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List of works by Karsten Rippe

A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling

scientific article published on 17 July 2005

A lattice model for transcription factor access to nucleosomal DNA.

scientific article published on October 2010

A spherical harmonics intensity model for 3D segmentation and 3D shape analysis of heterochromatin foci.

scientific article published on 17 March 2016

A three-dimensional colocalization RNA interference screening platform to elucidate the alternative lengthening of telomeres pathway

scientific article published on 7 June 2011

ALT-FISH quantifies alternative lengthening of telomeres activity by imaging of single-stranded repeats

scientific article published in 2022

Action at a distance: DNA-looping and initiation of transcription

scientific article published on December 1995

Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arrays

scientific article

Alternative lengthening of telomeres in childhood neuroblastoma from genome to proteome

scientific article published on 24 February 2021

Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy

scientific article published on 19 June 2009

Assembly and mobility of exon-exon junction complexes in living cells

scientific article published on 26 March 2009

Association states of nucleosome assembly protein 1 and its complexes with histones

scientific article published on 31 January 2005

Association states of the transcription activator protein NtrC from E. coli determined by analytical ultracentrifugation.

scientific article

Aurora Kinase B Regulates Telomerase Activity via a Centromeric RNA in Stem Cells

scientific article published on 4 June 2015

Binding affinity of Escherichia coli RNA polymerase*sigma54 holoenzyme for the glnAp2, nifH and nifL promoters

scientific article published on September 2002

Binding kinetics of human ISWI chromatin-remodelers to DNA repair sites elucidate their target location mechanism ⬇️

scientific article published on March 1, 2011

Biochemical characterization and mass spectrometric disulfide bond mapping of periplasmic alpha-amylase MalS of Escherichia coli.

scientific article published on August 1997

Calculating transcription factor binding maps for chromatin.

scientific article

Capturing chromosome conformation

scientific article (publication date: 15 February 2002)

Changing chromatin fiber conformation by nucleosome repositioning

scientific article

Chromatin remodelling in mammalian cells by ISWI-type complexes--where, when and why?

scientific article

Coding RNAs with a non-coding function: maintenance of open chromatin structure

scientific article published on September 2011

DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries

scientific article published on 04 April 2019

DNA binding and oligomerization of NtrC studied by fluorescence anisotropy and fluorescence correlation spectroscopy

scientific article

DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats.

scientific article

De novo assembly of a PML nuclear subcompartment occurs through multiple pathways and induces telomere elongation

scientific article

Defining the structural requirements for ribose 5-phosphate-binding and intersubunit cross-talk of the malarial pyridoxal 5-phosphate synthase

scientific article published on 17 September 2010

Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping.

scientific article

Dissecting chromatin interactions in living cells from protein mobility maps.

scientific article published in January 2011

Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels

scientific article published on 15 June 2020

Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories

scientific article

Dual color localization microscopy of cellular nanostructures.

scientific article

Dynamic organization of the cell nucleus.

scientific article published on 24 October 2007

Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells

scientific article published on 24 December 2016

Dynamics of telomeres and promyelocytic leukemia nuclear bodies in a telomerase-negative human cell line

scientific article

Epigenetic upregulation of lncRNAs at 13q14.3 in leukemia is linked to the In Cis downregulation of a gene cluster that targets NF-kB.

scientific article

Establishing epigenetic domains via chromatin-bound histone modifiers

scientific article published on 13 September 2013

Evolutionary dynamics and information hierarchies in biological systems

scientific article published on 20 May 2013

Exploring the conformational space of chromatin fibers and their stability by numerical dynamic phase diagrams

scientific article

Expression of CCCTC-binding factor (CTCF) is linked to poor prognosis in prostate cancer

scientific article published on 29 November 2019

Force spectroscopy of chromatin fibers: extracting energetics and structural information from Monte Carlo simulations

scientific article published on 3 February 2011

Genome organization: balancing stability and plasticity.

scientific article published on 03 August 2008

Genome-wide nucleosome positioning during embryonic stem cell development

scientific article

Genomic footprints of activated telomere maintenance mechanisms in cancer

scientific article published on 05 February 2020

Glioblastoma initiating cells are sensitive to histone demethylase inhibition due to epigenetic deregulation

scientific article published on 11 October 2019

HP1 is involved in regulating the global impact of DNA methylation on alternative splicing

scientific article

Helix-coil transition of parallel-stranded DNA. Thermodynamics of hairpin and linear duplex oligonucleotides

scientific article published in November 1989

Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells

scientific article

High-precision structural analysis of subnuclear complexes in fixed and live cells via spatially modulated illumination (SMI) microscopy

scientific article

Histone H2A C-terminus regulates chromatin dynamics, remodeling, and histone H1 binding

scientific article

Histone acetylation increases chromatin accessibility

scientific article published on 29 November 2005

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

scientific article

Hypermutation of the inactive X chromosome is a frequent event in cancer

scientific article published on 17 October 2013

IgE type multiple myeloma exhibits hypermutated phenotype and tumor reactive T cells

scientific article published in 2022

Increased vitamin D levels at birth and in early infancy increase offspring allergy risk—evidence for involvement of epigenetic mechanisms

article

Integrative genomic and transcriptomic analysis of leiomyosarcoma.

