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List of works by Roland Eils

3D segmentation and quantification of mouse embryonic stem cells in fluorescence microscopy images

4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin - poor tracks

scientific article

5th International Conference on Systems Biology (ICSB 2004), Heidelberg, October 9–13, 2004

A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes

article

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

scientific article

A comprehensive comparison of tools for differential ChIP-seq analysis.

scientific article

A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair

A contractile nuclear actin network drives chromosome congression in oocytes

scientific article published on 13 July 2005

A cryptic t(5;11)(q35;p15.5) in 2 children with acute myeloid leukemia with apparently normal karyotypes, identified by a multiplex fluorescence in situ hybridization telomere assay

scientific article published on 01 April 2002

A database system for comparative genomic hybridization analysis

scientific article published in July 2001

A framework for modelling gene regulation which accommodates non-equilibrium mechanisms

scientific article

A highly standardized, robust, and cost-effective method for genome-wide transcriptome analysis of peripheral blood applicable to large-scale clinical trials

article

A new strategy for the detection of subtelomeric rearrangements

scientific article

AP-1-controlled hepatocyte growth factor activation promotes keratinocyte migration via CEACAM1 and urokinase plasminogen activator/urokinase plasminogen receptor

scientific article

Active medulloblastoma enhancers reveal subgroup-specific cellular origins

scientific article published on 27 January 2016

Acute myeloid leukemias with reciprocal rearrangements can be distinguished by specific gene expression profiles

scientific article

Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin

scientific article published on 15 October 2020

Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis

scientific article

An RNAi screen identifies KIF15 as a novel regulator of the endocytic trafficking of integrin

scientific article published on 21 March 2014

An in silico Approach to Detect Efficient Malaria Drug Targets to Combat the Malaria Resistance Problem

scholarly article published 2009

An integrated genome research network for studying the genetics of alcohol addiction

scientific article published on October 2010

An optimized, fully automated system for fast and accurate identification of chromosomal rearrangements by multiplex-FISH (M-FISH).

scientific article

An ultrasensitive sorting mechanism for EGF receptor endocytosis

scientific article

Analysis of CD95 threshold signaling: triggering of CD95 (FAS/APO-1) at low concentrations primarily results in survival signaling

scientific article

Analysis of Mutational Signatures with YAPSA (Yet Another Package for Signature Analysis)

scientific article published on 22 November 2020

Analysis of chromosomal alterations in non-small cell lung cancer by multiplex-FISH, comparative genomic hybridization, and multicolor bar coding

scientific article published on July 2000

Analyzing the regulation of metabolic pathways in human breast cancer

scientific article

Applying Support Vector Machines for Gene Ontology based gene function prediction

scientific article

Argonaute--a database for gene regulation by mammalian microRNAs

scientific article

Artesunate activates mitochondrial apoptosis in breast cancer cells via iron-catalyzed lysosomal reactive oxygen species production

scientific article

Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes

scientific article

Author Correction: The landscape of genomic alterations across childhood cancers

scientific article published in Nature

Autoantibodies against the exocrine pancreas in autoimmune pancreatitis: gene and protein expression profiling and immunoassays identify pancreatic enzymes as a major target of the inflammatory process.

scientific article

Automated 3D light-sheet screening with high spatiotemporal resolution reveals mitotic phenotypes

scientific article published on 15 April 2020

Automated Analysis of Single-Molecule Photobleaching Data by Statistical Modeling of Spot Populations.

scientific article

Automated Analysis of siRNA Screens of Virus Infected Cells Based on Immunofluorescence Microscopy

Automated analysis of the mitotic phases of human cells in 3D fluorescence microscopy image sequences

article

Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time

scientific article

Automatic identification of subcellular phenotypes on human cell arrays

scientific article published on June 2004

BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence

scientific article

BRCA1-associated breast and ovarian cancer risks in Poland: no association with commonly studied polymorphisms

scientific article

Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation.

scientific article

Bayesian statistical modelling of human protein interaction network incorporating protein disorder information

scientific article

Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri

scientific article

BioModels: expanding horizons to include more modelling approaches and formats

scientific article published on 2 November 2017

Breast cancer: a candidate gene approach across the estrogen metabolic pathway

scientific article

Bronchoalveolar lavage fluid of lung cancer patients: Mapping the uncharted waters using proteomics technology

