SyBoSS - Systems Biology of Stem Cells and Reprogramming

Supported by the EU Seventh Research Framework Programme (FP7).

SyBoSS Publicationsuntil June 2014

2014 (14)

da Rocha, S. T., Boeva, V., Escamilla-Del-Arenal, M., Ancelin, K., Granier, C., Matias, N. R., Sanulli, S., Chow, J., Schulz, E., Picard, C., Kaneko, S., Helin, K., Reinberg, D., Stewart, A. F., Wutz, A., Margueron, R. and Heard, E. (2014). "Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to the Inactive X Chromosome." Mol Cell 53: 301-16.

Denissov, S., Hofemeister, H., Marks, H., Kranz, A., Ciotta, G., Singh, S., Anastassiadis, K., Stunnenberg, H. G. and Stewart, A. F. (2014). "Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant." Development 141: 526-37.

Dinkel, H., Van Roey, K., Michael, S., Davey, N. E., Weatheritt, R. J., Born, D., Speck, T., Kruger, D., Grebnev, G., Kuban, M., Strumillo, M., Uyar, B., Budd, A., Altenberg, B., Seiler, M., Chemes, L. B., Glavina, J., Sanchez, I. E., Diella, F. and Gibson, T. J. (2014). "The eukaryotic linear motif resource ELM: 10 years and counting." Nucleic Acids Res 42: D259-66.

Gendrel, A. V., Attia, M., Chen, C. J., Diabangouaya, P., Servant, N., Barillot, E. and Heard, E. (2014). "Developmental dynamics and disease potential of random monoallelic gene expression." Dev Cell 28: 366-80.

Kolovos, P., van de Werken, H. J., Kepper, N., Zuin, J., Brouwer, R. W., Kockx, C. E., Wendt, K. S., van, I. W. F., Grosveld, F. and Knoch, T. A. (2014). "Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements." Epigenetics Chromatin 7: 10

Meier, F., Giesert, F., Delic, S., Faus-Kessler, T., Matheus, F., Simeone, A., Holter, S. M., Kuhn, R., Weisenhorn, D. M., Wurst, W. and Prakash, N. (2014). "FGF/FGFR2 Signaling Regulates the Generation and Correct Positioning of Bergmann Glia Cells in the Developing Mouse Cerebellum." PLoS One 9: e101124.

Orchard, S., Ammari, M., Aranda, B., Breuza, L., Briganti, L., Broackes-Carter, F., Campbell, N. H., Chavali, G., Chen, C., del-Toro, N., Duesbury, M., Dumousseau, M., Galeota, E., Hinz, U., Iannuccelli, M., Jagannathan, S., Jimenez, R., Khadake, J., Lagreid, A., Licata, L., Lovering, R. C., Meldal, B., Melidoni, A. N., Milagros, M., Peluso, D., Perfetto, L., Porras, P., Raghunath, A., Ricard-Blum, S., Roechert, B., Stutz, A., Tognolli, M., van Roey, K., Cesareni, G. and Hermjakob, H. (2014). "The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases." Nucleic Acids Res 42: D358-63.

Pischedda, F., Szczurkowska, J., Cirnaru, M. D., Giesert, F., Vezzoli, E., Ueffing, M., Sala, C., Francolini, M., Hauck, S. M., Cancedda, L. and Piccoli, G. (2014). "A cell surface biotinylation assay to reveal membrane-associated neuronal cues: Negr1 regulates dendritic arborization." Mol Cell Proteomics 13: 733-48.

Schulz, E. G., Meisig, J., Nakamura, T., Okamoto, I., Sieber, A., Picard, C., Borensztein, M., Saitou, M., Bluthgen, N. and Heard, E. (2014). "The two active X chromosomes in female ESCs block exit from the pluripotent state by modulating the ESC signaling network." Cell Stem Cell 14: 203-16.

Tripathi, P. P., Di Giovannantonio, L. G., Sanguinetti, E., Acampora, D., Allegra, M., Caleo, M., Wurst, W., Simeone, A. and Bozzi, Y. (2014). "Increased dopaminergic innervation in the brain of conditional mutant mice overexpressing Otx2: effects on locomotor behavior and seizure susceptibility." Neuroscience 261: 173-83.

Van Roey, K., Uyar, B., Weatheritt, R. J., Dinkel, H., Seiler, M., Budd, A., Gibson, T. J. and Davey, N. E. (2014). "Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation." Chem Rev 114: 6733-78.

Wendt, K. S. and Grosveld, F. G. (2014). "Transcription in the context of the 3D nucleus." Curr Opin Genet Dev 25: 62-7.

Wurst, W. and Prakash, N. (2014). "Wnt1-regulated genetic networks in midbrain dopaminergic neuron development." J Mol Cell Biol 6: 34-41.

