Articles

Classification of protein–protein association rates based on biophysical informatics

Proteins form various complexes to carry out their versatile functions in cells. The dynamic properties of protein complex formation are mainly characterized by the association rates which measures how fast th...

Authors: Kalyani Dhusia and Yinghao Wu

HELLO: improved neural network architectures and methodologies for small variant calling

Modern Next Generation- and Third Generation- Sequencing methods such as Illumina and PacBio Circular Consensus Sequencing platforms provide accurate sequencing data. Parallel developments in Deep Learning hav...

Authors: Anand Ramachandran, Steven S. Lumetta, Eric W. Klee and Deming Chen

OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow

The advent of next generation sequencing has opened new avenues for basic and applied research. One application is the discovery of sequence variants causative of a phenotypic trait or a disease pathology. The...

Authors: Jochen Bathke and Gesine Lühken

Comprior: facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets

Reproducible benchmarking is important for assessing the effectiveness of novel feature selection approaches applied on gene expression data, especially for prior knowledge approaches that incorporate biologic...

Authors: Cindy Perscheid

Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation

The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ri...

Authors: Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch-Mizrachi and Eric P. Nawrocki

From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon

Numerous genomes are sequenced and made available to the community through the NCBI portal. However, and, unlike what happens for gene function annotation, annotation of promoter sequences and the underlying p...

Authors: Jorge Oliveira, Miguel Antunes, Claudia P. Godinho, Miguel C. Teixeira, Isabel Sá-Correia and Pedro T. Monteiro

CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis

The rise of spatial transcriptomics technologies is leading to new insights about how gene regulation happens in a spatial context. Determining which genes are expressed in similar spatial patterns can reveal ...

Authors: Yang Xu and Rachel Patton McCord

BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

Meiotic recombination is a vital biological process playing an essential role in genome's structural and functional dynamics. Genomes exhibit highly various recombination profiles along chromosomes associated ...

Authors: Yasmine Mansour, Annie Chateau and Anna-Sophie Fiston-Lavier

Integrative, multi-omics, analysis of blood samples improves model predictions: applications to cancer

Cancer genomic studies often include data collected from several omics platforms. Each omics data source contributes to the understanding of the underlying biological process via source specific (“individual”)...

Authors: Erica Ponzi, Magne Thoresen, Therese Haugdahl Nøst and Kajsa Møllersen

Maximum parsimony reconciliation in the DTLOR model

Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and th...

Authors: Jingyi Liu, Ross Mawhorter, Nuo Liu, Santi Santichaivekin, Eliot Bush and Ran Libeskind-Hadas

Correction to: NoRCE: non‑coding RNA sets cis enrichment tool

Authors: Gulden Olgun, Afshan Nabi and Oznur Tastan

A unified framework for the integration of multiple hierarchical clusterings or networks from multi-source data

Integrating data from different sources is a recurring question in computational biology. Much effort has been devoted to the integration of data sets of the same type, typically multiple numerical data tables...

Authors: Audrey Hulot, Denis Laloë and Florence Jaffrézic

Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps

A range of spatially resolved transcriptomic methods has recently emerged as a way to spatially characterize the molecular and cellular diversity of a tissue. As a consequence, an increasing number of computat...

Authors: Sergio Marco Salas, Daniel Gyllborg, Christoffer Mattsson Langseth and Mats Nilsson

COPLA, a taxonomic classifier of plasmids

Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is ne...

Authors: Santiago Redondo-Salvo, Roger Bartomeus-Peñalver, Luis Vielva, Kaitlin A. Tagg, Hattie E. Webb, Raúl Fernández-López and Fernando de la Cruz

Co-AMPpred for in silico-aided predictions of antimicrobial peptides by integrating composition-based features

Antimicrobial peptides (AMPs) are oligopeptides that act as crucial components of innate immunity, naturally occur in all multicellular organisms, and are involved in the first line of defense function. Recent...

Authors: Onkar Singh, Wen-Lian Hsu and Emily Chia-Yu Su

Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree

NCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on INSDC are organized in its hierarchical structure. Despite th...

Authors: Tetsu Sakamoto and J. Miguel Ortega

Mining a stroke knowledge graph from literature

Stroke has an acute onset and a high mortality rate, making it one of the most fatal diseases worldwide. Its underlying biology and treatments have been widely studied both in the “Western” biomedicine and the...

Authors: Xi Yang, Chengkun Wu, Goran Nenadic, Wei Wang and Kai Lu

MUREN: a robust and multi-reference approach of RNA-seq transcript normalization

Normalization of RNA-seq data aims at identifying biological expression differentiation between samples by removing the effects of unwanted confounding factors. Explicitly or implicitly, the justification of n...

Authors: Yance Feng and Lei M. Li

A neural network-based method for polypharmacy side effects prediction

Polypharmacy is a type of treatment that involves the concurrent use of multiple medications. Drugs may interact when they are used simultaneously. So, understanding and mitigating polypharmacy side effects ar...

