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  1. PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a se...

    Authors: Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen, Alexander Sczyrba, Sven Hartmeier and Robert Giegerich
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  2. Significance analysis at single gene level may suffer from the limited number of samples and experimental noise that can severely limit the power of the chosen statistical test. This problem is typically appro...

    Authors: Mirko Francesconi, Daniel Remondini, Nicola Neretti, John M Sedivy, Leon N Cooper, Ettore Verondini, Luciano Milanesi and Gastone Castellani
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  4. The DNA microarray technology allows the measurement of expression levels of thousands of genes under tens/hundreds of different conditions. In microarray data, genes with similar functions usually co-express ...

    Authors: Kin-On Cheng, Ngai-Fong Law, Wan-Chi Siu and Alan Wee-Chung Liew
    Citation: BMC Bioinformatics 2008 9:210
    Content type: Methodology article Published on:

  6. Genes that are co-expressed tend to be involved in the same biological process. However, co-expression is not a very reliable predictor of functional links between genes. The evolutionary conservation of co-ex...

    Authors: Martin Oti, Jeroen van Reeuwijk, Martijn A Huynen and Han G Brunner
    Citation: BMC Bioinformatics 2008 9:208
    Content type: Methodology article Published on:

  7. The increasing amount of published literature in biomedicine represents an immense source of knowledge, which can only efficiently be accessed by a new generation of automated information extraction tools. Nam...

    Authors: Markus Bundschus, Mathaeus Dejori, Martin Stetter, Volker Tresp and Hans-Peter Kriegel
    Citation: BMC Bioinformatics 2008 9:207
    Content type: Research article Published on:

  8. With the completion of the Human Genome Project and recent advancements in mutation detection technologies, the volume of data available on genetic variations has risen considerably. These data are stored in o...

    Authors: Timothy D Smith and Richard GH Cotton
    Citation: BMC Bioinformatics 2008 9:206
    Content type: Software Published on:

  9. Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a...

    Authors: Wei Yu, Melinda Clyne, Siobhan M Dolan, Ajay Yesupriya, Anja Wulf, Tiebin Liu, Muin J Khoury and Marta Gwinn
    Citation: BMC Bioinformatics 2008 9:205
    Content type: Software Published on:

  10. Single nucleotide polymorphisms (SNPs) are the most common genetic variations in the human genome and are useful as genomic markers. Oligonucleotide SNP microarrays have been developed for high-throughput geno...

    Authors: Cheng Li, Rameen Beroukhim, Barbara A Weir, Wendy Winckler, Levi A Garraway, William R Sellers and Matthew Meyerson
    Citation: BMC Bioinformatics 2008 9:204
    Content type: Research article Published on:

  11. Integrating data from multiple global assays and curated databases is essential to understand the spatio-temporal interactions within cells. Different experiments measure cellular processes at various widths a...

    Authors: Yuji Zhang, Jianhua Xuan, Benildo G de los Reyes, Robert Clarke and Habtom W Ressom
    Citation: BMC Bioinformatics 2008 9:203
    Content type: Research article Published on:

  12. Missing values frequently pose problems in gene expression microarray experiments as they can hinder downstream analysis of the datasets. While several missing value imputation approaches are available to the ...

    Authors: Johannes Tuikkala, Laura L Elo, Olli S Nevalainen and Tero Aittokallio
    Citation: BMC Bioinformatics 2008 9:202
    Content type: Research article Published on:

  13. Malaria parasite secretes various proteins in infected RBC for its growth and survival. Thus identification of these secretory proteins is important for developing vaccine/drug against malaria. The existing mo...

    Authors: Ruchi Verma, Ajit Tiwari, Sukhwinder Kaur, Grish C Varshney and Gajendra PS Raghava
    Citation: BMC Bioinformatics 2008 9:201
    Content type: Research article Published on:

  14. During the last decade, the use of microarrays to assess the transcriptome of many biological systems has generated an enormous amount of data. A common technique used to organize and analyze microarray data i...

    Authors: Piotr Kraj, Ashok Sharma, Nikhil Garge, Robert Podolsky and Richard A McIndoe
    Citation: BMC Bioinformatics 2008 9:200
    Content type: Software Published on:

  16. Determining the function of uncharacterized proteins is a major challenge in the post-genomic era due to the problem's complexity and scale. Identifying a protein's function contributes to an understanding of ...

