User Information

Reviews (2007)

  • Suderman, M. and Hallett, M. (2007) Tools for visually exploring biological networks. Bioinformatics. 23(20):2651. (pdf).

  • Helles, G. (2007) A comparative study of the reported performance of ab initio protein structure prediction algorithms. J. R. Soc. 5(21):387-96.

Software/Tool Papers (8/2007 - 5/2008)

Please send us your favorite if we missed it.

May 2008

  • Becker S, Palsson BO (2008) Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol 4:e1000082. [pdf]

  • Bogdan I, Rivers J, Beynon RJ, Coca D (2008) High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting. Bioinformatics May 3 (e-pub ahead of print).

  • Chi B, deLeeuw RJ, Coe BP, Ng RT, MacAulay C, et al. (2008) MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data. BMC Bioinformatics 20: 243. [pdf]

  • Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, et al. (2008) iTools: a framework for classification, categorization and integration of computational biology resources. PLoS ONE 3: e2265. [pdf] [Home Site].

  • Dolan PC, Denver DR (2008) TileQC: a system for tile-based quality control of Solexa data. BMC Bioinformatics 9:250. [pdf]

  • Lee SY, Skolnick J (2008) Benchmarking of TASSER_2.0: An improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophys J May 16 (e-pub ahead of print).

  • Li C (2008) Automating dChip: toward reproducible sharing of microarray data analysis. BMC Bioinformatics 9:231. [pdf]

  • Nicosia G, Stracquadanio G (2008) Generalized Pattern Search Algorithm for Peptide Structure Prediction. Biophys J May 16 (e-pub ahead of print).

  • Polpitiya AD, Qian WJ, Jaitly N, Petyuk VA, Adkins JN, et al. (2008) DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinformatics May 3 (e-pub ahead of print). [Home Site]

  • Porter CJ, Palidwor GA, Sandie R, Krzyzanowski PM, Muro EM, et al. (2007) StemBase: a resource for the analysis of stem cell gene expression data. Methods Mol Biol 407: 137-148.

  • Ritchie W, Theodule FX, Gautheret D (2008) Mireval: a web tool for simple microRNA prediction in genome sequences. Bioinformatics 24:1394-1396. [Home Site]

  • Sacan A, Ferhatosmanoglu HC, H (2008) CellTrack: An Open-Source Software for Cell Tracking and Motility Analysis. Bioinformatics May 29 (e-pub ahead of print). [Home Site]

  • White WT, Hendy MD (2008) Compressing DNA sequence databases with COIL. BMC Bioinformatics 9: 242. [pdf]

  • Wilm A, Higgins DG, Notredame C (2008) R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Research 36: e52. [pdf] [Download]

  • You FM, Huo N, Gu YQ, Luo MC, Ma Y, et al. (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253. [pdf] [Home Site]

April 2008

  • Castrignano, T., M. D'Antonio, A. Anselmo, D. Carrabino, A. D'Onorio De Meo, A. M. D'Erchia, F. Licciulli, M. Mangiulli, F. Mignone, G. Pavesi, E. Picardi, A. Riva, R. Rizzi, P. Bonizzoni and G. Pesole (2008). "A database resource for alternative splicing analysis." Bioinformatics 24(10): 1300-1304.

  • Daigle, B. J. J. and R. B. Altman (2008). "M-BISON: microarray-based integration of data sources using networks." BMC Bioinformatics 9: 214. [pdf]

  • Dandass, Y. S., S. C. Burgess, M. Lawrence and S. M. Bridges (2008). "Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research." BMC Bioinformatics 9: 197. [pdf]

  • Friedländer, M. R., W. Chen, C. Adamidi, J. Maaskola, R. Einspanier, S. Knespel and N. Rajewsky (2008). "Discovering microRNAs from deep sequencing data using miRDeep." Nat. Biotechnol. 26(4): 407-415.

  • Guo, Y., L. Yu, Z. Wen and M. Li (2008) "Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences." Nucleic Acids Res. Apr 4 (e-pub ahead of print) [pdf].

