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Items: 1 to 50 of 66

1.

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

Jandrasits C, Kröger S, Haas W, Renard BY.

PLoS Comput Biol. 2019 Dec 9;15(12):e1007527. doi: 10.1371/journal.pcbi.1007527. eCollection 2019 Dec.

2.

Reliable variant calling during runtime of Illumina sequencing.

Loka TP, Tausch SH, Renard BY.

Sci Rep. 2019 Nov 11;9(1):16502. doi: 10.1038/s41598-019-52991-z.

3.

Dendritic Cells Generated From Mops condylurus, a Likely Filovirus Reservoir Host, Are Susceptible to and Activated by Zaire Ebolavirus Infection.

Edenborough KM, Bokelmann M, Lander A, Couacy-Hymann E, Lechner J, Drechsel O, Renard BY, Radonić A, Feldmann H, Kurth A, Prescott J.

Front Immunol. 2019 Oct 11;10:2414. doi: 10.3389/fimmu.2019.02414. eCollection 2019.

4.

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

Seiler E, Trappe K, Renard BY.

PLoS Comput Biol. 2019 Jul 23;15(7):e1007208. doi: 10.1371/journal.pcbi.1007208. eCollection 2019 Jul.

5.

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

Bartoszewicz JM, Seidel A, Rentzsch R, Renard BY.

Bioinformatics. 2020 Jan 1;36(1):81-89. doi: 10.1093/bioinformatics/btz541.

PMID:
31298694
6.

Systems-level Analysis Reveals Multiple Modulators of Epithelial-mesenchymal Transition and Identifies DNAJB4 and CD81 as Novel Metastasis Inducers in Breast Cancer.

Uretmen Kagiali ZC, Sanal E, Karayel Ö, Polat AN, Saatci Ö, Ersan PG, Trappe K, Renard BY, Önder TT, Tuncbag N, Şahin Ö, Ozlu N.

Mol Cell Proteomics. 2019 Sep;18(9):1756-1771. doi: 10.1074/mcp.RA119.001446. Epub 2019 Jun 20.

PMID:
31221721
7.

Purple: A Computational Workflow for Strategic Selection of Peptides for Viral Diagnostics Using MS-Based Targeted Proteomics.

Lechner J, Hartkopf F, Hiort P, Nitsche A, Grossegesse M, Doellinger J, Renard BY, Muth T.

Viruses. 2019 Jun 8;11(6). pii: E536. doi: 10.3390/v11060536.

8.

Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis.

Schiebenhoefer H, Van Den Bossche T, Fuchs S, Renard BY, Muth T, Martens L.

Expert Rev Proteomics. 2019 May;16(5):375-390. doi: 10.1080/14789450.2019.1609944. Epub 2019 Apr 30.

PMID:
31002542
9.

Peptide-to-Protein Summarization: An Important Step for Accurate Quantification in Label-Based Proteomics.

Fischer M, Muth T, Renard BY.

Methods Mol Biol. 2019;1977:159-180. doi: 10.1007/978-1-4939-9232-4_11.

PMID:
30980328
10.

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

Dadi TH, Siragusa E, Piro VC, Andrusch A, Seiler E, Renard BY, Reinert K.

Bioinformatics. 2018 Sep 1;34(17):i766-i772. doi: 10.1093/bioinformatics/bty567.

PMID:
30423080
11.

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

Andrusch A, Dabrowski PW, Klenner J, Tausch SH, Kohl C, Osman AA, Renard BY, Nitsche A.

Bioinformatics. 2018 Sep 1;34(17):i715-i721. doi: 10.1093/bioinformatics/bty595.

12.

Parasitic Nematodes Exert Antimicrobial Activity and Benefit From Microbiota-Driven Support for Host Immune Regulation.

Rausch S, Midha A, Kuhring M, Affinass N, Radonic A, Kühl AA, Bleich A, Renard BY, Hartmann S.

Front Immunol. 2018 Oct 8;9:2282. doi: 10.3389/fimmu.2018.02282. eCollection 2018.

13.

Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development.

Ebner F, Kuhring M, Radonić A, Midha A, Renard BY, Hartmann S.

Front Immunol. 2018 Aug 15;9:1868. doi: 10.3389/fimmu.2018.01868. eCollection 2018.

14.

A Potential Golden Age to Come-Current Tools, Recent Use Cases, and Future Avenues for De Novo Sequencing in Proteomics.

Muth T, Hartkopf F, Vaudel M, Renard BY.

Proteomics. 2018 Sep;18(18):e1700150. doi: 10.1002/pmic.201700150. Epub 2018 Aug 22. Review.

PMID:
29968278
15.

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

Tausch SH, Strauch B, Andrusch A, Loka TP, Lindner MS, Nitsche A, Renard BY.

Bioinformatics. 2018 Nov 1;34(21):3750-3752. doi: 10.1093/bioinformatics/bty433.

