Author details

Full Name

David Koslicki

Affiliation

and the Huck Institutes of the Life Sciences, Penn State University, University Park

ORCID

Career Start Year

2011

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36752514	ARAX: a graph-based modular reasoning tool for translational biomedicine.	Bioinformatics	2023
37900350	An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges.	J Clin Transl Sci	2023
37344105	Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash.	Genome Res	2023
37131762	YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.	bioRxiv	2023
36752514	ARAX: a graph-based modular reasoning tool for translational biomedicine.	Bioinformatics	2023
37387190	Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L2UniFrac.	Bioinformatics	2023
37900350	An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges.	J Clin Transl Sci	2023
37387190	Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L2UniFrac.	Bioinformatics	2023
37344105	Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash.	Genome Res	2023
37131762	YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.	bioRxiv	2023
35108101	The Statistics of <i>k</i>-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches.	J Comput Biol	2022
36175836	RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine.	BMC Bioinformatics	2022
35758788	CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices.	Bioinformatics	2022
35758786	The minimizer Jaccard estimator is biased and inconsistent.	Bioinformatics	2022
37602759	KGML-xDTD: a knowledge graph-based machine learning framework for drug treatment prediction and mechanism description.	Gigascience	2022
36852763	TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles.	Gigascience	2022
35108101	The Statistics of <i>k</i>-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches.	J Comput Biol	2022
37602759	KGML-xDTD: a knowledge graph-based machine learning framework for drug treatment prediction and mechanism description.	Gigascience	2022
35758788	CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices.	Bioinformatics	2022
35758786	The minimizer Jaccard estimator is biased and inconsistent.	Bioinformatics	2022
36852763	TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles.	Gigascience	2022
36175836	RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine.	BMC Bioinformatics	2022
34446078	Technology dictates algorithms: recent developments in read alignment.	Genome Biol	2021
33742785	Application of MCAT questions as a testing tool and evaluation metric for knowledge graph-based reasoning systems.	Clin Transl Sci	2021
33649565	Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.	Nat Protoc	2021
34446078	Technology dictates algorithms: recent developments in read alignment.	Genome Biol	2021
33742785	Application of MCAT questions as a testing tool and evaluation metric for knowledge graph-based reasoning systems.	Clin Transl Sci	2021
33649565	Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.	Nat Protoc	2021
32264902	Improving the usability and comprehensiveness of microbial databases.	BMC Biol	2020
32264902	Improving the usability and comprehensiveness of microbial databases.	BMC Biol	2020
32912225	Metalign: efficient alignment-based metagenomic profiling via containment min hash.	Genome Biol	2020
32723395	Correction to: Improving the usability and comprehensiveness of microbial databases.	BMC Biol	2020
32912225	Metalign: efficient alignment-based metagenomic profiling via containment min hash.	Genome Biol	2020
32723395	Correction to: Improving the usability and comprehensiveness of microbial databases.	BMC Biol	2020
31167634	MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples.	BMC Genomics	2019
31167634	MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples.	BMC Genomics	2019
30832730	Assessing taxonomic metagenome profilers with OPAL.	Genome Biol	2019
30832730	Assessing taxonomic metagenome profilers with OPAL.	Genome Biol	2019
28735343	Exact probabilities for the indeterminacy of complex networks as perceived through press perturbations.	J Math Biol	2018
28735343	Exact probabilities for the indeterminacy of complex networks as perceived through press perturbations.	J Math Biol	2018
30377368	Striped UniFrac: enabling microbiome analysis at unprecedented scale.	Nat Methods	2018
29743478	Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia.	Transl Psychiatry	2018
29691633	EMDUniFrac: exact linear time computation of the UniFrac metric and identification of differentially abundant organisms.	J Math Biol	2018
29236975	IndeCut evaluates performance of network motif discovery algorithms.	Bioinformatics	2018
30377368	Striped UniFrac: enabling microbiome analysis at unprecedented scale.	Nat Methods	2018
29691633	EMDUniFrac: exact linear time computation of the UniFrac metric and identification of differentially abundant organisms.	J Math Biol	2018
29743478	Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia.	Transl Psychiatry	2018
29236975	IndeCut evaluates performance of network motif discovery algorithms.	Bioinformatics	2018
28967888	Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.	Nat Methods	2017
28967888	Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.	Nat Methods	2017

