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SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks BMC Bioinform. (IF 3.242) Pub Date : 2021-01-22 Tamer N. Jarada; Jon G. Rokne; Reda Alhajj
Drug repositioning is an emerging approach in pharmaceutical research for identifying novel therapeutic potentials for approved drugs and discover therapies for untreated diseases. Due to its time and cost efficiency, drug repositioning plays an instrumental role in optimizing the drug development process compared to the traditional de novo drug discovery process. Advances in the genomics, together
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Mining influential genes based on deep learning BMC Bioinform. (IF 3.242) Pub Date : 2021-01-22 Lingpeng Kong; Yuanyuan Chen; Fengjiao Xu; Mingmin Xu; Zutan Li; Jingya Fang; Liangyun Zhang; Cong Pian
Currently, large-scale gene expression profiling has been successfully applied to the discovery of functional connections among diseases, genetic perturbation, and drug action. To address the cost of an ever-expanding gene expression profile, a new, low-cost, high-throughput reduced representation expression profiling method called L1000 was proposed, with which one million profiles were produced.
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A stack LSTM structure for decoding continuous force from local field potential signal of primary motor cortex (M1) BMC Bioinform. (IF 3.242) Pub Date : 2021-01-22 Mehrdad Kashefi; Mohammad Reza Daliri
Brain Computer Interfaces (BCIs) translate the activity of the nervous system to a control signal which is interpretable for an external device. Using continuous motor BCIs, the user will be able to control a robotic arm or a disabled limb continuously. In addition to decoding the target position, accurate decoding of force amplitude is essential for designing BCI systems capable of performing fine
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MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning BMC Bioinform. (IF 3.242) Pub Date : 2021-01-18 Eliza Dhungel; Yassin Mreyoud; Ho-Jin Gwak; Ahmad Rajeh; Mina Rho; Tae-Hyuk Ahn
Diverse microbiome communities drive biogeochemical processes and evolution of animals in their ecosystems. Many microbiome projects have demonstrated the power of using metagenomics to understand the structures and factors influencing the function of the microbiomes in their environments. In order to characterize the effects from microbiome composition for human health, diseases, and even ecosystems
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DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms BMC Bioinform. (IF 3.242) Pub Date : 2021-01-18 Dipan Shaw; Hao Chen; Minzhu Xie; Tao Jiang
Long non-coding RNAs (lncRNAs) regulate diverse biological processes via interactions with proteins. Since the experimental methods to identify these interactions are expensive and time-consuming, many computational methods have been proposed. Although these computational methods have achieved promising prediction performance, they neglect the fact that a gene may encode multiple protein isoforms and
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Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data BMC Bioinform. (IF 3.242) Pub Date : 2021-01-15 Xinping Fan; Guanghao Luo; Yu S. Huang
Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task. We introduce Accucopy, a method to infer total copy numbers (TCNs) and allele-specific copy numbers (ASCNs) from challenging low-purity
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Drug perturbation gene set enrichment analysis (dpGSEA): a new transcriptomic drug screening approach BMC Bioinform. (IF 3.242) Pub Date : 2021-01-12 Mike Fang; Brian Richardson; Cheryl M. Cameron; Jean-Eudes Dazard; Mark J. Cameron
In this study, we demonstrate that our modified Gene Set Enrichment Analysis (GSEA) method, drug perturbation GSEA (dpGSEA), can detect phenotypically relevant drug targets through a unique transcriptomic enrichment that emphasizes biological directionality of drug-derived gene sets. We detail our dpGSEA method and show its effectiveness in detecting specific perturbation of drugs in independent public
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Impact of explicit area scaling on kinetic models involving multiple compartments BMC Bioinform. (IF 3.242) Pub Date : 2021-01-11 Pascal Holzheu; Ruth Großeholz; Ursula Kummer
Computational modelling of cell biological processes is a frequently used technique to analyse the underlying mechanisms and to generally understand the behaviour of these processes in the context of a pathway, network or even the whole cell. The most common technique in this context is the usage of ordinary differential equations that describe the kinetics of the relevant processes in mechanistic
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Set-theory based benchmarking of three different variant callers for targeted sequencing BMC Bioinform. (IF 3.242) Pub Date : 2021-01-07 Jose Arturo Molina-Mora; Mariela Solano-Vargas
Next generation sequencing (NGS) technologies have improved the study of hereditary diseases. Since the evaluation of bioinformatics pipelines is not straightforward, NGS demands effective strategies to analyze data that is of paramount relevance for decision making under a clinical scenario. According to the benchmarking framework of the Global Alliance for Genomics and Health (GA4GH), we implemented
