Articles

Predicting subcellular location of protein with evolution information and sequence-based deep learning

Protein subcellular localization prediction plays an important role in biology research. Since traditional methods are laborious and time-consuming, many machine learning-based prediction methods have been pro...

Authors: Zhijun Liao, Gaofeng Pan, Chao Sun and Jijun Tang

ILRC: a hybrid biomarker discovery algorithm based on improved L1 regularization and clustering in microarray data

Finding significant genes or proteins from gene chip data for disease diagnosis and drug development is an important task. However, the challenge comes from the curse of the data dimension. It is of great sign...

Authors: Kun Yu, Weidong Xie, Linjie Wang and Wei Li

A consensus-based ensemble approach to improve transcriptome assembly

Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. Multiple tools exist to perform...

Authors: Adam Voshall, Sairam Behera, Xiangjun Li, Xiao-Hong Yu, Kushagra Kapil, Jitender S. Deogun, John Shanklin, Edgar B. Cahoon and Etsuko N. Moriyama

Using neural networks to support high-quality evidence mapping

The Living Evidence Map Project at the Norwegian Institute of Public Health (NIPH) gives an updated overview of research results and publications. As part of NIPH’s mandate to inform evidence-based infection p...

Authors: Thomas B. Røst, Laura Slaughter, Øystein Nytrø, Ashley E. Muller and Gunn E. Vist

Context-aware multi-token concept recognition of biological entities

Concept recognition is a term that corresponds to the two sequential steps of named entity recognition and named entity normalization, and plays an essential role in the field of bioinformatics. However, the c...

Authors: Kwangmin Kim and Doheon Lee

A sui generis QA approach using RoBERTa for adverse drug event identification

Extraction of adverse drug events from biomedical literature and other textual data is an important component to monitor drug-safety and this has attracted attention of many researchers in healthcare. Existing...

Authors: Harshit Jain, Nishant Raj and Suyash Mishra

PIC-Me: paralogs and isoforms classifier based on machine-learning approaches

Paralogs formed through gene duplication and isoforms formed through alternative splicing have been important processes for increasing protein diversity and maintaining cellular homeostasis. Despite their reco...

Authors: Jooseong Oh, Sung-Gwon Lee and Chungoo Park

Comparability of reference-based and reference-free transcriptome analysis approaches at the gene expression level

Lately, high-throughput RNA sequencing has been extensively used to elucidate the transcriptome landscape and dynamics of cell types of different species. In particular, for most non-model organisms lacking co...

Authors: Sung-Gwon Lee, Dokyun Na and Chungoo Park

CL-ACP: a parallel combination of CNN and LSTM anticancer peptide recognition model

Anticancer peptides are defence substances with innate immune functions that can selectively act on cancer cells without harming normal cells and many studies have been conducted to identify anticancer peptide...

Authors: Huiqing Wang, Jian Zhao, Hong Zhao, Haolin Li and Juan Wang

Differential expression analysis using a model-based gene clustering algorithm for RNA-seq data

RNA-seq is a tool for measuring gene expression and is commonly used to identify differentially expressed genes (DEGs). Gene clustering is used to classify DEGs with similar expression patterns for the subsequ...

Authors: Takayuki Osabe, Kentaro Shimizu and Koji Kadota

Fast activation maximization for molecular sequence design

Optimization of DNA and protein sequences based on Machine Learning models is becoming a powerful tool for molecular design. Activation maximization offers a simple design strategy for differentiable models: o...

Authors: Johannes Linder and Georg Seelig

Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers

Sequencing partial 16S rRNA genes is a cost effective method for quantifying the microbial composition of an environment, such as the human gut. However, downstream analysis relies on binning reads into microb...

Authors: Brianna S. Chrisman, Kelley M. Paskov, Nate Stockham, Jae-Yoon Jung, Maya Varma, Peter Y. Washington, Christine Tataru, Shoko Iwai, Todd Z. DeSantis, Maude David and Dennis P. Wall

Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis

The 10th and 9th revisions of the International Statistical Classification of Diseases and Related Health Problems (ICD10 and ICD9) have been adopted worldwide as a well-recognized norm to share codes for dise...

