Publications

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Journals | Conferences | Books/Book Chapters | Publications (non-peer-reviewed) | Theses

Journals

Title: Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures
Author(s): Sarah A. Munro, Steven P. Lund, P. Scott Pine, Hans Binder, Djork-Arné Clevert, Ana Conesa, Joaquin Dopazo, Mario Fasold, Sepp Hochreiter, Huixiao Hong, Nedereh Jafari, David P. Kreil, Pawel P. Labaj, Sheng Li, Yang Liao, Simon M. Lin, Joseph Meehan, Christopher E. Mason, Javier Santoyo-Lopez, Robert A. Setterquist, Leming Shi, Wei Shi, Gordon K. Smyth, Nancy Stralis-Pavese, Zhenqiang Su, Weida Tong, Charles Wang, Jian Wang, Joshua Xu, Zhan Ye, Yong Yang, Ying Yu, Marc Salit
Published: Nature Communications 5, Article number: 5125, 25 September 2014 doi:10.1038/ncomms6125
Download: Draft Version arXiv
 
Title: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
Author(s): SEQC/MAQC-III Consortium
Published: Nature Biotechnology, 32:903–914, 2014 doi:10.1038/nbt.2957
Download: Full Text
 
Title: Furby: fuzzy force-directed bicluster visualization
Author(s): Marc Streit, Samuel Gratzl, Michael Gillhofer, Andreas Mayr, Andreas Mitterecker, Sepp Hochreiter
Published: BMC Bioinformatics, 15(Suppl 6):S4, 2014 doi:10.1186/1471-2105-15-S6-S4
Download: Abstract
Full Text
 
Title: Lck Mediates Signal Transmission from CD59 to the 1 TCR/CD3 Pathway in Jurkat T Cells
Author(s): Anna-M. Lipp, Kata Juhasz, Christian Paar, Christoph Ogris, Paul Eckerstorfer, Roland Thuenauer, Jan Hesse, Benedikt Nimmervoll, Hannes Stockinger, Gerhard J. Schütz, Ulrich Bodenhofer, Zsolt Balogi, Alois Sonnleitner
Published: PLoS ONE, 9(1):e85934, 2014 doi:10.1371/journal.pone.0085934
Abstract: PDF



Conferences

Title: Multi-Task Deep Networks for Drug Target Prediction
Author(s): Thomas Unterthiner, Andreas Mayr, Günter Klambauer, Marvin Steijaert, Hugo Ceulemans, Jörg Wegner, Sepp Hochreiter
Published: Conference Neural Information Processing Systems Foundation (NIPS 2014), Workshop on Transfer and Multi-task Learning, Montreal, Canada, December 8-13, 2014
Downdload: PDF
 
Title: Deep Learning for Drug Target Prediction
Author(s): Thomas Unterthiner, Andreas Mayr, Günter Klambauer, Marvin Steijaert, Hugo Ceulemans, Jörg Wegner, Sepp Hochreiter
Published: Conference Neural Information Processing Systems Foundation (NIPS 2014), Workshop on Representation and Learning Methods for Complex Outputs, Montreal, Canada, December 8-13, 2014
Downdload: PDF
 
Title: Aiding Drug Design with Deep Neural Networks
Author(s): Thomas Unterthiner, Andreas Mayr, Günter Klambauer, Marvin Steijaert, Jörg Wegner, Hugo Ceulemans, Sepp Hochreiter
Published: Conference Neural Information Processing Systems Foundation (NIPS 2014), Workshop on Machine Learning in Computational Biology, Montreal, Canada, December 8-13, 2014
Downdload: PDF
 
Title: Deep Learning as an Opportunity in Virtual Screening
Author(s): Thomas Unterthiner, Andreas Mayr, Günter Klambauer, Marvin Steijaert, Jörg Wegner, Hugo Ceulemans, Sepp Hochreiter
Published: Conference Neural Information Processing Systems Foundation (NIPS 2014), Workshop on Machine Learning for Clinical Data Analysis, Healthcare and Genomics, Montreal, Canada, December 8-13, 2014
Downdload: PDF
 
