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.
- Explainable Brain Age Prediction using coVariance Neural Networks. (arXiv:2305.18370v1 [q-bio.QM])
- Species interactions reproduce abundance correlations patterns in microbial communities. (arXiv:2305.19154v1 [q-bio.PE])
- Non-equilibrium antigen recognition in acute infections. (arXiv:2304.02794v2 [q-bio.PE] UPDATED)
- V1T: large-scale mouse V1 response prediction using a Vision Transformer. (arXiv:2302.03023v3 [cs.CV] UPDATED)
- End-to-End Full-Atom Antibody Design. (arXiv:2302.00203v4 [q-bio.BM] UPDATED)
- Endemic Oscillations for SARS-CoV-2 Omicron -- A SIRS model analysis. (arXiv:2211.09005v2 [q-bio.PE] UPDATED)
- Considering Hilbert's Approach: Problems from a Cell's Perspective. (arXiv:2210.04627v2 [q-bio.OT] UPDATED)
- Physical computation and compositionality. (arXiv:2210.00392v3 [quant-ph] UPDATED)
- Winning the lottery with neural connectivity constraints: faster learning across cognitive tasks with spatially constrained sparse RNNs. (arXiv:2207.03523v2 [q-bio.NC] UPDATED)
- The free energy principle made simpler but not too simple. (arXiv:2201.06387v3 [cond-mat.stat-mech] UPDATED)
- Individualized network analysis reveals a link between the gut microbiome, diet intervention and Gestational Diabetes Mellitus
- In vivo Protein Footprinting Reveals the Dynamic Conformational Changes of Proteome of Multiple Tissues in Progressing Alzheimer's Disease
- Replication initiation in bacteria: precision control based on protein counting
- Single-cell transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states associated with senescence
- StressME: unified computing framework of Escherichia coli metabolism, gene expression, and stress responses
- ZIPPI: proteome-scale sequence-based evaluation of protein-protein interaction models
- PhotoEukStein: Towards an omics-based definition of unicellular eukaryote phototrophs functional traits via metabolic modelling
- Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis
- Quantitative Geometric Modeling of Blood Cells from X-ray Histotomograms of Whole Zebrafish Larvae
- Transcriptional reprogramming by IL-2 variant generates metabolically active stem-like T cells
- Carriage of antimicrobial-resistant Enterobacterales among pregnant women and newborns in Amhara, Ethiopia
- Development and Validation of a Short Form of Suboptimal Health Status Questionnaire
- Increasing transmission of dengue virus across ecologically diverse regions of Ecuador and associated risk factors
- Investigation on the clinicopathological characteristics and BRCA1/2 gene variation of patients in breast cancer pedigrees in Northern Henan Province
- Incidence of SARS-CoV-2 infection and associated risk factors among staff and residents at homeless shelters in King County, Washington: an active surveillance study
- Societal feedback induces complex and chaotic dynamics in endemic infectious diseases
- Diet, pace of biological aging, and risk of dementia in the Framingham Heart Study
- Trends across time in socioeconomic differences in body mass index: a comparison of population and individual-level approaches
- Wastewater surveillance suggests unreported Mpox cases in a low-prevalence area
- Effectiveness of BNT162b2 mRNA vaccine third doses and previous infection in protecting against SARS-CoV-2 infections during the Delta and Omicron variant waves; the UK SIREN cohort study September 2021 to February 2022
- Forecasting COVID-19 activity in Australia to support pandemic response: May to October 2020
- SIMBA: single-cell embedding along with features
- Epidemiological inference for emerging viruses using segregating sites
- Deciphering subcellular organization with multiplexed imaging and deep learning
- Author Correction: The power of genetic diversity in genome-wide association studies of lipids
- Reproducibility metrics for context-specific CRISPR screens
- Coupled oscillator cooperativity as a control mechanism in chronobiology
- Between noise and function: Toward a taxonomy of the non-canonical translatome
- Genetic interactions under the microscope
- Deciphering tumor ecosystems at super resolution from spatial transcriptomics with TESLA
- Dimension reduction of dynamics on modular and heterogeneous directed networks
- Full Bayesian identification of linear dynamic systems using stable kernels
- Autocorrelation analysis for cryo-EM with sparsity constraints: Improved sample complexity and projection-based algorithms
- Dimension matters when modeling network communities in hyperbolic spaces
- Polygonal tessellations as predictive models of molecular monolayers
- A mathematical model of invasion and control of coconut rhinoceros beetle Oryctes rhinoceros (L.) in Guam
- Vaccine hesitancy promotes emergence of new SARS-CoV-2 variants
- Predator switching strength controls stability in diamond-shaped food web models
- Optimal foraging strategies for mutually avoiding competitors
- What explains the poor contraction of the viral load during paediatric HIV infection?
- Topological data analysis of antibody dynamics of severe and non-severe patients with COVID-19
- Demand-induced regime shift in fishery: A mathematical perspective
- Coupling dynamics of 2D Notch-Delta signalling
- A pipeline for testing drug mechanism of action and combination therapies: From microarray data to simulations via Linear-In-Flux-Expressions: Testing four-drug combinations for tuberculosis treatment
- Mobility and the spatial spread of sars-cov-2 in Belgium
- CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing
- Tight basis cycle representatives for persistent homology of large biological data sets
- Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths
- Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier
- Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression
- A Statistical Mechanics Approach to Describe Cell Reorientation Under Stretch
- A Mathematical Model of the Disruption of Glucose Homeostasis in Cancer Patients
- Ecological Effects of Predator Harvesting and Environmental Noises on Oceanic Coral Reefs
- Autoregulation of Transcription and Translation: A Qualitative Analysis
- Quantitative Assessment of a Dual Epidemic Caused by Tuberculosis and HIV in the Philippines
- 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
- The XBB.1.5 slightly increase the binding affinity for host receptor ACE2 and exhibit strongest immune escaping features: molecular modeling and free energy calculation
- Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties
- A Boolean-based machine learning framework identifies predictive biomarkers of HSP90-targeted therapy response in prostate cancer
- Disruption of DYRK1A-induced hyperphosphorylation of amyloid-beta and tau protein in Alzheimer’s disease: An integrative molecular modeling approach
- Editorial: Biomolecular function and activity modulated by membranes
- Aging and oocyte competence: A molecular cell perspective
- The use of multiplex imaging techniques to characterize tuberculous granuloma heterogeneity
- In vitro maturation of oocytes as a laboratory approach to polycystic ovarian syndrome (PCOS): From oocyte to embryo
- 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
- Evolutionary implications of host genetic control for engineering beneficial microbiomes
- Regulation of the microtubule network; the shaft matters!
- How prebiotic complexity increases through Darwinian evolution
- Control of tissue dimensions in the developing neural tube and somites
- Corrigendum to: Entropy as a measure of variability and stemness in single-cell transcriptomics
- An estimator for the recombination rate from a continuously observed diffusion of haplotype frequencies
- Phase field modeling and computation of vesicle growth or shrinkage
- Exact expressions and numerical evaluation of average evolvability measures for characterizing and comparing $$\textbf{G}$$ matrices
- Resource allocation in a PDE ecosystem model
- Bifurcations driven by generalist and specialist predation: mathematical interpretation of Fennoscandia phenomenon
Twitter Bio Models
New publication from @daimhulluni . Dr Kenneth Y. Wertheim and their colleagues used a genetic algorithm to personalise chemotherapy schedules for high-risk neuroblastoma patients #mathbio #neuroblastoma #optimisation #CancerResearch
https://www.mdpi.com/2072-6694/15/7/1986
Conference day 2: I had the honor to give a plenary talk this Friday and to be the chairman of a session this morning:) so many interesting talks given by talented researchers:) #mathbio #math #vanderbilt #alzheimer
I love my @BIRS_Math Sex Differences in Physiology workshop team! We are building a math model for surgical menopause this week in Banff! #womenshealth #mathbio
Excited to visit @prob_rick & @v_ciocanel to talk about our lab’s work on #evolutionarytherapy @DukeU Maths. Was supposed to come April 2020… great to meet students and eager to talk #mathbio
Another day, another reason to not sleep :(
Can't wait to tear through this.
#protein #ai #RFdiffusion #compbio
https://github.com/RosettaCommons/RFdiffusion
Very excited about the start of #FoundryFridays. The sharing of tips, tricks and insights, both simple and complex, by and between the #Bioinformatics and #CompBio community helps everyone to #AccelerateScience. And that makes the 🌎 better!
Introducing #FoundryFridays - a weekly post by @viascientifc with helpful hints, suggestions, tricks, and general insights into the amazing world of #biology, #multiomics and #bioinformatics. Today we will start by talking about something seemingly simple, - gene names.
Deadline extended to 30 June 2023 of TAC #Women in #AI of @AILSCI.
Looking forward for submissions!
🔗Found more at : https://bit.ly/3k8xEq1
#AI #drugdiscovery #Bioinformatics #compchem #compbio #machinelearning #deeplearning #womeninAI #WomenWhoCode @ELSpharma
Finally out! A Special Issue on Photosynthesis Research entirely dedicated to quantum and classical computational methods in #photosynthesis by @nikinikki87 and me! Read the editorial at https://doi.org/10.1007/s11120-023-01011-3 #compchem #compbio
Today the 10th PhD thesis from our group was submitted!🎉 Well done to @Matt_Madgwick who contributed to many studies in our group with his immerse expertise, and carried out a combined #MachineLearning & #SystemsBiology iCASE project to better predict #microbiome changes in #IBD
Investigating #Thymic Epithelial Cell Diversity Using #SystemsBiology by Honyin Chiu, Peter S. Linsley, & Steven F. Ziegler @BRIseattle | #BriefReview in #JI_systemsimmunology #ReadTheJI #systemsimmunology #stromalimmunology #stromalcells 👉 http://ow.ly/X1A550NrNfG
📢Don't miss out on the chance to register at a discounted rate for #ISMBECCB2023! Join us to explore the latest developments in systems modeling at the SysMod session (https://sysmod.info/). Submit your abstract before the deadline on April 20th. #systemsbiology
Today’s the day! Don't wait - Use code EARLY10 & register for #ISMBECCB2023 to lock in the savings & free cancellation. This special offer ends TODAY, March 30th.
https://www.iscb.org/ismbeccb2023-register
#ComputationalBiology #Bioinformatics #savings
Abstract submission tomorrow ‼️
Don’t miss the chance for travel grants & waivers to this #Interdisciplinary #Signaling Workshop for #ECR (PhD students,postdoc fellows)
#IBD #Cancer #Microbiome #Organoids #PrecisionMedicine #SystemsBiology
✅Talks
✅Knight tournaments
✅Teamwork
We're organizing the 3rd Interdisciplinary #SignalingWorkshop this summer focusing experimental + computational approaches related to Inflammation (#IBD), infection & cancer. Top speakers 👇and informal brainstormings supported Knight's tournaments. Pls RT http://signalingworkshop.org