#systemsbiology — Public Fediverse posts

My new paper: The Kinetic Elasticity Model proposes that PEM may emerge from slow GPCR desensitization/recovery kinetics - not simply from energy failure. Different upstream phenotypes may converge on a shared signaling bottleneck.

https://doi.org/10.5281/zenodo.23061587

#mecfs #cfs #CognitiveNeuroscience #neuroscience
#systemsbiology

A closed-loop artificial intelligence laboratory system capable of autonomously generating scientific hypotheses, designing and executing experiments, and analyzing the resulting biological data.
#SystemsBiology #ArtificialIntelligence #ComputationalBiology #Biotechnology #sflorg
https://www.sflorg.com/2026/09/bio09302601.html

🧬 What if some single-cell trajectories are technical artifacts masquerading as biology?

🔗 Graph Topology Reframes the Coherence of Cell-State Manifold Inference under Heterogeneous Single-Cell Observations. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0087

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#scRNAseq #SingleCellOmics #Transcriptomics #Genomics #Bioinformatics #SystemsBiology #CellBiology #CellState #CellTrajectory #Omics

Cell-fate partitioning after senescence induction: modeling SASP-driven escape trajectories

#CellularSenescence #SASP #CellCycleReentry #SenescenceEscape #TumorSuppression #NFkBSignaling #SystemsBiology #ComputationalCellBiology

The 𝗤𝘂𝗮𝗻𝘁𝘂𝗺 𝗕𝗶𝗼𝗹𝗼𝗴𝘆 𝗮𝗻𝗱 𝗕𝗶𝗼𝗽𝗵𝗼𝘁𝗼𝗻𝗶𝗰𝘀 section of CSBJ (A Science Partner Journal) is inviting submissions for its upcoming Special Issue:

“𝗤𝘂𝗮𝗻𝘁𝘂𝗺 𝗜𝗺𝗺𝘂𝗻𝗼𝗹𝗼𝗴𝘆 𝗮𝗻𝗱 𝘁𝗵𝗲 𝗗𝘆𝗻𝗮𝗺𝗶𝗰 𝗔𝗿𝗰𝗵𝗶𝘁𝗲𝗰𝘁𝘂𝗿𝗲 𝗼𝗳 𝗜𝗺𝗺𝘂𝗻𝗲 𝗦𝘆𝘀𝘁𝗲𝗺𝘀”

⏳ Submission Deadline: 30 November 2026

🔗 For more information and submission guidelines, please visit: https://spj.science.org/journal/csbj/qbio

#CallForPapers #QuantumImmunology #QuantumBiology #Immunology #SystemsBiology #Biophysics #SystemsImmunology #QuantumScience

📢 Call for Papers: Deep Learning for Next-Generation Bio-Data Mining

⏳ Submission Deadline: 30 November 2026

🔗 Submit your work: https://spj.science.org/journal/csbj/si/deep-learning-bio-data

#CallForPapers #DeepLearning #BioDataMining #ArtificialIntelligence #MachineLearning #Bioinformatics #ComputationalBiology #BiomedicalAI #Genomics #Transcriptomics #Multiomics #BiomedicalNLP #DrugDiscovery #SystemsBiology #HealthcareAI

🤖 Can artificial intelligence reveal how bacterial strains differ beneath the surface?

🔗 Predicting Strain-Specific Metabolic Capabilities in the Genus Pseudomonas with a Flux-to-AI Approach Reveals Hidden Cell Envelope Properties. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0190

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#Microbiology #ComputationalBiology #SystemsBiology #ArtificialIntelligence #Biotechnology #SyntheticBiology

Metaproteomics is the comprehensive study of the entire protein complement produced by complex microbial communities and their hosts, revealing the active physiological functions and interactions within ecosystems like the gut microbiome.
#Metaproteomics #Microbiology #SystemsBiology #AnalyticalChemistry #Pharmacology #Toxicology #sflorg
https://www.sflorg.com/2026/08/mcb08032601.html

Geriatric frailty is significantly associated with lower bacterial diversity and impaired functional capacity within the gut microbiota. A higher degree of frailty correlates directly with fewer microbial genes and diminished microbial diversity.
#Microbiology #Gerontology #SystemsBiology #sflorg
https://www.sflorg.com/2026/07/mcb07082601.html

Sharing a visualization from our ongoing methodological work on reprogramming factor dose-response modeling.

