Efforts towards accessible and reliable bioinformatics
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[1] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[2] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[3] Sattanathan Subramanian,et al. Pipelined data-flow delegated orchestration for data-intensive eScience workflows , 2013, Int. J. Web Inf. Syst..
[4] Jill P. Mesirov,et al. GenomeSpace: an environment for frictionless bioinformatics , 2013 .
[5] Thomas Lengauer,et al. Editorial. The Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99) , 1999, Bioinform..
[6] Shane S. Sturrock,et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..
[7] Christian Burks,et al. Molecular Biology Database List , 1999, Nucleic Acids Res..
[8] H. Bernstein. Recent changes to RasMol, recombining the variants. , 2000, Trends in biochemical sciences.
[9] D. Lipman,et al. National Center for Biotechnology Information , 2019, Springer Reference Medizin.
[10] Rodger Staden,et al. The current status and portability of our sequence handling software , 1986, Nucleic Acids Res..
[11] Sylvain Gaillard,et al. Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics , 2006, BMC Bioinformatics.
[12] Rodrigo Lopez,et al. The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI , 2015, Nucleic Acids Res..
[13] D. Botstein,et al. Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[14] G Vriend,et al. WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.
[15] S Henikoff,et al. Sequence analysis by electronic mail server. , 1993, Trends in biochemical sciences.
[16] Peter F. Stadler,et al. ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.
[17] Mark D. Wilkinson,et al. BioMOBY: An Open Source Biological Web Services Proposal , 2002, Briefings Bioinform..
[18] J. Eisen. The Genetic Data Environment , 1997 .
[19] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[20] Dieter Schmalstieg,et al. StratomeX: Visual Analysis of Large‐Scale Heterogeneous Genomics Data for Cancer Subtype Characterization , 2012, Comput. Graph. Forum.
[21] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[22] Daniel J. Blankenberg,et al. Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.
[23] I. Longden,et al. EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.
[24] Carole A. Goble,et al. The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud , 2013, Nucleic Acids Res..
[25] Geoffrey J. Barton,et al. The Jalview Java alignment editor , 2004, Bioinform..
[26] Nicolas Le Novère,et al. Identifiers.org and MIRIAM Registry: community resources to provide persistent identification , 2011, Nucleic Acids Res..
[27] Etsuko N. Moriyama,et al. Vector NTI, a balanced all-in-one sequence analysis suite , 2004, Briefings Bioinform..
[28] R. Staden. A strategy of DNA sequencing employing computer programs. , 1979, Nucleic acids research.
[29] Sarah M. Keating,et al. Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. , 2004, Systems biology.
[30] Amedeo Napoli,et al. BioRegistry: Automatic extraction of metadata for biological database retrieval and discovery , 2010, Int. J. Metadata Semant. Ontologies.
[31] Paulien Hogeweg,et al. The Roots of Bioinformatics in Theoretical Biology , 2011, PLoS Comput. Biol..
[32] Robert Schmieder,et al. SEQanswers: an open access community for collaboratively decoding genomes , 2012, Bioinform..
[33] Leighton Pritchard,et al. GenomeDiagram: a python package for the visualization of large-scale genomic data , 2006, Bioinform..
[34] Emmanuel Barillot,et al. HuGeMap: a distributed and integrated Human Genome Map database , 1998, Nucleic Acids Res..
[35] Carole A. Goble,et al. myExperiment: a repository and social network for the sharing of bioinformatics workflows , 2010, Nucleic Acids Res..
[36] Gary Benson,et al. Editorial: Nucleic Acids Research annual Web Server Issue in 2015 , 2015, Nucleic Acids Res..
[37] Vincent J. Henry,et al. OMICtools: an informative directory for multi-omic data analysis , 2014, Database J. Biol. Databases Curation.
[38] Gary D. Bader,et al. Cytoscape Web: an interactive web-based network browser , 2010, Bioinform..
[39] P. Argos,et al. SRS: information retrieval system for molecular biology data banks. , 1996, Methods in enzymology.
[40] Christopher J. Rawlings,et al. Ondex Web: web-based visualization and exploration of heterogeneous biological networks , 2013, Bioinform..
[41] Alex Bateman,et al. Ten Simple Rules for Editing Wikipedia , 2010, PLoS Comput. Biol..
[42] Jeffrey Chang,et al. Biopython: Python tools for computational biology , 2000, SIGB.
