The University of Queensland

Aging of intestinal stem cells and associated niche

Jardé, Thierry, Nefzger, Christian M., Polo, Jose M. and Abud, Helen E. (2020). Aging of intestinal stem cells and associated niche. The Stem Cell Niche during Ageing. (pp. 25-40) edited by Susie Nilsson. Cambridge, MA, United States: Academic Press. doi: 10.1016/bs.asn.2020.05.001

Production of high-titer lentiviral particles for stable genetic modification of mammalian cells

Larcombe, Michael R., Manent, Jan, Chen, Joseph, Mishra, Ketan, Liu, Xiaodong and Nefzger, Christian M. (2019). Production of high-titer lentiviral particles for stable genetic modification of mammalian cells. Mouse cell culture. (pp. 47-61) edited by Ivan Bertoncello. New York, NY, United States: Humana Press. doi: 10.1007/978-1-4939-9086-3_4

Isolation of reprogramming intermediates during generation of induced pluripotent stem cells from mouse embryonic fibroblasts

Nefzger, Christian M., Alaei, Sara and Polo, Jose M. (2015). Isolation of reprogramming intermediates during generation of induced pluripotent stem cells from mouse embryonic fibroblasts. Cell reprogramming: methods and protocols. (pp. 205-218) New York, NY USA: Springer. doi: 10.1007/978-1-4939-2848-4_17

Transient naive reprogramming corrects hiPS cells functionally and epigenetically

Buckberry, Sam, Liu, Xiaodong, Poppe, Daniel, Tan, Jia Ping, Sun, Guizhi, Chen, Joseph, Nguyen, Trung Viet, de Mendoza, Alex, Pflueger, Jahnvi, Frazer, Thomas, Vargas-Landín, Dulce B., Paynter, Jacob M., Smits, Nathan, Liu, Ning, Ouyang, John F., Rossello, Fernando J., Chy, Hun S., Rackham, Owen J. L., Laslett, Andrew L., Breen, James, Faulkner, Geoffrey J., Nefzger, Christian M., Polo, Jose M. and Lister, Ryan (2023). Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature, 620 (7975), 863-872. doi: 10.1038/s41586-023-06424-7

Macrophage ACE2 is necessary for SARS-CoV-2 replication and subsequent cytokine responses that restrict continued virion release

Labzin, Larisa I., Chew, Keng Yih, Eschke, Kathrin, Wang, Xiaohui, Esposito, Tyron, Stocks, Claudia J., Rae, James, Patrick, Ralph, Mostafavi, Helen, Hill, Brittany, Yordanov, Teodor E., Holley, Caroline L., Emming, Stefan, Fritzlar, Svenja, Mordant, Francesca L., Steinfort, Daniel P., Subbarao, Kanta, Nefzger, Christian M., Lagendijk, Anne K., Gordon, Emma J., Parton, Robert G., Short, Kirsty R., Londrigan, Sarah L. and Schroder, Kate (2023). Macrophage ACE2 is necessary for SARS-CoV-2 replication and subsequent cytokine responses that restrict continued virion release. Science Signaling, 16 (782), eabq1366. doi: 10.1126/scisignal.abq1366

High ploidy large cytoplasmic megakaryocytes are hematopoietic stem cells regulators and essential for platelet production

Heazlewood, Shen Y., Ahmad, Tanveer, Cao, Benjamin, Cao, Huimin, Domingues, Melanie, Sun, Xuan, Heazlewood, Chad K., Li, Songhui, Williams, Brenda, Fulton, Madeline, White, Jacinta F., Nebl, Tom, Nefzger, Christian M., Polo, Jose M., Kile, Benjamin T., Kraus, Felix, Ryan, Michael T., Sun, Yu B., Choong, Peter F. M., Ellis, Sarah L., Anko, Minna-Liisa and Nilsson, Susan K. (2023). High ploidy large cytoplasmic megakaryocytes are hematopoietic stem cells regulators and essential for platelet production. Nature Communications, 14 (1) 2099, 1-18. doi: 10.1038/s41467-023-37780-7

Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells

Gerdes, Patricia, Lim, Sue Mei, Ewing, Adam D., Larcombe, Michael R., Chan, Dorothy, Sanchez-Luque, Francisco J., Walker, Lucinda, Carleton, Alexander L., James, Cini, Knaupp, Anja S., Carreira, Patricia E., Nefzger, Christian M., Lister, Ryan, Richardson, Sandra R., Polo, Jose M. and Faulkner, Geoffrey J. (2022). Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells. Nature Communications, 13 (1) 7470, 1-18. doi: 10.1038/s41467-022-35180-x

Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations

Mizikovsky, Dalia, Naval Sanchez, Marina, Nefzger, Christian M, Cuellar Partida, Gabriel and Palpant, Nathan J (2022). Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations. Nucleic Acids Research, 50 (15) e87, 1-12. doi: 10.1093/nar/gkac413

Benchmarking of ATAC Sequencing Data From BGI’s Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions

Naval-Sanchez, Marina, Deshpande, Nikita, Tran, Minh, Zhang, Jingyu, Alhomrani, Majid, Alsanie, Walaa, Nguyen, Quan and Nefzger, Christian M. (2022). Benchmarking of ATAC Sequencing Data From BGI’s Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions. Frontiers in Molecular Biosciences, 9 900323, 1-15. doi: 10.3389/fmolb.2022.900323

Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential

Nefzger, Christian M., Jardé, Thierry, Srivastava, Akanksha, Schroeder, Jan, Rossello, Fernando J., Horvay, Katja, Prasko, Mirsada, Paynter, Jacob M., Chen, Joseph, Weng, Chen-Fang, Sun, Yu B. Y., Liu, Xiaodong, Chan, Eva, Deshpande, Nikita, Chen, Xiaoli, Li, Y. Jinhua, Pflueger, Jahnvi, Engel, Rebekah M., Knaupp, Anja S., Tsyganov, Kirill, Nilsson, Susan K., Lister, Ryan, Rackham, Owen J. L., Abud, Helen E. and Polo, Jose M. (2022). Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential. npj Regenerative Medicine, 7 (1) 31, 1-8. doi: 10.1038/s41536-022-00226-7

Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1–3 in mesendoderm cell differentiation

Sinniah, Enakshi, Wu, Zhixuan, Shen, Sophie, Naval-Sanchez, Marina, Chen, Xiaoli, Lim, Junxian, Helfer, Abbigail, Iyer, Abishek, Tng, Jiahui, Lucke, Andrew J., Reid, Robert C., Redd, Meredith A., Nefzger, Christian M., Fairlie, David P. and Palpant, Nathan J. (2022). Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1–3 in mesendoderm cell differentiation. Cell Reports, 39 (7) 110818, 1-21. doi: 10.1016/j.celrep.2022.110818

BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation

Keniry, Andrew, Jansz, Natasha, Gearing, Linden J., Wanigasuriya, Iromi, Chen, Joseph, Nefzger, Christian M., Hickey, Peter F., Gouil, Quentin, Liu, Joy, Breslin, Kelsey A., Iminitoff, Megan, Beck, Tamara, Tapia del Fierro, Andres, Whitehead, Lachlan, Jarratt, Andrew, Kinkel, Sarah A., Taberlay, Phillippa C., Willson, Tracy, Pakusch, Miha, Ritchie, Matthew E., Hilton, Douglas J., Polo, Jose M. and Blewitt, Marnie E. (2022). BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation. Nature Communications, 13 (1) 1658, 1658. doi: 10.1038/s41467-022-29333-1

Bone marrow regulatory T cells are a unique population, supported by niche-specific cytokines and plasmacytoid dendritic cells, and required for chronic graft-versus-host disease control

Nicholls, Jemma, Cao, Benjamin, Le Texier, Laetitia, Xiong, Laura Yan, Hunter, Christopher R., Llanes, Genesis, Aguliar, Ethan G., Schroder, Wayne A., Phipps, Simon, Lynch, Jason P., Cao, Huimin, Heazlewood, Shen Y., Williams, Brenda, Clouston, Andrew D., Nefzger, Christian M., Polo, Jose M., Nilsson, Susan K., Blazar, Bruce R. and MacDonald, Kelli P. A. (2021). Bone marrow regulatory T cells are a unique population, supported by niche-specific cytokines and plasmacytoid dendritic cells, and required for chronic graft-versus-host disease control. Frontiers in Cell and Developmental Biology, 9 737880, 737880. doi: 10.3389/fcell.2021.737880