CCM2 mediates death signaling by the TrkA receptor tyrosine kinase

scientific article published on September 2009

CGH-Profiler: data mining based on genomic aberration profiles

scientific article

COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis

scientific article published on 26 June 2020

CYP3A5 mediates basal and acquired therapy resistance in different subtypes of pancreatic ductal adenocarcinoma

scientific article published on 8 February 2016

Caspase-8 activity has an essential role in CD95/Fas-mediated MAPK activation

scientific article published on 6 October 2011

Caspase-8 cleaves its substrates from the plasma membrane upon CD95-induced apoptosis

scientific article

Cell segmentation-free inference of cell types from in situ transcriptomics data ⬇️

journal article from 'bioRxiv' published in 2020

Cell-specific CRISPR-Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins

scientific article published on 01 July 2019

Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen

scientific article

Classification of neuroblastoma patients by published gene-expression markers reveals a low sensitivity for unfavorable courses of MYCN non-amplified disease

article

Combinatorial treatment of CD95L and gemcitabine in pancreatic cancer cells induces apoptotic and RIP1-mediated necroptotic cell death network

scientific article

Comparative transcriptome profiling of amyloid precursor protein family members in the adult cortex

scientific article

Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3.

scientific article

Comparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patients

scientific article

Compartmentalization of interphase chromosomes observed in simulation and experiment

scientific article

Compensation of global movement for improved tracking of cells in time-lapse confocal microscopy image sequences

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.

scientific article

Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation

scientific article published on 27 December 2018

Computational design of anti-CRISPR proteins with improved inhibition potency

scientific article published on 13 April 2020

Computational identification of signalling pathways in Plasmodium falciparum

scientific article published on 26 November 2010

Computational imaging in cell biology

scientific article

Concurrent detection of autolysosome formation and lysosomal degradation by flow cytometry in a high-content screen for inducers of autophagy

scientific article

Contactless Investigation of Nuclear Mechanics of Normal and Lamin Mutant Cells Using a 3D Image- and Model-Based Framework

Contactless determination of nuclear compressibility using 3D image- and model-based analysis of drug-induced cellular deformation

scientific article published on 01 December 2010

Copy Number Alterations in Enzyme-Coding and Cancer-Causing Genes Reprogram Tumor Metabolism

scientific article

Core binding factor beta-smooth muscle myosin heavy chain chimeric protein involved in acute myeloid leukemia forms unusual nuclear rod-like structures in transformed NIH 3T3 cells

scientific article published on February 1996

Correlated receptor transport processes buffer single-cell heterogeneity

scientific article published on 25 September 2017

Coupling Cas9 to artificial inhibitory domains enhances CRISPR-Cas9 target specificity

scientific article published on 05 February 2020

Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies

scientific article

Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange.

scientific article published in July 2014

Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes

scientific article

Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes

scientific article

Cross-talk between the airway epithelium and activated immune cells defines severity in COVID-19

scientific article published on 05 May 2020

Customized Oligonucleotide Microarray Gene Expression–Based Classification of Neuroblastoma Patients Outperforms Current Clinical Risk Stratification

article

Cutis laxa, exocrine pancreatic insufficiency and altered cellular metabolomics as additional symptoms in a new patient with ATP6AP1-CDG.

scientific article published on 27 January 2018

DDX3X mutations in two girls with a phenotype overlapping Toriello-Carey syndrome.

scientific article published on 29 March 2017

DETERMINATION OF MITOTIC DELAYS IN 3D FLUORESCENCE MICROSCOPY IMAGES OF HUMAN CELLS USING AN ERROR-CORRECTING FINITE STATE MACHINE

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control

scientific article

Data-derived modeling characterizes plasticity of MAPK signaling in melanoma

scientific article (publication date: September 2014)

Databases for Systems Biology

Decision-tree based model analysis for efficient identification of parameter relations leading to different signaling states

scientific article (publication date: 2013)

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

scientific article

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

scientific article published in Nature Communications

Defective homologous recombination DNA repair as therapeutic target in advanced chordoma

scientific article published on 09 April 2019

Delayed viral clearance and exacerbated airway hyperinflammation in hypertensive COVID-19 patients ⬇️

journal article from 'medRxiv' published in 2020

Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images

scientific article published on September 2010

Detection of non-uniform multi-body motion in image time-series using saccades-enhanced phase correlation

Determination of Constitutive Properties of Single Cells and Intracellular Structures Using Image- and Model-Based Framework

