Bernhard Y. Renard

57 papers A* 1C 1Journal 50Unranked 5

Year	Rank	Type	Title / Venue / Authors
2025	C	`conf`	CombDNF: Disease-Specific drug combination predictions with network-based features on clinically validated data. CIBCB Pauline Hiort, Bernhard Y. Renard, Katharina Baum
2025	J	`jnl`	Electronic Health Records-based identification of newly diagnosed Crohn's Disease cases. Artif. Intell. Medicine Susanne Ibing, Julian Hugo, Florian Borchert, Linea Schmidt, Caroline Benson, Allison A. Marshall, Colleen Chasteau, Ujunwa Korie, Diana Paguay, Jan-Philipp Sachs, Bernhard Y. Renard, Judy H. Cho, Erwin P. Böttinger, Ryan C. Ungaro
2025	J	`jnl`	End-to-end simulation of nanopore sequencing signals with feed-forward transformers. Bioinform. Denis Beslic, Martin Kucklick, Susanne Engelmann, Stephan Fuchs, Bernhard Y. Renard, Nils Körber
2025	A*	`conf`	Identifying Drivers of Predictive Aleatoric Uncertainty. IJCAI Pascal Iversen, Simon Witzke, Katharina Baum, Bernhard Y. Renard
2024	J	`jnl`	Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2. BMC Bioinform. Fábio Malcher Miranda, Vasco Ariston de Carvalho Azevedo, Rommel Thiago Juca Ramos, Bernhard Y. Renard, Vitor Piro
2024	J	`jnl`	PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks. Bioinform. Tobias Pietz, Sukrit Gupta, Christoph N. Schlaffner, Saima Ahmed, Hanno Steen, Bernhard Y. Renard, Katharina Baum
2024	—	`conf`	Sparse Explanations of Neural Networks Using Pruned Layer-Wise Relevance Propagation. ECML/PKDD (4) Paulo Yanez Sarmiento, Simon Witzke, Nadja Klein, Bernhard Y. Renard
2024	J	`jnl`	Sparse Explanations of Neural Networks Using Pruned Layer-Wise Relevance Propagation. CoRR Paulo Yanez Sarmiento, Simon Witzke, Nadja Klein, Bernhard Y. Renard
2024	J	`jnl`	The three-year evolution of Germany's Digital Therapeutics reimbursement program and its path forward. npj Digit. Medicine Linea Schmidt, Marc Pawlitzki, Bernhard Y. Renard, Sven G. Meuth, Lars Masanneck
2023	J	`jnl`	Comprehensive evaluation of peptide Briefings Bioinform. Denis Beslic, Georg Tscheuschner, Bernhard Y. Renard, Michael G. Weller, Thilo Muth
2023	—	`conf`	Evaluating Tuning Strategies for Sequence Generation with Protein Language Models. MLCB Andrea Nathansen, Kevin Klein, Bernhard Y. Renard, Melania Nowicka, Jakub M. Bartoszewicz
2023	J	`jnl`	HiClass: a Python Library for Local Hierarchical Classification Compatible with Scikit-learn. J. Mach. Learn. Res. Fábio Malcher Miranda, Niklas Köhnecke, Bernhard Y. Renard
2023	J	`jnl`	Identifying Drivers of Predictive Uncertainty using Variance Feature Attribution. CoRR Pascal Iversen, Simon Witzke, Katharina Baum, Bernhard Y. Renard
2023	J	`jnl`	LazyFox: fast and parallelized overlapping community detection in large graphs. PeerJ Comput. Sci. Tim Garrels, Athar Khodabakhsh, Bernhard Y. Renard, Katharina Baum
2023	J	`jnl`	MpoxRadar: a worldwide MPXV genomic surveillance dashboard. Nucleic Acids Res. Ferdous Nasri, Kunaphas Kongkitimanon, Alice Wittig, Jorge Sánchez Cortés, Annika Brinkmann, Andreas Nitsche, Anna-Juliane Schmachtenberg, Bernhard Y. Renard, Stephan Fuchs
2023	—	`conf`	SimbaML: Connecting Mechanistic Models and Machine Learning with Augmented Data. Tiny Papers @ ICLR Maximilian Kleissl, Lukas Drews, Benedict B. Heyder, Julian Zabbarov, Pascal Iversen, Simon Witzke, Bernhard Y. Renard, Katharina Baum
2023	J	`jnl`	SimbaML: Connecting Mechanistic Models and Machine Learning with Augmented Data. CoRR Maximilian Kleissl, Lukas Drews, Benedict B. Heyder, Julian Zabbarov, Pascal Iversen, Simon Witzke, Bernhard Y. Renard, Katharina Baum
