Stochastic Language Models for Content Based DNA Sequence Classification. - Uwe Ohler; Heinrich Niemann (German Conference on Bioinformatics, 1998)

Multigrams for language identification. - Stefan Harbeck; Uwe Ohler (EUROSPEECH, 1999)

Discriminative training of language model classifiers. - Uwe Ohler; Stefan Harbeck; Heinrich Niemann (EUROSPEECH, 1999)

Information Theoretic Based Segments for Language Identification. - Stefan Harbeck; Uwe Ohler; Elmar Nöth; Heinrich Niemann (TSD, 1999)

Interpolated markov chains for eukaryotic promoter recognition. - Uwe Ohler; Stefan Harbeck; Heinrich Niemann; Elmar Nöth; Martin G. Reese (Bioinform., 1999)

Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. - Uwe Ohler; Heinrich Niemann; Guo-chun Liao; Gerald M. Rubin (ISMB (Supplement of Bioinformatics), 2001)

Recognition of Unknown Conserved Alternatively Spliced Exons. - Uwe Ohler; Noam Shomron; Christopher B. Burge (PLoS Comput. Biol., 2005)

Quantification of transcription factor expression from Arabidopsis images. - Daniel L. Mace; Jiyoung Lee 002; Richard W. Twigg; Juliette Colinas; Philip N. Benfey; Uwe Ohler (ISMB (Supplement of Bioinformatics), 2006)

Informative priors based on transcription factor structural class improve de novo motif discovery. - Leelavati Narlikar; Raluca Gordân; Uwe Ohler; Alexander J. Hartemink (ISMB (Supplement of Bioinformatics), 2006)

Advancing the State of the Art in Computational Gene Prediction. - William H. Majoros; Uwe Ohler (KDECB, 2006)

Optimized mixed Markov models for motif identification. - Weichun Huang; David M. Umbach; Uwe Ohler; Leping Li (BMC Bioinform., 2006)

Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events. - Dirk Holste; Uwe Ohler (PLoS Comput. Biol., 2008)

Complexity reduction in context-dependent DNA substitution models. - William H. Majoros; Uwe Ohler (Bioinform., 2009)

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes. - Arunachalam Manonmani; Karthik Jayasurya; Pavel Tomancak; Uwe Ohler (Bioinform., 2010)

Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images. - Daniel L. Mace; Nicole Varnado; Weiping Zhang; Erwin Frise; Uwe Ohler (Bioinform., 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)

imiRTP: An Integrated Method to Identifying miRNA-target Interactions in Arabidopsis thaliana. - Jiandong Ding; Shusi Yu; Uwe Ohler; Jihong Guan; Shuigeng Zhou (BIBM, 2011)

Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models. - Iulian Pruteanu-Malinici; Daniel L. Mace; Uwe Ohler (PLoS Comput. Biol., 2011)

Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation. - Dina Hafez; Ting Ni; Sayan Mukherjee 001; Jun Zhu; Uwe Ohler (Bioinform., 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)

Improved transcript isoform discovery using ORF graphs. - William H. Majoros; Niel Lebeck; Uwe Ohler; Song Li (Bioinform., 2014)

COUGER - co-factors associated with uniquely-bound genomic regions. - Alina Munteanu; Uwe Ohler; Raluca Gordân (Nucleic Acids Res., 2014)

JAMM: a peak finder for joint analysis of NGS replicates. - Mahmoud M. Ibrahim; Scott A. Lacadie; Uwe Ohler (Bioinform., 2015)

Cseq-Simulator: A Data Simulator for CLIP-Seq Experiments. - Wanja Kassuhn; Uwe Ohler; Philipp Drewe (PSB, 2016)

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)

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)

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; et al. (Nucleic Acids Res., 2017)

SSMART: sequence-structure motif identification for RNA-binding proteins. - Alina Munteanu; Neelanjan Mukherjee; Uwe Ohler (Bioinform., 2018)

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)

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 008; Nikolay Russkikh; et al. (NeurIPS (Competition and Demos), 2021)

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; et al. (Genom. Proteom. Bioinform., 2022)

Deep learning for prediction of population health costs. - Philipp Drewe-Boss; Dirk Enders; Jochen Walker; Uwe Ohler (BMC Medical Informatics Decis. Mak., 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)

Metadata-guided feature disentanglement for functional genomics. - Alexander Rakowski; Remo Monti; Viktoriia Huryn; Marta Lemanczyk; Uwe Ohler; Christoph Lippert (Bioinform., 2024)

Deep Learning for RNA Regulation and Multidimensional Transcriptomics (Dagstuhl Seminar 24491). - Annalisa Marsico; Uwe Ohler; Igor Ulitsky; Kathi Zarnack; Charlotte Capitanchik (Dagstuhl Reports, 2024)