12th and 13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2015/16)

Preface to the BMC-CIBB 2015-16 special issue

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

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

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

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

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

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

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

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

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

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

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

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