Determination of Material Properties of Cellular Structures Using Time Series of Microscopic Images and Numerical Model of Cell Mechanics

Deterministic and probabilistic approaches for tracking virus particles in time-lapse fluorescence microscopy image sequences.

scientific article published on 3 January 2009

Diagnosis of CoPAN by whole exome sequencing: Waking up a sleeping tiger's eye.

scientific article published on 10 May 2017

Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms

scientific article

Discovery of transcriptional programs in cerebral ischemia by in silico promoter analysis

scientific article

Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities

scientific article published on 24 December 2012

Dissecting the contribution of actin and vimentin intermediate filaments to mechanical phenotype of suspended cells using high-throughput deformability measurements and computational modeling

scientific article

Dissecting the genomic complexity underlying medulloblastoma

scientific article

Distinct gene expression patterns associated with FLT3- and NRAS-activating mutations in acute myeloid leukemia with normal karyotype

scientific article

Distinct molecular phenotype of malignant CD34(+) hematopoietic stem and progenitor cells in chronic myelogenous leukemia

scientific article

Disturbed trophoblast transition links preeclampsia progression from placenta to the maternal syndrome

scientific article published on 11 October 2022

Dynamics of HIV-1 assembly and release

scientific article (publication date: November 2009)

Dynamics within the CD95 death-inducing signaling complex decide life and death of cells

scientific article published on 9 March 2010

Early-onset childhood atopic dermatitis is related to NLRP2 repression.

scientific article

Editorial: Synthetic biology--ready for application

scientific article published in February 2015

Efficient keratinocyte differentiation strictly depends on JNK-induced soluble factors in fibroblasts

scientific article published on 16 November 2013

Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9

Engineered anti-CRISPR proteins for optogenetic control of CRISPR–Cas9

scholarly article by Felix Bubeck published in October 2018

Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells

scientific article published on 14 July 2014

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

scientific article

Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands

scientific article published in Nature Communications

Enhancers regulate progression of development in mammalian cells

scientific article

EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations.

scientific article published on 4 April 2018

Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children

scientific article published on 24 March 2016

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

scientific article

Erratum: Corrigendum: Autoantibodies Against the Exocrine Pancreas in Autoimmune Pancreatitis: Gene and Protein Expression Profiling and Immunoassays Identify Pancreatic Enzymes as a Major Target of the Inflammatory Process

article

Erratum: Corrigendum: Signatures of mutational processes in human cancer

scientific article published in Nature

Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico

scientific article published on 20 January 2008

Estimating the activity of transcription factors by the effect on their target genes

scientific article

Etiology-dependent molecular mechanisms in human hepatocarcinogenesis

scientific article published on February 2008

Evidence against a looped structure of the inactive human X-chromosome territory

scientific article

Familial Cancer Variant Prioritization Pipeline version 2 (FCVPPv2) applied to a papillary thyroid cancer family

scientific article published in Scientific Reports

Feature Selection for Evaluating Fluorescence Microscopy Images in Genome-Wide Cell Screens

Follicular T helper cells shape the HCV-specific CD4+ T cell repertoire after virus elimination

scientific article published on 01 February 2020

Four-dimensional imaging and quantitative reconstruction to analyse complex spatiotemporal processes in live cells

scientific article

Framework For Quality Assessment Of Whole Genome, Cancer Sequences

Framework for quality assessment of whole genome cancer sequences

scientific article published on 07 October 2020

From latent disseminated cells to overt metastasis: genetic analysis of systemic breast cancer progression

scientific article

GOPET: a tool for automated predictions of Gene Ontology terms

scientific article

Gene expression analysis on biochemical networks using the Potts spin model

scientific article

Gene expression profiling of Philadelphia chromosome (Ph)-negative CD34+ hematopoietic stem and progenitor cells of patients with Ph-positive CML in major molecular remission during therapy with imatinib

scientific article published in March 2005

Gene expression signature predicting pathologic complete response with gemcitabine, epirubicin, and docetaxel in primary breast cancer

scientific article published in April 2006

Gene network dynamics controlling keratinocyte migration

scientific article published on July 2008

Gene set inference from single-cell sequencing data using a hybrid of matrix factorization and variational autoencoders ⬇️

journal article from 'Nature Machine Intelligence' published in 2020

Genetic Interactions and Tissue Specificity Modulate the Association of Mutations with Drug Response

scientific article published on 11 December 2019

Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer.

