#systemsbiology — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #systemsbiology, aggregated by home.social.
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🦠 Could we outsmart antibiotic resistance by turning bacteria against themselves?
🔗 Rational Targeting and gRNA Design for Enhancing Quorum Quenching in Pseudomonas aeruginosa PAO1. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0089
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#AntimicrobialResistance #AMR #CRISPR #GeneEditing #SyntheticBiology #SystemsBiology #Microbiology #Biotechnology #DrugResistance #QuorumSensing #Biofilms #Genomics
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🦠 Could we outsmart antibiotic resistance by turning bacteria against themselves?
🔗 Rational Targeting and gRNA Design for Enhancing Quorum Quenching in Pseudomonas aeruginosa PAO1. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0089
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#AntimicrobialResistance #AMR #CRISPR #GeneEditing #SyntheticBiology #SystemsBiology #Microbiology #Biotechnology #DrugResistance #QuorumSensing #Biofilms #Genomics
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🦠 Could we outsmart antibiotic resistance by turning bacteria against themselves?
🔗 Rational Targeting and gRNA Design for Enhancing Quorum Quenching in Pseudomonas aeruginosa PAO1. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0089
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#AntimicrobialResistance #AMR #CRISPR #GeneEditing #SyntheticBiology #SystemsBiology #Microbiology #Biotechnology #DrugResistance #QuorumSensing #Biofilms #Genomics
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🦠 Could we outsmart antibiotic resistance by turning bacteria against themselves?
🔗 Rational Targeting and gRNA Design for Enhancing Quorum Quenching in Pseudomonas aeruginosa PAO1. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0089
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#AntimicrobialResistance #AMR #CRISPR #GeneEditing #SyntheticBiology #SystemsBiology #Microbiology #Biotechnology #DrugResistance #QuorumSensing #Biofilms #Genomics
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🦠 Could we outsmart antibiotic resistance by turning bacteria against themselves?
🔗 Rational Targeting and gRNA Design for Enhancing Quorum Quenching in Pseudomonas aeruginosa PAO1. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0089
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#AntimicrobialResistance #AMR #CRISPR #GeneEditing #SyntheticBiology #SystemsBiology #Microbiology #Biotechnology #DrugResistance #QuorumSensing #Biofilms #Genomics
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🧬 Could a single metric decode how genes are regulated across cells?
🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics
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🧬 Could a single metric decode how genes are regulated across cells?
🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics
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🧬 Could a single metric decode how genes are regulated across cells?
🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics
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🧬 Could a single metric decode how genes are regulated across cells?
🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics
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🧬 Could a single metric decode how genes are regulated across cells?
🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics
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Researchers have developed a method to deduce the complete protein landscape (proteome profile) of a living cell without destroying it by utilizing Raman spectroscopy. This light-based technique allows scientists to observe exactly how cells balance internal stability with the flexibility needed to survive changing environments.
#Biophysics #Proteomics #Optics #SystemsBiology #sflorg
https://www.sflorg.com/2026/04/phy04282601.html -
International Course on #Computational #SystemsBiology of #Cancer taking place at Institut Curie from September 21st – 25th, 2026 (Paris campus).
The course will review current methods and tools for analysing and interpreting multimodal genomic data, with a focus on generative artificial intelligence and network approaches, as well as concrete applications related to cancer.
More details and registration: https://training.institut-curie.org/courses/csbc2026
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Welcome to the latest edition of the "What Is" series, presented by the Scientific Frontline publication. In this research report, we delve into one of the most ambitious, technologically demanding, and philosophically profound frontiers in modern biological science: Connectomics.
#WhatIs #Neuroscience #SystemsBiology #ComputationalNeuroscience #ArtificialIntelligence #Bioinformatics #sflorg
https://www.sflorg.com/2026/04/wi04262601.html -
⚛️ Could life itself be a quantum phenomenon disguised as biology?
🔗 Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0024
📚 CSBJ Quantum Biology and Biophotonics: https://spj.science.org/journal/csbj/qbio
#QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences
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⚛️ Could life itself be a quantum phenomenon disguised as biology?
🔗 Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0024
📚 CSBJ Quantum Biology and Biophotonics: https://spj.science.org/journal/csbj/qbio
#QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences
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⚛️ Could life itself be a quantum phenomenon disguised as biology?
