Associate Professor Jessica Mar

ARC Future Fellow

Australian Institute for Bioengineering and Nanotechnology

Overview

Qualifications

  • Doctor of Philosophy, Harvard University

Publications

  • Taylor, Deanne M., Aronow, Bruce J., Tan, Kai, Bernt, Kathrin, Salomonis, Nathan, Greene, Casey S., Frolova, Alina, Henrickson, Sarah E., Wells, Andrew, Pei, Liming, Jaiswal, Jyoti K., Whitsett, Jeffrey, Hamilton, Kathryn E., MacParland, Sonya A., Kelsen, Judith, Heuckeroth, Robert O., Potter, S. Steven, Vella, Laura A., Terry, Natalie A., Ghanem, Louis R., Kennedy, Benjamin C., Helbig, Ingo, Sullivan, Kathleen E., Castelo-Soccio, Leslie, Kreigstein, Arnold, Herse, Florian, Nawijn, Martijn C., Koppelman, Gerard H., Haendel, Melissa, Harris, Nomi L., Rokita, Jo Lynne, Zhang, Yuanchao, Regev, Aviv, Rozenblatt-Rosen, Orit, Rood, Jennifer E., Tickle, Timothy L., Vento-Tormo, Roser, Alimohamed, Saif, Lek, Monkol, Mar, Jessica C., Loomes, Kathleen M., Barrett, David M., Uapinyoying, Prech, Beggs, Alan H., Agrawal, Pankaj B., Chen, Yi-Wen, Muir, Amanda B., Garmire, Lana X., Snapper, Scott B., Nazarian, Javad, Seeholzer, Steven H., Fazelinia, Hossein, Singh, Larry N., Faryabi, Robert B., Raman, Pichai, Dawany, Noor, Xie, Hongbo Michael, Devkota, Batsal, Diskin, Sharon J., Anderson, Stewart A., Rappaport, Eric F., Peranteau, William, Wikenheiser-Brokamp, Kathryn A., Teichmann, Sarah, Wallace, Douglas, Peng, Tao, Ding, Yang-yang, Kim, Man S., Xing, Yi, Kong, Sek Won, Bönnemann, Carsten G., Mandl, Kenneth D. and White, Peter S. (2019) The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Developmental Cell, 49 1: 10-29. doi:10.1016/j.devcel.2019.03.001

  • Mar, Jessica C. (2019) The rise of the distributions: why non-normality is important for understanding the transcriptome and beyond. Biophysical Reviews, . doi:10.1007/s12551-018-0494-4

  • Piqué, Daniel G., Montagna, Cristina, Greally, John M. and Mar, Jessica C. (2019) A novel approach to modelling transcriptional heterogeneity identifies the oncogene candidate CBX2 in invasive breast carcinoma. British Journal of Cancer, 120 7: 746-753. doi:10.1038/s41416-019-0387-8

View all Publications

Supervision

  • Doctor Philosophy

  • Doctor Philosophy

  • Doctor Philosophy

View all Supervision

Publications

Journal Article

  • Taylor, Deanne M., Aronow, Bruce J., Tan, Kai, Bernt, Kathrin, Salomonis, Nathan, Greene, Casey S., Frolova, Alina, Henrickson, Sarah E., Wells, Andrew, Pei, Liming, Jaiswal, Jyoti K., Whitsett, Jeffrey, Hamilton, Kathryn E., MacParland, Sonya A., Kelsen, Judith, Heuckeroth, Robert O., Potter, S. Steven, Vella, Laura A., Terry, Natalie A., Ghanem, Louis R., Kennedy, Benjamin C., Helbig, Ingo, Sullivan, Kathleen E., Castelo-Soccio, Leslie, Kreigstein, Arnold, Herse, Florian, Nawijn, Martijn C., Koppelman, Gerard H., Haendel, Melissa, Harris, Nomi L., Rokita, Jo Lynne, Zhang, Yuanchao, Regev, Aviv, Rozenblatt-Rosen, Orit, Rood, Jennifer E., Tickle, Timothy L., Vento-Tormo, Roser, Alimohamed, Saif, Lek, Monkol, Mar, Jessica C., Loomes, Kathleen M., Barrett, David M., Uapinyoying, Prech, Beggs, Alan H., Agrawal, Pankaj B., Chen, Yi-Wen, Muir, Amanda B., Garmire, Lana X., Snapper, Scott B., Nazarian, Javad, Seeholzer, Steven H., Fazelinia, Hossein, Singh, Larry N., Faryabi, Robert B., Raman, Pichai, Dawany, Noor, Xie, Hongbo Michael, Devkota, Batsal, Diskin, Sharon J., Anderson, Stewart A., Rappaport, Eric F., Peranteau, William, Wikenheiser-Brokamp, Kathryn A., Teichmann, Sarah, Wallace, Douglas, Peng, Tao, Ding, Yang-yang, Kim, Man S., Xing, Yi, Kong, Sek Won, Bönnemann, Carsten G., Mandl, Kenneth D. and White, Peter S. (2019) The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Developmental Cell, 49 1: 10-29. doi:10.1016/j.devcel.2019.03.001

