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Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.

Bioinformatics 2019 Oct 12. Epub 2019 Oct 12.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btz736DOI Listing
October 2019

Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment.

Environ Microbiol Rep 2019 08 12;11(4):487-494. Epub 2018 Sep 12.

Natural History Museum, University of Tartu, 14A Ravila, 50411, Tartu, Estonia.

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http://dx.doi.org/10.1111/1758-2229.12684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6618113PMC
August 2019

Interactive Tree Of Life (iTOL) v4: recent updates and new developments.

Nucleic Acids Res 2019 Jul;47(W1):W256-W259

EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gkz239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602468PMC
July 2019

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.

Microbiome 2019 06 3;7(1):84. Epub 2019 Jun 3.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1186/s40168-019-0684-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547473PMC
June 2019

Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology.

Gut 2019 Jun 15. Epub 2019 Jun 15.

Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1136/gutjnl-2019-319045DOI Listing
June 2019

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals.

Cell 2019 May 25;177(5):1308-1318.e10. Epub 2019 Apr 25.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Max Delbrück Center for Molecular Medicine, Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.03.015DOI Listing
May 2019

Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.

Curr Biol 2019 May 9;29(10):1712-1720.e7. Epub 2019 May 9.

Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2019.04.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6538971PMC
May 2019

iPath3.0: interactive pathways explorer v3.

Nucleic Acids Res 2018 07;46(W1):W510-W513

Department of Biological Information, Tokyo Institute of Technology, Tokyo 152-8550, Japan.

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http://dx.doi.org/10.1093/nar/gky299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031023PMC
July 2018

Quantifying compartment-associated variations of protein abundance in proteomics data.

Mol Syst Biol 2018 07 2;14(7):e8131. Epub 2018 Jul 2.

Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany

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http://dx.doi.org/10.15252/msb.20178131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056770PMC
July 2018

The Human Gut Microbiome: From Association to Modulation.

Cell 2018 03;172(6):1198-1215

European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.02.044DOI Listing
March 2018

Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.

Cell 2018 03 15;173(1):208-220.e20. Epub 2018 Mar 15.

Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.02.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5871717PMC
March 2018

Bioinformatics Analysis of Functional Associations of PTMs.

Methods Mol Biol 2017 ;1558:303-320

European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany.

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http://dx.doi.org/10.1007/978-1-4939-6783-4_14DOI Listing
February 2018

20 years of the SMART protein domain annotation resource.

Nucleic Acids Res 2018 01;46(D1):D493-D496

EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gkx922DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753352PMC
January 2018

MVP: a microbe-phage interaction database.

Nucleic Acids Res 2018 01;46(D1):D700-D707

Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China.

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http://dx.doi.org/10.1093/nar/gkx1124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753265PMC
January 2018

Subspecies in the global human gut microbiome.

Mol Syst Biol 2017 12 14;13(12):960. Epub 2017 Dec 14.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5740502PMC
http://dx.doi.org/10.15252/msb.20177589DOI Listing
December 2017

metaSNV: A tool for metagenomic strain level analysis.

PLoS One 2017 28;12(7):e0182392. Epub 2017 Jul 28.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182392PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533426PMC
October 2017

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.

Elife 2017 10 31;6. Epub 2017 Oct 31.

UMR 7144, team EPEP, Station Biologique de Roscoff, Centre Nationnal de la Recherche Scientifique, Roscoff, France.

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http://dx.doi.org/10.7554/eLife.26066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5663481PMC
October 2017

RTK: efficient rarefaction analysis of large datasets.

Bioinformatics 2017 Aug;33(16):2594-2595

Structural & Computational Biology Unit, EMBL, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btx206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870771PMC
August 2017

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.

Mol Biol Evol 2017 08;34(8):2115-2122

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1093/molbev/msx148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850834PMC
August 2017

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis.

Am J Physiol Gastrointest Liver Physiol 2017 Apr 30;312(4):G327-G339. Epub 2016 Dec 30.

Children's Hospital, University Medical Center, Johannes Gutenberg University, Mainz, Germany;

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http://dx.doi.org/10.1152/ajpgi.00293.2016DOI Listing
April 2017

Metabolic anchor reactions for robust biorefining.

Metab Eng 2017 03 21;40:1-4. Epub 2017 Feb 21.

European Molecular Biology Laboratory, Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ymben.2017.02.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5368410PMC
March 2017

GEAR: A database of Genomic Elements Associated with drug Resistance.

Sci Rep 2017 03 15;7:44085. Epub 2017 Mar 15.

Department of Computer Science and Technology, Tongji University, Shanghai 201804, China.

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http://dx.doi.org/10.1038/srep44085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5353689PMC
March 2017

Systematic identification of phosphorylation-mediated protein interaction switches.

PLoS Comput Biol 2017 03 27;13(3):e1005462. Epub 2017 Mar 27.

CellNetworks, Bioquant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1005462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386296PMC
March 2017

[Microbial Biomarkers for Early Cancer Detection].

Dtsch Med Wochenschr 2017 Feb 24;142(4):267-274. Epub 2017 Feb 24.

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http://dx.doi.org/10.1055/s-0042-110193DOI Listing
February 2017

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.

Nucleic Acids Res 2017 01 30;45(D1):D940-D944. Epub 2016 Oct 30.

