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  1. Protein kinases play crucial roles in cell growth, differentiation, and apoptosis. Abnormal function of protein kinases can lead to many serious diseases, such as cancer. Kinase inhibitors have potential for t...

    Authors: Maris Lapins and Jarl ES Wikberg
    Citation: BMC Bioinformatics 2010 11:339
    Content type: Research article Published on:

  2. Reverse-engineering approaches such as Bayesian network inference, ordinary differential equations (ODEs) and information theory are widely applied to deriving causal relationships among different elements suc...

    Authors: Cunlu Zou, Christophe Ladroue, Shuixia Guo and Jianfeng Feng
    Citation: BMC Bioinformatics 2010 11:337
    Content type: Research article Published on:

  3. Several tools have been developed to explore and search Gene Ontology (GO) databases allowing efficient GO enrichment analysis and GO tree visualization. Nevertheless, identification of highly specific GO-term...

    Authors: Marc Bruckskotten, Mario Looso, Franz Cemiĉ, Anne Konzer, Jürgen Hemberger, Marcus Krüger and Thomas Braun
    Citation: BMC Bioinformatics 2010 11:336
    Content type: Methodology article Published on:

  4. Graph drawing is one of the important techniques for understanding biological regulations in a cell or among cells at the pathway level. Among many available layout algorithms, the spring embedder algorithm is...

    Authors: Kaname Kojima, Masao Nagasaki and Satoru Miyano
    Citation: BMC Bioinformatics 2010 11:335
    Content type: Research article Published on:

  6. In water-soluble proteins it is energetically favorable to bury hydrophobic residues and to expose polar and charged residues. In contrast to water soluble proteins, transmembrane proteins face three distinct ...

    Authors: Kristoffer Illergård, Simone Callegari and Arne Elofsson
    Citation: BMC Bioinformatics 2010 11:333
    Content type: Research article Published on:

  8. Determining a suitable sample size is an important step in the planning of microarray experiments. Increasing the number of arrays gives more statistical power, but adds to the total cost of the experiment. Se...

    Authors: Ilari Scheinin, José A Ferreira, Sakari Knuutila, Gerrit A Meijer, Mark A van de Wiel and Bauke Ylstra
    Citation: BMC Bioinformatics 2010 11:331
    Content type: Software Published on:

  11. Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many m...

    Authors: Jay Vyas, Ronald J Nowling, Thomas Meusburger, David Sargeant, Krishna Kadaveru, Michael R Gryk, Vamsi Kundeti, Sanguthevar Rajasekaran and Martin R Schiller
    Citation: BMC Bioinformatics 2010 11:328
    Content type: Software Published on:

  12. The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in rece...

    Authors: Svetlana Kirillova, Silvio CE Tosatto and Oliviero Carugo
    Citation: BMC Bioinformatics 2010 11:327
    Content type: Software Published on:

  14. Because a priori knowledge about function of G protein-coupled receptors (GPCRs) can provide useful information to pharmaceutical research, the determination of their function is a quite meaningful topic in pr...

    Authors: Zhanchao Li, Xuan Zhou, Zong Dai and Xiaoyong Zou
    Citation: BMC Bioinformatics 2010 11:325
    Content type: Research article Published on:

  16. Cell volume determination plays a pivotal role in the investigation of the biophysical mechanisms underlying various cellular processes. Whereas light microscopy in principle enables one to obtain three dimens...

    Authors: Patrick Happel, Kerstin Möller, Ralf Kunz and Irmgard D Dietzel
    Citation: BMC Bioinformatics 2010 11:323
    Content type: Methodology article Published on:

  18. Cancer and other disorders are due to genomic lesions. SNP-microarrays are able to measure simultaneously both genotype and copy number (CN) at several Single Nucleotide Polymorphisms (SNPs) along the genome. ...

    Authors: Paola MV Rancoita, Marcus Hutter, Francesco Bertoni and Ivo Kwee
    Citation: BMC Bioinformatics 2010 11:321
    Content type: Research article Published on:

  19. Caspases are a family of proteases that have central functions in programmed cell death (apoptosis) and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins...

