BioPerl publications

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A sample of papers related to or using BioPerl.

Search Google Scholar for BioPerl references.

These lists are undoubtably incomplete please add to it where appropriate


Papers which should be cited when using BioPerl

The first paper is the main BioPerl citation for using the toolkit, the second is for Gbrowse and the third is for the PopGen modules.

  1. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, and Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002 Oct; 12(10) 1611-8. doi:10.1101/gr.361602 pmid:12368254. PubMed HubMed [bioperl2002]
  2. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, and Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res 2002 Oct; 12(10) 1599-610. doi:10.1101/gr.403602 pmid:12368253. PubMed HubMed [gbrowse2002]
  3. Stajich JE and Hahn MW. Disentangling the effects of demography and selection in human history. Mol Biol Evol 2005 Jan; 22(1) 63-73. doi:10.1093/molbev/msh252 pmid:15356276. PubMed HubMed [perlmorphism2005]
All Medline abstracts: PubMed HubMed

References to BioPerl in PubMed


Projects or Papers which cite BioPerl


  1. Kraemer ET and Ferrin TE. Molecules to maps: tools for visualization and interaction in support of computational biology. Bioinformatics 1998; 14(9) 764-71. pmid:9918946. PubMed HubMed [kraemer1998]
  2. Chervitz SA, Fuellen G, Dagdigian C, Brenner SE, Birney E, Korf I, Bioperl: Standard Perl modules for Bioinformatics 1999 BITS J. 1. (journal longer available) [bits1999]
  3. Pocock M, Down T, Hubbard T BioJava: open source components for bioinformatics 2000 ACM SIGBIO Newsletter 20(2):10-12. [biojava2000]
  4. Stajich JE and Birney E The Bioperl project: motivation and usage ACM SIGBIO Newsletter 2000 20(2):13-14. [bioperl2000]
  5. Chapman B, Chang J Biopython: Python tools for computational biology 2000 ACM SIGBIO Newsletter 20(2):15-19. [bipython2000]
  6. Ramu C, Gemund C, and Gibson TJ. Object-oriented parsing of biological databases with Python. Bioinformatics 2000 Jul; 16(7) 628-38. pmid:11038333. PubMed HubMed [ramu2000]
  7. Achard F, Vaysseix G, and Barillot E. XML, bioinformatics and data integration. Bioinformatics 2001 Feb; 17(2) 115-25. pmid:11238067. PubMed HubMed [achard2001]
  8. Stein L. Genome annotation: from sequence to biology. Nat Rev Genet 2001 Jul; 2(7) 493-503. doi:10.1038/35080529 pmid:11433356. PubMed HubMed [stein2001]
  9. Ramu C. SIR: a simple indexing and retrieval system for biological flat file databases. Bioinformatics 2001 Aug; 17(8) 756-8. pmid:11524384. PubMed HubMed [ramu2001]
  10. Wong RK, Shui WM Utilizing Multiple Bioinformatics Information Sources: An XML Database Approach 2001 Proceedings of the 2nd IEEE International Symposium on Bioinformatics and Bioengineering. [wong2001]
  11. Rubin E, Lithwick G, and Levy AA. Structure and evolution of the hAT transposon superfamily. Genetics 2001 Jul; 158(3) 949-57. pmid:11454746. PubMed HubMed [rubin2001]
  12. Gavaghan H A permanent education 2001 Nature 413(6858):4-5. [gavaghan2001]
  13. Hoskins J, Alborn WE Jr, Arnold J, Blaszczak LC, Burgett S, DeHoff BS, Estrem ST, Fritz L, Fu DJ, Fuller W, Geringer C, Gilmour R, Glass JS, Khoja H, Kraft AR, Lagace RE, LeBlanc DJ, Lee LN, Lefkowitz EJ, Lu J, Matsushima P, McAhren SM, McHenney M, McLeaster K, Mundy CW, Nicas TI, Norris FH, O'Gara M, Peery RB, Robertson GT, Rockey P, Sun PM, Winkler ME, Yang Y, Young-Bellido M, Zhao G, Zook CA, Baltz RH, Jaskunas SR, Rosteck PR Jr, Skatrud PL, and Glass JI. Genome of the bacterium Streptococcus pneumoniae strain R6. J Bacteriol 2001 Oct; 183(19) 5709-17. doi:10.1128/JB.183.19.5709-5717.2001 pmid:11544234. PubMed HubMed [hoskins2001]
  14. Fuellen G, Wagele JW, and Giegerich R. Minimum conflict: a divide-and-conquer approach to phylogeny estimation. Bioinformatics 2001 Dec; 17(12) 1168-78. pmid:11751225. PubMed HubMed [fuellen2001]
  15. Riikonen P, Boberg J, Salakoski T, and Vihinen M. BioWAP, mobile Internet service for bioinformatics. Bioinformatics 2001 Sep; 17(9) 855-6. pmid:11590108. PubMed HubMed [biowap]
All Medline abstracts: PubMed HubMed


