August 7, 2019

CURRICULUM VITA

I. BIOGRAPHICAL

Waterman, Michael S.msw@usc.eduhttp://dornsife.usc.edu/labs/msw/

Education

B. S. (Mathematics) Oregon State University 1964M. S. (Mathematics) Oregon State University 1966M. A. (Statistics) Michigan State University 1968Ph. D. (Statistics & Probability) Michigan State Univ. 1969

Permanent Positions

1969 - May 1974 Assistant Professor of Mathematics,Idaho State University

May 1974 - July 1975 Associate Professor of Mathematics,Idaho State University

July 1975 - Dec. 1980 Staff Member,Los Alamos Scientific Laboratory

Jan. 1980 - Dec. 1981 Project Leader,Los Alamos National Laboratory

Sept. 1982 - present Professor of Biological Sciences,Mathematics, Computer Science,and University ProfessorUniversity of Southern California

Other Positions

Summer 1965 Scientific Programmer,Lawrence Radiation Labs

Summer 1966 Statistician,Bell Telephone Labs

1

1968 - 1969 Statistician (part-time),Michigan Highway Dept.

May 1973 - July 1975 Consultant,Energy Incorporated

Summer 1974 - July 1975 Visiting Staff Member,Los Alamos Scientific Laboratory,

Sept. 1979 - June 1980 Visiting Professor of Mathematics,University of Hawaii

Jan. 1982 - June 1982 Visiting Research Professor of Structural Biology,Medical School, University of California at San Francisco

Fall 1988 Visiting Professor,Mt. Sinai Medical School, NYC

Spring 2000 Chalmers 150th Anniversary Visiting Professor,Chalmers University, Goteborg, Sweden

2000 - 2001 Aisenstadt Chair,Centre de Recherches MathematiquesUniversite’ de MontrealMontreal, Quebec

2000-2005 Professor-at-LargeKeck Graduate Institute of Life SciencesClaremont Colleges

2000-2005 Celera Genomics Fellow2008-2017 Cao Xingcheng Chair Professor

Tsinghua UniversitySchool of Information Science and Technology

2016 Visiting ScientistSimons Institute for the Theory of ComputingUniversity of California at Berkeley

2014-2019 Distinguished ProfessorFudan University

II. AWARDS AND HONORS

Outstanding Educator of America Awards, 1971 and 1972

NSF Faculty Research Participant, Los Alamos Scientific Laboratory, Summer 1974

New Research Initiatives Award from Director’s Office, Los Alamos National Labora-tory, 1976 and 1981

2

Outstanding Presentations Award of the SPES section of the American StatisticalAssociation at the 1977 Annual Meeting

Fellow of the American Association for the Advancement of Science (elected 1990)

Fellow of the Institute of Mathematical Statistics (1991)

USC Associates Endowed Professorship in Mathematics and Biology, 1991–present

USC Associates Award for Creativity in Research and Scholarship, March 1992

Jet Propulsion Laboratory Award for Filing Patent Application, 1992

Fellow of the John Simon Guggenheim Foundation, 1995–1996

Fellow of the American Academy of Arts and Sciences (1995)

University Professor, University of Southern California, 1998–present

Chalmers 150th Anniversary Visiting Professor, 2000

Celera Genomics Fellow, first Fellow appointed, 2000

Aisenstadt Chair, Universite’ de Montreal, 2001

Member of the National Academy of Sciences (2001)

Gairdner Foundation International Award, 2002

USC College Award for Excellence, 2004

Member of the French Academy of Sciences (elected 2005)

The Stanislaw Ulam Memorial Computational Biology Lecture, 2006 Award Recipient

Senior Scientist Accomplishment Award, International Society of Computational Biol-ogy, 2006

USC-Mellon Excellence in Mentoring Award, 2007

University of Southern California Presidential Medallion, 2008

American Mathematical Society Einstein Public Lecture, 2009

Inaugural Fellow of the Society for Industrial and Applied Mathematics (2009)

Inaugural Fellow of the International Society of Computational Biology (2009)

3

Outstanding Achievement Award, International Society of Intelligent Biological Medicine(2009)

Doctor Philosophiae Honoris Causa, Tel Aviv University, 2011

Fellow of Los Angeles Institute of the Humanities (2011)

Member of the National Academy of Engineering (2012)

Test of Time Award from RECOMB 2013 (for a conference paper published in 2001)

People’s Republic of China Friendship Award, 2013

Doctor Scientiarum Honoris Causa, University of Southern Denmark, 2013

Foreign Member of the Chinese Academy of Sciences (2013)

Honorary Professor, The Chinese University of Hong Kong, Shenzhen, 2014

Dan David Prize: The Future (Bioinformatics), 2015

Fellow of the National Academy of Inventors, 2018

III. GRANTS

National Science Foundation (NSF) Research Grants, 1971, 1972, 1975

National Institutes of Health Research Grants(with T. F. Smith), 1980, 1981

System Development Foundation Grant, Basic Research in Pattern Analysis with Prin-cipal Application to Molecular Biology: (direct costs)

(1) 1982-1985: $808,600

(2) 1985-1986: $76,024

(3) 1986-1987: $525,448

DOD, CY 1986, Molecular Biology Computer Facility for DNA and Protein SequenceAnalysis: $50,000 (co-PI)

National Institutes of Health Research Grant (GM36230), 1986-1998, Pattern Recog-nition for Analysis of Molecular Sequences: (direct costs only)

4

(1) 1986 award: $169,681

(2) 1987 award: $147,047

(3) 1988 award: $184,972

(4) 1989 award: $147,926

(5) 1990 award: $152,559

(6) 1991 award: $173,661

(7) 1992 award: $178,057

(8) 1993 award: $184,657

(9) 1994 award: $204,571

(10) 1995 award: $242,826

(11) 1996 award: $250,033

(12) 1997 award: $255,591

(13) 1998 award: $255,911

NSF (DMS 87-14251), 1988-1989, Center for Computational Studies of MolecularStructure and Function: $476,730

NSF (DMS-8815106),1988-1990, Mathematical Tools for Molecular Sequence Analysis

(1) 1988 award: $64,819

(2) 1989 award: $64,819

USC Faculty Research Award, Experiments for Genome Mapping, 1988-1989: $3,727

National Science Foundation Center for Mathematics and Molecular Biology maingrant at Berkeley (DMS-8720208), USC portion:

(1) 1988 award: $20,825

(2) 1989 award: $40,036

(3) 1990 award: $40,000

(4) 1991 award: $40,000

(5) 1992 award: $40,000

National Institutes of Health, (1S10RR04955-01), Campus Link in Molecular Biology:A Computer Network: $398,610 (co-PI)

5

Sloan Foundation, A Seminar Series in Mathematical Sciences and Molecular Biology,1/1/90 - 06/30/94,

(1) 1990 award: $25,000

(2) 1991 award: $25,000

National Science Foundation, Group Project in Probability, Statistics and Computa-tional Biology (DMS-90-05833), 6/1/90 - 6/30/95, (direct + indirect) (with SimonTavare and three others)

(1) 1990 award: $425,000

(2) 1991 award: $537,650

(3) 1992 award: $423,000

(4) 1993 award: $420,000

(5) 1994 award: $424,000

National Science Foundation, Statistical and Computational Problems in Genetics andMolecular Biology (BIR-95-04393), 7/1/95 - 6/30/99, (direct + indirect) (with SimonTavare)

(1) 1995 award: $200,000

(2) 1996 award: $200,000

(3) 1997 award: $200,000

(4) 1998 award: $200,000

(4) 1999 award: $200,000

Alfred P. Sloan Foundation, Project for Professional Master’s Programs in the Sciences.(Inter-departmental instructional project, USC.) Co-investigator, Computational Bi-ology track. 1997-2001. $360,726, direct costs.

Anchorgen, Inc. Scientific Collaboration on Sequence Assembly (ANCH /00), 11/01/00- 04/30/01, $25,000

National Science Foundation, “Computational Biology Support: Recomb 2001,2002,2003” (DBI-0100748), 06/01/01–05/31/04. $50,000, direct costs.

National Institutes of Health, “New Approach to DNA Fragment Assembly” (R01HG02366-01), 07/01/01–06/30/04. Held as part of a larger grant with Pavel Pevznerat UCSD. USC award at $210,000 for each of 3 years.

6

Department of Energy, Computational Biology Support, Recomb Conferences (DE-FG03-01ER63090), 02/15/01–02/14/03, $75,000, direct costs.

National Institutes of Health, “Computational Methods for Functional Genomics”(1R01 GM 67243), 07/01/02 to 06/30/06

(1) 2002 award: $406,250

(2) 2003 award: $406,250

(3) 2004 award: $406,250

(4) 2005 award: $406,250

National Institutes of Health, “Implications of Haplotype Structure in the HumanGenome” (5P50 HG002790), 9/1/2003–8/31/2009, $18,700,000 (PI with 11 coPIs).

(1) 2003 award: $3,513,797

(2) 2004 award: $3,582,129

(3) 2005 award: $3,719,700

(4) 2008 award: $3,823,699

(5) 2009 award: $3,461,387

National Science Foundation, “Program in Mathematics and Molecular Biology, Grad-uate Support” (RF-0287MDS107), 01/01/2005-12/31/2005 $40,000

National Science Foundation, “ISGA-PGR: A Genome-Wide Optical Map for Maize”(# 0501818, prime # 0501818), 05/15/05-04/30/07, PI David Schwartz (University ofWisconsin), Waterman, M.S.co-PI. Subcontract:

(1) 2005 award: $44,880

(2) 2006 award: $28,215

(3) 2007 award: $73,025

Seaver Foundation, “Gene Aging Nexus: A Web Platform for Integrated Data Mining”(SEAVER 2547), PI Xianghong Zhou, Waterman, M.S.coPI.

(1) 9/1/05-8/31/06, $150,000

(2) 9/1/05-6/30/07, $205,000

(3) 9/1/05-6/30/08, $70,000

National Institutes of Health, “Integrative Analysis of Cross-Platform Microarray Data”(5R01 GM 074163), 01/01/06-12/31/09, PI Xianghong Zhou, Waterman, M.S.coPI.

7

(1) 2005 award:$203,438

(2) 2006 award: $197,280

(3) 2007 award: $223,831

(4) 2008 award: $171,634

(5) 2009 award: 207,766

National Institutes of Health, “Single Molecule Genome Analysis of Oligodendroglioma”(5 R33 CA111933-02) PI David Schwartz (University of Wisconsin), subcontract toWaterman, M.S.. 09/01/2006-08/31/2009 $45,000

National Institutes of Health, “A Web Platform for Integrative Genomic Analysis inAging” (5 R21 AG031723), PI Xianghong Zhou, Waterman, M.S.coPI. 03/01/2008–02/28/2010

(1) 2008 award:$200,490

(2) 2009 award: $167,075

National Institutes of Health, “Computational and Statistical Studies for MultipleMolecular Networks” (1 R21 AG032743), PI Fengzhu Sun, Waterman, M.S.coPI. 08/01/2008–07/03/2010

(1) 2008 award: $167,075

(2) 2009 award: $200,388

(3) 2010 award: $200,388

National Institutes of Health, “Molecular Sequence Analysis Using Word Counts:Statistics, Power and Applications,” R21HG006199 Sun (PI) Waterman (Co-I), 07/22/2011-04/30/2013 Direct Costs: $275,000

National Institutes of Health, “Methods for Deep Sequencing Based RBP BindingMotif Characterization” NIH GM097230, 09/05/2011 - 05/31/2015 Role: Co-I (PI:Andrew Smith) 09/13/2011-06/30/2014 ( 0.6 person-month) Cost: $1,171,448

National Institutes of Health, “Statistical methods for the study of alternative splicingusing deep sequencing” Role: Co-I (PI: Liang Chen) (0.5 person-month) Total Cost:$1,392,672

National Institutes of Health, “MapGen Knowledge Base (MAPGenKB) and Coordi-nation Center,” U01HL08634 Zhou and Crandall (PIs) Waterman (Co-I) 08/25/2011-06/30/2016 Direct Costs: $3,682,888

