Optimizing spatio-temporal correlation structures for modeling food security in Africa: a simulation-based investigation
This study investigates the impact of spatio- temporal correlation using four spatio-temporal models: Spatio-Temporal Poisson Linear Trend Model (SPLTM), Poisson Temporal Model (TMS), Spatio-Temporal Poisson A... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 27, 2024 Category: Bioinformatics Authors: Adusei Bofa and Temesgen Zewotir Tags: Research Source Type: research
Exploring combinations of dimensionality reduction, transfer learning, and regularization methods for predicting binary phenotypes with transcriptomic data
Numerous transcriptomic-based models have been developed to predict or understand the fundamental mechanisms driving biological phenotypes. However, few models have successfully transitioned into clinical prac... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 26, 2024 Category: Bioinformatics Authors: S. R. Oshternian, S. Loipfinger, A. Bhattacharya and R. S. N. Fehrmann Tags: Research Source Type: research
Orthogonal multimodality integration and clustering in single-cell data
Multimodal integration combines information from different sources or modalities to gain a more comprehensive understanding of a phenomenon. The challenges in multi-omics data analysis lie in the complexity, h... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 25, 2024 Category: Bioinformatics Authors: Yufang Liu, Yongkai Chen, Haoran Lu, Wenxuan Zhong, Guo-Cheng Yuan and Ping Ma Tags: Research Source Type: research
Improvements in viral gene annotation using large language models and soft alignments
The annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute for viral proteins, which demonstrate limited homology to known protein... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 25, 2024 Category: Bioinformatics Authors: William L. Harrigan, Barbra D. Ferrell, K. Eric Wommack, Shawn W. Polson, Zachary D. Schreiber and Mahdi Belcaid Tags: Research Source Type: research
Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems
The Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 25, 2024 Category: Bioinformatics Authors: Leonardo Giannantoni, Roberta Bardini, Alessandro Savino and Stefano Di Carlo Tags: Research Source Type: research
OrthoRefine: automated enhancement of prior ortholog identification via synteny
Identifying orthologs continues to be an early and imperative step in genome analysis but remains a challenging problem. While synteny (conservation of gene order) has previously been used independently and in... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 25, 2024 Category: Bioinformatics Authors: J. Ludwig and J. Mr ázek Tags: Software Source Type: research
OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies
The results of high-throughput biology ( ‘omic’) experiments provide insight into biological mechanisms but can be challenging to explore, archive and share. The scale of these challenges continues to grow as o... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - April 24, 2024 Category: Bioinformatics Authors: Terrence R. Ernst, John D. Blischak, Paul Nordlund, Joe Dalen, Justin Moore, Akshay Bhamidipati, Pankaj Dwivedi, Joe LoGrasso, Marco Rocha Curado and Brett Warren Engelmann Tags: Software Source Type: research
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
