Prof. Dr. Alice McHardy participates in RESIST research projects B2, B10 and C1.

My Research Interest in RESIST

Our research interest in RESIST is to analyse clinical biomedical data sets from patients with infectious diseases studied together with other RESIST PIs, by development and application of suitable computational methodologies. These methods combine techniques from bioinformatics, machine learning and phylogenetic / population genetic inference. We focus specifically on biofilm formation in clinical Pseudomonas aeruginosa isolates, inflammatory diseases linked to the gut microbiome, as well as immune evasion of Hepatitis C viruses.

Our aim is to 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.

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Prof. McHardy about her scientific work

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Prof. Dr. Alice McHardy – Curriculum Vitae

Current Position

  • Since 2014

    Head of Department for “Computational Biology for Infection Research” at the Helmholtz Centre for Infection Research (HZI) and full professor, Carl-Friedrich-Gauss Department and Department of Life Sciences, Technical University of Braunschweig, Germany

Undergraduate and Postgraduate Training

  • 1995 – 2000 Diploma in Biochemistry, Department of Chemistry, Bielefeld University, Germany

  • 2001 – 2004 Dr. rer. nat. (Ph.D.) in Bioinformatics, Computer Science Department, Bielefeld University, Germany

Academic and Research Posts

  • 2004 – 2004 Postdoctoral researcher, Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Germany

  • 2005 – 2007 Postdoctoral researcher, then Permanent Research Staff, Bioinformatics & Pattern Discovery Group, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA

  • 2007 – 2012 Head of independent Max-Planck Research Group for “Computational Genomics & Epidemiology” (W2: eq. associate), Max-Planck Institute for Informatics, Saarbrücken, Germany

  • 2010 – 2014 Chair of “Algorithmic Bioinformatics” (W3: eq. full), Heinrich-Heine University Düsseldorf, Germany

  • Since 2014 Head of Department for “Computational Biology for Infection Research”, Helmholtz Centre for Infection Research, Braunschweig, Germany

  • Since 2014 Full professor, Carl-Friedrich-Gauss Department and Department of Life Sciences, Technical University of Braunschweig, Germany

Other Scientific Roles

  • 2013 – 2019 Associate Editor, PLOS Computational Biology

  • Since 2015 Coordinator of the TI Bioinformatics Platform, then TI Bioresources, Biodata and Digital Health, German Centre for Infection Research (DZIF)

  • Since 2015 Scientific Advisory Board for de.NBI (German Network for Bioinformatics Infrastructure)

  • Since 2016 Scientific Advisory Board, EMBL-EBI Metagenomics

  • Since 2017 Co-chair, “Microbiome” Community of Special Interest (COSI) of the International Society for Computational Biology (ISCB) and the ISMB/ECCB “Microbiome” Track

  • Since 2019 Deputy Editor, PLOS Computational Biology

  • Since 2019 Metagenomics Editor, Current Protocols in Bioinformatics

  • Since 2020 Scientific Advisory Board, Trends in Microbiology

  • Since 2020 Nominator for Nobel Prize in Physiology or Medicine

Awards and Prizes

  • 2002 Intelligent Systems for Molecular Biology (ISMB) ‚Best Poster‘ Award

  • 2006 IBM Invention Achievement Award

  • 2006 International Business Machines Corporation (IBM) ‚Research Division Technical Achievement Group‘ Award

  • 2008 Sponsorship ‚Fast Track Program‘, Robert Bosch Foundation

  • 2010 Invitation to 60th Nobel Laureate Meeting, Lindau, Germany

  • 2020, 2021 Highly Cited Researcher (Clarivate)

Patents

  • Rigoutsos I, Huynh T, Tsirigos A, McHardy AC, Miranda KC. US2008052008A1: Techniques for Linking Non-Coding and Gene-Coding Deoxyribonucleic Acid Sequences and Applications Thereof.

  • Bathe B, Bastuck C, Tauch A, McHardy AC. US2003100054A1: Nucleotide sequences which code for the ilvE gene.

  • Rigoutsos I, Huynh T, Tsirigos A, McHardy AC. US2011178283A1: Ribonucleic acid interference molecules and binding sites derived by analyzing intergenic and intronic regions of genomes.

  • McHardy AC, Steinbruck L. US2011280907A1: Method and system for building a phylogeny from genetic sequences and using the same for recommendation of vaccine strain candidates for the influenza virus.

