James Tisdall is the author of two standard, best-selling textbooks in bioinformatics,
Beginning Perl for Bioinformatics and Mastering Perl for Bioinformatics.
He is also the author of several papers and articles on bioinformatics programming
and other scientific topics such as complexity theory and information theory. He has
delivered bioinformatics training at leading institutions and bioinformatics conferences.
He has been a scientific research programmer for over twenty years. He has worked at
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His degrees are in mathematics (B.A. City College CUNY) and computer science
(M.S. Columbia University) and he has additional extensive graduate training in
mathematics, computer science, genetics and biology.
He pioneered the use in biology research of the Perl programming language,
the most popular bioinformatics language. As a manager, his specialty is
translating the researcher's needs into specific tasks for the programming staff.
His focus is designing bioinformatics programs that advance research goals. He enjoys
fast programming to respond to immediate research needs, as well as system building.
Here are some of his on-line articles about bioinformatics:
Why Biologists
Want to Program Computers
The economic and scientific benefits of biologists learning to program are explained.
Beginning
Bioinformatics
What the average Perl programmer needs to know
about the new field of bioinformatics.
Parsing
Protein Domains with Perl
Shows how to program in Perl using protein data,
with downloadable code examples.
A Chromosome at a Time with Perl, Part I
Programming strategies to get excellent performance
when dealing with very large biological data sets.
A Chromosome at a Time with Perl, Part II
More programming strategies to get excellent performance
when dealing with very large biological data sets.
Education Ph.D. Candidate, Computer and Information Science, University of Pennsylvania 1989 M.S. Computer Science, Columbia University 1988 B.A. Mathematics, Summa Cum Laude, City College CUNY Summary of Experience Positions Held Research Scientist in Genetic Discovery Dupont, Wilmington, Delaware January 2004-present. Research consultant and science writer. Biocomputing Associates, Philadelphia, Pennsylvania. September 2000-present. Manager, Computational Biology Group, Research Information Technology Facilities. The Fox Chase Cancer Center, Philadelphia, Pennsylvania. October 1995-August 2000. Computational Biologist and Head of Informatics Group. Mercator Genetics, Menlo Park, California. November 1994-October 1995. Programmer/Analyst IV and Systems Manager, Human Genome Project. Computational Biology and Informatics Laboratory (CBIL). Department of Human Genetics, School of Medicine, University of Pennsylvania. March 1992-November 1994. University and Dean's Fellow. Department of Computer and Information Science, University of Pennsylvania. 1990-1992. University Fellow. Department of Computer Science, University of Michigan. 1989-1990. Member Technical Staff, Speech Research, Information Principles Laboratory. AT&T Bell Laboratories, Murray Hill, New Jersey. 1984-1989. Selected Publications and Talks Course: Mastering Perl for Bioinformatics Drexel University and Bioadvance, (coming April 2004) Course: Beginning Perl for Bioinformatics Drexel University and Bioadvance, 2004 Mastering Perl for Bioinformatics (book) James Tisdall O'Reilly & Associates, 2003. Tutorial: Using Perl and Bioperl O'Reilly Bioinformatics Technology Conference, 2003. Functional Genomics: Integration of Computational, Visualization and Genomic Database Annotation Tools for Biological Pathway Analysis Michael Caudy, Lincoln D. Stein, James Tisdall O'Reilly Bioinformatics Technology Conference, 2003. Tutorial: Beginning Perl for Bioinformatics ISMB (Intelligent Systems for Molecular Biology) Conference, 2002. Tutorial: Beginning Perl for Bioinformatics O'Reilly Bioinformatics Technology Conference, 2002. Functional Genomics: Integration of Experimental Results With Online Annotation Databases Michael Caudy, Lincoln D. Stein, James Tisdall O'Reilly Bioinformatics Technology Conference, 2002. Telometric: A Tool Providing Simplified, Reproducible Measurements of Telomeric DNA from Constant Field Agarose Gels Grant, Broccoli, Manion, Muquit, Tisdall, Ochs BioTechniques, 31, 6, 2001. Beginning Perl for Bioinformatics (book) James Tisdall O'Reilly & Associates, 2001. Managing Bioinformatics Facilities Invited Talk, Wyeth Laboratories, 1998. Bioinformatics Challenges Invited Talk, SmithKlein Laboratories, 1997. Gerard - Compare and Analyze Affected and Unaffected Patient DNA Technical Memorandum, Mercator Genetics, 1995. Relational Databases and Object Oriented Methods in Bioinformatics Invited Talk, National Center for Genome Resources, 1994. Using Perl in Bioinformatics Facilities Invited Talk, Genome DataBase, Johns Hopkins, 1994. DNA WorkBench James Tisdall Reviewed in Trends in Biochemical Sciences October 1994. DNA WorkBench Tisdall, Searls, Overton WorkShop on Genome Sequencing and Analysis Cold Spring Harbor, 1993. DNA WorkBench James Tisdall UPenn Technical Memorandum MS-CIS-93-38 (LOGIC & COMPUTATION 61), 1993. Simultaneous Strong Separations of Probabilistic and Unambiguous Complexity Classes Eppstein, Hemachandra, Tisdall, and Yener Mathematical Systems Theory, 25, 1992. On Rhythm James Tisdall Bell Laboratories Technical Memorandum, 1988.Visit www.biocomputingassociates.com