome-Wide Co-Occurrence of Promoter Elements Reveals a Cis- (2003)
Priya Sudarsanam, Yitzhak Pilpel, George M. Church
Combinatorial regulation is an important feature of eukaryotic transcription. However, only a limited number of studies have characterized this aspect on a whole-genome level. We have conducted a...
Computational Identification of Transcription Factor (2003)
Zhou Zhu, Yitzhak Pilpel, George M. Church
addition, we also made de novo predictions for some unknown TF binding sites. q 2002 Elsevier Science Ltd. All rights reserved Keywords: computational biology; transcription factor; clustering; DNA...
Molecular Microbiology (2003) 48(3), 699 -- 712 (2003)
Nobuhisa Masuda, George M. Church
this paper are taken from http://bmb.med.miami.edu/EcoGene/ EcoWeb/.) Results and discussion Induction of acid resistance by overexpression of YdeP, YdeO and YhiE in exponentially growing cells We...
Oliver D. King, Jeffrey C. Lee, Daniel M, George M. Church, Frederick P. Roth
Motivation: Predicting the outcome of specific experiments (such as the growth of a particular mutant strain in a particular medium) has the potential to allow researchers to devote resources to...
Background: Overlapping but oppositely oriented transcripts have the potential to form senseantisense perfect double-stranded (ds) RNA duplexes. Over recent years, the number and variety of examples...
On the Complete Determination of Biological Systems (2003)
Douglas W. Selinger, Matthew A. Wright, George M. Church
one, was to compile a large number of systems that are interesting (those that define a general rule, break one or appeal to us as idiosyncratic human beings) or applicable (those that contribute to...
Computational discovery of sense-antisense transcription in the human and mouse genomes (2002)
Shendure, Jay, Church, George M
Abstract Background Overlapping but oppositely oriented transcripts have the potential to form sense-antisense perfect double-stranded (ds) RNA duplexes. Over recent years, the number and variety of...
A Statistical Model for Investigating Binding Probabilities (2002)
Martha L. Bulyk, George M. Church
this paper. We turn to this topic in the next section
Molecular Biology of the Cell (2002)
Barak A. Cohen, Yitzhak Pilpel, Robi D. Mitra, George M. Church
this report we focus on the response to H 2 O 2, but the full dataset is available at http://arep.med.harvard.edu/ExpressDB
Sarah A. Teichmann, Cyrus Chothia, George M. Church
Motivation: For large-scale structural assignment to sequences, as in computational structural genomics, a fast yet sensitive sequence search procedure is essential. A new approach using intermediate...
Jason D. Hughes, Preston W. Estep, Saeed Tavazoie, George M. Church
ns on randomly selected sets of genes and on sets of genes whose upstream regions contain known transcription factor binding sites serve as controls. # 2000 Academic Press Keywords: bioinformatics;...
Dynamic Simulation of the Human Red Blood Cell Metabolic Network (2001)
Neema Jamshidi, Jeremy S. Edwards, Tom Fahland, George M. Church, Bernhard O. Palsson
Summary: We have developed a Mathematica # application package to perform dynamic simulations of the red blood cell (RBC) metabolic network. The package relies on, and integrates, many years of...
Predicting Regulons and Their Cis-Regulatory Motifs By Comparative Genomics (2001)
Abigail Manson Mcguire, George M. Church
We have combined and compared three techniques for predicting functional interactions based on comparative genomics (methods based on conserved operons, protein fusions and correlated evolution) and...
Aligning Gene Expression Time Series With Time Warping Algorithms (2001)
Motivation: Increasingly, biological processes are being studied through time series of RNA expression data collected for large numbers of genes. Because common processes may unfold at varying rates...
Modeling Gene Expression With Differential Equations (2001)
Ting Chen, Hongyu L. He, George M. Church
this paper, we propose a linear differential equation model for gene expression and two algorithms to solve the differential equations. Potentially, our methods answer the practical questions in (1)...
A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001)
Chen, Ting, Kao, Ming-Yang, Tepel, Matthew, Rush, John, Church, George M.
The tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged prefix and suffix subsequences, and then measures mass/charge ratios of these ions. The de...
Margret R. Hoehe, Birgit Wendel, Klaus Rohde, Christina Flachmeier, Kenneth K. Kidd, George M. Church
in substance (heroin/cocaine) dependence. All known functionally relevant regions of this prime candidate gene were analyzed by multiplex sequence comparison in 250 cases and controls; 43 variants...
A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2000)
Ting Chen, Ming-yang Kao, Matthew Tepel, John Rush, George M. Church
The tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged molecules of prex and sux peptide subsequences, and then measures mass/charge ratios of...
Algorithms for Identifying Protein Cross-links via Tandem Mass Spectrometry (2000)
Ting Chen, Jake Jaffe, George M. Church
Cross-linking technology combined with tandem mass spectrometry is a powerful method that provides a rapid solution to the discovery of protein-protein interactions and protein structures. We studied...
localized amplification and contact replication of many individual DNA molecules (2000)
Robi D. Mitra, George M. Church
We describe a method to clone and amplify DNA by performing the polymerase chain reaction (PCR) in a thin polyacrylamide film poured on a glass microscope slide. The polyacrylamide matrix retards the...
Modeling Gene Expression With Differential Equations (2000)
Ting Chen, Hongyu L. He, George M. Church
this paper, we propose a linear differential equation model for gene expression and two algorithms to solve the differential equations. Potentially, our methods answer the practical questions in (1)...
Biclustering of Expression Data (2000)
Yizong Cheng, George M. Church
## ###### ############# ######### ## ########## ## ### ########### ## ########## #### #### ####### #### ####### ####### ###### ### ## ## ##### ## ####### #### ## ###### ############# ######## ##...
Systematic Management and Analysis of Yeast Gene Expression Data (2000)
John Aach, Wayne Rindone, George M. Church
roarrays, Serial Analysis of Gene Expression (SAGE), and other techniques (Velculescu et al. 1995; Lockhart et al. 1996; DeRisi et al. 1997), has led to the rapid accumulation of large expression...
Keith Robison, Abigail Manson Mcguire, George M. Church
Introduction Sequence-specic DNA-binding proteins perform a multitude of roles in a living cell and regulate a variety of processes including transcription. Escherichia coli contains at least 240...
Modeling Gene Expression With Differential Equations (1999)
Ting Chen, Hongyu L. He, George M. Church
this paper, we propose a linear differential equation model for gene expression and two algorithms to solve the differential equations. Potentially, our methods answer the practical questions in (1)...
Modeling Gene Expression With Differential Equations (1998)
Ting Chen, Hongyu L. He, George M. Church
this paper, we propose a linear di#erential equation model for gene expression and two algorithms to solve the di#erential equations. Potentially, our methods answer the practical questions in #1#...
Genetic elements within yeast mitochondrial and mouse immunoglobulin introns / (1984)
Church, George M. (George McDonald)
Thesis (Ph. D.)--Harvard University, 1984.
Predicting ligand-binding function in families of bacterial receptors
Johnson, Jason M., Church, George M.
The three-dimensional fold of a new protein sequence can often be inferred directly from sequence homology to a protein of known structure. The function of a new protein sequence is more difficult to...
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
Bulyk, Martha L., Huang, Xiaohua, Choo, Yen, Church, George M.
A key step in the regulation of networks that control gene expression is the sequence-specific binding of transcription factors to their DNA recognition sites. A more complete understanding of these...
Jelinsky, Scott A., Estep, Preston, Church, George M., Samson, Leona D.
Exposure to carcinogenic alkylating agents, oxidizing agents, and ionizing radiation modulates transcript levels for over one third of Saccharomyces cerevisiae's 6,200 genes. Computational analysis...
Bulyk, Martha L., Johnson, Philip L. F., Church, George M.
We can determine the effects of many possible sequence variations in transcription factor binding sites using microarray binding experiments. Analysis of wild-type and mutant Zif268 (Egr1) zinc...
Cohen, Barak A., Pilpel, Yitzhak, Mitra, Robi D., Church, George M.
