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 (10/2007 - 6/2009)

Please send us your favorite if we missed it.

May 2009

  • Blazewicz J, Bryja M, Figlerowicz M, Gawron P, Kasprzak M, Kirton E, Platt DP, J., Swiercz A, Szajkowski L (2009) Whole genome assembly from 454 sequencing output via modified DNA graph concept. Comput Biol Chem May 3 (e-pub ahead of print).

  • Brandon MC, Wallace DC, Baldi P (2009) Data structures and compression algorithms for genomic sequence data. Bioinformatics May 15 (e-pub ahead of print).

  • Davis FP, Eddy SR (2009) A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas. Bioinformatics May 4 (e-pub ahead of print).

  • Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, Primig M (2009) MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinformatics 10(1):151.

  • Holford ME, Rajeevan H, Zhao H, Kidd KK, Cheung KH (2009) Semantic web-based integration of cancer pathways and allele frequency data. Cancer Inform 8:19-30.

  • Hong MG, Pawitan Y, Magnusson PK, Prince JA (2009) Strategies and issues in the detection of pathway enrichment in genome-wide association studies. Hum Genet May 1. (e-pub ahead of print)]: .

  • Hussong R, Gregorius B, Tholey A, Hildebrandt A (2009) Highly accelerated feature detection in proteomics data sets using modern graphics processing units. Bioinformatics May 14 (e-pub ahead of print).

  • Kano Y, Baumgartner WAJ, McCrohon L, Ananiadou S, Cohen KB, Hunter L, Tsujii J (2009) U-Compare: share and compare text mining tools with UIMA. Bioinformatics May 4 (e-pub ahead of print).

  • Kofler R, Torres TT, Lelley T, Schlotterer C (2009) PanGEA: Identification of allele specific gene expression using the 454 technology. BMC Bioinformatics 210:143.

  • Le Fèvre F, Smidtas S, Combe C, Durot M, d'Alché-Buc F, Schachter V (2009) CycSim — an online tool for exploring and experimenting with genome-scale metabolic models. Bioinformatics May 6. (e-pub ahead of print).

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics May 18. (e-pub ahead of print).

  • Monzoorul HM, Tarini S, Dinakar K, Sharmila SM (2009) SOrt-ITEMS : Sequence Orthology based approach for Improved Taxonomic Estimation of Metagenomic Sequences. Bioinformatics May 13. (e-pub ahead of print).

  • Saladin A, Fiorucci S, Poulain P, Prevost C, Zacharias M (2009) PTools: an opensource molecular docking library. BMC Struct Biol 9(1):27.

  • Teo YY, Small KS (2009) A novel method for haplotype clustering and visualization. Genet Epidemiol May 28. (e-pub ahead of print).

  • Vishnepolsky B, Pirtskhalava M (2009) ALIGN_MTX-An optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment. Comput Biol Chem May 3. (e-pub ahead of print).

  • Zaslavskiy M, Bach F, Vert JP (2009) Global alignment of protein-protein interaction networks by graph matching methods. Bioinformatics 25(12):1259-1267.

April 2009

  • Bao H, Guo H, Wang J, Zhou R, Lu X, Shi S (2009) MapView: visualization of short reads alignment on a desktop computer. Bioinformatics 25(12) 1554-1555. [download]

  • Daemen A, Gevaert O, Ojeda F, Debucquoy A, Suykens JA, Sempoux C, Machiels JP, Haustermans K, De Moor B (2009) A kernel-based integration of genome-wide data for clinical decision support. Genome Med 1(4):39.