[43] Jason P. Mulvenna,et al. Bioclojure: a functional library for the manipulation of biological sequences , 2014, Bioinform..
[44] Rodger Staden,et al. Graphic methods to determine the function of nucleic acid sequences , 1984, Nucleic Acids Res..
[45] Jason E. Stewart,et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.
[46] Alessandro Vullo,et al. Ensembl 2015 , 2014, Nucleic Acids Res..
[47] Monica C Munoz-Torres,et al. Web Apollo: a web-based genomic annotation editing platform , 2013, Genome Biology.
[48] D. Higgins,et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.
[49] Emmanuel Barillot,et al. DBcat: a catalog of biological databases , 1999, Nucleic Acids Res..
[50] Kevin Thornton,et al. libsequence: a C++ class library for evolutionary genetic analysis , 2003, Bioinform..
[51] Mikko Koski,et al. Chipster: user-friendly analysis software for microarray and other high-throughput data , 2011, BMC Genomics.
[52] Gultekin Özsoyoglu,et al. Pathways Database System: An Integrated System for Biological Pathways , 2003, Bioinform..
[53] Hideaki Sugawara,et al. Biological SOAP servers and web services provided by the public sequence data bank , 2003, Nucleic Acids Res..
[54] Olivier Sallou,et al. Sprints, Hackathons and Codefests as community gluons in computational biology , 2013 .
[55] Geir Kjetil Sandve,et al. Identifying elemental genomic track types and representing them uniformly , 2011, BMC Bioinformatics.
[56] D. van der Spoel,et al. GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .
[57] Gregory D. Schuler,et al. Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.
[58] Burkhard Rost,et al. FreeContact: fast and free software for protein contact prediction from residue co-evolution , 2014, BMC Bioinformatics.
[59] Avner Schlessinger,et al. PredictProtein—an open resource for online prediction of protein structural and functional features , 2014, Nucleic Acids Res..
[60] Paul T. Spellman,et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB , 2006, BMC Bioinformatics.
[61] Matthew R. Pocock,et al. BioJava: open source components for bioinformatics , 2000, SIGB.
[62] S. Lewis,et al. The generic genome browser: a building block for a model organism system database. , 2002, Genome research.
[63] G. Cameron,et al. The EMBL data library. , 1988, Nucleic acids research.
[64] Martin Vingron,et al. The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources , 2004, Bioinform..
[65] Jean YH Yang,et al. Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.
[66] Gary D Bader,et al. BMC Biology BioMed Central , 2007 .
[67] Christian M. Zmasek,et al. phyloXML: XML for evolutionary biology and comparative genomics , 2009, BMC Bioinformatics.
[68] Don Gilbert,et al. Bioinformatics software resources. , 2004, Briefings in bioinformatics.
[69] Scott McMillan,et al. The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers , 2005, Nucleic Acids Res..
[70] Arek Kasprzyk,et al. BioMart: driving a paradigm change in biological data management , 2011, Database J. Biol. Databases Curation.
[71] Thomas L. Madden,et al. BLAST: at the core of a powerful and diverse set of sequence analysis tools , 2004, Nucleic Acids Res..
[72] Jon C. Ison,et al. Using registries to integrate bioinformatics tools and services into workbench environments , 2016, International Journal on Software Tools for Technology Transfer.
[73] Yves Moreau,et al. ISMB/ECCB 2015 , 2015, Bioinform..
[74] Nigel W. Hardy,et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project , 2008, Nature Biotechnology.
[75] Andreas D. Baxevanis,et al. The Molecular Biology Database Collection: an online compilation of relevant database resources , 2000, Nucleic Acids Res..
[76] Tomas Vitvar,et al. SAWSDL: Semantic Annotations for WSDL and XML Schema , 2007, IEEE Internet Computing.
[77] Rolf Apweiler,et al. The European Bioinformatics Institute’s data resources 2014 , 2013, Nucleic Acids Res..
[78] Kathryn F. Beal,et al. The Staden package, 1998. , 2000, Methods in molecular biology.
[79] Angel Herráez,et al. Biomolecules in the computer: Jmol to the rescue , 2006, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.
[80] Chris F. Taylor,et al. The MGED Ontology: a resource for semantics-based description of microarray experiments , 2006, Bioinform..
