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2024 Journal Article Superior induced pluripotent stem cell generation through Phactr-3-driven mechano-modulation of both early and late phases of cell reprogrammingChowdhury, 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, 28 0025, 0025. doi: 10.34133/bmr.0025 |
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2024 Journal Article Redox signalling regulates breast cancer metastasis via phenotypic and metabolic reprogramming due to p63 activation by HIF1αRen, 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 |
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2023 Journal Article Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathologyAguado, 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), 1561-1575. doi: 10.1038/s43587-023-00519-6 |
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2023 Journal Article Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell agingZheng, 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 |
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2023 Journal Article Deconstructing heterogeneity of replicative senescence in human mesenchymal stem cells at single cell resolutionTaherian 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 |
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2023 Journal Article scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing dataDharmaratne, 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 |
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2022 Journal Article Biophysical Reviews special issue call: quantitative methods to decipher cellular heterogeneity — from single-cell to spatial omic methodsHo, 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 |
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2022 Journal Article 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 dataWatson, 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) bbac387, 1-14. doi: 10.1093/bib/bbac387 |
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2022 Journal Article Impaired signaling for neuromuscular synaptic maintenance is a feature of Motor Neuron DiseaseDing, 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 |
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2022 Conference Publication Softer, faster, better! - Substrate mechanics drives superior somatic cell reprogramming outcomesCooper-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. |
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2022 Journal Article Redox signaling by glutathione peroxidase 2 links vascular modulation to metabolic plasticity of breast cancerRen, 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 |
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2022 Journal Article Computational methods for single-cell imaging and omics data integrationWatson, 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 |
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2021 Journal Article Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural networkGrapotte, 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 |
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2020 Journal Article The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic datade 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 |
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2020 Journal Article Investigating transcriptome-wide sex dimorphism by multi-level analysis of single-cell RNA sequencing data in ten mouse cell typesLu, 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 |
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2020 Journal Article Single-cell analysis of transcriptome and DNA methylome in human oocyte maturationYu, 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 |
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2020 Journal Article Metformin alters skeletal muscle transcriptome adaptations to resistance training in older adultsKulkarni, 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 |
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2020 Journal Article Identification of a novel subgroup of endometrial cancer patients with loss of thyroid hormone receptor beta expression and improved survivalPiqué, 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 |
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2020 Conference Publication Redox regulation of tumor cell heterogeneity in the PyMT mammary tumor model revealed by single cell RNA sequencingRen, 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 |
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2020 Journal Article Protein-protein interactions uncover candidate 'core genes' within omnigenic disease networksRatnakumar, 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 |
