Anna Alemany

STRAIGHT-IN Dual: a platform for dual, single-copyintegrations of DNA payloads and gene circuits into human induced pluripotent stem cells

STRAIGHT-IN Dual enables efficient, single-copy integration of two DNA payloads into hiPSCs, improving genetic engineering for synthetic biology applications.

Sex-specific DNA methylation in adult skeletal muscle

The paper examines DNA methylation patterns in adult skeletal muscle, finding that sex, not spatial location, drives methylation variation and sex-specific transcriptional programs.

De novo H3.3K27M-altered Diffuse Midline Glioma in human brainstem organoids to dissect GD2 CAR T cell function

This paper develops a human brainstem organoid model of H3.3K27M-altered DMG to study GD2 CAR T cell function and identify therapeutic targets.

Post-transcriptional regulatory mechanisms in human islets inferred from cell type-specific eQTLs detected by single-cell RNA-seq

The paper infers post-transcriptional regulatory mechanisms in human islets using cell type-specific eQTLs from single-cell RNA-seq data, linking variants to biological processes in health and disease.

Droplet-based Single-cell Total RNA-seq Reveals Differential Non-Coding Expression and Splicing Patterns during Mouse Development

The paper introduces VASA-seq, a method for total single-cell RNA-seq in mice, revealing non-coding RNA expression and alternative splicing during development.

DUX4 induces a homogeneous sequence of molecular changes, culminating in the activation of a stem-cell-like transcriptional network and induction of apoptosis in somatic cells

The paper investigates how DUX4 induces a sequence of transcriptional changes leading to apoptosis in somatic cells by activating a stem-cell-like network.

A genome-wide CRISPR/Cas phenotypic screen formodulators of DUX4 cytotoxicity reveals screen complications

The paper performs a genome-wide CRISPR/Cas9 screen to identify modulators of DUX4 cytotoxicity in FSHD but finds no key effectors other than DUX4 itself.

Functional modules from variable genes: Leveraging percolation to analyze noisy, high-dimensional data

The paper introduces a density-based clustering method using percolation theory to identify functionally related gene modules from noisy, high-dimensional RNA sequencing data across different organisms.

Embryonic signals perpetuate polar-like trophoblast stem cells and pattern the blastocyst axis.

The paper shows that embryonic signals convert trophoblast stem cells into polar-like cells that pattern the blastocyst axis in vitro.

Massively parallel clonal analysis using CRISPR/Cas9 induced genetic scars

scartrace uses Cas9-induced genetic scars for clonal analysis in zebrafish, aiming at lineage reconstruction across many cells at once rather than the small subsets imaging covers.