Author details

Full Name

Neil D Clarke

Affiliation

Yale-NUS College Singapore

ORCID

Career Start Year

1981

Papers

H Index

Expertise

CM4AI Collaborator

Nathan Sheffield (CM4AI)

PMID	Paper Title	Journal Title	Published Year
31324835	Gains and losses of metabolic function inferred from a phylotranscriptomic analysis of algae.	Sci Rep	2019
23558744	Differential binding of the related transcription factors Pho4 and Cbf1 can tune the sensitivity of promoters to different levels of an induction signal.	Nucleic Acids Res	2013
22570629	Dynamic deposition of histone variant H3.3 accompanies developmental remodeling of the Arabidopsis transcriptome.	PLoS Genet	2012
23185583	Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes.	PLoS One	2012
22987856	Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell.	J Integr Bioinform	2012
21750106	Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.	Genome Res	2011
20098497	Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local.	PLoS Comput Biol	2010
21179027	Integrative model of genomic factors for determining binding site selection by estrogen receptor-Î±.	Mol Syst Biol	2010
20953172	A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity.	Nature	2010
20591648	Protein engineering for bioenergy and biomass-based chemicals.	Curr Opin Struct Biol	2010
20186320	Towards a rigorous assessment of systems biology models: the DREAM3 challenges.	PLoS One	2010
20126276	Success in the DREAM3 signaling response challenge using simple weighted-average imputation: lessons for community-wide experiments in systems biology.	PLoS One	2010
20412781	Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst.	Dev Cell	2010
19193152	Inferring transcription factor targets from gene expression changes and predicted promoter occupancy.	J Comput Biol	2009
19348643	Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge.	Ann N Y Acad Sci	2009
18555785	Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.	Cell	2008
19111667	A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.	Mol Cell	2008
17654725	Domain definition and target classification for CASP7.	Proteins	2007
17894354	Automated server predictions in CASP7.	Proteins	2007
17894330	Assessment of CASP7 structure predictions for template free targets.	Proteins	2007
17671976	Assessment of intramolecular contact predictions for CASP7.	Proteins	2007
16923194	Inferring direct regulatory targets from expression and genome location analyses: a comparison of transcription factor deletion and overexpression.	BMC Genomics	2006
17053089	Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.	Genome Res	2006
15710749	DIP-chip: rapid and accurate determination of DNA-binding specificity.	Genome Res	2005
16207358	Explicit equilibrium modeling of transcription-factor binding and gene regulation.	Genome Biol	2005
16377560	Control of transcription through intragenic patterns of nucleosome composition.	Cell	2005
15221026	DNA binding and nucleotide flipping by the human DNA repair protein AGT.	Nat Struct Mol Biol	2004
15226427	Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts.	Mol Cell Biol	2004
12538241	Rank order metrics for quantifying the association of sequence features with gene regulation.	Bioinformatics	2003
12368093	Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities.	J Mol Biol	2002
11574685	Covalent capture of a human O(6)-alkylguanine alkyltransferase-DNA complex using N(1),O(6)-ethanoxanthosine, a mechanism-based crosslinker.	Nucleic Acids Res	2001
10813834	Assignment of enzyme substrate specificity by principal component analysis of aligned protein sequences: an experimental test using DNA glycosylase homologs.	Proteins	2000
10677686	Dominant sensitization variants of human O(6)-methylguanine-DNA-methyltransferase obtained by a mutational screen of surface residues.	Mutat Res	2000
10521423	Characterization of an 8-oxoguanine DNA glycosylase from Methanococcus jannaschii.	J Biol Chem	1999
10350454	The C-terminal domain of the adenine-DNA glycosylase MutY confers specificity for 8-oxoguanine.adenine mispairs and may have evolved from MutT, an 8-oxo-dGTPase.	Biochemistry	1999
9729739	Computer search algorithms in protein modification and design.	Curr Opin Struct Biol	1998
9489921	A hybrid sequence approach to the paracelsus challenge.	Proteins	1998
9851917	Zinc fingers in Caenorhabditis elegans: finding families and probing pathways.	Science	1998
9287154	Specificity of DNA repair methyltransferases determined by competitive inactivation with oligonucleotide substrates: evidence that Escherichia coli Ada repairs O6-methylguanine and O4-methylthymine with similar efficiency.	Biochemistry	1997
9126605	Construction and overexpression of a synthetic gene for human DNA methylguanine methyltransferase: renaturation and rapid purification of the protein.	Protein Expr Purif	1997
9108163	Formation of a covalent complex between methylguanine methyltransferase and DNA via disulfide bond formation between the active site cysteine and a thiol-containing analog of guanine.	Nucleic Acids Res	1997
8759343	Innervation of the chick cornea analyzed in vitro.	Invest Ophthalmol Vis Sci	1996
8988002	Specific recognition of A/G and A/7,8-dihydro-8-oxoguanine (8-oxoG) mismatches by Escherichia coli MutY: removal of the C-terminal domain preferentially affects A/8-oxoG recognition.	Biochemistry	1996
7664093	Novel metal-binding proteins by design.	Nat Struct Biol	1995
8563623	Covariation of residues in the homeodomain sequence family.	Protein Sci	1995
8592706	Metal search: a computer program that helps design tetrahedral metal-binding sites.	Proteins	1995
7579658	Sequence 'minimization': exploring the sequence landscape with simplified sequences.	Curr Opin Biotechnol	1995
7972014	A proposed mechanism for the self-splicing of proteins.	Proc Natl Acad Sci U S A	1994
7849596	Structural studies of the engrailed homeodomain.	Protein Sci	1994
1833818	The DNA binding arm of lambda repressor: critical contacts from a flexible region.	Science	1991

