Sanjay R Srivatsan

Designed Minibinders Rewire Receptor Signaling to Enable Functional Human Myogenic Reprogramming

This paper demonstrates that AI-designed receptor modulators can drive efficient human fibroblast-to-muscle transdifferentiation by rewiring extracellular signaling.

Midgestation metabolic constraint in purine metabolism drives distinct strategies for placenta and fetal growth

The paper shows that midgestational metabolic constraints in purine metabolism drive distinct strategies for placenta and fetal growth in mice and humans.

Reconstituting Mouse Embryogenesis Ex Utero from Gastrulation to Fetal Development Reveals Maternally Independent Metabolic Programs

This paper uses ex utero culture to study mouse embryogenesis from gastrulation to fetal development, revealing metabolically independent programs and environmental influences on metabolic transitions.

Capsule-Based Single-Cell Genome Sequencing

This paper introduces a semi-permeable capsule for single-cell genome sequencing, enabling uniform coverage and minimal cross-contamination for detecting genomic variants.

Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart

The paper uses single-nucleus ATAC-Seq and RNA-Seq to analyze age and sex differences in human heart cells, identifying gene expression and chromatin changes linked to these factors.

Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

The paper introduces SCOPE, an optics-free method to reconstruct 2D and 3D shapes using DNA barcode proximity graphs from sequencing data.

Multiplexed single cell transcriptomics optimizes mesodermal patterning and hemogenic endothelial output from murine embryonic stem cells

This study uses sci-Plex to analyze how Activin and BMP4 gradients affect mesoderm patterning and hemogenic endothelial cell production in mouse embryonic stem cells.

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

12.4 million single-nucleus transcriptomes from 83 staged mouse embryos (E8 to P0) yield 190 cell types, a zygote-to-pup cell-type tree, and rapid postnatal transcriptional shifts.

Induction and in silico staging of human gastruloids with neural tube, segmented somites & advanced cell types

This study induces human gastruloids with embryo-like structures using retinoic acid and shows they match E9.5 mouse embryos in developmental stage through single-cell RNA-seq and computational staging.

Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy

The paper uses a combined single-cell genetic and chemical screening platform to analyze kinase dependencies in glioblastoma response to targeted therapy, identifying adaptive signaling and potential combination therapies.

High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling

The paper introduces sciPlex-ATAC-seq for high-capacity multiplexing of single-cell chromatin accessibility, demonstrating its use in chemical epigenomics and immune stimulation studies.

Proteostasis governs differential temperature sensitivity across embryonic cell types

The paper uses single-cell RNA-seq to study temperature sensitivity in zebrafish embryos, finding that notochord sheath cells are particularly vulnerable due to protein misfolding.

Deep molecular, cellular and temporal phenotyping of developmental perturbations at whole organism scale

The paper presents single cell transcriptomic data from zebrafish embryos with genetic perturbations to analyze developmental variation and cell type composition.

Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development

The paper uses single-cell RNA sequencing to systematically phenotype mouse genetic models, identifying molecular and cellular changes across multiple mutants and wildtypes.

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

The paper integrates single-cell RNA-seq, ATAC-seq, and Hi-C data to study nuclear configuration and gene expression changes during stem cell differentiation and X inactivation, revealing discrete structural changes and delayed chromatin compaction.

Multipotent progenitors and hematopoietic stem cells arise independently during the endothelial to hematopoietic transition in the early mouse embryo

The paper shows that multipotent progenitors and HSC arise from distinct HE populations during mouse embryogenesis, identified through clonal assays and single-cell transcriptomics.

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

SwabExpress is a simplified COVID-19 testing protocol that eliminates the need for transport media and nucleic acid extraction, achieving high sensitivity and specificity.

Systematic reconstruction of the cellular trajectories of mammalian embryogenesis

This paper reconstructs cellular trajectories of mammalian embryogenesis using scRNA-seq data and identifies key transcription factors at branch points.

Visual Cell Sorting: A High-throughput, Microscope-based Method to Dissect Cellular Heterogeneity

This paper introduces a method to physically separate live cells based on visual phenotypes and uses it to study nuclear localization sequences and paclitaxel resistance in human cancers.

Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome

The paper analyzes MYOD-mediated reprogramming of human fibroblasts using single-cell RNA-Seq to identify molecular determinants of reprogramming success and failure.

Chromatin accessibility dynamics of myogenesis at single cell resolution

The paper introduces Cicero, a statistical method to link regulatory elements to target genes using single-cell chromatin accessibility data, and applies it to study myogenesis.