Nathan Goodman

Curriculum Vitae

March 2004

Education

Sep 77 - Jun 80.                          Harvard University                        PhD                        Applied Mathematics                        1980

Sep 74 - Jun 76.                          Mass. Institute of Technology                        MS                        Computer Science                        1976

Sep 68 - Feb 72.                          Mass. Institute of Technology                        BS                        Mathematics                        1972

PhD Thesis  Power of Semijoins in Distributed Database Query Processing, supervised by P.A. Bernstein.  Developed a technique for processing queries in relational distributed database sys­tems, called "semijoin reduction" and the theory of "tree database schemas" as a foundation for the technique.  This theory was subsequently elaborated by my student, Oded Shmueli, in his PhD the­sis, and by other associates.  The same theory, under the name "acyclic database schemes" was de­vel­oped in­de­pendently by Prof. J.D. Ullman and his associates.

MS Thesis  Coordination of Parallel Processes in the Actor Model of Computation, supervised by C. Hewitt.  Used Hewitt's "actor model" of computation to prove the correctness of parallel algo­rithms.  Hewitt's actor model was a precursor to today's "object oriented" approaches.  This was the first use of the theory to prove the correctness of a non-trivial parallel pro­gram.

Employment

Apr 02 – present. Institute for Systems Biology.  Senior Research Scientist. Research and development of disease focused community databases. Research on high performance computation for bioinformatics applications.

Jun 03 – present. Huntington’s Disease Drug Works.  Founder and Vice President. Non-profit organization conducting individualized therapeutic trials for people with Huntington’s Disease.

Apr 02 – Apr 03. University of Alaska at Fairbanks, Affiliate Professor of Bioinformatics. Assisted in establishment of bioinformatics research program which culminated in recruitment of Dr. Thomas Marr to head program.

Aug 01 – present. Independent bioinformatics consultant.  Consulting for software vendors, pharmaceutical companies, biotechs, and research organizations. 

Oct 00 – Jul 01. 3rd Millennium, Inc.  Senior Vice President.  Bioinformatics consulting firm.  Assisted president in management of consulting projects.  Principal investigator for company’s BioPathways research program.   Business development for microarray service line.

Mar 00 – Oct 00. Independent bioinformatics consultant.  Consulting for software vendors, pharmaceutical companies, biotechs, and research organizations. 

Feb 99-Mar 00.  Compaq Computer Corporation.  Director, Bioinformatics Center.   Managed a technical marketing group.  Development of solutions and sample applications that showcase Compaq and partner products.  Competitive benchmarking. Identification of important new partners, especially among small companies and academic laboratories.  Direct support of sales teams. Customer presentations and customer care. 

Jul 96-Feb 99.  The Jackson Laboratory.  Senior Staff Scientist.   Research on computing techniques and systems for molecular biology.  Gene discovery from genomic data.  Database integration.  Software sharing using component-based systems.  Flexible laboratory information management systems (LIMS) and databases. 

Jan 91 - Jun 96.  Whitehead Institute for Biomedical Research.  Senior Research Scientist, and Associate Director of Center for Genome Research. R&D on laboratory information management systems (LIMS) and databases for high throughput biological research projects. Founding member of Center.  Directed Informatics Core.

May 94- Dec 95.  Marble Associates, Inc.  President, and Chief Technology Officer.  Consulting firm spe­cializing in development of object-oriented business information systems. 

Feb 90 - Apr 94.  Nathan Goodman Database Consultants.  President and Founder.  Consulting in object oriented databases and distributed databases.

Mar 88 - Feb 90.  Codd and Date, Inc.  Senior Vice President.  Con­sulting and education services in relational database management.  Served on company's executive and management committees.

Mar 86 - Feb 88.  Kendall Square Research Corporation.  Founder, Vice President, and Chief Computer Scientist.  Startup company developing multi­processor supercomputers.  Responsible for software ar­chitecture and system per­formance analysis. Assisted with hardware architecture.  Man­aged Software Engineering Department from inception until late-1987.

Jun 85 - Mar 86.  Encore Computer Corporation.  Senior Consulting Engineer.  Startup company devel­oping general purpose, multiprocessor computers.  Managed technical support group responsible for   sys­tem performance analysis, customer application support, and quality assurance.

Jun 84 - May 85.  Sequoia Systems, Inc.  Product Development Manager, Database Products.  Startup com­pany developing multiprocessor computers for database and transaction processing.  Managed soft­ware engineering group responsible for database and transaction processing soft­ware products.

Sep 83 - May 84.  Department of Computer Science, Boston University.  Associate Pro­fessor of Computer Science.  (Granted tenure in May 1984.)  Taught introductory programming and ad­vanced database courses.  Research on relational query processing, transaction processing, ar­chitecture of relational database systems, and relational database theory.

Jul 80 - Aug 83.  Division of Applied Sciences, Harvard University.  Assistant Profes­sor of Computer Science.  Taught introductory computer science and graduate courses on database sys­tems and dis­tributed computing.  Research on relational query optimization, transaction processing, architecture of relational database systems, and relational database theory.

Jul 80 - Jun 83.  Computer Corporation of America.  Computer scientist (part time con­sultant).  Designed database recovery and failure handling subsystem of distributed object-oriented database system and system archi­tec­ture of distributed heterogeneous database system.

Oct 74 - Jun 80.  Computer Corporation of America.  Computer Scientist (77-80), Assis­tant Manager of Research Division (76-77), Systems Programmer (74-76).  During 1977-80, research and development related to distributed relational database system.  During 1976-77, business development. During 1974-76, de­veloped two large systems: database front-end for real-time seismic data and electronic mail product.  Note:  at­tended graduate school at MIT and Harvard during this period.

