|
Cell Plasticity - Systems Biology of Cell Differentiation
Third-party funded project |
Project title |
Cell Plasticity - Systems Biology of Cell Differentiation |
Principal Investigator(s) |
van Nimwegen, Erik
|
Co-Investigator(s) |
Zavolan, Mihaela
|
Project Members |
Pemberton-Ross, Peter Omidi Klishami, Saeed Balwierz, Piotr Arnold, Phil Geier, Florian Berninger, Philipp Kelley, Nicholas William
|
Organisation / Research unit |
Departement Biozentrum / Bioinformatics (van Nimwegen) |
Project Website |
http://www.cellplasticity.org |
Project start |
01.01.2010 |
Probable end |
31.12.2014 |
Status |
Completed |
Abstract |
The Systems Biology of Cell Plasticity in Health and Disease is an RTD project funded by the SystemsX.ch initiative. Coordinated by Dr. Susan Gasser, Cell Plasticity brings together 8 research teams, and several affiliated members. The common goal is to decode the regulation of stem cell status and cell differentiation, under both physiological and pathological conditions. Specifically, we will delineate genome-wide epigenetic and transcriptional events that occur during cell differentiation using systematic, quantitative approaches. We will relate this insight to gene regulation programs that have been computationally predicted and experimentally tested. In particular, we will model the interplay of transcription factor activities and chromatin modifications during cell differentiation by genetic perturbations in our experimental systems (hematopoiesis, neurogenesis, and the epithelial-mesenchymal transition). Ultimately, by performing the proposed integrated analysis, we aim to generate predictive models for the epigenetic contribution to the state of pluripotency and to cell differentiation.
see http://www.cellplasticity.org/Projects/ for a more detailed summary of the projects.
|
Financed by |
Swiss Government (Research Cooperations)
|
Published results () |
|
ID |
Autor(en) |
Titel |
ISSN / ISBN |
Erschienen in |
Art der Publikation |
|
1445147 |
Arnold, Phil; Schöler, Anne; Pachkov, Mikhail; Balwierz, Piotr J; Jørgensen, Helle; Stadler, Michael B; van Nimwegen, Erik; Schübeler, Dirk |
Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting |
1088-9051 |
Genome research |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
1471083 |
Pachkov, Mikhail; Balwierz, Piotr J.; Arnold, Phil; Ozonov, Evgeniy; van Nimwegen, Erik |
SwissRegulon : a database of genome-wide annotations of regulatory sites: recent updates |
0305-1048 ; 1362-4962 |
Nucleic Acids Research |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
1618773 |
Tiwari, N.; Meyer-Schaller, N.; Arnold, P.; Antoniadis, H.; Pachkov, M.; van Nimwegen, E.; Christofori, G. |
Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8) |
1932-6203 |
PLoS ONE |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
1166189 |
Arnold, Phil; Erb, Ionas; Pachkov, Mikhail; Molina, Nacho; van Nimwegen, Erik |
MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences |
1367-4803 |
Bioinformatics |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
1166190 |
Stadler, Michael B; Murr, Rabih; Burger, Lukas; Ivanek, Robert; Lienert, Florian; Schöler, Anne; van Nimwegen, Erik; Wirbelauer, Christiane; Oakeley, Edward J; Gaidatzis, Dimos; Tiwari, Vijay K; Schübeler, Dirk |
DNA-binding factors shape the mouse methylome at distal regulatory regions |
0028-0836 |
Nature |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
1445148 |
Tippmann, Sylvia C; Ivanek, Robert; Gaidatzis, Dimos; Schöler, Anne; Hoerner, Leslie; van Nimwegen, Erik; Stadler, Peter F; Stadler, Michael B; Schübeler, Dirk |
Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels |
1744-4292 |
Molecular systems biology |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
2055424 |
Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard |
Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming |
1535-6108 |
Cancer cell |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
3208053 |
Pemberton-Ross, Peter J; Pachkov, Mikhail; van Nimwegen, Erik |
ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data |
1046-2023 |
Methods |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
2637564 |
Baresic, Mario; Salatino, Silvia; Kupr, Barbara; van Nimwegen, Erik; Handschin, Christoph |
Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program |
1098-5549 |
Molecular and cellular biology |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
2420424 |
Diepenbruck, Maren; Waldmeier, Lorenz; Ivanek, Robert; Berninger, Philipp; Arnold, Phil; van Nimwegen, Erik; Christofori, Gerhard |
Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition |
0021-9533 ; 1477-9137 |
Journal of Cell Science |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
2420414 |
Balwierz, Piotr J; Pachkov, Mikhail; Arnold, Phil; Gruber, Andreas J; Zavolan, Mihaela; van Nimwegen, Erik |
ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs |
1088-9051 |
Genome research |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
2365922 |
Luisier, Raphaëlle; Unterberger, Elif B.; Goodman, Jay I.; Schwarz, Michael; Moggs, Jonathan; Terranova, Rémi; van Nimwegen, Erik |
Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion |
0305-1048 ; 1362-4962 |
Nucleic Acids Research |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
2326176 |
Vigano, Maria Alessandra; Ivanek, Robert; Balwierz, Piotr; Berninger, Philipp; van Nimwegen, Erik; Karjalainen, Klaus; Rolink, Antonius |
An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants. |
0014-2980 |
European journal of immunology |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
3931575 |
Omidi, Saeed; Zavolan, Mihaela; Pachkov, Mikhail; Breda, Jeremie; Berger, Severin; van Nimwegen, Erik |
Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors |
1553-734X ; 1553-7358 |
PLoS Computational Biology |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
3775473 |
Artimo, Panu; Duvaud, Séverine; Pachkov, Mikhail; Ioannidis, Vassilios; van Nimwegen, Erik; Stockinger, Heinz |
The ISMARA client |
2046-1402 |
F1000Research |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
4509680 |
Berger, Severin; Pachkov, Mikhail; Arnold, Phil; Omidi, Saeed; Kelley, Nicholas; Salatino, Silvia; van Nimwegen, Erik |
Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs |
1088-9051 ; 1549-5469 |
Genome Research |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
Cooperations () |
|
ID |
Kreditinhaber |
Kooperationspartner |
Institution |
Laufzeit - von |
Laufzeit - bis |
|
2331193 |
van Nimwegen, Erik |
Zavolan, Mihaela |
Biozentrum, University of Basel |
01.01.2000 |
31.12.2099 |
|
2331239 |
van Nimwegen, Erik |
Schübeler, Dirk |
FMI, Basel |
01.01.2010 |
31.12.2014 |
|
2337819 |
van Nimwegen, Erik |
Christofori, Gerhard |
Dep. Biomedicine, University of Basel |
01.01.2012 |
31.12.2020 |
|
2337835 |
van Nimwegen, Erik |
Rolink, Antonius |
Dep. Biomedicine, University of Basel |
01.01.2012 |
31.12.2020 |
|
2337883 |
van Nimwegen, Erik |
Bentires-Alj, Mohamed |
FMI, Basel |
01.01.2012 |
31.12.2020 |
|
|
|
|