| Year |
Citation |
Score |
| 2020 |
Grossmann P, Cristea S, Beerenwinkel N. Clonal evolution driven by superdriver mutations. Bmc Evolutionary Biology. 20: 89. PMID 32689942 DOI: 10.1186/S12862-020-01647-Y |
0.36 |
|
| 2020 |
Borgsmüller N, Bonet J, Marass F, Gonzalez-Perez A, Lopez-Bigas N, Beerenwinkel N. BnpC: Bayesian non-parametric clustering of single-cell mutation profiles. Bioinformatics (Oxford, England). PMID 32592465 DOI: 10.1093/Bioinformatics/Btaa599 |
0.347 |
|
| 2020 |
Pélissier A, Akrout Y, Jahn K, Kuipers J, Klein U, Beerenwinkel N, Rodríguez Martínez M. Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts. Cells. 9. PMID 32532145 DOI: 10.3390/Cells9061448 |
0.306 |
|
| 2020 |
Ringel T, Frey N, Ringnalda F, Janjuha S, Cherkaoui S, Butz S, Srivatsa S, Pirkl M, Russo G, Villiger L, Rogler G, Clevers H, Beerenwinkel N, Zamboni N, Baubec T, et al. Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance. Cell Stem Cell. 26: 431-440.e8. PMID 32142663 DOI: 10.1016/J.Stem.2020.02.007 |
0.317 |
|
| 2020 |
Dirmeier S, Dächert C, van Hemert M, Tas A, Ogando NS, van Kuppeveld F, Bartenschlager R, Kaderali L, Binder M, Beerenwinkel N. Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation. Plos Computational Biology. 16: e1007587. PMID 32040506 DOI: 10.1371/Journal.Pcbi.1007587 |
0.316 |
|
| 2020 |
Lang BM, Kuipers J, Misselwitz B, Beerenwinkel N. Predicting colorectal cancer risk from adenoma detection via a two-type branching process model. Plos Computational Biology. 16: e1007552. PMID 32023238 DOI: 10.1371/Journal.Pcbi.1007552 |
0.324 |
|
| 2020 |
Marass F, Castro-Giner F, Szczerba BM, Jahn K, Kuipers J, Aceto N, Beerenwinkel N. Computational Analysis of DNA and RNA Sequencing Data Obtained from Liquid Biopsies. Recent Results in Cancer Research. Fortschritte Der Krebsforschung. Progres Dans Les Recherches Sur Le Cancer. 215: 347-368. PMID 31605238 DOI: 10.1007/978-3-030-26439-0_18 |
0.301 |
|
| 2019 |
Hosseini SR, Diaz-Uriarte R, Markowetz F, Beerenwinkel N. Estimating the predictability of cancer evolution. Bioinformatics (Oxford, England). 35: i389-i397. PMID 31510665 DOI: 10.1093/Bioinformatics/Btz332 |
0.316 |
|
| 2019 |
Malikic S, Jahn K, Kuipers J, Sahinalp SC, Beerenwinkel N. Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data. Nature Communications. 10: 2750. PMID 31227714 DOI: 10.1038/S41467-019-10737-5 |
0.341 |
|
| 2019 |
Silverbush D, Cristea S, Yanovich-Arad G, Geiger T, Beerenwinkel N, Sharan R. Simultaneous Integration of Multi-omics Data Improves the Identification of Cancer Driver Modules. Cell Systems. 8: 456-466.e5. PMID 31103572 DOI: 10.1016/J.Cels.2019.04.005 |
0.34 |
|
| 2019 |
Schmich F, Kuipers J, Merdes G, Beerenwinkel N. netprioR: a probabilistic model for integrative hit prioritisation of genetic screens. Statistical Applications in Genetics and Molecular Biology. PMID 30840598 DOI: 10.1515/Sagmb-2018-0033 |
0.352 |
|
| 2019 |
Szczerba BM, Castro-Giner F, Vetter M, Krol I, Gkountela S, Landin J, Scheidmann MC, Donato C, Scherrer R, Singer J, Beisel C, Kurzeder C, Heinzelmann-Schwarz V, Rochlitz C, Weber WP, ... Beerenwinkel N, et al. Neutrophils escort circulating tumour cells to enable cell cycle progression. Nature. PMID 30728496 DOI: 10.1038/S41586-019-0915-Y |
0.321 |
|
| 2019 |
Bihr S, Ohashi R, Moore AL, Rüschoff JH, Beisel C, Hermanns T, Mischo A, Corrò C, Beyer J, Beerenwinkel N, Moch H, Schraml P. Expression and Mutation Patterns of PBRM1, BAP1 and SETD2 Mirror Specific Evolutionary Subtypes in Clear Cell Renal Cell Carcinoma. Neoplasia (New York, N.Y.). 21: 247-256. PMID 30660076 DOI: 10.1016/J.Neo.2018.12.006 |
0.321 |
|
| 2019 |
Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A. Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection. Scientific Reports. 9: 213. PMID 30659199 DOI: 10.1038/S41598-018-36135-3 |
0.331 |
|
| 2018 |
Singer J, Kuipers J, Jahn K, Beerenwinkel N. Single-cell mutation identification via phylogenetic inference. Nature Communications. 9: 5144. PMID 30514897 DOI: 10.1038/S41467-018-07627-7 |
0.366 |
|
| 2018 |
Kuipers J, Thurnherr T, Moffa G, Suter P, Behr J, Goosen R, Christofori G, Beerenwinkel N. Mutational interactions define novel cancer subgroups. Nature Communications. 9: 4353. PMID 30341300 DOI: 10.1038/S41467-018-06867-X |
0.371 |
|
| 2018 |
Lienkaemper C, Lamberti L, Drain J, Beerenwinkel N, Gavryushkin A. The geometry of partial fitness orders and an efficient method for detecting genetic interactions. Journal of Mathematical Biology. PMID 29736875 DOI: 10.1007/S00285-018-1237-7 |
0.303 |
|
| 2018 |
Lopes MB, Veríssimo A, Carrasquinha E, Casimiro S, Beerenwinkel N, Vinga S. Ensemble outlier detection and gene selection in triple-negative breast cancer data. Bmc Bioinformatics. 19: 168. PMID 29728051 DOI: 10.1186/S12859-018-2149-7 |
