Uwe Ohler

According to our database, Uwe Ohler authored at least 35 papers between 1998 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Deep Learning for RNA Regulation and Multidimensional Transcriptomics (Dagstuhl Seminar 24491).

Annalisa Marsico, Uwe Ohler, Igor Ulitsky, Kathi Zarnack, Charlotte Capitanchik

Dagstuhl Reports, December, 2024

Metadata-guided feature disentanglement for functional genomics.

Alexander Rakowski, Remo Monti, Viktoriia Huryn, Marta Lemanczyk, Uwe Ohler, Christoph Lippert

Bioinform., 2024

2022

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

Wolfgang Kopp, Altuna Akalin, Uwe Ohler

Nat. Mach. Intell., 2022

Deep learning for prediction of population health costs.

Philipp Drewe-Boss, Dirk Enders, Jochen Walker, Uwe Ohler

BMC Medical Informatics Decis. Mak., 2022

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

Jes-Niels Boeckel, Maximilian Möbius-Winkler, Marion Müller, Sabine Rebs, Nicole Eger, Laura Schoppe, Rewati Tappu, Karoline E. Kokot, Jasmin M. Kneuer, Susanne Gaul, Diana M. Bordalo, Alan Lai, Jan Haas, Mahsa Ghanbari, Philipp Drewe-Boss, Martin Liss, Hugo A. Katus, Uwe Ohler, Michael Gotthardt, Ulrich Laufs, Katrin Streckfuss-Bömeke, Benjamin Meder

Genom. Proteom. Bioinform., 2022

2021

Multimodal single cell data integration challenge: Results and lessons learned.

Christopher Lance, Malte D. Lücken, Daniel B. Burkhardt, Robrecht Cannoodt, Pia Rautenstrauch, Anna Laddach, Aidyn Ubingazhibov, Zhi-Jie Cao, Kaiwen Deng, Sumeer Khan, Qiao Liu, Nikolay Russkikh, Gleb Ryazantsev, Uwe Ohler, Angela Oliveira Pisco, Jonathan Bloom, Smita Krishnaswamy, Fabian J. Theis

Proceedings of the NeurIPS 2021 Competitions and Demonstrations Track, 2021

2019

Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 19342).

Rolf Backofen, Yael Mandel-Gutfreund, Uwe Ohler, Gabriele Varani

Dagstuhl Reports, 2019

2018

SSMART: sequence-structure motif identification for RNA-binding proteins.

Alina Munteanu, Neelanjan Mukherjee, Uwe Ohler

Bioinform., 2018

2017

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

Björn A. Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen Lott, Youri Hoogstrate, Wolfgang R. Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F. Stadler, Rolf Backofen

Nucleic Acids Res., 2017

Computational Challenges in RNA-Based Gene Regulation: Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 17252).

Rolf Backofen, Yael Mandel-Gutfreund, Uwe Ohler, Gabriele Varani

Dagstuhl Reports, 2017

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

Michael Piechotta, Emanuel Wyler, Uwe Ohler, Markus Landthaler, Christoph Dieterich

BMC Bioinform., 2017

2016

Cseq-Simulator: A Data Simulator for CLIP-Seq Experiments.

Wanja Kassuhn, Uwe Ohler, Philipp Drewe

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

2015

JAMM: a peak finder for joint analysis of NGS replicates.

Mahmoud M. Ibrahim, Scott A. Lacadie, Uwe Ohler

Bioinform., 2015

2014

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

Alina Munteanu, Uwe Ohler, Raluca Gordân

Nucleic Acids Res., 2014

Improved transcript isoform discovery using ORF graphs.

William H. Majoros, Niel Lebeck, Uwe Ohler, Song Li

Bioinform., 2014

2013

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

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

Bioinform., 2013

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

Dina Hafez, Ting Ni, Sayan Mukherjee, Jun Zhu, Uwe Ohler

Bioinform., 2013

2011

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

Iulian Pruteanu-Malinici, Daniel L. Mace, Uwe Ohler

PLoS Comput. Biol., 2011

imiRTP: An Integrated Method to Identifying miRNA-target Interactions in Arabidopsis thaliana.

Jiandong Ding, Shusi Yu, Uwe Ohler, Jihong Guan, Shuigeng Zhou

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

2010

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

William H. Majoros, Uwe Ohler

PLoS Comput. Biol., 2010

Extraction and comparison of gene expression patterns from 2D RNA <i>in situ</i> hybridization images.

Daniel L. Mace, Nicole Varnado, Weiping Zhang, Erwin Frise, Uwe Ohler

Bioinform., 2010

An alignment-free method to identify candidate orthologous enhancers in multiple <i>Drosophila</i> genomes.

Arunachalam Manonmani, Karthik Jayasurya, Pavel Tomancak, Uwe Ohler

Bioinform., 2010

2009

Complexity reduction in context-dependent DNA substitution models.

William H. Majoros, Uwe Ohler

Bioinform., 2009

2008

Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events.

Dirk Holste, Uwe Ohler

PLoS Comput. Biol., 2008

2006

Optimized mixed Markov models for motif identification.

Weichun Huang, David M. Umbach, Uwe Ohler, Leping Li

BMC Bioinform., 2006

Advancing the State of the Art in Computational Gene Prediction.

William H. Majoros, Uwe Ohler

Proceedings of the Knowledge Discovery and Emergent Complexity in Bioinformatics, 2006

Informative priors based on transcription factor structural class improve <i>de novo</i> motif discovery.

Leelavati Narlikar, Raluca Gordân, Uwe Ohler, Alexander J. Hartemink

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

Quantification of transcription factor expression from Arabidopsis images.

Daniel L. Mace, Jiyoung Lee, Richard W. Twigg, Juliette Colinas, Philip N. Benfey, Uwe Ohler

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

Recognition of Unknown Conserved Alternatively Spliced Exons.

Uwe Ohler, Noam Shomron, Christopher B. Burge

PLoS Comput. Biol., 2005

2001

Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition.

Uwe Ohler, Heinrich Niemann, Guo-chun Liao, Gerald M. Rubin

Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

1999

Interpolated markov chains for eukaryotic promoter recognition.

Uwe Ohler, Stefan Harbeck, Heinrich Niemann, Elmar Nöth, Martin G. Reese

Bioinform., 1999

Information Theoretic Based Segments for Language Identification.

Stefan Harbeck, Uwe Ohler, Elmar Nöth, Heinrich Niemann

Proceedings of the Text, Speech and Dialogue - Second International Workshop, 1999

Discriminative training of language model classifiers.

Uwe Ohler, Stefan Harbeck, Heinrich Niemann

Proceedings of the Sixth European Conference on Speech Communication and Technology, 1999

Multigrams for language identification.

Stefan Harbeck, Uwe Ohler

Proceedings of the Sixth European Conference on Speech Communication and Technology, 1999

1998

Stochastic Language Models for Content Based DNA Sequence Classification.

Uwe Ohler, Heinrich Niemann

Proceedings of the German Conference on Bioinformatics, 1998