  • Mar, Jessica C. (2019) The rise of the distributions: why non-normality is important for understanding the transcriptome and beyond. Biophysical Reviews, . doi:10.1007/s12551-018-0494-4

  • Piqué, Daniel G., Montagna, Cristina, Greally, John M. and Mar, Jessica C. (2019) A novel approach to modelling transcriptional heterogeneity identifies the oncogene candidate CBX2 in invasive breast carcinoma. British Journal of Cancer, 120 7: 746-753. doi:10.1038/s41416-019-0387-8

  • Xu, Chunliang, Gao, Xin, Wei, Qiaozhi, Nakahara, Fumio, Zimmerman, Samuel E., Mar, Jessica and Frenette, Paul S. (2018) Stem cell factor is selectively secreted by arterial endothelial cells in bone marrow. Nature Communications, 9 1: . doi:10.1038/s41467-018-04726-3

  • Boulais, Philip E., Mizoguchi, Toshihide, Zimmerman, Samuel, Nakahara, Fumio, Vivie, Judith, Mar, Jessica C., van Oudenaarden, Alexander and Frenette, Paul S. (2018) The majority of CD45- Ter119- CD31- bone marrow cell fraction is of hematopoietic origin and contains erythroid and lymphoid progenitors. Immunity, 49 4: 627-639. doi:10.1016/j.immuni.2018.2018.08.019

  • Chen, Shuonan and Mar, Jessica C. (2018) Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data. BMC Bioinformatics, 19 1: 232. doi:10.1186/s12859-018-2217-z

  • Kulkarni, Ameya S., Brutsaert, Erika F., Anghel, Valentin, Zhang, Kehao, Bloomgarden, Noah, Pollak, Michael, Mar, Jessica C., Hawkins, Meredith, Crandall, Jill P. and Barzilai, Nir (2018) Metformin regulates metabolic and nonmetabolic pathways in skeletal muscle and subcutaneous adipose tissues of older adults. Aging Cell, 17 2: e12723. doi:10.1111/acel.12723

  • Bueno, Raymund and Mar, Jessica C. (2017) Changes in gene expression variability reveal a stable synthetic lethal interaction network in BRCA2-ovarian cancers. Methods, 131 74-82. doi:10.1016/j.ymeth.2017.07.021

  • de Torrente, Laurence, Zimmerman, Samuel, Taylor, Deanne, Hasegawa, Yu, Wells, Christine A. and Mar, Jessica C. (2017) pathVar: a new method for pathway-based interpretation of gene expression variability. PeerJ, 2017 5: e3334. doi:10.7717/peerj.3334

  • Ito, Kyoko, Turcotte, Raphaël, Cui, Jinhua, Zimmerman, Samuel E., Pinho, Sandra, Mizoguchi, Toshihide, Arai, Fumio, Runnels, Judith M., Alt, Clemens, Teruya-Feldstein, Julie, Mar, Jessica C., Singh, Rajat, Suda, Toshio, Lin, Charles P., Frenette, Paul S. and Ito, Keisuke (2016) Self-renewal of a purified Tie2+ hematopoietic stem cell population relies on mitochondrial clearance. Science, 354 6316: 1156-1160. doi:10.1126/science.aaf5530

  • Taherian Fard, Atefeh, Srihari, Sriganesh, Mar, Jessica C. and Ragan, Mark A. (2016) Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks. NPJ Systems Biology and Applications, 2 16001. doi:10.1038/npjsba.2016.1

  • 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: e1002315. doi:10.1371/journal.pbio.1002315

  • Carbajo, Daniel, Magi, Shigeyuki, Itoh, Masayoshi, Kawaji, Hideya, Lassmann, Timo, Arner, Erik, Forrest, Alistair R. R., Carninci, Piero, Hayashizaki, Yoshihide, Daub, Carsten O., Okada-Hatakeyama, Mariko and Mar, Jessica C. (2015) Application of gene expression trajectories initiated from ErbB receptor activation highlights the dynamics of divergent promoter usage. Plos One, 10 12: . doi:10.1371/journal.pone.0144176

