Publications

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(Publications from 2009: SunEtAl2009)
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#HoldenEtAl2009 pmid=19076238
 
#HoldenEtAl2009 pmid=19076238
 
// Used [[SeqIO|Bio.SeqIO]], [[BioSQL]] and GenomeDiagram
 
// Used [[SeqIO|Bio.SeqIO]], [[BioSQL]] and GenomeDiagram
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#MilesEtAl2009 pmid=19640266
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// Used Biopython to work with genotypes for microsatellite locii
 
#MullerEtAl2009 pmid=19583843
 
#MullerEtAl2009 pmid=19583843
 
#NarayananEtAl pmid=19324053
 
#NarayananEtAl pmid=19324053

Revision as of 10:49, 20 August 2009

There is a separate shorter listing of Biopython papers you may wish to cite.

This is a list of papers citing, referencing or using Biopython, by year sorted alphabetically by author. In many cases these citations are just via the website, which is now discouraged with the publication of the Biopython application note [1]. Regrettably, in some cases the manuscripts themselves do not directly mention Biopython, but this has been confirmed explicitly by an author.

Contents

Publications from 2009

  1. Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, and de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3. doi:10.1093/bioinformatics/btp163 pmid:19304878. PubMed HubMed [CockEtAl2009]
    This application note covers the whole of Biopython
  2. Banach M, Stapor K, and Roterman I. Chaperonin structure: the large multi-subunit protein complex. Int J Mol Sci 2009 Mar; 10(3) 844-61. doi:10.3390/ijms10030844 pmid:19399224. PubMed HubMed [BanachEtAl2009]
    Used Bio.PDB and Bio.KDTree
  3. Chi SW, Zang JB, Mele A, and Darnell RB. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 2009 Jul 23; 460(7254) 479-86. doi:10.1038/nature08170 pmid:19536157. PubMed HubMed [ChiEtAl2009]
    General bioinformatics analysis including in silico random CLIP (crosslinking immunoprecipitation)
  4. Cox CJ, Foster PG, Hirt RP, Harris SR, and Embley TM. The archaebacterial origin of eukaryotes. Proc Natl Acad Sci U S A 2008 Dec 23; 105(51) 20356-61. doi:10.1073/pnas.0810647105 pmid:19073919. PubMed HubMed [CoxEtAl2009]
    Used Bio.Blast, Bio.Fasta, & Bio.Nexus
  5. Daily MD and Gray JJ. Allosteric communication occurs via networks of tertiary and quaternary motions in proteins. PLoS Comput Biol 2009 Feb; 5(2) e1000293. doi:10.1371/journal.pcbi.1000293 pmid:19229311. PubMed HubMed [DailyEtAl2009]
    Used Bio.SVDSuperimposer (and probably Bio.PDB as well)
  6. Garbino A, van Oort RJ, Dixit SS, Landstrom AP, Ackerman MJ, and Wehrens XH. Molecular evolution of the junctophilin gene family. Physiol Genomics 2009 May 13; 37(3) 175-86. doi:10.1152/physiolgenomics.00017.2009 pmid:19318539. PubMed HubMed [GarbinoEtAl2009]
  7. Holden N, Pritchard L, and Toth I. Colonization outwith the colon: plants as an alternative environmental reservoir for human pathogenic enterobacteria. FEMS Microbiol Rev 2009 Jul; 33(4) 689-703. doi:10.1111/j.1574-6976.2008.00153.x pmid:19076238. PubMed HubMed [HoldenEtAl2009]
    Used Bio.SeqIO, BioSQL and GenomeDiagram
  8. Miles LG, Isberg SR, Glenn TC, Lance SL, Dalzell P, Thomson PC, and Moran C. A genetic linkage map for the saltwater crocodile (Crocodylus porosus). BMC Genomics 2009 Jul 29; 10 339. doi:10.1186/1471-2164-10-339 pmid:19640266. PubMed HubMed [MilesEtAl2009]
    Used Biopython to work with genotypes for microsatellite locii
  9. Muller B, Richards AJ, Jin B, and Lu X. GOGrapher: A Python library for GO graph representation and analysis. BMC Res Notes 2009 Jul 7; 2 122. doi:10.1186/1756-0500-2-122 pmid:19583843. PubMed HubMed [MullerEtAl2009]
  10. Narayanan A, Sellers BD, and Jacobson MP. Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains. J Mol Biol 2009 May 22; 388(5) 941-53. doi:10.1016/j.jmb.2009.03.043 pmid:19324053. PubMed HubMed [NarayananEtAl]
    Used Bio.SVDSuperimposer (and probably Bio.PDB as well)
  11. Schanda P. 2009. Fast-pulsing longitudinal relaxation optimized techniques: Enriching the toolbox of fast biomolecular NMR spectroscopy. Progress in Nuclear Magnetic Resonance Spectroscopy: 'In press' doi:10.1016/j.pnmrs.2009.05.002 [Schanda2009]
    Used Bio.PDB
  12. Smith SA, Beaulieu JM, and Donoghue MJ. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol Biol 2009 Feb 11; 9 37. doi:10.1186/1471-2148-9-37 pmid:19210768. PubMed HubMed [SmithEtAl2009]
    Used Biopython to implement a pipeline with BioSQL
  13. Sun C, Wang X, Lin L. 2009. A Multi-level Disambiguation Framework for Gene Name Normalization. Acta Automatica Sinica 2009 Feb; 35(2) 193-197. doi:10.1016/S1874-1029(08)60073-7 [SunEtAl2009]
    Used Biopython to access MEDLINE
  14. Tanaka LY, Herskovic JR, Iyengar MS, and Bernstam EV. Sequential result refinement for searching the biomedical literature. J Biomed Inform 2009 Aug; 42(4) 678-84. doi:10.1016/j.jbi.2009.02.009 pmid:19272463. PubMed HubMed [TanakaEtAl2009]
    Used Biopython to access MEDLINE
  15. Torrance GM, Leader DP, Gilbert DR, and Milner-White EJ. A novel main chain motif in proteins bridged by cationic groups: the niche. J Mol Biol 2009 Jan 30; 385(4) 1076-86. doi:10.1016/j.jmb.2008.11.007 pmid:19038265. PubMed HubMed [TorranceEtAl2009]
    Used Biopython for the k-means algorithm
  16. Wiwanitkit V. FHM3 in familial hemiplegic migraine is more resistant to mutation than FHM1 and FHM2. J Neurol Sci 2009 Feb 15; 277(1-2) 76-9. doi:10.1016/j.jns.2008.10.012 pmid:19007941. PubMed HubMed [Wiwanitkit2009a]
    Used Biopython to work with ExPASy
  17. Wiwanitkit V. Weak linkage in androgen receptor: identification of mutation-prone points. Fertil Steril 2009 Jan; 91(1) e1-3. doi:10.1016/j.fertnstert.2007.06.089 pmid:17936280. PubMed HubMed [Wiwanitkit2009b]
    Used Biopython to work with ExPASy
All Medline abstracts: PubMed HubMed

