Niko Beerenwinkel - Publications

Affiliations: 
ETH/Uni Zurich, Zürich, Zürich, Switzerland 

103 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Wan C, Bachmann N, Mitov V, Blanquart F, Céspedes SP, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Fellay J, Roth V, Böni J, Perreau M, Klimkait T, Yerly S, et al. Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART. Nature Communications. 11: 5542. PMID 33139735 DOI: 10.1038/s41467-020-19198-7  0.32
2020 Thorball CW, Borghesi A, Bachmann N, Von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Roth V, Kok YL, Parbhoo S, Wieser M, Böni J, Perreau M, et al. Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment. Journal of Acquired Immune Deficiency Syndromes (1999). 85: 517-524. PMID 33136754 DOI: 10.1097/QAI.0000000000002473  0.32
2020 Thorball CW, Borghesi A, Bachmann N, Von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Roth V, Kok YL, Parbhoo S, Wieser M, Böni J, Perreau M, et al. Host genomics of the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment. Journal of Acquired Immune Deficiency Syndromes (1999). PMID 32826560 DOI: 10.1097/QAI.0000000000002473  0.32
2019 Bachmann N, von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Fellay J, Roth V, Kok YL, Thorball CW, Borghesi A, Parbhoo S, Wieser M, Böni J, et al. Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART. Nature Communications. 10: 3193. PMID 31324762 DOI: 10.1038/s41467-019-10884-9  0.32
2016 Andritschke D, Dilling S, Emmenlauer M, Welz T, Schmich F, Misselwitz B, Rämö P, Rottner K, Kerkhoff E, Wada T, Penninger JM, Beerenwinkel N, Horvath P, Dehio C, Hardt WD. A Genome-Wide siRNA Screen Implicates Spire1/2 in SipA-Driven Salmonella Typhimurium Host Cell Invasion. Plos One. 11: e0161965. PMID 27627128 DOI: 10.1371/journal.pone.0161965  0.4
2016 Montazeri H, Kuipers J, Kouyos R, Böni J, Yerly S, Klimkait T, Aubert V, Günthard HF, Beerenwinkel N. Large-scale inference of conjunctive Bayesian networks. Bioinformatics (Oxford, England). 32: i727-i735. PMID 27587695 DOI: 10.1093/bioinformatics/btw459  0.4
2016 Jahn K, Kuipers J, Beerenwinkel N. Tree inference for single-cell data. Genome Biology. 17: 86. PMID 27149953 DOI: 10.1186/s13059-016-0936-x  0.4
2016 Erzinger MM, Bovet C, Hecht KM, Senger S, Winiker P, Sobotzki N, Cristea S, Beerenwinkel N, Shay JW, Marra G, Wollscheid B, Sturla SJ. Sulforaphane Preconditioning Sensitizes Human Colon Cancer Cells towards the Bioreductive Anticancer Prodrug PR-104A. Plos One. 11: e0150219. PMID 26950072 DOI: 10.1371/journal.pone.0150219  0.4
2016 Beerenwinkel N, Greenman CD, Lagergren J. Computational Cancer Biology: An Evolutionary Perspective. Plos Computational Biology. 12: e1004717. PMID 26845763 DOI: 10.1371/journal.pcbi.1004717  0.4
2015 Seifert D, Di Giallonardo F, Töpfer A, Singer J, Schmutz S, Günthard HF, Beerenwinkel N, Metzner KJ. A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations. Journal of Molecular Biology. PMID 26711506 DOI: 10.1016/j.jmb.2015.12.012  0.4
2015 Yilmaz A, Engeler R, Constantinescu S, Kokkaliaris KD, Dimitrakopoulos C, Schroeder T, Beerenwinkel N, Paro R. Ectopic expression of Msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation. Stem Cell Research. 15: 542-553. PMID 26468601 DOI: 10.1016/j.scr.2015.09.012  0.4
2015 Schmich F, Szczurek E, Kreibich S, Dilling S, Andritschke D, Casanova A, Low SH, Eicher S, Muntwiler S, Emmenlauer M, Rämö P, Conde-Alvarez R, von Mering C, Hardt WD, Dehio C, ... Beerenwinkel N, et al. gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens. Genome Biology. 16: 220. PMID 26445817 DOI: 10.1186/s13059-015-0783-1  0.4
