Author details

Full Name

Michael S Waterman

Affiliation

Biocomplexity Institute and Initiative

ORCID

Career Start Year

1977

Papers

104

H Index

Expertise

CM4AI Collaborator

Christopher Churas (CM4AI)

PMID	Paper Title	Journal Title	Published Year
36780044	RNA Secondary Structures with Given Motif Specification: Combinatorics and Algorithms.	Bull Math Biol	2023
33275493	Multiscale Feedback Loops in SARS-CoV-2 Viral Evolution.	J Comput Biol	2021
34257466	Levenshtein Distance, Sequence Comparison and Biological Database Search.	IEEE Trans Inf Theory	2021
31345254	Benchmarking of alignment-free sequence comparison methods.	Genome Biol	2019
29040382	Generalized correlation measure using count statistics for gene expression data with ordered samples.	Bioinformatics	2018
28984181	Optimal choice of word length when comparing two Markov sequences using a Ï¿ <sup>2</sup>-statistic.	BMC Genomics	2017
28472388	CAFE: aCcelerated Alignment-FrEe sequence analysis.	Nucleic Acids Res	2017
24064230	New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.	Brief Bioinform	2014
25288767	Gene coexpression measures in large heterogeneous samples using count statistics.	Proc Natl Acad Sci U S A	2014
24895436	DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.	Nucleic Acids Res	2014
23053535	Topological classification and enumeration of RNA structures by genus.	J Math Biol	2013
23829649	A geometric interpretation for local alignment-free sequence comparison.	J Comput Biol	2013
22697250	Normal and compound poisson approximations for pattern occurrences in NGS reads.	J Comput Biol	2012
21723298	New powerful statistics for alignment-free sequence comparison under a pattern transfer model.	J Theor Biol	2011
21554016	Sequence alignment as hypothesis testing.	J Comput Biol	2011
21698123	Integrative analysis of many weighted co-expression networks using tensor computation.	PLoS Comput Biol	2011
20426691	The power of detecting enriched patterns: an HMM approach.	J Comput Biol	2010
22121326	New Generations: Sequencing Machines and Their Computational Challenges.	J Comput Sci Technol	2010
20973742	Alignment-free sequence comparison (II): theoretical power of comparison statistics.	J Comput Biol	2010
20534489	High-resolution human genome structure by single-molecule analysis.	Proc Natl Acad Sci U S A	2010
20122238	An integrative modular approach to systematically predict gene-phenotype associations.	BMC Bioinformatics	2010
19208108	The Seventh Asia Pacific Bioinformatics Conference (APBC2009).	BMC Bioinformatics	2009
19936062	A single molecule scaffold for the maize genome.	PLoS Genet	2009
19965430	The B73 maize genome: complexity, diversity, and dynamics.	Science	2009
20001252	Alignment-free sequence comparison (I): statistics and power.	J Comput Biol	2009
19630539	An integrative network approach to map the transcriptome to the phenome.	J Comput Biol	2009
19561337	HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome.	Bioinformatics	2009
17090592	Gene Aging Nexus: a web database and data mining platform for microarray data on aging.	Nucleic Acids Res	2007
17567986	Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi.	Genome Res	2007
17563310	A quantile method for sizing optical maps.	J Comput Biol	2007
17646346	A graph-based approach to systematically reconstruct human transcriptional regulatory modules.	Bioinformatics	2007
17646300	Systematic discovery of functional modules and context-specific functional annotation of human genome.	Bioinformatics	2007
17277422	On the length of the longest exact position match in a random sequence.	IEEE/ACM Trans Comput Biol Bioinform	2007
17277416	Accuracy assessment of diploid consensus sequences.	IEEE/ACM Trans Comput Biol Bioinform	2007
16597251	Alignment of optical maps.	J Comput Biol	2006
17043225	An algorithm for assembly of ordered restriction maps from single DNA molecules.	Proc Natl Acad Sci U S A	2006
17038176	Integrative missing value estimation for microarray data.	BMC Bioinformatics	2006
16500933	Refinement of optical map assemblies.	Bioinformatics	2006
15333454	HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms.	Bioinformatics	2005
15668398	An Eulerian path approach to local multiple alignment for DNA sequences.	Proc Natl Acad Sci U S A	2005
15078859	Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies.	Genome Res	2004
15285905	Haplotype reconstruction from SNP alignment.	J Comput Biol	2004
14769938	Whole-genome shotgun assembly and comparison of human genome assemblies.	Proc Natl Acad Sci U S A	2004
12802783	Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data.	Am J Hum Genet	2003
15338619	DNA sequence assembly and multiple sequence alignment by an Eulerian path approach.	Cold Spring Harb Symp Quant Biol	2003
14980012	An Eulerian path approach to global multiple alignment for DNA sequences.	J Comput Biol	2003
12902383	Estimating the repeat structure and length of DNA sequences using L-tuples.	Genome Res	2003
12032283	A dynamic programming algorithm for haplotype block partitioning.	Proc Natl Acad Sci U S A	2002
12374863	Distributional regimes for the number of k-word matches between two random sequences.	Proc Natl Acad Sci U S A	2002
12015891	Zinc finger gene clusters and tandem gene duplication.	J Comput Biol	2002

