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.
- Arrested coalescence of multicellular aggregates. (arXiv:2012.01455v1 [cond-mat.soft])
- Emergence of radial orientation selectivity: Effect of cell density changes and eccentricity in a layered network. (arXiv:1805.03749v2 [q-bio.NC] UPDATED)
- Optimal governance and implementation of vaccination programs to contain the COVID-19 pandemic. (arXiv:2011.06455v2 [cs.GT] UPDATED)
- An infection process near criticality: Influence of the initial condition. (arXiv:2009.08940v2 [q-bio.PE] UPDATED)
- A single-cell mathematical model of SARS-CoV-2 induced pyroptosis and the effects of anti-inflammatory intervention. (arXiv:2008.04172v2 [q-bio.SC] UPDATED)
- Complexity of modification problems for best match graphs. (arXiv:2006.16909v3 [cs.CC] UPDATED)
- Multicellular sensing at a feedback-induced critical point. (arXiv:2005.07010v2 [physics.bio-ph] UPDATED)
- Two-dimensional partial covariance mass spectrometry for the top-down analysis of intact proteins. (arXiv:2004.11949v2 [physics.chem-ph] UPDATED)
- Dr-COVID: Graph Neural Networks for SARS-CoV-2 Drug Repurposing. (arXiv:2012.02151v1 [cs.LG])
- Moment-generating function of output stream of leaky integrate-and-fire neuron. (arXiv:2012.01501v1 [q-bio.NC])
- An opponent process for alcohol addiction based on changes in endocrine gland mass
- Newfound coding potential of transcripts unveils missing members of human protein communities
- Spatio-temporal Dynamics of the Patterning of Arabidopsis Flower Meristem
- A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium.
- Sca1+ cells as direct isolate (ex vivo) versus in vitro cultured exhibit differential proteomic signatures in murine skeletal muscle
- Role of periodic forcing on the stochastic dynamics of a biomolecular clock
- Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition
- Prediction of Michaelis constants from structuralfeatures using deep learning
- Active and machine learning-based approaches to rapidly enhance microbial chemical production
- A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement
- Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data
- The effectiveness of population-wide, rapid antigen test based screening in reducing SARS-CoV-2 infection prevalence in Slovakia
- Identification of hippocampal volume as a mediator of the association between APOE4 and dementia
- Antiherpetic medication and incident dementia: observational cohort studies in four countries
- Novel Approach for Monte Carlo Simulation of the new COVID-19 Spread Dynamics
- Household factors and the risk of severe COVID-like illness early in the US pandemic
- A holistic approach for suppression of COVID-19 spread in workplaces and universities
- Modelling the Test, Trace and Quarantine Strategy to Control the COVID-19 Epidemic in the State of Sao Paulo, Brazil
- How to choose a time zero for patients in external control arms
- A Stochastic Compartmental Model for COVID-19
- Age-stratified discrete compartment model of the COVID-19 epidemic with application to Switzerland
- Frequency spectrum recurrence analysis
- State-level tracking of COVID-19 in the United States
- Mathematical formulation and parametric analysis of in vitro cell models in microfluidic devices: application to different stages of glioblastoma evolution
- SkipGNN: predicting molecular interactions with skip-graph networks
- Comparing the Efficacy of Cancer Therapies between Subgroups in Basket Trials
- Understanding and Engineering Chromatin as a Dynamical System across Length and Timescales
- The Most Logical Approach to Improve CAR T Cell Therapy
- Pairwise Stimulations of Pathogen-Sensing Pathways Predict Immune Responses to Multi-adjuvant Combinations
- Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells
- On instabilities of deep learning in image reconstruction and the potential costs of AI [Applied Mathematics]
- Theoretical issues in deep networks [Applied Mathematics]
- Evidence that coronavirus superspreading is fat-tailed [Applied Mathematics]
- How humans learn and represent networks [Colloquium Papers (free online)]
- Narrative structure of A Song of Ice and Fire creates a fictional world with realistic measures of social complexity [Anthropology]
- Lepidopteran mouthpart architecture suggests a new mechanism of fluid uptake by insects with long proboscises
- Ecological and evolutionary consequences of predator-prey role reversal: Allee effect and catastrophic predator extinction
- Quantifying antiviral effects against simian/human immunodeficiency virus induced by host immune response
- Cellular automata modeling suggests symmetric stem-cell division, cell death, and cell drift as key mechanisms driving adult spinal cord growth in teleost fish
- A mathematical model of kin selection in floral displays
- Squaring within the Colless index yields a better balance index
- Sensitivity analysis of the reaction occurrence and recurrence times in steady-state biochemical networks
- Four-tier response system and spatial propagation of COVID-19 in China by a network model
- European and US lockdowns and second waves during the COVID-19 pandemic
- Interaction of red crabs with yellow crazy ants during migration on Christmas Island
- Computational study on ratio-sensing in yeast galactose utilization pathway
- Bacteria use structural imperfect mimicry to hijack the host interactome
- SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes
- Control of filament length by a depolymerizing gradient
- The DIOS framework for optimizing infectious disease surveillance: Numerical methods for simulation and multi-objective optimization of surveillance network architectures
- Disease Emergence in Multi-Patch Stochastic Epidemic Models with Demographic and Seasonal Variability
- Modeling the Mechanisms by Which Coexisting Biomolecular RNAβProtein Condensates Form
- Phylosymmetric Algebras: Mathematical Properties of a New Tool in Phylogenetics
- Stationary Distribution of Telomere Lengths in Cells with Telomere Length Maintenance and its Parametric Inference
- Spatial Dynamics and Spread of Ecosystem Engineers: Two Patch Analysis
- Simulation-based assessment of model selection criteria during the application of benchmark dose method to quantal response data
- Ontological model of multi-agent Smart-system for predicting drug properties based on modified algorithms of artificial immune systems
- Quantifying the annual incidence and underestimation of seasonal influenza: A modelling approach
- Modelling HIV disease process and progression in seroconversion among South Africa women: using transition-specific parametric multi-state model
- Risk estimation of the SARS-CoV-2 acute respiratory disease outbreak outside China
- Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With Calmodulin
- Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations
- Exploring Allosteric Signaling in the Exit Tunnel of the Bacterial Ribosome by Molecular Dynamics Simulations and Residue Network Model
- Molecular Dynamics Investigations of Binding Mechanism for Triazoles Inhibitors to CYP51
- Probing the Structural Dynamics of the Plasmodium falciparum Tunneling-Fold Enzyme 6-Pyruvoyl Tetrahydropterin Synthase to Reveal Allosteric Drug Targeting Sites
- Cellular reprogramming: Mathematics meets medicine
- Thermoregulation: A journey from physiology to computational models and the intensive care unit
- Microbial metabolic noise
- The WNT/Ξ²βcatenin dependent transcription: A tissueβspecific business
- Bioengineering tools for probing intracellular events in T lymphocytes
- Synthetic genomes with altered genetic codes
- Engineering cell fate: Applying synthetic biology to cellular reprogramming
- Contents
- Current state of nonlinear-type timeβfrequency analysis and applications to high-frequency biomedical signals
- Seven myths of how transcription factors read the cis-regulatory code
- On the heterozygosity of an admixed population
- Mathematical models for the effect of anti-vascular endothelial growth factor on visual acuity
- Nonlocal and local models for taxis in cell migration: a rigorous limit procedure
- Counting phylogenetic networks of level 1 and 2
- Invasion analysis on a predatorβprey system in open advective environments
Twitter Bio Models
Instructors! The deadline for @biocollective's Spring Faculty Mentoring Network has been extended to 12/15! Join colleagues to customize and implement data-driven modules for your undergrad #biology courses.
#STEMEd #mathbio #sysbio #compbio
For those interested in adopting computational modeling and simulation modules that address systems #biology and quantitative reasoning skills--apply for the Spring 2021 Cell Collective Faculty Mentoring Network! App due 11/20.