1 - 50 of 64

David C Molik

Arthropod-Borne Animal Disease Research Unit

Career Start Year 2018

Number of shared co-authors 1

David Tse

Stanford University

Career Start Year 2013

Number of shared co-authors 0

Migun Shakya

Los Alamos National Laboratory

Career Start Year 2012

Number of shared co-authors 2

Corey M Hudson

Informatics Institute, University of Missouri

Career Start Year 2011

Number of shared co-authors 0

Nathan D Olson

National Institute of Standards and Technology

Career Start Year 2010

Number of shared co-authors 1

Jared T Simpson

Ontario Institute for Cancer Research

Career Start Year 2009

Number of shared co-authors 1

Chien-Chi Lo

Los Alamos National Laboratory

Career Start Year 2009

Number of shared co-authors 1

Georg Zeller

Max Planck Institute for Developmental Biology

Career Start Year 2007

Number of shared co-authors 2

Fangfang Xia

University of Chicago

Career Start Year 2007

Number of shared co-authors 0

Wataru Iwasaki

the University of Tokyo

Career Start Year 2006

Number of shared co-authors 0

Bonnie L Hurwitz

The University of Arizona

Career Start Year 2006

Number of shared co-authors 1

Curtis Huttenhower

Broad Institute of MIT and Harvard

Career Start Year 2006

Number of shared co-authors 5

Brandi L Cantarel

University of Texas Southwestern Medical Center

Career Start Year 2006

Number of shared co-authors 2

Metin Balaban

University of California San Diego

Career Start Year 2006

Number of shared co-authors 2

Davide Albanese

Fondazione Edmund Mach

Career Start Year 2006

Number of shared co-authors 1

Carl Kingsford

Carnegie Mellon University

Career Start Year 2005

Number of shared co-authors 1

Morgan G I Langille

Dalhousie University

Career Start Year 2004

Number of shared co-authors 5

Michael C Schatz

Johns Hopkins University

Career Start Year 2004

Number of shared co-authors 1

Kristoffer Forslund

Max Delbruck Center for Molecular Medicine (MDC)

Career Start Year 2003

Number of shared co-authors 2

Adam M Phillippy

National Human Genome Research Institute, National Institutes of Health

Career Start Year 2002

Number of shared co-authors 1

Haixu Tang

Indiana University

Career Start Year 2000

Number of shared co-authors 0

C Titus Brown

University of California davis

Career Start Year 1999

Number of shared co-authors 7

Shibu Yooseph

University of Central Florida

Career Start Year 1998

Number of shared co-authors 1

Eric J Alm

Massachusetts Institute of Technology 21 Ames St. Cambridge

Career Start Year 1998

Number of shared co-authors 4

James A Foster

University of Idaho

Career Start Year 1996

Number of shared co-authors 0

Susan Holmes

Stanford University

Career Start Year 1996

Number of shared co-authors 5

Folker Meyer

Institute for Artificial Intelligence, University of Duisburg-Essen

Career Start Year 1996

Number of shared co-authors 6

Bonnie Berger

Massachusetts Institute of Technology

Career Start Year 1994

Number of shared co-authors 1

Granger Sutton

J. Craig Venter Institute

Career Start Year 1993

Number of shared co-authors 1

Steven L Salzberg

Center for Computational Biology, Johns Hopkins University

Career Start Year 1992

Number of shared co-authors 2

row(s) 1 - 30 of 30

Serghei Mangul

School of Pharmacy, University of Southern California

Co-authored papers 7

Eleazar Eskin

Co-authored papers 5

Andreas Bremges

Co-authored papers 3

Alice C McHardy

Computational Biology of Infection Research, Helmholtz Centre for Infection Research

Co-authored papers 3

Fernando Meyer

Co-authored papers 3

Gail L Rosen

Drexel University

Co-authored papers 2

Eric W Deutsch

Institute for Systems Biology

Co-authored papers 2

Alexander Sczyrba

Center for Biotechnology (CeBiTec), Bielefeld University, Universitatsstrasse 27

Co-authored papers 2

Stephen A Ramsey

Oregon State University

Co-authored papers 2

Aaron E Darling

Co-authored papers 2

Nathan LaPierre

University of California los angeles

Co-authored papers 2

Alexey Gurevich

Co-authored papers 2

Peter Belmann

Co-authored papers 2

Chris Bizon

Renaissance Computing Institute (RENCI), University of North Carolina at Chapel Hill

Co-authored papers 2

Stefan Janssen

Co-authored papers 2

Jared C Roach

Institute for Systems Biology

Co-authored papers 2

Karamarie Fecho

Renaissance Computing Institute (RENCI), University of North Carolina at Chapel Hill

Co-authored papers 2

Adrian Fritz

Co-authored papers 2

Molly Megraw

Center for Quantitative Life Sciences, Oregon State University

Co-authored papers 1

Anne E Thessen

Biodiversity Information Standards, Coastal and Estuarine Research Federation, Oregon State University, Phycological Society of America, Society of Professional Consultants, The Data Detektiv, University of Colorado Anschutz Medical Campus, University of Maryland College Park, Women in the Enterprise of Science and Technology

Co-authored papers 1

Vicki Gardner

Renaissance Computing Institute (RENCI), University of North Carolina at Chapel Hill

Co-authored papers 1

Dongwan Kang

Co-authored papers 1

Robert A Edwards

Co-authored papers 1

Irit Rubin

Institute for Systems Biology

Co-authored papers 1

Sandrine Muller