Our Publications

• Nurhan Arslan, Bernhard Reuter, Joachim Buech, Thomas Lengauer, Martin Obermeier, Rolf Kaiser, Nico Pfeifer
  Hepatitis C Virus Saint Petersburg Variant Detection With Machine Learning Methods
  Journal of Medical Virology 2025, 97: e70169
   
• Katharina M. Götz, Amin T. Turki, Katharina Och, Dominik Selzer, Christian Brossette, Norbert Graf, Jochen Rauch, Stefan Theobald, Yvonne Braun, Kerstin Rohm, Gabriele Weiler, Simeon Rüdesheim, Matthias Schwab, Lisa Eisenberg, Nico Pfeifer, Stephan Kiefer, Ulf Schwarz, Claudia Riede, Sigrun Smola, Dietrich W. Beelen, Dominic Kaddu-Mulindwa, Jürgen Rissland, Jörg Bittenbring, Thorsten Lehr
  Model-Based Prediction of Clinically Relevant Thrombocytopenia after Allogeneic Hematopoietic Stem Cell Transplantation
  Clinical Pharmacology & Therapeutics 2025
   
• [medRxiv preprint] Marius de Arruda Botelho Herr, Cem Ata Baykara, Ali Burak Ünal, Nico Pfeifer, Mete Akgün
  Privacy-preserving AUC Computation in Distributed Machine Learning with PHT-meDIC
   
• Lara Tretschock, Kathrin Haßdenteufel, Léa L. Volmer, Armin Bauer, Stefan Stefanovic, Tobias Engler, Andreas D. Hartkopf, Nico Pfeifer, Pascal Escher, Marc Mausch, Oliver Heinze, Marc Sütterlin, Sara Y. Brucker, Andreas Schneeweiss, Thomas M. Deutsch, Markus Wallwiener
  ENABLE – eine digitale therapiebegleitende Plattform für Patientinnen mit invasivem Mammakarzinom
  Senologie 2024; 21(04): 265-267
   
• [arXiv preprint] Cem Ata Baykara, Ali Burak Ünal, Nico Pfeifer, Mete Akgün
  Privacy Preserving Federated Unsupervised Domain Adaptation with Application to Age Prediction from DNA Methylation Data
   
• [arXiv preprint] Şeyma Selcan Mağara, Noah Dietrich, Ali Burak Ünal, Mete Akgün
  Accelerating Privacy-Preserving Medical Record Linkage: A Three-Party MPC Approach
   
• [arXiv preprint] Anika Hannemann, Arjhun Swaminathan, Ali Burak Ünal, Mete Akgün
  Private, Efficient and Scalable Kernel Learning for Medical Image Analysis
   
• Sascha Welten, Marius de Arruda Botelho Herr, Lars Hempel, David Hieber, Peter Placzek, Michael Graf, Sven Weber, Laurenz Neumann, Maximilian Jugl, Liam Tirpitz, Karl Kindermann, Sandra Geisler, Luiz Olavo Bonino da Silva Santos, Stefan Decker, Nico Pfeifer, Oliver Kohlbacher & Toralf Kirsten
  A study on interoperability between two Personal Health Train infrastructures in leukodystrophy data analysis. 
  Sci Data 2024, 11, 663
   
• Ali Burak Ünal, Nico Pfeifer, Mete Akgün
  A privacy-preserving approach for cloud-based protein fold recognition
  Patterns 2024, 101023, ISSN 2666-3899
   
• Jacqueline Wistuba-Hamprecht, Bernhard Reuter, Rolf Fendel, Stephen L. Hoffman, Joseph J. Campo, Philip L. Felgner, Peter G. Kremsner, Benjamin Mordmüller, Nico Pfeifer
  Machine learning prediction of malaria vaccine efficacy based on antibody profiles
  PLoS Comput Biol 20(6) (2024): e1012131
   
• [arXiv preprint] Cem Ata Baykara, Ali Burak Ünal, Mete Akgün
  FHAUC: Privacy Preserving AUC Calculation for Federated Learning using Fully Homomorphic Encryption
   
