Dr Dmitry Ovchinnikov

Research Fellow & StemCore Manager

Australian Institute for Bioengineering and Nanotechnology
d.ovchinnikov@uq.edu.au
+61 7 334 63854

Overview

Dmitry A. Ovchinnikov is currently a CSO and general manager of the NCRIS/BPA-funded stem cell functional genomics facility, StemCore, and a Research Fellow in the Stem Cell Engineering Group at the Australian Institute for Bioengineering and Nanotechnology at the University of Queensland. His main research interests lie in the genetic manipulation of pluripotent stem cells for investigations into the stem cell biology and mechanisms of neurodegenerative diseases, e.g. Down's syndrome and Alzheimer's disease. He is utilizing both gene knockdown and overexpression approaches to dissect the roles of various signalling pathways and specific genes in the aetiologies of these conditions. His research interests include the generation of transgenic ESC and iPSC research tools for bioengineering applications, re-programming somatic cells to pluripotency (iPSC generation), seamless (traceless) correction of the disease-causing mutations, and other precise modifications of the human genome. More recently, he has also developed an interest in the transcriptomics and epigenetics of pluripotent cells, their derivatives and cancer cells. Previously, he led the Transgenic subgroup in the laboratory of Professor David Hume at UQ’s Institute for Molecular Biosciences, where he generated a number of transgenic mouse lines, some of which are widely used for investigations into macrophage function, and other in vivo studies. Dmitry received his Diploma in Biochemistry (Masters equivalent) from the Lomonosov Moscow State University in 1993. He completed his PhD studies in the laboratory of Professor Richard R. Behringer at the University of Texas MD Anderson Cancer Center, where he was involved in the development of transgenic resources and performed some of the first studies in mice utilising the conditional knockout-enabling Cre/loxP system.

Research Interests

  • Molecular genetics of human pluripotent stem cells
    My research interests revolve around genetic and epigenetic regulation of normal pluripotent stem cell maintenance and differentiation as well as mechanisms of development and progression of human genetically-based diseases (syndromes) and cancer. In particular, I have been involved in development of numerous transgenic human ES/iPS tools facilitating studies of both maintenance of pluripotency and directed differentiation, with particular focus on neural and cardiac cell development. I'm also creating platform technologies allowing for both up- and down-modulation of the function of single and groups of genes. Those include inducible gene overexpression systems and regulatable system for generation of pre-determined genomic alterations in pluripotent stem cells.

Research Impacts

In July, 2017 assumed leadership of the StemCore, a Stem Cells Limited / NCRIS(BPA) / UQ AIBN stem cell functional genomics facility

Invited participant in the Australian Academy of Sciences'/ The Royal Society's (UK) Theo Murphy High Flyers Think Tank - "The stem cell revolution: Lessons and imperatives for Australia", Sydney, July 22-24 2015

Qualifications

  • Doctor of Philosophy, University of California

Publications

  • Ovchinnikov, Dmitry A., Korn, Othmar, Virshup, Isaac, Wells, Christine A. and Wolvetang, Ernst J. (2018) The impact of APP on Alzheimer-like pathogenesis and gene expression in Down syndrome iPSC-derived neurons. Stem Cell Reports, 11 . doi:10.1016/j.stemcr.2018.05.004

  • Bellmaine, Stephanie F., Ovchinnikov, Dmitry A., Manallack, David T., Cuddy, Claire E., Elefanty, Andrew G., Stanley, Edouard G., Wolvetang, Ernst J., Williams, Spencer J. and Pera, Martin (2017) Inhibition of DYRK1A disrupts neural lineage specificationin human pluripotent stem cells. Elife, 6 . doi:10.7554/eLife.24502

  • Ovchinnikov, Dmitry A., Sun, Jane and Wolvetang, Ernst J. (2015) Generation of footprint-free induced pluripotent stem cells from human fibroblasts using episomal plasmid vectors. Methods in Molecular Biology, 1330 37-45. doi:10.1007/978-1-4939-2848-4_4

  • Arner, Erik, Beckhouse, Anthony, Briggs, James, Ovchinnikov, Dmitry, Wolvetang, Ernst, Wells, Christine and FANTOM Consortium (2015) Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science, 347 6225: 1010-1014. doi:10.1126/science.1259418

  • Ovchinnikov, Dmitry A.,, Hidalgo, Alejandro, Yang, Seung-Kwon, Zhang, Xinli, Hudson, James, Mazzone, Stuart B., Chen, Chen, Cooper-White, Justin J. and Wolvetang, Ernst J. (2014) Isolation of contractile cardiomyocytes from human pluripotent stem-cell-derived cardiomyogenic cultures using a human NCX1-EGFP reporter. Stem Cells and Development, 24 1: 11-20. doi:10.1089/scd.2014.0195

