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  1. Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with mo...

    Authors: Zeev Frenkel, Etienne Paux, David Mester, Catherine Feuillet and Abraham Korol
    Citation: BMC Bioinformatics 2010 11:584
    Content type: Methodology article Published on:

  3. The Gene Ontology (GO) is a well known controlled vocabulary describing the biological process, molecular function and cellular component aspects of gene annotation. It has become a widely used knowledge source i...

    Authors: Sidahmed Benabderrahmane, Malika Smail-Tabbone, Olivier Poch, Amedeo Napoli and Marie-Dominique Devignes
    Citation: BMC Bioinformatics 2010 11:588
    Content type: Methodology article Published on:

  4. Models for the simulation of metabolic networks require the accurate prediction of enzyme function. Based on a genomic sequence, enzymatic functions of gene products are today mainly predicted by sequence data...

    Authors: C Bannert, A Welfle, C aus dem Spring and D Schomburg
    Citation: BMC Bioinformatics 2010 11:589
    Content type: Methodology article Published on:

  8. This meeting report gives an overview of the keynote lectures and a selection of the student oral and poster presentations at the 6th International Society for Computational Biology Student Council Symposium t...

    Authors: Christiaan Klijn, Magali Michaut and Thomas Abeel
    Citation: BMC Bioinformatics 2010 11(Suppl 10):I1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 11 Supplement 10

  17. Authors: María Paula Magariños, John Overington, Santiago Carmona, Dhanasekaran Shanmugam, Maria Doyle, Stuart Ralph, Greg Crowther, Christiane Hertz-Fowler, Solomon Nwaka, Matt Berriman, David Roos, Wes Van Voorhis and Fernán Agüero
    Citation: BMC Bioinformatics 2010 11(Suppl 10):O10
    Content type: Oral presentation Published on:

    This article is part of a Supplement: Volume 11 Supplement 10

  22. The analysis of Inter-Alu PCR patterns obtained from human genomic DNA samples is a promising technique for a simultaneous analysis of many genomic loci flanked by Alu repetitive sequences in order to detect t...

    Authors: Maurizio Cardelli, Matteo Nicoli, Armando Bazzani and Claudio Franceschi
    Citation: BMC Bioinformatics 2010 11:593
    Content type: Research article Published on:

  23. The purpose of this manuscript is to provide, based on an extensive analysis of a proteomic data set, suggestions for proper statistical analysis for the discovery of sets of clinically relevant biomarkers. As...

    Authors: Mohammed Dakna, Keith Harris, Alexandros Kalousis, Sebastien Carpentier, Walter Kolch, Joost P Schanstra, Marion Haubitz, Antonia Vlahou, Harald Mischak and Mark Girolami
    Citation: BMC Bioinformatics 2010 11:594
    Content type: Research article Published on:

  26. Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. Howev...

    Authors: Enrico Glaab, Anaïs Baudot, Natalio Krasnogor and Alfonso Valencia
    Citation: BMC Bioinformatics 2010 11:597
    Content type: Methodology article Published on:

  27. Embryogenesis is the process by which the embryo is formed, develops, and establishes developmental hierarchies of tissues. The recent advance in microarray technology made it possible to investigate the tissu...

    Authors: Yao Yu, Tao Xu, Yongtao Yu, Pei Hao and Xuan Li
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  28. Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expan...

    Authors: Lee Sael and Daisuke Kihara
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  29. In the literature, there are fruitful algorithmic approaches for identification functional modules in protein-protein interactions (PPI) networks. Because of accumulation of large-scale interaction data on mul...

    Authors: Liping Jing and Michael K Ng
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  30. A bisection-type algorithm for the grammar-based compression of tree-structured data has been proposed recently. In this framework, an elementary ordered-tree grammar (EOTG) and an elementary unordered-tree gr...

    Authors: Yang Zhao, Morihiro Hayashida and Tatsuya Akutsu
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  31. Inference of causal regulators responsible for gene expression changes under different conditions is of great importance but remains rather challenging. To date, most approaches use direct binding targets of t...

    Authors: Qi Liu, Yejun Tan, Tao Huang, Guohui Ding, Zhidong Tu, Lei Liu, Yixue Li, Hongyue Dai and Lu Xie
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  32. Traditional Chinese Medicine (TCM) is characterized by the wide use of herbal formulae, which are capable of systematically treating diseases determined by interactions among various herbs. However, the combin...

    Authors: Shao Li, Bo Zhang, Duo Jiang, Yingying Wei and Ningbo Zhang
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  33. The environment has been playing an instrumental role in shaping and maintaining the morphological, physiological and biochemical diversities of prokaryotes. It has been debatable whether the whole-genome Guan...

    Authors: Hao Zheng and Hongwei Wu
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  34. Weak motif discovery in DNA sequences is an important but unresolved problem in computational biology. Previous algorithms that aimed to solve the problem usually require a large amount of memory or execution ...

