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2015 Journal Article Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated allelesLi, 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 |
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2014 Journal Article Divergent reprogramming routes lead to alternative stem-cell statesTonge, 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 |
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2014 Journal Article Genome-wide characterization of the routes to pluripotencyHussein, 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 ... Nagy, Andras (2014). Genome-wide characterization of the routes to pluripotency. Nature, 516 (7530), 198-+. doi: 10.1038/nature14046 |
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2014 Journal Article The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequencesWijetunga, 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 (1) 6195. doi: 10.1038/ncomms6195 |
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2014 Journal Article Gene expression variability as a unifying element of the pluripotency networkMason, 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 |
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2014 Journal Article Single-cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cellsHough, 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 |
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2014 Journal Article Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organizationMukhopadhyay, 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) e1004319, e1004319. doi: 10.1371/journal.pgen.1004319 |
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2014 Journal Article A promoter-level mammalian expression atlasForest, 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 ... Hayashizaki, Yoshihide (2014). A promoter-level mammalian expression atlas. Nature, 507 (7493), 462-470. doi: 10.1038/nature13182 |
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2013 Journal Article Not to be suppressed?: rethinking the host response at a root-parasite interfaceGoto, 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 |
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2013 Journal Article Arteriolar niches maintain haematopoietic stem cell quiescenceKunisaki, 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 |
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2013 Journal Article Temporal dynamics and transcriptional control using single-cell gene expression analysisKouno, 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) R118. doi: 10.1186/gb-2013-14-10-r118 |
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2012 Journal Article Interpreting cancer genomes using systematic host network perturbations by tumour virus proteinsRozenblatt-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 ... Vidal, Marc (2012). Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature, 487 (7408), 491-495. doi: 10.1038/nature11288 |
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2012 Journal Article Induced Pluripotent Stem Cells from Ataxia-Telangiectasia Recapitulate the Cellular PhenotypeNayler, 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 |
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2012 Journal Article Viral perturbations of host networks reflect disease etiologyGulbahce, 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. ... Barabási, Albert-László (2012). Viral perturbations of host networks reflect disease etiology. PLoS Computational Biology, 8 (6) e1002531, e1002531. doi: 10.1371/journal.pcbi.1002531 |
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2012 Journal Article nEASE: a method for gene ontology subclassification of high-throughput gene expression dataChittenden, 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) bts011, 726-728. doi: 10.1093/bioinformatics/bts011 |
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2012 Journal Article Genome-wide siRNA screen for mediators of NF-κB activationGewurz, 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 |
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2011 Journal Article Attract : A method for identifying core pathways that define cellular phenotypesMar, 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, e25445-1-e25445-6. doi: 10.1371/journal.pone.0025445 |
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2011 Journal Article Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growthZhao, 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 |
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2011 Journal Article Variance of gene expression identifies altered network constraints in neurological diseaseMar, 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, e1002207. doi: 10.1371/journal.pgen.1002207 |
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2011 Journal Article Canonical NF-κB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulationGewurz, 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 |
