Articles

A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation

The temporal coordination of biological processes by the circadian clock is an important mechanism, and its disruption has negative health outcomes, including cancer. Experimental and theoretical evidence sugg...

Authors: Adrien Rougny, Loïc Paulevé, Michèle Teboul and Franck Delaunay

Combining genetic algorithm with machine learning strategies for designing potent antimicrobial peptides

Current methods in machine learning provide approaches for solving challenging, multiple constraint design problems. While deep learning and related neural networking methods have state-of-the-art performance,...

Authors: Kyle Boone, Cate Wisdom, Kyle Camarda, Paulette Spencer and Candan Tamerler

Simultaneous learning of individual microRNA-gene interactions and regulatory comodules

MicroRNAs (miRNAs) function in post-transcriptional regulation of gene expression by binding to target messenger RNAs (mRNAs). Because of the key part that miRNAs play, understanding the correct regulatory rol...

Authors: Michael Roth, Pranjal Jain, Jinkyu Koo and Somali Chaterji

DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples

High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic refere...

Authors: Steffen Klasberg, Alexander H. Schmidt, Vinzenz Lange and Gerhard Schöfl

Censcyt: censored covariates in differential abundance analysis in cytometry

Innovations in single cell technologies have lead to a flurry of datasets and computational tools to process and interpret them, including analyses of cell composition changes and transition in cell states. The d...

Authors: Reto Gerber and Mark D. Robinson

MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics

Cis-regulatory elements (CREs) are DNA sequence segments that regulate gene expression. Among CREs are promoters, enhancers, Boundary Elements (BEs) and Polycomb Response Elements (PREs), all of which are enriche...

Authors: Bjørn André Bredesen and Marc Rehmsmeier

Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes

Genes implicated in tumorigenesis often exhibit diverse sets of genomic variants in the tumor cohorts within which they are frequently mutated. For many genes, neither the transcriptomic effects of these varia...

Authors: Michal R. Grzadkowski, Hannah D. Holly, Julia Somers and Emek Demir

Spectral phenotyping of embryonic development reveals integrative thermodynamic responses

Energy proxy traits (EPTs) are a novel approach to high dimensional organismal phenotyping that quantify the spectrum of energy levels within different temporal frequencies associated with mean pixel value flu...

Authors: Oliver Tills, John I. Spicer, Ziad Ibbini and Simon D. Rundle

DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information

Epitope prediction is a useful approach in cancer immunology and immunotherapy. Many computational methods, including machine learning and network analysis, have been developed quickly for such purposes. Howev...

Authors: Xiaoyun Yang, Liyuan Zhao, Fang Wei and Jing Li

A new method for exploring gene–gene and gene–environment interactions in GWAS with tree ensemble methods and SHAP values

The identification of gene–gene and gene–environment interactions in genome-wide association studies is challenging due to the unknown nature of the interactions and the overwhelmingly large number of possible...

Authors: Pål V. Johnsen, Signe Riemer-Sørensen, Andrew Thomas DeWan, Megan E. Cahill and Mette Langaas

The Coronavirus Network Explorer: mining a large-scale knowledge graph for effects of SARS-CoV-2 on host cell function

Leveraging previously identified viral interactions with human host proteins, we apply a machine learning-based approach to connect SARS-CoV-2 viral proteins to relevant host biological functions, diseases, an...

Authors: Andreas Krämer, Jean-Noël Billaud, Stuart Tugendreich, Dan Shiffman, Martin Jones and Jeff Green

Modern simulation utilities for genetic analysis

Statistical geneticists employ simulation to estimate the power of proposed studies, test new analysis tools, and evaluate properties of causal models. Although there are existing trait simulators, there is am...

Authors: Sarah S. Ji, Christopher A. German, Kenneth Lange, Janet S. Sinsheimer, Hua Zhou, Jin Zhou and Eric M. Sobel

Tamock: simulation of habitat-specific benchmark data in metagenomics

Simulated metagenomic reads are widely used to benchmark software and workflows for metagenome interpretation. The results of metagenomic benchmarks depend on the assumptions about their underlying ecosystems....

