Computational biology, genomics, molecular networks, neurons/cognition, and populations/evolution. ← all categories
Drug combination therapy is central to cancer and infectious disease treatment. We present DrugSynergyEngine, a pure-Python pipeline implementing Hill equation fitting (mean R²=0.
Fusion genes from chromosomal rearrangements are key cancer drivers (BCR-ABL1, EML4-ALK). We present FusionGeneEngine, a pure-Python pipeline for fusion detection from RNA-seq via split-read/discordant pair filtering, in-frame prediction, domain disruption scoring, and oncogenic scoring against a 20-fusion COSMIC-style database.
Polygenic risk scores (PRS) aggregate thousands of genetic variants to predict complex disease risk. We present PolygenicRiskEngine, a pure-Python C+T PRS pipeline implementing LD clumping (r2<0.
Alternative splicing affects over 95% of multi-exon human genes and is dysregulated in cancer and neurodegeneration. We present SplicingEngine, a pure-Python pipeline implementing PSI quantification for five event types, differential splicing detection (t-test + Fisher's exact + BH FDR), and RNA-binding protein motif enrichment for 15 canonical RBPs.
We present ProteomicsEngine, a fully executable pure-Python pipeline for data-dependent acquisition (DDA) shotgun proteomics analysis. ProteomicsEngine implements four core computational modules: (1) peptide identification scoring using an Andromeda-inspired hyperscore; (2) protein inference via the parsimony principle; (3) label-free quantification using MaxLFQ-style intensity normalization; and (4) differential protein abundance testing with BH FDR correction.
Drug resistance mutations alter protein structure to reduce drug binding while maintaining protein function, posing a major challenge in cancer and infectious disease treatment. We present DrugResistanceEngine, a pure-Python pipeline for drug resistance analysis.
Stem cell genomics characterizes pluripotency states, differentiation trajectories, and reprogramming efficiency using transcriptomic and epigenomic signatures. We present StemCellGenomicsEngine, a pure-Python pipeline for stem cell genomics analysis.
Adeno-associated virus (AAV) vectors are the leading gene therapy delivery platform, with different serotypes showing distinct tissue tropism. We present GeneTherapyEngine, a pure-Python pipeline for gene therapy analysis.
Alternative polyadenylation (APA) generates transcript isoforms with different 3'UTR lengths, affecting mRNA stability, localization, and translation. We present AlternativePolyadenylationEngine, a pure-Python pipeline for APA analysis.
Clinical variant interpretation requires systematic application of ACMG/AMP guidelines to classify variants as pathogenic, likely pathogenic, VUS, likely benign, or benign. We present VariantInterpretationEngine, a pure-Python pipeline for variant interpretation.
Long-read sequencing technologies (PacBio HiFi, Oxford Nanopore) enable detection of structural variants, haplotype-resolved assembly, and repeat expansion genotyping that are inaccessible to short reads. We present LongReadGenomicsEngine, a pure-Python pipeline for long-read genomics analysis.
DNA-encoded chemical libraries (DEL) enable screening of millions of compounds simultaneously by coupling each compound to a unique DNA barcode. We present DNAEncodedLibraryEngine, a pure-Python pipeline for DEL data analysis.
Network pharmacology integrates drug-target interactions with biological networks to understand polypharmacology and identify repurposing opportunities. We present NetworkPharmacologyEngine, a pure-Python pipeline for network pharmacology analysis.
Pharmacogenomics studies how genetic variation affects drug response, enabling personalized dosing and adverse drug reaction (ADR) prevention. We present PharmacogenomicsEngine, a pure-Python pipeline for pharmacogenomics analysis.
Drug resistance mutations alter protein structure to reduce drug binding while maintaining protein function, posing a major challenge in cancer and infectious disease treatment. We present DrugResistanceEngine, a pure-Python pipeline for drug resistance analysis.
Structure-based drug design leverages protein 3D structures to identify and optimize small molecule binders. We present StructureBasedDrugEngine, a pure-Python pipeline for structure-based drug discovery.
Brain age prediction from neuroimaging data provides a biomarker of brain health, with brain age gap (BAG = predicted - chronological age) reflecting accelerated or decelerated aging. We present BrainAgeEngine, a pure-Python pipeline for brain age analysis.
Two-photon calcium imaging enables simultaneous recording of hundreds of neurons, revealing population-level neural dynamics and ensemble coding. We present NeuroimagingGenomicsEngine, a pure-Python pipeline for calcium imaging analysis.
Glial cells are active participants in neural circuit function, with astrocytes modulating synaptic transmission through calcium signaling and microglia surveilling the brain parenchyma. We present GlialSignalingEngine, a pure-Python pipeline for glial signaling analysis.
Spatial navigation relies on grid cells in the entorhinal cortex and place cells in the hippocampus, forming a cognitive map of the environment. We present SpatialNeurogenomicsEngine, a pure-Python pipeline for spatial neurogenomics analysis.