BioPerl publications/2002

1. Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, and Stein L. Gramene: a resource for comparative grass genomics. Nucleic Acids Res. 2002 Jan 1;30(1):103-5.
2. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, and Clamp M. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41.
3. Reiser L, Mueller LA, and Rhee SY. Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems. Plant Mol Biol. 2002 Jan;48(1-2):59-74.
4. Roos DS, Crawford MJ, Donald RG, Fraunholz M, Harb OS, He CY, Kissinger JC, Shaw MK, and Striepen B. Mining the Plasmodium genome database to define organellar function: what does the apicoplast do?. Philos Trans R Soc Lond B Biol Sci. 2002 Jan 29;357(1417):35-46. DOI:10.1098/rstb.2001.1047 |
5. Thijs G, Moreau Y, De Smet F, Mathys J, Lescot M, Rombauts S, Rouze P, De Moor B, and Marchal K. INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling. Bioinformatics. 2002 Feb;18(2):331-2.
6. Stein L. Creating a bioinformatics nation. Nature. 2002 May 9;417(6885):119-20. DOI:10.1038/417119a |
7. Baxevanis AD, Ouellette BFF Bioinformatics (Second Edition) 2001 Wiley & Sons, ISBN:0471223921.
8. Mangalam HJ. tacg--a grep for DNA. BMC Bioinformatics. 2002;3:8.
9. Lenhard B and Wasserman WW. TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics. 2002 Aug;18(8):1135-6.
10. Thorisson GA and Stein LD. The SNP Consortium website: past, present and future. Nucleic Acids Res. 2003 Jan 1;31(1):124-7.
11. Birney E, Clamp M, and Hubbard T. Databases and tools for browsing genomes. Annu Rev Genomics Hum Genet. 2002;3:293-310. DOI:10.1146/annurev.genom.3.030502.101529 |
12. Heil J, Glanowski S, Scott J, Winn-Deen E, McMullen I, Wu L, Gire C, and Sprague A. An automated computer system to support ultra high throughput SNP genotyping. Pac Symp Biocomput. 2002:30-40.
13. Moreau L Agents for the Grid: A Comparison with Web Services (Part I: Transport Layer) Proceedings of the 2nd IEEE/ACM International Symposium on Cluster Computing and the Grid 2002.
14. Konagaya A OBIGrid: Towards a New Distributed Platform for Bioinformatics Proceedings of the 21st IEEE Symposium on Reliable Distributed Systems (SRDS'02) 2002.
15. Loraine AE, Helt G Visualization Techniques for Genomic Data Proceedings of the IEEE Computer Society Conference on Bioinformatics 2002.
16. Loraine AE, Helt GA, Cline MS, and Siani-Rose MA. Protein-based analysis of alternative splicing in the human genome. Proc IEEE Comput Soc Bioinform Conf. 2002;1:118-24.
17. Loraine AE and Helt GA. Visualization techniques for genomic data. Proc IEEE Comput Soc Bioinform Conf. 2002;1:321-6.
18. Salse J, Piégu B, Cooke R, and Delseny M. Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project. Nucleic Acids Res. 2002 Jun 1;30(11):2316-28.
19. Wilkinson MD and Links M. BioMOBY: an open source biological web services proposal. Brief Bioinform. 2002 Dec;3(4):331-41.
20. Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM, and Lewis SE. An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol. 2002;3(12):RESEARCH0081.
21. Wilkinson MD, Block D, and Crosby WL. Genquire: genome annotation browser/editor. Bioinformatics. 2002 Oct;18(10):1398-9.
22. Mangalam H. The Bio* toolkits--a brief overview. Brief Bioinform. 2002 Sep;3(3):296-302.
23. Matthiessen MW. Affordable biocomputing for everyone: using the Internet, freeware and open-source software. Trends Biochem Sci. 2002 Nov;27(11):586-8.
24. Berezikov E, Plasterk RH, and Cuppen E. GENOTRACE: cDNA-based local GENOme assembly from TRACE archives. Bioinformatics. 2002 Oct;18(10):1396-7.
25. Kivioja T, Arvas M, Kataja K, Penttilä M, Söderlund H, and Ukkonen E. Assigning probes into a small number of pools separable by electrophoresis. Bioinformatics. 2002;18 Suppl 1:S199-206.
26. Andrade MA, Ciccarelli FD, Perez-Iratxeta C, and Bork P. NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria. Genome Biol. 2002 Aug 15;3(9):RESEARCH0047.
27. Chen H and Sharp BM. Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region. BMC Bioinformatics. 2002 Oct 6;3:27.
28. Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, and Hogue CW. SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics. 2002 Oct 25;3:32.
29. McAdam RA, Quan S, Smith DA, Bardarov S, Betts JC, Cook FC, Hooker EU, Lewis AP, Woollard P, Everett MJ, Lukey PT, Bancroft GJ, Jacobs Jr WR Jr, and Duncan K. Characterization of a Mycobacterium tuberculosis H37Rv transposon library reveals insertions in 351 ORFs and mutants with altered virulence. Microbiology. 2002 Oct;148(Pt 10):2975-86.
30. Riikonen P, Boberg J, Salakoski T, and Vihinen M. Mobile access to biological databases on the Internet. IEEE Trans Biomed Eng. 2002 Dec;49(12):1477-9. DOI:10.1109/TBME.2002.805459 |
31. Wong L. Technologies for integrating biological data. Brief Bioinform. 2002 Dec;3(4):389-404.
32. Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, and Clamp ME. Apollo: a sequence annotation editor. Genome Biol. 2002;3(12):RESEARCH0082.