Bernhard Y. Renard

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 36

Top Topics

Reference Genome

Machine Learning

Horizontal Gene Transfer

Top Venues

Briefings Bioinform.

Publications

Paulo Yanez Sarmiento, Simon Witzke, Nadja Klein, Bernhard Y. Renard
Sparse Explanations of Neural Networks Using Pruned Layer-Wise Relevance Propagation. CoRR (2024)
Linea Schmidt, Marc Pawlitzki, Bernhard Y. Renard, Sven G. Meuth, Lars Masanneck
The three-year evolution of Germany's Digital Therapeutics reimbursement program and its path forward. npj Digit. Medicine 7 (1) (2024)
Fábio Malcher Miranda, Vasco Ariston de Carvalho Azevedo, Rommel Thiago Juca Ramos, Bernhard Y. Renard, Vitor Piro
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2. BMC Bioinform. 25 (1) (2024)
Pascal Iversen, Simon Witzke, Katharina Baum, Bernhard Y. Renard
Identifying Drivers of Predictive Uncertainty using Variance Feature Attribution. CoRR (2023)
Maximilian Kleissl, Lukas Drews, Benedict B. Heyder, Julian Zabbarov, Pascal Iversen, Simon Witzke, Bernhard Y. Renard, Katharina Baum
SimbaML: Connecting Mechanistic Models and Machine Learning with Augmented Data. CoRR (2023)
Denis Beslic, Georg Tscheuschner, Bernhard Y. Renard, Michael G. Weller, Thilo Muth
sequencing tools for monoclonal antibody assembly. Briefings Bioinform. 24 (1) (2023)
Fábio Malcher Miranda, Niklas Köhnecke, Bernhard Y. Renard
HiClass: a Python Library for Local Hierarchical Classification Compatible with Scikit-learn. J. Mach. Learn. Res. 24 (2023)
Ferdous Nasri, Kunaphas Kongkitimanon, Alice Wittig, Jorge Sánchez Cortés, Annika Brinkmann, Andreas Nitsche, Anna-Juliane Schmachtenberg, Bernhard Y. Renard, Stephan Fuchs
MpoxRadar: a worldwide MPXV genomic surveillance dashboard. Nucleic Acids Res. 51 (W1) (2023)
Tim Garrels, Athar Khodabakhsh, Bernhard Y. Renard, Katharina Baum
LazyFox: fast and parallelized overlapping community detection in large graphs. PeerJ Comput. Sci. 9 (2023)
Andrea Nathansen, Kevin Klein, Bernhard Y. Renard, Melania Nowicka, Jakub M. Bartoszewicz
Evaluating Tuning Strategies for Sequence Generation with Protein Language Models. MLCB (2023)
Maximilian Kleissl, Lukas Drews, Benedict B. Heyder, Julian Zabbarov, Pascal Iversen, Simon Witzke, Bernhard Y. Renard, Katharina Baum
SimbaML: Connecting Mechanistic Models and Machine Learning with Augmented Data. Tiny Papers @ ICLR (2023)
Alice Wittig, Fábio Miranda, Martin Hölzer, Tom Altenburg, Jakub M. Bartoszewicz, Sebastian Beyvers, Marius A. Dieckmann, Ulrich Genske, Sven H. Giese, Melania Nowicka, Hugues Richard, Henning Schiebenhoefer, Anna-Juliane Schmachtenberg, Paul Sieben, Ming Tang, Julius Tembrockhaus, Bernhard Y. Renard, Stephan Fuchs
CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance. Bioinform. 38 (17) (2022)
Tim Garrels, Athar Khodabakhsh, Bernhard Y. Renard, Katharina Baum
LazyFox: Fast and parallelized overlapping community detection in large graphs. CoRR (2022)
Tom Altenburg, Sven H. Giese, Shengbo Wang, Thilo Muth, Bernhard Y. Renard
Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides. Nat. Mach. Intell. 4 (4) (2022)
Fábio M. Miranda, Niklas Köhnecke, Bernhard Y. Renard
HiClass: a Python library for local hierarchical classification compatible with scikit-learn. CoRR (2021)
Jakub M. Bartoszewicz, Ulrich Genske, Bernhard Y. Renard
Deep learning-based real-time detection of novel pathogens during sequencing. Briefings Bioinform. 22 (6) (2021)
Vitor Piro, Temesgen Hailemariam Dadi, Enrico Seiler, Knut Reinert, Bernhard Y. Renard