@biocollective #STEMEd
https://qubeshub.org/news/blog/2020/11/spring-2021-fmn-announcement-cell-collective-faculty-mentoring-network
Excited to present our latest work at upcoming #CGSB20 this week on topological signatures of phenotypic heterogeneity in smallcell lung cancer @CompMolBioSymp @sysbioire @SMB_MathBiology #sysbio #mathbio #mathonco @Sabu_fm_Jupyter @gur9669 @kishorehari139 https://www.biorxiv.org/content/10.1101/2020.10.30.362228v1
We are getting everything ready for the #CGSB20 this week (3rd and 4th Dec)!
You can find all information on our website: https://cgsb-2020.webflow.io/
Last minute registration under: https://docs.google.com/forms/d/1Q-mmgiUpuFLJdhKndlnYP-huUqm3Eq_3JsRC1djkDUI/viewform?edit_requested=true
We find intriguing patterns for even vs. odd numbered polygons. Even-n polygons give rise to predominant 2 states (1010.., 0101..). Odd-n polygons generate 2n states with similar frequency and follow 'circular permutation' #synbio #mathbio. Work supported by @serbonline @IndiaDST
#Bioinformatics #CompBio #WomenWhoCode #WiDS @WiDS_Worldwide #STEM
This year ISCB has not received a single nomination for a female for the Overton Prize (https://iscb.org/iscb-awards/overton-prize)? Computational biologists within 10-year post-degree are eligible. The deadline is today! I am calling on the community to help!
If you're looking to sponsor an initiative or opportunity that amplifies the voices of Black womxn in the #compbio field, please email contact.blackwomencompbio@gmail.com with a proposal that our teams can explore together.
#GivingTuesday #BlackWomenCompBio #ThankYou
Additionally, we'd like to thank all of our donors in the #CompBio community for their support of our network as we grow. Every penny goes to maintaining our online platform and helps to ensure we can fund fruitful initiatives for our members and allies.
http://tinyurl.com/BWCB-give
One week countdown to our virtual Open House for the NYU MS Biomedical Informatics program. Come hang out and hear about our 12-month program. Tuesday Dec 8 @ 5:30!
@nyulangone
@nyugrossman
#CompBio #ClinicalInformatics #Bioinformatics
https://eventbrite.com/e/nyu-ms-in-biomedical-informatics-virtual-open-house-tickets-121054624641?utm-medium=discovery&utm-campaign=social&utm-content=attendeeshare&aff=estw&utm-source=tw&utm-term=listing
And a cool talk from @McManus_Lab, collab w @JG_Underwood & @vram142, using CRISPR arrays to probe gene interactions in cancer. Really nice #SystemsBiology look at convergence of pathways.
This session was a cavalcade of tools for realistic studies of complex biology β₯οΈ
Come do a PhD with Kathryn on funky light-sensing and transducing membrane proteins...from PIRANHAS! π―π― Applications in #systemsbiology & #syntheticbiology #synbio #findaphd
Would you like to do a #PhD with me?! π Currently advertising a PhD studentship to characterise far red-sensitive opsins from Piranha! π Apply by 29th Jan π Co-supervised by @kellier13 and @DarrenSmithdx #optogenetics #synbio #endocrinology
https://www.findaphd.com/phds/project/defining-novel-far-red-light-sensitive-protein-modules-for-endocrine-research-ref-rdf21-hls-app-garner/?p127647
#ScienceJobs:
Multiscale modelling of IVD cell activity & potential tissue turnover
Disc4All (@Disc4all_EU) Innovative Training network - Universitat Pompeu Fabra, Barcelona, Spain
https://jobrxiv.org/job/disc4all-innovative-training-network-h2020-msca-itn-etn-2020-ga-955735-universitat-pompeu-fabra-27778-multiscale-modelling-of-ivd-cell-activity-potential-tissue-turnover/
#PhD #Simulations #InSilicoMedicine #SystemsBiology #IntervertebralDisc
Support our PhD students tomorrow in the @CompMolBioSymp! @ANwaokorie is speaking at 10:45 am and @dekegelb is speaking at 1:05 pm! Hope to "see you" there! #womeninSTEM #PhDlife #researchtalks #systemsbiology #cancer
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