  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. pmid:11752266. PubMed HubMed [gramene]
  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. pmid:11752248. PubMed HubMed [ensembl2002]
  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. pmid:11860214. PubMed HubMed [reiser2002]
  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 pmid:11839180. PubMed HubMed [roos2002]
  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. pmid:11847086. PubMed HubMed [INCLUSive]
  6. Stein L. Creating a bioinformatics nation. Nature 2002 May 9; 417(6885) 119-20. doi:10.1038/417119a pmid:12000935. PubMed HubMed [stein2002]
  7. Baxevanis AD, Ouellette BFF Bioinformatics (Second Edition) 2001 Wiley & Sons, ISBN:0471223921. [baxevanis2002]
  8. Mangalam HJ. tacg--a grep for DNA. BMC Bioinformatics 2002; 3 8. pmid:11882250. PubMed HubMed [mangalam2002]
  9. Lenhard B and Wasserman WW. TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics 2002 Aug; 18(8) 1135-6. pmid:12176838. PubMed HubMed [TFBS]
  10. Thorisson GA and Stein LD. The SNP Consortium website: past, present and future. Nucleic Acids Res 2003 Jan 1; 31(1) 124-7. pmid:12519964. PubMed HubMed [TSC]
  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 pmid:12194990. PubMed HubMed [birney2002]
  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. pmid:11928485. PubMed HubMed [heil2002]
  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. [moreau2002]
  14. Konagaya A OBIGrid: Towards a New Distributed Platform for Bioinformatics Proceedings of the 21st IEEE Symposium on Reliable Distributed Systems (SRDS'02) 2002. [konagaya]
  15. Loraine AE, Helt G Visualization Techniques for Genomic Data Proceedings of the IEEE Computer Society Conference on Bioinformatics 2002. [loraine2002c]
  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. pmid:15838129. PubMed HubMed [loraine2002a]
  17. Loraine AE and Helt GA. Visualization techniques for genomic data. Proc IEEE Comput Soc Bioinform Conf 2002; 1 321-6. pmid:15838148. PubMed HubMed [loraine2002b]
  18. Salse J, Piegu 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. pmid:12034818. PubMed HubMed [salse2002]
  19. Wilkinson MD and Links M. BioMOBY: an open source biological web services proposal. Brief Bioinform 2002 Dec; 3(4) 331-41. pmid:12511062. PubMed HubMed [biomoby]
  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. pmid:12537570. PubMed HubMed [mungall2002]
  21. Wilkinson MD, Block D, and Crosby WL. Genquire: genome annotation browser/editor. Bioinformatics 2002 Oct; 18(10) 1398-9. pmid:12376386. PubMed HubMed [genquire]
  22. Mangalam H. The Bio* toolkits--a brief overview. Brief Bioinform 2002 Sep; 3(3) 296-302. pmid:12230038. PubMed HubMed [mangalamreview2002]
  23. Matthiessen MW. Affordable biocomputing for everyone: using the Internet, freeware and open-source software. Trends Biochem Sci 2002 Nov; 27(11) 586-8. pmid:12417135. PubMed HubMed [matthiessen2002]
  24. Berezikov E, Plasterk RH, and Cuppen E. GENOTRACE: cDNA-based local GENOme assembly from TRACE archives. Bioinformatics 2002 Oct; 18(10) 1396-7. pmid:12376385. PubMed HubMed [genotrace]
  25. Kivioja T, Arvas M, Kataja K, Penttila M, Soderlund H, and Ukkonen E. Assigning probes into a small number of pools separable by electrophoresis. Bioinformatics 2002; 18 Suppl 1 S199-206. pmid:12169548. PubMed HubMed [kivioja2002]
  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. pmid:12225586. PubMed HubMed [andrade2002]
  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. pmid:12366869. PubMed HubMed [oliz]
  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. pmid:12401134. PubMed HubMed [seqhound]
  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. pmid:12368431. PubMed HubMed [mcadams2002]
  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. pmid:12542244. PubMed HubMed [riikonen2002]
  31. Wong L. Technologies for integrating biological data. Brief Bioinform 2002 Dec; 3(4) 389-404. pmid:12511067. PubMed HubMed [wong2002]
  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. pmid:12537571. PubMed HubMed [harris2002]
All Medline abstracts: PubMed HubMed


