Articles

Modeling drug mechanism of action with large scale gene-expression profiles using GPAR, an artificial intelligence platform

Querying drug-induced gene expression profiles with machine learning method is an effective way for revealing drug mechanism of actions (MOAs), which is strongly supported by the growth of large scale and high...

Authors: Shengqiao Gao, Lu Han, Dan Luo, Gang Liu, Zhiyong Xiao, Guangcun Shan, Yongxiang Zhang and Wenxia Zhou

Drug-induced cell viability prediction from LINCS-L1000 through WRFEN-XGBoost algorithm

Predicting the drug response of the cancer diseases through the cellular perturbation signatures under the action of specific compounds is very important in personalized medicine. In the process of testing dru...

Authors: Jiaxing Lu, Ming Chen and Yufang Qin

mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessmen...

Authors: Bing Song, August E. Woerner and John Planz

MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes

High-throughput sequencing has increased the number of available microbial genomes recovered from isolates, single cells, and metagenomes. Accordingly, fast and comprehensive functional gene annotation pipelin...

Authors: Carlos A. Ruiz-Perez, Roth E. Conrad and Konstantinos T. Konstantinidis

PCirc: random forest-based plant circRNA identification software

Circular RNA (circRNA) is a novel type of RNA with a closed-loop structure. Increasing numbers of circRNAs are being identified in plants and animals, and recent studies have shown that circRNAs play an import...

Authors: Shuwei Yin, Xiao Tian, Jingjing Zhang, Peisen Sun and Guanglin Li

HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding

Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent hi...

Authors: Edwin A. Solares, Yuan Tao, Anthony D. Long and Brandon S. Gaut

DISTEVAL: a web server for evaluating predicted protein distances

Protein inter-residue contact and distance prediction are two key intermediate steps essential to accurate protein structure prediction. Distance prediction comes in two forms: real-valued distances and ‘binne...

Authors: Badri Adhikari, Bikash Shrestha, Matthew Bernardini, Jie Hou and Jamie Lea

MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanism

Accurate prediction of binding between class I human leukocyte antigen (HLA) and neoepitope is critical for target identification within personalized T-cell based immunotherapy. Many recent prediction tools de...

Authors: Yilin Ye, Jian Wang, Yunwan Xu, Yi Wang, Youdong Pan, Qi Song, Xing Liu and Ji Wan

MiBiOmics: an interactive web application for multi-omics data exploration and integration

Multi-omics experimental approaches are becoming common practice in biological and medical sciences underlining the need to design new integrative techniques and applications to enable the multi-scale characte...

Authors: Johanna Zoppi, Jean-François Guillaume, Michel Neunlist and Samuel Chaffron

SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model

Single-cell RNA sequencing (scRNA-seq) enables the possibility of many in-depth transcriptomic analyses at a single-cell resolution. It’s already widely used for exploring the dynamic development process of li...

Authors: Yan Zheng, Yuanke Zhong, Jialu Hu and Xuequn Shang

SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions

Statistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein–protein interaction (PPI) ...

Authors: Joaquim Aguirre-Plans, Alberto Meseguer, Ruben Molina-Fernandez, Manuel Alejandro Marín-López, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornes, Narcis Fernandez-Fuentes and Baldo Oliva

Examination of hydrogen cross-feeders using a colonic microbiota model

Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanog...

Authors: Nick W. Smith, Paul R. Shorten, Eric Altermann, Nicole C. Roy and Warren C. McNabb

recoup: flexible and versatile signal visualization from next generation sequencing

The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlyi...

Authors: Panagiotis Moulos

Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm

Protein–peptide interactions play a fundamental role in a wide variety of biological processes, such as cell signaling, regulatory networks, immune responses, and enzyme inhibition. Peptides are characterized ...

Authors: Pedro M. Martins, Lucianna H. Santos, Diego Mariano, Felippe C. Queiroz, Luana L. Bastos, Isabela de S. Gomes, Pedro H. C. Fischer, Rafael E. O. Rocha, Sabrina A. Silveira, Leonardo H. F. de Lima, Mariana T. Q. de Magalhães, Maria G. A. Oliveira and Raquel C. de Melo-Minardi

Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data

As the number of RNA-seq datasets that become available to explore transcriptome diversity increases, so does the need for easy-to-use comprehensive computational workflows. Many available tools facilitate ana...

Authors: Noel-Marie Plonski, Emily Johnson, Madeline Frederick, Heather Mercer, Gail Fraizer, Richard Meindl, Gemma Casadesus and Helen Piontkivska

Analysis of associations between emotions and activities of drug users and their addiction recovery tendencies from social media posts using structural equation modeling

Addiction to drugs and alcohol constitutes one of the significant factors underlying the decline in life expectancy in the US. Several context-specific reasons influence drug use and recovery. In particular em...

Authors: Deeptanshu Jha and Rahul Singh

Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy

Personalized cancer vaccines are emerging as one of the most promising approaches to immunotherapy of advanced cancers. However, only a small proportion of the neoepitopes generated by somatic DNA mutations in...

