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1

CONCEPTUAL CHANGE TEXTS IN CHEMISTRY TEACHING: A STUDY ON THE PARTICLE MODEL OF MATTER

Anne Beerenwinkel, Ilka Parchmann, Cornelia Gräsel

Journal:

International Journal of Science and Mathematics Education

Year:

2011

Language:

english

File:

PDF, 201 KB

english, 2011

2

Waiting Time Models of Cancer Progression

GERSTUNG, MORITZ, BEERENWINKEL, NIKO

Journal:

Mathematical Population Studies

Year:

2010

Language:

english

File:

PDF, 268 KB

english, 2010

3

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

4

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

5

ROCR: visualizing classifier performance in R

Sing, T., Sander, O., Beerenwinkel, N., Lengauer, T.

Journal:

Year:

2005

Language:

english

File:

PDF, 107 KB

english, 2005

6

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

7

Constructivism in Practice: an Exploratory Study of Teaching Patterns and Student Motivation in Physics Classrooms in Finland, Germany and Switzerland

Beerenwinkel, Anne, von Arx, Matthias

Journal:

Research in Science Education

Year:

2017

Language:

english

File:

PDF, 467 KB

english, 2017

8

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

9

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

10

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

11

Chemieschulbücher in der Unterrichtsplanung - Welche Bedeutung haben Schülervorstellungen?

Anne Beerenwinkel, Ilka Parchmann, Cornelia Gräsel

Journal:

Year:

2007

Language:

german

File:

PDF, 224 KB

german, 2007

12

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

13

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

14

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

15

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

16

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

17

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

18

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

19

Is the public willing to pay for hydrogen buses? A comparative study of preferences in four cities

Tanya O’Garra, Susana Mourato, Lisa Garrity, Patrick Schmidt, Anne Beerenwinkel, Matthias Altmann, David Hart, Cornelia Graesel, Simon Whitehouse

Journal:

Year:

2007

Language:

english

File:

PDF, 222 KB

english, 2007

20

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

21

Quantifying cancer progression with conjunctive Bayesian networks

Gerstung, M., Baudis, M., Moch, H., Beerenwinkel, N.

Journal:

Year:

2009

Language:

english

File:

PDF, 336 KB

english, 2009

22

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

Zagordi, O., Klein, R., Daumer, M., Beerenwinkel, N.

Journal:

Nucleic Acids Research

Year:

2010

Language:

english

File:

PDF, 2.12 MB

english, 2010

23

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

24

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

25

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

26

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

27

PROGRESSION RISK ASSESSMENT IN PROSTATE CANCER USING A NOVEL BIOINFORMATICS BASED GENETIC MODEL

B. Wullich, V. Jung, J. Rahnenführer, N. Beerenwinkel, M. Müller, W. Schulz, J. Kamradt, M. Stöckle

Journal:

European Urology Supplements

Year:

2006

Language:

english

File:

PDF, 47 KB

english, 2006

28

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

29

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

30

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

31

Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction

Dumcke, S., Brauer, J., Anchang, B., Spang, R., Beerenwinkel, N., Tresch, A.

Journal:

Year:

2014

Language:

english

File:

PDF, 608 KB

english, 2014

32

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

33

Challenges in RNA virus bioinformatics

Marz, M., Beerenwinkel, N., Drosten, C., Fricke, M., Frishman, D., Hofacker, I. L., Hoffmann, D., Middendorf, M., Rattei, T., Stadler, P. F., Topfer, A.

Journal:

Year:

2014

Language:

english

File:

PDF, 178 KB

english, 2014

34

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

35

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

36

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

37

Geno2pheno: interpreting genotypic HIV drug resistance tests

N. Beerenwinkel, T. Lengauer, J. Selbig, B. Schmidt, H. Walter, K. Korn, R. Kaiser, D. Hoffmann

Journal:

IEEE Intelligent Systems and their Applications

Year:

2001

Language:

english

File:

PDF, 281 KB

english, 2001

38

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

39

Cancer Evolution: Mathematical Models and Computational Inference

Beerenwinkel, N., Schwarz, R. F., Gerstung, M., Markowetz, F.

Journal:

Systematic Biology

Year:

2015

Language:

english

File:

PDF, 773 KB

english, 2015

40

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes

Beerenwinkel, N.

Journal:

Nucleic Acids Research

Year:

2003

Language:

english

File:

PDF, 338 KB

english, 2003

41

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

42

[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

43

[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

44

Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype

Beerenwinkel, N., Schmidt, B., Walter, H., Kaiser, R., Lengauer, T., Hoffmann, D., Korn, K., Selbig, J.

Journal:

Proceedings of the National Academy of Sciences

Year:

2002

Language:

english

File:

PDF, 547 KB

english, 2002

45

Cell Selection as Driving Force in Lung and Colon Carcinogenesis

Schollnberger, H., Beerenwinkel, N., Hoogenveen, R., Vineis, P.

Journal:

Cancer Research

Year:

2010

Language:

english

File:

PDF, 265 KB

english, 2010

46

Competition-colonization dynamics in an RNA virus

Ojosnegros, S., Beerenwinkel, N., Antal, T., Nowak, M. A., Escarmis, C., Domingo, E.

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 624 KB

english, 2010

47

Comparative lesion sequencing provides insights into tumor evolution

Jones, S., Chen, W.-d., Parmigiani, G., Diehl, F., Beerenwinkel, N., Antal, T., Traulsen, A., Nowak, M. A., Siegel, C., Velculescu, V. E., Kinzler, K. W., Vogelstein, B., Willis, J., Markowitz, S. D.

Journal:

Proceedings of the National Academy of Sciences

Year:

2008

Language:

english

File:

PDF, 779 KB

english, 2008

48

Tenofovir Resistance and Resensitization

Wolf, K., Walter, H., Beerenwinkel, N., Keulen, W., Kaiser, R., Hoffmann, D., Lengauer, T., Selbig, J., Vandamme, A.-M., Korn, K., Schmidt, B.

Journal:

Antimicrobial Agents and Chemotherapy

Year:

2003

Language:

english

File:

PDF, 133 KB

english, 2003

49

A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data

Beerenwinkel, N., Drton, M.

Journal:

Year:

2007

Language:

english

File:

PDF, 301 KB

english, 2007

50

Competition-colonization trade-off promotes coexistence of low-virulence viral strains

Ojosnegros, S., Delgado-Eckert, E., Beerenwinkel, N.

Journal:

Journal of The Royal Society Interface

Year:

2012

Language:

english

File:

PDF, 585 KB

english, 2012