Authors: Samuel M. Gerner, Alexandra B. Graf and Thomas Rattei

JEDi: java essential dynamics inspector — a molecular trajectory analysis toolkit

Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straig...

Authors: Charles C. David, Chris S. Avery and Donald J. Jacobs

Root Digger: a root placement program for phylogenetic trees

In phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such a...

Authors: Ben Bettisworth and Alexandros Stamatakis

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

RNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with it. In practice, there are a large number of individual steps a researcher must perform ...

Authors: Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe and Leonardo Collado-Torres

Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage

Brain image genetics provides enormous opportunities for examining the effects of genetic variations on the brain. Many studies have shown that the structure, function, and abnormality (e.g., those related to ...

Authors: Jin Li, Wenjie Liu, Huang Li, Feng Chen, Haoran Luo, Peihua Bao, Yanzhao Li, Hailong Jiang, Yue Gao, Hong Liang and Shiaofen Fang

Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars

Amyloid signaling motifs are a class of protein motifs which share basic structural and functional features despite the lack of clear sequence homology. They are hard to detect in large sequence databases eith...

Authors: Witold Dyrka, Marlena Gąsior-Głogowska, Monika Szefczyk and Natalia Szulc

Dynamic model updating (DMU) approach for statistical learning model building with missing data

Developing statistical and machine learning methods on studies with missing information is a ubiquitous challenge in real-world biological research. The strategy in literature relies on either removing the sam...

Authors: Rahi Jain and Wei Xu

GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments

Design of valid high-quality primers is essential for qPCR experiments. MRPrimer is a powerful pipeline based on MapReduce that combines both primer design for target sequences and homology tests on off-target...

Authors: Jeongmin Bae, Hajin Jeon and Min-Soo Kim

SMALF: miRNA-disease associations prediction based on stacked autoencoder and XGBoost

Identifying miRNA and disease associations helps us understand disease mechanisms of action from the molecular level. However, it is usually blind, time-consuming, and small-scale based on biological experimen...

Authors: Dayun Liu, Yibiao Huang, Wenjuan Nie, Jiaxuan Zhang and Lei Deng

Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Next-generation sequencing (NGS) represents a significant advancement in clinical genetics. However, its use creates several technical, data interpretation and management challenges. It is essential to follow ...

Authors: Maria Zanti, Kyriaki Michailidou, Maria A. Loizidou, Christina Machattou, Panagiota Pirpa, Kyproula Christodoulou, George M. Spyrou, Kyriacos Kyriacou and Andreas Hadjisavvas

The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma

lncRNA may be involved in the occurrence, metastasis, and chemical reaction of hepatocellular carcinoma (HCC) through various pathways associated with autophagy. Therefore, it is urgent to reveal more autophag...

Authors: Shiming Yang, Yaping Zhou, Xiangxin Zhang, Lu Wang, Jianfeng Fu, Xiaotong Zhao and Liu Yang

CarSite-II: an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniques

Carbonylation is a non-enzymatic irreversible protein post-translational modification, and refers to the side chain of amino acid residues being attacked by reactive oxygen species and finally converted into c...

Authors: Yun Zuo, Jianyuan Lin, Xiangxiang Zeng, Quan Zou and Xiangrong Liu

Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis

Next generation sequencing has allowed the discovery of miRNA isoforms, termed isomiRs. Some isomiRs are derived from imprecise processing of pre-miRNA precursors, leading to length variants. Additional variab...

Authors: Jose Francisco Sanchez Herrero, Raquel Pluvinet, Antonio Luna de Haro and Lauro Sumoy

Euler diagrams drawn with ellipses area-proportionally (Edeap)

Area-proportional Euler diagrams are frequently used to visualize data from Microarray experiments, but are also applied to a wide variety of other data from biosciences, social networks and other domains.