Publications from 2008

  1. Antao T, Lopes A, Lopes RJ, Beja-Pereira A, and Luikart G. LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 2008 Jul 28; 9 323. doi:10.1186/1471-2105-9-323 pmid:18662398. PubMed HubMed [AntaoEtAl2008]
    Used Bio.PopGen
  2. Cardona G, Rosselló F, and Valiente G. Extended Newick: it is time for a standard representation of phylogenetic networks. BMC Bioinformatics 2008 Dec 15; 9 532. doi:10.1186/1471-2105-9-532 pmid:19077301. PubMed HubMed [CardonaEtAl2008]
  3. Diella F, Gould CM, Chica C, Via A, and Gibson TJ. Phospho.ELM: a database of phosphorylation sites--update 2008. Nucleic Acids Res 2008 Jan; 36(Database issue) D240-4. doi:10.1093/nar/gkm772 pmid:17962309. PubMed HubMed [DiellaEtAl2008]
    Used with UniProt and PubMed
  4. Faircloth BC. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources 2008; 8(1) 92-94. doi:10.1111/j.1471-8286.2007.01884.x [Faircloth2008]
    Used Bio.SeqIO
  5. Feldhahn M, Thiel P, Schuler MM, Hillen N, Stevanovic S, Rammensee HG, and Kohlbacher O. EpiToolKit--a web server for computational immunomics. Nucleic Acids Res 2008 Jul 1; 36(Web Server issue) W519-22. doi:10.1093/nar/gkn229 pmid:18440979. PubMed HubMed [FeldhahnEtAl2008]
    Used Biopython for several unspecified tasks
  6. Fourment M and Gillings MR. A comparison of common programming languages used in bioinformatics. BMC Bioinformatics 2008 Feb 5; 9 82. doi:10.1186/1471-2105-9-82 pmid:18251993. PubMed HubMed [FourmentAndGillings2008]
  7. Frelinger J, Kepler TB, and Chan C. Flow: Statistics, visualization and informatics for flow cytometry. Source Code Biol Med 2008 Jun 17; 3 10. doi:10.1186/1751-0473-3-10 pmid:18559108. PubMed HubMed [FrelingerEtAl2008]
    Used PyCluster / Bio.Cluster
  8. Geraci F, Pellegrini M, and Renda ME. AMIC@: All MIcroarray Clusterings @ once. Nucleic Acids Res 2008 Jul 1; 36(Web Server issue) W315-9. doi:10.1093/nar/gkn265 pmid:18477631. PubMed HubMed [GeraciEtAl2008]
    Used PyCluster / Bio.Cluster and other unspecified parts of Biopython
  9. Gront D and Kolinski A. Utility library for structural bioinformatics. Bioinformatics 2008 Feb 15; 24(4) 584-5. doi:10.1093/bioinformatics/btm627 pmid:18227118. PubMed HubMed [GrontAndKolinski2008]
  10. Higa RH and Tozzi CL. A simple and efficient method for predicting protein-protein interaction sites. Genet Mol Res 2008 Sep 23; 7(3) 898-909. pmid:18949708. PubMed HubMed [HigaAndTozzi2008]
    Used Bio.PDB
  11. Kim N and Lee C. Bioinformatics detection of alternative splicing. Methods Mol Biol 2008; 452 179-97. doi:10.1007/978-1-60327-159-2_9 pmid:18566765. PubMed HubMed [KimAndLee2008]
  12. Langkilde A, Kristensen SM, Lo Leggio L, Mølgaard A, Jensen JH, Houk AR, Navarro Poulsen JC, Kauppinen S, and Larsen S. Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase. Acta Crystallogr D Biol Crystallogr 2008 Aug; D64(Pt 8) 851-63. doi:10.1107/S0907444908017083 pmid:18645234. PubMed HubMed [LangkildeEtAl2008]
    Used Bio.PDB
  13. Koczyk G and Berezovsky IN. Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure. Nucleic Acids Res 2008 Jul 1; 36(Web Server issue) W239-45. doi:10.1093/nar/gkn326 pmid:18502776. PubMed HubMed [KoczykAndBerezovsky2008]