scientific article published in June 2017

Genetic variants in apoptosis-related genes associated with colorectal hyperplasia

scientific article

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition

scientific article

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations

scientific article

Genome sequencing: a systematic review of health economic evidence

scientific article published on 12 December 2013

Genome-wide expression screens indicate a global role for protein kinase CK2 in chromatin remodeling

scientific article published in April 2003

Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells

scholarly article

Genomic analysis of single cytokeratin-positive cells from bone marrow reveals early mutational events in breast cancer

article

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma

scientific article published on 29 March 2019

Genomic features of renal cell carcinoma with venous tumor thrombus.

scientific article

Genomic footprints of activated telomere maintenance mechanisms in cancer

scientific article published on 05 February 2020

Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype

scientific article published on 18 December 2020

Global chromosome positions are transmitted through mitosis in mammalian cells

scientific article published in March 2003

Global gene expression profiling and cluster analysis in Xenopus laevis.

scientific article

Group testing for pathway analysis improves comparability of different microarray datasets

scientific article published on 7 August 2006

Herpesviral replication compartments move and coalesce at nuclear speckles to enhance export of viral late mRNA.

scientific article

HiGHmed – An Open Platform Approach to Enhance Care and Research across Institutional Boundaries

scientific article published on 17 July 2018

High-resolution genomic profiling reveals association of chromosomal aberrations on 1q and 16p with histologic and genetic subgroups of invasive breast cancer

scientific article

HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data

scientific article

Human resting CD4+ T cells are constitutively inhibited by TGF beta under steady-state conditions

scientific article published in June 2007

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

scientific article published on 17 October 2013

Hypermutation takes the driver's seat

scientific article

Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19

scientific article

ICGC PedBrain - dissecting the genomic complexity underlying medulloblastoma using whole-genome sequencing.

scientific article

Identification of DNA methylation changes at cis-regulatory elements during early steps of HSC differentiation using tagmentation-based whole genome bisulfite sequencing

scientific article

Identification of a subtle t(16;19)(p13.3;p13.3) in an infant with multiple congenital abnormalities using a 12-colour multiplex FISH telomere assay, M-TEL.

scientific article published on December 2000

Identification of immunotherapeutic targets by genomic profiling of rectal NET metastases.

scientific article published on 22 July 2016

Identification of regulatory networks in HSCs and their immediate progeny via integrated proteome, transcriptome, and DNA methylome analysis.

scientific article published on 21 August 2014

Identification of the Rage-dependent gene regulatory network in a mouse model of skin inflammation

scientific article

Identifying essential genes in bacterial metabolic networks with machine learning methods

scientific article

Identifying fusion events in fluorescence microscopy images

Identifying multimodal signatures underlying the somatic comorbidity of psychosis: the COMMITMENT roadmap

scientific article published on 15 October 2020

Identifying virus-cell fusion in two-channel fluorescence microscopy image sequences based on a layered probabilistic approach.

scientific article published on 6 June 2012

Image- and model-based analysis of constitutive properties of cellular structures

Impact of cancer mutational signatures on transcription factor motifs in the human genome

scientific article published on 20 May 2019

Impact of clinical exomes in neurodevelopmental and neurometabolic disorders.

scientific article published on 30 June 2017

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

article

Inferring a System Model of Subcellular Topoisomerase IIβ Localization Dynamics

article

Inferring genetic regulatory logic from expression data

scientific article

Inflammation-mediated skin tumorigenesis induced by epidermal c-Fos

scientific article

Informatics united: exemplary studies combining medical informatics, neuroinformatics and bioinformatics

scientific article published on January 1, 2003

Integrated genomic profiling identifies two distinct molecular subtypes with divergent outcome in neuroblastoma with loss of chromosome 11q

Integration of activating and inhibitory receptor signaling by regulated phosphorylation of Vav1 in immune cells

scientific article published on 31 May 2011

Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas

scientific article published on 17 December 2013

Integrative analysis of multi-omics data identified EGFR and PTGS2 as key nodes in a gene regulatory network related to immune phenotypes in head and neck cancer

scientific article published on 11 March 2020

Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer

scientific article

Integrative genomic and transcriptomic analysis of leiomyosarcoma.

