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Research Output 2004 2018

2018

Identification of dynamic undifferentiated cell states within the male germline

La, H. M., Mäkelä, J-A., Chan, A-L., Rossello, F. J., Nefzger, C. M., Legrand, J. M. D., De Seram, M., Polo, J. M. & Hobbs, R. M. 19 Jul 2018 In : Nature Communications. 9, 1, 18 p., 2819

Research output: Contribution to journalArticle

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

Ratnadiwakara, M., Archer, S. K., Dent, C. I., Ruiz De Los Mozos, I., Beilharz, T. H., Knaupp, A. S., Nefzger, C. M., Polo, J. M. & Anko, M-L. 2018 (Accepted/In press) In : eLife.

Research output: Contribution to journalArticle

Open Access
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TFAP2C regulates transcription in human naive pluripotency by opening enhancers

Pastor, W. A., Liu, W., Chen, D., Ho, J., Kim, R., Hunt, T. J., Lukianchikov, A., Liu, X., Polo, J. M., Jacobsen, S. E. & Clark, A. T. 1 May 2018 In : Nature Cell Biology. 20, 5, p. 553-564 12 p.

Research output: Contribution to journalArticle

2017

Cell Type of Origin Dictates the Route to Pluripotency

Nefzger, C. M., Rossello, F. J., Chen, J., Liu, X., Knaupp, A. S., Firas, J., Paynter, J. M., Pflueger, J., Buckberry, S., Lim, S. M., Williams, B., Alaei, S., Faye-Chauhan, K., Petretto, E., Nilsson, S. K., Lister, R., Ramialison, M., Powell, D. R., Rackham, O. J. L. & Polo, J. M. 5 Dec 2017 In : Cell Reports. 21, 10, p. 2649-2660 12 p.

Research output: Contribution to journalArticle

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

Liu, X. , Nefzger, C. M. , Rossello, F. J. , Chen, J. , Knaupp, A. S. , Firas, J. , Ford, E. , Pflueger, J. , Paynter, J. M. , Chy, H. S. , O'Brien, C. M. , Huang, C. , Mishra, K. , Hodgson-Garms, M. , Jansz, N. , Williams, S. M. , Blewitt, M. E. , Nilsson, S. K. , Schittenhelm, R. B. , Laslett, A. L. & 2 others Lister, R. & Polo, J. M. 31 Oct 2017 In : Nature Methods. 14, 11, p. 1055-1062 8 p.

Research output: Contribution to journalArticle

Open Access
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DEAD-Box RNA Binding Protein DDX5: Not a Black-Box during Reprogramming

Nefzger, C. & Polo, J. M. 6 Apr 2017 In : Cell Stem Cell. 20, 4, p. 419-420 2 p.

Research output: Contribution to journalShort Survey

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

Marino, E. , Richards, J. L. , McLeod, K. H. , Stanley, D. , Yap, Y. A. , Knight, J. , McKenzie, C. , Kranich, J. , Oliveira, A. C. , Rossello, F. J. , Krishnamurthy, B. , Nefzger, C. M. , Macia, L. , Thorburn, A. , Baxter, A. G. , Morahan, G. , Wong, L. H. , Polo, J. M. , Moore, R. J. , Lockett, T. J. & 4 others Clarke, J. M., Topping, D. L., Harrison, L. C. & Mackay, C. R. May 2017 In : Nature Immunology. 18, 5, p. 552-562 13 p.

Research output: Contribution to journalArticle

Muscle Stem Cells Undergo Extensive Clonal Drift during Tissue Growth via Meox1-Mediated Induction of G2 Cell-Cycle Arrest

Nguyen, P. D., Gurevich, D. B., Sonntag, C., Hersey, L., Alaei , S., Nim, H. T., Siegel, A., Hall, T. E., Rossello, F. J., Boyd, S. E., Polo, J. M. & Currie, P. D. 6 Jul 2017 In : Cell Stem Cell. 21, 1, p. 107-119.e6 19 p.