Jul 73 - Sep 74, Feb 72 - Aug 72, Sep 70 - Jan 72.   LOGO Project, Artificial Intelligence Laboratory, Massa­chusetts Institute of Technology.  Research Associate, Student Research Assistant , Student Worker.  LOGO is programming language and system for children, fa­mous for "turtle graphics", in­vented by Prof. Seymour Papert at MIT.  Worked on language design and software development.  Used LOGO to teach children.

Sep 72 - Jun 73.  School of Artificial Intelligence, University of Edinburgh, Scot­land.  Research Associ­ate.  Established pilot LOGO project.

PhD Students

Eric Harley. Graph Algorithms for Physical Mapping. Co-advisor with Dr. Anthony J. Bonner.  University of Toronto.  December 02 expected.

Richard Michael Bruskiewich. Fine Scale Mapping and Functional Analysis of the Werner Syndrome Locus (WRN). Co-advisor with Dr. Stephen Wood.  University of British Columbia. December 98. 

Johann Christoph Freytag.  Translating Relational Queries into Iterative Programs. Harvard University. June 85. 

Dennis Shasha.  Concurrency Control for Search Structures. Harvard University. June 84. 

Y.C. Tay.  A Mean Value Performance Model for Locking in Databases. Harvard University. June 84. 

Oded Shmueli.  The Fundamental Role of Tree Schemas in Relational Query Processing. Harvard University.  June 81. 


Professional Activities (Current)

It Guy columnist for Genome Technology magazine

Steering Committee, Washington Catalyst for Information-Based Medicine

Ad hoc Reviewer, Genome Study Section, National Institutes of Health

Professional Activities (Past)

Scientific Advisory Board, AnVil Informatics, Inc.

Technology Panel, Arctic Region Supercomputing Center (ARSC)

Genomics Review Committee, Canadian Institutes of Health Research

Working Group of the Human Genetic Cell Repository, National Institute of General Medical Sciences

Informatics Advisory Board, Pharmaceutical Research and Manufacturers of America (PhRMA) Foundation

External Review Board for Functional Genomics, Novartis, Inc.

Ad hoc Reviewer, Genome Canada

Advisory Board, Bioinformatics Program, University of Massachusetts at Lowell

Editorial Board, Cambridge Healthtech Institute

Co-Chair, Bioinformatics Committee, Massachusetts Biotech Council

Editor-in-Chief, Gene-COMBIS

Editorial Board, Information Systems

Editorial Board, The International Journal on Very Large Data Bases

Genomics Review Committee, Medical Research Committee (Canada)

Scientific Advisory Committee, European Bioinformatics Institute

Board of Scientific Advisors, Washington University Genome Sequencing Center

Board of Scientific Advisors, FlyBase: the Drosophila Community Database project

Advisor, Canadian Genome Analysis and Technology (CGAT) Program

Member, Joint Informatics Task Force, a working group of the NIH Program Advisory Committee on the Human Genome and of the Health and Environmental Research Advisory Committee of the Department of Energy

External Advisory Board, University of Southern California Human Brain Project

Scientific Advisory Board, 3rd Millennium, Inc.

Scientific Advisory Board, Molecular Applications Group

Malaria Advisory Board, Eikos, Inc.

Board of Directors, Marble Associates, Inc.

Program Committee Member

1999 International Conference on Very Large Database (VLDB)

1998 Conference on Intelligent Systems in Molecular Biology (ISMB)

1997 Conference on Intelligent Systems in Molecular Biology (ISMB)

1985 International Conference on Very Large Database (VLDB)

1984 International Conference on Very Large Database (VLDB)

1984 ACM Conference on Management of Data (SIGMOD)

1984 ACM Symposium on Principles of Database Systems (PODS)

1983 ACM Symposium on Principles of Distributed Computing (PODC)

1983 ACM Conference on Management of Data (SIGMOD)

1982 ACM Conference on Management of Data (SIGMOD)

Database Conference Tutorial Chairman

1984 International Conference on Very Large Database (VLDB)

Peer-reviewed Publications (articles, reviews, book chapters, and books)

Plans for HDBase - A Research Community Website for Huntington's Disease. Clinical Neuroscience Research: Special issue on Huntington's Disease, ed. C.L. Wellington and M.R. Hayden. Vol. 3, No. 3 (October 2003). N. Goodman, K. McCormick, D. Goldowitz, E. Hockly, C. Johnson, B. Kristal, M. MacDonald, R. Truant, M. van Beuzekom.

Biological Data Becomes Computer Literate: New Advances in Bioinformatics. Current Opinion in Biotechnology 13:68-71 (February 2002).  N. Goodman.

Uniform Integration of Genome Mapping Data Using Intersection Graphs.  Bioinformatics Vol. 17, No. 6 (June 2001).  E. Harley, A.J. Bonner,  N. Goodman.

LabBase: Data And Workflow Management for Large Scale Biological Research,  in Bioinformatics Databases and Systems, S.I. Letovsky, ed., Kluwer Academic Press, 1999.  N. Goodman, S. Rozen, L.D. Stein.

Revealing Hidden Interval Graph Structure in STS-Content Data, Bioinformatics Vol. 15, No. 4 (April 1999). E. Harley, A.J. Bonner,  N. Goodman.

The LabBase System for Data Management in Large Scale Biological Research Laboratories, Bioinformatics Vol. 14, No. 7 (August 1998).  N. Goodman, S. Rozen, A.G. Smith, L.D. Stein.

A Model System for Studying the Integration of Molecular Biology Databases. Bioinformatics Vol. 14, No. 7 (August 1998). J.B. Macauley, H. Wang, N. Goodman.

