Publications

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 CockEtAl2009. Regrettably, in some cases the manuscripts themselves do not directly mention Biopython, but this has been confirmed explicitly by an author.

Publications from 2010

We don’t plan to compile a listing manually, since most publications should be citing our application note CockEtAl2009 explicitly (and/or one of the module specific papers).

Publications from 2009

1. ArmanoAndManconi2009 pmid=19799773 // Used Bio.PDB 1. BanachEtAl2009 pmid=19399224 // Used Bio.PDB and Bio.KDTree 1. BerkholzEtAl2009 pmid=19906726 // Used Bio.PDB 1. ChiEtAl2009 pmid=19536157 // General bioinformatics analysis including in silico random CLIP (crosslinking immunoprecipitation) 1. BouvierEtAl2009 pmid=19910307 // Used Bio.PDB 1. CockEtAl2009 pmid=19304878 // This application note covers the whole of Biopython 1. CockEtAl2009b pmid=20015970 // This describes the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava and EMBOSS 1. CoxEtAl2009 pmid=19073919 // Used Bio.Blast, Bio.Fasta, & Bio.Nexus 1. DailyEtAl2009 pmid=19229311 // Used Bio.SVDSuperimposer (and probably Bio.PDB as well) 1. DonaireEtAl2009 pmid=19665162 // Used Biopython for removing adaptors from 454 sequencing reads 1. DudleyAndButte2009 pmid=20041221 // A bioinformatics review citing Biopython and other project. 1. GarbinoEtAl2009 pmid=19318539 2. GouldEtAl2009 pmid=19920119 // Used Biopython to retrieve information from SWISS-PROT and PubMed 1. HanAndZmasek2009 pmid=19860910 2. HoldenEtAl2009 pmid=19076238 // Used [Bio.SeqIO](SeqIO "wikilink"), [BioSQL](BioSQL "wikilink") and GenomeDiagram 1. IhekwabaEtAl2009 pmid=19895694 // Data mining 1. JankunKellyEtAl2009 pmid=19811691 // Used Biopython for working with sequence alignments 1. JonesEtAl2009 pmid=19849787 // Used Biopython for sequence manipulation 1. KorhonenEtAl2009 pmid=19773334 // Includes a Python wrapper with examples using it with Biopthon 1. LundborgEtAl2009 pmid=19926726 2. MacDonaldEtAl2009 N MacDonald, D Parks, R Beiko 2009. *SeqMonitor: Influenza Analysis Pipeline and Visualization.* PLoS Curr Influenza. RRN1040. 3. MilesEtAl2009 pmid=19640266 // Used Biopython to work with genotypes for microsatellite locii 1. MullerEtAl2009 pmid=19583843 2. NarayananEtAl pmid=19324053 // Used Bio.SVDSuperimposer (and probably Bio.PDB as well) 1. ParisienEtAl2009 pmid=19710185 // Used Bio.PDB 1. Schanda2009 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>](http://dx.doi.org/10.1016/j.pnmrs.2009.05.002) // Used Bio.PDB 1. SmithEtAl2009 pmid=19210768 // Used Biopython to implement a pipeline with BioSQL 1. StivalaEtAl2009 pmid=19450287 // PDB, SCOP and ASTRAL data 1. SunEtAl2009 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>](http://dx.doi.org/10.1016/S1874-1029(08)60073-7) // Used Biopython to access MEDLINE 1. SzaboEtAl2009 pmid=19778434 // Used Biopython for sequence manipulation and analysis 1. TanakaEtAl2009 pmid=19272463 // Used Biopython to access MEDLINE 1. Thomson2009 pmid=19812729 // A Linux distribution including Biopython 1. TorranceEtAl2009 pmid=19038265 // Used Biopython for the k-means algorithm 1. VanDerAuweraEtAl2009 pmid=19259779 // Used Biopython and Genome Diagram for plasmid map and alignment figures 1. WeilEtAl2009 pmid=19910254 // Used Biopython for sequence manipulation 1. Wiwanitkit2009a pmid=19007941 // Used Biopython to work with ExPASy 1. Wiwanitkit2009b pmid=17936280 // Used Biopython to work with ExPASy