Authors: Elham Sherafat, Jordan Force and Ion I. Măndoiu

Evolution of drug resistance in HIV protease

Drug resistance is a critical problem limiting effective antiviral therapy for HIV/AIDS. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice...

Authors: Dhara Shah, Christopher Freas, Irene T. Weber and Robert W. Harrison

Multi-view feature selection for identifying gene markers: a diversified biological data driven approach

In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene ...

Authors: Sudipta Acharya, Laizhong Cui and Yi Pan

Convex hulls in hamming space enable efficient search for similarity and clustering of genomic sequences

In molecular epidemiology, comparison of intra-host viral variants among infected persons is frequently used for tracing transmissions in human population and detecting viral infection outbreaks. Application o...

Authors: David S. Campo and Yury Khudyakov

An automated protocol for modelling peptide substrates to proteases

Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promi...

Authors: Rodrigo Ochoa, Mikhail Magnitov, Roman A. Laskowski, Pilar Cossio and Janet M. Thornton

Dependency parsing of biomedical text with BERT

Syntactic analysis, or parsing, is a key task in natural language processing and a required component for many text mining approaches. In recent years, Universal Dependencies (UD) has emerged as the leading fo...

Authors: Jenna Kanerva, Filip Ginter and Sampo Pyysalo

C-Norm: a neural approach to few-shot entity normalization

Entity normalization is an important information extraction task which has gained renewed attention in the last decade, particularly in the biomedical and life science domains. In these domains, and more gener...

Authors: Arnaud Ferré, Louise Deléger, Robert Bossy, Pierre Zweigenbaum and Claire Nédellec

Correction to: MicroBVS: Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package

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

Authors: Matthew D. Koslovsky and Marina Vannucci

Compositional zero-inflated network estimation for microbiome data

The estimation of microbial networks can provide important insight into the ecological relationships among the organisms that comprise the microbiome. However, there are a number of critical statistical challe...

Authors: Min Jin Ha, Junghi Kim, Jessica Galloway-Peña, Kim-Anh Do and Christine B. Peterson

LDscaff: LD-based scaffolding of de novo genome assemblies

Genome assembly is fundamental for de novo genome analysis. Hybrid assembly, utilizing various sequencing technologies increases both contiguity and accuracy. While such approaches require extra costly sequencing...

Authors: Zicheng Zhao, Yingxiao Zhou, Shuai Wang, Xiuqing Zhang, Changfa Wang and Shuaicheng Li

Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine 2020

The International Association for Intelligent Biology and Medicine (IAIBM) is a nonprofit organization that promotes intelligent biology and medical science. It hosts an annual International Conference on Inte...

Authors: Yan Guo, Li Shen, Xinghua Shi, Kai Wang, Yulin Dai and Zhongming Zhao

The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data

In genomics, we often assume that continuous data, such as gene expression, follow a specific kind of distribution. However we rarely stop to question the validity of this assumption, or consider how broadly a...

Authors: Laurence de Torrenté, Samuel Zimmerman, Masako Suzuki, Maximilian Christopeit, John M. Greally and Jessica C. Mar

Genome-wide detection of short tandem repeat expansions by long-read sequencing

Short tandem repeat (STR), or “microsatellite”, is a tract of DNA in which a specific motif (typically < 10 base pairs) is repeated multiple times. STRs are abundant throughout the human genome, and specific r...

Authors: Qian Liu, Yao Tong and Kai Wang

Effect of APOE ε4 on multimodal brain connectomic traits: a persistent homology study

Although genetic risk factors and network-level neuroimaging abnormalities have shown effects on cognitive performance and brain atrophy in Alzheimer’s disease (AD), little is understood about how apolipoprote...

Authors: Jin Li, Chenyuan Bian, Dandan Chen, Xianglian Meng, Haoran Luo, Hong Liang and Li Shen

Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction

Cryo-EM data generated by electron tomography (ET) contains images for individual protein particles in different orientations and tilted angles. Individual cryo-EM particles can be aligned to reconstruct a 3D ...

Authors: Adil Al-Azzawi, Anes Ouadou, Ye Duan and Jianlin Cheng

Fingerprint restoration using cubic Bezier curve

Fingerprint biometrics play an essential role in authentication. It remains a challenge to match fingerprints with the minutiae or ridges missing. Many fingerprints failed to match their targets due to the inc...

Authors: Yanglin Tu, Zengwei Yao, Jiao Xu, Yilin Liu and Zhe Zhang

In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells

Cancer stem cells (CSCs) have features such as the ability to self-renew, differentiate into defined progenies and initiate the tumor growth. Treatments of cancer include drugs, chemotherapy and radiotherapy o...

Authors: Monalisa Mandal, Sanjeeb Kumar Sahoo, Priyadarsan Patra, Saurav Mallik and Zhongming Zhao

Deep learning detection of informative features in tau PET for Alzheimer’s disease classification

Alzheimer’s disease (AD) is the most common type of dementia, typically characterized by memory loss followed by progressive cognitive decline and functional impairment. Many clinical trials of potential thera...

