Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups.

mdbabumiamssm24

Bioinformática

Microbiome Cancer Agent

AI-powered analysis of microbiome-cancer interactions including tumor microbiome profiling, immunotherapy response prediction, and microbiome-targeted therapeutic opportunities.

mdbabumiamssm24

Química Computacional

Bio Variant Calling Clinical Interpretation

Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications. Use when interpreting clinical significance of variants.

mdbabumiamssm24

Computación Científica

Bio Flow Cytometry Clustering Phenotyping

Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without predefined gates.

mdbabumiamssm24

Bioinformática

Chromosomal Instability Agent

AI-powered analysis of chromosomal instability (CIN) signatures for cancer prognosis, immunotherapy response prediction, and therapeutic vulnerability identification.

mdbabumiamssm24

Bioinformática

Interactive Annotation

Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation. Use when manually annotating cell types for training classifiers or validating automated phenotyping results.

mdbabumiamssm24

Química Computacional

Chemical Property Lookup

Compute RDKit-driven molecular properties (MW, logP, TPSA, QED, Lipinski) for a SMILES string to support downstream drug discovery tools.

mdbabumiamssm24

Depuración

Bio Methylation Calling

Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts. Use when extracting methylation levels from aligned bisulfite sequencing data for downstream analysis.

mdbabumiamssm24

Bioinformática

Methylation-Based Detection

Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Identifies cancer-specific methylation signatures and performs tissue-of-origin deconvolution. Use when using methylation biomarkers for early cancer detection or minimal residual disease.

mdbabumiamssm24

Bioinformática

Protein Structure Prediction

Predicts 3D protein structures from amino acid sequences using ESMFold or AlphaFold3 (mock).

mdbabumiamssm24

Herramientas de Laboratorio

Bio Experimental Design Sample Size

Estimates required sample sizes for differential expression, ChIP-seq, methylation, and proteomics studies. Use when budgeting experiments, writing grant proposals, or determining minimum replicates needed to achieve statistical significance for expected effect sizes.

mdbabumiamssm24

Bioinformática

Tcr Pmhc Prediction Agent

AI-powered TCR-peptide-MHC interaction prediction using AlphaFold3 and deep learning for therapeutic TCR discovery, neoantigen validation, and T cell immunogenicity assessment.

mdbabumiamssm24

Bioinformática

Immune Checkpoint Combination Agent

AI-powered analysis for predicting optimal immune checkpoint inhibitor combinations based on tumor microenvironment, biomarkers, and molecular profiling.

mdbabumiamssm24

Bioinformática

Bio Fragment Analysis

Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fragment ratios, and DELFI-style fragmentation profiles for cancer detection. Use when leveraging fragment patterns for tumor detection or tissue-of-origin analysis.

mdbabumiamssm24

Análisis de Datos

Bio Tcr Bcr Analysis Repertoire Visualization

Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs. Use when generating figures for repertoire comparisons, clonal dynamics, or V(D)J gene usage.

mdbabumiamssm24

Química Computacional

Virtual Screening

Performs structure-based virtual screening using AutoDock Vina 1.2 for molecular docking. Prepares receptor PDBQT files, generates ligand conformers, defines binding site boxes, and ranks compounds by predicted binding affinity. Use when screening chemical libraries against a protein structure to find potential binders.

mdbabumiamssm24

Bioinformática

Bio Microbiome Taxonomy Assignment

Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.

mdbabumiamssm24

Bioinformática

Tumor Heterogeneity Agent

AI-powered intratumor heterogeneity analysis for clonal architecture reconstruction, subclonal evolution tracking, and therapy resistance prediction using multi-region and longitudinal sequencing.

mdbabumiamssm24

Académico

Agentd Drug Discovery

Use the AgentD workflow to mine evidence, design molecules, and rank candidates with SAR plus ADMET annotations for early drug discovery tasks.

mdbabumiamssm24

Química Computacional

Bio Read Qc Umi Processing

Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, low-input RNA-seq, or targeted sequencing to distinguish PCR from biological duplicates.

mdbabumiamssm24

Bioinformática

Bio Tcr Bcr Analysis Immcantation Analysis

Analyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell phylogenetics using the Immcantation framework. Use when studying B cell affinity maturation, germinal center dynamics, or antibody evolution.

mdbabumiamssm24

Bioinformática

Bio Imaging Mass Cytometry Phenotyping

Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.

mdbabumiamssm24

Química Computacional

Bio Metabolomics Metabolite Annotation

Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untargeted metabolomics.

mdbabumiamssm24

Bioinformática

Bio Tcr Bcr Analysis Mixcr Analysis

Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune repertoire sequencing data to identify clonotypes and their frequencies.

mdbabumiamssm24

Química Computacional

Immunogenicity Scoring

Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features. Rank candidates for vaccine design. Use when prioritizing epitopes for vaccine development or identifying the most immunogenic neoantigens.

mdbabumiamssm24

Computación Científica

Bio Sequence Properties

Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence composition, computing physical properties, or comparing sequences.

mdbabumiamssm24

Bioinformática

Bio Cfdna Preprocessing

Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before downstream analysis.

mdbabumiamssm24

Química Computacional

Armored Cart Design Agent

AI-powered design of armored CAR-T cells with cytokine/chemokine expression for enhanced solid tumor efficacy, including IL-12, IL-15, IL-18, and IL-7 armoring strategies.

mdbabumiamssm24

Química Computacional

Bio Crispr Screens Screen Qc

Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recovery. Use when assessing screen quality before hit calling or diagnosing poor screen performance.

mdbabumiamssm24

Herramientas de Laboratorio

Chematagent Drug Discovery

Chemical Lab Agent

mdbabumiamssm24

Microbiologists | Skills Pool