Melissa Laird Smith

DNA 6mA marks transcriptionally active chromatin in malaria parasites

The paper identifies 6mA methylation in Plasmodium falciparum, showing it is associated with active chromatin and transcription, and identifies a methyltransferase involved in this modification.

Comparative genomic and transcriptomic analyses of Strongylus vulgaris reveal developmental and evolutionary deployment of parasitism in a migratory equine nematode

This paper presents a genomic and transcriptomic analysis of Strongylus vulgaris, revealing developmental and evolutionary aspects of its parasitic lifestyle and identifying key genes and isoforms involved in its biology.

Disruption of a CCR5-like immunoglobulin gene is linked to plague susceptibility in black-footed ferrets

The paper identifies a disrupted CCR5-like immunoglobulin gene in black-footed ferrets linked to increased susceptibility to plague caused by Yersinia pestis.

An integrated human immunoglobulin germline resource linking allele diversity to expressed repertoire structure

This paper constructs HUSA, a comprehensive germline resource linking allele diversity to expressed antibody repertoires by integrating long-read sequencing and AIRR-seq data.

LVV SMRTcap reveals extensive proviral variation in lentiviral vector-transduced CAR T cells

The paper uses long-read sequencing to analyze proviral variation in lentiviral vector-transduced CAR T cells, finding deletions and mutations affecting transgene function.

Fully Phased Telomere-to-Telomere Assemblies for Thoroughbred Horse and Donkey Haplotypes derived from a Mule Illuminate the Peculiar Evolution of Equid Centromeres

The paper presents telomere-to-telomere genome assemblies of a Thoroughbred horse and donkey derived from a mule, revealing insights into equid centromere evolution and plasticity.

Development and validation of HIV SMRTcap for the characterization of HIV-1 reservoirs across tissues and subtypes

The paper introduces HIV SMRTcap, a method for characterizing HIV-1 reservoirs by identifying integration sites and proviral integrity using long-read sequencing, and validates its performance across subtypes and tissue samples.

The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations

The paper identifies structural variants and coding polymorphisms in the human IGHC locus, revealing population-specific diversity and potential functional impacts.

Germline polymorphism in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire

This study shows that genetic variations in immunoglobulin light chain loci influence the diversity of expressed light chain antibodies, affecting amino acid sequences and gene usage.

Diverse priming outcomes under conditions of very rare precursor B cells

The paper investigates how vaccine antigen delivery and adjuvant selection affect the priming of rare HIV broadly neutralizing antibody-precursor B cells in non-human primates, finding that specific dosing and adjuvant combinations enhance their detection in germinal centers.

A Broad Survey and Functional Analysis of Immunoglobulin Loci Variation in Rhesus Macaques

The paper develops methodologies to generate and analyze immunoglobulin loci variation in rhesus macaques, revealing extensive diversity and expanding existing allele sets by 60%.

Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy chain locus

The paper introduces a method using ultra-long sequencing and bioinformatics to resolve haplotypes in the human immunoglobulin heavy chain locus, uncovering novel alleles and structural variants.

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.

Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire

The paper shows that genetic variation in the immunoglobulin heavy chain locus influences the diversity and characteristics of the human antibody repertoire.

Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation

The paper characterizes the immunoglobulin lambda chain locus in diverse populations, identifying novel alleles and highlighting limitations of short-read sequencing.

Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta and beta loci

This paper uses targeted long-read sequencing to accurately assemble and genotype TCR loci, discovering new alleles and improving variant detection compared to short-read methods.

Unbiased profiling of CRISPR RNA-guided transposition products by long-read sequencing

The paper uses long-read sequencing to analyze transposition products of RNA-guided transposons, finding they primarily use copy-and-paste mechanisms and report engineered variants with TnsAB fusion proteins.

exRNA Signatures in Extracellular Vesicles and their Tumor-Lineage from Prostate Cancer

The paper identifies exRNA signatures in circulating tumor extracellular vesicles (CTEVs) from prostate cancer patients and shows their differential expression post-tumor resection.

A novel framework for characterizing genomic haplotype diversity in the human immunoglobulin heavy chain locus

The paper introduces a framework combining long-read sequencing and a new tool to fully characterize haplotype diversity in the human immunoglobulin heavy chain locus, demonstrating high accuracy and scalability.

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.

In-host population dynamics of M. tuberculosis during treatment failure

The paper analyzes M. tuberculosis population dynamics during treatment failure using whole-genome sequencing data from clinical isolates to identify resistance mutations and in-host evolutionary patterns.

High-coverage, long-read sequencing of Han Chinese trio reference samples.

The paper presents high-coverage long-read sequencing data from a Han Chinese trio for developing and evaluating long-read bioinformatics methods.

Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons

FLEA is a tool for analyzing long-read sequencing data of HIV-1 env, improving accuracy in reconstructing viral sequences and analyzing evolutionary dynamics.

Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

The paper presents an improved Aedes aegypti genome assembly, AaegL5, which enhances biological understanding and vector control efforts by resolving key genomic features and identifying new targets for intervention.

Multiparameter cell characterization using nanofluidic technology facilitates real-time phenotypic and genotypic elucidation of intratumor heterogeneity

The paper uses a nanofluidic platform to enable single-cell phenotypic and genetic profiling of ovarian cancer cells, revealing clonal diversity and TP53 mutation patterns associated with tumor heterogeneity.

Amplification-free, CRISPR-Cas9 Targeted Enrichment and SMRT Sequencing of Repeat-Expansion Disease Causative Genomic Regions

Combining amplification-free CRISPR-Cas9 targeted enrichment with Single Molecule, Real-Time (SMRT) long-read sequencing captures and sequences human repeat-expansion disease loci across HTT, FMR1, C9orf72, and ATXN10 without PCR bias.