Recommended Links

10 Selected Publications (of > 110 original publications)

F. Meyer, A. Fritz, Z.-L. Deng, D. Koslicki, T. R. Lesker, A. Gurevich, G. Robertson, M. Alser, D. Antipov, F. Beghini, D. Bertrand, J. J. Brito, C. T. Brown, J. Buchmann, A. Buluç, B. Chen, R. Chikhi, P. T. Clausen, A. Cristian, P. W. Dabrowski, A. E. Darling, R. Egan, E. Eskin, E. Georganas, E. Goltsman, M. A. Gray, L. H. Hansen, S. Hofmeyr, P. Huang, L. Irber, H. Jia, T. S. Jørgensen, S. D. Kieser, T. Klemetsen, A. Kola, M. Kolmogorov, A. Korobeynikov, J. Kwan, N. LaPierre, C. Lemaitre, C. Li, A. Limasset, F. Malcher-Miranda, S. Mangul, V. R. Marcelino, C. Marchet, P. Marijon, D. Meleshko, D. R. Mende, A. Milanese, N. Nagarajan, J. Nissen, S. Nurk, L. Oliker, L. Paoli, P. Peterlongo, V. C. Piro, J. S. Porter, S. Rasmussen, E. R. Rees, K. Reinert, B. Renard, E. M. Robertsen, G. L. Rosen, H.-J. Ruscheweyh, V. Sarwal, N. Segata, E. Seiler, L. Shi, F. Sun, S. Sunagawa, S. J. Sørensen, A. Thomas, C. Tong, M. Trajkovski, J. Tremblay, G. Uritskiy, R. Vicedomini, Zhe. Wang, Zi. Wang, Zho. Wang, A. Warren, N. P. Willassen, K. Yelick, R. You, G. Zeller, Z. Zhao, S. Zhu, J. Zhu, R. Garrido-Oter, P. Gastmeier, S. Hacquard, S. Häußler, A. Khaledi, F. Maechler, F. Mesny, S. Radutoiu, P. Schulze-Lefert, N. Smit, T. Strowig, A. Bremges, A. Sczyrba, A. C. McHardy, Critical Assessment of Metagenome Interpretation – the second round of challenges. Nature methods in press (2021).

P. C. Münch, E. A. Franzosa, B. Stecher, A. C. McHardy*, C. Huttenhower* (*shared last authors), Identification of Natural CRISPR Systems and Targets in the Human Microbiome. Cell Host Microbe 29, 94-106 (2021).

D. Bankwitz, A. Bahai, M. Labuhn, M. Doepke, C. Ginkel, T. Khera, D. Todt, L. J. Ströh, L. Dold, F. Klein, F. Klawonn, T. Krey, P. Behrendt, M. Cornberg, A. C. McHardy*, T. Pietschmann* (*shared last authors), Hepatitis C reference viruses highlight potent antibody responses and diverse viral functional interactions with neutralising antibodies. Gut 70:1734-1745 (2021).

A. Khaledi, A. Weimann, M. Schniederjans, E. Asgari, T. H. Kuo, A. Oliver, G. Cabot, A. Kola, P. Gastmeier, M. Hogardt, D. Jonas, M. R. Mofrad, A. Bremges, A. C. McHardy*, S. Häussler* (*shared last authors), Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics. EMBO Mol Med 12, e10264 (2020).

F. Meyer, A. Bremges, P. Belmann, S. Janssen, A. C. McHardy*, D. Koslicki* (*shared last authors), Assessing taxonomic metagenome profilers with OPAL .Genome Biol 20, 51 (2019).

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 35, 2498-2500 (2019).

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, Critical Assessment of Metagenome Interpretation – a benchmark of metagenomics software. Nat Methods 14, 1063–1071 (2017).

Y. Bai, D. B. Muller, G. Srinivas, R. Garrido-Oter, E. Potthoff, M. Rott, N. Dombrowski, P. C. Munch, S. Spaepen, M. Remus-Emsermann, B. Huttel, A. C. McHardy, J. A. Vorholt, P. Schulze-Lefert, Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528, 364-9 (2015).

K. R. Patil, P. Haider, P. B. Pope, P. J. Turnbaugh, M. Morrison, T. Scheffer, A. C. McHardy, Taxonomic metagenome sequence assignment with structured output models. Nat Methods 8, 191-2 (2011).

A. C. McHardy, H. G. Martin, A. Tsirigos, P. Hugenholtz, I. Rigoutsos, Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods 4, 63-72 (2007).

Contact

  Prof. Dr. Alice McHardy
  Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI)
  Inhoffenstraße 7
38124 Braunschweig
  +49 531 39155271
  Alice.McHardy
@helmholtz-hzi.de