  • Hoff, K. J., M. Tech, T. Lingner, R. Daniel, B. Morgenstern and P. Meinicke (2008)."Gene prediction in metagenomic fragments: a large scale machine learning approach." BMC Bioinformatics 9: 217. [pdf]

  • Kim, P. G., H. G. Cho and K. Park (2008) "A scaffold analysis tool using mate-pair information in genome sequencing." J. Biomed Biotechnol 2008: 675741. [pdf]

  • Li, W., J. S. Carroll, M. Brown and S. Liu (2008) "xMAN: extreme MApping of OligoNucleotides." BMC Genomics 9 (Suppl 1): S20. [pdf]

  • Pavesi, G., F. Zambelli, C. Caggese and G. Pesole (2008) "Exalign: a new method for comparative analysis of exon-intron gene structures." Nucleic Acids Res. Apr 8 (e-pub ahead of print). [pdf]

  • Quandt, A., P. Hernandez, A. Masselot, C. Hernandez, S. Maffioletti, C. Pautasso, R. D. Appel and F. Lisacek (2008) "swissPIT: A novel approach for pipelined analysis of mass spectrometry data." Bioinformatics Apr 23 (e-pub ahead of print).

  • Schutz, F. and M. Delorenzi (2008) "MAMOT: Hidden MArkov Modeling Tool." Bioinformatics Apr 25 (e-pub ahead of print).

  • Siepen, J. A., Belhajjame, K.Selley, J. N. Embury, S. N. Paton, N. W. Goble, C. A. Oliver, S., Stevens, R., Zamboulis, L., Martin, N., Poulovassillis, A.,Jones, P., Côté, R., Hermjakob, H., Pentony, M. M., Jones, D. T., Orengo, C. A., Hubbard, S. J. (2008) "ISPIDER Central: an integrated database web-server for proteomics." Nucleic Acids Res. Apr 25 (e-pub ahead of print) [pdf]

  • Spasic, I., D. Schober, S. A. Sansone, D. Rebholz-Schuhmann, D. B. Kell and N. Paton (2008) "Facilitating the development of controlled vocabularies for metabolomics technologies with text mining." BMC Bioinformatics 9 (Suppl 5): S5. [pdf]

March 2008

  • Cahan, P., L. E. Godfrey, P. S. Eis, T. A. Richmond, R. R. Selzer, M. Brent, H. L. McLeod, T. J. Ley and T. A. Graubert (2008). "wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data." Nucleic Acids Res 36(7): e47. [pdf]

  • Choi, J. H., S. Kim, H. Tang, J. Andrews, D. G. Gilbert and J. K. Colbourne (2008). "A machine-learning approach to combined evidence validation of genome assemblies." Bioinformatics 24(6): 744-750. [pdf]

  • Denisov, G., B. Walenz, A. L. Halpern, J. Miller, N. Axelrod, S. Levy and G. Sutton (2008). "Consensus Generation and Variant Detection by Celera Assembler." Bioinformatics 24(8): 1035-1040. [pdf]

  • Ferro, M., M. Tardif, E. Reguer, R. Cahuzac, C. Bruley, T. Vermat, E. Nugues, M. Vigouroux, Y. Vandenbrouck, J. Garin and A. Viari (2008). "PepLine: A Software Pipeline for High-Throughput Direct Mapping of Tandem Mass Spectrometry Data on Genomic Sequences." J. Proteome Research 7(5): 1873-1883.

  • Hernandez, D., P. François, L. Farinelli, M. Osterås and J. Schrenzel (2008). "De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer." Genome Research Apr 3 (e-pub ahead of print).

  • Laborde, T., M. Tomita and A. Krishnan (2008). "GANDivAWeb: A Web Server for detecting early folding units ('foldons') from protein 3D structures." BMC Struct Biol. 8(1): 15. [pdf]

  • Lai, W., V. Choudhary and P. J. Park (2008). "CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms." Bioinformatics 24(7): 1014-1015. [Software].

