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  1. Gene expression profiling using microarrays has become an important genetic tool. Spotted arrays prepared in academic labs have the advantage of low cost and high design and content flexibility, but are often ...

    Authors: Xujing Wang, Shuang Jia, Lisa Meyer, Bixia Xiang, Li-Yen Chen, Nan Jiang, Carol Moreno, Howard J Jacob, Soumitra Ghosh and Martin J Hessner
    Citation: BMC Bioinformatics 2006 7:378
    Content type: Research article Published on:

  3. Automated comparison of complete sets of genes encoded in two genomes can provide insight on the genetic basis of differences in biological traits between species. Gene ontology (GO) is used as a common vocabu...

    Authors: Zhaotao Cai, Xizeng Mao, Songgang Li and Liping Wei
    Citation: BMC Bioinformatics 2006 7:374
    Content type: Methodology article Published on:

  4. Sphingosine 1-phosphate (S1P), a lysophospholipid, is involved in various cellular processes such as migration, proliferation, and survival. To date, the impact of S1P on human glioblastoma is not fully unders...

    Authors: Jeyakumar Natarajan, Daniel Berrar, Werner Dubitzky, Catherine Hack, Yonghong Zhang, Catherine DeSesa, James R Van Brocklyn and Eric G Bremer
    Citation: BMC Bioinformatics 2006 7:373
    Content type: Research article Published on:

  5. Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein ...

    Authors: Katrin Fundel and Ralf Zimmer
    Citation: BMC Bioinformatics 2006 7:372
    Content type: Research article Published on:

  7. Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological litera...

    Authors: David Chen, Hans-Michael Müller and Paul W Sternberg
    Citation: BMC Bioinformatics 2006 7:370
    Content type: Methodology article Published on:

  8. Biological tissues consist of various cell types that differentially contribute to physiological and pathophysiological processes. Determining and analyzing cell type-specific gene expression under diverse con...

    Authors: Martin Hoffmann, Dirk Pohlers, Dirk Koczan, Hans-Jürgen Thiesen, Stefan Wölfl and Raimund W Kinne
    Citation: BMC Bioinformatics 2006 7:369
    Content type: Methodology article Published on:

  9. Genome databases contain diverse kinds of information, including gene annotations and nucleotide and amino acid sequences. It is not easy to integrate such information for genomic study. There are few tools fo...

    Authors: Naoto Tanaka, Takashi Abe, Satoru Miyazaki and Hideaki Sugawara
    Citation: BMC Bioinformatics 2006 7:368
    Content type: Software Published on:

  10. We previously demonstrated that gene expression profiles during neuronal differentiation in vitro and hippocampal development in vivo were very similar, due to a conservation of the important second singular valu...

    Authors: Michal Dabrowski, Stein Aerts and Bozena Kaminska
    Citation: BMC Bioinformatics 2006 7:367
    Content type: Research article Published on:

  11. In the Bioinformatics field, a great deal of interest has been given to Non-negative matrix factorization technique (NMF), due to its capability of providing new insights and relevant information about the com...

    Authors: Alberto Pascual-Montano, Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M Carazo and Roberto D Pascual-Marqui
    Citation: BMC Bioinformatics 2006 7:366
    Content type: Software Published on:

  12. Identification of protein interaction networks has received considerable attention in the post-genomic era. The currently available biochemical approaches used to detect protein-protein interactions are all ti...

    Authors: Sylvain Pitre, Frank Dehne, Albert Chan, Jim Cheetham, Alex Duong, Andrew Emili, Marinella Gebbia, Jack Greenblatt, Mathew Jessulat, Nevan Krogan, Xuemei Luo and Ashkan Golshani
    Citation: BMC Bioinformatics 2006 7:365
    Content type: Research article Published on:

  13. In the area of protein structure prediction, recently a lot of effort has gone into the development of Model Quality Assessment Programs (MQAPs). MQAPs distinguish high quality protein structure models from in...

    Authors: Ingolf Sommer, Stefano Toppo, Oliver Sander, Thomas Lengauer and Silvio CE Tosatto
    Citation: BMC Bioinformatics 2006 7:364
    Content type: Methodology article Published on:

  14. Recent analyses in systems biology pursue the discovery of functional modules within the cell. Recognition of such modules requires the integrative analysis of genome-wide experimental data together with avail...

