Publications by authors named "Niko Beerenwinkel"

100Publications

Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times.

Stat Appl Genet Mol Biol 2020 Oct 21. Epub 2020 Oct 21.

Harvard TH Chan School of Public Health, 665 Huntington Ave, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1515/sagmb-2019-0026DOI Listing
October 2020

A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment.

PLoS Comput Biol 2020 Oct 2;16(10):e1008056. Epub 2020 Oct 2.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1008056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7591057PMC
October 2020

Clonal evolution driven by superdriver mutations.

BMC Evol Biol 2020 07 20;20(1):89. Epub 2020 Jul 20.

Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-020-01647-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7370525PMC
July 2020

BnpC: Bayesian non-parametric clustering of single-cell mutation profiles.

Bioinformatics 2020 Jun 27. Epub 2020 Jun 27.

Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btaa599DOI Listing
June 2020

Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance.

Cell Stem Cell 2020 03;26(3):431-440.e8

Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland; Department of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2020.02.007DOI Listing
March 2020

Predicting colorectal cancer risk from adenoma detection via a two-type branching process model.

PLoS Comput Biol 2020 02 5;16(2):e1007552. Epub 2020 Feb 5.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1007552DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001909PMC
February 2020

PyBDA: a command line tool for automated analysis of big biological data sets.

BMC Bioinformatics 2019 Nov 12;20(1):564. Epub 2019 Nov 12.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-019-3087-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6849186PMC
November 2019

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

Recent Results Cancer Res 2020 ;215:347-368

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-3-030-26439-0_18DOI Listing
October 2019

Inferring signalling dynamics by integrating interventional with observational data.

Bioinformatics 2019 07;35(14):i577-i585

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612850PMC
July 2019

Estimating the predictability of cancer evolution.

Bioinformatics 2019 07;35(14):i389-i397

Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612861PMC
July 2019

Probability, Statistics, and Computational Science.

Methods Mol Biol 2019 ;1910:33-70

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-9074-0_2DOI Listing
January 2020

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

Nat Commun 2019 06 21;10(1):2750. Epub 2019 Jun 21.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-019-10737-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588593PMC
June 2019

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

Cell Syst 2019 05 15;8(5):456-466.e5. Epub 2019 May 15.

Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2019.04.005DOI Listing
May 2019

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

Stat Appl Genet Mol Biol 2019 03 6;18(3). Epub 2019 Mar 6.

Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1515/sagmb-2018-0033DOI Listing
March 2019

A Hierarchical Regulatory Landscape during the Multiple Stages of EMT.

Dev Cell 2019 02 31;48(4):539-553.e6. Epub 2019 Jan 31.

Department of Biomedicine, University of Basel, Basel 4058, Switzerland. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S15345807183112
Publisher Site
http://dx.doi.org/10.1016/j.devcel.2018.12.023DOI Listing
February 2019

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

Neoplasia 2019 02 16;21(2):247-256. Epub 2019 Jan 16.

Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.neo.2018.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355619PMC
February 2019

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

Sci Rep 2019 01 18;9(1):213. Epub 2019 Jan 18.

Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-36135-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338737PMC
January 2019

Single-cell mutation identification via phylogenetic inference.

Nat Commun 2018 12 4;9(1):5144. Epub 2018 Dec 4.

Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-018-07627-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6279798PMC
December 2018

Microbiome interactions shape host fitness.

Proc Natl Acad Sci U S A 2018 12 3;115(51):E11951-E11960. Epub 2018 Dec 3.

Division of Genetics, Genomics & Development, Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720;

View Article

Download full-text PDF

Source
http://www.pnas.org/lookup/doi/10.1073/pnas.1809349115
Publisher Site
http://dx.doi.org/10.1073/pnas.1809349115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304949PMC
December 2018

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

Bioinformatics 2018 09;34(17):i964-i971

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

View Article

Download full-text PDF

Source
https://academic.oup.com/bioinformatics/article/34/17/i964/5
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/bty602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129288PMC
September 2018

Mutational interactions define novel cancer subgroups.

Nat Commun 2018 10 19;9(1):4353. Epub 2018 Oct 19.

Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41467-018-06867-x
Publisher Site
http://dx.doi.org/10.1038/s41467-018-06867-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6195543PMC
October 2018

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

J Math Biol 2018 10 7;77(4):951-970. Epub 2018 May 7.

Department of Computer Science, University of Otago, Dunedin, New Zealand.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00285-018-1237-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153669PMC
October 2018

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

BMC Bioinformatics 2018 05 4;19(1):168. Epub 2018 May 4.

IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, Lisboa, 1049-001, Portugal.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-018-2149-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5936001PMC
May 2018

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

Cell Rep 2018 04;23(4):942-950

Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2018.03.102DOI Listing
April 2018

ISMB/ECCB 2017 proceedings.

Bioinformatics 2017 07;33(14):i1-i2

Rutgers University, New Brunswick, NJ, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btx321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870677PMC
July 2017

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

Elife 2018 01 3;7. Epub 2018 Jan 3.

Growth and Development, Biozentrum, University of Basel, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.29815DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5752201PMC
January 2018

Bioinformatics for precision oncology.

