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Research Output 2004 2019

2019
2 Citations (Scopus)

DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns

Skvortsova, K., Masle-Farquhar, E., Luu, P. L., Song, J. Z., Qu, W., Zotenko, E., Gould, C. M., Du, Q., Peters, T. J., Colino-Sanguino, Y., Pidsley, R., Nair, S. S., Khoury, A., Smith, G. C., Miosge, L. A., Reed, J. H., Kench, J. G., Rubin, M. A., Horvath, L., Bogdanovic, O. & 5 others, Lim, S. M., Polo, J. M., Goodnow, C. C., Stirzaker, C. & Clark, S. J., 11 Feb 2019, In : Cancer Cell. 35, 2, p. 297-314 18 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Generation of mouse-induced pluripotent stem cells by lentiviral transduction

Liu, X., Chen, J., Firas, J., Paynter, J. M., Nefzger, C. M. & Polo, J. M., 2019, Mouse Cell Culture: Methods and Protocols. Bertoncello, I. (ed.). New York, NY: Humana Press, p. 63-76 14 p. (Methods in Molecular Biology; vol. 1940).

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

2 Citations (Scopus)

TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network

Seruggia, D., Oti, M., Tripathi, P., Canver, M. C., LeBlanc, L., Di Giammartino, D. C., Bullen, M. J., Nefzger, C. M., Sun, Y. B. Y., Farouni, R., Polo, J. M., Pinello, L., Apostolou, E., Kim, J., Orkin, S. H. & Das, P. P., 20 Jun 2019, In : Molecular Cell. 74, 6, p. 1148-1163 16 p.

Research output: Contribution to journalArticleResearchpeer-review

The application of human pluripotent stem cells to model the neuronal and glial components of neurodevelopmental disorders

Lee, K. M., Hawi, Z. H., Parkington, H. C., Parish, C. L., Kumar, P. V., Polo, J. M., Bellgrove, M. A. & Tong, J., 27 Aug 2019, (Accepted/In press) In : Molecular Psychiatry. 11 p.

Research output: Contribution to journalArticleResearchpeer-review

2018
16 Citations (Scopus)

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

Pflueger, C., Tan, D., Swain, T., Nguyen, T., Pflueger, J., Nefzger, C., Polo, J. M., Ford, E. & Lister, R., 1 Aug 2018, In : Genome Research. 28, 8, p. 1193-1206 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
3 Citations (Scopus)

Fine Tuning of Canonical Wnt Stimulation Enhances Differentiation of Pluripotent Stem Cells Independent of β-Catenin-Mediated T-Cell Factor Signaling

Chen, J., Nefzger, C. M., Rossello, F., Sun, Y. B. Y., Lim, S. M., Liu, X., De Boer, S., Knaupp, A. S., Li, J., Davidson, K. C., Polo, J. M. & Barberi, T., 1 Jun 2018, In : Stem Cells. 36, 6, p. 822-833 12 p.

Research output: Contribution to journalArticleResearchpeer-review

15 Citations (Scopus)

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 journalArticleResearchpeer-review

Open Access
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3 Citations (Scopus)

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., 9 May 2018, In : eLife. 7, 28 p., e37419.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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9 Citations (Scopus)

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 journalArticleResearchpeer-review

2017
15 Citations (Scopus)

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 journalArticleResearchpeer-review

Open Access
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24 Citations (Scopus)

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 journalArticleResearchpeer-review

Open Access
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2 Citations (Scopus)

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 SurveyOtherpeer-review

139 Citations (Scopus)

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 journalArticleResearchpeer-review

19 Citations (Scopus)

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 journalArticleResearchpeer-review

7 Citations (Scopus)

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 journalArticleResearchpeer-review

Open Access
File
2 Citations (Scopus)

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 ArticleOtherpeer-review

30 Citations (Scopus)

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 journalArticleResearchpeer-review

2016
4 Citations (Scopus)

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., Ankö, M-L., Nefzger, C. M. & Polo, J. M., 1 Jul 2016, In : Stem Cell Research. 17, 1, p. 49-53 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
92 Citations (Scopus)

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 journalLetterOtherpeer-review

9 Citations (Scopus)

A Versatile Strategy for Isolating a Highly Enriched Population of Intestinal Stem Cells

Nefzger, C. M., Jarde, T., Rossello, F. J., Horvay, K., Knaupp, A. S., Powell, D. R., Chen, J. Y., Abud, H. E. & Polo, J. M., 2016, In : Stem Cell Reports. 6, 3, p. 321 - 329 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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5 Citations (Scopus)

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 ArticleResearchpeer-review

2015
17 Citations (Scopus)
17 Citations (Scopus)

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 journalArticleResearchpeer-review

Open Access
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2 Citations (Scopus)

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)Otherpeer-review

22 Citations (Scopus)

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 journalArticleResearchpeer-review

Open Access
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14 Citations (Scopus)

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 journalArticleResearchpeer-review

2014
10 Citations (Scopus)

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

Nefzger, C. M., Alaei Shehni, S., Knaupp, A. S., Holmes, M. L. & Polo, J. M., 2014, In : Journal of Visualized Experiments. 91, (Art. No.: e51728), p. 1 - 8 8 p.

Research output: Contribution to journalArticleResearchpeer-review

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 journalArticleOther

12 Citations (Scopus)

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 journalArticleResearchpeer-review

7 Citations (Scopus)

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 / DebateResearchpeer-review

56 Citations (Scopus)

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 journalArticleResearchpeer-review

58 Citations (Scopus)

Phases of reprogramming

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

Research output: Contribution to journalArticleResearchpeer-review

Open Access
4 Citations (Scopus)

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 journalArticleOther

2013
73 Citations (Scopus)

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. DE., 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 journalArticleResearchpeer-review

Open Access
File
79 Citations (Scopus)

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 journalArticleResearchpeer-review

Open Access
119 Citations (Scopus)

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 journalArticleResearchpeer-review

49 Citations (Scopus)

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 journalArticleResearchpeer-review

49 Citations (Scopus)

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 journalArticleResearchpeer-review

Open Access
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2012
484 Citations (Scopus)

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 journalArticleResearchpeer-review

140 Citations (Scopus)

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 journalArticleResearchpeer-review

Open Access
2011
378 Citations (Scopus)

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 journalArticleResearchpeer-review

368 Citations (Scopus)

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 journalArticleResearchpeer-review

2010
158 Citations (Scopus)

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 journalArticleResearchpeer-review

188 Citations (Scopus)

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 journalArticleResearchpeer-review

79 Citations (Scopus)

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 journalArticleResearchpeer-review

804 Citations (Scopus)

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 journalArticleResearchpeer-review

21 Citations (Scopus)

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 journalArticleResearchpeer-review

46 Citations (Scopus)

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 SurveyOtherpeer-review

2009
125 Citations (Scopus)

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 journalArticleResearchpeer-review