Articles

SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations

Blood cancers (BCs) are responsible for over 720 K yearly deaths worldwide. Their prevalence and mortality-rate uphold the relevance of research related to BCs. Despite the availability of different resources ...

Authors: Nícia Rosário-Ferreira, Victor Guimarães, Vítor S. Costa and Irina S. Moreira

Practical identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis

Nonlinear mixed effects models provide a way to mathematically describe experimental data involving a lot of inter-individual heterogeneity. In order to assess their practical identifiability and estimate conf...

Authors: Ronan Duchesne, Anissa Guillemin, Olivier Gandrillon and Fabien Crauste

shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study

Quantitative, reverse transcription PCR (qRT-PCR) is currently the gold-standard for SARS-CoV-2 detection and it is also used for detection of other virus. Manual data analysis of a small number of qRT-PCR pla...

Authors: S. Olaechea-Lázaro, I. García-Santisteban, J. R. Pineda, I. Badiola, S. Alonso, Jose Ramon Bilbao and Nora Fernandez-Jimenez

A laminar augmented cascading flexible neural forest model for classification of cancer subtypes based on gene expression data

Correctly classifying the subtypes of cancer is of great significance for the in-depth study of cancer pathogenesis and the realization of personalized treatment for cancer patients. In recent years, classific...

Authors: Lianxin Zhong, Qingfang Meng, Yuehui Chen, Lei Du and Peng Wu

SamQL: a structured query language and filtering tool for the SAM/BAM file format

The Sequence Alignment/Map Format Specification (SAM) is one of the most widely adopted file formats in bioinformatics and many researchers use it daily. Several tools, including most high-throughput sequencin...

Authors: Christopher T. Lee and Manolis Maragkakis

DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification

Quantification of tumor heterogeneity is essential to better understand cancer progression and to adapt therapeutic treatments to patient specificities. Bioinformatic tools to assess the different cell populat...

Authors: Clémentine Decamps, Alexis Arnaud, Florent Petitprez, Mira Ayadi, Aurélia Baurès, Lucile Armenoult, Sergio Escalera, Isabelle Guyon, Rémy Nicolle, Richard Tomasini, Aurélien de Reyniès, Jérôme Cros, Yuna Blum and Magali Richard

Correction to: Avian Immunome DB: an example of a user‑friendly interface for extracting genetic information

Authors: Ralf C. Mueller, Nicolai Mallig, Jacqueline Smith, Lél Eöry, Richard I. Kuo and Robert H. S. Kraus

Modelling the bioinformatics tertiary analysis research process

With the advancements of Next Generation Techniques, a tremendous amount of genomic information has been made available to be analyzed by means of computational methods. Bioinformatics Tertiary Analysis is a c...

Authors: Sara Pidò, Pietro Crovari and Franca Garzotto

Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data

Pathway enrichment analysis (PEA) is a well-established methodology for interpreting a list of genes and proteins of interest related to a condition under investigation. This paper aims to extend our previous ...

Authors: Giuseppe Agapito and Mario Cannataro

On how to generalize species-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome

Understanding the genome, with all of its components and intrinsic relationships, is a great challenge. Conceptual modeling techniques have been used as a means to face this challenge. The heterogeneity and id...

Authors: Alberto García S. and Juan Carlos Casamayor

The expression landscape of JAK1 and its potential as a biomarker for prognosis and immune infiltrates in NSCLC

Janus-activated kinase-1 (JAK1) plays a crucial role in many aspects of cell proliferation, differentiation, apoptosis and immune regulation. However, correlations of JAK1 with prognosis and immune infiltration i...

Authors: Kaikai Shen, Yuqing Wei, Tangfeng Lv, Yong Song, Xiaogan Jiang, Zhiwei Lu, Ping Zhan, Xianghai Wang, Meng Fan and Weihua Lu

Detecting selection in low-coverage high-throughput sequencing data using principal component analysis

Identification of selection signatures between populations is often an important part of a population genetic study. Leveraging high-throughput DNA sequencing larger sample sizes of populations with similar an...

Authors: Jonas Meisner, Anders Albrechtsen and Kristian Hanghøj

multiMarker: software for modelling and prediction of continuous food intake using multiple biomarkers measurements

Metabolomic biomarkers offer potential for objective and reliable food intake assessment, and there is growing interest in using biomarkers in place of or with traditional self-reported approaches. Ongoing res...