0.322 |
|
| 2018 |
Dimitrakopoulos C, Kumar Hindupur S, Häfliger L, Behr J, Montazeri H, Hall MN, Beerenwinkel N. Network-based integration of multi-omics data for prioritizing cancer genes. Bioinformatics (Oxford, England). PMID 29547932 DOI: 10.1093/Bioinformatics/Bty148 |
0.328 |
|
| 2017 |
Singer J, Irmisch A, Ruscheweyh HJ, Singer F, Toussaint NC, Levesque MP, Stekhoven DJ, Beerenwinkel N. Bioinformatics for precision oncology. Briefings in Bioinformatics. PMID 29272324 DOI: 10.1093/Bib/Bbx143 |
0.303 |
|
| 2017 |
Crona K, Gavryushkin A, Greene D, Beerenwinkel N. Inferring genetic interactions from comparative fitness data. Elife. 6. PMID 29260711 DOI: 10.7554/Elife.28629 |
0.331 |
|
| 2017 |
Kuipers J, Jahn K, Raphael BJ, Beerenwinkel N. Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors. Genome Research. PMID 29030470 DOI: 10.1101/Gr.220707.117 |
0.375 |
|
| 2017 |
Pirkl M, Diekmann M, van der Wees M, Beerenwinkel N, Fröhlich H, Markowetz F. Inferring modulators of genetic interactions with epistatic nested effects models. Plos Computational Biology. 13: e1005496. PMID 28406896 DOI: 10.1371/Journal.Pcbi.1005496 |
0.328 |
|
| 2017 |
Kuipers J, Jahn K, Beerenwinkel N. Advances in understanding tumour evolution through single-cell sequencing. Biochimica Et Biophysica Acta. PMID 28193548 DOI: 10.1016/J.Bbcan.2017.02.001 |
0.368 |
|
| 2017 |
Hofmann AL, Behr J, Singer J, Kuipers J, Beisel C, Schraml P, Moch H, Beerenwinkel N. Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. Bmc Bioinformatics. 18: 8. PMID 28049408 DOI: 10.1186/S12859-016-1417-7 |
0.338 |
|
| 2016 |
Thurnherr T, Singer F, Stekhoven DJ, Beerenwinkel N. Genomic variant annotation workflow for clinical applications. F1000research. 5: 1963. PMID 27990260 DOI: 10.12688/F1000Research.9357.2 |
0.313 |
|
| 2016 |
Cristea S, Kuipers J, Beerenwinkel N. pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27936934 DOI: 10.1089/Cmb.2016.0171 |
0.356 |
|
| 2016 |
Dimitrakopoulos CM, Beerenwinkel N. Computational approaches for the identification of cancer genes and pathways. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. PMID 27863091 DOI: 10.1002/Wsbm.1364 |
0.369 |
|
| 2016 |
Posada-Cespedes S, Seifert D, Beerenwinkel N. Recent Advances in Inferring Viral Diversity from High-throughput Sequencing Data. Virus Research. PMID 27693290 DOI: 10.1016/J.Virusres.2016.09.016 |
0.33 |
|
| 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 |
0.367 |
|
| 2016 |
Betz-Stablein BD, Töpfer A, Littlejohn M, Yuen L, Colledge D, Sozzi V, Angus P, Thompson A, Revill P, Beerenwinkel N, Warner N, Luciani F. Single-molecule sequencing reveals complex genomic variation of hepatitis B virus during 15 years of chronic infection following liver transplantation. Journal of Virology. PMID 27252524 DOI: 10.1128/Jvi.00243-16 |
0.325 |
|
| 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 |
0.373 |
|
| 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 |
0.37 |
|
| 2016 |
Dazert E, Heim M, Beerenwinkel N, Hall MN. Abstract IA22: Mechanisms of evasive resistance in cancer Molecular Cancer Research. 14. DOI: 10.1158/1557-3125.Devbiolca15-Ia22 |
0.309 |
|
| 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 |
0.315 |
|
| 2015 |
Levesque MP, Dummer R, Beerenwinkel N. Perturbing resistance: a network perspective. Pigment Cell & Melanoma Research. PMID 26471867 DOI: 10.1111/Pcmr.12431 |
0.308 |
|
| 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 |
0.307 |
|
| 2015 |
Seifert D, Beerenwinkel N. Estimating Fitness of Viral Quasispecies from Next-Generation Sequencing Data. Current Topics in Microbiology and Immunology. PMID 26318139 DOI: 10.1007/82_2015_462 |
0.344 |
|
| 2015 |
Constantinescu S, Szczurek E, Mohammadi P, Rahnenführer J, Beerenwinkel N. TiMEx: a waiting time model for mutually exclusive cancer alterations. Bioinformatics (Oxford, England). PMID 26163509 DOI: 10.1093/Bioinformatics/Btv400 |
0.359 |
|
| 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 |
0.351 |
|
| 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 |
0.338 |
|
| 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 |
0.308 |
|
| 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 |
0.375 |
|
| 2015 |
Seifert D, Di Giallonardo F, Metzner KJ, Günthard HF, Beerenwinkel N. A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory. Genetics. 199: 191-203. PMID 25406469 DOI: 10.1534/Genetics.114.172312 |
0.346 |
|
| 2015 |
Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F. Cancer evolution: mathematical models and computational inference. Systematic Biology. 64: e1-25. PMID 25293804 DOI: 10.1093/Sysbio/Syu081 |