  • 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: e1005428. doi:10.1371/journal.pgen.1005428

  • Hussein, Samer M. I., Puri, Mira C., Tonge, Peter D., Benevento, Marco, Corso, Andrew J., Clancy, Jennifer L., Mosbergen, Rowland, Li, Mira, Lee, Dong-Sung, Cloonan, Nicole, Wood, David L. A., Munoz, Javier, Middleton, Robert, Korn, Othmar, Patel, Hardip R., White, Carl A., Shin, Jong-Yeon, Gauthier, Maely E., Le Cao, Kim-Anh, Kim, Jong-Il, Mar, Jessica C., Shakiba, Nika, Ritchie, William, Rasko, John E. J., Grimmond, Sean M., Zandstra, Peter W., Wells, Christine A., Preiss, Thomas, Seo, Jeong-Sun, Heck, Albert J. R., Rogers, Ian M. and Nagy, Andras (2015) Corrigendum: Genome-wide characterization of the routes to pluripotency. Nature, 523 7562: 626-626. doi:10.1038/nature14606

  • Tonge, Peter D., Corso, Andrew J., Monetti, Claudio, Hussein, Samer M. I., Puri, Mira C., Michael, Iacovos P., Li, Mira, Lee, Dong-Sung, Mar, Jessica C., Cloonan, Nicole, Wood, David L., Gauthier, Maely E., Korn, Othmar, Clancy, Jennifer L., Preiss, Thomas, Grimmond, Sean M., Shin, Jong-Yeon, Seo, Jeong-Sun, Wells, Christine A., Rogers, Ian M. and Nagy, Andras (2015) Erratum: Divergent reprogramming routes lead to alternative stem-cell states (Nature (2014) 516 (192-197) DOI: 10.1038/nature14047). Nature, 523 7562: . doi:10.1038/nature14607

  • Ramachandiran, Sampath, Adon, Arsene, Guo, Xiangxue, Wang, Yi, Wang, Huichen, Chen, Zhengjia, Kowalski, Jeanne, Sunay, Ustun R., Young, Andrew N., Brown, Theresa, Mar, Jessica C., Du, Yuhong, Fu, Haian, Mann, Karen P., Natkunam, Yasodha, Boise, Lawrence H., Saavedra, Harold I., Lossos, Izidore S. and Bernal-Mizrachi, Leon (2015) Chromosome instability in diffuse large B cell lymphomas is suppressed by activation of the noncanonical NF-κB pathway. International Journal of Cancer, 136 10: 2341-2351. doi:10.1002/ijc.29301

  • Li, Wenge, Calder, R. Brent, Mar, Jessica C. and Vijg, Jan (2015) Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles. Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis, 772 55-62. doi:10.1016/j.mrfmmm.2015.01.002

  • Tonge, Peter D., Corso, Andrew J., Monetti, Claudio, Hussein, Samer M. I., Puri, Mira C., Michael, Iacovos P., Li, Mira, Lee, Dong-Sung, Mar, Jessica C., Cloonan, Nicole, Wood, David L., Gauthier, Maely E., Korn, Othmar, Clancy, Jennifer L., Preiss, Thomas, Grimmond, Sean M., Shin, Jong-Yeon, Seo, Jeong-Sun, Wells, Christine A., Rogers, Ian M. and Nagy, Andras (2014) Divergent reprogramming routes lead to alternative stem-cell states. Nature, 516 7530: 192-197. doi:10.1038/nature14047

  • Hussein, Samer M. I., Puri, Mira C., Tonge, Peter D., Benevento, Marco, Corso, Andrew J., Clancy, Jennifer L., Mosbergen, Rowland, Li, Mira, Lee, Dong-Sung, Cloonan, Nicole, Wood, David L. A., Munoz, Javier, Middleton, Robert, Korn, Othmar, Patel, Hardip R., White, Carl A., Shin, Jong-Yeon, Gauthier, Maely E., Le Cao, Kim-Anh, Kim, Jong-Il, Mar, Jessica C., Shakiba, Nika, Ritchie, William, Rasko, John E. J., Grimmond, Sean M., Zandstra, Peter W., Wells, Christine A., Preiss, Thomas, Seo, Jeong-Sun, Heck, Albert J. R., Rogers, Ian M. and Nagy, Andras (2014) Genome-wide characterization of the routes to pluripotency. Nature, 516 7530: 198-+. doi:10.1038/nature14046