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinform. 36 (Supplement-1) (2020)
Hartwig Anzt, Felix Bach, Stephan Druskat, Frank Löffler, Axel Loewe, Bernhard Y. Renard, Gunnar Seemann, Alexander Struck, Elke Achhammer, Piush Aggarwal, Franziska Appel, Michael Bader, Lutz Brusch, Christian Busse, Gerasimos Chourdakis, Piotr Wojciech Dabrowski, Peter Ebert, Bernd Flemisch, Sven Friedl, Bernadette Fritzsch, Maximilian D. Funk, Volker Gast, Florian Goth, Jean-Noël Grad, Sibylle Hermann, Florian Hohmann, Stephan Janosch, Dominik Kutra, Jan Linxweiler, Thilo Muth, Wolfgang Peters-Kottig, Fabian Rack, Fabian H. C. Raters, Stephan Rave, Guido Reina, Malte Reißig, Timo Ropinski, Jörg Schaarschmidt, Heidi Seibold, Jan P. Thiele, Benjamin Uekermann, Stefan Unger, Rudolf Weeber
An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action. F1000Research 9 (2020)
Hartwig Anzt, Felix Bach, Stephan Druskat, Frank Löffler, Axel Loewe, Bernhard Y. Renard, Gunnar Seemann, Alexander Struck, Elke Achhammer, Piush Aggarwal, Franziska Appel, Michael Bader, Lutz Brusch, Christian Busse, Gerasimos Chourdakis, Piotr Wojtek Dabrowski, Peter Ebert, Bernd Flemisch, Sven Friedl, Bernadette Fritzsch, Maximilian D. Funk, Volker Gast, Florian Goth, Jean-Noël Grad, Sibylle Hermann, Florian Hohmann, Stephan Janosch, Dominik Kutra, Jan Linxweiler, Thilo Muth, Wolfgang Peters-Kottig, Fabian Rack, Fabian H. C. Raters, Stephan Rave, Guido Reina, Malte Reißig, Timo Ropinski, Jörg Schaarschmidt, Heidi Seibold, Jan P. Thiele, Benjamin Uekerman, Stefan Unger, Rudolf Weeber
An Environment for Sustainable Research Software in Germany and Beyond: Current State, Open Challenges, and Call for Action. CoRR (2020)
Robert Rentzsch, Carlus Deneke, Andreas Nitsche, Bernhard Y. Renard
Predicting bacterial virulence factors - evaluation of machine learning and negative data strategies. Briefings Bioinform. 21 (5) (2020)
Jakub M. Bartoszewicz, Anja Seidel, Robert Rentzsch, Bernhard Y. Renard
DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks. Bioinform. 36 (1) (2020)
Enrico Seiler, Kathrin Trappe, Bernhard Y. Renard
Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation. PLoS Comput. Biol. 15 (7) (2019)
Christine Jandrasits, Stefan Kröger, Walter Haas, Bernhard Y. Renard
Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters. PLoS Comput. Biol. 15 (12) (2019)
Tobias P. Loka, Simon H. Tausch, Piotr Wojtek Dabrowski, Aleksandar Radonic, Andreas Nitsche, Bernhard Y. Renard
PriLive: privacy-preserving real-time filtering for next-generation sequencing. Bioinform. 34 (14) (2018)
Thilo Muth, Bernhard Y. Renard
Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? Briefings Bioinform. 19 (5) (2018)
Andreas Andrusch, Piotr Wojtek Dabrowski, Jeanette Klenner, Simon H. Tausch, Claudia Kohl, Abdalla Osman, Bernhard Y. Renard, Andreas Nitsche
PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples. Bioinform. 34 (17) (2018)
Temesgen Hailemariam Dadi, Enrico Siragusa, Vitor Piro, Andreas Andrusch, Enrico Seiler, Bernhard Y. Renard, Knut Reinert
DREAM-Yara: an exact read mapper for very large databases with short update time. Bioinform. 34 (17) (2018)
Simon H. Tausch, Benjamin Strauch, Andreas Andrusch, Tobias P. Loka, Martin S. Lindner, Andreas Nitsche, Bernhard Y. Renard
LiveKraken--real-time metagenomic classification of illumina data. Bioinform. 34 (21) (2018)
Martina Fischer, Benjamin Strauch, Bernhard Y. Renard
Abundance estimation and differential testing on strain level in metagenomics data. Bioinform. 33 (14) (2017)