• Lorenz Dörner, Lucia Grosse, Felix Stange, Hanni Hille, Sylvia Kurz, Hannes Becker, Sebastian Volkmer, Melina Hippler, David Rieger, Paula Bombach, Johannes Rieger, Lina Weinert, Laura Svensson, Carolin Anders, Sila Cekin, Frank Paulsen, Öznur Öner, Kristina Ruhm, Holly Sundberg Malek, Yonne Möller, Marcos Tatagiba, Markus Wallwiener, Nils Eckert, Pascal Escher, Nico Pfeifer, Andrea Forschner, Armin Bauer, Daniel Zips , Michael Bitzer, Nisar Malek, Cihan Gani, Ghazaleh Tabatabai, Mirjam Renovanz
  App-based assessment of patient-reported outcomes in the Molecular Tumor Board in the Center for Personalized Medicine—(TRACE)
  Neuro-Oncology Practice XX(XX), 1–11, 2024
   
• Pontus Hedberg, Milosz Parczewski, Karol Serwin, Giulia Marchetti, Francesca Bai, Björn-Erik Ole Jensen, Joana P.V. Pereira, Francis Drobniewski, Henrik Reschreiter, Daniel Naumovas, Francesca Ceccherini-Silberstein, Gibran Horemheb Rubio Quintanares, Matilu Mwau, Cristina Toscano, Florian König, Nico Pfeifer, Maurizio Zazzi, Iuri Fanti, Francesca Incardona, Alessandro Cozzi-Lepri, Anders Sönnerborg, Pontus Nauclér
  In-hospital mortality during the wild-type, alpha, delta, and omicron SARS-CoV-2 waves: a multinational cohort study in the EuCARE project
  The Lancet Regional Health - Europe 2024, 100855, ISSN 2666-7762
   
• Anna Hake, Anja Germann, Corena de Beer, Alexander Thielen, Martin Däumer, Wolfgang Preiser, Hagen von Briesen, Nico Pfeifer
  Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models
  PLOS Computational Biology 2023, 19(12): e1010355
   
• 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
   
• Federica Bellerba, Nils Bardeck, Michael Boehm, Oriana D’Ecclesiis, Sara Raimondi, Elisa Tomezzoli, Mafalda Silva Miranda, Inês Martins Alves, Daniela Alves, Ana Abecasis, Valeria Gabellone, Elisa Gabrielli, Giulia Vaglio, Elham Shamsara, Nico Pfeifer, Chiara Mommo, Francesca Incardona, Rolf Kaiser, Sara Gandini
  SARS-CoV-2 trends in Italy, Germany and Portugal and school opening during the period of Omicron variant dominance: a quasi-experimental study
  International Journal of Infectious Diseases 2023, ISSN 1201-9712
   
• Pontus Hedberg, Benedetta Varisco, Francesca Bai, Anders Sönnerborg, Pontus Naucler, Nico Pfeifer, Alessandro Cozzi-Lepri, Francesca Ceccherini-Silberstein, Daniel Naumovas, Francis Drobniewski, Björn-Erik Ole Jensen, Cristina Toscano, Miłosz Parczewski, Gibran Horemheb Rubio Quintanares, Matilu Mwau, Jorge A. Pinto, Francesca Incardona, Chiara Mommo, Giulia Marchetti
  EuCARE-hospitalised study protocol: a cohort study of patients hospitalised with COVID-19 in the EuCARE project
  BMC Infectious Diseases volume 23, Article number: 690 (2023)
   
• Jonas C. Ditz, Bernhard Reuter, Nico Pfeifer
  Inherently interpretable position-aware convolutional motif kernel networks for biological sequencing data
  Scientific Reports 2023, 13, 17216
   
• Nicole Anderle, Felix Schäfer-Ruoff, Annette Staebler, Nicolas Kersten, André Koch, Cansu Önder, Anna-Lena Keller, Simone Liebscher, Andreas Hartkopf, Markus Hahn, Markus Templin, Sara Y. Brucker, Katja Schenke-Layland, Christian Schmees
  Breast cancer patient-derived microtumors resemble tumor heterogeneity and enable protein-based stratification and functional validation of individualized drug treatment
  Journal of Experimental & Clinical Cancer Research 2023, 42:210
   