8

National Science Foundation, “Inference of Markovian Properties of Molecular Se-quence Using Shotgun Reads and Applications,” NSF 1518001, F. Sun PI, Water-man (Co-I) 8/01/2015 -07/31/2018 Effort: 0.3 Summer Months Total Project Cost:$600,000

National Institutes of Health, “Computational Studies of Virus-host Interactions UsingMetagenomics Data and Applications” NIH R01 GM120624-01A1, F. Sun, N. Ahlgren,S. Highlander (multiple PI), Waterman (Co-I), 04/01/2017-03/30/2021

Total direct cost: $1,517,297

IV. PROFESSIONAL RECOGNITION AND SERVICE

Other Professional Activities

NSF Review Panel for Science Faculty Professional Development Program, February1978

NSF and NIH Committee on Nucleic Acid Data, March 1979

Formation Evaluation School, Unit I (Oil and Gas Consultants International), May11-22, 1981

Advisory Board: Molecular Biology Computer Research Resource, Harvard, 1987-1992

Collaborator: Center for Prokaroyotic Gene Analysis, U. of Illinois, 1987-1989

Associate Member, Canadian Institute of Advanced Research, 1987-2002

International Advisory Committee for Nucleotide Databases (NIH), 1988-1991

GenBank Advisory Committee (NIH), 1989-1991

Advisory Board, Protein Identification Resource, Georgetown University, 1988-1991

National Planning Committee on AIDS Modeling and Epidemiology, 1988

Working Group on California Human Genome Projects, 1988–1990

Panel on Math. Sci. in Genome and Protein Structure (Natl. Res. Council) 1990-1994

Member, Board of Directors of Global Pursuits Inc., 1991–1999

Member, Human Genome Organization (HUGO), 1991–present

9

Member, Scientific Advisory Board of Hyseq, Inc., 1993–2001

Electorate Nominating Committee, AAAS Section on Mathematics (A), 1995-1998

Panel Member, Alfred P. Sloan Foundation Postdoctoral Fellowships in ComputationalMolecular Biology, 1996–2003

Co-founder of the conference RECOMB in 1997. Member of Steering Committee 1997–2007. Member of Program Committee 1997–2010.

DOE Joint Genome Institute Advisory Board, 1997–2000

Member, Scientific Advisory Board of Genedata, 1997–2005

Member, Advisory Board on Bioinformatics Program, Boston University, 1997–2001

Member, site visit team for “Organelle Genome Megasequencing Program” for MedicalResearch Council of Canada, Montreal; April 25, 1997.

Member, Advisory Committee for Interfaces in Science Program, Burroughs WelcomeFund, 1998–2001

Member of Program Committee, 9th Genome Informatics Workshop (GIW’98), TokyoJapan, December 1998

Member of Scientific Advisory Committee, Institute for Pure and Applied Mathemat-ics, 1999–2002

Member of Computational Molecular Biology Panel, EURANDOM, The Netherlands,2000–2005

Session Chair, at the meeting “Mathematische Stochastik,” at Oberwolfach, Germany,March 12–18, 2000.

Member of Evaluation Panel of the Research Programme MaDaMe March 2000, Fin-land Academy of Science, Helsinki.

Advisor, Howard Hughes Medical Institute Computational Biology Competition, April2000

Member, Review and Site visit of Michigan Life Sciences Corridor proposal for Michi-gan Center for Biological Information, Washington Advisory Group, October 2000

Member, Scientific Advisory Board of Biodiscovery, 2000–2009

10

Member, Organizing Committee of the Program “Post-genome Knowledge Discovery,”Institute for Mathematical Sciences (IMS), Singapore, 2001–2005

Member, Scientific Advisory Board, Bioinformatics Institute, Biomedical ResearchCouncil, Singapore, 2002-2008

Member, Committee to Select the Gibbs Lecturer, American Mathematical Society,2003-2004

Program Committee, Alfred P. Sloan Foundation Fellowships in Computational andEvolutionary Molecular Biology, 2002–2005

Member, Panel Review Meeting for Ohio Biomedical Research and Technology TransferPartnership Awards, Washington Advisory Group, April 2002

Member, NIH Review Committee for Bioterrorism SBIR grant applications, April 16,2002

Board of Directors, Mathematical Biosciences Institute, Ohio State University, 2002-2004

Board of Directors, International Society of Computational Biology, 2002-2004

Member, Scientific Advisory Board of OpGen, 2002–2006

Member, NIH Special Emphasis Review Panel for ENCODE, July 14-15, 2003

Advisory Board, NYU IGERT Program, 2003–2006

Scientific Board of the Banff International Research Station (BIRS), 2003-2009

Member, Scientific and Academic Advisory Committee sub-committee to review Bioin-formatics/Proteomics & Genomics, Weizmann Institute of Science, Israel, November5–9, 2003.

Member, Shanghai Institute for Advanced Studies Committee: Perpectives on Com-putational Biology, Shanghai, China, February 19–21, 2004

DIMACS Program on K-12 Education, 2004–2010

NRC Report on Computational Biology, 2004–2005

Genome Center Genome External Advisory Board, University of California at Davis,2005–2007

11

Head, Review Committee for Life Sciences-Computer Sciences, Hebrew University,Jerusalem, Israel, December 5-9, 2005

Scientific Advisory Board, MAGNet (Multiscale Anlaysis of Genomic Networks, NIHNational Center in Biomedical Computing at Columbia University, 2005–2015

Chair, External Review Committee for The Academic Program in Computational Bi-ology, Hebrew University. December 5-9, 2005

Member, Genomics, Computational Biology and Technology Study Section, GCATStudy Section, Bethesda, March 2-3, 2006

Scientific Advisory Board, Chinese Academy of Sciences-Max Planck Gesellschaft In-stitute for Computational Biology (Shanghai), 2006–2018

Board of Directors, Defienens, 2005-2009

Co-chair, Third Recomb Satelite Workshop on Computational Methods for SNPs andHaplotypes, USC, January 28-29, 2007

Scientific Program Committee, Brazilian Symposium on Bioinformatics 2007

Program Committee, International Symposium on Combinatorial Optimization, Xi’an,China, August 12-15, 2007

Program Committee, Discovery in Massive or Complex Datasets: Common StatisticalThemes, NSF Workshop, October 16 and 17, 2007, Washington DC.

Conference Co-Chair, The Eight Annual Asian Pacific Bioinformatics Conference, Bei-jing China, January 13-16, 2009

Honorary General Chair and Steering Committee, International Joint Conferences onBioinformatics, Systems Biology and Intelligent Computing, August 3-6, 2009, Shang-hai, China

Mathematical Biosciences Institute, Board of Trustees (Ohio State University), 2009–2016

Committee to Select the Winner of the Birkhoff Prize, American Mathematical Society,February 2011 to January 2012.

California State Science Fair Category Judge (Senior: Mathematics and Software),April 16, 2013

Ford Foundation Fellowship Program Reviewer, 2016 and 2017

12

Member, External Advisory Committee, U54 Center for Cancer Systems Therapeutics(CaST), Columbia University, 2016–

Editorial Services

Editorial Board, Journal of Molecular Biology and Evolution, 1983-1993

Associate Editor, Bulletin of Mathematical Biology , 1984-2001

Communicating Editor, Advances in Applied Mathematics, 1986-2000

Editorial Board, Genomics, 1987-2002

Editorial Board, SIAM J. on Applied Mathematics, 1989-1991

Editorial Board, Molecular Phylogenetics and Evolution, 1992-1997

Co-Founder and Co-Editor-in-chief, Journal of Computational Biology, 1994-

Associate Editor, Annals of Combinatorics, 1996-

Editorial Board, Methodology and Computing in Applied Probability, 1997-

Editorial Board, Computational Methods in Science and Technology, 2000-

Editorial Board, BioMed Central Bioinformatics. 2001–

Advisory Board, Acta Biochimica et Biophysica Sinca, 2002-

Editorial Board, Proceedings of the National Academy of Sciences, 2002-2007

Editorial Board, Journal of Bioinformatics. 2003-

National Academy of Sciences, Temporaty Nominating Group for Foreign Associates,2012-

Editorial Committee, Annual Review of Biomedical Data Science, 2015-2020

Society Membership

Fellow of the Institute of Mathematical Statistics

Fellow of the American Association for the Advancement of Science

American Statistics Association

13

Society for Mathematical Biology

Fellow of the Society for Industrial and Applied Mathematics

Fellow of the International Society for Computational Biology

American Academy of Arts and Sciences

National Academy of Sciences

French Academy of Sciences

Fellow of the Los Angeles Institute of the Humanities

National Academy of Engineering

Chinese Academy of Sciences

Seminars

1998

“Statistical and Computational Aspects of Biological Database Searches,” KeynoteSpeaker, SIAMS-SEAS Annual Meeting, Tallahassee, Florida, March 20, 1998

Member of Program Committee and General Chair of the Steering Committee,RECOMB’98, New York City, March 22-25, 1998

Member of Organizing Committee, Understanding the Genome: Techno-logical and Mathematical Challenges, Mathematical Sciences ResearchInstitute, Berkeley California, May 21-23, 1998.

Invited participant: National Human Genome Research Institute’s FiveYear Planning Meeting, National Institutes of Health and Department ofEnergy, Airlie Center, Virginia, May 28-29, 1998.

“Sequence Alignment Methods,” Burrows Welcome Short Course, Math-ematics and Molecular Biology, Science for the 21st Century, June22-24, 1998, Berkeley, California

“Constructing Restriction Maps,” ISMB’98 (Intelligent Systems in Molec-ular Biology), Invited Speaker, Montreal, Canada, June 28–July 1, 1998

1999

14

Member of Program Committee and General Chair of the Steering Committee,RECOMB’98, New York City, April 11-14, 1998

“Estimating optical maps,” University of New Mexico, Albuquerque, New Mex-ico, April 26, 1999

“Estimating optical maps,” The Santa Fe Institute, Santa Fe, New Mexico, April27, 1999

“The Lost Art of Conversation,” Los Alamos National Laboratory, Los Alamos,New Mexico, May 8, 1999

“Constructing Restriction Maps,” Carniege Mellon University, May 12, 1999 Thiswas the first in a Series: Merck Distinguished Seminars in Computa-tional Biology

Genomics Workshop,, University of British Columbia, May 31—June 11, 1999(Co-Organizer with David Sankoff)

“Molecular Biology and Its Mathematics,” a three-hour lecture which began the11-th Lipari International Summer School. Computational Biologyheld June 20-July 3, 1999 in Lipari, Italy

“Estimating restriction maps,” the Plenary Lecture of the Sequencing, Foldingand Molecular Structure Session of the Theory and Mathematics in Bi-ology and Medicine conference in Amsterdam, June 29 – July 3, 1999 (Mylecture was June 30.)

