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  1. The detection of conserved motifs in promoters of orthologous genes (phylogenetic footprints) has become a common strategy to predict cis-acting regulatory elements. Several software tools are routinely used t...

    Authors: Rekin's Janky and Jacques van Helden
    Citation: BMC Bioinformatics 2008 9:37
    Content type: Research article Published on:

  3. This paper discusses the problem of automated annotation. It is a continuation of the previous work on the A4-algorithm (Adaptive algorithm of automated annotation) developed by Leontovich and others.

    Authors: Andrey M Leontovich, Konstantin Y Tokmachev and Hans C van Houwelingen
    Citation: BMC Bioinformatics 2008 9:31
    Content type: Methodology article Published on:

  4. Censored data are increasingly common in many microarray studies that attempt to relate gene expression to patient survival. Several new methods have been proposed in the last two years. Most of these methods,...

    Authors: Ramon Diaz-Uriarte
    Citation: BMC Bioinformatics 2008 9:30
    Content type: Software Published on:

  5. Analysis of complex samples with tandem mass spectrometry (MS/MS) has become routine in proteomic research. However, validation of database search results creates a bottleneck in MS/MS data processing. Recentl...

    Authors: Jiyang Zhang, Jianqi Li, Xin Liu, Hongwei Xie, Yunping Zhu and Fuchu He
    Citation: BMC Bioinformatics 2008 9:29
    Content type: Methodology article Published on:

  6. MAGE-ML has been promoted as a standard format for describing microarray experiments and the data they produce. Two characteristics of the MAGE-ML format compromise its use as a universal standard: First, MAGE...

    Authors: Don Maier, Farrell Wymore, Gavin Sherlock and Catherine A Ball
    Citation: BMC Bioinformatics 2008 9:28
    Content type: Software Published on:

  7. The models developed to characterize the evolution of multigene families (such as the birth-and-death and the concerted models) have also been applied on the level of sequence repeats inside a gene/protein. Ph...

    Authors: Botond Sipos, Kálmán Somogyi, István Andó and Zsolt Pénzes
    Citation: BMC Bioinformatics 2008 9:27
    Content type: Methodology article Published on:

  8. The variety of DNA microarray formats and datasets presently available offers an unprecedented opportunity to perform insightful comparisons of heterogeneous data. Cross-species studies, in particular, have th...

    Authors: Alexandre Kuhn, Ruth Luthi-Carter and Mauro Delorenzi
    Citation: BMC Bioinformatics 2008 9:26
    Content type: Software Published on:

  9. Normalization is essential in dual-labelled microarray data analysis to remove non-biological variations and systematic biases. Many normalization methods have been used to remove such biases within slides (Gl...

    Authors: Huiling Xiong, Dapeng Zhang, Christopher J Martyniuk, Vance L Trudeau and Xuhua Xia
    Citation: BMC Bioinformatics 2008 9:25
    Content type: Methodology article Published on:

  10. A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data ...

    Authors: Jonathan G Lees and Robert W Janes
    Citation: BMC Bioinformatics 2008 9:24
    Content type: Research article Published on:

  11. The inference of a genetic network is a problem in which mutual interactions among genes are deduced using time-series of gene expression patterns. While a number of models have been proposed to describe genet...

    Authors: Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Hideki Maeda, Koki Matsumura and Mariko Hatakeyama
    Citation: BMC Bioinformatics 2008 9:23
    Content type: Methodology article Published on:

  15. Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally develope...

    Authors: Mutlu Doğruel, Thomas A Down and Tim JP Hubbard
    Citation: BMC Bioinformatics 2008 9:19
    Content type: Methodology article Published on:

  17. Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions. One approach to recover this information is to use 3D temp...

    Authors: David M Kristensen, R Matthew Ward, Andreas Martin Lisewski, Serkan Erdin, Brian Y Chen, Viacheslav Y Fofanov, Marek Kimmel, Lydia E Kavraki and Olivier Lichtarge
    Citation: BMC Bioinformatics 2008 9:17
    Content type: Research article Published on:

  18. The huge amount of data generated by DNA chips is a powerful basis to classify various pathologies. However, constant evolution of microarray technology makes it difficult to mix data from different chip types...

