Model Board
Each subheading shows the most recent computational models published in each journal or preprint server. As journals publish, this page is autonomously updated and clicking the links will send you to the article.
- Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation. (arXiv:2302.03038v1 [q-bio.GN])
- How a simple chloroplast psbA gene mutation changed world agriculture. (arXiv:2302.03471v1 [q-bio.PE])
- Comparing apples to apples -- Using a modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets. (arXiv:2211.08527v2 [q-bio.NC] UPDATED)
- Meta-Learning Biologically Plausible Plasticity Rules with Random Feedback Pathways. (arXiv:2210.16414v5 [q-bio.NC] UPDATED)
- Neural-network solutions to stochastic reaction networks. (arXiv:2210.01169v2 [q-bio.MN] UPDATED)
- Recommendations and guidelines from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 2 -- Ex vivo imaging. (arXiv:2209.13371v2 [physics.med-ph] UPDATED)
- The role of ecosystem transpiration in creating alternate moisture regimes by influencing atmospheric moisture convergence. (arXiv:2205.14646v3 [physics.ao-ph] UPDATED)
- BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis. (arXiv:2112.08687v5 [q-bio.GN] UPDATED)
- Automated Huntington's Disease Prognosis via Biomedical Signals and Shallow Machine Learning. (arXiv:2302.03605v1 [eess.SP])
- NodeCoder: a graph-based machine learning platform to predict active sites of modeled protein structures. (arXiv:2302.03590v1 [q-bio.QM])
- Pgc-1α is an exercise-responsive regulator of myosteatosis in older individuals
- RxRx3: Phenomics Map of Biology
- Unraveling codon usage of Escherichia coli using machine learning
- Coupling Flux Balance Analysis with Reactive Transport Modeling through Machine Learning for Rapid and Stable Simulation of Microbial Metabolic Switching
- Metabolic modeling of sex-specific tissue predicts mechanisms of differences in toxicological responses
- From autopoiesis to self-optimization: Toward an enactive model of biological regulation
- SingleCellGGM enables gene expression program identification from single-cell transcriptomes and facilitates universal cell label transfer
- Mathematically mapping the network of cells in the tumor microenvironment
- Extended fractional-polynomial generalizations of diffusion and Fisher-KPP equations on directed networks: Modeling neurodegenerative progression
- ENVIRONMENT MODULATES PROTEIN HETEROGENEITY THROUGH TRANSCRIPTIONAL AND TRANSLATIONAL STOP CODON MISCODING
- A step-by-step Researcher's Guide to the use of an AI-based transformer in epidemiology: an exploratory analysis of ChatGPT using the STROBE checklist for observational studies
- Non-Communicable Disease Service Readiness in Nepal: A Further Analysis of Nepal Health Facility Survey- 2021
- Machine-learning-aided multiplexed nanobiosensor for COVID-19 population immunity profiling
- Patterns of testing in the extensive Danish national SARS-CoV-2 test set-up
- Quantification of impact of COVID-19 pandemic on cancer screening programmes -a case study from Argentina, Bangladesh, Colombia, Morocco, Sri Lanka and Thailand
- Month-to-month all-cause mortality forecasting: A method to rapidly detect changes in seasonal patterns
- Parental body mass index and offspring childhood body size and eating behaviour: causal inference via parental comparisons and extended children of twins structural equation modelling
- Incorporating data from multiple endpoints in the analysis of clinical trials: example from RSV vaccines
- Trials underestimate the impact of preventive treatment for household contacts exposed to multidrug-resistant tuberculosis: a simulation study
- A correction for Levin's formula in the presence of confounding
- Quantifying the direct and indirect protection provided by insecticide treated bed nets against malaria
- Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data
- Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network
- A value-based deep reinforcement learning model with human expertise in optimal treatment of sepsis
- Estimation of cell lineages in tumors from spatial transcriptomics data
- Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset
- Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition
- Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3
- MitoNet: A generalizable model for segmentation of individual mitochondria within electron microscopy datasets
- The in silico lab: Improving academic code using lessons from biology
- Bias in machine learning models can be significantly mitigated by careful training: Evidence from neuroimaging studies
- Non-equilibrium early-warning signals for critical transitions in ecological systems
- Insights from high-fidelity modeling of industrial rotary bell atomization
- James–Stein for the leading eigenvector
- On cheap entropy-sparsified regression learning
- Adaptive diversification and niche packing on rugged fitness landscapes
- Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching
- Effect of beneficial sweeps and background selection on genetic diversity in changing environments
- Editorial Board
- Computational model of articular cartilage regeneration induced by scaffold implantation in vivo
- Metabolic blood flow regulation in a hybrid model of the human retinal microcirculation
- A new lipid-structured model to investigate the opposing effects of LDL and HDL on atherosclerotic plaque macrophages
- Impulsive modelling of rust dynamics and predator releases for biocontrol
- Imperfect vaccine can yield multiple Nash equilibria in vaccination games
- Analysis of tumor-immune functional responses in a mathematical model of neoantigen cancer vaccines
- Unsupervised learning reveals interpretable latent representations for translucency perception
- Forecasting upper respiratory tract infection burden using high-dimensional time series data and forecast combinations
