List of works by Andreas Gnirke

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals

scientific article published on 30 August 2012

A rapid, low cost, and highly sensitive SARS-CoV-2 diagnostic based on whole genome sequencing

scientific article published on 26 April 2020

A unique regulatory phase of DNA methylation in the early mammalian embryo

scientific article published on 28 March 2012

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

scientific article published on October 2009

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

scientific article

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

scientific article (publication date: May 2010)

Activation of <i>Notch</i> and <i>Myc</i> Signaling via B-cell-Restricted Depletion of <i>Dnmt3a</i> Generates a Consistent Murine Model of Chronic Lymphocytic Leukemia

scientific article published on 22 October 2021

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

scientific article

Analyzing and minimizing bias in Illumina sequencing libraries

article by Daniel Aird et al published 11 October 2010 in Genome Biology

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

scientific article

Author Correction: Global delay in nascent strand DNA methylation.

scientific article published on 26 March 2018

Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade.

scientific article published on 6 April 2018

Capturing diverse microbial sequence with comprehensive and scalable probe design

scholarly article published 12 March 2018

Capturing sequence diversity in metagenomes with comprehensive and scalable probe design

scientific article published on 04 February 2019

Cellular source and mechanisms of high transcriptome complexity in the mammalian testis

scientific article published on 20 June 2013

Charting a dynamic DNA methylation landscape of the human genome

scientific article published on 07 August 2013

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

scientific article published on 23 October 2015

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus

scientific article

Comparative analysis of RNA sequencing methods for degraded or low-input samples

scientific article

Comparative genomic analysis of embryonic, lineage-converted, and stem cell-derived motor neurons

scientific article published on 21 November 2018

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

scientific article

Comprehensive comparative analysis of strand-specific RNA sequencing methods

scientific article

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

scientific article (publication date: 9 October 2009)

Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes

scientific article published on 9 June 2014

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL

scientific article published on 23 April 2019

DNA methylation dynamics during in vivo differentiation of blood and skin stem cells

scientific article published on 26 July 2012

DNA sequence and analysis of human chromosome 18

scientific article

Development and Validation of a Mass Spectrometry–Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease

article

Development and evaluation of RNA-seq methods

Dissecting neural differentiation regulatory networks through epigenetic footprinting

scientific article published on 24 December 2014

Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology.

scientific article published on 14 March 2018

Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect

scientific article published on 01 September 2020

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

scientific article

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

scientific article

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples

scientific article

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

scientific article published on 15 May 2019

Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

scientific article published on 20 September 2017

Erratum: Corrigendum: Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

scholarly article published in Nature Biotechnology

Erratum: Corrigendum: DNA sequence and analysis of human chromosome 18

scientific article published in Nature

Evaluation of bacterial ribosomal RNA (rRNA) depletion methods for sequencing microbial community transcriptomes.

scientific article published on 11 October 2010

Full-length transcriptome assembly from RNA-Seq data without a reference genome

scientific article

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

scientific article

Genetic determinants and epigenetic effects of pioneer-factor occupancy.

scientific article published on 22 January 2018

Genome sequencing reveals Zika virus diversity and spread in the Americas

scientific article (publication date: 18 February 2017)

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

scientific article published on 10 January 2010

Genome-scale DNA methylation maps of pluripotent and differentiated cells

scientific article

Genome-wide tracking of dCas9-methyltransferase footprints

scientific article published on 9 February 2018

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types

scientific article

Genomic epidemiology reveals multiple introductions of Zika virus into the United States ⬇️

scientific article

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

scientific article

Global delay in nascent strand DNA methylation.

scientific article published on 12 March 2018

Hi-C: a method to study the three-dimensional architecture of genomes

scientific article

High-throughput bisulfite sequencing in mammalian genomes

scientific article published on 12 May 2009

Hybrid selection for sequencing pathogen genomes from clinical samples

scientific article published on 11 August 2011

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

scientific article

Integrative analysis of the melanoma transcriptome

scientific article

Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia

scientific article

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

scientific article

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

scientific article

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

scientific article

Paired-end sequencing of Fosmid libraries by Illumina

scientific article

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

scientific article published on 10 December 2020

Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events

scientific article published on 25 August 2020

Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy

scientific article published on 03 December 2020

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

scientific article

Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells

scientific article

Quantitative comparison of genome-wide DNA methylation mapping technologies.

scientific article published on 19 September 2010

RNA-Seq methods for imperfect samples: development, evaluation and applications

scientific article published on 19 September 2011

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis

scientific article

Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines

scientific article

Reprogramming factor expression initiates widespread targeted chromatin remodeling

scientific article

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

scientific article

Simultaneous generation of many RNA-seq libraries in a single reaction

scientific article published on 2 March 2015

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

scientific article (publication date: 13 June 2013)

Small Molecule Targets TMED9 and Promotes Lysosomal Degradation to Reverse Proteinopathy

scientific article published on 01 July 2019

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

scientific article

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites

scientific article

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

scientific article

TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers

scientific article published on 08 June 2020

Targeted bisulfite sequencing of the dynamic DNA methylome

scientific article published on 3 December 2016

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells

scientific article published on 30 March 2015

Targeted exon sequencing by in-solution hybrid selection

scientific article

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

scientific article

Targets and genomic constraints of ectopic Dnmt3b expression

The African coelacanth genome provides insights into tetrapod evolution

scientific article

The genome of the model beetle and pest Tribolium castaneum

scientific article

The maternal-effect, selfish genetic element Medea is associated with a composite Tc1 transposon.

scholarly article

Transcription factor binding dynamics during human ES cell differentiation

scientific article

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells

scientific article published on 09 May 2013

Virus genomes reveal factors that spread and sustained the Ebola epidemic

scientific article (publication date: 12 April 2017)

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

article published in 2016

ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth

scientific article

Zika virus evolution and spread in the Americas

scientific article

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