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  1. The recent emergence of the H5N1 influenza virus from avian reservoirs has raised concern about future influenza strains of high virulence emerging that could easily infect humans. We analyzed differential gen...

    Authors: Ken Tatebe, Ahmet Zeytun, Ruy M Ribeiro, Robert Hoffmann, Kevin S Harrod and Christian V Forst
    Citation: BMC Bioinformatics 2010 11:170
    Content type: Research article Published on:

  3. In recent years, gene order data has attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. If gene orders are viewed as one character with...

    Authors: Jian Shi, Yiwei Zhang, Haiwei Luo and Jijun Tang
    Citation: BMC Bioinformatics 2010 11:168
    Content type: Research article Published on:

  5. An important objective of DNA microarray-based gene expression experimentation is determining inter-relationships that exist between differentially expressed genes and biological processes, molecular functions...

    Authors: Saurin D Jani, Gary L Argraves, Jeremy L Barth and W Scott Argraves
    Citation: BMC Bioinformatics 2010 11:166
    Content type: Software Published on:

  7. Gene clustering for annotating gene functions is one of the fundamental issues in bioinformatics. The best clustering solution is often regularized by multiple constraints such as gene expressions, Gene Ontolo...

    Authors: Jia Zeng, Shanfeng Zhu, Alan Wee-Chung Liew and Hong Yan
    Citation: BMC Bioinformatics 2010 11:164
    Content type: Methodology article Published on:

  8. Identifying candidate genes in genetic networks is important for understanding regulation and biological function. Large gene expression datasets contain relevant information about genetic networks, but mining...

    Authors: Anup Parikh, Eryong Huang, Christopher Dinh, Blaz Zupan, Adam Kuspa, Devika Subramanian and Gad Shaulsky
    Citation: BMC Bioinformatics 2010 11:163
    Content type: Research article Published on:

  9. In cancer, gene networks and pathways often exhibit dynamic behavior, particularly during the process of carcinogenesis. Thus, it is important to prioritize those genes that are strongly associated with the fu...

    Authors: Chen Wang, Jianhua Xuan, Huai Li, Yue Wang, Ming Zhan, Eric P Hoffman and Robert Clarke
    Citation: BMC Bioinformatics 2010 11:162
    Content type: Methodology article Published on:

  10. The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regul...

    Authors: Israel T Silva, Ricardo ZN Vêncio, Thiago YK Oliveira, Greice A Molfetta and Wilson A Silva Jr
    Citation: BMC Bioinformatics 2010 11:161
    Content type: Software Published on:

  11. Small molecular cofactors or ligands play a crucial role in the proper functioning of cells. Accurate annotation of their target proteins and binding sites is required for the complete understanding of reactio...

    Authors: Hifzur R Ansari and Gajendra PS Raghava
    Citation: BMC Bioinformatics 2010 11:160
    Content type: Research article Published on:

  12. Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools...

    Authors: Thomas Kuhn, Egon L Willighagen, Achim Zielesny and Christoph Steinbeck
    Citation: BMC Bioinformatics 2010 11:159
    Content type: Software Published on:

  13. Gene expression data can be analyzed by summarizing groups of individual gene expression profiles based on GO annotation information. The mean expression profile per group can then be used to identify interest...

    Authors: Jorn R De Haan, Ester Piek, Rene C van Schaik, Jacob de Vlieg, Susanne Bauerschmidt, Lutgarde MC Buydens and Ron Wehrens
    Citation: BMC Bioinformatics 2010 11:158
    Content type: Research article Published on:

  15. Oligonucleotide arrays have become one of the most widely used high-throughput tools in biology. Due to their sensitivity to experimental conditions, normalization is a crucial step when comparing measurements...

    Authors: Marc Hulsman, Anouk Mentink, Eugene P van Someren, Koen J Dechering, Jan de Boer and Marcel JT Reinders
    Citation: BMC Bioinformatics 2010 11:156
    Content type: Methodology article Published on:

  16. Computational comparison of two protein structures is the starting point of many methods that build on existing knowledge, such as structure modeling (including modeling of protein complexes and conformational...

    Authors: Zong Hong Zhang, Hwee Kuan Lee and Ivana Mihalek
    Citation: BMC Bioinformatics 2010 11:155
    Content type: Research article Published on:

  17. One of main aims of Molecular Biology is the gain of knowledge about how molecular components interact each other and to understand gene function regulations. Using microarray technology, it is possible to ext...

    Authors: Pietro Zoppoli, Sandro Morganella and Michele Ceccarelli
    Citation: BMC Bioinformatics 2010 11:154
    Content type: Methodology article Published on:

  19. Molecular studies of microbial diversity have provided many insights into the bacterial communities inhabiting the human body and the environment. A common first step in such studies is a survey of conserved m...

    Authors: James R White, Saket Navlakha, Niranjan Nagarajan, Mohammad-Reza Ghodsi, Carl Kingsford and Mihai Pop
    Citation: BMC Bioinformatics 2010 11:152
    Content type: Research article Published on:

  20. Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of ev...

    Authors: Pierre M Durand, Scott Hazelhurst and Theresa L Coetzer
    Citation: BMC Bioinformatics 2010 11:151
    Content type: Methodology article Published on:

  23. Mass spectrometry has become the analytical method of choice in metabolomics research. The identification of unknown compounds is the main bottleneck. In addition to the precursor mass, tandem MS spectra carry...