scientific article published on 10 January 2018

International network of cancer genome projects

scientific article

Intra- and interdimeric caspase-8 self-cleavage controls strength and timing of CD95-induced apoptosis

scientific article

Introducing Computational Systems Biology

article

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

scientific article

Large-scale tracking and classification for automatic analysis of cell migration and proliferation, and experimental optimization of high-throughput screens of neuroblastoma cells.

scientific article

Live cell dynamics of promyelocytic leukemia nuclear bodies upon entry into and exit from mitosis

scientific article

Live-cell assays to identify regulators of ER-to-Golgi trafficking

scientific article published on 3 January 2012

Local gene density predicts the spatial position of genetic loci in the interphase nucleus

article

Longitudinal trends of serum IgE and IL5RA expression throughout childhood are associated with asthma but not with persistent wheeze

scientific article published on 21 May 2019

Loss of function of PGAP1 as a cause of severe encephalopathy identified by Whole Exome Sequencing: Lessons of the bioinformatics pipeline

scientific article published on 4 June 2015

MEST mediates the impact of prenatal bisphenol A exposure on long-term body weight development

scientific article published on 20 April 2018

MYC/MIZ1-dependent gene repression inversely coordinates the circadian clock with cell cycle and proliferation.

scientific article

Machine learning based analyses on metabolic networks supports high-throughput knockout screens

scientific article

MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences

scientific article

Maternal phthalate exposure promotes allergic airway inflammation over 2 generations through epigenetic modifications

scientific article published on 6 April 2017

Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis

scientific article published on September 2004

Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.

scientific article

Meningiomas induced by low-dose radiation carry structural variants of NF2 and a distinct mutational signature

scientific article published on 4 May 2017

Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus

scientific article

MicroRNA profiling of primary high-grade soft tissue sarcomas

scientific article

Microarray analysis reveals differential gene expression patterns and regulation of single target genes contributing to the opposing phenotype of TrkA- and TrkB-expressing neuroblastomas.

scientific article

Microarray-based copy number and expression profiling in dedifferentiated and pleomorphic liposarcoma

scientific article published on 01 June 2002

Microarrays meet the Voltaire challenge: Drug discovery on a chip?

scientific article published on January 2006

Mining association rules from HIV-human protein interactions

scientific article published in December 2010

Mining quasi-bicliques from HIV-1-human protein interaction network: a multiobjective biclustering approach

scientific article published on March 2013

Mixed Integer Linear Programming based machine learning approach identifies regulators of telomerase in yeast

scientific article

Model-based dissection of CD95 signaling dynamics reveals both a pro- and antiapoptotic role of c-FLIPL.

scientific article

Model-based segmentation and quantification of fluorescent bacteria in 3D microscopy live cell images

scholarly article published 8 March 2007

Modeling glioblastoma invasion using human brain organoids and single-cell transcriptomics

scientific article published on 16 April 2020

Modulation of serines 17 and 24 in the LC3-interacting region of Bnip3 determines pro-survival mitophagy versus apoptosis

scientific article published on 3 December 2012

Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories

scientific article published on 01 December 2018

Motion detection and pattern tracking in microscopical images using phase correlation approach

Multi-parametric analysis and modeling of relationships between mitochondrial morphology and apoptosis

scientific article

Multiparametric image analysis reveals role of Caveolin1 in endosomal progression rather than internalization of EGFR.

scientific article

Mutant KIT as imatinib-sensitive target in metastatic sinonasal carcinoma.

scientific article published on 29 September 2016

Mutational patterns and regulatory networks in epigenetic subgroups of meningioma

scientific article published on 08 May 2019

Mutations in the SIX1/2 pathway and the DROSHA/DGCR8 miRNA microprocessor complex underlie high-risk blastemal type Wilms tumors

scientific article published in February 2015

NK cells switch from granzyme B to death receptor-mediated cytotoxicity during serial killing

scientific article published on 03 July 2019

NOTCH target gene HES5 mediates oncogenic and tumor suppressive functions in hepatocarcinogenesis

scientific article published on 13 February 2020

Negative feedback in the bone morphogenetic protein 4 (BMP4) synexpression group governs its dynamic signaling range and canalizes development

scientific article

Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling

scientific article

New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs

scientific article

New Insights into the Genetic Regulation of Plasmodium Falciparum Obtained by Bayesian Modeling

