Articles

Predicting enhancers in mammalian genomes using supervised hidden Markov models

Eukaryotic gene regulation is a complex process comprising the dynamic interaction of enhancers and promoters in order to activate gene expression. In recent years, research in regulatory genomics has contribu...

Authors: Tobias Zehnder, Philipp Benner and Martin Vingron

Linking entities through an ontology using word embeddings and syntactic re-ranking

Although there is an enormous number of textual resources in the biomedical domain, currently, manually curated resources cover only a small part of the existing knowledge. The vast majority of these informati...

Authors: İlknur Karadeniz and Arzucan Özgür

GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness

Biological knowledge, and therefore Gene Ontology annotation sets, for human genes is incomplete. Recent studies have reported that biases in available GO annotations result in biased estimates of functional s...

Authors: Meng Liu and Paul D. Thomas

UTAP: User-friendly Transcriptome Analysis Pipeline

RNA-Seq technology is routinely used to characterize the transcriptome, and to detect gene expression differences among cell types, genotypes and conditions. Advances in short-read sequencing instruments such ...

Authors: Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran and Dena Leshkowitz

A new massively parallel nanoball sequencing platform for whole exome research

Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well...

Authors: Yu Xu, Zhe Lin, Chong Tang, Yujing Tang, Yue Cai, Hongbin Zhong, Xuebin Wang, Wenwei Zhang, Chongjun Xu, Jingjing Wang, Jian Wang, Huanming Yang, Linfeng Yang and Qiang Gao

SSS-test: a novel test for detecting positive selection on RNA secondary structure

Long non-coding RNAs (lncRNAs) play an important role in regulating gene expression and are thus important for determining phenotypes. Most attempts to measure selection in lncRNAs have focused on the primary ...

Authors: Maria Beatriz Walter Costa, Christian Höner zu Siederdissen, Marko Dunjić, Peter F. Stadler and Katja Nowick

A likelihood ratio test for changes in homeolog expression bias

Gene duplications are a major source of raw material for evolution and a likely contributor to the diversity of life on earth. Duplicate genes (i.e., homeologs, in the case of a whole genome duplication) may r...

Authors: Ronald D. Smith, Taliesin J. Kinser, Gregory D. Conradi Smith and Joshua R. Puzey

FitTetra 2.0 – improved genotype calling for tetraploids with multiple population and parental data support

Genetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in ...

Authors: Konrad Zych, Gerrit Gort, Chris A. Maliepaard, Ritsert C. Jansen and Roeland E. Voorrips

GMASS: a novel measure for genome assembly structural similarity

Thanks to the recent advancements in next-generation sequencing (NGS) technologies, large amount of genomic data, which are short DNA sequences known as reads, has been accumulating. Diverse assemblers have be...

Authors: Daehong Kwon, Jongin Lee and Jaebum Kim

Replicability analysis in genome-wide association studies via Cartesian hidden Markov models

Replicability analysis which aims to detect replicated signals attracts more and more attentions in modern scientific applications. For example, in genome-wide association studies (GWAS), it would be of convin...

Authors: Pengfei Wang and Wensheng Zhu

MGSEA – a multivariate Gene set enrichment analysis

Gene Set Enrichment Analysis (GSEA) is a powerful tool to identify enriched functional categories of informative biomarkers. Canonical GSEA takes one-dimensional feature scores derived from the data of one pla...

Authors: Khong-Loon Tiong and Chen-Hsiang Yeang

Network meta-analysis correlates with analysis of merged independent transcriptome expression data

Using meta-analysis, high-dimensional transcriptome expression data from public repositories can be merged to make group comparisons that have not been considered in the original studies. Merging of high-dimen...

Authors: Christine Winter, Robin Kosch, Martin Ludlow, Albert D. M. E. Osterhaus and Klaus Jung

Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction

microRNAs (miRNAs) regulate gene expression at the post-transcriptional level and they play an important role in various biological processes in the human body. Therefore, identifying their regulation mechanis...

