Free Factories: Unified Infrastructure for Data Intensive Web Services (2009)
Er Wait Zaranek, Tom Clegg, Ward V, George M. Church
We introduce the Free Factory, a platform for deploying data-intensive web services using small clusters of commodity hardware and free software. Independently administered virtual machines called...
Tuberculosis Drug Resistance Mutation Database (2009)
Andreas Sandgren, Michael Strong, Preetika Muthukrishnan, Brian K. Weiner, George M. Church, Megan B. Murray
Meta-analysis of age-related gene expression profiles identifies common signatures of aging (2009)
De Magalhães, João Pedro, Curado, João, Church, George M.
Motivation: Numerous microarray studies of aging have been conducted, yet given the noisy nature of gene expression changes with age, elucidating the transcriptional features of aging and how these...
Rapid prototyping of 3D DNA-origami shapes with caDNAno (2009)
Douglas, Shawn M., Marblestone, Adam H., Teerapittayanon, Surat, Vazquez, Alejandro, Church, George M., Shih, William M.
DNA nanotechnology exploits the programmable specificity afforded by base-pairing to produce self-assembling macromolecular objects of custom shape. For building megadalton-scale DNA nanostructures,...
Multiplex padlock targeted sequencing reveals human hypermutable CpG variations (2009)
Li, Jin Billy, Gao, Yuan, Aach, John, Zhang, Kun, Kryukov, Gregory V., Xie, Bin, ...
Utilizing the full power of next-generation sequencing often requires the ability to perform large-scale multiplex enrichment of many specific genomic loci in multiple samples. Several technologies...
Evidence for large diversity in the human transcriptome created by Alu RNA editing (2009)
Barak, Michal, Levanon, Erez Y., Eisenberg, Eli, Paz, Nurit, Rechavi, Gideon, Church, George M., ...
Adenosine-to-inosine (A-to-I) RNA editing alters the original genomic content of the human transcriptome and is essential for maintenance of normal life in mammals. A-to-I editing in Alu repeats is...
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...
Ruvkun, Gary, Zuber, Maria T., Gilbert, Walter, Church, George M., Finney, Michael, Johnson, Sarah Stewart, ...
Ting Chen, Ming-yang Kao, Matthew Tepel, John Rush, George M. Church
Tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged molecules of prefix and suffix peptide subsequences, and then measures mass/charge ratios of...
Martha L. Bulyk, Abigail M. Mcguire, Nobuhisa Masuda, George M. Church
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...
Article The Complete Genome and Proteome of Mycoplasma mobile (2008)
Jacob D. Jaffe, Nicole Stange-thomann, Cherylyn Smith, David Decaprio, Sheila Fisher, Jonathan Butler, ...
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...
Leonard M. Anderson, Sung E. Choe, Rustam Y. Yukhananov, Rob L. Hopfner, George M. Church, Richard E. Pratt, ...
We have reported previously that LXRα can mediate a novel cAMP dependent increase in renin and c-myc gene transcription by binding as a monomer to a unique regulatory element, termed the CNRE. To...
2Department of Biological Chemistry and Molecular Pharmacology (2008)
Joseph T. Wade, George M. Church, Kevin Struhl
We perform a genome-wide analysis of the transition between transcriptional initiation and elongation in Escherichia coli by determining the association of core RNA polymerase (RNAP) and the...
André Catic, Cal Collins, George M. Church, Hidde L. Ploegh
1 Catic A, et al. Motivation: The conjugation of ubiquitin to target molecules involves several enzymatic steps. Little is known about the specificity of ubiquitination. How E3 ligases select their...
Localization to the Proteasome Is Sufficient for (2008)
Daniel M. Janse, Bernat Crosas, Daniel Finley, George M. Church
The majority of unstable proteins in eukaryotic cells are targeted for degradation through the ubiquitin-proteasome pathway. Substrates for degradation are recognized by the E1, E2, and E3 ubiquitin...
Methods Discovering functional transcription-factor combinations in the human cell cycle (2008)
Zhou Zhu, Jay Shendure, George M. Church
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...
1 RESEARCH ARTICLE MapQuant: Open-source software for large-scale (2008)
Protein Quantification, Kyriacos C. Leptos, David A. Sarracino, Jacob D. Jaffe, Bryan Krastins, George M. Church
Whole-cell protein quantification using MS has proven to be a challenging task. Detection efficiency varies significantly from peptide to peptide, molecular identities are not evident a priori, and...
Jacob D. Jaffe, D. R. Mani, Kyriacos C. Leptos, George M. Church, Michael A. Gillette, Steven A. Carr
Quantitative proteomics holds considerable promise for elucidation of basic biology and for clinical biomarker discovery. However, it has been difficult to fulfill this promise due to over-reliance...
