Articles

Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage

Following publication of the original article [1], the author reported that there are several errors in the original article;

Authors: Louis Ranjard, Thomas K. F. Wong and Allen G. Rodrigo

Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations

Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data,...

Authors: Antoine Buetti-Dinh, Malte Herold, Stephan Christel, Mohamed El Hajjami, Francesco Delogu, Olga Ilie, Sören Bellenberg, Paul Wilmes, Ansgar Poetsch, Wolfgang Sand, Mario Vera, Igor V. Pivkin, Ran Friedman and Mark Dopson

ShinyOmics: collaborative exploration of omics-data

Omics-profiling is a collection of increasingly prominent approaches that result in large-scale biological datasets, for instance capturing an organism’s behavior and response in an environment. It can be daun...

Authors: Defne Surujon and Tim van Opijnen

Lag penalized weighted correlation for time series clustering

The similarity or distance measure used for clustering can generate intuitive and interpretable clusters when it is tailored to the unique characteristics of the data. In time series datasets generated with hi...

Authors: Thevaa Chandereng and Anthony Gitter

PRAP: Pan Resistome analysis pipeline

Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species. Therefore, a pan-genome approach to analy...

Authors: Yichen He, Xiujuan Zhou, Ziyan Chen, Xiangyu Deng, Andrew Gehring, Hongyu Ou, Lida Zhang and Xianming Shi

Automatic construction of metabolic models with enzyme constraints

In order to improve the accuracy of constraint-based metabolic models, several approaches have been developed which intend to integrate additional biological information. Two of these methods, MOMENT and GECKO...

Authors: Pavlos Stephanos Bekiaris and Steffen Klamt

A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma

Integrating genome-wide gene expression patient profiles with regulatory knowledge is a challenging task because of the inherent heterogeneity, noise and incompleteness of biological data. From the computation...

Authors: Maxime Folschette, Vincent Legagneux, Arnaud Poret, Lokmane Chebouba, Carito Guziolowski and Nathalie Théret

Deep neural networks for human microRNA precursor detection

MicroRNAs (miRNAs) play important roles in a variety of biological processes by regulating gene expression at the post-transcriptional level. So, the discovery of new miRNAs has become a popular task in biolog...

Authors: Xueming Zheng, Xingli Fu, Kaicheng Wang and Meng Wang

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software

Cell-type heterogeneity of tumors is a key factor in tumor progression and response to chemotherapy. Tumor cell-type heterogeneity, defined as the proportion of the various cell-types in a tumor, can be inferr...

Authors: Clémentine Decamps, Florian Privé, Raphael Bacher, Daniel Jost, Arthur Waguet, Eugene Andres Houseman, Eugene Lurie, Pavlo Lutsik, Aleksandar Milosavljevic, Michael Scherer, Michael G. B. Blum and Magali Richard

The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment

Seed and accessibility constraints are core features to enable highly accurate sRNA target screens based on RNA-RNA interaction prediction. Currently, available tools provide different (sets of) constraints an...

Authors: Martin Raden, Teresa Müller, Stefan Mautner, Rick Gelhausen and Rolf Backofen

LDpop: an interactive online tool to calculate and visualize geographic LD patterns

Linkage disequilibrium (LD)—the non-random association of alleles at different loci—defines population-specific haplotypes which vary by genomic ancestry. Assessment of allelic frequencies and LD patterns from...

Authors: T. A. Alexander and M. J. Machiela

Improving the organization and interactivity of metabolic pathfinding with precomputed pathways

The rapid growth of available knowledge on metabolic processes across thousands of species continues to expand the possibilities of producing chemicals by combining pathways found in different species. Several...

Authors: Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett and Lydia E. Kavraki

Bayesian differential analysis of gene regulatory networks exploiting genetic perturbations

Gene regulatory networks (GRNs) can be inferred from both gene expression data and genetic perturbations. Under different conditions, the gene data of the same gene set may be different from each other, which ...

Authors: Yan Li, Dayou Liu, Tengfei Li and Yungang Zhu

Integrative analysis of time course metabolic data and biomarker discovery

Metabolomics time-course experiments provide the opportunity to understand the changes to an organism by observing the evolution of metabolic profiles in response to internal or external stimuli. Along with ot...

