Multi-label classification with XGBoost for metabolic pathway prediction
Metabolic pathway prediction is one possible approach to address the problem in system biology of reconstructing an organism ’s metabolic network from its genome sequence. Recently there have been developments ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 1, 2024 Category: Bioinformatics Authors: Hyunwhan Joe and Hong-Gee Kim Tags: Research Source Type: research
Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA –miRNA–mRNA networks
Non-coding RNAs represent a large part of the human transcriptome and have been shown to play an important role in disease such as cancer. However, their biological functions are still incompletely understood.... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 1, 2024 Category: Bioinformatics Authors: Rose-Marie Fraboulet, Yanis Si Ahmed, Marc Aubry, Sebastien Corre, Marie-Dominique Galibert and Yuna Blum Tags: Software Source Type: research
ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs
Transcriptome assembly from RNA-sequencing data in species without a reliable reference genome has to be performed de novo, but studies have shown that de novo methods often have inadequate ability to reconstr... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 1, 2024 Category: Bioinformatics Authors: Karl Johan Westrin, Warren W. Kretzschmar and Olof Emanuelsson Tags: Software Source Type: research
Multivariate pattern analysis: a method and software to reveal, quantify, and visualize predictive association patterns in multicollinear data
Strongly multicollinear covariates, such as those typically represented in metabolomics applications, represent a challenge for multivariate regression analysis. These challenges are commonly circumvented by r... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 31, 2024 Category: Bioinformatics Authors: Tim U. H. Baumeister, Eivind Aadland, Roger G. Linington and Olav M. Kvalheim Tags: Software Source Type: research
Learning self-supervised molecular representations for drug –drug interaction prediction
Drug –drug interactions (DDI) are a critical concern in healthcare due to their potential to cause adverse effects and compromise patient safety. Supervised machine learning models for DDI prediction need to be... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 30, 2024 Category: Bioinformatics Authors: Rogia Kpanou, Patrick Dallaire, Elsa Rousseau and Jacques Corbeil Tags: Research Source Type: research
CCL-DTI: contributing the contrastive loss in drug –target interaction prediction
The Drug –Target Interaction (DTI) prediction uses a drug molecule and a protein sequence as inputs to predict the binding affinity value. In recent years, deep learning-based models have gotten more attention.... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 30, 2024 Category: Bioinformatics Authors: Alireza Dehghan, Karim Abbasi, Parvin Razzaghi, Hossein Banadkuki and Sajjad Gharaghani Tags: Research Source Type: research
PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes
Genome streamlining, the process by which genomes become smaller and encode fewer genes over time, is a common phenomenon among pathogenic bacteria. This reduction is driven by selection for minimized energy e... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 30, 2024 Category: Bioinformatics Authors: Abigail Glascock, Eric Waltari, Gytis Dudas, Joan Wong and Vida Ahyong Tags: Software Source Type: research
PredictEFC: a fast and efficient multi-label classifier for predicting enzyme family classes
Enzymes play an irreplaceable and important role in maintaining the lives of living organisms. The Enzyme Commission (EC) number of an enzyme indicates its essential functions. Correct identification of the fi... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 30, 2024 Category: Bioinformatics Authors: Lei Chen, Chenyu Zhang and Jing Xu Tags: Research Source Type: research
Flux sampling in genome-scale metabolic modeling of microbial communities
Microbial communities play a crucial role in ecosystem function through metabolic interactions. Genome-scale modeling is a promising method to understand these interactions and identify strategies to optimize ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 29, 2024 Category: Bioinformatics Authors: Patrick E. Gelbach, Handan Cetin and Stacey D. Finley Tags: Research Source Type: research
Predicting lncRNA-disease associations using multiple metapaths in hierarchical graph attention networks
Many biological studies have shown that lncRNAs regulate the expression of epigenetically related genes. The study of lncRNAs has helped to deepen our understanding of the pathogenesis of complex diseases at t... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 29, 2024 Category: Bioinformatics Authors: Dengju Yao, Yuexiao Deng, Xiaojuan Zhan and Xiaorong Zhan Tags: Research Source Type: research
MIWE: detecting the critical states of complex biological systems by the mutual information weighted entropy
Complex biological systems often undergo sudden qualitative changes during their dynamic evolution. These critical transitions are typically characterized by a catastrophic progression of the system. Identifyi... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 27, 2024 Category: Bioinformatics Authors: Yuke Xie, Xueqing Peng and Peiluan Li Tags: Research Source Type: research
Fast computation of the eigensystem of genomic similarity matrices
The computation of a similarity measure for genomic data is a standard tool in computational genetics. The principal components of such matrices are routinely used to correct for biases due to confounding by p... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 25, 2024 Category: Bioinformatics Authors: Georg Hahn, Sharon M. Lutz, Julian Hecker, Dmitry Prokopenko, Michael H. Cho, Edwin K. Silverman, Scott T. Weiss and Christoph Lange Tags: Research Source Type: research
Anchor Clustering for million-scale immune repertoire sequencing data
The clustering of immune repertoire data is challenging due to the computational cost associated with a very large number of pairwise sequence comparisons. To overcome this limitation, we developed Anchor Clus... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 25, 2024 Category: Bioinformatics Authors: Haiyang Chang, Daniel A. Ashlock, Steffen P. Graether and Stefan M. Keller Tags: Research Source Type: research
InClust+: the deep generative framework with mask modules for multimodal data integration, imputation, and cross-modal generation
With the development of single-cell technology, many cell traits can be measured. Furthermore, the multi-omics profiling technology could jointly measure two or more traits in a single cell simultaneously. In ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 24, 2024 Category: Bioinformatics Authors: Lifei Wang, Rui Nie, Xuexia Miao, Yankai Cai, Anqi Wang, Hanwen Zhang, Jiang Zhang and Jun Cai Tags: Research Source Type: research
Tpgen: a language model for stable protein design with a specific topology structure
Natural proteins occupy a small portion of the protein sequence space, whereas artificial proteins can explore a wider range of possibilities within the sequence space. However, specific requirements may not b... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - January 23, 2024 Category: Bioinformatics Authors: Xiaoping Min, Chongzhou Yang, Jun Xie, Yang Huang, Nan Liu, Xiaocheng Jin, Tianshu Wang, Zhibo Kong, Xiaoli Lu, Shengxiang Ge, Jun Zhang and Ningshao Xia Tags: Research Source Type: research
