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  1. The vitamins are important cofactors in various enzymatic-reactions. In past, many inhibitors have been designed against vitamin binding pockets in order to inhibit vitamin-protein interactions. Thus, it is im...

    Authors: Bharat Panwar, Sudheer Gupta and Gajendra P S Raghava
    Citation: BMC Bioinformatics 2013 14:44
    Content type: Research article Published on:

  3. Gene clustering algorithms are massively used by biologists when analysing omics data. Classical gene clustering strategies are based on the use of expression data only, directly as in Heatmaps, or indirectly ...

    Authors: Marie Verbanck, Sébastien Lê and Jérôme Pagès
    Citation: BMC Bioinformatics 2013 14:42
    Content type: Methodology article Published on:

  4. Interferon-gamma (IFN-gamma) and interleukin-6 (IL-6) are multifunctional cytokines that regulate immune responses, cell proliferation, and tumour development and progression, which frequently have functionall...

    Authors: Yun-feng Qi, Yan-xin Huang, Hong-yan Wang, Yu Zhang, Yong-li Bao, Lu-guo Sun, Yin Wu, Chun-lei Yu, Zhen-bo Song, Li-hua Zheng, Ying Sun, Guan-nan Wang and Yu-xin Li
    Citation: BMC Bioinformatics 2013 14:41
    Content type: Research article Published on:

  7. Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use ...

    Authors: Kemal Sanli, Fredrik H Karlsson, Intawat Nookaew and Jens Nielsen
    Citation: BMC Bioinformatics 2013 14:38
    Content type: Software Published on:

  8. Motion analysis is one of the tools available to biologists to extract biologically relevant information from image datasets and has been applied to a diverse range of organisms. The application of motion anal...

    Authors: Oliver Tills, Tabitha Bitterli, Phil Culverhouse, John I Spicer and Simon Rundle
    Citation: BMC Bioinformatics 2013 14:37
    Content type: Research article Published on:

  9. One of the major issues in the fight against infectious diseases is the notable increase in multiple drug resistance in pathogenic species. For that reason, newly acquired high-throughput data on virulent micr...

    Authors: Arkadiusz Gladki, Szymon Kaczanowski, Pawel Szczesny and Piotr Zielenkiewicz
    Citation: BMC Bioinformatics 2013 14:36
    Content type: Research article Published on:

  10. Drug pharmacokinetics parameters, drug interaction parameters, and pharmacogenetics data have been unevenly collected in different databases and published extensively in the literature. Without appropriate pha...

    Authors: Heng-Yi Wu, Shreyas Karnik, Abhinita Subhadarshini, Zhiping Wang, Santosh Philips, Xu Han, Chienwei Chiang, Lei Liu, Malaz Boustani, Luis M Rocha, Sara K Quinney, David Flockhart and Lang Li
    Citation: BMC Bioinformatics 2013 14:35
    Content type: Database Published on:

  12. Illumina sequencing platform is widely used in genome research. Sequence reads quality assessment and control are needed for downstream analysis. However, software that provides efficient quality assessment an...

    Authors: Xi Yang, Di Liu, Fei Liu, Jun Wu, Jing Zou, Xue Xiao, Fangqing Zhao and Baoli Zhu
    Citation: BMC Bioinformatics 2013 14:33
    Content type: Software Published on:

  14. RNA-Seq has the potential to answer many diverse and interesting questions about the inner workings of cells. Estimating changes in the overall transcription of a gene is not straightforward. Changes in overal...

    Authors: Ellis Patrick, Michael Buckley and Yee Hwa Yang
    Citation: BMC Bioinformatics 2013 14:31
    Content type: Methodology article Published on:

  15. The size of the protein sequence database has been exponentially increasing due to advances in genome sequencing. However, experimentally characterized proteins only constitute a small portion of the database,...

    Authors: Wenlin Li, Qian Cong, Lisa N Kinch and Nick V Grishin
    Citation: BMC Bioinformatics 2013 14:30
    Content type: Research article Published on:

  16. Delineating the molecular drivers of cancer, i.e. determining cancer genes and the pathways which they deregulate, is an important challenge in cancer research. In this study, we aim to identify pathways of fr...

    Authors: Sepideh Babaei, Marc Hulsman, Marcel Reinders and Jeroen de Ridder
    Citation: BMC Bioinformatics 2013 14:29
    Content type: Methodology article Published on:

  17. Population inference is an important problem in genetics used to remove population stratification in genome-wide association studies and to detect migration patterns or shared ancestry. An individual’s genotyp...

