Advice to a Young Mathematical Biologist
Bull Math Biol. 2024 Apr 9;86(5):52. doi: 10.1007/s11538-024-01269-1.ABSTRACTThis paper offers advice to early-mid career researchers in Mathematical Biology from ten past and current Presidents of the Society for Mathematical Biology. The topics covered include deciding if a career in academia is right for you; finding and working with a mentor; building collaborations and working with those from other disciplines; formulating a research question; writing a paper; reviewing papers; networking; writing fellowship or grant proposals; applying for faculty positions; and preparing and giving lectures. While written with mathe...
Source: Bulletin of Mathematical Biology - April 9, 2024 Category: Bioinformatics Authors: Paul A Roberts Source Type: research
Advancing Drug-Target Interaction prediction with BERT and subsequence embedding
Comput Biol Chem. 2024 Apr 5;110:108058. doi: 10.1016/j.compbiolchem.2024.108058. Online ahead of print.ABSTRACTExploring the relationship between proteins and drugs plays a significant role in discovering new synthetic drugs. The Drug-Target Interaction (DTI) prediction is a fundamental task in the relationship between proteins and drugs. Unlike encoding proteins by amino acids, we use amino acid subsequence to encode proteins, which simulates the biological process of DTI better. For this research purpose, we proposed a novel deep learning framework based on Bidirectional Encoder Representation from Transformers (BERT), ...
Source: Computational Biology and Chemistry - April 9, 2024 Category: Bioinformatics Authors: Zhihui Yang Juan Liu Feng Yang Xiaolei Zhang Qiang Zhang Xuekai Zhu Peng Jiang Source Type: research
Mathematical Models of Early Hepatitis B Virus Dynamics in Humanized Mice
Bull Math Biol. 2024 Apr 9;86(5):53. doi: 10.1007/s11538-024-01284-2.ABSTRACTAnalyzing the impact of the adaptive immune response during acute hepatitis B virus (HBV) infection is essential for understanding disease progression and control. Here we developed mathematical models of HBV infection which either lack terms for adaptive immune responses, or assume adaptive immune responses in the form of cytolytic immune killing, non-cytolytic immune cure, or non-cytolytic-mediated block of viral production. We validated the model that does not include immune responses against temporal serum hepatitis B DNA (sHBV) and temporal s...
Source: Bulletin of Mathematical Biology - April 9, 2024 Category: Bioinformatics Authors: Stanca M Ciupe Harel Dahari Alexander Ploss Source Type: research
Advice to a Young Mathematical Biologist
Bull Math Biol. 2024 Apr 9;86(5):52. doi: 10.1007/s11538-024-01269-1.ABSTRACTThis paper offers advice to early-mid career researchers in Mathematical Biology from ten past and current Presidents of the Society for Mathematical Biology. The topics covered include deciding if a career in academia is right for you; finding and working with a mentor; building collaborations and working with those from other disciplines; formulating a research question; writing a paper; reviewing papers; networking; writing fellowship or grant proposals; applying for faculty positions; and preparing and giving lectures. While written with mathe...
Source: Bulletin of Mathematical Biology - April 9, 2024 Category: Bioinformatics Authors: Paul A Roberts Source Type: research
Flanked Block-Interchange Distance on Strings
(Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics)
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - April 9, 2024 Category: Bioinformatics Source Type: research
Computational screening identifies depsidones as promising Aurora A kinase inhibitors: extra precision docking and molecular dynamics studies
In this study, we explored the potential of depsidone analogues as inhibitors of Aurora A kinase through computational methods. A molecular docking studies of 260 depsidone molecules against Aurora A kinase, were conducted using extra precision docking mode of Glide. Three molecules, parmosidone A, chaetosidone A, and parmosidone E, showed promising docking scores compared to the reference inhibitor. These compounds exhibited strong interactions with the binding site of Aurora A kinase, involving hydrogen bonds and hydrophobic interactions. To further evaluate the stability of these interactions, we performed molecular dyn...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - April 9, 2024 Category: Bioinformatics Source Type: research
Computational model for drug research
Brief Bioinform. 2024 Mar 27;25(3):bbae158. doi: 10.1093/bib/bbae158.ABSTRACTThis special issue focuses on computational model for drug research regarding drug bioactivity prediction, drug-related interaction prediction, modelling for immunotherapy and modelling for treatment of a specific disease, as conveyed by the following six research and four review articles. Notably, these 10 papers described a wide variety of in-depth drug research from the computational perspective and may represent a snapshot of the wide research landscape.PMID:38581423 | PMC:PMC10998638 | DOI:10.1093/bib/bbae158 (Source: Briefings in Bioinformatics)
Source: Briefings in Bioinformatics - April 6, 2024 Category: Bioinformatics Authors: Xing Chen Li Huang Source Type: research
Correction to: Introducing π-HelixNovo for practical large-scale de novo peptide sequencing
Brief Bioinform. 2024 Mar 27;25(3):bbae134. doi: 10.1093/bib/bbae134.NO ABSTRACTPMID:38581650 | PMC:PMC10998637 | DOI:10.1093/bib/bbae134 (Source: Briefings in Bioinformatics)
Source: Briefings in Bioinformatics - April 6, 2024 Category: Bioinformatics Source Type: research
Correction to: Adjustment of scRNA-seq data to improve cell-type decomposition of spatial transcriptomics
Brief Bioinform. 2024 Mar 27;25(3):bbae155. doi: 10.1093/bib/bbae155.NO ABSTRACTPMID:38581651 | PMC:PMC10998650 | DOI:10.1093/bib/bbae155 (Source: Briefings in Bioinformatics)
Source: Briefings in Bioinformatics - April 6, 2024 Category: Bioinformatics Source Type: research
A new paradigm for applying deep learning to protein-ligand interaction prediction
This study presents a novel framework for DL-based prediction of protein-ligand interactions, contributing to the advancement of this field. The IGModel is available at GitHub repository https://github.com/zchwang/IGModel.PMID:38581420 | PMC:PMC10998640 | DOI:10.1093/bib/bbae145 (Source: Briefings in Bioinformatics)
Source: Briefings in Bioinformatics - April 6, 2024 Category: Bioinformatics Authors: Zechen Wang Sheng Wang Yangyang Li Jingjing Guo Yanjie Wei Yuguang Mu Liangzhen Zheng Weifeng Li Source Type: research
Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph
Brief Bioinform. 2024 Mar 27;25(3):bbae150. doi: 10.1093/bib/bbae150.ABSTRACTBoolean models of gene regulatory networks (GRNs) have gained widespread traction as they can easily recapitulate cellular phenotypes via their attractor states. Their overall dynamics are embodied in a state transition graph (STG). Indeed, two Boolean networks (BNs) with the same network structure and attractors can have drastically different STGs depending on the type of Boolean functions (BFs) employed. Our objective here is to systematically delineate the effects of different classes of BFs on the structural features of the STG of reconstructe...
Source: Briefings in Bioinformatics - April 6, 2024 Category: Bioinformatics Authors: Priyotosh Sil Ajay Subbaroyan Saumitra Kulkarni Olivier C Martin Areejit Samal Source Type: research
HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data
Brief Bioinform. 2024 Mar 27;25(3):bbae152. doi: 10.1093/bib/bbae152.ABSTRACTReliable cell type annotations are crucial for investigating cellular heterogeneity in single-cell omics data. Although various computational approaches have been proposed for single-cell RNA sequencing (scRNA-seq) annotation, high-quality cell labels are still lacking in single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) data, because of extreme sparsity and inconsistent chromatin accessibility between datasets. Here, we present a novel automated cell annotation method that transfers cell type information from a well-l...
Source: Briefings in Bioinformatics - April 6, 2024 Category: Bioinformatics Authors: Weihang Zhang Yang Cui Bowen Liu Martin Loza Sung-Joon Park Kenta Nakai Source Type: research
From tradition to innovation: conventional and deep learning frameworks in genome annotation
Brief Bioinform. 2024 Mar 27;25(3):bbae138. doi: 10.1093/bib/bbae138.ABSTRACTFollowing the milestone success of the Human Genome Project, the 'Encyclopedia of DNA Elements (ENCODE)' initiative was launched in 2003 to unearth information about the numerous functional elements within the genome. This endeavor coincided with the emergence of numerous novel technologies, accompanied by the provision of vast amounts of whole-genome sequences, high-throughput data such as ChIP-Seq and RNA-Seq. Extracting biologically meaningful information from this massive dataset has become a critical aspect of many recent studies, particularl...
Source: Briefings in Bioinformatics - April 6, 2024 Category: Bioinformatics Authors: Zhaojia Chen Noor Ul Ain Qian Zhao Xingtan Zhang Source Type: research
PUTransGCN: identification of piRNA-disease associations based on attention encoding graph convolutional network and positive unlabelled learning
Brief Bioinform. 2024 Mar 27;25(3):bbae144. doi: 10.1093/bib/bbae144.ABSTRACTPiwi-interacting RNAs (piRNAs) play a crucial role in various biological processes and are implicated in disease. Consequently, there is an escalating demand for computational tools to predict piRNA-disease interactions. Although there have been computational methods proposed for the detection of piRNA-disease associations, the problem of imbalanced and sparse dataset has brought great challenges to capture the complex relationships between piRNAs and diseases. In response to this necessity, we have developed a novel computational architecture, de...
Source: Briefings in Bioinformatics - April 6, 2024 Category: Bioinformatics Authors: Qiuhao Chen Liyuan Zhang Yaojia Liu Zhonghao Qin Tianyi Zhao Source Type: research
Bayesian functional analysis for untargeted metabolomics data with matching uncertainty and small sample sizes
Brief Bioinform. 2024 Mar 27;25(3):bbae141. doi: 10.1093/bib/bbae141.ABSTRACTUntargeted metabolomics based on liquid chromatography-mass spectrometry technology is quickly gaining widespread application, given its ability to depict the global metabolic pattern in biological samples. However, the data are noisy and plagued by the lack of clear identity of data features measured from samples. Multiple potential matchings exist between data features and known metabolites, while the truth can only be one-to-one matches. Some existing methods attempt to reduce the matching uncertainty, but are far from being able to remove the ...
Source: Briefings in Bioinformatics - April 6, 2024 Category: Bioinformatics Authors: Guoxuan Ma Jian Kang Tianwei Yu Source Type: research
