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1

Waiting Time Models of Cancer Progression

GERSTUNG, MORITZ, BEERENWINKEL, NIKO

Journal:

Mathematical Population Studies

Year:

2010

Language:

english

File:

PDF, 268 KB

english, 2010

2

Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model

Mohammadi, Pejman, di Iulio, Julia, Muñoz, Miguel, Martinez, Raquel, Bartha, István, Cavassini, Matthias, Thorball, Christian, Fellay, Jacques, Beerenwinkel, Niko, Ciuffi, Angela, Telenti, Amalio, Eme

Journal:

Year:

2014

Language:

english

File:

PDF, 3.78 MB

english, 2014

3

Models of RNA virus evolution and their roles in vaccine design

Samuel Ojosnegros, Niko Beerenwinkel

Journal:

Immunome Research

Year:

2010

Language:

english

File:

PDF, 615 KB

english, 2010

4

Ultra-deep sequencing for the analysis of viral populations

Niko Beerenwinkel, Osvaldo Zagordi

Journal:

Current Opinion in Virology

Year:

2011

Language:

english

File:

PDF, 309 KB

english, 2011

5

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

Mohammadi, Pejman, Beerenwinkel, Niko, Benenson, Yaakov

Journal:

Year:

2017

Language:

english

File:

PDF, 3.46 MB

english, 2017

6

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

Dirmeier, Simon, Emmenlauer, Mario, Dehio, Christoph, Beerenwinkel, Niko

Journal:

BMC Bioinformatics

Year:

2019

File:

PDF, 1.15 MB

2019

7

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Hufsky, Franziska, Lamkiewicz, Kevin, Almeida, Alexandre, Aouacheria, Abdel, Arighi, Cecilia, Bateman, Alex, Baumbach, Jan, Beerenwinkel, Niko, Brandt, Christian, Cacciabue, Marco, Chuguransky, Sara,

Journal:

Briefings in Bioinformatics

Year:

2020

File:

PDF, 2.30 MB

2020

8

Genome-wide expression and copy number analysis identifies driver genes in gingivobuccal cancers

Srikant Ambatipudi, Moritz Gerstung, Manishkumar Pandey, Tanuja Samant, Asawari Patil, Shubhada Kane, Rajiv S. Desai, Alejandro A. Schäffer, Niko Beerenwinkel, Manoj B. Mahimkar

Journal:

Genes, Chromosomes and Cancer

Year:

2012

Language:

english

File:

PDF, 708 KB

english, 2012

9

Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas

Ralf Ketter, Steffi Urbschat, Wolfram Henn, Wolfgang Feiden, Niko Beerenwinkel, Thomas Lengauer, Wolf-Ingo Steudel, Klaus D. Zang, Jörg Rahnenführer

Journal:

International Journal of Cancer

Year:

2007

Language:

english

File:

PDF, 400 KB

english, 2007

10

Construction of oncogenetic tree models reveals multiple pathways of oral cancer progression

Swapnali Pathare, Alejandro A. Schäffer, Niko Beerenwinkel, Manoj Mahimkar

Journal:

International Journal of Cancer

Year:

2009

Language:

english

File:

PDF, 265 KB

english, 2009

11

Evolution on distributive lattices

Niko Beerenwinkel, Nicholas Eriksson, Bernd Sturmfels

Journal:

Journal of Theoretical Biology

Year:

2006

Language:

english

File:

PDF, 253 KB

english, 2006

12

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

Osvaldo Zagordi, Arnab Bhattacharya, Nicholas Eriksson, Niko Beerenwinkel

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 229 KB

english, 2011

13

The Evolution of Virulence in RNA Viruses under

Edgar Delgado-Eckert, Samuel Ojosnegros, Niko Beerenwinkel

Journal:

Bulletin of Mathematical Biology

Year:

2011

Language:

english

File:

PDF, 1.08 MB

english, 2011

14

Evolutionary Games with Affine Fitness Functions: Applications to Cancer

Moritz Gerstung, Hani Nakhoul, Niko Beerenwinkel

Journal:

Dynamic Games and Applications

Year:

2011

Language:

english

File:

PDF, 584 KB

english, 2011

15

Reliable detection of subclonal single-nucleotide variants in tumour cell populations

Gerstung, Moritz, Beisel, Christian, Rechsteiner, Markus, Wild, Peter, Schraml, Peter, Moch, Holger, Beerenwinkel, Niko

Journal:

Nature Communications

Year:

2012

Language:

english

File:

PDF, 6.73 MB

english, 2012

16

Analysis of epistatic interactions and fitness landscapes using a new geometric approach

Niko Beerenwinkel, Lior Pachter, Bernd Sturmfels, Santiago F Elena, Richard E Lenski

Journal:

BMC Evolutionary Biology

Year:

2007

Language:

english

File:

PDF, 322 KB

english, 2007

17

Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing

Sakoparnig, Thomas, Kockmann, Tobias, Paro, Renato, Beisel, Christian, Beerenwinkel, Niko

Journal:

Journal of Computational Biology

Year:

2012

Language:

english

File:

PDF, 35.23 MB

english, 2012

18

Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy

Melanie Balduin, Saleta Sierra, Martin P Däumer, Jürgen K Rockstroh, Mark Oette, Gerd Fätkenheuer, Bernd Kupfer, Niko Beerenwinkel, Daniel Hoffmann, Joachim Selbig, Herbert J Pfister, Rolf Kaiser

Journal:

Journal of Clinical Virology

Year:

2005

Language:

english

File:

PDF, 258 KB

english, 2005

19

Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART

Clara Lehmann, Martin Däumer, Ibrahim Boussaad, Tobias Sing, Niko Beerenwinkel, Thomas Lengauer, Norbert Schmeisser, Christoph Wyen, Gerd Fätkenheuer, Rolf Kaiser

Journal:

Journal of Clinical Virology

Year:

2006

Language:

english

File:

PDF, 123 KB

english, 2006

20

Kinetic, Energetic, and Mechanical Differences between Dark-State Rhodopsin and Opsin

Kawamura, Shiho, Gerstung, Moritz, Colozo, Alejandro T., Helenius, Jonne, Maeda, Akiko, Beerenwinkel, Niko, Park, Paul S.-H., Müller, Daniel J.

Journal:

Year:

2013

Language:

english

File:

PDF, 2.20 MB

english, 2013

21

Sequencing approach to analyze the role of quasispecies for classical swine fever

Töpfer, Armin, Höper, Dirk, Blome, Sandra, Beer, Martin, Beerenwinkel, Niko, Ruggli, Nicolas, Leifer, Immanuel

Journal:

Year:

2013

Language:

english

File:

PDF, 516 KB

english, 2013

22

Probabilistic Inference of Viral Quasispecies Subject to Recombination

Töpfer, Armin, Zagordi, Osvaldo, Prabhakaran, Sandhya, Roth, Volker, Halperin, Eran, Beerenwinkel, Niko

Journal:

Journal of Computational Biology

Year:

2013

Language:

english

File:

PDF, 564 KB

english, 2013

23

Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias

McElroy, Kerensa, Zagordi, Osvaldo, Bull, Rowena, Luciani, Fabio, Beerenwinkel, Niko

Journal:

Year:

2013

Language:

english

File:

PDF, 354 KB

english, 2013

24

Patients with High-Grade Gliomas Harboring Deletions of Chromosomes 9p and 10q Benefit from Temozolomide Treatment

Wemmert, Silke, Ketter, Ralf, Rahnenfuhrer, Jorg, Beerenwinkel, Niko, Strowitzki, Martin, Feiden, Wolfgang, Hartmann, Christian, Lengauer, Thomas, Stockhammer, Florian, Zang, Klaus D., Meese, Eckart,

Journal:

Year:

2005

Language:

english

File:

PDF, 376 KB

english, 2005

25

Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

Zagordi, Osvaldo, Geyrhofer, Lukas, Roth, Volker, Beerenwinkel, Niko

Journal:

