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Grants and Funding: Extramural Programs (EP)

Dr. Russ Altman – PECASE Recipient 1997

Representing Biological Data for Molecular Modeling (R01-LM-006244)

Project Information

The first NLM-supported grantee to receive a PECASE award, in 1997, was Russ B. Altman, M.D., Ph.D., for his contribution to bioinformatics. Dr. Altman’s research focused on the application of bioinformatics to basic molecular biological problems. He is particularly interested in the analysis of protein and RNA structure and function, both in an individual problem-centered manner and on a functional genomic scale. Over the last decade, Dr. Altman, a Professor of Bioengineering, Genetics, and Medicine at the Stanford University School of Medicine, has received several grants from NIH and served with distinction on the Biomedical Library and Informatics Review Committee.

Quotes

What do you think the impact of this award has had on your research career?

This was incredibly important for me because it extended my first R01 grant for a few years, and allowed my nascent research program to gather more results before renewal. It also was a huge confidence builder for a young academic—always wondering if we are worthy of our post and if our work will be productive and impactful enough to attract support.

Photo of Dr. Russ Altman

Dr. Russ Altman

What is your best career advice to young investigators?

Focus on an initial area that is important but not super-competitive and establish your excellence in research and mentoring in that area before branching out. Make sure you publish papers in mid-tier journals along the way, and let the high-impact papers emerge more opportunistically. Don't forget about the parallel skills of speaking, writing, and meeting organization to make sure that your peers understand your research program and its excitement and results.

What do you think might be the most likely (and meaningful) discovery to emerge in your field in the next five? Ten years?

I think that we have turned a corner in machine understanding of human generated text, and so we will have bioinformatics tools that really can read and summarize science. I also think that we will begin to push the fruits of genomics into the clinics and deliver on the promise to use the sequenced genome to improve human health.

Tools

RiboWeb, now available at simtk.org

Publications

Publications related to this grant and listed in PubMed include:

Chang JT, Altman RB. Extracting and characterizing gene-drug relationships from the literature. Pharmacogenetics. 2004 Sep;14(9):577-86. PubMed PMID: 15475731.

Chang JT, Schütze H, Altman RB. Creating an online dictionary of abbreviations from MEDLINE. J Am Med Inform Assoc. 2002 Nov-Dec;9(6):612-20. PubMed PMID: 12386112; PubMed Central PMCID: PMC349378.

Chang JT, Schütze H, Altman RB. GAPSCORE: finding gene and protein names one word at a time. Bioinformatics. 2004 Jan 22;20(2):216-25. PubMed PMID: 14734313.

Mooney SD, Altman RB. MutDB: annotating human variation with functionally relevant data. Bioinformatics. 2003 Sep 22;19(14):1858-60. PubMed PMID: 14512363.

Mooney SD, Klein TE, Altman RB, Trifiro MA, Gottlieb B. A functional analysis of disease-associated mutations in the androgen receptor gene. Nucleic Acids Res.2003 Apr 15;31(8):e42. PubMed PMID: 12682377; PubMed Central PMCID: PMC153754.

Mooney SD, Liang MH, DeConde R, Altman RB. Structural characterization of proteins using residue environments. Proteins. 2005 Dec 1;61(4):741-7. PubMed PMID: 16245324; PubMed Central PMCID: PMC2483305.

Raychaudhuri S, Altman RB. A literature-based method for assessing the functional coherence of a gene group. Bioinformatics. 2003 Feb 12;19(3):396-401. PubMed PMID: 12584126; PubMed Central PMCID: PMC2669934.

Raychaudhuri S, Chang JT, Sutphin PD, Altman RB. Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res. 2002 Jan;12(1):203-14. PubMed PMID: 11779846; PubMed Central PMCID: PMC155261.

Raychaudhuri S, Schütze H, Altman RB. Using text analysis to identify functionally coherent gene groups. Genome Res. 2002 Oct;12(10):1582-90. PubMed PMID: 12368251; PubMed Central PMCID: PMC187532.

Raychaudhuri S, Stuart JM, Altman RB. Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac Symp Biocomput. 2000:455-66. PubMed PMID: 10902193; PubMed Central PMCID: PMC2669932.

Raychaudhuri S, Sutphin PD, Chang JT, Altman RB. Basic microarray analysis: grouping and feature reduction. Trends Biotechnol. 2001 May;19(5):189-93. Review. PubMed PMID: 11301132.

Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Missing value estimation methods for DNA microarrays. Bioinformatics. 2001 Jun;17(6):520-5. PubMed PMID: 11395428.

Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8348-53. Epub 2003 Jun 25. PubMed PMID: 12826619; PubMed Central PMCID: PMC166232.

Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics. 2002 Nov;18(11):1454-61. PubMed PMID: 12424116.

Waugh A, Gendron P, Altman R, Brown JW, Case D, Gautheret D, Harvey SC, Leontis N, Westbrook J, Westhof E, Zuker M, Major F. RNAML: a standard syntax for exchanging RNA information. RNA. 2002 Jun;8(6):707-17. PubMed PMID: 12088144; PubMed Central PMCID: PMC1370290.

Wei L, Altman RB, Chang JT. Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences. Pac Symp Biocomput. 1997:465-76. PubMed PMID: 9390315.