Authors: Takoua Jendoubi and Timothy M. D. Ebbels

DeepECA: an end-to-end learning framework for protein contact prediction from a multiple sequence alignment

Recently developed methods of protein contact prediction, a crucially important step for protein structure prediction, depend heavily on deep neural networks (DNNs) and multiple sequence alignments (MSAs) of t...

Authors: Hiroyuki Fukuda and Kentaro Tomii

Multiset sparse partial least squares path modeling for high dimensional omics data analysis

Recent technological developments have enabled the measurement of a plethora of biomolecular data from various omics domains, and research is ongoing on statistical methods to leverage these omics data to bett...

Authors: Attila Csala, Aeilko H. Zwinderman and Michel H. Hof

Microscopy cell nuclei segmentation with enhanced U-Net

Cell nuclei segmentation is a fundamental task in microscopy image analysis, based on which multiple biological related analysis can be performed. Although deep learning (DL) based techniques have achieved sta...

Authors: Feixiao Long

Optimization and expansion of non-negative matrix factorization

Non-negative matrix factorization (NMF) is a technique widely used in various fields, including artificial intelligence (AI), signal processing and bioinformatics. However existing algorithms and R packages ca...

Authors: Xihui Lin and Paul C. Boutros

Evolving knowledge graph similarity for supervised learning in complex biomedical domains

In recent years, biomedical ontologies have become important for describing existing biological knowledge in the form of knowledge graphs. Data mining approaches that work with knowledge graphs have been propo...

Authors: Rita T. Sousa, Sara Silva and Catia Pesquita

Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products

The order of genes in bacterial genomes is not random; for example, the products of genes belonging to an operon work together in the same pathway. The cotranslational assembly of protein complexes is deemed t...

Authors: Robert Esch and Rainer Merkl

Bayesian mixture regression analysis for regulation of Pluripotency in ES cells

Observed levels of gene expression strongly depend on both activity of DNA binding transcription factors (TFs) and chromatin state through different histone modifications (HMs). In order to recover the functio...

Authors: Mehran Aflakparast, Geert Geeven and Mathisca C.M. de Gunst

Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina

The green microalga Dunaliella salina accumulates a high proportion of β-carotene during abiotic stress conditions. To better understand the intracellular flux distribution leading to carotenoid accumulation, thi...

Authors: Melanie Fachet, Carina Witte, Robert J. Flassig, Liisa K. Rihko-Struckmann, Zaid McKie-Krisberg, Jürgen E. W. Polle and Kai Sundmacher

DynaVenn: web-based computation of the most significant overlap between ordered sets

In many research disciplines, ordered lists are compared. One example is to compare a subset of all significant genes or proteins in a primary study to those in a replication study. Often, the top of the lists...

Authors: Jérémy Amand, Tobias Fehlmann, Christina Backes and Andreas Keller

Alignment-free genomic sequence comparison using FCGR and signal processing

Alignment-free methods of genomic comparison offer the possibility of scaling to large data sets of nucleotide sequences comprised of several thousand or more base pairs. Such methods can be used for purposes ...

Authors: Daniel Lichtblau

The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa’s capacity for genomics research

Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic bioinformatics suppo...

Authors: Judit Kumuthini, Lyndon Zass, Sumir Panji, Samson P. Salifu, Jonathan K. Kayondo, Victoria Nembaware, Mamana Mbiyavanga, Ajayi Olabode, Ali Kishk, Gordon Wells and Nicola J. Mulder

ZDOG: zooming in on dominating genes with mutations in cancer pathways

Inference of cancer-causing genes and their biological functions are crucial but challenging due to the heterogeneity of somatic mutations. The heterogeneity of somatic mutations reveals that only a handful of...

Authors: Rudi Alberts, Jinyu Chen and Louxin Zhang

LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation

Recent advances in genome sequencing technologies and the cost drop in high-throughput sequencing continue to give rise to a deluge of data available for downstream analyses. Among others, evolutionary biologi...