2015 Vongrad V, Imig J, Mohammadi P, Kishore S, Jaskiewicz L, Hall J, Günthard HF, Beerenwinkel N, Metzner KJ. HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages. Plos One. 10: e0132127. PMID 26226348 DOI: 10.1371/journal.pone.0132127  0.4
2015 Moreau Y, Beerenwinkel N. ISMB/ECCB 2015. Bioinformatics (Oxford, England). 31: i1-i2. PMID 26072471 DOI: 10.1093/bioinformatics/btv303  0.4
2015 Montazeri H, Günthard HF, Yang WL, Kouyos R, Beerenwinkel N. Estimating the dynamics and dependencies of accumulating mutations with applications to HIV drug resistance. Biostatistics (Oxford, England). PMID 25979750 DOI: 10.1093/biostatistics/kxv019  0.4
2015 Siebourg-Polster J, Mudrak D, Emmenlauer M, Rämö P, Dehio C, Greber U, Fröhlich H, Beerenwinkel N. NEMix: single-cell nested effects models for probabilistic pathway stimulation. Plos Computational Biology. 11: e1004078. PMID 25879530 DOI: 10.1371/journal.pcbi.1004078  0.4
2015 Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N. BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies. Genome Biology. 16: 36. PMID 25786108 DOI: 10.1186/s13059-015-0592-6  0.4
2015 Sakoparnig T, Fried P, Beerenwinkel N. Identification of constrained cancer driver genes based on mutation timing. Plos Computational Biology. 11: e1004027. PMID 25569148 DOI: 10.1371/journal.pcbi.1004027  0.4
2015 Beerenwinkel N, Beretta S, Bonizzoni P, Dondi R, Pirola Y. Covering Pairs in Directed Acyclic Graphs Computer Journal. 58: 1673-1686. DOI: 10.1093/comjnl/bxu116  0.4
2015 Delgado-Eckert E, Beerenwinkel N. Genetic interactions and network reliability Systems Genetics: Linking Genotypes and Phenotypes. 51-64. DOI: 10.1017/CBO9781139012751.004  0.4
2015 Constantinescu S, Sturla SJ, Marra G, Wollscheid B, Beerenwinkel N. Computational data integration in toxicogenomics Computational Systems Toxicology. 371-392. DOI: 10.1007/978-1-4939-2778-4_15  0.4
2014 Prabhakaran S, Rey M, Zagordi O, Beerenwinkel N, Roth V. HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 11: 182-91. PMID 26355517 DOI: 10.1109/TCBB.2013.145  0.32
2014 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, et al. Simultaneous analysis of large-scale RNAi screens for pathogen entry. Bmc Genomics. 15: 1162. PMID 25534632 DOI: 10.1186/1471-2164-15-1162  0.4
2014 Gopalakrishnan S, Montazeri H, Menz S, Beerenwinkel N, Huisinga W. Estimating HIV-1 fitness characteristics from cross-sectional genotype data. Plos Computational Biology. 10: e1003886. PMID 25375675 DOI: 10.1371/journal.pcbi.1003886  0.4
2014 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, ... ... Beerenwinkel N, et al. Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Research. 42: e115. PMID 24972832 DOI: 10.1093/nar/gku537  0.4
2014 Mohammadi P, di Iulio J, Muñoz M, Martinez R, Bartha I, Cavassini M, Thorball C, Fellay J, Beerenwinkel N, Ciuffi A, Telenti A. Dynamics of HIV latency and reactivation in a primary CD4+ T cell model. Plos Pathogens. 10: e1004156. PMID 24875931 DOI: 10.1371/journal.ppat.1004156  0.4
2014 Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N. Viral quasispecies assembly via maximal clique enumeration. Plos Computational Biology. 10: e1003515. PMID 24675810 DOI: 10.1371/journal.pcbi.1003515  0.4
2014 Szczurek E, Beerenwinkel N. Modeling mutual exclusivity of cancer mutations. Plos Computational Biology. 10: e1003503. PMID 24675718 DOI: 10.1371/journal.pcbi.1003503  0.4
