Articles

Segmentor: a tool for manual refinement of 3D microscopy annotations

Recent advances in tissue clearing techniques, combined with high-speed image acquisition through light sheet microscopy, enable rapid three-dimensional (3D) imaging of biological specimens, such as whole mous...

Authors: David Borland, Carolyn M. McCormick, Niyanta K. Patel, Oleh Krupa, Jessica T. Mory, Alvaro A. Beltran, Tala M. Farah, Carla F. Escobar-Tomlienovich, Sydney S. Olson, Minjeong Kim, Guorong Wu and Jason L. Stein

WEScover: selection between clinical whole exome sequencing and gene panel testing

Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for sev...

Authors: In-Hee Lee, Yufei Lin, William Jefferson Alvarez, Carles Hernandez-Ferrer, Kenneth D. Mandl and Sek Won Kong

digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes

The insertion sequence elements (IS elements) represent the smallest and the most abundant mobile elements in prokaryotic genomes. It has been shown that they play a significant role in genome organization and...

Authors: Janka Puterová and Tomáš Martínek

Accel-Align: a fast sequence mapper and aligner based on the seed–embed–extend method

Improvements in sequencing technology continue to drive sequencing cost towards $100 per genome. However, mapping sequenced data to a reference genome remains a computationally-intensive task due to the depend...

Authors: Yiqing Yan, Nimisha Chaturvedi and Raja Appuswamy

Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets

Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcodi...

Authors: T. M. Porter and M. Hajibabaei

Identifying cell types from single-cell data based on similarities and dissimilarities between cells

With the development of the technology of single-cell sequence, revealing homogeneity and heterogeneity between cells has become a new area of computational systems biology research. However, the clustering of...

Authors: Yuanyuan Li, Ping Luo, Yi Lu and Fang-Xiang Wu

Estimating colocalization probability from limited summary statistics

Colocalization is a statistical method used in genetics to determine whether the same variant is causal for multiple phenotypes, for example, complex traits and gene expression. It provides stronger mechanisti...

Authors: Emily A. King, Fengjiao Dunbar, Justin Wade Davis and Jacob F. Degner

An improved DNA-binding hot spot residues prediction method by exploring interfacial neighbor properties

DNA-binding hot spots are dominant and fundamental residues that contribute most of the binding free energy yet accounting for a small portion of protein–DNA interfaces. As experimental methods for identifying...

Authors: Sijia Zhang, Lihua Wang, Le Zhao, Menglu Li, Mengya Liu, Ke Li, Yannan Bin and Junfeng Xia

Learning curves for drug response prediction in cancer cell lines

Motivated by the size and availability of cell line drug sensitivity data, researchers have been developing machine learning (ML) models for predicting drug response to advance cancer treatment. As drug sensit...

Authors: Alexander Partin, Thomas Brettin, Yvonne A. Evrard, Yitan Zhu, Hyunseung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James H. Doroshow and Rick L. Stevens

Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes

RNA viruses possess remarkable evolutionary versatility driven by the high mutability of their genomes. Frameshifting nucleotide insertions or deletions (indels), which cause the premature termination of prote...

Authors: Dongbin Park and Yoonsoo Hahn

Identifying collateral and synthetic lethal vulnerabilities within the DNA-damage response

A pair of genes is defined as synthetically lethal if defects on both cause the death of the cell but a defect in only one of the two is compatible with cell viability. Ideally, if A and B are two synthetic le...

Authors: Pietro Pinoli, Sriganesh Srihari, Limsoon Wong and Stefano Ceri

SSBER: removing batch effect for single-cell RNA sequencing data

With the continuous maturity of sequencing technology, different laboratories or different sequencing platforms have generated a large amount of single-cell transcriptome sequencing data for the same or differ...

Authors: Yin Zhang and Fei Wang

A novel essential protein identification method based on PPI networks and gene expression data

Some proposed methods for identifying essential proteins have better results by using biological information. Gene expression data is generally used to identify essential proteins. However, gene expression dat...

