A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks
Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among t... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 29, 2020 Category: Bioinformatics Authors: Elisabetta Sauta, Andrea Demartini, Francesca Vitali, Alberto Riva and Riccardo Bellazzi Tags: Methodology article Source Type: research

Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads
The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly incre... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 29, 2020 Category: Bioinformatics Authors: William S. Pearman, Nikki E. Freed and Olin K. Silander Tags: Research article Source Type: research

BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data
The use of RNA-sequencing (RNA-seq) in molecular biology research and clinical settings has increased significantly over the past decade. Despite its widespread adoption, there is a lack of simple and interact... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 29, 2020 Category: Bioinformatics Authors: Pirunthan Perampalam and Frederick A. Dick Tags: Software Source Type: research

Extracting chemical reactions from text using Snorkel
Enzymatic and chemical reactions are key for understanding biological processes in cells. Curated databases of chemical reactions exist but these databases struggle to keep up with the exponential growth of th... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 27, 2020 Category: Bioinformatics Authors: Emily K. Mallory, Matthieu de Rochemonteix, Alex Ratner, Ambika Acharya, Chris Re, Roselie A. Bright and Russ B. Altman Tags: Research article Source Type: research

ARTDeco: automatic readthrough transcription detection
Mounting evidence suggests several diseases and biological processes target transcription termination to misregulate gene expression. Disruption of transcription termination leads to readthrough transcription ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 26, 2020 Category: Bioinformatics Authors: Samuel J. Roth, Sven Heinz and Christopher Benner Tags: Software Source Type: research

SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data
Recently, it has become possible to collect next-generation DNA sequencing data sets that are composed of multiple samples from multiple biological units where each of these samples may be from a single cell o... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 26, 2020 Category: Bioinformatics Authors: Collin Giguere, Harsh Vardhan Dubey, Vishal Kumar Sarsani, Hachem Saddiki, Shai He and Patrick Flaherty Tags: Software Source Type: research

Discovery of significant porcine SNPs for swine breed identification by a hybrid of information gain, genetic algorithm, and frequency feature selection technique
The number of porcine Single Nucleotide Polymorphisms (SNPs) used in genetic association studies is very large, suitable for statistical testing. However, in breed classification problem, one needs to have a m... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 26, 2020 Category: Bioinformatics Authors: Kitsuchart Pasupa, Wanthanee Rathasamuth and Sissades Tongsima Tags: Methodology Article Source Type: research

Data-based RNA-seq simulations by binomial thinning
With the explosion in the number of methods designed to analyze bulk and single-cell RNA-seq data, there is a growing need for approaches that assess and compare these methods. The usual technique is to compar... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 24, 2020 Category: Bioinformatics Authors: David Gerard Tags: Methodology Article Source Type: research

A novel investigation of the effect of iterations in sliding semi-landmarks for 3D human facial images
Landmark-based approaches of two- or three-dimensional coordinates are the most widely used in geometric morphometrics (GM). As human face hosts the organs that act as the central interface for identification,... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 24, 2020 Category: Bioinformatics Authors: Azree Nazri, Olalekan Agbolade, Razali Yaakob, Abdul Azim Ghani and Yoke Kqueen Cheah Tags: Research article Source Type: research

Substitution matrix based color schemes for sequence alignment visualization
Visualization of multiple sequence alignments often includes colored symbols, usually characters encoding amino acids, according to some (physical) properties, such as hydrophobicity or charge. Typically, colo... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 24, 2020 Category: Bioinformatics Authors: Patrick Kunzmann, Benjamin E. Mayer and Kay Hamacher Tags: Software Source Type: research

RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp
Analysis of secondary structures is essential for understanding the functions of RNAs. Because RNA molecules thermally fluctuate, it is necessary to analyze the probability distributions of their secondary str... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 24, 2020 Category: Bioinformatics Authors: Hiroki Takizawa, Junichi Iwakiri and Kiyoshi Asai Tags: Methodology Article Source Type: research