  • Ovchinnikov, Dmitry A., Titmarsh, Drew M., Fortuna, Patrick R. J., Hidalgo, Alejandro, Alharbi, Samah, Whitworth, Deanne J., Cooper-White, Justin J. and Wolvetang, Ernst J. (2014) Transgenic human ES and iPS reporter cell lines for identification and selection of pluripotent stem cells in vitro. Stem Cell Research, 13 2: 251-261. doi:10.1016/j.scr.2014.05.006

  • Forest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Baillie, J. Kenneth, De Hoon, Michael J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicholas, Jorgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Altschuler, Intikhab, Albanese, Davide, Altschule, Gabriel M., Arakawa, Takahiro, Archer, John A. C., Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Burroughs, A. Maxwell, Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drablos, Finn, Edge, Albert S. B., Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guh, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Sui, Shannan J. Ho, Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Klinken, S. Peter, Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri-ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, De Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummer, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, Van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. L., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 'T Hoen, Peter A. C., Tagami, Michihira, Takahash, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, Van De Wetering ,Marc, Van Den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham,Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero and Hayashizaki, Yoshihide (2014) A promoter-level mammalian expression atlas. Nature, 507 7493: 462-470. doi:10.1038/nature13182

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Supervision

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Available Projects

  • Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development

    Hasegawa, Yu., Taylor, Deanne., Ovchinnikov, Dmitry A., Wolvetang, Ernst J., de Torrente, Laurence. and Mar, Jessica C. (2015) Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development. PLoS Genetics, 11 8: . doi:10.1371/journal.pgen.1005428

View all Available Projects

Publications

Featured Publications

  • Ovchinnikov, Dmitry A., Korn, Othmar, Virshup, Isaac, Wells, Christine A. and Wolvetang, Ernst J. (2018) The impact of APP on Alzheimer-like pathogenesis and gene expression in Down syndrome iPSC-derived neurons. Stem Cell Reports, 11 . doi:10.1016/j.stemcr.2018.05.004

  • Bellmaine, Stephanie F., Ovchinnikov, Dmitry A., Manallack, David T., Cuddy, Claire E., Elefanty, Andrew G., Stanley, Edouard G., Wolvetang, Ernst J., Williams, Spencer J. and Pera, Martin (2017) Inhibition of DYRK1A disrupts neural lineage specificationin human pluripotent stem cells. Elife, 6 . doi:10.7554/eLife.24502

  • Ovchinnikov, Dmitry A., Sun, Jane and Wolvetang, Ernst J. (2015) Generation of footprint-free induced pluripotent stem cells from human fibroblasts using episomal plasmid vectors. Methods in Molecular Biology, 1330 37-45. doi:10.1007/978-1-4939-2848-4_4

  • Arner, Erik, Beckhouse, Anthony, Briggs, James, Ovchinnikov, Dmitry, Wolvetang, Ernst, Wells, Christine and FANTOM Consortium (2015) Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science, 347 6225: 1010-1014. doi:10.1126/science.1259418

  • Ovchinnikov, Dmitry A.,, Hidalgo, Alejandro, Yang, Seung-Kwon, Zhang, Xinli, Hudson, James, Mazzone, Stuart B., Chen, Chen, Cooper-White, Justin J. and Wolvetang, Ernst J. (2014) Isolation of contractile cardiomyocytes from human pluripotent stem-cell-derived cardiomyogenic cultures using a human NCX1-EGFP reporter. Stem Cells and Development, 24 1: 11-20. doi:10.1089/scd.2014.0195

  • Ovchinnikov, Dmitry A., Titmarsh, Drew M., Fortuna, Patrick R. J., Hidalgo, Alejandro, Alharbi, Samah, Whitworth, Deanne J., Cooper-White, Justin J. and Wolvetang, Ernst J. (2014) Transgenic human ES and iPS reporter cell lines for identification and selection of pluripotent stem cells in vitro. Stem Cell Research, 13 2: 251-261. doi:10.1016/j.scr.2014.05.006

  • Forest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Baillie, J. Kenneth, De Hoon, Michael J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicholas, Jorgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Altschuler, Intikhab, Albanese, Davide, Altschule, Gabriel M., Arakawa, Takahiro, Archer, John A. C., Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Burroughs, A. Maxwell, Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drablos, Finn, Edge, Albert S. B., Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guh, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Sui, Shannan J. Ho, Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Klinken, S. Peter, Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri-ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, De Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummer, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, Van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. L., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 'T Hoen, Peter A. C., Tagami, Michihira, Takahash, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, Van De Wetering ,Marc, Van Den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham,Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero and Hayashizaki, Yoshihide (2014) A promoter-level mammalian expression atlas. Nature, 507 7493: 462-470. doi:10.1038/nature13182

