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BMC Bioinformatics

ISSN Print: 1471-2105

ISSN Online:

Website: http://www.biomedcentral.com/bmcbioinformatics

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Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information

Panwar Bharat,Gupta Sudheer,Raghava Gajendra P S

SRAdb: query and use public next-generation sequencing data from within R

Zhu Yuelin,Stephens Robert M,Meltzer Paul S,Davis Sean R

Negated bio-events: analysis and identification

Nawaz Raheel,Thompson Paul,Ananiadou Sophia

An integrated pharmacokinetics ontology and corpus for text mining

Wu Heng-Yi,Karnik Shreyas,Subhadarshini Abhinita,Wang Zhiping

MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis

Klepper Kjetil,Drabl？s Finn

Machine learning methods can replace 3D profile method in classification of amyloidogenic hexapeptides

Stanislawski Jerzy,Kotulska Malgorzata,Unold Olgierd

Accurate prediction of protein enzymatic class by N-to-1 Neural Networks

Volpato Viola,Adelfio Alessandro,Pollastri Gianluca

The taxonomic name resolution service: an online tool for automated standardization of plant names

Boyle Brad,Hopkins Nicole,Lu Zhenyuan,Raygoza Garay Juan Antonio

A Bayesian method and its variational approximation for prediction of genomic breeding values in multiple traits

Hayashi Takeshi,Iwata Hiroyoshi

Mojo Hand, a TALEN design tool for genome editing applications

Neff Kevin L,Argue David P,Ma Alvin C,Lee Han B

FANTOM: Functional and taxonomic analysis of metagenomes

Sanli Kemal,Karlsson Fredrik H,Nookaew Intawat,Nielsen Jens

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

Cotten Cameron,Reed Jennifer L

Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure

Bak？？ Yasin,Otu Hasan H,Ta？？？ Nivart,Meydan Cem

ACG: rapid inference of population history from recombining nucleotide sequences

O'Fallon Brendan D

HTQC: a fast quality control toolkit for Illumina sequencing data

Yang Xi,Liu Di,Liu Fei,Wu Jun

A novel application of motion analysis for detecting stress responses in embryos at different stages of development

Tills Oliver,Bitterli Tabitha,Culverhouse Phil,Spicer John I

A domain-centric solution to functional genomics via dcGO Predictor

Fang Hai,Gough Julian

xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data

Uppal Karan,Soltow Quinlyn A,Strobel Frederick H,Pittard W Stephen

SyntTax: a web server linking synteny to prokaryotic taxonomy

Oberto Jacques

Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

Doran Anthony G,Creevey Christopher J

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison

Seitzer Phillip,Huynh Tu Anh,Facciotti Marc T

XperimentR: painless annotation of a biological experiment for the laboratory scientist

Tomlinson Chris D,Barton Geraint R,Woodbridge Mark,Butcher Sarah A

Seq2Ref: a web server to facilitate functional interpretation

Li Wenlin,Cong Qian,Kinch Lisa N,Grishin Nick V

Discovery and analysis of consistent active sub-networks in cancers

Gaire Raj K,Smith Lorey,Humbert Patrick,Bailey James

Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

Suleiman A Khan, Ali Faisal, John P Mpindi, Juuso A Parkkinen, Tuomo Kalliokoski, Antti Poso, Olli P Kallioniemi, Krister Wennerberg, Samuel Kaski

MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments

Peter W Collingridge, Steven Kelly

Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval

Lei Yuan, Alexander Woodard, Shuiwang Ji, Yuan Jiang, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

Jose C A Santos, Houssam Nassif, David Page, Stephen H Muggleton, Michael J E Sternberg

Developing a powerful In Silico tool for the discovery of novel caspase-3 substrates: a preliminary screening of the human proteome

Muneef Ayyash, Hashem Tamimi, Yaqoub Ashhab

BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins

Matti Kankainen, Teija Ojala, Liisa Holm

Consensus embedding: theory, algorithms and application to segmentation and classification of biomedical data

Satish Viswanath, Anant Madabhushi

ICGE: an R package for detecting relevant clusters and atypical units in gene expression

Itziar Irigoien, Basilio Sierra, Concepcion Arenas

Analysis of energy-based algorithms for RNA secondary structure prediction

Monir Hajiaghayi, Anne Condon, Holger H Hoos

Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling

Julien Pelé, Jean-Michel Bécu, Hervé Abdi, Marie Chabbert

graphite - a Bioconductor package to convert pathway topology to gene network

Gabriele Sales, Enrica Calura, Duccio Cavalieri, Chiara Romualdi

Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry

Jaesik Jeong, Xue Shi, Xiang Zhang, Seongho Kim, Changyu Shen

Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs

Hani Z Girgis, Ivan Ovcharenko

PANDAseq: paired-end assembler for illumina sequences

Andre P Masella, Andrea K Bartram, Jakub M Truszkowski, Daniel G Brown, Josh D Neufeld

proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis

David Rosenkranz, Hans Zischler

Assessing statistical significance in causal graphs

Leonid Chindelevitch, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek

PyElph - a software tool for gel images analysis and phylogenetics

Ana Brandu？a Pavel, Cristian Ioan Vasile

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

Cyrille Lepoivre, Aurélie Bergon, Fabrice Lopez, Narayanan B Perumal, Catherine Nguyen, Jean Imbert, Denis Puthier

TDT-HET: A new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data

Douglas Londono, Steven Buyske, Stephen J Finch, Swarkar Sharma, Carol A Wise, Derek Gordon

Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets

Fangzhou Yao, Jeff Coquery, Kim-Anh Lê Cao

Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets

Richard J Giuly, Maryann E Martone, Mark H Ellisman

Self-organizing ontology of biochemically relevant small molecules

Leonid L Chepelev, Janna Hastings, Marcus Ennis, Christoph Steinbeck, Michel Dumontier

MIPHENO: data normalization for high throughput metabolite analysis

Shannon M Bell, Lyle D Burgoon, Robert L Last

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

Akhil Kumar, Patrick F Suthers, Costas D Maranas

Protein docking prediction using predicted protein-protein interface

Bin Li, Daisuke Kihara

Convergent evolution in structural elements of proteins investigated using cross profile analysis

Kentaro Tomii, Yoshito Sawada, Shinya Honda

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