    Used Bio.PDB
  14. Munteanu CR, González-Díaz H, and Magalhães AL. Enzymes/non-enzymes classification model complexity based on composition, sequence, 3D and topological indices. J Theor Biol 2008 Sep 21; 254(2) 476-82. doi:10.1016/j.jtbi.2008.06.003 pmid:18606172. PubMed HubMed [MunteanuEtAl2008]
    Used Bio.PDB
  15. Park D, Kim BC, Cho SW, Park SJ, Choi JS, Kim SI, Bhak J, and Lee S. MassNet: a functional annotation service for protein mass spectrometry data. Nucleic Acids Res 2008 Jul 1; 36(Web Server issue) W491-5. doi:10.1093/nar/gkn241 pmid:18448467. PubMed HubMed [ParkEtAl2008]
    Used Biopython to calculate hydropathy profiles
  16. Ponty Y, Istrate R, Porcelli E, and Clote P. LocalMove: computing on-lattice fits for biopolymers. Nucleic Acids Res 2008 Jul 1; 36(Web Server issue) W216-22. doi:10.1093/nar/gkn367 pmid:18556754. PubMed HubMed [PontyEtAl2008]
    Used Biopython to work with lattice structures, including superimposition.
  17. Raman K, Yeturu K, and Chandra N. targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC Syst Biol 2008 Dec 19; 2 109. doi:10.1186/1752-0509-2-109 pmid:19099550. PubMed HubMed [RamanEtAl2008]
    Used Bio.Blast
  18. Singh S. India takes an open source approach to drug discovery. Cell 2008 Apr 18; 133(2) 201-3. doi:10.1016/j.cell.2008.04.003 pmid:18423188. PubMed HubMed [SinghEtAl2008]
  19. Song J, Tan H, Takemoto K, and Akutsu T. HSEpred: predict half-sphere exposure from protein sequences. Bioinformatics 2008 Jul 1; 24(13) 1489-97. doi:10.1093/bioinformatics/btn222 pmid:18467349. PubMed HubMed [SongEtAl2008]
    Used Bio.PDB
  20. Southey BR, Sweedler JV, and Rodriguez-Zas SL. A python analytical pipeline to identify prohormone precursors and predict prohormone cleavage sites. Front Neuroinform 2008; 2 7. doi:10.3389/neuro.11.007.2008 pmid:19169350. PubMed HubMed [SoutheyEtAl2008]
  21. Walters J, Binkley E, Haygood R, and Romano LA. Evolutionary analysis of the cis-regulatory region of the spicule matrix gene SM50 in strongylocentrotid sea urchins. Dev Biol 2008 Mar 15; 315(2) 567-78. doi:10.1016/j.ydbio.2008.01.007 pmid:18262514. PubMed HubMed [WaltersEtAl2008]
    Used Biopython for sequence manipulation
  22. Whitworth DE and Cock PJ. Two-component systems of the myxobacteria: structure, diversity and evolutionary relationships. Microbiology 2008 Feb; 154(Pt 2) 360-72. doi:10.1099/mic.0.2007/013672-0 pmid:18227240. PubMed HubMed [WhitworthAndCock2008]
    Used Bio.SeqIO, Bio.AlignIO and Bio.Blast
  23. Wiwanitkit V. Identification of weak points prone for mutation in ferredoxin of Trichomonas vaginalis. Indian J Med Microbiol 2008 Apr-Jun; 26(2) 158-9. pmid:18445954. PubMed HubMed [Wiwanitkit2008a]
    Used Biopython for working with ExPASy
  24. Wiwanitkit V. Mutation-prone points in thrombin receptor. J Thromb Thrombolysis 2008 Apr; 25(2) 190-2. doi:10.1007/s11239-007-0167-9 pmid:18064407. PubMed HubMed [Wiwanitkit2008b]
    Used Biopython for working with ExPASy
All Medline abstracts: PubMed HubMed

