Articles

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods

Count data generated by next-generation sequencing assays do not measure absolute transcript abundances. Instead, the data are constrained to an arbitrary “library size” by the sequencing depth of the assay, a...

Authors: Thomas P. Quinn, Tamsyn M. Crowley and Mark F. Richardson

De novo profile generation based on sequence context specificity with the long short-term memory network

Long short-term memory (LSTM) is one of the most attractive deep learning methods to learn time series or contexts of input data. Increasing studies, including biological sequence analyses in bioinformatics, u...

Authors: Kazunori D. Yamada and Kengo Kinoshita

De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application

Many organisms, in particular bacteria, contain repetitive DNA fragments called tandem repeats. These structures are restored by DNA assemblers by mapping paired-end tags to unitigs, estimating the distance be...

Authors: Wiktor Kuśmirek and Robert Nowak

Random forest versus logistic regression: a large-scale benchmark experiment

The Random Forest (RF) algorithm for regression and classification has considerably gained popularity since its introduction in 2001. Meanwhile, it has grown to a standard classification approach competing wit...

Authors: Raphael Couronné, Philipp Probst and Anne-Laure Boulesteix

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data

Transfer of genetic material from microbes or viruses into the host genome is known as horizontal gene transfer (HGT). The integration of viruses into the human genome is associated with multiple cancers, and ...

Authors: Saurabh Baheti, Xiaojia Tang, Daniel R. O’Brien, Nicholas Chia, Lewis R. Roberts, Heidi Nelson, Judy C. Boughey, Liewei Wang, Matthew P. Goetz, Jean-Pierre A. Kocher and Krishna R. Kalari

Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data

Data generated by RNA sequencing (RNA-Seq) is now accumulating in vast amounts in public repositories, especially for human and mouse genomes. Reanalyzing these data has emerged as a promising approach to iden...

Authors: Yasunobu Okamura and Kengo Kinoshita

Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links

Netpredictor is an R package for prediction of missing links in any given unipartite or bipartite network. The package provides utilities to compute missing links in a bipartite and well as unipartite networks...

Authors: Abhik Seal and David J. Wild

GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing

Tandem repeats comprise significant proportion of the human genome including coding and regulatory regions. They are highly prone to repeat number variation and nucleotide mutation due to their repetitive and ...

Authors: Devika Ganesamoorthy, Minh Duc Cao, Tania Duarte, Wenhan Chen and Lachlan Coin

Discovering themes in biomedical literature using a projection-based algorithm

The need to organize any large document collection in a manner that facilitates human comprehension has become crucial with the increasing volume of information available. Two common approaches to provide a br...

Authors: Lana Yeganova, Sun Kim, Grigory Balasanov and W. John Wilbur

CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata

Public biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these interfaces typically reflect the ad hoc metadata specification practices of the associate...

Authors: Syed Ahmad Chan Bukhari, Marcos Martínez-Romero, Martin J. O’ Connor, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen, Kei-Hoi Cheung and Steven H. Kleinstein

An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease

There are different and complicated associations between genes and diseases. Finding the causal associations between genes and specific diseases is still challenging. In this work we present a method to predic...

Authors: Ryohei Eguchi, Mohammand Bozlul Karim, Pingzhao Hu, Tetsuo Sato, Naoaki Ono, Shigehiko Kanaya and Md. Altaf-Ul-Amin

npInv: accurate detection and genotyping of inversions using long read sub-alignment

Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombinat...

Authors: Haojing Shao, Devika Ganesamoorthy, Tania Duarte, Minh Duc Cao, Clive J. Hoggart and Lachlan J. M. Coin

Effective automated pipeline for 3D reconstruction of synapses based on deep learning

The locations and shapes of synapses are important in reconstructing connectomes and analyzing synaptic plasticity. However, current synapse detection and segmentation methods are still not adequate for accura...

Authors: Chi Xiao, Weifu Li, Hao Deng, Xi Chen, Yang Yang, Qiwei Xie and Hua Han

trumpet: transcriptome-guided quality assessment of m⁶A-seq data

Methylated RNA immunoprecipitation sequencing (MeRIP-seq or m⁶A-seq) has been extensively used for profiling transcriptome-wide distribution of RNA N6-Methyl-Adnosine methylation. However, due to the intrinsic pr...

Authors: Teng Zhang, Shao-Wu Zhang, Lin Zhang and Jia Meng

Alternative empirical Bayes models for adjusting for batch effects in genomic studies

Combining genomic data sets from multiple studies is advantageous to increase statistical power in studies where logistical considerations restrict sample size or require the sequential generation of data. How...

Authors: Yuqing Zhang, David F. Jenkins, Solaiappan Manimaran and W. Evan Johnson

A study on multi-omic oscillations in Escherichia coli metabolic networks

Two important challenges in the analysis of molecular biology information are data (multi-omic information) integration and the detection of patterns across large scale molecular networks and sequences. They a...