Book Chapter

Journal Article

  • Ovchinnikov, Dmitry A., Korn, Othmar, Virshup, Isaac, Wells, Christine A. and Wolvetang, Ernst J. (2018) The impact of APP on Alzheimer-like pathogenesis and gene expression in Down syndrome iPSC-derived neurons. Stem Cell Reports, 11 . doi:10.1016/j.stemcr.2018.05.004

  • Hidalgo, Alejandro, Glass, Nick, Ovchinnikov, Dmitry, Yang, Seung-Kwon, Zhang, Xinli, Mazzone, Stuart, Chen, Chen, Wolvetang, Ernst and Cooper-White, Justin (2018) Modelling ischemia-reperfusion injury (IRI) in vitro using metabolically matured induced pluripotent stem cell-derived cardiomyocytes. APL Bioengineering, 2 2: 026102. doi:10.1063/1.5000746

  • Fortuna, Patrick R. J., Bielefeldt-Ohmann, Helle, Ovchinnikov, Dmitry A., Wolvetang, Ernst Jurgen and Whitworth, Deanne Jeanette (2018) Cortical neurons derived from equine induced pluripotent stem cells are susceptible to neurotropic flavivirus infection and replication: an in vitro model for equine neuropathic diseases. Stem Cells and Development, 27 10: 704-715. doi:10.1089/scd.2017.0106

  • Weeratunga, Prasanna, Shahsavari, Arash, Ovchinnikov, Dmitry A., Wolvetang, Ernst J. and Whitworth, Deanne J. (2018) Induced pluripotent stem cells from a marsupial, the Tasmanian devil (Sarcophilus harrisii): insight into the evolution of mammalian pluripotency. Stem Cells and Development, 27 2: 112-122. doi:10.1089/scd.2017.0224

  • Bellmaine, Stephanie F., Ovchinnikov, Dmitry A., Manallack, David T., Cuddy, Claire E., Elefanty, Andrew G., Stanley, Edouard G., Wolvetang, Ernst J., Williams, Spencer J. and Pera, Martin (2017) Inhibition of DYRK1A disrupts neural lineage specificationin human pluripotent stem cells. Elife, 6 . doi:10.7554/eLife.24502

  • Noguchi, Shuhei, Arakawa, Takahiro, Fukuda, Shiro, Furuno, Masaaki, Hasegawa, Akira, Hori, Fumi, Ishikawa-Kato, Sachi, Kaida, Kaoru, Kaiho, Ai, Kanamori-Katayama, Mutsumi, Kawashima, Tsugumi, Kojima, Miki, Kubosaki, Atsutaka, Manabe, Ri-ichiroh, Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakazato, Kenichi, Ninomiya, Noriko, Nishiyori-Sueki, Hiromi, Noma, Shohei, Saijyo, Eri, Saka, Akiko, Sakai, Mizuho, Simon, Christophe, Suzuki, Naoko, Tagami, Michihira, Watanabe, Shoko, Yoshida, Shigehiro, Arner, Peter, Axton, Richard A., Babina, Magda, Baillie, J. Kenneth, Barnett, Timothy C., Beckhouse, Anthony G., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Carlisle, Ailsa J., Clevers, Hans C., Davis, Carrie A., Detmar, Michael, Dohi, Taeko, Edge, Albert S. B., Edinger, Matthias, Ehrlund, Anna, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Eslami, Afsaneh, Fagiolini, Michela, Fairbairn, Lynsey, Farach-Carson, Mary C., Faulkner, Geoffrey J., Ferrai, Carmelo, Fisher, Malcolm E., Forrester, Lesley M., Fujita, Rie, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gingeras, Thomas, Goldowitz, Daniel, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Hasegawa, Yuki, Herlyn, Meenhard, Heutink, Peter, Hitchens, Kelly J., Hume, David A., Ikawa, Tomokatsu, Ishizu, Yuri, Kai, Chieko, Kawamoto, Hiroshi, Kawamura, Yuki I., Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Klein, Sarah, Klinken, S. Peter, Knox, Alan J., Kojima, Soichi, Koseki, Haruhiko, Koyasu, Shigeo, Lee, Weonju, Lennartsson, Andreas, Mackay-sim, Alan, Mejhert, Niklas, Mizuno, Yosuke, Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Morris, Kelly J., Motohashi, Hozumi, Mummery, Christine L., Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Passier, Robert, Patrikakis, Margaret, Pombo, Ana, Pradhan-Bhatt, Swati, Qin, Xian-Yang, Rehli, Michael, Rizzu, Patrizia, Roy, Sugata, Sajantila, Antti, Sakaguchi, Shimon, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schmidl, Christian, Schneider, Claudio, Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sheng, Guojun, Shin, Jay W., Sugiyama, Daisuke, Sugiyama, Takaaki, Summers, Kim M., Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tomoiu, Andru, Toyoda, Hiroo, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Yamaguchi, Yoko, Yamamoto, Masayuki, Yanagi-Mizuochi, Chiyo, Yoneda, Misako, Yonekura, Yohei, Zhang, Peter G., Zucchelli, Silvia, Abugessaisa, Imad, Arner, Erik, Harshbarger, Jayson, Kondo, Atsushi, Lassmann, Timo, Lizio, Marina, Sahin, Serkan, Sengstag, Thierry, Severin, Jessica, Shimoji, Hisashi, Suzuki, Masanori, Suzuki, Harukazu, Kawai, Jun, Kondo, Naoto, Itoh, Masayoshi, Daub, Carsten O., Kasukawa, Takeya, Kawaji, Hideya, Carninci, Piero, Forrest, Alistair R. R. and Hayashizaki, Yoshihide (2017) FANTOM5 CAGE profiles of human and mouse samples. Scientific Data, 4 170112. doi:10.1038/sdata.2017.112

