Extracting cancer concepts from clinical notes using natural language processing: a systematic review
Extracting information from free texts using natural language processing (NLP) can save time and reduce the hassle of manually extracting large quantities of data from incredibly complex clinical notes of canc... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 29, 2023 Category: Bioinformatics Authors: Maryam Gholipour, Reza Khajouei, Parastoo Amiri, Sadrieh Hajesmaeel Gohari and Leila Ahmadian Tags: Research Source Type: research
Picky with peakpicking: assessing chromatographic peak quality with simple metrics in metabolomics
Chromatographic peakpicking continues to represent a significant bottleneck in automated LC –MS workflows. Uncontrolled false discovery rates and the lack of manually-calibrated quality metrics require research... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 28, 2023 Category: Bioinformatics Authors: William Kumler, Bryna J. Hazelton and Anitra E. Ingalls Tags: Research Source Type: research
SeQual-Stream: approaching stream processing to quality control of NGS datasets
Quality control of DNA sequences is an important data preprocessing step in many genomic analyses. However, all existing parallel tools for this purpose are based on a batch processing model, needing to have t... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 27, 2023 Category: Bioinformatics Authors: Óscar Castellanos-Rodríguez, Roberto R. Expósito and Juan Touriño Tags: Software Source Type: research
deltaXpress ( ΔXpress): a tool for mapping differentially correlated genes using single-cell qPCR data
High-throughput experiments provide deep insight into the molecular biology of different species, but more tools need to be developed to handle this type of data. At the transcriptomics level, quantitative Pol... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 27, 2023 Category: Bioinformatics Authors: Alexis Germ án Murillo Carrasco, Tatiane Katsue Furuya, Miyuki Uno, Tharcisio Citrangulo Tortelli Jr and Roger Chammas Tags: Software Source Type: research
Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops
We consider two key problems in genomics involving multiple traits: multi-trait genome wide association studies (GWAS), where the goal is to detect genetic variants associated with the traits; and multi-trait ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 26, 2023 Category: Bioinformatics Authors: Aur élie C. Lozano, Hantian Ding, Naoki Abe and Alexander E. Lipka Tags: Research Source Type: research
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
