Articles

Game theoretic centrality: a novel approach to prioritize disease candidate genes by combining biological networks with the Shapley value

Complex human health conditions with etiological heterogeneity like Autism Spectrum Disorder (ASD) often pose a challenge for traditional genome-wide association study approaches in defining a clear genotype t...

Authors: Min Woo Sun, Stefano Moretti, Kelley M. Paskov, Nate T. Stockham, Maya Varma, Brianna S. Chrisman, Peter Y. Washington, Jae-Yoon Jung and Dennis P. Wall

NPF:network propagation for protein function prediction

The accurate annotation of protein functions is of great significance in elucidating the phenomena of life, treating disease and developing new medicines. Various methods have been developed to facilitate the ...

Authors: Bihai Zhao, Zhihong Zhang, Meiping Jiang, Sai Hu, Yingchun Luo and Lei Wang

ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

While technological advances have made it possible to profile the immune system at high resolution, translating high-throughput data into knowledge of immune mechanisms has been challenged by the complexity of...

Authors: Michelle B. Atallah, Varun Tandon, Kamir J. Hiam, Hunter Boyce, Michelle Hori, Waleed Atallah, Matthew H. Spitzer, Edgar Engleman and Parag Mallick

SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing...

Authors: Stevenn Volant, Pierre Lechat, Perrine Woringer, Laurence Motreff, Pascal Campagne, Christophe Malabat, Sean Kennedy and Amine Ghozlane

Lag penalized weighted correlation for time series clustering

The similarity or distance measure used for clustering can generate intuitive and interpretable clusters when it is tailored to the unique characteristics of the data. In time series datasets generated with hi...

Authors: Thevaa Chandereng and Anthony Gitter

GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis

Nanopore sequencing enables portable, real-time sequencing applications, including point-of-care diagnostics and in-the-field genotyping. Achieving these outcomes requires efficient bioinformatic algorithms fo...

Authors: Hasindu Gamaarachchi, Chun Wai Lam, Gihan Jayatilaka, Hiruna Samarakoon, Jared T. Simpson, Martin A. Smith and Sri Parameswaran

scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data

Recent advances in single-cell RNA sequencing (scRNA-seq) technology have enabled the identification of individual cell types, such as epithelial cells, immune cells, and fibroblasts, in tissue samples contain...

Authors: Ji-Hye Choi, Hye In Kim and Hyun Goo Woo

smsMap: mapping single molecule sequencing reads by locating the alignment starting positions

Single Molecule Sequencing (SMS) technology can produce longer reads with higher sequencing error rate. Mapping these reads to a reference genome is often the most fundamental and computing-intensive step for ...

Authors: Ze-Gang Wei, Shao-Wu Zhang and Fei Liu

RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data

Ribosome profiling has been widely used for studies of translation under a large variety of cellular and physiological contexts. Many of these studies have greatly benefitted from a series of data-mining tools...

Authors: Fajin Li, Xudong Xing, Zhengtao Xiao, Gang Xu and Xuerui Yang

IDSSIM: an lncRNA functional similarity calculation model based on an improved disease semantic similarity method

It has been widely accepted that long non-coding RNAs (lncRNAs) play important roles in the development and progression of human diseases. Many association prediction models have been proposed for predicting l...

Authors: Wenwen Fan, Junliang Shang, Feng Li, Yan Sun, Shasha Yuan and Jin-Xing Liu

MutEnricher: a flexible toolset for somatic mutation enrichment analysis of tumor whole genomes

Analysis of somatic mutations from tumor whole exomes has fueled discovery of novel cancer driver genes. However, ~ 98% of the genome is non-coding and includes regulatory elements whose normal cellular functi...

Authors: Anthony R. Soltis, Clifton L. Dalgard, Harvey B. Pollard and Matthew D. Wilkerson

AdmixPipe: population analyses in Admixture for non-model organisms

Research on the molecular ecology of non-model organisms, while previously constrained, has now been greatly facilitated by the advent of reduced-representation sequencing protocols. However, tools that allow ...