Interplay between the EMT transcription factors ZEB1 and ZEB2 regulates hematopoietic stem and progenitor cell differentiation and hematopoietic lineage fidelity

Wang, Jueqiong, Farkas, Carlos, Benyoucef, Aissa, Carmichael, Catherine, Haigh, Katharina, Wong, Nick, Huylebroeck, Danny, Stemmler, Marc P., Brabletz, Simone, Brabletz, Thomas, Nefzger, Christian M., Goossens, Steven, Berx, Geert, Polo, Jose M. and Haigh, Jody J. (2021). Interplay between the EMT transcription factors ZEB1 and ZEB2 regulates hematopoietic stem and progenitor cell differentiation and hematopoietic lineage fidelity. PLoS Biology, 19 (9) e3001394, 1-33. doi: 10.1371/journal.pbio.3001394

Nicotinamide riboside attenuates age-associated metabolic and functional changes in hematopoietic stem cells

Sun, Xuan, Cao, Benjamin, Naval-Sanchez, Marina, Pham, Tony, Sun, Yu Bo Yang, Williams, Brenda, Heazlewood, Shen Y, Deshpande, Nikita, Li, Jinhua, Kraus, Felix, Rae, James, Nguyen, Quan, Yari, Hamed, Schröder, Jan, Heazlewood, Chad K, Fulton, Madeline, Hatwell-Humble, Jessica, Das Gupta, Kaustav, Kapetanovic, Ronan, Chen, Xiaoli, Sweet, Matthew J, Parton, Robert G, Ryan, Michael T, Polo, Jose M, Nefzger, Christian M and Nilsson, Susan K (2021). Nicotinamide riboside attenuates age-associated metabolic and functional changes in hematopoietic stem cells. Nature Communications, 12 (1) 2665, 1-17. doi: 10.1038/s41467-021-22863-0

Mesenchymal Niche-Derived Neuregulin-1 Drives Intestinal Stem Cell Proliferation and Regeneration of Damaged Epithelium

Jardé, Thierry, Chan, Wing Hei, Rossello, Fernando J., Kaur Kahlon, Tanvir, Theocharous, Mandy, Kurian Arackal, Teni, Flores, Tracey, Giraud, Mégane, Richards, Elizabeth, Chan, Eva, Kerr, Genevieve, Engel, Rebekah M., Prasko, Mirsada, Donoghue, Jacqueline F., Abe, Shin-ichi, Phesse, Toby J., Nefzger, Christian M., McMurrick, Paul J., Powell, David R., Daly, Roger J., Polo, Jose M. and Abud, Helen E. (2020). Mesenchymal Niche-Derived Neuregulin-1 Drives Intestinal Stem Cell Proliferation and Regeneration of Damaged Epithelium. Cell Stem Cell, 27 (4), 646-662.e7. doi: 10.1016/j.stem.2020.06.021

Reprogramming roadmap reveals route to human induced trophoblast stem cells

Liu, Xiaodong, Ouyang, John F., Rossello, Fernando J., Tan, Jia Ping, Davidson, Kathryn C., Valdes, Daniela S., Schröder, Jan, Sun, Yu B. Y., Chen, Joseph, Knaupp, Anja S., Sun, Guizhi, Chy, Hun S., Huang, Ziyi, Pflueger, Jahnvi, Firas, Jaber, Tano, Vincent, Buckberry, Sam, Paynter, Jacob M., Larcombe, Michael R., Poppe, Daniel, Choo, Xin Yi, O’Brien, Carmel M., Pastor, William A., Chen, Di, Leichter, Anna L., Naeem, Haroon, Tripathi, Pratibha, Das, Partha P., Grubman, Alexandra ... Polo, Jose M. (2020). Reprogramming roadmap reveals route to human induced trophoblast stem cells. Nature, 586 (7827), 101-107. doi: 10.1038/s41586-020-2734-6

Class-switch recombination occurs infrequently in germinal centers

Roco, Jonathan A., Mesin, Luka, Binder, Sebastian C., Nefzger, Christian, Gonzalez-Figueroa, Paula, Canete, Pablo F., Ellyard, Julia, Shen, Qian, Robert, Philippe A., Cappello, Jean, Vohra, Harpreet, Zhang, Yang, Nowosad, Carla R., Schiepers, Arien, Corcoran, Lynn M., Toellner, Kai-Michael, Polo, Jose M., Meyer-Hermann, Michael, Victora, Gabriel D. and Vinuesa, Carola G. (2019). Class-switch recombination occurs infrequently in germinal centers. Immunity, 51 (2), 337-350.e7. doi: 10.1016/j.immuni.2019.07.001