Publications from 2007

  1. Antao T, Beja-Pereira A, and Luikart G. MODELER4SIMCOAL2: a user-friendly, extensible modeler of demography and linked loci for coalescent simulations. Bioinformatics 2007 Jul 15; 23(14) 1848-50. doi:10.1093/bioinformatics/btm243 pmid:17488756. PubMed HubMed [AntaoEtAl2007]
  2. Avrova AO, Whisson SC, Pritchard L, Venter E, De Luca S, Hein I, and Birch PR. A novel non-protein-coding infection-specific gene family is clustered throughout the genome of Phytophthora infestans. Microbiology 2007 Mar; 153(Pt 3) 747-59. doi:10.1099/mic.0.2006/002220-0 pmid:17322195. PubMed HubMed [AvrovaEtAl2007]
  3. Bassi S. A primer on python for life science researchers. PLoS Comput Biol 2007 Nov; 3(11) e199. doi:10.1371/journal.pcbi.0030199 pmid:18052533. PubMed HubMed [Bassi2007]
  4. Bernauer J, Azé J, Janin J, and Poupon A. A new protein-protein docking scoring function based on interface residue properties. Bioinformatics 2007 Mar 1; 23(5) 555-62. doi:10.1093/bioinformatics/btl654 pmid:17237048. PubMed HubMed [BernauerEtAl2007]
  5. Domingues FS, Rahnenführer J, and Lengauer T. Conformational analysis of alternative protein structures. Bioinformatics 2007 Dec 1; 23(23) 3131-8. doi:10.1093/bioinformatics/btm499 pmid:17933849. PubMed HubMed [DominguesEtAl2007]
  6. Chapman MA, Chang J, Weisman D, Kesseli RV, and Burke JM. Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae). Theor Appl Genet 2007 Oct; 115(6) 747-55. doi:10.1007/s00122-007-0605-2 pmid:17634914. PubMed HubMed [ChapmanEtAl2007]
  7. Cock PJ and Whitworth DE. Evolution of gene overlaps: relative reading frame bias in prokaryotic two-component system genes. J Mol Evol 2007 Apr; 64(4) 457-62. doi:10.1007/s00239-006-0180-1 pmid:17479344. PubMed HubMed [CockAndWhitworth2007a]
  8. Cock PJ and Whitworth DE. Evolution of prokaryotic two-component system signaling pathways: gene fusions and fissions. Mol Biol Evol 2007 Nov; 24(11) 2355-7. doi:10.1093/molbev/msm170 pmid:17709334. PubMed HubMed [CockAndWhitworth2007b]
  9. Craddock T, Harwood CR, Hallinan J, and Wipat A. e-Science: relieving bottlenecks in large-scale genome analyses. Nat Rev Microbiol 2008 Dec; 6(12) 948-54. doi:10.1038/nrmicro2031 pmid:19008893. PubMed HubMed [CraddockEtAl2008]
  10. Ferrè F, Ponty Y, Lorenz WA, and Clote P. DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. Nucleic Acids Res 2007 Jul; 35(Web Server issue) W659-68. doi:10.1093/nar/gkm334 pmid:17567620. PubMed HubMed [FerreEtAl2007]
  11. Gentle IE, Perry AJ, Alcock FH, Likić VA, Dolezal P, Ng ET, Purcell AW, McConnville M, Naderer T, Chanez AL, Charrière F, Aschinger C, Schneider A, Tokatlidis K, and Lithgow T. Conserved motifs reveal details of ancestry and structure in the small TIM chaperones of the mitochondrial intermembrane space. Mol Biol Evol 2007 May; 24(5) 1149-60. doi:10.1093/molbev/msm031 pmid:17329230. PubMed HubMed [GentleEtAl2007]
  12. Grünberg R, Nilges M, and Leckner J. Biskit--a software platform for structural bioinformatics. Bioinformatics 2007 Mar 15; 23(6) 769-70. doi:10.1093/bioinformatics/btl655 pmid:17237072. PubMed HubMed [GrunbergEtAl2997]