Authors: Jiancheng Zhong, Chao Tang, Wei Peng, Minzhu Xie, Yusui Sun, Qiang Tang, Qiu Xiao and Jiahong Yang

IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome

Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SA...

Authors: Sanket Desai, Aishwarya Rane, Asim Joshi and Amit Dutt

Capsule-LPI: a LncRNA–protein interaction predicting tool based on a capsule network

Long noncoding RNAs (lncRNAs) play important roles in multiple biological processes. Identifying LncRNA–protein interactions (LPIs) is key to understanding lncRNA functions. Although some LPIs computational me...

Authors: Ying Li, Hang Sun, Shiyao Feng, Qi Zhang, Siyu Han and Wei Du

BoardION: real-time monitoring of Oxford Nanopore sequencing instruments

One of the main advantages of the Oxford Nanopore Technology (ONT) is the possibility of real-time sequencing. This gives access to information during the experiment and allows either to control the sequencing...

Authors: Aimeric Bruno, Jean-Marc Aury and Stefan Engelen

IIMLP: integrated information-entropy-based method for LncRNA prediction

The prediction of long non-coding RNA (lncRNA) has attracted great attention from researchers, as more and more evidence indicate that various complex human diseases are closely related to lncRNAs. In the era ...

Authors: Junyi Li, Huinian Li, Xiao Ye, Li Zhang, Qingzhe Xu, Yuan Ping, Xiaozhu Jing, Wei Jiang, Qing Liao, Bo Liu and Yadong Wang

CancerSiamese: one-shot learning for predicting primary and metastatic tumor types unseen during model training

The state-of-the-art deep learning based cancer type prediction can only predict cancer types whose samples are available during the training where the sample size is commonly large. In this paper, we consider...

Authors: Milad Mostavi, Yu-Chiao Chiu, Yidong Chen and Yufei Huang

PlncRNA-HDeep: plant long noncoding RNA prediction using hybrid deep learning based on two encoding styles

Long noncoding RNAs (lncRNAs) play an important role in regulating biological activities and their prediction is significant for exploring biological processes. Long short-term memory (LSTM) and convolutional ...

Authors: Jun Meng, Qiang Kang, Zheng Chang and Yushi Luan

DSCMF: prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization

In the development of science and technology, there are increasing evidences that there are some associations between lncRNAs and human diseases. Therefore, finding these associations between them will have a ...

Authors: Jin-Xing Liu, Ming-Ming Gao, Zhen Cui, Ying-Lian Gao and Feng Li

A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation

The temporal coordination of biological processes by the circadian clock is an important mechanism, and its disruption has negative health outcomes, including cancer. Experimental and theoretical evidence sugg...

Authors: Adrien Rougny, Loïc Paulevé, Michèle Teboul and Franck Delaunay

Combining genetic algorithm with machine learning strategies for designing potent antimicrobial peptides

Current methods in machine learning provide approaches for solving challenging, multiple constraint design problems. While deep learning and related neural networking methods have state-of-the-art performance,...

Authors: Kyle Boone, Cate Wisdom, Kyle Camarda, Paulette Spencer and Candan Tamerler

tRNA-derived fragments as novel potential biomarkers for relapsed/refractory multiple myeloma

tRNA-derived fragments have been reported to be key regulatory factors in human tumors. However, their roles in the progression of multiple myeloma remain unknown.

Authors: Cong Xu, Ting Liang, Fangrong Zhang, Jing Liu and Yunfeng Fu

Simultaneous learning of individual microRNA-gene interactions and regulatory comodules

MicroRNAs (miRNAs) function in post-transcriptional regulation of gene expression by binding to target messenger RNAs (mRNAs). Because of the key part that miRNAs play, understanding the correct regulatory rol...

Authors: Michael Roth, Pranjal Jain, Jinkyu Koo and Somali Chaterji

DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples

High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic refere...