Authors: Francesco Bardozzo, Pietro Lió and Roberto Tagliaferri

Comparison of metaheuristics to measure gene effects on phylogenetic supports and topologies

A huge and continuous increase in the number of completely sequenced chloroplast genomes, available for evolutionary and functional studies in plants, has been observed during the past years. Consequently, it ...

Authors: Régis Garnier, Christophe Guyeux, Jean-François Couchot, Michel Salomon, Bashar Al-Nuaimi and Bassam AlKindy

A deep learning approach to bilingual lexicon induction in the biomedical domain

Bilingual lexicon induction (BLI) is an important task in the biomedical domain as translation resources are usually available for general language usage, but are often lacking in domain-specific settings. In ...

Authors: Geert Heyman, Ivan Vulić and Marie-Francine Moens

NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability

Network controllability focuses on discovering combinations of external interventions that can drive a biological system to a desired configuration. In practice, this approach translates into finding a combine...

Authors: Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler and Ion Petre

Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes

Determining the value of kinetic constants for a metabolic system in the exact physiological conditions is an extremely hard task. However, this kind of information is of pivotal relevance to effectively simul...

Authors: Riccardo Colombo, Chiara Damiani, David Gilbert, Monika Heiner, Giancarlo Mauri and Dario Pescini

STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow

De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. G...

Authors: Igor Saggese, Elisa Bona, Max Conway, Francesco Favero, Marco Ladetto, Pietro Liò, Giovanni Manzini and Flavio Mignone

INBIA: a boosting methodology for proteomic network inference

The analysis of tissue-specific protein interaction networks and their functional enrichment in pathological and normal tissues provides insights on the etiology of diseases. The Pan-cancer proteomic project, ...

Authors: Davide S. Sardina, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti and Rosalba Giugno

Effect of the number of removed lymph nodes on prostate cancer recurrence and survival: evidence from an observational study

The aim of this article is to analyze the effect on biochemical recurrence and on overall survival of removing an extensive number of pelvic lymph nodes during prostate cancer surgery. The lack of evidence fro...

Authors: Chiara Gigliarano, Alessandro Nonis, Alberto Briganti, Marco Bonetti and Clelia Di Serio

Beyond the one-way ANOVA for ’omics data

With ever increasing accessibility to high throughput technologies, more complex treatment structures can be assessed in a variety of ’omics applications. This adds an extra layer of complexity to the analysis...

Authors: Kirsty L. Hassall and Andrew Mead

Mendelian randomisation analysis of clustered causal effects of body mass on cardiometabolic biomarkers

Recent advances in data analysis methods based on principles of Mendelian Randomisation, such as Egger regression and the weighted median estimator, add to the researcher’s ability to infer cause-effect links ...

Authors: Susana Conde, Xiaoguang Xu, Hui Guo, Markus Perola, Teresa Fazia, Luisa Bernardinelli and Carlo Berzuini

Deep learning models for bacteria taxonomic classification of metagenomic data

An open challenge in translational bioinformatics is the analysis of sequenced metagenomes from various environmental samples. Of course, several studies demonstrated the 16S ribosomal RNA could be considered ...

Authors: Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Giosue’ Lo Bosco, Giovanni Renda, Riccardo Rizzo, Salvatore Gaglio and Alfonso Urso

Modeling the covariates effects on the hazard function by piecewise exponential artificial neural networks: an application to a controlled clinical trial on renal carcinoma

In exploring the time course of a disease to support or generate biological hypotheses, the shape of the hazard function provides relevant information. For long follow-ups the shape of hazard function may be c...

Authors: Marco Fornili, Patrizia Boracchi, Federico Ambrogi and Elia Biganzoli

Preface to the BMC-CIBB 2015-16 special issue

Authors: Claudia Angelini, Andrea Bracciali, David Gilbert and Riccardo Rizzo

FC_analysis: a tool for investigating atomic force microscopy maps of force curves

The collection and analysis of Atomic Force Microscopy force curves is a well-established procedure to obtain high-resolution information of non-topographic data from any kind of sample, including biological s...

Authors: Simone Dinarelli, Marco Girasole and Giovanni Longo

BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing

Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each ...

Authors: Panu Somervuo, Patrik Koskinen, Peng Mei, Liisa Holm, Petri Auvinen and Lars Paulin

Correction to: The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure

Following publication of the original article [1], the authors reported that Figs. 1 and 3 were interchanged. The original article has been corrected.

Authors: Maxwell Shapiro, Stephen Meier and Thomas MacCarthy

BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization

Variation in chromatin organization across single cells can help shed important light on the mechanisms controlling gene expression, but scale, noise, and sparsity pose significant challenges for interpretatio...

Authors: Carl G. de Boer and Aviv Regev

Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0

Gene expression in plant chloroplasts and mitochondria is affected by RNA editing. Numerous C-to-U conversions, accompanied by reverse U-to-C exchanges in some plant clades, alter the genetic information encod...

Authors: Henning Lenz, Anke Hein and Volker Knoop

HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads

Haplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human individual. Long reads, which are nowadays...

