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ORCIDUwe Ohler
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- affiliation: Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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Journal Articles
- 2022
[j20]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:
SLM2 Is A Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy. Genom. Proteom. Bioinform. 20(1): 129-146 (2022)- [j19]Philipp Drewe-Boss, Dirk Enders, Jochen Walker, Uwe Ohler:
Deep learning for prediction of population health costs. BMC Medical Informatics Decis. Mak. 22(1): 32 (2022) - [j18]Wolfgang Kopp, Altuna Akalin, Uwe Ohler:
Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning. Nat. Mach. Intell. 4(2): 162-168 (2022) - 2018
- [j17]Alina Munteanu, Neelanjan Mukherjee, Uwe Ohler:
SSMART: sequence-structure motif identification for RNA-binding proteins. Bioinform. 34(23): 3990-3998 (2018) - 2017
- [j16]Michael Piechotta, Emanuel Wyler, Uwe Ohler, Markus Landthaler, Christoph Dieterich:
JACUSA: site-specific identification of RNA editing events from replicate sequencing data. BMC Bioinform. 18(1): 7:1-7:15 (2017) - [j15]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:
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Res. 45(Webserver-Issue): W560-W566 (2017) - 2015
- [j14]Mahmoud M. Ibrahim, Scott A. Lacadie, Uwe Ohler:
JAMM: a peak finder for joint analysis of NGS replicates. Bioinform. 31(1): 48-55 (2015) - 2014
- [j13]William H. Majoros, Niel Lebeck, Uwe Ohler, Song Li:
Improved transcript isoform discovery using ORF graphs. Bioinform. 30(14): 1958-1964 (2014) - [j12]Alina Munteanu, Uwe Ohler, Raluca Gordân:
COUGER - co-factors associated with uniquely-bound genomic regions. Nucleic Acids Res. 42(Webserver-Issue): 461-467 (2014) - 2013
- [j11]Iulian Pruteanu-Malinici, William H. Majoros, Uwe Ohler:
Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields. Bioinform. 29(13): 27-35 (2013) - [j10]Dina Hafez, Ting Ni, Sayan Mukherjee, Jun Zhu, Uwe Ohler:
Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation. Bioinform. 29(13): 108-116 (2013) - 2011
- [j9]Iulian Pruteanu-Malinici, Daniel L. Mace, Uwe Ohler:
Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models. PLoS Comput. Biol. 7(7) (2011) - 2010
- [j8]Daniel L. Mace, Nicole Varnado, Weiping Zhang, Erwin Frise, Uwe Ohler:
Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images. Bioinform. 26(6): 761-769 (2010) - [j7]Arunachalam Manonmani, Karthik Jayasurya, Pavel Tomancak, Uwe Ohler:
An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes. Bioinform. 26(17): 2109-2115 (2010) - [j6]William H. Majoros, Uwe Ohler:
Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs. PLoS Comput. Biol. 6(12) (2010) - 2009
- [j5]William H. Majoros, Uwe Ohler:
Complexity reduction in context-dependent DNA substitution models. Bioinform. 25(2): 175-182 (2009) - 2008
- [j4]Dirk Holste, Uwe Ohler:
Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events. PLoS Comput. Biol. 4(1) (2008) - 2006
- [j3]Weichun Huang, David M. Umbach, Uwe Ohler, Leping Li:
Optimized mixed Markov models for motif identification. BMC Bioinform. 7: 279 (2006) - 2005
- [j2]Uwe Ohler, Noam Shomron, Christopher B. Burge:
Recognition of Unknown Conserved Alternatively Spliced Exons. PLoS Comput. Biol. 1(2) (2005) - 1999
- [j1]Uwe Ohler, Stefan Harbeck, Heinrich Niemann, Elmar Nöth, Martin G. Reese:
Interpolated markov chains for eukaryotic promoter recognition. Bioinform. 15(5): 362-369 (1999)
Conference and Workshop Papers
- 2021
- [c11]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:
Multimodal single cell data integration challenge: Results and lessons learned. NeurIPS (Competition and Demos) 2021: 162-176 - 2016
- [c10]Wanja Kassuhn, Uwe Ohler, Philipp Drewe:
Cseq-Simulator: A Data Simulator for CLIP-Seq Experiments. PSB 2016: 433-444 - 2011
- [c9]Jiandong Ding, Shusi Yu, Uwe Ohler, Jihong Guan, Shuigeng Zhou:
imiRTP: An Integrated Method to Identifying miRNA-target Interactions in Arabidopsis thaliana. BIBM 2011: 100-104 - 2006
- [c8]Daniel L. Mace, Jiyoung Lee, Richard W. Twigg, Juliette Colinas, Philip N. Benfey, Uwe Ohler:
Quantification of transcription factor expression from Arabidopsis images. ISMB (Supplement of Bioinformatics) 2006: 323-331 - [c7]Leelavati Narlikar, Raluca Gordân, Uwe Ohler, Alexander J. Hartemink:
Informative priors based on transcription factor structural class improve de novo motif discovery. ISMB (Supplement of Bioinformatics) 2006: 384-392 - [c6]William H. Majoros, Uwe Ohler:
Advancing the State of the Art in Computational Gene Prediction. KDECB 2006: 81-106 - 2001
- [c5]Uwe Ohler, Heinrich Niemann, Guo-chun Liao, Gerald M. Rubin:
Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. ISMB (Supplement of Bioinformatics) 2001: 199-206 - 1999
- [c4]Stefan Harbeck, Uwe Ohler:
Multigrams for language identification. EUROSPEECH 1999: 375-378 - [c3]Uwe Ohler, Stefan Harbeck, Heinrich Niemann:
Discriminative training of language model classifiers. EUROSPEECH 1999 - [c2]Stefan Harbeck, Uwe Ohler, Elmar Nöth, Heinrich Niemann:
Information Theoretic Based Segments for Language Identification. TSD 1999: 187-192 - 1998
- [c1]Uwe Ohler, Heinrich Niemann:
Stochastic Language Models for Content Based DNA Sequence Classification. German Conference on Bioinformatics 1998
Informal and Other Publications
- 2020
- [i3]Philipp Drewe-Boss, Dirk Enders, Jochen Walker, Uwe Ohler:
Deep learning for prediction of population health costs. CoRR abs/2003.03466 (2020) - 2019
- [i2]Rolf Backofen, Yael Mandel-Gutfreund, Uwe Ohler, Gabriele Varani:
Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 19342). Dagstuhl Reports 9(8): 49-69 (2019) - 2017
- [i1]Rolf Backofen, Yael Mandel-Gutfreund, Uwe Ohler, Gabriele Varani:
Computational Challenges in RNA-Based Gene Regulation: Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 17252). Dagstuhl Reports 7(6): 86-108 (2017)
Coauthor Index
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