Adam P. Cribbs

The paper develops a spatial tri-omics workflow to map genetically distinct myeloma subclones in bone marrow, showing they occupy spatially and biologically distinct niches.

This study identifies BRD9 inhibition as a strategy to enhance radiosensitivity in glioblastoma by modulating the MYC pathway, without significant cytotoxicity under normal conditions.

This study identifies CBP/p300 inhibition as a strategy to overcome vincristine resistance in medulloblastoma by targeting genes involved in drug resistance.

This study compares nanopore direct RNA and PCR-cDNA sequencing protocols, showing distinct 5' and 3' coverage biases affecting transcript-level analysis but similar gene-level accuracy.

FlowBench evaluates agentic bioinformatics systems by decomposing performance into planning, fault recovery, interpretation, and output fidelity, revealing limitations in toolchain inference and fault handling.

The paper identifies HDAC6 as an epigenetic vulnerability in TMZ-resistant glioblastoma models and shows HDAC6 inhibitors can restore TMZ sensitivity.

This study uses spatial and single-cell transcriptomics to map cellular changes in human tendons across development and aging, identifying lineage-specific targets for therapeutic repair.

This study shows GSK-J4, a KDM6 inhibitor, induces metal and stress responses in multiple myeloma cells by increasing intracellular Zn2+ and activating metallothionein gene expression.

The paper creates a single-cell atlas of the healthy human Achilles tendon, identifying six fibroblast subtypes with distinct spatial distributions and transcriptional profiles.

This paper introduces FIRESCAPE, a radiolabeling method to study extracellular histone H3 clearance and effects, revealing distinct behaviors compared to intact nucleosomes.

The paper integrates multi-omics data from uterine fibroids, myometrium, and endometrium to identify differential splicing and molecular pathways associated with abnormal uterine bleeding.

This study compares long-read single-cell sequencing platforms, identifying common limitations and demonstrating their utility for isoform-resolved analyses.

The paper identifies BRPF1 as a key regulator of Taxol resistance in TNBC through genetic and chemical screens, showing its inhibition sensitizes resistant cells to chemotherapy.

This study identifies CD4+ tissue-resident memory Th17 (TRM17) cells as the main source of IL-17A in SpA synovium, showing their role in disease pathology and potential as therapeutic targets.

This study identifies RBBP4 as a critical regulator of cell cycle progression in TMZ-resistant glioblastoma through CRISPR screens and functional analyses.

This study uses single-nucleus RNA sequencing to analyze early cellular changes in human quadriceps tendons after rupture, identifying key cell types and pathways involved in the injury response.

UMIche provides a unified platform for UMI-centric simulation and analysis in bulk and single-cell sequencing to improve molecular quantification accuracy.

Tresor simulates transcriptomic reads with PCR error representation across sequencing technologies, showing cell-type-specific profiles similar to reference data after duplicate removal.

mclUMI improves UMI deduplication by using Markov clustering to dynamically remove PCR duplicates, outperforming existing methods in noisy sequencing conditions.

FlowAgent automates bioinformatics workflows with an agent-based system, improving reproducibility and accessibility through intelligent decision-making and natural language interfaces.

This study identifies ATF4-mediated metabolic stress response as a therapeutic target in chordoma, showing that EPRS inhibitors reduce cell viability and inhibit tumor growth in vivo.

This paper introduces T2, a method using RNA editing to estimate transcriptional age and identify transient transcriptional programs in human cells.

The paper introduces an anchor-enhanced bead design to reduce oligonucleotide synthesis errors in single-cell sequencing, improving UMI recovery and feature detection.

The paper uses proteomics and other methods to study endolysosomal changes in a goat model of atrial fibrillation, identifying upregulated pathways and specific proteins.

The paper demonstrates that PCR errors significantly affect UMI-based absolute counting in sequencing data and proposes a solution using homotrimeric nucleotide blocks to correct these errors.

DeepsmirUD predicts small molecule-mediated regulatory effects on miRNA expression using deep learning, achieving high accuracy and enabling drug repositioning insights.

This paper introduces scBUC-seq, a method to correct barcode and UMI errors in single-cell sequencing, enabling direct Nanopore transcriptome sequencing with improved accuracy.

This study shows that BRD9 and ncBAF complexes maintain somatic cell identity and hinder reprogramming, with BRD9 inhibition increasing iPSC generation efficiency.

tRNAnalysis is a high-throughput pipeline for small RNA-seq data analysis, focusing on tRNAs, with visualization and support for multiple samples.

CGAT-core is a Python framework for building scalable, reproducible computational biology workflows, demonstrated with an RNAseq analysis pipeline.