2014 Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf M, Rattei T, Stadler PF, Töpfer A. Challenges in RNA virus bioinformatics. Bioinformatics (Oxford, England). 30: 1793-9. PMID 24590443 DOI: 10.1093/bioinformatics/btu105  0.4
2014 Constantinescu S, Hecht K, Sobotzki N, Erzinger MM, Bovet C, Shay JW, Wollscheid B, Sturla SJ, Marra G, Beerenwinkel N. Transcriptomic responses of cancerous and noncancerous human colon cells to sulforaphane and selenium. Chemical Research in Toxicology. 27: 377-86. PMID 24383545 DOI: 10.1021/tx400427t  0.4
2014 Dümcke S, Bräuer J, Anchang B, Spang R, Beerenwinkel N, Tresch A. Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. Bioinformatics (Oxford, England). 30: 414-9. PMID 24292937 DOI: 10.1093/bioinformatics/btt696  0.4
2014 Töpfer A, Beerenwinkel N. Viral quasispecies assembly from paired-end reads 2014 Ieee 4th International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2014. DOI: 10.1109/ICCABS.2014.6863931  0.4
2013 Prabhakaran S, Rey M, Zagordi O, Beerenwinkel N, Roth V. HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. PMID 24216116 DOI: 10.1109/TCBB.2013.145  0.4
2013 Di Giallonardo F, Zagordi O, Duport Y, Leemann C, Joos B, Künzli-Gontarczyk M, Bruggmann R, Beerenwinkel N, Günthard HF, Metzner KJ. Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination. Plos One. 8: e74249. PMID 24058534 DOI: 10.1371/journal.pone.0074249  0.4
2013 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, et al. The individualized genetic barrier predicts treatment response in a large cohort of HIV-1 infected patients. Plos Computational Biology. 9: e1003203. PMID 24009493 DOI: 10.1371/journal.pcbi.1003203  0.4
2013 McElroy K, Zagordi O, Bull R, Luciani F, Beerenwinkel N. Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias. Bmc Genomics. 14: 501. PMID 23879730 DOI: 10.1186/1471-2164-14-501  0.4
2013 Kockmann T, Gerstung M, Schlumpf T, Xhinzhou Z, Hess D, Beerenwinkel N, Beisel C, Paro R. The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila. Genome Biology. 14: R18. PMID 23442797 DOI: 10.1186/gb-2013-14-2-r18  0.4
2013 Kawamura S, Gerstung M, Colozo AT, Helenius J, Maeda A, Beerenwinkel N, Park PS, Müller DJ. Kinetic, energetic, and mechanical differences between dark-state rhodopsin and opsin. Structure (London, England : 1993). 21: 426-37. PMID 23434406 DOI: 10.1016/j.str.2013.01.011  0.4
2013 Töpfer A, Höper D, Blome S, Beer M, Beerenwinkel N, Ruggli N, Leifer I. Sequencing approach to analyze the role of quasispecies for classical swine fever. Virology. 438: 14-9. PMID 23415390 DOI: 10.1016/j.virol.2012.11.020  0.4
2013 Töpfer A, Zagordi O, Prabhakaran S, Roth V, Halperin E, Beerenwinkel N. Probabilistic inference of viral quasispecies subject to recombination. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 113-23. PMID 23383997 DOI: 10.1089/cmb.2012.0232  0.4
2013 Mohammadi P, Desfarges S, Bartha I, Joos B, Zangger N, Muñoz M, Günthard HF, Beerenwinkel N, Telenti A, Ciuffi A. 24 hours in the life of HIV-1 in a T cell line. Plos Pathogens. 9: e1003161. PMID 23382686 DOI: 10.1371/journal.ppat.1003161  0.4
2012 Zagordi O, Däumer M, Beisel C, Beerenwinkel N. Read length versus depth of coverage for viral quasispecies reconstruction. Plos One. 7: e47046. PMID 23056573 DOI: 10.1371/journal.pone.0047046  0.4
2012 Beerenwinkel N, Günthard HF, Roth V, Metzner KJ. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Frontiers in Microbiology. 3: 329. PMID 22973268 DOI: 10.3389/fmicb.2012.00329  0.4
2012 Sakoparnig T, Beerenwinkel N. Efficient sampling for Bayesian inference of conjunctive Bayesian networks. Bioinformatics (Oxford, England). 28: 2318-24. PMID 22782551 DOI: 10.1093/bioinformatics/bts433  0.4
