Publications

The SystemsX RTD project BrainstemX/NeurostemX started in March 2013. 

 

(a) Publications acknowledging SystemsX.ch explicitly

  • Iber, D., Tanaka, S., Fried,. P., Germann, P., and Menshykau, D. (2015). Simulating Tissue Morphogenesis and Signaling, Springer Book Series: Methods in Molecular Biology. Book Title: Tissue Morphogenesis: Methods and Protocols. Editor: Celeste Nelson

  • Velten, B., Ünal, E., and Iber, D. Image-based Parameter Inference for Spatio-Temporal Models of Organogenesis. NOLTA 2014 (Luzern, CH), awarded price for best student paper

  • Vollmer, J., Menshykau, D., and Iber, D. (2013) Simulating Organogenesis in COMSOL: Cell-based Signaling Models. Proceedings of COMSOL Conference 2013, Rotterdam

  • Nobs, N, Baranek, C, Nestel, S, Kulik, A, Kapfhammer, J, Nitsch, C, Atanasoski, S (2014). Stage-specific requirement for cyclin D1 in glial progenitor cells of the cerebral cortex. Glia 62, 829-839

 

(b) Publications of at least two groups of BrainStemX

  • Lopez-Rios, J., Duchesne, A., Speziale, D., Andrey, G., Peterson, K. A., Germann, P., Unal, E., Liu, J., Floriot, S., Barbey, S., Gallard, Y., Müller-Gerbl, M., Courtney, A. D., Klopp, C., Rodriguez, S., Ivanek, R., Beisel, C., Wicking, C., Iber, D., Robert, B., McMahon, A. P., Duboule, D. and Zeller, R. (2014). Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. Nature 511, 46-51.

 

(c) Other publications with minor contributions of BrainStemX

  • Arbore, R., Sekii, K., Beisel, C., Ladurner, P., Berezikov, E., Schärer, L. (2015). Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits. Front Zool. 12:14.

  • Arnold, P., Erb, I., Pachkov, M., Molina, N. and van Nimwegen, E. (2012). MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinformatics 28, 487-494.

  • Arnold, P., Schöler, A., Pachkov, M., Balwierz, P. J., Jørgensen, H., Stadler, M. B., van Nimwegen, E. and Schübeler, D. (2013). Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome research 23, 60-73.

  • Azim, K., Hurtado-Chong, A., Fischer, B., Kumar, N., Zweifel, S., Taylor, V., Raineteau O. (2015). Transcriptional Hallmarks of Heterogeneous Neural Stem Cell Niches of the Subventricular Zone. Stem Cells 33, 2232-2242.

  • Balwierz, P. J., Pachkov, M., Arnold, P., Gruber, A. J., Zavolan, M. and van Nimwegen, E. (2014). ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome research 24, 869-884.

  • Baresic, M., Salatino, S., Kupr, B., van Nimwegen, E. and Handschin, C. (2014). Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program. Molecular and cellular biology, Molcular Cell Biol. 01710-01713.

  • Boda, E., Di Maria, S., Rosa, P., Taylor, V., Abbracchio, M.P. and Buffo, A. (2014). Early phenotypic asymmetry of sister oligodendrocyte progenitor cells after mitosis and its modulation by aging and extrinsic factors. Glia 63, 271-286.

  • Cloëtta, D., Thomanetz, V., Lustenberger, RM., Baranek, C., Lin, S., Oliveri, F., 1Atanasoski, S., and 1Rüegg, MA. (2013). Inactivation of mTORC1 in the developing brain induces microcephaly and affects gliogenesis. J Neurosci. 33, 7799-7810 1equal contribution.

  • Comoglio, F., Schlumpf, T., Schmid, V., Rohs, R., Beisel, C., Paro, R. (2015). High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins. Cell Rep. 2015 11(5):821-834.

  • Consortium, T. F. (2014). A promoter-level mammalian expression atlas. Nature 507, 462-470.

  • Diepenbruck, M., Waldmeier, L., Ivanek, R., Berninger, P., Arnold, P., van Nimwegen, E. and Christofori, G. (2014). Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial–mesenchymal transition. Journal of Cell Science 127, 1523-1536.

  • Dill, M. T., Makowska, Z., Trincucci, G., Gruber, A. J., Vogt, J. E., Filipowicz, M., Calabrese, D., Krol, I., Lau, D. T., Terracciano, L., van Nimwegen, E., Roth, V. and Heim, M. H. (2014). Pegylated IFN-alpha regulates hepatic gene expression through transient Jak/STAT activation. J Clin Invest 124, 1568-1581

  • Frank, T. and Tay, S. (2013). Flow-switching allows independently programmable, extremely stable, high-throughput diffusion-based gradients. Lab. Chip 2013, 13, 1273–1281.

  • Giachino, C., Barz, M., Tchorz, J.S., Tome, M., Gassmann, M., Bischofberger, J., Bettler, B., and Taylor, V. (2014). GABA suppresses neurogenesis in the adult hippocampus through GABAB receptors. Development 141, 83-90.

  • Giachino, C., Basak, O., Lugert, S., Knuckles, P., Obernier, K., Fiorelli, R., Frank, S., Raineteau, O., Alvarez-Buylla, A., and Taylor, V. (2014). Molecular diversity subdivides the adult forebrain neural stem cell population. Stem Cells 32, 70-84.

