Class introduction

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Optional Reading

Ruben, Adam. "How to Read a Scientific Paper." Science Magazine, January 2016. (Accessed November 28, 2017.)


Potency and pluripotent stem cells

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Martin, George R. "Isolation of a Pluripotent Cell Line from Early Mouse Embryos Cultured in Medium Conditioned by Teratocarcinoma Stem Cells." Proceedings of the National Academy of Sciences of the United States of America 78, no. 12 (1981): 7634–38.

Takahashi, Kazutoshi, and Shinya Yamanaka. "Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors." Cell 126, no. 4 (2006): 663–76.


Signatures and mechanisms of pluripotency: Transcriptional networks

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Silva, Jose, Wallace J. Nichols, et al. "Nanog is the Gateway to the Pluripotent Ground State." Cell 138, no. 4 (2009): 722–37.

Ang, Yin-Sin, Sui-Yi Tsai, et al. "Wdr5 Mediates Self–Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network." Cell 145, no. 2 (2011): 183–97.


Signatures and mechanisms of pluripotency: Bivalent chromatin domains

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Bernstein, Bradley E., Tarjei S. Mikkelsen, et al. "A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells." Cell 125, no. 2 (2006): 315–26.

Lesch, Bluma J., Sherman J. Silber, et al. "Parallel Evolution of Male Germline Epigenetic Poising and Somatic Development in Animals." Nature Genetics 48, no. 8 (2016): 888–94.


Germ cell identity

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Ephrussi A., R. Lehmann. "Induction of germ cell formation by oskar." Nature 358(1992): 387–392.

Ohinata, Yasuhide, Hiromichi Ohta, et al. "A Signaling Principle for the Specification of the Germ Cell Lineage in Mice." Cell 137, no. 3 (2009): 571–84.


Reprogramming of germ cells and stem cells

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Tursun, Baris, Tulsi Patel, et al. "Direct Conversion of C. Elegans Germ Cells into Specific Neuron Types." Science 331, no. 6015 (2011): 304–8.

Hayashi, Katsuhiko, Hiromichi Ohta, et al. "Reconstitution of the Mouse Germ Cell Specification Pathway in Culture by Pluripotent Stem Cells." Cell 146, no. 4 (2011): 519–32.


Reprogramming soma by pioneer transcription factors

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Lassar, Andrew B., Bruce M. Paterson, et al. "Transfection of a DNA Locus that Mediates the Conversion of 10T1/2 Fibroblasts to Myoblasts." Cell 47, no. 5 (1986): 649–56.

Wapinski, Orly L., Thomas Vierbuchen, et al. "Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons." Cell 155, no. 3 (2013): 621–35.


Defining hematopoietic identities: Part 1

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Akashi, Koichi, David Traver, et al. "A Clonogenic Common Myeloid Progenitor that Gives Rise to All Myeloid Lineages." Nature 404, no. 6774 (2000): 193–97.

Miyamoto, Toshihiro, Hironori Iwasaki, et al. "Myeloid or Lymphoid Promiscuity as a Critical Step in Hematopoietic Lineage Commitment." Developmental Cell 3, no. 1 (2002): 137–47.


Defining hematopoietic identities: Part 2

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Villani, Alexandra-Chloe, Rahul Satija, et al. "Single–Cell RNA–Seq Reveals New Types of Human Blood Dendritic Cells, Monocytes, and Progenitors." Science 356, no. 6335 (2017): eaah4573.

Velten, Lars, San Francisco Haas, et al. "Human Haematopoietic Stem Cell Lineage Commitment is a Continuous Process." Nature Cell Biology 19, no. 4 (2017): 271–81.


Regulatory mechanisms for immune cell identity: Chromatin and transcription factors

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Rhodes, Jordan, Margaret A. Hagen, et al. "Interplay of Pu.1 and Gata1 Determines Myelo–Erythroid Progenitor Cell Fate in Zebrafish." Developmental Cell 8, no. 1 (2005): 97–108.

Oravecz, Attila, Apostol Apostolov, et al. "Ikaros Mediates Gene Silencing in T cells Through Polycomb Repressive Complex 2." Nature Communications 6, no. 8823 (2015): 1–15.


Regulatory mechanisms for immune cell identity: Cell signaling

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Kikuchi, Kazu, Anne Y. Lai, et al. "IL–7 Receptor Signaling is Necessary for Stage Transition in Adult B Cell Development Through Up–Regulation of EBF." The Journal of Experimental Medicine 201, no. 8 (2005): 1197.

Veldhoen, Marc, Richard J. Hocking, et al. "TGFβ in the Context of an Inflammatory Cytokine Milieu Supports De Novo Differentiation of IL–17–Producing T Cells." Immunity 24, no. 2 (2006): 179–89.


Disorders of cell identity: The reproductive tract and germ cell identity

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Matson, Clinton K., Mark W. Murphy, et al. "DMRT1 Prevents Female Reprogramming in the Postnatal Mammalian Testis." Nature 476, no. 7358 (2011): 101–4.

Unhavaithaya, Y., T. H. Shin, et al. "MEP–1 and a Homolog of the NURD Complex Component Mi–2 Act Together to Maintain Germline–Soma Distinctions in C. Elegans." Cell 111, no. 7 (2002): 991–1002.


Disorders of cell identity: Hematopoiesis

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Mullighan, Charles G., Salil Goorha, et al. "Genome–wide Analysis of Genetic Alterations in Acute Lymphoblastic Leukaemia." Nature 446, no. 7137 (2007): 758–64.

Tremblay, Mathieu, Cedric S. Tremblay, et al. "Modeling T–cell Acute Lymphoblastic Leukemia Induced by the SCL and LMO1 Oncogenes." Genes & Development 24, no. 11 (2010): 1093–105.


Cellular reprogramming and therapeutics

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Pagliuca, Felicia Walton, Jeffrey R. Millman, et al. "Generation of Functional Human Pancreatic β Cells in Vitro." Cell 159, no. 2 (2014): 428–39.

Cao, Nan, Huang Yu, et al. "Conversion of Human Fibroblasts into Functional Cardiomyocytes by Small Molecules." Science 352, no. 6290 (2016): 1216–20.


Oral presentations and evaluations

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