  13. Hackney JA, Ehrenkaufer GM, and Singh U. Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference. Nucleic Acids Res 2007; 35(7) 2141-52. doi:10.1093/nar/gkm028 pmid:17355990. PubMed HubMed [HackneyEtAl2007]
    Describes the Bio.MEME module
  14. Kauff F, Cox CJ, and Lutzoni F. WASABI: an automated sequence processing system for multigene phylogenies. Syst Biol 2007 Jun; 56(3) 523-31. doi:10.1080/10635150701395340 pmid:17562476. PubMed HubMed [KauffEtAl2007]
  15. Ma BG, Chen LL, and Zhang HY. What determines protein folding type? An investigation of intrinsic structural properties and its implications for understanding folding mechanisms. J Mol Biol 2007 Jul 13; 370(3) 439-48. doi:10.1016/j.jmb.2007.04.051 pmid:17524416. PubMed HubMed [MaEtAl2007]
  16. Picardi E, Regina TM, Brennicke A, and Quagliariello C. REDIdb: the RNA editing database. Nucleic Acids Res 2007 Jan; 35(Database issue) D173-7. doi:10.1093/nar/gkl793 pmid:17175530. PubMed HubMed [PicardiEtAl2007]
  17. Pietal MJ, Tuszynska I, and Bujnicki JM. PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure. Bioinformatics 2007 Jun 1; 23(11) 1429-30. doi:10.1093/bioinformatics/btm124 pmid:17400727. PubMed HubMed [PietalEtAl2007]
  18. Rattei T, Ott S, Gutacker M, Rupp J, Maass M, Schreiber S, Solbach W, Wirth T, and Gieffers J. Genetic diversity of the obligate intracellular bacterium Chlamydophila pneumoniae by genome-wide analysis of single nucleotide polymorphisms: evidence for highly clonal population structure. BMC Genomics 2007 Oct 4; 8 355. doi:10.1186/1471-2164-8-355 pmid:17916241. PubMed HubMed [RatteiEtAl2007]
  19. Sander O, Sing T, Sommer I, Low AJ, Cheung PK, Harrigan PR, Lengauer T, and Domingues FS. Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Comput Biol 2007 Mar 30; 3(3) e58. doi:10.1371/journal.pcbi.0030058 pmid:17397254. PubMed HubMed [SanderEtAl2007]
  20. Tagami Y, Inaba N, Kutsuna N, Kurihara Y, and Watanabe Y. Specific enrichment of miRNAs in Arabidopsis thaliana infected with Tobacco mosaic virus. DNA Res 2007 Oct 31; 14(5) 227-33. doi:10.1093/dnares/dsm022 pmid:18056073. PubMed HubMed [TagamiEtAl2007]
  21. Watanabe H, Enomoto T, and Tanaka S. Ab initio study of molecular interactions in higher plant and Galdieria partita Rubiscos with the fragment molecular orbital method. Biochem Biophys Res Commun 2007 Sep 21; 361(2) 367-72. doi:10.1016/j.bbrc.2007.07.004 pmid:17651697. PubMed HubMed [WatanabeEtAl2007]
  22. Whisson SC, Boevink PC, Moleleki L, Avrova AO, Morales JG, Gilroy EM, Armstrong MR, Grouffaud S, van West P, Chapman S, Hein I, Toth IK, Pritchard L, and Birch PR. A translocation signal for delivery of oomycete effector proteins into host plant cells. Nature 2007 Nov 1; 450(7166) 115-8. doi:10.1038/nature06203 pmid:17914356. PubMed HubMed [WhissonEtAl2007]
  23. Won KJ, Hamelryck T, Prügel-Bennett A, and Krogh A. An evolutionary method for learning HMM structure: prediction of protein secondary structure. BMC Bioinformatics 2007 Sep 21; 8 357. doi:10.1186/1471-2105-8-357 pmid:17888163. PubMed HubMed [WonEtAl2007]
All Medline abstracts: PubMed HubMed

