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2020 – today
- 2024
[j37]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): 228 (2024)- [j36]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) - [c5]Paulo Yanez Sarmiento, Simon Witzke, Nadja Klein, Bernhard Y. Renard:
Sparse Explanations of Neural Networks Using Pruned Layer-Wise Relevance Propagation. ECML/PKDD (4) 2024: 336-351 - [i7]Paulo Yanez Sarmiento, Simon Witzke, Nadja Klein, Bernhard Y. Renard:
Sparse Explanations of Neural Networks Using Pruned Layer-Wise Relevance Propagation. CoRR abs/2404.14271 (2024) - 2023
- [j35]Denis Beslic, Georg Tscheuschner, Bernhard Y. Renard, Michael G. Weller, Thilo Muth:
Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly. Briefings Bioinform. 24(1) (2023) - [j34]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: 29:1-29:17 (2023) - [j33]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): 331-337 (2023) - [j32]Tim Garrels, Athar Khodabakhsh, Bernhard Y. Renard, Katharina Baum:
LazyFox: fast and parallelized overlapping community detection in large graphs. PeerJ Comput. Sci. 9: e1291 (2023) - [c4]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 - [c3]Andrea Nathansen, Kevin Klein, Bernhard Y. Renard, Melania Nowicka, Jakub M. Bartoszewicz:
Evaluating Tuning Strategies for Sequence Generation with Protein Language Models. MLCB 2023: 76-89 - [i6]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 abs/2304.04000 (2023) - [i5]Pascal Iversen, Simon Witzke, Katharina Baum, Bernhard Y. Renard:
Identifying Drivers of Predictive Uncertainty using Variance Feature Attribution. CoRR abs/2312.07252 (2023) - 2022
- [j31]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): 4223-4225 (2022) - [j30]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): 378-388 (2022) - [i4]Tim Garrels, Athar Khodabakhsh, Bernhard Y. Renard, Katharina Baum:
LazyFox: Fast and parallelized overlapping community detection in large graphs. CoRR abs/2210.03211 (2022) - 2021
- [j29]Jakub M. Bartoszewicz, Ulrich Genske, Bernhard Y. Renard:
Deep learning-based real-time detection of novel pathogens during sequencing. Briefings Bioinform. 22(6) (2021) - [i3]Fábio Malcher Miranda, Niklas Köhnecke, Bernhard Y. Renard:
HiClass: a Python library for local hierarchical classification compatible with scikit-learn. CoRR abs/2112.06560 (2021) - 2020
- [j28]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): 1596-1608 (2020) - [j27]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): 81-89 (2020) - [j26]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): i12-i20 (2020) - [i2]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:
An Environment for Sustainable Research Software in Germany and Beyond: Current State, Open Challenges, and Call for Action. CoRR abs/2005.01469 (2020) - [i1]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: 295 (2020)
2010 – 2019
- 2019
- [j25]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) - [j24]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) - 2018
- [j23]Thilo Muth, Bernhard Y. Renard:
Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? Briefings Bioinform. 19(5): 954-970 (2018) - [j22]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): 2376-2383 (2018) - [j21]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): i715-i721 (2018) - [j20]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): i766-i772 (2018) - [j19]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): 3750-3752 (2018) - 2017
- [j18]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): 917 (2017) - [j17]Martina Fischer, Benjamin Strauch, Bernhard Y. Renard:
Abundance estimation and differential testing on strain level in metagenomics data. Bioinform. 33(14): i124-i132 (2017) - 2016
- [j16]Martina Fischer, Bernhard Y. Renard:
iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification. Bioinform. 32(7): 1040-1047 (2016) - [j15]Vitor Piro, Martin S. Lindner, Bernhard Y. Renard:
DUDes: a top-down taxonomic profiler for metagenomics. Bioinform. 32(15): 2272-2280 (2016) - [j14]Kathrin Trappe, Tobias Marschall, Bernhard Y. Renard:
Detecting horizontal gene transfer by mapping sequencing reads across species boundaries. Bioinform. 32(17): 595-604 (2016) - 2015
- [j13]Robert Rentzsch, Bernhard Y. Renard:
Docking small peptides remains a great challenge: an assessment using AutoDock Vina. Briefings Bioinform. 16(6): 1045-1056 (2015) - [j12]Franziska Zickmann, Bernhard Y. Renard:
MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms. Bioinform. 31(12): 106-115 (2015) - [j11]Mathias Kuhring, Piotr Wojtek Dabrowski, Vitor Piro, Andreas Nitsche, Bernhard Y. Renard:
SuRankCo: supervised ranking of contigs in de novo assemblies. BMC Bioinform. 16: 240:1-240:7 (2015) - 2014
- [j10]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): 9-16 (2014) - [j9]Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard:
GIIRA - RNA-Seq driven gene finding incorporating ambiguous reads. Bioinform. 30(5): 606-613 (2014) - [j8]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): 149-156 (2014) - [c2]Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard:
RNA-seq driven gene identification. GCB 2014: 36-40 - 2013
- [j7]Martin S. Lindner, Maximilian Kollock, Franziska Zickmann, Bernhard Y. Renard:
Analyzing genome coverage profiles with applications to quality control in metagenomics. Bioinform. 29(10): 1260-1267 (2013) - 2012
- [j6]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) - 2011
- [j5]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): 987-993 (2011) - [j4]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: 324 (2011) - 2010
- [j3]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): 77-83 (2010) - [j2]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): 1535-1541 (2010)
2000 – 2009
- 2009
- [c1]Michael Hanselmann, Ullrich Köthe, Bernhard Y. Renard, Marc Kirchner, Ron M. A. Heeren, Fred A. Hamprecht:
Multivariate Watershed Segmentation of Compositional Data. DGCI 2009: 180-192 - 2008
- [j1]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)
Coauthor Index
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