Research Area
Science Use Cases
72 research projects covering life sciences, biomedical research, and physical sciences. Each one was planned, executed and written up by K-Dense Web, and links to its full report and session transcript.
Topics in this area
- Astronomy5
- Astrophysics2
- Biology/Safety1
- Biosignals1
- Cancer Biology9
- Cheminformatics2
- Chemistry10
- Drug Discovery3
- Epigenetics1
- Genomics8
- Heliophysics1
- Immunology4
- Mass Spectrometry2
- Metabolomics2
- Microbiology1
- Nanomedicine1
- Neuroscience6
- Nutrition1
- Physics4
- Proteomics2
- Quantum Chemistry1
- Spectroscopy2
- Synthetic Biology1
- Toxicology2
Beta Pictoris orbital stability simulation
Simulate Beta Pictoris orbital architecture and assess long-term dynamical stability of the debris disk system.
Tau pathway mapping and therapeutic audit
Map tau pathology pathways and audit therapeutic opportunities across anti-tau intervention strategies.
AME2020 SEMF Binding Energy Fit
Fit the semi-empirical mass formula to AME2020 binding energies and map residuals across the nuclear chart.
Simulating and reconstructing PLATON scintillator tracks
Simulate PLATON scintillator particle tracks and validate reconstruction performance against known geometries.
Sweetener and drug interactions on gut microbes
Screen sweetener–drug interaction effects on gut microbes and prioritize watchlist combinations for follow-up study.
Tara Oceans MAG–Nutrient Associations
Model 957 metagenome-assembled genomes across 93 ocean samples to identify 10 region-robust nutrient associations and design a confirmatory microcosm experiment.
ATLAS Higgs ML Challenge Classifier
Train and evaluate classifiers on the ATLAS Higgs ML Challenge with a documented end-to-end methodology pipeline.
Breast Cancer Spatial Prognostic Modeling
Test imaging mass cytometry features across 285 patients with leakage-controlled nested survival modeling, finding composition improves prognosis while spatial features do not generalize.
CO Fundamental Band from HITRAN
Fit the CO fundamental band using HITRAN line data and diagnose rotational residuals across the spectrum.
Graphene Tight-Binding Dispersion & Dirac Physics
Compute graphene tight-binding band structure and visualize Dirac-cone physics near the Fermi level.
Li Ionization Energy from Rydberg Series
Extract lithium ionization energy from Rydberg series spectroscopy fits with residual diagnostics.
BDE-db Bond Dissociation Enthalpy Prediction
Predict bond dissociation enthalpies from BDE-db and characterize model error distributions.
CRC Serum Metabolomics Classifier
Classify colorectal cancer from serum metabolomics with PCA diagnostics before and after batch correction.
Crohn's Anti-TNF Nonresponse Signature
Derive a cell-state-informed signature from ileal single-cell data and test it in an independent bulk cohort, revealing real biology but a platform shift that requires assay redesign.
Heart Failure Proteomics Module Discovery
Reanalyze LFQ proteomics from 34 human hearts to identify stable co-abundance modules across ischemic, dilated, and hypertrophic heart-failure etiologies.
METLIN Retention-Time QSAR Prediction
Predict METLIN chromatographic retention times with QSAR models against observed values.
MoNA MS/MS ClassyFire Classifier
Classify MoNA MS/MS spectra into ClassyFire chemical taxonomy with hierarchical label evaluation.
nmrshiftdb2 NMR Structure Elucidation
Elucidate molecular structures from nmrshiftdb2 NMR shifts using a multi-stage candidate funnel.
Plant Diversity & Gut Microbiome Analysis
Reassess the >30-plants-per-week hypothesis in 2,676 American Gut Project participants with compositional statistics and geographic transportability testing.
QM9 HOMO-LUMO Gap Prediction
Predict QM9 HOMO–LUMO gaps with ML regression and validate predicted-versus-true parity plots.
Reaction Barrier Prediction from Reactants & Products
Predict reaction activation barriers from reactant and product structures and compare model families.
SAMPL6 First-Principles pKa Prediction
Predict SAMPL6 pKa values from first principles and correlate predictions against experimental benchmarks.