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Identifying the sequence specificities of circRNA-binding proteins based on a capsule network architecture BMC Bioinform. (IF 3.242) Pub Date : 2021-01-07 Zhengfeng Wang; Xiujuan Lei
Circular RNAs (circRNAs) are widely expressed in cells and tissues and are involved in biological processes and human diseases. Recent studies have demonstrated that circRNAs can interact with RNA-binding proteins (RBPs), which is considered an important aspect for investigating the function of circRNAs. In this study, we design a slight variant of the capsule network, called circRB, to identify the
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H2V: a database of human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection BMC Bioinform. (IF 3.242) Pub Date : 2021-01-07 Nan Zhou; Jinku Bao; Yuping Ning
The ongoing global COVID-19 pandemic is caused by SARS-CoV-2, a novel coronavirus first discovered at the end of 2019. It has led to more than 50 million confirmed cases and more than 1 million deaths across 219 countries as of 11 November 2020, according to WHO statistics. SARS-CoV-2, SARS-CoV, and MERS-CoV are similar. They are highly pathogenic and threaten public health, impair the economy, and
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Modeling drug mechanism of action with large scale gene-expression profiles using GPAR, an artificial intelligence platform BMC Bioinform. (IF 3.242) Pub Date : 2021-01-07 Shengqiao Gao; Lu Han; Dan Luo; Gang Liu; Zhiyong Xiao; Guangcun Shan; Yongxiang Zhang; Wenxia Zhou
Querying drug-induced gene expression profiles with machine learning method is an effective way for revealing drug mechanism of actions (MOAs), which is strongly supported by the growth of large scale and high-throughput gene expression databases. However, due to the lack of code-free and user friendly applications, it is not easy for biologists and pharmacologists to model MOAs with state-of-art deep
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G-Tric: generating three-way synthetic datasets with triclustering solutions BMC Bioinform. (IF 3.242) Pub Date : 2021-01-07 João Lobo; Rui Henriques; Sara C. Madeira
Three-way data started to gain popularity due to their increasing capacity to describe inherently multivariate and temporal events, such as biological responses, social interactions along time, urban dynamics, or complex geophysical phenomena. Triclustering, subspace clustering of three-way data, enables the discovery of patterns corresponding to data subspaces (triclusters) with values correlated
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Predicting chemosensitivity using drug perturbed gene dynamics BMC Bioinform. (IF 3.242) Pub Date : 2021-01-07 Joshua D. Mannheimer; Ashok Prasad; Daniel L. Gustafson
One of the current directions of precision medicine is the use of computational methods to aid in the diagnosis, prognosis, and treatment of disease based on data driven approaches. For instance, in oncology, there has been a particular focus on development of algorithms and biomarkers that can be used for pre-clinical and clinical applications. In particular large-scale omics-based models to predict
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PyConvU-Net: a lightweight and multiscale network for biomedical image segmentation BMC Bioinform. (IF 3.242) Pub Date : 2021-01-07 Changyong Li; Yongxian Fan; Xiaodong Cai
With the development of deep learning (DL), more and more methods based on deep learning are proposed and achieve state-of-the-art performance in biomedical image segmentation. However, these methods are usually complex and require the support of powerful computing resources. According to the actual situation, it is impractical that we use huge computing resources in clinical situations. Thus, it is
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Drug-induced cell viability prediction from LINCS-L1000 through WRFEN-XGBoost algorithm BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Jiaxing Lu; Ming Chen; Yufang Qin
Predicting the drug response of the cancer diseases through the cellular perturbation signatures under the action of specific compounds is very important in personalized medicine. In the process of testing drug responses to the cancer, traditional experimental methods have been greatly hampered by the cost and sample size. At present, the public availability of large amounts of gene expression data
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mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Bing Song; August E. Woerner; John Planz
Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested by linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other. Therefore, a compatible and user-friendly
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MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Carlos A. Ruiz-Perez; Roth E. Conrad; Konstantinos T. Konstantinidis
High-throughput sequencing has increased the number of available microbial genomes recovered from isolates, single cells, and metagenomes. Accordingly, fast and comprehensive functional gene annotation pipelines are needed to analyze and compare these genomes. Although several approaches exist for genome annotation, these are typically not designed for easy incorporation into analysis pipelines, do
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PCirc: random forest-based plant circRNA identification software BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Shuwei Yin; Xiao Tian; Jingjing Zhang; Peisen Sun; Guanglin Li