  • Desmet FO, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C (2009) Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res 37(9):e67. [server]

  • Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Vooren SV, Moreau Y, Pettett RM, Carter NP (2009) DECIPHER: Database of chromosomal imbalance andphenotype in humans using Ensembl resources. Am J Hum Genet 84(4):524-533.[database]

  • Li H, Xing X, Ding G, Li Q, Wang C, Xie L, Zeng R, Li Y (2009) SysPTM - a systematic resource for proteomic research of post-translational modifications Mol Cell Proteomics Apr 14 (e-pub ahead of print). [server] [pdf]

  • Quandt A, Masselot A, Hernandez P, Hernandez C, Maffioletti S, Appel RD, Lisacek F (2009) SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid. Proteomics Apr 24. (e-pub ahead of print). [server]

  • Schatz MC (2009) CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics Apr 8 (e-pub ahead of print). [software]

  • Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR (2009) FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome Biol 10(4):R39.[pdf] [database]

  • Suchard MA, Rambaut A (2009) Many-Core algorithms for statistical phylogenetics. Bioinformatics Apr 15. (e-pub ahead of print). [software]

  • Tabei Y, Asai K (2009) A local multiple alignment method for detection of non-coding RNA sequences. Bioinformatics Apr 17. (e-pub ahead of print). [software]


March 2009

  • Antonov AV, Dietmann S, Wong P, Mewes HW (2009) TICL - a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics. FEBS Journal 2009 276(7):2084 - 2094. [server]

  • Bengtsson H, Ray A, Spellman P, Speed TP (2009) A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods. Bioinformatics 25(7):861 - 867.

  • Chelala C, Khan A, Lemoine NR (2009) SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics 25(5):655-661. [database]

  • Chen FC, Chen YZ, Chuang TJ (2009) CNVVdb: a database of copy number variations across vertebrate genomes. Bioinformatics Mar 25 (e-pub ahead of print). [database]

  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25. [pdf] [software]

  • Lee J, Kim SH (2009) PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI. Acta Crystallogr D Biol Crystallogr D65:399-402. [software]

  • Macpherson JI, Pinney JW, Robertson DL (2009) JNets: Exploring networks by integrating annotation. BMC Bioinformatics 10(1):95. [pdf] [software]

  • McComb T, Cairncross O, Noske AB, Wood DL, Marsh BJ, Ragan MAI (2009) Iloura: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data. Bioinformatics 25(9) 1208-1210. [software]

  • Messina DN, Sonnhammer EL (2009) DASher: a stand alone protein sequence client for DAS, the Distributed Annotation System. Bioinformatics Mar 17. (e-pub ahead of print). [software]

  • Nawrocki EP, Kolbe DL, Eddy SR (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics 25(10):1335-1337 [software]

  • Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH (2009) Local DNA topography correlates with functional noncoding regions of the human genome. Science 324(5925) 389 - 392. [abstract]

  • Rausch T, Koren S, Denisov G, Weese D, Emde AK, Doring A, Reinert K (2009) A Consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics 25(9) 1118 - 1124. [software]

  • Wang Y, Huang Z, Wu Y, Malmberg RL, Cai L (2009) RNATOPS-W: A web server for RNA structure searches of genomes. Bioinformatics 25(8):1080 - 1081. [server] [software]

  • Westesson O, Holmes I (2009) Accurate detection of recombinant breakpoints in whole-genome alignments. . PLoS Comput Biol 5(3):e1000318. [pdf] {software on request]

  • Xu H, Wang L, Sallans L, Freitas MA (2009) A hierarchical MS(2)/MS(3) database search algorithm for automated analysis of phosphopeptide tandem mass spectra. Proteomics 9(7)1763-1770.

February 2009

  • Ackermann M, Strimmer K (2009) A general modular framework for gene-set enrichment analysis. BMC Bioinformatics 10:47. [pdf]

  • Antonov AV, Dietmann S, Wong P, Igor R, Mewes HW (2009) PLIPS, an automatically collected database of protein lists reported by proteomics studies. J Proteome Res Feb 13. (e-pub ahead of print). [site]

  • Benoukraf T, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau JC, Spicuglia S, Ferrier P (2009) CoCAS: A ChIP-on-chip Analysis Suite. Bioinformatics Feb 4 (e-pub ahead of print).[software]

  • Biegert A, Söding J (2009) Sequence context-specific profiles for homology searching. Proc Natl Acad Sci USA Feb 20. (e-pub ahead of print) [pdf] [download]

  • Bryant DWJ, Wong WK, Mockler TC (2009) QSRA - a quality-value guided de novo short read assembler. BMC Bioinformatics 10(69). [pdf] [software]

  • Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, Manavski S, Vitulo N, Valle G (2009) PASS: a program to align short sequences. Bioinformatics Feb 13 (e-pub ahead of print) [software]

  • Eaves HL, Gao Y (2009) MOM: Maximum oligonucleotide mapping. Bioinformatics Feb 19 (e-pub ahead of print) [software]

  • Haynes BC, Brent MR (2009) Benchmarking regulatory network reconstruction with GRENDEL. Bioinformatics Feb 2 (e-pub ahead of print). [software]

  • Hur J, Schuyler AD, States DJ, Feldman EL (2009) SciMiner: Web-based literature mining tool for target identification and functional enrichment analysis. Bioinformatics Feb 2 (e-pub ahead of print). [software]

  • Jones AR, Siepen JA, Hubbard SJ, Paton NW (2009) Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics 9(5):1220 - 1229. [pdf]

  • Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB (2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol 10(2):R23. [pdf] [software]

  • Li H, Ding G, Xie L, Li Y (2009) PAnnBuilder: An R package for assembling proteomic annotation data. Bioinformatics Feb 23 (e-pub ahead of print). [software]

  • Lu Y, Sze SH (2009) Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Research 37(2):463-472. [software]

  • Paananen J, Wong G (2009) FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data. BMC Systems Biology 3:26. [pdf] [software]

  • Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R (2009) OnTheFly: A tool for automated document-based text annotation, data linking and network generation. Bioinformatics Feb 17 (e-pub ahead of print). [server]

  • Reynolds C, Damerell D, Jones S (2009) ProtorP: a protein–protein interaction analysis server. Bioinformatics 25(3):413 - 414. [server]

  • Schreyer A, Blundell T (2009) CREDO: a protein-ligand interaction database for drug discovery. Chem Biol Drug Des 73(2):157-167. [tools/api]

  • Vanlier J, Wu F, Qi F, Vinnakota KC, Han Y, Dash RK, Yang F, Beard DA (2009) BISEN: Biochemical Simulation Environment. Bioinformatics Feb 25 (e-pub ahead of print). [software]

January 2009

  • Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M (2009) Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics 10(1):31. [pdf] [site]

  • Bayjanov JR, Wels M, Starrenburg M, van Hylckama Vlieg JE, Siezen RJ, Molenaar D (2009) PanCGH: a genotype-calling algorithm for pangenome CGH data. Bioinformatics 25(3):309-314.

  • Chen TY, Ho JW, Liu H, Xie X (2009) An innovative approach for testing bioinformatics programs using metamorphic testing. BMC Bioinformatics 10(1):24. [pdf]

  • Chen Y, Chen W, Cobb MH, Zhao Y (2009) PTMap - A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites. Proc Natl Acad Sci USA 106(3):761-766.

  • Dubchak I, Poliakov A, Kislyuk A, Brudno M (2009) Multiple whole genome alignments without a reference organism. Genome Res Jan 28 (e-pub ahead of print).

  • Durinck S BJ, Spellman PT, Dudoit S. (2009) GenomeGraphs: integrated genomic data visualization with R. BMC Bioinformatics 10:2. [pdf] [download]

  • Gehlenborg N, Yan W, Lee IY, Yoo H, Nieselt K, Hwang D, Aebersold R, Hood L (2009) Prequips - An extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. Bioinformatics Jan 6. (e-pub ahead of print). [download]

  • Johnson AD, O'Donnell CJ (2009) An open access database of genome-wide association results. BMC Med Genet 2009 10(1):6. [pdf] [database]

  • Lee D, Seo H, Park C, Park K (2009) WeGAS: A web-based microbial genome annotation system. Biosci Biotechnol Biochem Jan 7 (e-pub ahead of print). [pdf]

  • Ma'ayan A, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn NS, Posner JM, Flores T, R. I (2009) SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. BMC Syst Biol 3(1):10. [pdf] [download]

  • Warren AS, Setubal JC (2009) The Genome Reverse Compiler: an explorative annotation tool. BMC Bioinformatics 10(1):35. [pdf] [download]