  1. Ernst P, Glatting KH, and Suhai S. A task framework for the web interface W2H. Bioinformatics 2003 Jan 22; 19(2) 278-82. pmid:12538250. PubMed HubMed [w2h]
  2. Pan X, Liu H, Clarke J, Jones J, Bevan M, and Stein L. ATIDB: Arabidopsis thaliana insertion database. Nucleic Acids Res 2003 Feb 15; 31(4) 1245-51. pmid:12582244. PubMed HubMed [ATIDB]
  3. Kossenkov A, Manion FJ, Korotkov E, Moloshok TD, and Ochs MF. ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database. Bioinformatics 2003 Mar 22; 19(5) 675-6. pmid:12651736. PubMed HubMed [ASAP]
  4. Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, and Tomita M. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics 2003 Jan 22; 19(2) 305-6. pmid:12538262. PubMed HubMed [G_language]
  5. Jamison DC. Open bioinformatics. Bioinformatics 2003 Apr 12; 19(6) 679-80. pmid:12691978. PubMed HubMed [Jamison2002]
  6. Clarke B, Lambrecht M, and Rhee SY. Arabidopsis genomic information for interpreting wheat EST sequences. Funct Integr Genomics 2003 Mar; 3(1-2) 33-8. doi:10.1007/s10142-002-0075-1 pmid:12590341. PubMed HubMed [clarke2003]
  7. Eckart JD and Sobral BW. A life scientist's gateway to distributed data management and computing: the PathPort/ToolBus framework. OMICS 2003 Spring; 7(1) 79-88. doi:10.1089/153623103322006661 pmid:12831562. PubMed HubMed [eckart2003]
  8. Moriyama M, Hoshida Y, Otsuka M, Nishimura S, Kato N, Goto T, Taniguchi H, Shiratori Y, Seki N, and Omata M. Relevance network between chemosensitivity and transcriptome in human hepatoma cells. Mol Cancer Ther 2003 Feb; 2(2) 199-205. pmid:12589037. PubMed HubMed [moriyama2003]
  9. Macas J, Neumann P, and Pozarkova D. Zaba: a novel miniature transposable element present in genomes of legume plants. Mol Genet Genomics 2003 Aug; 269(5) 624-31. doi:10.1007/s00438-003-0869-4 pmid:12898216. PubMed HubMed [zaba]
  10. Sandelin A, Hoglund A, Lenhard B, and Wasserman WW. Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. Funct Integr Genomics 2003 Jul; 3(3) 125-34. doi:10.1007/s10142-003-0086-6 pmid:12827523. PubMed HubMed [sandelin2003]
  11. Roberg-Perez K, Carlson CM, and Largaespada DA. MTID: a database of Sleeping Beauty transposon insertions in mice. Nucleic Acids Res 2003 Jan 1; 31(1) 78-81. pmid:12519952. PubMed HubMed [mtid]
  12. Sugawara H and Miyazaki S. Biological SOAP servers and web services provided by the public sequence data bank. Nucleic Acids Res 2003 Jul 1; 31(13) 3836-9. pmid:12824432. PubMed HubMed [sugawara2003]
  13. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, and Puhler A. GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 2003 Apr 15; 31(8) 2187-95. pmid:12682369. PubMed HubMed [meyer2003]
  14. Tuggle CK, Green JA, Fitzsimmons C, Woods R, Prather RS, Malchenko S, Soares BM, Kucaba T, Crouch K, Smith C, Tack D, Robinson N, O'Leary B, Scheetz T, Casavant T, Pomp D, Edeal BJ, Zhang Y, Rothschild MF, Garwood K, and Beavis W. EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human. Mamm Genome 2003 Aug; 14(8) 565-79. doi:10.1007/s00335-002-2263-7 pmid:12925889. PubMed HubMed [tuggle2003]
