Pan-genome de Bruijn graph using the bidirectional FM-index
Pan-genome graphs are gaining importance in the field of bioinformatics as data structures to represent and jointly analyze multiple genomes. Compacted de Bruijn graphs are inherently suited for this purpose, ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 26, 2023 Category: Bioinformatics Authors: Lore Depuydt, Luca Renders, Thomas Abeel and Jan Fostier Tags: Research Source Type: research
Deep learning, radiomics and radiogenomics applications in the digital breast tomosynthesis: a systematic review
Recent advancements in computing power and state-of-the-art algorithms have helped in more accessible and accurate diagnosis of numerous diseases. In addition, the development of de novo areas in imaging scien... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 26, 2023 Category: Bioinformatics Authors: Sadam Hussain, Yareth Lafarga-Osuna, Mansoor Ali, Usman Naseem, Masroor Ahmed and Jose Gerardo Tamez-Pe ña Tags: Research Source Type: research
EMDL_m6Am: identifying N6,2 ′-O-dimethyladenosine sites based on stacking ensemble deep learning
N6, 2'-O-dimethyladenosine (m6Am) is an abundant RNA methylation modification on vertebrate mRNAs and is present in the transcription initiation region of mRNAs. It has recently been experimentally shown to be as... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 25, 2023 Category: Bioinformatics Authors: Jianhua Jia, Zhangying Wei and Mingwei Sun Tags: Research Source Type: research
TreeKernel: interpretable kernel machine tests for interactions between -omics and clinical predictors with applications to metabolomics and COPD phenotypes
In this paper, we are interested in interactions between a high-dimensional -omics dataset and clinical covariates. The goal is to evaluate the relationship between a phenotype of interest and a high-dimension... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 25, 2023 Category: Bioinformatics Authors: Charlie M. Carpenter, Lucas Gillenwater, Russell Bowler, Katerina Kechris and Debashis Ghosh Tags: Research Source Type: research
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches
Technical progress in computational hardware allows researchers to use new approaches for sequence alignment problems. For a given sequence, we usually use smaller subsequences (anchors) to find possible candi... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 24, 2023 Category: Bioinformatics Authors: Valeriy Titarenko and Sofya Titarenko Tags: Research Source Type: research
Identification of transcription factor high accumulation DNA zones
Transcription factors (TF) play a crucial role in the regulation of gene transcription; alterations of their activity and binding to DNA areas are strongly involved in cancer and other disease onset and develo... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 20, 2023 Category: Bioinformatics Authors: Silvia Cascianelli, Gaia Ceddia, Alberto Marchesi and Marco Masseroli Tags: Software Source Type: research
Designs for the simultaneous inference of concentration –response curves
An important problem in toxicology in the context of gene expression data is the simultaneous inference of a large number of concentration –response relationships. The quality of the inference substantially dep... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 19, 2023 Category: Bioinformatics Authors: Leonie Sch ürmeyer, Kirsten Schorning and Jörg Rahnenführer Tags: Research Source Type: research
Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects
(Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 19, 2023 Category: Bioinformatics Authors: Yunqing Liu, Jiayi Zhao, Taylor S. Adams, Ningya Wang, Jonas C. Schupp, Weimiao Wu, John E. McDonough, Geoffrey L. Chupp, Naftali Kaminski, Zuoheng Wang and Xiting Yan Tags: Correction Source Type: research
Asterics: a simple tool for the ExploRation and Integration of omiCS data
The rapid development of omics acquisition techniques has induced the production of a large volume of heterogeneous and multi-level omics datasets, which require specific and sometimes complex analyses to obta... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 18, 2023 Category: Bioinformatics Authors: Élise Maigné, Céline Noirot, Julien Henry, Yaa Adu Kesewaah, Ludovic Badin, Sébastien Déjean, Camille Guilmineau, Arielle Krebs, Fanny Mathevet, Audrey Segalini, Laurent Thomassin, David Colongo, Christine Gaspin, Laurence Liaubet and Nathalie Vialan Tags: Software Source Type: research
Artificial Intelligence based wrapper for high dimensional feature selection
Feature selection is important in high dimensional data analysis. The wrapper approach is one of the ways to perform feature selection, but it is computationally intensive as it builds and evaluates models of ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 18, 2023 Category: Bioinformatics Authors: Rahi Jain and Wei Xu Tags: Research Source Type: research
Advances and challenges in Bioinformatics and Biomedical Engineering: IWBBIO 2020
This Supplement issue, presents five research articles which are distributed, mainly due to the subject they address, from the 8th International Work-Conference on Bioinformatics and Biomedical Engineering (IW... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 18, 2023 Category: Bioinformatics Authors: Olga Valenzuela, Mario Cannataro, Irena Rusur, Jianxin Wang, Zhongming Zhao and Ignacio Rojas Tags: Introduction Source Type: research
EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets
Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experienc... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 14, 2023 Category: Bioinformatics Authors: Dao-Feng Zhang, Wei He, Zongze Shao, Iftikhar Ahmed, Yuqin Zhang, Wen-Jun Li and Zhe Zhao Tags: Software Source Type: research
lifex-ep: a robust and efficient software for cardiac electrophysiology simulations
Simulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the need for streamlined, accurate, and high-performance computational too... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 13, 2023 Category: Bioinformatics Authors: Pasquale Claudio Africa, Roberto Piersanti, Francesco Regazzoni, Michele Bucelli, Matteo Salvador, Marco Fedele, Stefano Pagani, Luca Dede ’ and Alfio Quarteroni Tags: Software Source Type: research
cgMSI: pathogen detection within species from nanopore metagenomic sequencing data
Metagenomic sequencing is an unbiased approach that can potentially detect all the known and unidentified strains in pathogen detection. Recently, nanopore sequencing has been emerging as a highly potential to... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 12, 2023 Category: Bioinformatics Authors: Xu Zhu, Lili Zhao, Lihong Huang, Wenxian Yang, Liansheng Wang and Rongshan Yu Tags: Research Source Type: research
Unbiased image segmentation assessment toolkit for quantitative differentiation of state-of-the-art algorithms and pipelines
Image segmentation pipelines are commonly used in microscopy to identify cellular compartments like nucleus and cytoplasm, but there are few standards for comparing segmentation accuracy across pipelines. The ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 12, 2023 Category: Bioinformatics Authors: Vishakha Goyal, Nick J. Schaub, Ty C. Voss and Nathan A. Hotaling Tags: Research Source Type: research