2022	J	`jnl`	Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides. Nat. Mach. Intell. Tom Altenburg, Sven H. Giese, Shengbo Wang, Thilo Muth, Bernhard Y. Renard
2022	J	`jnl`	CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance. Bioinform. 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
2022	J	`jnl`	Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection. Bioinform. Jakub M. Bartoszewicz, Ferdous Nasri, Melania Nowicka, Bernhard Y. Renard
2022	J	`jnl`	DrDimont: explainable drug response prediction from differential analysis of multi-omics networks. Bioinform. Pauline Hiort, Julian Hugo, Justus Zeinert, Nataniel Müller, Spoorthi Kashyap, Jagath C. Rajapakse, Francisco Azuaje, Bernhard Y. Renard, Katharina Baum
2022	J	`jnl`	LazyFox: Fast and parallelized overlapping community detection in large graphs. CoRR Tim Garrels, Athar Khodabakhsh, Bernhard Y. Renard, Katharina Baum
2022	J	`jnl`	ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing. Bioinform. Jens-Uwe Ulrich, Ahmad Lutfi, Kilian Rutzen, Bernhard Y. Renard
2021	J	`jnl`	Deep learning-based real-time detection of novel pathogens during sequencing. Briefings Bioinform. Jakub M. Bartoszewicz, Ulrich Genske, Bernhard Y. Renard
2021	J	`jnl`	HiClass: a Python library for local hierarchical classification compatible with scikit-learn. CoRR Fábio Malcher Miranda, Niklas Köhnecke, Bernhard Y. Renard
2020	J	`jnl`	An Environment for Sustainable Research Software in Germany and Beyond: Current State, Open Challenges, and Call for Action. CoRR 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
2020	J	`jnl`	An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action. F1000Research 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
2020	J	`jnl`	DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks. Bioinform. Jakub M. Bartoszewicz, Anja Seidel, Robert Rentzsch, Bernhard Y. Renard
2020	J	`jnl`	Predicting bacterial virulence factors - evaluation of machine learning and negative data strategies. Briefings Bioinform. Robert Rentzsch, Carlus Deneke, Andreas Nitsche, Bernhard Y. Renard
2020	J	`jnl`	ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinform. Vitor Piro, Temesgen Hailemariam Dadi, Enrico Seiler, Knut Reinert, Bernhard Y. Renard
2019	J	`jnl`	Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters. PLoS Comput. Biol. Christine Jandrasits, Stefan Kröger, Walter Haas, Bernhard Y. Renard
2019	J	`jnl`	Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation. PLoS Comput. Biol. Enrico Seiler, Kathrin Trappe, Bernhard Y. Renard
2018	J	`jnl`	DREAM-Yara: an exact read mapper for very large databases with short update time. Bioinform. Temesgen Hailemariam Dadi, Enrico Siragusa, Vitor Piro, Andreas Andrusch, Enrico Seiler, Bernhard Y. Renard, Knut Reinert
2018	J	`jnl`	Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? Briefings Bioinform. Thilo Muth, Bernhard Y. Renard
2018	J	`jnl`	LiveKraken--real-time metagenomic classification of illumina data. Bioinform. Simon H. Tausch, Benjamin Strauch, Andreas Andrusch, Tobias P. Loka, Martin S. Lindner, Andreas Nitsche, Bernhard Y. Renard
2018	J	`jnl`	PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples. Bioinform. Andreas Andrusch, Piotr Wojtek Dabrowski, Jeanette Klenner, Simon H. Tausch, Claudia Kohl, Abdalla Osman, Bernhard Y. Renard, Andreas Nitsche