Publications from 2006

  1. Benita Y, Wise MJ, Lok MC, Humphery-Smith I, and Oosting RS. Analysis of high throughput protein expression in Escherichia coli. Mol Cell Proteomics 2006 Sep; 5(9) 1567-80. doi:10.1074/mcp.M600140-MCP200 pmid:16822774. PubMed HubMed [BenitaEtAl2006]
    This describes some of the Bio.SeqUtils module
  2. Bonis J, Furlong LI, and Sanz F. OSIRIS: a tool for retrieving literature about sequence variants. Bioinformatics 2006 Oct 15; 22(20) 2567-9. doi:10.1093/bioinformatics/btl421 pmid:16882651. PubMed HubMed [BonisEtAl2006]
  3. Casbon JA, Crooks GE, and Saqi MA. A high level interface to SCOP and ASTRAL implemented in python. BMC Bioinformatics 2006 Jan 10; 7 10. doi:10.1186/1471-2105-7-10 pmid:16403221. PubMed HubMed [CasbonEtAl2006]
    Describes additions to the Bio.SCOP module
  4. Croce O, Lamarre M, and Christen R. Querying the public databases for sequences using complex keywords contained in the feature lines. BMC Bioinformatics 2006 Jan 27; 7 45. doi:10.1186/1471-2105-7-45 pmid:16441875. PubMed HubMed [CroceEtAl2006]
  5. Ferreira AO, Myers CR, Gordon JS, Martin GB, Vencato M, Collmer A, Wehling MD, Alfano JR, Moreno-Hagelsieb G, Lamboy WF, DeClerck G, Schneider DJ, and Cartinhour SW. Whole-genome expression profiling defines the HrpL regulon of Pseudomonas syringae pv. tomato DC3000, allows de novo reconstruction of the Hrp cis clement, and identifies novel coregulated genes. Mol Plant Microbe Interact 2006 Nov; 19(11) 1167-79. doi:10.1094/MPMI-19-1167 pmid:17073300. PubMed HubMed [FerreiraEtAl2006]
  6. Friedberg I, Harder T, and Godzik A. JAFA: a protein function annotation meta-server. Nucleic Acids Res 2006 Jul 1; 34(Web Server issue) W379-81. doi:10.1093/nar/gkl045 pmid:16845030. PubMed HubMed [FriedbergEtAl2006]
  7. Gront D and Kolinski A. BioShell--a package of tools for structural biology computations. Bioinformatics 2006 Mar 1; 22(5) 621-2. doi:10.1093/bioinformatics/btk037 pmid:16407320. PubMed HubMed [GrontAndKolinski2006]
  8. Hegedűs T and Riordan JR. Search for proteins with similarity to the CFTR R domain using an optimized RDBMS solution, mBioSQL. Central European Journal of Biology 2006; 1(1) 29-42. doi:10.2478/s11535-006-0003-9 [HegedusAndRiordan2006]
  9. Lee KT, Park EW, Moon S, Park HS, Kim HY, Jang GW, Choi BH, Chung HY, Lee JW, Cheong IC, Oh SJ, Kim H, Suh DS, and Kim TH. Genomic sequence analysis of a potential QTL region for fat trait on pig chromosome 6. Genomics 2006 Feb; 87(2) 218-24. doi:10.1016/j.ygeno.2005.09.002 pmid:16326071. PubMed HubMed [LeeEtAl2006]
  10. Mattingly CJ, Rosenstein MC, Davis AP, Colby GT, Forrest JN Jr, and Boyer JL. The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks. Toxicol Sci 2006 Aug; 92(2) 587-95. doi:10.1093/toxsci/kfl008 pmid:16675512. PubMed HubMed [MattinglyEtAl2006]
  11. Munos B. Can open-source R&D reinvigorate drug research?. Nat Rev Drug Discov 2006 Sep; 5(9) 723-9. doi:10.1038/nrd2131 pmid:16915233. PubMed HubMed [Munos2006]
  12. Nilsen et al. Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence. Animal Genetics 2008; 39(2) 97-104 doi:10.1111/j.1365-2052.2007.01686.x [NilsenEtAl2006]
  13. Pritchard L, White JA, Birch PR, and Toth IK. GenomeDiagram: a python package for the visualization of large-scale genomic data. Bioinformatics 2006 Mar 1; 22(5) 616-7. doi:10.1093/bioinformatics/btk021 pmid:16377612. PubMed HubMed [PritchardEtAl2006]
    This describes GenomeDiagram, now part of the Bio.Graphics module
  14. Stajich JE and Lapp H. Open source tools and toolkits for bioinformatics: significance, and where are we?. Brief Bioinform 2006 Sep; 7(3) 287-96. doi:10.1093/bib/bbl026 pmid:16899494. PubMed HubMed [StajichAndLapp2006]
  15. Taylor J and Provart NJ. CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping. BMC Genet 2006 May 10; 7 27. doi:10.1186/1471-2156-7-27 pmid:16686952. PubMed HubMed [TaylorAndProvart2006]
    This describes the Bio.CAPS module.
  16. Ternes P, Sperling P, Albrecht S, Franke S, Cregg JM, Warnecke D, and Heinz E. Identification of fungal sphingolipid C9-methyltransferases by phylogenetic profiling. J Biol Chem 2006 Mar 3; 281(9) 5582-92. doi:10.1074/jbc.M512864200 pmid:16339149. PubMed HubMed [TernesEtAl2006]
  17. Toth IK, Pritchard L, and Birch PR. Comparative genomics reveals what makes an enterobacterial plant pathogen. Annu Rev Phytopathol 2006; 44 305-36. doi:10.1146/annurev.phyto.44.070505.143444 pmid:16704357. PubMed HubMed [TothEtAl2006]
  18. Windsor AJ, Schranz ME, Formanová N, Gebauer-Jung S, Bishop JG, Schnabelrauch D, Kroymann J, and Mitchell-Olds T. Partial shotgun sequencing of the Boechera stricta genome reveals extensive microsynteny and promoter conservation with Arabidopsis. Plant Physiol 2006 Apr; 140(4) 1169-82. doi:10.1104/pp.105.073981 pmid:16607030. PubMed HubMed [WindsorEtAl2006]
  19. Wuchty S. Topology and weights in a protein domain interaction network--a novel way to predict protein interactions. BMC Genomics 2006 May 23; 7 122. doi:10.1186/1471-2164-7-122 pmid:16716232. PubMed HubMed [Wuchty2006]
  20. Zapala MA and Schork NJ. Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables. Proc Natl Acad Sci U S A 2006 Dec 19; 103(51) 19430-5. doi:10.1073/pnas.0609333103 pmid:17146048. PubMed HubMed [ZapalaEtAl2006]
  21. Zotenko E, O'Leary DP, and Przytycka TM. Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification. BMC Struct Biol 2006 Jun 8; 6 12. doi:10.1186/1472-6807-6-12 pmid:16762072. PubMed HubMed [ZotenkoEtAl2006]
All Medline abstracts: PubMed HubMed

