IBD Sharing between Africans, Neandertals, and Denisovans _{Genome Biol. Evol.}

Author(s):	Gundula Povysil, Sepp Hochreiter
Published:	Genome Biol. Evol., 8(12): 3406-3416, 2016 doi:10.1093/gbe/evw234, opens an external URL in a new window

Weighted similarity-based clustering of chemical structures and bioactivity data in early drug discovery _{J. Bioinform. Comput. Biol.}

Author(s):	Nolen Joy Perualila-Tan, Ziv Shkedy, Willem Talloen, Hinrich W. H. Göhlmann, QSTAR Consortium, Marijke Van Moerbeke
Published:	J. Bioinform. Comput. Biol., 14(4):1650018, 2016 doi:10.1142/S0219720016500189, opens an external URL in a new window

A joint modeling approach for uncovering associations between gene expression, bioactivity and chemical structure in early drug discovery to guide lead selection and genomic biomarker development _{Stat. Appl. Genet. Mol. Biol.}

Author(s):	Nolen Perualila-Tan, Adetayo Kasim, Willem Talloen, Bie Verbist, Hinrich W.H. Göhlmann, QSTAR Consortium, Ziv Shkedy
Published:	Stat. Appl. Genet. Mol. Biol., 15(4):1544-6115, 2016 doi:10.1515/sagmb-2014-0086, opens an external URL in a new window

Transcriptome profiling of antimicrobial resistance in Pseudomonas aeruginosa _{Antimicrob. Agents Chemother.}

Author(s):	Ariane Khaledi, Monika Schniederjans, Sarah Pohl, Roman Rainer, Ulrich Bodenhofer, Boyang Xia, Frank Klawonn, Sebastian Bruchmann, Matthias Preusse, Denitsa Eckweiler, Andreas Dötsch, Susanne Häussler
Published:	Antimicrob. Agents Chemother., 60(8):4722-4733, 2016 doi:10.1128/AAC.00075-16, opens an external URL in a new window

Hsa-miR-375 is a predictor of local control in early stage breast cancer _{Clin. Epigenetics}

Author(s):	Franz Zehentmayr, Cornelia Hauser-Kronberger, Barbara Zellinger, Falk Hlubek, Claudia Schuster, Ulrich Bodenhofer, Gerd Fastner, Heinz Deutschmann, Philipp Steininger, Roland Reitsamer, Thorsten Fischer, Felix Sedlmayer
Published:	Clin. Epigenetics, 8:28, 2016 doi:10.1186/s13148-016-0198-1, opens an external URL in a new window
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DeepTox: Toxicity Prediction using Deep Learning _{Front. Environ. Sci.}

Author(s):	Andreas Mayr, Günter Klambauer, Thomas Unterthiner, Sepp Hochreiter
Published:	Front. Environ. Sci. 3:80., 2015 doi:10.3389/fenvs.2015.00080, opens an external URL in a new window
Download:	PDF, opens an external URL in a new window
Abstract:	Abstract, opens an external URL in a new window

Long Short-Term Memory For Autonomous Driving Cars _NIPS

Author(s):	Michael Treml, José Arjona-Medina, Thomas Unterthiner, Rupesh Durgesh, Felix Friedmann, Peter Schuberth, Andreas Mayr, Martin Heusel, Markus Hofmarcher, Michael Widrich, Ulrich Bodenhofer, Bernhard Nessler, Sepp Hochreiter
Published:	Workshop on Machine Learning for Intelligent Transport Systems, Conference Neural Information Processing Systems Foundation (NIPS 2016), December 5-10, 2016
Download:	PDF, opens an external URL in a new window

Deep Learning for predicting synergy effects of drug combinations _NIPS

Author(s):	Kristina Preuer, Günter Klambauer, Sepp Hochreiter
Published:	Women in Machine Learning Workshop, Conference Neural Information Processing Systems Foundation (NIPS 2016), December 5-10, 2016

HapRFN: a deep learning method for identifying short IBD segments _NIPS

Author(s):	Gundula Povysil, Djork-Arné Clevert, Sepp Hochreiter
Published:	Women in Machine Learning Workshop, Conference Neural Information Processing Systems Foundation (NIPS 2016), December 5-10, 2016