ABIDE Autism Classification with Site-Effect Analysis
Classify autism in ABIDE neuroimaging data while quantifying site-effect leakage across CV schemes.
EGFR Chemotype–Mutation Potency Matrix
Integrate TCGA-LUAD, ChEMBL, and PDB data to rank EGFR inhibitor chemotypes against six sensitizing and resistance mutations with explicit go/no-go gates.
Equitable CYP2C19 Genotyping Assay Design
Audit CYP2C19 allele coverage across 2,504 people from 26 populations to design a low-cost universal core assay with trigger-based ancestry-aware add-ons.
M. tuberculosis Rifampicin Resistance Panel
Prioritize 10 rpoB resistance variants from the WHO 2023 catalogue using epidemiological odds ratios, confidence grades, and structural proximity to rifampicin.
PFOS Placental Toxicogenomics
Integrate EPA ToxCast with a 64,734-cell maternal-fetal interface atlas to nominate PFOS–PPARγ signaling in extravillous trophoblasts for mechanistic testing.
Allen Brain Observatory Visual Stimulus Decoding
Decode visual stimuli from Allen Brain Observatory mouse cortex recordings with neural decoding models.
Allen Cell Types E/I Neuron Classification
Classify excitatory versus inhibitory cortical neurons from Allen Cell Types electrophysiology features.
AqSolDB Aqueous Solubility QSAR Model
Model aqueous solubility on AqSolDB with QSPR methods and report predictive performance.
Buchwald-Hartwig C-N Coupling Yield Prediction
Predict Buchwald–Hartwig C–N coupling yields and rank reaction-component importance.
CHB-MIT Pediatric Seizure Detection Classifier
Detect pediatric seizures in CHB-MIT EEG with channel-montage importance analysis.
Clustering and mapping of CyTOF bone marrow cells
Cluster and map CyTOF bone marrow cells with UMAP comparisons across clustering methods.
CPA Catalyst Selectivity ML Prediction
Predict CPA catalyst selectivity with machine learning and highlight the most informative molecular features.
EGFR pIC50 QSAR Prediction Model
Build an EGFR pIC50 QSAR model for kinase inhibitor potency prediction with graphical abstract reporting.
Gaia DR3 Pleiades cluster membership analysis
Determine Pleiades cluster membership from Gaia DR3 astrometry and photometry.
OC20 IS2RE Adsorption Energy Prediction
Predict OC20 IS2RE adsorption energies and evaluate parity across train, validation, and test splits.
Planck CMB TT power spectrum peak extraction and ΛCDM fitting
Extract Planck CMB TT acoustic peaks and fit ΛCDM cosmological parameters to the power spectrum.
Sitagliptin Multi-Step Synthetic Route Design
Design a multi-step sitagliptin synthetic route with stereochemical model visualization.
Systematic analysis of Tdap vaccine immune responses
Systematically analyze Tdap vaccine immune responses including IgG fold-rise by clinical covariates.
TCRβ repertoire-based CMV serostatus classifier
Classify CMV serostatus from TCRβ repertoire features using clonal burden score distributions.
TESS transit modeling of WASP-121b
Model TESS transit photometry of WASP-121b with MCMC posterior corner diagnostics.
Yellow fever vaccine transcriptomic time-course analysis
Analyze yellow fever vaccine transcriptomic time courses with pathway enrichment of immune responses.
ΛCDM cosmological fit to Pantheon+ supernovae
Fit ΛCDM cosmology to Pantheon+ supernova distances and summarize posterior constraints.
A Topological Test of the JWST-Era Cosmic Web
A graph-topology comparison of NASA's newly released COSMOS-Web map of 164,000 galaxies.
FGFR2 Inhibitor SAR Mining from Patent WO2020231990
A reproducible six-step pipeline that extracts 4-amino-pyrrolopyrimidine compounds from an image-only patent table, fuses ligand descriptors with FGFR2 co-crystal pocket geometry, and trains an explainable Random Forest model to surface the structural drivers of kinase activity.
Multiproxy Analysis of 1204 Solar Storm
Bridging historical solar events and modern space weather to provide a risk assessment of potential impacts to modern infrastructure.
