Publications

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

Journals

Title: Weighted similarity-based clustering of chemical structures and bioactivity data in early drug discovery
Author(s): Nolen Joy Perualila-Tan, Ziv Shkedy, Willem Talloen, Hinrich W. H. Göhlmann, QSTAR Consortium, Marijke Van Moerbeke
Published: J. Bioinform. Comput. Biol., 2016 (to appear) doi:10.1142/S0219720016500189
 
Title: 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
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., 2016 (to appear) doi:10.1515/sagmb-2014-0086
 
Title: Transcriptome profiling of antimicrobial resistance in Pseudomonas aeruginosa
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
 
Title: Hsa-miR-375 is a predictor of local control in early stage breast cancer
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
Download: PDF
 
Title: DeepTox: Toxicity Prediction using Deep Learning
Author(s): Andreas Mayr, Günter Klambauer, Thomas Unterthiner, Sepp Hochreiter
Published: Front. Environ. Sci. 3:80., 2015 doi:10.3389/fenvs.2015.00080
Download: PDF
Abstract: Abstract
 



Conferences

Title: Rectified Factor Networks for Biclusterin
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
Downdload: PDF
 
Title: Understanding Very Deep Networks via Volume Conservation
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
Downdload: PDF
 
Title: Fast and Accurate Deep Network Learning by Exponential Linear Units (ELUs)
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
Downdload: arXiv:1511.07289 [cs.LG] / PDF
 



Books/Book Chapters

Title: Applied Biclustering Methods for Big and High-Dimensional Data Using R
Editor(s): Adetayo Kasim, Ziv Shkedy, Sebastian Kaiser, Sepp Hochreiter, Willem Talloen
Published: Taylor & Francis Group, Chapman & Hall/CRC Biostatistics Series, ISBN 9781482208238, to appear 2016
 
Title: Introduction
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, ISBN 9781482208238, to appear 2016
 
Title: δ-biclustering and FLOC Algorithm
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, ISBN 9781482208238, to appear 2016
 
Title: The Plaid Model
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, ISBN 9781482208238, to appear 2016
 
Title: FABIA
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, ISBN 9781482208238, to appear 2016
 
Title: Gene Expression Experiments in Drug Discovery
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, ISBN 9781482208238, to appear 2016
 
Title: Biclustering Methods in Chemoinformatics and Molecular Modeling
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, ISBN 9781482208238, to appear 2016
 
Title: Ranking of Biclusters in Drug Discovery Experiments
Author(s): Nolen Joy Perualila, Ziv Shkedy, Sepp Hochreiter, and 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, ISBN 9781482208238, to appear 2016
 
Title: HapFABIA: Biclustering for Detecting Identity by Descent
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, ISBN 9781482208238, to appear 2016
 
Title: The BiclustGUI Package
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, ISBN 9781482208238, to appear 2016
 
Title: The biclustGUI Shiny App
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, ISBN 9781482208238, to appear 2016
 



Publications (non-peer-reviewed)



Theses

Title: Long Short-Term Memory and convolutional neural networks for SNV-based phenotype prediction
Published: Master Thesis, 2016
Author(s): Michael Widrich
 
Title: The Maximum Common Subgraph Kernel For Predicting Kinase Inhibitors
Published: Master Thesis, 2016
Author(s): Sabine Schwandegger
 
Title: Multiple Sequence Alignment with R
Published: Master Thesis, 2016
Author(s): Enrico Bonatesta, Christoph Kainrath
 
Title: Parallel Long Short Term Memory LSTM
Published: Master Thesis, 2016
Author(s): Martin Moser
 
Title: Deep Learning for Drug Combination Synergy Prediction
Published: Master Thesis, 2016
Author(s): Kristina Preuer
 
Title: Classification of (alternatively) spliced exons using state-of-the-art sequence kernels
Published: Master Thesis, 2016
Author(s): Alexander Kogler
 
Title: Accurate detection of tumor copy number variations in high-throughput sequencing data
Published: Master Thesis, 2016
Author(s): Patrick Praher
 
Title: panelcn.MOPS reaches clinical standards as a copy number variation detection tool for targeted panel sequencing
Published: Master Thesis, 2016
Author(s): Verena Haunschmid