SOV_refine: A further refined definition of segment overlap score and its significance for protein structure similarity

The segment overlap score (SOV) has been used to evaluate the predicted protein secondary structures, a sequence composed of helix (H), strand (E), and coil (C), by comparing it with the native or reference se...

Authors: Tong Liu and Zheng Wang

FLIM-FRET analyzer: open source software for automation of lifetime-based FRET analysis

Despite the broad use of FRET techniques, available methods for analyzing protein-protein interaction are subject to high labor and lack of systematic analysis. We propose an open source software allowing the ...

Authors: Jiho Kim, Yury Tsoy, Jan Persson and Regis Grailhe

goSTAG: gene ontology subtrees to tag and annotate genes within a set

Over-representation analysis (ORA) detects enrichment of genes within biological categories. Gene Ontology (GO) domains are commonly used for gene/gene-product annotation. When ORA is employed, often times the...

Authors: Brian D. Bennett and Pierre R. Bushel

LitDB - Keeping Track of Research Papers From Your Institute Made Simple

In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their s...

Authors: Jörn Bethune, Lars Kraemer, Ingo Thomsen, Andreas Keller, David Ellinghaus and Andre Franke

NET: a new framework for the vectorization and examination of network data

The analysis of complex networks both in general and in particular as pertaining to real biological systems has been the focus of intense scientific attention in the past and present. In this paper we introduc...

Authors: Jana Lasser and Eleni Katifori

Algorithm and software to automatically identify latency and amplitude features of local field potentials recorded in electrophysiological investigation

Local field potentials (LFPs) evoked by sensory stimulation are particularly useful in electrophysiological research. For instance, spike timing and current transmembrane current flow estimated from LFPs recor...

Authors: Maria Rubega, Claudia Cecchetto, Stefano Vassanelli and Giovanni Sparacino

DEApp: an interactive web interface for differential expression analysis of next generation sequence data

A growing trend in the biomedical community is the use of Next Generation Sequencing (NGS) technologies in genomics research. The complexity of downstream differential expression (DE) analysis is however still...

Authors: Yan Li and Jorge Andrade

Erratum to: A bedr way of genomic interval processing

Authors: Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu and Paul C. Boutros

PureCN: copy number calling and SNV classification using targeted short read sequencing

Matched sequencing of both tumor and normal tissue is routinely used to classify variants of uncertain significance (VUS) into somatic vs. germline. However, assays used in molecular diagnostics focus on known...

Authors: Markus Riester, Angad P. Singh, A. Rose Brannon, Kun Yu, Catarina D. Campbell, Derek Y. Chiang and Michael P. Morrissey

A bedr way of genomic interval processing

Next-generation sequencing is making it critical to robustly and rapidly handle genomic ranges within standard pipelines. Standard use-cases include annotating sequence ranges with gene or other genomic annota...

Authors: Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu and Paul C. Boutros

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing

Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it....

Authors: Toshiki Takeuchi, Atsuo Yamada, Takashi Aoki and Kunihiro Nishimura

TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data

In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. Howev...

Authors: Lindsay V. Clark and Erik J. Sacks

A new tool for prioritization of sequence variants from whole exome sequencing data

Whole exome sequencing (WES) has provided a means for researchers to gain access to a highly enriched subset of the human genome in which to search for variants that are likely to be pathogenic and possibly pr...

Authors: Brigitte Glanzmann, Hendri Herbst, Craig J. Kinnear, Marlo Möller, Junaid Gamieldien and Soraya Bardien

Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines

To reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are ...

Authors: John M. Macdonald and Paul C. Boutros

SV-STAT accurately detects structural variation via alignment to reference-based assemblies

Genomic deletions, inversions, and other rearrangements known collectively as structural variations (SVs) are implicated in many human disorders. Technologies for sequencing DNA provide a potentially rich sour...

Authors: Caleb F. Davis, Deborah I. Ritter, David A. Wheeler, Hongmei Wang, Yan Ding, Shannon P. Dugan, Matthew N. Bainbridge, Donna M. Muzny, Pulivarthi H. Rao, Tsz-Kwong Man, Sharon E. Plon, Richard A. Gibbs and Ching C. Lau

Implementation and clinical application of a deformation method for fast simulation of biological tissue formed by fibers and fluid

The aim of this paper is to provide a general discussion, algorithm, and actual working programs of the deformation method for fast simulation of biological tissue formed by fibers and fluid. In order to demon...

Authors: Ana Gabriella de Oliveira Sardinha, Ceres Nunes de Resende Oyama, Armando de Mendonça Maroja and Ivan F. Costa

MM2S: personalized diagnosis of medulloblastoma patients and model systems

Medulloblastoma (MB) is a highly malignant and heterogeneous brain tumour that is the most common cause of cancer-related deaths in children. Increasing availability of genomic data over the last decade had re...

Authors: Deena M.A. Gendoo and Benjamin Haibe-Kains

A flexible tool to plot a genomic map for single nucleotide polymorphisms

Most genetic association studies use single-nucleotide polymorphisms (SNPs) as the research targets. However, resources to visualize the genomic map of candidate SNPs in a programming manner are limited. We ha...

Authors: Fuquan Zhang

A generic schema and data collection forms applicable to diverse entomological studies of mosquitoes

Standardized schemas, databases, and public data repositories are needed for the studies of malaria vectors that encompass a remarkably diverse array of designs and rapidly generate large data volumes, often i...

Authors: Samson S. Kiware, Tanya L. Russell, Zacharia J. Mtema, Alpha D. Malishee, Prosper Chaki, Dickson Lwetoijera, Javan Chanda, Dingani Chinula, Silas Majambere, John E. Gimnig, Thomas A. Smith and Gerry F. Killeen

Conserved antigenic sites between MERS-CoV and Bat-coronavirus are revealed through sequence analysis

MERS-CoV is a newly emerged human coronavirus reported closely related with HKU4 and HKU5 Bat coronaviruses. Bat and MERS corona-viruses are structurally related. Therefore, it is of interest to estimate the d...

Authors: Refat Sharmin and Abul B. M. M. K. Islam

Implementation of the Rank-Weighted Co-localization (RWC) algorithm in multiple image analysis platforms for quantitative analysis of microscopy images

Quantitative co-localization studies strengthen the analysis of fluorescence microscopy-based assays and are essential for illustrating and understanding many cellular processes and interactions. In our earlie...

Authors: Vasanth R. Singan and Jeremy C. Simpson

Symmetrical treatment of “Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition”, for major depressive disorders

We previously presented a group theoretical model that describes psychiatric patient states or clinical data in a graded vector-like format based on modulo groups. Meanwhile, the Diagnostic and Statistical Manual...

Authors: Jitsuki Sawamura, Shigeru Morishita and Jun Ishigooka

PageRank as a method to rank biomedical literature by importance

Optimal ranking of literature importance is vital in overcoming article overload. Existing ranking methods are typically based on raw citation counts, giving a sum of ‘inbound’ links with no consideration of c...

Authors: Elliot J. Yates and Louise C. Dixon

PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB

One of the recent challenges of computational biology is development of new algorithms, tools and software to facilitate predictive modeling of big data generated by high-throughput technologies in biomedical ...

Authors: Samad Jahandideh, Fatemeh Sharifi, Lukasz Jaroszewski and Adam Godzik

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols

Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of ...

Authors: Alexandros Kanterakis, Joël Kuiper, George Potamias and Morris A. Swertz