Publications from 2005

  1. Toth IK, Pritchard L, and Birch PR. Comparative genomics reveals what makes an enterobacterial plant pathogen. Annu Rev Phytopathol 2006; 44 305-36. doi:10.1146/annurev.phyto.44.070505.143444 pmid:16704357. PubMed HubMed [TothEtAl2006]
  2. Boomsma W and Hamelryck T. Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. BMC Bioinformatics 2005 Jun 28; 6 159. doi:10.1186/1471-2105-6-159 pmid:15985178. PubMed HubMed [BoomsmaAndHamelryck2005]
  3. Armstrong MR, et al. An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. Proc Natl Acad Sci U S A 2005 May 24; 102(21) 7766-71. doi:10.1073/pnas.0500113102 pmid:15894622. PubMed HubMed [ArmstrongEtAl2005]
  4. Curk T, Demsar J, Xu Q, Leban G, Petrovic U, Bratko I, Shaulsky G, and Zupan B. Microarray data mining with visual programming. Bioinformatics 2005 Feb 1; 21(3) 396-8. doi:10.1093/bioinformatics/bth474 pmid:15308546. PubMed HubMed [CurkEtAl2005]
  5. Dimmic MW, Hubisz MJ, Bustamante CD, and Nielsen R. Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics 2005 Jun; 21 Suppl 1 i126-35. doi:10.1093/bioinformatics/bti1032 pmid:15961449. PubMed HubMed [DimmicEtAl2005]
  6. Feder M and Bujnicki JM. Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site. BMC Genomics 2005 Feb 18; 6 21. doi:10.1186/1471-2164-6-21 pmid:15720711. PubMed HubMed [FederAndBujnicki2005]
  7. Friedberg I and Godzik A. Fragnostic: walking through protein structure space. Nucleic Acids Res 2005 Jul 1; 33(Web Server issue) W249-51. doi:10.1093/nar/gki363 pmid:15980462. PubMed HubMed [FriedbergEtAl2005]
  8. Herskovic JR and Bernstam EV. Using incomplete citation data for MEDLINE results ranking. AMIA Annu Symp Proc 2005 316-20. pmid:16779053. PubMed HubMed [HerskovicAndBernstam2005]
  9. Hamelryck T. An amino acid has two sides: a new 2D measure provides a different view of solvent exposure. Proteins 2005 Apr 1; 59(1) 38-48. doi:10.1002/prot.20379 pmid:15688434. PubMed HubMed [Hamelryck2005]
  10. Johannessen BR, Skov LK, Kastrup JS, Kristensen O, Bolwig C, Larsen JN, Spangfort M, Lund K, and Gajhede M. Structure of the house dust mite allergen Der f 2: implications for function and molecular basis of IgE cross-reactivity. FEBS Lett 2005 Feb 14; 579(5) 1208-12. doi:10.1016/j.febslet.2004.11.115 pmid:15710415. PubMed HubMed [JohannessenEtAl2005]
  11. Majumdar I, Krishna SS, and Grishin NV. PALSSE: a program to delineate linear secondary structural elements from protein structures. BMC Bioinformatics 2005 Aug 11; 6 202. doi:10.1186/1471-2105-6-202 pmid:16095538. PubMed HubMed [MajumdarEtAl2005]
  12. Neerincx PB and Leunissen JA. Evolution of web services in bioinformatics. Brief Bioinform 2005 Jun; 6(2) 178-88. pmid:15975226. PubMed HubMed [NeerincxAndLeunissen2005]
  13. Olsen HG, Lien S, Gautier M, Nilsen H, Roseth A, Berg PR, Sundsaasen KK, Svendsen M, and Meuwissen TH. Mapping of a milk production quantitative trait locus to a 420-kb region on bovine chromosome 6. Genetics 2005 Jan; 169(1) 275-83. doi:10.1534/genetics.104.031559 pmid:15466433. PubMed HubMed [OlsenEtAl2005]
  14. Trissl S, Rother K, Müller H, Steinke T, Koch I, Preissner R, Frömmel C, and Leser U. Columba: an integrated database of proteins, structures, and annotations. BMC Bioinformatics 2005 Mar 31; 6 81. doi:10.1186/1471-2105-6-81 pmid:15801979. PubMed HubMed [TrisslEtAl2005]
  15. Whisson SC, Avrova AO, Lavrova O, and Pritchard L. Families of short interspersed elements in the genome of the oomycete plant pathogen, Phytophthora infestans. Fungal Genet Biol 2005 Apr; 42(4) 351-65. doi:10.1016/j.fgb.2005.01.004 pmid:15749054. PubMed HubMed [WhissonEtAl2005]
All Medline abstracts: PubMed HubMed

Publications from 2004

  1. Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ, Holeva MC, Thomson NR, Bentley SD, Churcher LJ, Mungall K, Atkin R, Bason N, Brooks K, Chillingworth T, Clark K, Doggett J, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Norbertczak H, Ormond D, Price C, Quail MA, Sanders M, Walker D, Whitehead S, Salmond GP, Birch PR, Parkhill J, and Toth IK. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc Natl Acad Sci U S A 2004 Jul 27; 101(30) 11105-10. doi:10.1073/pnas.0402424101 pmid:15263089. PubMed HubMed [BellEtAl2004]
  2. Chapman BA, Bowers JE, Schulze SR, and Paterson AH. A comparative phylogenetic approach for dating whole genome duplication events. Bioinformatics 2004 Jan 22; 20(2) 180-5. pmid:14734308. PubMed HubMed [ChapmanEtAl2004]
  3. Flanagan K, Stevens R, Pocock M, Lee P, and Wipat A. Ontology for genome comparison and genomic rearrangements. Comp Funct Genomics 2004; 5(6-7) 537-44. doi:10.1002/cfg.436 pmid:18629137. PubMed HubMed [FlanaganEtAl2004]
  4. de Hoon MJ, Imoto S, Nolan J, and Miyano S. Open source clustering software. Bioinformatics 2004 Jun 12; 20(9) 1453-4. doi:10.1093/bioinformatics/bth078 pmid:14871861. PubMed HubMed [DeHoonEtAl2004]
    This describes the Bio.Cluster module
  5. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, and Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004; 5(10) R80. doi:10.1186/gb-2004-5-10-r80 pmid:15461798. PubMed HubMed [GentlemanEtAl2004]
  6. King GJ. Bioinformatics: harvesting information for plant and crop science. Semin Cell Dev Biol 2004 Dec; 15(6) 721-31. doi:10.1016/j.semcdb.2004.09.006 pmid:15561592. PubMed HubMed [King2004]
  7. Swart EC, Hide WA, and Seoighe C. FRAGS: estimation of coding sequence substitution rates from fragmentary data. BMC Bioinformatics 2004 Jan 29; 5 8. doi:10.1186/1471-2105-5-8 pmid:15005802. PubMed HubMed [SwartEtAl2004]
All Medline abstracts: PubMed HubMed