🔗 Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0024
📚 CSBJ Quantum Biology and Biophotonics: https://spj.science.org/journal/csbj/qbio
#QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences
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⚛️ Could life itself be a quantum phenomenon disguised as biology?
🔗 Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0024
📚 CSBJ Quantum Biology and Biophotonics: https://spj.science.org/journal/csbj/qbio
#QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences
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⚛️ Could life itself be a quantum phenomenon disguised as biology?
🔗 Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0024
📚 CSBJ Quantum Biology and Biophotonics: https://spj.science.org/journal/csbj/qbio
#QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences
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📢 Call for Papers: Metabolome-Microbiome in Health and Diseases for One Health
⏳ Submission Deadline: 31 May 2026
🔗 Submit your work: https://spj.science.org/journal/csbj/si/metabolome-microbiome-health-diseases
#CallForPapers #Metabolomics #Microbiome #SystemsBiology #OneHealth #DiseaseBiology #MedicalInformatics #Phenomics
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📢 Call for Papers: Metabolome-Microbiome in Health and Diseases for One Health
⏳ Submission Deadline: 31 May 2026
🔗 Submit your work: https://spj.science.org/journal/csbj/si/metabolome-microbiome-health-diseases
#CallForPapers #Metabolomics #Microbiome #SystemsBiology #OneHealth #DiseaseBiology #MedicalInformatics #Phenomics
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🧬 Can AI truly decode gene expression, or is it being misled by too much data?
🔗 Artificial Intelligence in Bulk RNA-Seq: Challenges and Potential Solutions. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0039
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#ArtificialIntelligence #MachineLearning #Bioinformatics #Genomics #RNAseq #ComputationalBiology #SystemsBiology #AI #PrecisionMedicine #BigData #AIinHealthcare
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🧬 Can AI truly decode gene expression, or is it being misled by too much data?
🔗 Artificial Intelligence in Bulk RNA-Seq: Challenges and Potential Solutions. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0039
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#ArtificialIntelligence #MachineLearning #Bioinformatics #Genomics #RNAseq #ComputationalBiology #SystemsBiology #AI #PrecisionMedicine #BigData #AIinHealthcare
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🧬 Can AI truly decode gene expression, or is it being misled by too much data?
🔗 Artificial Intelligence in Bulk RNA-Seq: Challenges and Potential Solutions. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0039
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#ArtificialIntelligence #MachineLearning #Bioinformatics #Genomics #RNAseq #ComputationalBiology #SystemsBiology #AI #PrecisionMedicine #BigData #AIinHealthcare
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🧬 Can AI truly decode gene expression, or is it being misled by too much data?
🔗 Artificial Intelligence in Bulk RNA-Seq: Challenges and Potential Solutions. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0039
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#ArtificialIntelligence #MachineLearning #Bioinformatics #Genomics #RNAseq #ComputationalBiology #SystemsBiology #AI #PrecisionMedicine #BigData #AIinHealthcare
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🧬 Can AI truly decode gene expression, or is it being misled by too much data?
🔗 Artificial Intelligence in Bulk RNA-Seq: Challenges and Potential Solutions. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0039
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#ArtificialIntelligence #MachineLearning #Bioinformatics #Genomics #RNAseq #ComputationalBiology #SystemsBiology #AI #PrecisionMedicine #BigData #AIinHealthcare
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⚛️ Can we design drugs that stabilize biomolecular interactions instead of blocking them?
🔗 In Silico Analysis of Potential Stabilizer Binding Sites at Protein–RNA Interfaces. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0016
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#StructuralBiology #DrugDiscovery #ComputationalBiology #RNA #MolecularBiology #Bioinformatics #DrugDesign #SystemsBiology #MedicinalChemistry
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🤯 What if most “biological insights” are just mixed-up signals we never untangled?
🔗 Integrative Learning of Disentangled Representations from Single-Cell RNA-Sequencing Datasets. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0015
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#SystemsBiology #Genomics #Bioinformatics #ComputationalBiology #AIinBiology #SingleCell #MachineLearning #DataScience #LifeSciences
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🤯 What if most “biological insights” are just mixed-up signals we never untangled?
🔗 Integrative Learning of Disentangled Representations from Single-Cell RNA-Sequencing Datasets. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0015
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#SystemsBiology #Genomics #Bioinformatics #ComputationalBiology #AIinBiology #SingleCell #MachineLearning #DataScience #LifeSciences
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🧬 Can we map the cascade of gene activity that guides cells through differentiation?