Authors: Vu VH Pham, Junpeng Zhang, Lin Liu, Buu Truong, Taosheng Xu, Trung T. Nguyen, Jiuyong Li and Thuc D. Le

FitEllipsoid: a fast supervised ellipsoid segmentation plugin

The segmentation of a 3D image is a task that can hardly be automatized in certain situations, notably when the contrast is low and/or the distance between elements is small. The existing supervised methods re...

Authors: Bastien Kovac, Jérôme Fehrenbach, Ludivine Guillaume and Pierre Weiss

DSab-origin: a novel IGHD sensitive VDJ mapping method and its application on antibody response after influenza vaccination

Functional antibody genes are often assembled by VDJ recombination and then diversified by somatic hypermutation. Identifying the combination of sourcing germline genes is critical to understand the process of...

Authors: Qingchen Zhang, Lu Zhang, Chen Zhou, Yiyan Yang, Zuojing Yin, Dingfeng Wu, Kailin Tang and Zhiwei Cao

Partition-based optimization model for generative anatomy modeling language (POM-GAML)

This paper presents a novel approach for Generative Anatomy Modeling Language (GAML). This approach automatically detects the geometric partitions in 3D anatomy that in turn speeds up integrated non-linear opt...

Authors: Doga Demirel, Berk Cetinsaya, Tansel Halic, Sinan Kockara and Shahryar Ahmadi

Evaluation of Sirtuin-3 probe quality and co-expressed genes using literature cohesion

Gene co-expression studies can provide important insights into molecular and cellular signaling pathways. The GeneNetwork database is a unique resource for co-expression analysis using data from a variety of t...

Authors: Sujoy Roy, Kazi I. Zaman, Robert W. Williams and Ramin Homayouni

Keanu: a novel visualization tool to explore biodiversity in metagenomes

One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing F...

Authors: Adam Thrash, Mark Arick II, Robyn A. Barbato, Robert M. Jones, Thomas A. Douglas, Julie Esdale, Edward J. Perkins and Natàlia Garcia-Reyero

Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics

Several methods to handle data generated from bottom-up proteomics via liquid chromatography-mass spectrometry, particularly for peptide-centric quantification dealing with post-translational modification (PTM...

Authors: Philip Berg, Evan W. McConnell, Leslie M. Hicks, Sorina C. Popescu and George V. Popescu

Similarities and differences between variants called with human reference genome HG19 or HG38

Reference genome selection is a prerequisite for successful analysis of next generation sequencing (NGS) data. Current practice employs one of the two most recent human reference genome versions: HG19 or HG38....

Authors: Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong and Huixiao Hong

Predicting protein residue-residue contacts using random forests and deep networks

The ability to predict which pairs of amino acid residues in a protein are in contact with each other offers many advantages for various areas of research that focus on proteins. For example, contact predictio...

Authors: Joseph Luttrell IV, Tong Liu, Chaoyang Zhang and Zheng Wang

Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions

Gene families are sets of structurally and evolutionarily related genes – in one or multiple species – that typically share a conserved biological function. As such, the identification and subsequent analyses ...

Authors: Norbert Bokros, Sorina C. Popescu and George V. Popescu

Genome-wide tracts of homozygosity and exome analyses reveal repetitive elements with Barrets esophagus/esophageal adenocarcinoma risk

Barrett’s esophagus (BE) is most commonly seen as the condition in which the normal squamous epithelium lining of the esophagus is replaced by goblet cells. Many studies show that BE is a predisposing factor f...

Authors: Visanu Wanchai, Jing Jin, Emine Bircan, Charis Eng and Mohammed Orloff

Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA

Adverse Drug Reactions (ADRs) are of great public health concern. FDA-approved drug labeling summarizes ADRs of a drug product mainly in three sections, i.e., Boxed Warning (BW), Warnings and Precautions (WP),...

Authors: Leihong Wu, Taylor Ingle, Zhichao Liu, Anna Zhao-Wong, Stephen Harris, Shraddha Thakkar, Guangxu Zhou, Junshuang Yang, Joshua Xu, Darshan Mehta, Weigong Ge, Weida Tong and Hong Fang

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations

The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments...