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...
On the complete determination of biological systems (2007)
Douglas W. Selinger, Matthew A. Wright, George M. Church
The nascent field of systems biology ambitiously proposes to integrate information from large-scale biology projects to create computational models that are, in some sense, complete. However, the...
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...
Abigail Manson Mcguire, George M. Church
Predicting regulons and their cis-regulatory motifs by
Article Systematic Management and Analysis of Yeast Gene Expression Data (2007)
John Aach, Wayne Rindone, George M. Church
We report steps toward the systematic management, standardization, and analysis of functional genomics data. We developed the ExpressDB database for yeast RNA expression data and loaded it with...
Multiplex Sequencing of 1.5 Mb of the Mycobacterium leprae Genome (2007)
Douglas R. Smith, Peter Richterich, Marc Rubenfield, Philip W. Rice, Kathleen Falls, Joan Imrich, ...
The nucleotide sequence of 1.5 Mb of genomic DNA from Mycobacterium leprae was determined using computer-assisted multiplex sequencing technology. This brings the 2.8-Mb M. leprae genome sequence to...
Sarah A. Teichmann, Cyrus Chothia, George M. Church, Jong Park
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...
Neema Jamshidi, Jeremy S. Edwards, Tom Fahl, George M. Church, Bernhard O. Palsson
Dynamic simulation of the human red blood cell
Reveals Positional Patternsof, Douglas W. Selinger, Rini Mukherjee Saxena, Kevin J. Cheung, George M. Church, Carsten Rosenow
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- (2007)
Regulatory Cassette Of, 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...
Molecular Microbiology (2003) 48(3), 699 -- 712 (2007)
Blackwell Publishing Ltd, 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...
Polony Multiplex Analysis of Gene Expression (PMAGE (2007)
Et Al, Hypertrophic Cardiomyopathy, Jae Bum Kim, Jae Bum Kim, Gregory J. Porreca, Lei Song, ...
The following resources related to this article are available online at
Analyses of human–chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging
Synthetic biology projects in vitro (2007)
Forster, Anthony C., Church, George M.
Advances in the in vitro synthesis and evolution of DNA, RNA, and polypeptides are accelerating the construction of biopolymers, pathways, and organisms with novel functions. Known functions are...
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...
PEPPeR, a Platform for Experimental Proteomic Pattern Recognition (2006)
Jacob D. Jaffe, D. R. Mani, Kyriacos C. Leptos, George M. Church, Michael A. Gillette, Steven A. Carr
Quantitative proteomics holds considerable promise for elucidation of basic biology and for clinical biomarker discovery. However, it has been difficult to fulfill this promise due to over-reliance...
Su-in Lee, Aimée M. Dudley, George M. Church, Daphne Koller, Su-in Lee, Aimée M. Dudley, ...
Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification
Supplementary data References (2006)
Joseph T. Wade, George M. Church, Kevin Struhl, Email Alerting, Joseph T. Wade, George M. Church, ...
Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites
Allegra A. Petti, George M. Church, Email Alerting, Allegra A. Petti, George M. Church
doi:10.1101/gr.3847105
Synthetic biology projects in vitro (2006)
Forster, Anthony C., Church, George M.
Advances in the in vitro synthesis and evolution of DNA, RNA, and polypeptides are accelerating the construction of biopolymers, pathways, and organisms with novel functions. Known functions are...
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'...
using 1D-PAGE and LC/MS/MS (2005)
Q Rushdy Ahmad, Dat H Nguyen, Mark A Wingerd, George M Church, Martin A Steffen, George M Church, ...
Molecular weight assessment of proteins in total proteome profiles
You might find this additional information useful... This article cites 44 articles, 13 of which you can access free at:
Opinion Cells discover fire: Employing reactive oxygen species in development (2005)
and consequences for aging
Office Of Science, George M. Church, Jeremy Zucker
Contractor-Grantee Workshop III
Discovering functional transcription-factor combinations in the human cell cycle (2005)
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...
A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae (2005)
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...
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...
systems
Preferred in vivo ubiquitination sites (2004)
Catic, André, Collins, Cal, Church, George M., Ploegh, Hidde L.
Motivation: The conjugation of ubiquitin to target molecules involves several enzymatic steps. Little is known about the specificity of ubiquitination. How E3 ligases select their substrate and which...
The Complete Genome and Proteome of Mycoplasma mobile (2004)
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...
Grad, Yonatan H., Roth, Frederick P., Halfon, Marc S., Church, George M.
