Publications

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

Journals

Title: msa: an R package for multiple sequence alignment
Author(s): Ulrich Bodenhofer, Enrico Bonatesta, Christoph Kainrath, Sepp Hochreiter
Published: Bioinformatics, 31(24):3997-3999, 2015
doi:10.1093/bioinformatics/btv494
Download: PDF
 
Title: Prediction of human population responses to toxic compounds by a collaborative competition
Author(s): Federica Eduati, Lara M Mangravite, Tao Wang, Hao Tang, ... , Sepp Hochreiter, GŁnter Klambauer, Andreas Mayr, ... , Ivan Rusyn, Fred A Wright, Gustavo Stolovitzky, Yang Xie, Julio Saez-Rodriguez
Published: Nature Biotechnology, 33(9):933-940, 2015 doi:10.1038/nbt.3299
 
Title: Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map
Author(s): Günter Klambauer, Martin Wischenbart, Michael Mahr, Thomas Unterthiner, Andreas Mayr, Sepp Hochreiter
Published: Bioinformatics, 31(20):3392-3394, 2015 doi:10.1093/bioinformatics/btv373
Download: PDF
 
Title: KeBABS: an R package for kernel-based analysis of biological sequences
Author(s): Johannes Palme, Sepp Hochreiter, Ulrich Bodenhofer
Published: Bioinformatics, 31(15):2574-2576, 2015 doi:10.1093/bioinformatics/btv176
Download: PDF
Abstract: Abstract
 
Title: Using transcriptomics to guide lead optimization in drug discovery projects
Author(s): Bie Verbist, Günter Klambauer, Liesbet Vervoort, Willem Talloen, QSTAR Consortium, Ziv Shkedy, Olivier Thas, Andreas Bender, Hinrich W.H. Göhlmann, Sepp Hochreiter
Published: Drug Discovery Today, 20(5):505-513, 2015 doi:10.1016/j.drudis.2014.12.014
 
Title: Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis
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
Published: Mol. BioSyst., 11:86-96, 2015 doi:10.1039/C4MB00328D
Download: Abstract
 
Title: Graded dominance and related graded properties of fuzzy connectives
Author(s): Libor Behounek, Ulrich Bodenhofer, Petr Cintula, Susanne Saminger-Platz, Peter Sarkoci
Published: Fuzzy Sets and Systems, 262:78-101, 2015 doi:10.1016/j.fss.2014.04.025



Conferences

Title: ELU-Networks - Fast and Accurate CNN Learning on ImageNet
Author(s): Martin Heusel, Djork-Arné Clevert, Günter Klambauer, Andreas Mayr, Karin Schwarzbauer, Thomas Unterthiner, Sepp Hochreiter
Published: Poster at International Conference on Computer Vision (ICCV 2015), Santiago, Chile, December 13-16, 2015
Downdload: PDF
 
Title: Rectified Factor Networks
Author(s): Djork-Arné Clevert, Andreas Mayr, Thomas Unterthiner, Sepp Hochreiter
Published: Conference Neural Information Processing Systems Foundation (NIPS 2015), Montreal, Canada, December 7-12, 2015
Downdload: PDF, Supplement (PDF)
 
Title: panelcn. MOPS reaches clinical standards as a CNV detection tool for targeted panel sequencing data
Author(s): Verena Haunschmid, Gundula Povysil, Julia Vogt, Katharina Wimmer, Günter Klambauer, Sepp Hochreiter
Published: Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2015), Baltimore, USA, October 6-10, 2015
Abstract: PDF
 
Title: KeBABS: an R/Bioconductor package for kernel-based analysis of biological sequences
Author(s): Johannes Palme, Sepp Hochreiter, Ulrich Bodenhofer
Published: Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2015), Baltimore, USA, October 6-10, 2015
Abstract: PDF
 
Title: PODKAT: a software package implementing the position-dependent kernel association test
Author(s): Ulrich Bodenhofer, Sepp Hochreiter
Published: Poster at Annual Meeting of the American Society of Human Genetics (ASHG 2015), Baltimore, USA, October 6-10, 2015
Abstract: PDF
 
Title: Early Interbreeding between Ancestors of Humans, Neandertals, and Denisovans within Africa
Author(s): Gundula Povysil, Sepp Hochreiter
Published: Poster at Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2015), Vienna, Austria, July 12-16, 2015
Abstract: PDF
 



Books/Book Chapters



Publications (non-peer-reviewed)

Title: Toxicity Prediction using Deep Learning
Author(s): Thomas Unterthiner, Andreas Mayr, Günter Klambauer, Sepp Hochreiter
Published: arXiv.org, Mar 2015
Download: arXiv:1503.01445 [stat.ML]
 
Title: Rectified Factor Networks
Author(s): Djork-Arné Clevert, Thomas Unterthiner, Andreas Mayr, Hubert Ramsauer, Sepp Hochreiter
Published: arXiv.org, Feb 2015
Download: arXiv:1502.06464 [cs.LG]



Theses

Title: Support Vector Regression vs. Neural Network Regression in the Field of Predicting Drug-Target Binding Activities
Published: Master Thesis, 2015
Author(s): Alexander Pfaffinger
 
Title: Similarity-based clustering of big data: A parallel ensemble variant of leveraged affinity propagation
Published: Master Thesis, 2015
Author(s): Chrats Melkonian
 
Title: Development, application and analysis of a pipeline for genotype-to-phenotype whole-genome based predictions
Published: Master Thesis, 2015
Author(s): Roman Josef Rainer
 
Title: A copy number analysis and genome-wide association study of schizophrenia data
Published: Master Thesis, 2015
Author(s): Nadine Stein
 
Title: KeBABS - An R Package for Kernel-Based Analysis of Biological Sequences
Published: Master Thesis, 2015
Author(s): Johannes Palme
 
Title: Inferring Regulatory Interactions from Microarray Data Using the FABIA Biclustering Method: A Case Study for E.coli K-12
Published: Master Thesis, 2015
Author(s): Wilhelm Lichtberger
 
Title: Detecting CNVs in the 1000 Genomes Project Data Using cn.MOPS and Relating the Results to Transcriptome Sequencing Data
Published: Master Thesis, 2015
Author(s): Anna Maria Langmüller