SyBoSS - Systems Biology of Stem Cells and Reprogramming

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

Selected Publications

Publications of Francis Stewart

Andreu-Vieyra CV, Chen R, Agno J, Glaser S, Anastassiadis K, Stewart AF and Matzuk MM (2010) Mll2 is required in oocytes for bulk histone 3 lysine 4 trimethylation and global transcriptional silencing. PLoS Biology, 17, 8(8).

Buchanan L, Durand-Dubief B, Roguev A, Sakalar C, Wilhelm B, Stralfors A, Shevchenko A, Aasland R, Shevchenko A, Ekwall K and Stewart AF (2009) The S.pombe JmjC-protein, Msc1, prevents H2A.Z localization in centromeric and subtelomeric chromatin domains. PLoS Genetics, 5(11):e1000726.

Anastassiadis K, Fu J, Patsch C, Hu S, Weidlich S, Duerschke K, Buchholz F, Edenhofer F, Stewart AF (2009) Dre recombinase, like Cre, is a highly efficient site specific recombinase in E.coli, mammalian cells and mice Disease Models & Mechanisms 2, 508-15.

Erler A, Wegmann S, Elie-Caille C, Bradshaw CR, Maresca M, Seidel R, Habermann B, Muller D and Stewart AF. (2009) Conformational adaptability of Redβ during DNA annealing and implications for its structural relationship with Rad52. Journal of Molecular Biology, 391, 586-98.

Glaser S, Lubitz S, Loveland KL, Ohbo K, Robb L, Schwenk F, Seibler J, Röllig D, Kranz A, Anastassiadis K and Stewart AF (2009) The histone 3 lysine 4 methyltransferase, Mll2, is only required briefly during development and spermatogenesis. Epigenetics and Chromatin, 2:5

Shevchenko A, Roguev A, Schaft D, Buchanan L, Sakalar C, Habermann B, Shevchenko A, Stewart AF (2008) Chromatin Central; towards the comparative proteome by accurate mapping of a yeast proteomic environment. Genome Biology 9:R167.

Sarov, M., Pozniakovski, A., Schneider, S., Roguev, A., Ernst, S., Zhang, Y., Hyman, A.A. and Stewart, A.F. (2006) A recombineering pipeline for protein tagging and functional analysis, as applied to Caenorhabtidis elegans Nature Methods 3, 839 -44.

Publications of Andreas Beyer

1. Ucar D, Beyer A, Parthasarathy S, Workman CT (2009) Predicting functionality of protein-DNA

interactions by integrating diverse evidence; Bioinformatics 25(12):i137-44.

2. Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. (2008) eQED: an efficient method for

interpreting eQTL associations using protein networks. Mol. Systems Biol. 4:162.

3. Beyer A, Bandyopadhyay S, Ideker T (2007) Integrating physical and genetic maps: From

genomes to interaction networks. Nat. Rev. Genetics. 8(9):699-710.

4. Beyer A, Workman CT, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T (2006) Integrated

assessment and prediction of transcription factor binding. PLoS Comput. Biol. 2(6):e70.

5. Beyer A, Hollunder J, Nasheuer H-P, Wilhelm T (2004) Post-transcriptional expression regulation

in the yeast Saccharomyces cerevisiae on a genomic scale. Mol. Cell. Prot. 3:1083 - 1092.

Publications of Tony Hyman

1.     Bird AW, Hyman AA (2008) Building a spindle of the correct length in human cells requires the interaction between TPX2 and Aurora A. J Cell Biol.;182(2):289-300.

2.     Pelletier et al. (2006) Centriole assembly in Caenorhabditis elegans. Nature; 444(7119):619-23.

3.     Zhu et al. (2008) The mammalian SPD-2 ortholog Cep192 regulates centrosome biogenesis. Curr Biol. 18(2):136-41.

4.     Brouhard et al. (2008) XMAP215 is a processive microtubule polymerase. Cell. 11;132(1):79-88.

5.     Poser et al. (2008) BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods. 5(5):409-15.

6.     Sönnichsen et al. (2005) Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature. 434(7032):462-9.

7.     Boxem et al. (2008) A protein domain-based interactome network for C. elegans early embryogenesis. Cell;134(3):534-45.

8.     Petrásek et al. (2008) Characterization of protein dynamics in asymmetric cell division by scanning fluorescence correlation spectroscopy. Biophys J. 95(11):5476-86.

