User profiles for J. Klughammer

Johanna Klughammer

Broad Institute of MIT and Harvard
Verified email at broadinstitute.org
Cited by 5673

High-definition spatial transcriptomics for in situ tissue profiling

S Vickovic, G Eraslan, F Salmén, J Klughammer… - Nature …, 2019 - nature.com
… P(c j |b) and P(b|c j ) represent the posterior probability and the likelihood, respectively. P(b)…
cell type j and respective Θ j , we retained only nonzero elements of each Θ j and shuffled …

Specification of tissue-resident macrophages during organogenesis

…, CE Jacome-Galarza, K Händler, J Klughammer… - Science, 2016 - science.org
INTRODUCTION Embryonic development and tissue homeostasis depend on cooperation
between specialized cell types. Resident macrophages are professional phagocytes that …

Pooled CRISPR screening with single-cell transcriptome readout

…, C Schmidl, T Krausgruber, P Traxler, J Klughammer… - Nature …, 2017 - nature.com
… and stimulated conditions, respectively; and i and j are indices of the signature genes (n) and
… For m = 100, this is equivalent to μ a and μb being placed at index j = 20 and j = 80 of the Z …

[HTML][HTML] A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

…, O Cohen, J Klughammer, Y Rosen, J Gould… - Nature medicine, 2020 - nature.com
Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq)
profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq …

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

…, BE Johnson, J Klughammer, M Slyper, J Waldman… - Science, 2021 - science.org
INTRODUCTION Cells and tissues are made up of diverse molecular building blocks,
organized with nanoscale precision over extended length scales. Newly developed techniques …

Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation

…, AD Bretherick, TG Richardson, J Klughammer… - Nature …, 2021 - nature.com
Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to
understand mechanisms underpinning gene regulation and disease. In the present study, we …

[HTML][HTML] Artemisinins target GABAA receptor signaling and impair α cell identity

…, RA Romanov, C Sturtzel, CH Lardeau, J Klughammer… - Cell, 2017 - cell.com
Type 1 diabetes is characterized by the destruction of pancreatic β cells, and generating new
insulin-producing cells from other cell types is a major aim of regenerative medicine. One …

Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

…, LN Gonzalez Castro, AR Richman, J Klughammer… - Nature …, 2021 - nature.com
Single-cell RNA sequencing has revealed extensive transcriptional cell state diversity in
cancer, often observed independently of genetic heterogeneity, raising the central question of …

[PDF][PDF] Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics

…, A Nuzzo, P Datlinger, A Schönegger, J Klughammer… - Cell reports, 2015 - cell.com
Methods for single-cell genome and transcriptome sequencing have contributed to our
understanding of cellular heterogeneity, whereas methods for single-cell epigenomics are much …

The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space

J Klughammer, B Kiesel, T Roetzer, N Fortelny… - Nature medicine, 2018 - nature.com
Glioblastoma is characterized by widespread genetic and transcriptional heterogeneity, yet
little is known about the role of the epigenome in glioblastoma disease progression. Here, …