Circular RNA (circRNA) is a novel type of RNA with a closed-loop structure. Increasing numbers of circRNAs are being identified in plants and animals, and recent studies have shown that circRNAs play an important role in gene regulation. Therefore, identifying circRNAs from increasing amounts of RNA-seq data is very important. However, traditional circRNA recognition methods have limitations. In recent
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HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Edwin A. Solares; Yuan Tao; Anthony D. Long; Brandon S. Gaut
Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream
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DISTEVAL: a web server for evaluating predicted protein distances BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Badri Adhikari; Bikash Shrestha; Matthew Bernardini; Jie Hou; Jamie Lea
Protein inter-residue contact and distance prediction are two key intermediate steps essential to accurate protein structure prediction. Distance prediction comes in two forms: real-valued distances and ‘binned’ distograms, which are a more finely grained variant of the binary contact prediction problem. The latter has been introduced as a new challenge in the 14th Critical Assessment of Techniques
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MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanism BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Yilin Ye; Jian Wang; Yunwan Xu; Yi Wang; Youdong Pan; Qi Song; Xing Liu; Ji Wan
Accurate prediction of binding between class I human leukocyte antigen (HLA) and neoepitope is critical for target identification within personalized T-cell based immunotherapy. Many recent prediction tools developed upon the deep learning algorithms and mass spectrometry data have indeed showed improvement on the average predicting power for class I HLA-peptide interaction. However, their prediction
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MiBiOmics: an interactive web application for multi-omics data exploration and integration BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Johanna Zoppi; Jean-François Guillaume; Michel Neunlist; Samuel Chaffron
Multi-omics experimental approaches are becoming common practice in biological and medical sciences underlining the need to design new integrative techniques and applications to enable the multi-scale characterization of biological systems. The integrative analysis of heterogeneous datasets generally allows to acquire additional insights and generate novel hypotheses about a given biological system
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SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Yan Zheng; Yuanke Zhong; Jialu Hu; Xuequn Shang
Single-cell RNA sequencing (scRNA-seq) enables the possibility of many in-depth transcriptomic analyses at a single-cell resolution. It’s already widely used for exploring the dynamic development process of life, studying the gene regulation mechanism, and discovering new cell types. However, the low RNA capture rate, which cause highly sparse expression with dropout, makes it difficult to do downstream
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SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Joaquim Aguirre-Plans; Alberto Meseguer; Ruben Molina-Fernandez; Manuel Alejandro Marín-López; Gaurav Jumde; Kevin Casanova; Jaume Bonet; Oriol Fornes; Narcis Fernandez-Fuentes; Baldo Oliva
Statistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein–protein interaction (PPI) structures. In previous works we decomposed the statistical potentials in different terms, named Split-Statistical Potentials, accounting for the type of amino acid pairs, their hydrophobicity
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Examination of hydrogen cross-feeders using a colonic microbiota model BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Nick W. Smith; Paul R. Shorten; Eric Altermann; Nicole C. Roy; Warren C. McNabb
Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing. An existing mathematical model for microbial community growth and metabolism was
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recoup: flexible and versatile signal visualization from next generation sequencing BMC Bioinform. (IF 3.242) Pub Date : 2021-01-06 Panagiotis Moulos
The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlying signal generated to answer important qualitative and quantitative biological questions. As a result, the need for novel software able to reliably produce quick, comprehensive, and easily repeatable
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Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm BMC Bioinform. (IF 3.242) Pub Date : 2021-01-02 Pedro M. Martins; Lucianna H. Santos; Diego Mariano; Felippe C. Queiroz; Luana L. Bastos; Isabela de S. Gomes; Pedro H. C. Fischer; Rafael E. O. Rocha; Sabrina A. Silveira; Leonardo H. F. de Lima; Mariana T. Q. de Magalhães; Maria G. A. Oliveira; Raquel C. de Melo-Minardi
Protein–peptide interactions play a fundamental role in a wide variety of biological processes, such as cell signaling, regulatory networks, immune responses, and enzyme inhibition. Peptides are characterized by low toxicity and small interface areas; therefore, they are good targets for therapeutic strategies, rational drug planning and protein inhibition. Approximately 10% of the ethical pharmaceutical
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Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data BMC Bioinform. (IF 3.242) Pub Date : 2020-12-30 Noel-Marie Plonski; Emily Johnson; Madeline Frederick; Heather Mercer; Gail Fraizer; Richard Meindl; Gemma Casadesus; Helen Piontkivska
