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.
- Explaining Patterns in Data with Language Models via Interpretable Autoprompting. (arXiv:2210.01848v1 [cs.LG])
- Congruity of genomic and epidemiological data in modeling of local cholera outbreaks. (arXiv:2210.01956v1 [q-bio.QM])
- MAtt: A Manifold Attention Network for EEG Decoding. (arXiv:2210.01986v1 [cs.LG])
- ChemAlgebra: Algebraic Reasoning on Chemical Reactions. (arXiv:2210.02095v1 [cs.LG])
- Computing algebraic degrees of phylogenetic varieties. (arXiv:2210.02116v1 [q-bio.PE])
- Development and validation of deep learning based embryo selection across multiple days of transfer. (arXiv:2210.02120v1 [q-bio.QM])
- The metabolic origins of big size in aquatic mammals. (arXiv:2210.02183v1 [q-bio.PE])
- Machine learning in bioprocess development: From promise to practice. (arXiv:2210.02200v1 [cs.LG])
- Novel Radiomic Measurements of Tumor- Associated Vasculature Morphology on Clinical Imaging as a Biomarker of Treatment Response in Multiple Cancers. (arXiv:2210.02273v1 [q-bio.QM])
- Fitting a Directional Microstructure Model to Diffusion-Relaxation MRI Data with Self-Supervised Machine Learning. (arXiv:2210.02349v1 [eess.IV])
- Dynamic trade-offs between biomass accumulation and division determine bacterial cell size and proteome in fluctuating nutrient environments
- Suppression of Betacellulin expression is a key mechanism for omega-3 fatty acid mediated attenuation of nonalcoholic steatohepatitis
- Machine learning on large-scale proteomics data identifies tissue- and cell type-specific proteins
- Beyond BRCA: Discovery of novel causes and consequences of homologous recombination deficiencies
- Evaluating the potential of marine invertebrate and insect protein hydrolysates to reduce fetal bovine serum in cell culture media for cultivated fish production
- Minor intron containing genes: Achilles' heel of viruses?
- NHA1 is a cation/proton antiporter essential for the water-conserving functions of the rectal complex in Tribolium castaneum
- Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells
- Comprehensive analysis of intercellular communication in thermogenic adipose niche
- The trait coding rule in phenotype space
- Association of upper respiratory Streptococcus pneumoniae colonization with SARS-CoV-2 infection among adults
- Association between COVID-19 mRNA vaccination and COVID-19 illness and severity during Omicron BA.4 and BA.5 sublineage periods
- Identification of BcenGI15 genomic island harboring ST839 clone in a population of Burkholderia cenocepacia complex from a major tertiary care hospital in Northern India
- Radiomics analysis to predict pulmonary nodule malignancy using machine learning approaches
- Anemia and associated factors among 6-59 months age children attending health facilities in Northeast Ethiopia: A facility based cross sectional study
- Re-evaluating the robustness of Mendelian randomisation to measurement error
- Effectiveness of nirmatrelvir-ritonavir against hospital admission: a matched cohort study in a large US healthcare system
- Reduction in maternal mortality ratio varies by district in Sidama Regional State, southern Ethiopia: Estimates by cross-sectional studies using the sisterhood method and a household survey of pregnancy and birth outcomes
- Knockdown resistance (kdr) Associated organochlorine Resistance in human head lice: Systematic review and meta-analysis
- COVID-19 vaccine antibody response is associated with side-effects, chronic health conditions, and vaccine type in a large Northern California cohort
- An interpretable semi-supervised framework for patch-based classification of breast cancer
- Fat infiltration in the infarcted heart as a paradigm for ventricular arrhythmias
- Modelling health and economic impact of nutrition interventions: a systematic review
- Homeostatic coordination and up-regulation of neural activity by activity-dependent myelination
- Extraction of sensing data for desired scent impressions using mass spectra of odorant molecules
- Unraveling phenotypic plasticity and evolution in small cell lung cancer
- What are the current driving questions in immune repertoire research?
- Virtual screening for small-molecule pathway regulators by image-profile matching
- Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions
- Self-organization of plasticity and specialization in a primitively social insect
- On the parameter combinations that matter and on those that do not: data-driven studies of parameter (non)identifiability
- COVID-19 cases and deaths in the United States follow Taylor’s law for heavy-tailed distributions with infinite variance
- Reply to Dablander and Bury: Dealing with the unknown unknowns of deep learning
- Deep learning for tipping points: Preprocessing matters
- Digital computing through randomness and order in neural networks
- Hamilton’s rule, the evolution of behavior rules and the wizardry of control theory
- Ethnic homophily affects vaccine prioritization strategies
- Modeling of indirect cell–cell interaction networks mediated by IFN/IL-4 cytokine involved in atopic dermatitis
- Competitive evolution of H1N1 and H3N2 influenza viruses in the United States: A mathematical modeling study
- Modeling of ionizing radiation induced hair follicle regenerative dynamics
- Impacts of demographic and environmental stochasticity on population dynamics with cooperative effects
- Mathematical modeling for the combination treatment of IFN- and anti-PD-1 in cancer immunotherapy
- In silico modeling of endocrine organ-on-a-chip systems
- A simulation of parental and glycolytic tumor phenotype competition predicts observed responses to pH changes and increased glycolysis after anti-VEGF therapy
- SBML to bond graphs: From conversion to composition
- Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins
- Ten simple rules for unbiased teaching
- Ten simple rules for successfully supporting first-generation/low-income (FLI) students in STEM
- Measuring impact of vaccination among wildlife: The case of bait vaccine campaigns for classical swine fever epidemic among wild boar in Japan
- An ensemble n-sub-epidemic modeling framework for short-term forecasting epidemic trajectories: Application to the COVID-19 pandemic in the USA
- Long-Term Forecast of HIV/AIDS Epidemic in China with Fear Effect and 90-90-90 Strategies
- Estimation of Rates of Non-neutral Mutations When Bacteria are Exposed to Subinhibitory Levels of Antibiotics
- Can the Kuznetsov Model Replicate and Predict Cancer Growth in Humans?