Authors: Silvia D’Angelo, Isobel Claire Gormley, Aoife E. McNamara and Lorraine Brennan

rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects

The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been gen...

Authors: Manon Geerts, Achim Schnaufer and Frederik Van den Broeck

Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis

The rising consensus that the cell can dynamically allocate its resources provides an interesting angle for discovering the governing principles of cell growth and metabolism. Extensive efforts have been made ...

Authors: Hong Zeng, Reza Rohani, Wei E. Huang and Aidong Yang

Decline of protein structure rigidity with interatomic distance

Protein structural rigidity was analyzed in a non-redundant ensemble of high-resolution protein crystal structures by means of the Hirshfeld test, according to which the components (uX and uY) of the B-factors of...

Authors: Oliviero Carugo

Enumeration and comprehensive in-silico modeling of three-helix bundle structures composed of typical αα-hairpins

The design of protein structures from scratch requires special attention to the combination of the types and lengths of the secondary structures and the loops required to build highly designable backbone struc...

Authors: Koya Sakuma and Shintaro Minami

Improving structural variant clustering to reduce the negative effect of the breakpoint uncertainty problem

Structural variants (SVs) represent an important source of genetic variation. One of the most critical problems in their detection is breakpoint uncertainty associated with the inability to determine their exa...

Authors: Jan Geryk, Alzbeta Zinkova, Iveta Zedníková, Halina Simková, Vlastimil Stenzl and Marie Korabecna

EvoLaps: a web interface to visualize continuous phylogeographic reconstructions

Phylogeographic reconstructions serve as a basis to understand the spread and evolution of pathogens. Visualization of these reconstructions often lead to complex graphical representations which are difficult ...

Authors: François Chevenet, Denis Fargette, Stéphane Guindon and Anne-Laure Bañuls

A targeted solution for estimating the cell-type composition of bulk samples

To avoid false-positive findings and detect cell-type specific associations in methylation and transcription investigations with bulk samples, it is critical to know the proportions of the major cell-types.

Authors: Edwin J. C. G. van den Oord, Lin Y. Xie, Charles J. Tran, Min Zhao and Karolina A. Aberg

Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders

Accurate identification of Transcriptional Regulator binding locations is essential for analysis of genomic regions, including Cis Regulatory Elements. The customary NGS approaches, predominantly ChIP-Seq, can...

Authors: Quentin Ferré, Jeanne Chèneby, Denis Puthier, Cécile Capponi and Benoît Ballester

Ancestry inference using reference labeled clusters of haplotypes

We present ARCHes, a fast and accurate haplotype-based approach for inferring an individual’s ancestry composition. Our approach works by modeling haplotype diversity from a large, admixed cohort of hundreds o...

Authors: Yong Wang, Shiya Song, Joshua G. Schraiber, Alisa Sedghifar, Jake K. Byrnes, David A. Turissini, Eurie L. Hong, Catherine A. Ball and Keith Noto

In silico vaccine design and epitope mapping of New Delhi metallo-beta-lactamase (NDM): an immunoinformatics approach

Antibiotic resistance is a global health crisis. The adage that “prevention is better than cure” is especially true regarding antibiotic resistance because the resistance appears and spreads much faster than t...

Authors: Matin Fathollahi, Anwar Fathollahi, Hamid Motamedi, Jale Moradi, Amirhooshang Alvandi and Ramin Abiri

Identification of driver genes based on gene mutational effects and network centrality

As one of the deadliest diseases in the world, cancer is driven by a few somatic mutations that disrupt the normal growth of cells, and leads to abnormal proliferation and tumor development. The vast majority ...

Authors: Yun-Yun Tang, Pi-Jing Wei, Jian-ping Zhao, Junfeng Xia, Rui-Fen Cao and Chun-Hou Zheng

Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments

The use of sound to represent sequence data—sonification—has great potential as an alternative and complement to visual representation, exploiting features of human psychoacoustic intuitions to convey nuance m...

Authors: Edward J. Martin, Thomas R. Meagher and Daniel Barker

Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data

With the rapid advancement of genomic sequencing techniques, massive production of gene expression data is becoming possible, which prompts the development of precision medicine. Deep learning is a promising a...