Motivation: To date, computational searches for cis-regulatory modules (CRMs) have relied on two methods. The first, phylogenetic footprinting, has been used to find CRMs in non-coding sequence, but...
Preferred in vivo ubiquitination sites (2004)
Catic, André, Collins, Cal, Church, George M., Ploegh, Hidde L.
Motivation: The conjugation of ubiquitin to target molecules involves several enzymatic steps. Little is known about the specificity of ubiquitination. How E3 ligases select their substrate and which...
Grad, Yonatan H., Roth, Frederick P., Halfon, Marc S., Church, George M.
Motivation: To date, computational searches for cis-regulatory modules (CRMs) have relied on two methods. The first, phylogenetic footprinting, has been used to find CRMs in non-coding sequence, but...
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...
Filling gaps in a metabolic network using expression information (2004)
Kharchenko, Peter, Vitkup, Dennis, Church, George M.
Motivation: The metabolic models of both newly sequenced and well-studied organisms contain reactions for which the enzymes have not been identified yet. We present a computational approach for...
yMGV: a cross-species expression data mining tool (2004)
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...
Grad, Yonatan H., Roth, Frederick P., Halfon, Marc S., Church, George M.
Motivation: To date, computational searches for cis-regulatory modules (CRMs) have relied on two methods. The first, phylogenetic footprinting, has been used to find CRMs in non-coding sequence, but...
Preferred in vivo ubiquitination sites (2004)
Catic, André, Collins, Cal, Church, George M., Ploegh, Hidde L.
Motivation: The conjugation of ubiquitin to target molecules involves several enzymatic steps. Little is known about the specificity of ubiquitination. How E3 ligases select their substrate and which...
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...
Martha L. Bulyk, G. A. Whitmore, George M. Church
SUMMARY: There is considerable scientific interest in knowing the probability that a site-specific transcription factor will bind to a given DNA sequence. Microarray methods provide an effective...
Vol Suppl Pages, Oliver D. King, Jeffrey C. Lee, Aimée M. Dudley, Daniel M, George M. Church, ...
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...
Computational and experimental identification of C. elegans microRNAs (2003)
Yonatan Grad, John Aach, Gabriel D. Hayes, Brenda J. Reinhart, George M. Church, Gary Ruvkun, ...
MicroRNAs (miRNAs) constitute an extensive class of noncoding RNAs that are thought to regulate the expression of target genes via complementary base-pair interactions. To date, cloning has...
Digital Quantitative Measurements of Gene Expression (2003)
Venugopal Mikkilineni, Robi D. Mitra, Joshua Merritt, Jason R. Ditonno, George M. Church, Babatunde Ogunnaike, ...
Abstract: One of the primary goals of functional genomics is to provide a quantitative understanding of gene function. However, the success of this enterprise is dependent on the accuracy and...
Kevin Cheu Vasu, Kevin J. Cheung, Vasudeo Badarinarayana, Douglas W. Selinger, Daniel Janse, George M. Church
this paper, we report theappl5K59RS ofwhol579RSO5 microarrays toward understanding the significance of supercoilr - in the osmotic stress response. Osmotic shock is among the most commonenvironmental...
yMGV: a cross-species expression data mining tool (2003)
Gaeèlle Lel, Steâphane Le Crom, Freâdeâric Devaux, Steâphane Vialette, George M. Church, Claude Jacq
The yeast Microarray Global Viewer (yMGV @
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...
Predicting phenotype from patterns of annotation (2003)
King, Oliver D., Lee, Jeffrey C., Dudley, Aimée M., Janse, Daniel M., Church, George M., Roth, Frederick P.
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...
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...
Zhou Zhu, Yitzhak Pilpel, George M. Church
Understanding how the expression levels of thousands of genes are regulated at all times in the life of a cell remains one of the greatest challenges of molecular biology. A major component
Copyright American Society, 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...
Genome-Scale Metabolic Model of Helicobacter pylori 26695 (2002)
Christophe H. Schilling, Markus W. Covert, Iman Famili, George M. Church, Jeremy S. Edwards, ...
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 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...
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...
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...
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...
A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001)
Ting Chen, Ming-yang Kao, Matthew Tepel, John Rush, George M. Church
Tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged molecules of pre � x and suf � x peptide subsequences and then measures mass/charge ratios...
Dynamic simulation of the human red blood cell metabolic network (2001)
Jamshidi, Neema, Edwards, Jeremy S., Fahland, Tom, Church, George M., Palsson, Bernhard O.
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...
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...
