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Results: 1 to 20 of 46

1.

Correction: 24 Hours in the Life of HIV-1 in a T Cell Line.

Mohammadi P, Desfarges S, Bartha I, Joos B, Zangger N, Muñoz M, Günthard HF, Beerenwinkel N, Telenti A, Ciuffi A.

PLoS Pathog. 2015 Jun 15;11(6):e1005006. doi: 10.1371/journal.ppat.1005006. eCollection 2015 Jun.

2.

NEMix: single-cell nested effects models for probabilistic pathway stimulation.

Siebourg-Polster J, Mudrak D, Emmenlauer M, Rämö P, Dehio C, Greber U, Fröhlich H, Beerenwinkel N.

PLoS Comput Biol. 2015 Apr 16;11(4):e1004078. doi: 10.1371/journal.pcbi.1004078. eCollection 2015 Apr.

3.

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.

Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N.

Genome Biol. 2015 Feb 13;16:36. doi: 10.1186/s13059-015-0592-6.

4.

Identification of constrained cancer driver genes based on mutation timing.

Sakoparnig T, Fried P, Beerenwinkel N.

PLoS Comput Biol. 2015 Jan 8;11(1):e1004027. doi: 10.1371/journal.pcbi.1004027. eCollection 2015 Jan.

5.

Dynamic models of viral replication and latency.

Mohammadi P, Ciuffi A, Beerenwinkel N.

Curr Opin HIV AIDS. 2015 Mar;10(2):90-5. doi: 10.1097/COH.0000000000000136.

6.

Simultaneous analysis of large-scale RNAi screens for pathogen entry.

Rämö P, Drewek A, Arrieumerlou C, Beerenwinkel N, Ben-Tekaya H, Cardel B, Casanova A, Conde-Alvarez R, Cossart P, Csúcs G, Eicher S, Emmenlauer M, Greber U, Hardt WD, Helenius A, Kasper C, Kaufmann A, Kreibich S, Kühbacher A, Kunszt P, Low SH, Mercer J, Mudrak D, Muntwiler S, Pelkmans L, Pizarro-Cerdá J, Podvinec M, Pujadas E, Rinn B, Rouilly V, Schmich F, Siebourg-Polster J, Snijder B, Stebler M, Studer G, Szczurek E, Truttmann M, von Mering C, Vonderheit A, Yakimovich A, Bühlmann P, Dehio C.

BMC Genomics. 2014 Dec 22;15:1162. doi: 10.1186/1471-2164-15-1162.

7.

A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory.

Seifert D, Di Giallonardo F, Metzner KJ, Günthard HF, Beerenwinkel N.

Genetics. 2015 Jan;199(1):191-203. doi: 10.1534/genetics.114.172312. Epub 2014 Nov 17. Erratum in: Genetics. 2015 Apr;199(4):1271.

8.

Estimating HIV-1 fitness characteristics from cross-sectional genotype data.

Gopalakrishnan S, Montazeri H, Menz S, Beerenwinkel N, Huisinga W.

PLoS Comput Biol. 2014 Nov 6;10(11):e1003886. doi: 10.1371/journal.pcbi.1003886. eCollection 2014 Nov.

9.

Cancer evolution: mathematical models and computational inference.

Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F.

Syst Biol. 2015 Jan;64(1):e1-25. doi: 10.1093/sysbio/syu081. Epub 2014 Oct 7. Review.

10.

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations.

Giallonardo FD, Töpfer A, Rey M, Prabhakaran S, Duport Y, Leemann C, Schmutz S, Campbell NK, Joos B, Lecca MR, Patrignani A, Däumer M, Beisel C, Rusert P, Trkola A, Günthard HF, Roth V, Beerenwinkel N, Metzner KJ.

Nucleic Acids Res. 2014 Aug;42(14):e115. doi: 10.1093/nar/gku537. Epub 2014 Jun 27.

11.

Dynamics of HIV latency and reactivation in a primary CD4+ T cell model.

Mohammadi P, di Iulio J, Muñoz M, Martinez R, Bartha I, Cavassini M, Thorball C, Fellay J, Beerenwinkel N, Ciuffi A, Telenti A.

PLoS Pathog. 2014 May 29;10(5):e1004156. doi: 10.1371/journal.ppat.1004156. eCollection 2014 May.

12.

Viral quasispecies assembly via maximal clique enumeration.

Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003515. doi: 10.1371/journal.pcbi.1003515. eCollection 2014 Mar.

13.

Modeling mutual exclusivity of cancer mutations.

Szczurek E, Beerenwinkel N.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003503. doi: 10.1371/journal.pcbi.1003503. eCollection 2014 Mar.

14.

Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination.

Di Giallonardo F, Zagordi O, Duport Y, Leemann C, Joos B, Künzli-Gontarczyk M, Bruggmann R, Beerenwinkel N, Günthard HF, Metzner KJ.

PLoS One. 2013 Sep 18;8(9):e74249. doi: 10.1371/journal.pone.0074249. eCollection 2013.

15.

The individualized genetic barrier predicts treatment response in a large cohort of HIV-1 infected patients.

Beerenwinkel N, Montazeri H, Schuhmacher H, Knupfer P, von Wyl V, Furrer H, Battegay M, Hirschel B, Cavassini M, Vernazza P, Bernasconi E, Yerly S, Böni J, Klimkait T, Cellerai C, Günthard HF; Swiss HIV Cohort Study.

PLoS Comput Biol. 2013;9(8):e1003203. doi: 10.1371/journal.pcbi.1003203. Epub 2013 Aug 29.

16.

Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias.

McElroy K, Zagordi O, Bull R, Luciani F, Beerenwinkel N.

BMC Genomics. 2013 Jul 24;14:501. doi: 10.1186/1471-2164-14-501.

17.

The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila.

Kockmann T, Gerstung M, Schlumpf T, Xhinzhou Z, Hess D, Beerenwinkel N, Beisel C, Paro R.

Genome Biol. 2013 Feb 25;14(2):R18. doi: 10.1186/gb-2013-14-2-r18.

18.

Kinetic, energetic, and mechanical differences between dark-state rhodopsin and opsin.

Kawamura S, Gerstung M, Colozo AT, Helenius J, Maeda A, Beerenwinkel N, Park PS, Müller DJ.

Structure. 2013 Mar 5;21(3):426-37. doi: 10.1016/j.str.2013.01.011. Epub 2013 Feb 21.

19.

Probabilistic inference of viral quasispecies subject to recombination.

Töpfer A, Zagordi O, Prabhakaran S, Roth V, Halperin E, Beerenwinkel N.

J Comput Biol. 2013 Feb;20(2):113-23. doi: 10.1089/cmb.2012.0232.

20.

24 hours in the life of HIV-1 in a T cell line.

Mohammadi P, Desfarges S, Bartha I, Joos B, Zangger N, Muñoz M, Günthard HF, Beerenwinkel N, Telenti A, Ciuffi A.

PLoS Pathog. 2013 Jan;9(1):e1003161. doi: 10.1371/journal.ppat.1003161. Epub 2013 Jan 31.

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