    Authors: Thierry Rème, Dirk Hose, John De Vos, Aurélien Vassal, Pierre-Olivier Poulain, Véronique Pantesco, Hartmut Goldschmidt and Bernard Klein
    Citation: BMC Bioinformatics 2008 9:16
    Content type: Methodology article Published on:

  19. Ultraconserved elements are nucleotide or protein sequences with 100% identity (no mismatches, insertions, or deletions) in the same organism or between two or more organisms. Studies indicate that these conse...

    Authors: Scott Christley, Neil F Lobo and Greg Madey
    Citation: BMC Bioinformatics 2008 9:15
    Content type: Methodology article Published on:

  22. Gene expression data frequently contain missing values, however, most down-stream analyses for microarray experiments require complete data. In the literature many methods have been proposed to estimate missin...

    Authors: Guy N Brock, John R Shaffer, Richard E Blakesley, Meredith J Lotz and George C Tseng
    Citation: BMC Bioinformatics 2008 9:12
    Content type: Research article Published on:

  23. The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome [1] would not have been possible without advanced assembly algorithms....

    Authors: Andreas Döring, David Weese, Tobias Rausch and Knut Reinert
    Citation: BMC Bioinformatics 2008 9:11
    Content type: Software Published on:

  24. Advanced Text Mining (TM) such as semantic enrichment of papers, event or relation extraction, and intelligent Question Answering have increasingly attracted attention in the bio-medical domain. For such attem...

    Authors: Jin-Dong Kim, Tomoko Ohta and Jun'ichi Tsujii
    Citation: BMC Bioinformatics 2008 9:10
    Content type: Research article Published on:

  26. Protein sumoylation is an essential dynamic, reversible post translational modification that plays a role in dozens of cellular activities, especially the regulation of gene expression and the maintenance of g...

    Authors: Jialin Xu, Yun He, Boqin Qiang, Jiangang Yuan, Xiaozhong Peng and Xian-Ming Pan
    Citation: BMC Bioinformatics 2008 9:8
    Content type: Research article Published on:

  27. The zebrafish is a powerful model vertebrate amenable to high throughput in vivo genetic analyses. Examples include reverse genetic screens using morpholino knockdown, expression-based screening using enhancer tr...

    Authors: Michelle N Knowlton, Tongbin Li, Yongliang Ren, Brent R Bill, Lynda BM Ellis and Stephen C Ekker
    Citation: BMC Bioinformatics 2008 9:7
    Content type: Database Published on:

  28. Recent approaches for predicting the three-dimensional (3D) structure of proteins such as de novo or fold recognition methods mostly rely on simplified energy potential functions and a reduced representation of t...

    Authors: Jean-François Taly, Antoine Marin and Jean-François Gibrat
    Citation: BMC Bioinformatics 2008 9:6
    Content type: Research article Published on:

  29. Expressed sequence tag (EST) collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector region...

    Authors: Javier Forment, Francisco Gilabert, Antonio Robles, Vicente Conejero, Fernando Nuez and Jose M Blanca
    Citation: BMC Bioinformatics 2008 9:5
    Content type: Software Published on:

  30. In spite of two-dimensional gel electrophoresis (2-DE) being an effective and widely used method to screen the proteome, its data standardization has still not matured to the level of microarray genomics data ...

    Authors: Romesh Stanislaus, John M Arthur, Balaji Rajagopalan, Rick Moerschell, Brian McGlothlen and Jonas S Almeida
    Citation: BMC Bioinformatics 2008 9:4
    Content type: Research article Published on:

  31. High-throughput technologies like functional screens and gene expression analysis produce extended lists of candidate genes. Gene-Set Enrichment Analysis is a commonly used and well established technique to te...

    Authors: Florian Hahne, Alexander Mehrle, Dorit Arlt, Annemarie Poustka, Stefan Wiemann and Tim Beissbarth
    Citation: BMC Bioinformatics 2008 9:3
    Content type: Research article Published on:

  32. Inference of protein interaction networks from various sources of data has become an important topic of both systems and computational biology. Here we present a supervised approach to identification of gene e...

    Authors: Cuong C To and Jiri Vohradsky
    Citation: BMC Bioinformatics 2008 9:2
    Content type: Research article Published on:

  33. As an alternative to the frequently used "reference design" for two-channel microarrays, other designs have been proposed. These designs have been shown to be more profitable from a theoretical point of view (...

