Articles

iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach

Protein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure...

Authors: Guilhem Faure, Agnel Praveen Joseph, Pierrick Craveur, Tarun J. Narwani, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Joseph Rebehmed and Alexandre G. de Brevern

Social support for collaboration and group awareness in life science research teams

Next-generation sequencing (NGS) technologies have revolutionarily reshaped the landscape of ’-omics’ research areas. They produce a plethora of information requiring specific knowledge in sample preparation, ...

Authors: Delfina Malandrino, Ilaria Manno, Alberto Negro, Andrea Petta, Luigi Serra, Concita Cantarella and Vittorio Scarano

MZPAQ: a FASTQ data compression tool

Due to the technological progress in Next Generation Sequencing (NGS), the amount of genomic data that is produced daily has seen a tremendous increase. This increase has shifted the bottleneck of genomic proj...

Authors: Achraf El Allali and Mariam Arshad

IPCAPS: an R package for iterative pruning to capture population structure

Resolving population genetic structure is challenging, especially when dealing with closely related or geographically confined populations. Although Principal Component Analysis (PCA)-based methods and genomic...

Authors: Kridsadakorn Chaichoompu, Fentaw Abegaz, Sissades Tongsima, Philip James Shaw, Anavaj Sakuntabhai, Luísa Pereira and Kristel Van Steen

eUTOPIA: solUTion for Omics data PreprocessIng and Analysis

Application of microarrays in omics technologies enables quantification of many biomolecules simultaneously. It is widely applied to observe the positive or negative effect on biomolecule activity in perturbed...

Authors: Veer Singh Marwah, Giovanni Scala, Pia Anneli Sofia Kinaret, Angela Serra, Harri Alenius, Vittorio Fortino and Dario Greco

ProSave: an application for restoring quantitative data to manipulated subsets of protein lists

In proteomics studies, liquid chromatography tandem mass spectrometry data (LC-MS/MS) is quantified by spectral counts or by some measure of ion abundance. Downstream comparative analysis of protein content (e...

Authors: Daniel A. Machlab, Gabriel Velez, Alexander G. Bassuk and Vinit B. Mahajan

Simulating pedigrees ascertained for multiple disease-affected relatives

Studies that ascertain families containing multiple relatives affected by disease can be useful for identification of causal, rare variants from next-generation sequencing data.

Authors: Christina Nieuwoudt, Samantha J. Jones, Angela Brooks-Wilson and Jinko Graham

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

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

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

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

FlexDM: Simple, parallel and fault-tolerant data mining using WEKA

With the continued exponential growth in data volume, large-scale data mining and machine learning experiments have become a necessity for many researchers without programming or statistics backgrounds. WEKA (...

Authors: Madison Flannery, David M. Budden and Alexandre Mendes

MOtoNMS: A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation

Neuromusculoskeletal modeling and simulation enable investigation of the neuromusculoskeletal system and its role in human movement dynamics. These methods are progressively introduced into daily clinical prac...

Authors: Alice Mantoan, Claudio Pizzolato, Massimo Sartori, Zimi Sawacha, Claudio Cobelli and Monica Reggiani

CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks

Inference of gene networks from expression data is an important problem in computational biology. Many algorithms have been proposed for solving the problem efficiently. However, many of the available implemen...

Authors: Maciej Fronczuk, Adrian E. Raftery and Ka Yee Yeung

TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence

It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in...

Authors: Connor H. Fortin, Katharina V. Schulze and Gregory A. Babbitt

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many mul...

Authors: Carol L. Ecale Zhou

PrimerView: high-throughput primer design and visualization

High-throughput primer design is routinely performed in a wide number of molecular applications including genotyping specimens using traditional PCR techniques as well as assembly PCR, nested PCR, and primer w...

Authors: Damien M. O’Halloran

Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment

Malaria has been a major life threatening mosquito borne disease from long since. Unavailability of any effective vaccine and recent emergence of multi drug resistant strains of malaria pathogen Plasmodium falcip...

Authors: Md. Anayet Hasan, Md. Habibul Hasan Mazumder, Afrin Sultana Chowdhury, Amit Datta and Md. Arif Khan

popRange: a highly flexible spatially and temporally explicit Wright-Fisher simulator

Sequencing and genotyping technology advancements have led to massive, growing repositories of spatially explicit genetic data and increasing quantities of temporal data (i.e., ancient DNA). These data will al...

Authors: Kimberly F McManus

Wormpath: searching for molecular interaction networks in Caenorhabditis elegans

High-throughput transcriptional profiling using Next-Generation Sequencing (RNA-Seq) or microarray technology have become standard tools in molecular biology. Successful investigations of gene regulatory mecha...

Authors: Peter Frommolt and Björn Schumacher

MagiCMicroRna: a web implementation of AgiMicroRna using shiny

MicroRNA expression can be quantified using sequencing techniques or commercial microRNA-expression arrays. Recently, the AgiMicroRna R-package was published that enabled systematic preprocessing and statistical ...

Authors: Maarten LJ Coonen, Daniel HJ Theunissen, Jos CS Kleinjans and Danyel GJ Jennen

Membrainy: a ‘smart’, unified membrane analysis tool

The study of biological membranes using Molecular Dynamics has become an increasingly popular means by which to investigate the interactions of proteins, peptides and potentials with lipid bilayers. These inte...

Authors: Matthew Carr and Cait E MacPhee

AdmixKJump: identifying population structure in recently diverged groups

Correctly modeling population structure is important for understanding recent evolution and for association studies in humans. While pre-existing knowledge of population history can be used to specify expected...

Authors: Timothy D O’Connor

LocusTrack: Integrated visualization of GWAS results and genomic annotation

Genome-wide association studies (GWAS) are an important tool for the mapping of complex traits and diseases. Visual inspection of genomic annotations may be used to generate insights into the biological mechan...

Authors: Gabriel Cuellar-Partida, Miguel E Renteria and Stuart MacGregor

HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline

The graphical visualization of gene expression data using heatmaps has become an integral component of modern-day medical research. Heatmaps are used extensively to plot quantitative differences in gene expres...

Authors: Bohdan B Khomtchouk, Derek J Van Booven and Claes Wahlestedt

Erratum to: BatTool: an R package with GUI for assessing the effect of white-nose syndrome and other take events on Myotis spp. of bats

Authors: Richard A Erickson, Wayne E Thogmartin and Jennifer A Szymanski

Using the value of Lin’s concordance correlation coefficient as a criterion for efficient estimation of areas of leaves of eelgrass from noisy digital images

Eelgrass is a cosmopolitan seagrass species that provides important ecological services in coastal and near-shore environments. Despite its relevance, loss of eelgrass habitats is noted worldwide. Restoration ...

Authors: Héctor Echavarría-Heras, Cecilia Leal-Ramírez, Enrique Villa-Diharce and Oscar Castillo

Robust dose-response curve estimation applied to high content screening data analysis

Successfully automated sigmoidal curve fitting is highly challenging when applied to large data sets. In this paper, we describe a robust algorithm for fitting sigmoid dose-response curves by estimating four p...

Authors: Thuy Tuong Nguyen, Kyungmin Song, Yury Tsoy, Jin Yeop Kim, Yong-Jun Kwon, Myungjoo Kang and Michael Adsetts Edberg Hansen

Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments

Whole genomes, whole exomes and transcriptomes of tumour samples are sequenced routinely to identify the drivers of cancer. The systematic sequencing and analysis of tumour samples, as well other oncogenomic e...

Authors: Mike Gavrielides, Simon J Furney, Tim Yates, Crispin J Miller and Richard Marais