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Items: 1 to 50 of 150

1.

Computational Analysis of DNA and RNA Sequencing Data Obtained from Liquid Biopsies.

Marass F, Castro-Giner F, Szczerba BM, Jahn K, Kuipers J, Aceto N, Beerenwinkel N.

Recent Results Cancer Res. 2020;215:347-368. doi: 10.1007/978-3-030-26439-0_18.

PMID:
31605238
2.

Inferring signalling dynamics by integrating interventional with observational data.

Cardner M, Meyer-Schaller N, Christofori G, Beerenwinkel N.

Bioinformatics. 2019 Jul 15;35(14):i577-i585. doi: 10.1093/bioinformatics/btz325.

3.

Estimating the predictability of cancer evolution.

Hosseini SR, Diaz-Uriarte R, Markowetz F, Beerenwinkel N.

Bioinformatics. 2019 Jul 15;35(14):i389-i397. doi: 10.1093/bioinformatics/btz332.

4.

Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART.

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, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Hoffmann M, Bernasconi E, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ; Swiss HIV Cohort Study.

Nat Commun. 2019 Jul 19;10(1):3193. doi: 10.1038/s41467-019-10884-9.

5.

Probability, Statistics, and Computational Science.

Beerenwinkel N, Siebourg J.

Methods Mol Biol. 2019;1910:33-70. doi: 10.1007/978-1-4939-9074-0_2.

PMID:
31278661
6.

Tracing Clonal Dynamics Reveals that Two- and Three-dimensional Patient-derived Cell Models Capture Tumor Heterogeneity of Clear Cell Renal Cell Carcinoma.

Bolck HA, Corrò C, Kahraman A, von Teichman A, Toussaint NC, Kuipers J, Chiovaro F, Koelzer VH, Pauli C, Moritz W, Bode PK, Rechsteiner M, Beerenwinkel N, Schraml P, Moch H.

Eur Urol Focus. 2019 Jun 29. pii: S2405-4569(19)30164-6. doi: 10.1016/j.euf.2019.06.009. [Epub ahead of print]

7.

Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data.

Malikic S, Jahn K, Kuipers J, Sahinalp SC, Beerenwinkel N.

Nat Commun. 2019 Jun 21;10(1):2750. doi: 10.1038/s41467-019-10737-5.

8.

Simultaneous Integration of Multi-omics Data Improves the Identification of Cancer Driver Modules.

Silverbush D, Cristea S, Yanovich-Arad G, Geiger T, Beerenwinkel N, Sharan R.

Cell Syst. 2019 May 22;8(5):456-466.e5. doi: 10.1016/j.cels.2019.04.005. Epub 2019 May 15.

PMID:
31103572
9.

Identification and Validation of a Biomarker Signature in Patients With Resectable Pancreatic Cancer via Genome-Wide Screening for Functional Genetic Variants.

Dimitrakopoulos C, Vrugt B, Flury R, Schraml P, Knippschild U, Wild P, Hoerstrup S, Henne-Bruns D, Wuerl P, Graf R, Breitenstein S, Bond G, Beerenwinkel N, Grochola LF.

JAMA Surg. 2019 Jun 1;154(6):e190484. doi: 10.1001/jamasurg.2019.0484. Epub 2019 Jun 19.

PMID:
30942874
10.

netprioR: a probabilistic model for integrative hit prioritisation of genetic screens.

Schmich F, Kuipers J, Merdes G, Beerenwinkel N.

Stat Appl Genet Mol Biol. 2019 Mar 6;18(3). pii: /j/sagmb.2019.18.issue-3/sagmb-2018-0033/sagmb-2018-0033.xml. doi: 10.1515/sagmb-2018-0033.

PMID:
30840598
11.

Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection.

Carlisle LA, Turk T, Kusejko K, Metzner KJ, Leemann C, Schenkel CD, Bachmann N, Posada S, Beerenwinkel N, Böni J, Yerly S, Klimkait T, Perreau M, Braun DL, Rauch A, Calmy A, Cavassini M, Battegay M, Vernazza P, Bernasconi E, Günthard HF, Kouyos RD; Swiss HIV Cohort Study .

J Infect Dis. 2019 Jun 19;220(2):254-265. doi: 10.1093/infdis/jiz094.

PMID:
30835266
12.

Neutrophils escort circulating tumour cells to enable cell cycle progression.

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, Aceto N.

Nature. 2019 Feb;566(7745):553-557. doi: 10.1038/s41586-019-0915-y. Epub 2019 Feb 6.