Journal of Computational Biology

Year:

2010

Language:

english

File:

PDF, 6.34 MB

english, 2010

26

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model

Prabhakaran, Sandhya, Rey, Melanie, Zagordi, Osvaldo, Beerenwinkel, Niko, Roth, Volker

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 897 KB

english, 2014

27

Transcriptomic Responses of Cancerous and Noncancerous Human Colon Cells to Sulforaphane and Selenium

Constantinescu, Simona, Hecht, Katrin, Sobotzki, Nadine, Erzinger, Melanie M., Bovet, Cédric, Shay, Jerry W., Wollscheid, Bernd, Sturla, Shana J., Marra, Giancarlo, Beerenwinkel, Niko

Journal:

Chemical Research in Toxicology

Year:

2014

Language:

english

File:

PDF, 1.64 MB

english, 2014

28

Learning Multiple Evolutionary Pathways from Cross-Sectional Data

Beerenwinkel, Niko, Rahnenführer, Jörg, Däumer, Martin, Hoffmann, Daniel, Kaiser, Rolf, Selbig, Joachim, Lengauer, Thomas

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 146 KB

english, 2005

29

[IEEE 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - New Orleans, LA (2013.6.12-2013.6.14)] 2013 IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS) - Probing of viral diversity by global haplotype prediction

Topfer, Armin, Di Giallonardo, Francesca, Metzner, Karin J., Gunthard, Huldrych F., Beerenwinkel, Niko

Year:

2013

Language:

english

File:

PDF, 73 KB

english, 2013

30

[IEEE 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Miami, FL, USA (2014.6.2-2014.6.4)] 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Viral quasispecies assembly from paired-end reads

Topfer, Armin, Beerenwinkel, Niko

Year:

2014

Language:

english

File:

PDF, 80 KB

english, 2014

31

Predicting the Response to Combination Antiretroviral Therapy: Retrospective Validation of geno2pheno‐THEO on a Large Clinical Database

Altmann, André, Däumer, Martin, Beerenwinkel, Niko, Peres, Yardena, Schülter, Eugen, Büch, Joachim, Rhee, Soo‐Yon, Sönnerborg, Anders, Fessel, W. Jeffrey, Shafer, Robert W., Zazzi, Maurizio, Kaiser, R

Journal:

The Journal of Infectious Diseases

Year:

2009

Language:

english

File:

PDF, 238 KB

english, 2009

32

Dynamic models of viral replication and latency

Mohammadi, Pejman, Ciuffi, Angela, Beerenwinkel, Niko

Journal:

Current Opinion in HIV and AIDS

Year:

2015

Language:

english

File:

PDF, 593 KB

english, 2015

33

Simultaneous analysis of large-scale RNAi screens for pathogen entry

Rämö, Pauli, Drewek, Anna, Arrieumerlou, Cécile, Beerenwinkel, Niko, Ben-Tekaya, Houchaima, Cardel, Bettina, Casanova, Alain, Conde-Alvarez, Raquel, Cossart, Pascale, Csúcs, Gábor, Eicher, Simone, Emm

Journal:

Year:

2014

Language:

english

File:

PDF, 3.53 MB

english, 2014

34

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies

Yuan, Ke, Sakoparnig, Thomas, Markowetz, Florian, Beerenwinkel, Niko

Journal:

Year:

2015

Language:

english

File:

PDF, 1.36 MB

english, 2015

35

Estimating HIV Evolutionary Pathways and the Genetic Barrier to Drug Resistance

Beerenwinkel, Niko, Däumer, Martin, Sing, Tobias, Rahnenführer, Jörg, Lengauer, Thomas, Selbig, Joachim, Hoffmann, Daniel, Kaiser, Rolf

Journal:

The Journal of Infectious Diseases

Year:

2005

Language:

english

File:

PDF, 668 KB

english, 2005

36

Model Selection for Mixtures of Mutagenetic Trees

Yin, Junming, Beerenwinkel, Niko, Rahnenführer, Jörg, Lengauer, Thomas

Journal:

Statistical Applications in Genetics and Molecular Biology

Year:

2006

Language:

english

File:

PDF, 460 KB

english, 2006

37

Briefer Notices

Yin, Junming, Beerenwinkel, Niko, Rahnenführer, Jörg, Lengauer, Thomas

Journal:

American Political Science Review

Year:

1931

Language:

english

File:

PDF, 2.08 MB

english, 1931

38

Learning Monotonic Genotype-Phenotype Maps

Beerenwinkel, Niko, Knupfer, Patrick, Tresch, Achim

Journal:

Statistical Applications in Genetics and Molecular Biology

Year:

2011

Language:

english

File:

PDF, 518 KB

english, 2011

39

The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients

Beerenwinkel, Niko, Montazeri, Hesam, Schuhmacher, Heike, Knupfer, Patrick, von Wyl, Viktor, Furrer, Hansjakob, Battegay, Manuel, Hirschel, Bernard, Cavassini, Matthias, Vernazza, Pietro, Bernasconi,

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 547 KB

english, 2013

40

Identification of Constrained Cancer Driver Genes Based on Mutation Timing

Sakoparnig, Thomas, Fried, Patrick, Beerenwinkel, Niko, Wang, Edwin

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 922 KB

english, 2015

41

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data

Bragg, Lauren M., Stone, Glenn, Butler, Margaret K., Hugenholtz, Philip, Tyson, Gene W., Beerenwinkel, Niko

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.23 MB

english, 2013

42

Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks

Lasserre, Julia, Chung, Ho-Ryun, Vingron, Martin, Beerenwinkel, Niko

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.78 MB

english, 2013

43

Genetic Progression and the Waiting Time to Cancer

Beerenwinkel, Niko, Antal, Tibor, Dingli, David, Traulsen, Arne, Kinzler, Kenneth W., Velculescu, Victor E., Vogelstein, Bert, Nowak, Martin A.

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 359 KB

english, 2007

44

The Time Scale of Evolutionary Innovation

Chatterjee, Krishnendu, Pavlogiannis, Andreas, Adlam, Ben, Nowak, Martin A., Beerenwinkel, Niko

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.33 MB

english, 2014

45

24 Hours in the Life of HIV-1 in a T Cell Line

Mohammadi, Pejman, Desfarges, Sébastien, Bartha, István, Joos, Beda, Zangger, Nadine, Muñoz, Miguel, Günthard, Huldrych F., Beerenwinkel, Niko, Telenti, Amalio, Ciuffi, Angela, Emerman, Michael

Journal:

Year:

2013

Language:

english

File:

PDF, 873 KB

english, 2013

46

Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV

von Kleist, Max, Menz, Stephan, Huisinga, Wilhelm, Beerenwinkel, Niko

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 686 KB

english, 2010

47

Viral Population Estimation Using Pyrosequencing

Eriksson, Nicholas, Pachter, Lior, Mitsuya, Yumi, Rhee, Soo-Yon, Wang, Chunlin, Gharizadeh, Baback, Ronaghi, Mostafa, Shafer, Robert W., Beerenwinkel, Niko, Tesler, Glenn

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 436 KB

english, 2008

48

The Protective Role of Symmetric Stem Cell Division on the Accumulation of Heritable Damage

McHale, Peter T., Lander, Arthur D., Beerenwinkel, Niko

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.81 MB

english, 2014

49

Modeling Protective Anti-Tumor Immunity via Preventative Cancer Vaccines Using a Hybrid Agent-based and Delay Differential Equation Approach

Kim, Peter S., Lee, Peter P., Beerenwinkel, Niko

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.83 MB

english, 2012

50

Patterns of Proliferative Activity in the Colonic Crypt Determine Crypt Stability and Rates of Somatic Evolution

Zhao, Rui, Michor, Franziska, Beerenwinkel, Niko

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.77 MB

english, 2013