    Authors: Mirva Piippo, Niina Lietzén, Olli S Nevalainen, Jussi Salmi and Tuula A Nyman
    Citation: BMC Bioinformatics 2010 11:320
    Content type: Software Published on:

  20. The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between ...

    Authors: Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross Overbeek, Veronika Vonstein, Rick Stevens and Robert A Edwards
    Citation: BMC Bioinformatics 2010 11:319
    Content type: Software Published on:

  21. Genome-wide association studies (GWAS) based on single nucleotide polymorphisms (SNPs) revolutionized our perception of the genetic regulation of complex traits and diseases. Copy number variations (CNVs) prom...

    Authors: Lukas Forer, Sebastian Schönherr, Hansi Weissensteiner, Florian Haider, Thomas Kluckner, Christian Gieger, Heinz-Erich Wichmann, Günther Specht, Florian Kronenberg and Anita Kloss-Brandstätter
    Citation: BMC Bioinformatics 2010 11:318
    Content type: Software Published on:

  22. For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encode...

    Authors: Amber L Hartman, Sean Riddle, Timothy McPhillips, Bertram Ludäscher and Jonathan A Eisen
    Citation: BMC Bioinformatics 2010 11:317
    Content type: Software Published on:

  23. G protein-coupled receptors (GPCRs) represent a family of well-characterized drug targets with significant therapeutic value. Phylogenetic classifications may help to understand the characteristics of individu...

    Authors: Eelke van der Horst, Julio E Peironcely, Adriaan P IJzerman, Margot W Beukers, Jonathan R Lane, Herman WT van Vlijmen, Michael TM Emmerich, Yasushi Okuno and Andreas Bender
    Citation: BMC Bioinformatics 2010 11:316
    Content type: Research article Published on:

  26. The knowledge about proteins with specific interaction capacity to the protein partners is very important for the modeling of cell signaling networks. However, the experimentally-derived data are sufficiently ...

    Authors: Boris Sobolev, Dmitry Filimonov, Alexey Lagunin, Alexey Zakharov, Olga Koborova, Alexander Kel and Vladimir Poroikov
    Citation: BMC Bioinformatics 2010 11:313
    Content type: Research article Published on:

  28. Whole genome association studies using highly dense single nucleotide polymorphisms (SNPs) are a set of methods to identify DNA markers associated with variation in a particular complex trait of interest. One ...

    Authors: Stephen J Goodswen, Cedric Gondro, Nathan S Watson-Haigh and Haja N Kadarmideen
    Citation: BMC Bioinformatics 2010 11:311
    Content type: Database Published on:

  29. Partitioning of a protein into structural components, known as domains, is an important initial step in protein classification and for functional and evolutionary studies. While the systematic assignments of d...

    Authors: Kieran Alden, Stella Veretnik and Philip E Bourne
    Citation: BMC Bioinformatics 2010 11:310
    Content type: Software Published on:

  30. This paper introduces the notion of optimizing different norms in the dual problem of support vector machines with multiple kernels. The selection of norms yields different extensions of multiple kernel learni...

    Authors: Shi Yu, Tillmann Falck, Anneleen Daemen, Leon-Charles Tranchevent, Johan AK Suykens, Bart De Moor and Yves Moreau
    Citation: BMC Bioinformatics 2010 11:309
    Content type: Methodology article Published on:

  31. Signal transduction is the major mechanism through which cells transmit external stimuli to evoke intracellular biochemical responses. Diverse cellular stimuli create a wide variety of transcription factor act...