“Estimating restriction maps,” Inaugural lecture in the Bioinformatics Interdisci-plinary Seminar Series, California State University at Northridge, September14, 1999

2000

“Estimating restriction maps,” Inaugural lecture in the Computational BiologyLecture Series, Brown University, February 1, 2000

“Estimating restriction maps,” Com2MaC Workshop on Combinatorial and Com-putational Mathematics, February 15–17, 2000 in Pohang, Korea

“Sequencing DNA” and “Estimating restriction maps,” two of four lectures inWorkshop on Bioinformatics, Postech University, Pohang, Korea

“Estimating restriction maps,” Uppsala University Department of Mathematics,Uppsala Sweden, February 23, 2000

“Sequence alignment algorithms,” Sequence alignments statistics,” (both Febru-ary 24) and “Estimating restriction maps,” (February 26). Three lectures

15

delivered in ”Graduate Course in Bioinformatics” in Uppsala Sweden, Febru-ary 24–26, 2000

“Estimating restriction maps,” Chalmers University Department of Mathemati-cal Satistics, March 2, 2000

“Reading DNA: SBH and Shotgun,” Open Bioinformatics Day, Gothenborg, Swe-den, May 12, 2000

“Estimating restriction maps” and “Matching Restriction Maps,” Computer Sci-ence Department, Helsinki University, May 16, 2000

“Probability of Matching Random Restriction Maps,” Celera Genomics, June 14,2000

“Reading DNA Molecules,” Second lecture in the Harvey Mudd College 2000-2001 Speaker Series: Beyond the Human Genome Project, October 25, 2000

“Reading Genome Sequences,” Plenary Lecture in Session Bioinformatics andGenomics I, AIChE Annual 2000 Meeting, November 13, 2000

“Hearing Distant Echos,” Celera Genomics, November 16, 2000

2001

“Matching Random Restriction Maps,” EURANDOM, Eindhoven Netherlands,January 16, 2001

“DNA Sequence Assembly,” University of Idaho, February 16, 2001

“DNA Sequence Assembly,” University of California at Berkeley, February 16,2001

“Estimating Restriction Maps,” the first in a lecture series, The John KinneyMemorial Lectures, Michigan State University, March 14, 2001

“Reading DNA Molecules,” the first in a lecture series, The John Kinney Memo-rial Lectures, Michigan State University, March 15, 2001

“Reading DNA Molecules,” University of Michigan, March 16, 2001

“Estimating Optical Maps,” Aisenstadt Lecture Series, University of Montreal,March 20, 2001

“The Probability of Matching Random Maps,” Aisenstadt Lecture Series, Uni-versity of Montreal, March 22, 2001

“A New Approach to DNA Sequence Assembly,” Aisenstadt Lecture Series, Uni-versity of Montreal, March 23, 2001

16

“Sequence Comparison and Database Searches,” Aisenstadt Lecture Series, Uni-versity of Montreal, April 17, 2001

“Oceans and Islands: Physical Mapping of DNA,” Aisenstadt Lecture Series,University of Montreal, April 18, 2001

“A New Approach to DNA Sequence Assembly,” Lecture 42 in the series Matem-aticke’ Kolokvium, Charles University, Prague, Czech Republic, June 1, 2001

“Overview of Computational Biology,” International School on ComputationalBiology, Poznan Poland, June 4, 2001

”Database Searches, Algorithms and Statistics,” International School on Com-putational Biology, Poznan Poland, June 4, 2001

”Physical Mapping and Assembly: A Statistical Analysis,” International Schoolon Computational Biology, Poznan Poland, June 4, 2001

”Genome Sequence Assembly,” International School on Computational Biology,Poznan Poland, June 4, 2001

“A New Approach to DNA Sequence Assembly,” The 2nd International Sympo-sium on Bioinformatics (Korean Society for Bioinformatics), Pohang Scienceand Technology University, Korea, August 17, 2001

“Coverage in Mapping and Sequencing,” The 2nd International Symposium onBioinformatics (Korean Society for Bioinformatics), Pohang Science and Tech-nology University, Korea, August 17, 2001

“A New Approach to DNA Sequence Assembly,” Korean National University,Seoul, Korea, August 20, 2001

“Sequence Database Search Algorithms,” Korean Health Industry DevelopmentInstitute, Seoul Korea, August 20, 2001

“Statistics for Sequence Database Searches,” ISI Satellite Meeting on recent Ad-vances in Biostatistics,” Taejon, Korea, August 21, 2001

Participant and Discussant , 2001 Santa Cruz Human Genome Symposium, Au-gust 23-26, 2001

“DNA Sequence Assembly Using Eulerian Graphs,” Invited Plenary Lecture,First SIAM/EMS Conference on APPLIED MATHEMATICS IN OUR CHANG-ING WORLD, Berlin, September 2, 2001

“DNA Sequence Assembly,” Statistics Department, Oxford University, Oxford,England, September 7, 2001

17

“DNA Sequence Assembly Using Eulerian Paths,” Ninth Frank and Bobbie Fen-ner Conference in Medical Research: BIOINFORMATION SCIENCE, Aus-tralian Academy of Science, Canberra, September 30, 2001

“DNA Sequence Assembly Using Eulerian Graphs,” Genetics Department, Stan-ford University, October 25, 2001

“DNA Sequence Assembly Using Eulerian Paths,” Mathematics Department,University of Arizona, Tucson, November 9, 2001

2002

Bioinformatics Session organizer, Mathematics and Molecular Biology VII: Mod-elling Across the Scales–Atoms to Organisms, Santa Fe, New Mexico, January8, 2002

“A Word Count Statistic from Computational Biology,” Plenary Lecture, Inter-national Workshop on Applied Probability, Caracas, Venezuela, January 14,2002

“DNA Sequence Assembly Using Eulerian Graphs,” Keynote Lecture, Interna-tional Conference on Bioinformatics, Bangkok, Thailand, February 7, 2002

“DNA Sequence Assembly Using Eulerian Graphs,” J-BIG Tokyo Lecture Series,February 11, 2002

“DNA Sequence Assembly Using Eulerian Paths,” Department of Computer Sci-ence, Harvey Mudd College, Claremont, CA, February 14, 2002

“DNA Sequence Assembly Using Eulerian Graphs,” Owens Lecture, Wayne StateUniversity, Detroit, April 1, 2002

“DNA Sequence Assembly Using Eulerian Graphs,” Florida State University,Tallahassee, April 3, 2002

“DNA Sequence Assembly Using Eulerian Graphs,” Texas Tech University, Lub-bock, April 5, 2002

“Sequence Assembly Using Eulerian Graphs,” The Stanislaw Ulam Lecture, DIMACS-CTS (National Chiao Tung University) Conference on the Interconnectionsamong Codes, Designs, Graphs and Molecular Biology, Taiwan, May 24, 2002

“A Dynamic Programming Algorithm for Haplotype Block Partitioning,” IPAMFunctional Genomics Reunion Conference, UCLA, June 17, 2002

“A Word Count Statistic from Computational Biology,” Keynote Address, 2002Taipei International Statistical Symposium and Bernoulli Society EAPR Con-ference, Taipei, Taiwan, July 9, 2002

18

“Dynamic Programming Algorithms for Haplotype Block Partitioning,” Univer-sity of New South Wales, Sydney, Australia, August 26, 2002

“Dynamic Programming Algorithms for Haplotype Block Partitioning,” GarvanInstitute, Sydney, Australia, August 28, 2002

“Dynamic Programming Algorithms for Haplotype Block Partitioning,” Queens-land University, Brisbane, Australia, August 29, 2002

“A Word Count Statistic from Computational Biology,” Australian National Uni-versity, Canberra, September 5, 2002

“Dynamic Programming Algorithms for Haplotype Block Partitioning,” Aus-tralian National University, Canberra, September 5, 2002

“A Word Count Statistic from Computational Biology,” La Trobe University, LaTrobe University, Melbourne, Australia, September 6, 2002

“A Word Count Statistic from Computational Biology,” Walter and Eliza HallInstitute of Medical Research, Melbourne, Australia, September 6, 2002

“Computations Essential For Genomics,” Minds that Matter Symposium, Cal-gary, Alberta, Canada, October 21, 2002

“Computations Essential For Genomics,” Minds that Matter Symposium, Ed-monton, Alberta, Canada, October 22, 2002

“A Computational Theme in Genomics,” Gairdner International Genome Sym-posium, Toronto, Canada, October 24, 2002

“Dynamic Programming Algorithms for Haplotype Block Partitioning,” MaxPlank Institute for Molecular Genetics, Berlin, Germany, December 6, 2002

“Dynamic Programming Algorithms for Haplotype Block Partitioning,” Institutefor Bioinformatics, Hamburg, Germany, December 10, 2002

2003

“Dynamic programming algorithms for haplotype block partitioning: applica-tions to human chromosome 21 haplotype data,” Seventh Annual Conferenceon Computational Molecular Biology (RECOMB 2003), Berlin, April 13, 2003

“A computational theme in genomics,” New Frontiers in Biological Sciences,University of Southern California, April ,2003

“Dynamic programming algorithms for haplotype block partitioning in humanchromosomes,” Institut Henri Poincare’, Paris, France May 12, 2003

“Eulerian methods for DNA sequence assembly and multiple alignment,” InstitutHenri Poincare’, Paris, France May 13, 2003

19

“DNA sequence assembly and multiple alignment by the Eulerian path approach,”LXVIII CSHL Symposium: The Genome of Home Sapiens, Cold Spring Har-bor, June 1, 2003

“Dynamic programming algorithms for haplotype block partitioning,” KeynoteLecture, 11th International Conference on Intelligent Systems for MolecularBiology, Brisbane Australia, July 2, 2003

“Eulerian path methods for multiple sequence alignment,” Invited Speaker, Com-putational Systems in Bioinformatics, CSB 2003, Stanford, August 14, 2003

“Dynamic programming algorithms for haplotype block partitioning,” InvitedSpeaker, Bioinformatics Institute Scientific Workshop, Singapore, August 21,2003

“Partitioning human chromosomes,” Colorado State University, Pueblo, Col-orado, August 29, 2003

“A computational theme in genomics,” Building Dedication Ceremony, ColoradoState University, Pueblo, Colorado, August 30, 2003

“Dynamic programming algorithms for partitioning sequence variation in humanchromosomes,” Plenary Lecture, 6-th Hellenic-European Conference on Com-puter Mathematics and Its Applications, Athens, Greece, September 25, 2003

“Dynamic programming algorithms for partitioning sequence variation in humanchromosomes,” Plenary Lecture, 7-th Joint Conference on Information Sci-ences, Raleigh, North Carolina, September 27, 2003

“A word-count statistic from computational biology,” Peking University Sympo-sium on Mathematics: 90-th Anniversary, Plenary Lecture, Beijing, China,October 25, 2003

2004

“Algorithms for haplotype block partitioning and applications,” Case WesternReserve University, Cleveland, Ohio, January 29, 2004

“Algorithms for haplotype block partitioning and applications,” Iowa State Uni-versity, Ames, Iowa, February 2, 2004

“Algorithms for haplotype block partitioning,” University of Texas at El Paso,February 6, 2004

“Patterns of variation in human chromosome 21,” Chinese Academy of Sciences,Shanghai, China, June 8, 2004

20

“A word-count statistic from computational biology,” SIAM Conference in Dis-crete Mathematics, Nashville, TN June 13, 2004

“Charting common ancestry in human chromosomes,” 13th European Conferenceon Mathematics in Industry, plenary lecture, Eindhoven, The Netherlands,June 25, 2004

“A word-count statistic from computational biology,” Society of MathematicalBiology, Ann Arbor, Michigan, July 25, 2004

“A word-count statistic from computational biology,” Combinatorics, SpecialFunctions and Physics, in Honor of the 75th Birthday of James D. Louck,Nankai University, Tianjin, China, August 3, 2004

2005

“Whole genome optical mapping,” Keynote Lecture, Southern California AppliedMathematics Symposium, SIAM, Los Angeles, April 24, 2005

“Whole genome optical mapping,” Plenary Lecture, Symposium on High-PerformanceComputing, Cornell Theory Center, Cornell University, May 24, 2005

“Whole genome optical mapping,” Plenary Lecture, BIOINFO 2005, Pusan, Ko-rea, September 23, 2005

“Some roles of computation in molecular biology,” The National Academies KeckFutures Initiative Genomic Revolution Conference, Irvine, California, Novem-ber 11, 2005.