  • Lim, Yenkai, Wan, Yunxia, Vagenas, Dimitrios, Ovchinnikov, Dmitry A., Perry, Chris F. L., Davis, Melissa J. and Punyadeera, Chamindie (2016) Salivary DNA methylation panel to diagnose HPV-positive and HPV-negative head and neck cancers. BMC Cancer, 16 1: 749. doi:10.1186/s12885-016-2785-0

  • Hurst, Laurence D., Ghanbarian, Avazeh T., Forrest, Alistair R. R., Huminiecki, Lukasz, Rehli, Michael, Baillie, J. Kenneth, de Hoon, Michiel J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jorgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A. C., Arner, Peter, Babina, Magda, Baker, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Burroughs, A. Maxwell, Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drablos, Finn, Edge, Albert S. B., Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew ., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Klinken, S. Peter, Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay, Alan, Manabe, Riichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru., Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. ., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 't Hoen, Peter A.C., Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Suzan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero and Hayashizaki, Yoshihide (2015) The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome. PLoS Biology, 13 12: . doi:10.1371/journal.pbio.1002315

  • Ovchinnikov, Dmitry A., Sun, Jane and Wolvetang, Ernst J. (2015) Generation of footprint-free induced pluripotent stem cells from human fibroblasts using episomal plasmid vectors. Methods in Molecular Biology, 1330 37-45. doi:10.1007/978-1-4939-2848-4_4

  • Hasegawa, Yu., Taylor, Deanne., Ovchinnikov, Dmitry A., Wolvetang, Ernst J., de Torrente, Laurence. and Mar, Jessica C. (2015) Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development. PLoS Genetics, 11 8: . doi:10.1371/journal.pgen.1005428

  • Arner, Erik, Beckhouse, Anthony, Briggs, James, Ovchinnikov, Dmitry, Wolvetang, Ernst, Wells, Christine and FANTOM Consortium (2015) Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science, 347 6225: 1010-1014. doi:10.1126/science.1259418

  • Thakar, Nilay Y., Ovchinnikov, Dmitry A., Hastie, Marcus L., Kobe, Bostjan, Gorman, Jeffrey J. and Wolvetang, Ernst J. (2015) TRAF2 recruitment via T61 in CD30 drives NFκB activation and enhances hESC survival and proliferation.. Molecular Biology of the Cell, 26 5: 993-1006. doi:10.1091/mbc.E14-08-1290

  • Thakar, Nilay Yogeshkumar, Ovchinnikov, Dmitry Alexander, Hastie, Marcus Lachlan, Gorman, Jeffrey and Wolvetang, Ernst Jurgen (2015) RELB alters proliferation of human pluripotent stem cells via IMP3- and LIN28-mediated modulation of the expression of IGF2 and other cell-cycle regulators. Stem Cells and Development, 24 16: 1888-1900. doi:10.1089/scd.2014.0587

  • Liang, Cong, The FANTOM Consortium, Forrest, Alistair R. R., Wagner, Guenter P., Kenna, Tony, Beckhouse, Anthony, Blumenthal, Antje, Briggs, James, Hitchens, Kelly, Ovchinnikov, Dmitry, Vijayan, Dipti, Wells, Christine and Wolvetang, Ernst (2015) The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Nature Communications, 6 . doi:10.1038/ncomms7066