As the number of RNA-seq datasets that become available to explore transcriptome diversity increases, so does the need for easy-to-use comprehensive computational workflows. Many available tools facilitate analyses of one of the two major mechanisms of transcriptome diversity, namely, differential expression of isoforms due to alternative splicing, while the second major mechanism—RNA editing due to
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Analysis of associations between emotions and activities of drug users and their addiction recovery tendencies from social media posts using structural equation modeling BMC Bioinform. (IF 3.242) Pub Date : 2020-12-30 Deeptanshu Jha; Rahul Singh
Addiction to drugs and alcohol constitutes one of the significant factors underlying the decline in life expectancy in the US. Several context-specific reasons influence drug use and recovery. In particular emotional distress, physical pain, relationships, and self-development efforts are known to be some of the factors associated with addiction recovery. Unfortunately, many of these factors are not
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Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy BMC Bioinform. (IF 3.242) Pub Date : 2020-12-30 Elham Sherafat; Jordan Force; Ion I. Măndoiu
Personalized cancer vaccines are emerging as one of the most promising approaches to immunotherapy of advanced cancers. However, only a small proportion of the neoepitopes generated by somatic DNA mutations in cancer cells lead to tumor rejection. Since it is impractical to experimentally assess all candidate neoepitopes prior to vaccination, developing accurate methods for predicting tumor-rejection
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Evolution of drug resistance in HIV protease BMC Bioinform. (IF 3.242) Pub Date : 2020-12-30 Dhara Shah; Christopher Freas; Irene T. Weber; Robert W. Harrison
Drug resistance is a critical problem limiting effective antiviral therapy for HIV/AIDS. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice of therapy. These techniques can also be used to identify protease mutants for experimental studies of resistance and thereby assist in the development of next-generation therapies. Few studies
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Multi-view feature selection for identifying gene markers: a diversified biological data driven approach BMC Bioinform. (IF 3.242) Pub Date : 2020-12-30 Sudipta Acharya; Laizhong Cui; Yi Pan
In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene selection and identifying relevant and non-redundant marker genes from high dimensional gene expression data sets. In that context, designing an efficient feature selection algorithm exploiting
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Convex hulls in hamming space enable efficient search for similarity and clustering of genomic sequences BMC Bioinform. (IF 3.242) Pub Date : 2020-12-30 David S. Campo; Yury Khudyakov
In molecular epidemiology, comparison of intra-host viral variants among infected persons is frequently used for tracing transmissions in human population and detecting viral infection outbreaks. Application of Ultra-Deep Sequencing (UDS) immensely increases the sensitivity of transmission detection but brings considerable computational challenges when comparing all pairs of sequences. We developed
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An automated protocol for modelling peptide substrates to proteases BMC Bioinform. (IF 3.242) Pub Date : 2020-12-29 Rodrigo Ochoa; Mikhail Magnitov; Roman A. Laskowski; Pilar Cossio; Janet M. Thornton
Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promiscuity which can also be essential. Databases compiling specificity matrices derived from experimental assays have provided valuable insights into protease substrate recognition. Despite this
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Dependency parsing of biomedical text with BERT BMC Bioinform. (IF 3.242) Pub Date : 2020-12-29 Jenna Kanerva; Filip Ginter; Sampo Pyysalo
Syntactic analysis, or parsing, is a key task in natural language processing and a required component for many text mining approaches. In recent years, Universal Dependencies (UD) has emerged as the leading formalism for dependency parsing. While a number of recent tasks centering on UD have substantially advanced the state of the art in multilingual parsing, there has been only little study of parsing
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C-Norm: a neural approach to few-shot entity normalization BMC Bioinform. (IF 3.242) Pub Date : 2020-12-29 Arnaud Ferré; Louise Deléger; Robert Bossy; Pierre Zweigenbaum; Claire Nédellec
Entity normalization is an important information extraction task which has gained renewed attention in the last decade, particularly in the biomedical and life science domains. In these domains, and more generally in all specialized domains, this task is still challenging for the latest machine learning-based approaches, which have difficulty handling highly multi-class and few-shot learning problems
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Correction to: MicroBVS: Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package BMC Bioinform. (IF 3.242) Pub Date : 2020-12-28 Matthew D. Koslovsky; Marina Vannucci
An amendment to this paper has been published and can be accessed via the original article.