Bio-semantic relation extraction with attention-based external knowledge reinforcement
Semantic resources such as knowledge bases contains high-quality-structured knowledge and therefore require significant effort from domain experts. Using the resources to reinforce the information retrieval fr... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 24, 2020 Category: Bioinformatics Authors: Zhijing Li, Yuchen Lian, Xiaoyong Ma, Xiangrong Zhang and Chen Li Tags: Methodology article Source Type: research

Enhancing SVM for survival data using local invariances and weighting
The necessity to analyze medium-throughput data in epidemiological studies with small sample size, particularly when studying biomedical data may hinder the use of classical statistical methods. Support vector... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 19, 2020 Category: Bioinformatics Authors: Hector Sanz, Ferran Reverter and Clarissa Valim Tags: Methodology article Source Type: research

fcScan: a versatile tool to cluster combinations of sites using genomic coordinates
Finding combinations of homotypic or heterotypic genomic sites obeying a specific grammar in DNA sequences is a frequent task in bioinformatics. A typical case corresponds to the identification of cis-regulato... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 19, 2020 Category: Bioinformatics Authors: Abdullah El-Kurdi, Ghiwa Ali Khalil, Georges Khazen and Pierre Khoueiry Tags: Software Source Type: research

Uncovering the prognostic gene signatures for the improvement of risk stratification in cancers by using deep learning algorithm coupled with wavelet transform
The aim of gene expression-based clinical modelling in tumorigenesis is not only to accurately predict the clinical endpoints, but also to reveal the genome characteristics for downstream analysis for the purp... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 19, 2020 Category: Bioinformatics Authors: Yiru Zhao, Yifan Zhou, Yuan Liu, Yinyi Hao, Menglong Li, Xuemei Pu, Chuan Li and Zhining Wen Tags: Methodology article Source Type: research

Direct comparison shows that mRNA-based diagnostics incorporate information which cannot be learned directly from genomic mutations
Compared to the many uses of DNA-level testing in clinical oncology, development of RNA-based diagnostics has been more limited. An exception to this trend is the growing use of mRNA-based methods in early-sta... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 19, 2020 Category: Bioinformatics Authors: Hersh D. Ravkin, Ofer Givton, David B. Geffen and Eitan Rubin Tags: Research article Source Type: research

Power analysis for RNA-Seq differential expression studies using generalized linear mixed effects models
Power analysis becomes an inevitable step in experimental design of current biomedical research. Complex designs allowing diverse correlation structures are commonly used in RNA-Seq experiments. However, the f... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 19, 2020 Category: Bioinformatics Authors: Lianbo Yu, Soledad Fernandez and Guy Brock Tags: Methodology Article Source Type: research

CSN: unsupervised approach for inferring biological networks based on the genome alone
Most organisms cannot be cultivated, as they live in unique ecological conditions that cannot be mimicked in the lab. Understanding the functionality of those organisms ’ genes and their interactions by perform... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 15, 2020 Category: Bioinformatics Authors: Maya Galili and Tamir Tuller Tags: Methodology article Source Type: research

CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments
Single cell RNA sequencing (scRNAseq) has provided invaluable insights into cellular heterogeneity and functional states in health and disease. During the analysis of scRNAseq data, annotating the biological i... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 15, 2020 Category: Bioinformatics Authors: H. Atakan Ekiz, Christopher J. Conley, W. Zac Stephens and Ryan M. O ’Connell Tags: Software Source Type: research

ICEKAT: an interactive online tool for calculating initial rates from continuous enzyme kinetic traces
Continuous enzyme kinetic assays are often used in high-throughput applications, as they allow rapid acquisition of large amounts of kinetic data and increased confidence compared to discontinuous assays. Howe... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 14, 2020 Category: Bioinformatics Authors: Michael D. Olp, Kelsey S. Kalous and Brian C. Smith Tags: Software Source Type: research

Automated image analysis system for studying cardiotoxicity in human pluripotent stem cell-Derived cardiomyocytes
Cardiotoxicity, characterized by severe cardiac dysfunction, is a major problem in patients treated with different classes of anticancer drugs. Development of predictable human-based models and assays for drug... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 14, 2020 Category: Bioinformatics Authors: Lu Cao, Andries D. van der Meer, Fons J. Verbeek and Robert Passier Tags: Methodology Article Source Type: research

