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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: Research

    Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein s...

    Authors: Gayatri Kumar, Richa Mudgal, Narayanaswamy Srinivasan and Sankaran Sandhya

    Citation: Biology Direct 2018 13:8

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  2. Content type: Research

    There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow...

    Authors: Daniel H. Huson, Benjamin Albrecht, Caner Bağcı, Irina Bessarab, Anna Górska, Dino Jolic and Rohan B. H. Williams

    Citation: Biology Direct 2018 13:6

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  3. Content type: Research

    High-throughput methodologies such as microarrays and next-generation sequencing are routinely used in cancer research, generating complex data at different omics layers. The effective integration of omics data c...

    Authors: Margherita Francescatto, Marco Chierici, Setareh Rezvan Dezfooli, Alessandro Zandonà, Giuseppe Jurman and Cesare Furlanello

    Citation: Biology Direct 2018 13:5

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  4. Content type: Research

    The experience with running various types of classification on the CAMDA neuroblastoma dataset have led us to the conclusion that the results are not always obvious and may differ depending on type of analysis...

    Authors: Anna Leśniewska, Joanna Zyprych-Walczak, Alicja Szabelska-Beręsewicz and Michal J. Okoniewski

    Citation: Biology Direct 2018 13:3

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  5. Content type: Research

    Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip’s law, the observed distributions often deviate from a single power-law slope. ...

    Authors: Wing-Cheong Wong, Hong-kiat Ng, Erwin Tantoso, Richie Soong and Frank Eisenhaber

    Citation: Biology Direct 2018 13:2

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  6. Content type: Application note

    The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the ...

    Authors: Daria V. Dibrova, Kirill A. Konovalov, Vadim V. Perekhvatov, Konstantin V. Skulachev and Armen Y. Mulkidjanian

    Citation: Biology Direct 2017 12:29

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  7. Content type: Application note

    In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-...

    Authors: Olesya I. Klimchuk, Kirill A. Konovalov, Vadim V. Perekhvatov, Konstantin V. Skulachev, Daria V. Dibrova and Armen Y. Mulkidjanian

    Citation: Biology Direct 2017 12:26

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  8. Content type: Research

    Programmed ribosomal frameshifting (PRF) is a gene expression mechanism which enables the translation of two N-terminally coincident, C-terminally distinct protein products from a single mRNA. Many viruses uti...

    Authors: Adam M. Dinan, John F. Atkins and Andrew E. Firth

    Citation: Biology Direct 2017 12:24

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  9. Content type: Research

    Bacterial species present in multispecies microbial communities often react to the same chemical signal but at vastly different concentrations. The existence of different response thresholds with respect to th...

    Authors: János Juhász, Dóra Bihary, Attila Jády, Sándor Pongor and Balázs Ligeti

    Citation: Biology Direct 2017 12:22

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  10. Content type: Research

    Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided b...

    Authors: Kuang-Lim Chan, Tatiana V. Tatarinova, Rozana Rosli, Nadzirah Amiruddin, Norazah Azizi, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Nagappan Jayanthi, Petr Ponomarenko, Martin Triska, Victor Solovyev, Mohd Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy and Eng-Ti Leslie Low

    Citation: Biology Direct 2017 12:21

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  11. Content type: Research

    Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthe...

    Authors: Alice Toms and Rodolphe Barrangou

    Citation: Biology Direct 2017 12:20

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  12. Content type: Discovery notes

    We report a comprehensive computational dissection of the domain architecture of the SAMD9 family proteins that are involved in antivirus and antitumor response in humans. We show that the SAMD9 protein family...

    Authors: Sergei L. Mekhedov, Kira S. Makarova and Eugene V. Koonin

    Citation: Biology Direct 2017 12:13

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  13. Content type: Discovery notes

    The protein Gcn1 (General control non-derepressible 1) is found in virtually all eukaryotes, and is a key component of the general amino acid control signal transduction pathway. This pathway is best known for...

    Authors: Ramachandran Rakesh, Rangachari Krishnan, Evelyn Sattlegger and Narayanaswamy Srinivasan

    Citation: Biology Direct 2017 12:12

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  14. Content type: Research

    TRIF is a key protein in antiviral innate immunity, operating downstream of TLRs. TRIF activation leads to the production of interferon-β and pro-inflammatory cytokines. There is evidence from experiments to s...

    Authors: Jarjapu Mahita and Ramanathan Sowdhamini

    Citation: Biology Direct 2017 12:9

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  15. Content type: Research

    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...

    Authors: Mustafa Alshawaqfeh, Ahmad Bashaireh, Erchin Serpedin and Jan Suchodolski

    Citation: Biology Direct 2017 12:4

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  16. Content type: Research

    It is believed that all cancers occur due to the mutation or change in one or more genes. In order to investigate the significance of the biological pathways which are interrupted by these genetic mutations, w...

    Authors: Sinjini Sikdar, Somnath Datta and Susmita Datta

    Citation: Biology Direct 2016 11:65

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  17. Content type: Research

    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

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  18. Content type: APPLICATION NOTE

    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

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  19. Content type: Research

    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

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  20. Content type: Research

    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

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  21. Content type: Discovery notes

    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

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  22. Content type: Discovery notes

    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

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  23. Content type: Discovery notes

    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

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  24. Content type: Research

    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

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  25. Content type: Research

    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

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  26. Content type: Discovery notes

    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

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  27. Content type: Application note

    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

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  28. Content type: Research

    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

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  29. Content type: Review

    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

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  30. Content type: Research

    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

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  31. Content type: Research

    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

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  32. Content type: Review

    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

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  33. Content type: Discovery notes

    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

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