• Jonas Christian Ditz, Bernhard Reuter and Nico Pfeifer
  COmic: Convolutional Kernel Networks for Interpretable End-to-End Learning on (Multi-)Omics Data
  Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i76–i85, presented at MLCSB cosi of ISMB/ECCB 2023
   
• Jonas Christian Ditz, Jacqueline Wistuba-Hamprecht, Timo Maier, Rolf Fendel, Nico Pfeifer and Bernhard Reuter
  PlasmoFAB: A Benchmark to Foster Machine Learning for Plasmodium falciparum Protein Antigen Candidate Prediction
  Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i86–i93, presented at ISMB/ECCB 2023
   
• Christian Malte Boßelmann, Ulrike B.S. Hedrich, Holger Lerche, Nico Pfeifer
  Predicting functional effects of ion channel variants using new phenotypic machine learning methods
  PLoS Computational Biology 2023, 19(3):e1010959
   
• Filippo Grazioli,  Pierre Machart,  Anja Mösch,  Kai Li,  Leonardo V Castorina, Nico Pfeifer,  Martin Renqiang Min
  Attentive Variational Information Bottleneck for TCR–peptide interaction prediction
  Bioinformatics 2023, Volume 39, Issue 1, January 2023, btac820
   
• [bioRxiv preprint] Markus Wallner, Nicolas Kersten, Nico Pfeifer
  Multi-view confounder detection for biomedical studies
   
• Lukas Häger, Philipp Wendland, Stephanie Biergans, Simone Lederer, Marius de Arruda Botelho Herr, Christian Erhardt, Kristina Schmauder, Maik Kschischo, Nisar Peter Malek, Stefanie Bunk, Michael Bitzer, Beryl Primrose Gladstone, Siri Göpel
  External Validation of COVID-19 Risk Scores during Three Waves of Pandemic in a German Cohort—A Retrospective Study
  Journal of Personalized Medicine 2022, 12(11), 1775
   
• Maarten A. A. van de Klundert, Anastasiia Antonova, Giulia Di Teodoro, Rafael Ceña Diez, Nikoloz Chkhartishvili, Eva Heger, Anna Kuznetsova, Aleksey Lebedev, Aswathy Narayanan, Ekaterina Ozhmegova, Alexander Pronin, Andrey Shemshura, Alexandr Tumanov, Nico Pfeifer, Rolf Kaiser, Francesco Saladini, Maurizio Zazzi, Francesca Incardona, Marina Bobkova, Anders Sönnerborg
  Molecular Epidemiology of HIV-1 in Eastern Europe and Russia
  Viruses 2022, 14, 2099
   
• Felix Ruoff, Nicolas Kersten, Nicole Anderle, Sandra Jerbi, Aaron Stahl, André Koch, Annette Staebler, Andreas Hartkopf, Sara Y. Brucker, Markus Hahn, Katja Schenke‐Layland, Christian Schmees, Markus F. Templin
  Protein Profiling of Breast Carcinomas Reveals Expression of Immune-Suppressive Factors and Signatures Relevant for Patient Outcome
  Cancers 2022, 14, 4542
   
• Lisa Eisenberg, the XplOit consortium, Christian Brossette, Jochen Rauch, Andrea Grandjean, Hellmut Ottinger, Jürgen Rissland, Ulf Schwarz, Norbert Graf, Dietrich W. Beelen, Stephan Kiefer, Nico Pfeifer*, Amin T. Turki*
  Time-dependent prediction of mortality and cytomegalovirus reactivation after allogeneic hematopoietic cell transplantation using machine learning
  American Journal of Hematology, 2022
  *: equal contribution
   
