Predicting potential microbe-disease associations based on auto-encoder and graph convolution network
The increasing body of research has consistently demonstrated the intricate correlation between the human microbiome and human well-being. Microbes can impact the efficacy and toxicity of drugs through various... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 14, 2023 Category: Bioinformatics Authors: Shanghui Lu, Yong Liang, Le Li, Rui Miao, Shuilin Liao, Yongfu Zou, Chengjun Yang and Dong Ouyang Tags: Research Source Type: research
PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data
Detection of exotic plant pathogens and preventing their entry and establishment are critical for the protection of agricultural systems while securing the global trading of agricultural commodities. High-thro... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 13, 2023 Category: Bioinformatics Authors: Xiaojun Hu, Oscar P. Hurtado-Gonzales, Bishwo N. Adhikari, Ronald D. French-Monar, Martha Malapi, Joseph A. Foster and Clint D. McFarland Tags: Software Source Type: research
primerJinn: a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and performing in silico PCR
Multiplex PCR amplifies numerous targets in a single tube reaction and is essential in molecular biology and clinical diagnostics. One of its most important applications is in the targeted sequencing of pathog... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 12, 2023 Category: Bioinformatics Authors: Jason D. Limberis and John Z. Metcalfe Tags: Software Source Type: research
Rendering protein mutation movies with MutAmore
The success of AlphaFold2 in reliable protein three-dimensional (3D) structure prediction, assists the move of structural biology toward studies of protein dynamics and mutational impact on structure and function... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 12, 2023 Category: Bioinformatics Authors: Konstantin Weissenow and Burkhard Rost Tags: Software Source Type: research
A score-based method of immune status evaluation for healthy individuals with complete blood cell counts
With the COVID-19 outbreak, an increasing number of individuals are concerned about their health, particularly their immune status. However, as of now, there is no available algorithm that effectively assesses... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 11, 2023 Category: Bioinformatics Authors: Min Zhang, Chengkui Zhao, Qi Cheng, Jiayu Xu, Nan Xu, Lei Yu and Weixing Feng Tags: Research Source Type: research
An oscillating reaction network with an exact closed form solution in the time domain
Oscillatory behavior is critical to many life sustaining processes such as cell cycles, circadian rhythms, and notch signaling. Important biological functions depend on the characteristics of these oscillation... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 9, 2023 Category: Bioinformatics Authors: Joseph Hellerstein Tags: Research Source Type: research
Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer
Hierarchical classification offers a more specific categorization of data and breaks down large classification problems into subproblems, providing improved prediction accuracy and predictive power for undefin... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 8, 2023 Category: Bioinformatics Authors: Youpeng Yang, Qiuhong Zeng, Gaotong Liu, Shiyao Zheng, Tianyang Luo, Yibin Guo, Jia Tang and Yi Huang Tags: Research Source Type: research
Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs
Allele-specific binding (ASB) events occur when transcription factors (TFs) bind more favorably to one of the two parental alleles at heterozygous single nucleotide polymorphisms (SNPs). Evidence suggests that... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 8, 2023 Category: Bioinformatics Authors: Ying Li, Xiao-Ou Zhang, Yan Liu and Aiping Lu Tags: Software Source Type: research
pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods
Variability in datasets is not only the product of biological processes: they are also the product of technical biases. ComBat and ComBat-Seq are among the most widely used tools for correcting those technical... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 7, 2023 Category: Bioinformatics Authors: Abdelkader Behdenna, Maximilien Colange, Julien Haziza, Aryo Gema, Guillaume App é, Chloé-Agathe Azencott and Akpéli Nordor Tags: Software Source Type: research
Efficient design of synthetic gene circuits under cell-to-cell variability
Synthetic biologists use and combine diverse biological parts to build systems such as genetic circuits that perform desirable functions in, for example, biomedical or industrial applications. Computer-aided d... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 7, 2023 Category: Bioinformatics Authors: Baptiste Turpin, Eline Y. Bijman, Hans-Michael Kaltenbach and J örg Stelling Tags: Research Source Type: research
Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network
Basecalling long DNA sequences is a crucial step in nanopore-based DNA sequencing protocols. In recent years, the CTC-RNN model has become the leading basecalling model, supplanting preceding hidden Markov mod... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 7, 2023 Category: Bioinformatics Authors: Xuechun Xu, Nayanika Bhalla, Patrik St åhl and Joakim Jaldén Tags: Research Source Type: research
Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer
Synonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA maturation, and mRNA half-lives. The possibility that synonymous mutati... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 7, 2023 Category: Bioinformatics Authors: Yiyun Rao, Nabeel Ahmed, Justin Pritchard and Edward P. O ’Brien Tags: Research Source Type: research
G-bic: generating synthetic benchmarks for biclustering
Biclustering is increasingly used in biomedical data analysis, recommendation tasks, and text mining domains, with hundreds of biclustering algorithms proposed. When assessing the performance of these algorith... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 6, 2023 Category: Bioinformatics Authors: Eduardo N. Castanho, Jo ão P. Lobo, Rui Henriques and Sara C. Madeira Tags: Software Source Type: research
Detection for melanoma skin cancer through ACCF, BPPF, and CLF techniques with machine learning approach
Intense sun exposure is a major risk factor for the development of melanoma, an abnormal proliferation of skin cells. Yet, this more prevalent type of skin cancer can also develop in less-exposed areas, such a... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 6, 2023 Category: Bioinformatics Authors: P. Kavitha, G. Ayyappan, Prabhu Jayagopal, Sandeep Kumar Mathivanan, Saurav Mallik, Amal Al-Rasheed, Mohammed S. Alqahtani and Ben Othman Soufiene Tags: Research Source Type: research
Protein –protein interaction site prediction by model ensembling with hybrid feature and self-attention
Protein –protein interactions (PPIs) are crucial in various biological functions and cellular processes. Thus, many computational approaches have been proposed to predict PPI sites. Although significant progres... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - December 5, 2023 Category: Bioinformatics Authors: Hanhan Cong, Hong Liu, Yi Cao, Cheng Liang and Yuehui Chen Tags: Research Source Type: research