Zuin, J., Dixon, J. R., van der Reijden, M. I., Ye, Z., Kolovos, P., Brouwer, R. W., van de Corput, M. P., van de Werken, H. J., Knoch, T. A., van, I. W. F., Grosveld, F. G., Ren, B. and Wendt, K. S. (2014). "Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells." Proc Natl Acad Sci U S A 111: 996-1001.

submitted (1)

Kirk, I. K., Weinhold, N., Brunak, S. and Belling, K. (submitted). "Conserved synteny in mammalians reflects preservation of functional relationships through evolution." Mol Sys Biol.

 

2013    (20)

Ackermann, M., Sikora-Wohlfeld, W. and Beyer, A. (2013). "Impact of natural genetic variation on gene expression dynamics." PLoS Genet 9: e1003514.

Betschinger, J., Nichols, J., Dietmann, S., Corrin, P. D., Paddison, P. J. and Smith, A. (2013). "Exit from pluripotency is gated by intracellular redistribution of the bHLH transcription factor Tfe3." Cell 153: 335-47.

Bornigen, D., Pers, T. H., Thorrez, L., Huttenhower, C., Moreau, Y. and Brunak, S. (2013). "Concordance of gene expression in human protein complexes reveals tissue specificity and pathology." Nucleic Acids Res 41: e171.

Chen, C. J. and Heard, E. (2013). "Small RNAs derived from structural non-coding RNAs." Methods.

Gendrel, A. V., Tang, Y. A., Suzuki, M., Godwin, J., Nesterova, T. B., Greally, J. M., Heard, E. and Brockdorff, N. (2013). "Epigenetic functions of smchd1 repress gene clusters on the inactive X chromosome and on autosomes." Mol Cell Biol 33: 3150-65.

Ghamari, A., van de Corput, M. P., Thongjuea, S., van Cappellen, W. A., van Ijcken, W., van Haren, J., Soler, E., Eick, D., Lenhard, B. and Grosveld, F. G. (2013). "In vivo live imaging of RNA polymerase II transcription factories in primary cells." Genes Dev 27: 767-77.

Gibson, T. J., Seiler, M. and Veitia, R. A. (2013). "The transience of transient overexpression." Nat Methods 10: 715-21.

Giesert, F., Hofmann, A., Burger, A., Zerle, J., Kloos, K., Hafen, U., Ernst, L., Zhang, J., Vogt-Weisenhorn, D. M. and Wurst, W. (2013). "Expression analysis of Lrrk1, Lrrk2 and Lrrk2 splice variants in mice." PLoS One 8: e63778.

Hock, S., Ng, Y. K., Hasenauer, J., Wittmann, D., Lutter, D., Trumbach, D., Wurst, W., Prakash, N. and Theis, F. J. (2013). "Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation." BMC Syst Biol 7: 48.

Karimova, M., Abi-Ghanem, J., Berger, N., Surendranath, V., Pisabarro, M. T. and Buchholz, F. (2013). "Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system." Nucleic Acids Research 41.

Merkl, C., Saalfrank, A., Riesen, N., Kuhn, R., Pertek, A., Eser, S., Hardt, M. S., Kind, A., Saur, D., Wurst, W., Iglesias, A. and Schnieke, A. (2013). "Efficient generation of rat induced pluripotent stem cells using a non-viral inducible vector." PLoS One 8: e55170.

Mylona, A., Andrieu-Soler, C., Thongjuea, S., Martella, A., Soler, E., Jorna, R., Hou, J., Kockx, C., van Ijcken, W., Lenhard, B. and Grosveld, F. (2013). "Genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis." Blood 121: 2902-13.

Nora, E. P., Dekker, J. and Heard, E. (2013). "Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods?" Bioessays 35: 818-28.

Pourfarzad, F., Aghajanirefah, A., de Boer, E., Ten Have, S., Bryn van Dijk, T., Kheradmandkia, S., Stadhouders, R., Thongjuea, S., Soler, E., Gillemans, N., von Lindern, M., Demmers, J., Philipsen, S. and Grosveld, F. (2013). "Locus-specific proteomics by TChP: targeted chromatin purification." Cell Rep 4: 589-600.

Reber, S. B., Baumgart, J., Widlund, P. O., Pozniakovsky, A., Howard, J., Hyman, A. A. and Julicher, F. (2013). "XMAP215 activity sets spindle length by controlling the total mass of spindle microtubules." Nat Cell Biol 15: 1116-22.

Seitan, V. C., Faure, A. J., Zhan, Y., McCord, R. P., Lajoie, B. R., Ing-Simmons, E., Lenhard, B., Giorgetti, L., Heard, E., Fisher, A. G., Flicek, P., Dekker, J. and Merkenschlager, M. (2013). "Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments." Genome Res 23: 2066-77.

