Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed)
Genomes are inherently inhomogeneous, with features such as base composition, recombination, gene density, and gene expression varying along chromosomes. Evolutionary, biological, and biomedical analyses aim t... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 16, 2024 Category: Bioinformatics Authors: Claus Vogl, Mariia Karapetiants, Bur çin Yıldırım, Hrönn Kjartansdóttir, Carolin Kosiol, Juraj Bergman, Michal Majka and Lynette Caitlin Mikula Tags: Research Source Type: research
Designing and delivering bioinformatics project-based learning in East Africa
The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its go... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 14, 2024 Category: Bioinformatics Authors: Caleb K. Kibet, Jean-Baka Domelevo Entfellner, Daudi Jjingo, Etienne Pierre de Villiers, Santie de Villiers, Karen Wambui, Sam Kinyanjui and Daniel Masiga Tags: Research Source Type: research
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach
Protein toxins are defense mechanisms and adaptations found in various organisms and microorganisms, and their use in scientific research as therapeutic candidates is gaining relevance due to their effectivene... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 12, 2024 Category: Bioinformatics Authors: Jorge F. Beltr án, Lisandra Herrera-Belén, Fernanda Parraguez-Contreras, Jorge G. Farías, Jorge Machuca-Sepúlveda and Stefania Short Tags: Software Source Type: research
Biomarker discovery with quantum neural networks: a case-study in CTLA4-activation pathways
Biomarker discovery is a challenging task due to the massive search space. Quantum computing and quantum Artificial Intelligence (quantum AI) can be used to address the computational problem of biomarker disco... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 12, 2024 Category: Bioinformatics Authors: Phuong-Nam Nguyen Tags: Research Source Type: research
KEGG orthology prediction of bacterial proteins using natural language processing
The advent of high-throughput technologies has led to an exponential increase in uncharacterized bacterial protein sequences, surpassing the capacity of manual curation. A large number of bacterial protein seq... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 11, 2024 Category: Bioinformatics Authors: Jing Chen, Haoyu Wu and Ning Wang Tags: Research Source Type: research
Control of false discoveries in grouped hypothesis testing for eQTL data
Expression quantitative trait locus (eQTL) analysis aims to detect the genetic variants that influence the expression of one or more genes. Gene-level eQTL testing forms a natural grouped-hypothesis testing st... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 11, 2024 Category: Bioinformatics Authors: Pratyaydipta Rudra, Yi-Hui Zhou, Andrew Nobel and Fred A. Wright Tags: Research Source Type: research
DPI_CDF: druggable protein identifier using cascade deep forest
Drug targets in living beings perform pivotal roles in the discovery of potential drugs. Conventional wet-lab characterization of drug targets is although accurate but generally expensive, slow, and resource i... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 5, 2024 Category: Bioinformatics Authors: Muhammad Arif, Ge Fang, Ali Ghulam, Saleh Musleh and Tanvir Alam Tags: Research Source Type: research
Multiple phenotype association tests based on sliced inverse regression
Joint analysis of multiple phenotypes in studies of biological systems such as Genome-Wide Association Studies is critical to revealing the functional interactions between various traits and genetic variants, ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 4, 2024 Category: Bioinformatics Authors: Wenyuan Sun, Kyongson Jon and Wensheng Zhu Tags: Research Source Type: research
CAT-DTI: cross-attention and Transformer network with domain adaptation for drug-target interaction prediction
Accurate and efficient prediction of drug-target interaction (DTI) is critical to advance drug development and reduce the cost of drug discovery. Recently, the employment of deep learning methods has enhanced ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 2, 2024 Category: Bioinformatics Authors: Xiaoting Zeng, Weilin Chen and Baiying Lei Tags: Research Source Type: research
CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny
The rapid advancement of new genomic sequencing technology has enabled the development of multi-omic single-cell sequencing assays. These assays profile multiple modalities in the same cell and can often yield... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 2, 2024 Category: Bioinformatics Authors: Garth L. Kong, Thai T. Nguyen, Wesley K. Rosales, Anjali D. Panikar, John H. W. Cheney, Theresa A. Lusardi, William M. Yashar, Brittany M. Curtiss, Sarah A. Carratt, Theodore P. Braun and Julia E. Maxson Tags: Software Source Type: research
Predicting condensate formation of protein and RNA under various environmental conditions
Liquid –liquid phase separation (LLPS) by biomolecules plays a central role in various biological phenomena and has garnered significant attention. The behavior of LLPS is strongly influenced by the characteris... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 2, 2024 Category: Bioinformatics Authors: Ka Yin Chin, Shoichi Ishida, Yukio Sasaki and Kei Terayama Tags: Research Source Type: research
MFSynDCP: multi-source feature collaborative interactive learning for drug combination synergy prediction
Drug combination therapy is generally more effective than monotherapy in the field of cancer treatment. However, screening for effective synergistic combinations from a wide range of drug combinations is parti... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 1, 2024 Category: Bioinformatics Authors: Yunyun Dong, Yunqing Chang, Yuxiang Wang, Qixuan Han, Xiaoyuan Wen, Ziting Yang, Yan Zhang, Yan Qiang, Kun Wu, Xiaole Fan and Xiaoqiang Ren Tags: Research Source Type: research
Feature-specific quantile normalization and feature-specific mean –variance normalization deliver robust bi-directional classification and feature selection performance between microarray and RNAseq data
Cross-platform normalization seeks to minimize technological bias between microarray and RNAseq whole-transcriptome data. Incorporating multiple gene expression platforms permits external validation of experim... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 29, 2024 Category: Bioinformatics Authors: Daniel Skubleny, Sunita Ghosh, Jennifer Spratlin, Daniel E. Schiller and Gina R. Rayat Tags: Research Source Type: research
Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes
Metagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology particularly. The technology has revolutionized the studies of microbes and ena... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 29, 2024 Category: Bioinformatics Authors: Zhanshan (Sam) Ma Tags: Research Source Type: research
Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data
Even though high-throughput transcriptome sequencing is routinely performed in many laboratories, computational analysis of such data remains a cumbersome process often executed manually, hence error-prone and... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 29, 2024 Category: Bioinformatics Authors: Patrick Blumenkamp, Max Pfister, Sonja Diedrich, Karina Brinkrolf, Sebastian Jaenicke and Alexander Goesmann Tags: Software Source Type: research