PMID:
29868852
16.

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

Loka TP, Tausch SH, Dabrowski PW, Radonic A, Nitsche A, Renard BY.

Bioinformatics. 2018 Jul 15;34(14):2376-2383. doi: 10.1093/bioinformatics/bty128.

PMID:
29522157
17.

Comparative phosphoproteomic analysis reveals signaling networks regulating monopolar and bipolar cytokinesis.

Karayel Ö, Şanal E, Giese SH, Üretmen Kagıalı ZC, Polat AN, Hu CK, Renard BY, Tuncbag N, Özlü N.

Sci Rep. 2018 Feb 2;8(1):2269. doi: 10.1038/s41598-018-20231-5.

18.

seq-seq-pan: building a computational pan-genome data structure on whole genome alignment.

Jandrasits C, Dabrowski PW, Fuchs S, Renard BY.

BMC Genomics. 2018 Jan 15;19(1):47. doi: 10.1186/s12864-017-4401-3.

19.

MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go.

Muth T, Kohrs F, Heyer R, Benndorf D, Rapp E, Reichl U, Martens L, Renard BY.

Anal Chem. 2018 Jan 2;90(1):685-689. doi: 10.1021/acs.analchem.7b03544. Epub 2017 Dec 19.

20.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

21.

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

Fischer M, Strauch B, Renard BY.

Bioinformatics. 2017 Jul 15;33(14):i124-i132. doi: 10.1093/bioinformatics/btx237.

22.

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.

Piro VC, Matschkowski M, Renard BY.

Microbiome. 2017 Aug 14;5(1):101. doi: 10.1186/s40168-017-0318-y.

23.

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

Muth T, Renard BY.

Brief Bioinform. 2018 Sep 28;19(5):954-970. doi: 10.1093/bib/bbx033.

PMID:
28369237
24.

SLIMM: species level identification of microorganisms from metagenomes.

Dadi TH, Renard BY, Wieler LH, Semmler T, Reinert K.

PeerJ. 2017 Mar 28;5:e3138. doi: 10.7717/peerj.3138. eCollection 2017.

25.

PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data.

Deneke C, Rentzsch R, Renard BY.

Sci Rep. 2017 Jan 4;7:39194. doi: 10.1038/srep39194.

26.

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

Lindner MS, Strauch B, Schulze JM, Tausch SH, Dabrowski PW, Nitsche A, Renard BY.

Bioinformatics. 2017 Mar 15;33(6):917-319. doi: 10.1093/bioinformatics/btw659.

PMID:
27794555
27.

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

Trappe K, Marschall T, Renard BY.

Bioinformatics. 2016 Sep 1;32(17):i595-i604. doi: 10.1093/bioinformatics/btw423.

PMID:
27587679
28.

Metaproteomic data analysis at a glance: advances in computational microbial community proteomics.

Muth T, Renard BY, Martens L.

Expert Rev Proteomics. 2016 Aug;13(8):757-69. doi: 10.1080/14789450.2016.1209418. Epub 2016 Jul 20. Review.

PMID:
27376173
29.

DUDes: a top-down taxonomic profiler for metagenomics.

Piro VC, Lindner MS, Renard BY.

Bioinformatics. 2016 Aug 1;32(15):2272-80. doi: 10.1093/bioinformatics/btw150. Epub 2016 Mar 24.

PMID:
27153591
30.

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

Fischer M, Renard BY.

Bioinformatics. 2016 Apr 1;32(7):1040-7. doi: 10.1093/bioinformatics/btv675. Epub 2015 Nov 20.

PMID:
26589272
31.

Addition to "Phosphoproteomic Analysis of Aurora Kinase Inhibition in Monopolar Cytokinesis".

Polat AN, Karayel Ö, Giese SH, Harmanda B, Sanal E, Hu CK, Renard BY, Özlü N.

J Proteome Res. 2015 Dec 4;14(12):5408. doi: 10.1021/acs.jproteome.5b01002. Epub 2015 Nov 11. No abstract available.

PMID:
26561005
32.

Detection of Unknown Amino Acid Substitutions Using Error-Tolerant Database Search.

Giese SH, Zickmann F, Renard BY.

Methods Mol Biol. 2016;1362:247-64. doi: 10.1007/978-1-4939-3106-4_16.

PMID:
26519182
33.

First Draft Genome Sequence of Balamuthia mandrillaris, the Causative Agent of Amoebic Encephalitis.

Detering H, Aebischer T, Dabrowski PW, Radonić A, Nitsche A, Renard BY, Kiderlen AF.

Genome Announc. 2015 Sep 24;3(5). pii: e01013-15. doi: 10.1128/genomeA.01013-15.

34.

RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data.

Tausch SH, Renard BY, Nitsche A, Dabrowski PW.

