Peer-Reviewed Papers

Chang JT and Nevins JR. GATHER: a systems approach to interpreting genomic signatures. Bioinformatics, 2006.
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Kong LJ, Chang JT, Bild AH, and Nevins JR. Compensation and specificity of function within the E2F family. Oncogene, 2006.
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Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA, Marks JR, Dressman HK, West M, and Nevins JR. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature, 2005.
[ PMID ]

Delong M, Yao G, Wang Q, Dobra A, Black EP, Chang JT, Bild A, West M, Nevins JR, and Dressman H. DIG -- a system for gene annotation and functional discovery. Bioinformatics 21(13). 2005.
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Wren JD, Chang JT, Pustejovsky J, Adar E, Garner HR, and Altman RB. Biomedical Term Mapping Databases. Nucleic Acids Research 33(Database issue), 2005.
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Chang JT and Altman RB. Extracting and Characterizing Gene-Drug Relationships from the Literature. Pharmacogenetics 14(9), 2004.
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Chang JT, Schütze H, and Altman RB. GAPSCORE: Finding Gene and Protein Names One Word at a Time. Bioinformatics 20(2), 2004.
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Raychaudhuri S, Chang JT, Imam F, and Altman RB. The computational analysis of scientific literature to define and recognize gene expression clusters. Nucleic Acids Research 31(15): 4553-60, 2003.
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Chang JT, Schütze H, and Altman RB. Creating an Online Dictionary of Abbreviations from MEDLINE. The Journal of the American Medical Informatics Association 9(6): 612-20, 2002.
[ PMID | PDF | WWW ]

Raychaudhuri S, Chang JT, Sutphin PD, and Altman RB. Associating genes with Gene Ontology codes using a maximum entropy analysis of biomedical literature. Genome Research 12:203-214, 2002.
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Raychaudhuri S, Sutphin PD, Chang JT, and Altman RB. Basic microarray analysis: grouping and feature reduction. Trends in Biotechnology 19:189-193, 2001.
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Klein TE, Chang JT, Cho MK, Easton KL, Fergerson R, Hewett M, Lin Z, Liu Y, Liu S, Oliver DE, Rubin DL, Shafa F, Stuart JM, and Altman RB. Integrating genotype and phenotype information: an overview of the PharmGKB project. The Pharmacogenomics Journal 1, 167-170, 2001.
[ PMID ]

Chang JT, Raychaudhuri S, Altman RB. Including biological literature improves homology search. Pacific Symposium on Biocomputing 374-383, 2001.
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Wei L, Altman RB, and Chang JT. Using the radial distributions of physical featuresto compare amino acid environments and align amino acid sequences. Pacific Symposium on Biocomputing, Hawaii, 465-476, 1997.
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Book Chapters

Chang JT and Schütze H. Abbreviations in Biomedical Text. In Text Mining for Biology and Biomedicine. Sophia Ananiadou and John McNaught, Eds. Artech House Publishers, 2005.

Chang JT, Carrillo MW, Waugh A, Wei L, and Altman RB. Scoring Functions Sensitive to Alignment Error Have a More Difficult Search. In Structures and Mechanisms: From Ashes to Enzymes, Gareth R. Eaton, Don C. Wiley, and Oleg Jardetzky, eds., ACS Symposium Series Volume 827, Oxford University Press, 309-320, 2002.

Wei L, Chang JT, and Altman RB. In David Searls, Steven Salzberg, and Simon Kasif, Ed., Computation Methods in Molecular Biology. Elsevier Science, 207-225, 1998.

Tech Reports, Articles, and Other

Mooney S and Chang JT. Bioinformatics. In Shein-Chung Chow, Ed., Encyclopedia of Biopharmaceutical Statistics, Second Edition. Dekker, 2004.

Chang JT. Using Machine Learning to Extract Drug and Gene Relationships from Text. Doctoral Dissertation. Stanford University, September 2003.
[ PDF (1.8Mb) ]

Osborne M, Chang J, Cumiskey M, Mehra N, Rotemberg V, Sinclair G, Smillie M, Altman RB, and Webber B. Edinburgh-Stanford TREC 2003 Genomics Track: Notebook Paper. TREC Genomics Track, NIST, USA, 2003.

Chang JT and Altman RB. Promises of Text Processing: Natural Language Processing Meets AI. Drug Discovery Today. 7(19):992-993, 2002.
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Bernstam EV, Kamvar SD, Meric F, Dugan JM, Chang JT, Chizek SC, Stave C, Troyanskaya OG and Fagan LM. Oncology Patient Interface to MEDLINE. Proceedings of the American Society of Clinical Oncology 37th Annual Meeting 20:244a, 2001.

Chapman B and Chang JT. Biopython: Python Tools for Computational Biology. Sig-Bio Newsletter of the Association for Computing Machinery. 20(2):15-19, 2000.

Altman RB, Whirl M, Waugh A, Wei L, and Chang JT. A Paradox for Threading: Scoring Functions Sensitive to Alignment Error Have a More Difficult Search. 1997.

Tutorials and Invited Presentations

Chang JT. Python and Biopython Scripting for Busy Bioinformaticians. IEEE Computer Society Bioinformatics Conference, 2003.
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Chang JT and Raychaudhuri S. Towards Incorporating Scientific Literature into Biological Algorithms. Tutorial. Intelligent Systems in Molecular Biology, 2001.
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Chang JT. Python Scripting for Computational Biologists. Tutorial. Pacific Symposium on Biocomputing, 2001.

Chang JT. Including Biological Literature Improves Homology Search. Pacific Symposium on Biocomputing, 2001.

Chang JT. Biopython Coming of Age. Bioinformatics Open Source Conference, 2000.