1 - 50 of 56

Madan Mohan Babu

St. Jude Children's Research Hospital

Career Start Year 2002

Number of shared co-authors 1

Jeffrey B Bonanno

Albert Einstein College of Medicine

Career Start Year 1999

Number of shared co-authors 0

Yury Patskovsky

New York University Grossman School of Medicine

Career Start Year 1998

Number of shared co-authors 0

Christopher T Workman

Technical University of Denmark

Career Start Year 1995

Number of shared co-authors 1

Terry Gaasterland

Scripps Institution of Oceanography, University of California San Diego

Career Start Year 1994

Number of shared co-authors 2

Steven E Brenner

University of California berkeley

Career Start Year 1994

Number of shared co-authors 8

Finn Drabl??s

NTNU - Norwegian University of Science and Technology

Career Start Year 1994

Number of shared co-authors 1

Zhiping Weng

University of Massachusetts Medical School

Career Start Year 1992

Number of shared co-authors 15

Dietlind L Gerloff

Foundation for Applied Molecular Evolution (FfAME)

Career Start Year 1991

Number of shared co-authors 0

Robert B Russell

Heidelberg University

Career Start Year 1991

Number of shared co-authors 0

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 15

Cheryl H Arrowsmith

University of Toronto

Career Start Year 1989

Number of shared co-authors 5

P??r Nordlund

Karolinska Institutet, BioClinicum J6

Career Start Year 1989

Number of shared co-authors 0

Steven C Almo

Albert Einstein College of Medicine

Career Start Year 1988

Number of shared co-authors 0

Liang Tong

Columbia University

Career Start Year 1988

Number of shared co-authors 1

Mark W Knuth

Joint Center for Structural Genomics

Career Start Year 1988

Number of shared co-authors 1

Christopher W V Hogue

National University of Singapore

Career Start Year 1987

Number of shared co-authors 0

Adam Godzik

University of California Riverside

Career Start Year 1987

Number of shared co-authors 4

Stanley Fields

University of Washington

Career Start Year 1985

Number of shared co-authors 1

Aled M Edwards

University of Toronto

Career Start Year 1984

Number of shared co-authors 1

Opher Gileadi

Structural Genomics Consortium Karolinska Institute Stockholm Sweden.

Career Start Year 1984

Number of shared co-authors 0

Stephen K Burley

The State University of New Jersey

Career Start Year 1982

Number of shared co-authors 2

Gary D Stormo

Washington University in St. Louis

Career Start Year 1981

Number of shared co-authors 0

Udo Heinemann

Max-Delbruck-Center for Molecular Medicine in the Helmholtz Association (MDC)

Career Start Year 1980

Number of shared co-authors 0

Chris Sander

Broad Institute of MIT and Harvard

Career Start Year 1979

Number of shared co-authors 2

George M Church

Harvard Medical School

Career Start Year 1977

Number of shared co-authors 1

David T Jones

University College London

Career Start Year 1977

Number of shared co-authors 3

Gianni Cesareni

University of Rome 'Tor Vergata'

Career Start Year 1976

Number of shared co-authors 3

Ronald W Davis

Stanford University

Career Start Year 1968

Number of shared co-authors 4

Sung-Hou Kim

University of California berkeley

Career Start Year 1967

Number of shared co-authors 0

row(s) 1 - 30 of 30

Mikael Huss

Stockholm University

Co-authored papers 6

Yuriy L Orlov

Co-authored papers 5

Jason D Lieb

The University of Chicago

Co-authored papers 5

Huck-Hui Ng

Co-authored papers 3

Guillaume Bourque

Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University

Co-authored papers 3

Yijun Ruan

Co-authored papers 2

Randy J Read

Cambridge Institute for Medical Research, University of Cambridge

Co-authored papers 2

Vinsensius B Vega

Co-authored papers 2

Michael L Tress

Spanish National Cancer Research Centre (CNIO)

Co-authored papers 2

Bing Lim

Co-authored papers 2

Torsten Schwede

University of Basel

Co-authored papers 2

Timothy R Hughes

University of Toronto

Co-authored papers 1

Cynthia Sung

Health Services and Systems Research, Duke-NUS Medical School

Co-authored papers 1

Jeremy M Simon

University of North Carolina

Co-authored papers 1

Ryan M McDaniell

The Children's Hospital of Philadelphia

Co-authored papers 1

Atif Shahab

Co-authored papers 1

Gustavo Stolovitzky

IBM T.J. Watson Research Center

Co-authored papers 1

Linda L Grasfeder

Duke University Medical Center

Co-authored papers 1

John A Tainer

The University of Texas MD Anderson Cancer Center

Co-authored papers 1

Zheng Liu

Chinese Academy of Agricultural Sciences

Co-authored papers 1

Jeremy Berg

Co-authored papers 1

Zhancheng Zhang

Co-authored papers 1

Edison T Liu

USA The Jackson Laboratory Cancer Center

Co-authored papers 1

James U Bowie

Co-authored papers 1

Kimberly A Showers

Co-authored papers 1

Delwood Richardson

Co-authored papers 1

Paul G Giresi

Center for Personal Dynamic Regulomes

Co-authored papers 1

Lingyun Song

Center for Genomic & Computational Biology, Duke University

Co-authored papers 1

Daniel Marbach

Roche Pharma Research and Early Development

Co-authored papers 1

Deborah R Winter

Northwestern University Feinberg School of Medicine

Co-authored papers 1

1 - 30

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