Aguirre-Plans, Joaquim Meseguer, Alberto Molina-Fernandez, Ruben Marín-López, Manuel Alejandro Jumde, Gaurav Casanova, Kevin Bonet, Jaume Fornes, Oriol Fernandez-Fuentes, Narcis Oliva, Baldo
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Published in
BMC Bioinformatics
BackgroundStatistical 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, acco...
Haddad-Boubaker, Sondes Othman, Houcemeddine Touati, Rabeb Ayouni, Kaouther Lakhal, Marwa Ben Mustapha, Imen Ghedira, Kais Kharrat, Maher Triki, Henda
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BMC Bioinformatics
BackgroundCoronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, we investigated the putative implication of 12 vaccines, including BCG, OPV and MMR in the protection against COVID-19. Sequences of the main antigenic proteins in the investigated vaccines and SARS-CoV-2 proteins wer...
Pan, Juming
Published in
BMC Bioinformatics
BackgroundModel averaging has attracted increasing attention in recent years for the analysis of high-dimensional data. By weighting several competing statistical models suitably, model averaging attempts to achieve stable and improved prediction. In this paper, we develop a two-stage model averaging procedure to enhance accuracy and stability in p...
Liu, Bailong Zhu, Xiaoyan Zhang, Lei Liang, Zhizheng Li, Zhengwei
Published in
BMC Bioinformatics
BackgroundCumulative evidence from biological experiments has confirmed that miRNAs have significant roles to diagnose and treat complex diseases. However, traditional medical experiments have limitations in time-consuming and high cost so that they fail to find the unconfirmed miRNA and disease interactions. Thus, discovering potential miRNA-disea...
Guo, Lidong Xu, Mengyang Wang, Wenchao Gu, Shengqiang Zhao, Xia Chen, Fang Wang, Ou Xu, Xun Seim, Inge Fan, Guangyi
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Published in
BMC Bioinformatics
BackgroundSynthetic long reads (SLR) with long-range co-barcoding information are now widely applied in genomics research. Although several tools have been developed for each specific SLR technique, a robust standalone scaffolder with high efficiency is warranted for hybrid genome assembly.ResultsIn this work, we developed a standalone scaffolding ...
Hadifar, Shima Mostafaei, Shayan Behrouzi, Ava Fateh, Abolfazl Riahi, Parisa Siadat, Seyed Davar Vaziri, Farzam
Published in
BMC Bioinformatics
BackgroundA growing body of evidence has shown the association between tuberculosis (TB) infection and lung cancer. However, the possible effect of strain‐specific behavior of Mycobacterium tuberculosis (M.tb) population, the etiological agent of TB infection in this association has been neglected. In this context, this study was conducted to inves...
Kavran, Andrew J. Clauset, Aaron
Published in
BMC Bioinformatics
BackgroundLarge-scale biological data sets are often contaminated by noise, which can impede accurate inferences about underlying processes. Such measurement noise can arise from endogenous biological factors like cell cycle and life history variation, and from exogenous technical factors like sample preparation and instrument variation.ResultsWe d...
Shao, Danying Ahmed, Nabeel Soni, Nishant O’Brien, Edward P.
Published in
BMC Bioinformatics
BackgroundTranslation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this ...
Yohannes, Dawit A. Kaukinen, Katri Kurppa, Kalle Saavalainen, Päivi Greco, Dario
Published in
BMC Bioinformatics
BackgroundDeep immune receptor sequencing, RepSeq, provides unprecedented opportunities for identifying and studying condition-associated T-cell clonotypes, represented by T-cell receptor (TCR) CDR3 sequences. However, due to the immense diversity of the immune repertoire, identification of condition relevant TCR CDR3s from total repertoires has mo...
Fan, Jeremy Huang, Steven Chorlton, Samuel D.
Published in
BMC Bioinformatics
BackgroundAs the use of nanopore sequencing for metagenomic analysis increases, tools capable of performing long-read taxonomic classification (ie. determining the composition of a sample) in a fast and accurate manner are needed. Existing tools were either designed for short-read data (eg. Centrifuge), take days to analyse modern sequencer outputs...