Martin S. Lindner, Benjamin Strauch, Jakob M. Schulze, Simon H. Tausch, Piotr Wojtek Dabrowski, Andreas Nitsche, Bernhard Y. Renard
HiLive: real-time mapping of illumina reads while sequencing. Bioinform. 33 (6) (2017)
Kathrin Trappe, Tobias Marschall, Bernhard Y. Renard
Detecting horizontal gene transfer by mapping sequencing reads across species boundaries. Bioinform. 32 (17) (2016)
Martina Fischer, Bernhard Y. Renard
iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification. Bioinform. 32 (7) (2016)
Vitor Piro, Martin S. Lindner, Bernhard Y. Renard
DUDes: a top-down taxonomic profiler for metagenomics. Bioinform. 32 (15) (2016)
Robert Rentzsch, Bernhard Y. Renard
Docking small peptides remains a great challenge: an assessment using AutoDock Vina. Briefings Bioinform. 16 (6) (2015)
Mathias Kuhring, Piotr Wojtek Dabrowski, Vitor Piro, Andreas Nitsche, Bernhard Y. Renard
SuRankCo: supervised ranking of contigs in de novo assemblies. BMC Bioinform. 16 (2015)
Franziska Zickmann, Bernhard Y. Renard
MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms. Bioinform. 31 (12) (2015)
Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard
RNA-seq driven gene identification. GCB (2014)
Anke Penzlin, Martin S. Lindner, Joerg Doellinger, Piotr Wojtek Dabrowski, Andreas Nitsche, Bernhard Y. Renard
Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics. Bioinform. 30 (12) (2014)
Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard
GIIRA - RNA-Seq driven gene finding incorporating ambiguous reads. Bioinform. 30 (5) (2014)
Sven H. Giese, Franziska Zickmann, Bernhard Y. Renard
Specificity control for read alignments using an artificial reference genome-guided false discovery rate. Bioinform. 30 (1) (2014)
Martin S. Lindner, Maximilian Kollock, Franziska Zickmann, Bernhard Y. Renard
Analyzing genome coverage profiles with applications to quality control in metagenomics. Bioinform. 29 (10) (2013)
Martin Löwer, Bernhard Y. Renard, Jos de Graaf, Meike Wagner, Claudia Paret, Christoph Kneip, Özlem Türeci, Mustafa Diken, Cedrik M. Britten, Sebastian Kreiter, Michael Koslowski, John C. Castle, Ugur Sahin
Confidence-based Somatic Mutation Evaluation and Prioritization. PLoS Comput. Biol. 8 (9) (2012)
Bernhard Y. Renard, Martin Löwer, Yvonne Kuhne, Ulf Reimer, Andree Rothermel, Özlem Türeci, John C. Castle, Ugur Sahin
rapmad: Robust Analysis of Peptide Microarray Data. BMC Bioinform. 12 (2011)
Björn Voss, Michael Hanselmann, Bernhard Y. Renard, Martin S. Lindner, Ullrich Köthe, Marc Kirchner, Fred A. Hamprecht
SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists. Bioinform. 27 (7) (2011)
Marc Kirchner, Bernhard Y. Renard, Ullrich Köthe, Darryl J. Pappin, Fred A. Hamprecht, Hanno Steen, Judith A. J. Steen
Computational protein profile similarity screening for quantitative mass spectrometry experiments. Bioinform. 26 (1) (2010)
Xinghua Lou, Marc Kirchner, Bernhard Y. Renard, Ullrich Köthe, Sebastian Boppel, Christian Graf, Chung-Tien Lee, Judith A. J. Steen, Hanno Steen, Matthias P. Mayer, Fred A. Hamprecht
Deuteration distribution estimation with improved sequence coverage for HX/MS experiments. Bioinform. 26 (12) (2010)
Michael Hanselmann, Ullrich Köthe, Bernhard Y. Renard, Marc Kirchner, Ron M. A. Heeren, Fred A. Hamprecht
Multivariate Watershed Segmentation of Compositional Data. DGCI (2009)
Bernhard Y. Renard, Marc Kirchner, Hanno Steen, Judith A. J. Steen, Fred A. Hamprecht
NITPICK: peak identification for mass spectrometry data. BMC Bioinform. 9 (2008)