U. Ohler

Konrad U. Förstner, Philipp H. Schiffer, Jonathan L. Schmid-Burgk, 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

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

P. Benfey, Louisa M. Liberman, U. Ohler, 2013, Genome research.

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation.

Rolf Backofen, Uwe Ohler, Anika Erxleben, 2017, Journal of biotechnology.

Identifying RBP Targets with RIP-seq.

U. Ohler, N. Mukherjee, H. Wessels, 2016, Methods in molecular biology.

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

Uwe Ohler, Nikolaus Rajewsky, Altuna Akalin, 2017, Nucleic acids research.

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

Olaf Wolkenhauer, Rolf Backofen, Sebastian Will, 2017, Nucleic Acids Res..

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

Uwe Ohler, Philipp Drewe-Boss, U. Ohler, 2018, Genome Biology.

Recognition of Unknown Conserved Alternatively Spliced Exons

Christopher B. Burge, Uwe Ohler, Noam Shomron, 2005, PLoS Comput. Biol..

Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms

Osamu Takeuchi, Uwe Ohler, Daron M. Standley, 2015, Cell.

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

Shuigeng Zhou, Jihong Guan, Uwe Ohler, 2012, BMC Genomics.

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

S. Gerstberger, T. Tuschl, E. Larsson, 2014, RNA.

Spatio-temporal mRNA tracking in the early zebrafish embryo

M. Landthaler, U. Ohler, J. Junker, 2021, Nature Communications.

Spatio-temporal mRNA dynamics in the early zebrafish embryo

M. Landthaler, U. Ohler, J. Junker, 2020, bioRxiv.

Genome-wide identification of regulatory elements in Sertoli cells

G. Crawford, Lingyun Song, U. Ohler, 2017, Development.

Deep neural networks for interpreting RNA-binding protein target preferences

Uwe Ohler, Mahsa Ghanbari, U. Ohler, 2019, bioRxiv.

Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant.

U. Ohler, Lorenzo Calviello, Dermot Harnett, 2021, Methods in molecular biology.

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

Weiping Zhang, Uwe Ohler, Daniel L. Mace, 2010, Bioinform..

Stochastic segment models of eukaryotic promoter regions.

S Harbeck, H Niemann, G. Stemmer, 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

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

C. Dieterich, M. Landthaler, U. Ohler, 2017, BMC Bioinformatics.

Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data

Yunjiang Qiu, U. Ohler, M. Sander, 2021, BMC Genomics.

RNA localization is a key determinant of neurite-enriched proteome

N. Rajewsky, E. Mazzoni, M. Selbach, 2017, Nature Communications.

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

Christoph Dieterich, Uwe Ohler, Markus Landthaler, 2017, BMC Bioinformatics.

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

Alexander J. Hartemink, Uwe Ohler, Raluca Gordân, 2006, ISMB.

Transcriptional control of tissue formation throughout root development

Uwe Ohler, Teva Vernoux, Philip N Benfey, 2015, Science.

Computational Mapping of the Human-SARS-CoV-2 Protein-RNA Interactome

U. Ohler, F. Bittner, A. Marsico, 2021, bioRxiv.

Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root

Trevor M. Nolan, P. Benfey, Geoffrey Schiebinger, 2023, Science.

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

M. Landthaler, U. Ohler, M. Milek, 2018, RNA biology.

The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation

U. Ohler, D. Leister, Mathias Labs, 2020, International journal of molecular sciences.

Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes

C. Lippert, U. Ohler, S. Konigorski, 2021, Nature Communications.

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

Wolfgang Busch, Uwe Ohler, G. K. Fricke, 2012, Nature Methods.

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

U. Ohler, H. Wessels, Philipp Drewe-Boss, 2018, Genome Biology.

Deep learning for prediction of population health costs pdf

Uwe Ohler, Philipp Drewe-Boss, Dirk Enders, 2020, BMC Medical Informatics and Decision Making.

Quantification of transcription factor expression from Arabidopsis images

Uwe Ohler, Daniel L. Mace, Philip N. Benfey, 2006, ISMB.

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning

A. Akalin, U. Ohler, W. Kopp, 2022, Nature Machine Intelligence.

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

U. Ohler, Dilmurat Yusuf, Antje Hirsekorn, 2019, Genome Biology.

The protein expression landscape of the Arabidopsis root

P. Benfey, M. Megraw, U. Ohler, 2012, Proceedings of the National Academy of Sciences.

SSMART: Sequence-structure motif identification for RNA-binding proteins

Uwe Ohler, Alina Munteanu, Neelanjan Mukherjee, 2017, bioRxiv.