    Authors: R Mitchell Parry and May D Wang
    Citation: BMC Bioinformatics 2013 14:28
    Content type: Research article Published on:

  19. Identification of cis- and trans-acting factors regulating gene expression remains an important problem in biology. Bioinformatics analyses of regulatory regions are hampered by several difficulties. One is that ...

    Authors: Alexis Vandenbon, Yutaro Kumagai, Shunsuke Teraguchi, Karlou Mar Amada, Shizuo Akira and Daron M Standley
    Citation: BMC Bioinformatics 2013 14:26
    Content type: Methodology article Published on:

  21. Mass spectrometry-based protein identification is a very challenging task. The main identification approaches include de novo sequencing and database searching. Both approaches have shortcomings, so an integra...

    Authors: Penghao Wang and Susan R Wilson
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S24
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  22. Functional module identification in biological networks may provide new insights into the complex interactions among biomolecules for a better understanding of cellular functional organization. Most of existin...

    Authors: Yijie Wang and Xiaoning Qian
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  23. Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free gra...

    Authors: Zsuzsanna Sükösd, Bjarne Knudsen, James WJ Anderson, Ádám Novák, Jørgen Kjems and Christian NS Pedersen
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  24. The pandemic 2009-H1N1 influenza virus circulated in the human population and caused thousands deaths worldwide. Studies on pandemic influenza vaccines have shown that T cell recognition to conserved epitopes ...

    Authors: Chinh TT Su, Christian Schönbach and Chee-Keong Kwoh
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  25. Disulfide bonds constitute one of the most important cross-linkages in proteins and significantly influence protein structure and function. At the state-of-the-art, various methodological frameworks have been ...

    Authors: Rahul Singh and William Murad
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  26. Given a protein's amino acid sequence, the protein structure prediction problem is to find a three dimensional structure that has the native energy level. For many decades, it has been one of the most challeng...

    Authors: Swakkhar Shatabda, MA Hakim Newton, Mahmood A Rashid, Duc Nghia Pham and Abdul Sattar
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  27. The triplet distance is a distance measure that compares two rooted trees on the same set of leaves by enumerating all sub-sets of three leaves and counting how often the induced topologies of the tree are equ...

    Authors: Andreas Sand, Gerth Stølting Brodal, Rolf Fagerberg, Christian NS Pedersen and Thomas Mailund
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  28. Optimization procedures to identify gene knockouts for targeted biochemical overproduction have been widely in use in modern metabolic engineering. Flux balance analysis (FBA) framework has provided conceptual...

    Authors: Shaogang Ren, Bo Zeng and Xiaoning Qian
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  29. Protein structure prediction is an important but unsolved problem in biological science. Predicted structures vary much with energy functions and structure-mapping spaces. In our simplified ab initio protein stru...

    Authors: Mahmood A Rashid, MA Hakim Newton, Md Tamjidul Hoque, Swakkhar Shatabda, Duc Nghia Pham and Abdul Sattar
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  30. Gene Ontology (GO) has been widely used in biological databases, annotation projects, and computational analyses. Although the three GO categories are structured as independent ontologies, the biological relat...

    Authors: Jiajie Peng, Jin Chen and Yadong Wang
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  31. The over consumption of fossil fuels has led to growing concerns over climate change and global warming. Increasing research activities have been carried out towards alternative viable biofuel sources. Of seve...

    Authors: Nguyen Xuan Vinh, Madhu Chetty, Ross Coppel, Sandeep Gaudana and Pramod P Wangikar
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  32. MHC (Major Histocompatibility Complex) is a key player in the immune response of most vertebrates. The computational prediction of whether a given antigenic peptide will bind to a specific MHC allele is import...

    Authors: Cem Meydan, Hasan H Otu and Osman Uğur Sezerman
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  33. In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classificatio...

    Authors: Cheng-Yu Ma, Shu-Hsi Lin, Chi-Ching Lee, Chuan Yi Tang, Bonnie Berger and Chung-Shou Liao
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  34. The protein-protein interaction (PPI) is one of the most important features to understand biological processes. For a PPI, the physical domain-domain interaction (DDI) plays the key role for biology functions....

