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- Validation of double digest selective label database for sequenced prokaryotic genomes
- DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data
- PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches
- webMGR: an online tool for the multiple genome rearrangement problem
- Tmod: toolbox of motif discovery
- Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes
- Optimizing nucleotide sequence ensembles for combinatorial protein libraries using a genetic algorithm
- MATICCE: mapping transitions in continuous character evolution
- Ancestors 1.0: a web server for ancestral sequence reconstruction
- inGAP: an integrated next-generation genome analysis pipeline
Nucleic Acids Research
- A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data
- DNA structures from phosphate chemical shifts
- A rapid and sensitive method to detect siRNA-mediated mRNA cleavage in vivo using 5' RACE and a molecular beacon probe
- Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
- Specific local induction of DNA strand breaks by infrared multi-photon absorption
Bioinformatics
- Tmod: toolbox of motif discovery
- webMGR: an online tool for the multiple genome rearrangement problem
- PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches
- DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data
- Validation of double digest selective label database for sequenced prokaryotic genomes
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Validation of double digest selective label database for sequenced prokaryotic genomes
Submitted by bogdan on Sun, 2010-02-07 20:31Validation of double digest selective label database for sequenced prokaryotic genomes - Summary: A database for simulation of double digest selective label (DDSL) typing technique has been created and validated against a sequenced strain (Salmonella enterica serovar Typhimurium strain LT2).
DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data
Submitted by bogdan on Sun, 2010-02-07 20:30DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data - Summary: DNA copy number alterations (CNA) frequently underlie gene expression changes by increasing or decreasing gene dosage.
PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches
Submitted by bogdan on Sun, 2010-02-07 20:29Fortunately, R package developers finally got to the problem of parallel computations. An excerpt (below) from a recent Bioinformatics article is a good illustration.
webMGR: an online tool for the multiple genome rearrangement problem
Submitted by bogdan on Sun, 2010-02-07 20:27webMGR: an online tool for the multiple genome rearrangement problem - Summary: The algorithm MGR enables the reconstruction of rearrangement phylogenies based on gene or synteny block order in multiple genomes.
Tmod: toolbox of motif discovery
Submitted by bogdan on Sun, 2010-02-07 20:25Tmod: toolbox of motif discovery - Summary: Motif discovery is an important topic in computational transcriptional regulation studies.
Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes
Submitted by bogdan on Sun, 2010-02-07 20:23Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes - We present a new computational method for solving a classical problem, the identification problem of cis-regulatory motifs in a given set of promoter sequences, based on one key new idea.
Optimizing nucleotide sequence ensembles for combinatorial protein libraries using a genetic algorithm
Submitted by bogdan on Sun, 2010-02-07 20:21Optimizing nucleotide sequence ensembles for combinatorial protein libraries using a genetic algorithm - Protein libraries are essential to the field of protein engineering.
MATICCE: mapping transitions in continuous character evolution
Submitted by bogdan on Tue, 2009-12-29 23:33MATICCE: mapping transitions in continuous character evolution - Summary: MATICCE is a new software package in the R language for mapping phylogenetic transitions in organismal traits that have continuous distributions.
Ancestors 1.0: a web server for ancestral sequence reconstruction
Submitted by bogdan on Tue, 2009-12-29 23:32Ancestors 1.0: a web server for ancestral sequence reconstruction - Summary: The computational inference of ancestral genomes consists of five difficult steps: identifying syntenic regions, inferring ancestral arrangement of syntenic regions, aligning multiple sequences, reconstructing the insertion a
inGAP: an integrated next-generation genome analysis pipeline
Submitted by bogdan on Tue, 2009-12-29 23:32inGAP: an integrated next-generation genome analysis pipeline - Summary: We develop a novel mining pipeline, Integrative Next-generation Genome Analysis Pipeline (inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-thr