  • Giallonardo, F. D., Töpfer, A., Rey, M., Prabhakaran, S., Duport, Y., Leemann, C., Schmutz, S., Campbell, N. K., Joos, B., Lecca, M. R., Patrignani, A., Däumer, M., Beisel, C., Rusert, P., Trkola, A., Günthard, H. F., Roth, V., Beerenwinkel, N. and Metzner, K. J. (2014). Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Research, in press.

  • Kellogg, R. A., Gómez-Sjöberg, R., Leyrat, A.A. and Tay, S. (2014). High-throughput microfluidic single-cell analysis pipeline for studies of signaling dynamics Nature Protocol 9, 1713-1726.

  • Khorshid, M., Hausser, J., Zavolan, M. and van Nimwegen, E. (2013). A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nature Methods 10, 253-255.

  • Luisier, R., Unterberger, E. B., Goodman, J. I., Schwarz, M., Moggs, J., Terranova, R. and van Nimwegen, E. (2014). Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion. Nucleic Acids Research, gkt1415.

  • Lundberg, P., Karow, A., Nienhold, R., Looser, R., Hao-Shen, H., Nissen, I., Girsberger, S., Lehmann, T., Passweg, J., Stern, M., Beisel, C., Kralovics, R. and Skoda, R. C. (2014). Clonal evolution and clinical correlates of somatic mutations in myeloproliferative neoplasms. Blood 123, 2220-2228. 

  • Meier-Abt, F., Milani, E., Roloff, T., Brinkhaus, H., Duss, S., Meyer, D. S., Klebba, I., Balwierz, P. J., van Nimwegen, E. and Bentires-Alj, M. (2013). Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium. Breast Cancer Research 15, R36.

  • Menshykau, D., Germann, P., Lemereux, L., and Iber, D. (2013) Simulating Organogenesis in COMSOL: Parameter Optimization for PDE-based models. Proceedings of COMSOL Conference 2013, Rotterdam.

  • Moretti, F., Rolando, C., Winker, M., Ivanek, R., Taylor, V., Bustin, M., and Pertz, O. (2015). Growth cone localization of the mRNA encoding a chromatin regulator modulates neuronal outgrowth. Mol Cell Bio 35, 2035-2050.

  • Nato, G., Caramello, A., Trova, S., Avataneo, V., Rolando, C., Taylor, V., Buffo, A., Peretto, P., and Luzzati, F. (2015). Striatal astrocytes produce neuroblasts in an excitotoxic model of Huntington's disease. Development 142, 840-845.

  • Nobs, N., Nestel, S., Kulik, A., Nitsch, C., and Atanasoski, S. (2013). Cyclin D1 is required for proliferation of Olig2-expressing progenitor cells in the injured cerebral cortex. Glia 61, 1443-1455.

  • Pachkov, M., Balwierz, P. J., Arnold, P., Ozonov, E. and van Nimwegen, E. (2013). SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic acids research 41, D214-D220.

  • Rago L., Beattie R., Taylor V., Winter J. (2014). miR379-410 cluster miRNAs regulate neurogenesis and neuronal migration by fine-tuning N-cadherin. EMBO J. 33, 906-920.

  • Robins. S., Stewart, I., McNay, D.E., Taylor, V., Giachino, C., Goetz, M., Ninkovic, J., Briancon, N., Maratos-Flier, E., Flier, J.S., Kokoeva, M.V., and Placzek, M. (2013). Alpha-tanycytes of the adult hypothalamic third ventricle include distinct populations of FGF-responsive neural progenitors. Nature Communications 4, 2049.

  • Osterwalder, M., Speziale, D., Shoukry, M., Mohan, R., Ivanek, R., Kohler, M., Beisel, C., Wen, X., Scales, SJ., Christoffels, V.M., Visel, A., Lopez-Rios, J., Zeller, R. (2014). HAND2 targets define a network of transcriptional regulators that compartmentalize the early limb bud mesenchyme. Dev Cell. 2014 31(3):345-357.

  • Schwaninger CA, Menshykau D, and Iber D. (2015). Simulating organogenesis: Algorithms for the image-based determination of displacement fields. ACM Transactions on Modeling and Computer Simulation, 25.2: 10.

  • Steffen, P. A., Fonseca, J. P., Gänger, C., Dworschak, E., Kockmann, T., Beisel, C. and Ringrose, L. (2013). Quantitative in vivo analysis of chromatin binding of Polycomb and Trithorax group proteins reveals retention of ASH1 on mitotic chromatin. Nucleic Acids Research 41, 5235-5250.

  • Tanaka, S., and Iber, D. (2013). Simulation of a Microfluidic Gradient Generator using Lattice Boltzmann Methods. Current Synthetic and Systems Biology 1, 102.

  • Tanaka S, Sichau D, Iber D. (2015). LBIBCell: A Cell-Based Simulation Environment for Morphogenetic Problems. Bioinformatics 31, 2340-2347.

  • Tiwari, N., Meyer-Schaller, N., Arnold, P., Antoniadis, H., Pachkov, M., van Nimwegen, E. and Christofori, G. (2013a). Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PloS one 8, e57329.

  • Tiwari, N., Tiwari, V. K., Waldmeier, L., Balwierz, P. J., Arnold, P., Pachkov, M., Meyer-Schaller, N., Schübeler, D., van Nimwegen, E. and Christofori, G. (2013b). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming. Cancer Cell 23, 768-783.