[81] Sattanathan Subramanian,et al. Direct data transfer between SOAP web services in orchestration , 2012, IIWAS '12.
[82] Emmanuel Barillot,et al. DBcat: a catalog of 500 biological databases , 2000, Nucleic Acids Res..
[83] Ulf Leser,et al. A proposal for a standard CORBA interface for genome maps , 1999, Bioinform..
[84] R. Staden. Sequence data handling by computer. , 1977, Nucleic acids research.
[85] R. Staden. Further procedures for sequence analysis by computer. , 1978, Nucleic acids research.
[86] Aleksandra Pawlik,et al. BioJS: an open source standard for biological visualisation – its status in 2014 , 2014, F1000Research.
[87] Christopher J. Rawlings,et al. Graph-based analysis and visualization of experimental results with ONDEX , 2006, Bioinform..
[88] Enrico Pontelli,et al. Initial Implementation of a Comparative Data Analysis Ontology , 2009, Evolutionary bioinformatics online.
[89] László Kaján,et al. Cloud Prediction of Protein Structure and Function with PredictProtein for Debian , 2013, BioMed research international.
[90] Jiren Wang,et al. Soap-HT-BLAST: high throughput BLAST based on Web services , 2003, Bioinform..
[91] Enis Afgan,et al. Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy , 2012, Current protocols in bioinformatics.
[92] T. Oinn,et al. Soaplab - a unified Sesame door to analysis tools , 2003 .
[93] Calton Pu,et al. Design and application of PDBlib, a C++ macromolecular class library , 1994, Comput. Appl. Biosci..
[94] Tirso Pons,et al. Homology modeling, model and software evaluation: three related resources , 1998, Bioinform..
[95] Lennart Martens,et al. Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy. , 2007, Molecular & cellular proteomics : MCP.
[96] Teresa K. Attwood,et al. Concepts, historical milestones and the central place of bioinformatics in modern biology: a European perspective. , 2011 .
[97] Yukako Tohsato,et al. Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data , 2014, Bioinform..
[98] K. Bretonnel Cohen,et al. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains , 2014, Journal of Biomedical Semantics.
[99] R A Sayle,et al. RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.
[100] Hilmar Lapp,et al. NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata , 2012, Systematic biology.
[101] S. Tabassum. Editorial , 1968, Euroasian journal of hepato-gastroenterology.
[102] Gabor T. Marth,et al. Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web , 2013, Bioinform..
[103] Brian E. Granger,et al. IPython: A System for Interactive Scientific Computing , 2007, Computing in Science & Engineering.
[104] Reinhard Dölz. Hierarchical Access System for Sequence Libraries in Europe (HASSLE): a tool to access sequence databases remotely , 1994, Comput. Appl. Biosci..
[105] Haruki Nakamura,et al. PDBML: the representation of archival macromolecular structure data in XML , 2005, Bioinform..
[106] Maria Jesus Martin,et al. BioJS: an open source JavaScript framework for biological data visualization , 2013, Bioinform..
[107] Finn Drabløs,et al. MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis , 2012, BMC Bioinformatics.
[108] Robert Herzog,et al. WWW2GCG, a web interface to the GCG biological sequences analysis software , 1996, Comput. Graph..
[109] Tin Wee Tan,et al. Towards BioDBcore: a community-defined information specification for biological databases , 2010, Database J. Biol. Databases Curation.
[110] Gerrit Groenhof,et al. GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..
[111] Ross A. Overbeek,et al. The genetic data environment an expandable GUI for multiple sequence analysis , 1994, Comput. Appl. Biosci..
[112] Matthew R. Pocock,et al. Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..
[113] G D Schuler,et al. A workbench for multiple alignment construction and analysis , 1991, Proteins.
[114] Robert B. Russell,et al. Topic Pages: PLoS Computational Biology Meets Wikipedia , 2012, PLoS Comput. Biol..
[115] G. B. Petersen,et al. HOMED: a homologous sequence editor , 1987, Comput. Appl. Biosci..
[116] Michael Y. Galperin,et al. The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection , 2014, Nucleic Acids Res..
[117] V. Marx. Biology: The big challenges of big data , 2013, Nature.
[118] Toshihisa Takagi,et al. The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data , 2014, Nucleic Acids Res..
[119] Emily S. Charlson,et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications , 2011, Nature Biotechnology.