  • Xie X, Rigor P, Baldi P (2009) MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics 25(2):167-174. [download]

  • Yeung JM SP, Chan AS, Cherny SS. (2008) OpenADAM: an open source genome-wide association data management system for Affymetrix SNP arrays. BMC Genomics 9(1):636. [pdf] [download]

December 2008

  • Chen R, Mallelwar R, Thosar A, Venkatasubrahmanyam S, Butte AJ (2008) GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinformatics 9(1):548. [pdf] [download]

  • Hill J, Hambley M, Forster T, Mewissen M, Sloan TM, Scharinger F, Trew A, Ghazal P (2008) SPRINT: A new parallel framework for R. BMC Bioinformatics 9(1):558. [pdf] [download]

  • Kratz A, Tomita M, Krishnan A (2008) GeNESiS: gene network evolution simulation software. BMC Bioinformatics 9(1):541.[pdf] [database]

  • Nielsen J, Mailund T (2008) SNPFile - A software library and file format for large scale association mapping and population genetics studies. BMC Bioinformatics 9(1):526. [pdf] [download]

  • Paten B, Herrero J, Beal K, Birney E (2008) Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics Dec 4 (e-pub ahead of print). [download]

  • Pounds S, Cheng C, Mullighan C, Raimondi SC, Shurtleff S, Downing JR (2008) Reference Alignment of SNP Microarray Signals for Copy Number Analysis of Tumors. Bioinformatics Dec 3 (e-pub ahead of print). [download]

  • Rhee H, Lee JS (2008) MedRefSNP: a database of medically investigated SNPs. Hum Mutat Dec 22 (e-pub ahead of print).[site]

  • Stanislaus R, Carey M, Deus HF, Coombes K, Hennessy BT, Mills GB, Almeida JS (2008) RPPAML/RIMS: A meta data format and an information management system for Reverse Phase Protein Arrays. BMC Bioinformatics 9(1):555. [pdf] [download]

  • Yen CY, Meyer-Arendt K, Eichelberger B,  Sun S, Houel S, Old WM, Knight R, Ahn NG, Hunter LE, Resing KA (2008) A simulated MS/MS library for spectrum-to-spectrum searching in large-scale identification of proteins. Mol Cell Proteomics Dec 22 (e-pub ahead of print)

November 2008

  • Bryan K, Brennan L, Cunningham P (2008) MetaFIND: A feature analysis tool for metabolomics data. BMC Bioinformatics 9(1):470. [pdf] [download]

  • Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES (2008) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods Nov 30 (e-pub ahead of print).

  • Christley S, Lu Y, Li C, Xie X (2008) Human genomes as email attachments. Bioinformatics  Nov 7 (e-pub ahead of print). [download]

  • Huntley D, Tang YM, Nesterova TB, Butcher S, Brockdorff N (2008) Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features. BMC Bioinformatics 9(1):501. [pdf] [download]

  • Jensen JH, Hoeg-Jensen T, Padkjaer SB (2008) Building a BioChemformatics Database. J Chem Inf Model Nov 21 (e-pub ahead of print).

  • Ji H, Jiang H, Ma W, Johnson DS, Myers RM, et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26(11):1293-1300. [download]

  • Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE. (2008) CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics 9(1):482. [pdf] [download]

  • Mann B, Madera M, Sheng Q, Tang H, Mechref Y, Novotny MV (2008) ProteinQuant Suite: a bundle of automated software tools for label-free quantitative proteomics. Rapid Commun Mass Spectrom 22(23):3823-3834. [download]

  • Ondov BD, Varadarajan A, Passalacqua KD, Bergman NH (2008) Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications. Bioinformatics 24(23):2776-2777. [download]

  • Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R (2008) Arena3D: visualization of biological networks in 3D. BMC Syst Biol 2(1):104. [pdf] [download]

  • Reynolds C, Damerell D, Jones S (2008) ProtorP: A Protein-Protein Interaction Analysis Server. Bioinformatics  Nov 11 (e-pub ahead of print). [server]