• Jan Scheer, Alisa Volkert, Nicolas Brich, Lina Weinert, Nandhini Santhanam, Michael Krone, Thomas Ganslandt, Martin Boeker, Till Nagel
  Visualization techniques of time-oriented data for the comparison of single patients to multiple patients or cohorts: a scoping review
  Journal of Medical Internet Research, 2022
   
• Christian Malte Boßelmann, Ulrike B.S. Hedrich, Peter Müller, Lukas Sonnenberg, Shridhar Parthasarathy, Ingo Helbig, Holger Lerche, Nico Pfeifer
  Predicting the functional effects of voltage-gated potassium channel missense variants with multi-task learning
  eBioMedicine, 2022
   
• Gibran Horemheb Rubio*, Ralf Eggeling*, Norbert Schmeiβer, Nico Pfeifer, Thomas Lengauer, Barbara C. Gärtner, Christiane Prifert, Matthias Kochanek, Christoph Scheid, Ortwin Adams, Rolf Kaiser*, Respiratory Virus Network
  Respiratory viruses dynamics and interactions: ten years of surveillance in central Europe
  BMC Public Health, 2022, 1167
  *: equal contribution
   
• Allan Bayat, Angel Aledo-Serrano, Antonio Gil-Nagel, Christian M. Korff, Ashley Thomas, Christian Boßelmann, Yvonne Weber, Elena Gardella, Allan M. Lund, Monique G. M. de Sain-van der Velden, Rikke S. Møller
  Pyridoxine or pyridoxal-5-phosphate treatment for seizures in glycosylphosphatidylinositol deficiency: A cohort study
  Developmental Medicine & Child Neurology, 2022
   
• Kanika Vanshylla, Pinkus Tober-Lau, Henning Gruell, Friederike Münn, Ralf Eggeling, Nico Pfeifer, N Han Le, Irmgard Landgraf, Florian Kurth, Leif E Sander, Florian Klein
  Durability of omicron-neutralising serum activity after mRNA booster immunisation in older adults
  The Lancet Infectious Diseases, 2022
   
• Marius Lange, Volker Bergen, Michal Klein, Manu Setty, Bernhard Reuter, Mostafa Bakhti, Heiko Lickert, Meshal Ansari, Janine Schniering, Herbert B. Schiller, Dana Pe’er, Fabian J. Theis
  CellRank for directed single-cell fate mapping
  Nature Methods, 2022
   
• [arXiv preprint] Ali Burak Ünal, Nico Pfeifer, Mete Akgün
  ppAURORA: Privacy Preserving Area Under Receiver Operating Characteristic and Precision-Recall Curves with Secure 3-Party Computation
   
• [arXiv preprint] Jonas C. Ditz, Bernhard Reuter, Nico Pfeifer
  Convolutional Motif Kernel Networks
   
• Timm Weber, Julian Potthoff, Sven Bizu, Maurice Labuhn, Leona Dold, Till Schoofs, Marcel Horning, Meryem S. Ercanoglu, Christoph Kreer, Lutz Gieselmann, Kanika Vanshylla, Bettina Langhans, Hanna Janicki, Luisa J. Ströh, Elena Knops, Dirk Nierhoff, Ulrich Spengler, Rolf Kaiser, Pamela J. Bjorkman, Thomas Krey, Dorothea Bankwitz, Nico Pfeifer, Thomas Pietschmann, Andrew I. Flyak, Florian Klein
  Analysis of antibodies from HCV elite neutralizers identifies genetic determinants of broad neutralization
  Immunity, 2022
   
• David Blumenthal, Julian Matschinske, Nicolas Alcaraz, Arriel Benis, Martin Golebiewski, Dominik Grimm, Lukas Heumos, Tim Kacprowski, Olga Lazareva, Markus List, Zakaria Louadi, Josch Pauling, Nico Pfeifer, Richard Röttger, Veit Schwämmle, Gregor Sturm, Alberto Traverso, Kristel Van Steen, Martiela Freitas, Gerda Villalba Silva, Leonard Wee, Nina Wenke, Massimiliano Zanin, Olga Zolotareva, Jan Baumbach
  The AIMe registry for artificial intelligence in biomedical research
  Nature Methods, 2021
   
