HormoNet: a deep learning approach for hormone-drug interaction prediction
Several experimental evidences have shown that the human endogenous hormones can interact with drugs in many ways and affect drug efficacy. The hormone drug interactions (HDI) are essential for drug treatment ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 28, 2024 Category: Bioinformatics Authors: Neda Emami and Reza Ferdousi Tags: Research Source Type: research
GPAD: a natural language processing-based application to extract the gene-disease association discovery information from OMIM
Thousands of genes have been associated with different Mendelian conditions. One of the valuable sources to track these gene-disease associations (GDAs) is the Online Mendelian Inheritance in Man (OMIM) databa... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 27, 2024 Category: Bioinformatics Authors: K. M. Tahsin Hassan Rahit, Vladimir Avramovic, Jessica X. Chong and Maja Tarailo-Graovac Tags: Research Source Type: research
Correction: Modifying the false discovery rate procedure based on the information theory under arbitrary correlation structure and its performance in high-dimensional genomic data
(Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 23, 2024 Category: Bioinformatics Authors: Sedighe Rastaghi, Azadeh Saki and Hamed Tabesh Tags: Correction Source Type: research
PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes
One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery se... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 22, 2024 Category: Bioinformatics Authors: Katelyn McNair, Peter Salamon, Robert A. Edwards and Anca M. Segall Tags: Research Source Type: research
SNVstory: inferring genetic ancestry from genome sequencing data
Genetic ancestry, inferred from genomic data, is a quantifiable biological parameter. While much of the human genome is identical across populations, it is estimated that as much as 0.4% of the genome can diff... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 20, 2024 Category: Bioinformatics Authors: Audrey E. Bollas, Andrei Rajkovic, Defne Ceyhan, Jeffrey B. Gaither, Elaine R. Mardis and Peter White Tags: Software Source Type: research
A novel microbe-drug association prediction model based on graph attention networks and bilayer random forest
In recent years, the extensive use of drugs and antibiotics has led to increasing microbial resistance. Therefore, it becomes crucial to explore deep connections between drugs and microbes. However, traditiona... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 20, 2024 Category: Bioinformatics Authors: Haiyue Kuang, Zhen Zhang, Bin Zeng, Xin Liu, Hao Zuo, Xingye Xu and Lei Wang Tags: Research Source Type: research
Fusing graph transformer with multi-aggregate GCN for enhanced drug –disease associations prediction
Identification of potential drug –disease associations is important for both the discovery of new indications for drugs and for the reduction of unknown adverse drug reactions. Exploring the potential links bet... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 20, 2024 Category: Bioinformatics Authors: Shihui He, Lijun Yun and Haicheng Yi Tags: Research Source Type: research
CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data
With the increase of the dimensionality in flow cytometry data over the past years, there is a growing need to replace or complement traditional manual analysis (i.e. iterative 2D gating) with automated data a... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 20, 2024 Category: Bioinformatics Authors: Philippe Hauchamps, Babak Bayat, Simon Delandre, Mehdi Hamrouni, Marie Toussaint, Stephane Temmerman, Dan Lin and Laurent Gatto Tags: Research Source Type: research
Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences
The breakthrough high-throughput measurement of the cis-regulatory activity of millions of randomly generated promoters provides an unprecedented opportunity to systematically decode the cis-regulatory logic t... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 20, 2024 Category: Bioinformatics Authors: Il-Youp Kwak, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Daniel J. Garry, Jianyi Zhang and Wuming Gong Tags: Research Source Type: research
Generic model to unravel the deeper insights of viral infections: an empirical application of evolutionary graph coloring in computational network biology
In this study, we demonstrate the gra... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 16, 2024 Category: Bioinformatics Authors: Arnab Kole, Arup Kumar Bag, Anindya Jyoti Pal and Debashis De Tags: Research Source Type: research
Drug –target affinity prediction with extended graph learning-convolutional networks
High-performance computing plays a pivotal role in computer-aided drug design, a field that holds significant promise in pharmaceutical research. The prediction of drug –target affinity (DTA) is a crucial stage... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 16, 2024 Category: Bioinformatics Authors: Haiou Qi, Ting Yu, Wenwen Yu and Chenxi Liu Tags: Research Source Type: research
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format
The STRUCTURE software has gained popularity as a tool for population structure and genetic analysis. Nevertheless, formatting data to meet STRUCTURE's specific requirements can be daunting and susceptible to ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 15, 2024 Category: Bioinformatics Authors: Adam Bessa-Silva Tags: Software Source Type: research
123VCF: an intuitive and efficient tool for filtering VCF files
The advent of Next-Generation Sequencing (NGS) has catalyzed a paradigm shift in medical genetics, enabling the identification of disease-associated variants. However, the vast quantum of data produced by NGS ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 14, 2024 Category: Bioinformatics Authors: Milad Eidi, Samaneh Abdolalizadeh, Soheila Moeini, Masoud Garshasbi and Javad Zahiri Tags: Software Source Type: research
Interpretable deep learning methods for multiview learning
Technological advances have enabled the generation of unique and complementary types of data or views (e.g. genomics, proteomics, metabolomics) and opened up a new era in multiview learning research with the p... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 14, 2024 Category: Bioinformatics Authors: Hengkang Wang, Han Lu, Ju Sun and Sandra E. Safo Tags: Research Source Type: research
Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond
Biological networks have proven invaluable ability for representing biological knowledge. Multilayer networks, which gather different types of nodes and edges in multiplex, heterogeneous and bipartite networks... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 14, 2024 Category: Bioinformatics Authors: Anthony Baptista, Galadriel Bri ère and Anaïs Baudot Tags: Research Source Type: research
