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  1. The joint analysis of several categorical variables is a common task in many areas of biology, and is becoming central to systems biology investigations whose goal is to identify potentially complex interactio...

    Authors: Corinne Dahinden, Giovanni Parmigiani, Mark C Emerick and Peter Bühlmann
    Citation: BMC Bioinformatics 2007 8:476
    Content type: Methodology article Published on:

  3. The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated f...

    Authors: Michael C Schatz, Cole Trapnell, Arthur L Delcher and Amitabh Varshney
    Citation: BMC Bioinformatics 2007 8:474
    Content type: Software Published on:

  4. Eukaryotic cells have developed mechanisms to respond to external environmental or physiological changes (stresses). In order to increase the activities of stress-protection functions in response to an environ...

    Authors: Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li and Bor-Sen Chen
    Citation: BMC Bioinformatics 2007 8:473
    Content type: Methodology article Published on:

  5. Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis,...

    Authors: Srinath Sridhar, Fumei Lam, Guy E Blelloch, R Ravi and Russell Schwartz
    Citation: BMC Bioinformatics 2007 8:472
    Content type: Research article Published on:

  8. Ribozymes are small catalytic RNAs that possess the dual functions of sequence-specific RNA recognition and site-specific cleavage. Trans-cleaving ribozymes can inhibit translation of genes at the messenger RNA (...

    Authors: Yu Shao, Susan Wu, Chi Yu Chan, Jessie R Klapper, Erasmus Schneider and Ye Ding
    Citation: BMC Bioinformatics 2007 8:469
    Content type: Research article Published on:

  9. High-throughput peptide and protein identification technologies have benefited tremendously from strategies based on tandem mass spectrometry (MS/MS) in combination with database searching algorithms. A major ...

    Authors: Nico Pfeifer, Andreas Leinenbach, Christian G Huber and Oliver Kohlbacher
    Citation: BMC Bioinformatics 2007 8:468
    Content type: Research article Published on:

  10. In the analysis of networks we frequently require the statistical significance of some network statistic, such as measures of similarity for the properties of interacting nodes. The structure of the network ma...

    Authors: Thomas Thorne and Michael PH Stumpf
    Citation: BMC Bioinformatics 2007 8:467
    Content type: Methodology article Published on:

  11. Subcellular location prediction of proteins is an important and well-studied problem in bioinformatics. This is a problem of predicting which part in a cell a given protein is transported to, where an amino ac...

    Authors: Takeyuki Tamura and Tatsuya Akutsu
    Citation: BMC Bioinformatics 2007 8:466
    Content type: Research article Published on:

  12. Simple Sequence Repeats (SSRs), or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched f...

    Authors: Alexis Dereeper, Xavier Argout, Claire Billot, Jean-François Rami and Manuel Ruiz
    Citation: BMC Bioinformatics 2007 8:465
    Content type: Software Published on:

  15. The construction of literature-based networks of gene-gene interactions is one of the most important applications of text mining in bioinformatics. Extracting potential gene relationships from the biomedical l...

    Authors: Hyunsoo Kim, Haesun Park and Barry L Drake
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  16. With more and more research dedicated to literature mining in the biomedical domain, more and more systems are available for people to choose from when building literature mining applications. In this study, w...

    Authors: Manabu Torii, Zhang-zhi Hu, Min Song, Cathy H Wu and Hongfang Liu
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  17. A huge amount of biomedical textual information has been produced and collected in MEDLINE for decades. In order to easily utilize biomedical information in the free text, document clustering and text summariz...

    Authors: Illhoi Yoo, Xiaohua Hu and Il-Yeol Song
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  18. Annotating genes and their products with Gene Ontology codes is an important area of research. One approach is to use the information available about these genes in the biomedical literature. The goal in this ...

    Authors: Padmini Srinivasan and Xin Ying Qiu
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  19. As systems biology has begun to draw growing attention, bio-network inference and analysis have become more and more important. Though there have been many efforts for bio-network inference, they are still far...