• Felix Erne*, Daniel Dehncke*, Steven C. Herath, Fabian Springer, Nico Pfeifer, Ralf Eggeling**, Markus Alexander Küper**
  Deep Learning in the Detection of Rare Fractures – Development of a “Deep Learning Convolutional Network” Model for Detecting Acetabular Fractures
  *: shared authorship
  **: shared last authorship
  Zeitschrift für Orthopädie und Unfallchirurgie, 26 July 2021
   
• Michael Korenkov, Nareshkumar Poopalasingam, Matthias Madler, Kanika Vanshylla, Ralf Eggeling, Maike Wirtz, Irina Fish, Felix Dewald, Lutz Gieselmann, Clara Lehmann, Gerd Fätkenheuer, Henning Gruell, Nico Pfeifer, Eva Heger, and Florian Klein
  Evaluation of a rapid antigen test to detect SARS-CoV-2 infection and identify potentially infectious individuals
  Journal of Clinical Microbiology, 02 July 2021
   
• Kanika Vanshylla, Veronica Di Cristanziano, Franziska Kleipass, Felix Dewald, Philipp Schommers, Lutz Gieselmann, Henning Gruell, Maike Schlotz, Meryem S. Ercanoglu, Ricarda Stumpf, Petra Mayer, Matthias Zehner, Eva Heger, Wibke Johannis, Carola Horn, Isabelle Suárez, Norma Jung, Susanne Salomon, Kirsten Alexandra Eberhardt, Birgit Gathof, Gerd Fätkenheuer, Nico Pfeifer, Ralf Eggeling, Max Augustin, Clara Lehmann, Florian Klein
  Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2 infectionin humans
  Cell Host and Microbe May 2021
   
• Nina Marty, Siriphan Saeng-Aroon, Eva Heger, Alexander Thielen, Martin Obermeier, Nico Pfeifer, Rolf Kaiser, Thomas Klimkait
  Adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia
  Journal of Clinical Virology February 2021
   
• S. Käppel, R. Eggeling, F. Rümpler, M. Groth, R. Melzer, G. Theißen
  DNA-binding properties of the MADS-domain transcription factor SEPALLATA3 and mutant variants characterized by SELEX-seq
  Plant Molecular Biology 2021
   
• A. B. Ünal, M. Akgün, N. Pfeifer
  ESCAPED: Efficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare
  Proceedings of the AAAI Conference on Artificial Intelligence 2021, 35(11), 9988-9996. Retrieved from ojs.aaai.org/index.php/AAAI/article/view/17199
   
• 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
   
• M. Akgün, A. Burak Ünal, B. Ergüner, N. Pfeifer, O. Kohlbacher
  Identifying Disease-Causing Mutations with Privacy Protection, 
  Bioinformatics, Volume 36, Issue 21, 1 November 2020
   
• J. Ditz, A. Schwarz, G. R. Müller-Putz
  Perturbation-evoked potentials can be classified from single-trial EEG
  April 2020, Journal of Neural Engineering
   
• H. Chen, A. Burak Ünal, M. Akgün, N. Pfeifer
  Privacy-preserving SVM on Outsourced Genomic Data via Secure Multi-party Computation
  March 2020, IWSPA '20: Proceedings of the Sixth International Workshop on Security and Privacy Analytics (Association for Computing Machinery, Pages 61–69) 
   
• S. Ehrhardt, M. Zehner, V. Krähling, H. Cohen-Dvashi, C. Kreer, N. Elad, H. Gruell, M.S. Ercanoglu, P. Schommers, L. Grieselmann, R. Eggeling, C. Dahlke, T. Wolf, N. Pfeifer, M. Addo, R. Diskin, S. Becker, F. Klein
  Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV
  Nature Medicine 2019, 25, 1589–1600
   
• A. B. Ünal, M. Akgün, N. Pfeifer
  A framework with randomized encoding for a fast privacy preserving calculation of non-linear kernels for machine learning applications in precision medicine
  CANS 2019, Lecture Notes in Computer Science
   
• M. Döring, C. Kreer, N. Lehnen, F. Klein, N. Pfeifer
  Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features
  Sci. Rep. 2019, 9, 10748.
   
