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  1. Structural variations caused by a wide range of physico-chemical and biological sources directly influence the function of a protein. For enzymatic proteins, the structure and chemistry of the catalytic bindin...

    Authors: Drew H Bryant, Mark Moll, Brian Y Chen, Viacheslav Y Fofanov and Lydia E Kavraki
    Citation: BMC Bioinformatics 2010 11:242
    Content type: Research article Published on:

  2. Feature gene extraction is a fundamental issue in microarray-based biomarker discovery. It is normally treated as an optimization problem of finding the best predictive feature genes that can effectively and s...

    Authors: Chi Kin Chow, Hai Long Zhu, Jessica Lacy and Winston P Kuo
    Citation: BMC Bioinformatics 2010 11:241
    Content type: Methodology article Published on:

  3. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identificat...

    Authors: Lihua J Zhu, Claude Gazin, Nathan D Lawson, Hervé Pagès, Simon M Lin, David S Lapointe and Michael R Green
    Citation: BMC Bioinformatics 2010 11:237
    Content type: Software Published on:

  4. Sequence alignment is one of the most important techniques to analyze biological systems. It is also true that the alignment is not complete and we have to develop it to look for more accurate method. In parti...

    Authors: Toshihide Hara, Keiko Sato and Masanori Ohya
    Citation: BMC Bioinformatics 2010 11:235
    Content type: Software Published on:

  5. Differential co-expression analysis is an emerging strategy for characterizing disease related dysregulation of gene expression regulatory networks. Given pre-defined sets of biological samples, such analysis ...

    Authors: Johannes M Freudenberg, Siva Sivaganesan, Michael Wagner and Mario Medvedovic
    Citation: BMC Bioinformatics 2010 11:234
    Content type: Research article Published on:

  6. Phenomenological information about regulatory interactions is frequently available and can be readily converted to Boolean models. Fully quantitative models, on the other hand, provide detailed insights into t...

    Authors: Jan Krumsiek, Sebastian Pölsterl, Dominik M Wittmann and Fabian J Theis
    Citation: BMC Bioinformatics 2010 11:233
    Content type: Software Published on:

  7. Phosphorylation is a ubiquitous and fundamental regulatory mechanism that controls signal transduction in living cells. The number of identified phosphoproteins and their phosphosites is rapidly increasing as ...

    Authors: Haruna Imamura, Nozomu Yachie, Rintaro Saito, Yasushi Ishihama and Masaru Tomita
    Citation: BMC Bioinformatics 2010 11:232
    Content type: Research article Published on:

  8. Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RN...

    Authors: Mariusz Popenda, Marta Szachniuk, Marek Blazewicz, Szymon Wasik, Edmund K Burke, Jacek Blazewicz and Ryszard W Adamiak
    Citation: BMC Bioinformatics 2010 11:231
    Content type: Database Published on:

  9. Bisulfite sequencing is a popular method to analyze DNA methylation patterns at high resolution. A region of interest is targeted by PCR and about 20-50 subcloned DNA molecules are usually analyzed, to determi...

    Authors: Christian Rohde, Yingying Zhang, Richard Reinhardt and Albert Jeltsch
    Citation: BMC Bioinformatics 2010 11:230
    Content type: Software Published on:

  10. Modern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their ...

    Authors: Alain B Tchagang, Alexander Gawronski, Hugo Bérubé, Sieu Phan, Fazel Famili and Youlian Pan
    Citation: BMC Bioinformatics 2010 11:229
    Content type: Software Published on:

  12. High-throughput DNA methylation arrays are likely to accelerate the pace of methylation biomarker discovery for a wide variety of diseases. A potential problem with a standard set of probes measuring the methy...