Brief Bioinform 2019 05;20(3):778-788

Department of Biosystems Science and Engineering of ETH Zurich in Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bib/bbx143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6585151PMC
May 2019

Inferring genetic interactions from comparative fitness data.

Elife 2017 12 20;6. Epub 2017 Dec 20.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.28629DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737811PMC
December 2017

Predicting cancer type from tumour DNA signatures.

Genome Med 2017 Nov 28;9(1):104. Epub 2017 Nov 28.

Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, 4058, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13073-017-0493-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706302PMC
November 2017

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

Sci Rep 2017 11 22;7(1):16051. Epub 2017 Nov 22.

Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Navi Mumbai, 410210, India.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-017-16247-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5700126PMC
November 2017

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

Genome Res 2017 11 13;27(11):1885-1894. Epub 2017 Oct 13.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.220707.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668945PMC
November 2017

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

BMC Med Inform Decis Mak 2017 Jun 5;17(1):80. Epub 2017 Jun 5.

Division of Gastroenterology, University Hospital Zurich (USZ), Rämistrasse 100, 8091, Zurich, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12911-017-0458-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5460500PMC
June 2017

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

Transl Oncol 2017 Jun 21;10(3):396-409. Epub 2017 Apr 21.

Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Navi Mumbai, 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, India. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tranon.2017.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5403767PMC
June 2017

Inferring modulators of genetic interactions with epistatic nested effects models.

PLoS Comput Biol 2017 04 13;13(4):e1005496. Epub 2017 Apr 13.

University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1005496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5407847PMC
April 2017

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

Front Microbiol 2017 30;8:95. Epub 2017 Jan 30.

Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich Zurich, Switzerland.

View Article

Download full-text PDF

Source
http://journal.frontiersin.org/article/10.3389/fmicb.2017.00
Publisher Site
http://dx.doi.org/10.3389/fmicb.2017.00095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5277004PMC
January 2017

Advances in understanding tumour evolution through single-cell sequencing.

Biochim Biophys Acta Rev Cancer 2017 Apr 11;1867(2):127-138. Epub 2017 Feb 11.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbcan.2017.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813714PMC
April 2017

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

Cell Syst 2017 02 8;4(2):207-218.e14. Epub 2017 Feb 8.

Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2017.01.003DOI Listing
February 2017

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

Nat Commun 2017 01 27;8:14348. Epub 2017 Jan 27.

Eidgenössische Technische Hochschule (ETH) Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland.

View Article

Download full-text PDF

Source
http://www.nature.com/doifinder/10.1038/ncomms14348
Publisher Site
http://dx.doi.org/10.1038/ncomms14348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5290147PMC
January 2017

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

BMC Bioinformatics 2017 Jan 3;18(1). Epub 2017 Jan 3.

Department of Biosystems Science and Engineering, ETH Zurich, Mattenstr, Basel, 26, 4058, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-016-1417-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209852PMC
January 2017

Genomic variant annotation workflow for clinical applications.

F1000Res 2016 12;5:1963. Epub 2016 Aug 12.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.12688/f1000research.9357.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5130070PMC
August 2016

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

J Comput Biol 2017 Jun 12;24(6):603-615. Epub 2016 Dec 12.

1 Department of Biosystems Science and Engineering, ETH Zürich , Basel, Switzerland .

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/cmb.2016.0171DOI Listing
June 2017

Computational approaches for the identification of cancer genes and pathways.

Wiley Interdiscip Rev Syst Biol Med 2017 01 11;9(1). Epub 2016 Nov 11.

Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/wsbm.1364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215607PMC
January 2017

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

Virus Res 2017 07 28;239:17-32. Epub 2016 Sep 28.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB, Basel, Switzerland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virusres.2016.09.016DOI Listing
July 2017

Large-scale inference of conjunctive Bayesian networks.

Bioinformatics 2016 09;32(17):i727-i735

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btw459DOI Listing
September 2016

Linear effects models of signaling pathways from combinatorial perturbation data.

Bioinformatics 2016 06;32(12):i297-i305

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland SIB Swiss Institute of Bioinformatics.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btw268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908352PMC
June 2016

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

Front Microbiol 2016 19;7:713. Epub 2016 May 19.

Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich Zurich, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2016.00713DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4871866PMC
May 2016

Tree inference for single-cell data.

Genome Biol 2016 May 5;17:86. Epub 2016 May 5.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-016-0936-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858868PMC
May 2016

Computational Cancer Biology: An Evolutionary Perspective.

PLoS Comput Biol 2016 Feb 4;12(2):e1004717. Epub 2016 Feb 4.

Science for Life Laboratory, School of Computer Science and Communication, Swedish E-Science Research Center, KTH Royal Institute of Technology, Solna, Sweden.

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1004717
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1004717DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742235PMC
February 2016

A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations.

J Mol Biol 2016 Jan 19;428(1):238-250. Epub 2015 Dec 19.

Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2015.12.012DOI Listing
January 2016

Perturbing resistance: a network perspective.

