Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model

Autor: Joke Blom, Carsten Carlberg, Frank J. Bruggeman, Katja N. Rybakova, Aleksandra Tomaszewska, Simon van Mourik, Hans V. Westerhoff

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, 153-161. Oxford University Press
ISSUE=43;STARTPAGE=153;ENDPAGE=161;ISSN=0305-1048;TITLE=Nucleic Acids Research
Nucleic Acids Research, 43(1), 153-161. Oxford University Press
Rybakova, E N, Tomaszewska, A, van Mourik, A, Blom, J, Westerhoff, H V, Carlberg, C & Bruggeman, F J 2015, ' Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model. ', Nucleic Acids Research, no. 43, 1, pp. 153-161 . https://doi.org/10.1093/nar/gku1272
Nucleic acids research
Nucleic acids research, 43(1), 153-161
Nucleic acids research 43 (2015) 1

Changes in transcription factor levels, epigenetic status, splicing kinetics and mRNA degradation can each contribute to changes in the mRNA dynamics of a gene. We present a novel method to identify which of these processes is changed in cells in res

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d90581f1a1a3882229874215d4450f73
https://doi.org/10.1093/nar/gku1272

Systems Biology towards life in silico: mathematics of the control of living cells

Autor: Barbara M. Bakker, Martijn J. Moné, Hanna M. Härdin, Alexey Kolodkin, Hans van Leeuwen, Jacky L. Snoep, Klaas Krab, Marco Eijken, Frank J. Bruggeman, Riaan Conradie, Stephen J. Wilkinson, Katja N. Rybakova, Jan H. van Schuppen, Hans V. Westerhoff

Publikováno v: Westerhoff, H V, Kolodkin, A N, Conradie, R, Wilkinson, S J, Bruggeman, F J, Krab, K, Schuppen, J H, Hardin, H M, Bakker, B M, Mone, M J, Rybakova, E N, Eijken, M, van Leeuwen, J P & Snoep, J L 2009, ' Systems Biology towards life in silico: mathematics of the control of living cells. ', Journal of Mathematical Biology, vol. 58, pp. 7-34 . https://doi.org/10.1007/s00285-008-0160-8
Journal of Mathematical Biology, 58, 7-34. Springer Verlag
Journal of Mathematical Biology, 58(1-2), 7-34. Springer-Verlag
Westerhoff, H V, Kolodkin, A, Conradie, R, Wilkinson, S J, Bruggeman, F J, Krab, K, van Schuppen, J H, Hardin, H, Bakker, B M, Moné, M J, Rybakova, K N, Eijken, M, van Leeuwen, H J P & Snoep, J L 2009, ' Systems biology towards life in silico : mathematics of the control of living cells ', Journal of Mathematical Biology, vol. 58, no. 1-2, pp. 7-34 . https://doi.org/10.1007/s00285-008-0160-8

Systems Biology is the science that aims to understand how biological function absent from macromolecules in isolation, arises when they are components of their system. Dedicated to the memory of Reinhart Heinrich, this paper discusses the origin and

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::36889fd3574c120799520fceae6b637d
https://hdl.handle.net/1871/27365

Origins of Stochastic Intracellular Processes and Consequences for Cell-to-Cell Variability and Cellular Survival Strategies

Autor: Katja N. Rybakova, Anne Schwabe, Maciej Dobrzyński, Pernette J. Verschure, Frank J. Bruggeman

Quantitative analyses of the dynamics of single cells have become a powerful approach in current cell biology. They give us an unprecedented opportunity to study dynamics of molecular networks at a high level of accuracy in living single cells. Genet

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::2153d6ffedcb3c4aa1696c2cec004f6f
https://doi.org/10.1016/b978-0-12-385118-5.00028-1

RETRACTED: Population-Level Transcription Cycles Derive from Stochastic Timing of Single-Cell Transcription

Autor: Hans V. Westerhoff, Aleksandra Tomaszewska, Martijn J. Moné, Tatjana Degenhardt, Katja N. Rybakova, Carsten Carlberg, Frank J. Bruggeman

Publikováno v: Degenhardt, T, Rybakova, E N, Tomaszewska, A, Mone, M J, Westerhoff, H V, Bruggeman, F J & Carlberg, C 2009, ' Population-level transcription cycles derive from stochastic timing of single-cell transcription. ', Cell, vol. 138, pp. 489-501 . https://doi.org/10.1016/j.cell.2009.05.029
Cell, 138, 489-501. Cell Press

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).This article has been retracted at the request of the authors.In this paper we used computational approaches to show t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3d3d0cf9913be4e2954ee83efdbb9b5e