- Reaction Network Analysis of Metabolic Insulin Signaling
- Effect of Movement on the Early Phase of an Epidemic
- 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
- A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations
- CAT-CPI: Combining CNN and transformer to learn compound image features for predicting compound-protein interactions
- In silico design of refined ferritin-SARS-CoV-2 glyco-RBD nanoparticle vaccine
- ProDFace: A web-tool for the dissection of protein-DNA interfaces
- Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool
- Insights into the sperm chromatin and implications for male infertility from a protein perspective
- Evolution of precision oncology‐guided treatment paradigms
- In silico modeling for the hepatic circulation and transport: From the liver organ to lobules
- Pathogenesis of neural tube defects: The regulation and disruption of cellular processes underlying neural tube closure
- Development and diseases of the coronary microvasculature and its communication with the myocardium
- Editorial overview: The metabolic network
- 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
- Operating diagrams for a three-tiered microbial food web in the chemostat
- From individual-based epidemic models to McKendrick-von Foerster PDEs: a guide to modeling and inferring COVID-19 dynamics
- Noise-driven bifurcations in a neural field system modelling networks of grid cells
- Inference in Gaussian state-space models with mixed effects for multiple epidemic dynamics
- Scaling relations for auxin waves
Twitter Bio Models
Like when that sneaky bug of your code refuses to get nailed down and yet you have to present results about your model soon #compbio #mathbio
✅✅ Save the date!
The workshop *MoDiS 2023: Modelling Diffusive Systems* will take place at ICMS Edinburgh, 11-15 Sep 2023.
#mathbio #workshop
As mentioned earlier today, I am sad not to be in Heidelberg for this year’s @SMB_MathBiology @ecmtb2022 #mathbio meeting but if you are attending you will be glad that much better scientists (and presenters) than yours truly will be describing there
I’m an @ESMTBio poster prize winner!! #mathbio
💡💡💡Open position: Postdoc & Senior researcher, IBS Biomedical Math Group, Korea.
Deadline: Nov 15, 2022.
See https://www.ibs.re.kr/bimag/hiring/ for more details.
#mathbio #postdoc
'A #biology-informed similarity metric for simulated patches of human #cell #membrane' by @harshbhatia85 @RUSH1L @jjayaram7 et al @Livermore_Lab @LLNL_SciTech hits 500 downloads! https://bit.ly/3c5XBDc #machinelearning #compbio #AI #HPC #datascience #compchem #TensorFlow #health
Delighted to share that miR2Trait has been published today in @PeerJLife -- a journey over four years in the making.
MiR2trait provides an ecosystem of services for working with miRNA-disease associations
#Bioinformatics #Biotechnology #Genomics #CompBio
https://peerj.com/articles/14146
Call for Judges for the first Wikipedia-ISCB LATAM contest.
EOI form: https://forms.gle/LFrpBxZJoCPgBgGR8
For details, contact: Dr Nelly Sélem at nselem@matmor.unam.mx.
@iscb @iscbsc @nselem35 @propicee @i_am_kilpatrick @GonzaParra_ #Wikipedia #LATAM #CompBio #SpanishWiki #Bioinformatics
NOW >3000 DOWNLOADS!🥳'Site2Vec: a reference frame invariant #algorithm for #vector embedding of #protein–ligand binding sites' by Arnab Bhadra and Kalidas Yeturu @iit_tirupati @IndiaDST - https://bit.ly/2OpchBu #machinelearning #bioinformatics #compchem #compbio #drugdiscovery
Andrea Califano #systemsbiology @ColumbiaMPT speaking about single cell analysis
New Research: The role of mathematical models in designing mechanopharmacological therapies for asthma https://www.frontiersin.org/articles/10.3389/fsysb.2022.929426?utm_source=S-TWT&utm_medium=SNET&utm_campaign=ECO_FSYSB_XXXXXXXX_auto-dlvrit #SystemsBiology
#NCICSBC supports cancer #systemsbiology research that integrates experimental and computational approaches to understand the complexities of cancer: https://csbconsortium.org/
October 19th is the application deadline for @theNCI #fundingopportunity that supports research centers for cancer #systemsbiology, which will be a part of @NCIsysbio (#NCICSBC): https://grants.nih.gov/grants/guide/rfa-files/RFA-CA-21-048.html