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  5. Genomic deletions and duplications are important in the pathogenesis of diseases, such as cancer and mental retardation, and have recently been shown to occur frequently in unaffected individuals as polymorphi...

    Authors: Ágnes Baross, Allen D Delaney, H Irene Li, Tarun Nayar, Stephane Flibotte, Hong Qian, Susanna Y Chan, Jennifer Asano, Adrian Ally, Manqiu Cao, Patricia Birch, Mabel Brown-John, Nicole Fernandes, Anne Go, Giulia Kennedy, Sylvie Langlois…
    Citation: BMC Bioinformatics 2007 8:368
    Content type: Research article Published on:

  6. Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been estab...

    Authors: Jan Küntzer, Christina Backes, Torsten Blum, Andreas Gerasch, Michael Kaufmann, Oliver Kohlbacher and Hans-Peter Lenhof
    Citation: BMC Bioinformatics 2007 8:367
    Content type: Database Published on:

  7. In recent years, RNA molecules that are not translated into proteins (ncRNAs) have drawn a great deal of attention, as they were shown to be involved in many cellular functions. One of the most important compu...

    Authors: Yair Horesh, Tirza Doniger, Shulamit Michaeli and Ron Unger
    Citation: BMC Bioinformatics 2007 8:366
    Content type: Methodology article Published on:

  12. Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of applica...

    Authors: Wolfgang Huber, Vincent J Carey, Li Long, Seth Falcon and Robert Gentleman
    Citation: BMC Bioinformatics 2007 8(Suppl 6):S8
    Content type: Review Published on:

    This article is part of a Supplement: Volume 8 Supplement 6

  13. This is an introductory review on how genes interact to produce biological functions. Transcriptional interactions involve the binding of proteins to regulatory DNA. Specific binding sites can be identified by...

    Authors: Michael Lässig
    Citation: BMC Bioinformatics 2007 8(Suppl 6):S7
    Content type: Review Published on:

    This article is part of a Supplement: Volume 8 Supplement 6

  14. The genomewide pattern of changes in mRNA expression measured using DNA microarrays is typically a complex superposition of the response of multiple regulatory pathways to changes in the environment of the cel...

    Authors: Harmen J Bussemaker, Lucas D Ward and Andre Boorsma
    Citation: BMC Bioinformatics 2007 8(Suppl 6):S6
    Content type: Review Published on:

    This article is part of a Supplement: Volume 8 Supplement 6

  15. In this review we give an overview of computational and statistical methods to reconstruct cellular networks. Although this area of research is vast and fast developing, we show that most currently used method...

    Authors: Florian Markowetz and Rainer Spang
    Citation: BMC Bioinformatics 2007 8(Suppl 6):S5
    Content type: Review Published on:

    This article is part of a Supplement: Volume 8 Supplement 6

  16. Over the last two decades a large number of algorithms has been developed for regulatory motif finding. Here we show how many of these algorithms, especially those that model binding specificities of regulator...

    Authors: Erik van Nimwegen
    Citation: BMC Bioinformatics 2007 8(Suppl 6):S4
    Content type: Review Published on:

    This article is part of a Supplement: Volume 8 Supplement 6

  18. Considering that 80 genomes have been sequenced, providing us with the static information of the genome, it is still a long way to reveal the relationship between complex genotypes and phenotypes. The transcri...

    Authors: Silke Sperling
    Citation: BMC Bioinformatics 2007 8(Suppl 6):S2
    Content type: Review Published on:

    This article is part of a Supplement: Volume 8 Supplement 6

  20. Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many environments, the methods themselve...

    Authors: Michael C Wendl, Scott Smith, Craig S Pohl, David J Dooling, Asif T Chinwalla, Kevin Crouse, Todd Hepler, Shin Leong, Lynn Carmichael, Mike Nhan, Benjamin J Oberkfell, Elaine R Mardis, LaDeana W Hillier and Richard K Wilson
    Citation: BMC Bioinformatics 2007 8:362
    Content type: Methodology article Published on:

  21. In an epitope-based vaccine setting, the use of conserved epitopes would be expected to provide broader protection across multiple strains, or even species, than epitopes derived from highly variable genome re...

    Authors: Huynh-Hoa Bui, John Sidney, Wei Li, Nicolas Fusseder and Alessandro Sette
    Citation: BMC Bioinformatics 2007 8:361
    Content type: Software Published on:

  22. The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualizat...

    Authors: Stan Gaj, Arie van Erk, Rachel IM van Haaften and Chris TA Evelo
    Citation: BMC Bioinformatics 2007 8:360
    Content type: Methodology article Published on:

  23. High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ...

    Authors: Srinka Ghosh, Heather A Hirsch, Edward A Sekinger, Philipp Kapranov, Kevin Struhl and Thomas R Gingeras
    Citation: BMC Bioinformatics 2007 8:359
    Content type: Methodology article Published on:

  24. Arabidopsis thaliana is the model species of current plant genomic research with a genome size of 125 Mb and approximately 28,000 genes. The function of half of these genes is currently unknown. The purpose of th...

    Authors: Hui Lan, Rachel Carson, Nicholas J Provart and Anthony J Bonner
    Citation: BMC Bioinformatics 2007 8:358
    Content type: Research article Published on:

  25. The prediction of the secondary structure of proteins is one of the most studied problems in bioinformatics. Despite their success in many problems of biological sequence analysis, Hidden Markov Models (HMMs) ...