Publications from 2008

1. AntaoEtAl2008 pmid=18662398 // Used Bio.PopGen 1. CardonaEtAl2008 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19077301) [HubMed](http://www.hubmed.org/display.cgi?uids=19077301) 2. DiellaEtAl2008 pmid=17962309 // Used with UniProt and PubMed 1. Faircloth2008 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>](http://dx.doi.org/10.1111/j.1471-8286.2007.01884.x) // Used [Bio.SeqIO](SeqIO "wikilink") 1. FeldhahnEtAl2008 pmid=18440979 // Used Biopython for several unspecified tasks 1. FourmentAndGillings2008 pmid=18251993 2. FrelingerEtAl2008 pmid=18559108 // Used PyCluster / Bio.Cluster 1. GeraciEtAl2008 pmid=18477631 // Used PyCluster / Bio.Cluster and other unspecified parts of Biopython 1. GrontAndKolinski2008 pmid=18227118 2. HigaAndTozzi2008 pmid=18949708 // Used Bio.PDB 1. KimAndLee2008 pmid=18566765 2. LangkildeEtAl2008 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18645234) [HubMed](http://www.hubmed.org/display.cgi?uids=18645234) // Used Bio.PDB 1. KoczykAndBerezovsky2008 pmid=18502776 // Used Bio.PDB 1. MunteanuEtAl2008 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18606172) [HubMed](http://www.hubmed.org/display.cgi?uids=18606172) // Used Bio.PDB 1. ParkEtAl2008 pmid=18448467 // Used Biopython to calculate hydropathy profiles 1. PontyEtAl2008 pmid=18556754 // Used Biopython to work with lattice structures, including superimposition. 1. RamanEtAl2008 pmid=19099550 // Used Bio.Blast 1. SinghEtAl2008 pmid=18423188 2. SongEtAl2008 pmid=18467349 // Used Bio.PDB 1. SoutheyEtAl2008 pmid=19169350 2. WaltersEtAl2008 pmid=18262514 // Used Biopython for sequence manipulation 1. WhitworthAndCock2008 pmid=18227240 // Used [Bio.SeqIO](SeqIO "wikilink"), [Bio.AlignIO](AlignIO "wikilink") and Bio.Blast 1. Wiwanitkit2008a pmid=18445954 // Used Biopython for working with ExPASy 1. Wiwanitkit2008b pmid=18064407 // Used Biopython for working with ExPASy Publications from 2007 ====================== 1. AntaoEtAl2007 pmid=17488756 2. AvrovaEtAl2007 pmid=17322195 3. Bassi2007 pmid=18052533 4. BernauerEtAl2007 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17237048) [HubMed](http://www.hubmed.org/display.cgi?uids=17237048) 5. DominguesEtAl2007 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17933849) [HubMed](http://www.hubmed.org/display.cgi?uids=17933849) 6. ChapmanEtAl2007 pmid=17634914 7. CockAndWhitworth2007a pmid=17479344 8. CockAndWhitworth2007b pmid=17709334 9. CraddockEtAl2008 pmid=19008893 10. FerreEtAl2007 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17567620) [HubMed](http://www.hubmed.org/display.cgi?uids=17567620) 11. GentleEtAl2007 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17329230) [HubMed](http://www.hubmed.org/display.cgi?uids=17329230) 12. GrunbergEtAl2997 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17237072) [HubMed](http://www.hubmed.org/display.cgi?uids=17237072) 13. HackneyEtAl2007 pmid=17355990 // Describes the Bio.MEME module 1. KauffEtAl2007 pmid=17562476 2. MaEtAl2007 pmid=17524416 3. PicardiEtAl2007 pmid=17175530 4. PietalEtAl2007 pmid=17400727 5. RatteiEtAl2007 pmid=17916241 6. SanderEtAl2007 pmid=17397254 7. TagamiEtAl2007 pmid=18056073 8. WatanabeEtAl2007 pmid=17651697 9. WhissonEtAl2007 pmid=17914356 10. WonEtAl2007 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17888163) [HubMed](http://www.hubmed.org/display.cgi?uids=17888163) Publications from 2006 ====================== 1. BenitaEtAl2006 pmid=16822774 // This describes some of the Bio.SeqUtils module 1. BonisEtAl2006 pmid=16882651 2. CasbonEtAl2006 pmid=16403221 // Describes additions to the Bio.SCOP module 1. CroceEtAl2006 pmid=16441875 2. FerreiraEtAl2006 pmid=17073300 3. FriedbergEtAl2006 pmid=16845030 4. GrontAndKolinski2006 pmid=16407320 5. HegedusAndRiordan2006 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>](http://dx.doi.org/10.2478/s11535-006-0003-9) 6. LeeEtAl2006 pmid=16326071 7. MattinglyEtAl2006 pmid=16675512 8. Munos2006 pmid=16915233 9. NilsenEtAl2006 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>](http://dx.doi.org/10.1111/j.1365-2052.2007.01686.x) 10. PritchardEtAl2006 pmid=16377612 // This describes GenomeDiagram, now part of the Bio.Graphics module 1. StajichAndLapp2006 pmid=16899494 2. TaylorAndProvart2006 pmid=16686952 // This describes the Bio.CAPS module. 