New concepts to improve resolution and sensitivity of molecular cytogenetic diagnostics by multicolor fluorescence in situ hybridization

scientific article published on May 2001

New insights into the genetic regulation of Plasmodium falciparum obtained by Bayesian modeling

scientific article published on 29 November 2007

Non-rigid alignment of multi-channel fluorescence microscopy images of live cells for improved classification of subcellular particle motion

scholarly article published 26 February 2009

Non-rigid multi-frame registration of cell nuclei in live cell fluorescence microscopy image data

scientific article

Non-rigid registration of 3D multi-channel microscopy images of cell nuclei

scientific article published on 01 January 2006

Nonlinear elastic model for image registration and soft tissue simulation based on piecewise St. Venant-Kirchhoff material approximation

Nonrigid registration of 2-D and 3-D dynamic cell nuclei images for improved classification of subcellular particle motion

scientific article published on 13 September 2010

Nonrigid registration of 3-d multichannel microscopy images of cell nuclei

scientific article published in April 2008

Normalizing for individual cell population context in the analysis of high-content cellular screens

scientific article

Nuclear NR4A2 (Nurr1) Immunostaining is a Novel Marker for Acinic Cell Carcinoma of the Salivary Glands Lacking the Classic NR4A3 (NOR-1) Upregulation

scientific article published on 24 April 2020

Nuclear NR4A3 Immunostaining Is a Specific and Sensitive Novel Marker for Acinic Cell Carcinoma of the Salivary Glands

scientific article published on 01 September 2019

Nuclear architecture and the induction of chromosomal aberrations

scientific article published on November 1996

Nuclear envelope breakdown proceeds by microtubule-induced tearing of the lamina

scientific article published on January 2002

Nucleosome repositioning during differentiation of a human myeloid leukemia cell line

scientific article

OTP: An automatized system for managing and processing NGS data

scientific article published on 10 August 2017

Olfactory transmucosal SARS-CoV-2 invasion as a port of central nervous system entry in individuals with COVID-19

scientific article published on 30 November 2020

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

scientific article

On the role of spatial phase and phase correlation in vision, illusion, and cognition

scientific article

One, two or three? Probing the stoichiometry of membrane proteins by single-molecule localization microscopy

scientific article

Optimal experimental design for parameter estimation of a cell signaling model

scientific article (publication date: November 2009)

Optogenetic Control of Nuclear Protein Import in Living Cells Using Light-Inducible Nuclear Localization Signals (LINuS).

scientific article published on 2 June 2016

Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein

scientific article published on 16 December 2020

Optogenetic control of nuclear protein export

scientific article

Pancreatic Ductal Adenocarcinoma Subtyping Using the Biomarkers Hepatocyte Nuclear Factor-1A and Cytokeratin-81 Correlates with Outcome and Treatment Response

scientific article published on 3 November 2017

PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways

scientific article published on 24 March 2010

Pathways of urothelial cancer progression suggested by Bayesian network analysis of allelotyping data

scientific article

Pedigree based DNA sequencing pipeline for germline genomes of cancer families

scientific article

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

scientific article published on 26 August 2019

Phenocopy--a strategy to qualify chemical compounds during hit-to-lead and/or lead optimization

scientific article

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

scientific article

Precision oncology based on omics data: The NCT Heidelberg experience

scientific article

Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains

scientific article published on 14 June 2006

Prediction of clinical outcome and biological characterization of neuroblastoma by expression profiling

scientific article published in November 2005

Prediction of small molecule binding property of protein domains with Bayesian classifiers based on Markov chains.

scientific article

Prenatal maternal stress and wheeze in children: novel insights into epigenetic regulation

scientific article published on 28 June 2016

Probing compressibility of the nuclear interior in wild-type and lamin deficient cells using microscopic imaging and computational modeling

scientific article published on 9 September 2011

Prognostic impact of gene expression-based classification for neuroblastoma.

scientific article published on 21 June 2010

Prospective multicentric validation of a novel prediction model for paroxysmal atrial fibrillation

scientific article published on 19 November 2020

Proteomic bronchiolitis obliterans syndrome risk monitoring in lung transplant recipients

scientific article

Putative second hit rare genetic variants in families with seemingly GBA-associated Parkinson's disease

scientific article published on 05 January 2021

Quantification of fluorescent spots in time series of 3D confocal microscopy images of endoplasmic reticulum exit sites based on the HMAX transform