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

Uwe Ohler, William H. Majoros, U. Ohler, 2010, PLoS Comput. Biol..

Discriminative training of language model classifiers

Heinrich Niemann, Stefan Harbeck, Uwe Ohler, 1999, EUROSPEECH.

A computational map of the human-SARS-CoV-2 protein–RNA interactome predicted at single-nucleotide resolution

U. Ohler, A. Marsico, Mahsa Ghanbari, 2023, NAR genomics and bioinformatics.

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

Pavel Tomancak, Uwe Ohler, Arunachalam Manonmani, 2010, Bioinform..

6th European Congress of Immunology, 1-4 September 2021, Virtual meeting.

Konrad U. Förstner, Philipp H. Schiffer, M. Nöthen, 2021, European journal of immunology.

The protein expression landscape of the Arabidopsis root.

P. Benfey, M. Megraw, U. Ohler, 2012, Proceedings of the National Academy of Sciences of the United States of America.

Liam tackles complex multimodal single-cell data integration challenges

U. Ohler, Pia Rautenstrauch, 2022, bioRxiv.

Promoter Prediction on a Genomic Scale – the Adh Experience

U. Ohler, U Ohler, Genome Project, 2000 .

Explaining Deep Neural Networks for the Prediction of Translation Rates

U. Ohler, Frederick Korbel, Ekaterina Eroshok, 2023, bioRxiv.

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

Uwe Ohler, William H. Majoros, Iulian Pruteanu-Malinici, 2013, Bioinform..

Improved transcript isoform discovery using ORF graphs

Song Li, Uwe Ohler, William H. Majoros, 2014, Bioinform..

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

P. Hsu, P. Benfey, U. Ohler, 2016, Proceedings of the National Academy of Sciences.

Mapping the complexity of transcription control in higher eukaryotes

Pavel Tomancak, Uwe Ohler, U. Ohler, 2010, Genome Biology.

Integrative classification of human coding and non-coding genes based on RNA metabolism profiles

U. Ohler, N. Mukherjee, Lorenzo Calviello, 2016, bioRxiv.

Quantification of translation uncovers the functions of the alternative transcriptome

U. Ohler, Lorenzo Calviello, Antje Hirsekorn, 2019, Nature Structural & Molecular Biology.

A transcription factor affinity-based code for mammalian transcription initiation.

Fernando C Pereira, A. Hatzigeorgiou, M. Megraw, 2009, Genome research.

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

U. Ohler, Dilmurat Yusuf, Antje Hirsekorn, 2018, bioRxiv.

Escholarship@umms Program in Gene Function and Expression Publications and Presentations Program in Gene Function and Expression a Stele-enriched Gene Regulatory Network in the Arabidopsis Root Repository Citation a Stele-enriched Gene Regulatory Network in the Arabidopsis Root a Stele-enriched Gene

P. Benfey, S. Ahnert, M. Megraw, 2022 .

Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit.

V. Tarabykin, I. Vida, M. Selbach, 2020, Molecular cell.

Stress-induced nuclear speckle reorganization is linked to activation of immediate early gene splicing

U. Ohler, J. Messens, Johanna Schott, 2023, The Journal of cell biology.

Inaugural Article: The protein expression landscape of the Arabidopsis root

P. Benfey, M. Megraw, U. Ohler, 2012 .

MatK impacts Differential Chloroplast Translation of Ribosomal and Photosynthetic genes by limiting spliced tRNA-K(UUU) abundance

U. Ohler, Reimo Zoschke, H. Ruwe, 2023, bioRxiv.

Toward Identification of Functional Sequences and Variants in Noncoding DNA.

U. Ohler, Remo Monti, 2023, Annual review of biomedical data science.

Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation

E. Mazzoni, V. Kaartinen, A. Tsirigos, 2024, Science Immunology.

Janggu - Deep learning for genomics

Uwe Ohler, Annalaura Tamburrini, Remo Monti, 2019, bioRxiv.

Finding RNA structure in the unstructured RBPome

Bonnie Berger, Uwe Ohler, Yaron Orenstein, 2018, BMC Genomics.