TAF5L and TAF6L maintain self-renewal of embryonic stem cells via the MYC regulatory network

Seruggia, Davide, Oti, Martin, Tripathi, Pratibha, Canver, Matthew C., LeBlanc, Lucy, Di Giammartino, Dafne C., Bullen, Michael J., Nefzger, Christian M., Sun, Yu Bo Yang, Farouni, Rick, Polo, Jose M., Pinello, Luca, Apostolou, Effie, Kim, Jonghwan, Orkin, Stuart H. and Das, Partha Pratim (2019). TAF5L and TAF6L maintain self-renewal of embryonic stem cells via the MYC regulatory network. Molecular Cell, 74 (6), 1148-+. doi: 10.1016/j.molcel.2019.03.025

Generation of mouse-induced pluripotent stem cells by lentiviral transduction

Liu, Xiaodong, Chen, Joseph, Firas, Jaber, Paynter, Jacob M., Nefzger, Christian M. and Polo, Jose M. (2019). Generation of mouse-induced pluripotent stem cells by lentiviral transduction. Methods in Molecular Biology, 1940, 63-76. doi: 10.1007/978-1-4939-9086-3_5

Propagation and maintenance of mouse embryonic stem cells

Paynter, Jacob M., Chen, Joseph, Liu, Xiaodong and Nefzger, Christian M. (2019). Propagation and maintenance of mouse embryonic stem cells. Methods in Molecular Biology, 1940, 33-45. doi: 10.1007/978-1-4939-9086-3_3

Generation of four iPSC lines from peripheral blood mononuclear cells (PBMCs) of an attention deficit hyperactivity disorder (ADHD) individual and a healthy sibling in an Australia-Caucasian family

Tong, Janette, Lee, Kyung Min, Liu, Xiaodong, Nefzger, Christian M., Vijayakumar, Prasidhee, Hawi, Ziarih, Pang, Ken C., Parish, Clare L., Polo, Jose M. and Bellgrove, Mark A. (2019). Generation of four iPSC lines from peripheral blood mononuclear cells (PBMCs) of an attention deficit hyperactivity disorder (ADHD) individual and a healthy sibling in an Australia-Caucasian family. Stem Cell Research, 34 101353. doi: 10.1016/j.scr.2018.11.014

A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs

Pflueger, Christian, Tan, Dennis, Swain, Tessa, Trung Nguyen,, Pflueger, Jahnvi, Nefzger, Christian, Polo, Jose M., Ford, Ethan and Lister, Ryan (2018). A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. Genome Research, 28 (8), 1193-1206. doi: 10.1101/gr.233049.117

Identification of dynamic undifferentiated cell states within the male germline

La, Hue M., Makela, Juho-Antti, Chan, Ai-Leen, Rossello, Fernando J., Nefzger, Christian M., Legrand, Julien M. D., De Seram, Mia, Polo, Jose M. and Hobbs, Robin M. (2018). Identification of dynamic undifferentiated cell states within the male germline. Nature Communications, 9 (1) 2819. doi: 10.1038/s41467-018-04827-z

Fine tuning of canonical Wnt stimulation enhances differentiation of pluripotent stem cells independent of beta-catenin-mediated T-cell factor signaling

Chen, Joseph, Nefzger, Christian M., Rossello, Fernando J., Sun, Yu B. Y., Lim, Sue Mei, Liu, Xiaodong, de Boer, Suzan, Knaupp, Anja S., Li, Jinhua, Davidson, Kathryn C., Polo, Jose M. and Barberi, Tiziano (2018). Fine tuning of canonical Wnt stimulation enhances differentiation of pluripotent stem cells independent of beta-catenin-mediated T-cell factor signaling. Stem Cells, 36 (6), 822-833. doi: 10.1002/stem.2794

SRSF3 promotes pluripotency through Nanog mRNA export and coordination of the pluripotency gene expression program