Figure: "OSKM factor stoichiometry shapes reprogramming trajectories"

#iPSC #CellularReprogramming #StemCellBiology #Yamanaka #Pluripotency #SystemsBiology

Sharing a visualization developed in the context of our ongoing work on somatic cell reprogramming trajectories.

Figure: Single-cell transcriptomic heterogeneity during OSKM reprogramming

#CellularReprogramming #iPSC #SingleCellTranscriptomics #Pluripotency #SystemsBiology

Sharing a visualization developed for didactic and exploratory purposes, addressing the temporal dynamics of OSKM-mediated reprogramming in somatic cells.

#CellularReprogramming #YamanakaFactors #iPSC #Pluripotency #Epigenetics #Senescence #PartialReprogramming #SystemsBiology

Transient OSKM induction dynamics in aged fibroblasts: relative transcript abundance over a 6-day doxycycline pulse-chase.

#PartialReprogramming #YamanakaFactors #CellularRejuvenation #EpigeneticReprogramming #OSKM #AgingBiology #TranscriptionalDynamics #SystemsBiology

Call for Papers:

Omics and Metabolic Networks in Microbial Xenobiotic Degradation and Detoxification.

Special Issue aims to bring together research and reviews that integrate omics data, metabolic network analysis, and ecological perspectives to elucidate microbial mechanisms involved in xenobiotic degradation and detoxification.

#Xenobiotics #biodegradation #Metagenomics #SystemsBiology #environment #Bioremediation #ecology

https://www.sciencedirect.com/special-issue/334118/omics-and-metabolic-networks-in-microbial-xenobiotic-degradation-and-detoxification

🤖 Have we built AI powerful enough to design proteins, but too complicated for most scientists to use?

🔗 BioPipelines: Accessible Computational Protein and Ligand Design for Chemical Biologists. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0129

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#BioPipelines #ProteinEngineering #ComputationalBiology #ProteinDesign #SyntheticBiology #Bioinformatics #AlphaFold #SystemsBiology #AI

📢 Call for Papers: Computational Spatial Omics - Multimodal Strategies for Systems Biology and Biomedical Discovery

⏳ Submission Deadline: 31 December 2026

🔗 Submit your work: https://spj.science.org/journal/csbj/si/computational-spatial-omics

#CallForPapers #SpatialOmics #SpatialTranscriptomics #SpatialProteomics #Metabolomics #Lipidomics #Multiomics #ComputationalBiology #SystemsBiology #Bioinformatics #AIinHealthcare #DigitalPathology #GraphNeuralNetworks #PrecisionMedicine

🧠 What if missing data is not a flaw, but one of the most informative parts of a complex system?

🔗 Informative Missingness in Nominal Data: A Graph-Theoretic Approach to Revealing Hidden Structure. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0099

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#DataScience #BigData #GraphTheory #ComputationalBiology #NetworkScience #Bioinformatics #SystemsBiology #BiomedicalResearch #MissingData

"INTOXICOM Workshop Report: Systems Biology Models for Toxicology" https://doi.org/10.37044/osf.io/zf2qj_v1

"The workshop took place under the INTOXICOM Implementation Study workshop series (Integrating the toxicology community into ELIXIR 2024) and aimed to strengthen connections between systems biologyand toxicology by bridging ELIXIR resources with systems toxicology modelling approaches usedfor chemical risk assessment." https://index.biohackrxiv.org/2026/05/20/zf2qj.html