  • Parisien, M. and F. Major (2008). "The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data." Nature 452 (7183): 51-55.

  • Sanchez-Villeda, H., S. Schroeder, S. Flint-Garcia, K. E. Guill, M. Yamasaki and M. D. McMullen (2008). "DNAAlignEditor: DNA Alignment editor tool." BMC Bioinformatics 9: 154. [pdf] [software]

  • Sturm, M., A. Bertsch, C. Groepl, A. Hildebrandt, R. Hussong, E. Lange, N. Pfeifer, O. Schulz-Trieglaff, A. Zerck, K. Reinert and O. Kohlbacher (2008). "OpenMS - An open-source software framework for mass spectrometry." BMC Bioinformatics 9(163 ). [pdf]

  • Visvanathan, M., M. Breit, B. Pfeifer, C. Baumgartner, R. Modre-Osprian and B. Tilg (2008). "DMSP - Database for Modeling Signaling Pathways. Combining Biological and Mathematical Modeling Knowledge for Pathways." Methods Inf Med. 47(2): 140-148.

  • Zhang, J., S. He, C. X. Ling, X. Cao, R. Zeng and W. Gao (2008). "PeakSelect: preprocessing tandem mass spectra for better peptide identification." Rapid Commun. Mass Spectrometry 22(8): 1203-1212.

February 2008

  • Cai, J.J. (2008) "PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution." J Hered. Feb 29 (e-pub ahead of print). Software.

  • Fourment, M. and Gillings, M.R. (2008) "A comparison of common programming languages used in bioinformatics." BMC Bioinformatics. 9:82. [pdf] NOTE: This paper is currently our most popular download. Our team does not dispute its general conclusions, these are anecdotally shared by most developers. However, the methodology is deeply flawed. Please visit the comments on this paper.

  • Ge, D., Zhang, K., Need, A., Martin, O., Fellay, J., Urban, T.J., Telenti, A., and Goldstein, D.B. (2008) "WGAViewer: A Software for Genomic Annotation of Whole Genome Association Studies." Genome Research 18(4): 640-643

  • Hamilton, N.A. and Teasdale, R.D. (2008) "Visualizing and clustering high throughput sub-cellular localization imaging." BMC Bioinformatics 9:81. [pdf].

  • Kalaev, M., Smoot, M., Ideker, T., and Sharan, R. (2008) "NetworkBLAST: comparative analysis of protein networks." Bioinformatics 24(4):594-596. Software.

  • Li, R., Li, Y., Kristiansen, K., and Wang, J. (2008) "SOAP: short oligonucleotide alignment program." Bioinformatics 24(5):713-714. [Software].

  • Liu, Q., Olman, V., Liu, H., Ye, X., Qiu, S., and Xu, Y. (2008) "RNACluster: An integrated tool for RNA secondary structure comparison and clustering." J Computational Chem. 29(9):1517-1526 .

  • Morris, J.S., Clark, B.N., and Gutstein, H.B. (2008) "Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data." Bioinformatics. 24(4):529-536. [pdf]

  • Rohde, C., Zhang, Y., Jurkowski, T.P., Stamerjohanns, H., Reinhardt, R., and Jeltsch, A. (2008) "Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis." Nucleic Acids Res. Feb 22 (e-pub ahead of print). [Software].

  • Sharikov, Y., Walker, R.C., Greenberg, J., Kouznetsova, V., Nigam, S.K., Miller, M. A, Masliah, E., Tsigelny, I.F. (2008) "MAPAS: a tool for predicting membrane-contacting protein surfaces." Nature Methods 5(2):119.

  • Zhang, S., Kumar, K., Jiang, X., Wallqvist, A., and Reifman, J. (2008) "DOVIS: an implementation for high-throughput virtual screening using AutoDock." BMC Bioinformatics. 9:126. [pdf]

January 2008

  • Brylinski, M. and Skolnick, J. (2007) A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation Proc Natl Acad Sci USA.105(1):129-134.