Authors: Steffen Klasberg, Alexander H. Schmidt, Vinzenz Lange and Gerhard Schöfl

Censcyt: censored covariates in differential abundance analysis in cytometry

Innovations in single cell technologies have lead to a flurry of datasets and computational tools to process and interpret them, including analyses of cell composition changes and transition in cell states. The d...

Authors: Reto Gerber and Mark D. Robinson

MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics

Cis-regulatory elements (CREs) are DNA sequence segments that regulate gene expression. Among CREs are promoters, enhancers, Boundary Elements (BEs) and Polycomb Response Elements (PREs), all of which are enriche...

Authors: Bjørn André Bredesen and Marc Rehmsmeier

Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes

Genes implicated in tumorigenesis often exhibit diverse sets of genomic variants in the tumor cohorts within which they are frequently mutated. For many genes, neither the transcriptomic effects of these varia...

Authors: Michal R. Grzadkowski, Hannah D. Holly, Julia Somers and Emek Demir

Spectral phenotyping of embryonic development reveals integrative thermodynamic responses

Energy proxy traits (EPTs) are a novel approach to high dimensional organismal phenotyping that quantify the spectrum of energy levels within different temporal frequencies associated with mean pixel value flu...

Authors: Oliver Tills, John I. Spicer, Ziad Ibbini and Simon D. Rundle

DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information

Epitope prediction is a useful approach in cancer immunology and immunotherapy. Many computational methods, including machine learning and network analysis, have been developed quickly for such purposes. Howev...

Authors: Xiaoyun Yang, Liyuan Zhao, Fang Wei and Jing Li

A new method for exploring gene–gene and gene–environment interactions in GWAS with tree ensemble methods and SHAP values

The identification of gene–gene and gene–environment interactions in genome-wide association studies is challenging due to the unknown nature of the interactions and the overwhelmingly large number of possible...

Authors: Pål V. Johnsen, Signe Riemer-Sørensen, Andrew Thomas DeWan, Megan E. Cahill and Mette Langaas

The Coronavirus Network Explorer: mining a large-scale knowledge graph for effects of SARS-CoV-2 on host cell function

Leveraging previously identified viral interactions with human host proteins, we apply a machine learning-based approach to connect SARS-CoV-2 viral proteins to relevant host biological functions, diseases, an...

Authors: Andreas Krämer, Jean-Noël Billaud, Stuart Tugendreich, Dan Shiffman, Martin Jones and Jeff Green

Modern simulation utilities for genetic analysis

Statistical geneticists employ simulation to estimate the power of proposed studies, test new analysis tools, and evaluate properties of causal models. Although there are existing trait simulators, there is am...

Authors: Sarah S. Ji, Christopher A. German, Kenneth Lange, Janet S. Sinsheimer, Hua Zhou, Jin Zhou and Eric M. Sobel

Tamock: simulation of habitat-specific benchmark data in metagenomics

Simulated metagenomic reads are widely used to benchmark software and workflows for metagenome interpretation. The results of metagenomic benchmarks depend on the assumptions about their underlying ecosystems....

Authors: Samuel M. Gerner, Alexandra B. Graf and Thomas Rattei

JEDi: java essential dynamics inspector — a molecular trajectory analysis toolkit

Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straig...

Authors: Charles C. David, Chris S. Avery and Donald J. Jacobs

Root Digger: a root placement program for phylogenetic trees

In phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such a...

Authors: Ben Bettisworth and Alexandros Stamatakis

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

RNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with it. In practice, there are a large number of individual steps a researcher must perform ...

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

Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage

Brain image genetics provides enormous opportunities for examining the effects of genetic variations on the brain. Many studies have shown that the structure, function, and abnormality (e.g., those related to ...

Authors: Jin Li, Wenjie Liu, Huang Li, Feng Chen, Haoran Luo, Peihua Bao, Yanzhao Li, Hailong Jiang, Yue Gao, Hong Liang and Shiaofen Fang

Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars

Amyloid signaling motifs are a class of protein motifs which share basic structural and functional features despite the lack of clear sequence homology. They are hard to detect in large sequence databases eith...

