Publications

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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

Error fetching PMID 19799773:
Error fetching PMID 19399224:
Error fetching PMID 19906726:
Error fetching PMID 19536157:
Error fetching PMID 19304878:
Error fetching PMID 20015970:
Error fetching PMID 19073919:
Error fetching PMID 19229311:
Error fetching PMID 19665162:
Error fetching PMID 19318539:
Error fetching PMID 19860910:
Error fetching PMID 19076238:
Error fetching PMID 19811691:
Error fetching PMID 19849787:
Error fetching PMID 19773334:
Error fetching PMID 19926726:
Error fetching PMID 19640266:
Error fetching PMID 19583843:
Error fetching PMID 19324053:
Error fetching PMID 19710185:
Error fetching PMID 19210768:
Error fetching PMID 19272463:
Error fetching PMID 19038265:
Error fetching PMID 19007941:
Error fetching PMID 17936280:
  1. Error fetching PMID 19304878: [CockEtAl2009]
    This application note covers the whole of Biopython

  2. Error fetching PMID 19799773: [ArmanoAndManconi2009]
    Used Bio.PDB

  3. Error fetching PMID 19399224: [BanachEtAl2009]
    Used Bio.PDB and Bio.KDTree

  4. Error fetching PMID 19906726: [BerkholzEtAl2009]
    Used Bio.PDB

  5. Error fetching PMID 19536157: [ChiEtAl2009]
    General bioinformatics analysis including in silico random CLIP (crosslinking immunoprecipitation)

  6. Error fetching PMID 20015970: [CockEtAl2009b]
    This describes the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava and EMBOSS

  7. Error fetching PMID 19073919: [CoxEtAl2009]
    Used Bio.Blast, Bio.Fasta, & Bio.Nexus

  8. Error fetching PMID 19229311: [DailyEtAl2009]
    Used Bio.SVDSuperimposer (and probably Bio.PDB as well)

  9. Error fetching PMID 19665162: [DonaireEtAl2009]
    Used Biopython for removing adaptors from 454 sequencing reads

  10. Error fetching PMID 19318539: [GarbinoEtAl2009]
  11. Error fetching PMID 19860910: [HanAndZmasek2009]
  12. Error fetching PMID 19076238: [HoldenEtAl2009]
    Used Bio.SeqIO, BioSQL and GenomeDiagram

  13. Error fetching PMID 19811691: [JankunKellyEtAl2009]
    Used Biopython for working with sequence alignments

  14. Error fetching PMID 19849787: [JonesEtAl2009]
    Used Biopython for sequence manipulation

  15. Error fetching PMID 19773334: [KorhonenEtAl2009]
    Includes a Python wrapper with examples using it with Biopthon

  16. Error fetching PMID 19926726: [LundborgEtAl2009]
  17. N MacDonald, D Parks, R Beiko 2009. SeqMonitor: Influenza Analysis Pipeline and Visualization. PLoS Curr Influenza. RRN1040.

    [MacDonaldEtAl2009]

  18. Error fetching PMID 19640266: [MilesEtAl2009]
    Used Biopython to work with genotypes for microsatellite locii

  19. Error fetching PMID 19583843: [MullerEtAl2009]
  20. Error fetching PMID 19324053: [NarayananEtAl]
    Used Bio.SVDSuperimposer (and probably Bio.PDB as well)

  21. Error fetching PMID 19710185: [ParisienEtAl2009]
    Used Bio.PDB

  22. 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

  23. Error fetching PMID 19210768: [SmithEtAl2009]
    Used Biopython to implement a pipeline with BioSQL

  24. 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

  25. Error fetching PMID 19272463: [TanakaEtAl2009]
    Used Biopython to access MEDLINE

  26. Error fetching PMID 19038265: [TorranceEtAl2009]
    Used Biopython for the k-means algorithm

  27. Error fetching PMID 19007941: [Wiwanitkit2009a]
    Used Biopython to work with ExPASy

  28. Error fetching PMID 17936280: [Wiwanitkit2009b]
    Used Biopython to work with ExPASy

All Medline abstracts: PubMed HubMed

Publications from 2008

Error fetching PMID 18662398:
Error fetching PMID 17962309:
Error fetching PMID 18440979:
Error fetching PMID 18251993:
Error fetching PMID 18559108:
Error fetching PMID 18477631:
Error fetching PMID 18227118:
Error fetching PMID 18949708:
Error fetching PMID 18566765:
Error fetching PMID 18502776:
Error fetching PMID 18448467:
Error fetching PMID 18556754:
Error fetching PMID 19099550:
Error fetching PMID 18423188:
Error fetching PMID 18467349:
Error fetching PMID 19169350:
Error fetching PMID 18262514:
Error fetching PMID 18227240:
Error fetching PMID 18445954:
Error fetching PMID 18064407:
  1. Error fetching PMID 18662398: [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. Error fetching PMID 17962309: [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. Error fetching PMID 18440979: [FeldhahnEtAl2008]
    Used Biopython for several unspecified tasks