Authors: Emanuel Maldonado and Agostinho Antunes

Benchmarking the PEPOP methods for mimicking discontinuous epitopes

Computational methods provide approaches to identify epitopes in protein Ags to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was de...

Authors: Vincent Demolombe, Alexandre G. de Brevern, Franck Molina, Géraldine Lavigne, Claude Granier and Violaine Moreau

Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach

Reactivation of the telomerase reverse transcriptase gene TERT is a central feature for unlimited proliferation of the majority of cancers. However, the underlying regulatory processes are only partly understood.

Authors: Alexandra M. Poos, Theresa Kordaß, Amol Kolte, Volker Ast, Marcus Oswald, Karsten Rippe and Rainer König

A novel method detecting the key clinic factors of portal vein system thrombosis of splenectomy & cardia devascularization patients for cirrhosis & portal hypertension

Portal vein system thrombosis (PVST) is potentially fatal for patients if the diagnosis is not timely or the treatment is not proper. There hasn’t been any available technique to detect clinic risk factors to ...

Authors: Mingzhao Wang, Linglong Ding, Meng Xu, Juanying Xie, Shengli Wu, Shengquan Xu, Yingmin Yao and Qingguang Liu

Protein sequence information extraction and subcellular localization prediction with gapped k-Mer method

Subcellular localization prediction of protein is an important component of bioinformatics, which has great importance for drug design and other applications. A multitude of computational tools for proteins su...

Authors: Yu-hua Yao, Ya-ping Lv, Ling Li, Hui-min Xu, Bin-bin Ji, Jing Chen, Chun Li, Bo Liao and Xu-ying Nan

Multi-cancer samples clustering via graph regularized low-rank representation method under sparse and symmetric constraints

Identifying different types of cancer based on gene expression data has become hotspot in bioinformatics research. Clustering cancer gene expression data from multiple cancers to their own class is a significa...

Authors: Juan Wang, Cong-Hai Lu, Jin-Xing Liu, Ling-Yun Dai and Xiang-Zhen Kong

The exploration of disease-specific gene regulatory networks in esophageal carcinoma and stomach adenocarcinoma

Feed-forward loops (FFLs), consisting of miRNAs, transcription factors (TFs) and their common target genes, have been validated to be important for the initialization and development of complex diseases, inclu...

Authors: Guimin Qin, Luqiong Yang, Yuying Ma, Jiayan Liu and Qiuyan Huo

PCA via joint graph Laplacian and sparse constraint: Identification of differentially expressed genes and sample clustering on gene expression data

In recent years, identification of differentially expressed genes and sample clustering have become hot topics in bioinformatics. Principal Component Analysis (PCA) is a widely used method in gene expression d...

Authors: Chun-Mei Feng, Yong Xu, Mi-Xiao Hou, Ling-Yun Dai and Jun-Liang Shang

An efficient gene selection method for microarray data based on LASSO and BPSO

The main goal of successful gene selection for microarray data is to find compact and predictive gene subsets which could improve the accuracy. Though a large pool of available methods exists, selecting the op...

Authors: Ying Xiong, Qing-Hua Ling, Fei Han and Qing-Hua Liu

PEIS: a novel approach of tumor purity estimation by identifying information sites through integrating signal based on DNA methylation data

Tumor purity plays an important role in understanding the pathogenic mechanism of tumors. The purity of tumor samples is highly sensitive to tumor heterogeneity. Due to Intratumoral heterogeneity of genetic an...

Authors: Shudong Wang, Lihua Wang, Yuanyuan Zhang, Shanchen Pang and Xinzeng Wang

VariFAST: a variant filter by automated scoring based on tagged-signatures

Variant calling and refinement from whole genome/exome sequencing data is a fundamental task for genomics studies. Due to the limited accuracy of NGS sequencing and variant callers, IGV-based manual review is ...

Authors: Hang Zhang, Ke Wang, Juan Zhou, Jianhua Chen, Yizhou Xu, Dong Wang, Xiaoqi Li, Renliang Sun, Mancang Zhang, Zhuo Wang and Yongyong Shi

The coming era of artificial intelligence in biological data science

Authors: Henry Han and Wenbin Liu

Identification of infectious disease-associated host genes using machine learning techniques

With the global spread of multidrug resistance in pathogenic microbes, infectious diseases emerge as a key public health concern of the recent time. Identification of host genes associated with infectious dise...