Authors: Taeho Jo, Kwangsik Nho, Shannon L. Risacher and Andrew J. Saykin

Integrative approach for detecting membrane proteins

Membrane proteins are key gates that control various vital cellular functions. Membrane proteins are often detected using transmembrane topology prediction tools. While transmembrane topology prediction tools ...

Authors: Munira Alballa and Gregory Butler

ARPIR: automatic RNA-Seq pipelines with interactive report

RNA-Seq is an increasing used methodology to study either coding and non-coding RNA expression. There are many software tools available for each phase of the RNA-Seq analysis and each of them uses different al...

Authors: Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini and Maria Paola Martelli

Predicting substitutions to modulate disorder and stability in coiled-coils

Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disorder...

Authors: Yasaman Karami, Paul Saighi, Rémy Vanderhaegen, Denis Gerlier, Sonia Longhi, Elodie Laine and Alessandra Carbone

A2A: a platform for research in biomedical literature search

Finding relevant literature is crucial for many biomedical research activities and in the practice of evidence-based medicine. Search engines such as PubMed provide a means to search and retrieve published lit...

Authors: Maciej Rybinski, Sarvnaz Karimi, Vincent Nguyen and Cecile Paris

Inter-protein residue covariation information unravels physically interacting protein dimers

Predicting physical interaction between proteins is one of the greatest challenges in computational biology. There are considerable various protein interactions and a huge number of protein sequences and synth...

Authors: Sara Salmanian, Hamid Pezeshk and Mehdi Sadeghi

Inferring time-dependent population growth rates in cell cultures undergoing adaptation

The population growth rate is an important characteristic of any cell culture. During sustained experiments, the growth rate may vary due to competition or adaptation. For instance, in presence of a toxin or a...

Authors: H. Jonathan G. Lindström and Ran Friedman

Menoci: lightweight extensible web portal enhancing data management for biomedical research projects

Biomedical research projects deal with data management requirements from multiple sources like funding agencies’ guidelines, publisher policies, discipline best practices, and their own users’ needs. We descri...

Authors: M. Suhr, C. Lehmann, C. R. Bauer, T. Bender, C. Knopp, L. Freckmann, B. Öst Hansen, C. Henke, G. Aschenbrandt, L. K. Kühlborn, S. Rheinländer, L. Weber, B. Marzec, M. Hellkamp, P. Wieder, U. Sax…

Selected abstracts of “Bioinformatics: from Algorithms to Applications 2020” conference

Authors:

Graph embeddings on gene ontology annotations for protein–protein interaction prediction

Protein–protein interaction (PPI) prediction is an important task towards the understanding of many bioinformatics functions and applications, such as predicting protein functions, gene-disease associations an...

Authors: Xiaoshi Zhong and Jagath C. Rajapakse

DRACP: a novel method for identification of anticancer peptides

Millions of people are suffering from cancers, but accurate early diagnosis and effective treatment are still tough for all doctors. Common ways against cancer include surgical operation, radiotherapy and chem...

Authors: Tianyi Zhao, Yang Hu and Tianyi Zang

Filtering de novo indels in parent-offspring trios

Identification of de novo indels from whole genome or exome sequencing data of parent-offspring trios is a challenging task in human disease studies and clinical practices. Existing computational approaches us...

Authors: Yongzhuang Liu, Jian Liu and Yadong Wang

BioRel: towards large-scale biomedical relation extraction

Although biomedical publications and literature are growing rapidly, there still lacks structured knowledge that can be easily processed by computer programs. In order to extract such knowledge from plain text...

Authors: Rui Xing, Jie Luo and Tengwei Song

NDRindex: a method for the quality assessment of single-cell RNA-Seq preprocessing data

Single-cell RNA sequencing can be used to fairly determine cell types, which is beneficial to the medical field, especially the many recent studies on COVID-19. Generally, single-cell RNA data analysis pipelin...

Authors: Ruiyu Xiao, Guoshan Lu, Wanqian Guo and Shuilin Jin

Combining sequence and network information to enhance protein–protein interaction prediction

Protein–protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to th...

Authors: Leilei Liu, Xianglei Zhu, Yi Ma, Haiyin Piao, Yaodong Yang, Xiaotian Hao, Yue Fu, Li Wang and Jiajie Peng

Identifying diseases that cause psychological trauma and social avoidance by GCN-Xgboost

With the rapid development of medical treatment, many patients not only consider the survival time, but also care about the quality of life. Changes in physical, psychological and social functions after and du...

Authors: Huijuan Xu, Hairong Wang, Chenshan Yuan, Qinghua Zhai, Xufeng Tian, Lei Wu and Yuanyuan Mi

Predicting functions of maize proteins using graph convolutional network

Maize (Zea mays ssp. mays L.) is the most widely grown and yield crop in the world, as well as an important model organism for fundamental research of the function of genes. The functions of Maize proteins are an...

Authors: Guangjie Zhou, Jun Wang, Xiangliang Zhang, Maozu Guo and Guoxian Yu