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
Published: Nature Communications 5, Article number: 5125, 25 September 2014 doi:10.1038/ncomms6125
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
 
Title: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
Published: Nature Biotechnology, published online 24 August 2014 doi:10.1038/nbt.2957
Author(s): SEQC/MAQC-III Consortium
Download: Full Text
 
Title: Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis
Published: Accepted for publication in Mol. BioSyst., 2014 doi:10.1039/C4MB00328D
Author(s): Aakash Chavan Ravindranath, Nolen Perualila-Tan, Adetayo Kasim, Georgios Drakakis, Sonia Liggi, Suzanne C. Brewerton, Daniel Mason, Michael J. Bodkin, David A. Evans, Aditya Bhagwat, Willem Talloen, Hinrich W. H. Göhlmann, QSTAR Consortium, Ziv Shkedy, Andreas Bender
Download: Abstract
 
Title: Furby: fuzzy force-directed bicluster visualization
Published: BMC Bioinformatics, 15(Suppl 6):S4, 2014 doi:10.1186/1471-2105-15-S6-S4
Author(s): Marc Streit, Samuel Gratzl, Michael Gillhofer, Andreas Mayr, Andreas Mitterecker, Sepp Hochreiter
Download: Abstract
Full Text
 
Title: Lck Mediates Signal Transmission from CD59 to the 1 TCR/CD3 Pathway in Jurkat T Cells
Published: PLoS ONE, 9(1):e85934, 2014 doi:10.1371/journal.pone.0085934
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
Abstract: PDF
 



Conferences

Title: Utilizing Private Variants in Large Genome-Wide Association Studies: Issues, Techniques, Experiences
Published: Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2014), San Diego, USA, October 18-22, 2014
Author(s): Ulrich Bodenhofer, Sepp Hochreiter
Abstract: PDF
 
Title: Detection of Copy Number Variations in Cancer Genomes from High Throughput Sequencing Data
Published: Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2014), San Diego, USA, October 18-22, 2014
Author(s): Günter Klambauer, Sepp Hochreiter
Abstract: PDF
 
Title: Population specific patterns of novel haplotype groups at the PAH locus
Published: Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2014), San Diego, USA, October 18-22, 2014
Author(s): Gundula Povysil, Stefanie Wieser, Sepp Hochreiter, Johannes Zschocke
Abstract: PDF
 
Title: Identity by descent between humans, Denisovans, and Neandertals
Published: Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2014), San Diego, USA, October 18-22, 2014
Author(s): Sepp Hochreiter, Gundula Povysil
Abstract: PDF
 



Books/Book Chapters



Publications (non-peer-reviewed)

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



Theses

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