[120] Toshihisa Takagi,et al. TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services , 2010, Nucleic Acids Res..
[121] Ivo L. Hofacker,et al. Vienna RNA secondary structure server , 2003, Nucleic Acids Res..
[122] Patricia Rodriguez-Tomé,et al. The European Bioinformatics Institute (EBI) databases , 1994, Nucleic Acids Res..
[123] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[124] Tim Berners-Lee,et al. The World-Wide Web , 1994, CACM.
[125] Galt P. Barber,et al. BigWig and BigBed: enabling browsing of large distributed datasets , 2010, Bioinform..
[126] Ronny Lorenz,et al. The Vienna RNA Websuite , 2008, Nucleic Acids Res..
[127] Marta Bleda,et al. Genome Maps, a new generation genome browser , 2013, Nucleic Acids Res..
[128] Other Contributors Are Indicated Where They Contribute. The Free Software Foundation , 2017 .
[129] Rainer Fuchs,et al. CLUSTAL V: improved software for multiple sequence alignment , 1992, Comput. Appl. Biosci..
[130] Sameer Velankar,et al. SOAP-based services provided by the European Bioinformatics Institute , 2005, Nucleic Acids Res..
[131] Mark Johnson,et al. NCBI BLAST: a better web interface , 2008, Nucleic Acids Res..
[132] Ulf Leser,et al. EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation , 1999, German Conference on Bioinformatics.
[133] Brent S. Pedersen,et al. BioStar: An Online Question & Answer Resource for the Bioinformatics Community , 2011, PLoS Comput. Biol..
[134] Gordon Gremme,et al. AnnotationSketch: a genome annotation drawing library , 2009, Bioinform..
[135] Peter Woollard,et al. The minimum information required for reporting a molecular interaction experiment (MIMIx) , 2007, Nature Biotechnology.
[136] Patricia Rodriguez-Tomé,et al. Mapplet: a CORBA-based genome map viewer , 1998, Bioinform..
[137] Tiziana Margaria,et al. Semantics-based composition of EMBOSS services , 2011, J. Biomed. Semant..
[138] Greg Brown,et al. A performance and energy comparison of FPGAs, GPUs, and multicores for sliding-window applications , 2012, FPGA '12.
[139] R D Appel,et al. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. , 1994, Trends in biochemical sciences.
[140] Mark A. Williams,et al. The Bioinformatics Template Library—generic Components for Biocomputing , 2001 .
[141] Dan M. Bolser,et al. The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis , 2011, Nucleic Acids Res..
[142] Hideaki Sugawara,et al. Web API for biology with a workflow navigation system , 2009, Nucleic Acids Res..
[143] C. Sander,et al. The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.
[144] Bartek Wilczynski,et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..
[145] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[146] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer , 2011, Nature Biotechnology.
[147] Anton Nekrutenko,et al. Galaxy CloudMan: delivering cloud compute clusters , 2010, BMC Bioinformatics.
[148] Gary D Bader,et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions , 2011, Nature Methods.
[149] Christian Blouin,et al. libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny , 2005, BMC Bioinformatics.
[150] A. Nekrutenko,et al. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.
[151] Hilmar Lapp,et al. The Bioinformatics Open Source Conference (BOSC) 2013 , 2015, Bioinform..
[152] Kjell Petersen,et al. Analysis of Gene‐Expression Data Using J‐Express , 2008, Current protocols in bioinformatics.
[153] Rodrigo Lopez,et al. The EMBL-EBI bioinformatics web and programmatic tools framework , 2015, Nucleic Acids Res..
[154] Natalya F. Noy,et al. BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse , 2009 .
[155] R Staden,et al. The staden sequence analysis package , 1996, Molecular biotechnology.
[156] David L. Wild,et al. Protein analyst - a distributed object environment for protein sequence and structure analysis , 1999, Bioinform..
[157] Andreas Prlic,et al. BioJava: an open-source framework for bioinformatics in 2012 , 2012, Bioinform..
[158] R. Lister,et al. Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.
[159] Geoffrey J. Barton,et al. Java bioinformatics analysis web services for multiple sequence alignment—JABAWS:MSA , 2011, Bioinform..
[160] Patricia Rodriguez-Tomé. The BioCatalog , 1998, Bioinform..
[161] Chris F. Taylor,et al. The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.