    Authors: Shih Chi Peng, David Shan Hill Wong, Kai Che Tung, Yan Yu Chen, Chun Cheih Chao, Chien Hua Peng, Yung Jen Chuang and Chuan Yi Tang
    Citation: BMC Bioinformatics 2010 11:308
    Content type: Methodology article Published on:

  32. We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the re...

    Authors: Gerd Gruenert, Bashar Ibrahim, Thorsten Lenser, Maiko Lohel, Thomas Hinze and Peter Dittrich
    Citation: BMC Bioinformatics 2010 11:307
    Content type: Research article Published on:

  33. Accurately covering the conformational space of amino acid side chains is essential for important applications such as protein design, docking and high resolution structure prediction. Today, the most common w...

    Authors: Tim Harder, Wouter Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer E Johansson and Thomas Hamelryck
    Citation: BMC Bioinformatics 2010 11:306
    Content type: Research article Published on:

  34. Methylation of CpG islands within the DNA promoter regions is one mechanism that leads to aberrant gene expression in cancer. In particular, the abnormal methylation of CpG islands may silence associated genes...

    Authors: Leandro A Loss, Anguraj Sadanandam, Steffen Durinck, Shivani Nautiyal, Diane Flaucher, Victoria EH Carlton, Martin Moorhead, Yontao Lu, Joe W Gray, Malek Faham, Paul Spellman and Bahram Parvin
    Citation: BMC Bioinformatics 2010 11:305
    Content type: Methodology article Published on:

  35. There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rear...

    Authors: Adriana Muñoz, Chunfang Zheng, Qian Zhu, Victor A Albert, Steve Rounsley and David Sankoff
    Citation: BMC Bioinformatics 2010 11:304
    Content type: Research article Published on:

  36. Many functional proteins have a symmetric structure. Most of these are multimeric complexes, which are made of non-symmetric monomers arranged in a symmetric manner. However, there are also a large number of p...

    Authors: Changhoon Kim, Jodi Basner and Byungkook Lee
    Citation: BMC Bioinformatics 2010 11:303
    Content type: Research article Published on:

  38. Guanosine triphosphate (GTP)-binding proteins play an important role in regulation of G-protein. Thus prediction of GTP interacting residues in a protein is one of the major challenges in the field of the comp...

    Authors: Jagat S Chauhan, Nitish K Mishra and Gajendra PS Raghava
    Citation: BMC Bioinformatics 2010 11:301
    Content type: Research article Published on:

  39. Feature selection is an important pre-processing task in the analysis of complex data. Selecting an appropriate subset of features can improve classification or clustering and lead to better understanding of t...

    Authors: Assaf Gottlieb, Roy Varshavsky, Michal Linial and David Horn
    Citation: BMC Bioinformatics 2010 11:300
    Content type: Research article Published on:

  40. Typically, pooling of mRNA samples in microarray experiments implies mixing mRNA from several biological-replicate samples before hybridization onto a microarray chip. Here we describe an alternative smart poo...

    Authors: Raghunandan M Kainkaryam, Angela Bruex, Anna C Gilbert, John Schiefelbein and Peter J Woolf
    Citation: BMC Bioinformatics 2010 11:299
    Content type: Research article Published on:

  46. Metabolic pathway is a highly regulated network consisting of many metabolic reactions involving substrates, enzymes, and products, where substrates can be transformed into products with particular catalytic e...

    Authors: Lei Chen, Kai-Yan Feng, Yu-Dong Cai, Kuo-Chen Chou and Hai-Peng Li
    Citation: BMC Bioinformatics 2010 11:293
    Content type: Research article Published on:

  49. Despite the recent success of genome-wide association studies in identifying novel loci contributing effects to complex human traits, such as type 2 diabetes and obesity, much of the genetic component of varia...

    Authors: Reedik Mägi and Andrew P Morris
    Citation: BMC Bioinformatics 2010 11:288
    Content type: Software Published on:

  50. High-throughput screens comparing growth rates of arrays of distinct micro-organism cultures on solid agar are useful, rapid methods of quantifying genetic interactions. Growth rate is an informative phenotype...

    Authors: Conor Lawless, Darren J Wilkinson, Alexander Young, Stephen G Addinall and David A Lydall
    Citation: BMC Bioinformatics 2010 11:287
    Content type: Software Published on:

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