  • Ovchinnikov, Dmitry A. and Wolvetang, Ernst J. (2014) Opportunities and limitations of modelling Alzheimer’s disease with induced pluripotent stem cells. Journal of Clinical Medicine, 3 4: 1357-1372. doi:10.3390/jcm3041357

  • Alamein, Mohammad A., Wolvetang, Ernst J., Ovchinnikov, Dmitry A., Stephens, Sebastien, Sanders, Katherine and Warnke, Patrick H. (2014) Polymeric nanofibrous substrates stimulate pluripotent stem cells to form three-dimensional multilayered patty-like spheroids in feeder-free culture and maintain their pluripotency.. Journal of Tissue Engineering and Regenerative Medicine, 9 9: 1078-1083. doi:10.1002/term.1960

  • Verardo, Roberto, Piazza, Silvano, Klaric, Enio, Ciani, Yari, Bussadori, Giulio, Marzinotto, Stefania, Mariuzzi, Laura, Cesselli, Daniela, Beltrami, Antonio P., Mano, Miguel, Itoh, Masayoshi, Kawaji, Hideya, Lassmann, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Beltrami, Carlo A., The Fantom Consortium, Schneider, Claudio, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014) Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer. Stem Cells (Durham), 32 11: 2998-3011. doi:10.1002/stem.1791

  • Ovchinnikov, Dmitry A.,, Hidalgo, Alejandro, Yang, Seung-Kwon, Zhang, Xinli, Hudson, James, Mazzone, Stuart B., Chen, Chen, Cooper-White, Justin J. and Wolvetang, Ernst J. (2014) Isolation of contractile cardiomyocytes from human pluripotent stem-cell-derived cardiomyogenic cultures using a human NCX1-EGFP reporter. Stem Cells and Development, 24 1: 11-20. doi:10.1089/scd.2014.0195

  • Ovchinnikov, Dmitry A., Titmarsh, Drew M., Fortuna, Patrick R. J., Hidalgo, Alejandro, Alharbi, Samah, Whitworth, Deanne J., Cooper-White, Justin J. and Wolvetang, Ernst J. (2014) Transgenic human ES and iPS reporter cell lines for identification and selection of pluripotent stem cells in vitro. Stem Cell Research, 13 2: 251-261. doi:10.1016/j.scr.2014.05.006

  • Whitworth, Deanne J., Frith, Jessica E, Frith, Thomas J. R., Ovchinnikov, Dmitry A., Cooper-White, Justin J. and Wolvetang, Ernst J. (2014) Derivation of mesenchymal stromal cells from canine induced pluripotent stem cells by inhibition of the TGFbeta/activin signaling pathway. Stem Cells and Development, Online Ahead of Print 24: 3021-3033. doi:10.1089/scd.2013.0634

  • Ovchinnikov, Dmitry A., Wan, Yunxia, Coman, William B., Pandit, Pratibala, Cooper-White, Justin J., Herman, James G. and Punyadeera, Chamindie (2014) DNA methylation at the novel CpG sites in the promoter of MED15/PCQAP gene as a biomarker for head and neck cancers. Biomarker Insights, 9 53-60. doi:10.4137/BMI.S16199

  • Hasegawa, Yuki, Tang, Dave, Takahashi, Naoko, Hayashizaki, Yoshihide, Forrest, Alistair R. R., the FANTOM consortium, Suzuki, Harukazu, Blumenthal, Antje, Kenna, Tony, Briggs, James, Beckhouse, Anthony G., Hitchens, Kelly J., Ovchinnikov, Dmitry A., Vijayan, Dipti, Wells, Christine A. and Wolvetang, Ernst (2014) CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Scientific Reports, 4 Art No: 5228: 277-279. doi:10.1038/srep05228

  • Fort, Alexandre, Hashimoto, Kosuke, Yamada, Daisuke, Salimullah, Md, Keya, Chaman A., Saxena, Alka, Bonetti, Alessandro, Voineagu, Irina, Bertin, Nicolas, Kratz, Anton, Noro, Yukihiko, Wong, Chee-Hong, de Hoon, Michiel, Andersson, Robin, Sandelin, Albin, Suzuki, Harukazu, Wei, Chia-Lin, Koseki, Haruhiko, Hasegawa, Yuki, Forrest, Alistair R. R., Carninci, Piero, FANTOM Consortium, Beckhouse, Anthony, Blumenthal, Antje, Briggs, James, Hitchens, Kelly, Kenna, Tony, Ovchinnikov, Dmitry, Vijayan, Dipti, Wells, Christine and Wolvetang, Ernst (2014) Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nature Genetics, 46 6: 558-566. doi:10.1038/ng.2965

