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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 6. doi: 10.1038/s41586-019-0915-y. [Epub ahead of print]


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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 May 7. doi: 10.1007/s00285-018-1237-7. [Epub ahead of print]


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.


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.


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.


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.


ISMB/ECCB 2017 proceedings.

Beerenwinkel N, Bromberg Y.

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


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:.


Bioinformatics for precision oncology.

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

Brief Bioinform. 2017 Dec 18. doi: 10.1093/bib/bbx143. [Epub ahead of print]


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics.

Cristea S, Kuipers J, Beerenwinkel N.

J Comput Biol. 2017 Jun;24(6):603-615. doi: 10.1089/cmb.2016.0171. Epub 2016 Dec 12.


Computational approaches for the identification of cancer genes and pathways.

Dimitrakopoulos CM, Beerenwinkel N.

Wiley Interdiscip Rev Syst Biol Med. 2017 Jan;9(1). doi: 10.1002/wsbm.1364. Epub 2016 Nov 11. Review.


Recent advances in inferring viral diversity from high-throughput sequencing data.

Posada-Cespedes S, Seifert D, Beerenwinkel N.

Virus Res. 2017 Jul 15;239:17-32. doi: 10.1016/j.virusres.2016.09.016. Epub 2016 Sep 28. Review.


A Genome-Wide siRNA Screen Implicates Spire1/2 in SipA-Driven Salmonella Typhimurium Host Cell Invasion.

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.

PLoS One. 2016 Sep 14;11(9):e0161965. doi: 10.1371/journal.pone.0161965. eCollection 2016.


Large-scale inference of conjunctive Bayesian networks.

Montazeri H, Kuipers J, Kouyos R, Böni J, Yerly S, Klimkait T, Aubert V, Günthard HF, Beerenwinkel N; Swiss HIV Cohort Study.

Bioinformatics. 2016 Sep 1;32(17):i727-i735. doi: 10.1093/bioinformatics/btw459.


Linear effects models of signaling pathways from combinatorial perturbation data.

Szczurek E, Beerenwinkel N.

Bioinformatics. 2016 Jun 15;32(12):i297-i305. doi: 10.1093/bioinformatics/btw268.


Single-Molecule Sequencing Reveals Complex Genome Variation of Hepatitis B Virus during 15 Years of Chronic Infection following Liver Transplantation.

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.

J Virol. 2016 Jul 27;90(16):7171-7183. doi: 10.1128/JVI.00243-16. Print 2016 Aug 15.


The Common Gut Microbe Eubacterium hallii also Contributes to Intestinal Propionate Formation.

Engels C, Ruscheweyh HJ, Beerenwinkel N, Lacroix C, Schwab C.

Front Microbiol. 2016 May 19;7:713. doi: 10.3389/fmicb.2016.00713. eCollection 2016.


Tree inference for single-cell data.

Jahn K, Kuipers J, Beerenwinkel N.

Genome Biol. 2016 May 5;17:86. doi: 10.1186/s13059-016-0936-x.


Sulforaphane Preconditioning Sensitizes Human Colon Cancer Cells towards the Bioreductive Anticancer Prodrug PR-104A.

Erzinger MM, Bovet C, Hecht KM, Senger S, Winiker P, Sobotzki N, Cristea S, Beerenwinkel N, Shay JW, Marra G, Wollscheid B, Sturla SJ.

PLoS One. 2016 Mar 7;11(3):e0150219. doi: 10.1371/journal.pone.0150219. eCollection 2016.


Computational Cancer Biology: An Evolutionary Perspective.

Beerenwinkel N, Greenman CD, Lagergren J.

PLoS Comput Biol. 2016 Feb 4;12(2):e1004717. doi: 10.1371/journal.pcbi.1004717. eCollection 2016 Feb. Review. No abstract available.

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