  15. Massey SE, Moura G, Beltrao P, Almeida R, Garey JR, Tuite MF, and Santos MA. Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp. Genome Res 2003 Apr; 13(4) 544-57. doi:10.1101/gr.811003 pmid:12670996. PubMed HubMed [massey2003]
  16. King MW, Nguyen T, Calley J, Harty MW, Muzinich MC, Mescher AL, Chalfant C, N'Cho M, McLeaster K, McEntire J, Stocum D, Smith RC, and Neff AW. Identification of genes expressed during Xenopus laevis limb regeneration by using subtractive hybridization. Dev Dyn 2003 Feb; 226(2) 398-409. doi:10.1002/dvdy.10250 pmid:12557218. PubMed HubMed [king2003]
  17. Gimelli G, Pujana MA, Patricelli MG, Russo S, Giardino D, Larizza L, Cheung J, Armengol L, Schinzel A, Estivill X, and Zuffardi O. Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions. Hum Mol Genet 2003 Apr 15; 12(8) 849-58. pmid:12668608. PubMed HubMed [gimelli2003]
  18. Hoebeke M, Nicolas P, and Bessieres P. MuGeN: simultaneous exploration of multiple genomes and computer analysis results. Bioinformatics 2003 May 1; 19(7) 859-64. pmid:12724296. PubMed HubMed [MuGeN]
  19. Adams MW, Dailey HA, DeLucas LJ, Luo M, Prestegard JH, Rose JP, and Wang BC. The Southeast Collaboratory for Structural Genomics: a high-throughput gene to structure factory. Acc Chem Res 2003 Mar; 36(3) 191-8. doi:10.1021/ar0101382 pmid:12641476. PubMed HubMed [adams2003]
  20. Raymond J, Zhaxybayeva O, Gogarten JP, and Blankenship RE. Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach. Philos Trans R Soc Lond B Biol Sci 2003 Jan 29; 358(1429) 223-30. doi:10.1098/rstb.2002.1181 pmid:12594930. PubMed HubMed [raymond2003]
  21. Yu J, Farjo R, MacNee SP, Baehr W, Stambolian DE, and Swaroop A. Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina. Genome Biol 2003; 4(10) R65. doi:10.1186/gb-2003-4-10-r65 pmid:14519200. PubMed HubMed [yu2003]
  22. Gatherer D and McEwan NR. Analysis of sequence periodicity in E. coli proteins: empirical investigation of the "duplication and divergence" theory of protein evolution. J Mol Evol 2003 Aug; 57(2) 149-58. doi:10.1007/s00239-002-2462-1 pmid:14562959. PubMed HubMed [gatherer2003]
  23. McCallum J and Ganesh S. Text mining of DNA sequence homology searches. Appl Bioinformatics 2003; 2(3 Suppl) S59-63. pmid:15130818. PubMed HubMed [mccallum2003]
  24. Della Vedova G and Dondi R. A library of efficient bioinformatics algorithms. Appl Bioinformatics 2003; 2(2) 117-21. pmid:15130828. PubMed HubMed [della_vedova2003]
  25. Lipovich L and King MC. Novel transcriptional units and unconventional gene pairs in the human genome: toward a sequence-level basis for primate-specific phenotypes?. Cold Spring Harb Symp Quant Biol 2003; 68 461-70. pmid:15338649. PubMed HubMed [lipovich2002]