Authors: Michael Wybrow, Peter Rodgers and Fadi K. Dib

A new Bayesian piecewise linear regression model for dynamic network reconstruction

Linear regression models are important tools for learning regulatory networks from gene expression time series. A conventional assumption for non-homogeneous regulatory processes on a short time scale is that ...

Authors: Mahdi Shafiee Kamalabad and Marco Grzegorczyk

Selected papers from the 15th and 16th international conference on Computational Intelligence Methods for Bioinformatics and Biostatistics

Authors: Paolo Cazzaniga, Maria Raposo, Daniela Besozzi, Ivan Merelli, Antonino Staiano, Angelo Ciaramella, Riccardo Rizzo and Luca Manzoni

Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models

Genome-wide reconstructions of metabolism opened the way to thorough investigations of cell metabolism for health care and industrial purposes. However, the predictions offered by Flux Balance Analysis (FBA) c...

Authors: Marco S. Nobile, Vasco Coelho, Dario Pescini and Chiara Damiani

Evaluation of open search methods based on theoretical mass spectra comparison

Mass spectrometry remains the privileged method to characterize proteins. Nevertheless, most of the spectra generated by an experiment remain unidentified after their analysis, mostly because of the modificati...

Authors: Albane Lysiak, Guillaume Fertin, Géraldine Jean and Dominique Tessier

Tremor assessment using smartphone sensor data and fuzzy reasoning

Tremor severity assessment is an important step for the diagnosis and treatment decision-making of essential tremor (ET) patients. Traditionally, tremor severity is assessed by using questionnaires (e.g., ETRS...

Authors: Caro Fuchs, Marco S. Nobile, Guillaume Zamora, Aurélie Degeneffe, Pieter Kubben and Uzay Kaymak

Advantages of using graph databases to explore chromatin conformation capture experiments

High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of DNA interactions and 3D chromosome folding at the genome-wide scale. Usually, these data are represented as matrices descri...

Authors: Daniele D’Agostino, Pietro Liò, Marco Aldinucci and Ivan Merelli

MADGAN: unsupervised medical anomaly detection GAN using multiple adjacent brain MRI slice reconstruction

Unsupervised learning can discover various unseen abnormalities, relying on large-scale unannotated medical images of healthy subjects. Towards this, unsupervised methods reconstruct a 2D/3D single medical ima...

Authors: Changhee Han, Leonardo Rundo, Kohei Murao, Tomoyuki Noguchi, Yuki Shimahara, Zoltán Ádám Milacski, Saori Koshino, Evis Sala, Hideki Nakayama and Shin’ichi Satoh

Machine learning to reveal an astute risk predictive framework for Gynecologic Cancer and its impact on women psychology: Bangladeshi perspective

In this research, an astute system has been developed by using machine learning and data mining approach to predict the risk level of cervical and ovarian cancer in association to stress.

Authors: Sayed Asaduzzaman, Md. Raihan Ahmed, Hasin Rehana, Setu Chakraborty, Md. Shariful Islam and Touhid Bhuiyan

Hydropathicity-based prediction of pain-causing NaV1.7 variants

Mutation-induced variations in the functional architecture of the NaV1.7 channel protein are causally related to a broad spectrum of human pain disorders. Predicting in silico the phenotype of NaV1.7 variant i...

Authors: Makros N. Xenakis, Dimos Kapetis, Yang Yang, Monique M. Gerrits, Jordi Heijman, Stephen G. Waxman, Giuseppe Lauria, Catharina G. Faber, Ronald L. Westra, Patrick J. Lindsey and Hubert J. Smeets

scSensitiveGeneDefine: sensitive gene detection in single-cell RNA sequencing data by Shannon entropy

Single-cell RNA sequencing (scRNA-seq) is the most widely used technique to obtain gene expression profiles from complex tissues. Cell subsets and developmental states are often identified via differential gen...

Authors: Zechuan Chen, Zeruo Yang, Xiaojun Yuan, Xiaoming Zhang and Pei Hao

Predicting rifampicin resistance mutations in bacterial RNA polymerase subunit beta based on majority consensus

Mutations in an enzyme target are one of the most common mechanisms whereby antibiotic resistance arises. Identification of the resistance mutations in bacteria is essential for understanding the structural ba...

