Bernhard Y. Renard

According to our database, Bernhard Y. Renard authored at least 45 papers between 2008 and 2024.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2024

Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2.

Fábio Malcher Miranda, Vasco Ariston de Carvalho Azevedo, Rommel Thiago Juca Ramos, Bernhard Y. Renard, Vitor Piro

BMC Bioinform., December, 2024

The three-year evolution of Germany's Digital Therapeutics reimbursement program and its path forward.

Linea Schmidt, Marc Pawlitzki, Bernhard Y. Renard, Sven G. Meuth, Lars Masanneck

npj Digit. Medicine, 2024

Sparse Explanations of Neural Networks Using Pruned Layer-Wise Relevance Propagation.

Paulo Yanez Sarmiento, Simon Witzke, Nadja Klein, Bernhard Y. Renard

Proceedings of the Machine Learning and Knowledge Discovery in Databases. Research Track, 2024

2023

MpoxRadar: a worldwide MPXV genomic surveillance dashboard.

Ferdous Nasri, Kunaphas Kongkitimanon, Alice Wittig, Jorge Sánchez Cortés, Annika Brinkmann, Andreas Nitsche, Anna-Juliane Schmachtenberg, Bernhard Y. Renard, Stephan Fuchs

Nucleic Acids Res., July, 2023

Comprehensive evaluation of peptide <i>de novo</i> sequencing tools for monoclonal antibody assembly.

Denis Beslic, Georg Tscheuschner, Bernhard Y. Renard, Michael G. Weller, Thilo Muth

Briefings Bioinform., January, 2023

LazyFox: fast and parallelized overlapping community detection in large graphs.

Tim Garrels, Athar Khodabakhsh, Bernhard Y. Renard, Katharina Baum

PeerJ Comput. Sci., 2023

HiClass: a Python Library for Local Hierarchical Classification Compatible with Scikit-learn.

Fábio Malcher Miranda, Niklas Köhnecke, Bernhard Y. Renard

J. Mach. Learn. Res., 2023

Identifying Drivers of Predictive Uncertainty using Variance Feature Attribution.

Pascal Iversen, Simon Witzke, Katharina Baum, Bernhard Y. Renard

CoRR, 2023

Evaluating Tuning Strategies for Sequence Generation with Protein Language Models.

Andrea Nathansen, Kevin Klein, Bernhard Y. Renard, Melania Nowicka, Jakub M. Bartoszewicz

Proceedings of the Machine Learning in Computational Biology, November 30, 2023

SimbaML: Connecting Mechanistic Models and Machine Learning with Augmented Data.

Maximilian Kleissl, Lukas Drews, Benedict B. Heyder, Julian Zabbarov, Pascal Iversen, Simon Witzke, Bernhard Y. Renard, Katharina Baum

Proceedings of the First Tiny Papers Track at ICLR 2023, 2023

2022

Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides.

Tom Altenburg, Sven H. Giese, Shengbo Wang, Thilo Muth, Bernhard Y. Renard

Nat. Mach. Intell., 2022

CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance.

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

Bioinform., 2022

2021

Deep learning-based real-time detection of novel pathogens during sequencing.

Jakub M. Bartoszewicz, Ulrich Genske, Bernhard Y. Renard

Briefings Bioinform., 2021

2020

An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action.

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

F1000Research, 2020

An Environment for Sustainable Research Software in Germany and Beyond: Current State, Open Challenges, and Call for Action.

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 Uekermann, Stefan Unger, Rudolf Weeber

CoRR, 2020

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences.

Vitor Piro, Temesgen Hailemariam Dadi, Enrico Seiler, Knut Reinert, Bernhard Y. Renard

Bioinform., 2020

DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks.

Jakub M. Bartoszewicz, Anja Seidel, Robert Rentzsch, Bernhard Y. Renard

Bioinform., 2020

Predicting bacterial virulence factors - evaluation of machine learning and negative data strategies.

Robert Rentzsch, Carlus Deneke, Andreas Nitsche, Bernhard Y. Renard

Briefings Bioinform., 2020

2019

Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation.

Enrico Seiler, Kathrin Trappe, Bernhard Y. Renard

PLoS Comput. Biol., 2019

Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.

Christine Jandrasits, Stefan Kröger, Walter Haas, Bernhard Y. Renard

PLoS Comput. Biol., 2019

2018

LiveKraken--real-time metagenomic classification of illumina data.

Simon H. Tausch, Benjamin Strauch, Andreas Andrusch, Tobias P. Loka, Martin S. Lindner, Andreas Nitsche, Bernhard Y. Renard

Bioinform., 2018

PriLive: privacy-preserving real-time filtering for next-generation sequencing.