PDAC RAS Mutation Landscape
Global pancreatic cancer analysis of KRAS, NRAS, and HRAS mutation prevalence by allele and continent, with pan-RAS therapy eligibility and clinical-trial benchmarking.
CD20×CD3 Bispecific Antibody Biomarker Discovery
Multi-omic biomarker analysis for glofitamab/mosunetuzumab stratification in DLBCL using cBioPortal, DepMap, and FAERS with Phase III SAP recommendations.
PDAC Neoantigen Landscape & iNeST Strategy
PDAC neoantigen landscape analysis with TMB benchmarking, KRAS structural modeling, and individualized neoantigen therapy optimization.
GBM Clinical Trial Landscape Analysis
Analyze 1,913 glioblastoma clinical trials identifying the immunotherapy gap (682 trials, 0 approvals) and novel target pipeline attrition.
PDAC KRAS Mutation Survival Analysis
Analyze KRAS variant distribution and survival outcomes in 2,336 pancreatic adenocarcinoma patients from MSK cBioPortal data.
Deadliest Animal Venoms Safety Guide
Emergency response guide for the 5 deadliest venoms: cone snail, box jellyfish, wandering spider, inland taipan, and funnel-web.
NGS Variant Callers in Clinical Practice
Comprehensive review of germline and somatic variant callers for clinical genomics with ACMG/AMP classification frameworks.
Renal Cancer Drug Response Stratification
Stratify 97 ccRCC patients by predicted response to standard therapies and identify drug repurposing candidates.
Indian Vegetarian Diet Optimization
Generate nutritionally optimized 7-day meal plans for urban Indians across activity levels with regional diversity.
Doxorubicin Mechanism of Action
Elucidate doxorubicin's mechanism in MCF7 cells through differential expression, pathway enrichment, and drug connectivity.
HNSCC Treatment Response Biomarkers
Build ML classifier for head and neck cancer treatment response using 270 patient samples with AUC=0.76.
Tox21 Liver Toxicity Prediction
Predict liver toxicity using Tox21 SR-MMP endpoint with XGBoost and SHAP-based structural interpretation.
T2-Low Asthma Endotype Discovery
Identify molecular endotypes in 679 asthma patients using nasal airway RNA-Seq and pathway-based clustering.
Epigenetic Clock Drug Discovery
Identify master transcription factors regulating 866 epigenetic clock CpG sites and map FDA-approved drug targets.
LC-MS Ion Suppression Prediction
Predict ion suppression factors in LC-MS metabolomics using chromatographic context features and SHAP interpretability.
Longevity Gene Analysis
Map model organism longevity genes to human orthologs and evaluate their validation through GWAS studies.
Lycopene Biosynthesis Optimization
Optimize enzyme expression ratios for lycopene production in E. coli using FBA and kinetic bottleneck analysis.
MS Fragmentation Rule Mining
Discover fragmentation patterns from 1,267 GNPS spectra with FDR-corrected statistical enrichment analysis.
JWST Exoplanet Target Prioritization
Rank 124 habitable zone exoplanets for JWST atmospheric characterization using TSM/ESM metrics and observability windows.
Nanoparticle Protein Corona Prediction
Build ML models to predict protein corona composition on gold nanoparticles using physicochemical properties.
Wearable Seizure Prediction
Explore heart-brain coupling for seizure prediction using EEG/ECG analysis and phase-amplitude coupling methods.
ECG Stress Detection Pipeline
Build HRV-based stress classifier from WESAD ECG data achieving 97% accuracy with XGBoost and Random Forest models.
Natural Products Chemical Space
Cluster 715K+ compounds from the COCONUT database to identify bacterial-derived drug candidates using ML dimensionality reduction.
Quantum Chemistry VQE Benchmarking
Benchmark variational quantum eigensolver algorithms for molecular simulations on H₂, LiH, BeH₂, and H₂O systems.
TMT Proteomics Spike-in Validation
Validate TMT 6-plex quantification accuracy using Erwinia carotovora spike-in proteins with 97% correlation to ground truth.
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