Gloria Sheynkman

Targeted proteomics informed by long-read RNA-sequencing reveals protein isoform expression associated with bone mineral density

This study uses genetics-guided targeted mass spectrometry to detect protein isoforms associated with bone mineral density, confirming their expression in clinical samples.

Sperm development requires TMC5-dependent mechanoresponsive calcium entry

This study identifies TMC5 as essential for mechanoresponsive calcium entry during spermiogenesis, linking mechanical cues to sperm development and male infertility.

LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery

LRP2 is a proteogenomics pipeline that integrates long-read RNA sequencing and mass spectrometry to detect novel protein isoforms and improve their translation inference.

Isocall enables scalable transcript identification from long-read RNA-sequencing data

Isocall is a scalable method for joint transcript identification from long-read RNA-seq data, showing high precision and handling large datasets efficiently.

Perplexity as a Metric for Isoform Diversity in the Human Transcriptome

The paper introduces perplexity as a metric to quantify isoform diversity in the human transcriptome using long-read RNA-sequencing data, showing it provides interpretable and reproducible measurements.

Tonotopic Specialization of MYO7A Isoforms in Auditory Hair Cells

The paper identifies a novel MYO7A isoform, MYO7A-N, and shows its distinct expression and function in outer hair cells, contributing to hearing sensitivity and cochlear frequency resolution.

eSIG-Net: Accurate prediction of single-mutation induced perturbations on protein interactions using a language model

eSIG-Net predicts how single mutations affect protein interactions using a sequence-based interaction language model, outperforming existing methods.

Beyond gene length: Exon-intron architecture and isoform potential in the evolution of eukaryotic complexity

The paper shows that exon count increases beyond a certain point in eukaryotic evolution and saturates at ~10 exons per gene, suggesting it contributes to genomic complexity.

A Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification

This study benchmarks PacBio Kinnex long-read RNA sequencing against Illumina short-read RNA-seq, finding Kinnex provides more accurate transcript discovery and quantification with comparable gene-level performance.

Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics

The paper develops a workflow using long-read RNA-seq and MS data to construct haplotype-resolved proteomes, enabling detection of variant and allele-specific protein isoforms.

The Septin Cytoskeleton is a Novel Regulator of Intestinal Epithelial Barrier Integrity and Mucosal Inflammation

This study investigates the role of SEPT9 in intestinal epithelial barrier integrity and inflammation, finding that its loss disrupts tight junctions and increases susceptibility to colitis.

Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox

The paper develops a CRISPR/Cas13d-based method to specifically knockdown RNA isoforms and provides computational tools for experimental design and analysis.

Protein sequencing with single amino acid resolution discerns peptides that discriminate tropomyosin proteoforms

This study evaluates the Platinum sequencer's ability to detect proteoform-informative peptides, distinguishing TPM1/TPM2 paralogs, spliceforms, and PTMs.

Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity

Biosurfer identifies sources of protein isoform diversity by analyzing long-read RNA-seq data, revealing common mechanisms like alternative transcription start sites and 'ragged codons'.

Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

The paper identifies two categories of transcription factor isoforms with distinct molecular functions and shows they contribute to gene regulatory complexity.

Alternative splicing is coupled to gene expression in a subset of variably expressed genes

The paper shows that alternative splicing is coupled to gene expression in a subset of variably expressed genes across multiple tissues.

AI-readiness criteria for biomedical data

The paper defines AI-readiness criteria for biomedical data, encompassing seven dimensions, and evaluates them across flagship datasets to ensure ethical and explainable AI practices.

Long read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease

This paper connects disease-associated splicing QTLs to protein isoform effects using long-read RNA-seq and GWAS data in osteoblasts.

IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection

The paper introduces LRP-IS-PRM, a method using long-read RNAseq to inform targeted proteomics with IS-PRM, identifying five new protein isoforms in human stem cells.

IsoBayes: a Bayesian approach for single-isoform proteomics inference

IsoBayes infers protein isoform presence and abundance using Bayesian methods integrating proteomics and transcriptomics data, showing good sensitivity and specificity in simulations and real datasets.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development

The paper analyzes single-cell long-read mRNA isoform regulation across mouse brain regions, cell types, and development, finding pervasive isoform variability and cell-type specific splicing patterns.

Characterization of protein isoform diversity in human umbilical vein endothelial cells (HUVECs) via long-read proteogenomics

The paper uses long-read proteogenomics to characterize protein isoform diversity in HUVECs, identifying novel transcripts and isoforms with potential functional implications.

Endothelial Cell Cycle State Determines Propensity for Arterial-Venous Fate

This study shows that endothelial cell cycle states determine arterial-venous fate, with early G1 for venous and late G1 for arterial specification.

Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data

The paper benchmarks variant callers on long-read RNA-seq data and proposes a pipeline to improve their performance using spliced alignment files.

Genetic regulation of human aortic smooth muscle cell gene expression and splicing predict causal coronary artery disease genes

The paper identifies eQTLs and sQTLs in human aortic SMCs that colocalize with CAD GWAS loci, highlighting splicing regulation as a mechanism for CAD risk.

Characterization of a Disease-Associated NPNT Functional Splicing Genetic Variant in Human Lung Tissue via Long-Read Sequencing

The paper identifies a genetic variant in NPNT associated with COPD risk and lung function through splicing analysis using long-read sequencing.

ORF Capture-Seq: a versatile method for targeted identification of full-length isoforms

ORF Capture-Seq enables targeted full-length isoform sequencing by using cloned ORFs as probes, significantly increasing isoform detection compared to unenriched samples.

A reference map of the human protein interactome

The paper presents HuRI, a comprehensive human protein-protein interaction map, and demonstrates its utility in understanding cellular function and disease mechanisms.

Full-length mRNA sequencing uncovers a widespread coupling between transcription and mRNA processing

The paper uses full-length mRNA sequencing to uncover widespread coupling between transcription and mRNA processing events in breast cancer cells and human tissues.