    Authors: Hailong Meng, Andrew R Joyce, Daniel E Adkins, Priyadarshi Basu, Yankai Jia, Guoya Li, Tapas K Sengupta, Barbara K Zedler, E Lenn Murrelle and Edwin JCG van den Oord
    Citation: BMC Bioinformatics 2010 11:227
    Content type: Methodology article Published on:

  13. Copy number variations (CNVs) and polymorphisms (CNPs) have only recently gained the genetic community's attention. Conservative estimates have shown that CNVs and CNPs might affect more than 10% of the genome...

    Authors: Louis-Philippe Lemieux Perreault, Gregor U Andelfinger, Géraldine Asselin and Marie-Pierre Dubé
    Citation: BMC Bioinformatics 2010 11:226
    Content type: Software Published on:

  14. Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription factors in the literature, however, for many...

    Authors: Denitsa Alamanova, Philip Stegmaier and Alexander Kel
    Citation: BMC Bioinformatics 2010 11:225
    Content type: Research article Published on:

  15. Whole-genome sequence alignment is an essential process for extracting valuable information about the functions, evolution, and peculiarities of genomes under investigation. As available genomic sequence data ...

    Authors: Ryuichiro Nakato and Osamu Gotoh
    Citation: BMC Bioinformatics 2010 11:224
    Content type: Research article Published on:

  16. The antigen receptors, immunoglobulins (IG) and T cell receptors (TR), are specific molecular components of the adaptive immune response of vertebrates. Their genes are organized in the genome in several loci ...

    Authors: Jérôme Lane, Patrice Duroux and Marie-Paule Lefranc
    Citation: BMC Bioinformatics 2010 11:223
    Content type: Research article Published on:

  17. A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. Th...

    Authors: Andreas Bremges, Stefanie Schirmer and Robert Giegerich
    Citation: BMC Bioinformatics 2010 11:222
    Content type: Methodology article Published on:

  18. Genome-wide expression studies have developed exponentially in recent years as a result of extensive use of microarray technology. However, expression signals are typically calculated using the assignment of "...

    Authors: Alberto Risueño, Celia Fontanillo, Marcel E Dinger and Javier De Las Rivas
    Citation: BMC Bioinformatics 2010 11:221
    Content type: Database Published on:

  19. Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With jour...

    Authors: Andreas Prlić, Marco A Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T Yukich, Peter W Rose, Philip E Bourne and J Lynn Fink
    Citation: BMC Bioinformatics 2010 11:220
    Content type: Software Published on:

  20. Quantitative proteomics technologies have been developed to comprehensively identify and quantify proteins in two or more complex samples. Quantitative proteomics based on differential stable isotope labeling ...

    Authors: Fan Mo, Qun Mo, Yuanyuan Chen, David R Goodlett, Leroy Hood, Gilbert S Omenn, Song Li and Biaoyang Lin
    Citation: BMC Bioinformatics 2010 11:219
    Content type: Software Published on:

  21. An adaptive coarse-grained (kinetic) Monte Carlo (ACGMC) simulation framework is applied to reaction and diffusion dynamics in inhomogeneous domains. The presented model is relevant to the diffusion and dimeri...

    Authors: Stuart Collins, Michail Stamatakis and Dionisios G Vlachos
    Citation: BMC Bioinformatics 2010 11:218
    Content type: Methodology article Published on:

  22. Genome-Wide Association (GWA) analysis is a powerful method for identifying loci associated with complex traits and drug response. Parts of GWA analyses, especially those involving thousands of individuals and...

    Authors: Unitsa Sangket, Surakameth Mahasirimongkol, Wasun Chantratita, Pichaya Tandayya and Yurii S Aulchenko
    Citation: BMC Bioinformatics 2010 11:217
    Content type: Software Published on:

  23. Subtle alternative splicing events involving tandem splice sites separated by a short (2-12 nucleotides) distance are frequent and evolutionarily widespread in eukaryotes, and a major contributor to the comple...

