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Results: 18

1.

Improved therapy-success prediction with GSS estimated from clinical HIV-1 sequences.

Pironti A, Pfeifer N, Kaiser R, Walter H, Lengauer T.

J Int AIDS Soc. 2014 Nov 2;17(4 Suppl 3):19743. doi: 10.7448/IAS.17.4.19743. eCollection 2014.

PMID:
25397488
[PubMed - in process]
Free PMC Article
2.

Association between HIV-1 coreceptor usage and resistance to broadly neutralizing antibodies.

Pfeifer N, Walter H, Lengauer T.

J Acquir Immune Defic Syndr. 2014 Oct 1;67(2):107-12. doi: 10.1097/QAI.0000000000000283.

PMID:
25072615
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Primarily oseltamivir-resistant influenza A (H1N1pdm09) virus evolving into a multidrug-resistant virus carrying H275Y and I223R neuraminidase substitutions.

Grund S, Gkioule C, Termos T, Pfeifer N, Kobbe G, Verheyen J, Adams O.

Antivir Ther. 2014 Jun 18. doi: 10.3851/IMP2811. [Epub ahead of print]

PMID:
24941247
[PubMed - as supplied by publisher]
4.

Personalized HIV therapy to control drug resistance.

Lengauer T, Pfeifer N, Kaiser R.

Drug Discov Today Technol. 2014 Mar;11:57-64. doi: 10.1016/j.ddtec.2014.02.004. Review.

PMID:
24847654
[PubMed - indexed for MEDLINE]
Free Article
5.

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.

Kalinina OV, Pfeifer N, Lengauer T.

Retrovirology. 2013 Nov 11;10:130. doi: 10.1186/1742-4690-10-130.

PMID:
24215935
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.

Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, John M, Haas DW, Martinez-Picado J, Dalmau J, López-Galíndez C, Casado C, Rauch A, Günthard HF, Bernasconi E, Vernazza P, Klimkait T, Yerly S, O'Brien SJ, Listgarten J, Pfeifer N, Lippert C, Fusi N, Kutalik Z, Allen TM, Müller V, Harrigan PR, Heckerman D, Telenti A, Fellay J.

Elife. 2013 Oct 29;2:e01123. doi: 10.7554/eLife.01123.

PMID:
24171102
[PubMed - in process]
Free PMC Article
7.

Distinct HIV-1 escape patterns selected by cytotoxic T cells with identical epitope specificity.

Yagita Y, Kuse N, Kuroki K, Gatanaga H, Carlson JM, Chikata T, Brumme ZL, Murakoshi H, Akahoshi T, Pfeifer N, Mallal S, John M, Ose T, Matsubara H, Kanda R, Fukunaga Y, Honda K, Kawashima Y, Ariumi Y, Oka S, Maenaka K, Takiguchi M.

J Virol. 2013 Feb;87(4):2253-63. doi: 10.1128/JVI.02572-12. Epub 2012 Dec 12.

PMID:
23236061
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1.

Carlson JM, Brumme CJ, Martin E, Listgarten J, Brockman MA, Le AQ, Chui CK, Cotton LA, Knapp DJ, Riddler SA, Haubrich R, Nelson G, Pfeifer N, Deziel CE, Heckerman D, Apps R, Carrington M, Mallal S, Harrigan PR, John M, Brumme ZL; International HIV Adaptation Collaborative.

J Virol. 2012 Dec;86(24):13202-16. doi: 10.1128/JVI.01998-12. Epub 2012 Oct 10.

PMID:
23055555
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data.

Pfeifer N, Lengauer T.

Bioinformatics. 2012 Sep 15;28(18):i589-i595. doi: 10.1093/bioinformatics/bts373.

PMID:
22962486
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Widespread impact of HLA restriction on immune control and escape pathways of HIV-1.

Carlson JM, Listgarten J, Pfeifer N, Tan V, Kadie C, Walker BD, Ndung'u T, Shapiro R, Frater J, Brumme ZL, Goulder PJ, Heckerman D.

J Virol. 2012 May;86(9):5230-43. doi: 10.1128/JVI.06728-11. Epub 2012 Feb 29.

PMID:
22379086
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics.

Bertsch A, Jung S, Zerck A, Pfeifer N, Nahnsen S, Henneges C, Nordheim A, Kohlbacher O.

J Proteome Res. 2010 May 7;9(5):2696-704. doi: 10.1021/pr1001803.

PMID:
20201589
[PubMed - indexed for MEDLINE]
12.

Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach.

Pfeifer N, Leinenbach A, Huber CG, Kohlbacher O.

J Proteome Res. 2009 Aug;8(8):4109-15. doi: 10.1021/pr900064b.

PMID:
19492844
[PubMed - indexed for MEDLINE]
13.

LC-MSsim--a simulation software for liquid chromatography mass spectrometry data.

Schulz-Trieglaff O, Pfeifer N, Gröpl C, Kohlbacher O, Reinert K.

BMC Bioinformatics. 2008 Oct 8;9:423. doi: 10.1186/1471-2105-9-423.

PMID:
18842122
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

OpenMS - an open-source software framework for mass spectrometry.

Sturm M, Bertsch A, Gröpl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O.

BMC Bioinformatics. 2008 Mar 26;9:163. doi: 10.1186/1471-2105-9-163.

PMID:
18366760
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

Pfeifer N, Leinenbach A, Huber CG, Kohlbacher O.

BMC Bioinformatics. 2007 Nov 30;8:468.

PMID:
18053132
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Gradient-based optimization of kernel-target alignment for sequence kernels applied to bacterial gene start detection.

Igel C, Glasmachers T, Mersch B, Pfeifer N, Meinicke P.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Apr-Jun;4(2):216-26.

PMID:
17473315
[PubMed - indexed for MEDLINE]
17.

TOPP--the OpenMS proteomics pipeline.

Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M.

Bioinformatics. 2007 Jan 15;23(2):e191-7.

PMID:
17237091
[PubMed - indexed for MEDLINE]
Free Article
18.

TICO: a tool for improving predictions of prokaryotic translation initiation sites.

Tech M, Pfeifer N, Morgenstern B, Meinicke P.

Bioinformatics. 2005 Sep 1;21(17):3568-9. Epub 2005 Jun 30.

PMID:
15994191
[PubMed - indexed for MEDLINE]
Free Article
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