PLoS One. 2015 Sep 17;10(9):e0137896. doi: 10.1371/journal.pone.0137896. eCollection 2015.

35.

Phosphoproteomic Analysis of Aurora Kinase Inhibition in Monopolar Cytokinesis.

Polat AN, Karayel Ö, Giese SH, Harmanda B, Sanal E, Hu CK, Renard BY, Özlü N.

J Proteome Res. 2015 Sep 4;14(9):4087-98. doi: 10.1021/acs.jproteome.5b00645. Epub 2015 Aug 25. Erratum in: J Proteome Res. 2015 Dec 4;14(12):5408.

PMID:
26270265
36.

SuRankCo: supervised ranking of contigs in de novo assemblies.

Kuhring M, Dabrowski PW, Piro VC, Nitsche A, Renard BY.

BMC Bioinformatics. 2015 Jul 30;16:240. doi: 10.1186/s12859-015-0644-7.

37.

Estimating the computational limits of detection of microbial non-model organisms.

Kuhring M, Renard BY.

Proteomics. 2015 Oct;15(20):3580-4. doi: 10.1002/pmic.201400598. Epub 2015 Aug 17.

PMID:
26136362
38.

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

Zickmann F, Renard BY.

Bioinformatics. 2015 Jun 15;31(12):i106-15. doi: 10.1093/bioinformatics/btv236.

39.

The Proteome of the Isolated Chlamydia trachomatis Containing Vacuole Reveals a Complex Trafficking Platform Enriched for Retromer Components.

Aeberhard L, Banhart S, Fischer M, Jehmlich N, Rose L, Koch S, Laue M, Renard BY, Schmidt F, Heuer D.

PLoS Pathog. 2015 Jun 4;11(6):e1004883. doi: 10.1371/journal.ppat.1004883. eCollection 2015 Jun.

40.

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

Rentzsch R, Renard BY.

Brief Bioinform. 2015 Nov;16(6):1045-56. doi: 10.1093/bib/bbv008. Epub 2015 Apr 21.

PMID:
25900849
41.

IPred - integrating ab initio and evidence based gene predictions to improve prediction accuracy.

Zickmann F, Renard BY.

BMC Genomics. 2015 Feb 26;16:134. doi: 10.1186/s12864-015-1315-9.

42.

Metagenomic profiling of known and unknown microbes with microbeGPS.

Lindner MS, Renard BY.

PLoS One. 2015 Feb 2;10(2):e0117711. doi: 10.1371/journal.pone.0117711. eCollection 2015.

43.

Quantitative comparison of a human cancer cell surface proteome between interphase and mitosis.

Özlü N, Qureshi MH, Toyoda Y, Renard BY, Mollaoglu G, Özkan NE, Bulbul S, Poser I, Timm W, Hyman AA, Mitchison TJ, Steen JA.

EMBO J. 2015 Jan 13;34(2):251-65. doi: 10.15252/embj.201385162. Epub 2014 Dec 4.

44.

Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a Member of the Zaïre Lineage.

Calvignac-Spencer S, Schulze JM, Zickmann F, Renard BY.

PLoS Curr. 2014 Jun 16;6. pii: ecurrents.outbreaks.c0e035c86d721668a6ad7353f7f6fe86. doi: 10.1371/currents.outbreaks.c0e035c86d721668a6ad7353f7f6fe86.

45.

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

Penzlin A, Lindner MS, Doellinger J, Dabrowski PW, Nitsche A, Renard BY.

Bioinformatics. 2014 Jun 15;30(12):i149-56. doi: 10.1093/bioinformatics/btu267.

46.

Pre- and post-processing workflow for affinity purification mass spectrometry data.

Fischer M, Zilkenat S, Gerlach RG, Wagner S, Renard BY.

J Proteome Res. 2014 May 2;13(5):2239-49. doi: 10.1021/pr401249b. Epub 2014 Apr 23.

PMID:
24641689
47.

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

Zickmann F, Lindner MS, Renard BY.

Bioinformatics. 2014 Mar 1;30(5):606-13. doi: 10.1093/bioinformatics/btt577. Epub 2013 Oct 11.

PMID:
24123675
48.

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

Giese SH, Zickmann F, Renard BY.

Bioinformatics. 2014 Jan 1;30(1):9-16. doi: 10.1093/bioinformatics/btt255. Epub 2013 May 17.

PMID:
23685787
49.

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

Lindner MS, Kollock M, Zickmann F, Renard BY.

Bioinformatics. 2013 May 15;29(10):1260-7. doi: 10.1093/bioinformatics/btt147. Epub 2013 Apr 14.

PMID:
23589648
50.

iPiG: integrating peptide spectrum matches into genome browser visualizations.

Kuhring M, Renard BY.

PLoS One. 2012;7(12):e50246. doi: 10.1371/journal.pone.0050246. Epub 2012 Dec 4.

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