2012 Gerstung M, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, Beerenwinkel N. Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nature Communications. 3: 811. PMID 22549840 DOI: 10.1038/ncomms1814  0.4
2012 Siebourg J, Merdes G, Misselwitz B, Hardt WD, Beerenwinkel N. Stability of gene rankings from RNAi screens. Bioinformatics (Oxford, England). 28: 1612-8. PMID 22513992 DOI: 10.1093/bioinformatics/bts192  0.4
2012 Ojosnegros S, Delgado-Eckert E, Beerenwinkel N. Competition-colonization trade-off promotes coexistence of low-virulence viral strains. Journal of the Royal Society, Interface / the Royal Society. 9: 2244-54. PMID 22513722 DOI: 10.1098/rsif.2012.0160  0.4
2012 Beerenwinkel N, Siebourg J. Probability, statistics, and computational science. Methods in Molecular Biology (Clifton, N.J.). 855: 77-110. PMID 22407706 DOI: 10.1007/978-1-61779-582-4_3  0.4
2012 Sakoparnig T, Kockmann T, Paro R, Beisel C, Beerenwinkel N. Binding profiles of chromatin-modifying proteins are predictive for transcriptional activity and promoter-proximal pausing. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 126-38. PMID 22300315 DOI: 10.1089/cmb.2011.0258  0.4
2012 Ambatipudi S, Gerstung M, Pandey M, Samant T, Patil A, Kane S, Desai RS, Schäffer AA, Beerenwinkel N, Mahimkar MB. Genome-wide expression and copy number analysis identifies driver genes in gingivobuccal cancers. Genes, Chromosomes & Cancer. 51: 161-73. PMID 22072328 DOI: 10.1002/gcc.20940  0.4
2011 Beerenwinkel N, Zagordi O. Ultra-deep sequencing for the analysis of viral populations. Current Opinion in Virology. 1: 413-8. PMID 22440844 DOI: 10.1016/j.coviro.2011.07.008  0.4
2011 Gerstung M, Eriksson N, Lin J, Vogelstein B, Beerenwinkel N. The temporal order of genetic and pathway alterations in tumorigenesis. Plos One. 6: e27136. PMID 22069497 DOI: 10.1371/journal.pone.0027136  0.4
2011 Pathare SM, Gerstung M, Beerenwinkel N, Schäffer AA, Kannan S, Pai P, Pathak KA, Borges AM, Mahimkar MB. Clinicopathological and prognostic implications of genetic alterations in oral cancers. Oncology Letters. 2: 445-451. PMID 21546976 DOI: 10.3892/ol.2011.271  0.4
2011 Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. Bmc Bioinformatics. 12: 119. PMID 21521499 DOI: 10.1186/1471-2105-12-119  0.4
2011 Lefebvre G, Desfarges S, Uyttebroeck F, Muñoz M, Beerenwinkel N, Rougemont J, Telenti A, Ciuffi A. Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell. Journal of Virology. 85: 6205-11. PMID 21507965 DOI: 10.1128/JVI.00252-11  0.4
2011 Ambatipudi S, Gerstung M, Gowda R, Pai P, Borges AM, Schäffer AA, Beerenwinkel N, Mahimkar MB. Genomic profiling of advanced-stage oral cancers reveals chromosome 11q alterations as markers of poor clinical outcome. Plos One. 6: e17250. PMID 21386901 DOI: 10.1371/journal.pone.0017250  0.4
2011 Beerenwinkel N, Knupfer P, Tresch A. Learning monotonic genotype-phenotype maps. Statistical Applications in Genetics and Molecular Biology. 10: Article 3. PMID 21291413 DOI: 10.2202/1544-6115.1603  0.4
2011 Delgado-Eckert E, Ojosnegros S, Beerenwinkel N. The evolution of virulence in RNA viruses under a competition-colonization trade-off. Bulletin of Mathematical Biology. 73: 1881-908. PMID 21082274 DOI: 10.1007/s11538-010-9596-2  0.4
2011 Gerstung M, Nakhoul H, Beerenwinkel N. Evolutionary Games with Affine Fitness Functions: Applications to Cancer Dynamic Games and Applications. 1: 370-385. DOI: 10.1007/s13235-011-0029-0  0.4
2010 Ojosnegros S, Beerenwinkel N. Models of RNA virus evolution and their roles in vaccine design. Immunome Research. 6: S5. PMID 21067547 DOI: 10.1186/1745-7580-6-S2-S5  0.4