Authors: Steven M. Mussmann, Marlis R. Douglas, Tyler K. Chafin and Michael E. Douglas

A topological data analysis based classification method for multiple measurements

Machine learning models for repeated measurements are limited. Using topological data analysis (TDA), we present a classifier for repeated measurements which samples from the data space and builds a network gr...

Authors: Henri Riihimäki, Wojciech Chachólski, Jakob Theorell, Jan Hillert and Ryan Ramanujam

Statistical shape analysis of tap roots: a methodological case study on laser scanned sugar beets

The efficient and robust statistical analysis of the shape of plant organs of different cultivars is an important investigation issue in plant breeding and enables a robust cultivar description within the bree...

Authors: Behrend Heeren, Stefan Paulus, Heiner Goldbach, Heiner Kuhlmann, Anne-Katrin Mahlein, Martin Rumpf and Benedikt Wirth

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assemble...

Authors: Yi Yue, Hao Huang, Zhao Qi, Hui-Min Dou, Xin-Yi Liu, Tian-Fei Han, Yue Chen, Xiang-Jun Song, You-Hua Zhang and Jian Tu

Construction and optimization of gene expression signatures for prediction of survival in two-arm clinical trials

Gene expression signatures for the prediction of differential survival of patients undergoing anti-cancer therapies are of great interest because they can be used to prospectively stratify patients entering ne...

Authors: Joachim Theilhaber, Marielle Chiron, Jennifer Dreymann, Donald Bergstrom and Jack Pollard

METROID: an automated method for robust quantification of subcellular fluorescence events at low SNR

In cell biology, increasing focus has been directed to fast events at subcellular space with the advent of fluorescent probes. As an example, voltage sensitive dyes (VSD) have been used to measure membrane pot...

Authors: Marcelo Zoccoler and Pedro X. de Oliveira

SPAligner: alignment of long diverged molecular sequences to assembly graphs

Graph-based representation of genome assemblies has been recently used in different contexts — from improved reconstruction of plasmid sequences and refined analysis of metagenomic data to read error correctio...

Authors: Tatiana Dvorkina, Dmitry Antipov, Anton Korobeynikov and Sergey Nurk

Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer

Horizontal gene transfer, i.e. the acquisition of genetic material from nonparent organism, is considered an important force driving species evolution. Many cases of horizontal gene transfer from prokaryotes t...

Authors: Maria A. Daugavet, Sergey V. Shabelnikov and Olga I. Podgornaya

imputeqc: an R package for assessing imputation quality of genotypes and optimizing imputation parameters

The imputation of genotypes increases the power of genome-wide association studies. However, the imputation quality should be assessed in each particular case. Nevertheless, not all imputation softwares contro...

Authors: Gennady V. Khvorykh and Andrey V. Khrunin

CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities

Illumina paired-end reads are often used for 16S analysis in metagenomic studies. Since DNA fragment size is usually smaller than the sum of lengths of paired reads, reads can be merged for downstream analysis...

Authors: Yulia Kondratenko, Anton Korobeynikov and Alla Lapidus

Extending rnaSPAdes functionality for hybrid transcriptome assembly

De novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impos...

Authors: Andrey D. Prjibelski, Giuseppe D. Puglia, Dmitry Antipov, Elena Bushmanova, Daniela Giordano, Alla Mikheenko, Domenico Vitale and Alla Lapidus

SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles

A number of simulators have been developed for emulating next-generation sequencing data by incorporating known errors such as base substitutions and indels. However, their practicality may be degraded by func...

Authors: Zhenhua Yu, Fang Du, Rongjun Ban and Yuanwei Zhang

Drug-target interactions prediction using marginalized denoising model on heterogeneous networks

Drugs achieve pharmacological functions by acting on target proteins. Identifying interactions between drugs and target proteins is an essential task in old drug repositioning and new drug discovery. To recomm...

Authors: Chunyan Tang, Cheng Zhong, Danyang Chen and Jianyi Wang

An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma

Melanoma phenotype and the dynamics underlying its progression are determined by a complex interplay between different types of regulatory molecules. In particular, transcription factors (TFs), microRNAs (miRN...