Quantification of frap experiments in live cell image sequences by combining segmentation and registration

scholarly article published March 2011

Quantification of substrate and cellular strains in stretchable 3D cell cultures: an experimental and computational framework

scientific article published on 7 March 2017

Quantitative Single-Molecule Localization Microscopy (qSMLM) of Membrane Proteins Based on Kinetic Analysis of Fluorophore Blinking Cycles.

scientific article published in January 2017

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

scientific article published on 21 November 2015

Quantitative comparison of DNA detection by GFP-lac repressor tagging, fluorescence in situ hybridization and immunostaining

scientific article

Quantitative diagnosis of breast tumors by morphometric classification of microenvironmental myoepithelial cells using a machine learning approach

scientific article

Quantitative motion analysis and visualization of cellular structures

scientific article

RIP: the regulatory interaction predictor--a machine learning-based approach for predicting target genes of transcription factors

scientific article published on 20 June 2011

RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens

scientific article

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment

scientific article

Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing

scientific article

Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma

scientific article

RecurrentRHOAmutations in pediatric Burkitt lymphoma treated according to the NHL-BFM protocols

article

Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design

scientific article

Resolution improvement by 3‐D reconstructions from tilted views in axial tomography and confocal theta microscopy

Response to olaparib in a PALB2 germline mutated prostate cancer and genetic events associated with resistance.

scientific article published in April 2019

Revised risk estimation and treatment stratification of low- and intermediate-risk neuroblastoma patients by integrating clinical and molecular prognostic markers

scientific article published on 17 September 2014

Rigid and non-rigid registration of polarized light imaging data for 3D reconstruction of the temporal lobe of the human brain at micrometer resolution

scientific article published on 06 July 2018

Role of the ESCRT Complexes in Telomere Biology

scientific article published on 8 November 2016

SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches

scientific article (preprint)

SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells

scientific article published on 04 April 2020

SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells

scientific article

SIPA1L3 identified by linkage analysis and whole-exome sequencing as a novel gene for autosomal recessive congenital cataract.

scientific article published on 25 March 2015

STK25 protein mediates TrkA and CCM2 protein-dependent death in pediatric tumor cells of neural origin

scientific article

Screening drug effects in patient-derived cancer cells links organoid responses to genome alterations.

scientific article published on 27 November 2017

Secretory meningiomas are defined by combined KLF4 K409Q and TRAF7 mutations

scientific article

Segregation and potential functional impact of a rare stop-gain PABPC4L variant in familial atypical Parkinsonism

scientific article published on 19 September 2019

Separate and variably shaped chromosome arm domains are disclosed by chromosome arm painting in human cell nuclei

scientific article

Shape normalization of 3D cell nuclei using elastic spherical mapping

scientific article

ShinyButchR: Interactive NMF-based decomposition workflow of genome-scale datasets

scientific article published on 29 October 2020

Simulation of the distribution of chromosome targets in cell nuclei under topological constraints

Single nucleus and in situ RNA sequencing reveals cell topographies in the human pancreas

scientific article published on 16 November 2020

Single-Fluorescent Protein Reporters Allow Parallel Quantification of Natural Killer Cell-Mediated Granzyme and Caspase Activities in Single Target Cells

article by Clarissa Liesche et al published 2018 in Frontiers in Immunology

Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy

scientific article published on 05 October 2021

Single-cell-based image analysis of high-throughput cell array screens for quantification of viral infection

scientific article published on April 2009

So rare we need to hunt for them: reframing the ethical debate on incidental findings

scientific article published on 30 July 2015

Somatic mutations and promotor methylation of the ryanodine receptor 2 is a common event in the pathogenesis of head and neck cancer

scientific article published on 19 June 2019

Spatial distributions of early and late replicating chromatin in interphase chromosome territories

scientific article published on September 1998

Spatial niche formation but not malignant progression is a driving force for intratumoural heterogeneity

scientific article published on 13 June 2016

Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort.

scientific article

SplicingCompass: differential splicing detection using RNA-seq data

scientific article

Structural analysis of interphase X-chromatin based on statistical shape theory

article published in 2008

Subclassification and individual survival time prediction from gene expression data of neuroblastoma patients by using CASPAR.

scientific article

Subtelomeric chromosome rearrangements are detected using an innovative 12-color FISH assay (M-TEL)

scientific article published on 01 April 2001

Suppression of early hematogenous dissemination of human breast cancer cells to bone marrow by retinoic Acid-induced 2.