Authors: Victoria Bourgeais, Farida Zehraoui, Mohamed Ben Hamdoune and Blaise Hanczar

Non-small-cell lung cancer classification via RNA-Seq and histology imaging probability fusion

Adenocarcinoma and squamous cell carcinoma are the two most prevalent lung cancer types, and their distinction requires different screenings, such as the visual inspection of histology slides by an expert path...

Authors: Francisco Carrillo-Perez, Juan Carlos Morales, Daniel Castillo-Secilla, Yésica Molina-Castro, Alberto Guillén, Ignacio Rojas and Luis Javier Herrera

Predicting chemotherapy response using a variational autoencoder approach

Multiple studies have shown the utility of transcriptome-wide RNA-seq profiles as features for machine learning-based prediction of response to chemotherapy in cancer. While tumor transcriptome profiles are pu...

Authors: Qi Wei and Stephen A. Ramsey

Concentration optimization of combinatorial drugs using Markov chain-based models

Combinatorial drug therapy for complex diseases, such as HSV infection and cancers, has a more significant efficacy than single-drug treatment. However, one key challenge is how to effectively and efficiently ...

Authors: Shuang Ma, Dan Dang, Wenxue Wang, Yuechao Wang and Lianqing Liu

Constructing xenobiotic maps of metabolism to predict enzymes catalyzing metabolites capable of binding to DNA

The liver plays a major role in the metabolic activation of xenobiotics (drugs, chemicals such as pollutants, pesticides, food additives...). Among environmental contaminants of concern, heterocyclic aromatic ...

Authors: Mael Conan, Nathalie Théret, Sophie Langouet and Anne Siegel

Identifying homogeneous subgroups of patients and important features: a topological machine learning approach

This paper exploits recent developments in topological data analysis to present a pipeline for clustering based on Mapper, an algorithm that reduces complex data into a one-dimensional graph.

Authors: Ewan Carr, Mathieu Carrière, Bertrand Michel, Frédéric Chazal and Raquel Iniesta

Reverse engineering gene regulatory network based on complex-valued ordinary differential equation model

The growing researches of molecular biology reveal that complex life phenomena have the ability to demonstrating various types of interactions in the level of genomics. To establish the interactions between ge...

Authors: Bin Yang, Wenzheng Bao, Wei Zhang, Haifeng Wang, Chuandong Song, Yuehui Chen and Xiuying Jiang

ncDLRES: a novel method for non-coding RNAs family prediction based on dynamic LSTM and ResNet

Studies have proven that the same family of non-coding RNAs (ncRNAs) have similar functions, so predicting the ncRNAs family is helpful to the research of ncRNAs functions. The existing calculation methods ma...

Authors: Linyu Wang, Xiaodan Zhong, Shuo Wang and Yuanning Liu

KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases

Protein kinases are among the largest druggable family of signaling proteins, involved in various human diseases, including cancers and neurodegenerative disorders. Despite their clinical relevance, nearly 30%...

Authors: Liang-Chin Huang, Rahil Taujale, Nathan Gravel, Aarya Venkat, Wayland Yeung, Dominic P. Byrne, Patrick A. Eyers and Natarajan Kannan

Fast and exact quantification of motif occurrences in biological sequences

Identification of motifs and quantification of their occurrences are important for the study of genetic diseases, gene evolution, transcription sites, and other biological mechanisms. Exact formulae for estima...

Authors: Mattia Prosperi, Simone Marini and Christina Boucher

DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction

The study of gene essentiality is fundamental to understand the basic principles of life, as well as for applications in many fields. In recent decades, dozens of sets of essential genes have been determined u...

Authors: Jimena Solana, Emilio Garrote-Sánchez and Rosario Gil

Boolean factor graph model for biological systems: the yeast cell-cycle network

The desire to understand genomic functions and the behavior of complex gene regulatory networks has recently been a major research focus in systems biology. As a result, a plethora of computational and modelin...

Authors: Stephen Kotiang and Ali Eslami

Randomized boosting with multivariable base-learners for high-dimensional variable selection and prediction

Statistical boosting is a computational approach to select and estimate interpretable prediction models for high-dimensional biomedical data, leading to implicit regularization and variable selection when comb...