  • Wijetunga, N. Ari, Delahaye, Fabien, Zhao, Yong M., Golden, Aaron, Mar, Jessica C., Einstein, Francine H. and Greally, John M. (2014) The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences. Nature Communications, 5 . doi:10.1038/ncomms6195

  • Mason, Elizabeth, Mar, Jessica C., Laslett, Andrew, Pera, Martin F., Quackenbush, John, Wolvetang, Ernst and Wells C. (2014) Gene expression variability as a unifying element of the pluripotency network. Stem Cell Reports, 3 2: 365-377. doi:10.1016/j.stemcr.2014.06.008

  • Hough, Shelley R., Thornton, Matthew, Mason, Elizabeth, Mar, Jessica C., Wells, Christine A. and Pera, Martin F. (2014) Single-cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cells. Stem Cell Reports, 2 6: 881-895. doi:10.1016/j.stemcr.2014.04.014

  • Mukhopadhyay, Rituparna, Lajugie, Julien, Fourel, Nicolas, Selzer, Ari, Schizas, Michael, Bartholdy, Boris, Mar, Jessica, Lin, Chii Mei, Martin, Melvenia M., Ryan, Michael, Aladjem, Mirit I. and Bouhassira, Eric E. (2014) Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization. PLoS Genetics, 10 5: . doi:10.1371/journal.pgen.1004319

  • 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

  • Goto, Derek B., Miyazawa, Hikota, Mar, Jessica C. and Sato, Masanao (2013) Not to be suppressed?: rethinking the host response at a root-parasite interface. Plant Science, 213 9-17. doi:10.1016/j.plantsci.2013.08.004

  • Kunisaki, Yuya, Bruns, Ingmar, Scheiermann, Christoph, Ahmed, Jalal, Pinho, Sandra, Zhang, Dachuan, Mizoguchi, Toshihide, Wei, Qiaozhi, Lucas, Daniel, Ito, Keisuke, Mar, Jessica C., Bergman, Aviv and Frenette, Paul S. (2013) Arteriolar niches maintain haematopoietic stem cell quiescence. Nature, 502 7473: 637-643. doi:10.1038/nature12612

  • Kouno, Tsukasa, de Hoon, Michiel, Mar, Jessica C., Tomaru, Yasuhiro, Kawano, Mitsuoki, Carninci, Piero, Suzuki, Harukazu, Hayashizaki, Yoshihide and Shin, Jay W. (2013) Temporal dynamics and transcriptional control using single-cell gene expression analysis. Genome Biology, 14 10: . doi:10.1186/gb-2013-14-10-r118

  • Rozenblatt-Rosen, Orit, Deo, Rahul C., Padi, Megha, Adelmant, Guillaume, Calderwood, Michael A., Rolland, Thomas, Grace, Miranda, Dricot, Amélie, Askenazi, Manor, Tavares, Maria, Pevzner, Samuel J., Abderazzaq, Fieda, Byrdsong, Danielle, Carvunis, Anne-Ruxandra, Chen, Alyce A., Cheng, Jingwei, Correll, Mick, Duarte, Melissa, Fan, Changyu, Feltkamp, Mariet C., Ficarro, Scott B., Franchi, Rachel, Garg, Brijesh K., Gulbahce, Natali, Hao, Tong, Holthaus, Amy M., James, Robert, Korkhin, Anna, Litovchick, Larisa, Mar, Jessica C., Pak, Theodore R., Rabello, Sabrina, Rubio, Renee, Shen, Yun, Singh, Saurav, Spangle, Jennifer M., Tasan, Murat, Wanamaker, Shelly, Webber, James T., Roecklein-Canfield, Jennifer, Johannsen, Eric, Barabási, Albert-László, Beroukhim, Rameen, Kieff, Elliott, Cusick, Michael E., Hill, David E., Münger, Karl, Marto, Jarrod A., Quackenbush, John, Roth, Frederick P., Decaprio, James A. and Vidal, Marc (2012) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature, 487 7408: 491-495. doi:10.1038/nature11288

  • Nayler, Sam, Gatei, Magtouf, Kozlov, Sergei, Gatti, Richard, Mar, Jessica C., Wells, Christine A., Lavin, Martin and Wolvetang, Ernst (2012) Induced Pluripotent Stem Cells from Ataxia-Telangiectasia Recapitulate the Cellular Phenotype. Stem Cells Translational Medicine, 1 7: 523-535. doi:10.5966/sctm.2012-0024