Jason D. Hughes, Preston W. Estep, Saeed Tavazoie, George M. Church
The recent increase in the number of sequenced genomes and the amount of genome-scale experimental data allows the use of computational techniques to investigate cis-acting sequences controlling
T. Chen, Ting Chen, Ming-yang Kao, Matthew Tepel, John Rush, George M. Church
) Ting Chen Ming-Yang Kao y Matthew Tepel z John Rush x George M. Church -- Abstract The tandem mass spectrometry fragments molecules of the same peptide sequence into charged prefix and suffix...
Single Molecule Profiling of Alternative Pre-mRNA Splicing (2000)
R Eports, R. A. Reenan, C. J. Hanrahan, B. Ganetzky, P. J. Aruscavage, B. L. Bass, ...
Alternative pre-messenger RNA splicing is an important mechanism for generating protein diversity and may explain in part how mammalian complexity arises from a surprisingly small complement of...
Teichmann, Sarah A., Chothia, Cyrus, Church, George M., Park, Jong
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...
Conservation of DNA Regulatory Motifs and Discovery of New Motifs in Microbial Genomes (2000)
McGuire, Abigail Manson, Hughes, Jason D., Church, George M.
Predicting regulons and their cis-regulatory motifs by comparative genomics (2000)
Manson McGuire, Abigail, 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...
Modeling gene expression with differential equations (1999)
Ting Chen, Hongyu L. He, George M. Church
We propose a di erential equation model for gene expression and provide two methods to construct the model from a set of temporal data. We model both transcription and translation by kinetic...
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)...
Jason M. Johnson, George M. Church
The emergence of drug-resistant strains of bacteria is a signi®cant and growing human health problem. Active ef¯ux pumps with broad speci-®city are involved in the intrinsic and acquired
Keith Robison, Abigail Manson Mcguire, George M. Church
Sequence-speci®c 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 proteins that
Complete Genome Sequence of Methanobacterium thermoautotrophicum ΔH: Functional . . . (1997)
Douglas R. Smith, Craig Deloughery, Hongmei Lee, Joann Dubois, ...
the ORF-encoded polypeptides are related to sequences with unknown functions, and 496 (27%) have little or no homology to sequences in public databases. Comparisons with Eucarya-, Bacteria-, and...
Multiplex Sequencing of 1.5 Mb of the Mycobacterium leprae Genome (1997)
Smith, Douglas R., Richterich, Peter, Rubenfield, Marc, Rice, Philip W., Butler, Carol, Lee, Hong-Mei, ...
Barak A. Cohen, Yitzhak Pilpel, Robi D. Mitra, George M. Church
duplication with subsequent divergence of paralogs could be a major force in the evolution of new gene functions. In practice the functional differences between closely related homologues produced by...
Cytosine specific DNA sequencing with hydrogen peroxide (1995)
Richterich, Peter, Lakey, Nathan D., Lee, Hong-Mei, Mao, Jen-i, Smith, Doug, Church, George M.
Genetic elements within yeast mitochondrial and mouse immunoglobulin introns / (1984)
Church, George M. (George McDonald)
Thesis (Ph. D.)--Harvard University, 1984.
The cleavage site of the restriction endonuclease Ava II (1978)
J. Gregor Sutcliffe, George M. Church
We have determined that the type II restriction enzyme Ava II, isolated from Anabaena variabilis, recognizes and cuts the sequence
The cleavage site of the restriction endonuclease Ava II (1978)
Sutcliffe, J.Gregor, Church, George M.
We have determined that the type II restriction enzyme Ava II, isolated from Anabaena variabilis, recognizes and cuts the sequence 5′ - G↓GTCC - 3′ 3′ - CCAG↑G - 5′ The eight Ava II sites...
S. C. Abrahams, L. Sussman, Stephen R. Holbrook, George M. Church, Sung-hou Kim
A method of structure-factor least-squares refinement of constrained groups linked by distance restraints has been developed for the refinement of macromolecular structures. Each constrained group...
RNA-ligand interactions. (I) magnesium binding sites in yeast tRNA phe (1977)
Stephen R. Holbrook, Joel L. Sussman, R. Wade Warrant, George M. Church
X-ray crystallographic studies indicate that there are at least four site-specifically bound hydrated Mg2+ ions, [Mg(H20)n]2+, in yeast tRNAPhe. The size and the octahedral coordination geometry,...
RNA - ligand interactions:(I) magnesium binding sites in yeast tRNAPhe (1977)
Holbrook, Stephen R., Sussman, Joel L., Warrant, R. Wade, Church, George M., Kim, Sung-Hou
X-ray crystallographic studies indicate that there are at least four site-specifically bound hydrated Mg2+ ions, [Mg(H2O)n]2+, in yeast tRNAPhe. The size and the octahedral coordination geometry,...
