The University of Queensland

Superior induced pluripotent stem cell generation through Phactr-3-driven mechano-modulation of both early and late phases of cell reprogramming

Chowdhury, Mohammad Mahfuz, Zimmerman, Samuel, Leeson, Hannah, Nefzger, Christian Maximilian, Mar, Jessica Cara, Laslett, Andrew, Polo, Jose Maria, Wolvetang, Ernst and Cooper-White, Justin (2024). Superior induced pluripotent stem cell generation through Phactr-3-driven mechano-modulation of both early and late phases of cell reprogramming. Biomaterials Research. doi: 10.34133/bmr.0025

Redox signalling regulates breast cancer metastasis via phenotypic and metabolic reprogramming due to p63 activation by HIF1α

Ren, Zuen, Dharmaratne, Malindrie, Liang, Huizhi, Benard, Outhiriaradjou, Morales-Gallego, Miriam, Suyama, Kimita, Kumar, Viney, Fard, Atefeh Taherian, Kulkarni, Ameya S., Prystowsky, Michael, Mar, Jessica C., Norton, Larry and Hazan, Rachel B. (2024). Redox signalling regulates breast cancer metastasis via phenotypic and metabolic reprogramming due to p63 activation by HIF1α. British Journal of Cancer, 130 (6), 908-924. doi: 10.1038/s41416-023-02522-5

Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology

Aguado, Julio, Amarilla, Alberto A., Taherian Fard, Atefeh, Albornoz, Eduardo A., Tyshkovskiy, Alexander, Schwabenland, Marius, Chaggar, Harman K., Modhiran, Naphak, Gómez-Inclán, Cecilia, Javed, Ibrahim, Baradar, Alireza A., Liang, Benjamin, Peng, Lianli, Dharmaratne, Malindrie, Pietrogrande, Giovanni, Padmanabhan, Pranesh, Freney, Morgan E., Parry, Rhys, Sng, Julian D. J., Isaacs, Ariel, Khromykh, Alexander A., Valenzuela Nieto, Guillermo, Rojas-Fernandez, Alejandro, Davis, Thomas P., Prinz, Marco, Bengsch, Bertram, Gladyshev, Vadim N., Woodruff, Trent M., Mar, Jessica C. ... Wolvetang, Ernst J. (2023). Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology. Nature Aging, 3 (12), 1-15. doi: 10.1038/s43587-023-00519-6

Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell aging

Zheng, Huiwen, Vijg, Jan, Fard, Atefeh Taherian and Mar, Jessica Cara (2023). Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell aging. Genome Biology, 24 (1) 238, 1-26. doi: 10.1186/s13059-023-03036-2

Deconstructing heterogeneity of replicative senescence in human mesenchymal stem cells at single cell resolution

Taherian Fard, Atefeh, Leeson, Hannah C., Aguado, Julio, Pietrogrande, Giovanni, Power, Dominique, Gómez-Inclán, Cecilia, Zheng, Huiwen, Nelson, Christopher B., Soheilmoghaddam, Farhad, Glass, Nick, Dharmaratne, Malindrie, Watson, Ebony R., Lu, Jennifer, Martin, Sally, Pickett, Hilda A., Cooper-White, Justin, Wolvetang, Ernst J. and Mar, Jessica C. (2023). Deconstructing heterogeneity of replicative senescence in human mesenchymal stem cells at single cell resolution. GeroScience, 46 (1), 1-17. doi: 10.1007/s11357-023-00829-y

scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data

Dharmaratne, Malindrie, Kulkarni, Ameya S., Taherian Fard, Atefeh and Mar, Jessica C. (2023). scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data. GigaScience, 12 giac126, 1-18. doi: 10.1093/gigascience/giac126

Biophysical Reviews special issue call: quantitative methods to decipher cellular heterogeneity — from single-cell to spatial omic methods

Ho, Joshua W. K., Chen, Xi, He, Mu, Huang, Yuanhua, Mar, Jessica C., Shih, David J. H. and Wu, Angela R. (2022). Biophysical Reviews special issue call: quantitative methods to decipher cellular heterogeneity — from single-cell to spatial omic methods. Biophysical Reviews, 14 (5), 1079-1080. doi: 10.1007/s12551-022-00994-y

