List of works - Uwe Ohler

A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells

scientific article

A microfluidic device and computational platform for high-throughput live imaging of gene expression

scientific article

A paired-end sequencing strategy to map the complex landscape of transcription initiation

scientific article

A stele-enriched gene regulatory network in the Arabidopsis root

scientific article

A transcription factor affinity-based code for mammalian transcription initiation

scientific article published on 13 January 2009

A viral microRNA functions as an orthologue of cellular miR-155

scientific article

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes

scientific article

Analysis of the miRNA targetome in EBV-infected B cells

scientific article published on 19 April 2012

Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements

scientific article

Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields ⬇️

scientific article published on July 1, 2013

Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models ⬇️

scientific article published on July 21, 2011

Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome

scientific article published on 5 September 2017

Brassinosteroid gene regulatory networks at cellular resolution in the <i>Arabidopsis</i> root

scientific article published on 31 March 2023

COUGER--co-factors associated with uniquely-bound genomic regions

scientific article published on 26 May 2014

CSEQ-SIMULATOR: A DATA SIMULATOR FOR CLIP-SEQ EXPERIMENTS.

scientific article

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

scientific article

Complexity reduction in context-dependent DNA substitution models

scientific article

Computational analysis of core promoters in the Drosophila genome

scientific article

DDX54 regulates transcriptome dynamics during DNA damage response

scientific article published on 8 June 2017

Deciphering human ribonucleoprotein regulatory networks

Deep learning for genomics using Janggu

scientific article published on 13 July 2020

Deep neural networks for interpreting RNA binding protein target preferences

Detecting actively translated open reading frames in ribosome profiling data

scientific article

Detection of broadly expressed neuronal genes in C. elegans

scientific article published on 15 September 2006

Determinants of promoter and enhancer transcription directionality in metazoans

scientific article published in Nature Communications

Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy

scientific article

Divergent transcription and epigenetic directionality of human promoters

scientific article published on 26 April 2016

Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation

article

Evidence-ranked motif identification

scientific article published on 15 February 2010

Expanding the map of protein-RNA interaction sites via cell fusion followed by PAR-CLIP.

scientific article

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection

scientific article

Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images

scientific article

FMRP targets distinct mRNA sequence elements to regulate protein expression

scientific journal article

Finding RNA structure in the unstructured RBPome

scientific article published on 20 February 2018

Fine time course expression analysis identifies cascades of activation and repression and maps a putative regulator of mammalian sex determination

scientific article

Gene expression divergence recapitulates the developmental hourglass model

scientific article

Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation

scientific article

Genome-wide identification of regulatory elements in Sertoli cells

scientific article published on 13 January 2017

Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach ⬇️

scientific article published on June 11, 2012

Global identification of functional microRNA-mRNA interactions in Drosophila

scientific article published on 09 April 2019

Global target mRNA specification and regulation by the RNA-binding protein ZFP36.

scientific article

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

scientific article published on 9 November 2016

High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis

scientific article published on 22 September 2011

Human promoters are intrinsically directional

scientific article

Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction

scientific article published on 26 October 2006

Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets

scientific article

Identifying RBP Targets with RIP-seq

scientific article published in January 2016

Improved transcript isoform discovery using ORF graphs

scientific article

Informative priors based on transcription factor structural class improve de novo motif discovery

scientific article

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

scientific article

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

scientific article published on 10 March 2020

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

scientific article

Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability

scientific article published on 30 June 2011

JACUSA: site-specific identification of RNA editing events from replicate sequencing data

scientific article

JAMM: a peak finder for joint analysis of NGS replicates

scientific article published on 15 September 2014

Mapping the complexity of transcription control in higher eukaryotes

scientific article published on 30 April 2010

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes

scientific article published on 26 October 2017

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships

scientific article published on 29 May 2009

MicroRNA target site identification by integrating sequence and binding information

scientific article published on 26 May 2013

Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs ⬇️

scientific article published on December 16, 2010

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome

scientific article published on 9 July 2009

Optimized mixed Markov models for motif identification

scientific article

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

scientific article

Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures

scientific article

Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification

scientific article

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment

scientific article published on 7 August 2006

Perspectives on Unidirectional versus Divergent Transcription

scientific article published in November 2015

Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools

scientific article

Predicting cell-type-specific gene expression from regions of open chromatin

scientific article published on September 2012

Promoting developmental transcription

scientific article

Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT

scientific article published in 2022

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction

scientific article published on 01 March 2019

Quantification of transcription factor expression from Arabidopsis images

scientific article published in July 2006

Quantification of translation uncovers the functions of the alternative transcriptome