[162] Barend Mons,et al. Open PHACTS: semantic interoperability for drug discovery. , 2012, Drug discovery today.
[163] Geoffrey J. Barton,et al. Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..
[164] Maureen J Donlin,et al. Using the Generic Genome Browser (GBrowse) , 2007, Current protocols in bioinformatics.
[165] Johannes Goll,et al. A new reference implementation of the PSICQUIC web service , 2013, Nucleic Acids Res..
[166] Steve Pettifer,et al. WIWS: a protein structure bioinformatics Web service collection , 2010, Nucleic Acids Res..
[167] Mark D. Wilkinson,et al. The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation , 2011 .
[168] Ron D. Appel,et al. ExPASy: the proteomics server for in-depth protein knowledge and analysis , 2003, Nucleic Acids Res..
[169] D Gilbert. Free software in molecular biology for Macintosh and MS Windows computers. , 2000, Methods in molecular biology.
[170] Ronald J. Vetter,et al. Mosaic and the World Wide Web , 1994, Computer.
[171] Dawn Field,et al. Open software for biologists: from famine to feast , 2006, Nature Biotechnology.
[172] Rodrigo Lopez,et al. Analysis Tool Web Services from the EMBL-EBI , 2013, Nucleic Acids Res..
[173] Thure Etzold,et al. SRS - an indexing and retrieval tool for flat file data libraries , 1993, Comput. Appl. Biosci..
[174] M. Andreessen. MCSA Mosaic Technical Summary , 1993 .
[175] Olivier Sallou,et al. Community-driven development for computational biology at Sprints, Hackathons and Codefests , 2014, BMC Bioinformatics.
[176] S. B. Needleman,et al. A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.
[177] Vassilios Ioannidis,et al. ExPASy: SIB bioinformatics resource portal , 2012, Nucleic Acids Res..
[178] D. Womble,et al. GCG: The Wisconsin Package of sequence analysis programs. , 2000, Methods in molecular biology.
[179] J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.
[180] Rodger Staden,et al. An improved sequence handling package that runs on the Apple Macintosh , 1990, Comput. Appl. Biosci..
[181] Rodrigo Lopez,et al. A new bioinformatics analysis tools framework at EMBL–EBI , 2010, Nucleic Acids Res..
[182] Domenica D'Elia,et al. The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community , 2009, BMC Bioinformatics.
[183] Sean R. Eddy,et al. The Distributed Annotation System , 2001, BMC Bioinformatics.
[184] Pawel Sztromwasser,et al. Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows , 2011, J. Integr. Bioinform..
[185] Gordon Gremme,et al. GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations , 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[186] Jonathan Crabtree,et al. Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG , 2014, Bioinform..
[187] J A Eisen,et al. The Genetic Data Environment. A user modifiable and expandable multiple sequence analysis package. , 1997, Methods in molecular biology.
[188] Carole A. Goble,et al. Community-driven computational biology with Debian Linux , 2010, BMC Bioinformatics.
[189] Rodrigo Lopez,et al. Public services from the European Bioinformatics Institute , 2003, Briefings Bioinform..
[190] Surendra Kumar,et al. AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses , 2009, BMC Bioinformatics.
[191] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[192] Steve Pettifer,et al. Utopia documents: linking scholarly literature with research data , 2010, Bioinform..
[193] Allan Kuchinsky,et al. Exploring Biological Networks with Cytoscape Software , 2008, Current protocols in bioinformatics.
[194] J. Felsenstein. CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.
[195] Paweł Sztromwasser. Throughput and robustness of bioinformatics pipelines for genome-scale data analysis , 2014 .
[196] L. Stein. Creating a bioinformatics nation , 2002, Nature.
[197] Jan Krüger,et al. Playing with pesticides. , 1998, BMC Bioinformatics.
[198] Daniel MacLean,et al. Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics , 2012, Bioinform..
[199] R A Harper. EMBnet: an institute without walls. , 1996, Trends in biochemical sciences.
[200] Jason E. Stewart,et al. Design and implementation of microarray gene expression markup language (MAGE-ML) , 2002, Genome Biology.
[201] Steve Pettifer,et al. An active registry for bioinformatics web services , 2009, Bioinform..
[202] Rodrigo Lopez,et al. Public web-based services from the European Bioinformatics Institute , 2004, Nucleic Acids Res..