• T. Talvitie, R. Eggeling, M. Koivisto
  Learning Bayesian networks with local structure, mixed variables, and exact algorithms
  International Journal of Approximate Reasoning, 2019
   
• B. Roeder, N. Kersten, M. Herr, N. Speicher, N. Pfeifer
  web-rMKL: A web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning,
  Nucleic Acids Research, Volume 47, Issue W1, 02 July 2019
   
• L. Handl, A. Jalali, M. Scherer, R. Eggeling, N. Pfeifer
  Weighted Elastic Net for Unsupervised Domain Adaptation with Application to Age Prediction from DNA Methylation Data
  Proceedings of ISMB/ECCB 2019,
  Bioinformatics 2019, Volume 35, Issue 14, July 2019, Pages i154–i163
   
• R. Eggeling, J. Viinikka, A. Vuoksenmaa, M. Koivisto
  On Structure Priors for Learning Bayesian Networks
  AISTATS 2019
   
• R. Eggeling, I. Grosse, M. Koivisto
  Algorithms for learning parsimonious context trees
  Machine Learning, 2019
   
• 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 479–484
   
• Y. Bar-On, H. Gruell, T. Schoofs, J. Pai, L. Nogueira, A. Butler, K. Millard, C. Lehmann, I. Suárez, T. Oliveira, T. Karagounis, Y. Cohen, C. Wyen, S. Scholten, L. Handl, S. Belblidia, J. Dizon, J. Vehreschild, M. Pack, I. Shimeliovich, K. Jain, K. Fiddike, K. Seaton, N. Yates, J. Horowitz, R. Gulick, N. Pfeifer, G. Tomaras, M. Seaman, G. Fätkenheuer, M. Caskey, F. Klein, M. C. Nussenzweig
  Safety and antiviral activity of combination HIV-1 broadly neutralizing antibodies in viremic individuals
  Nature Medicine 2018
   
• 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
   
• R. Apweiler, T. Beissbarth, M.R. Berthold, N. Blüthgen, Y. Burmeister, O. Dammann, A. Deutsch, F. Feuerhake, A. Franke, J. Hasenauer, S. Hoffmann, T. Höfer, P.L. Jansen, L. Kaderali, U. Klingmüller, I. Koch, O. Kohlbacher, L. Kuepfer, F. Lammert, D. Maier, N. Pfeifer, N. Radde, M. Rehm, I. Roeder, J. Saez-Rodriguez, U. Sax, B. Schmeck, A. Schuppert, B. Seilheimer, F.J. Theis, J. Vera, O. Wolkenhauer 
  Whither systems medicine?
  Exp Mol Med. 2018 Mar 2;50(3):e453.
   
• 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
   
• N. K. Speicher and N. Pfeifer
  Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples
  J Integr Bioinform 2017, 14(2)
   
• S. Nikumbh, P. Ebert, and N. Pfeifer
  All Fingers Are Not the Same: Handling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels
  In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Schloss Dagstuhl; 2017. [Leibniz International Proceedings in Informatics, vol. 88]
   
• S. Nikumbh and N. Pfeifer
  Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization
  BMC Bioinformatics 2017, 18, 218
   
• A. Pironti, N. Pfeifer, H. Walter, B.O. Jensen, M. Zazzi, P. Gomes, R. Kaiser, T. Lengauer
  Using drug exposure for predicting drug resistance – A data-driven genotypic interpretation tool
  PLoS One 2017, 12, e0174992
   
• 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 185–191
   
• M. Döring, P. Borrego, J. Büch, A. Martins, G. Friedrich, R. J. Camacho, J. Eberle, R. Kaiser, T. Lengauer, N. Taveira, N. Pfeifer
  A genotypic method for determining HIV-2 coreceptor usage enables epidemiological studies and clinical decision support
  Retrovirology 2016, 13:85
   
