Pavel-Kravchenko/Bioinformatics

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Build tries, Aho-Corasick, and suffix arrays with Kasai LCP to index DNA/text and match many patterns in one pass. Use for genome motif scanning, k-mer indexing, longest-repeat search, or BWA/FM-index groundwork.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Interpret AlphaFold2/AF3 pLDDT/PAE scores, fetch AlphaFold DB models by UniProt ID, and rank RFdiffusion/ProteinMPNN designs. Use when asked about pLDDT, PAE, AF2 vs AF3, AlphaFold DB fetch, or design triage.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Code DDPM/DDIM diffusion samplers, linear/cosine noise schedules, and DDRM inverse-problem solving (denoising, inpainting, super-resolution) in NumPy/PyTorch. Use for forward/reverse diffusion, score matching, or DDIM sampling.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Predict CAGE/DNase/ATAC/ChIP-seq tracks from raw DNA with Enformer/Borzoi, run in-silico mutagenesis (ISM), and score noncoding variant effects. Use when predicting enhancer/promoter activity from sequence, running ISM, scoring a noncoding SNP, or prioritizing GWAS/eQTL variants.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Choose Borzoi (RNA-seq coverage, 32bp) vs Epiformer (sequence+PhyloP, chromatin accessibility) vs AlphaGenome for epigenomic prediction. Use when picking a model for RNA-seq, ATAC/DNase, or variant-effect scoring.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Generate ESM2 protein embeddings (fair-esm/transformers) and predict structure with ESMFold. Use when embedding sequences, scoring mutations zero-shot, annotating protein function, or doing fast MSA-free structure prediction.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Tokenize scRNA-seq via Geneformer gene-rank or scGPT expression-bin encoding; annotate cell types, simulate in-silico knockouts. Use for foundation-model cell annotation, Geneformer/scGPT tokenization, or perturbation prediction.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Embed DNA with genomic foundation models (Nucleotide Transformer, HyenaDNA, Evo) via HuggingFace transformers; k-mer tokenize, probe promoter motifs. Use for DNA LLMs, genomic embeddings, or NT/HyenaDNA/Evo choice.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Fine-tune LLMs (Mistral/Llama/Qwen) with LoRA/QLoRA via HuggingFace PEFT, bitsandbytes NF4, and trl SFTTrainer. Use when doing LoRA/QLoRA fine-tuning, PEFT, instruction tuning, or SFTTrainer on limited GPU memory.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Track LLM fine-tuning runs with pandas/dataclasses + W&B/MLflow/TensorBoard: log per-epoch loss, run one-factor ablations (LoRA rank, LR), build a run registry. Use for hyperparameter ablations or picking an early-stop epoch.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Score splicing variant effects with SpliceAI/Pangolin delta scores (DSAG/DSAL/DSDG/DSDL) and AlphaGenome. Use when scoring a VCF for splice disruption, interpreting DS thresholds, or ranking cryptic splice-site variants.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Triage variant scores for structural follow-up; pick AlphaFold2 vs AlphaFold3 vs RoseTTAFold2 and gate results on pLDDT/PAE. Use for monomer/complex/ligand model choice or ranking variants by structural confidence.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

ColPali-style Vision RAG: embed rendered PDF pages, retrieve via ColBERT MaxSim, feed top-k pages to Qwen2-VL, no OCR. Use for PDF/document QA over figures and tables, multimodal retrieval, or Recall@k/MRR eval.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Score protein point mutations zero-shot with ESM-1v/ESM-2 masked-LM log-odds, ensembled, benchmarked on ProteinGym DMS. Use when predicting mutation effects, ranking missense variants, scoring VUS fitness with no labels.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Build an Aho-Corasick automaton (trie + BFS failure links) to find every pattern occurrence in one O(n+m+z) text pass. Use for restriction-site/primer/motif search or replacing per-pattern KMP/regex loops over many fixed patterns.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Implement a self-balancing AVL binary search tree in Python with rotation-based rebalancing (LL/RR/LR/RL) guaranteeing O(log n) insert/delete/search. Use when a user asks to build/implement an AVL tree, keep a sorted index balanced under insert/delete, explain balance factor or tree rotations, or avoid O(n)…

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Compute GCD/LCM via Euclid's algorithm, find roots with Newton's method, and count k-mers using dict/Counter vs O(n^2) list-scan. Use for GCD/LCM math, root-finding, k-mer counting, or Big-O complexity questions.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

BFS (queue) and DFS (stack/recursion) traversal in pure Python for shortest unweighted path, k-hop neighborhood, connected components, cycle detection on PPI/regulatory networks. Use for shortest path or cycle detection.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Implement/debug a binary search tree in Python: insert, search, delete (3 cases), successor/predecessor, inorder/level-order traversal. Use for BST coding, O(log n) vs O(n) degenerate cases, or choosing AVL/Red-Black.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Implement bubble/merge/shell/quicksort in Python; compare Big-O time/space/stability. Use when asked to sort an array, code a sort from scratch, explain quicksort complexity, or fix O(n^2) worst case on sorted input.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Derive Big O time/space complexity of loops and recursion via recurrence relations; simplify expressions, compare growth at scale. Use when asked the complexity of code, hunting O(n^2) loops, or worst-case cost.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Build a DFA transition table via the KMP prefix function, then scan text in O(n) with zero backtracking. Use when repeatedly searching one fixed pattern (motif, restriction site, primer) against many sequences or texts.

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Compute single-source shortest paths in a non-negative-weight graph with Dijkstra's algorithm (binary-heap priority queue, O((V+E) log V)); reconstruct paths and find network diameter. Use when finding shortest/cheapest/most-reliable path, routing, weighted PPI/interaction-network distance, or ranking paths by…

Pavel-Kravchenko/Bioinformatics

Skill Claude CodeCodex

Implement resizable arrays with ctypes-backed doubling/shrinking; prove append is amortized O(1). Use when asked why list.append is O(1), to build a DynamicArray class, or to compare list vs numpy append speed.