Authors: Ranjan Kumar Barman, Anirban Mukhopadhyay, Ujjwal Maulik and Santasabuj Das

Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation

Cellular memory is a ubiquitous function of biological systems. By generating a sustained response to a transient inductive stimulus, often due to bistability, memory is central to the robust control of many i...

Authors: A. B. M. Shamim Ul Hasan, Hiroyuki Kurata and Sebastian Pechmann

ki67 nuclei detection and ki67-index estimation: a novel automatic approach based on human vision modeling

The protein ki67 (pki67) is a marker of tumor aggressiveness, and its expression has been proven to be useful in the prognostic and predictive evaluation of several types of tumors. To numerically quantify the...

Authors: Barbara Rita Barricelli, Elena Casiraghi, Jessica Gliozzo, Veronica Huber, Biagio Eugenio Leone, Alessandro Rizzi and Barbara Vergani

Deep mixed model for marginal epistasis detection and population stratification correction in genome-wide association studies

Genome-wide Association Studies (GWAS) have contributed to unraveling associations between genetic variants in the human genome and complex traits for more than a decade. While many works have been invented as...

Authors: Haohan Wang, Tianwei Yue, Jingkang Yang, Wei Wu and Eric P. Xing

IILLS: predicting virus-receptor interactions based on similarity and semi-supervised learning

Viral infectious diseases are the serious threat for human health. The receptor-binding is the first step for the viral infection of hosts. To more effectively treat human viral infectious diseases, the hidden...

Authors: Cheng Yan, Guihua Duan, Fang-Xiang Wu and Jianxin Wang

Efficient computation of stochastic cell-size transient dynamics

How small, fast-growing bacteria ensure tight cell-size distributions remains elusive. High-throughput measurement techniques have propelled efforts to build modeling tools that help to shed light on the relat...

Authors: Cesar Augusto Nieto-Acuna, Cesar Augusto Vargas-Garcia, Abhyudai Singh and Juan Manuel Pedraza

iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks

Since protein-DNA interactions are highly essential to diverse biological events, accurately positioning the location of the DNA-binding residues is necessary. This biological issue, however, is currently a ch...

Authors: Binh P. Nguyen, Quang H. Nguyen, Giang-Nam Doan-Ngoc, Thanh-Hoang Nguyen-Vo and Susanto Rahardja

Model-based cell clustering and population tracking for time-series flow cytometry data

Modern flow cytometry technology has enabled the simultaneous analysis of multiple cell markers at the single-cell level, and it is widely used in a broad field of research. The detection of cell populations i...

Authors: Kodai Minoura, Ko Abe, Yuka Maeda, Hiroyoshi Nishikawa and Teppei Shimamura

Rearrangement analysis of multiple bacterial genomes

Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to...

Authors: Mehwish Noureen, Ipputa Tada, Takeshi Kawashima and Masanori Arita

Topological structure analysis of chromatin interaction networks

Current Hi-C technologies for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made into analysis ...

Authors: Juris Viksna, Gatis Melkus, Edgars Celms, Kārlis Čerāns, Karlis Freivalds, Paulis Kikusts, Lelde Lace, Mārtiņš Opmanis, Darta Rituma and Peteris Rucevskis

Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data

Removing duplicates might be considered as a well-resolved problem in next-generation sequencing (NGS) data processing domain. However, as NGS technology gains more recognition in clinical application, researc...

Authors: Shifu Chen, Yanqing Zhou, Yaru Chen, Tanxiao Huang, Wenting Liao, Yun Xu, Zhicheng Li and Jia Gu

Old drug repositioning and new drug discovery through similarity learning from drug-target joint feature spaces

Detection of new drug-target interactions by computational algorithms is of crucial value to both old drug repositioning and new drug discovery. Existing machine-learning methods rely only on experimentally va...

Authors: Yi Zheng, Hui Peng, Xiaocai Zhang, Zhixun Zhao, Xiaoying Gao and Jinyan Li