Boland, M.J. et al. Adult mice generated from induced pluripotent stem cells. Nature 461, 91–94 (2009).
Kang, L., Wang, J., Zhang, Y., Kou, Z. & Gao, S. iPS cells can support full-term development of tetraploid blastocyst-complemented embryos. Cell Stem Cell 5, 135–138 (2009).
Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).
Zhao, X.Y. et al. iPS cells produce viable mice through tetraploid complementation. Nature 461, 86–90 (2009).
Ieda, M. et al. Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors. Cell 142, 375–386 (2010).
Jopling, C., Boue, S. & Izpisua Belmonte, J.C. Dedifferentiation, transdifferentiation and reprogramming: three routes to regeneration. Nat. Rev. Mol. Cell Biol. 12, 79–89 (2011).
Tsunemoto, R.K., Eade, K.T., Blanchard, J.W. & Baldwin, K.K. Forward engineering neuronal diversity using direct reprogramming. EMBO J. 34, 1445–1455 (2015).
Vierbuchen, T. et al. Direct conversion of fibroblasts to functional neurons by defined factors. Nature 463, 1035–1041 (2010).
Arkin, M.R., Tang, Y. & Wells, J.A. Small-molecule inhibitors of protein-protein interactions: progressing toward the reality. Chem. Biol. 21, 1102–1114 (2014).
Laraia, L., McKenzie, G., Spring, D.R., Venkitaraman, A.R. & Huggins, D.J. Overcoming chemical, biological, and computational challenges in the development of inhibitors targeting protein-protein interactions. Chem. Biol. 22, 689–703 (2015).
Carey, B.W. et al. Reprogramming factor stoichiometry influences the epigenetic state and biological properties of induced pluripotent stem cells. Cell Stem Cell 9, 588–598 (2011).
Hanna, J. et al. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 462, 595–601 (2009).
Stadtfeld, M., Maherali, N., Borkent, M. & Hochedlinger, K. A reprogrammable mouse strain from gene-targeted embryonic stem cells. Nat. Methods 7, 53–55 (2010).
Ichida, J.K. et al. A small-molecule inhibitor of TGF-β signaling replaces sox2 in reprogramming by inducing NANOG. Cell Stem Cell 5, 491–503 (2009).
Lyssiotis, C.A. et al. Reprogramming of murine fibroblasts to induced pluripotent stem cells with chemical complementation of Klf4. Proc. Natl. Acad. Sci. USA 106, 8912–8917 (2009).
Staerk, J. et al. Pan-Src family kinase inhibitors replace Sox2 during the direct reprogramming of somatic cells. Angew. Chem. Int. Ed. 50, 5734–5736 (2011).
Qin, H. et al. Systematic identification of barriers to human iPSC generation. Cell 158, 449–461 (2014).
Borkent, M. et al. A serial shRNA screen for roadblocks to reprogramming identifies the protein modifier SUMO2. Stem Cell Rep. 6, 704–716 (2016).
Melidoni, A.N., Dyson, M.R., Wormald, S. & McCafferty, J. Selecting antagonistic antibodies that control differentiation through inducible expression in embryonic stem cells. Proc. Natl. Acad. Sci. USA 110, 17802–17807 (2013).
Xie, J., Zhang, H., Yea, K. & Lerner, R.A. Autocrine signaling based selection of combinatorial antibodies that transdifferentiate human stem cells. Proc. Natl. Acad. Sci. USA 110, 8099–8104 (2013).
Zhang, H., Wilson, I.A. & Lerner, R.A. Selection of antibodies that regulate phenotype from intracellular combinatorial antibody libraries. Proc. Natl. Acad. Sci. USA 109, 15728–15733 (2012).
Zhang, H. et al. Selecting agonists from single cells infected with combinatorial antibody libraries. Chem. Biol. 20, 734–741 (2013).
Zhang, H., Xie, J. & Lerner, R.A. A proximity based general method for identification of ligand and receptor interactions in living cells. Biochem. Biophys. Res. Commun. 454, 251–255 (2014).
Liu, T. et al. Construction and screening of a lentiviral secretome library. Cell Chem. Biol. 24, 767–771.e3 (2017).
Stadtfeld, M., Maherali, N., Breault, D.T. & Hochedlinger, K. Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell 2, 230–240 (2008).
Hou, P. et al. Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science 341, 651–654 (2013).
Radzisheuskaya, A. & Silva, J.C. Do all roads lead to Oct4? the emerging concepts of induced pluripotency. Trends Cell Biol. 24, 275–284 (2014).
Hazen, J.L. et al. The complete genome sequences, unique mutational spectra, and developmental potency of adult neurons revealed by cloning. Neuron 89, 1223–1236 (2016).
Maherali, N. & Hochedlinger, K. Tgfbeta signal inhibition cooperates in the induction of iPSCs and replaces Sox2 and cMyc. Curr. Biol. 19, 1718–1723 (2009).
Shu, J. et al. Induction of pluripotency in mouse somatic cells with lineage specifiers. Cell 153, 963–975 (2013).
Korshunova, I. et al. Characterization of BASP1-mediated neurite outgrowth. J. Neurosci. Res. 86, 2201–2213 (2008).
Maekawa, S., Maekawa, M., Hattori, S. & Nakamura, S. Purification and molecular cloning of a novel acidic calmodulin binding protein from rat brain. J. Biol. Chem. 268, 13703–13709 (1993).
Mosevitsky, M.I. et al. The BASP1 family of myristoylated proteins abundant in axonal termini. Primary structure analysis and physico-chemical properties. Biochimie 79, 373–384 (1997).
Hu, X. et al. Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell 14, 512–522 (2014).
Li, R. et al. A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell 7, 51–63 (2010).
Carpenter, B. et al. BASP1 is a transcriptional cosuppressor for the Wilms' tumor suppressor protein WT1. Mol. Cell. Biol. 24, 537–549 (2004).
Toska, E. et al. Repression of transcription by WT1-BASP1 requires the myristoylation of BASP1 and the PIP2-dependent recruitment of histone deacetylase. Cell Rep. 2, 462–469 (2012).
Huang, S. Reprogramming cell fates: reconciling rarity with robustness. BioEssays 31, 546–560 (2009).
Buganim, Y. et al. Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. Cell 150, 1209–1222 (2012).
Buganim, Y. et al. The developmental potential of iPSCs is greatly influenced by reprogramming factor selection. Cell Stem Cell 15, 295–309 (2014).
Feng, B. et al. Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. Nat. Cell Biol. 11, 197–203 (2009).
Motamedi, F.J. et al. WT1 controls antagonistic FGF and BMP-pSMAD pathways in early renal progenitors. Nat. Commun. 5, 4444 (2014).
Melidoni, A.N., Dyson, M.R. & McCafferty, J. Selection of antibodies interfering with cell surface receptor signaling using embryonic stem cell differentiation. Methods Mol. Biol. 1341, 111–132 (2015).
Schlaeger, T.M. et al. A comparison of non-integrating reprogramming methods. Nat. Biotechnol. 33, 58–63 (2015).
Imai, K. & Takaoka, A. Comparing antibody and small-molecule therapies for cancer. Nat. Rev. Cancer 6, 714–727 (2006).
Blanchard, J.W. et al. Selective conversion of fibroblasts into peripheral sensory neurons. Nat. Neurosci. 18, 25–35 (2015).
Bolger, A.M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Anders, S., Pyl, P.T. & Huber, W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).