Authors: Nivedita Singh, Martin Eberhardt, Olaf Wolkenhauer, Julio Vera and Shailendra K. Gupta

A performant bridge between fixed-size and variable-size seeding

Seeding is usually the initial step of high-throughput sequence aligners. Two popular seeding strategies are fixed-size seeding (k-mers, minimizers) and variable-size seeding (MEMs, SMEMs, maximal spanning seeds)...

Authors: Arne Kutzner, Pok-Son Kim and Markus Schmidt

BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint

Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such a challenge at the whole...

Authors: Vincent Henry, Fatiha Saïs, Olivier Inizan, Elodie Marchadier, Juliette Dibie, Anne Goelzer and Vincent Fromion

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

Understanding the relation between the human microbiome and modulating factors, such as diet, may help researchers design intervention strategies that promote and maintain healthy microbial communities. Numero...

Authors: Matthew D. Koslovsky and Marina Vannucci

A robust nonlinear low-dimensional manifold for single cell RNA-seq data

Modern developments in single-cell sequencing technologies enable broad insights into cellular state. Single-cell RNA sequencing (scRNA-seq) can be used to explore cell types, states, and developmental traject...

Authors: Archit Verma and Barbara E. Engelhardt

Graph-based prediction of Protein-protein interactions with attributed signed graph embedding

Protein-protein interactions (PPIs) are central to many biological processes. Considering that the experimental methods for identifying PPIs are time-consuming and expensive, it is important to develop automat...

Authors: Fang Yang, Kunjie Fan, Dandan Song and Huakang Lin

Predicting DNA binding protein-drug interactions based on network similarity

The study of DNA binding protein (DBP)-drug interactions can open a breakthrough for the treatment of genetic diseases and cancers. Currently, network-based methods are widely used for protein-drug interaction...

Authors: Wei Wang, Hehe Lv and Yuan Zhao

Performance evaluation of lossy quality compression algorithms for RNA-seq data

Recent advancements in high-throughput sequencing technologies have generated an unprecedented amount of genomic data that must be stored, processed, and transmitted over the network for sharing. Lossy genomic...

Authors: Rongshan Yu, Wenxian Yang and Shun Wang

GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences

Bacterial gene loss and acquisition is a well-known phenomenon which contributes to bacterial adaptation through changes in important phenotypes such as virulence, antibiotic resistance and metabolic capabilit...

Authors: Migle Gabrielaite and Rasmus L. Marvig

SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering

The three-dimensional (3D) structure of the genome plays a crucial role in gene expression regulation. Chromatin conformation capture technologies (Hi-C) have revealed that the genome is organized in a hierarc...

Authors: Kellen G. Cresswell, John C. Stansfield and Mikhail G. Dozmorov

LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks

Gene Regulatory Networks (GRNs) have been previously studied by using Boolean/multi-state logics. While the gene expression values are usually scaled into the range [0, 1], these GRN inference methods apply a ...

Authors: Seyed Amir Malekpour, Amir Reza Alizad-Rahvar and Mehdi Sadeghi

Enhancer prediction in the human genome by probabilistic modelling of the chromatin feature patterns

The binding sites of transcription factors (TFs) and the localisation of histone modifications in the human genome can be quantified by the chromatin immunoprecipitation assay coupled with next-generation sequ...

Authors: Maria Osmala and Harri Lähdesmäki

FluConvert and IniFlu: a suite of integrated software to identify novel signatures of emerging influenza viruses with increasing risk

The pandemic threat of influenza has attracted great attention worldwide. To assist public health decision-makers, new suites of tools are needed to rapidly process and combine viral information retrieved from...

Authors: Chin-Rur Yang, Chwan-Chuen King, Li-Yu Daisy Liu and Chia-Chi Ku

HEnRY: a DZIF LIMS tool for the collection and documentation of biomaterials in multicentre studies

Well-characterized biomaterials of high quality have great potential for acceleration and quality improvement in translational biomedical research. To improve accessibility of local sample collections, efforts...