Broad-coverage biomedical relation extraction with SemRep
In the era of information overload, natural language processing (NLP) techniques are increasingly needed to support advanced biomedical information management and discovery applications. In this paper, we pres... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 14, 2020 Category: Bioinformatics Authors: Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman and Dongwook Shin Tags: Software Source Type: research

TAMA: improved metagenomic sequence classification through meta-analysis
Microorganisms are important occupants of many different environments. Identifying the composition of microbes and estimating their abundance promote understanding of interactions of microbes in environmental ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 12, 2020 Category: Bioinformatics Authors: Mikang Sim, Jongin Lee, Daehwan Lee, Daehong Kwon and Jaebum Kim Tags: Software Source Type: research

Cluster correlation based method for lncRNA-disease association prediction
In recent years, increasing evidences have indicated that long non-coding RNAs (lncRNAs) are deeply involved in a wide range of human biological pathways. The mutations and disorders of lncRNAs are closely ass... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 11, 2020 Category: Bioinformatics Authors: Qianqian Yuan, Xingli Guo, Yang Ren, Xiao Wen and Lin Gao Tags: Methodology article Source Type: research

methCancer-gen: a DNA methylome dataset generator for user-specified cancer type based on conditional variational autoencoder
Recently, DNA methylation has drawn great attention due to its strong correlation with abnormal gene activities and informative representation of the cancer status. As a number of studies focus on DNA methylat... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 11, 2020 Category: Bioinformatics Authors: Joungmin Choi and Heejoon Chae Tags: Research Article Source Type: research

Multi-task learning sparse group lasso: a method for quantifying antigenicity of influenza A(H1N1) virus using mutations and variations in glycosylation of Hemagglutinin
In addition to causing the pandemic influenza outbreaks of 1918 and 2009, subtype H1N1 influenza A viruses (IAVs) have caused seasonal epidemics since 1977. Antigenic property of influenza viruses are determin... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 11, 2020 Category: Bioinformatics Authors: Lei Li, Deborah Chang, Lei Han, Xiaojian Zhang, Joseph Zaia and Xiu-Feng Wan Tags: Methodology article Source Type: research

MEPHAS: an interactive graphical user interface for medical and pharmaceutical statistical analysis with R and Shiny
Even though R is one of the most commonly used statistical computing environments, it lacks a graphical user interface (GUI) that appeals to students, researchers, lecturers, and practitioners in medicine and ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 11, 2020 Category: Bioinformatics Authors: Yi Zhou, Siu-wai Leung, Shosuke Mizutani, Tatsuya Takagi and Yu-Shi Tian Tags: Software Source Type: research

SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data
With the rapid development of single-cell genomics, technologies for parallel sequencing of the transcriptome and genome in each single cell is being explored in several labs and is becoming available. This br... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 11, 2020 Category: Bioinformatics Authors: Yue Hu, Xi Xi, Qian Yang and Xuegong Zhang Tags: Methodology article Source Type: research

Identifying novel associations in GWAS by hierarchical Bayesian latent variable detection of differentially misclassified phenotypes
Heterogeneity in the definition and measurement of complex diseases in Genome-Wide Association Studies (GWAS) may lead to misdiagnoses and misclassification errors that can significantly impact discovery of di... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 7, 2020 Category: Bioinformatics Authors: Afrah Shafquat, Ronald G. Crystal and Jason G. Mezey Tags: Research article Source Type: research

Self-analysis of repeat proteins reveals evolutionarily conserved patterns
Protein repeats can confound sequence analyses because the repetitiveness of their amino acid sequences lead to difficulties in identifying whether similar repeats are due to convergent or divergent evolution.... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 7, 2020 Category: Bioinformatics Authors: Matthew Merski, Krzysztof M łynarczyk, Jan Ludwiczak, Jakub Skrzeczkowski, Stanisław Dunin-Horkawicz and Maria W. Górna Tags: Research article Source Type: research