Pigment Cell Melanoma Res 2016 Jan;29(1):5-7

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/pcmr.12431DOI Listing
January 2016

Ectopic expression of Msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation.

Stem Cell Res 2015 Nov 30;15(3):542-553. Epub 2015 Sep 30.

Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel 4058, Switzerland; Faculty of Science, University of Basel, Basel, Switzerland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scr.2015.09.012DOI Listing
November 2015

BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data.

Bioinformatics 2016 04 5;32(7):976-83. Epub 2015 Sep 5.

Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btv520DOI Listing
April 2016

Estimating Fitness of Viral Quasispecies from Next-Generation Sequencing Data.

Curr Top Microbiol Immunol 2016 ;392:181-200

ETH Zurich, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/82_2015_462
Publisher Site
http://dx.doi.org/10.1007/82_2015_462DOI Listing
June 2016

HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages.

PLoS One 2015 30;10(7):e0132127. Epub 2015 Jul 30.

University Hospital Zurich, Division of Infectious Diseases and Hospital Epidemiology, University of Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132127PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520458PMC
May 2016

TiMEx: a waiting time model for mutually exclusive cancer alterations.

Bioinformatics 2016 04 9;32(7):968-75. Epub 2015 Jul 9.

Department of Biosystems Science and Engineering, ETH Zürich, Swiss Institute of Bioinformatics, Basel 4058, Switzerland and.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btv400DOI Listing
April 2016

ISMB/ECCB 2015.

Bioinformatics 2015 Jun;31(12):i1-2

Department of Biosystems Science and Engineering, ETH Zürich, Basel, SwitzerlandProceedings Chairs ISMB/ECCB 2015.

View Article

Download full-text PDF

Source
https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btv303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765879PMC
June 2015

Estimating the dynamics and dependencies of accumulating mutations with applications to HIV drug resistance.

Biostatistics 2015 Oct 14;16(4):713-26. Epub 2015 May 14.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland and SIB Swiss Institute of Bioinformatics, Basel, Switzerland

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/biostatistics/kxv019DOI Listing
October 2015

NEMix: single-cell nested effects models for probabilistic pathway stimulation.

PLoS Comput Biol 2015 Apr 16;11(4):e1004078. Epub 2015 Apr 16.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1004078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4400057PMC
April 2015

Identification of constrained cancer driver genes based on mutation timing.

PLoS Comput Biol 2015 Jan 8;11(1):e1004027. Epub 2015 Jan 8.

Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1004027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287396PMC
January 2015

Dynamic models of viral replication and latency.

Curr Opin HIV AIDS 2015 Mar;10(2):90-5

aInstitute of Microbiology, University Hospital of Lausanne, University of Lausanne, Lausanne bDepartment of Biosystems Science and Engineering, ETH Zurich cSwiss Institute of Bioinformatics, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1097/COH.0000000000000136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4323573PMC
March 2015

Estimating HIV-1 fitness characteristics from cross-sectional genotype data.

PLoS Comput Biol 2014 Nov 6;10(11):e1003886. Epub 2014 Nov 6.

Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute of Mathematics, University of Potsdam, Potsdam, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1003886DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4222584PMC
November 2014

Cancer evolution: mathematical models and computational inference.

Syst Biol 2015 Jan 7;64(1):e1-25. Epub 2014 Oct 7.

Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom; Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB20RE, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/sysbio/syu081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265145PMC
January 2015

Dynamics of HIV latency and reactivation in a primary CD4+ T cell model.

PLoS Pathog 2014 May 29;10(5):e1004156. Epub 2014 May 29.

Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; University of Lausanne, Lausanne, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1004156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038609PMC
May 2014

Viral quasispecies assembly via maximal clique enumeration.

PLoS Comput Biol 2014 Mar 27;10(3):e1003515. Epub 2014 Mar 27.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1003515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967922PMC
March 2014

Modeling mutual exclusivity of cancer mutations.

PLoS Comput Biol 2014 Mar 27;10(3):e1003503. Epub 2014 Mar 27.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1003503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967923PMC
March 2014

Challenges in RNA virus bioinformatics.

Bioinformatics 2014 Jul 3;30(13):1793-9. Epub 2014 Mar 3.

Friedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, Universitätsklinikum Bonn, Institut für Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, Technische Universität Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, Helmholtz Center Munich-German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany, Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny 141700, Russia, Institut für theoretische Chemie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria, Institute of Virology, Technical University of Munich, Trogerstr. 30, 81675 München, Germany, University of Leipzig, Faculty of Mathematics and Computer Science, Institute for Computer Science, Augustusplatz 10, 04109 Leipzig, Germany, Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Universität Wien, Althanstraße 14, 1090 Wien, Austria, Department of Computer Science and Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany and The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USAFriedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, Universitätsklinikum Bonn, Institut für Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, Technische Universität Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, Helmholtz

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btu105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110044PMC
July 2014

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

Chem Res Toxicol 2014 Mar 13;27(3):377-86. Epub 2014 Jan 13.

Department of Biosystems Science and Engineering, ETH Zurich , Basel 4058, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/tx400427tDOI Listing
March 2014