    Authors: Chun-Yu Lin, Yung-Chiang Chen, Yu-Shu Lo and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  35. Development of computational tools that can accurately predict presence and location of B-cell epitopes on pathogenic proteins has a valuable application to the field of vaccinology. Because of the highly vari...

    Authors: Scott Yi-Heng Lin, Cheng-Wei Cheng and Emily Chia-Yu Su
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  36. Polyadenylation is present in all three domains of life, making it the most conserved post-transcriptional process compared with splicing and 5'-capping. Even though most mammalian poly(A) sites contain a high...

    Authors: Eric S Ho, Samuel I Gunderson and Siobain Duffy
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  37. Markov state models have been widely used to study conformational changes of biological macromolecules. These models are built from short timescale simulations and then propagated to extract long timescale dyn...

    Authors: Chen Gu, Huang-Wei Chang, Lutz Maibaum, Vijay S Pande, Gunnar E Carlsson and Leonidas J Guibas
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  38. Gene expression profiles can show significant changes when genetically diseased cells are compared with non-diseased cells. Biological networks are often used to identify active subnetworks (ASNs) of the diseases...

    Authors: Raj K Gaire, Lorey Smith, Patrick Humbert, James Bailey, Peter J Stuckey and Izhak Haviv
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  39. Even a single amino acid substitution in a protein sequence may result in significant changes in protein stability, structure, and therefore in protein function as well. In the post-genomic era, computational ...

    Authors: Lukas Folkman, Bela Stantic and Abdul Sattar
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  40. Mutation of a single amino acid residue can cause changes in a protein, which could then lead to a loss of protein function. Predicting the protein stability changes can provide several possible candidates for...

    Authors: Chi-Wei Chen, Jerome Lin and Yen-Wei Chu
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  41. Functional RNA molecules participate in numerous biological processes, ranging from gene regulation to protein synthesis. Analysis of functional RNA motifs and elements in RNA sequences can obtain useful infor...

    Authors: Tzu-Hao Chang, Hsi-Yuan Huang, Justin Bo-Kai Hsu, Shun-Long Weng, Jorng-Tzong Horng and Hsien-Da Huang
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  42. MicroRNAs (miRNA) are regulatory genes that target and repress other RNA molecules via sequence-specific binding. Several biological processes are regulated across many organisms by evolutionarily conserved mi...

    Authors: Joseph W Carl Jr, Joanne Trgovcich and Sridhar Hannenhalli
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  43. One of the main types of genetic variations in cancer is Copy Number Variations (CNV). Whole exome sequenicng (WES) is a popular alternative to whole genome sequencing (WGS) to study disease specific genomic v...

    Authors: Kaushalya C Amarasinghe, Jason Li and Saman K Halgamuge
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

    The Erratum to this article has been published in BMC Bioinformatics 2013 14:S26

  44. Accurate secondary structure prediction provides important information to undefirstafinding the tertiary structures and thus the functions of ncRNAs. However, the accuracy of the native structure derivation of...

    Authors: Rujira Achawanantakun and Yanni Sun
    Citation: BMC Bioinformatics 2013 14(Suppl 2):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  45. Maximum Likelihood (ML)-based phylogenetic inference using Felsenstein’s pruning algorithm is a standard method for estimating the evolutionary relationships amongst a set of species based on DNA sequence data...

    Authors: Zheming Jin and Jason D Bakos
    Citation: BMC Bioinformatics 2013 14:25
    Content type: Software Published on:

  46. Protein pairs that have the same secondary structure packing arrangement but have different topologies have attracted much attention in terms of both evolution and physical chemistry of protein structures. Fur...

    Authors: Shintaro Minami, Kengo Sawada and George Chikenji
    Citation: BMC Bioinformatics 2013 14:24
    Content type: Methodology article Published on:

  47. New technology has resulted in high-throughput screens for pairwise genetic interactions in yeast and other model organisms. For each pair in a collection of non-essential genes, an epistasis score is obtained...

    Authors: Andrew Gallant, Mark DM Leiserson, Maxim Kachalov, Lenore J Cowen and Benjamin J Hescott
    Citation: BMC Bioinformatics 2013 14:23
    Content type: Software Published on:

  49. Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting ...

    Authors: Yasin Bakış, Hasan H Otu, Nivart Taşçı, Cem Meydan, Neş’e Bilgin, Sırrı Yüzbaşıoğlu and O Uğur Sezerman
    Citation: BMC Bioinformatics 2013 14:20
    Content type: Methodology article Published on:

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