Kitt D. Paraiso

cloneXplorer: A high-throughput clone discovery platform based on conical microwell arrays

The paper introduces cloneXplorer, a platform for generating antigen-specific T cell clones from peripheral blood using conical microwell arrays, and demonstrates its ability to identify and isolate functionally defined T cells.

Molecule template estimation using Validator Barcodes in multiplex PCR for adaptive immune repertoire profiling

This paper introduces Validator Barcodes (VBCs) as a simpler alternative to UMIs for estimating template molecules in TCR and BCR sequencing, showing comparable results to UMI-based methods.

Identification of functional non-coding variants associated with orofacial cleft

This study identifies functional non-coding variants associated with orofacial cleft by combining GWAS, reporter assays, and stem cell modeling.

Functional annotation of de novo variants found near GWAS loci associated with cleft lip with or without cleft palate

The paper annotates de novo variants near GWAS loci for cleft lip with or without cleft palate, finding noncoding variants in enhancer regions associated with craniofacial development genes.

Foxi2 and Sox3 are master regulators controlling ectoderm germ layer specification

This study identifies Foxi2 and Sox3 as master regulators of ectoderm specification in Xenopus, showing they control gene expression and epigenetic landscape through super-enhancers.

The CD4 T cell-independent IgG response during persistent virus infection favors emergence of neutralization-escape variants

Pre-existing and acquired CD4 T cell deficiency facilitates outgrowth of Ab-escape viral variants during persistent infection.

High incidence and geographic distribution of cleft palate cases in Finland are associated with a regulatory variant in IRF6

The paper identifies a regulatory variant in IRF6 associated with increased cleft palate risk in Finland and shows it disrupts IRF6 enhancer function.

Cell Type- and Tissue-specific Enhancers in Craniofacial Development

The paper identifies 14,000 human craniofacial enhancers across developmental stages and shows 56% are conserved in mice, providing cell type- and stage-specific activity profiles.

Uncovering the mesendoderm gene regulatory network through multi-omic data integration

The paper builds a genome-scale gene regulatory network for vertebrate mesendoderm development using multi-omic data integration and validates novel transcription factor interactions.

Maternal and zygotic factors sequentially shape the tissue regionalization of chromatin landscapes in early vertebrate embryos

The paper shows maternal and zygotic transcription factors sequentially shape chromatin landscapes in early vertebrate embryos, leading to distinct enhancer marks in germ layers.

Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endodermal gene regulatory network

The paper identifies Sox17 and β-catenin interactions at enhancers that regulate endoderm gene expression and repression of mesectoderm fates during Xenopus gastrulation.