  • Rönnerblad, Michelle, Andersson, Robin, Olofsson, Tor, Douagi, Iyadh, Karimi, Mohsen, Lehmann, Sören, Hoof, Ilka, de Hoon, Michiel, Itoh, Masayoshi, Nagao-Sato, Sayaka, Kawaji, Hideya, Lassmann, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Sandelin, Albin, Ekwall, Karl, Amer, Erik, Lennartsson, Andreas, for the FANTOM consortium, Wells, Christine, Wolvetang, Ernst, Blumenthal, Antje, Kenna, Tony, Hitchens, Kelly, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth, Nielsen, Lars and Vijayan, Dipti (2014) Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. Blood, 123 17: e79-e89. doi:10.1182/blood-2013-02-482893

  • Motakis, Efthymios, Guhl, Sven, Ishizu, Yuri, Itoh, Masayoshi, Kawaji, Hideya, de Hoon, Michiel, Lassman, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Zuberbier, Torsten, Forrest, Alistair R. R., Babina, Magda, for The FANTOM Consortium, Wells, Christine, Wolvetang, Ernst, Beckhouse, Anthony, Fearnley, Liam, Hitchens, Kelly, Kenna, Tony, Le Cao, Kim-Anh, Mason, Elizabeth, Nielsen, Lars, Vijayan, Dipti, Blumenthal, Antje, Ovchinnikov, Dmitry and Briggs, James (2014) Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood, 123 17: 58-67. doi:10.1182/blood-2013-02-483792

  • Whitworth, Deanne J., Ovchinnikov, Dmitry A., Sun, Jane, Fortuna, Patrick R. J. and Wolvetang, Ernst J. (2014) Generation and characterization of leukemia inhibitory factor-dependent equine induced pluripotent stem cells from adult dermal fibroblasts. Stem Cells and Development, Fast Track Articles 13: 1-9. doi:10.1089/scd.2013.0461

  • Forest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Baillie, J. Kenneth, De Hoon, Michael J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicholas, Jorgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Altschuler, Intikhab, Albanese, Davide, Altschule, Gabriel M., Arakawa, Takahiro, Archer, John A. C., Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Burroughs, A. Maxwell, Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drablos, Finn, Edge, Albert S. B., Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guh, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Sui, Shannan J. Ho, Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Klinken, S. Peter, Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri-ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, De Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummer, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, Van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. L., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 'T Hoen, Peter A. C., Tagami, Michihira, Takahash, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, Van De Wetering ,Marc, Van Den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham,Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero and Hayashizaki, Yoshihide (2014) A promoter-level mammalian expression atlas. Nature, 507 7493: 462-470. doi:10.1038/nature13182

  • Hurst, Laurence D., Sachenkova, Oxana, Daub, Carsten, Forrest, Alistair R. R., the FANTOM consortium, Huminiecki, Lukasz, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014) A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators. Genome Biology, 15 7: . doi:10.1186/s13059-014-0413-3

  • Tomaru, Yasuhiro, Hasegawa, Ryota, Suzuki, Takahiro, Sato, Taiji, Kubosaki, Atsutaka, Suzuki, Masanori, Kawaji, Hideya, Forrest, Alistair R. R., Hayashizaki, Yoshihide, FANTOM Consortium, Shin, Jay W., Suzuki, Harukazu, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Fearnley, Liam, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014) A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation. Nucleic Acids Research, 42 14: 8905-8913. doi:10.1093/nar/gku567

  • Grison, Alice, Zucchelli, Silvia, Urzi, Alice, Zamparo, Ilaria, Lazarevic, Dejan, Pascarella, Giovanni, Roncaglia, Paola, Giorgetti, Alejandro, Garcia-Esparcia, Paula, Vlachouli, Christina, Simone, Roberto, Persichetti, Francesca, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Carloni, Paolo, Ferrer, Isidro, Lodovichi, Claudia, Plessy, Charles, the FANTOM Consortium, Carninci, Piero, Gustincich, Stefano, Beckhouse, Anthony, Briggs, James, Hitchens, Kelly, Kenna, Tony, Ovchinnikov, Dmitry, Vijayan, Dipti, Wells, Christine, Wolvetang, Ernst, Blumenthal, Antje, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014) Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules. BMC Genomics, 15 1: . doi:10.1186/1471-2164-15-729

  • Titmarsh, Drew M., Ovchinnikov, Dmitry A., Wolvetang, Ernst J. and Cooper-White, Justin J. (2013) Full factorial screening of human embryonic stem cell maintenance with multiplexed microbioreactor arrays. Biotechnology Journal, 8 7: 822-834. doi:10.1002/biot.201200375

