Publications

Barbieri, M., Fraser, J., Lavitas, L. M., Chotalia, M., Dostie, J., Pombo, A., and Nicodemi, M. (2013) A polymer model explains the complexity of large-scale chromatin folding, Nucleus 4.

Barbieri, M., Chotalia, M., Fraser, J., Lavitas, L. M., Dostie, J., Pombo, A., and Nicodemi, M. (2013) A model of the large-scale organization of chromatin, Biochemical Society transactions 41, 508-512.

Ferraiuolo, M. A., Sanyal, A., Naumova, N., Dekker, J., and Dostie, J. (2012) From cells to chromatin: capturing snapshots of genome organization with 5C technology, Methods 58, 255-267.

Barbieri, M., Chotalia, M., Fraser, J., Lavitas, L. M., Dostie, J., Pombo, A., and Nicodemi, M. (2012) Complexity of chromatin folding is captured by the strings and binders switch model, Proceedings of the National Academy of Sciences of the United States of America 109, 16173-16178.

Ethier, S. D., Miura, H., and Dostie, J. (2012) Discovering genome regulation with 3C and 3C-related technologies, Biochimica et biophysica acta 1819, 401-410.

Dostie, J., and Bickmore, W. A. (2012) Chromosome organization in the nucleus - charting new territory across the Hi-Cs, Current opinion in genetics & development 22, 125-131.

Assadian, S., El-Assaad, W., Wang, X. Q., Gannon, P. O., Barres, V., Latour, M., Mes-Masson, A. M., Saad, F., Sado, Y., Dostie, J., and Teodoro, J. G. (2012) p53 inhibits angiogenesis by inducing the production of Arresten, Cancer research 72, 1270-1279.

Fraser, J., Ethier, S. D., Miura, H., and Dostie, J. (2012) A Torrent of data: mapping chromatin organization using 5C and high-throughput sequencing, Methods in enzymology 513, 113-141.

Rousseau, M., Fraser, J., Ferraiuolo, M. A., Dostie, J., and Blanchette, M. (2011) Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling, BMC bioinformatics 12, 414.

Wang, X. Q., Crutchley, J. L., and Dostie, J. (2011) Shaping the Genome with Non-Coding RNAs, Current genomics 12, 307-321.

Ferraiuolo, M. A., Rousseau, M., Miyamoto, C., Shenker, S., Wang, X. Q., Nadler, M., Blanchette, M., and Dostie, J. (2010) The three-dimensional architecture of Hox cluster silencing, Nucleic acids research 38, 7472-7484.

Crutchley, J. L., Wang, X. Q., Ferraiuolo, M. A., and Dostie, J. (2010) Chromatin conformation signatures: ideal human disease biomarkers?, Biomarkers in medicine 4, 611-629.

Fraser, J., Rousseau, M., Blanchette, M., and Dostie, J. (2010) Computing chromosome conformation, Methods in molecular biology 674, 251-268.

D'Haene, B., Attanasio, C., Beysen, D., Dostie, J., Lemire, E., Bouchard, P., Field, M., Jones, K., Lorenz, B., Menten, B., Buysse, K., Pattyn, F., Friedli, M., Ucla, C., Rossier, C., Wyss, C., Speleman, F., De Paepe, A., Dekker, J., Antonarakis, S. E., and De Baere, E. (2009) Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening, PLoS genetics 5, e1000522.

Consortium, F., Suzuki, H., Forrest, A. R., van Nimwegen, E., Daub, C. O., Balwierz, P. J., Irvine, K. M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M. J., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M., Asahara, H., Bailey, T., Bajic, V. B., Bauer, D., Beckhouse, A. G., Bertin, N., Bjorkegren, J., Brombacher, F., Bulger, E., Chalk, A. M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engstrom, P. G., Essack, M., Faulkner, G. J., Fink, J. L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S. M., Gustafsson, M., Hashimoto, M., Hashimoto, T., Hatakeyama, M., Heinzel, S., Hide, W., Hofmann, O., Hornquist, M., Huminiecki, L., Ikeo, K., Imamoto, N., Inoue, S., Inoue, Y., Ishihara, R., Iwayanagi, T., Jacobsen, A., Kaur, M., Kawaji, H., Kerr, M. C., Kimura, R., Kimura, S., Kimura, Y., Kitano, H., Koga, H., Kojima, T., Kondo, S., Konno, T., Krogh, A., Kruger, A., Kumar, A., Lenhard, B., Lennartsson, A., Lindow, M., Lizio, M., Macpherson, C., Maeda, N., Maher, C. A., Maqungo, M., Mar, J., Matigian, N. A., Matsuda, H., Mattick, J. S., Meier, S., Miyamoto, S., Miyamoto-Sato, E., Nakabayashi, K., Nakachi, Y., Nakano, M., Nygaard, S., Okayama, T., Okazaki, Y., Okuda-Yabukami, H., Orlando, V., Otomo, J., Pachkov, M., Petrovsky, N., Plessy, C., Quackenbush, J., Radovanovic, A., Rehli, M., Saito, R., Sandelin, A., Schmeier, S., Schonbach, C., Schwartz, A. S., Semple, C. A., Sera, M., Severin, J., Shirahige, K., Simons, C., St Laurent, G., Suzuki, M., Suzuki, T., Sweet, M. J., Taft, R. J., Takeda, S., Takenaka, Y., Tan, K., Taylor, M. S., Teasdale, R. D., Tegner, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C. A., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D. A., Riken Omics Science, C., Arakawa, T., Fukuda, S., Imamura, K., Kai, C., Kaiho, A., Kawashima, T., Kawazu, C., Kitazume, Y., Kojima, M., Miura, H., Murakami, K., Murata, M., Ninomiya, N., Nishiyori, H., Noma, S., Ogawa, C., Sano, T., Simon, C., Tagami, M., Takahashi, Y., Kawai, J., and Hayashizaki, Y. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line, Nature genetics 41, 553-562.

Fraser, J., Rousseau, M., Shenker, S., Ferraiuolo, M. A., Hayashizaki, Y., Blanchette, M., and Dostie, J. (2009) Chromatin conformation signatures of cellular differentiation, Genome biology 10, R37.

Dostie, J., Zhan, Y., and Dekker, J. (2007) Chromosome conformation capture carbon copy technology, Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] Chapter 21, Unit 21 14.

Dostie, J., Richmond, T. A., Arnaout, R. A., Selzer, R. R., Lee, W. L., Honan, T. A., Rubio, E. D., Krumm, A., Lamb, J., Nusbaum, C., Green, R. D., and Dekker, J. (2006) Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements, Genome research 16, 1299-1309.

Miele, A., Gheldof, N., Tabuchi, T. M., Dostie, J., and Dekker, J. (2006) Mapping chromatin interactions by chromosome conformation capture, Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] Chapter 21, Unit 21 11.

Koritzinsky, M., Magagnin, M. G., van den Beucken, T., Seigneuric, R., Savelkouls, K., Dostie, J., Pyronnet, S., Kaufman, R. J., Weppler, S. A., Voncken, J. W., Lambin, P., Koumenis, C., Sonenberg, N., and Wouters, B. G. (2006) Gene expression during acute and prolonged hypoxia is regulated by distinct mechanisms of translational control, The EMBO journal 25, 1114-1125.

Dostie, J., and Dekker, J. (2007) Mapping networks of physical interactions between genomic elements using 5C technology, Nature protocols 2, 988-1002.