Tobias P. Loka, Simon H. Tausch, Piotr Wojtek Dabrowski, Aleksandar Radonic, Andreas Nitsche, Bernhard Y. Renard

Bioinform., 2018

DREAM-Yara: an exact read mapper for very large databases with short update time.

Temesgen Hailemariam Dadi, Enrico Siragusa, Vitor Piro, Andreas Andrusch, Enrico Seiler, Bernhard Y. Renard, Knut Reinert

Bioinform., 2018

PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples.

Andreas Andrusch, Piotr Wojtek Dabrowski, Jeanette Klenner, Simon H. Tausch, Claudia Kohl, Abdalla Osman, Bernhard Y. Renard, Andreas Nitsche

Bioinform., 2018

Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification?

Thilo Muth, Bernhard Y. Renard

Briefings Bioinform., 2018

2017

HiLive: real-time mapping of illumina reads while sequencing.

Martin S. Lindner, Benjamin Strauch, Jakob M. Schulze, Simon H. Tausch, Piotr Wojtek Dabrowski, Andreas Nitsche, Bernhard Y. Renard

Bioinform., 2017

Abundance estimation and differential testing on strain level in metagenomics data.

Martina Fischer, Benjamin Strauch, Bernhard Y. Renard

Bioinform., 2017

2016

Detecting horizontal gene transfer by mapping sequencing reads across species boundaries.

Kathrin Trappe, Tobias Marschall, Bernhard Y. Renard

Bioinform., 2016

DUDes: a top-down taxonomic profiler for metagenomics.

Vitor Piro, Martin S. Lindner, Bernhard Y. Renard

Bioinform., 2016

iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification.

Martina Fischer, Bernhard Y. Renard

Bioinform., 2016

2015

SuRankCo: supervised ranking of contigs in de novo assemblies.

Mathias Kuhring, Piotr Wojtek Dabrowski, Vitor Piro, Andreas Nitsche, Bernhard Y. Renard

BMC Bioinform., 2015

MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms.

Franziska Zickmann, Bernhard Y. Renard

Bioinform., 2015

Docking small peptides remains a great challenge: an assessment using AutoDock Vina.

Robert Rentzsch, Bernhard Y. Renard

Briefings Bioinform., 2015

2014

GIIRA - RNA-Seq driven gene finding incorporating ambiguous reads.

Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard

Bioinform., 2014

Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics.

Anke Penzlin, Martin S. Lindner, Joerg Doellinger, Piotr Wojtek Dabrowski, Andreas Nitsche, Bernhard Y. Renard

Bioinform., 2014

Specificity control for read alignments using an artificial reference genome-guided false discovery rate.

Sven H. Giese, Franziska Zickmann, Bernhard Y. Renard

Bioinform., 2014

RNA-seq driven gene identification.

Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard

Proceedings of the German conference on bioinformatics 2014, September 28, 2014

2013

Analyzing genome coverage profiles with applications to quality control in metagenomics.

Martin S. Lindner, Maximilian Kollock, Franziska Zickmann, Bernhard Y. Renard

Bioinform., 2013

2012

Confidence-based Somatic Mutation Evaluation and Prioritization.

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

PLoS Comput. Biol., 2012

2011

rapmad: Robust Analysis of Peptide Microarray Data.

Bernhard Y. Renard, Martin Löwer, Yvonne Kuhne, Ulf Reimer, Andree Rothermel, Özlem Türeci, John C. Castle, Ugur Sahin

BMC Bioinform., 2011

SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists.

Björn Voss, Michael Hanselmann, Bernhard Y. Renard, Martin S. Lindner, Ullrich Köthe, Marc Kirchner, Fred A. Hamprecht

Bioinform., 2011

2010

Deuteration distribution estimation with improved sequence coverage for HX/MS experiments.

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

Bioinform., 2010

Computational protein profile similarity screening for quantitative mass spectrometry experiments.

Marc Kirchner, Bernhard Y. Renard, Ullrich Köthe, Darryl J. Pappin, Fred A. Hamprecht, Hanno Steen, Judith A. J. Steen

Bioinform., 2010

2009

Multivariate Watershed Segmentation of Compositional Data.

Michael Hanselmann, Ullrich Köthe, Bernhard Y. Renard, Marc Kirchner, Ron M. A. Heeren, Fred A. Hamprecht

Proceedings of the Discrete Geometry for Computer Imagery, 2009

2008

NITPICK: peak identification for mass spectrometry data.

Bernhard Y. Renard, Marc Kirchner, Hanno Steen, Judith A. J. Steen, Fred A. Hamprecht

BMC Bioinform., 2008