    Authors: Aaron P Gabow, Sonia M Leach, William A Baumgartner, Lawrence E Hunter and Debra S Goldberg
    Citation: BMC Bioinformatics 2008 9:198
    Content type: Research article Published on:

  18. Microarray-based pooled DNA experiments that combine the merits of DNA pooling and gene chip technology constitute a pivotal advance in biotechnology. This new technique uses pooled DNA, thereby reducing costs...

    Authors: Hsin-Chou Yang, Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice LT Yu, Mitchell B Diccianni, Jer-Yuarn Wu, Yuan-Tsong Chen and Cathy SJ Fann
    Citation: BMC Bioinformatics 2008 9:196
    Content type: Software Published on:

  19. With the advent of high throughput biotechnology data acquisition platforms such as micro arrays, SNP chips and mass spectrometers, data sets with many more variables than observations are now routinely being ...

    Authors: Harri T Kiiveri
    Citation: BMC Bioinformatics 2008 9:195
    Content type: Methodology article Published on:

  21. Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear.

    Authors: Nikiforos Karamanis, Ruth Seal, Ian Lewin, Peter McQuilton, Andreas Vlachos, Caroline Gasperin, Rachel Drysdale and Ted Briscoe
    Citation: BMC Bioinformatics 2008 9:193
    Content type: Software Published on:

  23. Polymerase chain reaction (PCR) is used in directed sequencing for the discovery of novel polymorphisms. As the first step in PCR directed sequencing, effective PCR primer design is crucial for obtaining high-...

    Authors: Kelvin Li, Anushka Brownley, Timothy B Stockwell, Karen Beeson, Tina C McIntosh, Dana Busam, Steve Ferriera, Sean Murphy and Samuel Levy
    Citation: BMC Bioinformatics 2008 9:191
    Content type: Software Published on:

  24. Comparative genomics aims to detect signals of evolutionary conservation as an indicator of functional constraint. Surprisingly, results of the ENCODE project revealed that about half of the experimentally ver...

    Authors: Janis Dingel, Pavol Hanus, Niccolò Leonardi, Joachim Hagenauer, Jürgen Zech and Jakob C Mueller
    Citation: BMC Bioinformatics 2008 9:190
    Content type: Research article Published on:

  25. Haplotype reconstruction is important in linkage mapping and association mapping of quantitative trait loci (QTL). One widely used statistical approach for haplotype reconstruction is simulated annealing (SA),...

    Authors: Sang Hong Lee, Julius HJ Van der Werf and Brian P Kinghorn
    Citation: BMC Bioinformatics 2008 9:189
    Content type: Methodology article Published on:

  27. Availability of information about transcription factors (TFs) is crucial for genome biology, as TFs play a central role in the regulation of gene expression. While manual literature curation is expensive and l...

    Authors: Hui Yang, Goran Nenadic and John A Keane
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  28. In this paper we focus on the problem of automatically constructing ICD-9-CM coding systems for radiology reports. ICD-9-CM codes are used for billing purposes by health institutes and are assigned to clinical...

    Authors: Richárd Farkas and György Szarvas
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  29. This paper describes and evaluates a sentence selection engine that extracts a GeneRiF (Gene Reference into Functions) as defined in ENTREZ-Gene based on a MEDLINE record. Inputs for this task include both a g...

    Authors: Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Anaïs Mottaz, Anne-Lise Veuthey and Patrick Ruch
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  30. This paper describes the design of an event ontology being developed for application in the machine understanding of infectious disease-related events reported in natural language text. This event ontology is ...

    Authors: Ai Kawazoe, Hutchatai Chanlekha, Mika Shigematsu and Nigel Collier
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  31. Much effort is currently made to develop the Gene Ontology (GO). Due to the dynamic nature of information it addresses, GO undergoes constant updates whose results are released at regular intervals as separate...

    Authors: Jong C Park, Tak-eun Kim and Jinah Park
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  32. Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction (PPI) extraction. Howe...

    Authors: Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter and Tapio Salakoski
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  33. Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or...

    Authors: Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Daisuke Okanohara, Takuya Matsuzaki, Yuka Tateisi and Jun'ichi Tsujii
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  34. Efficient features play an important role in automated text classification, which definitely facilitates the access of large-scale data. In the bioscience field, biological structures and terminologies are des...