scientific article published on 29 June 2020

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

scientific article published on 21 February 2017

RNA localization is a key determinant of neurite-enriched proteome

scientific article published on 19 September 2017

Recognition of unknown conserved alternatively spliced exons

scientific article

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling

article

SLM2 Is A Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy

scientific article published in 2022

Spatial preferences of microRNA targets in 3' untranslated regions

scientific article

Spatio-temporal mRNA tracking in the early zebrafish embryo

scientific article published on 07 June 2021

Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events

scientific article

Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits

scientific article

The Drosophila Translational Control Element (TCE) Is Required for High-Level Transcription of Many Genes That Are Specifically Expressed in Testes ⬇️

scientific article published on September 11, 2012

The MTE, a new core promoter element for transcription by RNA polymerase II.

scientific article

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

scientific article published on 05 June 2017

The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery

scientific article

The mRNA-bound proteome of the early fly embryo

scientific article published on 28 April 2016

The viral and cellular microRNA targetome in lymphoblastoid cell lines

scientific article published in January 2012

Towards a deeper annotation of human lncRNAs

scientific article published on 22 May 2019

Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level

scientific article

Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots

scholarly article

Transcriptional control of tissue formation throughout root development

scientific article

Translocation of sickle cell erythrocyte microRNAs into Plasmodium falciparum inhibits parasite translation and contributes to malaria resistance

scientific article

Using machine learning to identify disease-relevant regulatory RNAs

scientific article published on 17 September 2013

Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines

scientific article

omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

scientific article published on 30 August 2017

List of works by Uwe Ohler

A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells

A microfluidic device and computational platform for high-throughput live imaging of gene expression

A paired-end sequencing strategy to map the complex landscape of transcription initiation

A stele-enriched gene regulatory network in the Arabidopsis root

A transcription factor affinity-based code for mammalian transcription initiation

A viral microRNA functions as an orthologue of cellular miR-155

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes

Analysis of the miRNA targetome in EBV-infected B cells

Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements

Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields ⬇️

Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models ⬇️

Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome

Brassinosteroid gene regulatory networks at cellular resolution in the <i>Arabidopsis</i> root

COUGER--co-factors associated with uniquely-bound genomic regions

CSEQ-SIMULATOR: A DATA SIMULATOR FOR CLIP-SEQ EXPERIMENTS.

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

Complexity reduction in context-dependent DNA substitution models

Computational analysis of core promoters in the Drosophila genome

DDX54 regulates transcriptome dynamics during DNA damage response

Deciphering human ribonucleoprotein regulatory networks

Deep learning for genomics using Janggu

Deep neural networks for interpreting RNA binding protein target preferences

Detecting actively translated open reading frames in ribosome profiling data

Detection of broadly expressed neuronal genes in C. elegans

Determinants of promoter and enhancer transcription directionality in metazoans

Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy

Divergent transcription and epigenetic directionality of human promoters

Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation

Evidence-ranked motif identification

Expanding the map of protein-RNA interaction sites via cell fusion followed by PAR-CLIP.

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection

Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images

FMRP targets distinct mRNA sequence elements to regulate protein expression

Finding RNA structure in the unstructured RBPome

Fine time course expression analysis identifies cascades of activation and repression and maps a putative regulator of mammalian sex determination

Gene expression divergence recapitulates the developmental hourglass model

Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation

Genome-wide identification of regulatory elements in Sertoli cells

Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach ⬇️

Global identification of functional microRNA-mRNA interactions in Drosophila

Global target mRNA specification and regulation by the RNA-binding protein ZFP36.

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis

Human promoters are intrinsically directional

Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction

Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets

Identifying RBP Targets with RIP-seq

Improved transcript isoform discovery using ORF graphs

Informative priors based on transcription factor structural class improve de novo motif discovery

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability

JACUSA: site-specific identification of RNA editing events from replicate sequencing data

JAMM: a peak finder for joint analysis of NGS replicates

Mapping the complexity of transcription control in higher eukaryotes

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships

MicroRNA target site identification by integrating sequence and binding information

Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs ⬇️

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome

Optimized mixed Markov models for motif identification

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures

Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment

Perspectives on Unidirectional versus Divergent Transcription

Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools

Predicting cell-type-specific gene expression from regions of open chromatin

Promoting developmental transcription

Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction

Quantification of transcription factor expression from Arabidopsis images

Quantification of translation uncovers the functions of the alternative transcriptome

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

RNA localization is a key determinant of neurite-enriched proteome

Recognition of unknown conserved alternatively spliced exons

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling

SLM2 Is A Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy