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.
- Attention-aware contrastive learning for predicting T cell receptor-antigen binding specificity. (arXiv:2206.11255v1 [q-bio.QM])
- Optimal allocation in annual plants with density dependent fitness. (arXiv:2206.11416v1 [q-bio.PE])
- Self-Supervised Learning Of Brain Dynamics From Broad Neuroimaging Data. (arXiv:2206.11417v1 [q-bio.NC])
- Weighted Concordance Index Loss-based Multimodal Survival Modeling for Radiation Encephalopathy Assessment in Nasopharyngeal Carcinoma Radiotherapy. (arXiv:2206.11458v1 [eess.IV])
- A Review of Published Machine Learning Natural Language Processing Applications for Protocolling Radiology Imaging. (arXiv:2206.11502v1 [cs.CV])
- Restoring speech intelligibility for hearing aid users with deep learning. (arXiv:2206.11567v1 [cs.SD])
- Single-phase deep learning in cortico-cortical networks. (arXiv:2206.11769v1 [q-bio.NC])
- Predicting the meal macronutrient composition from continuous glucose monitors. (arXiv:2206.11878v1 [q-bio.QM])
- Algorithms for determining transposons in gene sequences. (arXiv:1506.02424v3 [q-bio.GN] UPDATED)
- Continuous limits of large plant-pollinator random networks and some applications. (arXiv:2201.05219v2 [math.PR] UPDATED)
- Characterization of proteome-size scaling by integrative omics reveals mechanisms of proliferation control in cancer
- Glycolysis revisited: from steady state growth to glucose pulses
- A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis
- Prediction of representative phenotypes using multi-output subset selection
- Multi-Platform Proteomic Analysis of Alzheimer s Disease Cerebrospinal Fluid and Plasma Reveals Network Biomarkers Associated with Proteostasis and the Matrisome
- Tailoring and optimizing fatty acid production by oleaginous yeasts through the systematic exploration of their physiological fitness
- Agent-based vs. equation-based multi-scale modeling for macrophage polarization
- Host genetic variants regulates CCR5 expression on immune cells: a study in people living with HIV and healthy controls
- One model fits all: combining inferenceand simulation of gene regulatorynetworks
- Myeloid-derived suppressor cell dynamics control outcomes in the metastatic niche
- Is socioeconomic status associated with risk of childhood type 1 diabetes? A comprehensive review
- Heterogeneity and district-level factors associated with COVID-19 mortality during three epidemic waves in Indonesia: a nationwide ecological study
- From individual to population disease risk: population-averaged polygenic risk scores
- New, fast, and precise method of COVID-19 detection in nasopharyngeal and tracheal aspirate samples combining optical spectroscopy and machine learning
- Prevalence of Hepatitis B viral infection and associated factors among adults in Moyo district, North-Western Uganda
- Hill numbers at the edge of a pandemic: rapid SARS-COV2 surveillance without alignments or trees
- Factors associated with the uptake of Intermittent Preventive Treatment (IPTp-SP) for malaria in pregnancy: further analysis of the 2018 Nigeria Demographic and Health Survey
- Interplay of Human Metabolome and Gut Microbiome in Major Depression
- Dietary Exposure to Oxidized Lipids in US Infants
- Natural course of post COVID-19 condition and implications for trial design and outcome selection: A population-based longitudinal cohort study
- Inferring the spread of COVID-19: the role of time-varying reporting rate in epidemiological modelling
- 3pHLA-score improves structure-based peptide-HLA binding affinity prediction
- Probing TDP-43 condensation using an in silico designed aptamer
- A deep learning method for miRNA/isomiR target detection
- The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase
- Advancing remote homology detection: A step toward understanding and accurately predicting protein function
- Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation
- Diploid hepatocytes drive physiological liver renewal in adult humans
- Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells
- Localized electrical stimulation triggers cell-type-specific proliferation in biofilms
- Interpretable modeling of genotype–phenotype landscapes with state-of-the-art predictive power
- On getting it right by being wrong: A case study of how flawed research may become self-fulfilling at last
- Multidimensional political apportionment
- Public health implications of opening National Football League stadiums during the COVID-19 pandemic
- Finger stability in precision grips
- Mechanism of carbachol-induced 40 Hz gamma oscillations and the effects of NMDA activation on oscillatory dynamics in a model of the CA3 subfield of the hippocampus
- A new real-time analog circuit of Ca2+ Li-Rinzel astrocyte model based on analytical method
- Square Root Identities for Harvested Beverton–Holt Models
- A direct comparison of methods for assessing the threat from emerging infectious diseases in seasonally varying environments
- Propagation of invasive plant species in the presence of a road
- R Markdown as a dynamic interface for teaching: Modules from math and biology classrooms
- Learning transmission dynamics modelling of COVID-19 using comomodels
- Data-driven models for replication kinetics of Orthohantavirus infections
- Combining mathematical modeling and deep learning to make rapid and explainable predictions of the patient-specific response to anticoagulant therapy under venous flow
- Life-History traits and the replicator equation
- Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study
- A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale
- MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments
- Modeling cortical synaptic effects of anesthesia and their cholinergic reversal
- Ten simple rules for improving communication among scientists
- Mentoring Undergraduate Research in Mathematical Modeling
- Orchard Networks are Trees with Additional Horizontal Arcs