Authors: Witold Dyrka, Marlena Gąsior-Głogowska, Monika Szefczyk and Natalia Szulc

Dynamic model updating (DMU) approach for statistical learning model building with missing data

Developing statistical and machine learning methods on studies with missing information is a ubiquitous challenge in real-world biological research. The strategy in literature relies on either removing the sam...

Authors: Rahi Jain and Wei Xu

GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments

Design of valid high-quality primers is essential for qPCR experiments. MRPrimer is a powerful pipeline based on MapReduce that combines both primer design for target sequences and homology tests on off-target...

Authors: Jeongmin Bae, Hajin Jeon and Min-Soo Kim

SMALF: miRNA-disease associations prediction based on stacked autoencoder and XGBoost

Identifying miRNA and disease associations helps us understand disease mechanisms of action from the molecular level. However, it is usually blind, time-consuming, and small-scale based on biological experimen...

Authors: Dayun Liu, Yibiao Huang, Wenjuan Nie, Jiaxuan Zhang and Lei Deng

Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Next-generation sequencing (NGS) represents a significant advancement in clinical genetics. However, its use creates several technical, data interpretation and management challenges. It is essential to follow ...

Authors: Maria Zanti, Kyriaki Michailidou, Maria A. Loizidou, Christina Machattou, Panagiota Pirpa, Kyproula Christodoulou, George M. Spyrou, Kyriacos Kyriacou and Andreas Hadjisavvas

The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma

lncRNA may be involved in the occurrence, metastasis, and chemical reaction of hepatocellular carcinoma (HCC) through various pathways associated with autophagy. Therefore, it is urgent to reveal more autophag...

Authors: Shiming Yang, Yaping Zhou, Xiangxin Zhang, Lu Wang, Jianfeng Fu, Xiaotong Zhao and Liu Yang

CarSite-II: an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniques

Carbonylation is a non-enzymatic irreversible protein post-translational modification, and refers to the side chain of amino acid residues being attacked by reactive oxygen species and finally converted into c...

Authors: Yun Zuo, Jianyuan Lin, Xiangxiang Zeng, Quan Zou and Xiangrong Liu

Selected papers from the 15th and 16th international conference on Computational Intelligence Methods for Bioinformatics and Biostatistics

Authors: Paolo Cazzaniga, Maria Raposo, Daniela Besozzi, Ivan Merelli, Antonino Staiano, Angelo Ciaramella, Riccardo Rizzo and Luca Manzoni

Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models

Genome-wide reconstructions of metabolism opened the way to thorough investigations of cell metabolism for health care and industrial purposes. However, the predictions offered by Flux Balance Analysis (FBA) c...

Authors: Marco S. Nobile, Vasco Coelho, Dario Pescini and Chiara Damiani

Evaluation of open search methods based on theoretical mass spectra comparison

Mass spectrometry remains the privileged method to characterize proteins. Nevertheless, most of the spectra generated by an experiment remain unidentified after their analysis, mostly because of the modificati...

Authors: Albane Lysiak, Guillaume Fertin, Géraldine Jean and Dominique Tessier

Tremor assessment using smartphone sensor data and fuzzy reasoning

Tremor severity assessment is an important step for the diagnosis and treatment decision-making of essential tremor (ET) patients. Traditionally, tremor severity is assessed by using questionnaires (e.g., ETRS...

Authors: Caro Fuchs, Marco S. Nobile, Guillaume Zamora, Aurélie Degeneffe, Pieter Kubben and Uzay Kaymak

Advantages of using graph databases to explore chromatin conformation capture experiments

High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of DNA interactions and 3D chromosome folding at the genome-wide scale. Usually, these data are represented as matrices descri...

Authors: Daniele D’Agostino, Pietro Liò, Marco Aldinucci and Ivan Merelli