The LabFlow System for Workflow Management in Large Scale Biological Research Laboratories, Proceedings of the Sixth International Conference on Computational Biology: Intelligent Systems for Molecular Biology (ISMB '98). AAAI Press (June 1998).  N. Goodman, S. Rozen, L.D. Stein.

A Map of 75 Human Ribosomal Protein Genes. Genome Research (May 1998).  N. Kenmochi, T.S. Kawaguchi, S. Rozen, E. Davis, N. Goodman, T. J. Hudson, T. Tanaka, D.C. Page.

Informatics - Genome and Genetics Databases.  Current Opinion in Genetics and Development, Vol. 7, No. 6, pp 750-756 (December 1997).  M. Ashburner, N. Goodman.

Current Status of the Plasmodium falciparum Genome Project.  Molecular and Biochemical Parasitology 79:1-12 (1996).  J.B. Dame, D.E. Arnot, P.F. Bourke, D. Chakrabarti, Z. Christodoulou, R.L. Coppel, A.F. Cowman, A.G. Craig, K. Fischer, J. Foster, N. Goodman, K. Hinterberg, A.A. Holder, D.C. Holt, D.J. Kemp, M. Lanzer, A. Lim, C.I. Newbold, J.V. Ravetch, G.R. Reddy, J. Rubio, S.M. Schuster, X-z Su, J.K. Thompson, F. Vital, T.E. Wellems, E.B. Werner.

Good Maps are Straight,  Proceedings of the Fourth International Conference on Computational Biology: Intelligent Systems for Molecular Biology (ISMB '96) , AAAI Press (June 1996).  E. Harley, A.J. Bonner,  N. Goodman.

A Comprehensive Genetic Map of the Mouse Genome, Nature, 380:149-152 (March 1996).  W.F. Dietrich, J. Miller, R. Steen, M.A. Merchant, D. Damron-Boles, Z. Husain, R. Dredge, M.J. Daly, K.A. Ingalls, T. J. O'Connor, C.A. Evans, M.M. DeAngelis, D.M. Levinson, L. Kruglyak, N. Goodman, N.G. Copeland, N.A. Jenkins, T.L.  Hawkins, L. Stein, D.C. Page, E. S. Lander

An STS-Based Map of the Human Genome, Science, 270:1945-1955 (December 1995).  T.J. Hudson, L.D. Stein, S.S. Gerety, J. Ma, A.B. Castle, J.Silva, D.K. Slonim, R. Baptista, L. Kruglyak, S.-H. Xu, X. Hu, A.M.E. Colbert, C. Rosenberg,  M.P.Reeve-Daly, S. Rozen, L. Hui, X. Wu, C. Vestergaard, K.M. Wilson, J.S. Bae, S. Maitra, S. Ganiatsas, C.A. Evans, M.M. DeAngelis, K.A. Ingalls, R.W. Nahf, L.T. Horton, Jr., M.O. Anderson, A.J. Collymore, W.Ye, V. Kouyoumjian, I.S. Zemsteva, J.Tam, R. Devine, D.F. Courtney, M.T. Renaud, H. Nguyen, T.J. O'Connor, C.Fizames, S. Faure, G. Gyapay, C. Dib, J. Morissette, J.B. Orlin, B.W. Birren, N. Goodman, J. Weissenbach, T.L. Hawkins, S. Foote, D.C. Page, E.S. Lander.

Managing Laboratory Workflow with LabBase,  Proceedings of the First World Congress on Computational Medicine, Public Health and Biotechnology, World Scientific Publishing Company (1995).  L.D. Stein, S. Rozen,  N. Goodman.

LabBase:  A Database to Manage Laboratory Data in a Large-Scale Genome-Mapping Project,  IEEE Transactions on Engineering in Medicine and Biology (September 1995).  N. Goodman, S. Rozen,  L.D. Stein.

An Object Oriented DBMS War Story:  Developing a Genome Mapping Database in C++, in Modern Database Management:  Object-Oriented and Multidatabase Technologies, W. Kim, ed., 1994, ACM Press: New York, NY.  N. Goodman.

Splicing UNIX into a Genome Mapping Laboratory,  Proceeding of the Summer USENIX Conference (June 1994).  L.D. Stein, A. Marquis, E. Dredge, M.P. Reeve, M.J. Daly, S. Rozen,  N. Goodman.

A Genetic Map of the Mouse with 4,006 Simple Sequence Length Polymorphisms, Nature Genetics, 7:220-245 (June 1994).  W. F. Dietrich, J. C. Miller, R.G. Steen, M. Merchant, D. Damron, R. Nahf, A. Gross, D.C. Joyce, M. Wessel, R.D. Dredge, A. Marquis, L.D. Stein, N. Goodman, D.C. Page, E.S. Lander.

Constructing a Domain-Specific DBMS Using a Persistent Object System, in Persistent Object Systems, M.P. Atkinson, V. Benzake, and D. Maier, eds., 1995, Springer-Verlag and British Computer Society Workshops in Computing Series.  Also in Proceedings Sixth International Workshop on Persistent Object Systems (September 1994).  S. Rozen, L.D. Stein, N. Goodman.

Building a Laboratory Information System Around a C++-Based Object-Oriented DBMS   Proceedings of the 1994 Conference on Very Large Databases (September 1994).  N. Goodman, S. Rozen, L.D. Stein

Requirements for a Deductive Query Language in a Genome Mapping Database,  in Applications of Logic Databases, R. Ramakrishnan, ed., 1995, Kluwer Press.  N. Goodman, S. Rozen,  L.D. Stein.  Also in Proceedings of the Workshop on Programming with Logic Databases (November 1993).