    Authors: Sebastian Wolf, Stephan Schmidt, Matthias Müller-Hannemann and Steffen Neumann
    Citation: BMC Bioinformatics 2010 11:148
    Content type: Methodology article Published on:

  24. Algorithms and software for CNV detection have been developed, but they detect the CNV regions sample-by-sample with individual-specific breakpoints, while common CNV regions are likely to occur at the same ge...

    Authors: Teo Shu Mei, Agus Salim, Stefano Calza, Ku Chee Seng, Chia Kee Seng and Yudi Pawitan
    Citation: BMC Bioinformatics 2010 11:147
    Content type: Research article Published on:

  25. While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor and a similar structure; pairwise sequence...

    Authors: Michael L Sierk, Michael E Smoot, Ellen J Bass and William R Pearson
    Citation: BMC Bioinformatics 2010 11:146
    Content type: Methodology article Published on:

  26. The challenge of remote homology detection is that many evolutionarily related sequences have very little similarity at the amino acid level. Kernel-based discriminative methods, such as support vector machine...

    Authors: Bobbie-Jo M Webb-Robertson, Kyle G Ratuiste and Christopher S Oehmen
    Citation: BMC Bioinformatics 2010 11:145
    Content type: Methodology article Published on:

  27. The prediction of protein-protein interactions is an important step toward the elucidation of protein functions and the understanding of the molecular mechanisms inside the cell. While experimental methods for...

    Authors: Martial Hue, Michael Riffle, Jean-Philippe Vert and William S Noble
    Citation: BMC Bioinformatics 2010 11:144
    Content type: Research article Published on:

  28. Multiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template or multiple DNA templates using more than one primer set (comprising a forward primer and a reverse primer) in one...

    Authors: Zhiyong Shen, Wubin Qu, Wen Wang, Yiming Lu, Yonghong Wu, Zhifeng Li, Xingyi Hang, Xiaolei Wang, Dongsheng Zhao and Chenggang Zhang
    Citation: BMC Bioinformatics 2010 11:143
    Content type: Software Published on:

  30. The budding yeast Saccharomyces cerevisiae is one of the most widely studied model organisms in aging-related science. Although several genetic modifiers of yeast longevity have been identified, the utility of th...

    Authors: Brady Olsen, Christopher J Murakami and Matt Kaeberlein
    Citation: BMC Bioinformatics 2010 11:141
    Content type: Software Published on:

  32. Stable isotope tracing with ultra-high resolution Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR-MS) can provide simultaneous determination of hundreds to thousands of metabolite isotopolo...

    Authors: Hunter NB Moseley
    Citation: BMC Bioinformatics 2010 11:139
    Content type: Methodology article Published on:

  33. Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological signifi...

    Authors: Mallika Veeramalai, David Gilbert and Gabriel Valiente
    Citation: BMC Bioinformatics 2010 11:138
    Content type: Methodology article Published on:

  36. MicroRNAs have been discovered as important regulators of gene expression. To identify the target genes of microRNAs, several databases and prediction algorithms have been developed. Only few experimentally co...

    Authors: Haroon Naeem, Robert Küffner, Gergely Csaba and Ralf Zimmer
    Citation: BMC Bioinformatics 2010 11:135
    Content type: Software Published on:

  38. A large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases ...

    Authors: José Afonso Guerra-Assunção and Anton J Enright
    Citation: BMC Bioinformatics 2010 11:133
    Content type: Software Published on:

  40. Protein-coding gene detection in prokaryotic genomes is considered a much simpler problem than in intron-containing eukaryotic genomes. However there have been reports that prokaryotic gene finder programs hav...

    Authors: Andrew S Warren, Jeremy Archuleta, Wu-chun Feng and João Carlos Setubal
    Citation: BMC Bioinformatics 2010 11:131
    Content type: Methodology article Published on:

  41. The most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome of an individual are aligned to a reference genome sequence for the same species. ...

    Authors: Aakrosh Ratan, Yu Zhang, Vanessa M Hayes, Stephan C Schuster and Webb Miller
    Citation: BMC Bioinformatics 2010 11:130
    Content type: Software Published on:

  46. Identification of novel drug targets and their inhibitors is a major challenge in the field of drug designing and development. Diaminopimelic acid (DAP) pathway is a unique lysine biosynthetic pathway present ...

    Authors: Aarti Garg, Rupinder Tewari and Gajendra PS Raghava
    Citation: BMC Bioinformatics 2010 11:125
    Content type: Methodology article Published on:

  47. Quantification of different types of cells is often needed for analysis of histological images. In our project, we compute the relative number of proliferating hepatocytes for the evaluation of the regeneratio...

    Authors: Tetyana Ivanovska, Andrea Schenk, André Homeyer, Meihong Deng, Uta Dahmen, Olaf Dirsch, Horst K Hahn and Lars Linsen
    Citation: BMC Bioinformatics 2010 11:124
    Content type: Methodology article Published on:

  48. Mitochondrial DNA (mtDNA) is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping...

    Authors: Hansi Weißensteiner, Sebastian Schönherr, Günther Specht, Florian Kronenberg and Anita Brandstätter
    Citation: BMC Bioinformatics 2010 11:122
    Content type: Database Published on:

  49. DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration...

    Authors: Florian Battke, Stephan Symons and Kay Nieselt
    Citation: BMC Bioinformatics 2010 11:121
    Content type: Software Published on:

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