European molecular biology laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gkw1013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210522PMC
January 2017

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Nucleic Acids Res 2017 01 18;45(D1):D362-D368. Epub 2016 Oct 18.

Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland

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http://dx.doi.org/10.1093/nar/gkw937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210637PMC
January 2017

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

Nucleic Acids Res 2017 01 24;45(D1):D529-D534. Epub 2016 Oct 24.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany

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http://dx.doi.org/10.1093/nar/gkw989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210662PMC
January 2017

Global genetic capacity for mixotrophy in marine picocyanobacteria.

ISME J 2016 12 3;10(12):2946-2957. Epub 2016 May 3.

Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/ismej.2016.64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5148188PMC
December 2016

The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.

J Cell Biol 2016 Nov 8;215(4):543-558. Epub 2016 Nov 8.

Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany

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http://dx.doi.org/10.1083/jcb.201601090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119934PMC
November 2016

CART-a chemical annotation retrieval toolkit.

Bioinformatics 2016 09 2;32(18):2869-71. Epub 2016 Jun 2.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, Berlin, Germany Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btw233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018367PMC
September 2016

MOCAT2: a metagenomic assembly, annotation and profiling framework.

Bioinformatics 2016 08 8;32(16):2520-3. Epub 2016 Apr 8.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btw183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978931PMC
August 2016

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.

Nucleic Acids Res 2016 07 19;44(W1):W242-5. Epub 2016 Apr 19.

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gkw290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987883PMC
July 2016

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.

Mol Biol Evol 2016 06 26;33(6):1635-8. Epub 2016 Feb 26.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.

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http://dx.doi.org/10.1093/molbev/msw046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868116PMC
June 2016

A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.

Nat Protoc 2016 06 5;11(6):1021-38. Epub 2016 May 5.

European Molecular Biology Laboratory (EMBL) Structural and Computational Biology Unit, Heidelberg, Germany.

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http://dx.doi.org/10.1038/nprot.2016.059DOI Listing
June 2016

Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

Nat Commun 2016 Apr 21;7:11334. Epub 2016 Apr 21.

Institute for Computer Science and Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf 40225, Germany.

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http://dx.doi.org/10.1038/ncomms11334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844684PMC
April 2016

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

Science 2016 Apr;352(6285):586-9

Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany. Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany. Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.

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http://dx.doi.org/10.1126/science.aad8852DOI Listing
April 2016

Bacterial antisense RNAs are mainly the product of transcriptional noise.

Sci Adv 2016 Mar 4;2(3):e1501363. Epub 2016 Mar 4.

EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.

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http://dx.doi.org/10.1126/sciadv.1501363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783119PMC
March 2016

Spatiotemporal variation of mammalian protein complex stoichiometries.

Genome Biol 2016 Mar 14;17:47. Epub 2016 Mar 14.

European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.

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http://dx.doi.org/10.1186/s13059-016-0912-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791834PMC
March 2016

Gut Microbiota Linked to Sexual Preference and HIV Infection.

EBioMedicine 2016 Mar 28;5:135-46. Epub 2016 Jan 28.

IrsiCaixa AIDS Research Institute, Ctra de Canyet s/n, 08916 Badalona, Catalonia, Spain; Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500 Vic, Catalonia, Spain; Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain; HIV Unit & Lluita Contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Ctra de Canyet s/n, 08916 Badalona, Catalonia, Spain.

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http://dx.doi.org/10.1016/j.ebiom.2016.01.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816837PMC
March 2016

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.

Nucleic Acids Res 2016 Feb 14;44(3):1192-202. Epub 2016 Jan 14.

European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany Max-Delbrück-Centre (MDC) for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany

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http://dx.doi.org/10.1093/nar/gkw004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756857PMC
February 2016

The exploration of network motifs as potential drug targets from post-translational regulatory networks.

Sci Rep 2016 Feb 8;6:20558. Epub 2016 Feb 8.

Department of Computer Science and Technology, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China.

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http://dx.doi.org/10.1038/srep20558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744934PMC
February 2016

The SIDER database of drugs and side effects.

Nucleic Acids Res 2016 Jan 19;44(D1):D1075-9. Epub 2015 Oct 19.

European Molecular Biology Laboratory, Structural and Computational Biology Unit, Molecular Medicine Partnership Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany

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http://dx.doi.org/10.1093/nar/gkv1075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702794PMC
January 2016

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

Nucleic Acids Res 2016 Jan 17;44(D1):D286-93. Epub 2015 Nov 17.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg 69117, Germany Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany

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http://nar.oxfordjournals.org/content/early/2015/11/17/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1248
Publisher Site
http://dx.doi.org/10.1093/nar/gkv1248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702882PMC
January 2016

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.

Nucleic Acids Res 2016 Jan 20;44(D1):D380-4. Epub 2015 Nov 20.

Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden

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http://dx.doi.org/10.1093/nar/gkv1277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702904PMC
January 2016

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.

Nat Commun 2016 Jan 26;7:10410. Epub 2016 Jan 26.

Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Haartmaninkatu 3, PO Box 21, 00014 Helsinki, Finland.

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http://dx.doi.org/10.1038/ncomms10410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737757PMC
January 2016

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.

Cell Syst 2015 Sep 17;1(3):224-37. Epub 2015 Sep 17.

European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2015.08.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4802414PMC
September 2015