0.355 |
|
| 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 |
0.336 |
|
| 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 |
0.351 |
|
| 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 |
0.343 |
|
| 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 |
0.326 |
|
| 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 |
0.334 |
|
| 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 |
0.301 |
|
| 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 |
0.339 |
|
| 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 |
0.366 |
|
| 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 |
0.334 |
|
| 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 |
0.326 |
|
| 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 |
0.375 |
|
| 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 |
0.319 |
|
| 2013 |
Töpfer A, Boskova V, Daumer M, Thielen A, Seifert D, Beerenwinkel N. Visualization of viral populations F1000research. 4. DOI: 10.7490/F1000Research.1092903.1 |
0.324 |
|
| 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 |
0.334 |
|
| 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 |
0.368 |
|
| 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 |
0.373 |
|
| 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 |
0.331 |
|
| 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 |
0.32 |
|
| 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 |
0.302 |
|
| 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 |
0.302 |
|
| 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 |
0.332 |
|
| 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 |
0.349 |
|
| 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 |
0.314 |
|
| 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 |
0.32 |
|
| 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 |
0.359 |
|
| 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 |
0.337 |
|
| 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 |
0.322 |
|
| 2010 |
Ojosnegros S, Beerenwinkel N, Domingo E. Competition-colonization dynamics: An ecology approach to quasispecies dynamics and virulence evolution in RNA viruses. Communicative & Integrative Biology. 3: 333-6. PMID 20798818 DOI: 10.4161/Cib.3.4.11658 |
0.331 |
|
| 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 |
0.343 |
|
| 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 |
0.347 |
|
| 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 |
0.32 |
|
| 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 |
0.331 |
|
| 2010 |
Gerstung M, Beerenwinkel N. Waiting time models of cancer progression Mathematical Population Studies. 17: 115-135. DOI: 10.1080/08898480.2010.490994 |
0.36 |
|
| 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 |
0.371 |
|
| 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 |
0.306 |
|
| 2009 |
Altmann A, Däumer M, Beerenwinkel N, Peres Y, Schülter E, Büch J, Rhee SY, Sönnerborg A, Fessel WJ, Shafer RW, Zazzi M, Kaiser R, Lengauer T. Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. The Journal of Infectious Diseases. 199: 999-1006. PMID 19239365 DOI: 10.1086/597305 |
0.324 |
|
| 2009 |
Beerenwinkel N, Sullivant S. Markov models for accumulating mutations Biometrika. 96: 645-661. DOI: 10.1093/Biomet/Asp023 |
0.366 |
|
| 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 |
0.352 |
|
| 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 |
0.351 |
|
| 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 |
0.37 |
|
| 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 |
0.33 |
|
| 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 |
0.547 |
|
| 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 |
0.362 |
|
| 2007 |
Beerenwinkel N, Eriksson N, Sturmfels B. Conjunctive Bayesian networks Bernoulli. 13: 893-909. DOI: 10.3150/07-Bej6133 |
0.301 |
|
| 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 |
0.342 |
|
| 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 |
0.307 |
|
| 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 |
0.32 |
|
| 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 |
0.33 |
|
| 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 |
0.304 |
|
| 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 |
0.346 |
|
| 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 |
0.343 |
|
| 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 |
0.34 |
|
| 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 |
0.346 |
|
| 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 |
0.317 |
|
| 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 |
0.319 |
|
| 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 |
0.323 |
|
| 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 |
0.302 |
|
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