PMID:
30728496
13.

A Hierarchical Regulatory Landscape during the Multiple Stages of EMT.

Meyer-Schaller N, Cardner M, Diepenbruck M, Saxena M, Tiede S, Lüönd F, Ivanek R, Beerenwinkel N, Christofori G.

Dev Cell. 2019 Feb 25;48(4):539-553.e6. doi: 10.1016/j.devcel.2018.12.023. Epub 2019 Jan 31.

PMID:
30713070
14.

Expression and Mutation Patterns of PBRM1, BAP1 and SETD2 Mirror Specific Evolutionary Subtypes in Clear Cell Renal Cell Carcinoma.

Bihr S, Ohashi R, Moore AL, Rüschoff JH, Beisel C, Hermanns T, Mischo A, Corrò C, Beyer J, Beerenwinkel N, Moch H, Schraml P.

Neoplasia. 2019 Feb;21(2):247-256. doi: 10.1016/j.neo.2018.12.006. Epub 2019 Jan 16.

15.

Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection.

Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A.

Sci Rep. 2019 Jan 18;9(1):213. doi: 10.1038/s41598-018-36135-3.

16.

Single-cell mutation identification via phylogenetic inference.

Singer J, Kuipers J, Jahn K, Beerenwinkel N.

Nat Commun. 2018 Dec 4;9(1):5144. doi: 10.1038/s41467-018-07627-7.

17.

Microbiome interactions shape host fitness.

Gould AL, Zhang V, Lamberti L, Jones EW, Obadia B, Korasidis N, Gavryushkin A, Carlson JM, Beerenwinkel N, Ludington WB.

Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):E11951-E11960. doi: 10.1073/pnas.1809349115. Epub 2018 Dec 3.

18.

Single cell network analysis with a mixture of Nested Effects Models.

Pirkl M, Beerenwinkel N.

Bioinformatics. 2018 Sep 1;34(17):i964-i971. doi: 10.1093/bioinformatics/bty602.

19.

SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics.

Singer F, Irmisch A, Toussaint NC, Grob L, Singer J, Thurnherr T, Beerenwinkel N, Levesque MP, Dummer R, Quagliata L, Rothschild SI, Wicki A, Beisel C, Stekhoven DJ.

BMC Med Inform Decis Mak. 2018 Oct 29;18(1):89. doi: 10.1186/s12911-018-0680-0.

20.

Mutational interactions define novel cancer subgroups.

Kuipers J, Thurnherr T, Moffa G, Suter P, Behr J, Goosen R, Christofori G, Beerenwinkel N.

Nat Commun. 2018 Oct 19;9(1):4353. doi: 10.1038/s41467-018-06867-x.

21.

From hype to reality: data science enabling personalized medicine.

Fröhlich H, Balling R, Beerenwinkel N, Kohlbacher O, Kumar S, Lengauer T, Maathuis MH, Moreau Y, Murphy SA, Przytycka TM, Rebhan M, Röst H, Schuppert A, Schwab M, Spang R, Stekhoven D, Sun J, Weber A, Ziemek D, Zupan B.

BMC Med. 2018 Aug 27;16(1):150. doi: 10.1186/s12916-018-1122-7.

22.

Principles of Systems Biology, No. 31.

Cho H, Berger B, Peng J, Galitzine C, Vitek O, Beltran PMJ, Cristea IM, Görtler F, Solbrig S, Wettig T, Oefner PJ, Spang R, Altenbuchinger M, Basso RS, Hochbaum D, Vandin F, Silverbush D, Cristea S, Yanovich G, Geiger T, Beerenwinkel N, Sharan R, Zhou Z, Luhmann N, Alikhan NF, Achtman M.

Cell Syst. 2018 Aug 22;7(2):133-135. doi: 10.1016/j.cels.2018.08.005.

23.

Correction: Context-dependent deposition and regulation of mRNAs in P-bodies.

Wang C, Schmich F, Srivatsa S, Weidner J, Beerenwinkel N, Spang A.

Elife. 2018 Aug 23;7. pii: e41300. doi: 10.7554/eLife.41300. No abstract available.

24.

Improved pathway reconstruction from RNA interference screens by exploiting off-target effects.

Srivatsa S, Kuipers J, Schmich F, Eicher S, Emmenlauer M, Dehio C, Beerenwinkel N.

Bioinformatics. 2018 Jul 1;34(13):i519-i527. doi: 10.1093/bioinformatics/bty240.

