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In Print : Apr 30, 2009

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Bao H, Guo H, Wang J, Zhou R, Lu X, Shi S. MapView: visualization of short reads alignment on a desktop computer. [Bioinformatics. 2009 Apr 15. (e-pub ahead of print)]: Describes a visual analytics tool called MapView that represents large-scale short-read alignment data and genetic variation analysis. "MapView can handle hundreds of millions of short reads on a desktop computer with limited memory" and enables automated genetic variation detection, according to the paper's abstract. Available here.


Daemen A, Gevaert O, Ojeda F, Debucquoy A, Suykens JA, Sempoux C, Machiels JP, Haustermans K, De Moor B. A kernel-based integration of genome-wide data for clinical decision support. [Genome Med. 2009 Apr 3;1(4):39]: Describes a kernel-based approach for combining many genome-wide data sources in order to support clinical decision-making. Integration occurs "within the patient domain at the level of kernel matrices before building the classifier," the authors state in the paper's abstract. The method uses a weighted least squares support vector machine as its supervised classification algorithm. The authors note that in an example looking at cancer data, "the prediction of all outcomes improved when more than one genome-wide data set was considered," which "suggests that integrating multiple genome-wide data sources increases the predictive performance of clinical decision support models."


Desmet FO, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. [Nucleic Acids Res. 2009 Apr 1. (e-pub ahead of print)]: Describes Human Splicing Finder, a tool to predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence. HSF contains "all available matrices for auxiliary sequence prediction," as well as new ones for binding sites of the 9G8 and Tra2-beta serine-arginine proteins and the hnRNP A1 ribonucleoprotein, according to the paper's abstract. Available here.


Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Vooren SV, Moreau Y, Pettett RM, Carter NP. DECIPHER: Database of chromosomal imbalance andphenotype in humans using Ensembl resources. [Am J Hum Genet. 2009 Apr 1. (e-pub ahead of print)]: Discusses DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources), a database intended to help clinicians interpret problematic genotype-phenotype correlations. DECIPHER incorporates a suite of tools "designed to aid the interpretation of submicroscopic chromosomal imbalance, inversions, and translocations," the paper's abstract states. DECIPHER catalogs common copy-number changes in normal populations," and thus, by exclusion, enables changes that are novel and potentially pathogenic to be identified." Available here.


Li H, Xing X, Ding G, Li Q, Wang C, Xie L, Zeng R, Li Y. SysPTM - a systematic resource for proteomic research of post-translational modifications. [Mol Cell Proteomics. 2009 Apr 14 (e-pub ahead of print)]: Introduces a curated, web-accessible database of post-translational modifications called SysPTM. SysPTM includes a knowledge base of manually curated multi-type modification data, as well as four data-mining tools. The database currently contains information on 117,349 experimentally determined PTM sites on 33,421 proteins involving nearly 50 PTM types. Available here.


Quandt A, Masselot A, Hernandez P, Hernandez C, Maffioletti S, Appel RD, Lisacek F. SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid. [Proteomics. 2009 Apr 24. (e-pub ahead of print)]: Describes the Swiss protein identification toolbox, or swissPIT project, which "provides the scientific community with an expandable multitool platform for automated in-depth analysis of MS data." Currently, swissPIT supports four different programs implementing two different search strategies to identify MS/MS spectra. Available here.


Schatz MC. CloudBurst: highly sensitive read mapping with MapReduce. [Bioinformatics. 2009 Apr 8. (e-pub ahead of print)]: Presents CloudBurst, a new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes. The algorithm is modeled after the short-read mapping program RMAP, "and reports either all alignments or the unambiguous best alignment for each read with any number of mismatches or differences," according to the paper's abstract. "This level of sensitivity could be prohibitively time consuming, but CloudBurst uses the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes." According to the authors, CloudBurst's running time "scales linearly with the number of reads mapped, and with near linear speedup as the number of processors increases." Available here.


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. FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. [Genome Biol. 2009 Apr 19;10(4):R39]: Describes EdgeExpressDB, a database and set of interfaces for interpreting biological networks and comparing large expression datasets. The database summarizes gene expression patterns "in the context of alternative promoter structures and regulatory transcription factors and microRNAs using intuitive gene-centric and sub-network views," according to the paper's abstract. Available here.


Suchard MA, Rambaut A. Many-Core algorithms for statistical phylogenetics. [Bioinformatics. 2009 Apr 15. (e-pub ahead of print)]: Presents algorithms and methods for evaluating phylogenies under arbitrary molecular evolutionary models on graphics processing units. The authors implement the approach in an existing Bayesian framework to estimate the phylogeny of 62 complete mitochondrial genomes of carnivores under a 60-state codon model and report a "near 90-fold speed increase over an optimized CPU-based computation" and a more than 140-fold increase over the currently available implementation, "making this the first practical use of codon models for phylogenetic inference over whole mitochondrial or microorganism genomes." Available here.


Tabei Y, Asai K. A local multiple alignment method for detection of non-coding RNA sequences. [Bioinformatics. 2009 Apr 17. (e-pub ahead of print)]: Proposes a new local multiple alignment method for the detection of non-coding RNAs. The authors note that the alignment construction procedure is "inspired" by ProDA, a local multiple aligner program for protein sequences with repeated and shuffled elements. "In benchmark experiments, we demonstrate the high ability of the implemented software, SCARNA LM, for local multiple alignment for the detection of ncRNAs," the authors note in the paper's abstract. Available here.

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