Genome Maps IV, Science, 262:67-82 (October 1993).  N.G. Copeland, D.J. Gilbert, N.A. Jenkins, J.H. Nadeau, J.T. Eppig, L.J. Maltais, J.C. Miller, W.F. Dietrich, R.G. Steen, S.E. Lincoln, A. Weaver, D.C. Joyce, M. Merchant, M. Wessel, H. Katz, L.D. Stein, M.P. Reeve, M.J. Daly, R.D. Dredge, A. Marquis, N. Goodman,  E.S. Lander.

SSLP Genetic Map of the Mouse (Mus musculus) 2N=40, in Genetic Maps, S. J. O'Brien, ed., 1993.  W.F. Dietrich, J. C.Miller, H. Katz, D. Joyce, R. Steen, S.E. Lincoln, M.J. Daly, M.P. Reeve, A. Weaver, P. Anagnostopoulos, N. Goodman, N.C. Dracopoli, E.S. Lander.

Genome Informatics, The New Biologist, Vol. 3, No. 11 (November 91).  N. Goodman.

A Model for Concurrency in Nested Transaction Systems, Journal of the ACM, Vol. 36, No. 2 (April 89).  C. Beeri, P.A. Bernstein, N. Goodman.

On the Translation of Relational Queries into Iterative Programs,  ACM Transactions on Database Systems, Vol. 14, No. 1 (March 89).  J.C. Freytag, N. Goodman.

Concurrent Search Structure Algorithms, ACM Transactions on Database Systems, Vol. 13, No. 1 (March 88).  N. Goodman, D. Shasha.

Concurrency Control and Recovery in Database Systems, (Book) Addison-Wesley, 1987.  P.A. Bernstein, V. Hadzollacos

A Proof Technique for Concurrency Control and Recovery Algorithms for Repli­cated Databases, Distributed Computing 1 (1986).  P.A. Bernstein, N. Goodman.

Serializability Theory for Replicated Distributed Databases, Journal of Computer and Systems Science, Vol. 31, No. 3 (September 86).  P.A. Bernstein, N. Goodman.

Translating Aggregate Queries into Iterative Programs, Proceedings 12th International Conference on Very Large Databases (August 86).  J.C. Freytag, N. Goodman.

Rule Based Translation of Relational Queries into Iterative Programs, Proceedings 1986 ACM SIGMOD Conference on Management of Data (May 86).  J.C. Freytag, N. Goodman.

Distributed Database Concurrency Control:  Introduction, in Encyclopedia of Systems and Control, Pergamon Press Ltd., 1985.  N. Goodman

Locking Performance in Centralized Databases, ACM Transactions on Database Systems, Vol. 10, No. 4 (December 85).  Y.C. Tay, R. Suri, N. Goodman.

Multirelations (Relations with Duplicates) -- Semantics and Languages, Proceed­ings 11th International Conference on Very Large Databases (August 85).  N. Goodman, A. Klausner.

A Mean Value Performance Model for Locking in Databases:  The No Waiting Case, Journal of the ACM, Vol. 32, No. 3. (July 85).  Y.C. Tay , R. Suri, N. Goodman.

Semantically Based Concurrency Control for Search Structures, Proceedings 4th ACM Symposium on Principles of Database Systems (April 85).  N. Goodman, D. Shasha.

An Algorithm for Concurrency Control and Recovery in Replicated Distributed Databases, ACM Transactions on Database Systems, Vol. 9., No. 4 (December 84).  P.A. Bernstein, N. Goodman.

GYO Reductions, Canonical Connections, Tree and Cyclic Schemas and Tree Projec­tions, Journal of Computer and Systems Science, Vol. 29., No. 4 (December 84).  N. Goodman, O. Shmueli, Y.C. Tay.  (Preliminary version also in Proceedings 2nd ACM Symposium on Prin­ciples of Database Systems (Mar 83)).

Site Initialization, Recovery, and Back-up in a Distributed Database System, IEEE Transactions on Software Engineering, Vol. SE-10, No. 6 (November 84).  R. Attar, P.A. Bernstein, N. Goodman.

Choice and Performance in Locking for Databases, Proceedings 10th International Con­ference on Very Large Databases (August 84).  R. Suri, Y.C. Tay, N. Goodman.

A Characterization of Multivalued Dependencies Equivalent to a Join Dependency, Information Processing Letters, Vol. 8., No. 5 (June 84).  N. Goodman, O. Shmueli.

A Mean Value Performance Model for Locking in Databases:  The Waiting Case, Proceedings 3rd ACM Symposium on Principles of Database Systems (April 84).  R. Suri, Y.C. Tay, N. Goodman.

The Tree Projection Theorem and Relational Query Processing, Journal of Computer and Systems Science, Vol. 28., No. 1 (February 84).  N. Goodman, O. Shmueli.

NP-Complete Problems Simplified on Tree Schemas, Acta Informatica, Vol 20, pp. 171-178 (1983).  N. Goodman, O. Shmueli.

Multiversion Concurrency Control -- Theory and Algorithms, ACM Transactions on Database Systems, Vol 8., No. 4 (December 83).  P.A. Bernstein, N. Goodman.

Syntactic Characterization of Tree Database Schemas, Journal of the ACM, Vol. 30, No. 4 (October 83).  N. Goodman, O. Shmueli.

Recovery Algorithms for Database Systems, Proceedings 9th IFIP Congress (September 83).  P.A. Bernstein, N. Goodman, V. Hadzollacos.