2006

“Whole genome optical mapping,” Invited Lecture, Sequence Analysis TowardsSystem Biology, IPAM, UCLA, January 13, 2006

“Whole genome optical mapping,” Keynote Lecture, The Fourth Asia-PacificBioinformatics Conference, Taipei, Taiwan, February 13, 2006

“Stan Ulam and Computational Biology,” The Stanislaw Ulam Memorial Com-putational Biology Lecture, RECOMB 2006, Venice, Italy, April 3, 2006

“Life as a Resident Faculty at PIRC,” Keynote Address, Explore Parent Dinner,USC, April 10, 2006

“Whole genome optical mapping,” Myrna Samuels Memorial Lecture, PurdueUniversity, April 13, 2006

21

“Whole genome optical mapping,” Invited lecture, Walter M. Fitch Legacy Sym-posium, Genomes, Evolution, & Bioinformatics (SMBE Annual Meeting),Tempe, AZ, May 25, 2006

“Optical Mapping of the Maize Genome,” Plenary Lecture, Algorithmic Biology2006, UCSD, La Jolla, CA, November 30, 2006

“Constructing a map of the maize genome,” Plenary Lecture, International Con-ference on Bioinformatics, New Delhi, India, December 18, 2006

2007

“Computers and genomes,” IMS Public Lecture, National University of Singa-pore, March 7, 2007

“Bioinformatics of optical mapping,” Keynote Address, New Zealand Imagina-tive Partnering-Innovative Science Conference Programme, Auckland, NewZealand, March 14, 2007

“Optical Mapping of the Maize Genome,” Keynote Lecture, Sixth IEEE Interna-tional Workshop on High performance Computing, Long Beach, CA, March26, 2007

“Bioinformatics at USC,” Engineering School Presentation at Tsinghua Univer-sity, May 24, 2007

“Opening Lecture,” Tsinghau University Bioinformatics Summer School, July27, 2007

“Mathematics, Computers and Genomes,” Keynote Address, 2007 Conference onSystems Biology, Michigan State University, October 27, 2007

2008

“Whole-genome optical mapping,” Computer Science Distinguished Intel Lec-ture, University of California at Riverside, January 28, 2008

“Bioinformatics and Systems Biology,” Tsinghua University University, BeijingChina, May 22, 2008

“A Word Count Statistic in Computational Biology,” Nankai University, TianJin, China, May 25, 2008

“Eulerian Paths and DNA Sequence Assembly,” The Moshe Flatto Lecture Series2008, Beer-Sheva, Israel, November 27, 2008

22

2009

“Sequence Analysis Using Eulerian graphs,” Keynote Speech, Asian Pacific Bioin-formatics Conference, Beijing, China, January 16, 2009

“Reading DNA Sequences: 18th Century Mathematics for 21st Century Tech-nology,” Sixth Annual Carl M. Franklin Lecture on Science and Society, Uni-versity of Southern California, February 27, 2009

“Eulerian Paths and Reading DNA Sequences: 18th Century Mathematics for21st Century Technology,” Lecture for opening of School of Mathematical andStatistical Sciences, Arizona State University, March 18, 2009

“Reading DNA Sequences: 21st Century Technology with 18th Century Math-ematics,” Einstein Public Lecture in Mathematics, American MathematicalSociety, Raleigh, North Carolina, April 4, 2009

“Eulerian graphs and new generation DNA sequencing,” The 9th IEEE Inter-national Conference on Bioinformatics and Bioengineering, Keynote speech,Taichung, Taiwan, June 23, 2009

“Words, words, words,” International Workshop on Probability Theory, Statisticsand Their Application to Biology, Plenary lecture, Peiking University, BeijingChina June 26, 2009

“Words, words, words,” Fudan University, Shanghai, China, September 6, 2009

“Reading DNA Sequences Along Eulerian Paths,” CAS-MPG Partner Institutefor Computational Biology (PICB), Shanghai, China, September 7, 2009

“Euler’s Konigsberg Bridges and DNA Sequence Assembly,” Frontiers of Biomolec-ular Engineering, Boston University, Boston, September 25, 2009

“Comparing Sequences Without Alignment,” Computer Science Department,UCLA, Los Angeles, October 27, 2009

“A Word Count Statistic,” Max Planck Institute for Molecular Genetics, Berlin,December 2, 2009

2010

“Reading DNA Sequences: 18th Century, Mathematics for 21st Century Technol-ogy,” Distinguished Lecture Series, Department of Computer Science, WayneState University, April 9, 2010

“Reading DNA Sequences Along Eulerian Paths,” Mathematical Biosciences In-stitute, Ohio State University, March 15, 2010

23

“Sequence Comparison Using Word Counts,” Mathematics Department, AarhusUniversity, Denmark, April 13, 2010

“Alignment-free Sequence Comparison Using Word Counts,” Probability and Be-yond, A Conference in Honor of Louis Chen on His 70-th Birthday, Singapore,June 26, 2010

“Eulerian Graphs and Reading DNA Sequences,” Plenary Lecture, InternationalConference on Statistics and Society, Beijing, China, July 11, 2010

“A Word Count Statistic,” Beijing University Bioinformatics Center, July 9, 2010

“Computational Biology in the 21-st Century,” TNList Academic Summit on ITVision 2020, Tsinghua University, Beijing, China, July 12, 2010

“Sequence Comparison Without Alignment,” USC CAMS Colloquium, Septem-ber 30, 2010

“Reading DNA Sequences Along Eulerian Paths,” Discover Science Lecture Se-ries, University of Nevada at Reno, November 4, 2010

2011

“Sequence Comparison Without Alignment,” UCSD Distinguished ComputerScience Lecture Series, February 9, 2011

“Reading DNA Sequences Along Eulerian Paths,” Genomics Lecture Series, Cal-ifornia State University at Los Angeles, March 2, 2011

“Sequence Comparison Without Alignment,” Mathematics Department, Univer-sity of Nevada at Reno, April 7, 2011

“Reading DNA Sequences Along Eulerian Paths,”Computer Science Department,Tel Aviv University, May 15, 2011

“Reading DNA Sequences Along Eulerian Paths,” National Chung Hsing Uni-versity, Taiwan, November 14, 2011

“Reading DNA Sequences Along Eulerian Paths,” Academia Sinica, Taiwan,November 16, 2011

“Reading DNA Sequences Along Eulerian Paths,” National Chiao Tung Univer-sity, Taiwan, November 17, 2011

2012

24

“Sequence Comparison Without Alignment,” The Applied Mathematics Distin-guished Research Lecture, University of Colorado at Boulder, March 2, 2012

“Eulerian Graphs and Reading DNA Sequences,” Plenary Address, 2012 SIAMFront Range Student Conference, Denver CO, March 3, 2012

2013

“Reading DNA Sequences along Eulerian Paths,” Jiaotong University, Xi’an,China September 23, 2013

“Reading DNA Sequences along Eulerian Paths,” Tsinghua University GlobalVision Lectures, No. 136 in the Series. September 25, 2013

2014

“RNA Combinatorics I: Secondary Structure,” Fudan University, Shanghai, China,May 15, 2014

“Reading DNA Sequences along Eulerian Paths,” First in a series of MastersLectures, Chinese University of Hong Kong at Shenzhen, May 19, 2014

“Alignment-free Local Sequence Comparison Algorithms,” Tsinghua Chair Pro-fessors Workshop, Beijing, China, May 22, 2014

“Sequence Comparison Using Word Counts,” Plenary Lecture, International Work-shop on Applied Probability (IWAP2014), Antalya, Turkey, June 17, 2014

“DNA Sequencing in the 21-st Century: Algorithms and Estimation,” PlenaryLecture, IEEE International Symposium on Information Theory, HonoluluHawaii, June 30, 2014

“Mathematical and Statistical Problems from DNA Sequencing,” DistinguishedLecture Series, City University of Hong Kong, September 8, 2014

“Careers in Bioinformatics,” Bosi Lecture Forum which is a graduate student runspecial seminar series, Fudan University, October 23, 2014

“At the Confluence of Genomics, Mathematics, Statistics and Computer Sci-ence,” The Future Science Forum at the Pujiang Innovation Forum, ShanghaiChina, October 26, 2014

2015

“DNA Sequencing in the 21st Century,” 2015 Milne Public Lecture in Mathe-matics, Statistics, and Computer Science, Oregon State University, March 30,2015

25

“Using Word Counts for Alignment Free Sequence Analysis,” Oregon State Uni-versity, April 1, 2015

“Why So Late?” Dan David Prize acceptance speech, Tel Aviv University, May17, 2015.

“Big Data from DNA Sequencing,” Dan David Prize Lecture, Tel Aviv University,May 18, 2105

“DNA and the Age of Information,” LA Institute of the Humanities, October 9,2105

“DNA Sequencing in the 21st Century,” Plenary Lecture, Retrospect and Prospectof Computational Biuology Research, Partner Institute of Computational Bi-ology, Shanghai November 5, 2015

“Ask the Masters,” International Symposium on Evolutionary Genomics andBioinformatics 2015, Academia Sinica, Taiwan, November 6, 2015

“DNA Sequencing in the 21st Century,” Plenary Lecture, International Sympo-sium on Evolutionary Genomics and Bioinformatics 2015, Academia Sinica,Taiwan, November 7, 2015

“DNA and the Age of Information,” Plenary Lecture, Fudan Science and Tech-nology Forum, Shanghai, China, December 17-18, 2105

2016

“Fundamentals of Stringology II: Probability and Statistics for Sequence Align-ment,” Simons Institute for the Theory of Computing, Berkeley CA Jan 19,2016

“Probability and Statistics for Bio-Sequence Database Searches,” Keynote Speech,The Third Taihu International Statistics Forum, Shanghai China July 10,2016

“Statistical Issues for Sequence Comparison: Analysis by Position and Analysisby Pattern,” Plenary Lecture, KAUST Research Conference: ComputationalSystems Biology in Biomedicine, Saudi Arabia, December 5-7, 2016.

2017

“Combinatorial and Probabilistic Aspects of Genetic Sequence Alignment,” Cen-ter for Combinatorics, Nankai University, Tianjin, China, May 10, 2017

“Remarks on an Article by Richard Messing,” Algorithmic Challenges in Ge-nomics Reunion, Simons Institute for the Theory of Computing, BerkeleyCA, June 28, 2017

26

“The Changing Landscape of Biological Sequence Analysis,” Plenary lecture,Beyond Sequence Alignment Symposium, Biocomplexity Institute, VirginiaTech, October 16, 2017

2018

“Mathematical Approaches to RNA Structure,” University of Virginia, June 4,2018

V. REPORTS AND CONFERENCE PROCEEDINGS

1. Waterman, M.S. 1972 Allocating defense missiles to maximize expected distance be-tween the target and closest penetrating offensive missile. Bell Telephone LaboratoriesTechnical Memorandum 66-4263-12, 1966. This work appears in Mathematical Modelsof Target Coverage and Missile Allocation by A. R. Eckler and S. A. Burr, MilitaryOperations Research Society.

2. Waterman, M.S. Decimals and partial quotients of Euler’s constant and LN(2). Ac-cepted by UMT of the AMS.

3. Waterman, M.S. (January 1974) A Statistical Evaluation of the Marviken Data. Workperformed for the U. S. A. E. C. by Energy Incorporated . 144 pages.

4. Waterman, M.S. (1975) Introduction to Statistics (32 pages). A correspondence studycourse written for and published by Correspondence Study Office, University of IdahoCampus, Moscow, ID 83843.

5. Johnson, R.W. and Waterman, M.S. (Jan. 1976) Jacobi Algorithms for Integers. LosAlamos Scientific Laboratory Publication LA-6187-MS. 15 pages.

6. Martz, H.F., Waller, R.A. and Waterman, M.S. (July 1976) Fitting beta prior distri-butions in Bayesian reliability analysis. Los Alamos Scientific Laboratory PublicationLA-6395-MS. 23 pages.

7. Zeigler, R.K., Bement, T.R., Whiteman, D. and Waterman, M.S. (1977) Some prob-lems associated with the analysis of National Uranium Resource Evaluation (NURE)data Proceedings of the Second ERDA Statistical Symposium, LA-6758-C, 212-238.

8. Waller, R.A., Johnson, M.M., Martz, H.F. and Waterman, M.S. (1977) Gamma priordistribution selection for Bayesian analysis of failure rate and reliability in NuclearSystems Reliability Engineering and Risk Assessment (SIAM) edited by J. B. Fusselland G. R. Burdick.

