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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. While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of doma...

    Authors: Choon-Kong Yap, Birgit Eisenhaber, Frank Eisenhaber and Wing-Cheong Wong
    Citation: Biology Direct 2016 11:63
  2. Transcriptome data from the gene knockout experiment in mouse is widely used to investigate functions of genes and relationship to phenotypes. When a gene is knocked out, it is important to identify which gene...

    Authors: Benjamin Hur, Sangsoo Lim, Heejoon Chae, Seokjun Seo, Sunwon Lee, Jaewoo Kang and Sun Kim
    Citation: Biology Direct 2016 11:57
  3. Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary...

    Authors: Lukasz P. Kozlowski
    Citation: Biology Direct 2016 11:55
  4. It has been demonstrated that a pathway-based feature selection method that incorporates biological information within pathways during the process of feature selection usually outperforms a gene-based feature ...

    Authors: Suyan Tian, Howard H. Chang and Chi Wang
    Citation: Biology Direct 2016 11:50
  5. Recent analyses of next-generation sequencing datasets have shown that cell-specific regulatory elements in stem cells are marked with distinguishable patterns of transcription factor (TF) binding and epigenet...

    Authors: Esra Kurum, Bérénice A. Benayoun, Ankit Malhotra, Joshy George and Duygu Ucar
    Citation: Biology Direct 2016 11:47
  6. Histone lysine methyltransferases (HKMTs), catalyze mono-, di- and trimethylation of lysine residues, resulting in a regulatory pattern that controls gene expression. Their involvement in many different cellul...

    Authors: Tamas Lazar, Eva Schad, Beata Szabo, Tamas Horvath, Attila Meszaros, Peter Tompa and Agnes Tantos
    Citation: Biology Direct 2016 11:30
  7. Evolutionary relationship between class III nucleotide cyclases and an uncharacterized set of bacterial proteins from Actinobacteria, Bacteroidetes and Proteobacteria has been recognized and analyzed. Detailed...

    Authors: Gayatri Ramakrishnan, Abha Jain, Nagasuma Chandra and Narayanaswamy Srinivasan
    Citation: Biology Direct 2016 11:27
  8. Viruses are the simplest replicating units, characterized by a limited number of coding genes and an exceptionally high rate of overlapping genes. We sought a unified evolutionary explanation that accounts for...

    Authors: Nadav Brandes and Michal Linial
    Citation: Biology Direct 2016 11:26
  9. Recent advances in sequencing technologies enable the large-scale identification of genes that are affected by various genetic alterations in cancer. However, understanding tumor development requires insights ...

    Authors: Bálint Mészáros, András Zeke, Attila Reményi, István Simon and Zsuzsanna Dosztányi
    Citation: Biology Direct 2016 11:23
  10. Short leader genes usually do not encode stable proteins, although their importance in expression control of bacterial genomes is widely accepted. Such genes are often involved in the control of attenuation re...

    Authors: Semen A. Korolev, Oleg A. Zverkov, Alexandr V. Seliverstov and Vassily A. Lyubetsky
    Citation: Biology Direct 2016 11:20
  11. Genotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to ...

    Authors: Salvatore Camiolo, Gaurav Sablok and Andrea Porceddu
    Citation: Biology Direct 2016 11:8
  12. In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated...

    Authors: Sandeep Singh, Harinder Singh, Abhishek Tuknait, Kumardeep Chaudhary, Balvinder Singh, S. Kumaran and Gajendra P. S. Raghava
    Citation: Biology Direct 2015 10:73
  13. Genomic studies have greatly expanded our knowledge of structural non-coding RNAs (ncRNAs). These RNAs fold into characteristic secondary structures and perform specific-structure dependent biological function...

    Authors: Avinash Achar and Pål Sætrom
    Citation: Biology Direct 2015 10:61
  14. While hundreds of genes have been implicated already in the etiology of schizophrenia, the exact cause is not known or the disease is considered multigenic in origin. Recent discoveries of new types of RNAs an...

    Authors: Vadim Gumerov and Hedi Hegyi
    Citation: Biology Direct 2015 10:59
  15. γ-glutamyltranspeptidase (GGT) is a bi-substrate enzyme conserved in all three domains of life. It catalyzes the cleavage and transfer of γ-glutamyl moiety of glutathione to either water (hydrolysis) or substr...

    Authors: Ved Vrat Verma, Rani Gupta and Manisha Goel
    Citation: Biology Direct 2015 10:49
  16. Oligonucleotide microarrays belong to the basic tools of molecular biology and allow for simultaneous assessment of the expression level of thousands of genes. Analysis of microarray data is however very compl...

    Authors: Roman Jaksik, Marta Iwanaszko, Joanna Rzeszowska-Wolny and Marek Kimmel
    Citation: Biology Direct 2015 10:46
  17. Spodoptera is an important polyphagous agricultural insect pest in the tropical world. The genomic details are limited to understand the pest biology at molecular level. In the present...

    Authors: Pavan Kumar Kakumani, Rohit Shukla, Vivek N. Todur, Pawan Malhotra, Sunil K. Mukherjee and Raj K. Bhatnagar
    Citation: Biology Direct 2015 10:44
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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

Annual Journal Metrics

  • 2022 Citation Impact
    5.5 - 2-year Impact Factor
    3.8 - 5-year Impact Factor
    0.893 - SNIP (Source Normalized Impact per Paper)
    1.117 - SJR (SCImago Journal Rank)

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