=: Readings in Bioinformatics :=

Bioinformatics Journal Club

School of Information and Library Science

Readings in Bioinformatics

Send suggestions to macmw -[at]- ils.unc.edu .
Last updated: 2002.01.11

Introductory / Overview

Brazma, Alvis. On the Importance of Standardisation in Life Sciences. Bioinformatics 2001 17: 113-114.
http://bioinformatics.oupjournals.org/content/vol17/issue2/

Ouzounis, Christos. Two or three myths about bioinformatics. Bioinformatics 2000 16: 187-189.
http://bioinformatics.oupjournals.org/content/vol16/issue3/

Achard, Frédéric et al. XML, bioinformatics and data integration. Bioinformatics 2001 17: 115-125.
http://bioinformatics.oupjournals.org/cgi/content/abstract/17/2/115

Sander, Chris. Bioinformatics - Challenges in 2001. Bioinformatics 2001 17: 1-2.
http://bioinformatics.oupjournals.org/content/vol17/issue1/

Searls, David B. Reading the book of life. Bioinformatics 2001 17: 579-580.
http://bioinformatics.oupjournals.org/content/vol17/issue7/

Roos, David S. Bioinformatics--Trying to Swim in a Sea of Data. Science Volume 291, Number 5507, Issue of 16 Feb 2001, pp. 1260-1261.
http://www.sciencemag.org/cgi/content/full/291/5507/1260

Brenner, Sydney. Hunting the Metaphor. [review of Davies' Cracking the Genome). Science Volume 291, Number 5507, Issue of 16 Feb 2001, pp. 1265-1266.
http://www.sciencemag.org/cgi/content/full/291/5507/1265
A review of a book that is a good introduction to genome sequencing and the HGP, but also an insightful and humorous piece on its own.

Fields, Stanley (2001). The interplay of biology and technology. Proc Natl Acad Sci 98: 10051-10054
http://www.pnas.org/cgi/content/full/98/18/10051

Allen, John. In silico veritas: Data-mining and automated discovery: the truth is in there. EMBO Reports 2:7:542-544.
http://embo-reports.oupjournals.org/cgi/content/full/2/7/542

Luscombe NM, Greenbaum D, Gerstein M. What is bioinformatics? A proposed definition and overview of the field. Methods of information in medicine 2001;40(4):346-58.
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11552348&dopt=Abstract
See also
http://bioinfo.mbb.yale.edu/what-is-it/

Greenbaum D., et al. (2001) Interrelating Different Types of Genomic Data, from Proteome to Secretome: 'Oming in on Function. Genome Research 11:1463-1468.
http://www.genome.org/cgi/content/abstract/11/9/1463

Thornton, Janet M. (2001). From Genome to Function. Science 292:5524:2095.
http://www.sciencemag.org/cgi/content/summary/292/5524/2095

Stevens, Robert, et al. A classification of tasks in bioinformatics. Bioinformatics 2001 17: 180-188.
http://bioinformatics.oupjournals.org/cgi/content/abstract/17/2/180

Proteomics

Fields, Stanley. Proteomics in Genomeland. Science Feb 16 2001: 1221-1224.
http://www.sciencemag.org/cgi/content/full/291/5507/1221
Nice overview of the current state of the art of proteomics technology, discussion of future tech, and problems to be addressed.

Brower, V. Proteomics: biology in the post-genomic era. EMBO Reports 2:7:558-560.
http://embo-reports.oupjournals.org/cgi/content/full/2/7/558
Non-technical overview including discussion of commercial activities in proteomics.

Sperling K. From proteomics to genomics. Electrophoresis. 2001 Aug;22(14):2835-7.
http://www3.interscience.wiley.com/cgi-bin/abstract/85011011/START
Historical development of 2D GE and evolution into quantitative protein analysis via mass spec.

Nordhoff, E. et al. Large-gel two-dimensional electrophoresis-matrix assisted laser desorption/ionization-time of flight-mass spectrometry: An analytical challenge for studying complex protein mixtures. Electrophoresis. 2001 Aug;22(14):2844-2855.
http://www3.interscience.wiley.com/cgi-bin/abstract/85011013/START
"Automated identification of proteins in sequence databases by mass spectrometric peptide mapping requires a powerful search engine that makes full use of the information contained in the experimental data [...]."

T. Chen, M.-Y. Kao, M. Tepel, J. Rush, and G.M. Church (2001). A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry. Journal of Computational Biology 8:3:325-338.
http://www.liebertpub.com/CMB/TOC/default1.asp

Srinivas, PR et al. Proteomics in Early Detection of Cancer. Clinical Chemistry 2001 Oct;47(10):1901-1911.
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11568117&dopt=Abstract
The abstract looks good but I haven't been able to read it yet; UNC doesn't subscribe.

Genomics & Genome Annotation

Unfortunately, these are all in Nature, with whom UNC is currently in dispute re: electronic access. They are all at HSL in paper.

Stein, L. Genome Annotation: From Sequence to Biology. Nat Rev Genet 2:7:493-503

Hasty, J. et al. Computational studies of gene regulatory networks: in numero molecular biology. Nat Rev Genet 2:4:268-279.

Shoemaker, D. et al. Experimental annotation of the human genome using microarray technology. Nature 409:6822:922-927.

White, K. Functional genomics and the study of development, variation and evolution. Nat Rev Genet 2:7:528-537.