  26. Paquola AC, Machado AA, Reis EM, Da Silva AM, and Verjovski-Almeida S. Zerg: a very fast BLAST parser library. Bioinformatics 2003 May 22; 19(8) 1035-6. pmid:12761068. PubMed HubMed [zerg]
  27. Della Vedova G and Dondi R. A library of efficient bioinformatics algorithms. Appl Bioinformatics 2003; 2(2) 117-21. pmid:15130828. PubMed HubMed [vedova2003]
  28. Hahn MW, Stajich JE, and Wray GA. The effects of selection against spurious transcription factor binding sites. Mol Biol Evol 2003 Jun; 20(6) 901-6. doi:10.1093/molbev/msg096 pmid:12716998. PubMed HubMed [Hahn2003]
  29. Navarro JD, Niranjan V, Peri S, Jonnalagadda CK, and Pandey A. From biological databases to platforms for biomedical discovery. Trends Biotechnol 2003 Jun; 21(6) 263-8. pmid:12788546. PubMed HubMed [Navarro2003]
  30. Doctor KS, Reed JC, Godzik A, and Bourne PE. The apoptosis database. Cell Death Differ 2003 Jun; 10(6) 621-33. doi:10.1038/sj.cdd.4401230 pmid:12761571. PubMed HubMed [doctor2003]
  31. Moilanen JS and Majamaa K. Phylogenetic network and physicochemical properties of nonsynonymous mutations in the protein-coding genes of human mitochondrial DNA. Mol Biol Evol 2003 Aug; 20(8) 1195-210. doi:10.1093/molbev/msg121 pmid:12777521. PubMed HubMed [moilanen2003]
  32. Lenhard B, Wahlestedt C, and Wasserman WW. GeneLynx mouse: integrated portal to the mouse genome. Genome Res 2003 Jun; 13(6B) 1501-4. doi:10.1101/gr.951403 pmid:12819149. PubMed HubMed [genelynx]
  33. Saunders NF, Thomas T, Curmi PM, Mattick JS, Kuczek E, Slade R, Davis J, Franzmann PD, Boone D, Rusterholtz K, Feldman R, Gates C, Bench S, Sowers K, Kadner K, Aerts A, Dehal P, Detter C, Glavina T, Lucas S, Richardson P, Larimer F, Hauser L, Land M, and Cavicchioli R. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res 2003 Jul; 13(7) 1580-8. doi:10.1101/gr.1180903 pmid:12805271. PubMed HubMed [saunders2003]
  34. Yang G and Hall TC. MAK, a computational tool kit for automated MITE analysis. Nucleic Acids Res 2003 Jul 1; 31(13) 3659-65. pmid:12824388. PubMed HubMed [yang2003]
  35. Nair R and Rost B. LOC3D: annotate sub-cellular localization for protein structures. Nucleic Acids Res 2003 Jul 1; 31(13) 3337-40. pmid:12824321. PubMed HubMed [loc3d]
  36. Goto N, Nakao MC, Kawashima S, Katayama T, Kanehisa M BioRuby: Open-Source Bioinformatics Library 2003 Genome Informatics 14:629-630. [bioruby2003]
  37. Garner HR, Pertsemlidis A Computational biology: biological insight from 1s and 0s 2003 BIOSILIOCO 1(1):27-35. [garner2003]
  38. Lord PW, Stevens RD, Brass A, and Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 2003 Jul 1; 19(10) 1275-83. pmid:12835272. PubMed HubMed [lord2003]
  39. Shah SP, McVicker GP, Mackworth AK, Rogic S, and Ouellette BF. GeneComber: combining outputs of gene prediction programs for improved results. Bioinformatics 2003 Jul 1; 19(10) 1296-7. pmid:12835277. PubMed HubMed [genecomber]
  40. Hoon S, Ratnapu KK, Chia JM, Kumarasamy B, Juguang X, Clamp M, Stabenau A, Potter S, Clarke L, and Stupka E. Biopipe: a flexible framework for protocol-based bioinformatics analysis. Genome Res 2003 Aug; 13(8) 1904-15. doi:10.1101/gr.1363103 pmid:12869579. PubMed HubMed [biopipe]