25.

The geometry of partial fitness orders and an efficient method for detecting genetic interactions.

Lienkaemper C, Lamberti L, Drain J, Beerenwinkel N, Gavryushkin A.

J Math Biol. 2018 Oct;77(4):951-970. doi: 10.1007/s00285-018-1237-7. Epub 2018 May 7.

26.

Ensemble outlier detection and gene selection in triple-negative breast cancer data.

Lopes MB, Veríssimo A, Carrasquinha E, Casimiro S, Beerenwinkel N, Vinga S.

BMC Bioinformatics. 2018 May 4;19(1):168. doi: 10.1186/s12859-018-2149-7.

27.

Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells.

Golumbeanu M, Cristinelli S, Rato S, Munoz M, Cavassini M, Beerenwinkel N, Ciuffi A.

Cell Rep. 2018 Apr 24;23(4):942-950. doi: 10.1016/j.celrep.2018.03.102.

28.

A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila.

Torres J, Monti R, Moore AL, Seimiya M, Jiang Y, Beerenwinkel N, Beisel C, Beira JV, Paro R.

Elife. 2018 Mar 21;7. pii: e32697. doi: 10.7554/eLife.32697.

29.

Network-based integration of multi-omics data for prioritizing cancer genes.

Dimitrakopoulos C, Hindupur SK, Häfliger L, Behr J, Montazeri H, Hall MN, Beerenwinkel N.

Bioinformatics. 2018 Jul 15;34(14):2441-2448. doi: 10.1093/bioinformatics/bty148.

30.

ISMB/ECCB 2017 proceedings.

Beerenwinkel N, Bromberg Y.

Bioinformatics. 2017 Jul 15;33(14):i1-i2. doi: 10.1093/bioinformatics/btx321. No abstract available.

31.

Context-dependent deposition and regulation of mRNAs in P-bodies.

Wang C, Schmich F, Srivatsa S, Weidner J, Beerenwinkel N, Spang A.

Elife. 2018 Jan 3;7. pii: e29815. doi: 10.7554/eLife.29815. Erratum in: Elife. 2018 Aug 23;7:.

32.

Bioinformatics for precision oncology.

Singer J, Irmisch A, Ruscheweyh HJ, Singer F, Toussaint NC, Levesque MP, Stekhoven DJ, Beerenwinkel N.

Brief Bioinform. 2019 May 21;20(3):778-788. doi: 10.1093/bib/bbx143.

33.

Editorial: the influence of genetic factors in mediating the effects of tobacco smoke in IBD-Authors' reply.

Lang BM, Beerenwinkel N, Misselwitz B.

Aliment Pharmacol Ther. 2018 Jan;47(2):307-308. doi: 10.1111/apt.14447. No abstract available.

34.

Inferring genetic interactions from comparative fitness data.

Crona K, Gavryushkin A, Greene D, Beerenwinkel N.

Elife. 2017 Dec 20;6. pii: e28629. doi: 10.7554/eLife.28629.

35.

Myeloid differentiation primary response gene (MyD) 88 signalling is not essential for intestinal fibrosis development.

Lutz C, Weder B, Hünerwadel A, Fagagnini S, Lang B, Beerenwinkel N, Rossel JB, Rogler G, Misselwitz B, Hausmann M.

Sci Rep. 2017 Dec 15;7(1):17678. doi: 10.1038/s41598-017-17755-7.

36.

Predicting cancer type from tumour DNA signatures.

Soh KP, Szczurek E, Sakoparnig T, Beerenwinkel N.

Genome Med. 2017 Nov 28;9(1):104. doi: 10.1186/s13073-017-0493-2.

37.

Recurring Amplification at 11q22.1-q22.2 Locus Plays an Important Role in Lymph Node Metastasis and Radioresistance in OSCC.

Bhosale PG, Pandey M, Cristea S, Shah M, Patil A, Beerenwinkel N, Schäffer AA, Mahimkar MB.

Sci Rep. 2017 Nov 22;7(1):16051. doi: 10.1038/s41598-017-16247-y.

38.

Genetic polymorphisms associated with smoking behaviour predict the risk of surgery in patients with Crohn's disease.

Lang BM, Biedermann L, van Haaften WT, de Vallière C, Schuurmans M, Begré S, Zeitz J, Scharl M, Turina M, Greuter T, Schreiner P, Heinrich H, Kuntzen T, Vavricka SR, Rogler G, Beerenwinkel N, Misselwitz B; Swiss IBD Cohort Study Group.