A Concurrency Control Theory for Nested Transactions, Proceedings 2nd ACM Sympo­sium on Principles of Distributed Computing, (August 83).  C. Beeri, P.A. Bernstein, N. Goodman, M.Y. Lai.

The Failure and Recovery Problem for Replicated Databases, Proceedings 2nd ACM Symposium on Principles of Distributed Computing (August 83).  P.A. Bernstein, N. Goodman.

Overview of an Ada Compatible Distributed Database Manager, Proceedings 1983 ACM SIGMOD Conference on Management of Data (June 83).  A. Chan, U Dayal, S. Fox , N. Goodman, D Ries,  D. Skeen.

Analyzing Concurrency Control Algorithms When User and System Level Opera­tions Differ, IEEE Transactions on Software Engineering, Vol. SE-9, No. 3 (May 83).  P.A. Bernstein, N. Goodman, M.Y. Lai.

A Reliability Algorithm for a Distributed Database System, Proceedings 2nd ACM Symposium on Principles of Database Systems (March 83).  A. Chan, U. Dayal, S. Fox, N. Goodman, D. Ries  D. Skeen.

A Simple Analytic Model for Performance of Exclusive Locking in Database Sys­tems, Proceedings 2nd ACM Symposium on Principles of Database Systems (March 83).  R. Suri, Y.C. Tay, N. Goodman.

Tree Queries:  A Simple Class of Relational Queries, ACM Transactions on Database Sys­tems, Vol. 7 No. 4 (December 82).  N. Goodman, O. Shmueli.

A Sophisticate's Introduction to Database Concurrency Control, Proceedings 8th In­ternational Conference on Very Large Databases (September 82).  P.A. Bernstein, N. Goodman.

Concurrency Control for Multiversion Database Systems, Proceedings 1st ACM Sympo­sium on Principles of Distributed Computing (August 82).  P.A. Bernstein, N. Goodman.

Query Optimization for CODASYL Databases, Proceedings 1982 ACM SIGMOD Conference on Management of Data (June 82).  U. Dayal, N. Goodman.

An Extended Relational Algebra with Control Over Duplicate Elimination, Proceed­ings 1st ACM Symposium on Principles of Database Systems (March 82).  U. Dayal, N. Goodman, R.H. Katz.

The Tree Property is Fundamental for Query Processing, Proceedings 1st ACM Sympo­sium on Principles of Database Systems (March 82).  N. Goodman, O. Shmueli.

Transforming Cyclic Queries into Trees, Proceedings 1st ACM Symposium on Principles of Database Systems (March 82).  N. Goodman, O. Shmueli.

Limitations of the Chase, Information Processing Letters,. Vol. 13, Nos. 4, 5 (end 81).  N. Goodman, O. Shmueli.

Power of Inequality Semijoins, Information Systems, Vol. 6, No. 4 (December 81).  P.A. Bernstein, N. Goodman.

Query Processing in a System for Distributed Databases (SDD-1), ACM Transactions on Database Systems, Vol. 6., No 4, (December 81).  P.A. Bernstein, N. Goodman, C.L. Reeve, J.B. Rothnie, E. Wong.

Power of Natural Semijoins, SIAM Journal of Computing, Vol. 10, No. 4 (November 81).  P.A. Bernstein, N. Goodman.

Laying Phantoms to Rest, Proceedings COMPSAC '81 (November 81).  P.A. Bernstein, N. Goodman, M.Y. Lai.

View Processing in MULTIBASE, Proceedings 2nd International Conference on Entity-Rela­tionship Approach to Information Modeling and Analysis (October 81).  N. Goodman, R.H. Katz.

Concurrency Control in Distributed Database Systems, ACM Computing Surveys, Vol. 13, No. 2 (June 81).  P.A. Bernstein, N. Goodman.

MULTIBASE:  A System for Integrating Heterogeneous Databases, Proceedings 1981 National Computer Conference (May 81).  J.M. Smith et al.

Two Part Proof Schema for Database Concurrency Control, Proceedings 5th Berkeley Workshop on Distributed Data Management and Computer Networks (February 81).  P.A. Bernstein, N. Goodman, M.Y. Lai.

Database Architecture in a Network Environment, in Protocols and Techniques for Data Communication Networks, F.F. Kuo, ed., Prentice Hall, 1980.  T. Marill, J.B. Rothnie, N. Goodman.

What Does Boyce-Codd Normal Form Do?, Proceedings 6th International Conference on Very Large Databases(October 80).  P.A. Bernstein, N. Goodman.

Timestamp Based Algorithms for Concurrency Control in Distributed Database Systems, Proceedings 6th International Conference on Very Large Databases(October 80).  P.A. Bernstein, N. Goodman.

Introduction to a System for Distributed Databases (SDD-1), ACM Transactions on Database Systems, Vol. 5, No. 1 (March 80).  P.A. Bernstein, S. Fox, N. Goodman, M.M. Hammer, T.A. Landers, J.B. Rothnie, D.W. Shipman  E. Wong.

Full Reducers for Relational Queries Using Multi-Attribute Semijoins, Proceedings 1979 Computer Networking Symposium (December 79).  P.A. Bernstein, N. Goodman.

Approaches to Concurrency Control in Distributed Databases, Proceedings 1979 Na­tional Computer Conference (June 79).  P.A. Bernstein, N. Goodman.

A Sophisticate's Introduction to Database Normalization Theory, Proceedings 4th In­ternational Conference on Very Large Databases (September 78).  C. Beeri, P.A. Bern­stein, N. Goodman.

Database Systems:  Problems of the 80's, Computer, Vol. 11, No. 9 (September 78).  P.A. Bernstein, N. Goodman, S. Schuster, D.W. Shipman, D.C.P. Smith.

The Concurrency Control Mechanism of SDD-1 (The Fully Redundant Case), IEEE Transactions on Software Engineering, Vol. SE-4, No. 3 (May 78).  P.A. Bernstein, N. Goodman, C. Papadimitriou, J.B. Rothnie.

The Redundant Update Methodology of SDD-1 (The Fully Redundant Case), Proceed­ings COMPSAC '77 (November 77).  P.A. Bernstein, N. Goodman, C. Papadimitriou, J.B. Rothnie.

Survey of Research and Development in Distributed Database Systems, Proceedings 3rd International Conference on Very Large Databases (October 77).  J.B. Rothnie, N. Goodman.

An Overview of the Preliminary Design of SDD-1:  A System for Distributed Databases, Proceedings 2nd Berkeley Workshop on Distributed Data Management and Com­puter Networks (May 77).  J.B. Rothnie, N. Goodman.

Abstracts

T1DBase: Community Website for Type 1 Diabetes Research. Abstracts of the Immunology of Diabetes Society Seventh Annual Meeting (IDS-7).  (March 2004). N. Goodman, O. Burren, C. Cavnor, G. Dolman, P. Edlefsen, V. Everett, G. Glusman, B. Healy, E. Helton, A. Lam, D. Laneri, L. Rowen, H. Schuilenburg, N. Walker, Y. Wang, M. Whiting, J. Mychaleckyj, J.A. Todd, L. Smink.

First Steps on a Bioinformatics Program for Huntington’s Disease. HD2002: Changes, Advances, and Good News (CAG)n, Hereditary Disease Foundation (August 2002). N. Goodman.

Integration of Microarray Data With and Without Standards. Abstracts of Objects in Bio- & Chem-Informatics 2001 (OiBC-2001), Object Management Group (OMG) Life Sciences Research Domain Task Force (July 2001). J. Pollard, N. Goodman.

An Analysis Information Management System (AIMS) for the Hereditary Disease Array Group. Abstracts of the BioDiscovery Symposium on Experimental Design and Statistical Analysis in Array Technology (May 2001). R. Green, J. Pollard, N. Goodman.

Functional Analysis of the DEAH DNA Helicase Gene Subfamily. Abstracts of the 1998 American Society of Human Genetics Meeting (October 1998). R. M. Bruskiewich, K. Sjolander, N. Goodman, A. Rose, S. Wood.

First Steps Toward a Laboratory Informatics System for Positional Cloning of Complex Traits in Mouse. Abstracts of the 1997 International Mouse Genome Conference (October 1997). J.B. Macauley, A.G. Smith, H. Wang, D.N. Larkins, M.M. Miller, J. Pincus, N. Goodman.

LabBase and LabFlow: Software to Support the Workflow Paradigm for Genome Laboratory Informatics. Abstracts of the 1997 International Genome Sequencing and Analysis Conference, TIGR Science Education Foundation, Inc. (September 1997).  N. Goodman, S. Rozen, A.G. Smith, D.N. Larkins.

Field of Dreams: State-of-the-Art in Mammalian Genome Databases Suggests Strategies for the Future. Abstracts of the 1997 International Genome Sequencing and Analysis Conference, TIGR Science Education Foundation, Inc. (September 1997). J.B. Macauley, H. Wang, N. Goodman.

Seizing the Opportunity to Forge Practical Standards for Componentry in Bioinformatics. Abstracts of the 1997 ACEDB Conference and Workshop (ACE97) (July 1997). M.J. Cowley, N. Goodman.

The bioWidget QA Process: A Guide for Developers. Abstracts of Objects in Bioinformatics- Reusable Software Components and Distributed Computing for the Biological Sciences, European Bioinformatics Institute (June 1997). M.J. Cowley, J.A. Kadin, N. Goodman.

Information Systems to Manage Laboratory Data and Workflow for High Throughput Mapping. Abstracts of the 1997 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1997). S. Rozen, P. Young, R. Steen, V. Wang, W. Fitzhugh, R. Nahf, N. Goodman, L.D. Stein.

The Importance of Standards and Componentry in Meeting the Genome Informatics Challenges of the Next Five Years, Meeting on the Interconnection of Molecular Biology Databases (July 1995), Victor Markowitz, ed.  N. Goodman, S. Rozen,  L.D. Stein.

Towards an STS-Content Map of the Human Genome, Abstracts of the 1995 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1995).  T.  Hudson, S. Gerety, L.D. Stein, J. Ma, A. Castle, S-h. Xu, X. Hu, J. Silva, K. Wilson, A. Colbert, X. Wu, L. Horton, M. Anderson, A. Collymore, W. Ye, R. Kouyoumjiam, J. Tam, I, Zemtseva, R. Devine, R. Baptista, R. Nahf, N. Goodman, J.B. Orlin, S. Foote, D. C. Page, E. S. Lander.

Mapping the Mouse Genome:  7,000 Marker Genetic Map Complete, Physical Map Underway, Abstracts of the 1995 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1995).  W. F. Dietrich, J.C. Miller, R.G. Steen, M. Merchant, D. Damron, M. Haldi, C. Strickland, P. Lim, R.D. Dredge, L.D. Stein, R. Resnick, N. Goodman, D. C. Page, E. S. Lander.  

A Software Package for Managing Laboratory Workflow, Abstracts of the 1995 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1995).  L.D. Stein, S. Rozen,  N. Goodman.

Easily Shared, Component-Based Genome Software, Abstracts of the 1995 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1995).  N. Goodman, S. Rozen,  L.D. Stein.

A Suite of Software Programs for Managing Complex Laboratory Projects, Abstracts of the 1994 International Mouse Genome Conference (November 1994).  L.D. Stein, L. Bennett, R.D. Dredge, A.Marquis, R. Nahf, R. Resnick, C. Rosenberg, S. Rozen and N. Goodman

The Case for Componentry in Genome Information Systems, Meeting on the Interconnection of Molecular Biology Databases (August 1994), Peter D. Karp, organizer.  L.D. Stein, S. Rozen,  N. Goodman.

Construction of Genomic Maps in Mouse and Human: Whitehead/MIT Center for Genome Research Report, Abstracts of the 1994 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1994).  E. S. Lander, D. C. Page, N. Goodman, W. F. Dietrich, T.  Hudson, J.C. Miller, S. Foote, L.D. Stein, T. Hawkins, R.G. Steen, M. Merchant, D. Damron, R. Nahf, S. Gerety, J. Ma, S-H. Xu, X. Hu, J. Bae, J. Silva, J. Valle, S. Maitra, A. Colbert, L. Horton, M. Anderson, R.D. Dredge, M.P. Reeve, A. Marquis, M.J. Daly, A. Kaufman, C. Rosenberg, J.B. Orlin, K. Ingalls, T. O'Connor-Morin, C. Evans, M. Haldi, C. Strickland, P. Lim.

A 3500-Marker SSLP Genetic Map of the Mouse, Abstracts of the 1994 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1994).  J.C. Miller, W. F. Dietrich, R.G. Steen, M. Merchant, D. Damron, R. Nahf, A. Gross, M. Wessel, D.C. Joyce, R.D. Dredge, A. Marquis, L.D. Stein, N. Goodman, D. C. Page, E. S. Lander.  

LabBase: Tracking Experimental Data in High Throughput Mapping Projects, Abstracts of the 1994 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1994).  S. Rozen, L.D. Stein, N. Goodman.

Managing the Information Flow in Large Scale Laboratory Projects:  the Experience at the Whitehead/MIT Center for Genome Research , Abstracts of the 1994 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1994).  L.D. Stein, A. Marquis,R.D. Dredge, M.P. Reeve, M.J. Daly, N. Goodman.

Plug-and-Play Information-Retrieval Interfaces,  Abstracts of the ACM Workshop on Information Retrieval and Genomics (May 1994), John Guidi, organizer.  L.D. Stein, S. Rozen,  N. Goodman.

A Contig Assembly Algorithm for Mapping the Human Genome, Abstracts of MacroMolecules, Genes, and Computers: Chapter Three, Waterville Valley (August 1993).  M.P. Reeve, A. Kaufman, S.E. Lincoln, S. Foote, J.B. Orlin, E.S.Lander, N. Goodman.

The Design of MapBase: A Database for Large Scale Genome Mapping, Abstracts of the 1993 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1993).  N. Goodman, M.P. Reeve, P. Anagnostopoulos, L. Stein.

Progress Toward Maps of the Mouse and Human Genomes, Abstracts of the 1993 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1993).  W.F. Dietrich, J. C. Miller,  S. Foote, T. Hudson, D.C. Joyce, R.G. Steen, M. Merchant, M. Wessel, B. Trivedi, R. Bivins, K. Kusumi, J.S. Smith, J. Segre, S. Ganiatsas, A. Colbert, S. Gerety, S. Maitra, S-H. Xu, L. Stein, M.P. Reeve, S.E. Lincoln, M.J. Daly, N. Goodman, D.C. Page, E.S. Lander

Progress Toward a Complete Map of the Mouse Genome, Abstracts of the 1992 Genome Mapping and Sequencing Workshop, Cold Spring Harbor Laboratory (May 1992).  N.C. Dracopoli, J. Miller,  R. Steen, W. Dietrich, H. Katz, A. Weaver, S.E. Lincoln, M.J. Daly, N. Goodman, K. Kusumi, J.S. Smith, A. MacMurray, E.S. Lander.

Reports, Letters-to-the-Editor, and Courses

DNA Microarray Informatics: Key Technological Trends and Commercial Opportunities, (Report), Cambridge Healthtech Institute (February 2002). M. Branca, N. Goodman.

 

Microarray Informatics, (On-line Course), GeneEd, Inc (October 2001). J. Pollard, N. Goodman.  Available at http://www.geneed.com/courses/courses.html.

 

Conquering Microarray Analytics and Informatics, (Half-day seminar), Cambridge Healthtech Institute (June 2001). J. Pollard, R. Carel, N. Goodman.  Revised version of microarray seminar taught in April 2001.

 

Bioinformatics: Getting Results in the Era of High-Throughput Genomics, (Report), Cambridge Healthtech Institute (May 2001). M. Branca, T.V. Venkatesh, N. Goodman.

 

Getting Grounded in Microarray Informatics: Leading Challenges, Approaches, and Software Solutions, (Half-day seminar), Cambridge Healthtech Institute (April 2001). J. Pollard, N. Goodman.

 

To Be or Not to Be Science. Letter to the Editor,  in HMS Beagle: The BioMedNet Magazine, Issue 45 (January 1999) (http://www.biomednet.com/hmsbeagle/45/people/letters.htm#tobescience).  N. Goodman.

Comments on "Process Synchronization in Database Systems", ACM Transactions on Database Systems, Vol. 4, No. 4 (December 79).  P.A. Bernstein, M. Casanova, N. Goodman.

Magazine Articles (Genome Technolgy)

Messy Interactions,  Genome Technology (March 2004). N. Goodman.  Protein interaction databases.

Access Ability,  Genome Technology (January/February 2004). N. Goodman.  Open access data policies.

