Peer Bork, European Molecular Biology Laboratory (EMBL), Heidelberg, GERMANY
Biological Networks at different spatial scales
Networks are found in biological systems that range from small
biomolecules via cellular processes and species to entire
ecosystems; each of these scales usually comes with their own
biological research discipline. Using computational approaches, we
integrate heterogeneous data to uncover functional aspects of
diverse biological networks and we try to bridge between spacial
scales and research disciplines. I will illustrate our approach
with examples from biomolecular network analysis (proteins and
small molecules) and networks of microbes using the ecosystem human
gut as an example (networks of drugs and bugs), but will also
extend to planetary scale using microbial community networks in the
worlds oceans.
Bibliography
Richness of human gut microbiome correlates with metabolic markers.
Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T; MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O.
Nature. 2013 Aug 29;500(7464):541-6. doi: 10.1038/nature12506.
Genomic variation landscape of the human gut microbiome.
Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P.
Nature. 2013 Jan 3;493(7430):45-50. doi: 10.1038/nature11711.
for details see group page: http://www.bork.embl.de
Enterotypes of the human gut microbiome.
Arumugam M, Raes J et al.
Nature. 2011 May 12;473(7346):174-80. doi: 10.1038/nature09944.
A human gut microbial gene catalogue established by metagenomic sequencing.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J; MetaHIT Consortium, Bork P, Ehrlich SD, Wang J.
Nature. 2010 Mar 4;464(7285):59-65. doi: 10.1038/nature08821.
Proteome organization in a genome-reduced bacterium.
Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC.
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Comparative assessment of large-scale data sets of protein-protein interactions.
von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P.
Nature. 2002 May 23;417(6887):399-403. Epub 2002