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Compositional zero-inflated network estimation for microbiome data BMC Bioinform. (IF 3.242) Pub Date : 2020-12-28 Min Jin Ha; Junghi Kim; Jessica Galloway-Peña; Kim-Anh Do; Christine B. Peterson
The estimation of microbial networks can provide important insight into the ecological relationships among the organisms that comprise the microbiome. However, there are a number of critical statistical challenges in the inference of such networks from high-throughput data. Since the abundances in each sample are constrained to have a fixed sum and there is incomplete overlap in microbial populations
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LDscaff: LD-based scaffolding of de novo genome assemblies BMC Bioinform. (IF 3.242) Pub Date : 2020-12-28 Zicheng Zhao; Yingxiao Zhou; Shuai Wang; Xiuqing Zhang; Changfa Wang; Shuaicheng Li
Genome assembly is fundamental for de novo genome analysis. Hybrid assembly, utilizing various sequencing technologies increases both contiguity and accuracy. While such approaches require extra costly sequencing efforts, the information provided millions of existed whole-genome sequencing data have not been fully utilized to resolve the task of scaffolding. Genetic recombination patterns in population
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Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine 2020 BMC Bioinform. (IF 3.242) Pub Date : 2020-12-28 Yan Guo; Li Shen; Xinghua Shi; Kai Wang; Yulin Dai; Zhongming Zhao
The International Association for Intelligent Biology and Medicine (IAIBM) is a nonprofit organization that promotes intelligent biology and medical science. It hosts an annual International Conference on Intelligent Biology and Medicine (ICIBM), which was initially established in 2012. Due to the coronavirus (COVID-19) pandemic, the ICIBM 2020 was held for the first time as a virtual online conference
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The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data BMC Bioinform. (IF 3.242) Pub Date : 2020-12-28 Laurence de Torrenté; Samuel Zimmerman; Masako Suzuki; Maximilian Christopeit; John M. Greally; Jessica C. Mar
In genomics, we often assume that continuous data, such as gene expression, follow a specific kind of distribution. However we rarely stop to question the validity of this assumption, or consider how broadly applicable it may be to all genes that are in the transcriptome. Our study investigated the prevalence of a range of gene expression distributions in three different tumor types from the Cancer
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Genome-wide detection of short tandem repeat expansions by long-read sequencing BMC Bioinform. (IF 3.242) Pub Date : 2020-12-28 Qian Liu; Yao Tong; Kai Wang
Short tandem repeat (STR), or “microsatellite”, is a tract of DNA in which a specific motif (typically < 10 base pairs) is repeated multiple times. STRs are abundant throughout the human genome, and specific repeat expansions may be associated with human diseases. Long-read sequencing coupled with bioinformatics tools enables the estimation of repeat counts for STRs. However, with the exception of
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Effect of APOE ε4 on multimodal brain connectomic traits: a persistent homology study BMC Bioinform. (IF 3.242) Pub Date : 2020-12-28 Jin Li; Chenyuan Bian; Dandan Chen; Xianglian Meng; Haoran Luo; Hong Liang; Li Shen
Although genetic risk factors and network-level neuroimaging abnormalities have shown effects on cognitive performance and brain atrophy in Alzheimer’s disease (AD), little is understood about how apolipoprotein E (APOE) ε4 allele, the best-known genetic risk for AD, affect brain connectivity before the onset of symptomatic AD. This study aims to investigate APOE ε4 effects on brain connectivity from
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Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction BMC Bioinform. (IF 3.242) Pub Date : 2020-12-28 Adil Al-Azzawi; Anes Ouadou; Ye Duan; Jianlin Cheng
Cryo-EM data generated by electron tomography (ET) contains images for individual protein particles in different orientations and tilted angles. Individual cryo-EM particles can be aligned to reconstruct a 3D density map of a protein structure. However, low contrast and high noise in particle images make it challenging to build 3D density maps at intermediate to high resolution (1–3 Å). To overcome
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Fingerprint restoration using cubic Bezier curve BMC Bioinform. (IF 3.242) Pub Date : 2020-12-28 Yanglin Tu; Zengwei Yao; Jiao Xu; Yilin Liu; Zhe Zhang