How does the structure of data impact cell–cell similarity? Evaluating how structural properties influence the performance of proximity metrics in single cell RNA-seq data

Watson, Ebony Rose, Mora, Ariane, Taherian Fard, Atefeh and Mar, Jessica Cara (2022). How does the structure of data impact cell–cell similarity? Evaluating how structural properties influence the performance of proximity metrics in single cell RNA-seq data. Briefings in Bioinformatics, 23 (6), 1-14. doi: 10.1093/bib/bbac387

Impaired signaling for neuromuscular synaptic maintenance is a feature of Motor Neuron Disease

Ding, Qiao, Kesavan, Kaamini, Lee, Kah Meng, Wimberger, Elyse, Robertson, Thomas, Gill, Melinder, Power, Dominique, Chang, Jeryn, Fard, Atefeh T., Mar, Jessica C., Henderson, Robert D., Heggie, Susan, McCombe, Pamela A., Jeffree, Rosalind L., Colditz, Michael J., Hilliard, Massimo A., Ng, Dominic C. H., Steyn, Frederik J., Phillips, William D., Wolvetang, Ernst J., Ngo, Shyuan T. and Noakes, Peter G. (2022). Impaired signaling for neuromuscular synaptic maintenance is a feature of Motor Neuron Disease. Acta Neuropathologica Communications, 10 (1) 61, 61. doi: 10.1186/s40478-022-01360-5

Redox signaling by glutathione peroxidase 2 links vascular modulation to metabolic plasticity of breast cancer

Ren, Zuen, Liang, Huizhi, Galbo, Phillip M., Dharmaratne, Malindrie, Kulkarni, Ameya S., Fard, Atefeh Taherian, Aoun, Marie Louise, Martinez-Lopez, Nuria, Suyama, Kimita, Benard, Outhiriaradjou, Zheng, Wei, Liu, Yang, Albanese, Joseph, Zheng, Deyou, Mar, Jessica C., Singh, Rajat, Prystowsky, Michael B., Norton, Larry and Hazan, Rachel B. (2022). Redox signaling by glutathione peroxidase 2 links vascular modulation to metabolic plasticity of breast cancer. Proceedings of the National Academy of Sciences, 119 (8) e2107266119. doi: 10.1073/pnas.2107266119

Computational methods for single-cell imaging and omics data integration

Watson, Ebony Rose, Taherian Fard, Atefeh and Mar, Jessica Cara (2022). Computational methods for single-cell imaging and omics data integration. Frontiers in Molecular Biosciences, 8 768106, 768106. doi: 10.3389/fmolb.2021.768106

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad M. N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro ... Lecellier, Charles-Henri (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1) 3297. doi: 10.1038/s41467-021-23143-7

The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data

de Torrente, Laurence, Zimmerman, Samuel, Suzuki, Masako, Christopeit, Maximilian, Greally, John M. and Mar, Jessica C. (2020). The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data. BMC Bioinformatics, 21 (Suppl 21) 562, 562. doi: 10.1186/s12859-020-03892-w

Investigating transcriptome-wide sex dimorphism by multi-level analysis of single-cell RNA sequencing data in ten mouse cell types

Lu, Tianyuan and Mar, Jessica C. (2020). Investigating transcriptome-wide sex dimorphism by multi-level analysis of single-cell RNA sequencing data in ten mouse cell types. Biology of Sex Differences, 11 (1) 61, 61. doi: 10.1186/s13293-020-00335-2

Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation

Yu, Bo, Doni Jayavelu, Naresh, Battle, Stephanie L., Mar, Jessica C., Schimmel, Timothy, Cohen, Jacques and Hawkins, R. David (2020). Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation. PLoS One, 15 (11) e0241698, e0241698. doi: 10.1371/journal.pone.0241698

Metformin alters skeletal muscle transcriptome adaptations to resistance training in older adults

Kulkarni, Ameya S., Peck, Bailey D., Walton, R. Grace, Kern, Philip A., Mar, Jessica C., Windham, Samuel T., Bamman, Marcas M., Barzilai, Nir and Peterson, Charlotte A. (2020). Metformin alters skeletal muscle transcriptome adaptations to resistance training in older adults. Aging, 12 (20), 19852-19866. doi: 10.18632/aging.104096

