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2020 Journal Article Snai2 maintains bone marrow niche cells by repressing osteopontin expressionWei, Qiaozhi, Nakahara, Fumio, Asada, Noboru, Zhang, Dachuan, Gao, Xin, Xu, Chunliang, Alfieri, Alan, Brodin, N. Patrik, Zimmerman, Samuel E., Mar, Jessica C., Guha, Chandan, Guo, Wenjun and Frenette, Paul S. (2020). Snai2 maintains bone marrow niche cells by repressing osteopontin expression. Developmental Cell, 53 (5), 503-513. doi: 10.1016/j.devcel.2020.04.012 |
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2019 Journal Article A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknessesAndriani, Grasiella A., Maggi, Elaine, Piqué, Daniel, Zimmerman, Samuel E., Lee, Moonsook, Quispe-Tintaya, Wilber, Maslov, Alexander, Campisi, Judith, Vijg, Jan, Mar, Jessica C. and Montagna, Cristina (2019). A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknesses. Scientific Reports, 9 (1) 10508, 10508. doi: 10.1038/s41598-019-46606-w |
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2019 Journal Article Aneuvis: web-based exploration of numerical chromosomal variation in single cellsPiqué, Daniel G., Andriani, Grasiella A., Maggi, Elaine, Zimmerman, Samuel E., Greally, John M., Montagna, Cristina and Mar, Jessica C. (2019). Aneuvis: web-based exploration of numerical chromosomal variation in single cells. BMC Bioinformatics, 20 (1) 336, 336. doi: 10.1186/s12859-019-2842-1 |
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2019 Journal Article A comparison of survival analysis methods for cancer gene expression RNA-Sequencing dataRaman, Pichai, Zimmerman, Samuel, Rathi, Komal S., de Torrenté, Laurence, Sarmady, Mahdi, Wu, Chao, Leipzig, Jeremy, Taylor, Deanne M., Tozeren, Aydin and Mar, Jessica C. (2019). A comparison of survival analysis methods for cancer gene expression RNA-Sequencing data. Cancer Genetics, 235-236, 1-12. doi: 10.1016/j.cancergen.2019.04.004 |
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2019 Journal Article The Pediatric Cell Atlas: defining the growth phase of human development at single-cell resolutionTaylor, 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 ... 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 |
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2019 Journal Article The rise of the distributions: why non-normality is important for understanding the transcriptome and beyondMar, Jessica C. (2019). The rise of the distributions: why non-normality is important for understanding the transcriptome and beyond. Biophysical Reviews, 11 (1), 89-94. doi: 10.1007/s12551-018-0494-4 |
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2019 Conference Publication Investigating skewness to understand gene expression heterogeneity in large patient cohortsChurch, Benjamin V., Williams, Henry T. and Mar, Jessica C. (2019). Investigating skewness to understand gene expression heterogeneity in large patient cohorts. The International Conference on Intelligent Biology and Medicine (ICIBM 2019), Columbia, OH, United States, 9-11 June 2019. London, United Kingdom: BioMed Central. doi: 10.1186/s12859-019-3252-0 |
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2019 Journal Article A novel approach to modelling transcriptional heterogeneity identifies the oncogene candidate CBX2 in invasive breast carcinomaPiqué, 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 |
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2019 Journal Article Estrogen activates Alzheimer's disease genesRatnakumar, Abhirami, Zimmerman, Samuel E., Jordan, Bryen A. and Mar, Jessica C. (2019). Estrogen activates Alzheimer's disease genes. Alzheimer's and Dementia: Translational Research and Clinical Interventions, 5 (C), 906-917. doi: 10.1016/j.trci.2019.09.004 |
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2018 Journal Article Stem cell factor is selectively secreted by arterial endothelial cells in bone marrowXu, 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) 2449. doi: 10.1038/s41467-018-04726-3 |
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2018 Journal Article The majority of CD45- Ter119- CD31- bone marrow cell fraction is of hematopoietic origin and contains erythroid and lymphoid progenitorsBoulais, 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 |
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2018 Journal Article Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression dataChen, 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, 232. doi: 10.1186/s12859-018-2217-z |
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2018 Journal Article Metformin regulates metabolic and nonmetabolic pathways in skeletal muscle and subcutaneous adipose tissues of older adultsKulkarni, 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, e12723. doi: 10.1111/acel.12723 |
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2017 Journal Article Changes in gene expression variability reveal a stable synthetic lethal interaction network in BRCA2-ovarian cancersBueno, 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 |
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2017 Journal Article pathVar: a new method for pathway-based interpretation of gene expression variabilityde 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, e3334. doi: 10.7717/peerj.3334 |
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2016 Journal Article Self-renewal of a purified Tie2+ hematopoietic stem cell population relies on mitochondrial clearanceIto, 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 |
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2016 Journal Article Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networksTaherian 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 (1) 16001, 16001. doi: 10.1038/npjsba.2016.1 |
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2015 Journal Article The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosomeHurst, 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. ... Hayashizaki, Yoshihide (2015). The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome. PLoS Biology, 13 (12) e1002315, e1002315. doi: 10.1371/journal.pbio.1002315 |
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2015 Journal Article Application of gene expression trajectories initiated from ErbB receptor activation highlights the dynamics of divergent promoter usageCarbajo, 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) e0144176, e0144176. doi: 10.1371/journal.pone.0144176 |
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2015 Journal Article Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic DevelopmentHasegawa, 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, e1005428. doi: 10.1371/journal.pgen.1005428 |