Authors: Raziyeh Masumshah, Rosa Aghdam and Changiz Eslahchi

Uncovering the effects of heterogeneity and parameter sensitivity on within-host dynamics of disease: malaria as a case study

The fidelity and reliability of disease model predictions depend on accurate and precise descriptions of processes and determination of parameters. Various models exist to describe within-host dynamics during ...

Authors: Shade Horn, Jacky L. Snoep and David D. van Niekerk

PDBeCIF: an open-source mmCIF/CIF parsing and processing package

Biomacromolecular structural data outgrew the legacy Protein Data Bank (PDB) format which the scientific community relied on for decades, yet the use of its successor PDBx/Macromolecular Crystallographic Infor...

Authors: Glen van Ginkel, Lukáš Pravda, José M. Dana, Mihaly Varadi, Peter Keller, Stephen Anyango and Sameer Velankar

neoDL: a novel neoantigen intrinsic feature-based deep learning model identifies IDH wild-type glioblastomas with the longest survival

Neoantigen based personalized immune therapies achieve promising results in melanoma and lung cancer, but few neoantigen based models perform well in IDH wild-type GBM, and the association between neoantigen i...

Authors: Ting Sun, Yufei He, Wendong Li, Guang Liu, Lin Li, Lu Wang, Zixuan Xiao, Xiaohan Han, Hao Wen, Yong Liu, Yifan Chen, Haoyu Wang, Jing Li, Yubo Fan, Wei Zhang and Jing Zhang

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

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

Feature selection for RNA cleavage efficiency at specific sites using the LASSO regression model in Arabidopsis thaliana

RNA degradation is important for the regulation of gene expression. Despite the identification of proteins and sequences related to deadenylation-dependent RNA degradation in plants, endonucleolytic cleavage-d...

Authors: Daishin Ueno, Harunori Kawabe, Shotaro Yamasaki, Taku Demura and Ko Kato

GAT-LI: a graph attention network based learning and interpreting method for functional brain network classification

Autism spectrum disorders (ASD) imply a spectrum of symptoms rather than a single phenotype. ASD could affect brain connectivity at different degree based on the severity of the symptom. Given their excellent ...

Authors: Jinlong Hu, Lijie Cao, Tenghui Li, Shoubin Dong and Ping Li

METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs

Due to the complexity of microbial communities, de novo assembly on next generation sequencing data is commonly unable to produce complete microbial genomes. Metagenome assembly binning becomes an essential st...

Authors: Zhenmiao Zhang and Lu Zhang

Disease ontologies for knowledge graphs

Data integration to build a biomedical knowledge graph is a challenging task. There are multiple disease ontologies used in data sources and publications, each having its hierarchy. A common task is to map bet...

Authors: Natalja Kurbatova and Rowan Swiers

SAUTE: sequence assembly using target enrichment

Illumina is the dominant sequencing technology at this time. Short length, short insert size, some systematic biases, and low-level carryover contamination in Illumina reads continue to make assembly of repeat...

Authors: Alexandre Souvorov and Richa Agarwala

Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing

As exome sequencing (ES) integrates into clinical practice, we should make every effort to utilize all information generated. Copy-number variation can lead to Mendelian disorders, but small copy-number varian...

Authors: Dayne L. Filer, Fengshen Kuo, Alicia T. Brandt, Christian R. Tilley, Piotr A. Mieczkowski, Jonathan S. Berg, Kimberly Robasky, Yun Li, Chris Bizon, Jeffery L. Tilson, Bradford C. Powell, Darius M. Bost, Clark D. Jeffries and Kirk C. Wilhelmsen

HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences

SARS-CoV-2 related research has increased in importance worldwide since December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the most notable and concerning currently are the UK va...

Authors: Phuoc Thien Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant and Teemu Smura

Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks

Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Effector proteins are the tools such pathogens use to infect the cell, predicting effectors de ...

Authors: Ruth Kristianingsih and Dan MacLean

MSCFS: inferring circRNA functional similarity based on multiple data sources

More and more evidence shows that circRNA plays an important role in various biological processes and human health. Therefore, inferring the circRNA’s potential functions and obtaining circRNA functional simil...

Authors: Liang Shu, Cheng Zhou, Xinxu Yuan, Jingpu Zhang and Lei Deng

Publisher Correction to: TrancriptomeReconstructoR: data‑driven annotation of complex transcriptomes

Authors: Maxim Ivanov, Albin Sandelin and Sebastian Marquardt

MitoTox: a comprehensive mitochondrial toxicity database

Mitochondria play essential roles in regulating cellular functions. Some drug treatments and molecular interventions have been reported to have off-target effects damaging mitochondria and causing severe side ...

Authors: Yu-Te Lin, Ko-Hong Lin, Chi-Jung Huang and An-Chi Wei

SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency

Introns are generally removed from primary transcripts to form mature RNA molecules in a post-transcriptional process called splicing. An efficient splicing of primary transcripts is an essential step in gene ...

