User profiles for Christoph Hafemeister

Christoph Hafemeister

Postdoctoral Research Associate, St. Anna Children's Cancer Research Institute
Verified email at ccri.at
Cited by 16865

[PDF][PDF] Comprehensive integration of single-cell data

T Stuart, A Butler, P Hoffman, C Hafemeister… - cell, 2019 - cell.com
Single-cell transcriptomics has transformed our ability to characterize cell states, but deep
biological understanding requires more than a taxonomic listing of clusters. As new methods …

[HTML][HTML] Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

C Hafemeister, R Satija - Genome biology, 2019 - Springer
Single-cell RNA-seq (scRNA-seq) data exhibits significant cell-to-cell variation due to
technical factors, including the number of molecules detected in each cell, which can confound …

Simultaneous epitope and transcriptome measurement in single cells

M Stoeckius, C Hafemeister, W Stephenson… - Nature …, 2017 - nature.com
High-throughput single-cell RNA sequencing has transformed our understanding of complex
cell populations, but it does not provide phenotypic information such as cell-surface protein …

Developmental diversification of cortical inhibitory interneurons

C Mayer, C Hafemeister, RC Bandler, R Machold… - Nature, 2018 - nature.com
Diverse subsets of cortical interneurons have vital roles in higher-order brain functions. To
investigate how this diversity is generated, here we used single-cell RNA sequencing to …

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

ML Arrieta‐Ortiz, C Hafemeister, AR Bate… - Molecular systems …, 2015 - embopress.org
Organisms from all domains of life use gene regulation networks to control cell growth,
identity, function, and responses to environmental challenges. Although accurate global …

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

A Greenfield, C Hafemeister, R Bonneau - Bioinformatics, 2013 - academic.oup.com
Motivation: Inferring global regulatory networks (GRNs) from genome-wide data is a computational
challenge central to the field of systems biology. Although the primary data currently …

EGRINs (Environmental Gene Regulatory Influence Networks) in rice that function in the response to water deficit, high temperature, and agricultural environments

O Wilkins, C Hafemeister, A Plessis… - The Plant …, 2016 - academic.oup.com
Environmental gene regulatory influence networks (EGRINs) coordinate the timing and rate
of gene expression in response to environmental signals. EGRINs encompass many layers …

[HTML][HTML] Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis

…, R Perez, M Subramaniam, C Hafemeister… - Nature …, 2020 - nature.com
Single-cell RNA-sequencing (scRNA-Seq) is a compelling approach to directly and
simultaneously measure cellular composition and state, which can otherwise only be estimated by …

[HTML][HTML] Large-scale simultaneous measurement of epitopes and transcriptomes in single cells

M Stoeckius, C Hafemeister, W Stephenson… - Nature …, 2017 - ncbi.nlm.nih.gov
Recent high-throughput single-cell sequencing approaches have been transformative for
understanding complex cell populations, but are unable to provide additional phenotypic …

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

A Plessis, C Hafemeister, O Wilkins, ZJ Gonzaga… - Elife, 2015 - elifesciences.org
10.7554/eLife.08411.001 Plants rely on transcriptional dynamics to respond to multiple
climatic fluctuations and contexts in nature. We analyzed the genome-wide gene expression …