    Authors: Doheon Lee, Sangwoo Kim and Younghoon Kim
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  20. Biomedical ontologies are emerging as critical tools in genomic and proteomic research, where complex data in disparate resources need to be integrated. A number of ontologies describe properties that can be a...

    Authors: Darren A Natale, Cecilia N Arighi, Winona C Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith and Cathy H Wu
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  21. The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of t...

    Authors: Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios and Luis Mendoza
    Citation: BMC Bioinformatics 2007 8:462
    Content type: Software Published on:

  23. Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desi...

    Authors: Daniel H Huson, Daniel C Richter, Christian Rausch, Tobias Dezulian, Markus Franz and Regula Rupp
    Citation: BMC Bioinformatics 2007 8:460
    Content type: Software Published on:

  24. Peptides binding to Major Histocompatibility Complex (MHC) class II molecules are crucial for initiation and regulation of immune responses. Predicting peptides that bind to a specific MHC molecule plays an im...

    Authors: Menaka Rajapakse, Bertil Schmidt, Lin Feng and Vladimir Brusic
    Citation: BMC Bioinformatics 2007 8:459
    Content type: Research article Published on:

  39. In this meeting report we give an overview of the 3rd International Society for Computational Biology Student Council Symposium. Furthermore, we explain the role of the Student Council and the symposium series...

    Authors: Nils Gehlenborg, Manuel Corpas and Sarath Chandra Janga
    Citation: BMC Bioinformatics 2007 8(Suppl 8):I1
    Content type: Meeting report Published on:

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

  42. Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between nami...

    Authors: J Christopher Bare, Paul T Shannon, Amy K Schmid and Nitin S Baliga
    Citation: BMC Bioinformatics 2007 8:456
    Content type: Software Published on:

  44. The central role of transcription factors (TFs) in higher eukaryotes has led to much interest in deciphering transcriptional regulatory interactions. Even in the best case, experimental identification of TF ta...

    Authors: Henning Redestig, Daniel Weicht, Joachim Selbig and Matthew A Hannah
    Citation: BMC Bioinformatics 2007 8:454
    Content type: Methodology article Published on:

  45. Gene clustering has been widely used to group genes with similar expression pattern in microarray data analysis. Subsequent enrichment analysis using predefined gene sets can provide clues on which functional ...

    Authors: Tae-Min Kim, Yeun-Jun Chung, Mun-Gan Rhyu and Myeong Ho Jung
    Citation: BMC Bioinformatics 2007 8:453
    Content type: Methodology article Published on:

  46. The identification of transcription factors (TFs) associated with a biological process is fundamental to understanding its regulatory mechanisms. From microarray data, however, the activity changes of TFs ofte...

    Authors: Chao Cheng, Xiting Yan, Fengzhu Sun and Lei M Li
    Citation: BMC Bioinformatics 2007 8:452
    Content type: Methodology article Published on:

  47. α-Synuclein is a Parkinson's-disease-related protein. It forms aggregates in vivo, and these aggregates cause cell cytotoxicity. Aggregation inhibitors are expected to reduce α-synuclein cytotoxicity, and an aggr...

    Authors: Koichi Abe, Natsuki Kobayashi, Koji Sode and Kazunori Ikebukuro
    Citation: BMC Bioinformatics 2007 8:451
    Content type: Research article Published on:

  48. Human genetic variations primarily result from single nucleotide polymorphisms (SNPs) that occur approximately every 1000 bases in the overall human population. The non-synonymous SNPs (nsSNPs) that lead to am...

    Authors: Jian Tian, Ningfeng Wu, Xuexia Guo, Jun Guo, Juhua Zhang and Yunliu Fan
    Citation: BMC Bioinformatics 2007 8:450
    Content type: Software Published on:

  49. Improvements in genome sequence annotation revealed discrepancies in the original probeset/gene assignment in Affymetrix microarray and the existence of differences between annotations and effective alignments...

    Authors: Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sergio Ferrari, Doron Lancet, Gian Antonio Danieli and Silvio Bicciato
    Citation: BMC Bioinformatics 2007 8:446
    Content type: Software Published on:

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