Department of Computer Science

Prof. Dr. Nico Pfeifer

Office C115
Email: surname at informatik.uni-tuebingen.de
Appointments via mm-sekretariatspam prevention@inf.uni-tuebingen.de

Academic Career
Since 2017
W3 Professor

Computer Science (Methods in Medical Informatics), Universität Tübingen

Since 2013
Group Leader

Statistical Learning in Computational Biology, Max Planck Institute for Informatics

2011–2012
Post-Doc

Statistical Learning in Computational Biology, Max Planck Institute for Informatics

2009–2011
Post-Doc

Machine Learning in Computational Biology, Microsoft Research

2009
Dr. rer. nat.

Bioinformatics/Computational Biology, Universität Tübingen (Germany)

2005
M.Sc. in Applied Computer Science

Universität Göttingen (Germany)

2004
B.Sc. in Applied Computer Science (direction: Bioinformatics)

Universität Göttingen (Germany)

Selected Publications

1.     C. Kreer, M. Zehner ,T. Weber, M. S. Ercanoglu, L. Gieselmann, C. Rohde, S. Halwe, M. Korenkov, P. Schommers, K. Vanshylla, V. Di Cristanziano, H. Janicki, R. Brinker, A. Ashurov, V. Krähling, A. Kupke, H. Cohen-Dvashi, M. Koch, J. M. Eckert, S. Lederer, N. Pfeifer, T. Wolf, M. J.G.T. Vehreschild, C. Wendtner, R. Diskin, H. Gruell, S. Becker, and F. Klein
Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients
Cell 2020, 182(6):1663-1673

2.     M. Döring, J. Büch, G. Friedrich, A. Pironti, P. Kalaghatgi, E. Knops, E. Heger, M. Obermeier, M. Daeumer, A. Thielen, R. Kaiser, T. Lengauer, N. Pfeifer
geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data
Nucleic Acids Research 2018, 46(W1):W271–W277

3.     P. Mendoza, H. Gruell, L. Nogueira, J. Pai, A. Butler, K. Millard, C. Lehmann, I. Suárez, T. Oliveira, J. Lorenzi, Y. Cohen, C. Wyen, T. Kümmerle, T. Karagounis, C.-L. Lu, L. Handl, C. Unson-O’Brien, R. Patel, C. Ruping, M. Schlotz, M. Witmer-Pack, I. Shimeliovich, G. Kremer, E. Thomas, K. Seaton, J. Horowitz, A. West, P. Bjorkman, G. Tomaras, R. Gulick, N. Pfeifer, G. Fätkenheuer, M. Seaman, F. Klein, M. Caskey, M. C. Nussenzweig
Combination therapy with anti-HIV-1 antibodies maintains viral suppression,
Nature 2018, 561, pp 479–4842.

4.     A. Hake and N. Pfeifer
Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time,
PLOS Computational Biology 2017, 13(10):e1005789

5.     M. Caskey, T. Schoofs, H. Gruell, A. Settler, T. Karagounis, E. F. Kreider, B. Murrell, N. Pfeifer, L. Nogueira, T. Y. Oliveira, G. H. Learn, Y. Z. Cohen, C. Lehmann, D. Gillor, I. Shimeliovich, C. Unson-O’Brien, D. Weiland, A. Robles, T. Kümmerle, C. Wyen, R. Levin, M. Witmer-Pack, K. Eren, C. Ignacio, S. Kiss, A. P. West, Jr, H. Mouquet, B. S. Zingman, R. M. Gulick, T. Keler, P. J. Bjorkman, M. S. Seaman, B. H. Hahn, G. Fätkenheuer, S. J. Schlesinger, M. C. Nussenzweig, F. Klein
Antibody 10-1074 suppresses viremia in HIV-1-infected individuals,
Nature Medicine 2017, 23, pp 185–1912.2.

6.     J. F. Scheid*, J. A. Horwitz*, Y. Bar-On, E. F. Kreider, C.-L. Lu, J. C. C. Lorenzi, A. Feldmann, M. Braunschweig, L. Nogueira, T. Oliveira, I. Shimeliovich, R. Patel, L. Burke, Y. Z. Cohen, S. Hadrigan, A. Settler, M. Witmer-Pack, A. P. West, Jr., B. Juelg, T. Keler, T. Hawthorne, B. Zingman, R. M. Gulick, N. Pfeifer, G. H. Learn, M. S. Seaman, P. J. Bjorkman, F. Klein, S. J. Schlesinger, B. D. Walker, B. H. Hahn, M. C. Nussenzweig, and M. Caskey
HIV-1 antibody 3BNC117 suppresses viral rebound in humans during treatment interruption
Nature 2016, 535, pp 556–560
*: equal contribution

7.     J. M. Carlson†, V. Y. Du*, N. Pfeifer*, A. Bansal, V. Y. F. Tan, K. Power, C. J. Brumme, A. Kreimer, C. E. DeZiel, N. Fusi, M. Schaefer, A. Gladden-Young, M. Brockman, J. Gilmour, M. A. Price, W. Kilembe, R. Haubrich, M. John, S. Mallal, R. Shapiro, J. Frater, P. R. Harrigan, T. Ndung’u, S. Allen, D. Heckerman, J. Sidney, T. M. Allen, P. J. R. Goulder, Z. L. Brumme, E. Hunter†, P. A. Goepfert†,
Impact of Pre-adapted HIV Transmission,
Nature Medicine 2016, 22, pp 606-613
*: equal contribution, †: These authors jointly supervised this work

8.     T. Schoofs*, F. Klein*, M. Braunschweig*, K. F. Kreider, A. Feldmann, L. Nogueira, T. Oliveira, J. C. C. Lorenzi, E. H. Parrish, G. H. Learn, A. P. West, P. J. Bjorkman, S. J. Schlesinger, M. S. Seaman, J. Czartoski, M. J. McElrath, N. Pfeifer, B. H. Hahn, M. Caskey, and M. C. Nussenzweig
HIV-1 Immunotherapy with Monoclonal Antibody 3BNC117 Elicits Host Immune Responses against HIV-1,
Science 2016, 352 (6288), pp 997-1001
*: equal contribution

9.     N. K. Speicher and N. Pfeifer
Integrating Different Data Types by Regularized Unsupervised Multiple Kernel Learning with Application to Cancer Subtype Discovery,
Proceedings of ISMB/ECCB 2015, Bioinformatics 2015, 31, pp i268-i275

10.     N. Pfeifer, H. Walter, T. Lengauer
Association between HIV-1 coreceptor usage and resistance to broadly neutralizing antibodies,
JAIDS 2014, 67 (2), pp 107-112

11.  N. Pfeifer and T. Lengauer
Improving HIV coreceptor usage prediction in the clinic using hints from next generation sequencing data
“Proceedings of the 11th European Conference on Computational Biology (ECCB 2012)”, Bioinformatics 2012 28, i589-i595.

Click here for all publications.