Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures _{Nature Communications 5}

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, opens an external URL in a new window
Download:	Draft Version arXiv, opens an external URL in a new window

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium _{Nature Biotechnology}

Author(s):	SEQC/MAQC-III Consortium
Published:	Nature Biotechnology, 32:903–914, 2014 doi:10.1038/nbt.2957, opens an external URL in a new window
Download:	Full Text, opens an external URL in a new window

Furby: fuzzy force-directed bicluster visualization _{BMC Bioinformatics}

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, opens an external URL in a new window
Download:	Abstract, opens an external URL in a new window Full Text, opens an external URL in a new window

Lck Mediates Signal Transmission from CD59 to the 1 TCR/CD3 Pathway in Jurkat T Cells _{PLoS ONE}

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, opens an external URL in a new window
Abstract:	PDF, opens an external URL in a new window

Multi-Task Deep Networks for Drug Target Prediction _NIPS

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, opens an external URL in a new window

Deep Learning for Drug Target Prediction _NIPS

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, opens an external URL in a new window

Aiding Drug Design with Deep Neural Networks _NIPS

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
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Deep Learning as an Opportunity in Virtual Screening _NIPS

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, opens an external URL in a new window

Rectified Factor Networks and Dropout _NIPS

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, opens an external URL in a new window

Deep Learning as an Opportunity in Virtual Screening _NIPS

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, opens an external URL in a new window

Utilizing Private Variants in Large Genome-Wide Association Studies: Issues, Techniques, Experiences _ASHG 

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, opens an external URL in a new window

Detection of Copy Number Variations in Cancer Genomes from High Throughput Sequencing Data _ASHG

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, opens an external URL in a new window

Population specific patterns of novel haplotype groups at the PAH locus _ASHG

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, opens an external URL in a new window

Identity by descent between humans, Denisovans, and Neandertals _ASHG

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, opens an external URL in a new window

A Cloud-based GWAS Analysis Pipeline for Clinical Researchers _CLOSER

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, opens an external URL in a new window

FABIA: A Probabilistic Model for Biclustering and its Application to Analyzing Big Data in Drug Design _ISMB

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

Detecting biomarkers on label-free mass spectrometry data using biclustering _ISMB

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

Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions _ISMB

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

DeepSAR: Drug Target Prediction using Deep Learning _ISMB

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

Sharing of Very Short IBD Segments between Humans, Neandertals, and Denisovans _bioRxiv

Author(s):	Gundula Povysil, Sepp Hochreiter
Published:	bioRxiv, online April 7, 2014, doi:10.1101/003988, opens an external URL in a new window

 

Machine Learning Techniques for the Analysis of High-Throughput DNA and RNA Sequencing Data

Author(s):	Günter Klambauer
Published:	PhD Thesis, 2014