Ratnadiwakara, Madara, Archer, Stuart K., Dent, Craig I., De Los Mozos, Igor Ruiz, Beilharz, Traude H., Knaupp, Anja S., Nefzger, Christian M., Polo, Jose M. and Anko, Minna-Liisa (2018). SRSF3 promotes pluripotency through Nanog mRNA export and coordination of the pluripotency gene expression program. Elife, 7. doi: 10.7554/eLife.37419

Method of derivation and differentiation of mouse embryonic stem cells generating synchronous neuronal networks

Gazina, Elena V., Morrisroe, Emma, Mendis, Gunarathna D. C., Michalska, Anna E., Chen, Joseph, Nefzger, Christian M., Rollo, Benjamin N., Reid, Christopher A., Pera, Martin F. and Petrou, Steven (2018). Method of derivation and differentiation of mouse embryonic stem cells generating synchronous neuronal networks. Journal of Neuroscience Methods, 293, 53-58. doi: 10.1016/j.jneumeth.2017.08.018

Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming

Knaupp, Anja S., Buckberry, Sam, Pflueger, Jahnvi, Lim, Sue Mei, Ford, Ethan, Larcombe, Michael R., Rossello, Fernando J., de Mendoza, Alex, Alaei, Sara, Firas, Jaber, Holmes, Melissa L., Nair, Shalima S., Clark, Susan J., Nefzger, Christian M., Lister, Ryan and Polo, Jose M. (2017). Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming. Cell Stem Cell, 21 (6), 834-845+. doi: 10.1016/j.stem.2017.11.007

Cell type of origin dictates the route to pluripotency

Nefzger, Christian M., Rossello, Fernando J., Chen, Joseph, Liu, Xiaodong, Knaupp, Anja S., Firas, Jaber, Paynter, Jacob M., Pflueger, Jahnvi, Buckberry, Sam, Lim, Sue Mei, Williams, Brenda, Alaei, Sara, Faye-Chauhan, Keshav, Petretto, Enrico, Nilsson, Susan K., Lister, Ryan, Ramialison, Mirana, Powell, David R., Rackham, Owen J. L. and Polo, Jose M. (2017). Cell type of origin dictates the route to pluripotency. Cell Reports, 21 (10), 2649-2660. doi: 10.1016/j.celrep.2017.11.029

Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming

Liu, Xiaodong, Nefzger, Christian M., Rossello, Fernando J., Chen, Joseph, Knaupp, Anja S., Firas, Jaber, Ford, Ethan, Pflueger, Jahnvi, Paynter, Jacob M., Chy, Hun S., O'Brien, Carmel M., Huang, Cheng, Mishra, Ketan, Hodgson-Garms, Margeaux, Jansz, Natasha, Williams, Sarah M., Blewitt, Marnie E., Nilsson, Susan K., Schittenhelm, Ralf B., Laslett, Andrew L., Lister, Ryan and Polo, Jose M. (2017). Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming. Nature Methods, 14 (11), 1055-1062+. doi: 10.1038/NMETH.4436

Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes (vol 18, pg 552, 2017)

Marino, Eliana, Richards, James L., McLeod, Keiran H., Stanley, Dragana, Yap, Yu Anne, Knight, Jacinta, McKenzie, Craig, Kranich, Jan, Oliveira, Ana Carolina, Rossello, Fernando J., Krishnamurthy, Balasubramanian, Nefzger, Christian M., Macia, Laurence, Thorburn, Alison, Baxter, Alan G., Morahan, Grant, Wong, Lee H., Polo, Jose M., Moore, Robert J., Lockett, Trevor J., Clarke, Julie M., Topping, David L., Harrison, Leonard C. and Mackay, Charles R. (2017). Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes (vol 18, pg 552, 2017). Nature Immunology, 18 (11), 1271-1271. doi: 10.1038/ni1117-1271c

Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes (vol 18, pg 552, 2017)

Marino, Eliana, Richards, James L., McLeod, Keiran H., Stanley, Dragana, Yap, Yu Anne, Knight, Jacinta, McKenzie, Craig, Kranich, Jan, Oliveira, Ana Carolina, Rossello, Fernando J., Krishnamurthy, Balasubramanian, Nefzger, Christian M., Macia, Laurence, Thorburn, Alison, Baxter, Alan G., Morahan, Grant, Wong, Lee H., Polo, Jose M., Moore, Robert J., Lockett, Trevor J., Clarke, Julie M., Topping, David L., Harrison, Leonard C. and Mackay, Charles R. (2017). Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes (vol 18, pg 552, 2017). Nature Immunology, 18 (8), 951-951. doi: 10.1038/ni0817-951c

Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes

Marino, Eliana, Richards, James L., McLeod, Keiran H., Stanley, Dragana, Yap, Yu Anne, Knight, Jacinta, McKenzie, Craig, Kranich, Jan, Oliveira, Ana Carolina, Rossello, Fernando J., Krishnamurthy, Balasubramanian, Nefzger, Christian M., Macia, Laurence, Thorburn, Alison, Baxter, Alan G., Morahan, Grant, Wong, Lee H., Polo, Jose M., Moore, Robert J., Lockett, Trevor J., Clarke, Julie M., Topping, David L., Harrison, Leonard C. and Mackay, Charles R. (2017). Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes. Nature Immunology, 18 (5), 552-562. doi: 10.1038/ni.3713

DEAD-box RNA binding protein DDX5: not a black-box during reprogramming

Nefzger, Christian M. and Polo, Jose M. (2017). DEAD-box RNA binding protein DDX5: not a black-box during reprogramming. Cell Stem Cell, 20 (4), 419-420. doi: 10.1016/j.stem.2017.03.006

New monoclonal antibodies to defined cell surface proteins on human pluripotent stem cells

O'Brien, Carmel M., Chy, Hun S., Zhou, Qi, Blumenfeld, Shiri, Lambshead, Jack W., Liu, Xiaodong, Kie, Joshua, Capaldo, Bianca D., Chung, Tung-Liang, Adams, Timothy E., Tram Phan,, Bentley, John D., McKinstry, William J., Oliva, Karen, McMurrick, Paul J., Wang, Yu-Chieh, Rossello, Fernando J., Lindeman, Geoffrey J., Chen, Di, Jarde, Thierry, Clark, Amander T., Abud, Helen E., Visvader, Jane E., Nefzger, Christian M., Polo, Jose M., Loring, Jeanne F. and Laslett, Andrew L. (2017). New monoclonal antibodies to defined cell surface proteins on human pluripotent stem cells. Stem Cells, 35 (3), 626-640. doi: 10.1002/stem.2558

An improved reprogrammable mouse model harbouring the reverse tetracycline-controlled transcriptional transactivator 3

Alaei, S., Knaupp, A. S., Lim, S. M., Chen, J., Holmes, M. L., Anko, M. L., Nefzger, C. M. and Polo, J. M. (2016). An improved reprogrammable mouse model harbouring the reverse tetracycline-controlled transcriptional transactivator 3. Stem Cell Research, 17 (1), 49-53. doi: 10.1016/j.scr.2016.05.008

A versatile strategy for isolating a highly enriched population of intestinal stem cells

Nefzger, Christian M., Jarde, Thierry, Rossello, Fernando J., Horvay, Katja, Knaupp, Anja S., Powell, David R., Chen, Joseph, Abud, Helen E. and Polo, Jose M. (2016). A versatile strategy for isolating a highly enriched population of intestinal stem cells. Stem Cell Reports, 6 (3), 321-329. doi: 10.1016/j.stemcr.2016.01.014

A predictive computational framework for direct reprogramming between human cell types

Rackham, Owen J. L., Firas, Jaber, Fang, Hai, Oates, Matt E., Holmes, Melissa L., Knaupp, Anja S., Suzuki, Harukazu, Nefzger, Christian M., Daub, Carsten O., Shin, Jay W., Petretto, Enrico, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Polo, Jose M. and Gough, Julian (2016). A predictive computational framework for direct reprogramming between human cell types. Nature Genetics, 48 (3), 331-335. doi: 10.1038/ng.3487

Snai1 regulates cell lineage allocation and stem cell maintenance in the mouse intestinal epithelium

Horvay, Katja, Jarde, Thierry, Casagranda, Franca, Perreau, Victoria M., Haigh, Katharina, Nefzger, Christian M., Akhtar, Reyhan, Gridley, Thomas, Berx, Geert, Haigh, Jody J., Barker, Nick, Polo, Jose M., Hime, Gary R. and Abud, Helen E. (2015). Snai1 regulates cell lineage allocation and stem cell maintenance in the mouse intestinal epithelium. The EMBO Journal, 34 (10), 1319-1335. doi: 10.15252/embj.201490881