  6. Error fetching PMID 18251993: [FourmentAndGillings2008]
  7. Error fetching PMID 18559108: [FrelingerEtAl2008]
    Used PyCluster / Bio.Cluster

  8. Error fetching PMID 18477631: [GeraciEtAl2008]
    Used PyCluster / Bio.Cluster and other unspecified parts of Biopython

  9. Error fetching PMID 18227118: [GrontAndKolinski2008]
  10. Error fetching PMID 18949708: [HigaAndTozzi2008]
    Used Bio.PDB

  11. Error fetching PMID 18566765: [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. Error fetching PMID 18502776: [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. Error fetching PMID 18448467: [ParkEtAl2008]
    Used Biopython to calculate hydropathy profiles

  16. Error fetching PMID 18556754: [PontyEtAl2008]
    Used Biopython to work with lattice structures, including superimposition.

  17. Error fetching PMID 19099550: [RamanEtAl2008]
    Used Bio.Blast

  18. Error fetching PMID 18423188: [SinghEtAl2008]
  19. Error fetching PMID 18467349: [SongEtAl2008]
    Used Bio.PDB

  20. Error fetching PMID 19169350: [SoutheyEtAl2008]
  21. Error fetching PMID 18262514: [WaltersEtAl2008]
    Used Biopython for sequence manipulation

  22. Error fetching PMID 18227240: [WhitworthAndCock2008]
    Used Bio.SeqIO, Bio.AlignIO and Bio.Blast

  23. Error fetching PMID 18445954: [Wiwanitkit2008a]
    Used Biopython for working with ExPASy

  24. Error fetching PMID 18064407: [Wiwanitkit2008b]
    Used Biopython for working with ExPASy

All Medline abstracts: PubMed HubMed

Publications from 2007

Error fetching PMID 17488756:
Error fetching PMID 17322195:
Error fetching PMID 18052533:
Error fetching PMID 17634914:
Error fetching PMID 17479344:
Error fetching PMID 17709334:
Error fetching PMID 19008893:
Error fetching PMID 17355990:
Error fetching PMID 17562476:
Error fetching PMID 17524416:
Error fetching PMID 17175530:
Error fetching PMID 17400727:
Error fetching PMID 17916241:
Error fetching PMID 17397254:
Error fetching PMID 18056073:
Error fetching PMID 17651697:
Error fetching PMID 17914356:
  1. Error fetching PMID 17488756: [AntaoEtAl2007]
  2. Error fetching PMID 17322195: [AvrovaEtAl2007]
  3. Error fetching PMID 18052533: [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. Error fetching PMID 17634914: [ChapmanEtAl2007]
  7. Error fetching PMID 17479344: [CockAndWhitworth2007a]
  8. Error fetching PMID 17709334: [CockAndWhitworth2007b]
  9. Error fetching PMID 19008893: [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. Error fetching PMID 17355990: [HackneyEtAl2007]
    Describes the Bio.MEME module

  14. Error fetching PMID 17562476: [KauffEtAl2007]
  15. Error fetching PMID 17524416: [MaEtAl2007]
  16. Error fetching PMID 17175530: [PicardiEtAl2007]
  17. Error fetching PMID 17400727: [PietalEtAl2007]
  18. Error fetching PMID 17916241: [RatteiEtAl2007]
  19. Error fetching PMID 17397254: [SanderEtAl2007]
  20. Error fetching PMID 18056073: [TagamiEtAl2007]
  21. Error fetching PMID 17651697: [WatanabeEtAl2007]
  22. Error fetching PMID 17914356: [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

Error fetching PMID 16822774:
Error fetching PMID 16882651:
Error fetching PMID 16403221:
Error fetching PMID 16441875:
Error fetching PMID 17073300:
Error fetching PMID 16845030:
Error fetching PMID 16407320:
Error fetching PMID 16326071:
Error fetching PMID 16675512:
Error fetching PMID 16915233:
Error fetching PMID 16377612:
Error fetching PMID 16899494:
Error fetching PMID 16686952:
Error fetching PMID 16339149:
Error fetching PMID 16704357:
Error fetching PMID 16716232:
Error fetching PMID 17146048:
Error fetching PMID 16762072:
  1. Error fetching PMID 16822774: [BenitaEtAl2006]
    This describes some of the Bio.SeqUtils module

  2. Error fetching PMID 16882651: [BonisEtAl2006]
  3. Error fetching PMID 16403221: [CasbonEtAl2006]
    Describes additions to the Bio.SCOP module

  4. Error fetching PMID 16441875: [CroceEtAl2006]
  5. Error fetching PMID 17073300: [FerreiraEtAl2006]
  6. Error fetching PMID 16845030: [FriedbergEtAl2006]
  7. Error fetching PMID 16407320: [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. Error fetching PMID 16326071: [LeeEtAl2006]
  10. Error fetching PMID 16675512: [MattinglyEtAl2006]
  11. Error fetching PMID 16915233: [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. Error fetching PMID 16377612: [PritchardEtAl2006]
    This describes GenomeDiagram, now part of the Bio.Graphics module

  14. Error fetching PMID 16899494: [StajichAndLapp2006]
  15. Error fetching PMID 16686952: [TaylorAndProvart2006]
    This describes the Bio.CAPS module.