#systemsBiology #toxicology #INTOXICOM

https://www.europesays.com/ie/496885/ From whole-body to organ-specific biological age clocks #Ageing #ComputationalBiologyAndBioinformatics #Éire #general #Health #IE #Ireland #LifeSciences #SystemsBiology

📢 We are pleased to announce that authors can now submit manuscripts directly from bioRxiv to CSBJ through the 𝗯𝗶𝗼𝗥𝘅𝗶𝘃-𝘁𝗼-𝗝𝗼𝘂𝗿𝗻𝗮𝗹 (B2J) transfer service.

🙏We sincerely thank Cold Spring Harbor Laboratory (CSHL) for integrating CSBJ into the B2J service.

#CSBJ #bioRxiv #AAAS #OpenScience #Preprints #SystemsBiology #StructuralBiology #Biotechnology #ComputationalBiology #Omics #Nanoscience #MedicalInformatics #Biomedicine #AdvancedMaterials #Biomaterials #QuantumBiology #Biophotonics

🦠 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

🧬 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

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

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

📢 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

🧬 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

⚛️ 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

🤯 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

🧬 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

3 Questions: Using AI to accelerate the discovery and design of therapeutic drugs | MIT News https://www.byteseu.com/1773397/ #3Questions #AI #AIInDrugDevelopment #ArtificialIntelligence #ComputationalBiology #GenerativeAiInHealthCare #HarvardMITHealthSciencesAndTechnology(HST) #interview #JamesJCollins #MITIMES #MITJameelClinic #PhareBio #ReginaBarzilay #SyntheticBiology #SystemsBiology #TommiSJaakkola

#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

ESU to host free Science Saturday in celebration of Kansas’ 165th birthday | Free https://www.byteseu.com/1727180/ #animals #biogeography #biology #ConservationBiology #DavidTraylorZooOfEmporia #EarthSciences #ecology #EnvironmentalScience #EnvironmentalSocialScience #Kingdoms(biology) #NaturalEnvironment #NaturalResources #nature #organisms #PhysicalGeography #Science #SystemsBiology #SystemsEcology

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/

Meet CoralME: A new way to see the hidden metabolism of your gut

The community of microbes living in your gut is small to the eye but huge for your health.…
#NewsBeep #News #Health #AU #Australia #CellSystemsstudy #computationalmodeling #coralME #gutbacteriametabolism #gutmicrobiome #InflammatoryBowelDisease #microbiometherapy #personalizednutrition #Systemsbiology #UCSanDiego
https://www.newsbeep.com/au/304285/

🧬 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

Multi-omic profiling reveals age-related immune dynamics in healthy adults

The Sound Life study cohort Healthy 25- to 35-year-old and 55- to 65-year-old adult donors were prospectively recruited from the greater Seattle,…
#NewsBeep #News #US #USA #UnitedStates #UnitedStatesOfAmerica #Health #Cellularimmunity #HumanitiesandSocialSciences #multidisciplinary #Science #SystemsBiology #Transcriptomics #Vaccines
https://www.newsbeep.com/us/259764/

🧬 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

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.

#MachineLeaning #SystemsBiology #BreastCancer

New review out: "Metabolic Modeling of Host–Microbe Interactions". In the article, we:
Outline strategies for coupling host and microbial genome scale metabolic models #GEM
Highlight successful applications revealing #HostMicrobiome cross-feeding
Discuss challenges (regulation, dynamics, model validation) and possible solutions
Outline fields which are worthwhile exploring from a #SystemsBiology perspective

https://doi.org/10.1016/j.csbj.2025.10.006

#MetabolicModeling #MicrobiomeScience #ComputationalBiology

Tribute to Béla Novák (1956–2025) by Alexis Barr, Francis Barr and John Tyson, in J Cell Sci.

#CellBiology #SystemsBiology #CellCycle

https://doi.org/10.1242/jcs.264438