DAE-CFR: detecting microRNA-disease associations using deep autoencoder and combined feature representation
MicroRNA (miRNA) has been shown to play a key role in the occurrence and progression of diseases, making uncovering miRNA-disease associations vital for disease prevention and therapy. However, traditional lab... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 29, 2024 Category: Bioinformatics Authors: Yanling Liu, Ruiyan Zhang, Xiaojing Dong, Hong Yang, Jing Li, Hongyan Cao, Jing Tian and Yanbo Zhang Tags: Research Source Type: research
GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes
Michaelis constant (KM) is one of essential parameters for enzymes kinetics in the fields of protein engineering, enzyme engineering, and synthetic biology. As overwhelming experimental measurements of KM are dif... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 28, 2024 Category: Bioinformatics Authors: Xiao He and Ming Yan Tags: Research Source Type: research
Utilizing genomic signatures to gain insights into the dynamics of SARS-CoV-2 through Machine and Deep Learning techniques
The global spread of the SARS-CoV-2 pandemic, originating in Wuhan, China, has had profound consequences on both health and the economy. Traditional alignment-based phylogenetic tree methods for tracking epide... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 27, 2024 Category: Bioinformatics Authors: Ahmed M. A. Elsherbini, Amr Hassan Elkholy, Youssef M. Fadel, Gleb Goussarov, Ahmed Mohamed Elshal, Mohamed El-Hadidi and Mohamed Mysara Tags: Research Source Type: research
Classifying breast cancer subtypes on multi-omics data via sparse canonical correlation analysis and deep learning
Classifying breast cancer subtypes is crucial for clinical diagnosis and treatment. However, the early symptoms of breast cancer may not be apparent. Rapid advances in high-throughput sequencing technology hav... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 27, 2024 Category: Bioinformatics Authors: Yiran Huang, Pingfan Zeng and Cheng Zhong Tags: Research Source Type: research
SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images
Cancer is one of the leading causes of deaths worldwide. Survival analysis and prediction of cancer patients is of great significance for their precision medicine. The robustness and interpretability of the su... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 27, 2024 Category: Bioinformatics Authors: Shuo Wang, Yuanning Liu, Hao Zhang and Zhen Liu Tags: Research Source Type: research
Slideflow: deep learning for digital histopathology with real-time whole-slide visualization
Deep learning methods have emerged as powerful tools for analyzing histopathological images, but current methods are often specialized for specific domains and software environments, and few open-source option... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 27, 2024 Category: Bioinformatics Authors: James M. Dolezal, Sara Kochanny, Emma Dyer, Siddhi Ramesh, Andrew Srisuwananukorn, Matteo Sacco, Frederick M. Howard, Anran Li, Prajval Mohan and Alexander T. Pearson Tags: Software Source Type: research
biomapp::chip: large-scale motif analysis
Discovery biological motifs plays a fundamental role in understanding regulatory mechanisms. Computationally, they can be efficiently represented as kmers, making the counting of these elements a critical aspect ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 26, 2024 Category: Bioinformatics Authors: Jader M. Caldonazzo Garbelini, Danilo S. Sanches and Aurora T. Ramirez Pozo Tags: Software Source Type: research
HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses
The RNA-Recognition motif (RRM) is a protein domain that binds single-stranded RNA (ssRNA) and is present in as much as 2% of the human genome. Despite this important role in biology, RRM-ssRNA interactions ar... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 26, 2024 Category: Bioinformatics Authors: Anna Kravchenko, Sjoerd Jacob de Vries, Malika Sma ïl-Tabbone and Isaure Chauvot de Beauchene Tags: Research Source Type: research
COSAP: Comparative Sequencing Analysis Platform
Recent improvements in sequencing technologies enabled detailed profiling of genomic features. These technologies mostly rely on short reads which are merged and compared to reference genome for variant identi... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 26, 2024 Category: Bioinformatics Authors: Mehmet Arif Ergun, Omer Cinal, Berkant Bak ışlı, Abdullah Asım Emül and Mehmet Baysan Tags: Software Source Type: research
m6A-TCPred: a web server to predict tissue-conserved human m6A sites using machine learning approach
N6-methyladenosine (m6A) is the most prevalent post-transcriptional modification in eukaryotic cells that plays a crucial role in regulating various biological processes, and dysregulation of m6A status is involv... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 25, 2024 Category: Bioinformatics Authors: Gang Tu, Xuan Wang, Rong Xia and Bowen Song Tags: Research Source Type: research
Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes
Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains, or species to infer the relative abundances of sequences present in a sample. This observation plays an importan... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 23, 2024 Category: Bioinformatics Authors: Jasper van Bemmelen, Davida S. Smyth and Jasmijn A. Baaijens Tags: Research Source Type: research
Improving somatic exome sequencing performance by biological replicates
Next-generation sequencing (NGS) technologies offer fast and inexpensive identification of DNA sequences. Somatic sequencing is among the primary applications of NGS, where acquired (non-inherited) variants ar... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 22, 2024 Category: Bioinformatics Authors: Yunus Emre Cebeci, Rumeysa Aslihan Erturk, Mehmet Arif Ergun and Mehmet Baysan Tags: Research Source Type: research
HIHISIV: a database of gene expression in HIV and SIV host immune response
In the battle of the host against lentiviral pathogenesis, the immune response is crucial. However, several questions remain unanswered about the interaction with different viruses and their influence on disea... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 22, 2024 Category: Bioinformatics Authors: Raquel L. Costa, Luiz Gadelha, Mirela D ’arc, Marcelo Ribeiro-Alves, David L. Robertson, Jean-Marc Schwartz, Marcelo A. Soares and Fábio Porto Tags: Database Source Type: research
Cell4D: a general purpose spatial stochastic simulator for cellular pathways
With the generation of vast compendia of biological datasets, the challenge is how best to interpret ‘omics data alongside biochemical and other small-scale experiments to gain meaningful biological insights. ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 21, 2024 Category: Bioinformatics Authors: Donny Chan, Graham L. Cromar, Billy Taj and John Parkinson Tags: Software Source Type: research
NanoBERTa-ASP: predicting nanobody paratope based on a pretrained RoBERTa model
Nanobodies, also known as VHH or single-domain antibodies, are unique antibody fragments derived solely from heavy chains. They offer advantages of small molecules and conventional antibodies, making them prom... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - March 21, 2024 Category: Bioinformatics Authors: Shangru Li, Xiangpeng Meng, Rui Li, Bingding Huang and Xin Wang Tags: Research Source Type: research