Authors: Stefano Beretta, Murray D. Patterson, Simone Zaccaria, Gianluca Della Vedova and Paola Bonizzoni

SimCAL: a flexible tool to compute biochemical reaction similarity

Computation of reaction similarity is a pre-requisite for several bioinformatics applications including enzyme identification for specific biochemical reactions, enzyme classification and mining for specific i...

Authors: Tadi Venkata Sivakumar, Anirban Bhaduri, Rajasekhara Reddy Duvvuru Muni, Jin Hwan Park and Tae Yong Kim

Correction to: Realizing drug repositioning by adapting a recommendation system to handle the process

Following publication of the original article [1], the authors reported that there was an error in the spelling of the name of one of the authors.

Authors: Makbule Gulcin Ozsoy, Tansel Özyer, Faruk Polat and Reda Alhajj

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining

For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers...

Authors: John A. Bachman, Benjamin M. Gyori and Peter K. Sorger

MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data

Circadian rhythms comprise oscillating molecular interactions, the disruption of the homeostasis of which would cause various disorders. To understand this phenomenon systematically, an accurate technique to i...

Authors: Hitoshi Iuchi, Masahiro Sugimoto and Masaru Tomita

GenoGAM 2.0: scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes

GenoGAM (Genome-wide generalized additive models) is a powerful statistical modeling tool for the analysis of ChIP-Seq data with flexible factorial design experiments. However large runtime and memory requirem...

Authors: Georg Stricker, Mathilde Galinier and Julien Gagneur

PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes

Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionall...

Authors: Thomas H. Clarke, Lauren M. Brinkac, Jason M. Inman, Granger Sutton and Derrick E. Fouts

ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies

Identifying motifs in biological networks is essential in uncovering key functions served by these networks. Finding non-overlapping motif instances is however a computationally challenging task. The fact that...

Authors: Yuanfang Ren, Aisharjya Sarkar and Tamer Kahveci

BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data

The advent of next-generation sequencing (NGS) has made whole-genome sequencing of cohorts of individuals a reality. Primary datasets of raw or aligned reads of this sort can get very large. For scientific que...

Authors: Kristiina Ausmees, Aji John, Salman Z. Toor, Andreas Hellander and Carl Nettelblad

ToTem: a tool for variant calling pipeline optimization

High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters...

Authors: Nikola Tom, Ondrej Tom, Jitka Malcikova, Sarka Pavlova, Blanka Kubesova, Tobias Rausch, Miroslav Kolarik, Vladimir Benes, Vojtech Bystry and Sarka Pospisilova

AUCTSP: an improved biomarker gene pair class predictor

The Top Scoring Pair (TSP) classifier, based on the concept of relative ranking reversals in the expressions of pairs of genes, has been proposed as a simple, accurate, and easily interpretable decision rule f...

Authors: Dimitri Kagaris, Alireza Khamesipour and Constantin T. Yiannoutsos

Multiobjective grammar-based genetic programming applied to the study of asthma and allergy epidemiology

Asthma and allergies prevalence increased in recent decades, being a serious global health problem. They are complex diseases with strong contextual influence, so that the use of advanced machine learning tool...

Authors: Rafael V. Veiga, Helio J. C. Barbosa, Heder S. Bernardino, João M. Freitas, Caroline A. Feitosa, Sheila M. A. Matos, Neuza M. Alcântara-Neves and Maurício L. Barreto

Semi-supervised machine learning for automated species identification by collagen peptide mass fingerprinting

Biomolecular methods for species identification are increasingly being utilised in the study of changing environments, both at the microscopic and macroscopic levels. High-throughput peptide mass fingerprintin...

Authors: Muxin Gu and Michael Buckley

Detecting Succinylation sites from protein sequences using ensemble support vector machine

Lysine succinylation is a new kind of post-translational modification which plays a key role in protein conformation regulation and cellular function control. To understand the mechanism of succinylation profo...

Authors: Qiao Ning, Xiaosa Zhao, Lingling Bao, Zhiqiang Ma and Xiaowei Zhao

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios

The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transpl...

Authors: Maria Luisa Matey-Hernandez, Søren Brunak and Jose M. G. Izarzugaza

Proteome-wide analysis of human motif-domain interactions mapped on influenza A virus

The influenza A virus (IAV) is a constant threat for humans worldwide. The understanding of motif-domain protein participation is essential to combat the pathogen.

Authors: Carlos A. García-Pérez, Xianwu Guo, Juan García Navarro, Diego Alonso Gómez Aguilar and Edgar E. Lara-Ramírez

Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for intrasample comparison for the discovery and validation of g...

Authors: Marcel Smid, Robert R. J. Coebergh van den Braak, Harmen J. G. van de Werken, Job van Riet, Anne van Galen, Vanja de Weerd, Michelle van der Vlugt-Daane, Sandra I. Bril, Zarina S. Lalmahomed, Wigard P. Kloosterman, Saskia M. Wilting, John A. Foekens, Jan N. M. IJzermans, John W. M. Martens and Anieta M. Sieuwerts