Articles

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

DeepUbi: a deep learning framework for prediction of ubiquitination sites in proteins

Protein ubiquitination occurs when the ubiquitin protein binds to a target protein residue of lysine (K), and it is an important regulator of many cellular functions, such as signal transduction, cell division...

Authors: Hongli Fu, Yingxi Yang, Xiaobo Wang, Hui Wang and Yan Xu

Identifying cancer prognostic modules by module network analysis

The identification of prognostic genes that can distinguish the prognostic risks of cancer patients remains a significant challenge. Previous works have proven that functional gene sets were more reliable for ...

Authors: Xiong-Hui Zhou, Xin-Yi Chu, Gang Xue, Jiang-Hui Xiong and Hong-Yu Zhang

CirGO: an alternative circular way of visualising gene ontology terms

Prioritisation of gene ontology terms from differential gene expression analyses in a two-dimensional format remains a challenge with exponentially growing data volumes. Typically, gene ontology terms are repr...

Authors: Irina Kuznetsova, Artur Lugmayr, Stefan J. Siira, Oliver Rackham and Aleksandra Filipovska

Statistical assessment and visualization of synergies for large-scale sparse drug combination datasets

Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but requi...

Authors: Arnaud Amzallag, Sridhar Ramaswamy and Cyril H. Benes

Parameter estimation in models of biological oscillators: an automated regularised estimation approach

Dynamic modelling is a core element in the systems biology approach to understanding complex biosystems. Here, we consider the problem of parameter estimation in models of biological oscillators described by d...

Authors: Jake Alan Pitt and Julio R. Banga

Functional Heatmap: an automated and interactive pattern recognition tool to integrate time with multi-omics assays

Life science research is moving quickly towards large-scale experimental designs that are comprised of multiple tissues, time points, and samples. Omic time-series experiments offer answers to three big questi...

Authors: Joshua R. Williams, Ruoting Yang, John L. Clifford, Daniel Watson, Ross Campbell, Derese Getnet, Raina Kumar, Rasha Hammamieh and Marti Jett

Iterative unsupervised domain adaptation for generalized cell detection from brightfield z-stacks

Cell counting from cell cultures is required in multiple biological and biomedical research applications. Especially, accurate brightfield-based cell counting methods are needed for cell growth analysis. With ...

Authors: Kaisa Liimatainen, Lauri Kananen, Leena Latonen and Pekka Ruusuvuori

FunMappOne: a tool to hierarchically organize and visually navigate functional gene annotations in multiple experiments

Functional annotation of genes is an essential step in omics data analysis. Multiple databases and methods are currently available to summarize the functions of sets of genes into higher level representations,...

Authors: Giovanni Scala, Angela Serra, Veer Singh Marwah, Laura Aliisa Saarimäki and Dario Greco

BioVR: a platform for virtual reality assisted biological data integration and visualization

Functional characterization of single nucleotide variants (SNVs) involves two steps, the first step is to convert DNA to protein and the second step is to visualize protein sequences with their structures. As ...

Authors: Jimmy F. Zhang, Alex R. Paciorkowski, Paul A. Craig and Feng Cui

MultiDomainBenchmark: a multi-domain query and subject database suite

Genetic sequence database retrieval benchmarks play an essential role in evaluating the performance of sequence searching tools. To date, all phylogenetically diverse benchmarks known to the authors include on...

Authors: Hyrum D. Carroll, John L. Spouge and Mileidy Gonzalez

ADS-HCSpark: A scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark

The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical ...

Authors: Anghong Xiao, Zongze Wu and Shoubin Dong

WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations

With the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software ...

Authors: Yongzhi Yang, Ying Li, Qiao Chen, Yongshuai Sun and Zhiqiang Lu

Disease Pathway Cut for Multi-Target drugs

Biomarker discovery studies have been moving the focus from a single target gene to a set of target genes. However, the number of target genes in a drug should be minimum to avoid drug side-effect or toxicity....

Authors: Sunjoo Bang, Sangjoon Son, Sooyoung Kim and Hyunjung Shin

IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis

Reconstruction of protein-protein interaction networks (PPIN) has been riddled with controversy for decades. Particularly, false-negative and -positive interactions make this progress even more complicated. Al...

Authors: Minoo Ashtiani, Payman Nickchi, Soheil Jahangiri-Tazehkand, Abdollah Safari, Mehdi Mirzaie and Mohieddin Jafari

From POS tagging to dependency parsing for biomedical event extraction

Given the importance of relation or event extraction from biomedical research publications to support knowledge capture and synthesis, and the strong dependency of approaches to this information extraction tas...

Authors: Dat Quoc Nguyen and Karin Verspoor

Predicting protein functions by applying predicate logic to biomedical literature

A large number of computational methods have been proposed for predicting protein functions. The underlying techniques adopted by most of these methods revolve around predicting the functions of an unannotated...

Authors: Kamal Taha, Youssef Iraqi and Amira Al Aamri

Analyzing a co-occurrence gene-interaction network to identify disease-gene association

Understanding the genetic networks and their role in chronic diseases (e.g., cancer) is one of the important objectives of biological researchers. In this work, we present a text mining system that constructs ...