    Authors: Ana C Fierro, Raphael Thuret, Kristof Engelen, Gilles Bernot, Kathleen Marchal and Nicolas Pollet
    Citation: BMC Bioinformatics 2008 9:1
    Content type: Research article Published on:

  35. The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types...

    Authors: Egon L Willighagen, Noel M O'Boyle, Harini Gopalakrishnan, Dazhi Jiao, Rajarshi Guha, Christoph Steinbeck and David J Wild
    Citation: BMC Bioinformatics 2007 8:487
    Content type: Software Published on:

  36. Much recent work in bioinformatics has focused on the inference of various types of biological networks, representing gene regulation, metabolic processes, protein-protein interactions, etc. A common setting i...

    Authors: Jean-Philippe Vert, Jian Qiu and William S Noble
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 10

  37. For splice site recognition, one has to solve two classification problems: discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems typically rely on Markov Chains to...

    Authors: Sören Sonnenburg, Gabriele Schweikert, Petra Philips, Jonas Behr and Gunnar Rätsch
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 10

  38. High-throughput methods can directly detect the set of interacting proteins in model species but the results are often incomplete and exhibit high false positive and false negative rates. A number of researche...

    Authors: Yanjun Qi, Judith Klein-Seetharaman and Ziv Bar-Joseph
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 10

  39. Many important high throughput projects use in situ hybridization and may require the analysis of images of spatial cross sections of organisms taken with cellular level resolution. Projects creating gene express...

    Authors: Manjunatha Jagalur, Chris Pal, Erik Learned-Miller, R Thomas Zoeller and David Kulp
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 10

  40. Quantitative analysis of differential protein expressions requires to align temporal elution measurements from liquid chromatography coupled to mass spectrometry (LC/MS). We propose multiple Canonical Correlation...

    Authors: Bernd Fischer, Volker Roth and Joachim M Buhmann
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 10

  41. Gene expression measurements during the development of the fly Drosophila melanogaster are routinely used to find functional modules of temporally co-expressed genes. Complimentary large data sets of in situ RNA ...

    Authors: Ivan G Costa, Roland Krause, Lennart Opitz and Alexander Schliep
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 10

  42. In vertebrates, a large part of gene transcriptional regulation is operated by cis-regulatory modules. These modules are believed to be regulating much of the tissue-specificity of gene expression.

    Authors: Xiaoyu Chen and Mathieu Blanchette
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 10

  44. An ever increasing number of techniques are being used to find genes with similar profiles from microarray studies. Visualization of gene expression profiles can aid this process, potentially contributing to t...

    Authors: Yvonne E Pittelkow and Susan R Wilson
    Citation: BMC Bioinformatics 2007 8:486
    Content type: Methodology article Published on:

  45. The quality of cDNA microarray data is crucial for expanding its application to other research areas, such as the study of gene regulatory networks. Despite the fact that a number of algorithms have been sugge...

    Authors: Hye Young Kim, Seo Eun Lee, Min Jung Kim, Jin Il Han, Bo Kyung Kim, Yong Sung Lee, Young Seek Lee and Jin Hyuk Kim
    Citation: BMC Bioinformatics 2007 8:485
    Content type: Research article Published on:

  47. In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results i...

    Authors: Arnaud Droit, Joanna M Hunter, Michèle Rouleau, Chantal Ethier, Aude Picard-Cloutier, David Bourgais and Guy G Poirier
    Citation: BMC Bioinformatics 2007 8:483
    Content type: Database Published on:

  48. Predicting protein complexes from experimental data remains a challenge due to limited resolution and stochastic errors of high-throughput methods. Current algorithms to reconstruct the complexes typically rel...

    Authors: Wasinee Rungsarityotin, Roland Krause, Arno Schödl and Alexander Schliep
    Citation: BMC Bioinformatics 2007 8:482
    Content type: Research article Published on:

  49. Reliable transcription factor binding site (TFBS) prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the...

    Authors: Victor G Levitsky, Elena V Ignatieva, Elena A Ananko, Igor I Turnaev, Tatyana I Merkulova, Nikolay A Kolchanov and TC Hodgman
    Citation: BMC Bioinformatics 2007 8:481
    Content type: Research article Published on:

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