1.     P. Schommers, D. S. Kim, M. Schlotz, C. Kreer, R. Eggeling, A. Hake, M. Stecher, J. Park, C. E. Radford, A. S. Dingens, M. S. Ercanoglu, H. Gruell, S. Odidika, M. Dahlhaus, L. Gieselmann, E. Ahmadov, R. Y. Lawong, E. Heger, E. Knops, C. Wyen, T. Kümmerle, K. Römer, S. Scholten, T. Wolf, C. Stephan, I. Suárez, N. Raju, A. Adhikari, S. Esser, H. Streeck, R. Duerr, A. J. Nanfack, S. Zolla-Pazner, C. Geldmacher, O. Geisenberger, A. Kroidl, W. William, L. Maganga, N. E. Ntinginya, I. S. Georgiev, J. J. Vehreschild, M. Hoelscher, G. Fätkenheuer, J. J. Lavinder, J. D. Bloom, M. S. Seaman, C. Lehmann, N. Pfeifer, G. Georgiou, F. Klein
Dynamics and durability of HIV-1 neutralization are determined by viral replication
Nature Medicine 2023 

2.     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

3.     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

4.     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.

5.     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

6.     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.

7.     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

8.     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

9.     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

10.     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

11.     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

12.  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.