[203] G. Schuler,et al. Entrez: molecular biology database and retrieval system. , 1996, Methods in enzymology.
[204] Inge Jonassen,et al. J-Express: exploring gene expression data using Java , 2001, Bioinform..
[205] Korbinian Strimmer,et al. APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..
[206] Robert D. Finn,et al. Rfam: Wikipedia, clans and the “decimal” release , 2010, Nucleic Acids Res..
[207] Rutger A. Vos,et al. BIO::Phylo-phyloinformatic analysis using perl , 2011, BMC Bioinformatics.
[208] Fumikazu Konishi,et al. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies , 2013, J. Biomed. Semant..
[209] Matthew R. Pocock,et al. The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.
[210] Hagen Blankenburg,et al. Integrating biological data – the Distributed Annotation System , 2008, BMC Bioinformatics.
[211] Robert Buels,et al. JBrowse: A Next-Generation Genome Browser , 2014 .
[212] Paul Kavanagh,et al. The Open Source Definition , 2004 .
[213] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[214] Michelle D. Brazas,et al. A decade of web server updates at the bioinformatics links directory: 2003–2012 , 2012, Nucleic Acids Res..
[215] Matthias Schwab,et al. Making scientific computations reproducible , 2000, Comput. Sci. Eng..
[216] Renzo Kottmann,et al. A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). , 2008, Omics : a journal of integrative biology.
[217] Carole A. Goble,et al. Taverna: a tool for building and running workflows of services , 2006, Nucleic Acids Res..
[218] Pjotr Prins,et al. BioRuby: bioinformatics software for the Ruby programming language , 2010, Bioinform..
[219] Finn Drabløs,et al. The Genomic HyperBrowser: an analysis web server for genome-scale data , 2013, Nucleic Acids Res..
[220] Pierre Tufféry,et al. BIOINFORMATICS ORIGINAL PAPER , 2022 .
[221] E. L. Cabot,et al. Simultaneous editing of multiple nucleic acid and protein sequences with ESEE , 1989, Comput. Appl. Biosci..
[222] Atsuko Yamaguchi,et al. TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model , 2014, Nucleic Acids Res..
[223] W. Taylor. A flexible method to align large numbers of biological sequences , 2005, Journal of Molecular Evolution.
[224] Walter Fontana,et al. Fast folding and comparison of RNA secondary structures , 1994 .
[225] Tim J. P. Hubbard,et al. Dalliance: interactive genome viewing on the web , 2011, Bioinform..
[226] O Ritter,et al. X-HUSAR, an X-based graphical interface for the analysis of genomic sequences. , 1995, Computer methods and programs in biomedicine.
[227] Philip Lijnzaad,et al. The Ensembl genome database project , 2002, Nucleic Acids Res..
[228] R Staden,et al. An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. , 1982, Nucleic acids research.
[229] D. Haussler,et al. Assembly of the working draft of the human genome with GigAssembler. , 2001, Genome research.
[230] Kei-Hoi Cheung,et al. BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.
[231] Dieter Schmalstieg,et al. Caleydo: connecting pathways and gene expression , 2009, Bioinform..
[232] J. Tate,et al. The RNA WikiProject: community annotation of RNA families. , 2008, RNA.
[233] Hiroaki Kitano,et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..
[234] Carole A. Goble,et al. The myGrid ontology: bioinformatics service discovery , 2007, Int. J. Bioinform. Res. Appl..
[235] Rodrigo Lopez,et al. Web services at the European Bioinformatics Institute-2009 , 2009, Nucleic Acids Res..
[236] Michael Y. Galperin,et al. The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection , 2013, Nucleic Acids Res..
[237] M Parker. Biological data access through Gopher. , 1993, Trends in biochemical sciences.
[238] Steve Pettifer,et al. BioXSD: the common data-exchange format for everyday bioinformatics web services , 2010, Bioinform..
[239] D D Womble. Web-based interfaces for the GCG sequence analysis programs. , 2000, Methods in molecular biology.
[240] Peter M. Kasson,et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..
[241] Michael Y. Galperin,et al. The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection , 2011, Nucleic Acids Res..
[242] Rodrigo Lopez,et al. Web Services at the European Bioinformatics Institute , 2007, Nucleic Acids Res..
