Mora: abundance aware metagenomic read re-assignment for disentangling similar strains
Taxonomic classification of reads obtained by metagenomic sequencing is often a first step for understanding a microbial community, but correctly assigning sequencing reads to the strain or sub-species level h... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 23, 2024 Category: Bioinformatics Authors: Andrew Zheng, Jim Shaw and Yun William Yu Tags: Research Source Type: research
SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses
The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 22, 2024 Category: Bioinformatics Authors: Luan Pinto Rabelo, Davidson Sodr é, Rodrigo Petry Corrêa de Sousa, Luciana Watanabe, Grazielle Gomes, Iracilda Sampaio and Marcelo Vallinoto Tags: Software Source Type: research
TEC-miTarget: enhancing microRNA target prediction based on deep learning of ribonucleic acid sequences
MicroRNAs play a critical role in regulating gene expression by binding to specific target sites within gene transcripts, making the identification of microRNA targets a prominent focus of research. Convention... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 20, 2024 Category: Bioinformatics Authors: Tingpeng Yang, Yu Wang and Yonghong He Tags: Research Source Type: research
Noisecut: a python package for noise-tolerant classification of binary data using prior knowledge integration and max-cut solutions
Classification of binary data arises naturally in many clinical applications, such as patient risk stratification through ICD codes. One of the key practical challenges in data classification using machine lea... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 20, 2024 Category: Bioinformatics Authors: Moein E. Samadi, Hedieh Mirzaieazar, Alexander Mitsos and Andreas Schuppert Tags: Software Source Type: research
Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning
Accurately identifying drug-target interaction (DTI), affinity (DTA), and binding sites (DTS) is crucial for drug screening, repositioning, and design, as well as for understanding the functions of target. Alt... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 20, 2024 Category: Bioinformatics Authors: Xin Zeng, Guang-Peng Su, Shu-Juan Li, Shuang-Qing Lv, Meng-Liang Wen and Yi Li Tags: Software Source Type: research
A protein network refinement method based on module discovery and biological information
The identification of essential proteins can help in understanding the minimum requirements for cell survival and development to discover drug targets and prevent disease. Nowadays, node ranking methods are a ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 20, 2024 Category: Bioinformatics Authors: Li Pan, Haoyue Wang, Bo Yang and Wenbin Li Tags: Research Source Type: research
MMGAT: a graph attention network framework for ATAC-seq motifs finding
Motif finding in Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data is essential to reveal the intricacies of transcription factor binding sites (TFBSs) and their pivotal roles in gene... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 20, 2024 Category: Bioinformatics Authors: Xiaotian Wu, Wenju Hou, Ziqi Zhao, Lan Huang, Nan Sheng, Qixing Yang, Shuangquan Zhang and Yan Wang Tags: Research Source Type: research
TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing
High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, ‘N’s. PCR duplicates introduced i... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 18, 2024 Category: Bioinformatics Authors: Jianqiao Hu, Sai Luo, Ming Tian and Adam Yongxin Ye Tags: Software Source Type: research
Biomedical semantic text summarizer
Text summarization is a challenging problem in Natural Language Processing, which involves condensing the content of textual documents without losing their overall meaning and information content, In the domai... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 16, 2024 Category: Bioinformatics Authors: Mahira Kirmani, Gagandeep Kour, Mudasir Mohd, Nasrullah Sheikh, Dawood Ashraf Khan, Zahid Maqbool, Mohsin Altaf Wani and Abid Hussain Wani Tags: Research Source Type: research
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes
With the rapid increase in throughput of long-read sequencing technologies, recent studies have explored their potential for taxonomic classification by using alignment-based approaches to reduce the impact of... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 16, 2024 Category: Bioinformatics Authors: Rafael Peres da Silva, Chayaporn Suphavilai and Niranjan Nagarajan Tags: Research Source Type: research
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