🔗 Pseudotimecascade Visualizes Gene Expression Cascade in Pseudotime Analysis. Computational and Structural Biotechnology Journal (CSBJ). https://spj.science.org/doi/epdf/10.34133/csbj.0007
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#SingleCell #Genomics #Bioinformatics #SystemsBiology #GeneExpression #ComputationalBiology
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🧬 Can we map the cascade of gene activity that guides cells through differentiation?
🔗 Pseudotimecascade Visualizes Gene Expression Cascade in Pseudotime Analysis. Computational and Structural Biotechnology Journal (CSBJ). https://spj.science.org/doi/epdf/10.34133/csbj.0007
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#SingleCell #Genomics #Bioinformatics #SystemsBiology #GeneExpression #ComputationalBiology
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📊 Bioinformatics - Jan 2025
• Population-scale modeling maps the tumor immune microenvironment
• RNA–small molecule prediction advances structure-free drug discovery
• Improved microbiome analytics refine association testing -
#Bacterial #plasmids utilize two distinct survival strategies—stealth and manipulation—to drive a "stealth-first" mechanism where #antimicrobial resistance genes are initially acquired by stealthy plasmids before being rapidly disseminated by manipulative ones.
#Biology #MolecularBiology #Bioinformatics #SystemsBiology #sflorg
https://www.sflorg.com/2026/01/bio01272601.html -
Lead Bioinformatician
Arinale Biosciences, Inc.We are seeking a lead bioinformatician to establish robust interpretative frameworks for novel NGS-based assays.
See the full job description on jobRxiv: https://jobrxiv.org/job/arinale-biosciences-inc-27778-lead-bioinformatician/
#bioinformatics #BulkRNAsequencing #computationalbiology #DNAsequencing #systemsbiology #ScienceJobs #hiring #research
https://jobrxiv.org/job/arinale-biosciences-inc-27778-lead-bioinformatician/?fsp_sid=7697 -
I feel in debt for the amazing discussions I had over 3 years with colleagues, too many to list here (but listed in the acks!) #ComplexSystems #NetworkScience #SystemsBiology #Evolution #NonEquilibrium #Evolvability 👉 Paper: iopscience.iop.org/article/10.1... 8/
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🧬 Can combining LLMs with full-length RNA isoforms unlock hidden cellular diversity?
🔗 Advancing automated cell type annotation with large language models and single-cell isoform sequencing. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.008
📚 CSBJ: https://www.csbj.org/
#LargeLanguageModels #Genomics #CellBiology #SingleCellRNASequencing #AlternativeSplicing #LLMs #SystemsBiology
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🧬 Can treating codon sequences like physical systems unlock better mRNA and protein expression?
🔗 A statistical-physics approach for codon usage optimisation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.07.020
📚 CSBJ: https://www.csbj.org/
#Genomics #CodonOptimization #SyntheticBiology #GeneticEngineering #SystemsBiology #GeneDesign #MolecularBiology
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🧬 How can AI bridge the gap between histology and spatial transcriptomics?
🔗 SegDecon bridges histology and transcriptomics through AI-based nuclei segmentation and image-informed spatial deconvolution. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.041
📚 CSBJ: https://www.csbj.org/
#SpatialTranscriptomics #Histology #Genomics #SystemsBiology #NucleiSegmentation #AI #CellBiology #TissueBiology #Bioimaging
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🧬 How can AI bridge the gap between histology and spatial transcriptomics?
🔗 SegDecon bridges histology and transcriptomics through AI-based nuclei segmentation and image-informed spatial deconvolution. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.041
📚 CSBJ: https://www.csbj.org/
#SpatialTranscriptomics #Histology #Genomics #SystemsBiology #NucleiSegmentation #AI #CellBiology #TissueBiology #Bioimaging
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🔥 How does cryotherapy reshape your metabolism after intense exercise?
🔗 1H NMR urinary metabolomic analysis in recreational athletes: Impact of physical exercise, high intensity interval training and whole body cryostimulation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.05.007
📚 CSBJ: https://www.csbj.org/
#Metabolomics #SportsScience #HIIT #Cryotherapy #MetabolicHealth #NMR #SportsMedicine #ExercisePhysiology #AthleteRecovery #SystemsBiology #SportsMedicine
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🧬 Can cells “remember” their identity without changing their DNA?
