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In Print: Bioinformatics Tool-Related Papers of Note, Sept. 2004


Alam I, Dress A, Rehmsmeier, Fuellen G. Comparative homology agreement search: An effective combination of homology-search methods. [Proc. Natl. Acad. Sci. USA 2004 101 (38): 13814-13819]: Discusses a tool called comparative homology agreement search (CHASE), which integrates different search strategies to obtain a consensus homology. Availability: Upon request from author ([email protected]).

Aubert J, Bar-Hen A, Daudin JJ, Robin S. Determination of the differentially expressed genes in microarray experiments using local FDR. [BMC Bioinformatics 2004, 5:125]: Discusses the use of process intensity estimation methods to give estimates of the local false discovery rate (FDR) — the expected proportion of false positive genes in a set of genes — which may be considered as the probability for a gene to be false positive. Availability:

Berg J, Lässig M. Local graph alignment and motif search in biological networks. [Proc Natl Acad Sci USA. 2004 Sep 24]: Describes a search algorithm for topological motifs called graph alignment, a procedure with some analogies to sequence alignment. The algorithm is applied to the gene regulation network of Escherichia coli.

Camps-Valls G, Chalk A, Serrano-Lopez A, Martin-Guerrero J, Sonnhammer E. Profiled support vector machines for antisense oligonucleotide efficacy prediction. [BMC Bioinformatics 2004, 5:135]: Presents the use of support vector machines for prediction and analysis of antisense oligonucleotide efficacy. Availability:

Edwards RJ, Shields DC. GASP: Gapped Ancestral Sequence Prediction for Proteins. [BMC Bioinformatics. 2004 Sep 6;5(1):123]: Presents a new algorithm, GASP (Gapped Ancestral Sequence Prediction), for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Availability: Upon request from author ([email protected]).

Garwood K, McLaughlin T, Garwood C, et al. PEDRo: A database for storing, searching and disseminating experimental proteomics data. [BMC Genomics 2004, 5:68]: Describes the design, implementation, and use of the Proteome Experimental Data Repository (PEDRo), which makes proteomics data sets available for browsing, searching and downloading. Availability:

Gentleman R, Carey V, Bates D, et al. Bioconductor: open software development for computational biology and bioinformatics. [Genome Biology 2004, 5:R80]: Discusses the Bioconductor project, an open source software development initiative for computational biology and bioinformatics. Availability:

Getz G, Starovolsky A, Domany E. FSSP to SCOP and CATH (F2CS) Prediction Server. [arXiv pre-print server:]: Describes F2CS 2.00, an automated prediction method for SCOP and CATH protein classification. Availability:

Gordon PM, Sensen CW. Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays. [Nucleic Acids Res. 2004 Sep 29;32(17):e133]: Presents Osprey, a software package for calculating optimal oligonucleotides for DNA sequencing and the creation of microarrays based on either PCR-products or directly spotted oligomers. Availability:

Huang Y, Kowalski D. PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability. [BMC Bioinformatics 2004, 5:134]: Introduces PatternFinder, a web server that searches DNA sequences for matches to specific or flexible patterns, and analyzes DNA helical stability. Availability:

Karney C, Ferrara J, Brunner S. Method for Computing Protein Binding Affinity. [arXiv pre-print archive:]: Describes a method for computing the binding affinity of a ligand to a protein that involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein, and a special Monte Carlo move that allows transitions between the unbound and bound states.

Lopez-Campos GH, Martin-Sanchez F. AMANDA (Array MANagement Database): A Tool for Managing Microarray Experiments Data and Clinical Sample Annotation. [Medinfo. 2004;2004(CD):1728]: Introduces AMANDA (Array MANagement Database), a relational database designed to store and handle all the information related with microarray experiments that incorporates features specially designed for the clinical annotation of samples and sample collection procedures.

Maki Y, Takahashi Y, Arikawa Y, et al. An Integrated Comprehensive Workbench For Inferring Genetic Networks: Voyagene. [Journal of Bioinformatics and Computational Biology 2004 2(3): 533-550]: Discusses a network-inferring system for genetic interactions, named VoyaGene, which can analyze expression profiles by combining five inferring models: clustering, threshold-test, Bayesian, multi-level digraph and S-system models. Availability:

Mao L, Resat H. Probabilistic representation of gene regulatory networks. [Bioinformatics 2004 20(14):2258-2269]: Describes a probabilistic approach to the modeling of gene regulatory networks that allows for fluctuations in gene expression levels. The algorithm uses a simple representation for the genes, and accounts for the repression or induction of the genes and for the biological variations among isogenic populations simultaneously. Availability: Upon request from author ([email protected]).

Palopoli L, Terracina G. CooPPS: A System for the Cooperative Prediction of Protein Structures. [Journal of Bioinformatics and Computational Biology 2004 2(3): 471-495]: Describes a method for jointly applying several different protein structure prediction tools and combining their results in order to improve the quality of the predictions. Availability:

Pazos F, Sternberg M. Automated prediction of protein function and detection of functional sites from structure. [Proc Natl Acad Sci USA. 2004 Sep 29 (Epub ahead of print)]: Describes Phunctioneer, a method for structure-based function prediction using automatically extracted functional sites. The method relates proteins with the same function through structural alignments and extracts 3D profiles of conserved residues.

Pevzner PA, Tang H, Tesler G. De novo repeat classification and fragment assembly. [Genome Res. 2004 Sep;14(9):1786-96]: Introduces an algorithmic approach for classifying repetitive sequences that represents all repeats in a genome as a mosaic of sub-repeats. According to the authors, the concept also leads to new approaches to multiple alignment and fragment assembly that can improve on Phrap and Arachne.

Salzberg S, Chuche D, DiCuccio M, Yaschenko E, Ostell J. The Genome Assembly Archive: A New Public Resource. [PLoS Biol. 2004 September; 2 (9): e285]: Discusses the Assembly Archive, which was developed to store both an archival record of how a particular assembly was constructed and the alignments of any set of traces to a reference genome. The Assembly Archive’s first entries are a set of seven closely related strains of Bacillus anthracis. Availability:

Schmollinger M, Nieselt K, Kaufmann M, Morgenstern B. DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors. [BMC Bioinformatics. 2004 Sep 9;5(1):128]: Introduces a parallel version of the multi-alignment program DIALIGN. The paper discusses two ways of dividing the program into independent sub-routines that can be run on different processors: pair-wise sequence alignments that are used as a first step to multiple alignment; and heuristics for alignments of large genomic sequences that split up the sequences into sub-sequences based on a previously introduced anchored alignment procedure. Availability:

Von Öhsen N, Sommer I, Zimmer R, Lengauer T. Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. [Bioinformatics 2004 20(14):2228-2235]: Introduces Arby, a protein structure prediction server that combines several homology-based methods for predicting the three-dimensional structure of a protein, given its sequence. The methods used include a threading approach and a profile-profile alignment approach that incorporates secondary structure predictions. Availability:

Zheng C, Zhou H, Xie B, Han Y, Yap C, Chen Y. TRMP: a database of therapeutically relevant multiple pathways. [Bioinformatics 2004 20(14):2236-2241]: Introduces a database of known therapeutically relevant multiple pathways, which provides information about multiple pathways with related therapeutic targets, corresponding drugs/ligands, targeted disease conditions, constituent individual pathways, and structural and functional information about each protein in the pathways. Availability:

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