Research output: Contribution to journalArticle

New Monoclonal Antibodies to Defined Cell Surface Proteins on Human Pluripotent Stem Cells

O'Brien, C. M. , Chy, H. S. , Zhou, Q. , Blumenfeld, S. , Lambshead, J. W. , Liu, X. , Kie, J. , Capaldo, B. D. , Chung, T-L. , Adams, T. E. , Phan, T. , Bentley, J. D. , McKinstry, W. J. , Oliva, K. , McMurrick, P. J. , Wang, Y-C. , Rossello, F. J. , Lindeman, G. J. , Chen, D. , Jarde, T. & 7 others Clark, A. T., Abud, H. E., Visvader, J. E., Nefzger, C. M., Polo, J. M., Loring, J. F. & Laslett, A. L. 1 Mar 2017 In : Stem Cells. 35, 3, p. 626-640 15 p.

Research output: Contribution to journalArticle

Open Access
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Towards understanding transcriptional networks in cellular reprogramming

Firas, J. & Polo, J. M. 1 Oct 2017 In : Current Opinion in Genetics and Development. 46, 8 p.

Research output: Contribution to journalReview Article

Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming

Knaupp, A. S., Buckberry, S., Pflueger, J., Lim, S. M., Ford, E., Larcombe, M. R., Rossello, F. J., de Mendoza, A., Alaei, S., Firas, J., Holmes, M. L., Nair, S. S., Clark, S. J., Nefzger, C. M., Lister, R. & Polo, J. M. 7 Dec 2017 In : Cell Stem Cell. 21, 6, p. 834-845.e6 18 p.

Research output: Contribution to journalArticle

2016
Open Access

A predictive computational framework for direct reprogramming between human cell types

Rackham, O. J. L., Firas, J., Fang, H., Oates, M. E., Holmes, M. L., Knaupp, A. S., The FANTOM Consortium, Suzuki, H., Nefzger, C. M., Daub, C. O., Shin, J. W., Petretto, E., Forrest, A. R. R., Hayashizaki, Y., Polo, J. M. & Gough, J. 18 Jan 2016 In : Nature Genetics. 48, 3, p. 331-335 5 p.

Research output: Contribution to journalLetter

Open Access
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Computational methods for direct cell conversion

Kamaraj, U. S., Gough, J., Polo, J. M., Petretto, E. & Rackham, O. J. L. 16 Dec 2016 In : Cell Cycle. 15, 24, p. 3343-3354 12 p.

Research output: Contribution to journalReview Article

2015

APP intracellular domain acts as a transcriptional regulator of miR-663 suppressing neuronal differentiation

Shu, R., Wong, W. S. F., Ma, Q-H., Yang, Z. Z., Zhu, H., Liu, F. J., Wang, P., Ma, J., Yan, S., Polo, J. M., Bernard, C. C. A., Stanton, L. W., Dawe, G. S. & Xiao, Z. 1 Jan 2015 In : Cell Death and Disease. 6, 2, 12 p., e1651

Research output: Contribution to journalArticle

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

Nefzger, C. M., Alaei Shehni, S. & Polo, J. M. 2015 Cell Reprogramming: Methods and Protocols. Verma, P. J. & Sumer, H. (eds.). 1st ed. Totowa NJ USA: Humana Press, p. 205 - 218 14 p. (Methods in Molecular Biology: Springer Protocols; vol. 1330)

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)

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

Horvay, K., Jarde, T., Casagranda, F., Perreau, V. M., Haigh, K., Nefzger, C. M., Akhtar, R., Gridley, T., Berx, G., Haigh, J. J., Barker, N., Polo, J. M., Hime, G. R. & Abud, H. E. 2015 In : EMBO Journal. 34, 10, p. 1319 - 1335 17 p.

Research output: Contribution to journalArticle

Open Access
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Transcription factor-mediated reprogramming: epigenetics and therapeutic potential

Firas, J., Liu, E. X., Lim, S. M. & Polo, J. M. 2015 In : Immunology and Cell Biology. 93, 3, p. 284 - 289 6 p.

