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Results: 1 to 20 of 69

1.

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 Oct 1;42(14):e115. doi: 10.1093/nar/gku537. Epub 2014 Jun 27.

PMID:
24972832
[PubMed - in process]
Free Article
2.

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.

PMID:
24875931
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
24675810
[PubMed - in process]
Free PMC Article
4.

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.

PMID:
24675718
[PubMed - in process]
Free PMC Article
5.

Challenges in RNA virus bioinformatics.

Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf M, Rattei T, Stadler PF, Töpfer A.

Bioinformatics. 2014 Jul 1;30(13):1793-9. doi: 10.1093/bioinformatics/btu105. Epub 2014 Mar 3.

PMID:
24590443
[PubMed - in process]
6.

Transcriptomic responses of cancerous and noncancerous human colon cells to sulforaphane and selenium.

Constantinescu S, Hecht K, Sobotzki N, Erzinger MM, Bovet C, Shay JW, Wollscheid B, Sturla SJ, Marra G, Beerenwinkel N.

Chem Res Toxicol. 2014 Mar 17;27(3):377-86. doi: 10.1021/tx400427t. Epub 2014 Jan 13.

PMID:
24383545
[PubMed - in process]
7.

Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction.

Dümcke S, Bräuer J, Anchang B, Spang R, Beerenwinkel N, Tresch A.

Bioinformatics. 2014 Feb 1;30(3):414-9. doi: 10.1093/bioinformatics/btt696. Epub 2013 Nov 30.

PMID:
24292937
[PubMed - indexed for MEDLINE]
8.

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model.

Prabhakaran S, Rey M, Zagordi O, Beerenwinkel N, Roth V.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov 8. [Epub ahead of print]

PMID:
24216116
[PubMed - as supplied by publisher]
9.

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.

PMID:
24058534
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
24009493
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
23879730
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
23442797
[PubMed - in process]
Free PMC Article
13.

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.

PMID:
23434406
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Sequencing approach to analyze the role of quasispecies for classical swine fever.

Töpfer A, Höper D, Blome S, Beer M, Beerenwinkel N, Ruggli N, Leifer I.

Virology. 2013 Mar 30;438(1):14-9. doi: 10.1016/j.virol.2012.11.020. Epub 2013 Feb 13.

PMID:
23415390
[PubMed - indexed for MEDLINE]
Free Article
15.

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.

PMID:
23383997
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
23382686
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Read length versus depth of coverage for viral quasispecies reconstruction.

Zagordi O, Däumer M, Beisel C, Beerenwinkel N.

PLoS One. 2012;7(10):e47046. doi: 10.1371/journal.pone.0047046. Epub 2012 Oct 3.

PMID:
23056573
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data.

Beerenwinkel N, Günthard HF, Roth V, Metzner KJ.

Front Microbiol. 2012 Sep 11;3:329. doi: 10.3389/fmicb.2012.00329. eCollection 2012.

PMID:
22973268
[PubMed]
Free PMC Article
19.

Efficient sampling for Bayesian inference of conjunctive Bayesian networks.

Sakoparnig T, Beerenwinkel N.

Bioinformatics. 2012 Sep 15;28(18):2318-24. doi: 10.1093/bioinformatics/bts433. Epub 2012 Jul 10.

PMID:
22782551
[PubMed - indexed for MEDLINE]
Free Article
20.

Reliable detection of subclonal single-nucleotide variants in tumour cell populations.

Gerstung M, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, Beerenwinkel N.

Nat Commun. 2012 May 1;3:811. doi: 10.1038/ncomms1814.

PMID:
22549840
[PubMed - indexed for MEDLINE]

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