Computational Biology of Infection Research

The Department of “Computational Biology for Infection Research” studies the human microbiome, viral and bacterial pathogens, and human cell lineages within individual patients by analysis of large-scale biological and epidemiological data sets with computational techniques. Focusing on high throughput meta’omics, population genomic and single cell sequencing data, we produce testable hypotheses, such as sets of key sites or relevant genes associated with the presence of a disease, of antibiotic resistance or pathogenic evasion of immune defense. We interact with experimental collaborators to verify our findings and to promote their translation into medical treatment or diagnosis procedures. To achieve its research goals, the department also develops novel algorithms and software.

Leader

Selected Publications

Publications

2017

2016

 

2015

 

2014

 

2013

 

2012

 

2011

 

2010

 

2009

 

2008

  • M.G. Kalyuzhnaya, A. Lapidus, N. Ivanova, A.C. Copeland, A.C. McHardy, E. Szeto, A. Salamov, I.V. Grigoriev, D. Suciu, S.R. Levine, V.M. Markowitz, I. Rigoutsos, S.G. Tringe, D.C. Bruce, P.M. Richardson, M.E. Lidstrom, L. Chistoserdova
    High-resolution metagenomics targets specific functional types in complex microbial communities

    Nature Biotechnology 2008, 26(9):  1029-1034
  • A.C. McHardy
    Finding genes in genome sequence

    Methods in Molecular Biology 2008, 452(2): 163-177
  • L.Z. Holland, R. Albalat, K. Azumi, E. Benito-Gutiérrez, M.J. Blow, M. Bronner-Fraser, F. Brunet, T. Butts, S. Candiani, L.J. Dishaw, D.E. Ferrier, J. Garcia-Fernàndez, J.J. Gibson-Brown, C. Gissi, A. Godzik, F. Hallböök, D. Hirose, K. Hosomichi, T. Ikuta, H. Inoko, M. Kasahara, J. Kasamatsu, T. Kawashima, A. Kimura, M. Kobayashi, Z. Kozmik, K. Kubokawa, V. Laudet, G.W. Litman, A.C. McHardy, D. Meulemans, M. Nonaka, R.P. Olinski, Z. Pancer, L.A. Pennacchio, M. Pestarino, J.P. Rast, I. Rigoutsos, M. Robinson-Rechavi, G. Roch, H. Saiga, Y. Sasakura, M. Satake, Y. Satou, M. Schubert, N. Sherwood, T. Shiina, N. Takatori, J. Tello, P. Vopalensky, S. Wada, A. Xu, Y. Ye, K. Yoshida, F. Yoshizaki, J.K. Yu, Q. Zhang, C.M. Zmasek, P.J. de Jong, K. Osoegawa, N.H. Putnam, D.S. Rokhsar, N. Satoh, P.W. Holland
    The amphioxus genome illuminates vertebrate origins and cephalochordate biology

    Genome Research 2008, 18(7): 1100-1111
  • K.H. Gartemann, B. Abt, T. Bekel, A. Burger, J. Engemann, M. Flügel, L. Gaigalat, A. Goesmann, I. Gräfen, J. Kalinowski, O. Kaup, O. Kirchner, L. Krause, B. Linke, A.C. McHardy, F. Meyer, S. Pohle, C. Rückert, S. Schneiker, E.M. Zellermann, A. Pühler, R. Eichenlaub, O. Kaiser, D. Bartels
    The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity

    Journal of Bacteriology 2008, 190(6): 2138-2149
  • B. Adams, A.C. McHardy, C. Lundegaard, T. Lengauer
    Viral Bioinformatics
    in Modern Genome Annotation, D. Frishman, A. Valencia (Editors) Springer Verlag, 2009, 429-452

2007

 

2006

 

2005

 

2004

 

2003

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