Elizabeth Tseng

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.

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.

Cell-type-specific splicing of transcription regulators and Ptbp1 by Rbfox1/2/3 in the developing neocortex

The paper identifies cell-type-specific splicing of transcription regulators and Ptbp1 by Rbfox1/2/3 in the developing neocortex, showing differential splicing impacts on neuronal migration and differentiation.

Standardized Nomenclature and Reporting for PacBio HiFi Sequencing and Analysis of rAAV Gene Therapy Vectors

This paper establishes standardized nomenclature and reporting for analyzing rAAV vectors using PacBio HiFi sequencing to improve quality assessment and vector design.

SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms

SQANTI3 extends long-read transcriptome quality control with transcript-end subcategories, a short-read TSS ratio, rules or random-forest filters and a rescue module, raising SIRV-benchmarked F-score stepwise.

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.

Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos)

The paper uses long-read RNA sequencing to analyze isoform expression in brown bears during active and hibernation seasons, finding differential isoform usage in tissues even when genes are not differentially expressed.

VCFCons: a versatile VCF-based consensus sequence generator for small genomes

VCFCons generates consensus sequences from VCF files with customizable filtering for SARS-CoV-2 surveillance, producing accurate sequences accepted by GISAID and NCBI.

Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex

This study uses long-read RNA sequencing to analyze isoform diversity in human and mouse cerebral cortex, revealing widespread alternative splicing and novel transcripts.

I-CONVEX: Fast and Accurate de Novo Transcriptome Recovery from Long Reads

I-CONVEX improves de novo transcriptome recovery from long reads by providing fast, alignment-free isoform clustering with high consensus accuracy.

An improved pig reference genome sequence to enable pig genetics and genomics research

The paper presents improved pig reference genomes using long-read sequencing, enhancing continuity and accuracy for pig genetics and genomics research.

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.

Variant Phasing and Haplotypic Expression from Single-molecule Long-read Sequencing in Maize

The paper develops a tool for haplotype phasing and expression analysis in maize using single-molecule long-read sequencing, revealing allele-specific and imprinted gene expression.

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

The paper presents haplotype-resolved cattle genomes to identify structural variants and adaptation traits, finding expanded immune-related gene families and a fatty acid desaturase copy under positive selection in indicine cattle.

The landscape of SNCA transcripts across synucleinopathies: New insights from long reads sequencing analysis

This study uses long-read sequencing to analyze SNCA transcripts in synucleinopathies, revealing new insights into alternative splicing and structural variants.

Targeted Long-Read RNA Sequencing Demonstrates Transcriptional Diversity Driven by Splice-Site Variation in MYBPC3

The paper uses targeted long-read RNA sequencing to identify transcriptional diversity caused by a splice-site variant in MYBPC3 associated with hypertrophic cardiomyopathy.

Single molecule real time (SMRT) full length RNA-sequencing reveals novel and distinct mRNA isoforms in human bone marrow cell subpopulations

The paper uses SMRT full-length RNA sequencing to identify novel mRNA isoforms in human bone marrow progenitor and differentiated cells, revealing distinct transcript and protein isoforms that distinguish cell subpopulations.

SpaRC: Scalable Sequence Clustering using Apache Spark

SpaRC clusters large-scale sequence data using Apache Spark, achieving scalability and performance across transcriptomics and metagenomics datasets.

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

The paper uses long-read sequencing to analyze structural variations in the SK-BR-3 breast cancer cell line, revealing complex rearrangements and novel gene fusions.

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.

Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbird Archilochus colubris

The paper uses full-length transcript sequencing to analyze the transcriptome of the ruby-throated hummingbird, revealing sequence divergence in lipid metabolic genes.

Universal Alternative Splicing Of Noncoding Exons

The paper identifies that nearly all noncoding exons undergo alternative splicing, generating a vast repertoire of regulatory RNAs and highlighting conserved splicing patterns across species.

Widespread polycistronic transcripts in mushroom-forming fungi revealed by single-molecule long-read mRNA sequencing

The paper identifies widespread polycistronic transcripts in mushroom-forming fungi using long-read sequencing and shows short-read assembly is inadequate for isoform discovery.