Exploring the dynamics and interplay of human papillomavirus and cervical tumorigenesis by integrating biological data into a mathematical model
Cervical cancer is the fourth most common tumor in women worldwide, mostly resulting from high-risk human papillomavirus (HR-HPV) with persistent infection. (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 5, 2020 Category: Bioinformatics Authors: Wenting Wu, Lei Song, Yongtao Yang, Jianxin Wang, Hongtu Liu and Le Zhang Tags: Research Source Type: research

Main findings and advances in bioinformatics and biomedical engineering- IWBBIO 2018
In the current supplement, we are proud to present seventeen relevant contributions from the 6th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2018), which was held during ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 5, 2020 Category: Bioinformatics Authors: Olga Valenzuela, Fernando Rojas, Ignacio Rojas and Peter Glosekotter Tags: Introduction Source Type: research

TS: a powerful truncated test to detect novel disease associated genes using publicly available gWAS summary data
In the last decade, a large number of common variants underlying complex diseases have been identified through genome-wide association studies (GWASs). Summary data of the GWASs are freely and publicly availab... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 4, 2020 Category: Bioinformatics Authors: Jianjun Zhang, Xuan Guo, Samantha Gonzales, Jingjing Yang and Xuexia Wang Tags: Research Article Source Type: research

Transfer posterior error probability estimation for peptide identification
In shotgun proteomics, database searching of tandem mass spectra results in a great number of peptide-spectrum matches (PSMs), many of which are false positives. Quality control of PSMs is a multiple hypothesi... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 4, 2020 Category: Bioinformatics Authors: Xinpei Yi, Fuzhou Gong and Yan Fu Tags: Methodology Article Source Type: research

Blast2Fish: a reference-based annotation web tool for transcriptome analysis of non-model teleost fish
Transcriptome analysis by next-generation sequencing has become a popular technique in recent years. This approach is quite suitable for non-model organism study, as de novo assembly is independent of prior ge... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 4, 2020 Category: Bioinformatics Authors: Chun-Hsi Tso, Jen-Leih Wu and Ming-Wei Lu Tags: Software Source Type: research

Prediction model construction of mouse stem cell pluripotency using CpG and non-CpG DNA methylation markers
Genome-wide studies of DNA methylation across the epigenetic landscape provide insights into the heterogeneity of pluripotent embryonic stem cells (ESCs). Differentiating into embryonic somatic and germ cells,... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 4, 2020 Category: Bioinformatics Authors: Soobok Joe and Hojung Nam Tags: Research article Source Type: research

Comparative analysis of similarity measurements in miRNAs with applications to miRNA-disease association predictions
As regulators of gene expression, microRNAs (miRNAs) are increasingly recognized as critical biomarkers of human diseases. Till now, a series of computational methods have been proposed to predict new miRNA-di... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 4, 2020 Category: Bioinformatics Authors: Hailin Chen, Ruiyu Guo, Guanghui Li, Wei Zhang and Zuping Zhang Tags: Research article Source Type: research

wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data
Analysing whole genome bisulfite sequencing datasets is a data-intensive task that requires comprehensive and reproducible workflows to generate valid results. While many algorithms have been developed for tas... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 1, 2020 Category: Bioinformatics Authors: Marius W öste, Elsa Leitão, Sandra Laurentino, Bernhard Horsthemke, Sven Rahmann and Christopher Schröder Tags: Software Source Type: research

Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure
Whenever suitable template structures are not available, usage of fragment-based protein structure prediction becomes the only practical alternative as pure ab initio techniques require massive computational r... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 1, 2020 Category: Bioinformatics Authors: Jad Abbass and Jean-Christophe Nebel Tags: Methodology article Source Type: research

Negative binomial additive model for RNA-Seq data analysis
High-throughput sequencing experiments followed by differential expression analysis is a widely used approach for detecting genomic biomarkers. A fundamental step in differential expression analysis is to mode... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - May 1, 2020 Category: Bioinformatics Authors: Xu Ren and Pei-Fen Kuan Tags: Software Source Type: research