Research output: Contribution to journalArticle

2014

Epigenetic Changes During Reprogramming

Alaei Shehni, S., Knaupp, A. S. & Polo, J. M. 2014 In : Australian Biochemist. 45, 1, p. 17 - 20 4 p.

Research output: Contribution to journalArticle

Epigenetic memory in somatic cell nuclear transfer and induced pluripotency: evidence and implications

Firas, J., Liu, E. X. & Polo, J. M. 2014 In : Differentiation. 88, 1, p. 29 - 32 4 p.

Research output: Contribution to journalArticle

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

Firas, J., Liu, E. X., Nefzger, C. & Polo, J. M. 2014 In : Differentiation. 87, 5, p. 193 - 199 7 p.

Research output: Contribution to journalComment / Debate

Haematopoietic stem cell induction by somite-derived endothelial cells controlled by meox1

Nguyen, P., Hollway, G. E., Sonntag, C., Miles, L. B., Hall, T. E., Berger, S., Fernandez, K. J., Gurevich, D., Cole, N. J., Alaei Shehni, S., Ramialison, M. S. M., Sutherland, R. L., Polo, J. M., Lieschke, G. & Currie, P. D. 2014 In : Nature. 512, 7514, p. 314 - 318 5 p.

Research output: Contribution to journalArticle

Phases of reprogramming

David, L. & Polo, J. M. 2014 In : Stem Cell Research. 12, 3, p. 754 - 761 8 p.

Research output: Contribution to journalArticle

Open Access

Reprogramming can be a transforming experience

Hobbs, R. M. & Polo, J. M. 2014 In : Cell Stem Cell. 14, 3, p. 269 - 271 3 p.

Research output: Contribution to journalArticle

2013

Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity

De, S., Shaknovich, R., Riester, M., Elemento, O., Geng, H. D. E., Kormaksson, M., Jiang, Y., Woolcock, B., Johnson, N., Polo, J. M., Cerchietti, L., Gascoyne, R. D., Melnick, A. & Michor, F. 2013 In : PLoS Genetics. 9, 1, 14 p., e1003137

Research output: Contribution to journalArticle

Open Access
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A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters

Hatzi, K., Jiang, Y., Huang, C., Garrett-Bakelman, F., Gearhart, M. D., Giannopoulou, E. G., Zumbo, P., Kirouac, K., Bhaskara, S., Polo, J. M., Kormaksson, M., MacKerell Jr, A. D., Xue, F., Mason, C. E., Hiebert, S. W., Prive, G. G., Cerchietti, L., Bardwell, V. J., Elemento, O. & Melnick, A. 2013 In : Cell Reports. 4, 3, p. 578 - 588 11 p.

Research output: Contribution to journalArticle

Open Access

Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming

Apostolou, E., Ferrari, F., Walsh, R. M., Bar-Nur, O., Stadtfeld, M., Cheloufi, S., Stuart, H. T., Polo, J. M., Ohsumi, T., Borowsky, M. L., Kharchenko, P. V., Park, P. J. & Hochedlinger, K. 2013 In : Cell Stem Cell. 12, 6, p. 699 - 712 14 p.

Research output: Contribution to journalArticle

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

Kelly, R. D. W., Rodda, A. E., Dickinson, A., Mahmud, A., Nefzger, C., Lee, W., Forsythe, J. S., Polo, J. M., Trounce, I. A., McKenzie, M., Nisbet, D. R. & St John, J. C. 2013 In : Stem Cells. 31, 4, p. 703 - 716 14 p.

Research output: Contribution to journalArticle

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

Kaur, G., Costa, M., Nefzger, C., Silva, J., Fierro-Gonzalez, J. C., Polo, J. M., Bell, T. D. M. & Plachta, N. 2013 In : Nature Communications. 4, 1637, p. 1 - 13 13 p.

