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Caffeine causes cell cycle arrest at G0/G1 and increases of ubiquitinated proteins, ATP and mitochondrial membrane potential in renal cells
Caffeine causes cell cycle arrest at G0/G1 and increases of ubiquitinated proteins, ATP and mitochondrial membrane potential in renal cells
Available online 21 September 2023Author links open overlay panel, , , Highlights•From 936 proteins identified, caffeine i...
Biological informed graph neural network for tumor mutation burden prediction and immunotherapy-related pathway analysis in gastric cancer
Biological informed graph neural network for tumor mutation burden prediction and immunotherapy-related pathway analysis in gastric cancer
Interpretable biologically informed deep semi-graph neural network. The PGLCN consists three core modules: biological grap...
Molecular dynamics analysis of Superoxide Dismutase 1 mutations suggests decoupling between mechanisms underlying ALS onset and progression
Molecular dynamics analysis of Superoxide Dismutase 1 mutations suggests decoupling between mechanisms underlying ALS onset and progression
Amyotrophic lateral sclerosisSuperoxide Dismutase type 1 (SOD1)Diseaseassociated SOD1 mutationsMolecular dynamics (MD) sim...
ASCARIS: Positional Feature Annotation and Protein Structure-Based Representation of Single Amino Acid Variations
ASCARIS: Positional Feature Annotation and Protein Structure-Based Representation of Single Amino Acid Variations
Software/Web server ArticleASCARIS: Positional Feature Annotation and Protein Structure-Based Representation of Single Ami...
Deciphering m6A dynamics at a single-base level during planarian anterior-posterior axis specification
Deciphering m6A dynamics at a single-base level during planarian anterior-posterior axis specification
AbbreviationsPCGspositional control genesRAGsregeneration-associated genesAPAalternative polyadenylation3’ UTR3’ untransla...
Family-wide analysis of integrin structures predicted by AlphaFold2
Family-wide analysis of integrin structures predicted by AlphaFold2
Volume 21, 2023, Pages 4497-4507Author links open overlay panel, , AbstractRecent advances in protein structure prediction...
LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries
LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries
Available online 14 September 2023Author links open overlay panel, , , , AbstractEnzymes are potent catalysts with high sp...
Multimodal Analysis and the Oncology Patient: Creating a Hospital System for Integrated Diagnostics and Discovery
Multimodal Analysis and the Oncology Patient: Creating a Hospital System for Integrated Diagnostics and Discovery
We propose that an information technology and computational framework that would unify access to hospital digital informat...
Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes
Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes
Available online 15 September 2023Author links open overlay panel, , , Highlights•Enzyme-constrained model for Clostridium...
Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data
Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data
In anthropological, medical, and forensic studies, the nonrecombinant region of the human Y chromosome (NRY) enables accur...
Delineating highly transcribed noncoding elements landscape in breast cancer
Delineating highly transcribed noncoding elements landscape in breast cancer
KeywordsHighly transcribed noncoding elementsChromatin characterizationConsensus motif analysesSubtype specific transcript...
DBTRG: De Bruijn Trim Rotation Graph Encoding for Reliable DNA Storage
DBTRG: De Bruijn Trim Rotation Graph Encoding for Reliable DNA Storage
Available online 11 September 2023Author links open overlay panel, , , , Highlights•Dynamic binary sequence and original b...
Uncultured Prokaryotic Genomes in the Spotlight: An Examination of Publicly Available Data from Metagenomics and Single-Cell Genomics
Uncultured Prokaryotic Genomes in the Spotlight: An Examination of Publicly Available Data from Metagenomics and Single-Cell Genomics
Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-indepen...
Bst polymerase — a humble relative of Taq polymerase
Bst polymerase — a humble relative of Taq polymerase
DNA polymerases are a superfamily of enzymes synthesizing DNA using DNA as a template. They are essential for nucleic acid...
Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection
Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection
Available online 13 September 2023Author links open overlay panel, , , , Highlights•The long-term dissimilarity of the cer...
A drug repurposing method based on inhibition effect on gene regulatory network
A drug repurposing method based on inhibition effect on gene regulatory network
Numerous computational drug repurposing methods have emerged as efficient alternatives to costly and time-consuming tradit...
Featured interactome of homocysteine-inducible endoplasmic reticulum protein uncovers novel binding partners in response to ER stress
Featured interactome of homocysteine-inducible endoplasmic reticulum protein uncovers novel binding partners in response to ER stress
Homocysteine-inducible endoplasmic reticulum protein (HERP) is an endoplasmic reticulum (ER)-resident protein and importan...
