Mihaela Pertea

Bramble improves transcript quantification by projecting spliced genomic alignments into transcriptomic coordinates, enhancing accuracy across simulated datasets.

EviAnn improves eukaryotic genome annotation by using transcript alignments and protein homology, outperforming existing tools with less computational time.

StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts, reducing errors and enhancing precision and sensitivity in both short- and long-read data.

The paper presents HIV Atlas, a reference-quality annotation of HIV-1 and SIV transcriptional diversity, and demonstrates its utility in improving transcriptome analysis.

TranSigner improves transcript abundance estimation by accurately assigning long reads to transcripts, outperforming existing tools in simulated and experimental data.

The paper identifies isoswitching, a phenomenon of isoform usage changes in human brain development and aging, and shows it can predict age across the lifespan using RNA-seq data.

OpenSpliceAI improves SpliceAI by implementing it in PyTorch, enabling faster processing and retraining on non-human species with reduced memory usage.

LiftOn improves genome annotation by integrating DNA and protein alignments, enabling accurate annotation transfer between closely and distantly related species.

Splam improves spliced alignments by accurately predicting splice junctions in DNA, outperforming existing methods like SpliceAI across human and non-human species.

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.

SPIT detects differential transcript usage in complex diseases by quantifying population heterogeneity and identifying subgroups with distinct DTU events, revealing new events in schizophrenia brain samples.

CHESS 3 improves upon previous versions by using better algorithms and filtering to create a more accurate catalog of human genes and transcripts.

ORFanage identifies ORFs in known and novel transcripts, improving annotations in RefSeq and GENCODE databases and enabling analysis of large RNA-seq datasets.

EASTR corrects systematic alignment errors in multi-exon genes by detecting and removing falsely spliced transcripts, improving alignment accuracy across species.

The paper assembles a gapless, reference-quality genome from a Southern Han Chinese individual and identifies gene-level differences compared to a reference genome.

The paper uses 3D protein structures to evaluate human protein isoforms for biological functionality, refining genome annotations.

The paper improves transcriptome assembly by combining long and short reads using StringTie, achieving higher accuracy and transcript count than either method alone.

The paper presents a new reference genome, PR1, from a Puerto Rican individual, highlighting its completeness and annotations compared to existing genomes.

This paper introduces Bolotie, a method to detect recombination in SARS-CoV-2 genomes, identifying hundreds of recombinant isolates and showing some persist in the population.

The paper assembles and annotates a population-specific Ashkenazi human reference genome, showing improved contiguity and completeness compared to GRCh38.

StringTie2 assembles error-prone long reads, recovering on average 8.3 and 2.6 times as many correct transcripts as FLAIR and Traphlor, and outperforms Scallop on short reads.

The paper compiles RNA sequencing data from 9,795 experiments to create a new human gene catalog, identifying novel genes and transcripts while highlighting extensive transcriptional noise.