Author details

Full Name

Kyle Ellrott

Affiliation

Oregon Health & Science University

ORCID

0000-0002-6573-5900

Career Start Year

2002

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36874953	recountmethylation enables flexible analysis of public blood DNA methylation array data.	Bioinform Adv	2023
34146471	A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery.	Cell Syst	2021
35072136	GA4GH: International policies and standards for data sharing across genomic research and healthcare.	Cell Genom	2021
31424527	neoepiscope improves neoepitope prediction with multivariant phasing.	Bioinformatics	2020
32097025	Exploring Integrative Analysis Using the BioMedical Evidence Graph.	JCO Clin Cancer Inform	2020
32246132	A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.	Nat Genet	2020
31506093	Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges.	Genome Biol	2019
29653567	Population-level distribution and putative immunogenicity of cancer neoepitopes.	BMC Cancer	2018
30253747	Valection: design optimization for validation and verification studies.	BMC Bioinformatics	2018
30400818	Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.	Genome Biol	2018
29385983	Germline contamination and leakage in whole genome somatic single nucleotide variant detection.	BMC Bioinformatics	2018
29596782	Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.	Cell Syst	2018
29211761	Prophetic Granger Causality to infer gene regulatory networks.	PLoS One	2017
28988802	A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.	Cell Syst	2017
29092953	TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.	Cancer Res	2017
25984700	Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.	Nat Methods	2015
24675517	Global optimization of somatic variant identification in cancer genomes with a global community challenge.	Nat Genet	2014
23109555	The UCSC Cancer Genomics Browser: update 2013.	Nucleic Acids Res	2013
24071849	The Cancer Genome Atlas Pan-Cancer analysis project.	Nat Genet	2013
24071850	Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas.	Nat Genet	2013
20961957	TOPSAN: a dynamic web database for structural genomics.	Nucleic Acids Res	2011
19913036	Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain.	J Mol Biol	2010
20836087	The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu.	Protein Sci	2010
20944232	Structure of the Î³-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-Î³-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases.	Acta Crystallogr Sect F Struct Biol Cryst Commun	2010
20944230	Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved Î±+Î² core domain and an auxiliary C-terminal treble-clef zinc finger.	Acta Crystallogr Sect F Struct Biol Cryst Commun	2010
20944225	Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron.	Acta Crystallogr Sect F Struct Biol Cryst Commun	2010
20944224	Structure of Bacteroides thetaiotaomicron BT2081 at 2.05â¿¿Ã¿ resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism.	Acta Crystallogr Sect F Struct Biol Cryst Commun	2010
20944223	A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2â¿¿Ã¿ resolution.	Acta Crystallogr Sect F Struct Biol Cryst Commun	2010
20944222	Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules.	Acta Crystallogr Sect F Struct Biol Cryst Commun	2010
20944221	The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.	Acta Crystallogr Sect F Struct Biol Cryst Commun	2010
20944219	The structure of KPN03535 (gi\|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold.	Acta Crystallogr Sect F Struct Biol Cryst Commun	2010
20944209	Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism.	Acta Crystallogr Sect F Struct Biol Cryst Commun	2010
20944208	The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation.	Acta Crystallogr Sect F Struct Biol Cryst Commun	2010
20532204	Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families.	PLoS Comput Biol	2010
19567872	Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes.	J Biol Chem	2009
18075160	A historical perspective of template-based protein structure prediction.	Methods Mol Biol	2008
18574864	Improving the performance of protein threading using insertion/deletion frequency arrays.	J Bioinform Comput Biol	2008
17951836	Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays.	Comput Syst Bioinformatics Conf	2007
17503397	A generalized threading model using integer programming that allows for secondary structure element deletion.	Genome Inform	2006
15215441	PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction.	Nucleic Acids Res	2004
14555633	A computational pipeline for protein structure prediction and analysis at genome scale.	Bioinformatics	2003
14560049	PROSPECT II: protein structure prediction program for genome-scale applications.	Protein Eng	2003
12503319	Restriction enzyme recognition sequence search program.	Biotechniques	2002
12385991	Identifying transcription factor binding sites through Markov chain optimization.	Bioinformatics	2002

1 - 44 of 44

Michael T Zimmermann

Medical College of Wisconsin

Career Start Year 2009

Number of shared co-authors 10

Jian Peng

University of Illinois

Career Start Year 2009

Number of shared co-authors 1

Allison P Heath

Children's Hospital of Philadelphia

Career Start Year 2007

Number of shared co-authors 12

Vladimir Vacic

Stanley Institute for Cognitive Genomics

Career Start Year 2005

Number of shared co-authors 3

Semin Lee

Ulsan National Institute of Science and Technology (UNIST)