27

9. Martz, H.F. and Waterman, M.S. (1977) Statistical analysis and planning of multi-hundred-watt impact tests. Los Alamos Scientific Laboratory Publication LA-6886-MS. 13 pages.

10. Beyer, W.A. and Waterman, M.S. (1978) A conditioned random walk with applica-tions. Los Alamos Scientific Laboratory Publication LA-6990-MS. 18 pages.

11. Johnson, M.E., Monash, E.A. and Waterman, M.S. (1978) Modeling and optimizing agas-water reservoir. Los Alamos Scientific Laboratory Publication, LA-7088. 27 pages.

12. Smith, T.F. and Waterman, M.S. (1978) Evolutionary distance and secondary struc-ture for biomolecules. Los Alamos Scientific Laboratory Publication, LA-7153-MS. 21pages.

13. Howell, J.A., Smith, T.F. and Waterman, M.S. Using MACSYMA to compute gener-ating functions for RNA. Proceedings 1979 MACSYMA Users Conference, 126-139.

14. Waterman, M.S. (1988) Pattern matching in DNA sequences. Volume 4, Proceedings1988 IMACS, 4-6.

15. Waterman, M.S. (1988) Mathematical results for mapping DNA. Texas Tech Univer-sity, Mathematics Series. Visiting Scholars Lectures, 1986-1987 Volume 15, 137-147.

16. Goldstein, L. and Waterman, M.S. (1988) A simulated annealing approach to mappingDNA. Computing Science and Statistics. Proceedings of the 20th Symposium on theInterface: Computationally Intense Methods in Statistics. Eds. Wegman, Gantz, andMiller, 147-151.

17. Chow, E.T., Hunkapillar, T., Peterson, J.C., Zimmerman, B.A. and Waterman, M.S.A systolic array processor for biological information signal processing Proceedings ofthe 1991 International Conference on Supercomputing (ICS-91), ACM Order Number415911, (June 17-21, 1991) 216-223.

18. Chow, E.T., Hunkapillar, T., Peterson, J.C. and Waterman, M.S. Biological informa-tion signal processor Proceedings of the IEEE Applications-Specific Array ProcessorsConference, IEEE Computer Society Press, Order Number 2237, (September 1991)144-160.

19. Mathematical bioinformatics (T. Lengauer, D. Schomburg, M. Waterman (editors))Dagstuhl-Seminar-Report; 46 07.09.-11.09.92 (9237) (1992).

20. Churchill, G., Burks, B., Eggert, E., Engle, M.L., Waterman, M.S. Assembling DNAsequence fragments by shuffling and simulated annealing Los Alamos Scientific Labo-ratory Publication, LA-UR-2287. (1993) 25 pages.

28

21. Branscomb, E., Cartwright, P., Cinkosky, M.J., Davison, D., Fasman, K.H., Fields, C.,Gilna, P., Kingsbury, D.T., Marr, T. Slezak, T., Smith, F.R., Spengler, S., Uberbacher,E., and Waterman, M. (1993) DOE informatics summit meeting report. April 26-27,1993. Baltimore, MD. (Available via Gopher at gopher.gdb.org, and via the WorldWide Web at http://www.gdb.org/hopkins.html).

22. Pevzner, P.A. and Waterman, M.S. Open combinatorial problems in computationalbiology (1995) Invited Paper Proceedings Third Israel Symposium on the Theory ofComputing and Systems IEEE Computer Society Press, Order Number PR6915, (Jan-uary 4-6, 1995) 158-173.

23. Vingron, M. and Waterman, M.S. Statistical significance of local alignments with gaps.Bioinformatics: From Nucleic Acids and proteins to Cell Metabolism. GBF Mono-graphs Vol. 18., Schomburg, D., and Lessel, U., Eds. (1995) 75-84.

24. Komatsoulis, G.A. and Waterman, M.S. Chimeric alignment by dynamic program-ming: algorithm and biological uses (1997) Proceedings First Annual Conference onComputational Molecular Biology (RECOMB97) ACM Press, Order Number 508971,(January 19 - 22, 1997) 174-180.

25. Waterman, M.S. and Vingron, M. Statistical and computational aspects of biologicaldatabase searches. (1997) Proceedings of the International Symposium on TheoreticalBiophysics and Biomathematics Inner Mongolia University Press, pp. 1-6.

26. Sun, F., Benson, G., Arnheim, A., and Waterman, M.S.Pooling strategies for establish-ing genome maps using FISH. (1997) Proceedings First Annual Conference on Compu-tational Molecular Biology (RECOMB97) ACM Press, Order Number 508971, (Jan-uary 19 - 22, 1997) 294-299.

27. Komatsoulis, G.A. and Waterman, M.S. (1997) Statistics in Molecular Biology: An Ex-ample from Detection of Chimeric i6S RNA Artifacts Computing Science and Statistics,29(3), 210-217.

28. Dancik, V. and Waterman, M.S.Simple maximum likelihood methods for the opticalmapping problem (1998) Genome Informatics No. 8 Universal Academy Press, Inc.(ISSN 0919-9454), pp 1-8.

29. Pevzner, P., Tang, H. , and Waterman, M.S.A new approach to fragment assemblyin DNA sequencing. (2001) Proceedings Fifth Annual Conference on ComputationalMolecular Biology (RECOMB97) ACM Press, Order Number 508011, (April 22-25,2001), 256-267.

29

30. Tang, M, Waterman, M.S., and Yooseph, sS. Zinc finger gene clusters and tandem geneduplication. (2001) Proceedings Fifth Annual Conference on Computational MolecularBiology (RECOMB97) ACM Press, Order Number 508011, (April 22-25, 2001), 297-304.

31. Waterman, M.S.Eric Lander to Give von Neumann Lecture in Philadelphia. SIAMNews, 35, June 2002, 1;13.

32. Li, L., Kim, J., and Waterman, M.S.Haplotype reconstruction from SNP alignmentProceedings Seventh Annual Conference on Computational Molecular Biology (RE-COMB 2003)T. Lengauer, W. Miller, S. Istrail, P. Pevzner and M.S. Waterman, Edi-tors. ACM Press, Order Number 508031, (April 10-13, 2003), 207-216

33. Zhang, K., Sun, F., Waterman, M.S., and Chen, T. Dynamic programming algorithmsfor haplotype block partitioning: applications to human chromosome 21 haplotypedata Proceedings Seventh Annual Conference on Computational Molecular Biology(RECOMB 2003)T. Lengauer, W. Miller, S. Istrail, P. Pevzner and M.S. Waterman,Editors. ACM Press, Order Number 508031, (April 10-13, 2003), 332-340

34. Waterman, M.S.and Zhang, Yu. Eulerian Methods for Multiple Sequence AlignmentProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003 IEEE ComputerSociety, Order Number PR02000, 11-14 August) 29.

35. Waterman, M.S.. “Dynamic programming algorithms for partitioning sequence varia-tion in human chromosomes,” Proceedings of the 7-th Joint Conference on InformationSciences, 2003 JCIS/Association for Intelligent Machinery, Inc. ISBN No. 0-970789-2-5. p. 53.

36. Zhang K., Chen, T., Waterman MS, Sun, F., (2004) A set of dynamic algorithms forhaplotype block partition and tag SNP selection via haplotype data and genotype data.Computational Methods for SNPs and Haplotype Inference, Istrail, S., Waterman,M.S., and Clark A., Editors, LNBI 2983, Springer, 96-112.

37. Zhang, K.Chen, T., Waterman, M.S., Qin, Z., Liu, J., and Sun, F.(2004) Computa-tional Methods for SNPs and Haplotype Inference. S. Istrail et al, Editors, LectureNotes in Computer Science, Springer (2004) p. 96-112.

38. Waterman, M.S.(2006) Stan Ulam and Computational Biology. Proceedings TenthAnnual Conference on Computational Molecular Biology (RECOMB 2006) A. Apos-tolico et al, Editors. Lecture Notes in Bioinformatics (LNBI 3909), Springer (2006).p. 159.

30

39. Zhang, K., Sun, F., Waterman, M.S.and Chen, T. . “Dynamic programming algorithmsfor partitioning sequence variation in human chromosomes,” Computer Mathematicsand Its Applications; Advances and Developments (1994-2005)” E.A. Lipitakis, Editor,LEA Publishers (2006), p. 431-442.

VI. PUBLICATIONS

1. Waterman, M.S.(1970) Some ergodic properties of multi-dimensional F -expansions. Z.Wahrscheinlichkeitstheorie verw. Geb., 16 77-103.

2. Waterman, M.S.(l971) A Kuzmin theorem for a class of number theoretic endomor-phisms. Acta Arith., 19 31-41.

3. Waterman, M.S.(l971) A note on the reparametrization of an exponential family. Ann.Math. Statist., 42 752-754.

4. Beyer, W.A. and Waterman, M.S.(l972) Ergodic computations with continued frac-tions and Jacobi’s algorithm. Numer. Math., 19 195-205. (1973) Errata, 20 430.

5. Schweiger, F. and Waterman, M.S.(l973) Some remarks on Kuzmin’s theorem for F -expansions. J. Number Theory, 5 123-131.

6. Waterman, M.S.(1974) A restricted least squares problem. Technometrics, 16 135.

7. Beyer, W.A. and Waterman, M.S.(1974) Error analysis of a computation of Euler’sconstant. Math. Comp., 28 599-604.

8. Waterman, M.S.(1975) Remarks on invariant measures for number theoretic transfor-mations. Monatsh. Math., 79 157-163.

9. Waterman, M.S.(1975) Cantor series for vectors. Math. Month., 82 622-625.

10. Waterman, M.S.(1975) On Jacobi’s solution of linear Diophantine equations. Math.Mag., 48 159-163.

11. Waterman, M.S.(1975) F -expansions of rationals. Aequationes Math., 13 263-268.

12. Waterman, M.S.(1976) On the approximation of invariant measures for continued frac-tions. Rocky Mountain J. Math., 6 181-189.

13. Johnson, R.W. and Waterman, M.S.(1976) The algorithms of Euclid and Jacobi. Int.J. Math. Educ. Sci. and Technol., 7 307-313.

31

14. Waterman, M.S., Smith, T.F. and Beyer, W.A. (l976) Some biological sequence metrics.Adv. Math., 20 367-387.

15. Lowe, V.W. and Waterman, M.S.(1976) On the variance of a product with applicationto uranium estimation. J. Inst. Nuc. Mat. Manag., V 36-41.

16. Waterman, M.S.(1977) A Jacobi algorithm and metric theory for greatest commondivisors. J. Math. Anal. Appl., 59 288-300.

17. Waterman, M.S.(1977) Multidimensional greatest common divisor and Lehmer algo-rithms. BIT, 17 465-478.

18. Waterman, M.S., Smith, T.F., Singh, M. and Beyer, W.A. (1977) Additive evolutionarytrees. J. Theor. Biol., 64 199-213.

19. Bement, T.R. and Waterman, M.S.(1977) Locating maximum variance segments insequential data. J. Int. Assoc. Math. Geol., 9 55-61.

20. Beyer, W.A. and Waterman, M.S.(1977) Symmetries for conditioned ruin problems.Math. Mag., 50 42-45.

21. Waller, R.A. and Waterman, M.S.(1977) Percentiles for the gamma distribution. SIAMReview, 19 146.

22. Waterman, M.S.(1977) Least squares with non-negative regression coefficients. J.Statist. Comput. Simul., 6 67-70.

23. Beckman, R.J. and Waterman, M.S.(1977) On the random distribution of nucleoli inmetabolic cells. J. Theor. Biol., 69 561-562.

24. Waterman, M.S.and Lowe, V.W. (1977-1978) Reconstruction of an account’s past. J.Inst. of Nuc. Mat. Mgmt., VI 55-57.

25. Waterman, M.S.and Whiteman, D.E. (1978) Estimation of probability densities byempirical density functions. Int. J. Math. Educ. Sci. Tech., 9 127-137.