Fingerprint biometrics play an essential role in authentication. It remains a challenge to match fingerprints with the minutiae or ridges missing. Many fingerprints failed to match their targets due to the incompleteness. In this work, we modeled the fingerprints with Bezier curves and proposed a novel algorithm to detect and restore fragmented ridges in incomplete fingerprints. In the proposed model
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In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells BMC Bioinform. (IF 3.242) Pub Date : 2020-12-28 Monalisa Mandal; Sanjeeb Kumar Sahoo; Priyadarsan Patra; Saurav Mallik; Zhongming Zhao
Cancer stem cells (CSCs) have features such as the ability to self-renew, differentiate into defined progenies and initiate the tumor growth. Treatments of cancer include drugs, chemotherapy and radiotherapy or a combination. However, treatment of cancer by various therapeutic strategies often fail. One possible reason is that the nature of CSCs, which has stem-like properties, make it more dynamic
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Deep learning detection of informative features in tau PET for Alzheimer’s disease classification BMC Bioinform. (IF 3.242) Pub Date : 2020-12-28 Taeho Jo; Kwangsik Nho; Shannon L. Risacher; Andrew J. Saykin
Alzheimer’s disease (AD) is the most common type of dementia, typically characterized by memory loss followed by progressive cognitive decline and functional impairment. Many clinical trials of potential therapies for AD have failed, and there is currently no approved disease-modifying treatment. Biomarkers for early detection and mechanistic understanding of disease course are critical for drug development
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Integrative approach for detecting membrane proteins BMC Bioinform. (IF 3.242) Pub Date : 2020-12-21 Munira Alballa; Gregory Butler
Membrane proteins are key gates that control various vital cellular functions. Membrane proteins are often detected using transmembrane topology prediction tools. While transmembrane topology prediction tools can detect integral membrane proteins, they do not address surface-bound proteins. In this study, we focused on finding the best techniques for distinguishing all types of membrane proteins. This
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ARPIR: automatic RNA-Seq pipelines with interactive report BMC Bioinform. (IF 3.242) Pub Date : 2020-12-21 Giulio Spinozzi; Valentina Tini; Alessia Adorni; Brunangelo Falini; Maria Paola Martelli
RNA-Seq is an increasing used methodology to study either coding and non-coding RNA expression. There are many software tools available for each phase of the RNA-Seq analysis and each of them uses different algorithms. Furthermore, the analysis consists of several steps regarding alignment (primary-analysis), quantification, differential analysis (secondary-analysis) and any tertiary-analysis and can
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Predicting substitutions to modulate disorder and stability in coiled-coils BMC Bioinform. (IF 3.242) Pub Date : 2020-12-21 Yasaman Karami; Paul Saighi; Rémy Vanderhaegen; Denis Gerlier; Sonia Longhi; Elodie Laine; Alessandra Carbone
Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disordered regions in proteins are characterized by lack of stable secondary and tertiary structure under physiological conditions in vitro. They are increasingly recognized as important for protein function
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A2A: a platform for research in biomedical literature search BMC Bioinform. (IF 3.242) Pub Date : 2020-12-21 Maciej Rybinski; Sarvnaz Karimi; Vincent Nguyen; Cecile Paris
Finding relevant literature is crucial for many biomedical research activities and in the practice of evidence-based medicine. Search engines such as PubMed provide a means to search and retrieve published literature, given a query. However, they are limited in how users can control the processing of queries and articles—or as we call them documents—by the search engine. To give this control to both
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Inter-protein residue covariation information unravels physically interacting protein dimers BMC Bioinform. (IF 3.242) Pub Date : 2020-12-17 Sara Salmanian; Hamid Pezeshk; Mehdi Sadeghi
Predicting physical interaction between proteins is one of the greatest challenges in computational biology. There are considerable various protein interactions and a huge number of protein sequences and synthetic peptides with unknown interacting counterparts. Most of co-evolutionary methods discover a combination of physical interplays and functional associations. However, there are only a handful