    Authors: He Quan Sun, Malcolm Yoke Hean Low, Wen Jing Hsu and Jagath C Rajapakse
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  35. Clostridium beijerinckii is a valuable bacteria species which has the ability of ABE (acetone, butanol and ethanol) production. It has been shown that Phosphotransferase (PTS) is an important and common system fo...

    Authors: Yixiang Shi, Yi-Xue Li and Yuan-Yuan Li
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  36. The human leukocyte antigen system (HLA) contains many highly variable genes. HLA genes play an important role in the human immune system, and HLA gene matching is crucial for the success of human organ transp...

    Authors: Minzhu Xie, Jing Li and Tao Jiang
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  37. MicroRNAs (simply miRNAs) are derived from larger hairpin RNA precursors and play essential regular roles in both animals and plants. A number of computational methods for miRNA genes finding have been propose...

    Authors: Jiandong Ding, Shuigeng Zhou and Jihong Guan
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  38. The characterization of structural variations (SV) such as insertions, deletions and copy number variations is a critical step in the process of understanding the full genetic architecture of organisms. Copy n...

    Authors: Dan He, Nicholas Furlotte and Eleazar Eskin
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  39. As an obligate intracellular parasite, Apicomplexa interacts with the host in the special living environment, competing for energy and nutrients from the host cells by manipulating the host metabolism. Previou...

    Authors: Tao Xu, Jie Ping, Yao Yu, Fudong Yu, Yongtao Yu, Pei Hao and Xuan Li
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  40. Most mass spectrometry (MS) based proteomic studies depend on searching acquired tandem mass (MS/MS) spectra against databases of known protein sequences. In these experiments, however, a large number of high ...

    Authors: Kang Ning and Alexey I Nesvizhskii
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  41. Microarray has been widely used to measure the gene expression level on the genome scale in the current decade. Many algorithms have been developed to reconstruct gene regulatory networks based on microarray d...

    Authors: Wanlin Liu, Dong Li, Qijun Liu, Yunping Zhu and Fuchu He
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  42. A ‘head-to-head’ (h2h) gene pair is defined as a genomic locus in which two adjacent genes are divergently transcribed from opposite strands of DNA. In our previous work, this gene organization was found to be...

    Authors: Yun-Qin Chen, Hui Yu, Yi-Xue Li and Yuan-Yuan Li
    Citation: BMC Bioinformatics 2010 11(Suppl 11):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 11

  43. Bioinformatics is confronted with a new data explosion due to the availability of high throughput DNA sequencers. Data storage and analysis becomes a problem on local servers, and therefore it is needed to swi...

    Authors: Angela CM Luyf, Barbera DC van Schaik, Michel de Vries, Frank Baas, Antoine HC van Kampen and Silvia D Olabarriaga
    Citation: BMC Bioinformatics 2010 11:598
    Content type: Research article Published on:

  44. Traditional genome alignment methods consider sequence alignment as a variation of the string edit distance problem, and perform alignment by matching characters of the two sequences. They are often computatio...

    Authors: Minh Duc Cao, Trevor I Dix and Lloyd Allison
    Citation: BMC Bioinformatics 2010 11:599
    Content type: Methodology article Published on:

  45. Expression levels for 47294 transcripts in lymphoblastoid cell lines from all 270 HapMap phase II individuals, and genotypes (both HapMap phase II and III) of 3.96 million single nucleotide polymorphisms (SNPs...

    Authors: Kristian Holm, Espen Melum, Andre Franke and Tom H Karlsen
    Citation: BMC Bioinformatics 2010 11:600
    Content type: Software Published on:

  46. We propose a sequence clustering algorithm and compare the partition quality and execution time of the proposed algorithm with those of a popular existing algorithm. The proposed clustering algorithm uses a gr...

    Authors: David J Russell, Samuel F Way, Andrew K Benson and Khalid Sayood
    Citation: BMC Bioinformatics 2010 11:601
    Content type: Methodology article Published on:

  48. Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, t...

    Authors: Ronald C Taylor
    Citation: BMC Bioinformatics 2010 11(Suppl 12):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 12

  49. Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas suc...

    Authors: Judy Qiu, Jaliya Ekanayake, Thilina Gunarathne, Jong Youl Choi, Seung-Hee Bae, Hui Li, Bingjing Zhang, Tak-Lon Wu, Yang Ruan, Saliya Ekanayake, Adam Hughes and Geoffrey Fox
    Citation: BMC Bioinformatics 2010 11(Suppl 12):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 12

  50. The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates ...

    Authors: Steffen Möller, Hajo Nils Krabbenhöft, Andreas Tille, David Paleino, Alan Williams, Katy Wolstencroft, Carole Goble, Richard Holland, Dominique Belhachemi and Charles Plessy
    Citation: BMC Bioinformatics 2010 11(Suppl 12):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 12

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