Authors: Ling Wan, Justin Song, Virginia He, Jennifer Roman, Grace Whah, Suyuan Peng, Luxia Zhang and Yongqun He

A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction

Ubiquitylation is an important post-translational modification of proteins that not only plays a central role in cellular coding, but is also closely associated with the development of a variety of diseases. T...

Authors: Mengqi Luo, Zhongyan Li, Shangfu Li and Tzong-Yi Lee

AdmixSim 2: a forward-time simulator for modeling complex population admixture

Computer simulations have been widely applied in population genetics and evolutionary studies. A great deal of effort has been made over the past two decades in developing simulation tools. However, there are ...

Authors: Rui Zhang, Chang Liu, Kai Yuan, Xumin Ni, Yuwen Pan and Shuhua Xu

Functional glyco-metagenomics elucidates the role of glycan-related genes in environments

Glycan-related genes play a fundamental role in various processes for energy acquisition and homeostasis maintenance while adapting to the environment in which the organism exists; however, their role in the m...

Authors: Hayato Takihara, Nobuaki Miura, Kiyoko F. Aoki-Kinoshita and Shujiro Okuda

RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix

The functions of RNA molecules are mainly determined by their secondary structures. These functions can also be predicted using bioinformatic tools that enable the alignment of multiple RNAs to determine funct...

Authors: Tomasz Woźniak, Małgorzata Sajek, Jadwiga Jaruzelska and Marcin Piotr Sajek

Identifying piRNA targets on mRNAs in C. elegans using a deep multi-head attention network

Piwi-interacting RNAs (piRNAs) are the small non-coding RNAs (ncRNAs) that silence genomic transposable elements. And researchers found out that piRNA also regulates various endogenous transcripts. However, th...

Authors: Tzu-Hsien Yang, Sheng-Cian Shiue, Kuan-Yu Chen, Yan-Yuan Tseng and Wei-Sheng Wu

Reference-agnostic representation and visualization of pan-genomes

The pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species.

Authors: Qihua Liang and Stefano Lonardi

ClineHelpR: an R package for genomic cline outlier detection and visualization

Patterns of multi-locus differentiation (i.e., genomic clines) often extend broadly across hybrid zones and their quantification can help diagnose how species boundaries are shaped by adaptive processes, both ...

Authors: Bradley T. Martin, Tyler K. Chafin, Marlis R. Douglas and Michael E. Douglas

Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes

Identifying human protein-phenotype relationships has attracted researchers in bioinformatics and biomedical natural language processing due to its importance in uncovering rare and complex diseases. Since exp...

Authors: Morteza Pourreza Shahri and Indika Kahanda

Annotation depth confounds direct comparison of gene expression across species

Comparisons of the molecular framework among organisms can be done on both structural and functional levels. One of the most common top-down approaches for functional comparisons is RNA sequencing. This estima...

Authors: Elias Oziolor, Seda Arat and Matthew Martin

Tailored graphical lasso for data integration in gene network reconstruction

Identifying gene interactions is a topic of great importance in genomics, and approaches based on network models provide a powerful tool for studying these. Assuming a Gaussian graphical model, a gene associat...

Authors: Camilla Lingjærde, Tonje G. Lien, Ørnulf Borgan, Helga Bergholtz and Ingrid K. Glad

Quantitative prediction model for affinity of drug–target interactions based on molecular vibrations and overall system of ligand-receptor

The study of drug–target interactions (DTIs) affinity plays an important role in safety assessment and pharmacology. Currently, quantitative structure–activity relationship (QSAR) and molecular docking (MD) ar...

Authors: Xian-rui Wang, Ting-ting Cao, Cong Min Jia, Xue-mei Tian and Yun Wang

Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data

Circular RNA (circRNA) is an emerging class of RNA molecules attracting researchers due to its potential for serving as markers for diagnosis, prognosis, or therapeutic targets of cancer, cardiovascular, and a...

Authors: Dat Thanh Nguyen, Quang Thinh Trac, Thi-Hau Nguyen, Ha-Nam Nguyen, Nir Ohad, Yudi Pawitan and Trung Nghia Vu

CirPred, the first structure modeling and linker design system for circularly permuted proteins

This work aims to help develop new protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein follo...

