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List of works by Wolfgang Huber

A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells.

scientific article published on 23 December 2015

A clash of cultures in discussions of the P value

scientific article

A compendium to ensure computational reproducibility in high-dimensional classification tasks

scientific article published on 19 December 2004

A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles

scientific article published on 13 November 2020

A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes

scientific article published on 8 January 2015

A genetic interaction map of cell cycle regulators

scientific article

A global map of human gene expression

scientific article

A high-resolution map of transcription in the yeast genome

scientific article published on 28 March 2006

A large-scale RNAi screen identifies Deaf1 as a regulator of innate immune responses in Drosophila.

scientific article published on 13 October 2009

A map of directional genetic interactions in a metazoan cell

scientific article

A user guide for the online exploration and visualization of PCAWG data

scientific article published on 07 July 2020

Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes

scientific article published on 09 October 2019

Addressing accuracy and precision issues in iTRAQ quantitation

scientific article published on 10 April 2010

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions.

scientific article

Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

scientific article published on 30 November 2017

An Optogenetic Method to Modulate Cell Contractility during Tissue Morphogenesis

scientific article published on 18 November 2015

An autologous culture model of nodal B-cell lymphoma identifies ex vivo determinants of response to bispecific antibodies

scientific article published on 01 December 2021

Analysis of cell-based RNAi screens.

scientific article published on January 2006

Analyzing ChIP-chip data using bioconductor

scientific article

Antisense expression increases gene expression variability and locus interdependency

scientific article

Array-based genotyping in S.cerevisiae using semi-supervised clustering

scientific article published on 23 February 2009

Assessing affymetrix GeneChip microarray quality

scientific article

Authoring Bioconductor workflows with BiocWorkflowTools

Bidirectional promoters generate pervasive transcription in yeast

scientific article (publication date: 19 February 2009)

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

scientific article

Bioconductor: open software development for computational biology and bioinformatics

scientific article

Biological plasticity rescues target activity in CRISPR knock outs

scientific article published on 28 October 2019

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

scientific article

CellH5: a format for data exchange in high-content screening

scientific article

Clustering phenotype populations by genome-wide RNAi and multiparametric imaging.

scientific article published on June 2010

CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data

scientific article

Combinatorial effects of four histone modifications in transcription and differentiation

scientific article published on 8 November 2007

Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions

scientific article

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

scientific article

Contributions of the EMERALD project to assessing and improving microarray data quality

scientific article

Control of tissue morphology by Fasciclin III-mediated intercellular adhesion.

scientific article

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

2013 scientific article

Coverage and error models of protein-protein interaction data by directed graph analysis

scientific article

Cytogenetic and morphologic typing of 58 papillary renal cell carcinomas: evidence for a cytogenetic evolution of type 2 from type 1 tumors

article

Data-driven hypothesis weighting increases detection power in genome-scale multiple testing

scientific article

Detecting differential usage of exons from RNA-seq data

scientific article

Differential expression analysis for sequence count data

scientific article

Differential expression analysis for sequence count data

article

Directional tissue migration through a self-generated chemokine gradient.

scientific article published on 25 September 2013

Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling.

scientific article published on 14 August 2017

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

scientific article published on 15 June 2020

Dissection of CD20 regulation in lymphoma using RNAi

scientific article published on 18 August 2016

Drift and conservation of differential exon usage across tissues in primate species

scientific article published on 03 September 2013

Drug-based perturbation screen uncovers synergistic drug combinations in Burkitt lymphoma

scientific article published in Scientific Reports

Drug-perturbation-based stratification of blood cancer

scientific article published on 11 December 2017

Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay

scientific article

EBImage--an R package for image processing with applications to cellular phenotypes.

scientific article published on April 2010

Energy metabolism is co-determined by genetic variants in chronic lymphocytic leukemia and influences drug sensitivity

scientific article published on 21 February 2019

Enhancer loops appear stable during development and are associated with paused polymerase

scientific article published on 2 July 2014

Enterotypes of the human gut microbiome

scientific article

Estimating node degree in bait-prey graphs

article

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

scientific article

Expression Atlas: gene and protein expression across multiple studies and organisms.

scientific article

Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi.

scientific article

Fast Monte Carlo algorithm for nonequilibrium systems

scientific article published in April 1996

FourCSeq: analysis of 4C sequencing data

scientific article

From ORFeome to biology: a functional genomics pipeline

scientific article

Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle

scientific article

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency

scientific article published on 07 November 2018

Gene expression across mammalian organ development

scientific article published on 26 June 2019

Gene expression in kidney cancer is associated with cytogenetic abnormalities, metastasis formation, and patient survival

article

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

scientific article

Genome-wide allele- and strand-specific expression profiling

scientific article published on 16 June 2009

Genome-wide analysis of mRNA decay patterns during early Drosophila development

scientific article

Genome-wide survey of post-meiotic segregation during yeast recombination

scientific article published on 11 April 2011

Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality

scientific article published on 21 March 2007

Graphs in molecular biology

scientific article

HTSeq--a Python framework to work with high-throughput sequencing data

scientific article (publication date: 15 January 2015)

High-content siRNA screen reveals global ENaC regulators and potential cystic fibrosis therapy targets.

scientific article

High-resolution mapping of meiotic crossovers and non-crossovers in yeast

scientific article

High-resolution transcription atlas of the mitotic cell cycle in budding yeast

scientific article (publication date: 2010)