  • Starcevic A, Zucko J, Simunkovic J, Long PF, Cullum J, Hranueli D (2008) ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structure. Nucleic Acids Res 36(21):6882 - 6892. [pdf] [download]

October 2008

  • Amigo J, Salas A, Phillips C, Carracedo A (2008) SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access. BMC Bioinformatics 9:428. [pdf] [download]

  • Daub J, Gardner PP, Tate J, Ramsköld D, Manske M, et al. (2008) The RNA WikiProject: Community annotation of RNA families. RNA e-pub ahead of print. [home site]

  • Delcher AL, Koren S, Miller JR, Venter E, Walenz BP, et al. (2008) Aggressive assembly of pyrosequencing reads with mates. Bioinformatics e-pub ahead of print. [download]

  • Descorps-Declere S, Barba M, Labedan B (2008) Matching curated genome databases: a non trivial task. BMC Genomics 9(1):501. [pdf] [server]

  • Gilchrist MJ, Christensen MB, Harland R, Pollet N, Smith JC, et al. (2008) Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data. BMC Bioinformatics 9(1):442. [pdf]

  • Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, et al. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 26(10):1155-1160. [home site]

  • Hon G, Ren B, Wang W (2008) ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol 4(10):e1000201. [download]

  • Kessner D, Chambers M, Burke R, Agus D, Mallick P (2008) ProteoWizard: open source software for rapid proteomics tools development. . Bioinformatics 24(21):2534-2536.[download]

  • Li W, Wooley JC, Godzik, A (2008) Probing metagenomics by rapid cluster analysis of very large datasets. PLoS ONE 3(10):e3375. [server]

  • Ondov B, Varadarajan A, Passalacqua KD, Bergman NH (2008) Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic application:. Bioinformatics Oct 7; e-pub ahead of print. [download]

  • Pencheva T, Lagorce D, Pajeva I, Villoutreix BO, Miteva MA (2008) AMMOS: Automated molecular mechanics optimization tool for in silico screening. BMC Bioinformatics 9(1):438. [pdf] [download]

  • Price MN, Dehal PS, Arkin AP (2008) FastBLAST: Homology relationships for millions of proteins. PLoS ONE 3(10):e3589.[download]

  • Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, et al. (2008) Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics 9:431

  • Schulz-Trieglaff O, Pfeifer N, GrÖpl C, Kohlbacher O, Reinert K (2008) LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics 9:423. [pdf] [download]

  • Zhang Z, Cheung KH, Townsend JP (2008) Bringing Web 2.0 to bioinformatics. Brief Bioinform Oct 8: e-pub ahead of print.

  • Zhu Y, Davis S, Stephens R, Meltzer PS, Chen Y (2008) GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus (GEO) Bioinformatics Oct 17: e-pub ahead of print. [server]

September 2008

  • Arita M, Suwa K (2008) Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database. BioData Min 1(1):7. [pdf]

  • Boyle AP, Guinney J, Crawford GE, Furey TS (2008) F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags. Bioinformatics (Sept 10 e-publication ahead of print). [download]

  • Brohée S, Faust K, Lima-Mendez G, Vanderstocken G, van Helden J (2008) Network Analysis Tools: from biological networks to clusters and pathways. Nat Protoc 3(10):1616 -1629. [server]

  • Creighton CJ, Nagaraja AK, Hanash SM, Matzuk MM, Gunaratne PH (2008) A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions. RNA (Sep 23 e-publication ahead of print). [download]

  • Jacob L, Hoffmann B, Stoven V, Vert JP (2008) Virtual screening of GPCRs: an in silico chemogenomics approach. BMC Bioinformatics 9:363. [pdf]

  • Meyer F, Paarmann D, D'Souza M, Olson RD, Glass EM, et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. [pdf] [server]

  • Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, et al. (2008) MeltDB: A software platform for the analysis and integration of metabolomics experiment data. Bioinformatics (Sep 2 e-publication ahead of print). [server] (login required)

  • Ohtsubo Y, Ikeda-Ohtsubo W, Nagata Y, Tsuda M (2008) GenomeMatcher: A graphical user interface for DNA sequence comparison. BMC Bioinformatics 9(1):376. [pdf] [download]