Sikora-Wohlfeld, W., Ackermann, M., Christodoulou, E. G., Singaravelu, K. and Beyer, A. (2013). "Assessing computational methods for transcription factor target gene identification based on ChIP-seq data." PLoS Comput Biol 9: e1003342.

Surendranath, V., Theis, M., Habermann, B. H. and Buchholz, F. (2013). "Designing efficient and specific endoribonuclease-prepared siRNAs." Methods Mol Biol 942: 193-204.

Thieme, S., Gyarfas, T., Richter, C., Ozhan, G., Fu, J., Alexopoulou, D., Muders, M. H., Michalk, I., Jakob, C., Dahl, A., Klink, B., Bandola, J., Bachmann, M., Schrock, E., Buchholz, F., Stewart, A. F., Weidinger, G., Anastassiadis, K. and Brenner, S. (2013). "The histone demethylase UTX regulates stem cell migration and hematopoiesis." Blood 121: 2462-73.

Van Roey, K., Dinkel, H., Weatheritt, R. J., Gibson, T. J. and Davey, N. E. (2013). "The switches.ELM resource: a compendium of conditional regulatory interaction interfaces." Sci Signal 6: rs7.

2012 (15)

Bradley, A., Anastassiadis, K., Ayadi, A., Battey, J. F., Bell, C., Birling, M. C., Bottomley, J., Brown, S. D., Burger, A., Bult, C. J., Bushell, W., Collins, F. S., Desaintes, C., Doe, B., Economides, A., Eppig, J. T., Finnell, R. H., Fletcher, C., Fray, M., Frendewey, D., Friedel, R. H., Grosveld, F. G., Hansen, J., Herault, Y., Hicks, G., Horlein, A., Houghton, R., Hrabe de Angelis, M., Huylebroeck, D., Iyer, V., de Jong, P. J., Kadin, J. A., Kaloff, C., Kennedy, K., Koutsourakis, M., Lloyd, K. C., Marschall, S., Mason, J., McKerlie, C., McLeod, M. P., von Melchner, H., Moore, M., Mujica, A. O., Nagy, A., Nefedov, M., Nutter, L. M., Pavlovic, G., Peterson, J. L., Pollock, J., Ramirez-Solis, R., Rancourt, D. E., Raspa, M., Remacle, J. E., Ringwald, M., Rosen, B., Rosenthal, N., Rossant, J., Ruiz Noppinger, P., Ryder, E., Schick, J. Z., Schnutgen, F., Schofield, P., Seisenberger, C., Selloum, M., Simpson, E. M., Skarnes, W. C., Smedley, D., Stanford, W. L., Stewart, A. F., Stone, K., Swan, K., Tadepally, H., Teboul, L., Tocchini-Valentini, G. P., Valenzuela, D., West, A. P., Yamamura, K., Yoshinaga, Y. and Wurst, W. (2012). "The mammalian gene function resource: the International Knockout Mouse Consortium." Mamm Genome 23: 580-6.

Chakraborty, D., Kappei, D., Theis, M., Nitzsche, A., Ding, L., Paszkowski-Rogacz, M., Surendranath, V., Berger, N., Schulz, H., Saar, K., Hubner, N. and Buchholz, F. (2012). "Combined RNAi and localization for functionally dissecting long noncoding RNAs." Nature Methods 9: 360-U59.

Chen, C. J., Servant, N., Toedling, J., Sarazin, A., Marchais, A., Duvernois-Berthet, E., Cognat, V., Colot, V., Voinnet, O., Heard, E., Ciaudo, C. and Barillot, E. (2012). "ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data." Bioinformatics 28: 3147-9.

Ding, L., Poser, I., Paszkowski-Rogacz, M. and Buchholz, F. (2012). "From RNAi screens to molecular function in embryonic stem cells." Stem Cell Rev 8: 32-42.

Dinkel, H., Michael, S., Weatheritt, R. J., Davey, N. E., Van Roey, K., Altenberg, B., Toedt, G., Uyar, B., Seiler, M., Budd, A., Jodicke, L., Dammert, M. A., Schroeter, C., Hammer, M., Schmidt, T., Jehl, P., McGuigan, C., Dymecka, M., Chica, C., Luck, K., Via, A., Chatr-Aryamontri, A., Haslam, N., Grebnev, G., Edwards, R. J., Steinmetz, M. O., Meiselbach, H., Diella, F. and Gibson, T. J. (2012). "ELM--the database of eukaryotic linear motifs." Nucleic Acids Res 40: D242-51.