  • Droit, A., Hunter, J.M., Rouleau, M., Ethier, C., Picard-Cloutier, A., Bourgais, D., and Poirier, G.G. (2007) PARPs Database: A LIMS systems for protein-protein interaction data mining or Laboratory Information management system. BMC Bioinformatics. 8(1):483.

  • Givan, S.A., Sullivan, C.M., and Carrington, J.C. (2007) The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases. BMC Bioinformatics. 8:479. Server. [pdf]

  • Gross, S.S., Do, C.B., Sirota, M., and Batzoglou, S. (2007) CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol. . 8(12):R269

  • Laibe, C. and Le Novere, N. (2007) MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Syst Biol. 1(1):58.

  • Li, C. and Li, M. (2008) GWAsimulator: a rapid whole-genome simulation program. Bioinformatics. 24(1):140-142.

  • Mayer, U. (2008) Protein Information Crawler (PIC): Extensive spidering of multiple protein information resources for large protein sets. Proteomics. 8(1):42-44.

  • Pandya, G.A., Holmes, M.H., Sunkara, S., Sparks, A., Bai, Y., Verratti, K., Saeed, K., Venepally, P., Jarrahi, B., Fleischmann, R.D., and Peterson, S.N. (2007) A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform. Nucleic Acids Res. 35(21):e148. [pdf]

  • Zemla, A., Geisbrecht, B., Smith, J., Lam, M.K., B., Wagner, M., Slezak, T., and Zhou, C.E. (2007) STRALCP — structure alignment-based clustering of proteins. . Nucleic Acids Res.35(22):e150. [pdf]

  • Zimin, A.V., Smith, D.R., Sutton, G., and Yorke, J.A. (2008) Assembly reconciliation. Bioinformatics. 24 (1):42-45.

  • Adler, J. Reimand, J. Jänes, R. Kolde, H. Peterson and J. Vilo (2008) KEGGanim: pathway animations for high-throughput data. Bioinformatics  24(4) 588-590. http://biit.cs.ut.ee/KEGGanim/

  • C. Beauheim, F. Wymore, M. Nitzberg, Z. Zachariah, H. Jin, J. Skene, C. Ball and G. Sherlock (2007) OntologyWidget — a reusable, embeddable widget for easily locating ontology terms. BMC Bioinformatics 8:338.  http://smd.stanford.edu/ontologyWidget
  • S. Bhave, C. Hornbaker, T. Phang, L. Saba, R. Lapadat, K. Kechris, J. Gaydos, McGoldrick D, Dolbey A, S. Leach, B. Soriano, A. Ellington, E. Ellington, K. Jones, J. Mangion, J. Belknap, R. Williams, Hunter LE, P. Hoffman and B. Tabakoff (2007) The PhenoGen Informatics website: tools for analyses of complex traits. BMC Genetics  8(1):59.  http://phenogen.uchsc.edu/
  • J. Chen, E. Linstead, S. Swamidass, D. Wang and P. Baldi (2007) ChemDB update — full-text search and virtual chemical space. Bioinformatics  23(17): 2348 - 2351. http://cdb.ics.uci.edu/CHEM/Web/
  • S. Chen, T. Zhao, G. Gordon and R. Murphy (2007) Automated image analysis of protein localization in budding yeast. Bioinformatics  23(13): i66-i71. http://murphylab.web.cmu.edu/software

  • A. Droit, J. M. Hunter, M. Rouleau, C. Ethier, A. Picard-Cloutier, D. Bourgais and G. G. Poirier (2007) PARPs Database: A LIMS systems for protein-protein interaction data mining or Laboratory Information management system. BMC Bioinformatics 19(8):483.
  • J. Faith, A. Olson, T. Gardner and R. Sachidanandam (2007) Lightweight Genome Viewer: portable software for browsing genomics data in its chromosomal context. BMC Bioinformatics 8:344.  http://lwgv.sourceforge.net/
  • Y. Gao, D. Douguet, A. Tovchigrechko and I. Vakser (2007) DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking. Proteins: Structure, Function, and Bioinformatics  69(4):845 - 851.  http://dockground.bioinformatics.ku.edu/
  • S. Gräf, F. Nielsen, S. Kurtz, M. Huynen, E. Birney, H. Stunnenberg and P. Flicek (2007) Optimized design and assessment of whole genome tiling arrays. Bioinformatics  23(13): i195-i204.  http://www.ebi.ac.uk/~graef/arraydesign/.

