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
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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
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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.