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

  • A. Sczyrba*, P. Hofmann*, P. Belmann*, D. Koslicki, S. Janssen, J. Droge, I. Gregor, S.  Majda, J. Fiedler, E. Dahms, A. Bremges, A. Fritz, R. Garrido-Oter, T. Sparholt Jorgensen, N. Shapiro, P. D. Blood, A. Gurevich, Y. Bai, D. Turaev, M. Z. DeMaere, R. Chikhi, N. Nagarajan, C. Quince, F. Meyer, Monika Balvočiūtė, L. H. Hansen, S. J. Sorensen, B. K. H. Chia, B. Denis, J. L. Froula, Z. Wang, R. Egan, D. D. Kang, J. J. Cook, C. Deltel, M. Beckstette, C. Lemaitre, P. Peterlongo, G. Rizk, D. Lavenier, Y.-W. Wu, S. W. Singer, C. Jain, M. Strous, H. Klingenberg, P. Meinicke, M. Barton, T. Lingner, H.-H. Lin, Y.-C. Liao, G. Gueiros Z. Silva, D. A. Cuevas, R. A. Edwards, S. Saha, V. C. Piro, B. Y. Renard, M. Pop, H.-P. Klenk, M. Goker, N. Kyrpides, T. Woyke, J. A. Vorholt, P. Schulze-Lefert, E. M. Rubin, A. E. Darling, T. Rattei, A. C. McHardy  (*shared first authors)
    Critical Assessment of Metagenome Interpretation − a benchmark of metagenomics software.
    Nat Methods 2017, 14: 1063
  • E. Asgari, P. C. Munch, T. R. Lesker, A. C. McHardy*, M. R. K. Mofrad* (*shared last authors)
    DiTaxa: Nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection.
    Bioinformatics 2018, Epub: bty954
  • F. Meyer, A. Bremges, P. Belmann, S. Janssen, A. C. McHardy*, D. Koslicki* (*shared last authors)
    Assessing taxonomic metagenome profilers with OPAL.
    Genome Biol 2019, 20:51
  • A. Fritz, P. Hofmann, S. Majda, E. Dahms, J. Droge, J. Fiedler, T. R. Lesker, P. Belmann, M. Z. DeMaere, A. E. Darling, A. Sczyrba, A. Bremges, A. C. McHardy
    CAMISIM: simulating metagenomes and microbial communities.
    Microbiome 2019, 7:17

Publications

2019

2018

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
    Nat Biotechnol 2008, 26: 1029
  • A.C. McHardy
    Finding genes in genome sequence
    Methods in Molecular Biology 2008, 452: 163
  • 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 Res 2008, 18: 1100
  • 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: 2138
  • B. Adams, A.C. McHardy, C. Lundegaard, T. Lengauer
    Viral Bioinformatics
    in Modern Genome Annotation, D. Frishman, A. Valencia (Editors) Springer Verlag, 2009: 429

2007

2006

2005

2004

2003

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