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Bioinformatics Tool-Related Papers of Note, July 2008

Carvalho PC, Fischer JS, Chen EI, Yates JR 3rd, Barbosa VC. PatternLab for proteomics: a tool for differential shotgun proteomics. [BMC Bioinformatics. 2008 Jul 21;9:316]: Describes PatternLab, a software tool for proteomics that includes two methods to pinpoint differences in protein profiles. The first method, ACFold, uses a combined criterion based on expression fold changes, the AC test, and the false-discovery rate to offer a "bird's-eye view" of differentially expressed proteins, according to the paper’s abstract. The second method, called nSVM for natural support vector machine, addresses experimental designs having multiple readings from each state. Available here

Djebbari A, Quackenbush J. Seeded Bayesian Networks: constructing genetic networks from microarray data. [BMC Syst Biol. 2008 Jul 4;2:57]: Presents a method that relies on information about gene-gene interactions to infer biologically relevant pathways from microarray data. The approach uses networks derived from the literature and protein-protein interaction data as “seeds for a Bayesian network analysis of microarray results,” according to the paper’s abstract. The authors demonstrate that seeded Bayesian Networks “have the ability to identify high-confidence gene-gene interactions, which can then be validated by comparison to other sources of pathway data.” Software implementing these methods is available as part of the TM4 microarray analysis package, available here

Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. [Bioinformatics. 2008 Aug 1;24(15):1729-30]: Describes a software application for interpreting ChIP-Seq data that includes the ability to identify areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. Available here.

Gao M, Skolnick J. DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. [Nucleic Acids Res. 2008 Jul;36(12):3978-92]: Introduces DNA-binding Domain Hunter, or DBD-Hunter, a method for identifying DNA-binding proteins and associated binding sites. The method combines structural comparison and the evaluation of a statistical potential that describes interactions between DNA base pairs and protein residues. Available here.

Helsens K, Timmerman E, Vandekerckhove J, Gevaert K, Martens L. Peptizer: A tool for assessing false positive peptide identifications and manually validating selected results. [Mol Cell Proteomics. 2008 Jul 30. (e-pub ahead of print)]: Describes Peptizer, a proteomics post-processing tool helps identify false-positive peptide identifications. “Existing post-processing tools typically rely on a fixed or semi-fixed set of assumptions in their attempts to optimize both the sensitivity and the specificity of peptide and protein identification using MS/MS spectra,” but are unable to “adapt to emerging technology-specific peculiarity,” the authors note in the abstract. Peptizer “solves this adaptability issue by making use of pluggable assumptions.” Available here

Huang ZX, Tian HY, Hu ZF, Zhou YB, Zhao J, Yao KT. GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords. [BMC Bioinformatics. 2008 Jul 13;9(1):308]: Describes GenCLiP (Gene Cluster with Literature Profiles), which searches gene lists to identify functional clusters of genes based on literature profiling. Available here

Larsen LS, Wassman CD, Hatfield GW, Lathrop RH. Computationally Optimised DNA Assembly of synthetic genes. [Int J Bioinform Res Appl. 2008;4(3):324-36]: Describes methods to overcome two key challenges in gene synthesis: improper assembly of oligonucleotides and oligonucleotide defects incurred during chemical synthesis. To address the first issue, the authors developed the CODA (Computationally Optimized DNA Assembly) algorithm, which uses the “degeneracy of the genetic code” to design overlapping oligonucleotides with thermodynamic properties for self-assembly into a single, linear, DNA product, according to the paper’s abstract. To address the second problem, the authors developed a hierarchical assembly strategy that “reduces the incorporation of defective oligonucleotides into full-length gene constructs.”

Ortutay C, Vihinen M. PseudoGeneQuest — service for identification of different pseudogene types in the human genome. [BMC Bioinformatics. 2008 Jul 2;9:299]: Introduces PseudoGeneQuest, an online tool to search the human genome for a given query sequence and to identify different types of pseudogenes — nonfunctional copies of genes — as well as novel genes and gene fragments. The service can detect pseudogenes that have arisen either by retrotransposition or segmental genome duplication, “many of which are not listed in the public pseudogene databases,” according to the paper’s abstract. Available here

Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN. 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. 2008 Jul 18;9(1):313]: Describes SpliceCenter, a suite of web-based applications designed to study the impact of splice variation on the interpretation of genomics data. SpliceCenter includes programs for analysis of RT-PCR primer/probe sets, effectors of RNAi, microarrays, and protein-targeting technologies. As an example, the authors note that RT-PCR validation of gene expression microarray results “may be unsuccessful if the two technologies target different splice variants,” so researchers require knowledge of the specific splice variants that are targeted. Available here.

Smith AA, Vollrath A, Bradfield CA, Craven M. Similarity queries for temporal toxicogenomic expression profiles. [PLoS Comput Biol. 2008 Jul 18;4(7):e1000116]: Discusses an approach for “answering similarity queries about gene expression time series that is motivated by the task of characterizing the potential toxicity of various chemicals,” according to the paper’s abstract. The method employs an alignment algorithm based on time warping that has several advantages over previous approaches, according to the authors: “It allows the user to impose fairly strong biases on the form that the alignments can take, and it permits a type of local alignment in which the entirety of only one series has to be aligned.” The method also uses a “relaxed spline interpolation” to predict expression responses for unmeasured time points.

Theodosiou T, Darzentas N, Angelis L, Ouzounis CA. PuReD-MCL: a graph-based PubMed document clustering methodology. [Bioinformatics. 2008 Jul 1. (e-pub ahead of print)]: Discusses a text-mining tool for PubMed called PuReD-MCL (Pubmed Related Documents-MCL), which is based on the graph clustering algorithm MCL. According to the paper’s abstract, PuReD-MCL avoids using natural language processing techniques, but instead “takes advantage of existing resources, available from PubMed,” and then clusters documents using the MCL graph clustering algorithm, which is based on graph flow simulation. Available here

Xu H, Wei CL, Lin F, Sung WK. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. [Bioinformatics. 2008 Jul 29. (e-pub ahead of print)]: Discusses ChIPDiff, a software package for the genome-wide comparison of histone modification sites identified by ChIP-seq. The software enables researchers to identify differential histone modification sites. ChIPDiff employs a hidden Markov model to infer the states of histone modification changes at each genomic location. Available here.

Xu S, McCusker J, Krauthammer M. Yale Image Finder (YIF): a new search engine for retrieving biomedical images. [Bioinformatics. 2008 Jul 9. (e-pub ahead of print)]: Presents Yale Image Finder, or YIF, a publicly accessible search engine that allows users to retrieve biomedical images and associated papers based on the text carried inside the images. Retrieved images link back to their source papers, allowing users to find related papers starting with an image of interest. Currently, YIF has indexed more than 140,000 images from more than 34,000 public-access biomedical journal papers, according to the authors. Available here.  

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