  • S. S. Gross, C. B. Do, M. Sirota and S. Batzoglou (2007) CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol. 8(12):R269. http://contra.stanford.edu/contrast/

  • V. Hollich and E. L.L. Sonnhammer (2007) PfamAlyzer: domain-centric homology search. 23:3382-3383. http://pfamalyzer.sbc.su.se/pfamalyzer/
  • J. Huang, A. Gusnanto, K. O'Sullivan, J. Staaf, A. Borg, Y. Pawitan and (2007) Robust smooth segmentation approach for array CGH data analysis. Bioinformatics  23(18):2463-2469.  http://www.meb.ki.se/~yudpaw
  • X. Jiang, X. Jiang, G. Han, M. Ye and H. Zou (2007) Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics. BMC Bioinformatics 8:323.  [pdf]

  • C. Laibe and N. Le Novere (2007) MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Syst Biol. 1(1):58. http://www.ebi.ac.uk/compneur-srv/miriam/
  • J. Lee, D. Havaleshko, H. Cho, J. Weinstein, E. Kaldjian, J. Karpovich, A. Grimshaw and D. Theodorescu (2007) A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery. Proc Natl Acad Sci USA. 104(32):13086-91.  http://www.coxen.org

  • C. Li and M. Li (2008) GWAsimulator: a rapid whole-genome simulation program. Bioinformatics 24(1):140-142. http://biostat.mc.vanderbilt.edu/GWAsimulator

  • U. Mayer (2008) Protein Information Crawler (PIC): Extensive spidering of multiple protein information resources for large protein sets.Proteomics 8(1):42-44. http://www.zoo.uni-heidelberg.de/mfa/PIC.
  • J. Pandey, M. Koyutürk, Y. Kim, W. Szpankowski, S. Subramaniam and A. Grama (2007) Functional annotation of regulatory pathways. Bioinformatics  23(13): i377-i386.  http://www.cs.purdue.edu/homes/jpandey/narada/.

  • G. A. Pandya, M. H. Holmes, S. Sunkara, A. Sparks, Y. Bai, K. Verratti, K. Saeed, P. Venepally, B. Jarrahi, R. D. Fleischmann and S. N. Peterson (2007) A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform. Nucleic Acids Res. 35(21):e148.
  • T. Shtatland, D. Guettler, M. Kossodo, M. Pivovarov and R. Weissleder (2007) PepBank — a database of peptides based on sequence text mining and public peptide data sources. BMC Bioinformatics 8:280.  http://pepbank.mgh.harvard.edu/.
  • D. Winter, B. Vinegar, H. Nahal, R. Ammar, G. Wilson and N. Provart (2007) An "electronic fluorescent pictograph" browser for exploring and analyzing large-scale biological data sets. PLoS ONE  2: e718.  http://www.bar.utoronto.ca/
  • Z. Xiang, Y. Tian and Y. He (2007) PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biol. 8: R150.  http://www.phidias.us/

  • G. B. Zemla A, Smith J, Lam M, Kirkpatrick B, Wagner M, Slezak T, Zhou CE. (2007) STRALCP — structure alignment-based clustering of proteins. Nucleic Acids Res.  Nov 26 (e-pub ahead of print). http://as2ts.llnl.gov/AS2TS/STRALCP/index.html

  • A. V. Zimin, D. R. Smith, G. Sutton and J. A. Yorke (2007) Assembly reconciliation. Bioinformatics  24(1):42-45.