Publications from 2003

  1. Bowers JE, Chapman BA, Rong J, and Paterson AH. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 2003 Mar 27; 422(6930) 433-8. doi:10.1038/nature01521 pmid:12660784. PubMed HubMed [BowersEtAl2003]
  2. 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 [ErnstEtAl2003]
  3. Goto, N, Nakao, NC, Kawashima, S, Katayama, T, Kanehisa, T. BioRuby: Open-Source Bioinformatics Library. Genome Informatics 2003; 14, 629-630. [GotoEtAl2003]
    This paper describes BioRuby
  4. Hamelryck T and Manderick B. PDB file parser and structure class implemented in Python. Bioinformatics 2003 Nov 22; 19(17) 2308-10. pmid:14630660. PubMed HubMed [HamelryckAndManderick2003]
    This describes the Bio.PDB module
  5. De Hoon, MJL, Chapman, BA, Friedberg, I. Bioinformatics and computational biology with biopython. Genome Informatics 2003; 14, 298-299. [DeHoonEtAl2003]
  6. Horner DS and Pesole G. The estimation of relative site variability among aligned homologous protein sequences. Bioinformatics 2003 Mar 22; 19(5) 600-6. pmid:12651718. PubMed HubMed [HornerAndPesole2003]
  7. Kummerfeld SK, Weiss AS, Fekete A, and Jermiin LS. AMID: autonomous modeler of intragenic duplication. Appl Bioinformatics 2003; 2(3) 169-76. pmid:15130804. PubMed HubMed [KummerfieldEtAl2003]
  8. Linding R, Russell RB, Neduva V, and Gibson TJ. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res 2003 Jul 1; 31(13) 3701-8. pmid:12824398. PubMed HubMed [LindingEtAl2003]
  9. 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 [SugawaraEtAl2003]
  10. Wroe CJ, Stevens R, Goble CA, and Ashburner M. A methodology to migrate the gene ontology to a description logic environment using DAML+OIL. Pac Symp Biocomput 2003 624-35. pmid:12603063. PubMed HubMed [WroeEtAl2003]
All Medline abstracts: PubMed HubMed

Publications from 2002

  1. Chang JT, Schütze H, and Altman RB. Creating an online dictionary of abbreviations from MEDLINE. J Am Med Inform Assoc 2002 Nov-Dec; 9(6) 612-20. pmid:12386112. PubMed HubMed [ChangEtA2002]
  2. 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 [LenhardAndWasserman2002]
  3. Mangalam H. The Bio* toolkits--a brief overview. Brief Bioinform 2002 Sep; 3(3) 296-302. pmid:12230038. PubMed HubMed [Mangalam2002]
  4. Raychaudhuri S, Chang JT, Sutphin PD, and Altman RB. Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res 2002 Jan; 12(1) 203-14. doi:10.1101/gr.199701 pmid:11779846. PubMed HubMed [RaychaudhuriEtAl2002a]
  5. Raychaudhuri S, Schütze H, and Altman RB. Using text analysis to identify functionally coherent gene groups. Genome Res 2002 Oct; 12(10) 1582-90. doi:10.1101/gr.116402 pmid:12368251. PubMed HubMed [RaychaudhuriEtAl2002b]
  6. Stajich JE, et al. 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 [StajichEtAl2002]
    This paper describes BioPerl
  7. Stein L. Creating a bioinformatics nation. Nature 2002 May 9; 417(6885) 119-20. doi:10.1038/417119a pmid:12000935. PubMed HubMed [Stein2002]
All Medline abstracts: PubMed HubMed

Publications from 2001

  1. Achard F, Vaysseix G, and Barillot E. XML, bioinformatics and data integration. Bioinformatics 2001 Feb; 17(2) 115-25. pmid:11238067. PubMed HubMed [AchardEtAl2001]
  2. Chang JT, Raychaudhuri S, and Altman RB. Including biological literature improves homology search. Pac Symp Biocomput 2001 374-83. pmid:11262956. PubMed HubMed [ChangEtAl2001]
  3. Gemünd C, Ramu C, Altenberg-Greulich B, and Gibson TJ. Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries. Nucleic Acids Res 2001 Mar 15; 29(6) 1272-7. pmid:11238992. PubMed HubMed [GemundEtAl2001]
  4. Kawagashira N, et al. Multiple Zinc Finger Motifs with Comparison of Plant and Insect. Genome Informatics 2001; 12, 368-369 [KawagashiraEtAl2001]
  5. 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]
  6. Woodwark KC. Meeting review: the Bioinformatics Open Source Conference 2001 (BOSC 2001). Comp Funct Genomics 2001; 2(5) 327-9. doi:10.1002/cfg.107 pmid:18629243. PubMed HubMed [Woodwark2001]
All Medline abstracts: PubMed HubMed

Publications from 2000

  1. Chapman BA and Chang JT. Biopython: Python tools for computational biology. ACM SIGBIO Newsletter 2000; 20, 15-19. [ChapmanAndChang2000]
    This serves as the official project announcement.
  2. Ramu C, Gemünd C, and Gibson TJ. Object-oriented parsing of biological databases with Python. Bioinformatics 2000 Jul; 16(7) 628-38. pmid:11038333. PubMed HubMed [RamuEtAl2000]

Publications from 1999

  1. Sanner MF. Python: a programming language for software integration and development. J Mol Graph Model 1999 Feb; 17(1) 57-61. pmid:10660911. PubMed HubMed [Sanner1999]

Note the Biopython project started in 1999.

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