26. Waterman, M.S.(1978) Secondary structure of single stranded nucleic acids. Adv.Math. Suppl. Stud., I 167-212.

27. Kahaner, D. and Waterman, M.S.(1978) Asymptotics for gamma and beta percentiles.J. Stat. Comp. Sim., 6 315-316.

28. Martz Jr., H.F. and Waterman, M.S.(1978) A Bayesian model for determining theoptimal test stress for a single test unit. Technometrics, 20 179-185.

32

29. Waterman, M.S.and Smith, T.F. (1978) On the similarity of dendrograms. J. Theor.Biol., 73 789-800.

30. Smith, T.F. and Waterman, M.S. (1978) RNA secondary structure. Math. Biosci., 42257-266.

31. Stein, P.R. and Waterman, M.S.(1978) On some new sequences generalizing the Cata-lan and Motzkin numbers. Discrete Math., 26 261-272.

32. Beyer, W.A. and Waterman, M.S.(1979) Moments of absorption time for a conditionedrandom walk. Stud. Appl. Math., 60 83-90.

33. Waterman, M.S.(1979) Combinatorics of RNA hairpins and cloverleaves. Stud. Appl.Math., 60 91-96.

34. Johnson, M.E., Monash, E.A. and Waterman, M.S.(1979) Modeling and optimizing agas-water reservoir. I: Enhanced recovery with waterflooding. J. Int. Assoc. Math.Geol., 11 63-74.

35. Smith, T.F. and Waterman, M.S.(1980) Protein constraints induced by multiframeencoding. Math. Biosci., 49 17-26.

36. Smith, T.F. and Waterman, M.S.(1980) New stratigraphic correlation techniques. J.Geol., 88 451-457.

37. Howell, J.A., Smith, T.F. and Waterman, M.S.(1980) Computation of generating func-tions for biological molecules. SIAM J. Appl. Math, 39 119-133.

38. Smith, T.F. and Waterman, M.S.(1980) How alike are two trees? Math. Month., 87,552-553.

39. Smith, T.F., Waterman, M.S. and Fitch, W.M. (1981) Comparative biosequence met-rics. J. Mol. Evol., 18 38-46.

40. Smith, T.F. and Waterman, M.S.(1981) Comparison of biosequences. Adv. Appl.Math., 2 482-489.

41. Smith, T.F. and Waterman, M.S.(1981) Overlapping genes and information theory. J.Theor. Biol., 91 379-380.

42. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subse-quences. J. Mol. Biol., 147 195-197.

43. McKay, M.D. and Waterman, M.S.(1982) Self-descriptive strings. Math. Gaz., 66 1-4.

33

44. Lipman, D.J., Smith, T.F., Beckman, R.J. and Waterman, M.S.(1982) Hierarchicalanalysis of influenza A hemagglutinin gene sequences. Nucleic Acids Research, 105375-5389.

45. Smith, T.F., Waterman, M.S. and Sadler, J.R. (1983) Statistical characterization ofnucleic acid sequence functional domains. Nucleic Acids Research, 11 2205-2220.

46. Sadler, J.R., Waterman, M.S. and Smith, T.F. (1983) Regulatory pattern identificationin nucleic acid sequences. Nucleic Acids Research, 11 2221-2231.

47. Waterman, M.S.(1983) Sequence alignments in the neighborhood of the optimum withgeneral application to dynamic programming. Proc. Natl. Acad. Sci. USA 80 3123-3124.

48. Waterman, M.S.(1983) Frequencies of restriction sites. Nucleic Acids Research, 118951-8956.

49. Lipman, D.J., Wilbur, W.J., Smith, T.F. and Waterman, M.S.(1984) On the statisticalsignificance of nucleic acid similarities. Nucleic Acids Research, 12 215-226.

50. Waterman, M.S., Smith, T.F. and Katcher, H. (1984) Algorithms for restriction mapcomparisons. Nucleic Acids Research, 12 237-242.

51. Waterman, M.S.(1984) Some applications of information theory to cellular automata.Physica D 45-51.

52. Waterman, M.S.(1984) How do you spell DNA? Nature, 309 118.

53. Waterman, M.S.(1984) Efficient sequence alignment algorithms. J. Theor. Biol., 108333-337.

54. Waterman, M.S.(1984) General methods of sequence comparison. Bull. Math. Biol.,46 473-500.

55. Waterman, M.S., Arratia, R. and Galas, D.J. (1984) Pattern recognition in severalsequences; consensus and alignment. Bull. Math. Biol., 46 515-527.

56. Waterman, M.S.and Perlwitz, M.D. (1984) Line geometries for sequence comparisons.Bull. Math. Biol., 46 567-577.

57. Byers, T. and Waterman, M.S.(1984) Determining all optimal and near-optimal solu-tions when solving shortest path problems by dynamic programming. Oper. Res., 321381-1384.

34

58. Arratia, R. and Waterman, M.S.(1985) An Erdos-Renyi law with shifts. Adv. Math.,55 13-23.

59. Breen, S., Waterman, M.S. and Zhang, N. (1985) Renewal theory for several patterns.J. Appl. Prob. 22 228-234.

60. Smith, T.F., Waterman, M.S. and Burks, C. (1985) The statistical distribution ofnucleic acid similarities. Nucleic Acids Research, 13 645-656.

61. Darling, R.W.R. and Waterman, M.S.(1985) Matching rectangles in d-dimensions; al-gorithms and laws of large numbers. Adv. Math., 55 13-23.

62. Waterman, M.S.(1985) Dynamic programming algorithms for picture comparison. Adv.Appl. Math., 6 129-134.

63. Arratia, R. and Waterman, M.S. (1985) Critical phenomena in sequence matching.Ann. Prob., 13 1236-1249.

64. Waterman, M.S.and Byers, T.H. (1985) A dynamic programming algorithm to find allsolutions in the neighborhood of the optimum. Math. Biosci., 77 179-188.

65. Beyer, W.A., Sellers, P.H. and Waterman, M.S.(1985) Stanislaw M. Ulam’s contribu-tions to theoretical biology. Let. Math. Phys., 10 231-242.

66. Galas, D.J., Eggert, M. and Waterman, M.S. (1985) Rigorous pattern recognitionmethods for DNA sequences: analysis of promoter sequences from E. coli.. J. Mol.Biol., 186 117-128.

67. Waterman, M.S.(1985) Book review: Time Warps, String Edits, and Macromolecules:The Theory and Practice of Sequence Comparison. Math. Biosci., 76 243-244.

68. Waterman, M.S.(1986) Probability distributions for DNA sequence comparisons. Lent.Life Sci., 17 29-56.

69. Darling, R.W.R. and Waterman, M.S.(1986) Extreme value distribution for the largestcube in a random lattice. SIAM J. Appl. Math., 46 118-132.

70. Gordon, L., Schilling, M. and Waterman, M.S.(1986) An extreme value theory for longhead runs. Prob. Theor. Rel. Fields, 72 279-287.

71. Arratia, R., Gordon, L. and Waterman, M.S.(1986) An extreme value theory for se-quence matching. Ann. Stat., 14 971-993.

72. Waterman, M.S.and Griggs, J.R. (1986) Interval graphs and maps of DNA. Bull. Math.Biol., 48 189-195.

35

73. Griggs, J.R., Hanlon, P.J. and Waterman, M.S.(1986) Sequence alignments with matchedsections. SIAM J. Alg. Disc. Meth., 7 604-608.

74. Waterman, M.S.(1986) Multiple sequence alignment by consensus. Nucleic Acids Re-search, 14 9095-9102.

75. Waterman, M.S.and Smith, T.F. (1986) Rapid dynamic programming methods forRNA secondary structure. Adv. Appl. Math., 7 455-464.

76. Waterman, M.S.and Raymond Jr., R.R. (1987) The match game:new stratigraphiccorrelation algorithms. Math. Geol., 19 194-207.

77. Waterman, M.S., Gordon, L. and Arratia, R. (1987) Phase transitions in sequencematches and nucleic acid structure. Proc. Natl. Acad. Sci. USA, 84 1239-1243.

78. Goldstein, L. and Waterman, M.S.(1987) Mapping DNA by stochastic relaxation. Adv.Appl. Math., 8 194-207.

79. Waterman, M.S.and Eggert, M. (1987) A new algorithm for best subsequence align-ments with application to tRNA-rRNA comparisons. J. Mol. Biol., 197 723-728.

80. Arratia, R., Morris, P. and Waterman, M.S.(1988) Stochastic scrabble: large deviationsfor sequences with scores. J. Appl. Prob. 25 106-119.

81. Lander, E.S. and Waterman, M.S.(1988) Genomic mapping by fingerprinting randomclones: a mathematical analysis. Genomics, 2 231-239.

82. Perlwitz, M.D., Burks, C. and Waterman, M.S.(1988) Pattern analysis of the geneticcode. Adv. Appl. Math. 9 7-21.

83. Waterman, M.S.(1988) Computer analysis of nucleic acid sequences. Meth. Enzym.164 765-793.

84. Goldstein, L. and Waterman, M.S.(1988) Neighborhood size in the simulated annealingalgorithm. Amer. J. Math. Manag. Sci. 8 409-424.

85. Waterman, M.S.(1989) Sequence alignments. In Mathematical Methods for DNA Se-quences. Ed. by M.S. Waterman. CRC Press, 53-92.

86. Waterman, M.S.(1989) Consensus patterns in sequences. In Mathematical Methodsfor DNA Sequences. Ed. by M.S. Waterman. CRC Press, 93-115.

87. Waterman, M.S.(1989) Consensus methods for folding single-stranded nucleic acids.In Mathematical Methods for DNA Sequences. Ed. by M.S. Waterman. CRC Press,185-224.

36

88. Arratia, R. and Waterman, M.S.(1989) The Erdos-Renyi strong law for pattern match-ing with a given proportion of mismatches. Ann. Prob., 17 1152-1169.

89. Churchill, G.A., Daniels, D.L. and Waterman, M.S.(1990) The distribution of restric-tion enzyme sites in Ercherichia coli. Nucleic Acids Research, 18 589-597.

90. Waterman, M.S.and Gordon, L. (1990) Multiple hypothesis testing for sequence com-parisons. In Computers and DNA, Addison-Wesley, 127-135.

91. Waterman, M.S.(1990) Genomic sequence databases. Genomics, 6 700-701.

92. Waterman, M.S.and Jones, R. (1990) Consensus methods for DNA and protein se-quence alignment. Meth. Enzym., 183 221-236. Ed. Russell F. Doolittle, AcademicPress, Inc.

93. Arratia, R., Gordon, L. and Waterman, M.S.(1990) The Erdos-Renyi law in distribu-tion, for coin tossing and sequence matching. Ann. Stat., 18 539-570.

94. Tang, B. and Waterman, M.S.(1990) The expected fraction of clonable DNA. Bull.Math. Biol., 52 455-475.

95. Branscomb, E., Slezak, T., Pae, R., Galas, D., Carrano, A.V. and Waterman, M.S.(1990) Optimizing restriction fragment fingerprinting methods for ordering large ge-nomic libraries. Genomics, 8 351-366.

96. Griggs, R.J., Hanlon, P.J., Odlyzko, A.M. and Waterman, M.S.(1990) On the numberof alignments of k sequences. Graphs and Combinatorics, 6 133-146.

97. Waterman, M.S.(1990) Comment on: Poisson approximation and the Chen-Steinmethod, by R. Arratia, L. Goldstein and L. Gordon. Stat. Sci., 5 427-429.

98. Arratia, R., Lander, E.S., Tavare, S. and Waterman, M.S. (1991) Genomic mappingby anchoring random clones: a mathematical analysis. Genomics, 11 806-827.

99. Schmitt, W. and Waterman, M.S.(1991) Multiple solutions of DNA restriction mappingproblems. Adv. Appl. Math., 12 412-427.

100. Waterman, M.S., Joyce, J. and Eggert, M. (1991) Computer alignment of sequences.In Phylogenetic Analysis of DNA Sequences, Oxford University Press, 59-72.