W254 in furin functions as a molecular gate: Elucidation of putative drug tunneling and docking by non-equilibrium molecular dynamics
W254 in furin functions as a molecular gate: Elucidation of putative drug tunneling and docking by non-equilibrium molecular dynamics
Furins are serine endoproteases that process precursor proteins into their biologically active forms, and they play essent...
Corrigendum to “Exploiting cheminformatic and machine learning to navigate the available chemical space of potential small molecule inhibitors of SARS-CoV-2″ [Computational and Structural Biotechnology Journal 19 (2021) 424–438]
Corrigendum to “Exploiting cheminformatic and machine learning to navigate the available chemical space of potential small molecule inhibitors of SARS-CoV-2″ [Computational and Structural Biotechnology Journal 19 (2021) 424–438]
Volume 21, 2023, Page 4408Author links open overlay panelAbhinit Kumar a 1, Saurabh Loharch a 1, Sunil Kumar a 1, Rajesh P...
Clinical Decision Support systems: A step forward in establishing the clinical laboratory as a decision maker hub
Clinical Decision Support systems: A step forward in establishing the clinical laboratory as a decision maker hub
Clinical Decision Support SystemsClinical laboratoryElectronic health recordsQuality improvementOperational ManagementArti...
HIV Infection Detection Using CRISPR/Cas Systems: Present and Future Prospects
HIV Infection Detection Using CRISPR/Cas Systems: Present and Future Prospects
Available online 7 September 2023Author links open overlay panel, Highlights•Description of the mechanisms of different ty...
Proteome deconvolution of liver biopsies reveals hepatic cell composition as an important marker of fibrosis
Proteome deconvolution of liver biopsies reveals hepatic cell composition as an important marker of fibrosis
Available online 4 September 2023Author links open overlay panel, , , , , , , , , AbstractHuman liver tissue is composed o...
Current understanding of nucleoside analogs inhibiting the SARS-CoV-2 RNA-dependent RNA polymerase
Current understanding of nucleoside analogs inhibiting the SARS-CoV-2 RNA-dependent RNA polymerase
Since the outbreak of the COVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RN...
Dominant constraints on the evolution of rhythmic gene expression
Dominant constraints on the evolution of rhythmic gene expression
Circadian rhythmsRhythmic gene expressionCircadian evolutionTranscription-translation feedback loop (TTFL)Energy expenditu...
Mining the nanotube-forming Bacillus amyloliquefaciens MR14M3 Genome for Determining anti-Candida auris and anti-Candida albicans Potential by Pathogenicity and Comparative Genomics Analysis
Mining the nanotube-forming Bacillus amyloliquefaciens MR14M3 Genome for Determining anti-Candida auris and anti-Candida albicans Potential by Pathogenicity and Comparative Genomics Analysis
genome miningBacillusantifungal activitycytotoxicityCandida aurisbiosynthesis-related gene clusterscomparative genomicsbio...
Protons Taken Hostage: Dynamic H-Bond Networks of the pH-sensing GPR68
Protons Taken Hostage: Dynamic H-Bond Networks of the pH-sensing GPR68
proton-sensing G Protein Coupled Receptorsprotocol for structural modeling and model assessmentgraph theorydynamic hydroge...
The World of GPCR dimers - mapping Dopamine Receptor D2 Homodimers in Different Activation States and Configuration Arrangements
The World of GPCR dimers - mapping Dopamine Receptor D2 Homodimers in Different Activation States and Configuration Arrangements
G protein-coupled receptors (GPCRs) are known to dimerize, but the molecular and structural basis of GPCR dimers is not we...
Diversity of RNA viruses in agricultural insects
Diversity of RNA viruses in agricultural insects
Recent advancements in next-generation sequencing (NGS) technology and bioinformatics tools have revealed a vast array of ...
Thresholding Gini Variable Importance with a Single-Trained Random Forest: An Empirical Bayes Approach
Thresholding Gini Variable Importance with a Single-Trained Random Forest: An Empirical Bayes Approach
Random forests (RFs) are a widely used modelling tool capable of feature selection via a variable importance measure (VIM)...
Stability of human gut microbiome: comparison of ecological modelling and observational approaches
Stability of human gut microbiome: comparison of ecological modelling and observational approaches
The gut microbiome plays a pivotal role in the human body, and perturbations in its composition have been linked to variou...
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