Daniela Puiu

Efficient evidence-based genome annotation with EviAnn

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

Deleterious mitochondrial heteroplasmy drives high-risk clonal hematopoiesis and hematological malignancy

The paper shows that inherited and somatic mitochondrial DNA heteroplasmies contribute to hematological malignancies and high-risk clonal hematopoiesis, with most disease-related burden acquired during life.

Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project

The paper analyzes microbial content in 5,734 whole-genome sequencing samples from TCGA to provide a comprehensive reference dataset for future cancer microbiome studies.

Longitudinal change in mitochondrial heteroplasmy exhibits positive selection for deleterious variants

This study shows that deleterious mitochondrial DNA mutations increase over time and are associated with higher mortality risk, suggesting positive selection rather than genetic drift.

Mitochondrial heteroplasmy improves risk prediction for myeloid neoplasms

This study shows that mitochondrial heteroplasmy improves risk prediction for myeloid neoplasms when added to existing CHIP-based models.

Quantifying constraint in the human mitochondrial genome

The paper develops a mitochondrial constraint model applied to gnomAD data, revealing strong depletion of expected variation and identifying constrained regions in mtDNA.

A genome sequence for the threatened whitebark pine

The paper produces a high-quality genome sequence for whitebark pine and identifies NLR genes associated with resistance to white pine blister rust.

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

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

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

A Draft Human Pangenome Reference

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

Recombination between heterologous human acrocentric chromosomes

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

Automated assembly of high-quality diploid human reference genomes

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

Deleterious heteroplasmic mitochondrial mutations increase risk of overall and cancer-specific mortality

This study identifies that heteroplasmic mitochondrial mutations increase mortality risk and are linked to cancer incidence and outcomes, particularly leukemia.

High-quality genome and methylomes illustrate features underlying evolutionary success of oaks

This study presents a high-quality genome and methylome analysis of Quercus lobata, identifying genomic features linked to oak evolutionary success, including gene duplications and methylation patterns.

A Bioinformatics Pipeline for Estimating Mitochondria DNA Copy Number and Heteroplasmy Levels from Whole Genome Sequencing Data

This paper presents a bioinformatics pipeline to estimate mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data, showing improved accuracy in capturing mitochondrial genetic features.

A reference-quality, fully annotated genome from a Puerto Rican individual

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

Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia

This study uses GWAS to identify candidate genes for drought tolerance in coast redwood and giant sequoia, finding 78 and 6 marker-trait associations respectively.

Assembly and Annotation of an Ashkenazi Human Reference Genome

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

High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome

This paper presents a chromosome-scale walnut genome assembly, improving gene prediction and enabling better analysis of genetic diversity and proteomic changes.

Chromosome-scale assembly of the bread wheat genome, Triticum aestivum, reveals over 5700 new genes

The paper presents an updated wheat genome assembly, Triticum 4.0, which includes 15.07 gigabases of sequence and over 5700 new genes, improving upon previous assemblies.

The giant sequoia genome and proliferation of disease resistance genes

This paper presents the first genome assembly of the giant sequoia, enabling analysis of disease resistance genes for conservation and evolutionary studies.

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

The paper presents the first near-complete assembly of the hexaploid bread wheat genome using a combination of short and long-read sequencing technologies.

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm

The paper introduces a hybrid assembly method using long reads and short accurate reads to improve genome contiguity for a highly repetitive plant genome.