Ohno [Ohno, S. (1970) in Evolution by Gene Duplication, Springer, New York] proposed that gene duplication with subsequent divergence of paralogs could be a major force in the evolution of new gene...
Predicting regulons and their cis-regulatory motifs by comparative genomics
McGuire, Abigail Manson, Church, George M.
We have combined and compared three techniques for predicting functional interactions based on comparative genomics (methods based on conserved operons, protein fusions and correlated evolution) and...
Dudley, Aimée M., Aach, John, Steffen, Martin A., Church, George M.
Gene expression ratios derived from spotted-glass microarray experiments have become invaluable to researchers by providing sensitive and comprehensive indicators of the molecular underpinnings of...
Computational discovery of sense-antisense transcription in the human and mouse genomes
Shendure, Jay, Church, George M
Overlapping but oppositely oriented transcripts have the potential to form sense-antisense perfect double-stranded (ds) RNA duplexes. A bioinformatics approach has identified over 217 candidate...
Genome-Scale Metabolic Model of Helicobacter pylori 26695
Schilling, Christophe H., Covert, Markus W., Famili, Iman, Church, George M., Edwards, Jeremy S., Palsson, Bernhard O.
A genome-scale metabolic model of Helicobacter pylori 26695 was constructed from genome sequence annotation, biochemical, and physiological data. This represents an in silico model largely derived...
Analysis of optimality in natural and perturbed metabolic networks
Segrè, Daniel, Vitkup, Dennis, Church, George M.
An important goal of whole-cell computational modeling is to integrate detailed biochemical information with biological intuition to produce testable predictions. Based on the premise that...
Escherichia coli Gene Expression Responsive to Levels of the Response Regulator EvgA
Masuda, Nobuhisa, Church, George M.
To investigate the function of the EvgA response regulator, we compared the genome-wide transcription profile of EvgA-overexpressing and EvgA-lacking Escherichia coli strains by oligonucleotide...
Digital genotyping and haplotyping with polymerase colonies
Mitra, Robi D., Butty, Vincent L., Shendure, Jay, Williams, Benjamin R., Housman, David E., Church, George M.
Polymerase colony (polony) technology amplifies multiple individual DNA molecules within a thin acrylamide gel attached to a microscope slide. Each DNA molecule included in the reaction produces an...
Merritt, Joshua, DiTonno, Jason R., Mitra, Robi D., Church, George M., Edwards, Jeremy S.
We describe a strategy to analyze the impact of single nucleotide mutations on protein function. Our method utilizes a combination of yeast functional complementation, growth competition of mutant...
Halfon, Marc S., Grad, Yonatan, Church, George M., Michelson, Alan M.
Gene expression is regulated by transcription factors that interact with cis-regulatory elements. Predicting these elements from sequence data has proven difficult. We describe here a successful...
Sudarsanam, Priya, Pilpel, Yitzhak, Church, George M.
Combinatorial regulation is an important feature of eukaryotic transcription. However, only a limited number of studies have characterized this aspect on a whole-genome level. We have conducted a...
yMGV: a cross-species expression data mining tool
Lelandais, Gaëlle, Le Crom, Stéphane, Devaux, Frédéric, Vialette, Stéphane, Church, George M., Jacq, Claude, ...
The yeast Microarray Global Viewer (yMGV @ http://transcriptome.ens.fr/ymgv) was created 3 years ago as a database that houses a collection of Saccharomyces cerevisiae and Schizosaccharo myces pombe...
Identification of many microRNAs that copurify with polyribosomes in mammalian neurons
Kim, John, Krichevsky, Anna, Grad, Yonatan, Hayes, Gabriel D., Kosik, Kenneth S., Church, George M., ...
Localized translation in mammalian dendrites may play a role in synaptic plasticity and contribute to the molecular basis for learning and memory. The regulatory mechanisms that control localized...
Bulyk, Martha L., McGuire, Abigail M., Masuda, Nobuhisa, Church, George M.
Various computational approaches have been developed for predicting cis-regulatory DNA elements in prokaryotic genomes. We describe a novel method for predicting transcription-factor-binding sites in...