101. Navidi, W., Arnheim, N. and Waterman, M.S.(1992) A multiple-tubes approach for ac-curate genotyping of very small DNA samples by using PCR: statistical considerations.Am. J. Hum. Genet., 50 347-359.

37

102. Smith, T.F. and Waterman, M.S. (1992) The continuing case of the Florida dentist.Science, 256 1155-1156.

103. Schoniger, M. and Waterman, M.S. (1992) A local algorithm for DNA sequence align-ment with inversions. Bull. Math. Biol., 54 521-536.

104. von Haeseler, A., Blum, B., Simpson, L., Strum, N. and Waterman, M.S. (1992) Com-puter methods for locating kinetoplastid cryptogenes. Nucleic Acids Research, 202717-2724.

105. Goldstein, L. and Waterman, M.S. (1992) Poisson, compound Poisson, and processapproximations for testing statistical significance in sequence comparisons. Bull. Math.Biol., 54 785-812.

106. Waterman, M.S., Eggert, M. and Lander, E.S. (1992) Parametric sequence compar-isons. Proc. Natl. Acad. Sci. USA, 89 6090-6093.

107. Churchill, G.A. and Waterman, M.S. (1992) The accuracy of DNA sequences: estimat-ing sequence quality. Genomics, 14 89-98.

108. Pevzner, P. and Waterman, M.S. (1992) Matrix longest subsequence problems, dual-ity and Hilbert bases. Lecture Notes in Computer Science. Combinatorial PatternMatching,Third Annual Symposium, 644 77-87.

109. Huang, X. and Waterman, M.S. (1992) Dynamic programming algorithms for restric-tion map comparison. Comp. Appl. Bio. Sci., 8 511-520.

110. Pevzner, P. and Waterman, M.S. (1993) Generalized sequence alignment and duality.Adv. Appl. Math., 14 139-171.

111. Pevzner, P. and Waterman, M.S. (1993) A fast filtration for the substring matchingproblem. Lecture Notes in Computer Science. Combinatorial Pattern Matching,FourthAnnual Symposium, 684 197-214.

112. Penner, R.C. and Waterman, M.S. (1993) Spaces of RNA secondary structures. Adv.Math., 101 31-49.

113. Waterman, M.S.and von Haeseler, A. (1993) Designer algorithms for cryptogene searches.New Zealand J. Bot., 31 269-274.

114. Vingron, M. and Waterman, M.S.(1994) Sequence alignment and penalty choices:review of concepts, case studies and implications. J. Mol. Biol., 235 1-12.

38

115. Arratia, R. and Waterman, M.S.(1994) A phase transition for the score in matchingrandom sequences allowing deletions. Ann. Appl. Prob., 4(1) 200-225.

116. Waterman, M.S.and Vingron, M. (1994) Rapid and accurate estimates of statisticalsignificance for sequence database searches. Proc. Natl. Acad. Sci. USA, 91 4625-4628.

117. Waterman, M.S.(1994) Parametric and ensemble sequence alignment algorithms. Bull.Math. Biol., 56 743-767.

118. Waterman, M.S.(1994) Estimating of statistical significance of sequence alignments.Phil. Trans. R. Soc. London B, 344 383-390.

119. Goldstein, L. and Waterman, M.S.(1994) Approximations to profile score distributions.J. Comp. Biol., 1 93-104.

120. Schmitt, W.R. and Waterman, M.S.(1994) Linear trees and RNA secondary structure.Disc. Appl. Math., 51 317-323.

121. Waterman, M.S.and Vingron, M. (1994) Sequence comparison significance and Poissonapproximation. Statistical Sciences, 9 367-381.

122. Benson, G. and Waterman, M.S.(1994) A method for fast database search for all k-nucleotide repeats. Nucleic Acids Research, 22 4828-4836.

123. Waterman, M.S.(1994) Genomes, maps and sequences Lecture Notes in Biomathe-matics, 100 28-52.

124. Pevzner, P.A. and Waterman, M.S.(1995) Multiple filtration and approximate patternmatching. Algorithmica, 13 135-154.

125. Port, E., Sun, F., Martin, D. and Waterman, M.S.(1995) Genomic mapping by end-characterized random clones: a mathematical analysis. Genomics, 26 84-100.

126. Lander, E., and Waterman, M.S.(1995) The secrets of life. Calculating the Secrets ofLife National Academy Press, E. Lander and Waterman, M.S., Eds. 1-24.

127. Waterman, M.S.(1995) Hearing distant echos. Calculating the Secrets of Life NationalAcademy Press, E. Lander and Waterman, M.S., Eds. 90-113.

128. Idury, R., andWaterman, M.S.(1995) A new algorithm for DNA sequence assembly. J.Comp. Biol., 2 291-306.

129. Waterman, M.S.(1995) Combinatorics in molecular biology. Handbook of Combina-torics, Elsevier Science, R. Graham, M. Grotschel, and L. Lovasz, Eds. 1983-2001.

39

130. Sun, F., Arnheim, N., and Waterman, M.S.(1995) Whole genome amplification ofsingle cells: mathematical analysis of PEP and tagged PCR. Nucleic Acids Research,23 3034-3040.

131. Sun, F., Galas, D., and Waterman, M.S.(1996) A mathematical analysis of in vitromolecular selection-amplification. J. Mol. Biol., 258 650-660.

132. Arratia, R., Martin, D., Reinert, G., and Waterman, M.S.(1996) Poisson processapproximation for sequence repeats, and sequencing by hybridization. J. Comp. Biol.,3 425-463.

133. Steel, M., Goldstein, L., and Waterman, M.S.(1996) A central limit theorem for parsi-mony length of trees. Appl. Probab., 28 1051-1071.

134. Vingron, M. and Waterman, M.S.(1996) Alignment networks and electrical networks.Discrete Math., 71 297-309.

135. Xiong, M. and Waterman, M.S.(1997) A phase transition for the minimum free energyof secondary structures of a random RNA. Adv. Appl. Math., 18 111-132.

136. Komatsoulis, G.A. and Waterman, M.S.(1997) A new computational method for de-tection of chimeric 16S rRNA artifacts generated by PCR amplification from mixedbacterial populations. Appl. and Environ. Microbiology, 63 2338-2346.

137. Sun, F. and Waterman, M.S.(1997) Single chromosome amplification and branchingprocesses Adv. Appl. Probab., 29 629-668.

138. Sun, F., Benson, G., Arnheim, A., and Waterman, M.S.(1997) Pooling strategies forestablishing genome maps using FISH. J. Comp. Biol., 4 467-486.

139. Lee, J.K., Dancik, V., and Waterman, M.S.(1997) Estimation for restriction sitesobserved by optical mapping using reversible-jump Markov chain monte carlo. J.Comp. Biol., 5 505-516.

140. Beschler, E.F., Buchsbaum, D.A., Schwartz, J.T., Stanley, R.P., Taylor, B.D., andWaterman, M.S.(2000) Gian-Carlo Rota (1932–1999) Notices of the AMS, February2000, 47 203-216.

141. Reinert, G., Scabath, S., and Waterman, M.S.(2000) Probabilistic and statistical prop-erties of words J. Comp. Biol., 7 1-48.

142. Waterman, M.S.(2000) Mathematical sciences and the new biology. A chapter in thebook Essays on the Future, In Honor of Nick Metropolis, Birkh’auser Boston, S. Heckerand G.-C. Rota, Eds. 265-276.

40

143. Pevzner, P., Tang, H., and Waterman, M.S.(2001) An Eulerian path approach to DNAfragment assembly Proc. Natl. Acad. Sci. USA, 98 9748-9753.

144. Tang M and Waterman, M.S.(2001) Local matching of random restriction maps Journalof Applied Probability, 38 335-356.

145. Zhang,K., Deng, M., Chen, T., Waterman, M.S., and Sun, F. (2002) A dynamic pro-gramming algorithm for haplotype block partitioning Proc. Natl. Acad. Sci. USA, 997335-7339.

146. Tang, M., Waterman, M.S., and Yooseph, S. (2002) Zinc finger gene clusters andtandem gene duplication Journal of Computational Biology, 9 429-446.

147. Lippert, R.A., Huang, H., and Waterman, M.S.(2002) Distributional regimes for thenumber of k-word matches between two random sequences. Proc. Natl. Acad. Sci.USA, 99 13980-13989.

148. Zhang K, Sun F, Waterman MS, Chen T. (2003) Haplotype block partition with limitedresources and applications to human chromosome 21 haplotype data. Am J HumGenet. 73 63-73.

149. Li, X. and Waterman, M.S.(2003) Estimating the repeat structure and length of DNAsequences using l-tuples. Genome Research, 13 1916-1922.

150. Zhang, Y. and Waterman, M.S.(2003) An Eulerian path approach to global multiplealignment for DNA sequences. Journal of Computational Biology, 10 803-820.

151. Zhang, K., Sun, F., Waterman, M.S., and Chen, T., (2003) Dynamic programmingalgorithms for partitioning sequence variation in human chromosomes HERMIS, 4 15-26.

152. Istrail, S., Sutton, G., Florea, L., Halpern, A., Mobarry, C., Lippert, R., Walenz,B., Shatkay, H., Dew, I., Miller, J., Bolanos, R., Edwards, N., Fasulo, D., Flanigan,M., Halldorsson, B., Hannenhalli, S., Nusskern, D., Shue, B., Zheng, X., Turner, R.,Yooseph, S., Delcher, A., Huson , D., Kravitz, S., Mouchard, L., Reinert, K., Reming-ton, K., Clark, A., Waterman, M.S., Adams, M., Myers, E., and Venter J.C. (2004)Whole Genome Shotgun Assembly and Comparison of Human Genome AssembliesProc. Natl. Acad. Sci. USA, 101 1916-1921.

153. Zhang, Y. and Waterman, M.S.(2004) DNA sequence assembly and multiple sequencealignment by an Eulerian path approach Cold spring Harbor Symposium of QualitativeBiology, LXVIII 205-212.

41

154. Li, L.M., Kim, J.H., and Waterman, M.S.(2004) Haplotype reconstruction from SNPalignment, Journal of Computational Biology, 11 505-516.

155. Zhang, K., Qin, Z., Chen, T., and Waterman, M.S., and Sun, F. (2004) Haplotypeblock partitioning and tag SNP selection using genotype data and their application toassociation studies, Genome Research, 14 908-916.

156. Zhang Y and Waterman MS. (2005) An Eulerian path approach to local multiplealignment for DNA sequences. Proc Natl Acad Sci U S A 1021285-1290.

157. Zhang, K., Qin, Z., Chen, T., Liu, J., Waterman, M.S., and Sun, F. (2005) HapBlock:Haplotype Block Partitioning and Tag SNP Selection Software Using a Set of DynamicProgramming Algorithms. Bioinformatics 21 131-134.

158. Valouev A, Li L, Liu YC, Schwartz DC, Yang Y, Zhang Y, and Waterman MS. (2006)Alignment of optical maps. J Comput Biol. 13 442-462.

159. Valouev A, Zhang Y, Schwartz DC, and Waterman MS. (2006) Refinement of opticalmap assemblies. Bioinformatics. 22 1217-1224.

160. Valouev A, Schwartz DC, Zhou S, and Waterman MS. (2006) An algorithm for assemblyof ordered restriction maps from single DNA molecules. Proc Natl Acad Sci U S A103:15770-15775

161. Pan F, Chiu CH, Pulapura S, Mehan MR, Nunez-Iglesias J, Zhang K, Kamath K,Waterman MS, Finch CE, and Zhou XJ. (2007) Gene Aging Nexus: a web databaseand data mining platform for microarray data on aging. Nucleic Acids Res. 35

162. Reinert G., and Waterman, M.S.(2007) On the length of the longest exact posi-tion match in a random sequence. IEEE/ACM Trans Comput Biol Bioinform Jan-Mar;4(1):153-6.

163. Kim JH, Waterman, M.S., and Li LM. (2007) Accuracy assessment of diploid consensussequences. IEEE/ACM Trans Comput Biol Bioinform Jan-Mar;4(1):88-97.