1. TernesEtAl2006 pmid=16339149 2. TothEtAl2006 pmid=16704357 3. WindsorEtAl2006 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16607030) [HubMed](http://www.hubmed.org/display.cgi?uids=16607030) 4. Wuchty2006 pmid=16716232 5. ZapalaEtAl2006 pmid=17146048 6. ZotenkoEtAl2006 pmid=16762072 Publications from 2005 ====================== 1. BoomsmaAndHamelryck2005 pmid=15985178 2. ArmstrongEtAl2005 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15894622) [HubMed](http://www.hubmed.org/display.cgi?uids=15894622) 3. CurkEtAl2005 pmid=15308546 4. DimmicEtAl2005 pmid=15961449 5. FederAndBujnicki2005 pmid=15720711 6. FriedbergEtAl2005 pmid=15980462 7. HerskovicAndBernstam2005 pmid=16779053 8. Hamelryck2005 pmid=15688434 9. JohannessenEtAl2005 pmid=15710415 10. MajumdarEtAl2005 pmid=16095538 11. NeerincxAndLeunissen2005 pmid=15975226 12. OlsenEtAl2005 pmid=15466433 13. TothEtAl2006 pmid=16704357 14. TrisslEtAl2005 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15801979) [HubMed](http://www.hubmed.org/display.cgi?uids=15801979) 15. WhissonEtAl2005 pmid=15749054 Publications from 2004 ====================== 1. BellEtAl2004 pmid=15263089 2. ChapmanEtAl2004 pmid=14734308 3. FlanaganEtAl2004 pmid=18629137 4. DeHoonEtAl2004 pmid=14871861 // This describes the Bio.Cluster module 1. GentlemanEtAl2004 pmid=15461798 2. King2004 pmid=15561592 3. SwartEtAl2004 pmid=15005802 Publications from 2003 ====================== 1. BowersEtAl2003 pmid=12660784 2. ErnstEtAl2003 pmid=12538250 3. GotoEtAl2003 Goto, N, Nakao, NC, Kawashima, S, Katayama, T, Kanehisa, T. *BioRuby: Open-Source Bioinformatics Library.* Genome Informatics 2003; 14, 629-630. // This paper describes [BioRuby](http://www.bioruby.org) 1. HamelryckAndManderick2003 pmid=14630660 // This describes the Bio.PDB module 1. DeHoonEtAl2003 De Hoon, MJL, Chapman, BA, Friedberg, I. *Bioinformatics and computational biology with Biopython.* Genome Informatics 2003; 14, 298-299. 2. HornerAndPesole2003 pmid=12651718 3. KummerfieldEtAl2003 pmid=15130804 4. LindingEtAl2003 pmid=12824398 5. SugawaraEtAl2003 pmid=12824432 6. WroeEtAl2003 pmid=12603063 Publications from 2002 ====================== 1. ChangEtA2002 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. . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12386112) [HubMed](http://www.hubmed.org/display.cgi?uids=12386112) 2. LenhardAndWasserman2002 pmid=12176838 3. Mangalam2002 pmid=12230038 4. RaychaudhuriEtAl2002a pmid=11779846 5. RaychaudhuriEtAl2002b 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12368251) [HubMed](http://www.hubmed.org/display.cgi?uids=12368251) 6. StajichEtAl2002 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> . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12368254) [HubMed](http://www.hubmed.org/display.cgi?uids=12368254) // This paper describes [BioPerl](http://www.bioperl.org) 1. Stein2002 pmid=12000935 Publications from 2001 ====================== 1. AchardEtAl2001 pmid=11238067 2. ChangEtAl2001 pmid=11262956 3. GemundEtAl2001 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. . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11238992) [HubMed](http://www.hubmed.org/display.cgi?uids=11238992) 4. KawagashiraEtAl2001 Kawagashira N, *et al*. *Multiple Zinc Finger Motifs with Comparison of Plant and Insect.* Genome Informatics 2001; 12, 368-369 5. Ramu2001 pmid=11524384 6. Woodwark2001 pmid=18629243 Publications from 2000 ====================== 1. ChapmanAndChang2000 Chapman BA and Chang JT. *Biopython: Python tools for computational biology.* ACM SIGBIO Newsletter 2000; 20, 15-19. // This serves as the official project announcement. 1. RamuEtAl2000 Ramu C, Gemünd C, and Gibson TJ. *Object-oriented parsing of biological databases with Python*. Bioinformatics 2000 Jul; 16(7) 628-38. . [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11038333) [HubMed](http://www.hubmed.org/display.cgi?uids=11038333) Publications from 1999 ====================== 1. Sanner1999 pmid=10660911 Note the Biopython project started in 1999.