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  1. Software

    SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information

    The molecular assays that test gene expression, transcriptional, and epigenetic regulation are increasingly diverse and numerous. The information generated by each type of assay individually gives an insight i...

    N. Ari Wijetunga, Andrew D. Johnston, Ryo Maekawa, Fabien Delahaye, Netha Ulahannan, Kami Kim and John M. Greally

    BMC Bioinformatics 2017 18:41

    Published on: 18 January 2017

  2. Database

    ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana

    Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides wit...

    Rashmi R. Hazarika, Barbara De Coninck, Lidia R. Yamamoto, Laura R. Martin, Bruno P. A. Cammue and Vera van Noort

    BMC Bioinformatics 2017 18:37

    Published on: 17 January 2017

  3. Software

    iGC—an integrated analysis package of gene expression and copy number alteration

    With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional anal...

    Yi-Pin Lai, Liang-Bo Wang, Wei-An Wang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu and Eric Y. Chuang

    BMC Bioinformatics 2017 18:35

    Published on: 14 January 2017

  4. Methodology Article

    TTCA: an R package for the identification of differentially expressed genes in time course microarray data

    The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quic...

    Marco Albrecht, Damian Stichel, Benedikt Müller, Ruth Merkle, Carsten Sticht, Norbert Gretz, Ursula Klingmüller, Kai Breuhahn and Franziska Matthäus

    BMC Bioinformatics 2017 18:33

    Published on: 14 January 2017

  5. Research Article

    Predicting probable Alzheimer’s disease using linguistic deficits and biomarkers

    The manual diagnosis of neurodegenerative disorders such as Alzheimer’s disease (AD) and related Dementias has been a challenge. Currently, these disorders are diagnosed using specific clinical diagnostic crit...

    Sylvester O. Orimaye, Jojo S-M. Wong, Karen J. Golden, Chee P. Wong and Ireneous N. Soyiri

    BMC Bioinformatics 2017 18:34

    Published on: 14 January 2017

  6. Research article

    MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation

    The current state-of-the-art in cancer diagnosis and treatment is not ideal; diagnostic tests are accurate but invasive, and treatments are “one-size fits-all” instead of being personalized. Recently, miRNA’s ...

    Nikhil Cheerla and Olivier Gevaert

    BMC Bioinformatics 2017 18:32

    Published on: 13 January 2017

  7. Software

    SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes

    Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative...

    Reedik Mägi, Yury V. Suleimanov, Geraldine M. Clarke, Marika Kaakinen, Krista Fischer, Inga Prokopenko and Andrew P. Morris

    BMC Bioinformatics 2017 18:25

    Published on: 11 January 2017

  8. Methodology article

    An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids

    Detection and preventing entry of exotic viruses and viroids at the border is critical for protecting plant industries trade worldwide. Existing post entry quarantine screening protocols rely on time-consuming...

    Roberto A. Barrero, Kathryn R. Napier, James Cunnington, Lia Liefting, Sandi Keenan, Rebekah A. Frampton, Tamas Szabo, Simon Bulman, Adam Hunter, Lisa Ward, Mark Whattam and Matthew I. Bellgard

    BMC Bioinformatics 2017 18:26

    Published on: 11 January 2017

  9. Research article

    Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces

    Many critical biological processes are strongly related to protein-RNA interactions. Revealing the protein structure motifs for RNA-binding will provide valuable information for deciphering protein-RNA recogni...

    Zhi-Ping Liu, Shutang Liu, Ruitang Chen, Xiaopeng Huang and Ling-Yun Wu

    BMC Bioinformatics 2017 18:27

    Published on: 11 January 2017

  10. Database

    GTB – an online genome tolerance browser

    Accurate methods capable of predicting the impact of single nucleotide variants (SNVs) are assuming ever increasing importance. There exists a plethora of in silico algorithms designed to help identify and priori...

    Hashem A. Shihab, Mark F. Rogers, Michael Ferlaino, Colin Campbell and Tom R. Gaunt

    BMC Bioinformatics 2017 18:20

    Published on: 6 January 2017

  11. Software

    MPD: multiplex primer design for next-generation targeted sequencing

    Targeted resequencing offers a cost-effective alternative to whole-genome and whole-exome sequencing when investigating regions known to be associated with a trait or disease. There are a number of approaches ...

    Thomas S. Wingo, Alex Kotlar and David J. Cutler

    BMC Bioinformatics 2017 18:14

    Published on: 5 January 2017

  12. Methodology article

    The use of novel selectivity metrics in kinase research

    Compound selectivity is an important issue when developing a new drug. In many instances, a lack of selectivity can translate to increased toxicity. Protein kinases are particularly concerned with this issue b...

    Nicolas Bosc, Christophe Meyer and Pascal Bonnet

    BMC Bioinformatics 2017 18:17

    Published on: 5 January 2017

  13. Software

    KinMap: a web-based tool for interactive navigation through human kinome data

    Annotations of the phylogenetic tree of the human kinome is an intuitive way to visualize compound profiling data, structural features of kinases or functional relationships within this important class of prot...

    Sameh Eid, Samo Turk, Andrea Volkamer, Friedrich Rippmann and Simone Fulle

    BMC Bioinformatics 2017 18:16

    Published on: 5 January 2017

  14. Software

    T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes

    Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequenc...

    Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos and Grigoris D. Amoutzias

    BMC Bioinformatics 2017 18:13

    Published on: 5 January 2017

  15. Research article

    Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant

    The cyclin-dependent kinase 2 (CDK2) together with its cyclin E and A partners is a central regulator of cell growth and division. Deregulation of CDK2 activity is associated with diseases such as cancer. The ...

    Jinyu Li, Jörg Vervoorts, Paolo Carloni, Giulia Rossetti and Bernhard Lüscher

    BMC Bioinformatics 2017 18:15

    Published on: 5 January 2017

  16. Methodology Article

    PERGOLA: fast and deterministic linkage mapping of polyploids

    A large share of agriculturally and horticulturally important plant species are polyploid. Linkage maps are used to locate associations between genes and traits by breeders and geneticists. Linkage map creatio...

    Fabian Grandke, Soumya Ranganathan, Nikkie van Bers, Jorn R. de Haan and Dirk Metzler

    BMC Bioinformatics 2017 18:12

    Published on: 4 January 2017

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