  • Gulbahce, Natali, Yan, Han, Dricot, Amélie, Padi, Megha, Byrdsong, Danielle, Franchi, Rachel, Lee, Deok-Sun, Rozenblatt-Rosen, Orit, Mar, Jessica C., Calderwood, Michael A., Baldwin, Amy, Zhao, Bo, Santhanam, Balaji, Braun, Pascal, Simonis, Nicolas, Huh, Kyung-Won, Hellner, Karin, Grace, Miranda, Chen, Alyce, Rubio, Renee, Marto, Jarrod A., Christakis, Nicholas A., Kieff, Elliott, Roth, Frederick P., Roecklein-Canfield, Jennifer, DeCaprio, James A., Cusick, Michael E., Quackenbush, John, Hill, David E., Münger, Karl, Vidal, Marc and Barabási, Albert-László (2012) Viral perturbations of host networks reflect disease etiology. PLoS Computational Biology, 8 6: . doi:10.1371/journal.pcbi.1002531

  • Chittenden, Thomas W., Howe, Eleanor A., Taylor, Jennifer M., Mar, Jessica C., Aryee, Martin J., Gómez, Harold, Sultana, Razvan, Braisted, John, Nair, Sarita J., Quackenbush, John and Holmes, Chris (2012) nEASE: a method for gene ontology subclassification of high-throughput gene expression data. Bioinformatics, 28 5: 726-728. doi:10.1093/bioinformatics/bts011

  • Gewurz, Benjamin E., Towfic, Fadi, Mar, Jessica C., Shinners, Nicholas P., Takasaki, Kaoru, Zhao, Bo, Cahir-McFarland, Ellen D., Quackenbush, John, Xavier, Ramnik J. and Kieff, Elliott (2012) Genome-wide siRNA screen for mediators of NF-κB activation. Proceedings of the National Academy of Sciences of the United States of America, 109 7: 2467-2472. doi:10.1073/pnas.1120542109

  • Mar, Jessica C., Matigian, Nicholas A., Quackenbush, John and Wells, Christine A. (2011) Attract : A method for identifying core pathways that define cellular phenotypes. PLoS One, 6 10 Article # e25445: e25445-1-e25445-6. doi:10.1371/journal.pone.0025445

  • Zhao, Bo, Zou, James, Wang, Hongfang, Johannsen, Eric, Peng, Chih-Wen, Quackenbush, John, Mar, Jessica C., Morton, Cynthia Casson, Freedman, Matthew L., Blacklow, Stephen C., Aster, Jon C., Bernstein, Bradley E. and Kieff, Elliott (2011) Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. Proceedings of the National Academy of Sciences of the United States of America, 108 36: 14902-14907. doi:10.1073/pnas.1108892108

  • Mar, Jessica C., Matigian, Nicholas A., Mackay-Sim, Alan, Mellick, George D., Sue, Carolyn M., Silburn, Peter A., McGrath, John J., Quackenbush, John and Wells, Christine A. (2011) Variance of gene expression identifies altered network constraints in neurological disease. PLoS Genetics, 7 8: e1002207. doi:10.1371/journal.pgen.1002207

  • Gewurz, Benjamin E., Mar, Jessica C., Padi, Megha, Zhao, Bo, Shinners, Nicholas P., Takasaki, Kaoru, Bedoya, Edward, Zou, James Y., Cahir-Mcfarland, Ellen, Quackenbush, John and Kieff, Elliott (2011) Canonical NF-κB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation. Journal of Virology, 85 13: 6764-6773. doi:10.1128/JVI.00422-11

  • Mar, Jessica C., Wells, Christine A. and Quackenbush, John (2011) Defining an informativeness metric for clustering gene expression data. Bioinformatics, 27 8: 1094-1100. doi:10.1093/bioinformatics/btr074

  • Zhao, Bo, Mar, Jessica C., Maruo, Seiji, Lee, Sungwook, Gewurz, Benjamin E., Johannsen, Eric, Holton, Kristina, Rubio, Renee, Takada, Kenzo, Quackenbush, John and Kieff, Elliott (2011) Epstein-Barr virus nuclear antigen 3C regulated genes in lymphoblastoid cell lines. Proceedings of the National Academy of Sciences, 108 1: 337-342. doi:10.1073/pnas.1017419108