  41. Janssen P, Enright AJ, Audit B, Cases I, Goldovsky L, Harte N, Kunin V, and Ouzounis CA. COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics 2003 Jul 22; 19(11) 1451-2. pmid:12874064. PubMed HubMed [janseen2003]
  42. Korf I. Serial BLAST searching. Bioinformatics 2003 Aug 12; 19(12) 1492-6. pmid:12912829. PubMed HubMed [serialblast]
  43. Bowen NJ, Jordan IK, Epstein JA, Wood V, and Levin HL. Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe. Genome Res 2003 Sep; 13(9) 1984-97. doi:10.1101/gr.1191603 pmid:12952871. PubMed HubMed [bowen2003]
  44. Cannon SB and Young ND. OrthoParaMap: distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies. BMC Bioinformatics 2003 Sep 2; 4 35. doi:10.1186/1471-2105-4-35 pmid:12952558. PubMed HubMed [orthoparamap]
  45. Carlson CM, Dupuy AJ, Fritz S, Roberg-Perez KJ, Fletcher CF, and Largaespada DA. Transposon mutagenesis of the mouse germline. Genetics 2003 Sep; 165(1) 243-56. pmid:14504232. PubMed HubMed [carlson2003]
  46. Pichon C and Felden B. Intergenic sequence inspector: searching and identifying bacterial RNAs. Bioinformatics 2003 Sep 1; 19(13) 1707-9. pmid:15593399. PubMed HubMed [pichon2003]
  47. Cannon SB, Kozik A, Chan B, Michelmore R, and Young ND. DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization. Genome Biol 2003; 4(10) R68. doi:10.1186/gb-2003-4-10-r68 pmid:14519203. PubMed HubMed [diaghunter]
  48. Allen M, Heinzmann A, Noguchi E, Abecasis G, Broxholme J, Ponting CP, Bhattacharyya S, Tinsley J, Zhang Y, Holt R, Jones EY, Lench N, Carey A, Jones H, Dickens NJ, Dimon C, Nicholls R, Baker C, Xue L, Townsend E, Kabesch M, Weiland SK, Carr D, von Mutius E, Adcock IM, Barnes PJ, Lathrop GM, Edwards M, Moffatt MF, and Cookson WO. Positional cloning of a novel gene influencing asthma from chromosome 2q14. Nat Genet 2003 Nov; 35(3) 258-63. doi:10.1038/ng1256 pmid:14566338. PubMed HubMed [allen2003]
  49. Iacovoni JS. GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genome. Bioinformatics 2003 Nov 22; 19(17) 2316-8. pmid:14630663. PubMed HubMed [genehuggers]
  50. Shah NH, King DC, Shah PN, and Fedoroff NV. A tool-kit for cDNA microarray and promoter analysis. Bioinformatics 2003 Sep 22; 19(14) 1846-8. pmid:14512358. PubMed HubMed [shah2003]
  51. Redmond S, Vadivelu J, and Field MC. RNAit: an automated web-based tool for the selection of RNAi targets in Trypanosoma brucei. Mol Biochem Parasitol 2003 Apr 25; 128(1) 115-8. pmid:12706807. PubMed HubMed [rnait]
  52. Gardy JL, Spencer C, Wang K, Ester M, Tusnady GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, and Brinkman FS. PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res 2003 Jul 1; 31(13) 3613-7. pmid:12824378. PubMed HubMed [psortb]
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All Medline abstracts: PubMed HubMed