Title: Rectified Factor Networks and Dropout
Author(s): Djork-Arné Clevert, Thomas Unterthiner, Sepp Hochreiter
Published: Conference Neural Information Processing Systems Foundation (NIPS 2014), Workshop on Deep Learning and Representation Learning, Montreal, Canada, December 8-13, 2014
Downdload: PDF
 
Title: Deep Learning as an Opportunity in Virtual Screening
Author(s): Thomas Unterthiner, Andreas Mayr, Günter Klambauer, Marvin Steijaert, Jörg Wegner, Hugo Ceulemans, Sepp Hochreiter
Published: Conference Neural Information Processing Systems Foundation (NIPS 2014), Workshop on Deep Learning and Representation Learning, Montreal, Canada, December 8-13, 2014
Downdload: PDF
 
Title: Utilizing Private Variants in Large Genome-Wide Association Studies: Issues, Techniques, Experiences
Author(s): Ulrich Bodenhofer, Sepp Hochreiter
Published: Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2014), San Diego, USA, October 18-22, 2014
Abstract: PDF
 
Title: Detection of Copy Number Variations in Cancer Genomes from High Throughput Sequencing Data
Author(s): Günter Klambauer, Sepp Hochreiter
Published: Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2014), San Diego, USA, October 18-22, 2014
Abstract: PDF
 
Title: Population specific patterns of novel haplotype groups at the PAH locus
Author(s): Gundula Povysil, Stefanie Wieser, Sepp Hochreiter, Johannes Zschocke
Published: Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2014), San Diego, USA, October 18-22, 2014
Abstract: PDF
 
Title: Identity by descent between humans, Denisovans, and Neandertals
Author(s): Sepp Hochreiter, Gundula Povysil
Published: Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2014), San Diego, USA, October 18-22, 2014
Abstract: PDF
 
Title: A Cloud-based GWAS Analysis Pipeline for Clinical Researchers
Author(s): Paul Heinzlreiter, James Richard Perkins, Oscar Torreno, Johan Karlsson, Juan Antonio Ranea, Andreas Mitterecker, Miguel Blanca, Oswaldo Trelles
Published: Proc. of the 4th International Conference on Cloud Computing and Services Science (CLOSER 2014), ISBN 978-989-758-019-2, Barcelona, Spain, pp. 387-394, April 2014, doi:10.5220/0004802103870394



Books/Book Chapters



Publications (non-peer-reviewed)

Title: FABIA: A Probabilistic Model for Biclustering and its Application to Analyzing Big Data in Drug Design
Author(s): Djork-Arné Clevert, Günter Klambauer, Andreas Mayr, Andreas Mitterecker, Sepp Hochreiter
Published: Poster at 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, USA, July 11 - July 15 2014
 
Title: Detecting biomarkers on label-free mass spectrometry data using biclustering
Author(s): Andreas Mitterecker, Djork-Arné Clevert, Sepp Hochreiter
Published: Poster at 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, USA, July 11 - July 15 2014
 
Title: Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions
Author(s): Thomas Unterthiner, Günter Klambauer, Sepp Hochreiter
Published: Poster at 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, USA, July 11 - July 15 2014
 
Title: DeepSAR: Drug Target Prediction using Deep Learning
Author(s): Andreas Mayr, Alexander Pfaffinger, Thomas Unterthiner, Günter Klambauer, Marvin Steijaert, Jörg K. Wegner, Hugo Ceulemans, Sepp Hochreiter
Published: Poster at 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, USA, July 11 - July 15 2014
 
Title: Sharing of Very Short IBD Segments between Humans, Neandertals, and Denisovans
Author(s): Gundula Povysil, Sepp Hochreiter
Published: bioRxiv, online April 7, 2014, doi:10.1101/003988



Theses

Title: Machine Learning Techniques for the Analysis of High-Throughput DNA and RNA Sequencing Data
Author(s): Günter Klambauer
Published: PhD Thesis, 2014