🔗 Epigenetic memory: The role of the crosstalk between histone modifications and DNA methylation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.08.034
📚 CSBJ: https://www.csbj.org/
#Epigenetics #Chromatin #GeneRegulation #DNA #MolecularBiology #SyntheticBiology #CellEngineering #Genomics #SystemsBiology #DNAmethylation
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It's tomorrow!
Gwenn has done stellar work and taken things much farther than I've been able to follow — good thing that Véronique Stoven was her main advisor — and I'm very impressed by all that she has achieved and how much she's grown.
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Tribute to Béla Novák (1956–2025) by Alexis Barr, Francis Barr and John Tyson, in J Cell Sci.
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What is cause, what is effect,
If the effect causes the cause to change?
Where effect and cause, and cause and effect,
Are entangled in a complex web,
The mind is lost
And ponders in vain
The principal cause of all.Source: A First Course in Systems Biology, 3rd ed, 2025, CRC
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🧪 Could digital modeling redefine how we grow CHO cells for biologics?
🔗 Wheels turning: CHO cell modeling moves into a digital biomanufacturing era. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.06.035
📚 CSBJ: https://www.csbj.org/
#Biomanufacturing #CHOCells #DigitalTwins #BiotechInnovation #DigitalBiomanufacturing #Bioprocessing #Biologics #CellCulture #GenomeScaleModels #SmartManufacturing #BiopharmaInnovation #SystemsBiology #Biotechnology #Bioinformatics
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🔎 How can AI-powered tools help scientists uncover hidden connections in disease research?
🔗 Darling (v2.0): Mining disease-related databases for the detection of biomedical entity associations. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.06.025
📚 CSBJ: https://www.csbj.org/
#AIinScience #BiomedicalTextMining #Genomics #PrecisionMedicine #Bioinformatics #OpenScience #BiomedicalResearch #BiomedicalAI #LiteratureMining #SystemsBiology #Omics #KnowledgeDiscovery
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🧬 Are we overcomplicating proteomics—when a few unique sequences can tell the whole story?
🔗 Uniquome: Construction and decoding of a novel proteomic atlas that contains new peptide entities. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.05.027
📚 CSBJ: https://www.csbj.org/
#Proteomics #Uniquome #PeptideAtlas #Bioinformatics #PrecisionBiology #TranslationalResearch #SystemsBiology #MolecularBiology #PrecisionMedicine
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🚨 New paper out!
Novel algorithms for uncertainty quantification in systems biology using conformal inference.
Joint work with Alberto Portela and Marcos Matabuena.📄 Read more: https://doi.org/10.1371/journal.pcbi.1013098
#SystemsBiology #UQ -
🦠 How do dormant bacteria know when to wake up?
🔗 An ecological and stochastic perspective on persisters resuscitation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.12.002
📚 CSBJ: https://www.csbj.org/
#Microbiology #AntibioticResistance #SystemsBiology #InfectionRelapse #Persisters #StochasticProcesses #StochasticBiology #InfectionControl
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A synthetic protein-level neural network in mammalian cells
https://www.science.org/doi/10.1126/science.add8468Bringing neural networks to life
A synthetic protein-based winner-take-all neural network controls cell fate decisions
https://www.science.org/doi/10.1126/science.adu1327Chen et al. describe a protein-level synthetic circuit framework that implements a “winner-take-all” neural network capable of classifying the relative abundance of multiple inputs to modify the circuit output. This network replicates various classification circuits by adjusting the relative concentrations of a few components. By connecting this circuit to molecular pathways that regulate apoptosis, the authors demonstrate the promise of this approach for programming cell fate outcomes. This could be extended to design complex neural circuits that augment the computational capacity of cells.
perceptein: a combination of protein and perceptron.
biorxiv:
https://www.biorxiv.org/content/10.1101/2022.07.10.499405v1.full.pdfhttps://phys.org/news/2024-12-perceptein-protein-based-artificial-neural.html
#neuralNetworks #biochem #systemsbiology #proteins #cellbiology
#bioengineering #technology -
new paper: "Making PBPK models more reproducible in practice" https://doi.org/10.1093/bib/bbae569
"We make a proposal aiming to harmonize abbreviations used in PBPK models.
To illustrate these recommendations, we present an original and reproducible PBPK model code in MATLAB, alongside an example of
MATLAB code converted to Systems Biology Markup Language format using MOCCASIN."