Research output: Contribution to journalArticle

Open Access
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2012

A molecular roadmap of reprogramming somatic cells into iPS cells

Polo, J. M., Anderssen, E., Walsh, R. M., Schwarz, B. A., Nefzger, C., Lim, S. M., Borkent, M., Apostolou, E., Alaei Shehni, S., Cloutier, J., Bar-Nur, O., Cheloufi, S., Stadtfeld, M., Figueroa, M. E., Robinton, D., Natesan, S., Melnick, A., Zhu, J., Ramaswamy, S. & Hochedlinger, K. 2012 In : Cell. 151, 7, p. 1617 - 1632 16 p.

Research output: Contribution to journalArticle

Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency

Hansson, J., Reza Rafiee, M., Reiland, S., Polo, J. M., Gehring, J., Okawa, S., Huber, W., Hochedlinger, K. & Krijgsveld, J. 2012 In : Cell Reports. 2, 6, p. 1579 - 1592 14 p.

Research output: Contribution to journalArticle

Open Access
2011

Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells

Ohi, Y., Qin, H., Hong, C., Blouin, L., Polo, J. M., Guo, T., Qi, Z., Downey, S. L., Manos, P. D., Rossi, D. J., Yu, J., Hebrok, M., Hochedlinger, K., Costello, J. F., Song, J. S. & Ramalho-Santos, M. May 2011 In : Nature Cell Biology. 13, 5, p. 541-549 9 p.

Research output: Contribution to journalArticle

Sox2+ adult stem and progenitor cells are important for tissue regeneration and survival of mice

Arnold, K., Sarkar, A., Yram, M. A., Polo, J. M., Bronson, R., Sengupta, S., Seandel, M., Geijsen, N. & Hochedlinger, K. 2011 In : Cell Stem Cell. 9, 4, p. 317 - 329 13 p.

Research output: Contribution to journalArticle

2010

A murine ESC-like state facilitates transgenesis and homologous recombination in human pluripotent stem cells

Buecker, C., Chen, H. H., Polo, J. M., Daheron, L., Bu, L., Barakat, T. S., Okwieka, P., Porter, A., Gribnau, J., Hochedlinger, K. & Geijsen, N. 4 Jun 2010 In : Cell Stem Cell. 6, 6, p. 535-546 12 p.

Research output: Contribution to journalArticle

A Small-Molecule Inhibitor of BCL6 Kills DLBCL Cells In Vitro and In Vivo

Cerchietti, L. C., Ghetu, A. F., Zhu, X-H., Da Silva, G. F., Zhong, S., Matthews, M., Bunting, K. L., Polo, J. M., Farès, C., Arrowsmith, C. H., Yang, S. N., Garcia, M., Coop, A., MacKerell Jr, A. D., Privé, G. G. & Melnick, A. 13 Apr 2010 In : Cancer Cell. 17, 4, p. 400-411 12 p.

Research output: Contribution to journalArticle

BCL6 is critical for the development of a diverse primary B cell repertoire

Duy, C. , Yu, J. J. , Nahar, R. , Swaminathan, S. , Kweon, S. M. , Polo, J. M. , Valls, E. , Klemm, L. , Shojaee, S. , Cerchietti, L. , Schuh, W. , Jäck, H. M. , Hurtz, C. , Ramezani-Rad, P. , Herzog, S. , Jumaa, H. , Koeffler, H. P. , De Alborán, I. M. , Melnick, A. M. , Ye, B. H. & 1 others Müschen, M. 7 Jun 2010 In : Journal of Experimental Medicine. 207, 6, p. 1209-1221 13 p.

Research output: Contribution to journalArticle

Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells

Polo, J. M., Liu, S., Figueroa, M. E., Kulalert, W., Eminli, S., Tan, K. Y., Apostolou, E., Stadtfeld, M., Li, Y., Shioda, T., Natesan, S., Wagers, A. J., Melnick, A., Evans, T. & Hochedlinger, K. Aug 2010 In : Nature Biotechnology. 28, 8, p. 848-855 8 p.