- Delays, Masks, the Elderly, and Schools: First Covid-19 Wave in the Czech Republic
- Relation Between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions
- Transmission Dynamics of Tuberculosis with Age-specific Disease Progression
- 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
- Editorial: Interaction of Biomolecules and Bioactive Compounds With the SARS-CoV-2 Proteins: Molecular Simulations for the Fight Against Covid-19
- Comparative Structural Dynamics of Isoforms of Helicobacter pylori Adhesin BabA Bound to Lewis b Hexasaccharide via Multiple Replica Molecular Dynamics Simulations
- Cyclic Attractors Are Critical for Macrophage Differentiation, Heterogeneity, and Plasticity
- Editorial: Web Tools for Modeling and Analysis of Biomolecular Interactions
- Computational Investigation of Bending Properties of RNA AUUCU, CCUG, CAG, and CUG Repeat Expansions Associated With Neuromuscular Disorders
- Energy metabolism in mammalian sperm motility
- From infection to repair: Understanding the workings of our innate immune cells
- Explainable deep learning in healthcare: A methodological survey from an attribution view
- Modeling cholesterol metabolism and atherosclerosis
- The sense of taste: Development, regeneration, and dysfunction
- Organelle dysfunction and its contribution to metabolic impairments in aging and age-related diseases
- Metabolic dynamics during the cell cycle
- Synthetic metabolism approaches: A valuable resource for systems biology
- Enhanced underground metabolism challenges life at high temperature–metabolic thermoadaptation in hyperthermophilic Archaea
- Contents
- Bistability in deterministic and stochastic SLIAR-type models with imperfect and waning vaccine protection
- A mechanistic derivation of the Monod bioreaction equation for a limiting nutrient
- A PDMP model of the epithelial cell turn-over in the intestinal crypt including microbiota-derived regulations
- Generating function approach to the effective degree SIR model
- ‘Holey’ niche! finding holes in niche hypervolumes using persistence homology
Twitter Bio Models
It was so fun to see old friends and meet new ones while speaking on this panel today. It’s inspiring to see these brilliant #mathbio women working at @Optum for the week!
Great career panel at #WIMB2022 featuring an awesome spectrum of career paths using math and analytical skills in healthcare industry and academia
Open Problems in Mathematical Biology
https://arxiv.org/abs/2206.09516
@SeanVittadello and I wrote this in commemoration of our friend and colleague Edmund Crampin.
This is our first stab at surveying some open problems and opportunities in #mathbio. We would welcome your feedback.
Last call for our postdoc and senior researcher positions (Due June 30th)!
#MathBio #Biophysics #SystemsBiology #ComputationalBiology #StochasticAnalysis #Sleep #CircadianRhythms #DigitalMedicine #MoodDisorders #SingleCellSequencing #ReactionNetwork
https://www.ibs.re.kr/bimag/hiring/
New work out now with @adamlmaclean and @RoussosTorres - Myeloid-derived suppressor cell dynamics control outcomes in the metastatic niche
Lots of fun to write and develop in #JuliaLang, check it out! #mathonco #mathbio
https://www.biorxiv.org/content/10.1101/2022.06.15.496246v1
Myeloid-derived suppressor cell dynamics control outcomes in the metastatic niche.
Modeling tumor-MDSC dynamics w stochastic delay diff eq & Bayesian inference. MDSC par >> tumor par in importance. in #JuliaLang @jessemkreger @RoussosTorres #mathonco
https://www.biorxiv.org/content/10.1101/2022.06.15.496246v1
Interestingly this small mathematical biology conference hosted a community talk for people from the town. What an excellent idea!! #ScienceCommunication #mathbio
Our #compbio students close the week with an Introductory lecture on Metastasis by Adrienne Boire, MD, PhD.
Code Ocean customer @Sema4 wanted to set up an environment for fast, automated and secure access by researchers. See how they used the Code Ocean platform to achieve this goal and expedite research:
https://hubs.ly/Q01f7_6t0
#genomics #compbio #computationalresearch
Proud our work was inspired by MD done in collaboration with Lipi Thurkal @Sci_Lipi #compbio and Crick @TheCrick Schreiber team #autophagy #membrane https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbiorxiv.org%2Fcgi%2Fcontent%2Fshort%2F2022.06.10.495627v1&data=05%7C01%7C%7C6f22cd44798241b66be008da4afe86a2%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637904754289469543%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=kJGQ4JobKI2NRzlGAd1cMpAApwyIpDvBxdlmx5N8%2BGs%3D&reserved=0
With about a week until I start my #newPI journey @McMasterOBGYN @machealthsci, the Wilson lab logo is ready to go!
Are you an undergrad or prospective grad student interested in #genomics, #epigenomics, #placenta, #cfDNA, #compbio, please reach out!
New Research: Standardization of Human Metabolic Stoichiometric Models: Challenges and Directions https://www.frontiersin.org/articles/10.3389/fsysb.2022.899980?utm_source=S-TWT&utm_medium=SNET&utm_campaign=ECO_FSYSB_XXXXXXXX_auto-dlvrit #SystemsBiology
#ICYMI the slides and recording from @theNCI pre-application webinar for the #fundingopportunity that supports Research Centers for Cancer #SystemsBiology, which will be a part of #NCICSBC, can be found at https://www.cancer.gov/about-nci/organization/dcb/funding/resources. #FlashbackFriday
Just before the coffe break, @chrisondakeys on the resilience of the core bacterial metabolism at different temperatures! And here #systemsbiology rocks!
Explicando a importância da #privacidade na #Blockchain e na #dApp @abakhus e ostentando um sequenciador de #DNA minaturizado #MinION da @nanopore
#multiomics #systemsbiology #datascience #tokenization #privacy #sensitivedata
Presenting the #Abakhus #dApp during the #RioCryptoHub event. The miniaturized #MinION #DNA sequencer from @nanopore was also featured. Thanks to Douglas Miranda for organizing such a nice event. 📸 Werneck
#privacy #web3 #tokenization #multiomics #systemsbiology #datascience