 

Publications of Bill Skarnes

1. Brennan J, Skarnes WC. (2008) Gene trapping in mouse embryonic stem cells. Methods Mol Biol. 461:133-48.

2. Gao et al (2008) ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a. Proc Natl Acad Sci U S A. 105:6656-61.

3. Henion et al. (2005) Beta1,3-N-acetylglucosaminyltransferase 1 glycosylation is required for axon pathfinding by olfactory sensory neurons. J Neurosci 25:1894-903

4. Wang et al.(2004) Polybromo protein BAF180 functions in mammalian cardiac chamber maturation. Genes Dev 18:3106-16

5. Skarnes et al.(2004) A public gene trap resource for mouse functional genomics. Nat Genet 36:543-4.

6. Kelly et al.(2004) The Wnt co-receptors Lrp5 and Lrp6 are essential for gastrulation in mice. Development 131:2803-15

Publications of Edith Heard

1.     Patrat, C., Okamoto, I., Diabangouya, P., Vialon, V., Le Baccon, P., Chow, J. and Heard E. Dynamic changes in paternal X-chromosome activity during imprinted X inactivation in mice (in press, PNAS)

2.     Augui, S., Filion, G., Huart, S., Guggiari, M., Maresca, M., Stewart, A.F. and Heard, E. (2007) Sensing X-chromosome pairs prior to X inactivation via a novel X-pairing region of the Xic . Science 318, 1632-1636.

3.     Okamoto, I.,  Arnaud, D., Otte, AP, Disteche, C., Avner, P. and Heard E. (2005) Evidence for de novo imprinted X-chromosome inactivation independent of meiotic inactivation in mice.  Nature 438: 369-373.

4.     Okamoto, I., Otte, A., Allis, C. D., Reinberg, D. and Heard, E. (2004) Epigenetic dynamics of imprinted X inactivation during early mouse development. Science 303: 644-649.

 

Publications of Austin Smith

1.   Silva et al 2008). Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol 6, e253.

2.   Ying et al (2008). The ground state of embryonic stem cell self-renewal Nature 453, 519-3

3.   Buehr et al (2008). Capture of authentic embryonic stem cells from rat blastocysts. Cell 135, 1287-1298.

4.   Guo et al (2009). Klf4 reverts developmentally programmed restriction of ground state pluripotency. Development 136, 1063-1069.

5.   Pollard et al (2009) Glioma stem cell lines expanded in adherent culture have tumour-specific phenotypes and are suitable for chemical and genetic screens. Cell Stem Cell: in press.

 

Publications of Frank Grosveld

1.    Rodriguez P, Bonte E, Krijgsveld J, Kolodziej KE, Guyot B, Heck A, Vyas P, de Boer E, Grosveld F, Strouboulis J. GATA-1 forms distinct activating and repressive complexes in erythroid cells. EMBO J. 2005;24:2354-66.

2.    Splinter E, Heath H, Kooren J, Palstra RJ, Klous P, Grosveld F, Galjart N, de Laat W. CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev. 2006;20:2349-54

3.    Gontan C, Güttler T, Engelen E, Demmers J, Fornerod M, Grosveld F, Tibboel D, Görlich D, Rottier R, Poot R. Exportin 4 mediates a novel nuclear import pathway for Sox family transcription factors. J Cell Biol. 2009;185:27-34

4.    Monkhorst K, Jonkers I, Rentmeester E, Grosveld F, Gribnau J. X inactivation counting & choice is a stochastic process: evidence for involvement of an X-linked activator Cell 2008; 132:410-21.

Publications of Toby Gibson


Gibson, T. J. (2009). Cell regulation: determined to signal discrete cooperation. Trends Biochem. Sci. 34, 471-482.

Gould, C. M., Diella, F., Via, A., Puntervoll, P., Gemund, C., Chabanis-Davidson, S., Michael, S., Sayadi, A., Bryne, J. C., Chica, C., Seiler, M., Davey, N. E., Haslam, N., Weatheritt, R. J., Budd, A., Hughes, T., Pas, J., Rychlewski, L., Trave, G., Aasland, R., Helmer-Citterich, M., Linding, R., and Gibson, T. J. (2010). ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res. 38, D167-80.

Haslam, N. J., and Gibson, T. J. (2010). EpiC: an open resource for exploring epitopes to aid antibody-based experiments. J Proteome Res 9, 3759-3763.

Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948.

Taussig, M. J., Stoevesandt, O., Borrebaeck, C. A., Bradbury, A. R., Cahill, D., Cambillau, C., de Daruvar, A., Dubel, S., Eichler, J., Frank, R., Gibson, T. J., Gloriam, D., Gold, L., Herberg, F. W., Hermjakob, H., Hoheisel, J. D., Joos, T. O., Kallioniemi, O., Koegl, M., Konthur, Z., Korn, B., Kremmer, E., Krobitsch, S., Landegren, U., van der Maarel, S., McCafferty, J., Muyldermans, S., Nygren, P. A., Palcy, S., Pluckthun, A., Polic, B., Przybylski, M., Saviranta, P., Sawyer, A., Sherman, D. J., Skerra, A., Templin, M., Ueffing, M., and Uhlen, M. (2007). ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods 4, 13-17.

 

Publications of Soren Brunak

1.     A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S. Proc Natl Acad Sci U S A.105:20870-5, 2008

2.     Linear motif atlas for phosphorylation-dependent signaling. Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R, Science Signaling, 2008 Sep 2;1(35):ra2, 2008.

3.     A human phneome-interactome network of protein complexes implicated in genetic disorders, K. Lage, E.O. Karlberg, Z.M. Størling, P.I. Olason, A.G. Pedersen, O. Rigina, Z. Tumer, Y. Moreau, F. Pociot, N. Tommerup, and S. Brunak. Nature Biotech., 25, 309-16, 2007.

4.     Co-evolution of transcriptional and posttranslational cell cycle regulation, L.J. Jensen, T.S. Jensen, U. de Lichtenberg, S. Brunak and P. Bork, Nature, 443, 594-597, 2006.

5.   Dynamic protein complex formation during the cell cycle, U. de Lichtenberg, L.  Juhl Jensen,  S.Brunak, P. Bork, Science, 307, 724-727, 2005.

Publications of Matthias Mann

1. L. M. de Godoy et al., Nature 455, 1251 (Oct 30, 2008).

2. T. Bonaldi et al., Mol Cell 31, 762 (Sep 5, 2008).

3.  J. R. Z. Wisniewski, A.; Nagaraj, N. Mann, M., Nature Methods  (2009).

4. JV Olsen et al, Cell Oct 2006

5. H Daub et al, Mol Cell 2008 31:438-48.

Publications of Prof Chuna Choudhary

1. Kaidi A, Weinert BT, Choudhary C, Jackson SP. Human SIRT6 promotes DNA end resection through CtIP deacetylation. Science. 2010 Sep 10;329(5997):1348-53.
2. Choudhary C and Mann M. Decoding signaling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol. 2010 Jun;11(6):427-39.
3. Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther T, Olsen JV, Mann M. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science; 2009 Aug 14;325(5942):834-40.
4. Choudhary C, Olsen JV, Brandts C, Cox J, Böhmer FD, Gerke V, Schmidt-Arras D, Berdel WE, Müller-Tidow C, Mann M, Serve H. Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes. Mol Cell. 2009 Oct 23;36(2):326-39. 

 

Publications of Wolfgang Wurst

 