  • Briggs, James A., Mason, Elizabeth A., Ovchinnikov, Dmitry A., Wells, Christine A. and Wolvetang, Ernst J. (2013) Concise review: new paradigms for down syndrome research using induced pluripotent stem cells: tackling complex human genetic disease. Stem Cells Translational Medicine, 2 3: 175-184. doi:10.5966/sctm.2012-0117

  • Briggs, James A., Sun, Jane, Shepherd, Jill, Ovchinnikov, Dmitry A., Chung, Tung-Liang, Nayler, Sam P., Kao, Li-Pin, Morrow, Carl A., Thakar, Nilay Y., Soo, Set-Yen, Peura, Teija, Grimmond, Sean and Wolvetang, Ernst J. (2013) Integration-free induced pluripotent stem cells model genetic and neural developmental features of Down Syndrome etiology. Stem Cells, 31 3: 467-478. doi:10.1002/stem.1297

  • Ovchinnikov, Dmitry A., Cooper, Matthew A., Pandit, Pratibala, Coman, William B., Cooper-White, Justin J., Keith, Patricia, Wolvetang, Ernst J., Slowey, Paul D. and Punyadeera, Chamindie (2012) Tumor-suppressor gene promoter hypermethylation in saliva of head and neck cancer patients. Translational Oncology, 5 5: 321-326. doi:10.1593/tlo.12232

  • Whitworth, Deanne J., Ovchinnikov, Dmitry A. and Wolvetang, Ernst J. (2012) Generation and characterization of LIF-dependent canine induced pluripotent stem cells from adult dermal fibroblasts. Stem Cells and Development, 21 12: 2288-2297. doi:10.1089/scd.2011.0608

  • Smart, Chanel E., Askarian Amiri, Marjan E., Wronski, Ania, Dinger, Marcel E., Crawford, Joanna, Ovchinnikov, Dmitry A., Vargas, Ana Cristina, Reid, Lynne, Simpson, Peter T., Song, Sarah, Wiesner, Christiane, French, Juliet D., Dave, Richa K., da Silva, Leonard, Purdon, Amy, Andrew, Megan, Mattick, John S., Lakhani, Sunil R., Brown, Melissa A. and Kellie, Stuart (2012) Expression and function of the protein tyrosine phosphatase receptor J (PTPRJ) in normal mammary epithelial cells and breast tumors. PLoS One, 7 7: e40742.1-e40742.13. doi:10.1371/journal.pone.0040742

  • Kao, Li-Pin, Ovchinnikov, Dmitry and Wolvetang, Ernst (2012) The effect of ethidium bromide and chloramphenicol on mitochondrial biogenesis in primary human fibroblasts. Toxicology and Applied Pharmacology, 261 1: 42-49. doi:10.1016/j.taap.2012.03.009

  • Van Zuylen, Wendy J., Garceau, Valerie, Idris, Adi, Schroder, Kate, Irvine, Katharine M., Lattin, Jane E., Ovchinnikov, Dmitry A., Perkins, Andrew C., Cook, Andrew D., Hamilton, John A., Hertzog, Paul J., Stacey, Katryn J., Kellie, Stuart, Hume, David A. and Sweet, Matthew J. (2011) Macrophage activation and differentiation signals regulate Schlafen-4 gene expression: Evidence for Schlafen-4 as a modulator of myelopoiesis. PLoS One, 6 1: e15723-1-e15723-13. doi:10.1371/journal.pone.0015723

  • Ovchinnikov, Dmitry A., DeBats, Claire E. E., Sester, David P., Sweet, Matthew J. and Hume, David A. (2010) A conserved distal segment of the mouse CSF-1 receptor promoter is required for maximal expression of a reporter gene in macrophages and osteoclasts of transgenic mice. Journal of Leukocyte Biology, 87 5: 815-822. doi:10.1189/jlb.0809557

  • Ovchinnikov, Dmitry (2009) Alcian blue/alizarin red staining of cartilage and bone in mouse. Cold Spring Harbor Protocols, 3: . doi:10.1101/pdb.prot5170

  • Ovchinnikov, Dmitry (2008) Macrophages in the embryo and beyond: Much more than just giant phagocytes. Genesis, 46 9: 447-462. doi:10.1002/dvg.20417

  • Ovchinnikov, Dmitry A., van Zuylen, Wendy J. M., DeBats, Claire E. E., Alexander, Kylie A., Kellie, Stuart and Hume, David A. (2008) Expression of Gal4-dependent transgenes in cells of the mononuclear phagocyte system labeled with enhanced cyan fluorescent protein using Csf1r-Gal4VP16/UAS-ECFP double-transgenic mice. Journal of Leukocyte Biology, 83 2: 430-433. doi:10.1189/jlb.0807585

  • van Zuijlen, WJM, Cook, AD, Ovchinnikov, DA, Kellie, S and Hume, DA (2007) The role of schlafen in macrophages and inflammation. Inflammation Research, 56 S389-S389.