• A. Pironti, H. Walter, N. Pfeifer, E. Knops, N. Lübke, J. Büch, S. Di Gamberetto, R. Kaiser, T. Lengauer
  Determination of phenotypic resistance cutoffs from routine clinical data
  JAIDS 2016, 74(5):e129-e137
   
• J. F. Scheid*, Joshua 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
   
• P. Kalaghatgi, N. Pfeifer, and T. Lengauer
  Family-joining: A fast distance-based method for constructing generally labeled trees
  Molecular Biology and Evolution 2016, 33 (10), pp 2720-2734
   
• 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, M. A. 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
  + These authors jointly supervised this work
  * These authors contributed equally to this work
  Free access via the Springer Nature sharing initiative: pdf
  Check out the video explaining the main findings: MSR webpage
   
• 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 therapy with monoclonal antibody 3BNC117 elicits host immune responses against HIV-1
  Science 2016, 352 (6288), pp 997-1001
  *: equal contribution
   
• A. Jalali and N. Pfeifer
  Interpretable per Case Weighted Ensemble Method for Cancer Associations
  BMC Genomics 2016, 17:501
   
• 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, i268-i275
   
• A. Pironti, S. Sierra, R. Kaiser, T. Lengauer, and N. Pfeifer
  Effects of sequence alterations on results from genotypic tropism testing.
  J. Clin. Virol. 2015, 65, pp 68-73
   
• V. Kouri, R. Khouri, Y. Alemán, Y. Abrahantes, J. Vercauteren, A.-C. Pineda-Peña, K. Theys, S. Megens, M. Moutschen, N. Pfeifer, J. Van Weyenbergh, A. B. Pérez, J. Pérez, L. Pérez, K. Van Laethem, and A.-M. Vandamme
  CRF19_cpx is an evolutionary fit HIV-1 variant strongly associated with rapid progression to AIDS in Cuba.
  EBioMedicine 2015, 2 (3), pp 244-254
   
• M. Döring, G. Gasparoni, J. Gries, K. Nordström, P. Lutsik, J. Walter, and N. Pfeifer
  Identification and analysis of methylation call differences between bisulfite microarray and bisulfite sequencing data with statistical learning techniques 
  BMC Bioinformatics 2015, 16(Suppl 3):A7
   
• N. Pfeifer, H. Walter, and T. Lengauer
  Association between HIV-1 coreceptor usage and resistance to broadly neutralizing antibodies
  JAIDS 2014, 67 (2), pp 107-112
   
• S. Grund, C. Gkioule, T. Termos, N. Pfeifer, G. Kobbe, J. Verheyen, O. Adams
  Primarily oseltamivir resistant influenza A (H1N1pdm09) virus evolving into a multi-drug resistant virus carrying H275Y and I223R neuraminidase substitutions.
  Antivir Ther. 2014
   
• T. Lengauer, N. Pfeifer, and R. Kaiser
  Personalized HIV therapy to control drug resistance
  Drug Discovery Today: Technologies 2014, 11, pp 57-64
   
• O. Kalinina, N. Pfeifer, and T. Lengauer
  Modelling binding between CCR5 and CXCR4 receptors and their ligands suggests the surface electrostatic potential of the co-receptor to be a key player in the HIV-1 tropism
  Retrovirology 2013, 10:130
   
• I. Bartha, J. Carlson, C. Brumme, P. McLaren, Z. Brumme, M. John, D. Haas, J. Martinez-Picado, J. Dalmau, C. López Galíndez, C. Casado, A. Rauch, H. Günthard, E. Bernasconi, P. Vernazza, T. Klimkait, S. Yerly, S. O’Brien, J. Listgarten, N. Pfeifer, C. Lippert, N. Fusi, Z. Kutalik, T. Allen, V. Müller, P. R. Harrigan, D. Heckerman, A. Telenti, and J. Fellay
  A Genome-to-Genome Analysis of Associations between Human Genetic Variation, HIV-1 Sequence Diversity, and Viral Control
  eLife 2013, 2:e01123
  News coverage (Wired)
   