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Inferring time-dependent population growth rates in cell cultures undergoing adaptation BMC Bioinform. (IF 3.242) Pub Date : 2020-12-17 H. Jonathan G. Lindström; Ran Friedman
The population growth rate is an important characteristic of any cell culture. During sustained experiments, the growth rate may vary due to competition or adaptation. For instance, in presence of a toxin or a drug, an increasing growth rate indicates that the cells adapt and become resistant. Consequently, time-dependent growth rates are fundamental to follow on the adaptation of cells to a changing
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Menoci: lightweight extensible web portal enhancing data management for biomedical research projects BMC Bioinform. (IF 3.242) Pub Date : 2020-12-17 M. Suhr; C. Lehmann; C. R. Bauer; T. Bender; C. Knopp; L. Freckmann; B. Öst Hansen; C. Henke; G. Aschenbrandt; L. K. Kühlborn; S. Rheinländer; L. Weber; B. Marzec; M. Hellkamp; P. Wieder; U. Sax; H. Kusch; S. Y. Nussbeck
Biomedical research projects deal with data management requirements from multiple sources like funding agencies’ guidelines, publisher policies, discipline best practices, and their own users’ needs. We describe functional and quality requirements based on many years of experience implementing data management for the CRC 1002 and CRC 1190. A fully equipped data management software should improve documentation
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Selected abstracts of “Bioinformatics: from Algorithms to Applications 2020” conference BMC Bioinform. (IF 3.242) Pub Date : 2020-12-17
Fourth International Conference “Bioinformatics: From Algorithms to Applications” (BiATA 2020) Alla Lapidus1,*, Anton Korobeynikov1 1Center for Algorithmic Biotechnologies, Saint Petersburg State University, Saint Petersburg, Russia, 199034 Correspondence: Alla Lapidus - a.lapidus@spbu.ru BMC Bioinformatics 2020, 21(Suppl 20): I1 International Conference “Bioinformatics: from Algorithms to Applications”
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Graph embeddings on gene ontology annotations for protein–protein interaction prediction BMC Bioinform. (IF 3.242) Pub Date : 2020-12-16 Xiaoshi Zhong; Jagath C. Rajapakse
Protein–protein interaction (PPI) prediction is an important task towards the understanding of many bioinformatics functions and applications, such as predicting protein functions, gene-disease associations and disease-drug associations. However, many previous PPI prediction researches do not consider missing and spurious interactions inherent in PPI networks. To address these two issues, we define
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DRACP: a novel method for identification of anticancer peptides BMC Bioinform. (IF 3.242) Pub Date : 2020-12-16 Tianyi Zhao; Yang Hu; Tianyi Zang
Millions of people are suffering from cancers, but accurate early diagnosis and effective treatment are still tough for all doctors. Common ways against cancer include surgical operation, radiotherapy and chemotherapy. However, they are all very harmful for patients. Recently, the anticancer peptides (ACPs) have been discovered to be a potential way to treat cancer. Since ACPs are natural biologics
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Filtering de novo indels in parent-offspring trios BMC Bioinform. (IF 3.242) Pub Date : 2020-12-16 Yongzhuang Liu; Jian Liu; Yadong Wang
Identification of de novo indels from whole genome or exome sequencing data of parent-offspring trios is a challenging task in human disease studies and clinical practices. Existing computational approaches usually yield high false positive rate. In this study, we developed a gradient boosting approach for filtering de novo indels obtained by any computational approaches. Through application on the
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BioRel: towards large-scale biomedical relation extraction BMC Bioinform. (IF 3.242) Pub Date : 2020-12-16 Rui Xing; Jie Luo; Tengwei Song
Although biomedical publications and literature are growing rapidly, there still lacks structured knowledge that can be easily processed by computer programs. In order to extract such knowledge from plain text and transform them into structural form, the relation extraction problem becomes an important issue. Datasets play a critical role in the development of relation extraction methods. However,
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