Jouneau, A., Ciaudo, C., Sismeiro, O., Brochard, V., Jouneau, L., Vandormael-Pournin, S., Coppee, J. Y., Zhou, Q., Heard, E., Antoniewski, C. and Cohen-Tannoudji, M. (2012). "Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles." RNA 18: 253-64.

Marks, H., Kalkan, T., Menafra, R., Denissov, S., Jones, K., Hofemeister, H., Nichols, J., Kranz, A., Stewart, A. F., Smith, A. and Stunnenberg, H. G. (2012). "The transcriptional and epigenomic foundations of ground state pluripotency." Cell 149: 590-604.

Mellett, M., Atzei, P., Horgan, A., Hams, E., Floss, T., Wurst, W., Fallon, P. G. and Moynagh, P. N. (2012). "Orphan receptor IL-17RD tunes IL-17A signalling and is required for neutrophilia." Nat Commun 3: 1119.

Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., Gribnau, J., Barillot, E., Bluthgen, N., Dekker, J. and Heard, E. (2012). "Spatial partitioning of the regulatory landscape of the X-inactivation centre." Nature 485: 381-5.

Peng, C., Li, N., Ng, Y. K., Zhang, J., Meier, F., Theis, F. J., Merkenschlager, M., Chen, W., Wurst, W. and Prakash, N. (2012). "A unilateral negative feedback loop between miR-200 microRNAs and Sox2/E2F3 controls neural progenitor cell-cycle exit and differentiation." J Neurosci 32: 13292-308.

Sarac, O. S., Pancaldi, V., Bahler, J. and Beyer, A. (2012). "Topology of functional networks predicts physical binding of proteins." Bioinformatics 28: 2137-45.

Schulz, E. G. and Heard, E. (2012). "Role and control of X chromosome dosage in mammalian development." Curr Opin Genet Dev 23: 109-15.

Servant, N., Lajoie, B. R., Nora, E. P., Giorgetti, L., Chen, C. J., Heard, E., Dekker, J. and Barillot, E. (2012). "HiTC: exploration of high-throughput 'C' experiments." Bioinformatics 28: 2843-4.

Toedling, J., Servant, N., Ciaudo, C., Farinelli, L., Voinnet, O., Heard, E. and Barillot, E. (2012). "Deep-sequencing protocols influence the results obtained in small-RNA sequencing." PLoS One 7: e32724.

Van Roey, K., Gibson, T. J. and Davey, N. E. (2012). "Motif switches: decision-making in cell regulation." Curr Opin Struct Biol 22: 378-85.

2011 (8)

Bird, A. W., Erler, A., Fu, J., Heriche, J. K., Maresca, M., Zhang, Y., Hyman, A. A. and Stewart, A. F. (2011). "High-efficiency counterselection recombineering for site-directed mutagenesis in bacterial artificial chromosomes." Nat Methods 9: 103-9.

Davey, N. E., Van Roey, K., Weatheritt, R. J., Toedt, G., Uyar, B., Altenberg, B., Budd, A., Diella, F., Dinkel, H. and Gibson, T. J. (2011). "Attributes of short linear motifs." Mol Biosyst 8: 268-81.

Elefsinioti, A., Sarac, O. S., Hegele, A., Plake, C., Hubner, N. C., Poser, I., Sarov, M., Hyman, A., Mann, M., Schroeder, M., Stelzl, U. and Beyer, A. (2011). "Large-scale de novo prediction of physical protein-protein association." Mol Cell Proteomics 10: M111 010629.

Gendrel, A. V. and Heard, E. (2011). "Fifty years of X-inactivation research." Development 138: 5049-55.

Nitzsche, A., Paszkowski-Rogacz, M., Matarese, F., Janssen-Megens, E. M., Hubner, N. C., Schulz, H., de Vries, I., Ding, L., Huebner, N., Mann, M., Stunnenberg, H. G. and Buchholz, F. (2011). "RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity." PLoS One 6: e19470.

Pines, A., Kelstrup, C. D., Vrouwe, M. G., Puigvert, J. C., Typas, D., Misovic, B., de Groot, A., von Stechow, L., van de Water, B., Danen, E. H., Vrieling, H., Mullenders, L. H. and Olsen, J. V. (2011). "Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells." Mol Cell Biol 31: 4964-77.

Rigbolt, K. T., Prokhorova, T. A., Akimov, V., Henningsen, J., Johansen, P. T., Kratchmarova, I., Kassem, M., Mann, M., Olsen, J. V. and Blagoev, B. (2011). "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation." Sci Signal 4: rs3.

Wagner, S. A., Beli, P., Weinert, B. T., Nielsen, M. L., Cox, J., Mann, M. and Choudhary, C. (2011). "A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles." Mol Cell Proteomics 10: M111 013284.

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