High-throughput flow cytometry-based assay to identify apoptosis-inducing proteins

scientific article published on 3 May 2007

Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency

scientific article published on December 2012

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

scientific article

Human haematopoietic stem cell lineage commitment is a continuous process

scientific article

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

Importing ArrayExpress datasets into R/Bioconductor

scientific article published on 08 June 2009

Improved binding site assignment by high-resolution mapping of RNA-protein interactions using iCLIP

scientific article published on 11 August 2015

In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation

scientific article

Independent filtering increases detection power for high-throughput experiments

scientific article

Inferring tumor-specific cancer dependencies through integrating ex vivo drug response assays and drug-protein profiling

scientific article published in 2022

MDM4 Is Targeted by 1q Gain and Drives Disease in Burkitt Lymphoma

scientific article published on 18 April 2019

Making the most of high-throughput protein-interaction data

scientific article

Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping.

scientific article published on 7 April 2013

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

scientific article

Mapping of signaling networks through synthetic genetic interaction analysis by RNAi

scientific article published on 6 March 2011

Measuring genetic interactions in human cells by RNAi and imaging

scientific article published on 11 September 2014

Microarray data quality control improves the detection of differentially expressed genes

scientific article

Model-based variance-stabilizing transformation for Illumina microarray data.

scientific article

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

scientific article (publication date: 2014)

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

scientific article published on 20 June 2018

Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination

scientific article

Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia

scientific article published on 01 July 2021

Mutational landscape and complexity in CLL.

scientific article

Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause

scientific article published on February 2016

Nonparametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-binding Proteins

scientific article published on 03 October 2019

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

scientific article published on 23 December 2015

Orchestrating high-throughput genomic analysis with Bioconductor

scientific article

Orchestrating single-cell analysis with Bioconductor

scientific article published on 02 December 2019

Organelle proteomics experimental designs and analysis

scientific article

Parameter estimation for the calibration and variance stabilization of microarray data

scientific article

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

scientific article

Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications ⬇️

scientific article published on November 25, 2010

Protein quality control at the inner nuclear membrane

scientific article published on December 2014

Proteome-wide identification of ubiquitin interactions using UbIA-MS.

scientific article published on 15 February 2018

Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP

scientific article published on 11 March 2019

Publisher Correction: Orchestrating single-cell analysis with Bioconductor

scientific article published on 01 February 2020

Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF

scientific article published on 01 December 2019

RNA-Seq workflow: gene-level exploratory analysis and differential expression

scientific article published on 14 October 2015

Recurrent CDKN1B (p27) mutations in hairy cell leukemia

scientific article

Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions

scientific article

Reporting p Values

scientific article published on 01 March 2019

Research Techniques Made Simple: Bioinformatics for Genome-Scale Biology

scientific article published on September 2017

Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts

scientific article published on 26 June 2007

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository

scientific article

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

scientific article

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

scientific article published on 3 June 2015

Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells

scientific article

Software for computing and annotating genomic ranges

scientific article

SomaticSignatures: Inferring Mutational Signatures from Single Nucleotide Variants

SomaticSignatures: inferring mutational signatures from single-nucleotide variants.

scientific article

Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts

scientific article published on 17 August 2006

Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments

scientific article

Systematic comparison of surface coatings for protein microarrays

scholarly article by Birgit Guilleaume published in December 2005

TRRAP is essential for regulating the accumulation of mutant and wild-type p53 in lymphoma

scientific article published on 13 April 2018

Tandem fluorescent protein timers for in vivo analysis of protein dynamics

scientific article published on 24 June 2012

The Bioconductor channel in F1000Research

scientific article published on 10 July 2015

The LIFEdb database in 2006

scientific article

The RNA-Binding Protein YBX3 Controls Amino Acid Levels by Regulating SLC mRNA Abundance

scientific article published on 01 June 2019

The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs

scientific article published on 3 December 2015

The Small Non-coding Vault RNA1-1 Acts as a Riboregulator of Autophagy

scientific article published on 14 February 2019

The genomic and transcriptomic landscape of a HeLa cell line

scientific article

Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry.

scientific article published on 17 September 2015

Thermal proteome profiling monitors ligand interactions with cellular membrane proteins.

scientific article published on 2 November 2015

TimerQuant: a modelling approach to tandem fluorescent timer design and data interpretation for measuring protein turnover in embryos

scientific article

Top-down standards will not serve systems biology

scientific article published in Nature

Transcript Isoform Differences Across Human Tissues Are Predominantly Driven By Alternative Start And Termination Sites Of Transcription

Transcript mapping with high-density oligonucleotide tiling arrays

scientific article published on 20 June 2006

Transcriptome-wide profiling and posttranscriptional analysis of hematopoietic stem/progenitor cell differentiation toward myeloid commitment

scientific article

Transparency and reproducibility in artificial intelligence

scientific article published on 14 October 2020

Two independent modes of chromatin organization revealed by cohesin removal

scientific article published on 27 September 2017

Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities

scientific article

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

scientific article (publication date: 2002)

Variation in transcription factor binding among humans

scientific article

arrayMagic: two-colour cDNA microarray quality control and preprocessing

scientific article published on 28 September 2004

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data

scientific article

cAMP response element-binding protein is a primary hub of activity-driven neuronal gene expression

scientific article published in December 2011

gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection

scientific article published on 02 March 2020

h5vc: scalable nucleotide tallies with HDF5.

scientific article

matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements

scientific article published in 2004

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