Authors: Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf and Dirar Homouz

Predicting clinically promising therapeutic hypotheses using tensor factorization

Determining which target to pursue is a challenging and error-prone first step in developing a therapeutic treatment for a disease, where missteps are potentially very costly given the long-time frames and hig...

Authors: Jin Yao, Mark R. Hurle, Matthew R. Nelson and Pankaj Agarwal

Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms

It is possible to predict whether a tuberculosis (TB) patient will fail to respond to specific antibiotics by sequencing the genome of the infecting Mycobacterium tuberculosis (Mtb) and observing whether the path...

Authors: Tra-My Ngo and Yik-Ying Teo

CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

Non-coding RNAs (ncRNAs) are emerging as key regulators and play critical roles in a wide range of tumorigenesis. Recent studies have suggested that long non-coding RNAs (lncRNAs) could interact with microRNAs...

Authors: Qiu Xiao, Jiawei Luo, Cheng Liang, Jie Cai, Guanghui Li and Buwen Cao

Shambhala: a platform-agnostic data harmonizer for gene expression data

Harmonization techniques make different gene expression profiles and their sets compatible and ready for comparisons. Here we present a new bioinformatic tool termed Shambhala for harmonization of multiple hum...

Authors: Nicolas Borisov, Irina Shabalina, Victor Tkachev, Maxim Sorokin, Andrew Garazha, Andrey Pulin, Ilya I. Eremin and Anton Buzdin

DeepPVP: phenotype-based prioritization of causative variants using deep learning

Prioritization of variants in personal genomic data is a major challenge. Recently, computational methods that rely on comparing phenotype similarity have shown to be useful to identify causative variants. In ...

Authors: Imane Boudellioua, Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos and Robert Hoehndorf

Estimation of duplication history under a stochastic model for tandem repeats

Tandem repeat sequences are common in the genomes of many organisms and are known to cause important phenomena such as gene silencing and rapid morphological changes. Due to the presence of multiple copies of ...

Authors: Farzad Farnoud, Moshe Schwartz and Jehoshua Bruck

CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features

We previously reported on CERENKOV, an approach for identifying regulatory single nucleotide polymorphisms (rSNPs) that is based on 246 annotation features. CERENKOV uses the xgboost classifier and is designed...

Authors: Yao Yao, Zheng Liu, Qi Wei and Stephen A. Ramsey

Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers

The main objectives of this study were sequencing, assembling, and annotation of chloroplast genome of one of the main Siberian boreal forest tree conifer species Siberian larch (Larix sibirica Ledeb.) and detect...

Authors: Eugeniya I. Bondar, Yuliya A. Putintseva, Nataliya V. Oreshkova and Konstantin V. Krutovsky

Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

De novo assembling of large genomes, such as in conifers (~ 12–30 Gbp), which also consist of ~ 80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assemb...

Authors: Dmitry A. Kuzmin, Sergey I. Feranchuk, Vadim V. Sharov, Alexander N. Cybin, Stepan V. Makolov, Yuliya A. Putintseva, Natalya V. Oreshkova and Konstantin V. Krutovsky

MIGREW: database on molecular identification of genes for resistance in wheat

Population structure of fungal infections in wheat differs between wheat varieties and environments. Taking into account evolution of host-pathogen interactions, genetic diversity of both wheat and fungus must...

Authors: Fedor V. Kazantsev, Ekaterina S. Skolotneva, Vasiliy N. Kelbin, Elena A. Salina and Sergey A. Lashin

Application of the geographic population structure (GPS) algorithm for biogeographical analyses of wild and captive gorillas

The utilization of high resolution genome data has important implications for the phylogeographical evaluation of non-human species. Biogeographical analyses can yield detailed understanding of their populatio...

Authors: Ranajit Das and Priyanka Upadhyai

A new version of the ANDSystem tool for automatic extraction of knowledge from scientific publications with expanded functionality for reconstruction of associative gene networks by considering tissue-specific gene expression

Consideration of tissue-specific gene expression in reconstruction and analysis of molecular genetic networks is necessary for a proper description of the processes occurring in a specified tissue. Currently, ...

Authors: Vladimir A. Ivanisenko, Pavel S. Demenkov, Timofey V. Ivanisenko, Elena L. Mishchenko and Olga V. Saik

Bioinformatics research at BGRS-2018

Authors: Tatiana V. Tatarinova, Ming Chen and Yuriy L. Orlov

Inverse similarity and reliable negative samples for drug side-effect prediction

In silico prediction of potential drug side-effects is of crucial importance for drug development, since wet experimental identification of drug side-effects is expensive and time-consuming. Existing computationa...

Authors: Yi Zheng, Hui Peng, Shameek Ghosh, Chaowang Lan and Jinyan Li

Functional homogeneity and specificity of topological modules in human proteome

Functional modules in protein-protein interaction networks (PPIN) are defined by maximal sets of functionally associated proteins and are vital to understanding cellular mechanisms and identifying disease asso...