Hairballs: How to Deal With Dataset Detritus,  Genome Technology (October 2003). N. Goodman.  Visualization software for biological graphs.

You Want Fires With That?,  Genome Technology (September 2003). N. Goodman.  Assessment of bioinformatics job market.

Can’t Get There From Here,  Genome Technology (June 2003). N. Goodman.  Survey of pathway databases and websites, including a comparison of MAPK cascade in four databases.

Microarrays: Hazardous to Your Science,  Genome Technology (April 2003). N. Goodman.  Survey of analytical rigor (or lack thereof) in microarray papers published in top journals.

Welcome to the Terrible Twos,  Genome Technology (February 2003). N. Goodman.  Comparative analysis of one gene in the human and mouse genomes.

Text Mining: Help Is on the Way,  Genome Technology (January 2003). N. Goodman.  Software that helps extract information from the literature.

A Holly-Jolly Season for Open Source,  Genome Technology (December 2002). N. Goodman.  Introduction to BioPerl, a major open source bioinformatics package.

SNPs: Living HapMappily Ever After,  Genome Technology (November 2002). N. Goodman.  The rationale and prospects for genome-wide haplotype mapping.

Catch a Rising Star,  Genome Technology (October 2002). N. Goodman.  Quick look at several hot bioinformatics technologies: knowledge mining, pathway modeling, high performance sequence analysis, and community software.

Enlightenment Is Near,  Genome Technology (September 2002). N. Goodman.  Online bioinformatics courses and good old fashioned books.

Bioinformatics Tower of Babel,  Genome Technology (August 2002). N. Goodman.  Data integration problems and commercial solutions.

View from the Waterworks: The World of NCBI,  Genome Technology (July 2002). N. Goodman.  High performance bioinformatics at NCBI.

A Plethora of Protein Data, a Shortage of Solutions,  Genome Technology (June 2002). N. Goodman.  Comparison of major protein databases.

Drug Development for Dummies,  Genome Technology (May 2002). N. Goodman.  Overview of drug R&D process  for informaticians.

Ome Sweet Ome,  Genome Technology (April 2002). N. Goodman.  Proposal for omic approach to whole genome comparison.

A DIM SUMmary of Microarray Software,  Genome Technology (March 2002). N. Goodman.  Survey of microarray software.

Happy Birthday Human Genome,  Genome Technology (February 2002). N. Goodman.  Human genome data resources a year after the big publications.

How Smart is your Database?  Genome Technology (January 2002). N. Goodman.  How data semantics can lead to better databases.

A Letter to Santa,  Genome Technology (December 2001). N. Goodman.  Open source bioinformatics software.

Cruising the Single (Nucleotide Polymorphism) Scene,  Genome Technology (November 2001). N. Goodman.  Public databases of single nucleotide polymorphisms (SNPs).

Seduced by the S-Word,  Genome Technology (October 2001). N. Goodman.  The role of standards in microarray informatics.

Hail to Bioinformatics U,  Genome Technology (September 2001). N. Goodman.  Survey of graduate programs in bioinformatics.

Pondering the Games Proteins Play,  Genome Technology (August 2001). N. Goodman.  Informatics issues in biological pathways.

The Case of the Missing Genes,  Genome Technology (July 2001). N. Goodman.  The gene-number paradox: the discordance between gene-number estimates from human EST and genome sequence data.

Under the Hood,  Genome Technology (June 2001). N. Goodman.  Internals of microarray databases.

Who Wants To Be a Bioinformatics Millionaire?  Genome Technology (May 2001). N. Goodman.  Bioinformatics business models.

Now What?  Genome Technology (April 2001). N. Goodman.  The case for a Human Transcriptome Project.

Sampling the Menu of Microarray Software.  Genome Technology (March 2001). N. Goodman.  Survey of microarray analysis software.

The Wicked Truth About Annotation Databases.  Genome Technology (February 2001). N. Goodman.  Problems in the draft human genome annotation.

Farming for the New Biology.  Genome Technology (January 2001). N. Goodman.  Introduction to compute clusters. 

Wild, Wild Proteomics.  Genome Technology (December 2000). N. Goodman.  Challenges of modeling proteins in databases. 

Microarray Mining Made Easy - Almost.  Genome Technology (November 2000). N. Goodman.  Introduction to microarray analysis issues. 

Field of Genes. Genome Technology (October 2000). N. Goodman.  Proposal for integrated, gene-centric databases. 

Private Portals: Where’s the Payback? Genome Technology (September 2000). N. Goodman.  Survey of popular genome Web portals. 

Magazine Articles (Other)

The Fundamental Principles for Constructing a Successful Biological Laboratory Informatics System.  Scientific Computing and Automation July: 29-36 (July 1996).  N. Goodman.

The Object Data Model in Action, InfoDB, Vol. 6, No. 2 (Fall 91).  N. Goodman.

The Object Data Model, InfoDB, Vol. 6, No. 1 (Spring/Summer 91).  N. Goodman.

The Object Database Debate, InfoDB, Vol. 5, No. 4 (Winter 90/91).  N. Goodman.

Concurrency Control in Complex Transactions, InfoDB, Vol. 5, No. 3 (Fall 90).  N. Goodman.

View Update is Practical, InfoDB, Vol. 5, No. 2 (Summer 90).  N. Goodman.

Bill of Materials in Relational Databases, InfoDB, Vol. 5, No. 1 (Spring/Summer90).  N. Goodman.

The Benchmark Game:  Round 2, InfoDB,  Vol. 4, No. 4 (Winter 89/90).  N. Goodman.

Object Oriented Database Systems, InfoDB, Vol. 4, No. 3 (Fall 89).  N. Goodman.