Authors: Verônica R. de Melo Costa, Julianus Pfeuffer, Annita Louloupi, Ulf A. V. Ørom and Rosario M. Piro

Correction to: Moonlighting protein prediction using physico‑chemical and evolutional properties via machine learning methods

Authors: Farshid Shirafkan, Sajjad Gharaghani, Karim Rahimian, Reza Hasan Sajedi and Javad Zahiri

SCOUR: a stepwise machine learning framework for predicting metabolite-dependent regulatory interactions

The topology of metabolic networks is both well-studied and remarkably well-conserved across many species. The regulation of these networks, however, is much more poorly characterized, though it is known to be...

Authors: Justin Y. Lee, Britney Nguyen, Carlos Orosco and Mark P. Styczynski

Single-cell classification using graph convolutional networks

Analyzing single-cell RNA sequencing (scRNAseq) data plays an important role in understanding the intrinsic and extrinsic cellular processes in biological and biomedical research. One significant effort in thi...

Authors: Tianyu Wang, Jun Bai and Sheida Nabavi

Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria

Gene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in cellular subsystems, critical for the coherent functioning of cells. Her...

Authors: Ian Leifer, Mishael Sánchez-Pérez, Cecilia Ishida and Hernán A. Makse

Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization

Microbiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and opti...

Authors: Emily Goren, Chong Wang, Zhulin He, Amy M. Sheflin, Dawn Chiniquy, Jessica E. Prenni, Susannah Tringe, Daniel P. Schachtman and Peng Liu

Consensus clustering applied to multi-omics disease subtyping

Facing the diversity of omics data and the difficulty of selecting one result over all those produced by several methods, consensus strategies have the potential to reconcile multiple inputs and to produce rob...

Authors: Galadriel Brière, Élodie Darbo, Patricia Thébault and Raluca Uricaru

Performance of Web tools for predicting changes in protein stability caused by mutations

Despite decades on developing dedicated Web tools, it is still difficult to predict correctly the changes of the thermodynamic stability of proteins caused by mutations. Here, we assessed the reliability of fi...

Authors: Anna Marabotti, Eugenio Del Prete, Bernardina Scafuri and Angelo Facchiano

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature, allowing not only the identification of known phyla and strains but a...

Authors: Carlo Ferravante, Domenico Memoli, Domenico Palumbo, Paolo Ciaramella, Antonio Di Loria, Ylenia D’Agostino, Giovanni Nassa, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz and Giorgio Giurato

PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity

Tumors are composed by a number of cancer cell subpopulations (subclones), characterized by a distinguishable set of mutations. This phenomenon, known as intra-tumor heterogeneity (ITH), may be studied using C...

Authors: Marilisa Montemurro, Elena Grassi, Carmelo Gabriele Pizzino, Andrea Bertotti, Elisa Ficarra and Gianvito Urgese

Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing

Systems biology increasingly relies on deep sequencing with combinatorial index tags to associate biological sequences with their sample, cell, or molecule of origin. Accurate data interpretation depends on th...

Authors: Lior Galanti, Dennis Shasha and Kristin C. Gunsalus

ANMDA: anti-noise based computational model for predicting potential miRNA-disease associations

A growing proportion of research has proved that microRNAs (miRNAs) can regulate the function of target genes and have close relations with various diseases. Developing computational methods to exploit more po...

Authors: Xue-Jun Chen, Xin-Yun Hua and Zhen-Ran Jiang

BiGAN: LncRNA-disease association prediction based on bidirectional generative adversarial network

An increasing number of studies have shown that lncRNAs are crucial for the control of hormones and the regulation of various physiological processes in the human body, and deletion mutations in RNA are relate...

Authors: Qiang Yang and Xiaokun Li

Genome-wide identification and expression analysis of Raffinose synthetase family in cotton

The Raffinose synthetase (RAFS) genes superfamily is critical for the synthesis of raffinose, which accumulates in plant leaves under abiotic stress. However, it remains unclear whether RAFS contributes to resist...

Authors: Ruifeng Cui, Xiaoge Wang, Waqar Afzal Malik, Xuke Lu, Xiugui Chen, Delong Wang, Junjuan Wang, Shuai Wang, Chao Chen, Lixue Guo, Quanjia Chen and Wuwei Ye

Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network

Authors: Tianqi Wu, Zhiye Guo, Jie Hou and Jianlin Cheng

StrongestPath: a Cytoscape application for protein–protein interaction analysis

StrongestPath is a Cytoscape 3 application that enables the analysis of interactions between two proteins or groups of proteins in a collection of protein–protein interaction (PPI) network or signaling network...

Authors: Zaynab Mousavian, Mehran Khodabandeh, Ali Sharifi-Zarchi, Alireza Nadafian and Alireza Mahmoudi