Metadata, Ontologies, & Language

Pearson, Helen (2001). Biology's name game. Nature (online)
http://www.nature.com/nsu/010607/010607-12.html

Gene Ontology Consortium. Gene Ontology: Tool for the unification of biology. Nature Genetics 25:25-29
http://www.geneontology.org/GO_nature_genetics.pdf

Gene Ontology Consortium. Creating the Gene Ontology Resource: Design and Implementation. Genome Research 11:1425-1433.
http://www.genome.org/cgi/content/abstract/11/8/1425

Dolin R.H., et al. Kaiser permanente's "metadata-driven" national clinical intranet. Medinfo 2001;10(Pt 1):319-23.
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11604755&dopt=Abstract

Darmoni S.J. Doc'cismef: a search tool based on "encapsulated" mesh thesaurus. Medinfo 2001;10(Pt 1):314-8.
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11604754&dopt=Abstract

Anagnostaki A, Pavlopoulos S, Koutsouris D. XML and the VITAL standard: the document-oriented approach for open telemedicine applications. Medinfo 2001;10(Pt 1):77-81.
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11604709&dopt=Abstract

Karp, Peter D. An ontology for biological function based on molecular interactions. Bioinformatics 2000 16: 269-285
http://bioinformatics.oupjournals.org/cgi/content/abstract/16/3/269

Kazic, Toni. Semiotes: a semantics for sharing. Bioinformatics 2000 16: 1129-1144.
http://bioinformatics.oupjournals.org/cgi/content/abstract/16/12/1129

Rzhetsky, Andrey, et al. A knowledge model for analysis and simulation of regulatory networks. Bioinformatics 2000 16: 1120-1128.
http://bioinformatics.oupjournals.org/cgi/content/abstract/16/12/1120

Searls, David B. Reading the book of life. Bioinformatics 2001 17:579-580.
http://bioinformatics.oupjournals.org/content/vol17/issue7/

Searls, David B. (2001). From Jabberwocky to Genome: Lewis Carroll and Computational Biology. Journal of Computational Biology 8:3:339.
http://www.liebertpub.com/CMB/TOC/default1.asp

A. Marathe, A.E. Condon, and R.M. Corn (2001). On Combinatorial DNA Word Design. Journal of Computational Biology 8:3:201-220.
http://www.liebertpub.com/CMB/TOC/default1.asp

Avise, John C. (2001). Evolving Genomic Metaphors: A New Look at the Language of DNA. Science. 294:5540:86-87 (5 Oct 2001).

Nelkin, Dorothy (2001). Molecular metaphors: the gene in popular discourse. Nature Review Genetics. Vol 2:555-559 (July 2001).

Databases, Distributed Databases, & Data Integration

Nucleic Acids Research 2001 database issue
http://nar.oupjournals.org/content/vol29/issue1/
Annual review of the primary bio DBs

Xie, Guochun. Storing biological sequence databases in relational form. Bioinformatics 2000 16: 288-289.
http://bioinformatics.oupjournals.org/cgi/content/abstract/16/3/288

Stein, L. et al. A Distributed Annotation System (DAS)
http://das.wustl.edu/

Karp, Peter. Pathway Databases: A Case Study in Computational Symbolic Theories. Science 293:2040-2044.
http://www.sciencemag.org/cgi/content/full/293/5537/2040

Stevens, Robert. TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources. Bioinformatics 2000 16: 184-186.
http://bioinformatics.oupjournals.org/cgi/content/abstract/16/2/184

Tools

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410
The seminal article on BLAST.

Altschul, S.F., Boguski, M.S., Gish, W. & Wootton, J.C. (1994) "Issues in searching molecular sequence databases." Nature Genet. 6:119-129.

Giegerich, Robert. A systematic approach to dynamic programming in bioinformatics. Bioinformatics 2000 16: 665-677.
http://bioinformatics.oupjournals.org/cgi/content/abstract/16/8/665

Jonathan Bingham and Sucha Sudarsanam. Visualizing large hierarchical clusters in hyperbolic space. Bioinformatics 2000 16: 660-661.
http://bioinformatics.oupjournals.org/cgi/content/abstract/16/7/660
Use of an hyperbolic tree interface for visualization

Fuchs, Rainer. Analyse This...Or: Intelligent Help for The Rest of Us. Bioinformatics 2000 16: 491-493.
http://bioinformatics.oupjournals.org/content/vol16/issue6/
The danger of unintentional usability and the need for intelligent interfaces

The journal Bioinformatics has many software and database tools in each issue.

Problems

Jongeneel, C. Victor. The need for a human gene index. Bioinformatics 2000 16: 1059-1061
http://bioinformatics.oupjournals.org/content/vol17/issue7/

Anderson, N.G., Matheson, A., Anderson, N.L. Back to the future: The human protein index (HPI) and the agenda for post-proteomic biology. Proteomics 2001; 1:3-12.

Rechenmann, Francois. From data to knowledge. Bioinformatics 2000 16: 411.
http://bioinformatics.oupjournals.org/cgi/reprint/16/5/411

Board, John A. Jr. "Grand Challenges in Biomedical Computing." In Pilkington, Theo C. et al, High-Performance Computing in Biomedicine. CRC Press, 1993.

Etc.

S-Star
http://s-star.org/main.htm
"S-Star.org is an alliance between six different universities [...]" [and] "aims to provide a bioinformatics education to interested students everywhere, regardless of background, with the help of the Internet."

Bioinformatics Journal Club