    Authors: Monica Chagoyen, Pedro Carmona-Saez, Concha Gil, Jose M Carazo and Alberto Pascual-Montano
    Citation: BMC Bioinformatics 2006 7:363
    Content type: Methodology article Published on:

  17. Recent technological advances have enabled high-throughput measurements of protein-protein interactions in the cell, producing large protein interaction networks for various species at an ever-growing pace. Ho...

    Authors: Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan and Trey Ideker
    Citation: BMC Bioinformatics 2006 7:360
    Content type: Research article Published on:

  18. Numerous feature selection methods have been applied to the identification of differentially expressed genes in microarray data. These include simple fold change, classical t-statistic and moderated t-statisti...

    Authors: Ian B Jeffery, Desmond G Higgins and Aedín C Culhane
    Citation: BMC Bioinformatics 2006 7:359
    Content type: Research article Published on:

  20. Protein sequence alignment is one of the basic tools in bioinformatics. Correct alignments are required for a range of tasks including the derivation of phylogenetic trees and protein structure prediction. Num...

    Authors: Tomas Ohlson, Varun Aggarwal, Arne Elofsson and Robert M MacCallum
    Citation: BMC Bioinformatics 2006 7:357
    Content type: Methodology article Published on:

  23. We present an effective, rapid, systematic data mining approach for identifying genes or proteins related to a particular interest. A selected combination of programs exploring PubMed abstracts, universal gene...

    Authors: Pavel Pospisil, Lakshmanan K Iyer, S James Adelstein and Amin I Kassis
    Citation: BMC Bioinformatics 2006 7:354
    Content type: Methodology article Published on:

  24. Studies of differential expression that use Affymetrix GeneChip arrays are often carried out with a limited number of replicates. Reasons for this include financial considerations and limits on the available a...

    Authors: Anne-Mette K Hein and Sylvia Richardson
    Citation: BMC Bioinformatics 2006 7:353
    Content type: Research article Published on:

  25. Immunological prevention of cancer has been obtained in HER-2/neu transgenic mice using a vaccine that combines 3 different immune stimuli (Triplex vaccine) that is repeatedly administered for the entire lifes...

    Authors: Pier-Luigi Lollini, Santo Motta and Francesco Pappalardo
    Citation: BMC Bioinformatics 2006 7:352
    Content type: Methodology article Published on:

  27. Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Dis...

    Authors: Alexander F Auch, Stefan R Henz, Barbara R Holland and Markus Göker
    Citation: BMC Bioinformatics 2006 7:350
    Content type: Research article Published on:

  28. Microarray technologies have become common tools in biological research. As a result, a need for effective computational methods for data analysis has emerged. Numerous different algorithms have been proposed ...

    Authors: Matti Nykter, Tommi Aho, Miika Ahdesmäki, Pekka Ruusuvuori, Antti Lehmussola and Olli Yli-Harja
    Citation: BMC Bioinformatics 2006 7:349
    Content type: Methodology article Published on:

  29. Increasing amounts of data from large scale whole genome analysis efforts demands convenient tools for manipulation, visualization and investigation. Whole genome plots offer an intuitive window to the analysi...

    Authors: Rohit Ghai, Hannes Lindemann and Trinad Chakraborty
    Citation: BMC Bioinformatics 2006 7:348
    Content type: Software Published on:

  31. A structure alignment method based on a local geometric property is presented and its performance is tested in pairwise and multiple structure alignments. In this approach, the writhing number, a quantity orig...

    Authors: Peter L Chang, Andrew W Rinne and T Gregory Dewey
    Citation: BMC Bioinformatics 2006 7:346
    Content type: Methodology article Published on:

  34. Modeling of gene expression data from time course experiments often involves the use of linear models such as those obtained from principal component analysis (PCA), independent component analysis (ICA), or ot...