Identification of a novel subgroup of endometrial cancer patients with loss of thyroid hormone receptor beta expression and improved survival

Piqué, Daniel G., Greally, John M. and Mar, Jessica C. (2020). Identification of a novel subgroup of endometrial cancer patients with loss of thyroid hormone receptor beta expression and improved survival. BMC Cancer, 20 (1) 857, 857. doi: 10.1186/s12885-020-07325-y

Protein-protein interactions uncover candidate 'core genes' within omnigenic disease networks

Ratnakumar, Abhirami, Weinhold, Nils, Mar, Jessica C. and Riaz, Nadeem (2020). Protein-protein interactions uncover candidate 'core genes' within omnigenic disease networks. PLoS Genetics, 16 (7) e1008903, e1008903. doi: 10.1371/journal.pgen.1008903

Snai2 maintains bone marrow niche cells by repressing osteopontin expression

Wei, 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

A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknesses

Andriani, 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

Aneuvis: web-based exploration of numerical chromosomal variation in single cells

Piqué, 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

A comparison of survival analysis methods for cancer gene expression RNA-Sequencing data

Raman, 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

The Pediatric Cell Atlas: defining the growth phase of human development at single-cell resolution

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 ... 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

The rise of the distributions: why non-normality is important for understanding the transcriptome and beyond

Mar, 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

A novel approach to modelling transcriptional heterogeneity identifies the oncogene candidate CBX2 in invasive breast carcinoma

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

Estrogen activates Alzheimer's disease genes

Ratnakumar, 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

Stem cell factor is selectively secreted by arterial endothelial cells in bone marrow

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) 2449. doi: 10.1038/s41467-018-04726-3

The majority of CD45- Ter119- CD31- bone marrow cell fraction is of hematopoietic origin and contains erythroid and lymphoid progenitors

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

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data

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, 232. doi: 10.1186/s12859-018-2217-z

Metformin regulates metabolic and nonmetabolic pathways in skeletal muscle and subcutaneous adipose tissues of older adults

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, e12723. doi: 10.1111/acel.12723

Changes in gene expression variability reveal a stable synthetic lethal interaction network in BRCA2-ovarian cancers

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

pathVar: a new method for pathway-based interpretation of gene expression variability

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, e3334. doi: 10.7717/peerj.3334

Self-renewal of a purified Tie2+ hematopoietic stem cell population relies on mitochondrial clearance

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

Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks

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 (1) 16001, 16001. doi: 10.1038/npjsba.2016.1

The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome

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. ... 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

Application of gene expression trajectories initiated from ErbB receptor activation highlights the dynamics of divergent promoter usage

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) e0144176, e0144176. doi: 10.1371/journal.pone.0144176

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) e1005428, e1005428. doi: 10.1371/journal.pgen.1005428

Corrigendum: Genome-wide characterization of the routes to pluripotency

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 ... Nagy, Andras (2015). Corrigendum: Genome-wide characterization of the routes to pluripotency. Nature, 523 (7562), 626-626. doi: 10.1038/nature14606

Erratum: Divergent reprogramming routes lead to alternative stem-cell states (Nature (2014) 516 (192-197) DOI: 10.1038/nature14047)

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), 626-626. doi: 10.1038/nature14607

Chromosome instability in diffuse large B cell lymphomas is suppressed by activation of the noncanonical NF-κB pathway

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

Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles

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

Divergent reprogramming routes lead to alternative stem-cell states

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

Genome-wide characterization of the routes to pluripotency

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 ... Nagy, Andras (2014). Genome-wide characterization of the routes to pluripotency. Nature, 516 (7530), 198-+. doi: 10.1038/nature14046

The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences

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 (1) 6195. doi: 10.1038/ncomms6195

Gene expression variability as a unifying element of the pluripotency network

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

Single-cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cells

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

Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization

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) e1004319, e1004319. doi: 10.1371/journal.pgen.1004319

A promoter-level mammalian expression atlas

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 ... Hayashizaki, Yoshihide (2014). A promoter-level mammalian expression atlas. Nature, 507 (7493), 462-470. doi: 10.1038/nature13182