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...
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...
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...
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...
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...
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...
Identifying metabolic enzymes with multiple types of association evidence
Kharchenko, Peter, Chen, Lifeng, Freund, Yoav, Vitkup, Dennis, Church, George M
Expression dynamics of a cellular metabolic network
Kharchenko, Peter, Church, George M, Vitkup, Dennis
Toward the goal of understanding system properties of biological networks, we investigate the global and local regulation of gene expression in the Saccharomyces cerevisiae metabolic network. Our...
Towards synthesis of a minimal cell
Forster, Anthony C, Church, George M
Construction of a chemical system capable of replication and evolution, fed only by small molecule nutrients, is now conceivable. This could be achieved by stepwise integration of decades of work on...
Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability
Tolonen, Andrew C, Aach, John, Lindell, Debbie, Johnson, Zackary I, Rector, Trent, Steen, Robert, ...
Nitrogen (N) often limits biological productivity in the oceanic gyres where Prochlorococcus is the most abundant photosynthetic organism. The Prochlorococcus community is composed of strains, such...
Lee, Su-In, Pe'er, Dana, Dudley, Aimée M., Church, George M., Koller, Daphne
Sequence polymorphisms affect gene expression by perturbing the complex network of regulatory interactions. We propose a probabilistic method, called Geronemo, which directly aims to identify the...
Chromosomal periodicity of evolutionarily conserved gene pairs
Wright, Matthew A., Kharchenko, Peter, Church, George M., Segrè, Daniel
Chromosomes are compacted hundreds of times to fit in the cell, packaged into dynamic folds whose structures are largely unknown. Here, we examine patterns in gene locations to infer large-scale...
Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus
Kettler, Gregory C, Martiny, Adam C, Huang, Katherine, Zucker, Jeremy, Coleman, Maureen L, Rodrigue, Sebastien, ...
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...
Snitkin, Evan S, Dudley, Aimée M, Janse, Daniel M, Wong, Kaisheen, Church, George M, Segrè, Daniel
An iterative approach that integrates high-throughput measurements of yeast deletion mutants and flux balance model predictions improves understanding of both experimental and computational results.
Hippocrates revisited? Old ideals and new realities
Lunshof, Jeantine E., Chadwick, Ruth, Church, George M.
Individual genomics has arrived, personal decisions to make use of it are a new reality. What are the implications for the patient–physician relationship? In this article we address three factors...
Schwartz, Daniel, Chou, Michael F., Church, George M.
Protein post-translational modifications are an important biological regulatory mechanism, and the rate of their discovery using high throughput techniques is rapidly increasingly. To make use of...
Tuberculosis Drug Resistance Mutation Database
Sandgren, Andreas, Strong, Michael, Muthukrishnan, Preetika, Weiner, Brian K, Church, George M, Murray, Megan B
Andreas Sandgren and colleagues describe a new comprehensive resource on drug resistance mutations inM. tuberculosis.
PEPPeR: A Platform for Experimental Proteomic Pattern Recognition
Jaffe, Jacob D., Mani, D. R., Leptos, Kyriacos C., Church, George M., Gillette, Michael A., Carr, Steven A.
Large-scale identification of genetic design strategies using local search
Lun, Desmond S, Rockwell, Graham, Guido, Nicholas J, Baym, Michael, Kelner, Jonathan A, Berger, Bonnie, ...
In the past decade, computational methods have been shown to be well suited to unraveling the complex web of metabolic reactions in biological systems. Methods based on flux–balance analysis (FBA)...
Rapid prototyping of 3D DNA-origami shapes with caDNAno
Douglas, Shawn M., Marblestone, Adam H., Teerapittayanon, Surat, Vazquez, Alejandro, Church, George M., Shih, William M.
DNA nanotechnology exploits the programmable specificity afforded by base-pairing to produce self-assembling macromolecular objects of custom shape. For building megadalton-scale DNA nanostructures,...
Lee, Je-Hyuk, Park, In-Hyun, Gao, Yuan, Li, Jin Billy, Li, Zhe, Daley, George Q., ...
Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in...
Evidence for large diversity in the human transcriptome created by Alu RNA editing
Barak, Michal, Levanon, Erez Y., Eisenberg, Eli, Paz, Nurit, Rechavi, Gideon, Church, George M., ...
Adenosine-to-inosine (A-to-I) RNA editing alters the original genomic content of the human transcriptome and is essential for maintenance of normal life in mammals. A-to-I editing in Alu repeats is...