    Authors: Peter D Wentzell, Tobias K Karakach, Sushmita Roy, M Juanita Martinez, Christopher P Allen and Margaret Werner-Washburne
    Citation: BMC Bioinformatics 2006 7:343
    Content type: Methodology article Published on:

  36. The Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data

    Authors: Randi Vita, Kerrie Vaughan, Laura Zarebski, Nima Salimi, Ward Fleri, Howard Grey, Muthu Sathiamurthy, John Mokili, Huynh-Hoa Bui, Philip E Bourne, Julia Ponomarenko, Romulo de Castro Jr, Russell K Chan, John Sidney, Stephen S Wilson, Scott Stewart…
    Citation: BMC Bioinformatics 2006 7:341
    Content type: Database Published on:

  38. Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of suc...

    Authors: Elaine C Meng, Eric F Pettersen, Gregory S Couch, Conrad C Huang and Thomas E Ferrin
    Citation: BMC Bioinformatics 2006 7:339
    Content type: Software Published on:

  40. Accurate interpretation of data obtained by unsupervised analysis of large scale expression profiling studies is currently frequently performed by visually combining sample-gene heatmaps and sample characteris...

    Authors: Roel GW Verhaak, Mathijs A Sanders, Maarten A Bijl, Ruud Delwel, Sebastiaan Horsman, Michael J Moorhouse, Peter J van der Spek, Bob Löwenberg and Peter JM Valk
    Citation: BMC Bioinformatics 2006 7:337
    Content type: Software Published on:

  41. Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. Innate protein repea...

    Authors: Mridul K Kalita, Gowthaman Ramasamy, Sekhar Duraisamy, Virander S Chauhan and Dinesh Gupta
    Citation: BMC Bioinformatics 2006 7:336
    Content type: Database Published on:

  42. Microarrays are routinely used to assess mRNA transcript levels on a genome-wide scale. Large amount of microarray datasets are now available in several databases, and new experiments are constantly being perf...

    Authors: Mattia Pelizzola, Norman Pavelka, Maria Foti and Paola Ricciardi-Castagnoli
    Citation: BMC Bioinformatics 2006 7:335
    Content type: Software Published on:

  43. Word sense disambiguation (WSD) is critical in the biomedical domain for improving the precision of natural language processing (NLP), text mining, and information retrieval systems because ambiguous words neg...

    Authors: Hua Xu, Marianthi Markatou, Rositsa Dimova, Hongfang Liu and Carol Friedman
    Citation: BMC Bioinformatics 2006 7:334
    Content type: Research article Published on:

  44. DNA microarrays are popular tools for measuring gene expression of biological samples. This ever increasing popularity is ensuring that a large number of microarray studies are conducted, many of which with da...

    Authors: Mathieu Miron, Owen Z Woody, Alexandre Marcil, Carl Murie, Robert Sladek and Robert Nadon
    Citation: BMC Bioinformatics 2006 7:333
    Content type: Methodology article Published on:

  45. Gene regulation and metabolic reactions are two primary activities of life. Although many works have been dedicated to study each system, the coupling between them is less well understood. To bridge this gap, ...

    Authors: Chen-Hsiang Yeang and Martin Vingron
    Citation: BMC Bioinformatics 2006 7:332
    Content type: Research article Published on:

  46. Comparison of large protein datasets has become a standard task in bioinformatics. Typically researchers wish to know whether one group of proteins is significantly enriched in certain annotation attributes or...

    Authors: Thorsten Schmidt and Dmitrij Frishman
    Citation: BMC Bioinformatics 2006 7:331
    Content type: Software Published on:

  47. A complete understanding of the regulatory mechanisms of gene expression is the next important issue of genomics. Many bioinformaticians have developed methods and algorithms for predicting transcriptional reg...

    Authors: Seon-Young Kim and YongSung Kim
    Citation: BMC Bioinformatics 2006 7:330
    Content type: Methodology article Published on:

  48. Quantitative descriptions of amino acid similarity, expressed as probabilistic models of evolutionary interchangeability, are central to many mainstream bioinformatic procedures such as sequence alignment, hom...

    Authors: Blazej Bulka, Marie desJardins and Stephen J Freeland
    Citation: BMC Bioinformatics 2006 7:329
    Content type: Software Published on:

  50. ESTs are a tremendous resource for determining the exon-intron structures of genes, but even extensive EST sequencing tends to leave many exons and genes untouched. Gene prediction systems based exclusively on...

    Authors: Chaochun Wei and Michael R Brent
    Citation: BMC Bioinformatics 2006 7:327
    Content type: Research article Published on:

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