  16. Error fetching PMID 16339149: [TernesEtAl2006]
  17. Error fetching PMID 16704357: [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. Error fetching PMID 16716232: [Wuchty2006]
  20. Error fetching PMID 17146048: [ZapalaEtAl2006]
  21. Error fetching PMID 16762072: [ZotenkoEtAl2006]
All Medline abstracts: PubMed HubMed

Publications from 2005

Error fetching PMID 15985178:
Error fetching PMID 15308546:
Error fetching PMID 15961449:
Error fetching PMID 15720711:
Error fetching PMID 15980462:
Error fetching PMID 16779053:
Error fetching PMID 15688434:
Error fetching PMID 15710415:
Error fetching PMID 16095538:
Error fetching PMID 15975226:
Error fetching PMID 15466433:
Error fetching PMID 16704357:
Error fetching PMID 15749054:
  1. Error fetching PMID 16704357: [TothEtAl2006]
  2. Error fetching PMID 15985178: [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. Error fetching PMID 15308546: [CurkEtAl2005]
  5. Error fetching PMID 15961449: [DimmicEtAl2005]
  6. Error fetching PMID 15720711: [FederAndBujnicki2005]
  7. Error fetching PMID 15980462: [FriedbergEtAl2005]
  8. Error fetching PMID 16779053: [HerskovicAndBernstam2005]
  9. Error fetching PMID 15688434: [Hamelryck2005]
  10. Error fetching PMID 15710415: [JohannessenEtAl2005]
  11. Error fetching PMID 16095538: [MajumdarEtAl2005]
  12. Error fetching PMID 15975226: [NeerincxAndLeunissen2005]
  13. Error fetching PMID 15466433: [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. Error fetching PMID 15749054: [WhissonEtAl2005]
All Medline abstracts: PubMed HubMed

Publications from 2004

Error fetching PMID 15263089:
Error fetching PMID 14734308:
Error fetching PMID 18629137:
Error fetching PMID 14871861:
Error fetching PMID 15461798:
Error fetching PMID 15561592:
Error fetching PMID 15005802:
  1. Error fetching PMID 15263089: [BellEtAl2004]
  2. Error fetching PMID 14734308: [ChapmanEtAl2004]
  3. Error fetching PMID 18629137: [FlanaganEtAl2004]
  4. Error fetching PMID 14871861: [DeHoonEtAl2004]
    This describes the Bio.Cluster module

  5. Error fetching PMID 15461798: [GentlemanEtAl2004]
  6. Error fetching PMID 15561592: [King2004]
  7. Error fetching PMID 15005802: [SwartEtAl2004]
All Medline abstracts: PubMed HubMed

Publications from 2003

Error fetching PMID 12660784:
Error fetching PMID 12538250:
Error fetching PMID 14630660:
Error fetching PMID 12651718:
Error fetching PMID 15130804:
Error fetching PMID 12824398:
Error fetching PMID 12824432:
Error fetching PMID 12603063:
  1. Error fetching PMID 12660784: [BowersEtAl2003]
  2. Error fetching PMID 12538250: [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. Error fetching PMID 14630660: [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. Error fetching PMID 12651718: [HornerAndPesole2003]
  7. Error fetching PMID 15130804: [KummerfieldEtAl2003]
  8. Error fetching PMID 12824398: [LindingEtAl2003]
  9. Error fetching PMID 12824432: [SugawaraEtAl2003]
  10. Error fetching PMID 12603063: [WroeEtAl2003]
All Medline abstracts: PubMed HubMed

Publications from 2002

Error fetching PMID 12176838:
Error fetching PMID 12230038:
Error fetching PMID 11779846:
Error fetching PMID 12000935:
  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. Error fetching PMID 12176838: [LenhardAndWasserman2002]
  3. Error fetching PMID 12230038: [Mangalam2002]
  4. Error fetching PMID 11779846: [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. Error fetching PMID 12000935: [Stein2002]
All Medline abstracts: PubMed HubMed

Publications from 2001

Error fetching PMID 11238067:
Error fetching PMID 11262956:
Error fetching PMID 11524384:
Error fetching PMID 18629243:
  1. Error fetching PMID 11238067: [AchardEtAl2001]
  2. Error fetching PMID 11262956: [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. Error fetching PMID 11524384: [Ramu2001]
  6. Error fetching PMID 18629243: [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

Error fetching PMID 10660911:
  1. Error fetching PMID 10660911: [Sanner1999]

Note the Biopython project started in 1999.

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