2010 Zagordi O, Klein R, Däumer M, Beerenwinkel N. Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Research. 38: 7400-9. PMID 20671025 DOI: 10.1093/nar/gkq655  0.4
2010 Schöllnberger H, Beerenwinkel N, Hoogenveen R, Vineis P. Cell selection as driving force in lung and colon carcinogenesis. Cancer Research. 70: 6797-803. PMID 20656803 DOI: 10.1158/0008-5472.CAN-09-4392  0.4
2010 Zagordi O, Geyrhofer L, Roth V, Beerenwinkel N. Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 417-28. PMID 20377454 DOI: 10.1089/cmb.2009.0164  0.4
2010 Ojosnegros S, Beerenwinkel N, Antal T, Nowak MA, Escarmís C, Domingo E. Competition-colonization dynamics in an RNA virus. Proceedings of the National Academy of Sciences of the United States of America. 107: 2108-12. PMID 20080701 DOI: 10.1073/pnas.0909787107  0.4
2010 Gerstung M, Beerenwinkel N. Waiting time models of cancer progression Mathematical Population Studies. 17: 115-135. DOI: 10.1080/08898480.2010.490994  0.4
2009 Gerstung M, Baudis M, Moch H, Beerenwinkel N. Quantifying cancer progression with conjunctive Bayesian networks. Bioinformatics (Oxford, England). 25: 2809-15. PMID 19692554 DOI: 10.1093/bioinformatics/btp505  0.4
2009 Pathare S, Schäffer AA, Beerenwinkel N, Mahimkar M. Construction of oncogenetic tree models reveals multiple pathways of oral cancer progression. International Journal of Cancer. Journal International Du Cancer. 124: 2864-71. PMID 19267402 DOI: 10.1002/ijc.24267  0.4
2009 Beerenwinkel N, Sullivant S. Markov models for accumulating mutations Biometrika. 96: 645-661. DOI: 10.1093/biomet/asp023  0.4
2009 Saeed F, Khokhar A, Zagordi O, Beerenwinkel N. Multiple sequence alignment system for pyrosequencing reads Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5462: 362-375. DOI: 10.1007/978-3-642-00727-9_34  0.4
2008 Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, Beerenwinkel N. Viral population estimation using pyrosequencing. Plos Computational Biology. 4: e1000074. PMID 18437230 DOI: 10.1371/journal.pcbi.1000074  0.4
2008 Jones S, Chen WD, Parmigiani G, Diehl F, Beerenwinkel N, Antal T, Traulsen A, Nowak MA, Siegel C, Velculescu VE, Kinzler KW, Vogelstein B, Willis J, Markowitz SD. Comparative lesion sequencing provides insights into tumor evolution. Proceedings of the National Academy of Sciences of the United States of America. 105: 4283-8. PMID 18337506 DOI: 10.1073/pnas.0712345105  0.4
2008 Beerenwinkel N, Roomp K, Däumer M. Evolution of Drug Resistance in HIV Bioinformatics-From Genomes to Therapies. 3: 1457-1495. DOI: 10.1002/9783527619368.ch40  0.4
2007 Sing T, Low AJ, Beerenwinkel N, Sander O, Cheung PK, Domingues FS, Büch J, Däumer M, Kaiser R, Lengauer T, Harrigan PR. Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antiviral Therapy. 12: 1097-106. PMID 18018768  0.4
2007 Beerenwinkel N, Antal T, Dingli D, Traulsen A, Kinzler KW, Velculescu VE, Vogelstein B, Nowak MA. Genetic progression and the waiting time to cancer. Plos Computational Biology. 3: e225. PMID 17997597 DOI: 10.1371/journal.pcbi.0030225  0.4
2007 Ahlenstiel G, Roomp K, Däumer M, Nattermann J, Vogel M, Rockstroh JK, Beerenwinkel N, Kaiser R, Nischalke HD, Sauerbruch T, Lengauer T, Spengler U. Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level. Clinical and Vaccine Immunology : Cvi. 14: 1266-73. PMID 17715334 DOI: 10.1128/CVI.00169-07  0.4
2007 Ketter R, Urbschat S, Henn W, Feiden W, Beerenwinkel N, Lengauer T, Steudel WI, Zang KD, Rahnenführer J. Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas. International Journal of Cancer. Journal International Du Cancer. 121: 1473-80. PMID 17557299 DOI: 10.1002/ijc.22855  0.4