The amino-acid mutational spectrum of human genetic disease
Vitkup, Dennis, Sander, Chris, Church, George M
The human disease spectrum is compared to the spectra of mutual amino-acid mutation frequencies, non-disease polymorphisms in human genes, and substitutions fixed between species.
Cheung, Kevin J., Badarinarayana, Vasudeo, Selinger, Douglas W., Janse, Daniel, Church, George M.
Changes in DNA supercoiling are induced by a wide range of environmental stresses in Escherichia coli, but the physiological significance of these responses remains unclear. We now demonstrate that...
Selinger, Douglas W., Saxena, Rini Mukherjee, Cheung, Kevin J., Church, George M., Rosenow, Carsten
Subgenic-resolution oligonucleotide microarrays were used to study global RNA degradation in wild-type Escherichia coli MG1655. RNA chemical half-lives were measured for 1036 open reading frames...
The Complete Genome and Proteome of Mycoplasma mobile
Jaffe, Jacob D., Stange-Thomann, Nicole, Smith, Cherylyn, DeCaprio, David, Fisher, Sheila, Butler, Jonathan, ...
Although often considered “minimal” organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete...
Discovering functional transcription-factor combinations in the human cell cycle
Zhu, Zhou, Shendure, Jay, Church, George M.
With the completion of full genome sequences and advancement in high-throughput technologies, in silico methods have been successfully used to integrate diverse data sources toward unraveling the...
Molecular weight assessment of proteins in total proteome profiles using 1D-PAGE and LC/MS/MS
Ahmad, Q Rushdy, Nguyen, Dat H, Wingerd, Mark A, Church, George M, Steffen, Martin A
A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae
Petti, Allegra A., Church, George M.
Recent computational and experimental work suggests that functional modules underlie much of cellular physiology and are a useful unit of cellular organization from the perspective of systems...
Estrada, Beatriz, Choe, Sung E, Gisselbrecht, Stephen S, Michaud, Sebastien, Raj, Lakshmi, Busser, Brian W, ...
An important but largely unmet challenge in understanding the mechanisms that govern the formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the...
Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
Choe, Sung E, Boutros, Michael, Michelson, Alan M, Church, George M, Halfon, Marc S
A 'spike-in' experiment for Affymetrix GeneChips is described that provides a defined dataset of 3,860 RNA species. A 'best route' combination of analysis methods is presented which allows detection...
Wade, Joseph T., Reppas, Nikos B., Church, George M., Struhl, Kevin
Genomes of eukaryotic organisms are packaged into nucleosomes that restrict the binding of transcription factors to accessible regions. Bacteria do not contain histones, but they have...
Identifying metabolic enzymes with multiple types of association evidence
Kharchenko, Peter, Chen, Lifeng, Freund, Yoav, Vitkup, Dennis, Church, George M
Predicting ligand-binding function in families of bacterial receptors
Johnson, Jason M., Church, George M.
The three-dimensional fold of a new protein sequence can often be inferred directly from sequence homology to a protein of known structure. The function of a new protein sequence is more difficult to...
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
Bulyk, Martha L., Huang, Xiaohua, Choo, Yen, Church, George M.
A key step in the regulation of networks that control gene expression is the sequence-specific binding of transcription factors to their DNA recognition sites. A more complete understanding of these...
Jelinsky, Scott A., Estep, Preston, Church, George M., Samson, Leona D.
Exposure to carcinogenic alkylating agents, oxidizing agents, and ionizing radiation modulates transcript levels for over one third of Saccharomyces cerevisiae's 6,200 genes. Computational analysis...
Bulyk, Martha L., Johnson, Philip L. F., Church, George M.
We can determine the effects of many possible sequence variations in transcription factor binding sites using microarray binding experiments. Analysis of wild-type and mutant Zif268 (Egr1) zinc...
Cohen, Barak A., Pilpel, Yitzhak, Mitra, Robi D., Church, George M.
Ohno [Ohno, S. (1970) in Evolution by Gene Duplication, Springer, New York] proposed that gene duplication with subsequent divergence of paralogs could be a major force in the evolution of new gene...