  • Chittenden, Thomas W., Pak, Jane, Rubio, Renee, Cheng, Hailing, Holton, Kristina, Prendergast, Niall, Glinskii, Vladimir, Cai, Yi, Culhane, Aedin, Bentink, Stefan, Schwede, Mathew, Mar, Jessica C., Howe, Eleanor A., Aryee, Martin, Sultana, Razvan, Lanahan, Anthony A., Taylor, Jennifer M., Holmes, Chris, Hahn, William C., Zhao, Jean J., Iglehart, J. Dirk and Quackenbush, John (2010) Therapeutic implications of GIPC1 silencing in cancer. PLoS ONE, 5 12: . doi:10.1371/journal.pone.0015581

  • Mar, Jessica C. and Quackenbush, John (2009) Decomposition of gene expression state space trajectories. PLoS Computational Biology, 5 12: . doi:10.1371/journal.pcbi.1000626

  • Hellner, Karin, Mar, Jessica, Fang, Frank, Quackenbush, John and Münger, Karl (2009) HPV16 E7 oncogene expression in normal human epithelial cells causes molecular changes indicative of an epithelial to mesenchymal transition. Virology, 391 1: 57-63. doi:10.1016/j.virol.2009.05.036

  • Suzuki, H, Forrest, ARR, van Nimwegen, E, Daub, CO, Balwierz, PJ, Irvine, KM, Lassmann, T, Ravasi, T, Hasegawa, Y, de Hoon, MJL, 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, VB, Bauer, D, Beckhouse, AG, Bertin, N, Bjorkegren, J, Brombacher, F, Bulger, E, Chalk, AM, Chiba, J, Cloonan, N, Dawe, A, Dostie, J, Engstrom, PG, Essack, M, Faulkner, GJ, Fink, JL, Fredman, D, Fujimori, K, Furuno, M, Gojobori, T, Gough, J, Grimmond, SM, 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, MC, 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, CA, Maqungo, M, Mar, J, Matigian, NA, Matsuda, H, Mattick, JS, 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, AS, Semple, CA, Sera, M, Severin, J, Shirahige, K, Simons, C, Laurent, GS, Suzuki, M, Suzuki, T, Sweet, MJ, Taft, RJ, Takeda, S, Takenaka, Y, Tan, K, Taylor, MS, Teasdale, RD, Tegner, J, Teichmann, S, Valen, E, Wahlestedt, C, Waki, K, Waterhouse, A, Wells, Christine A., Winther, O, Wu, L, Yamaguchi, K, Yanagawa, H, Yasuda, J, Zavolan, M, Hume, DA, 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, Hayashizaki, Y, FANTOM Consortium and Riken Omics Science Center (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics, 41 5: 553-562. doi:10.1038/ng.375

  • Mar, Jessica C., Kimura, Yasumasa, Schroder, Kate, Irvine, Katherine M., Hayashizaki, Yoshihide, Suzuki, Harukazu, Hume, David and Quackenbush, John (2009) Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinformatics, 10 110.1-110.10. doi:10.1186/1471-2105-10-110

  • Silver, Daniel P., Dimitrov, Stoil D., Feunteun, Jean, Gelman, Rebecca, Drapkin, Ronny, Lu, Shihua D., Shestakova, Elena, Velmurugan, Soundarapandian, DeNunzio, Nicholas, Dragomir, Serban, Mar, Jessica, Liu, Xiaoling, Rottenberg, Sven, Jonkers, Jos, Ganesan, Shridar and Livingston, David M. (2007) Further Evidence for BRCA1 Communication with the Inactive X Chromosome. Cell, 128 5: 991-1002. doi:10.1016/j.cell.2007.02.025

  • Mar, Jessica C., Rubio, Renee and Quackenbush, John (2006) Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples. Genome Biology, 7 12: . doi:10.1186/gb-2006-7-12-r119

  • Haas, David W., Geraghty, Daniel E., Andersen, Janet, Mar, Jessica, Motsinger, Alison A., D'Aquila, Richard T., Unutmaz, Derya, Benson, Constance A., Ritchie, Marylyn D. and Landay, Alan (2006) Immunogenetics of CD4 lymphocyte count recovery during antiretroviral therapy: An AIDS clinical trials group study. Journal of Infectious Diseases, 194 8: 1098-1107. doi:10.1086/507313

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Principal Advisor

    Other advisors:

  • Doctor Philosophy — Principal Advisor

    Other advisors:

  • Doctor Philosophy — Principal Advisor

  • Doctor Philosophy — Principal Advisor

    Other advisors:

  • Doctor Philosophy — Associate Advisor