    Authors: Kyoung-Jae Won, Thomas Hamelryck, Adam Prügel-Bennett and Anders Krogh
    Citation: BMC Bioinformatics 2007 8:357
    Content type: Research article Published on:

  28. Computational methods to predict transcription factor binding sites (TFBS) based on exhaustive algorithms are guaranteed to find the best patterns but are often limited to short ones or impose some constraints...

    Authors: Fathi Elloumi and Martha Nason
    Citation: BMC Bioinformatics 2007 8:354
    Content type: Methodology article Published on:

  31. Odorant binding proteins (OBPs) are believed to shuttle odorants from the environment to the underlying odorant receptors, for which they could potentially serve as odorant presenters. Although several sequenc...

    Authors: Ganesan Pugalenthi, Ke Tang, PN Suganthan, G Archunan and R Sowdhamini
    Citation: BMC Bioinformatics 2007 8:351
    Content type: Research article Published on:

  32. The design of long oligonucleotides for spotted DNA microarrays requires detailed attention to ensure their optimal performance in the hybridization process. The main challenge is to select an optimal oligonuc...

    Authors: Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser and Zbynek Bozdech
    Citation: BMC Bioinformatics 2007 8:350
    Content type: Methodology article Published on:

  33. The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are succes...

    Authors: Heng Li, Liang Guan, Tao Liu, Yiran Guo, Wei-Mou Zheng, Gane Ka-Shu Wong and Jun Wang
    Citation: BMC Bioinformatics 2007 8:349
    Content type: Methodology article Published on:

  34. Although molecular pathway information and the International HapMap Project data can help biomedical researchers to investigate the aetiology of complex diseases more effectively, such information is missing o...

    Authors: Hwanseok Rhee and Jin-Sung Lee
    Citation: BMC Bioinformatics 2007 8:348
    Content type: Database Published on:

  36. The most popular methods for significance analysis on microarray data are well suited to find genes differentially expressed across predefined categories. However, identification of features that correlate wit...

    Authors: Lars Gidskehaug, Endre Anderssen, Arnar Flatberg and Bjørn K Alsberg
    Citation: BMC Bioinformatics 2007 8:346
    Content type: Research article Published on:

  38. Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standa...

    Authors: Jeremiah J Faith, Andrew J Olson, Timothy S Gardner and Ravi Sachidanandam
    Citation: BMC Bioinformatics 2007 8:344
    Content type: Software Published on:

  39. Modelling of time series data should not be an approximation of input data profiles, but rather be able to detect and evaluate dynamical changes in the time series data. Objective criteria that can be used to ...

    Authors: Ryoko Morioka, Shigehiko Kanaya, Masami Y Hirai, Mitsuru Yano, Naotake Ogasawara and Kazuki Saito
    Citation: BMC Bioinformatics 2007 8:343
    Content type: Research article Published on:

  41. MicroRNAs (miRNAs) are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs...

    Authors: Ting-Hua Huang, Bin Fan, Max F Rothschild, Zhi-Liang Hu, Kui Li and Shu-Hong Zhao
    Citation: BMC Bioinformatics 2007 8:341
    Content type: Software Published on:

  43. Expressed sequence tags (ESTs) analyses are a fundamental tool for gene identification in organisms. Given a preliminary EST sample from a certain library, several statistical prediction problems arise. In par...

    Authors: Antonio Lijoi, Ramsés H Mena and Igor Prünster
    Citation: BMC Bioinformatics 2007 8:339
    Content type: Methodology article Published on:

  44. Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate...

    Authors: Catherine C Beauheim, Farrell Wymore, Michael Nitzberg, Zachariah K Zachariah, Heng Jin, JH Pate Skene, Catherine A Ball and Gavin Sherlock
    Citation: BMC Bioinformatics 2007 8:338
    Content type: Software Published on:

  45. In past number of methods have been developed for predicting subcellular location of eukaryotic, prokaryotic (Gram-negative and Gram-positive bacteria) and human proteins but no method has been developed for m...

    Authors: Mamoon Rashid, Sudipto Saha and Gajendra PS Raghava
    Citation: BMC Bioinformatics 2007 8:337
    Content type: Research article Published on:

  46. Combinatorial complexity is a challenging problem in detailed and mechanistic mathematical modeling of signal transduction. This subject has been discussed intensively and a lot of progress has been made withi...

    Authors: Markus Koschorreck, Holger Conzelmann, Sybille Ebert, Michael Ederer and Ernst Dieter Gilles
    Citation: BMC Bioinformatics 2007 8:336
    Content type: Research article Published on:

  48. Cells dynamically adapt their gene expression patterns in response to various stimuli. This response is orchestrated into a number of gene expression modules consisting of co-regulated genes. A growing pool of...

    Authors: Jochen Supper, Martin Strauch, Dierk Wanke, Klaus Harter and Andreas Zell
    Citation: BMC Bioinformatics 2007 8:334
    Content type: Methodology article Published on:

  49. The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence.

    Authors: Andreas Prlić, Thomas A Down, Eugene Kulesha, Robert D Finn, Andreas Kähäri and Tim JP Hubbard
    Citation: BMC Bioinformatics 2007 8:333
    Content type: Research article Published on:

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