1 - 50 of 104

Nozomu Yachie

The University of British Columbia

Career Start Year 2006

Number of shared co-authors 1

Peter Huggins

Carnegie Mellon University

Career Start Year 2006

Number of shared co-authors 0

Gang Fang

Icahn School of Medicine at Mount Sinai

Career Start Year 2005

Number of shared co-authors 6

Carl Kingsford

Carnegie Mellon University

Career Start Year 2005

Number of shared co-authors 1

Martin C Frith

Artificial Intelligence Research Center, University of Tokyo

Career Start Year 2001

Number of shared co-authors 0

C Titus Brown

University of California davis

Career Start Year 1999

Number of shared co-authors 5

Vineet Bafna

University of California San Diego

Career Start Year 1998

Number of shared co-authors 22

Ian Korf

University of California davis

Career Start Year 1998

Number of shared co-authors 14

Ian Holmes

University of California berkeley

Career Start Year 1998

Number of shared co-authors 14

Jeremy Buhler

Washington University in St. Louis

Career Start Year 1997

Number of shared co-authors 0

Louxin Zhang

National University of Singapore

Career Start Year 1996

Number of shared co-authors 0

Stefano Lonardi

University of California Riverside

Career Start Year 1996

Number of shared co-authors 16

Richa Agarwala

National Center for Biotechnology Information, National Institutes of Health

Career Start Year 1995

Number of shared co-authors 18

Vsevolod J Makeev

Vavilov Institute of General Genetics, Russian Academy of Sciences

Career Start Year 1995

Number of shared co-authors 0

Terry Gaasterland

Scripps Institution of Oceanography, University of California San Diego

Career Start Year 1994

Number of shared co-authors 3

Simon Kasif

Boston University

Career Start Year 1993

Number of shared co-authors 8

Inna Dubchak

Lawrence Berkeley National Laboratory

Career Start Year 1993

Number of shared co-authors 15

Tao Jiang

University of California riverside

Career Start Year 1992

Number of shared co-authors 2

Steven L Salzberg

Center for Computational Biology, Johns Hopkins University

Career Start Year 1992

Number of shared co-authors 28

Ewan Birney

European Bioinformatics Institute

Career Start Year 1992

Number of shared co-authors 25

Jaap Heringa

VU University Amsterdam

Career Start Year 1991

Number of shared co-authors 0

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 14

Mark Borodovsky

Georgia Institute of Technology

Career Start Year 1989

Number of shared co-authors 5

Owen White

Institute for Genome Sciences, University of Maryland School of Medicine

Career Start Year 1988

Number of shared co-authors 17

David Haussler

Genomics Institute, University of California Santa Cruz

Career Start Year 1986

Number of shared co-authors 23

Dan Graur

University of Houston

Career Start Year 1982

Number of shared co-authors 4

Gary D Stormo

Washington University in St. Louis

Career Start Year 1981

Number of shared co-authors 1

Andrey A Mironov

Lomonosov Moscow State University

Career Start Year 1979

Number of shared co-authors 1

William R Pearson

University of Virginia

Career Start Year 1974

Number of shared co-authors 0

Richard Durbin

University of Cambridge

Career Start Year 1964

Number of shared co-authors 22

row(s) 1 - 30 of 30

Xianghong Jasmine Zhou

David Geffen School of Medicine, University of California at Los Angeles

Co-authored papers 8

David C Schwartz

University of Wisconsin-Madison

Co-authored papers 8

Temple F Smith

Co-authored papers 7

Anton Valouev

Keck School of Medicine, University of Southern California

Co-authored papers 5

Michael R Mehan

University of Southern California

Co-authored papers 5

Shiguo Zhou

Sage Science Inc.

Co-authored papers 4

Eric S Lander

Vanderbilt-Ingram Cancer Center, Vanderbilt University

Co-authored papers 3

Haiyan Huang

Washington State University

Co-authored papers 3

Xuegong Zhang

Co-authored papers 2

Fusheng Wei

University of Science and Technology Beijing

Co-authored papers 2

Dan Forrest

Co-authored papers 2

Konstantinos Potamousis

University of Wisconsin-Madison

Co-authored papers 2

Shibu Yooseph

University of Central Florida

Co-authored papers 2

Zhaohui S Qin

Emory University

Co-authored papers 2

Doreen Ware

USDA ARS NAA Robert W. Holley Center for Agriculture and Health

Co-authored papers 2

Wenyuan Li

Harvard Medical School

Co-authored papers 2

Christopher Churas (CM4AI)

University of California San Diego

Co-authored papers 2

Gary A Churchill

Tufts University

Co-authored papers 2

Shiran Pasternak

Co-authored papers 2

Miron Livny

Morgridge Institute for Research

Co-authored papers 2

Rod A Wing

Arizona Genomics Institute, University of Arizona

Co-authored papers 2

John Nguyen

Co-authored papers 2

Evan E Eichler

University of Washington

Co-authored papers 2

Steve Goldstein

University of Wisconsin-Madison

Co-authored papers 2

Bixiong Chris Shue

Co-authored papers 1

Jeffrey M Kidd

University of Michigan Medical School ann arbor

Co-authored papers 1

Clark Mobarry

Co-authored papers 1

Hagit Shatkay

University of Delaware

Co-authored papers 1

W John Wilbur

National Center for Biotechnology Information, National Institutes of Health

Co-authored papers 1

Sandra W Clifton

Garvan Institute of Medical Research

Co-authored papers 1

1 - 30

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