Research output: Contribution to journalArticle

SAFB1 mediates repression of immune regulators and apoptotic genes in breast cancer cells

Hammerich-Hille, S., Kaipparettu, B. A., Tsimelzon, A., Creighton, C. J., Jiang, S., Polo, J. M., Melnick, A., Meyer, R. & Oesterreich, S. 5 Feb 2010 In : Journal of Biological Chemistry. 285, 6, p. 3608-3616 9 p.

Research output: Contribution to journalArticle

When fibroblasts MET iPSCs

Polo, J. M. & Hochedlinger, K. Jul 2010 In : Cell Stem Cell. 7, 1, p. 5-6 2 p.

Research output: Contribution to journalShort Survey

2009

A peptomimetic inhibitor of BCL6 with potent antilymphoma effects in vitro and in vivo

Cerchietti, L. C., Yang, S. N., Shaknovich, R., Hatzi, K., Polo, J. M., Chadburn, A., Dowdy, S. F. & Melnick, A. 9 Apr 2009 In : Blood. 113, 15, p. 3397-3405 9 p.

Research output: Contribution to journalArticle

BCL6 modulates tonic BCR signaling in diffuse large B-cell lymphomas by repressing the SYK phosphatase, PTPROt

Juszczynski, P., Chen, L., O'Donnell, E., Polo, J. M., Ranuncolo, S. M., Dalla-Favera, R., Melnick, A. & Shipp, M. A. 17 Dec 2009 In : Blood. 114, 26, p. 5315-5321 7 p.

Research output: Contribution to journalArticle

Immortalization eliminates a roadblock during cellular reprogramming into iPS cells

Utikal, J., Polo, J. M., Stadtfeld, M., Maherali, N., Kulalert, W., Walsh, R. M., Khalil, A., Rheinwald, J. G. & Hochedlinger, K. 27 Aug 2009 In : Nature. 460, 7259, p. 1145-1148 4 p.

Research output: Contribution to journalArticle

The BCL6 transcriptional program features repression of multiple oncogenes in primary B cells and is deregulated in DLBCL

Ci, W., Polo, J. M., Cerchietti, L., Shaknovich, R., Wang, L., Shao, N. Y., Ye, K., Farinha, P., Horsman, D. E., Gascoyne, R. D., Elemento, O. & Melnick, A. 2009 In : Blood. 113, 22, p. 5536-5548 13 p.

Research output: Contribution to journalArticle

2008

B-cell lymphoma 6 and the molecular pathogenesis of diffuse large B-cell lymphoma

Ci, W., Polo, J. M. & Melnick, A. Jul 2008 In : Current Opinion in Hematology. 15, 4, p. 381-390 10 p.

Research output: Contribution to journalReview Article

BCL6-mediated attenuation of DNA damage sensing triggers growth arrest and senescence through a p53-dependent pathway in a cell context-dependent manner

Ranuncolo, S. M., Wang, L., Polo, J. M., Dell'Oso, T., Dierov, J., Gaymes, T. J., Rassool, F., Carroll, M. & Melnick, A. 15 Aug 2008 In : Journal of Biological Chemistry. 283, 33, p. 22565-22572 8 p.

Research output: Contribution to journalArticle

BCL6 represses CHEK1 and suppresses DNA damage pathways in normal and malignant B-cells

Ranuncolo, S. M., Polo, J. M. & Melnick, A. Jul 2008 In : Blood Cells, Molecules, and Diseases. 41, 1, p. 95-99 5 p.

Research output: Contribution to journalArticle

CtBP is an essential corepressor for BCL6 autoregulation

Mendez, L. M., Polo, J. M., Yu, J. J., Krupski, M., Ding, B. B., Melnick, A. & Ye, B. H. Apr 2008 In : Molecular and Cellular Biology. 28, 7, p. 2175-2186 12 p.

Research output: Contribution to journalArticle