Speeding up Semantic Segmentation for Autonomous Driving _NIPS

Author(s):	Michael Treml, José Arjona-Medina, Thomas Unterthiner, Rupesh Durgesh, Felix Friedmann, Peter Schuberth, Andreas Mayr, Martin Heusel, Markus Hofmarcher, Michael Widrich, Ulrich Bodenhofer, Bernhard Nessler, Sepp Hochreiter
Published:	Workshop on Machine Learning for Intelligent Transport Systems, Conference Neural Information Processing Systems Foundation (NIPS 2016), December 5-10, 2016
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panelcn.MOPS: CNV detection in targeted panel sequencing data for diagnostic use _ASGH

Author(s):	Gundula Povysil, Antigoni Tzika, Julia Vogt, Verena Haunschmid, Ludwine Messiaen, Katharina Wimmer, Günter Klambauer, Sepp Hochreiter
Published:	Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2016), Vancouver, Canada, October 18-22, 2016
Download:	PDF, opens an external URL in a new window

HapRNF: a deep learning method to identify short IBD segments _ASHG

Author(s):	Gundula Povysil, Djork-Arné Clevert, Sepp Hochreiter
Published:	Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2016), Vancouver, Canada, October 18-22, 2016
Download:	PDF, opens an external URL in a new window

Deep Learning for Drug Target Prediction _{GTC Europe}

Author(s):	Thomas Unterthiner, Andreas Mayr, Günter Klambauer, Sepp Hochreiter
Published:	Poster at GPU Technology Conference Europe (GTC Europe), September 26-29, 2016 Best-Paper Award

Long Short-Term Memory For Autonomous Driving Cars _{GTC Europe}

Author(s):	Michael Treml
Published:	Poster at GPU Technology Conference Europe (GTC Europe), September 26-29, 2016

Rectified Factor Networks for Biclustering _ICLR

Author(s):	Djork-Arné Clevert, Thomas Unterthiner, Sepp Hochreiter
Published:	Workshop Paper at International Conference on Learning Representations (ICLR 2016), San Juan, Puerto Rico, May 2-4, 2016
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Understanding Very Deep Networks via Volume Conservation _ICLR

Author(s):	Thomas Unterthiner, Sepp Hochreiter
Published:	Workshop Paper at International Conference on Learning Representations (ICLR 2016), San Juan, Puerto Rico, May 2-4, 2016
Download:	PDF, opens an external URL in a new window

Fast and Accurate Deep Network Learning by Exponential Linear Units (ELUs) _ICLR

Author(s):	Djork-Arné Clevert, Thomas Unterthiner, Sepp Hochreiter
Published:	International Conference on Learning Representations (ICLR 2016), San Juan, Puerto Rico, May 2-4, 2016
Download:	arXiv:1511.07289 [cs.LG], opens an external URL in a new window / PDF, opens an external URL in a new window

Applied Biclustering Methods for Big and High-Dimensional Data Using R _{Taylor & Francis Group}

Editor(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published:	Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, opens an external URL in a new window, ISBN 9781482208238, 2016

Introduction _{Applied Biclustering Methods for Big and High-Dimensional Data Using R}

Author(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Editor(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published:	Applied Biclustering Methods for Big and High-Dimensional Data Using R, Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, opens an external URL in a new window, ISBN 9781482208238, pp. 1-10, 2016

δ-biclustering and FLOC Algorithm _{Applied Biclustering Methods for Big and High-Dimensional Data Using R}

Author(s):	Adetayo Kasim, Sepp Hochreiter, Ziv Shkedy
Editor(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published:	Applied Biclustering Methods for Big and High-Dimensional Data Using R, Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, opens an external URL in a new window, ISBN 9781482208238, pp. 37-48, 2016

The Plaid Model _{Applied Biclustering Methods for Big and High-Dimensional Data Using R}

Author(s):	Ziv Shkedy, Ewoud De Troyer, Adetayo Kasim, Sepp Hochreiter, Heather Turner
Editor(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published:	Applied Biclustering Methods for Big and High-Dimensional Data Using R, Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, opens an external URL in a new window, ISBN 9781482208238, pp. 73-88, 2016

FABIA _{Applied Biclustering Methods for Big and High-Dimensional Data Using R}

Author(s):	Sepp Hochreiter
Editor(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published:	Applied Biclustering Methods for Big and High-Dimensional Data Using R, Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, opens an external URL in a new window, ISBN 9781482208238, pp. 99-117, 2016

Gene Expression Experiments in Drug Discovery _{Applied Biclustering Methods for Big and High-Dimensional Data Using R}

Author(s):	Willem Talloen, Hinrich W.H. Göhlmann, Bie Verbist, Nolen Joy Perualila, Ziv Shkedy, Adetayo Kasim, QSTAR Consortium
Editor(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published:	Applied Biclustering Methods for Big and High-Dimensional Data Using R, Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, opens an external URL in a new window, ISBN 9781482208238, pp. 159-174, 2016