Not to be suppressed?: rethinking the host response at a root-parasite interface

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

Arteriolar niches maintain haematopoietic stem cell quiescence

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

Temporal dynamics and transcriptional control using single-cell gene expression analysis

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) R118. doi: 10.1186/gb-2013-14-10-r118

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins

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 ... Vidal, Marc (2012). Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature, 487 (7408), 491-495. doi: 10.1038/nature11288

Induced Pluripotent Stem Cells from Ataxia-Telangiectasia Recapitulate the Cellular Phenotype

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

Viral perturbations of host networks reflect disease etiology

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. ... 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

nEASE: a method for gene ontology subclassification of high-throughput gene expression data

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) bts011, 726-728. doi: 10.1093/bioinformatics/bts011

Genome-wide siRNA screen for mediators of NF-κB activation

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

Attract : A method for identifying core pathways that define cellular phenotypes

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, e25445-1-e25445-6. doi: 10.1371/journal.pone.0025445

Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth

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

Variance of gene expression identifies altered network constraints in neurological disease

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, e1002207. doi: 10.1371/journal.pgen.1002207

Canonical NF-κB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation

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

Defining an informativeness metric for clustering gene expression data

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

Epstein-Barr virus nuclear antigen 3C regulated genes in lymphoblastoid cell lines

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

Therapeutic implications of GIPC1 silencing in cancer

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) e15581, e15581. doi: 10.1371/journal.pone.0015581

Decomposition of gene expression state space trajectories

Mar, Jessica C. and Quackenbush, John (2009). Decomposition of gene expression state space trajectories. PLoS Computational Biology, 5 (12) e1000626. doi: 10.1371/journal.pcbi.1000626

HPV16 E7 oncogene expression in normal human epithelial cells causes molecular changes indicative of an epithelial to mesenchymal transition

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

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

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 ... 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

Data-driven normalization strategies for high-throughput quantitative RT-PCR

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 (1) 110, 110.1-110.10. doi: 10.1186/1471-2105-10-110

Further Evidence for BRCA1 Communication with the Inactive X Chromosome

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

Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples

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) R119. doi: 10.1186/gb-2006-7-12-r119

Immunogenetics of CD4 lymphocyte count recovery during antiretroviral therapy: An AIDS clinical trials group study

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

Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation

Mar, Jessica C., Harlow, Timothy J . and Ragan, Mark A. (2005). Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation. BMC Evolutionary Biology, 5 (1), 8.1-8.20. doi: 10.1186/1471-2148-5-8

Model-based clustering in gene expression microarrays: an application to breast cancer data

Mar, J.C. and McLachlan, G.J. (2003). Model-based clustering in gene expression microarrays: an application to breast cancer data. International Journal of Software Engineering and Knowledge Engineering, 13 (6), 579-592. doi: 10.1142/S0218194003001482

Softer, faster, better! - Substrate mechanics drives superior somatic cell reprogramming outcomes

Cooper-White, Justin, Chowdhury, Mahfuz, Wolvetang, Ernst, Zimmerman, Samuel, Mar, Jessica, Polo, Jose, Laslett, Andrew and Nefzger, Christian (2022). Softer, faster, better! - Substrate mechanics drives superior somatic cell reprogramming outcomes. TERMIS 6th World Congress, Maastricht, Netherlands, 15-19 November 2021. New Rochelle, NY United States: Mary Ann Liebert.

Redox regulation of tumor cell heterogeneity in the PyMT mammary tumor model revealed by single cell RNA sequencing

Ren, Zuen, Dharmaratne, Malindrie, Kulkarni, Ameya, Fard, Atefeh Taherian, Mar, Jessica, Galbo, Phillip M., Liu, Yang, Zheng, Deyou, Liang, Huizhi, Benard, Outhiriaradjou, Suyama, Kimita, Prystowsky, Michael B., Norton, Larry and Hazan, Rachel B. (2020). Redox regulation of tumor cell heterogeneity in the PyMT mammary tumor model revealed by single cell RNA sequencing. AACR Annual Meeting, Online, 22-24 June, 2020. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2020-4426

Investigating skewness to understand gene expression heterogeneity in large patient cohorts

Church, 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