Cell surface marker mediated purification of iPS cell intermediates from a reprogrammable mouse model

Nefzger, Christian M., Alaei, Sara, Knaupp, Anja S., Holmes, Melissa L. and Polo, Jose M. (2014). Cell surface marker mediated purification of iPS cell intermediates from a reprogrammable mouse model. Jove-Journal of Visualized Experiments (91). doi: 10.3791/51728

GM-CSF and MEF-conditioned media support feeder-free reprogramming of mouse granulocytes to iPS cells

Firas, Jaber, Liu, Xiaodong, Nefzger, Christian M. and Polo, Jose M. (2014). GM-CSF and MEF-conditioned media support feeder-free reprogramming of mouse granulocytes to iPS cells. Differentiation, 87 (5), 193-199. doi: 10.1016/j.diff.2014.05.003

Mitochondrial DNA haplotypes define gene expression patterns in pluripotent and differentiating embryonic stem cells

Kelly, Richard D. W., Rodda, Andrew E., Dickinson, Adam, Mahmud, Arsalan, Nefzger, Christian M., Lee, William, Forsythe, John S., Polo, Jose M., Trounce, Ian A., McKenzie, Matthew, Nisbet, David R. and St John, Justin C. (2013). Mitochondrial DNA haplotypes define gene expression patterns in pluripotent and differentiating embryonic stem cells. Stem Cells, 31 (4), 703-716. doi: 10.1002/stem.1313

Probing transcription factor diffusion dynamics in the living mammalian embryo with photoactivatable fluorescence correlation spectroscopy

Kaur, Gurpreet, Costa, Mauro W., Nefzger, Christian M., Silva, Juan, Fierro-Gonzalez, Juan Carlos, Polo, Jose M., Bell, Toby D. M. and Plachta, Nicolas (2013). Probing transcription factor diffusion dynamics in the living mammalian embryo with photoactivatable fluorescence correlation spectroscopy. Nature Communications, 4 (1) 1637. doi: 10.1038/ncomms2657

A molecular roadmap of reprogramming somatic cells into iPS cells

Polo, Jose M., Anderssen, Endre, Walsh, Ryan M., Schwarz, Benjamin A., Nefzger, Christian M., Lim, Sue Mei, Borkent, Marti, Apostolou, Effie, Alaei, Sara, Cloutier, Jennifer, Bar-Nur, Ori, Cheloufi, Sihem, Stadtfeld, Matthias, Figueroa, Maria Eugenia, Robinton, Daisy, Natesan, Sridaran, Melnick, Ari, Zhu, Jinfang, Ramaswamy, Sridhar and Hochedlinger, Konrad (2012). A molecular roadmap of reprogramming somatic cells into iPS cells. Cell, 151 (7), 1617-1632. doi: 10.1016/j.cell.2012.11.039

Lmx1a allows context-specific isolation of progenitors of GABAergic or Dopaminergic neurons during neural differentiation of embryonic stem cells

Nefzger, Christian M., Su, Colin T., Fabb, Stewart A., Hartley, Brigham J., Beh, Siew J., Zeng, Wendy R., Haynes, John M. and Pouton, Colin W. (2012). Lmx1a allows context-specific isolation of progenitors of GABAergic or Dopaminergic neurons during neural differentiation of embryonic stem cells. Stem Cells, 30 (7), 1349-1361. doi: 10.1002/stem.1105

Midbrain and forebrain patterning delivers immunocytochemically and functionally similar populations of neuropeptide Y containing GABAergic neurons

Khaira, S. K., Nefzger, C. M., Beh, S. J., Pouton, C. W. and Haynes, J. M. (2011). Midbrain and forebrain patterning delivers immunocytochemically and functionally similar populations of neuropeptide Y containing GABAergic neurons. Neurochemistry International, 59 (3), 413-420. doi: 10.1016/j.neuint.2011.02.016

Directed expression of Gata2, Mash1, and Foxa2 synergize to induce the serotonergic neuron phenotype during in vitro differentiation of embryonic stem cells

Nefzger, Christian M., Haynes, John M. and Pouton, Colin W. (2011). Directed expression of Gata2, Mash1, and Foxa2 synergize to induce the serotonergic neuron phenotype during in vitro differentiation of embryonic stem cells. Stem Cells, 29 (6), 928-939. doi: 10.1002/stem.640

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.