    Authors: Hongning Wang, Minlie Huang, Shilin Ding and Xiaoyan Zhu
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  35. In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other sema...

    Authors: Antonio Jimeno, Ernesto Jimenez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  36. One of the difficulties in mapping biomedical named entities, e.g. genes, proteins, chemicals and diseases, to their concept identifiers stems from the potential variability of the terms. Soft string matching ...

    Authors: Yoshimasa Tsuruoka, John McNaught and Sophia Ananiadou
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  39. Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines ...

    Authors: Robin P Smith, William J Buchser, Marcus B Lemmon, Jose R Pardinas, John L Bixby and Vance P Lemmon
    Citation: BMC Bioinformatics 2008 9:186
    Content type: Software Published on:

  40. We present a methodology for high-throughput design of oligonucleotide fingerprints for microarray-based pathogen diagnostic assays. The oligonucleotide fingerprints, or DNA microarray probes, are designed for...

    Authors: Ravi Vijaya Satya, Nela Zavaljevski, Kamal Kumar and Jaques Reifman
    Citation: BMC Bioinformatics 2008 9:185
    Content type: Methodology article Published on:

  41. The number of protein targets with a known or predicted tri-dimensional structure and of drug-like chemical compounds is growing rapidly and so is the need for new therapeutic compounds or chemical probes. Per...

    Authors: Nicolas Sauton, David Lagorce, Bruno O Villoutreix and Maria A Miteva
    Citation: BMC Bioinformatics 2008 9:184
    Content type: Methodology article Published on:

  42. The systematic capture of appropriately annotated experimental data is a prerequisite for most bioinformatics analyses. Data capture is required not only for submission of data to public repositories, but also...

    Authors: Daniel Jameson, Kevin Garwood, Chris Garwood, Tim Booth, Pinar Alper, Stephen G Oliver and Norman W Paton
    Citation: BMC Bioinformatics 2008 9:183
    Content type: Software Published on:

  43. The identification and study of proteins from metagenomic datasets can shed light on the roles and interactions of the source organisms in their communities. However, metagenomic datasets are characterized by ...

    Authors: Shibu Yooseph, Weizhong Li and Granger Sutton
    Citation: BMC Bioinformatics 2008 9:182
    Content type: Methodology article Published on:

  44. A major obstacle in treatment of HIV is the ability of the virus to mutate rapidly into drug-resistant variants. A method for predicting the susceptibility of mutated HIV strains to antiviral agents would prov...

    Authors: Maris Lapins, Martin Eklund, Ola Spjuth, Peteris Prusis and Jarl ES Wikberg
    Citation: BMC Bioinformatics 2008 9:181
    Content type: Research article Published on:

  45. The expressed sequence tag (EST) methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analys...

    Authors: Ralf Schmid and Mark L Blaxter
    Citation: BMC Bioinformatics 2008 9:180
    Content type: Software Published on:

  46. Multi-dimensional scaling (MDS) is aimed to represent high dimensional data in a low dimensional space with preservation of the similarities between data points. This reduction in dimensionality is crucial for...

    Authors: Jengnan Tzeng, Henry Horng-Shing Lu and Wen-Hsiung Li
    Citation: BMC Bioinformatics 2008 9:179
    Content type: Methodology article Published on:

  47. Ornithine decarboxylase antizymes are proteins which negatively regulate cellular polyamine levels via their affects on polyamine synthesis and cellular uptake. In virtually all organisms from yeast to mammals...

    Authors: Michaël Bekaert, Ivaylo P Ivanov, John F Atkins and Pavel V Baranov
    Citation: BMC Bioinformatics 2008 9:178
    Content type: Software Published on:

  48. Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequ...

    Authors: Michael Richter, Thierry Lombardot, Ivaylo Kostadinov, Renzo Kottmann, Melissa Beth Duhaime, Jörg Peplies and Frank Oliver Glöckner
    Citation: BMC Bioinformatics 2008 9:177
    Content type: Software Published on:

  49. With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such dat...

    Authors: Qi Liu, Yu Yang, Chun Chen, Jiajun Bu, Yin Zhang and Xiuzi Ye
    Citation: BMC Bioinformatics 2008 9:176
    Content type: Methodology article Published on:

  50. Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between...

    Authors: Gabriel Cardona, Francesc Rosselló and Gabriel Valiente
    Citation: BMC Bioinformatics 2008 9:175
    Content type: Software Published on:

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