Role of environmental specificity in CASP results
Recently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical As... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 11, 2023 Category: Bioinformatics Authors: Irena Roterman, Katarzyna Stapor and Leszek Konieczny Tags: Research Source Type: research
Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools
Single-stranded nucleic acids (ssNAs) have important biological roles and a high biotechnological potential linked to their ability to bind to numerous molecular targets. This depends on the different spatial ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 8, 2023 Category: Bioinformatics Authors: Thomas Binet, S éverine Padiolleau-Lefèvre, Stéphane Octave, Bérangère Avalle and Irene Maffucci Tags: Research Source Type: research
A model-based clustering via mixture of hierarchical models with covariate adjustment for detecting differentially expressed genes from paired design
The causes of many complex human diseases are still largely unknown. Genetics plays an important role in uncovering the molecular mechanisms of complex human diseases. A key step to characterize the genetics o... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 8, 2023 Category: Bioinformatics Authors: Yixin Zhang, Wei Liu and Weiliang Qiu Tags: Research Source Type: research
ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications
Processing raw genomic data for downstream applications such as imputation, association studies, and modeling requires numerous third-party bioinformatics software tools. It is highly time-consuming and resour... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 8, 2023 Category: Bioinformatics Authors: Noah Herrick and Susan Walsh Tags: Software Source Type: research
Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides
In proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications remains challenging, as it is difficult to strike a balance between reasonable execution time, a ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 8, 2023 Category: Bioinformatics Authors: Gr égoire Prunier, Mehdi Cherkaoui, Albane Lysiak, Olivier Langella, Mélisande Blein-Nicolas, Virginie Lollier, Emile Benoist, Géraldine Jean, Guillaume Fertin, Hélène Rogniaux and Dominique Tessier Tags: Software Source Type: research
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering
Categorizing cells into distinct types can shed light on biological tissue functions and interactions, and uncover specific mechanisms under pathological conditions. Since gene expression throughout a populati... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 7, 2023 Category: Bioinformatics Authors: Hanjing Jiang, Yabing Huang, Qianpeng Li and Boyuan Feng Tags: Research Source Type: research
Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone
The aqueous environment directs the protein folding process towards the generation of micelle-type structures, which results in the exposure of hydrophilic residues on the surface (polarity) and the concentrat... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 7, 2023 Category: Bioinformatics Authors: Irena Roterman, Katarzyna Stapor and Leszek Konieczny Tags: Research Source Type: research
Hybrid deep learning approach to improve classification of low-volume high-dimensional data
The performance of machine learning classification methods relies heavily on the choice of features. In many domains, feature generation can be labor-intensive and require domain knowledge, and feature selecti... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 7, 2023 Category: Bioinformatics Authors: Pegah Mavaie, Lawrence Holder and Michael K. Skinner Tags: Research Source Type: research
Sctensor detects many-to-many cell –cell interactions from single cell RNA-sequencing data
Complex biological systems are described as a multitude of cell –cell interactions (CCIs). Recent single-cell RNA-sequencing studies focus on CCIs based on ligand–receptor (L–R) gene co-expression but the analy... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 7, 2023 Category: Bioinformatics Authors: Koki Tsuyuzaki, Manabu Ishii and Itoshi Nikaido Tags: Software Source Type: research
Multilayer network alignment based on topological assessment via embeddings
Network graphs allow modelling the real world objects in terms of interactions. In a multilayer network, the interactions are distributed over layers (i.e., intralayer and interlayer edges). Network alignment ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 6, 2023 Category: Bioinformatics Authors: Pietro Cinaglia, Marianna Milano and Mario Cannataro Tags: Software Source Type: research
Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data
Microhaplotypes have the potential to be more cost-effective than SNPs for applications that require genetic panels of highly variable loci. However, development of microhaplotype panels is hindered by a lack ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 3, 2023 Category: Bioinformatics Authors: Thomas A. Delomas and Stuart C. Willis Tags: Research Source Type: research
Predicting active enhancers with DNA methylation and histone modification
Enhancers play a crucial role in gene regulation, and some active enhancers produce noncoding RNAs known as enhancer RNAs (eRNAs) bi-directionally. The most commonly used method for detecting eRNAs is CAGE-seq... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 2, 2023 Category: Bioinformatics Authors: Ximei Luo, Qun Li, Yifan Tang, Yan Liu, Quan Zou, Jie Zheng, Ying Zhang and Lei Xu Tags: Research Source Type: research
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models
The PubMed archive contains more than 34 million articles; consequently, it is becoming increasingly difficult for a biomedical researcher to keep up-to-date with different knowledge domains. Computationally e... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 1, 2023 Category: Bioinformatics Authors: Robert J. Millikin, Kalpana Raja, John Steill, Cannon Lock, Xuancheng Tu, Ian Ross, Lam C. Tsoi, Finn Kuusisto, Zijian Ni, Miron Livny, Brian Bockelman, James Thomson and Ron Stewart Tags: Software Source Type: research
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug –drug interactions
During drug development, it is essential to gather information about the change of clinical exposure of a drug (object) due to the pharmacokinetic (PK) drug-drug interactions (DDIs) with another drug (precipit... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 1, 2023 Category: Bioinformatics Authors: Joel Zirkle, Xiaomei Han, Rebecca Racz, Mohammadreza Samieegohar, Anik Chaturbedi, John Mann, Shilpa Chakravartula and Zhihua Li Tags: Research Source Type: research
Structure-informed clustering for population stratification in association studies
Identifying variants associated with complex traits is a challenging task in genetic association studies due to linkage disequilibrium (LD) between genetic variants and population stratification, unrelated to ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - October 31, 2023 Category: Bioinformatics Authors: Aritra Bose, Myson Burch, Agniva Chowdhury, Peristera Paschou and Petros Drineas Tags: Research Source Type: research