Authors: Qing Ning, Dali Wang, Fei Cheng, Yuheng Zhong, Qi Ding and Jing You

GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases

Graphs are mathematical structures widely used for expressing relationships among elements when representing biomedical and biological information. On top of these representations, several analyses are perform...

Authors: Nicola Licheri, Vincenzo Bonnici, Marco Beccuti and Rosalba Giugno

The BioCyc Metabolic Network Explorer

The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks. Any metabolic network visualizat...

Authors: Suzanne Paley and Peter D. Karp

Gene-set distance analysis (GSDA): a powerful tool for gene-set association analysis

Identifying sets of related genes (gene sets) that are empirically associated with a treatment or phenotype often yields valuable biological insights. Several methods effectively identify gene sets in which in...

Authors: Xueyuan Cao and Stan Pounds

Correlation AnalyzeR: functional predictions from gene co-expression correlations

Co-expression correlations provide the ability to predict gene functionality within specific biological contexts, such as different tissue and disease conditions. However, current gene co-expression databases ...

Authors: Henry E. Miller and Alexander J. R. Bishop

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping ...

Authors: Sagnik Banerjee, Priyanka Bhandary, Margaret Woodhouse, Taner Z. Sen, Roger P. Wise and Carson M. Andorf

AutoDTI++: deep unsupervised learning for DTI prediction by autoencoders

Drug–target interaction (DTI) plays a vital role in drug discovery. Identifying drug–target interactions related to wet-lab experiments are costly, laborious, and time-consuming. Therefore, computational metho...

Authors: Seyedeh Zahra Sajadi, Mohammad Ali Zare Chahooki, Sajjad Gharaghani and Karim Abbasi

Constructing and analysing dynamic models with modelbase v1.2.3: a software update

Computational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding of various regulatory processes, metabolic fluxes, effects of drug therapies, ...

Authors: Marvin van Aalst, Oliver Ebenhöh and Anna Matuszyńska

MAPS: machine-assisted phenotype scoring enables rapid functional assessment of genetic variants by high-content microscopy

Genetic testing is widely used in evaluating a patient’s predisposition to hereditary diseases. In the case of cancer, when a functionally impactful mutation (i.e. genetic variant) is identified in a disease-r...

Authors: Jesse T. Chao, Calvin D. Roskelley and Christopher J. R. Loewen

A flexible ChIP-sequencing simulation toolkit

A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data. Accurate simulation of ChIP-seq data can mitigate this ch...

Authors: An Zheng, Michael Lamkin, Yutong Qiu, Kevin Ren, Alon Goren and Melissa Gymrek

Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources

Transcriptional regulation is complex, requiring multiple cis (local) and trans acting mechanisms working in concert to drive gene expression, with disruption of these processes linked to multiple diseases. Previ...

Authors: Neel Patel and William S. Bush

Correction to: Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters

An amendment to this paper has been published and can be accessed via the original article.

Authors: Snorre Sulheim, Fredrik A. Fossheim, Alexander Wentzel and Eivind Almaas

Eye-color and Type-2 diabetes phenotype prediction from genotype data using deep learning methods

Genotype–phenotype predictions are of great importance in genetics. These predictions can help to find genetic mutations causing variations in human beings. There are many approaches for finding the associatio...

Authors: Muhammad Muneeb and Andreas Henschel

Cancer immune control dynamics: a clinical data driven model of systemic immunity in patients with metastatic melanoma

Recent clinical advances in cancer immuno-therapeutics underscore the need for improved understanding of the complex relationship between cancer and the multiple, multi-functional, inter-dependent, cellular an...

Authors: Harold P. Frisch, Allan Sprau, Virginia F. McElroy, James D. Turner, Laura R. E. Becher, Wendy K. Nevala, Alexey A. Leontovich and Svetomir N. Markovic