Publications - Statistical Learning in Computational Biology

Publications

• 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
• 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, published ahead-of-print
• 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, 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
• 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
  Accepted for presentation at ISMB/ECCB 2015
  "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
• 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
• 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
• 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.
• M. Tech, N. Pfeifer, B. Morgenstern, P. Meinicke:
  TICO: a tool for improving predictions of prokaryotic translation initiation sites
  Bioinformatics 2005 21, 3568 - 3569.