Biclustering Methods in Chemoinformatics and Molecular Modeling _{Applied Biclustering Methods for Big and High-Dimensional Data Using} 

Author(s):	Nolen Joy Perualila, Ziv Shkedy, Aakash Chavan Ravindranath, Georgios Drakakis, Sonia Liggi, Andreas Bender, Adetayo Kasim, QSTAR Consortium, Willem Talloen, Hinrich W.H. Göhlmann
Editor(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published:	Applied Biclustering Methods for Big and High-Dimensional Data Using R, Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, opens an external URL in a new window, ISBN 9781482208238, pp. 175-202, 2016

Ranking of Biclusters in Drug Discovery Experiments _{Applied Biclustering Methods for Big and High-Dimensional Data Using R}

Author(s):	Nolen Joy Perualila, Ziv Shkedy, Sepp Hochreiter, Djork-Arné Clevert
Editor(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published:	Applied Biclustering Methods for Big and High-Dimensional Data Using R, Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, opens an external URL in a new window, ISBN 9781482208238, pp. 223-238, 2016

HapFABIA: Biclustering for Detecting Identity by Descent _{Applied Biclustering Methods for Big and High-Dimensional Data Using R}

Author(s):	Sepp Hochreiter
Editor(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published:	Applied Biclustering Methods for Big and High-Dimensional Data Using R, Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, opens an external URL in a new window, ISBN 9781482208238, pp. 239-259, 2016

The BiclustGUI Package _{Applied Biclustering Methods for Big and High-Dimensional Data Using R}

Author(s):	Ewoud De Troyer, Martin Otava, Jitao David Zhang, Setia Pramana, Tatsiana Khamiakova, Sebastian Kaiser, Martin Sill, Aedin Culhane, Daniel Gusenleitner,Pierre Gestraud, Gabor Csardi, Mengsteab Aregay, Sepp Hochreiter, Gunter Klambauer, Djork-Arné Clevert, Tobias Verbeke, Nolen Joy Perualila, Adetayo Kasim, Ziv Shkedy
Editor(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published:	Applied Biclustering Methods for Big and High-Dimensional Data Using R, Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, opens an external URL in a new window, ISBN 9781482208238, pp. 321-348, 2016

biclustGUI Shiny App _{Applied Biclustering Methods for Big and High-Dimensional Data Using R}

Author(s):	Ewoud De Troyer, Rudradev Sengupta, Martin Otava, Jitao David Zhang, Sebastian Kaiser, Aedin Culhane, Daniel Gusenleitner, Pierre Gestraud, Gabor Csardi, Sepp Hochreiter, Gunter Klambauer, Djork-Arné Clevert, Nolen Joy Perualila, Adetayo Kasim, Ziv Shkedy
Editor(s):	Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published:	Applied Biclustering Methods for Big and High-Dimensional Data Using R, Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, opens an external URL in a new window, ISBN 9781482208238, pp. 373-383, 2016

Multi-Target Deep Neural Networks for Toxicity Prediction _{Master Thesis}

Published:	Master Thesis, 2016
Author(s):	Thomas Unterthiner

Long Short-Term Memory and convolutional neural networks for SNV-based phenotype prediction _{Master Thesis}

Published:	Master Thesis, 2016
Author(s):	Michael Widrich

The Maximum Common Subgraph Kernel For Predicting Kinase Inhibitors _{Master Thesis}

Published:	Master Thesis, 2016
Author(s):	Sabine Schwandegger

Multiple Sequence Alignment with R _{Master Thesis}

Published:	Master Thesis, 2016
Author(s):	Enrico Bonatesta, Christoph Kainrath

Parallel Long Short Term Memory LSTM _{Master Thesis}

Published:	Master Thesis, 2016
Author(s):	Martin Moser

Deep Learning for Drug Combination Synergy Prediction _{Master Thesis}

Published:	Master Thesis, 2016
Author(s):	Kristina Preuer

Classification of (alternatively) spliced exons using state-of-the-art sequence kernels _{Master Thesis}

Published:	Master Thesis, 2016
Author(s):	Alexander Kogler

Accurate detection of tumor copy number variations in high-throughput sequencing data _{Master Thesis}

Published:	Master Thesis, 2016
Author(s):	Patrick Praher

panelcn.MOPS reaches clinical standards as a copy number variation detection tool for targeted panel sequencing _{Master Thesis}

Published:	Master Thesis, 2016
Author(s):	Verena Haunschmid