[243] Yves Moreau,et al. ECCB 2014: The 13th European Conference on Computational Biology , 2014, Bioinform..
[244] Hernán F. Morales,et al. BioSmalltalk: a pure object system and library for bioinformatics , 2013, Bioinform..
[245] J. Thompson,et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.
[246] G. K. Sandve,et al. The Genomic HyperBrowser: inferential genomics at the sequence level , 2010, Genome Biology.
[247] Carole A. Goble,et al. BioCatalogue: a universal catalogue of web services for the life sciences , 2010, Nucleic Acids Res..
[248] Andreas Prlic,et al. Sequence analysis , 2003 .
[249] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[250] S. Schuster,et al. Model of Tryptophan Metabolism, Readily Scalable Using Tissue-specific Gene Expression Data* , 2013, The Journal of Biological Chemistry.
[251] Benjamin T. Porebski,et al. Interactive visualization tools for the structural biologist , 2013, Journal of applied crystallography.
[252] Akira R. Kinjo,et al. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium* , 2010, J. Biomed. Semant..
[253] J. Devereux,et al. A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..
[254] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..
[255] D. Higgins,et al. See Blockindiscussions, Blockinstats, Blockinand Blockinauthor Blockinprofiles Blockinfor Blockinthis Blockinpublication Clustal: Blockina Blockinpackage Blockinfor Blockinperforming Multiple Blockinsequence Blockinalignment Blockinon Blockina Minicomputer Article Blockin Blockinin Blockin , 2022 .
[256] Oliver Hofmann,et al. ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level , 2010, Bioinform..
[257] Peter Murray-Rust,et al. Development of chemical markup language (CML) as a system for handling complex chemical content , 2001 .
[258] Rodger Staden,et al. An X windows and UNIX implementation of our sequence analysis package , 1991, Comput. Appl. Biosci..
[259] Di Tommaso Paolo,et al. A novel tool for highly scalable computational pipelines , 2014 .
[260] Jill P Mesirov,et al. Accessible Reproducible Research , 2010, Science.
[261] Jian Hu,et al. Design and implementation of a CORBA-based genome mapping system prototype , 1998, Bioinform..
[262] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[263] H. Mangalam,et al. The Bio* toolkits--a brief overview. , 2002, Briefings in bioinformatics.
[264] John Chilton,et al. Portable workflow and tool descriptions with the CWL , 2015 .
[265] Terri K. Attwood,et al. The EMBRACE web service collection , 2010, Nucleic Acids Res..
[266] Burkhard Rost,et al. The PredictProtein server , 2003, Nucleic Acids Res..
[267] Katerina Michalickova,et al. BIR Pipeline for Preparation of Phylogenomic Data , 2015, Evolutionary bioinformatics online.
[268] Pietro Liò,et al. The BioMart community portal: an innovative alternative to large, centralized data repositories , 2015, Nucleic Acids Res..
[269] Patrick Lambrix,et al. Workshop on laboratory protocol standards for the Molecular Methods Database. , 2013, New biotechnology.
[270] Robert D. Finn,et al. Integrating sequence and structural biology with DAS , 2007, BMC Bioinformatics.
[271] Mudita Singhal,et al. COPASI - a COmplex PAthway SImulator , 2006, Bioinform..
[272] Sattanathan Subramanian,et al. Optimizing the Data-Traffic of Centrally Coordinated Scientific Workflow Systems , 2010, 2010 IEEE International Conference on Web Services.
[273] Kim Rutherford,et al. Artemis: sequence visualization and annotation , 2000, Bioinform..
[274] Robert D. Finn,et al. Making your database available through Wikipedia: the pros and cons , 2011, Nucleic Acids Res..
[275] Knut Reinert,et al. SeqAn An efficient, generic C++ library for sequence analysis , 2008, BMC Bioinformatics.
[276] Steve Pettifer,et al. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats , 2013, Bioinform..
[277] R. Durbin,et al. The Sequence Ontology: a tool for the unification of genome annotations , 2005, Genome Biology.
[278] Minoru Kanehisa,et al. KEGG API: A Web Service Using SOAP/WSDL to Access the KEGG System , 2003 .
[279] Vladimir Makarenkov,et al. Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations , 2012, PloS one.
[280] Reinhard Dölz. The EMBnet Project-European Molecular Biology Network , 1992, Comput. Networks ISDN Syst..