- Criticality in probabilistic models of spreading dynamics in brain networks: Epileptic seizures
- Temporal progression along discrete coding states during decision-making in the mouse gustatory cortex
- A linear discriminant analysis model of imbalanced associative learning in the mushroom body compartment
- Modeling Syphilis and HIV Coinfection: A Case Study in the USA
- Evaluation of the Relative Performance of the Subflattenings Method for Phylogenetic Inference
- On Parameter Identifiability in Network-Based Epidemic Models
- Correction to: Relation Between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions
- Asymptotic Analysis of Optimal Vaccination Policies
- The impact of natural disasters on the spread of COVID-19: a geospatial, agent-based epidemiology model
- The effect of men who have sex with men (MSM) on the spread of sexually transmitted infections
- Assessing countermeasures during a hepatitis A virus outbreak among men who have sex with men
- Analysis of international traveler mobility patterns in Tokyo to identify geographic foci of dengue fever risk
- On the relationship between inhibition and receptor occupancy by nondepolarizing neuromuscular blocking drugs
- Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides
- Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
- Effect of naturally-occurring mutations on the stability and function of cancer-associated NQO1: Comparison of experiments and computation
- Thermal tuning of protein hydration in a hyperthermophilic enzyme
- Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study
- The evolution of cannabinoid receptors in cancer
- The use of multiplex imaging techniques to characterize tuberculous granuloma heterogeneity
- Interleukin‐17 as a spatiotemporal bridge from acute to chronic inflammation: Novel insights from computational modeling
- Advances in biomarker discovery using circulating cell‐free DNA for early detection of hepatocellular carcinoma
- Neurodegeneration in multiple sclerosis
- Mechanisms of enhancer function in neuronal systems in health and disease
- Mechanochemical feedback loops in contact-dependent fate patterning
- Heterogeneity and developmental dynamics of mammalian neocortical progenitors
- Critical phenomena in embryonic organization
- Robust cell identity specifications through transitions in the collective state of growing developmental systems
- Optimal control of bioproduction in the presence of population heterogeneity
- A coupled algebraic-delay differential system modeling tick-host interactive behavioural dynamics and multi-stability
- Effects of dispersal rates in a two-stage reaction-diffusion system
- Mathematical analysis of topological and random m-order spread models
- conditions for Turing and wave instabilities in reaction–diffusion systems
Twitter Bio Models
We are hiring senior and postdoc researchers for biomedical mathematics. Due is Feb. 6th.
If you have an interest in using math for real-world problems, BIMAG is the right place for you!
@ls_SIAM @SMB_MathBiology @ESMTBio @ICSB2023
#MathBio
https://www.ibs.re.kr/bimag/job-application/hiring/
"The Lost Art of Mathematical Modelling" by Gyllingberg, L., @Abebab, & @Soccermatics
http://arxiv.org/abs/2301.08559
#ComplexSystems #MathBio
Check out more work by @chadisaadroy @UCBerkeley at https://chadisaadroy.wordpress.com/
#EpiTwitter #MathBio #Statistics #ComplexSystems
Open position as a postdoctoral Research Associate in Mathematical Modelling of Epigenetic Regulation at the Centre de Recerca Matemàtica, Barcelona.
Deadline: 31st of March 2023.
See more: https://esmtb.org/event-5129689
#postdocjobs #mathbio
PhD position in Theoretical Eco-Evolutionary Dynamics (m/f/x) at the Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin
Deadline: 31 Jan 2023
https://karriere-igb.softgarden.io/job/26308733/PhD-position-in-Theoretical-Eco-Evolutionary-Dynamics-m-f-x-?jobDbPVId=66770784&l=en
#phdposition #mathbio
Thursdays = #CAPS_Talks
We are back to share another interesting journey of learning. This week it's about 'Diving deep into the sea of #protein #domains''. Do not miss!
📆 9th Feb, 3 pm
Link: http://bitly.ws/zLhu
Passcode: D6WJL8
#FreeToAttend
#Pfam #SCOP #compbio #InterPro
This week's fanart is by Sha Sun, Xia Li, and Malaiyalam Mariappan
°
#biology #research #cell #compbio #ER #structural #protein #folding #communication #sciart
Protein docking w/ Met your macros but
+ surface potential someone offers
& unlikely candidates to buy you steak dinner
🤝
"Fit'n'is protein into the pi-hole
hopin' laws of physics don't apply"
#CompBio #CompChem #IIFYM
#Research "Machine learning for longitudinal mortality risk prediction in patients with malignant neoplasm in São Paulo, Brazil" Available on @AILSCI!
🔗Find out more here: https://bit.ly/40tcwLI
#Machinelearning #AI #predictivemodel #cancer #compbio
New preprint on work led by Connor Moore on sex-specific #metabolic #models used to predict mechanisms of differential toxicological responses. #systemsbiology https://www.biorxiv.org/content/10.1101/2023.02.07.527430v1
One week ago, I joined @MPI_Biochem in Martinsried near Munich to found a new department for #MachineLearning and #SystemsBiology. An exciting new chapter has begun for my lab and me! @maxplanckpress #Munich #Martinsried
Postdoctoral Fellow – Computational Biology & Omics Data Analytics
https://cbirt.net/job/postdoctoral-fellow-computational-biology-omics-data-analytics/ via @CbirtDirector
👉 #PhD #Bioinformatics #computationalbiology #systemsbiology #statisticalgenetics
#Job #Jobs #JobSeekers #jobalerts #jobsearch #jobfairy #postdoc #postdocposition
Watch the video record of the second Coffee break with TRANSFAC that was held on 7th of February 2023 https://youtu.be/OXpnmgrxJJg
#bioinformatics #PromoterAnalysis #TranscriptionFactors #TranscriptionFactorBindingSite #TFBS #sitemodel #NGS #TRANSFAC #GeneRegulation #SystemsBiology