Articles

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

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

SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles

The human leukocyte antigen (HLA) gene family plays a key role in the immune response and thus is crucial in many biomedical and clinical settings. Utilizing Sanger sequencing, the golden standard technology f...

Authors: Yong Zhang, Yongsheng Chen, Huixin Xu, Junbin Fang, Zijian Zhao, Weipeng Hu, Xiaoqin Yang, Jia Ye, Yun Cheng, Jiayin Wang, Weiqiang Sun, Jian Wang, Huanming Yang, Jing Yan and Lin Fang

SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

Spliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Neverthele...

Authors: Javier Calvelo, Hernán Juan, Héctor Musto, Uriel Koziol and Andrés Iriarte

Bioinformatics recipes: creating, executing and distributing reproducible data analysis workflows

Bioinformaticians collaborating with life scientists need software that allows them to involve their collaborators in the process of data analysis.

Authors: Natay Aberra, Aswathy Sebastian, Aaron P. Maloy, Christopher B. Rees, Meredith L. Bartron and Istvan Albert

Critique of the pairwise method for estimating qPCR amplification efficiency: beware of correlated data!

A recently proposed method for estimating qPCR amplification efficiency E analyzes fluorescence intensity ratios from pairs of points deemed to lie in the exponential growth region on the amplification curves for...

Authors: Joel Tellinghuisen

Visualizing metabolic network dynamics through time-series metabolomic data

New technologies have given rise to an abundance of -omics data, particularly metabolomic data. The scale of these data introduces new challenges for the interpretation and extraction of knowledge, requiring t...

Authors: Lea F. Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur E. Sigurjónsson, Óttar Rolfsson, Julian Heinrich and Andreas Dräger

iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots

The interaction between proteins and nucleic acids plays pivotal roles in various biological processes such as transcription, translation, and gene regulation. Hot spots are a small set of residues that contri...

Authors: Xiaolei Zhu, Ling Liu, Jingjing He, Ting Fang, Yi Xiong and Julie C. Mitchell

PDXGEM: patient-derived tumor xenograft-based gene expression model for predicting clinical response to anticancer therapy in cancer patients

Cancer is a highly heterogeneous disease with varying responses to anti-cancer drugs. Although several attempts have been made to predict the anti-cancer therapeutic responses, there remains a great need to de...

Authors: Youngchul Kim, Daewon Kim, Biwei Cao, Rodrigo Carvajal and Minjung Kim

HPG-DHunter: an ultrafast, friendly tool for DMR detection and visualization

Software tools for analyzing DNA methylation do not provide graphical results which can be easily identified, but huge text files containing the alignment of the samples and their methylation status at a resol...

Authors: Lisardo Fernández, Mariano Pérez, Ricardo Olanda, Juan M. Orduña and Joan Marquez-Molins

Diversity-guided Lamarckian random drift particle swarm optimization for flexible ligand docking

Protein-ligand docking has emerged as a particularly important tool in drug design and development, and flexible ligand docking is a widely used method for docking simulations. Many docking software packages c...

Authors: Chao Li, Jun Sun and Vasile Palade

Optical map guided genome assembly

The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thu...

Authors: Miika Leinonen and Leena Salmela

DUGMO: tool for the detection of unknown genetically modified organisms with high-throughput sequencing data for pure bacterial samples

The European Community has adopted very restrictive policies regarding the dissemination and use of genetically modified organisms (GMOs). In fact, a maximum threshold of 0.9% of contaminating GMOs is tolerate...

Authors: Julie Hurel, Sophie Schbath, Stéphanie Bougeard, Mathieu Rolland, Mauro Petrillo and Fabrice Touzain

Comparison of smartphone-based retinal imaging systems for diabetic retinopathy detection using deep learning

Diabetic retinopathy (DR), the most common cause of vision loss, is caused by damage to the small blood vessels in the retina. If untreated, it may result in varying degrees of vision loss and even blindness. ...

Authors: Mahmut Karakaya and Recep E. Hacisoftaoglu

Proceedings of the 2019 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

Authors: Jonathan D. Wren, Yongsheng Bai, Zhaohui S. Qin, Da Yan and Ramin Homayouni

Toward a more holistic method of genome assembly assessment

A key use of high throughput sequencing technology is the sequencing and assembly of full genome sequences. These genome assemblies are commonly assessed using statistics relating to contiguity of the assembly...

Authors: Adam Thrash, Federico Hoffmann and Andy Perkins

Drug-target interaction prediction using semi-bipartite graph model and deep learning

Identifying drug-target interaction is a key element in drug discovery. In silico prediction of drug-target interaction can speed up the process of identifying unknown interactions between drugs and target pro...

Authors: Hafez Eslami Manoochehri and Mehrdad Nourani

MMiRNA-Viewer², a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network

Although there are many studies on the characteristics of miRNA-mRNA interactions using miRNA and mRNA sequencing data, the complexity of the change of the correlation coefficients and expression values of the...

Authors: Yongsheng Bai, Steve Baker, Kevin Exoo, Xingqin Dai, Lizhong Ding, Naureen Aslam Khattak, Hongtao Li, Hannah Liu and Xiaoming Liu

MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials

Protein model quality assessment (QA) is an essential procedure in protein structure prediction. QA methods can predict the qualities of protein models and identify good models from decoys. Clustering-based me...

Authors: Tong Liu and Zheng Wang

Sparse reduced-rank regression for integrating omics data

The problem of assessing associations between multiple omics data including genomics and metabolomics data to identify biomarkers potentially predictive of complex diseases has garnered considerable research i...

Authors: Haileab Hilafu, Sandra E. Safo and Lillian Haine

DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring

During transcription, numerous transcription factors (TFs) bind to targets in a highly coordinated manner to control the gene expression. Alterations in groups of TF-binding profiles (i.e. “co-binding changes”...

Authors: Jing Zhang, Jason Liu, Donghoon Lee, Shaoke Lou, Zhanlin Chen, Gamze Gürsoy and Mark Gerstein

A cell-level quality control workflow for high-throughput image analysis

Image-based high throughput (HT) screening provides a rich source of information on dynamic cellular response to external perturbations. The large quantity of data generated necessitates computer-aided quality...

Authors: Minhua Qiu, Bin Zhou, Frederick Lo, Steven Cook, Jason Chyba, Doug Quackenbush, Jason Matzen, Zhizhong Li, Puiying Annie Mak, Kaisheng Chen and Yingyao Zhou

USMPep: universal sequence models for major histocompatibility complex binding affinity prediction

Immunotherapy is a promising route towards personalized cancer treatment. A key algorithmic challenge in this process is to decide if a given peptide (neoepitope) binds with the major histocompatibility comple...

Authors: Johanna Vielhaben, Markus Wenzel, Wojciech Samek and Nils Strodthoff

Prediction of heart disease and classifiers’ sensitivity analysis

Heart disease (HD) is one of the most common diseases nowadays, and an early diagnosis of such a disease is a crucial task for many health care providers to prevent their patients for such a disease and to sav...

Authors: Khaled Mohamad Almustafa

Accounting for grouped predictor variables or pathways in high-dimensional penalized Cox regression models

The standard lasso penalty and its extensions are commonly used to develop a regularized regression model while selecting candidate predictor variables on a time-to-event outcome in high-dimensional data. Howe...

Authors: Shaima Belhechmi, Riccardo De Bin, Federico Rotolo and Stefan Michiels