2018	J	`jnl`	PriLive: privacy-preserving real-time filtering for next-generation sequencing. Bioinform. Tobias P. Loka, Simon H. Tausch, Piotr Wojtek Dabrowski, Aleksandar Radonic, Andreas Nitsche, Bernhard Y. Renard
2017	J	`jnl`	Abundance estimation and differential testing on strain level in metagenomics data. Bioinform. Martina Fischer, Benjamin Strauch, Bernhard Y. Renard
2017	J	`jnl`	HiLive: real-time mapping of illumina reads while sequencing. Bioinform. Martin S. Lindner, Benjamin Strauch, Jakob M. Schulze, Simon H. Tausch, Piotr Wojtek Dabrowski, Andreas Nitsche, Bernhard Y. Renard
2016	J	`jnl`	DUDes: a top-down taxonomic profiler for metagenomics. Bioinform. Vitor Piro, Martin S. Lindner, Bernhard Y. Renard
2016	J	`jnl`	Detecting horizontal gene transfer by mapping sequencing reads across species boundaries. Bioinform. Kathrin Trappe, Tobias Marschall, Bernhard Y. Renard
2016	J	`jnl`	iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification. Bioinform. Martina Fischer, Bernhard Y. Renard
2015	J	`jnl`	Docking small peptides remains a great challenge: an assessment using AutoDock Vina. Briefings Bioinform. Robert Rentzsch, Bernhard Y. Renard
2015	J	`jnl`	MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms. Bioinform. Franziska Zickmann, Bernhard Y. Renard
2015	J	`jnl`	SuRankCo: supervised ranking of contigs in de novo assemblies. BMC Bioinform. Mathias Kuhring, Piotr Wojtek Dabrowski, Vitor Piro, Andreas Nitsche, Bernhard Y. Renard
2014	J	`jnl`	GIIRA - RNA-Seq driven gene finding incorporating ambiguous reads. Bioinform. Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard
2014	J	`jnl`	Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics. Bioinform. Anke Penzlin, Martin S. Lindner, Joerg Doellinger, Piotr Wojtek Dabrowski, Andreas Nitsche, Bernhard Y. Renard
2014	—	`conf`	RNA-seq driven gene identification. GCB Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard
2014	J	`jnl`	Specificity control for read alignments using an artificial reference genome-guided false discovery rate. Bioinform. Sven H. Giese, Franziska Zickmann, Bernhard Y. Renard
2013	J	`jnl`	Analyzing genome coverage profiles with applications to quality control in metagenomics. Bioinform. Martin S. Lindner, Maximilian Kollock, Franziska Zickmann, Bernhard Y. Renard
2012	J	`jnl`	Confidence-based Somatic Mutation Evaluation and Prioritization. PLoS Comput. Biol. 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
2011	J	`jnl`	SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists. Bioinform. Björn Voss, Michael Hanselmann, Bernhard Y. Renard, Martin S. Lindner, Ullrich Köthe, Marc Kirchner, Fred A. Hamprecht
2011	J	`jnl`	rapmad: Robust Analysis of Peptide Microarray Data. BMC Bioinform. Bernhard Y. Renard, Martin Löwer, Yvonne Kuhne, Ulf Reimer, Andree Rothermel, Özlem Türeci, John C. Castle, Ugur Sahin
2010	J	`jnl`	Computational protein profile similarity screening for quantitative mass spectrometry experiments. Bioinform. Marc Kirchner, Bernhard Y. Renard, Ullrich Köthe, Darryl J. Pappin, Fred A. Hamprecht, Hanno Steen, Judith A. J. Steen
2010	J	`jnl`	Deuteration distribution estimation with improved sequence coverage for HX/MS experiments. Bioinform. 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
2009	—	`conf`	Multivariate Watershed Segmentation of Compositional Data. DGCI Michael Hanselmann, Ullrich Köthe, Bernhard Y. Renard, Marc Kirchner, Ron M. A. Heeren, Fred A. Hamprecht
2008	J	`jnl`	NITPICK: peak identification for mass spectrometry data. BMC Bioinform. Bernhard Y. Renard, Marc Kirchner, Hanno Steen, Judith A. J. Steen, Fred A. Hamprecht