164. Li, H., Valouv, A., Schwartz, D., Waterman, M.S.and Lei, L.M. (2007) A quantilemethod for sizing optical maps. J Comput Biol. 14 255-266.

165. Huang Yu, Li Haifeng, Hu Haiyan, Yan Xifeng, Waterman, M.S., Huang Hiayan,andZhou Xianghong, (2007) Systematic discovery of functional modules and context-specific functional annotation of the human genome. Bioinformatics 23(13): i222-229.

166. Kim JH, Waterman, M.S., and Li LM. (2007) Diploid reconstruction of Ciona intesti-nalis and comparison with Ciona savignyi. Genome research, 17: 1101-1110

42

167. Mehan M.R., Nunez-Iglesias J., Kalakrishnan M., Waterman, M.S., and Zhou X.,(2008) An integrative network approach to map the transcriptome to the phenome.Lecture Notes in Computer Science Vol. 4955 232-245.

168. Zhang M.Q., Waterman, M.S., and X. Zhang, (2009) Introduction: The Seventh AsiaPacific Bioinformatics Conference (APBC2009), BMC Bioinformatics, 10(Suppl 1):S1.

169. Kim JH, Kim W-C, Waterman, M.S., Park, S, and Li LM, (2009) HAOLOWSER: awhole-genome haplotype browser for personal genome and metagenome. Bioinformat-ics, 25 (18) 2430-2431.

170. Schnable, P.S. and 157 authors (including Waterman, M.S.), (2009) The B73 maizegenome: complexity, diversity and dynamics, Science, 326 (5956), 1112-1115.

171. Zhou, S., Fusheng, W., Nguyen, J., Bechner, M., Potamousis, K., Goldstein S., Pape,L., Mehan, M.R., Churas, C., Pasternak, S., Forrest, D., Wise, R., Ware, D., Wing,R.A., Waterman, M.S., Livny, M., and Schwartz, D.C. (2009) A single molecule scaffoldfor the maize genome, PLoS Genetics 5: e711.

172. Reinert, G., Chew, D., Sun, F., and Waterman, M.S., (2009) Alignment-free sequencecomparison (I): statistics and power, J Comput Biol. 16 1615-1634.

173. Schwartz, D.C. and Waterman, M.S., (2010) New generations: sequencing machinesand their computational challenges, J. Compt. Sci. and Tech. 25 3-9.

174. Zhai, Z., Ku, S-Y, Luan, Y., Reinert, G., Waterman, M.S.and Sun, F. (2010) Thepower of detecting enriched patterns: an HMM approach, J Comput Biol. 17 581-592.

175. Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, Sarkar D,Valouev A, Churs C, Kidd JM, Kohn S, Runheim R, Lamers C, Forrest D, Newton MA,Eichler EE, Kent-First M, Surti U, Livny M, and Schwartz DC (2010) High-resolutionhuman genome structure by single-molecule analysis, PNAS, 2010

176. Reinert, G., Chew, D., Sun, F., and Waterman, M.S., (2010) Alignment-free sequencecomparison (II): theoretical power of comparison statistics, J Comput Biol. 17 No.11: 1349-1372.

177. Li, W., Liu, C-C., Zhang, T., Li, H., Waterman, M.S., and Zhou, X.J., (2010) Inte-grative analysis of many weighted co-expression networks using tensor computation,PLoS Comput Biol, 7(6): e1001106.

43

178. Mehan, MR, Nunez-Iglesias, J, Dai, C, Waterman, MS, and Zhou, XJ (2010). Anintegrative modular approach to systematically predict gene-phenotype associations.BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S62.

179. Li, X., Wan, L., Li, J., Reinert, G., Waterman, M.S., and Sun, F., (2011) New powerfulstatistics for alignment-free sequence comparison under a pattern transfer model, J.Theor. Biol., 284 (1), 106-116.

180. Meng, L., Zhang, X., Sun, F., and Waterman, M.S., (2011) Sequence alignment ashypothesis testing, J. Comput. Biol., 18(5), 677-691.

181. Zhai, Z., Reinert, G., Song, K., Waterman, M.S., Luan, Y., and Sun, F. (2012) Nor-mal and compound Poisson approximations for pattern occurrences in NGS reads J.Comput. Biol., 19(6), 839-854.

182. Andersen, J.E., Penner, R.C., Reidys, C.M. and Waterman, M.S., (2013) Topologicalclassification and enumeration of RNA structures by genus, 67(5), J. Math. Biol.,1261-1278.

183. Behnamghader, E., Waterman, M.S., and Smith A.D., (2013) A geometric interpreta-tion for local alignment-free sequence comparison J. Comput. Biol., 20(7), 471-485.

184. Song, K. , Ren, J., Reinert, G., Deng, M., Waterman, M.S., and Sun, F. (2014) Newdevelopments of alignment-free sequence comparison: measures, statistics and next-generation sequencing, Brief. Bioinform. 15 (3), 343-353.

185. Liu CC*, Tseng YT*, Li W, Wu CY, Mayzus I, Rzhetsky A, Sun F, Waterman M,Chen JJ, Chaudhary PM, Loscalzo J, Crandall E, Zhou XJ. (2014). (*Joint first-author) DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. Nucleic Acid Research 2014 June; DOI: 10.1093/nar/gku412.

186. Wang, R., Waterman, M.S., and Huang, H. (2014) Gene coexpression measures in largeheterogeneous samples using count statistics. PNAS 46, 16371-16376.

187. Waterman, M.S.(2016) Questions I Was Asked, International Chinese Statistical As-sociation Bulletin 28(1), 48-51.

188. Bai,X., Tang, K., Ren, J., Waterman, M.S.and Sun, F. (2017) Optimal choice of wordlength when comparing two Markov sequences using a chi-square-statistic. Acceptedby ICIMB (2016). BMC Genomics 18:732

189. Lu, YY, Tang, K., Ren, J., Fuhrman, J., Waterman, M.S., Sun, F. (2017) CAFE:aCcelerated Alignment-FrEe sequence analysis NAR 45, W1, 554-559.

44

190. Wang, R., Waterman, M.S., and Huang, H. (2018) Generalized correlation measureusing count statistics for gene expression data with ordered samples, Bioinformatics34, Issue 4, 617624, https://doi.org/10.1093/bioinformatics/btx641

191. Zielezinski, A., Girgis, H., Bernard, G., Leimeister, C-A., Tang,K., Dencker, T., Lau,A., Rhling, S., Choi, J., Waterman, M.S., Comin, M., Kim, S-H., Vinga, S., Almeida,J., Chan, C., James, B., Sun, F., Morgenstern, B., and Karlowski. W., (2019) Bench-marking of alignment-free sequence comparison methods BMC Gemone Biology 20article 144.

VII. BOOKS AND EDITED VOLUMES

1. Mathematical Methods for DNA Sequences. (1989), M.S. Waterman, Editor. CRCPress. 283 pages.

2. Mathematical Analysis of Molecular Sequences, M.S. Waterman, Guest Editor. SpecialIssue: Bulletin of Mathematical Biology 51, Issue #1, (1989).

3. Calculating the Secrets of Life (1995) E. Lander and Waterman, M.S., Editors. Na-tional Academy Press, Washington DC. 285 pages.

4. Introduction to Computational Biology: Sequences, Maps and Genomes. (1995), M.S.Waterman. Chapman Hall, 431 pages.

5. Genetic Mapping and DNA Sequencing (1996), T. Speed and M.S. Waterman, Editors.81 IMA Volumes in Mathematics and its Applications, Springer-Verlag. 215 pages.

6. Proceedings First Annual Conference on Computational Molecular Biology (RECOMB1997) M.S. Waterman, S. Istrail and P. Pevzner, Editors. ACM Press, Order Number508971, (January 19 - 22, 1997)

7. Proceedings Second Annual Conference on Computational Molecular Biology (RE-COMB 1998)S. Istrail, P. Pevzner and M.S. Waterman, Editors. ACM Press, OrderNumber 508981, (March 22-25, 1998)

8. Mathematical Support for Molecular Biology. (1999), M. Farach-Colton, F.S. Roberts,M. Vingron, and M.S. Waterman, Editors. American Mathematical Society, 288 pages.

9. Proceedings Third Annual Conference on Computational Molecular Biology (RECOMB1999)S. Istrail, P. Pevzner and M.S. Waterman, Editors. ACM Press, Order Number508991, (April 11-14, 1999)

45

10. Russian translation of Mathematical Methods for DNA Sequences (1989): Matem-aticheskie metody dlja analiza posledovatel’nostej DNK pod red. M. Uotermena. MIRPublishers (1999).

11. Proceedings Fourth Annual Conference on Computational Molecular Biology (RE-COMB 2000)R. Shamir, S. Miyano, S. Istrail, P. Pevzner and M.S. Waterman, Editors.ACM Press, Order Number 508001, (April 8-11, 2000)

12. Proceedings Fifth Annual Conference on Computational Molecular Biology (RECOMB2001)T. Lengauer, D. Sankoff, S. Istrail, P. Pevzner and M.S. Waterman, Editors. ACMPress, Order Number 508011, (April 22-25, 2001)

13. Proceedings Sixth Annual Conference on Computational Molecular Biology (RECOMB2002)T. Lengauer, E. Meyers , S. Istrail, P. Pevzner and M.S. Waterman, Editors.ACM Press, Order Number , (April 18-21, 2002)

14. Proceedings Seventh Annual Conference on Computational Molecular Biology (RE-COMB 2003)T. Lengauer, W. Miller, S. Istrail, P. Pevzner and M.S. Waterman, Edi-tors. ACM Press, Order Number 508031, (April 10-13, 2003)

15. Computational Methods for SNPs and Haplotype Inference, Istrail, S., Waterman,M.S., and Clark A., Editors, LNBI 2983, Springer (2004).

16. Proceedings Eighth Annual Conference on Computational Molecular Biology (RE-COMB 2004) D. Gusfield, P. Bourne, S. Istrail, P. Pevzner and M.S. Waterman,Editors. ACM Press, Order Number 508041, (March 27-31, 2004)

17. Proceedings Ninth Annual Conference on Computational Molecular Biology (RECOMB2005) S. Miyano, J. Meserov, S. Kasif, S. Istrail, P. Pevzner and M.S. Waterman, Ed-itors. Lecture Notes in Bioinformatics (LNBI 3500), Springer (2005).

Mathematics and 21st Century Biology, member of Editorial Committee, NationalResearch Council, National Academies Press (2005).

18. Computational Genome Analysis, An Introduction R. Deonier, S, Tavare, and M.S.Waterman, Springer, 2005.

19. Proceedings Tenth Annual Conference on Computational Molecular Biology (RECOMB2006) A. Apostolico, C. Guerra, S. Istrail, and M. Waterman, Editors. Lecture Notesin Bioinformatics (LNBI 3909), Springer (2006).

20. Computational Methods for SNPs and Haplotype Inference: DIMACS/RECOMB Satel-lite Workshop, Piscataway, NJ, USA, November 21-22, 2002. Revised Papers S. Istrail,

46

Waterman, M.S., and A. Clark, Editors, Lecture Notes in Computer Science, (LNCS2983), Springer (2004).

VIII. PATENTS

1. System and Method for Fragmentation Mapping. U.S. Patent Application SN 889,981.U.S. Patent No. 4,771,384 (September 1988). D.L. Daniels, J.L. Schroeder, F.R.Blattner and M.S. Waterman.

2. Sequence Information Signal Processor for Local and Global String Comparisons. U.S.Patent Application 08/154,633. U.S. Patent No. 5,632,041 (May 20, 1997). E.T.Chow, J.C. Peterson, T.J. Hunkapillar, M.S. Waterman.

3. Oligoprobe Designation: A Computerized Method for Designing Optimal DNA Probes.U.S. Patent No. US5556749A (Sept 17,1996). M. Mitsuhashi, A. Cooper, M. Water-man, P. Pevzner.

47