    Authors: Rileen Sinha, Thorsten Lenser, Niels Jahn, Ulrike Gausmann, Swetlana Friedel, Karol Szafranski, Klaus Huse, Philip Rosenstiel, Jochen Hampe, Stefan Schuster, Michael Hiller, Rolf Backofen and Matthias Platzer
    Citation: BMC Bioinformatics 2010 11:216
    Content type: Database Published on:

  24. Automated protein function prediction methods are the only practical approach for assigning functions to genes obtained from model organisms. Many of the previously reported function annotation methods are of ...

    Authors: Jaehee Jung, Gangman Yi, Serenella A Sukno and Michael R Thon
    Citation: BMC Bioinformatics 2010 11:215
    Content type: Software Published on:

  25. Analysis of data from high-throughput experiments depends on the availability of well-structured data that describe the assayed biomolecules. Procedures for obtaining and organizing such meta-data on genes, tr...

    Authors: Henning Redestig, Miyako Kusano, Atsushi Fukushima, Fumio Matsuda, Kazuki Saito and Masanori Arita
    Citation: BMC Bioinformatics 2010 11:214
    Content type: Software Published on:

  26. Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabilities of organisms and interpreting experim...

    Authors: Jan Schellenberger, Junyoung O Park, Tom M Conrad and Bernhard Ø Palsson
    Citation: BMC Bioinformatics 2010 11:213
    Content type: Database Published on:

  27. Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequen...

    Authors: Jeffrey Martin, Wenhan Zhu, Karla D Passalacqua, Nicholas Bergman and Mark Borodovsky
    Citation: BMC Bioinformatics 2010 11(Suppl 3):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  28. Biological networks offer us a new way to investigate the interactions among different components and address the biological system as a whole. In this paper, a reverse-phase protein microarray (RPPM) is used ...

    Authors: Dong-Chul Kim, Xiaoyu Wang, Chin-Rang Yang and Jean Gao
    Citation: BMC Bioinformatics 2010 11(Suppl 3):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  29. Similaritysearch in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed tha...

    Authors: Xiaohong Wang, Jun Huan, Aaron Smalter and Gerald H Lushington
    Citation: BMC Bioinformatics 2010 11(Suppl 3):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  30. Ortholog detection methods present a powerful approach for finding genes that participate in similar biological processes across different organisms, extending our understanding of interactions between genes a...

    Authors: Fadi Towfic, Susan VanderPIas, Casey A OIiver, OIiver Couture, Christopher K TuggIe, M Heather West GreenIee and Vasant Honavar
    Citation: BMC Bioinformatics 2010 11(Suppl 3):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  31. In eukaryotes, alternative splicing often generates multiple splice variants from a single gene. Here weexplore the use of RNA sequencing (RNA-Seq) datasets to address the isoform quantification problem. Given...

    Authors: Brian E Howard and Steffen Heber
    Citation: BMC Bioinformatics 2010 11(Suppl 3):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  32. Detecting epistatic interactions associated with complex and common diseases can help to improve prevention, diagnosis and treatment of these diseases. With the development of genome-wide association studies (...

    Authors: Bing Han, Meeyoung Park and Xue-wen Chen
    Citation: BMC Bioinformatics 2010 11(Suppl 3):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  33. We present a novel conformal Bayesian network (CBN) to classify strains of Mycobacterium tuberculosis Complex (MTBC) into six major genetic lineages based on two high-throuput biomarkers: mycobacterial interspers...

    Authors: Minoo Aminian, Amina Shabbeer and Kristin P Bennett
    Citation: BMC Bioinformatics 2010 11(Suppl 3):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  34. Protein-protein interactions play a key role in biological processes of proteins within a cell. Recent high-throughput techniques have generated protein-protein interaction data in a genome-scale. A wide range...

    Authors: Young-Rae Cho and Aidong Zhang
    Citation: BMC Bioinformatics 2010 11(Suppl 3):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  35. Protein translation is a vital cellular process for any living organism. The availability of interaction databases provides an opportunity for researchers to exploit the immense amount of data in silico such as s...