scientific article published on 10 January 2018

Isolation of the protein and RNA content of active sites of transcription from mammalian cells ⬇️

scientific article published on 25 February 2016

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks

scientific article published on 22 May 2019

Loss of CCAAT-enhancer-binding protein alpha (CEBPA) is linked to poor prognosis in PTEN deleted and TMPRSS2:ERG fusion type prostate cancers

scientific article published on 14 November 2018

Loss of cooperativity of secreted CD40L and increased dose-response to IL4 on CLL cell viability correlates with enhanced activation of NF-kB and STAT6

scientific article published on 27 May 2014

Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development

scientific article published on August 2012

Making contacts on a nucleic acid polymer ⬇️

scientific article published on December 1, 2001

Mobility of multi-subunit complexes in the nucleus: accessibility and dynamics of chromatin subcompartments.

scientific article

Modeling nucleosome position distributions from experimental nucleosome positioning maps

scientific article published on 11 July 2013

Multiscale analysis of dynamics and interactions of heterochromatin protein 1 by fluorescence fluctuation microscopy

scientific article

NAP1 modulates binding of linker histone H1 to chromatin and induces an extended chromatin fiber conformation

scientific article published on 16 August 2005

NUDT9, a member of the Nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase.

scientific article

NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data

scientific article

Nuclear architecture by RNA.

scientific article published on 24 January 2012

Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation

scientific article published on 22 January 2008

Nucleosome repositioning during differentiation of a human myeloid leukemia cell line

scientific article

Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development.

scientific article

On the significance of Toc-GTPase homodimers

scientific article

PML induces compaction, TRF2 depletion and DNA damage signaling at telomeres and promotes their alternative lengthening

scientific article published on 23 April 2015

Parallel-stranded DNA under topological stress: rearrangement of (dA)15.(dT)15 to a d(A.A.T)n triplex

scientific article published on December 1991

Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs

scientific article published on August 1994

Pheno-seq - linking visual features and gene expression in 3D cell culture systems

scientific article published on 26 August 2019

Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow

scientific article

Quantifying transient binding of ISWI chromatin remodelers in living cells by pixel-wise photobleaching profile evolution analysis ⬇️

scientific article published on November 5, 2012

RNA: Networks & Imaging

scientific article published on 22 August 2006

Rational design and molecular characterization of a chimaeric response regulator protein.

scientific article

Reactivity of parallel-stranded DNA to chemical modification reagents

scientific article published on 01 October 1990

Real-time observation of light-controlled transcription in living cells.

scientific article published on 9 November 2017

Regulation of nucleolus assembly by non-coding RNA polymerase II transcripts ⬇️

scientific article

Retrieving Chromatin Patterns from Deep Sequencing Data Using Correlation Functions.

scientific article

Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells.

scientific article

SIRT6 recruits SNF2H to DNA break sites, preventing genomic instability through chromatin remodeling

scientific article

Scanning force microscopy of Escherichia coli RNA polymerase.sigma54 holoenzyme complexes with DNA in buffer and in air

scientific article published on 01 November 1998

Simultaneous binding of two DNA duplexes to the NtrC-enhancer complex studied by two-color fluorescence cross-correlation spectroscopy.

scientific article published on March 2000

Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming

scientific article published on 23 April 2020

Specificity mechanisms in the control of transcription

scientific article published on April 1996

Spectroscopic properties and helical stabilities of 25-nt parallel-stranded linear DNA duplexes

scientific article published on 01 November 1989

Statistical–mechanical lattice models for protein–DNA binding in chromatin ⬇️

scientific article published on September 30, 2010

Structure and function of the hetero-oligomeric cysteine synthase complex in plants

scientific article published on 18 August 2010

Substrate properties of 25-nt parallel-stranded linear DNA duplexes

scientific article published on 01 November 1989

Superhelix dimensions of a 1868 base pair plasmid determined by scanning force microscopy in air and in aqueous solution.

scientific article published on May 1997

Suv4-20h2 mediates chromatin compaction and is important for cohesin recruitment to heterochromatin.

scientific article published on 18 April 2013

TERRA and the state of the telomere

scientific article

Taking into account nucleosomes for predicting gene expression ⬇️

scientific article published on March 21, 2013

Targeting chromatin remodelers: signals and search mechanisms.

scientific article published on 16 June 2011

TelNet - a database for human and yeast genes involved in telomere maintenance

scientific article published on 18 May 2018

Telomere dysfunction and chromothripsis

scientific article published on 9 February 2016

TelomereHunter - in silico estimation of telomere content and composition from cancer genomes

scientific article published on 28 May 2019

Tethering RNA to chromatin for fluorescence microscopy based analysis of nuclear organization

scientific article published on 14 February 2017

The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments

scientific article

The effect of internucleosomal interaction on folding of the chromatin fiber

scientific article published on 25 July 2008

The effect of the DNA conformation on the rate of NtrC activated transcription of Escherichia coli RNA polymerase.sigma(54) holoenzyme

scientific article published on 01 July 2000

The hydrogen-bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick

scientific article published on 01 March 1991

The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility.

scientific article

Three-dimensional organization of promyelocytic leukemia nuclear bodies.

scientific article

Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase x sigma 54 holoenzyme by scanning force microscopy

scientific article published in July 1997

X-ray crystal structure of Saccharomyces cerevisiae Pdx1 provides insights into the oligomeric nature of PLP synthases

scientific article

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