Authors: Stephanie Heinen, Nick Schulze, Bernd Franke, Florian Klein, Clara Lehmann, Maria J. G. T. Vehreschild, Claas Gloistein, Melanie Stecher and Jörg Janne Vehreschild

Deep user identification model with multiple biometric data

Recognition is an essential function of human beings. Humans easily recognize a person using various inputs such as voice, face, or gesture. In this study, we mainly focus on DL model with multi-modality which...

Authors: Hyoung-Kyu Song, Ebrahim AlAlkeem, Jaewoong Yun, Tae-Ho Kim, Hyerin Yoo, Dasom Heo, Myungsu Chae and Chan Yeob Yeun

PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST

Recent advances in DNA sequencing technologies have enabled significant leaps in capacity to generate large volumes of DNA sequence data, which has spurred a rapid growth in the use of bioinformatics as a mean...

Authors: Cinque Soto, Jessica A. Finn, Jordan R. Willis, Samuel B. Day, Robert S. Sinkovits, Taylor Jones, Samuel Schmitz, Jens Meiler, Andre Branchizio and James E. Crowe Jr

Synthetic repurposing of drugs against hypertension: a datamining method based on association rules and a novel discrete algorithm

Drug repurposing aims to detect the new therapeutic benefits of the existing drugs and reduce the spent time and cost of the drug development projects. The synthetic repurposing of drugs may prove to be more u...

Authors: Yosef Masoudi-Sobhanzadeh and Ali Masoudi-Nejad

Incorporating representation learning and multihead attention to improve biomedical cross-sentence n-ary relation extraction

Most biomedical information extraction focuses on binary relations within single sentences. However, extracting n-ary relations that span multiple sentences is in huge demand. At present, in the cross-sentence...

Authors: Di Zhao, Jian Wang, Yijia Zhang, Xin Wang, Hongfei Lin and Zhihao Yang

AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids

Polyploid organisms such as wheat complicate even the simplest of procedures in molecular biology. Whilst knowledge of genomic sequences in crops is increasing rapidly, the scientific community is still a long...

Authors: Alexander Coulton and Keith J. Edwards

Evolutionary chemical binding similarity approach integrated with 3D-QSAR method for effective virtual screening

Despite continued efforts using chemical similarity methods in virtual screening, currently developed approaches suffer from time-consuming multistep procedures and low success rates. We recently developed a m...

Authors: Prasannavenkatesh Durai, Young-Joon Ko, Cheol-Ho Pan and Keunwan Park

PFBNet: a priori-fused boosting method for gene regulatory network inference

Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge...

Authors: Dandan Che, Shun Guo, Qingshan Jiang and Lifei Chen

Conditional permutation importance revisited

Random forest based variable importance measures have become popular tools for assessing the contributions of the predictor variables in a fitted random forest. In this article we reconsider a frequently used ...

Authors: Dries Debeer and Carolin Strobl

Keras R-CNN: library for cell detection in biological images using deep neural networks

A common yet still manual task in basic biology research, high-throughput drug screening and digital pathology is identifying the number, location, and type of individual cells in images. Object detection meth...

Authors: Jane Hung, Allen Goodman, Deepali Ravel, Stefanie C. P. Lopes, Gabriel W. Rangel, Odailton A. Nery, Benoit Malleret, Francois Nosten, Marcus V. G. Lacerda, Marcelo U. Ferreira, Laurent Rénia, Manoj T. Duraisingh, Fabio T. M. Costa, Matthias Marti and Anne E. Carpenter

Leveraging Bayesian networks and information theory to learn risk factors for breast cancer metastasis

Even though we have established a few risk factors for metastatic breast cancer (MBC) through epidemiologic studies, these risk factors have not proven to be effective in predicting an individual’s risk of develo...

Authors: Xia Jiang, Alan Wells, Adam Brufsky, Darshan Shetty, Kahmil Shajihan and Richard E. Neapolitan

Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data

Stable isotope tracing has become an invaluable tool for probing the metabolism of biological systems. However, data analysis and visualization from metabolic tracing studies often involve multiple software pa...

Authors: Avi Kumar, Jack Mitchener, Zachary A. King and Christian M. Metallo

Efficient implied alignment

Authors: Alex J. Washburn and Ward C. Wheeler