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. Research

    Consistent metagenomic biomarker detection via robust PCA

    Recent developments of high throughput sequencing technologies allow the characterization of the microbial communities inhabiting our world. Various metagenomic studies have suggested using microbial taxa as p...

    Mustafa Alshawaqfeh, Ahmad Bashaireh, Erchin Serpedin and Jan Suchodolski

    Biology Direct 2017 12:4

    Published on: 31 January 2017

  2. Research

    xHMMER3x2: Utilizing HMMER3’s speed and HMMER2’s sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

    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...

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

    Biology Direct 2016 11:63

    Published on: 29 November 2016

  3. APPLICATION NOTE

    CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments

    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...

    Benjamin Hur, Sangsoo Lim, Heejoon Chae, Seokjun Seo, Sunwon Lee, Jaewoo Kang and Sun Kim

    Biology Direct 2016 11:57

    Published on: 24 October 2016

  4. Research

    IPC – Isoelectric Point Calculator

    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...

    Lukasz P. Kozlowski

    Biology Direct 2016 11:55

    Published on: 21 October 2016

  5. Discovery notes

    Intrinsic protein disorder in histone lysine methylation

    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...

    Tamas Lazar, Eva Schad, Beata Szabo, Tamas Horvath, Attila Meszaros, Peter Tompa and Agnes Tantos

    Biology Direct 2016 11:30

    Published on: 30 June 2016

  6. Research

    Gene overlapping and size constraints in the viral world

    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...

    Nadav Brandes and Michal Linial

    Biology Direct 2016 11:26

    Published on: 21 May 2016

  7. Application note

    Altools: a user friendly NGS data analyser

    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 ...

    Salvatore Camiolo, Gaurav Sablok and Andrea Porceddu

    Biology Direct 2016 11:8

    Published on: 17 February 2016

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