• Y. Yagita, N. Kuse, K. Kuroki, H. Gatanaga, J. M. Carlson, T. Chikata, Z. L. Brumme, H. Murakoshi, T. Akahoshi, N. Pfeifer, S. Mallal, M. John, T. Ose, H. Matsubara, R. Kanda, Y. Fukunaga, K. Honda, Y. Kawashima, Y. Ariumi, S. Oka, K. Maenaka, M. Takiguchi
  Distinct HIV-1 Escape Patterns Selected by CTLs with Identical Epitope Specificity
  J. Virol. 2013, 87 (4), pp 2253-2263
   
• J. M. Carlson, C. Brumme, E. Martin, J. Listgarten, M. Brockman, A. Le, C. Chui, L. Cotton, D. Knapp, S. Riddler, R. Haubrich, G. Nelson, N. Pfeifer, C. DeZiel, D. Heckerman, R. Apps, M. Carrington, S. Mallal, R. Harrigan, M. John, and Z. Brumme
  Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1 
  J. Virol. 2012, 86 (24), pp 13202-13216
   
• 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.
   
• J. M. Carlson, J. Listgarten, N. Pfeifer, V. Tan, C. Kadie, B. D. Walker, T. Ndung’u, R. Shapiro, J. Frater, Z. L. Brumme, P. J. R. Goulder, D. Heckerman
  Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1
  J. Virol. 2012, 86 (9), pp 5230-5243
   
• A. Bertsch, S. Jung, A. Zerck, N. Pfeifer, S. Nahnsen, C. Henneges, A. Nordheim, and O. Kohlbacher:
  Optimal de novo Design of MRM Experiments for Rapid Assay Development in Targeted Proteomics.
  Journal of Proteome Research 2010, 9 (5), pp 2696-2704
   
• N. Pfeifer, A. Leinenbach, C. G. Huber, O. Kohlbacher:
  Improving Peptide Identification in Proteome Analysis by a Two-Dimensional Retention Time Filtering Approach.
  Journal of Proteome Research 2009, 8 (8), pp 4109-4115
   
• O. Schulz-Trieglaff, N. Pfeifer, C. Gröpel, O. Kohlbacher, K. Reinert:
  LC-MSsim – a simulation software for Liquid Chromatography Mass Spectrometry data
  BMC Bioinformatics 2008, 9:423
   
• N. Pfeifer and O. Kohlbacher:
  Multiple Instance Learning Allows MHC Class II Epitope Predictions across Alleles
  Lecture Notes in Bioinformatics: Proceedings of WABI 2008, pp 210-221
   
• M. Sturm, A. Bertsch, C. Gröpl, A. Hildebrandt, R. Hussong, E. Lange, N. Pfeifer, O. Schulz-Trieglaff, A. Zerck, K. Reinert, O. Kohlbacher:
  OpenMS – An open-source software framework for mass spectrometry.
  BMC Bioinformatics 2008, 9:163.
   
• N. Pfeifer, A. Leinenbach, C. G. Huber, O. Kohlbacher:
  Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics.
  BMC Bioinformatics 2007, 8:468.
   
• C. Igel, T. Glasmachers, B. Mersch, N. Pfeifer, P. Meinicke:
  Gradient-based Optimization of Kernel-Target Alignment for Sequence Kernels Applied to Bacterial Gene Start Detection.
  IEEE/ACM Transactions on Computational Biology and Bioinformatics 2007, Vol. 4, No. 2:216-226.
   
• O. Kohlbacher, K. Reinert, C. Gröpl, E. Lange, N. Pfeifer, O. Schulz-Trieglaff, M. Sturm:
  TOPP – The OpenMS Proteomics Pipeline 
  “Proceedings of the 5th European Conference on Computational Biology (ECCB 2006)”, Bioinformatics 2007 23, e191-e197.
   
• M. Tech, N. Pfeifer, B. Morgenstern, P. Meinicke:
  TICO: a tool for improving predictions of prokaryotic translation initiation sites
  Bioinformatics 2005 21, 3568 – 3569.