2007 Altmann A, Beerenwinkel N, Sing T, Savenkov I, Doumer M, Kaiser R, Rhee SY, Fessel WJ, Shafer RW, Lengauer T. Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance. Antiviral Therapy. 12: 169-78. PMID 17503659  0.4
2007 Oette M, Kaiser R, Däumer M, Fätkenheuer G, Rockstroh JK, Knechten H, Mitrenga D, Beerenwinkel N, Sagir A, Pfister H, Häussinger D. [Epidemiology of primary drug resistance in chronically HIV-infected patients in Nordrhein-Westfalen, Germany, 2001-2005]. Deutsche Medizinische Wochenschrift (1946). 132: 977-82. PMID 17457780 DOI: 10.1055/s-2007-979365  0.4
2007 Beerenwinkel N, Pachter L, Sturmfels B, Elena SF, Lenski RE. Analysis of epistatic interactions and fitness landscapes using a new geometric approach. Bmc Evolutionary Biology. 7: 60. PMID 17433106 DOI: 10.1186/1471-2148-7-60  0.4
2007 Beerenwinkel N, Drton M. A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data. Biostatistics (Oxford, England). 8: 53-71. PMID 16569743 DOI: 10.1093/biostatistics/kxj033  0.4
2007 Beerenwinkel N, Eriksson N, Sturmfels B. Conjunctive Bayesian networks Bernoulli. 13: 893-909. DOI: 10.3150/07-BEJ6133  0.4
2007 Sing T, Beerenwinkel N. Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype Advances in Neural Information Processing Systems. 1297-1304.  0.4
2007 Beerenwinkel N, Pachter L, Sturmfels B. Epistasis and shapes of fitness landscapes Statistica Sinica. 17: 1317-1342.  0.4
2006 Yin J, Beerenwinkel N, Rahnenführer J, Lengauer T. Model selection for mixtures of mutagenetic trees. Statistical Applications in Genetics and Molecular Biology. 5: Article17. PMID 17049028 DOI: 10.2202/1544-6115.1164  0.4
2006 Lehmann C, Däumer M, Boussaad I, Sing T, Beerenwinkel N, Lengauer T, Schmeisser N, Wyen C, Fätkenheuer G, Kaiser R. Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART. Journal of Clinical Virology : the Official Publication of the Pan American Society For Clinical Virology. 37: 300-4. PMID 17005445 DOI: 10.1016/j.jcv.2006.08.008  0.4
2006 Svicher V, Sing T, Santoro MM, Forbici F, Rodríguez-Barrios F, Bertoli A, Beerenwinkel N, Bellocchi MC, Gago F, d'Arminio Monforte A, Antinori A, Lengauer T, Ceccherini-Silberstein F, Perno CF. Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors. Journal of Virology. 80: 7186-98. PMID 16809324 DOI: 10.1128/JVI.02084-05  0.4
2006 Beerenwinkel N, Eriksson N, Sturmfels B. Evolution on distributive lattices. Journal of Theoretical Biology. 242: 409-20. PMID 16650439 DOI: 10.1016/j.jtbi.2006.03.013  0.4
2006 Roomp K, Beerenwinkel N, Sing T, Schülter E, Büch J, Sierra-Aragon S, Däumer M, Hoffmann D, Kaiser R, Lengauer T, Selbig J. Arevir: A secure platform for designing personalized antiretroviral therapies against HIV Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4075: 185-194. DOI: 10.1007/11799511_16  0.4
2005 Wemmert S, Ketter R, Rahnenführer J, Beerenwinkel N, Strowitzki M, Feiden W, Hartmann C, Lengauer T, Stockhammer F, Zang KD, Meese E, Steudel WI, von Deimling A, Urbschat S. Patients with high-grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment. Neoplasia (New York, N.Y.). 7: 883-93. PMID 16242071 DOI: 10.1593/neo.05307  0.4
2005 Balduin M, Sierra S, Däumer MP, Rockstroh JK, Oette M, Fätkenheuer G, Kupfer B, Beerenwinkel N, Hoffmann D, Selbig J, Pfister HJ, Kaiser R. Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy. Journal of Clinical Virology : the Official Publication of the Pan American Society For Clinical Virology. 34: 277-87. PMID 16191482 DOI: 10.1016/j.jcv.2005.08.007  0.4
