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