Aliment Pharmacol Ther. 2018 Jan;47(1):55-66. doi: 10.1111/apt.14378. Epub 2017 Oct 20.

39.

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors.

Kuipers J, Jahn K, Raphael BJ, Beerenwinkel N.

Genome Res. 2017 Nov;27(11):1885-1894. doi: 10.1101/gr.220707.117. Epub 2017 Oct 13.

40.

NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis.

Singer J, Ruscheweyh HJ, Hofmann AL, Thurnherr T, Singer F, Toussaint NC, Ng CKY, Piscuoglio S, Beisel C, Christofori G, Dummer R, Hall MN, Krek W, Levesque MP, Manz MG, Moch H, Papassotiropoulos A, Stekhoven DJ, Wild P, Wüst T, Rinn B, Beerenwinkel N.

Bioinformatics. 2018 Jan 1;34(1):107-108. doi: 10.1093/bioinformatics/btx540.

41.

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb.

Monti R, Barozzi I, Osterwalder M, Lee E, Kato M, Garvin TH, Plajzer-Frick I, Pickle CS, Akiyama JA, Afzal V, Beerenwinkel N, Dickel DE, Visel A, Pennacchio LA.

PLoS Comput Biol. 2017 Aug 21;13(8):e1005720. doi: 10.1371/journal.pcbi.1005720. eCollection 2017 Aug.

42.

CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies.

Prakash MK, Lang B, Heinrich H, Valli PV, Bauerfeind P, Sonnenberg A, Beerenwinkel N, Misselwitz B.

BMC Med Inform Decis Mak. 2017 Jun 5;17(1):80. doi: 10.1186/s12911-017-0458-9.

43.

Chromosomal Alterations and Gene Expression Changes Associated with the Progression of Leukoplakia to Advanced Gingivobuccal Cancer.

Bhosale PG, Cristea S, Ambatipudi S, Desai RS, Kumar R, Patil A, Kane S, Borges AM, Schäffer AA, Beerenwinkel N, Mahimkar MB.

Transl Oncol. 2017 Jun;10(3):396-409. doi: 10.1016/j.tranon.2017.03.008. Epub 2017 Apr 21.

44.

Inferring modulators of genetic interactions with epistatic nested effects models.

Pirkl M, Diekmann M, van der Wees M, Beerenwinkel N, Fröhlich H, Markowetz F.

PLoS Comput Biol. 2017 Apr 13;13(4):e1005496. doi: 10.1371/journal.pcbi.1005496. eCollection 2017 Apr.

45.

Trophic Interactions of Infant Bifidobacteria and Eubacterium hallii during L-Fucose and Fucosyllactose Degradation.

Schwab C, Ruscheweyh HJ, Bunesova V, Pham VT, Beerenwinkel N, Lacroix C.

Front Microbiol. 2017 Jan 30;8:95. doi: 10.3389/fmicb.2017.00095. eCollection 2017.

46.

Advances in understanding tumour evolution through single-cell sequencing.

Kuipers J, Jahn K, Beerenwinkel N.

Biochim Biophys Acta Rev Cancer. 2017 Apr;1867(2):127-138. doi: 10.1016/j.bbcan.2017.02.001. Epub 2017 Feb 11. Review.

47.

Automated Design of Synthetic Cell Classifier Circuits Using a Two-Step Optimization Strategy.

Mohammadi P, Beerenwinkel N, Benenson Y.

Cell Syst. 2017 Feb 22;4(2):207-218.e14. doi: 10.1016/j.cels.2017.01.003. Epub 2017 Feb 8.

48.

αV-class integrins exert dual roles on α5β1 integrins to strengthen adhesion to fibronectin.

Bharadwaj M, Strohmeyer N, Colo GP, Helenius J, Beerenwinkel N, Schiller HB, Fässler R, Müller DJ.

Nat Commun. 2017 Jan 27;8:14348. doi: 10.1038/ncomms14348.

49.

Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers.

Hofmann AL, Behr J, Singer J, Kuipers J, Beisel C, Schraml P, Moch H, Beerenwinkel N.

BMC Bioinformatics. 2017 Jan 3;18(1):8. doi: 10.1186/s12859-016-1417-7.

50.

Genomic variant annotation workflow for clinical applications.

Thurnherr T, Singer F, Stekhoven DJ, Beerenwinkel N.

Version 2. F1000Res. 2016 Aug 12 [revised 2016 Jan 1];5:1963. eCollection 2016.

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