    Authors: Daniel D Wu, Xiaohua Hu, EK Park, Xiaofeng Wang, Jiali Feng and Xindong Wu
    Citation: BMC Bioinformatics 2010 11(Suppl 3):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  36. Protein folding rate is an important property of a protein. Predicting protein folding rate is useful for understanding protein folding process and guiding protein design. Most previous methods of predicting p...

    Authors: Guan Ning Lin, Zheng Wang, Dong Xu and Jianlin Cheng
    Citation: BMC Bioinformatics 2010 11(Suppl 3):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 3

  37. Advances in biotechnology and in high-throughput methods for gene analysis have contributed to an exponential increase in the number of scientific publications in these fields of study. While much of the data ...

    Authors: Sérgio Matos, Joel P Arrais, João Maia-Rodrigues and José Luis Oliveira
    Citation: BMC Bioinformatics 2010 11:212
    Content type: Software Published on:

  39. We present here the recent update of AMS algorithm for identification of post-translational modification (PTM) sites in proteins based only on sequence information, using artificial neural network (ANN) method...

    Authors: Subhadip Basu and Dariusz Plewczynski
    Citation: BMC Bioinformatics 2010 11:210
    Content type: Research article Published on:

  40. Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical method...

    Authors: Federico Plazzi, Ronald R Ferrucci and Marco Passamonti
    Citation: BMC Bioinformatics 2010 11:209
    Content type: Methodology article Published on:

  41. A key stage for all microarray analyses is the extraction of feature-intensities from an image. If this step goes wrong, then subsequent preprocessing and processing stages will stand little chance of rectifyi...

    Authors: Mike L Smith, Mark J Dunning, Simon Tavaré and Andy G Lynch
    Citation: BMC Bioinformatics 2010 11:208
    Content type: Research article Published on:

  43. Previous studies on insect DNA barcoding provide contradictory results and suggest not consistent performances across orders. This work aims at providing a general evaluation of insect DNA barcoding and "mini-...

    Authors: Massimiliano Virgilio, Thierry Backeljau, Bruno Nevado and Marc De Meyer
    Citation: BMC Bioinformatics 2010 11:206
    Content type: Research article Published on:

  44. Profile HMMs (hidden Markov models) provide effective methods for modeling the conserved regions of protein families. A limitation of the resulting domain models is the difficulty to pinpoint their much shorte...

    Authors: Kevin Horan, Christian R Shelton and Thomas Girke
    Citation: BMC Bioinformatics 2010 11:205
    Content type: Research article Published on:

  45. A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendo...

    Authors: Annalisa Marsico, Andreas Henschel, Christof Winter, Anne Tuukkanen, Boris Vassilev, Kerstin Scheubert and Michael Schroeder
    Citation: BMC Bioinformatics 2010 11:204
    Content type: Research article Published on:

  46. Bisulfite sequencing using next generation sequencers yields genome-wide measurements of DNA methylation at single nucleotide resolution. Traditional aligners are not designed for mapping bisulfite-treated rea...

    Authors: Pao-Yang Chen, Shawn J Cokus and Matteo Pellegrini
    Citation: BMC Bioinformatics 2010 11:203
    Content type: Software Published on:

  47. Mathematical modeling is being applied to increasingly complex biological systems and datasets; however, the process of analyzing and calibrating against experimental data is often challenging and a rate limit...

    Authors: Kyoung Ae Kim, Sabrina L Spencer, John G Albeck, John M Burke, Peter K Sorger, Suzanne Gaudet and Do Hyun Kim
    Citation: BMC Bioinformatics 2010 11:202
    Content type: Methodology article Published on:

  49. DNA copy number aberration (CNA) is very important in the pathogenesis of tumors and other diseases. For example, CNAs may result in suppression of anti-oncogenes and activation of oncogenes, which would cause...

    Authors: Fuhai Li, Xiaobo Zhou, Wanting Huang, Chung-Che Chang and Stephen TC Wong
    Citation: BMC Bioinformatics 2010 11:200
    Content type: Research article Published on:

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