scientific article

Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care.

scientific article published on February 2004

Systemic spread is an early step in breast cancer

scientific article (publication date: 2008)

Systems Biology

Systems biological analysis of epidermal growth factor receptor internalization dynamics for altered receptor levels

scientific article published on 17 March 2009

Systems biology and artificial life: towards predictive modeling of biological systems

scientific article published in January 2008

TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus

scientific article published on 09 September 2016

TRACKING OF VIRUS PARTICLES IN TIME-LAPSE FLUORESCENCE MICROSCOPY IMAGE SEQUENCES

Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing

scientific article published in January 2018

Tagmentation-based whole-genome bisulfite sequencing

scientific article

The 3D positioning of ANT2 and ANT3 genes within female X chromosome territories correlates with gene activity.

scientific article

The Human Cell Atlas

scientific article

The Human Cell Atlas

The Human Cell Atlas White Paper ⬇️

journal article from 'arXiv:1810.05192 [q-bio]' published in 2018

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

scientific article

The benzene metabolite 1,4-benzoquinone reduces regulatory T-cell function: A potential mechanism for tobacco smoke-associated atopic dermatitis

scientific article published on 5 March 2017

The landscape of genomic alterations across childhood cancers

scientific article published on 28 February 2018

The landscape of viral associations in human cancers

scientific article published on 05 February 2020

The mutational pattern of primary lymphoma of the central nervous system determined by whole-exome sequencing

scientific article published on 5 September 2014

The openEHR Genomics Project

scientific article published on 01 June 2020

The role of Vimentin in Regulating Cell Invasive Migration in Dense Cultures of Breast Carcinoma Cells.

scientific article

The transcriptomic and epigenetic map of vascular quiescence in the continuous lung endothelium.

scientific article

The whole-genome landscape of medulloblastoma subtypes

scientific article published in July 2017

Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes

scientific article published on 26 April 2005

Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure

scientific article

Time-lapse imaging of neuroblastoma cells to determine cell fate upon gene knockdown

scientific article (publication date: 2012)

Time-resolved analysis and visualization of dynamic processes in living cells

scientific article

Topological analysis of 3D cell nuclei using finite element template-based spherical mapping

Topology of double minutes (dmins) and homogeneously staining regions (HSRs) in nuclei of human neuroblastoma cell lines

scientific article

Topology of genes and nontranscribed sequences in human interphase nuclei

article

Tracking Virus Particles in Fluorescence Microscopy Images Using Multi-Scale Detection and Multi-Frame Association

scientific article published on 17 July 2015

Tracking and quantitative analysis of dynamic movements of cells and particles

scientific article published on June 2010

Tracking multiple particles in fluorescence microscopy images via probabilistic data association

article published in 2011

Tracking virus particles in fluorescence microscopy images using two-step multi-frame association

scholarly article published May 2012

Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant

scientific article published on 7 December 2017

Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation

scientific article published on 24 January 2006

Translating expression profiling into a clinically feasible test to predict neuroblastoma outcome

scientific article published in March 2007

Tropical--parameter estimation and simulation of reaction-diffusion models based on spatio-temporal microscopy images

scientific article published on 29 August 2006

Understanding apoptosis by systems biology approaches

scientific article published on 03 August 2009

Understanding life and death at CD95.

scientific article published in January 2011

Unraveling mitotic protein networks by 3D multiplexed epitope drug screening

scientific article published on 13 August 2018

Using Bayesian multinomial classifier to predict whether a given protein sequence is intrinsically disordered

scientific article published on 14 June 2008

Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli

scientific article

Visualizing telomere dynamics in living mammalian cells using PNA probes

scientific article

Web-based design and analysis tools for CRISPR base editing

article by Gue-Ho Hwang et al published 27 December 2018 in BMC Bioinformatics

Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer

scientific article published in Nature Communications

Whole-genome analysis of gene expression associates the ubiquitin-proteasome system with the cardiomyopathy phenotype in disease-sensitized congenic mouse strains

article

Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4

scientific article published on 17 February 2020

Workflows for microscopy image analysis and cellular phenotyping

scientific article published on 27 July 2017

circlize Implements and enhances circular visualization in R.

scientific article

gtrellis: an R/Bioconductor package for making genome-level Trellis graphics.

scientific article

miR-17-5p regulates endocytic trafficking through targeting TBC1D2/Armus

scientific article

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