EMBL MDC, Berlin-Buch

Deciphering function and evolution of biological systems

The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales:

  • genes and proteins,

  • protein networks and cellular processes, and

  • phenotypes and environments.

They require both tool development and applications. Some selected  projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes.

The group is partially associated with Max Delbrück Center for Molecular Medicine (MDC), Berlin.

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Selected publications and News
Towards the biogeography of prokaryotic genes.
Coelho LP, Alves R, Del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, Pan S, Jia L, Ferretti P, Sunagawa S, Zhao XM, Nielsen HB, Huerta-Cepas J, Bork P
Nature 2021 Dec 15; [Epub ahead of print], 10.1038/s41586-021-04233-4
Combinatorial, additive and dose-dependent drug-microbiome associations.
Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, Markó L, Aron-Wisnewsky J, Nielsen T, Moitinho-Silva L, Schmidt TSB, Falony G, Vieira-Silva S, Adriouch S, Alves RJ, Assmann K, Bastard JP, Birkner T, Caesar R, Chilloux J, Coelho LP, Fezeu L, Galleron N, Helft G, Isnard R, Ji B, Kuhn M, Le Chatelier E, Myridakis A, Olsson L, Pons N, Prifti E, Quinquis B, Roume H, Salem JE, Sokolovska N, Tremaroli V, Valles-Colomer M, Lewinter C, Sřndertoft NB, Pedersen HK, Hansen TH, MetaCardis Consortium , Gřtze JP, Křber L, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Oppert JM, Letunic I, Nielsen J, Bäckhed F, Ehrlich SD, Dumas ME, Raes J, Pedersen O, Clément K, Stumvoll M, Bork P
Nature 2021 Dec;600(7889):500-505, 10.1038/s41586-021-04177-9
Unravelling the collateral damage of antibiotics on gut bacteria.
Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, Müller P, Garcia-Santamarina S, Cacace E, Zhang B, Gekeler C, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KR, Zimmermann M, Stecher B, Zeller G, Bork P, Typas A
Nature 2021 Nov 13; 599(7883): 120-124, 10.1038/s41586-021-03986-2
Bioaccumulation of therapeutic drugs by human gut bacteria.
Klünemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, Hövelmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR
Nature 2021 Sep, 597(7877): 533-538, DOI: 10.1038/s41579-020-0368-1
Dispersal strategies shape persistence and evolution of human gut bacteria.
Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P
Cell Host Microbe 2021 07 14; 29(7): 1167-1176.e9. , DOI: 10.1016/j.chom.2021.05.008
SCIENCE special issue: TARA OCEANS, 2015 May 22
Tara Oceans studies plankton at planetary scale
P. Bork, C. Bowler, C. de Vargas, G. Gorsky, E. Karsenti, and P. Wincker
Science 2015 May 22. Vol. 348 no. 6237 p. 873 DOI: 10.1126/science.aac5605

Structure and function of the global ocean microbiome
Sunagawa S, Coelho L, Chaffron S, Kultima JR, Labadie K, etc. Tara Oceans coordinators
Science 2015 May 22. Vol. 348 no. 6237 DOI: 10.1126/science.1261359

Environmental characteristics of Agulhas rings affect interocean plankton transport
Villar E, Farrant GK, Follows M, Garczarek L, etc. and Tara Oceans Coordinators.
Science 2015 May 22. Vol. 348 no. 6237 DOI: 10.1126/science.1261447

Patterns and ecological drivers of ocean viral communities
Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, etc. and Tara Oceans Coordinators.
Science 2015 May 22. Vol. 348 no. 6237 DOI: 10.1126/science.1261498

Eukaryotic plankton diversity in the sunlit ocean
de Vargas C, Audic S, Henry N, Decelle J, etc. and Tara Oceans Coordinators.
Science 2015 May 22. Vol. 348 no. 6237 DOI: 10.1126/science.1261605

Determinants of community structure in the global plankton interactome
Lima-Mendez G, Faust K, Henry N, Decelle J, etc. and Tara Oceans Coordinators.
Science 2015 May 22. Vol. 348 no. 6237 DOI: 10.1126/science.1262073
my.microbes Team
2011 Sep 08
Nature, 2011 Sep 09: Social network wants to sequence your gut, and Scientist: Get Your Gut Sequenced
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