  • Rae, Fiona, Woods, Kyra, Sasmono, Tedjo, Campanale, Naomi, Taylor, Darrin, Ovchinnikov, Dmitry A., Grimmond, Sean M., Hume, David A., Ricardo, Sharon D. and Little, Melissa H. (2007) Characterisation and trophic functions of murine embryonic macrophages based upon the use of a Csf1r-EGFP transgene reporter. Developmental Biology, 308 1: 232-246. doi:10.1016/j.ydbio.2007.05.027

  • Fidalgo, J. P., Fletcher, B., Muscat, G., Ovchinnikov, D. and Cassady, A. I. (2007) Characterization of the role of peroxisome proliferator-activated receptor (PPAR)-delta in osteoclast biology. Calcified Tissue International, 80 S90-S90.

  • Yoon, Byeong S., Pogue, Robert, Ovchinnikov, Dmitri A., Yoshii, Isaac, Mishina, Yuji, Behringer, Richard R. and Lyons, Karen M. (2006) BMPs regulate multiple aspects of growth-plate chondrogenesis through opposing actions on FGF pathways. Development, 133 23: 4667-4678. doi:10.1242/dev.02680

  • Ovchinnikov, Dmitry A., Selever, Jennifer, Wang, Ying, Chen, You-Tzung, Mishina, Yuji, Martin, James F. and Behringer, Martin R. (2006) BMP receptor type IA in limb bud mesenchyme regulates distal outgrowth and patterning. Developmental Biology, 295 1: 103-115. doi:10.1016/j.ydbio.2006.03.013

  • Yoon, Byeong S., Ovchinnikov, Dmitry A., Yoshii, Isaac, Behringer, Richard R. and Lyons, Karen M. (2005) Bmpr1a and Bmpr1b have overlapping functions and are essential for chondrogenesis in vivo. Proceedings of the National Academy of Sciences of the United States of America, 102 14: 5062-5067. doi:10.1073/pnas.0500031102

  • Iwata, T, Chen, L, Li, CI, Ovchinnikov, DA, Behringer, RR, Francomano, CA and Deng, CX (2000) A neonatal lethal mutation in FGFR3 uncouples proliferation and differentiation of growth plate chondrocytes in embryos. Human Molecular Genetics, 9 11: 1603-1613. doi:10.1093/hmg/9.11.1603

  • Ovchinnikov, DA, Deng, JM, Ogunrinu, G and Behringer, RR (2000) Co/2a1-directed expression of Cre recombinase in differentiating chondrocytes in transgenic mice. Genesis, 26 2: 145-146. doi:10.1002/(SICI)1526-968X(200002)26:2<145::AID-GENE14>3.0.CO;2-C

  • Chen H., Lun Y., Ovchinnikov D., Kokubo H., Oberg K.C., Pepicelli C.V., Gan L., Lee B. and Johnson R.L. (1998) Limb and kidney defects in Lmx1b mutant mice suggest an involvement of LMX1B in human nail patella syndrome. Nature Genetics, 19 1: 51-55. doi:10.1038/ng0598-51

  • Chen, HX, Ovchinnikov, D, Pressman, CL, Aulehla, A, Lun, Y and Johnson, RL (1998) Multiple calvarial defects in lmx1b mutant mice. Developmental Genetics, 22 4: 314-320. doi:10.1002/(SICI)1520-6408(1998)22:4<314::AID-DVG2>3.0.CO;2-9

  • Bogdanov, YD, Ovchinnikov, DA, Balaban, PM and Belyavsky, AV (1994) Novel Gene Hcs1 Specifically Expressed in the Giant Interneurons of the Terrestrial Snail. Neuroreport, 5 5: 589-592. doi:10.1097/00001756-199401000-00014

Conference Publication

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Associate Advisor

  • Doctor Philosophy — Associate Advisor

  • Doctor Philosophy — Associate Advisor

    Other advisors:

Completed Supervision

Possible Research Projects

Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.

  • Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development

    Hasegawa, Yu., Taylor, Deanne., Ovchinnikov, Dmitry A., Wolvetang, Ernst J., de Torrente, Laurence. and Mar, Jessica C. (2015) Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development. PLoS Genetics, 11 8: . doi:10.1371/journal.pgen.1005428