Authors: Rama Kaalia and Jagath C. Rajapakse

Identification and analysis of structurally critical fragments in HopS2

Among the diverse roles of the Type III secretion-system (T3SS), one of the notable functions is that it serves as unique nano machineries in gram-negative bacteria that facilitate the translocation of effecto...

Authors: Sapna M. Borah and Anupam Nath Jha

Computational discovery and annotation of conserved small open reading frames in fungal genomes

Small open reading frames (smORF/sORFs) that encode short protein sequences are often overlooked during the standard gene prediction process thus leading to many sORFs being left undiscovered and/or misannotat...

Authors: Shuhaila Mat-Sharani and Mohd Firdaus-Raih

GCAC: galaxy workflow system for predictive model building for virtual screening

Traditional drug discovery approaches are time-consuming, tedious and expensive. Identifying a potential drug-like molecule using high throughput screening (HTS) with high confidence is always a challenging ta...

Authors: Deepak R. Bharti, Anmol J. Hemrom and Andrew M. Lynn

Understanding the evolutionary trend of intrinsically structural disorders in cancer relevant proteins as probed by Shannon entropy scoring and structure network analysis

Malignant diseases have become a threat for health care system. A panoply of biological processes is involved as the cause of these diseases. In order to unveil the mechanistic details of these diseased states...

Authors: Sagnik Sen, Ashmita Dey, Sourav Chowdhury, Ujjwal Maulik and Krishnananda Chattopadhyay

Automated craniofacial landmarks detection on 3D image using geometry characteristics information

Indirect anthropometry (IA) is one of the craniofacial anthropometry methods to perform the measurements on the digital facial images. In order to get the linear measurements, a few definable points on the str...

Authors: Arpah Abu, Chee Guan Ngo, Nur Idayu Adira Abu-Hassan and Siti Adibah Othman

GlyStruct: glycation prediction using structural properties of amino acid residues

Glycation is a one of the post-translational modifications (PTM) where sugar molecules and residues in protein sequences are covalently bonded. It has become one of the clinically important PTM in recent times...

Authors: Hamendra Manhar Reddy, Alok Sharma, Abdollah Dehzangi, Daichi Shigemizu, Abel Avitesh Chandra and Tatushiko Tsunoda

Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum

In the current scenario, designing of world-wide effective malaria vaccine against Plasmodium falciparum remain challenging despite the significant progress has been made in last few decades. Conventional vaccino...

Authors: Manisha Pritam, Garima Singh, Suchit Swaroop, Akhilesh Kumar Singh and Satarudra Prakash Singh

Benchmarking of different molecular docking methods for protein-peptide docking

Molecular docking studies on protein-peptide interactions are a challenging and time-consuming task because peptides are generally more flexible than proteins and tend to adopt numerous conformations. There ar...

Authors: Piyush Agrawal, Harinder Singh, Hemant Kumar Srivastava, Sandeep Singh, Gaurav Kishore and Gajendra P. S. Raghava

Development of electronic medical records for clinical and research purposes: the breast cancer module using an implementation framework in a middle income country- Malaysia

Advances in medical domain has led to an increase of clinical data production which offers enhancement opportunities for clinical research sector. In this paper, we propose to expand the scope of Electronic Me...

Authors: Nurul Aqilah Mohd Nor, Nur Aishah Taib, Marniza Saad, Hana Salwani Zaini, Zahir Ahmad, Yamin Ahmad and Sarinder Kaur Dhillon

Drug candidate identification based on gene expression of treated cells using tensor decomposition-based unsupervised feature extraction for large-scale data

Although in silico drug discovery is necessary for drug development, two major strategies, a structure-based and ligand-based approach, have not been completely successful. Currently, the third approach, infer...

Authors: Y-h. Taguchi

EpiMethEx: a tool for large-scale integrated analysis in methylation hotspots linked to genetic regulation

DNA methylation is an epigenetic mechanism of genomic regulation involved in the maintenance of homeostatic balance. Dysregulation of DNA methylation status is one of the driver alterations occurring in neopla...

Authors: Saverio Candido, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi, Giulia Russo, Giuseppe Sgroi, Valentina Di Salvatore, Massimo Libra and Francesco Pappalardo

Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites

Glutarylation, the addition of a glutaryl group (five carbons) to a lysine residue of a protein molecule, is an important post-translational modification and plays a regulatory role in a variety of physiologic...

Authors: Kai-Yao Huang, Hui-Ju Kao, Justin Bo-Kai Hsu, Shun-Long Weng and Tzong-Yi Lee

Discovering MoRFs by trisecting intrinsically disordered protein sequence into terminals and middle regions

Molecular Recognition Features (MoRFs) are short protein regions present in intrinsically disordered protein (IDPs) sequences. MoRFs interact with structured partner protein and upon interaction, they undergo ...

Authors: Ronesh Sharma, Alok Sharma, Ashwini Patil and Tatsuhiko Tsunoda

BioReader: a text mining tool for performing classification of biomedical literature

Scientific data and research results are being published at an unprecedented rate. Many database curators and researchers utilize data and information from the primary literature to populate databases, form hy...

Authors: Christian Simon, Kristian Davidsen, Christina Hansen, Emily Seymour, Mike Bogetofte Barnkob and Lars Rønn Olsen