2005 Beerenwinkel N, Sing T, Lengauer T, Rahnenführer J, Roomp K, Savenkov I, Fischer R, Hoffmann D, Selbig J, Korn K, Walter H, Berg T, Braun P, Fätkenheuer G, Oette M, et al. Computational methods for the design of effective therapies against drug resistant HIV strains. Bioinformatics (Oxford, England). 21: 3943-50. PMID 16144807 DOI: 10.1093/bioinformatics/bti654  0.4
2005 Beerenwinkel N, Rahnenführer J, Däumer M, Hoffmann D, Kaiser R, Selbig J, Lengauer T. Learning multiple evolutionary pathways from cross-sectional data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 584-98. PMID 16108705 DOI: 10.1089/cmb.2005.12.584  0.4
2005 Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinformatics (Oxford, England). 21: 3940-1. PMID 16096348 DOI: 10.1093/bioinformatics/bti623  0.4
2005 Beerenwinkel N, Däumer M, Sing T, Rahnenfuhrer J, Lengauer T, Selbig J, Hoffmann D, Kaiser R. Estimating HIV evolutionary pathways and the genetic barrier to drug resistance. The Journal of Infectious Diseases. 191: 1953-60. PMID 15871130 DOI: 10.1086/430005  0.4
2005 Rahnenführer J, Beerenwinkel N, Schulz WA, Hartmann C, von Deimling A, Wullich B, Lengauer T. Estimating cancer survival and clinical outcome based on genetic tumor progression scores. Bioinformatics (Oxford, England). 21: 2438-46. PMID 15705654 DOI: 10.1093/bioinformatics/bti312  0.4
2005 Beerenwinkel N, Rahnenführer J, Kaiser R, Hoffmann D, Selbig J, Lengauer T. Mtreemix: a software package for learning and using mixture models of mutagenetic trees. Bioinformatics (Oxford, England). 21: 2106-7. PMID 15657098 DOI: 10.1093/bioinformatics/bti274  0.4
2005 Beerenwinkel N, Drton M. Mutagenetic tree models Algebraic Statistics For Computational Biology. 278-290. DOI: 10.1017/CBO9780511610684.018  0.4
2005 Sing T, Svicher V, Beerenwinkel N, Ceccherini-Silberstein F, Däumer M, Kaiser R, Walter H, Korn K, Hoffmann D, Oette M, Rockstroh JK, Fätkenheuer G, Perno CF, Lengauer T. Characterization of novel HIV drug resistance mutations using clustering, multidimensional scaling and SVM-based feature ranking Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3721: 285-296. DOI: 10.1007/11564126_30  0.4
2003 Wolf K, Walter H, Beerenwinkel N, Keulen W, Kaiser R, Hoffmann D, Lengauer T, Selbig J, Vandamme AM, Korn K, Schmidt B. Tenofovir resistance and resensitization. Antimicrobial Agents and Chemotherapy. 47: 3478-84. PMID 14576105 DOI: 10.1128/AAC.47.11.3478-3484.2003  0.4
2003 Beerenwinkel N, Lengauer T, Däumer M, Kaiser R, Walter H, Korn K, Hoffmann D, Selbig J. Methods for optimizing antiviral combination therapies. Bioinformatics (Oxford, England). 19: i16-25. PMID 12855433 DOI: 10.1093/bioinformatics/btg1001  0.4
2003 Beerenwinkel N, Däumer M, Oette M, Korn K, Hoffmann D, Kaiser R, Lengauer T, Selbig J, Walter H. Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Research. 31: 3850-5. PMID 12824435 DOI: 10.1093/nar/gkg575  0.4
2002 Beerenwinkel N, Schmidt B, Walter H, Kaiser R, Lengauer T, Hoffmann D, Korn K, Selbig J. Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype. Proceedings of the National Academy of Sciences of the United States of America. 99: 8271-6. PMID 12060770 DOI: 10.1073/pnas.112177799  0.4
2001 Beerenwinkel N, Lengauer T, Selbig J, Schmidt B, Walter H, Korn K, Kaiser R, Hoffmann D. Geno2pheno: Interpreting genotypic HIV drug resistance tests Ieee Intelligent Systems and Their Applications. 16: 35-41. DOI: 10.1109/5254.972080  0.4
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