Books that use or describe BioPerl

(Note: some of these only mention the toolkit in passing.)

  1. edited by Peter Williams. Methods in microbiology. London: Academic, 1998. isbn:0-125-21525-8. [williams1998]
  2. Rex A. Dwyer. Genomic Perl. Cambridge; Cambridge University Press, 2003. isbn:0-521-80177-X. [dwyer2002]
  3. S. B. Primrose, Richard M. Twyman, Sandy B. Primrose. Principles of Genome Analysis. Blackwell Publishers. isbn:1-405-10120-2. [primrose2002]
  4. Arthur M. Lesk. Introduction to bioinformatics. Oxford; Oxford University Press, 2002. isbn:0-199-25196-7. [lesk2002]
  5. edited by Tushar K. Ghosh... [et al.]. Science and technology of terrorism and counterterrorism. New York: Marcel Dekker, 2002. isbn:0-824-70870-9. [ghosh2002]
  6. Chris Town (Editor). Functional Genomics. Springer. isbn:1-402-00456-7. [town2002]
  7. James D. Tisdall. Beginning Perl for bioinformatics. Beijing; O'Reilly, 2001. isbn:0-596-00080-4. [tisdall2002]
  8. Stephen A., Ph.D. Karwetz (Editor), David D., Ph.D. Womble (Editor). Introduction to Bioinformatics. Humana Press. isbn:1-588-29241-X. [karwetz2003]
  9. James D. Tisdall; foreword by Lincoln Stein. Mastering Perl for bioinformatics. Sebastopol, CA; O'Reilly, 2003. isbn:0-596-00307-2. [tisdall2003]
  10. D. Curtis Jamison. Perl programming for biologists. Hoboken, N.J.: Wiley-Liss, 2003. isbn:0-471-43059-5. [jamison2003]
  11. by Ian Korf, Mark Yandell and Joseph Bedell; [foreword by Stephen Altschul]. BLAST. Sebastopol, CA: O'Reilly & Associates, 2003. isbn:0-596-00299-8. [blast2003]
  12. Giovanni Parmigiani... [et al.] editors. The analysis of gene expression data. New York: Springer-Verlag, 2003. isbn:0-387-95577-1. [parmigiani2003]
  13. Zoe Lacroix, Zoé Lacroix (Editor), Terence Critchlow (Editor). Bioinformatics. Morgan Kaufmann. isbn:1-558-60829-X. [lacroix2003]
  14. David W. Mount. Bioinformatics. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 2004. isbn:0-879-69687-7. [mount2004]
  15. Röbbe Wünschiers, R÷bbe Wnnschiers. Computational Biology. Springer. isbn:3-540-21142-X. [wunschiers2004]
  16. Michael Moorhouse, Paul Barry. Bioinformatics Biocomputing and Perl . John Wiley & Sons. isbn:047085331X. [moorhouse2004]
  17. Olaf R. P. Bininda-Emonds. Phylogenetic Supertrees: Combining Information To Reveal The Tree Of Life. Kluwer Academic Publishers. isbn:1-402-02328-6. [binindaemonds2004]
  18. Arun Jagota. Perl for Bioinformatics, Second Edition. Bioinformatics By The Bay Press. isbn:0-970-02974-8. [jagota2004]
  19. edited by Andreas D. Baxevanis, B. F. Francis Ouellette. Bioinformatics. Hoboken, N.J.: John Wiley, 2005. isbn:0-471-47878-4. [baxevanis_ouellette2004]
  20. Van G. Wilson. Sumoylation: Molecular Biology and Biochemistry. Taylor & Francis. isbn:0-954-52328-8. [wilson2004]
  21. Limsoon Wong (Editor). The Practical Bioinformatician. World Scientific Publishing Company. isbn:9-812-38846-X. [wong2004]
  22. Ethan Cerami. XML for bioinformatics. New York: Springer, 2005. isbn:0-387-23028-9. [cerami2005]
  23. Mike S. Lee. Integrated Strategies for Drug Discovery Using Mass Spectrometry. Wiley-Interscience. isbn:0-471-46127-X. [mikeslee_book2005]
  24. Sudhir Srivastava (Editor). Informatics In Proteomics. CRC. isbn:1-574-44480-8. [Srivastava2005]
  25. [edited by] Sean Ekins. Computer applications in pharmaceutical research and development. Hoboken, N.J.: John Wiley & Sons, 2006. isbn:0-471-73779-8. [elkins_wang2006]
  26. Laurence T. Yang, Minyi Guo. High-Performance Computing . Wiley-Interscience. isbn:0-471-65471-X. [yang_guo2005]
  27. Eugene Thacker. The global genome. Cambridge, Mass.: MIT Press, 2005. isbn:0-262-20155-0. [thacker2005]
  28. Maozhen Li, Mark Baker. The grid. Hoboken, NJ: Wiley, 2005. isbn:0-470-09417-6. [libaker2005]
  29. Christoph W. Sensen (Editor). Handbook of Genome Research . Wiley. isbn:3-527-31348-6. [sensen2005]
  30. Neil A. Winegarden (Editor), PhD, Mark Takahashi (Editor). Promoter and CpG Island Microarrays. Dna Press. isbn:0-974-87656-9. [winegarden2005]
  31. Alan R. Kimmel (Editor), Brian Oliver (Editor). DNA Microarrays, Part B: Databases and Statistics, Volume 411. Academic Press. isbn:0-121-82816-6. [oliver2006]
  32. Andras Falus (Editor). Immunogenomics and Human Disease. John Wiley & Sons. isbn:0-470-01530-6. [falus2006]
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