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List of works by Martin Hemberg

A dominated coupling from the past algorithm for the stochastic simulation of networks of biochemical reactions

scientific article

A robust activity marking system for exploring active neuronal ensembles.

scientific article published on 23 September 2016

Adult Human Glioblastomas Harbor Radial Glia-like Cells

scientific article published on 30 January 2020

Adult Human Glioblastomas Harbor Radial Glia-like Cells

scientific article published on 01 July 2020

Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

scientific article published on 16 March 2020

Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences

scientific article published on 19 November 2020

Bhlhb5 and Prdm8 Form a Repressor Complex Involved in Neuronal Circuit Assembly ⬇️

scientific article published on January 26, 2012

Challenges in unsupervised clustering of single-cell RNA-seq data

scientific article published on 01 May 2019

Chromatin remodeling inactivates activity genes and regulates neural coding

scientific article

Computational Stem Cell Biology: Open Questions and Guiding Principles

scientific article published on 01 January 2021

Conservation of transcription factor binding events predicts gene expression across species ⬇️

scientific article published on May 26, 2011

Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data

scientific article

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

scientific article

Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers

scientific article published on 05 January 2015

False signals induced by single-cell imputation

scientific article published on 02 November 2018

Fast searches of large collections of single-cell data using scfind

scientific article published on 01 March 2021

Genome-Wide Activity-Dependent MeCP2 Phosphorylation Regulates Nervous System Development and Function ⬇️

scientific article published on October 6, 2011

Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection

scientific article published on December 2008

Genome-wide identification and characterization of functional neuronal activity-dependent enhancers

scientific article

Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways

scientific article

Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci

Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci.

scientific article

High-throughput functional comparison of promoter and enhancer activities

scientific article published on 16 June 2016

Identifying cell populations with scRNASeq.

scientific article published on 13 July 2017

Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites

scientific article

M3Drop: dropout-based feature selection for scRNASeq

scientific article published on 01 August 2019

MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers

scientific article published on 19 March 2015

MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments

scientific article

MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development

scientific article published on 13 February 2020

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis.

scientific article

Obstacles to detecting isoforms using full-length scRNA-seq data

scientific article published on 23 March 2020

Perfect sampling of the master equation for gene regulatory networks

scientific article published on 27 April 2007

Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment

scientific article published on May 2017

Promoter decommissioning by the NuRD chromatin remodeling complex triggers synaptic connectivity in the mammalian brain

scientific journal article

Publisher Correction: Challenges in unsupervised clustering of single-cell RNA-seq data

scientific article published on 01 May 2019

Quantification of mRNA in single cells and modelling of RT-qPCR induced noise

scientific article

Quantitative profiling of peptides from RNAs classified as noncoding

scientific article published on 18 November 2014

Quantitative transcription factor analysis of undifferentiated single human embryonic stem cells

scientific article published on 8 October 2009

SC3: consensus clustering of single-cell RNA-seq data

scientific article

Simulation-based benchmarking of isoform quantification in single-cell RNA-seq

scientific article published on 07 November 2018

Single-cell genomics

scientific article published on 01 July 2018

Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis

scientific article published on 20 March 2018

Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

scientific article published on 04 May 2020

Stochastic kinetics of viral capsid assembly based on detailed protein structures.

scientific article

Summing up the parts of the hypothalamus

scientific article published on 01 February 2017

Supervised clustering for single-cell analysis

scientific article published on 01 October 2019

Tau promotes neurodegeneration through global chromatin relaxation

scientific article

Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution

scientific article published on October 2017

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription. ⬇️

scientific article published on August 2017

The Human Cell Atlas

scientific article

The Human Cell Atlas

The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle

scientific article

The Malaria Cell Atlas: a comprehensive reference of single parasite transcriptomes across the complete Plasmodium life cycle: file S1

scientific article published on 22 January 2019

Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts

scientific article published on 24 April 2020

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

scientific article

TransposonUltimate: software for transposon classification, annotation and detection

scientific article published on 14 February 2022

TransposonUltimate: software for transposon classification, annotation and detection

scientific article published on 30 April 2021

Trophic levels and trophic tangles: the prevalence of omnivory in real food webs

scientific article

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

scientific article published on 07 December 2020

f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome

scientific article published on 14 March 2016

scmap: projection of single-cell RNA-seq data across data sets

scientific article published on 02 April 2018

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