Authors: Teng-Ruei Chen, Yen-Cheng Lin, Yu-Wei Huang, Chih-Chieh Chen and Wei-Cheng Lo

Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities

Taxonomic classification of genetic markers for microbiome analysis is affected by the numerous choices made from sample preparation to bioinformatics analysis. Paired-end read merging is routinely used to cap...

Authors: Daniel P. Dacey and Frédéric J. J. Chain

Identification of prostate cancer specific methylation biomarkers from a multi-cancer analysis

Detecting prostate cancer at a non-aggressive stage is the main goal of prostate cancer screening. DNA methylation has been widely used as biomarkers for cancer diagnosis and prognosis, however, with low clini...

Authors: Yiyi Pu, Chao Li, Haining Yuan and Xiaoju Wang

FoldHSphere: deep hyperspherical embeddings for protein fold recognition

Current state-of-the-art deep learning approaches for protein fold recognition learn protein embeddings that improve prediction performance at the fold level. However, there still exists aperformance gap at th...

Authors: Amelia Villegas-Morcillo, Victoria Sanchez and Angel M. Gomez

CoolBox: a flexible toolkit for visual analysis of genomics data

Data visualization, especially the genome track plots, is crucial for genomics researchers to discover patterns in large-scale sequencing dataset. Although existing tools works well for producing a normal view...

Authors: Weize Xu, Quan Zhong, Da Lin, Ya Zuo, Jinxia Dai, Guoliang Li and Gang Cao

Comparison of sequencing data processing pipelines and application to underrepresented African human populations

Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools an...

Authors: Gwenna Breton, Anna C. V. Johansson, Per Sjödin, Carina M. Schlebusch and Mattias Jakobsson

Fast parallel construction of variable-length Markov chains

Alignment-free methods are a popular approach for comparing biological sequences, including complete genomes. The methods range from probability distributions of sequence composition to first and higher-order ...

Authors: Joel Gustafsson, Peter Norberg, Jan R. Qvick-Wester and Alexander Schliep

CorDiffViz: an R package for visualizing multi-omics differential correlation networks

Differential correlation networks are increasingly used to delineate changes in interactions among biomolecules. They characterize differences between omics networks under two different conditions, and can be ...

Authors: Shiqing Yu, Mathias Drton, Daniel E. L. Promislow and Ali Shojaie

Protein–protein interaction prediction based on ordinal regression and recurrent convolutional neural networks

Protein protein interactions (PPIs) are essential to most of the biological processes. The prediction of PPIs is beneficial to the understanding of protein functions and thus is helpful to pathological analysi...

Authors: Weixia Xu, Yangyun Gao, Yang Wang and Jihong Guan

Wavelet Screening: a novel approach to analyzing GWAS data

Traditional methods for single-variant genome-wide association study (GWAS) incur a substantial multiple-testing burden because of the need to test for associations with a vast number of single-nucleotide poly...

Authors: William R. P. Denault, Håkon K. Gjessing, Julius Juodakis, Bo Jacobsson and Astanand Jugessur

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

Identification, visualization, statistical analysis and mathematical modeling of high-feedback loops in gene regulatory networks

Feedback loops in gene regulatory networks play pivotal roles in governing functional dynamics of cells. Systems approaches demonstrated characteristic dynamical features, including multistability and oscillat...

Authors: Benjamin Nordick and Tian Hong

Spatial rank-based multifactor dimensionality reduction to detect gene–gene interactions for multivariate phenotypes

Identifying interaction effects between genes is one of the main tasks of genome-wide association studies aiming to shed light on the biological mechanisms underlying complex diseases. Multifactor dimensionali...

Authors: Mira Park, Hoe-Bin Jeong, Jong-Hyun Lee and Taesung Park

LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA–protein interaction identification

Long noncoding RNAs (lncRNAs) play important roles in various biological and pathological processes. Discovery of lncRNA–protein interactions (LPIs) contributes to understand the biological functions and mecha...

Authors: Liqian Zhou, Zhao Wang, Xiongfei Tian and Lihong Peng

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

On the robustness of generalization of drug–drug interaction models

Deep learning methods are a proven commodity in many fields and endeavors. One of these endeavors is predicting the presence of adverse drug–drug interactions (DDIs). The models generated can predict, with rea...

Authors: Rogia Kpanou, Mazid Abiodoun Osseni, Prudencio Tossou, Francois Laviolette and Jacques Corbeil

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