Projects - AI Gene Review

C. elegans Projects

Ciliopathy Pathway diagram

Mitophagy Pathway diagram

Proteostasis Pathway diagram

P Granules

Surveillance Immunity Pathway diagram

UPR Stress Pathway diagram

Yeast Projects

Cell Cycle

DNA Repair & Chromatin

Epigenetics & Histone Inheritance

Metabolic Engineering

Replicative Aging

Human / Mammalian Projects

Allergens

Alzheimer Disease

Chimeric mRNA Trans-Fusions in Immunity

ClinGen Mendelian Disease Genes

Glycobiology Resources dossier Pathway modules

PAINT (No-IBA Genes)

Ferroptosis

Isoform-Specific Functions

PINK1-Parkin Mitophagy

Mitochondrial Interactome (MitoMatch)

Human Proteostasis Network

Neuron Development

Neuroblast Proliferation (vertebrate vs protostome disambiguation)

cGAS-STING Pathway

Extracellular Matrix

Evidence-Source Sufficiency

Mechanobiology

Deliverome GO Collaboration

ER-Phagy

Integrated Stress Response

MicroRNA Degradation / TDMD

NLRP3 Inflammasome

Ribosome Quality Control

Stress Granules

Stilbene Cleavage Oxygenases (SCO / LSD family)

Unfolded Protein Binding (GO:0051082 obsoletion)

ER-PM Tethering (GO:0061817 obsoletion)

Mitochondrion-ER Tethering (GO:1990456 obsoletion)

Mitochondrion Targeting Sequence Binding (GO:0030943 obsoletion)

Synaptic Vesicle Docking (GO:0099148 obsoletion)

Vesicle Targeting (GO:0006903 obsoletion)

Protein Localization to ER Exit Site (GO:0070973 obsoletion)

Calcitriol Biosynthesis from Calciol (GO:0036378 obsoletion)

Substrate Localization to Autophagosome (GO:0061753 obsoletion)

Cargo Receptor Ligand Activity (GO:0140355 obsoletion)

Succinate Dehydrogenase gp2term (GO:0008177 enables→contributes_to)

KW-1110 TRAF-inhibition KW2GO remapping (GO:0039527 → GO:0140476)

Bacterial Projects

Antimicrobial Resistance (CARD/ARO)

B. subtilis

Cellulosome

Plant Bioenergy Modules

Biosynthetic Gene Cluster Complexes

Nitrogen Cycle

P. putida Genome-wide Curation Module plan

Lipoate Biosynthesis (GO:0009107 obsoletion)

Plant Projects

A. thaliana Heat Stress

Nicotine Biosynthesis

Ent-Kaurene Oxidation (GO:0010241 obsoletion)

Other Organism Projects

Cephalopod Neuro Genes

Tardigrade Stress Response

Pancrustacea Metamorphosis Gene Families

Satellite Model Organisms

Parasites

Fungal Conidiation Cascade (Aspergillus / Neurospora)

Naked Mole Rat (HETGA) Annotation Review

Cross-Cutting & Methodology

Protein Families

Amino Acid Activation (43 tRNA aminoacylation BP obsoletions)

Biomolecular Condensates (scaffold vs client curation) GO and annotation audit

UniProt Subcellular Locations (SL) Unique Terms Membrane · Cytoskeleton · Secreted · Mitochondria Methodology

COSCIENTIST (AI co-scientist compute-driven hypotheses)

Pathway Satisfiability (context-resolved module logic)

Genome-wide Validation (system-level plausibility of annotation sets)

Ad-Hoc Bioinformatics

Anti-CRISPR Systems

Contested Function (Pseudo-enzymes)

UniProt CAUTION Notes

Enzyme Specificity

Mitochondrial Fatty Acid β-Oxidation

Function Knowledge Gaps

IBA Annotation Review

IEP Evidence Code Review

InterPro Mapping Review

Iron-Sulfur Cluster Biogenesis

Metabolic Model Analysis

Metabolomics Interpretation with GO / GO-CAM Tools landscape

METEA MLL Cluster

Miscitation Review Register

NITV2 Pathways

Over-Annotation Patterns

Behaviour Annotations (Over-Annotation)

Review Quality Audit (Boilerplate)

Miscitation Audit Citation defect register Anomaly detectors

Retracted Literature Behind Annotations Retraction register

Pseudoenzymes

Phosphorylation Refactor

Protein Complex Functions

RHEA → GO Contribution & Gaps

TCDB → GO Transporter-Activity Mapping & Gaps

Pfam → GO Precision Gaps Results

NCBIFAM / CDD → GO Contribution & Gaps

Swiss-Prot Keywords

UniPathway Unique Terms

Surveillance Immunity Curation

Function Prediction Evaluation

ProtNLM, BioReason, DeepECTransformer, Affinage, and annotation-transfer reviews

Propagation by Homology

ISO, ISS/ISA, IBA, and electronic orthology transfers, with a donor → target browser

BioReason-Pro Comparison

ProtNLM2 Evaluation

Validating E. coli ML Predictions

Cuproptosis (Copper-Dependent Cell Death)

TreeGrafter Inference Evaluation