Authors: Aleksandra I. Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh and Jonathan D. Wren

Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference

Authors: Jonathan D. Wren, Robert J. Doerkson, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda and Shraddha Thakkar

Local edge-enhanced active contour for accurate skin lesion border detection

Dermoscopy is one of the common and effective imaging techniques in diagnosis of skin cancer, especially for pigmented lesions. Accurate skin lesion border detection is the key to extract important dermoscopic...

Authors: Mustafa Bayraktar, Sinan Kockara, Tansel Halic, Mutlu Mete, Henry K. Wong and Kamran Iqbal

SV-Pop: population-based structural variant analysis and visualization

Genetic structural variation underpins a multitude of phenotypes, with significant implications for a range of biological outcomes. Despite their crucial role, structural variants (SVs) are often neglected and...

Authors: Matt Ravenhall, Susana Campino and Taane G. Clark

PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome

A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. The ever-increasing genomic and proteomic data has greatly facilitated the vaccine des...

Authors: Kanwal Naz, Anam Naz, Shifa Tariq Ashraf, Muhammad Rizwan, Jamil Ahmad, Jan Baumbach and Amjad Ali

GRIBCG: a software for selection of sgRNAs in the design of balancer chromosomes

Balancer chromosomes are tools used by fruit fly geneticists to prevent meiotic recombination. Recently, CRISPR/Cas9 genome editing has been shown capable of generating inversions similar to the chromosomal re...

Authors: Brian B. Merritt and Lily S. Cheung

JOA: Joint Overlap Analysis of multiple genomic interval sets

Next-generation sequencing (NGS) technologies have produced large volumes of genomic data. One common operation on heterogeneous genomic data is genomic interval intersection. Most of the existing tools impose...

Authors: Burçak Otlu and Tolga Can

RhoTermPredict: an algorithm for predicting Rho-dependent transcription terminators based on Escherichia coli, Bacillus subtilis and Salmonella enterica databases

In bacterial genomes, there are two mechanisms to terminate the DNA transcription: the “intrinsic” or Rho-independent termination and the Rho-dependent termination. Intrinsic terminators are characterized by a...

Authors: Marco Di Salvo, Simone Puccio, Clelia Peano, Stephan Lacour and Pietro Alifano

Probabilistic ancestry maps: a method to assess and visualize population substructures in genetics

Principal component analysis (PCA) is a standard method to correct for population stratification in ancestry-specific genome-wide association studies (GWASs) and is used to cluster individuals by ancestry. Usi...

Authors: Héléna A. Gaspar and Gerome Breen

GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display

RNA-seq, wherein RNA transcripts expressed in a sample are sequenced and quantified, has become a widely used technique to study disease and development. With RNA-seq, transcription abundance can be measured, ...

Authors: Karl Stamm, Aoy Tomita-Mitchell and Serdar Bozdag

The influence of different types of translational inaccuracies on the genetic code structure

The standard genetic code is a recipe for assigning unambiguously 21 labels, i.e. amino acids and stop translation signal, to 64 codons. However, at early stages of the translational machinery development, the...

Authors: Paweł BłaŻej, Małgorzata Wnetrzak, Dorota Mackiewicz and Paweł Mackiewicz

svist4get: a simple visualization tool for genomic tracks from sequencing experiments

High-throughput sequencing often provides a foundation for experimental analyses in the life sciences. For many such methods, an intermediate layer of bioinformatics data analysis is the genomic signal track c...

Authors: Artyom A. Egorov, Ekaterina A. Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev and Ivan V. Kulakovskiy

Positive-unlabelled learning of glycosylation sites in the human proteome

As an important type of post-translational modification (PTM), protein glycosylation plays a crucial role in protein stability and protein function. The abundance and ubiquity of protein glycosylation across t...

Authors: Fuyi Li, Yang Zhang, Anthony W. Purcell, Geoffrey I. Webb, Kuo-Chen Chou, Trevor Lithgow, Chen Li and Jiangning Song

CellSim: a novel software to calculate cell similarity and identify their co-regulation networks

Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct repr...

