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Bioinformatics

Section edited by Frank Eisenhaber and Sandor Pongor

The Bioinformatics section will be the publishing channel for scientific articles that report about theoretical, computational and data analysis approaches applied to biological, medical and other life science related problems, and the results and insights that have been achieved with them. Special emphasis is given to manuscripts that deal with biological mechanism interpretation to biomolecular sequence data and data from other experimental high-throughput techniques. This section also covers all fields of bioinformatics and computational biology that might not be handled by other subsections of Biology Direct. Hypotheses are welcome as long as they are based on rigorous scientific standards and as they fit existing data. Manuscripts describing new methods or software developments need to demonstrate that a major improvement has been achieved, and this has led to either improved accuracy by orders of magnitude, lowered resource consumption and/or some new biological insight.

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  1. Content type: Review

    High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and car...

    Authors: Ola Spjuth, Erik Bongcam-Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimera, Aleksi Kallio, Eija Korpelainen, Maciej M Kańduła, Milko Krachunov, David P Kreil, Ognyan Kulev, Paweł P. Łabaj, Samuel Lampa, Luca Pireddu, Sebastian Schönherr…

    Citation: Biology Direct 2015 10:43

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  2. Content type: Research

    Antibiotic resistance is a major biomedical problem upon which public health systems demand solutions to construe the dynamics and epidemiological risk of resistant bacteria in anthropogenically-altered enviro...

    Authors: Marcelino Campos, Carlos Llorens, José M. Sempere, Ricardo Futami, Irene Rodriguez, Purificación Carrasco, Rafael Capilla, Amparo Latorre, Teresa M. Coque, Andres Moya and Fernando Baquero

    Citation: Biology Direct 2015 10:41

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  3. Content type: Research

    Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. A simplis...

    Authors: Wing-Cheong Wong, Choon-Kong Yap, Birgit Eisenhaber and Frank Eisenhaber

    Citation: Biology Direct 2015 10:39

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  4. Content type: Research

    In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contai...

    Authors: Richa Mudgal, Sankaran Sandhya, Nagasuma Chandra and Narayanaswamy Srinivasan

    Citation: Biology Direct 2015 10:38

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  5. Content type: Research

    Mutations in nucleotide sequences provide a foundation for genetic variability, and selection is the driving force of the evolution and molecular adaptation. Despite considerable progress in the understanding ...

    Authors: Alexander Goncearenco and Igor N Berezovsky

    Citation: Biology Direct 2014 9:29

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  6. Content type: Research

    Moonlighting proteins perform two or more cellular functions, which are selected based on various contexts including the cell type they are expressed, their oligomerization status, and the binding of different...

    Authors: Ishita Khan, Yuqian Chen, Tiange Dong, Xioawei Hong, Rikiya Takeuchi, Hirotada Mori and Daisuke Kihara

    Citation: Biology Direct 2014 9:30

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  7. Content type: Research

    We have previously suggested a method for proteome wide analysis of variation at functional residues wherein we identified the set of all human genes with nonsynonymous single nucleotide variation (nsSNV) in t...

    Authors: Hayley Dingerdissen, Daniel S Weaver, Peter D Karp, Yang Pan, Vahan Simonyan and Raja Mazumder

    Citation: Biology Direct 2014 9:9

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  8. Content type: Research

    H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an imp...

    Authors: Hufeng Zhou, Shangzhi Gao, Nam Ninh Nguyen, Mengyuan Fan, Jingjing Jin, Bing Liu, Liang Zhao, Geng Xiong, Min Tan, Shijun Li and Limsoon Wong

    Citation: Biology Direct 2014 9:5

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  9. Content type: Research

    The generation of interferon-gamma (IFN-γ) by MHC class II activated CD4+ T helper cells play a substantial contribution in the control of infections such as caused by Mycobacterium tuberculosis. In the past, num...

    Authors: Sandeep Kumar Dhanda, Pooja Vir and Gajendra PS Raghava

    Citation: Biology Direct 2013 8:30

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  10. Content type: Discovery notes

    Translation elongation factors eEF1A1 and eEF1A2 are 92% identical but exhibit non-overlapping expression patterns. While the two proteins are predicted to have similar tertiary structures, it is notable that ...

    Authors: Dinesh C Soares and Catherine M Abbott

    Citation: Biology Direct 2013 8:29

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  11. Content type: Research

    In the past, numerous methods have been developed for predicting antigenic regions or B-cell epitopes that can induce B-cell response. To the best of authors’ knowledge, no method has been developed for predic...

    Authors: Sudheer Gupta, Hifzur Rahman Ansari, Ankur Gautam and Gajendra PS Raghava

    Citation: Biology Direct 2013 8:27

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  12. Content type: Discovery notes

    The bacterial SOS response is an elaborate program for DNA repair, cell cycle regulation and adaptive mutagenesis under stress conditions. Using sensitive sequence and structure analysis, combined with context...

    Authors: L Aravind, Swadha Anand and Lakshminarayan M Iyer

    Citation: Biology Direct 2013 8:20

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  13. Content type: Discovery notes

    tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequenci...

    Authors: Guilherme Loss-Morais, Peter M Waterhouse and Rogerio Margis

    Citation: Biology Direct 2013 8:6

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  14. Content type: Discovery notes

    Twintrons represent a special intronic arrangement in which introns of two different types occupy the same gene position. Consequently, alternative splicing of these introns requires two different spliceosomes...

    Authors: Jessin Janice, Marcin Jąkalski and Wojciech Makałowski

    Citation: Biology Direct 2013 8:4

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  15. Content type: Discovery notes

    Clusters of localized hypermutation in human breast cancer genomes, named “kataegis” (from the Greek for thunderstorm), are hypothesized to result from multiple cytosine deaminations catalyzed by AID/APOBEC pr...

    Authors: Artem G Lada, Alok Dhar, Robert J Boissy, Masayuki Hirano, Aleksandr A Rubel, Igor B Rogozin and Youri I Pavlov

    Citation: Biology Direct 2012 7:47

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  16. Content type: Discovery notes

    Ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. Previous studies have revealed the presence of eutBC gen...

    Authors: Neelam Khatri, Indu Khatri, Srikrishna Subramanian and Saumya Raychaudhuri

    Citation: Biology Direct 2012 7:45

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  17. Content type: Discovery notes

    It has been recently discovered that transposable elements show high activity in the brain of mammals, however, the magnitude of their influence on its functioning is unclear so far. In this paper, I use flux ...

    Authors: György Abrusán

    Citation: Biology Direct 2012 7:41

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  18. Content type: Discovery notes

    Members of the Arabidopsis LSH1 and Oryza G1 (ALOG) family of proteins have been shown to function as key developmental regulators in land plants. However, their precise mode of action remains unclear. Using sens...

    Authors: Lakshminarayan M Iyer and L Aravind

    Citation: Biology Direct 2012 7:39

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  19. Content type: Discovery notes

    Viruses with large genomes encode numerous proteins that do not directly participate in virus biogenesis but rather modify key functional systems of infected cells. We report that a distinct group of giant vir...

    Authors: Natalya Yutin and Eugene V Koonin

    Citation: Biology Direct 2012 7:34

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  20. Content type: Research

    B lymphocyte stimulator (BLyS) is a member of the tumor necrosis factor superfamily of ligands that mediates its action through three known receptors. BLyS has been shown to enhance the production of antibodie...

    Authors: Dennis O Gor, Xuedong Ding, Qing Li, Dilara Sultana, Salamatu S Mambula, Richard J Bram and Neil S Greenspan

    Citation: Biology Direct 2011 6:9

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