  1. Enard, W., Enard W, Gehre S, Hammerschmidt K, Hölter SM, Blass T, Somel M, Brückner MK, Schreiweis C, Winter C, Sohr R, Becker L, Wiebe V, Nickel B, Giger T, Müller U, Groszer M, Adler T, Aguilar A, Bolle I, Calzada-Wack J, Dalke C, Ehrhardt N, Favor J, Fuchs H, Gailus-Durner V, Hans W, Hölzlwimmer G, Javaheri A, Kalaydjiev S, Kallnik M, Kling E, Kunder S, Mossbrugger I, Naton B, Racz I, Rathkolb B, Rozman J, Schrewe A, Busch DH, Graw J, Ivandic B, Klingenspor M, Klopstock T, Ollert M, Quintanilla-Martinez L, Schulz H, Wolf E, Wurst W, Zimmer A, Fisher SE, Morgenstern R, Arendt T, de Angelis MH, Fischer J, Schwarz J, Pääbo S. (2009). "A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice." Cell 137(5): 961-71.
  2. Pham TT, Giesert F, Röthig A, Floss T, Kallnik M, Weindl K, Hölter SM, Ahting U, Prokisch H, Becker L, Klopstock T, Hrabé de Angelis M, Beyer K, Görner K, Kahle PJ, Vogt Weisenhorn DM, Wurst W. (2009). "DJ-1 deficient mice show less TH positive neurons in the ventral tegmental area and exhibit non-motoric behavioural impairments." Genes Brain Behav.
  3. Wizenmann A, Brunet I, Lam JS, Sonnier L, Beurdeley M, Zarbalis K, Weisenhorn-Vogt D, Weinl C, Dwivedy A, Joliot A, Wurst W, Holt C, Prochiantz A (2009). "Extracellular Engrailed participates in the topographic guidance of retinal axons in vivo." Neuron 64(3): 355-66.
  4. Collins, F. S., J. Rossant and W. Wurst (2007). "A mouse for all reasons." Cell 128(1): 9-13.
  5. Prakash, N., C. Brodski, T. Naserke, E. Puelles, R. Gogoi, A. Hall, M. Panhuysen, D. Echevarria, L. Sussel, D. M. Weisenhorn, S. Martinez, E. Arenas, A. Simeone and W. Wurst (2006). "A Wnt1-regulated genetic network controls the identity and fate of midbrain-dopaminergic progenitors in vivo." Development 133(1): 89-98.
  6. Muller, M. B., S. Zimmermann, I. Sillaber, T. P. Hagemeyer, J. M. Deussing, P. Timpl, M. S. Kormann, S. K. Droste, R. Kuhn, J. M. Reul, F. Holsboer and W. Wurst (2003). "Limbic corticotropin-releasing hormone receptor 1 mediates anxiety-related behavior and hormonal adaptation to stress." Nat Neurosci 6(10): 1100-7.
  7. Sillaber, I., G. Rammes, S. Zimmermann, B. Mahal, W. Zieglgansberger, W. Wurst, F. Holsboer and R. Spanagel (2002). "Enhanced and delayed stress-induced alcohol drinking in mice lacking functional CRH1 receptors." Science 296(5569): 931-3.
  8. Wiles, M. V., F. Vauti, J. Otte, E. M. Fuchtbauer, P. Ruiz, A. Fuchtbauer, H. H. Arnold, H. Lehrach, T. Metz, H. von Melchner and W. Wurst (2000). "Establishment of a gene-trap sequence tag library to generate mutant mice from embryonic stem cells." Nat Genet 24(1): 13-4.
  9. Broccoli, V., E. Boncinelli and W. Wurst (1999). "The caudal limit of Otx2 expression positions the isthmic organizer." Nature 401(6749): 164-8.
  10. Timpl, P., R. Spanagel, I. Sillaber, A. Kresse, J. M. Reul, G. K. Stalla, V. Blanquet, T. Steckler, F. Holsboer and W. Wurst (1998). "Impaired stress response and reduced anxiety in mice lacking a functional corticotropin-releasing hormone receptor 1." Nat Genet 19(2): 162-6.

 

Publications of Frank Bucholz

1.     Kittler et al, (2004) An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature 432, 1036-1040.

2.     Kittler et al, (2007) Genome-wide RNAi profiling of cell cycle progression in human tissue culture cells. Nature Cell Biology, 9(12):1401-1412.

3.     Poser et al, (2008) BAC TransgeneOmics: A high-throughput method for exploration of protein function in mammals. Nature Methods, 5(5):409-15.

4.     Sarkar et al, (2007) HIV-1 Proviral DNA Excision Using an Evolved Recombinase. Science, 29;316(5833):1912-5.

5.     Ding et al, (2009) A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Cell Stem Cell 4, 403–415..

                      

Publications of Chris Workman

1.     Ucar D, Beyer A, Parthasarathy S, Workman CT, Predicting functionality of protein-DNA interactions by integrating diverse evidence, ISMB 2009, Bioinformatics 25(12):i137-44.

2.     Bergholdt R, Størling ZM, Lage K, Karlberg EO, Olason PI, Aalund M, Nerup J, Brunak S, Workman CT, Pociot F. Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. Genome Biol. 2007 8(11):R253

3.     Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A systems approach to mapping DNA damage response pathways. Science, 2006 312(5776):1054-9.

4.     Beyer A, Workman C, Hollunder J, Radke D, Moller U, Wilhelm T & Ideker T. (2006) Integrated Assessment and Prediction of Transcription Factor Binding. PLoS Comput. Biol. 16;2(6):e70.

5.     Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol. 23(1): 137-44.

 

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