Authors: Leijie Li, Dongxue Che, Xiaodan Wang, Peng Zhang, Siddiq Ur Rahman, Jianbang Zhao, Jiantao Yu, Shiheng Tao, Hui Lu and Mingzhi Liao

DEvis: an R package for aggregation and visualization of differential expression data

Existing tools for the aggregation and visualization of differential expression data have discrete functionality and require that end-users rely on multiple software packages with complex dependencies or manua...

Authors: Adam Price, Adrian Caciula, Cheng Guo, Bohyun Lee, Juliet Morrison, Angela Rasmussen, W. Ian Lipkin and Komal Jain

Predicting blood pressure from physiological index data using the SVR algorithm

Blood pressure diseases have increasingly been identified as among the main factors threatening human health. How to accurately and conveniently measure blood pressure is the key to the implementation of effec...

Authors: Bing Zhang, Huihui Ren, Guoyan Huang, Yongqiang Cheng and Changzhen Hu

‘apparent’: a simple and flexible R package for accurate SNP-based parentage analysis in the absence of guiding information

The accurate determination of parent-progeny relationships within both in situ natural populations and ex situ genetic resource collections can greatly enhance plant breeding/domestication efforts and support ...

Authors: Arthur T. O. Melo and Iago Hale

isma: an R package for the integrative analysis of mutations detected by multiple pipelines

Recent comparative studies have brought to our attention how somatic mutation detection from next-generation sequencing data is still an open issue in bioinformatics, because different pipelines result in a lo...

Authors: Noemi Di Nanni, Marco Moscatelli, Matteo Gnocchi, Luciano Milanesi and Ettore Mosca

MaGIC: a machine learning tool set and web application for monoallelic gene inference from chromatin

A large fraction of human and mouse autosomal genes are subject to random monoallelic expression (MAE), an epigenetic mechanism characterized by allele-specific gene expression that varies between clonal cell ...

Authors: Svetlana Vinogradova, Sachit D. Saksena, Henry N. Ward, Sébastien Vigneau and Alexander A. Gimelbrant

Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information

Group structures among genes encoded in functional relationships or biological pathways are valuable and unique features in large-scale molecular data for survival analysis. However, most of previous approache...

Authors: Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen and Nengjun Yi

Predicting protein-ligand binding residues with deep convolutional neural networks

Ligand-binding proteins play key roles in many biological processes. Identification of protein-ligand binding residues is important in understanding the biological functions of proteins. Existing computational...

Authors: Yifeng Cui, Qiwen Dong, Daocheng Hong and Xikun Wang

FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods

Accurate identification of perturbed signaling pathways based on differentially expressed genes between sample groups is one of the key factors in the understanding of diseases and druggable targets. Most path...

Authors: Fatemeh Mansoori, Maseud Rahgozar and Kaveh Kavousi

SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package

Next-Generation Sequencing (NGS) is now widely used in biomedical research for various applications. Processing of NGS data requires multiple programs and customization of the processing pipelines according to...

Authors: Taewoon Joo, Ji-Hye Choi, Ji-Hye Lee, So Eun Park, Youngsic Jeon, Sae Hoon Jung and Hyun Goo Woo

ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments

The investigation of intracellular metabolism is the mainstay in the biotechnology and physiology settings. Intracellular metabolic rates are commonly evaluated using labeling pattern of the identified metabol...

Authors: Di Du, Lin Tan, Yumeng Wang, Bo Peng, John N. Weinstein, Fredric E. Wondisford, Xiaoyang Su and Philip L. Lorenzi

SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data

High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) has become a routine tool for biodiversity survey and ecological studies. By including sample-specific tags in the primers prior PC...

Authors: Yoann Dufresne, Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawlowski and Tristan Cordier

Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information

Long non-coding RNAs play an important role in human complex diseases. Identification of lncRNA-disease associations will gain insight into disease-related lncRNAs and benefit disease diagnoses and treatment. ...

Authors: Xiao-Nan Fan, Shao-Wu Zhang, Song-Yao Zhang, Kunju Zhu and Songjian Lu