Authors: Christian Staerk and Andreas Mayr

TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes

Transcription factors (TFs) are the upstream regulators that orchestrate gene expression, and therefore a centrepiece in bioinformatics studies. While a core strategy to understand the biological context of ge...

Authors: Rasmus Magnusson and Zelmina Lubovac-Pilav

FALCON2: a web server for high-quality prediction of protein tertiary structures

Accurate prediction of protein tertiary structures is highly desired as the knowledge of protein structures provides invaluable insights into protein functions. We have designed two approaches to protein struc...

Authors: Lupeng Kong, Fusong Ju, Haicang Zhang, Shiwei Sun and Dongbo Bu

Finding functional associations between prokaryotic virus orthologous groups: a proof of concept

The field of viromics has greatly benefited from recent developments in metagenomics, with significant efforts focusing on viral discovery. However, functional annotation of the increasing number of viral geno...

Authors: Nikolaos Pappas and Bas E. Dutilh

Frequent contiguous pattern mining over biological sequences of protein misfolded diseases

Proteins are integral part of all living beings, which are building blocks of many amino acids. To be functionally active, amino acids chain folds up in a complex way to give each protein a unique 3D shape, wh...

Authors: Mohammad Shahedul Islam, Md. Abul Kashem Mia, Mohammad Shamsur Rahman, Mohammad Shamsul Arefin, Pranab Kumar Dhar and Takeshi Koshiba

SWnet: a deep learning model for drug response prediction from cancer genomic signatures and compound chemical structures

One of the major challenges in precision medicine is accurate prediction of individual patient’s response to drugs. A great number of computational methods have been developed to predict compounds activity usi...

Authors: Zhaorui Zuo, Penglei Wang, Xiaowei Chen, Li Tian, Hui Ge and Dahong Qian

CellProfiler 4: improvements in speed, utility and usability

Imaging data contains a substantial amount of information which can be difficult to evaluate by eye. With the expansion of high throughput microscopy methodologies producing increasingly large datasets, automa...

Authors: David R. Stirling, Madison J. Swain-Bowden, Alice M. Lucas, Anne E. Carpenter, Beth A. Cimini and Allen Goodman

Mining microbe–disease interactions from literature via a transfer learning model

Interactions of microbes and diseases are of great importance for biomedical research. However, large-scale of microbe–disease interactions are hidden in the biomedical literature. The structured databases for...

Authors: Chengkun Wu, Xinyi Xiao, Canqun Yang, JinXiang Chen, Jiacai Yi and Yanlong Qiu

Research on RNA secondary structure predicting via bidirectional recurrent neural network

RNA secondary structure prediction is an important research content in the field of biological information. Predicting RNA secondary structure with pseudoknots has been proved to be an NP-hard problem. Traditi...

Authors: Weizhong Lu, Yan Cao, Hongjie Wu, Yijie Ding, Zhengwei Song, Yu Zhang, Qiming Fu and Haiou Li

An integrated strategy for target SSR genotyping with toleration of nucleotide variations in the SSRs and flanking regions

With the broad application of high-throughput sequencing and its reduced cost, simple sequence repeat (SSR) genotyping by sequencing (SSR-GBS) has been widely used for interpreting genetic data across differen...

Authors: Yongxue Huo, Yikun Zhao, Liwen Xu, Hongmei Yi, Yunlong Zhang, Xianqing Jia, Han Zhao, Jiuran Zhao and Fengge Wang

RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources

RNA regulates a variety of biological functions by interacting with other molecules. The ligand often binds in the RNA pocket to trigger structural changes or functions. Thus, it is essential to explore and vi...

Authors: Ting Zhou, Huiwen Wang, Chen Zeng and Yunjie Zhao

A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells

In mammalian cells the endoplasmic reticulum (ER) comprises a highly complex reticular morphology that is spread throughout the cytoplasm. This organelle is of particular interest to biologists, as its dysfunc...

Authors: M. Elena Garcia-Pardo, Jeremy C. Simpson and Niamh C. O’Sullivan

DI2: prior-free and multi-item discretization of biological data and its applications

A considerable number of data mining approaches for biomedical data analysis, including state-of-the-art associative models, require a form of data discretization. Although diverse discretization approaches ha...

Authors: Leonardo Alexandre, Rafael S. Costa and Rui Henriques