CYPminer: an automated cytochrome P450 identification, classification, and data analysis tool for genome data sets across kingdoms
Cytochrome P450 monooxygenases (termed CYPs or P450s) are hemoproteins ubiquitously found across all kingdoms, playing a central role in intracellular metabolism, especially in metabolism of drugs and xenobiot... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 29, 2020 Category: Bioinformatics Authors: Ohgew Kweon, Seong-Jae Kim, Jae Hyun Kim, Seong Won Nho, Dongryeoul Bae, Jungwhan Chon, Mark Hart, Dong-Heon Baek, Young-Chang Kim, Wenjun Wang, Sung-Kwan Kim, John B. Sutherland and Carl E. Cerniglia Tags: Software Source Type: research

SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation
Technological developments in the emerging field of spatial transcriptomics have opened up an unexplored landscape where transcript information is put in a spatial context. Clustering commonly constitutes a ce... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 29, 2020 Category: Bioinformatics Authors: Joseph Bergenstr åhle, Ludvig Bergenstråhle and Joakim Lundeberg Tags: Software Source Type: research

circRNAprofiler: an R-based computational framework for the downstream analysis of circular RNAs
Circular RNAs (circRNAs) are a newly appreciated class of non-coding RNA molecules. Numerous tools have been developed for the detection of circRNAs, however computational tools to perform downstream functiona... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 29, 2020 Category: Bioinformatics Authors: Simona Aufiero, Yolan J. Reckman, Anke J. Tijsen, Yigal M. Pinto and Esther E. Creemers Tags: Software Source Type: research

YSMR: a video tracking and analysis program for bacterial motility
Motility in bacteria forms the basis for taxis and is in some pathogenic bacteria important for virulence. Video tracking of motile bacteria allows the monitoring of bacterial swimming behaviour and taxis on t... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 29, 2020 Category: Bioinformatics Authors: Julian Schwanbeck, Ines Oehmig, Jer ôme Dretzke, Andreas E. Zautner, Uwe Groß and Wolfgang Bohne Tags: Software Source Type: research

vivaGen – a survival data set generator for software testing
An amendment to this paper has been published and can be accessed via the original article. (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 29, 2020 Category: Bioinformatics Authors: Matthias Gietzelt, Christian Karmen, Petra Knaup-Gregori and Matthias Ganzinger Tags: Software Source Type: research

High dimensional model representation of log-likelihood ratio: binary classification with expression data
Binary classification rules based on a small-sample of high-dimensional data (for instance, gene expression data) are ubiquitous in modern bioinformatics. Constructing such classifiers is challenging due to (a... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 25, 2020 Category: Bioinformatics Authors: Ali Foroughi pour, Maciej Pietrzak, Lori A Dalton and Grzegorz A. Rempa ła Tags: Methodology Article Source Type: research

A single-model quality assessment method for poor quality protein structure
Quality assessment of protein tertiary structure prediction models, in which structures of the best quality are selected from decoys, is a major challenge in protein structure prediction, and is crucial to det... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 25, 2020 Category: Bioinformatics Authors: Jianquan Ouyang, Ningqiao Huang and Yunqi Jiang Tags: Methodology article Source Type: research

GiniClust3: a fast and memory-efficient tool for rare cell type identification
With the rapid development of single-cell RNA sequencing technology, it is possible to dissect cell-type composition at high resolution. A number of methods have been developed with the purpose to identify rar... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 25, 2020 Category: Bioinformatics Authors: Rui Dong and Guo-Cheng Yuan Tags: Software Source Type: research

On Sackin ’s original proposal: the variance of the leaves’ depths as a phylogenetic balance index
The Sackin indexS of a rooted phylogenetic tree, defined as the sum of its leaves ’ depths, is one of the most popular balance indices in phylogenetics, and Sackin’s paper (Syst Zool 21:225–6, 1972) is usually cit... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 23, 2020 Category: Bioinformatics Authors: Tom ás M. Coronado, Arnau Mir, Francesc Rosselló and Lucía Rotger Tags: Research Article Source Type: research

TooT-T: discrimination of transport proteins from non-transport proteins
Membrane transport proteins (transporters) play an essential role in every living cell by transporting hydrophilic molecules across the hydrophobic membranes. While the sequences of many membrane proteins are ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 23, 2020 Category: Bioinformatics Authors: Munira Alballa and Gregory Butler Tags: Research Source Type: research