  • Rabani M, Kertesz M, Segal E (2008) Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci USA 105(39):14885 - 14890. [server and download]

  • Ranzinger R, Herget S, Wetter T, von der Lieth CW (2008) GlycomeDB - integration of open-access carbohydrate structure databases. BMC Bioinformatics 9:384.[pdf] [database]

  • Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M (2008) Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res (Aug 29 e-publication ahead of print).[download]

  • Vera G, Jansen RC, Suppi RL (2008) R/parallel - speeding up bioinformatics analysis with R. BMC Bioinformatics 9:390. [pdf] [download]

  • Wirawan A, Kwoh CK, Nim TH, Schmidt B (2008) CBESW: Sequence Alignment on the Playstation 3. BMC Bioinformatics 9:377. [pdf] [download]

  • Xiong B, Liu K, Wu J, Burk DL, Jiang H, et al. (2008) DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks. Bioinformatics 24(18):2117-2118. [download]

  • Zhu Y, Li H, Miller DJ, Wang Z, Xuan J, et al. (2008) caBIG VISDA: modeling, visualization, and discovery for cluster analysis of genomic data. BMC Bioinformatics 9:383. [pdf] [download]

  • Zimmermann O, Hansmann UH (2008) LOCUSTRA: Accurate Prediction of Local Protein Structure Using a Two-Layer Support Vector Machine Approach. J Chem Inf Model (Sep 3 e-publication ahead of print). [server]

August 2008

  • Andronescu M, Bereg V, Hoos HH, Condon A (2008) RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database. BMC Bioinformatics 9:340. [pdf] [database]

  • Cui J, Liu Q, Puett D, Xu Y (2008) Computational Prediction of Human Proteins That Can Be Secreted into the Bloodstream. Bioinformatics e-publication ahead of print. [Server]

  • De Bona F, Ossowski S, Schneeberger K, Ratsch G (2008) Optimal spliced alignments of short sequence reads. Bioinformatics 24(16):i174-i180.

  • Filangi O, Beausse Y, Assi A, Legrand L, Larre JM, et al. (2008) BioMAJ: a flexible framework for databanks synchronization and processing. Bioinformatics 24(16):1823-1825. [download]

  • Ganesan H, Rakitianskaia AS, Davenport CF, Tümmler B, Reva ON (2008) The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage. BMC Bioinformatics 9:333. [pdf] [server]

  • Ji S, Sun L, Jin R, Kumar S, Ye J (2008) Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinformatics 24(17):1881-1888.

  • Jiang H, Wong WH (2008) SeqMap: mapping massive amounts of oligonucleotides to the genome. Bioinformatics e-publication ahead of print. [download]

  • Lehmann J, Stadler PF, Prohaska SJ (2008) SynBlast: assisting the analysis of conserved synteny information. BMC Bioinformatics 9:351. [pdf] [download]

  • Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res e-publication ahead of print. [pdf] [download]

  • Marchisio MA, Stelling J (2008) Computational design of synthetic gene circuits with composable parts. Bioinformatics 24(17):1903-1910.

  • Nagy A, Hegyi H, Farkas K, Tordai H, Kozma E, et al. (2008) Identification and correction of abnormal, incomplete, and mispredicted proteins in public databases. BMC Bioinformatics 9:353. [pdf] [database]

  • Samal BB, Eiden LE (2008) pathFinder: a static network analysis tool for pharmacological analysis of signal transduction pathways. Sci Signal 1(31, pt4). [server]

  • Zhang F, Liu J, Chen J, Deng HW (2008) HAPSIMU: a genetic simulation platform for population-based association studies. BMC Bioinformatics 9:33. [pdf] [download]

July 2008

  • Carvalho PC, Fischer JS, Chen EI, Yates JRr, Barbosa VC (2008) PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics 9:316. [pdf] [Home Site]

  • Djebbari A, Quackenbush J (2008) Seeded Bayesian Networks: constructing genetic networks from microarray data. BMC Syst Biol 2:57. [pdf] [Implementation in TM4 microarray package]

  • Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, et al. (2008) FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24(15):1729-1730. [download]

  • Gao M, Skolnick J (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res 36(12):3978-3992. [pdf] [server]

  • Helsens K, Timmerman E, Vandekerckhove J, Gevaert K, Martens L (2008) Peptizer: A tool for assessing false positive peptide identifications and manually validating selected results. Mol Cell Proteomics e-publication ahead of print. [pdf] [download]

  • Huang ZX, Tian HY, Hu ZF, Zhou YB, Zhao J, et al. (2008) GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords. BMC Bioinformatics 9(1):308. [pdf] [download]

  • Larsen LS, Wassman CD, Hatfield GW, Lathrop RH (2008) Computationally optimised DNA assembly of synthetic genes. Int J Bioinform Res Appl 4(3):324-336.

  • Ortutay C, Vihinen M (2008) PseudoGeneQuest - a service for identification of different pseudogene types in the human genome. BMC Bioinformatics 9:299. [pdf] [server]

  • Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, et al. (2008) SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC Bioinformatics 9(1):313. [pdf] [server].

  • Smith AA, Vollrath A, Bradfield CA, Craven M (2008) Similarity queries for temporal toxicogenomic expression profiles. PLoS Comput Biol 4(7):e1000116. [pdf]

  • Theodosiou T, Darzentas N, Angelis L, Ouzounis CA (2008) PuReD-MCL: a graph-based PubMed document clustering methodology. Bioinformatics e-publication ahead of print. Server Reported to be here but the link was broken when tested.

  • Xu H, Wei CL, Lin F, Sung WK (2008) An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics e-publication ahead of print. [download]

  • Xu S, McCusker J, Krauthammer M (2008) Yale Image Finder (YIF): a new search engine for retrieving biomedical images. Bioinformatics e-publication ahead of print. [server]

June 2008

  • Bergmann FT, Sauro HM (2008) Comparing simulation results of SBML Capable Simulators. Bioinformatics e-publication ahead of print. [Home Site]

  • Goll J, Rajagopala SV, Shiau SC, Wu H, Lamb BT, et al. (2008) MPIDB: The microbial protein interaction database. Bioinformatics e-publication ahead of print. [Home Site]

  • Hsing M, Cherkasov A (2008) Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins. BMC Bioinformatics 9(1):293. [pdf] [Home Site]

  • Huang W, Marth GT (2008) EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res. e-publication ahead of print. [Download]

  • Jelier R, 't Hoen PA, Sterrenburg E, den Dunnen JT, van Ommen GJ, et al. (2008) Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease. BMC Bioinformatics 9:291. [pdf]

  • Keskin O, Nussinov R, Gursoy A (2008) Prism: protein-protein interaction prediction by structural matching. Methods Mol Biol 484:505-521. [Home Site] [Server]

  • Kundrotas PJ, Lensink MF, Alexov E (2008) Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles. Int J Biol Macromol. e-publication ahead of print.

  • Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, et al. (2008) Database indexing for production MegaBLAST searches. Bioinformatics e-publication ahead of print. The published link in the Journal was incorrect. The correct link is here.

  • Sanderson MJ, Boss D, Chen D, Cranston KA, Wehe A (2008) The PhyLoTA browser: Processing GenBank for molecular phylogenetics research. Syst Biol 57(3):335-346. [Home Site]

  • Wright J, Wagner A (2008) The Systems Biology Research Tool: evolvable open-source software. BMC Systems Biology 2:55. [pdf] [Home Site]

  • Zhang HL, Lin HH, Tao L, Ma XH, Dai JL, et al. (2008) Prediction of antibiotic resistance proteins from sequence-derived properties irrespective of sequence similarity. Int J Antimicrob Agents e-publication ahead of print.

  • Zhao Z, Fu B, Alanis FJ, Summa CM (2008) Feedback algorithm and web-server for protein structure alignment. J Comput Biol 15(5):505-524. [server]

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-publication 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-publication 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-publication 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-publication 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-publication 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-publication 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-publication 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-publication ahead of print).

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