Career Start Year 2005

Number of shared co-authors 28

Yana Bromberg

Rutgers University

Career Start Year 2003

Number of shared co-authors 2

Predrag Radivojac

Indiana University

Career Start Year 2002

Number of shared co-authors 9

Suleyman Cenk Sahinalp

National Cancer Institute, National Institutes of Health

Career Start Year 2001

Number of shared co-authors 17

Sean D Mooney

University of Washington

Career Start Year 2001

Number of shared co-authors 25

Maricel G Kann

University of Maryland

Career Start Year 2000

Number of shared co-authors 1

Haixu Tang

Indiana University

Career Start Year 2000

Number of shared co-authors 5

Kevin Bryson

University of Glasgow

Career Start Year 1999

Number of shared co-authors 8

Quang M Trinh

Ontario Institute for Cancer Research

Career Start Year 1999

Number of shared co-authors 5

Rachel Karchin

Johns Hopkins University

Career Start Year 1998

Number of shared co-authors 27

Vineet Bafna

University of California San Diego

Career Start Year 1998

Number of shared co-authors 10

Sarah J Wheelan

National Human Genome Research Institute, National Institutes of Health

Career Start Year 1998

Number of shared co-authors 3

Lars Juhl Jensen

Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

Career Start Year 1998

Number of shared co-authors 3

Fabien Campagne

Weill Cornell Medical College

Career Start Year 1998

Number of shared co-authors 1

Iddo Friedberg

Iowa State University

Career Start Year 1997

Number of shared co-authors 10

Ron Shamir

Tel Aviv University

Career Start Year 1995

Number of shared co-authors 1

Steven J M Jones

University of British Columbia

Career Start Year 1995

Number of shared co-authors 65

Steven E Brenner

University of California berkeley

Career Start Year 1994

Number of shared co-authors 50

Bonnie Berger

Massachusetts Institute of Technology

Career Start Year 1994

Number of shared co-authors 9

Terry Gaasterland

Scripps Institution of Oceanography, University of California San Diego

Career Start Year 1994

Number of shared co-authors 6

Ioannis Xenarios

University of Lausanne

Career Start Year 1994

Number of shared co-authors 15

Zhiping Weng

University of Massachusetts Medical School

Career Start Year 1992

Number of shared co-authors 20

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 50

Aleksandar Milosavljevic

Baylor College of Medicine

Career Start Year 1991

Number of shared co-authors 42

Nomi L Harris

Lawrence Berkely National Laboratory, Massachusetts Institute of Technology, Princeton University

Career Start Year 1990

Number of shared co-authors 29

Vincent Ferretti

Ontario Institute for Cancer Research

Career Start Year 1986

Number of shared co-authors 18

row(s) 1 - 30 of 30

John Wooley

University of California

Co-authored papers 15

Adam Godzik

University of California Riverside

Co-authored papers 15

Lukasz Jaroszewski

University of California Riverside School of Medicine

Co-authored papers 14

Joshua M Stuart

University of California at Santa Cruz

Co-authored papers 14

Sanjay Krishna

Institute of Science, Banaras Hindu University

Co-authored papers 14

Constantina Bakolitsa

University of California berkeley

Co-authored papers 14

Dana Weekes

Joint Center for Structural Genomics, Sanford-Burnham Medical Research Institute

Co-authored papers 14

Herbert L Axelrod

Joint Center for Structural Genomics

Co-authored papers 13

Andrew T Morse

Co-authored papers 13

Dennis Carlton

Co-authored papers 13

Joanna C Grant

Joint Center for Structural Genomics

Co-authored papers 13

Lian Duan

Brown University

Co-authored papers 13

Connie Chen

University of California davis

Co-authored papers 13

Kevin K Jin

Cardiovascular Institute, Stanford University School of Medicine

Co-authored papers 13

Debanu Das

Accelero Biostructures Inc., USA XPose Therapeutics Inc.

Co-authored papers 13

Christine B Trame

Joint Center for Structural Genomics ( http:/www.jcsg.org )

Co-authored papers 13

Mark W Knuth

Joint Center for Structural Genomics

Co-authored papers 13

Marc-Andr?? Elsliger

Joint Center for Structural Genomics

Co-authored papers 13

Carol L Farr

Joint Center for Structural Genomics

Co-authored papers 13

Edward Nigoghossian

Genomics Institute of the Novartis Research Foundation

Co-authored papers 13

Anna Grzechnik

Co-authored papers 13

Ashley M Deacon

Accelero Biostructures Inc., USA XPose Therapeutics Inc.

Co-authored papers 13

Henry van den Bedem

University of California San Francisco

Co-authored papers 13

Heath E Klock

Merck & Co., Inc.

Co-authored papers 13

Linda Okach

Co-authored papers 13

Marc C Deller

Incyte Corporation

Co-authored papers 13

Ian A Wilson

The Scripps Research Institute, USA The Skaggs Institute for Chemical Biology

Co-authored papers 13

Thomas Clayton

Celgene/Bristol-Myers Squibb Corporation

Co-authored papers 13

Polat Abdubek

Regeneron Pharmaceuticals, Inc.

Co-authored papers 13

Mitchell D Miller

Rice University

Co-authored papers 13

1 - 30

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