TY - JOUR AU - Hansson, J. AU - Rafiee, M. R. AU - Reiland, S. AU - Polo, J. M. AU - Gehring, J. AU - Okawa, S. PY - 2012 DA - 2012// TI - Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency JO - Cell Rep VL - 2 UR - https://doi.org/10.1016/j.celrep.2012.10.014 DO - 10.1016/j.celrep.2012.10.014 ID - Hansson2012 ER - TY - JOUR AU - Benevento, M. AU - Tonge, P. D. AU - Puri, M. C. AU - Hussein, S. M. I. AU - Cloonan, N. AU - Wood, D. L. PY - 2014 DA - 2014// TI - Proteome adaptation in cell reprogramming proceeds via distinct transcriptional networks JO - Nat Commun VL - 5 UR - https://doi.org/10.1038/ncomms6613 DO - 10.1038/ncomms6613 ID - Benevento2014 ER - TY - JOUR AU - Polo, J. M. AU - Endre, A. AU - Walsh, R. M. AU - Schwarz, B. A. AU - Nefzger, C. M. AU - Lim, S. M. PY - 2012 DA - 2012// TI - A molecular roadmap of reprogramming somatic cells into iPS cells JO - Cell VL - 151 UR - https://doi.org/10.1016/j.cell.2012.11.039 DO - 10.1016/j.cell.2012.11.039 ID - Polo2012 ER - TY - JOUR AU - Clancy, J. L. AU - Patel, H. R. AU - Hussein, S. M. I. AU - Tonge, P. D. AU - Cloonan, N. AU - Corso, A. J. PY - 2014 DA - 2014// TI - Small RNA changes en route to distinct cellular states of induced pluripotency JO - Nat Commun VL - 5 UR - https://doi.org/10.1038/ncomms6522 DO - 10.1038/ncomms6522 ID - Clancy2014 ER - TY - JOUR AU - Tonge, P. D. AU - Corso, A. J. AU - Monetti, C. AU - Hussein, S. M. I. AU - Puri, M. C. AU - Michael, I. P. PY - 2014 DA - 2014// TI - Divergent reprogramming routes lead to alternative stem-cell states JO - Nature VL - 516 UR - https://doi.org/10.1038/nature14047 DO - 10.1038/nature14047 ID - Tonge2014 ER - TY - JOUR AU - Hussein, S. M. I. AU - Puri, M. C. AU - Tonge, P. D. AU - Benevento, M. AU - Corso, A. J. AU - Clancy, J. L. PY - 2014 DA - 2014// TI - Genome-wide characterization of the routes to pluripotency JO - Nature VL - 516 UR - https://doi.org/10.1038/nature14046 DO - 10.1038/nature14046 ID - Hussein2014 ER - TY - JOUR AU - Lee, D. -. S. AU - Shin, J. -. Y. AU - Tonge, P. D. AU - Puri, M. C. AU - Lee, S. AU - Park, H. PY - 2014 DA - 2014// TI - An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator JO - Nat Commun VL - 5 UR - https://doi.org/10.1038/ncomms6619 DO - 10.1038/ncomms6619 ID - Lee2014 ER - TY - JOUR AU - Goldberg, A. D. AU - Allis, C. D. AU - Bernstein, E. PY - 2007 DA - 2007// TI - Epigenetics: a landscape takes shape JO - Cell VL - 128 UR - https://doi.org/10.1016/j.cell.2007.02.006 DO - 10.1016/j.cell.2007.02.006 ID - Goldberg2007 ER - TY - JOUR AU - Cahan, P. AU - Li, H. AU - Morris, S. A. AU - Lummertz da Rocha, E. AU - Daley, G. Q. AU - Collins, J. J. PY - 2014 DA - 2014// TI - CellNet: Network Biology Applied to Stem Cell Engineering JO - Cell VL - 158 UR - https://doi.org/10.1016/j.cell.2014.07.020 DO - 10.1016/j.cell.2014.07.020 ID - Cahan2014 ER - TY - JOUR AU - Rackham, O. J. L. AU - Firas, J. AU - Fang, H. AU - Oates, M. E. AU - Holmes, M. L. AU - Knaupp, A. S. PY - 2016 DA - 2016// TI - A predictive computational framework for direct reprogramming between human cell types JO - Nat Genet VL - 48 UR - https://doi.org/10.1038/ng.3487 DO - 10.1038/ng.3487 ID - Rackham2016 ER - TY - JOUR AU - Samavarchi-Tehrani, P. AU - Payman, S. -. T. AU - Azadeh, G. AU - Laurent, D. AU - Hoon-ki, S. AU - Beyer, T. A. PY - 2010 DA - 2010// TI - Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming JO - Cell Stem Cell VL - 7 UR - https://doi.org/10.1016/j.stem.2010.04.015 DO - 10.1016/j.stem.2010.04.015 ID - Samavarchi-Tehrani2010 ER - TY - JOUR AU - Zavolan, M. AU - Kanitz, A. PY - 2017 DA - 2017// TI - RNA splicing and its connection with other regulatory layers in somatic cell reprogramming JO - Curr Opin Cell Biol VL - 52 UR - https://doi.org/10.1016/j.ceb.2017.12.002 DO - 10.1016/j.ceb.2017.12.002 ID - Zavolan2017 ER - TY - JOUR AU - Brown, R. L. AU - Reinke, L. M. AU - Damerow, M. S. AU - Perez, D. AU - Chodosh, L. A. AU - Yang, J. PY - 2011 DA - 2011// TI - CD44 splice isoform switching in human and mouse epithelium is essential for epithelial-mesenchymal transition and breast cancer progression JO - J Clin Invest VL - 121 UR - https://doi.org/10.1172/JCI44540 DO - 10.1172/JCI44540 ID - Brown2011 ER - TY - JOUR AU - Warzecha, C. C. AU - Sato, T. K. AU - Nabet, B. AU - Hogenesch, J. B. AU - Carstens, R. P. PY - 2009 DA - 2009// TI - ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing JO - Mol Cell VL - 33 UR - https://doi.org/10.1016/j.molcel.2009.01.025 DO - 10.1016/j.molcel.2009.01.025 ID - Warzecha2009 ER - TY - JOUR AU - Cieply, B. AU - Park, J. W. AU - Nakauka-Ddamba, A. AU - Bebee, T. W. AU - Guo, Y. AU - Shang, X. PY - 2016 DA - 2016// TI - Multiphasic and dynamic changes in alternative splicing during induction of pluripotency are coordinated by numerous RNA-binding proteins JO - Cell Rep VL - 15 UR - https://doi.org/10.1016/j.celrep.2016.03.025 DO - 10.1016/j.celrep.2016.03.025 ID - Cieply2016 ER - TY - JOUR AU - Kim, Y. -. D. AU - Kim, H. -. S. AU - Lee, J. AU - Choi, J. -. K. AU - Han, E. AU - Eun Jeong, J. PY - 2018 DA - 2018// TI - ESRP1-induced CD44 v3 is important for controlling pluripotency in human pluripotent stem cells JO - Stem Cells VL - 36 UR - https://doi.org/10.1002/stem.2864 DO - 10.1002/stem.2864 ID - Kim2018 ER - TY - STD TI - Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, et al. Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. elife. 2016;5. https://doi.org/10.7554/eLife.16797. ID - ref17 ER - TY - JOUR AU - Ghule, P. N. AU - Medina, R. AU - Lengner, C. J. AU - Mandeville, M. AU - Qiao, M. AU - Dominski, Z. PY - 2011 DA - 2011// TI - Reprogramming the pluripotent cell cycle: restoration of an abbreviated G1 phase in human induced pluripotent stem (iPS) cells JO - J Cell Physiol VL - 226 UR - https://doi.org/10.1002/jcp.22440 DO - 10.1002/jcp.22440 ID - Ghule2011 ER - TY - JOUR AU - Ruiz, S. AU - Panopoulos, A. D. AU - Herrerías, A. AU - Bissig, K. -. D. AU - Lutz, M. AU - Berggren, W. T. PY - 2011 DA - 2011// TI - A high proliferation rate is required for cell reprogramming and maintenance of human embryonic stem cell identity JO - Curr Biol VL - 21 UR - https://doi.org/10.1016/j.cub.2010.11.049 DO - 10.1016/j.cub.2010.11.049 ID - Ruiz2011 ER - TY - JOUR AU - Roccio, M. AU - Schmitter, D. AU - Knobloch, M. AU - Okawa, Y. AU - Sage, D. AU - Lutolf, M. P. PY - 2013 DA - 2013// TI - Predicting stem cell fate changes by differential cell cycle progression patterns JO - Development VL - 140 UR - https://doi.org/10.1242/dev.086215 DO - 10.1242/dev.086215 ID - Roccio2013 ER - TY - JOUR AU - Abyzov, A. AU - Mariani, J. AU - Palejev, D. AU - Zhang, Y. AU - Haney, M. S. AU - Tomasini, L. PY - 2012 DA - 2012// TI - Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells JO - Nature VL - 492 UR - https://doi.org/10.1038/nature11629 DO - 10.1038/nature11629 ID - Abyzov2012 ER - TY - JOUR AU - Kodama, Y. AU - Shumway, M. AU - Leinonen, R. PY - 2012 DA - 2012// TI - The Sequence Read Archive: explosive growth of sequencing data JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr854 DO - 10.1093/nar/gkr854 ID - Kodama2012 ER - TY - JOUR AU - Han, H. AU - Irimia, M. AU - Ross, P. J. AU - Sung, H. -. K. AU - Alipanahi, B. AU - David, L. PY - 2013 DA - 2013// TI - MBNL proteins repress ES-cell-specific alternative splicing and reprogramming JO - Nature VL - 498 UR - https://doi.org/10.1038/nature12270 DO - 10.1038/nature12270 ID - Han2013 ER - TY - JOUR AU - Lu, X. AU - Göke, J. AU - Sachs, F. AU - Jacques, P. -. É. AU - Liang, H. AU - Feng, B. PY - 2013 DA - 2013// TI - SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells JO - Nat Cell Biol VL - 15 UR - https://doi.org/10.1038/ncb2839 DO - 10.1038/ncb2839 ID - Lu2013 ER - TY - JOUR AU - Ohta, S. AU - Nishida, E. AU - Yamanaka, S. AU - Yamamoto, T. PY - 2013 DA - 2013// TI - Global splicing pattern reversion during somatic cell reprogramming JO - Cell Rep VL - 5 UR - https://doi.org/10.1016/j.celrep.2013.09.016 DO - 10.1016/j.celrep.2013.09.016 ID - Ohta2013 ER - TY - JOUR AU - Venables, J. P. AU - Lapasset, L. AU - Gadea, G. AU - Fort, P. AU - Klinck, R. AU - Irimia, M. PY - 2013 DA - 2013// TI - MBNL1 and RBFOX2 cooperate to establish a splicing programme involved in pluripotent stem cell differentiation JO - Nat Commun VL - 4 UR - https://doi.org/10.1038/ncomms3480 DO - 10.1038/ncomms3480 ID - Venables2013 ER - TY - JOUR AU - Lu, Y. AU - Loh, Y. -. H. AU - Li, H. AU - Cesana, M. AU - Ficarro, S. B. AU - Parikh, J. R. PY - 2014 DA - 2014// TI - Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells JO - Cell Stem Cell VL - 15 UR - https://doi.org/10.1016/j.stem.2014.04.002 DO - 10.1016/j.stem.2014.04.002 ID - Lu2014 ER - TY - JOUR AU - Cacchiarelli, D. AU - Trapnell, C. AU - Ziller, M. J. AU - Soumillon, M. AU - Cesana, M. AU - Karnik, R. PY - 2015 DA - 2015// TI - Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency JO - Cell VL - 162 UR - https://doi.org/10.1016/j.cell.2015.06.016 DO - 10.1016/j.cell.2015.06.016 ID - Cacchiarelli2015 ER - TY - JOUR AU - Castello, A. AU - Fischer, B. AU - Eichelbaum, K. AU - Horos, R. AU - Beckmann, B. M. AU - Strein, C. PY - 2012 DA - 2012// TI - Insights into RNA biology from an atlas of mammalian mRNA-binding proteins JO - Cell VL - 149 UR - https://doi.org/10.1016/j.cell.2012.04.031 DO - 10.1016/j.cell.2012.04.031 ID - Castello2012 ER - TY - JOUR AU - Dagher, S. F. AU - Wang, J. L. AU - Patterson, R. J. PY - 1995 DA - 1995// TI - Identification of galectin-3 as a factor in pre-mRNA splicing JO - Proc Natl Acad Sci U S A VL - 92 UR - https://doi.org/10.1073/pnas.92.4.1213 DO - 10.1073/pnas.92.4.1213 ID - Dagher1995 ER - TY - JOUR AU - Uhlén, M. AU - Fagerberg, L. AU - Hallström, B. M. AU - Lindskog, C. AU - Oksvold, P. AU - Mardinoglu, A. PY - 2015 DA - 2015// TI - Proteomics. Tissue-based map of the human proteome JO - Science VL - 347 UR - https://doi.org/10.1126/science.1260419 DO - 10.1126/science.1260419 ID - Uhlén2015 ER - TY - JOUR AU - Yu, J. AU - Vodyanik, M. A. AU - Smuga-Otto, K. AU - Antosiewicz-Bourget, J. AU - Frane, J. L. AU - Tian, S. PY - 2007 DA - 2007// TI - Induced pluripotent stem cell lines derived from human somatic cells JO - Science VL - 318 UR - https://doi.org/10.1126/science.1151526 DO - 10.1126/science.1151526 ID - Yu2007 ER - TY - JOUR AU - Zhang, J. AU - Ratanasirintrawoot, S. AU - Chandrasekaran, S. AU - Wu, Z. AU - Ficarro, S. B. AU - Yu, C. PY - 2016 DA - 2016// TI - LIN28 regulates stem cell metabolism and conversion to primed pluripotency JO - Cell Stem Cell VL - 19 UR - https://doi.org/10.1016/j.stem.2016.05.009 DO - 10.1016/j.stem.2016.05.009 ID - Zhang2016 ER - TY - JOUR AU - Chambers, I. AU - Silva, J. AU - Colby, D. AU - Nichols, J. AU - Nijmeijer, B. AU - Robertson, M. PY - 2007 DA - 2007// TI - Nanog safeguards pluripotency and mediates germline development JO - Nature VL - 450 UR - https://doi.org/10.1038/nature06403 DO - 10.1038/nature06403 ID - Chambers2007 ER - TY - JOUR AU - Li, R. AU - Ronghui, L. AU - Jialiang, L. AU - Su, N. AU - Ting, Z. AU - Xiaobing, Q. PY - 2010 DA - 2010// TI - A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts JO - Cell Stem Cell VL - 7 UR - https://doi.org/10.1016/j.stem.2010.04.014 DO - 10.1016/j.stem.2010.04.014 ID - Li2010 ER - TY - JOUR AU - O’Malley, J. AU - Skylaki, S. AU - Iwabuchi, K. A. AU - Chantzoura, E. AU - Ruetz, T. AU - Johnsson, A. PY - 2013 DA - 2013// TI - High-resolution analysis with novel cell-surface markers identifies routes to iPS cells JO - Nature VL - 499 UR - https://doi.org/10.1038/nature12243 DO - 10.1038/nature12243 ID - O’Malley2013 ER - TY - JOUR AU - Huang, R. Y. -. J. AU - Guilford, P. AU - Thiery, J. P. PY - 2012 DA - 2012// TI - Early events in cell adhesion and polarity during epithelial-mesenchymal transition JO - J Cell Sci VL - 125 UR - https://doi.org/10.1242/jcs.099697 DO - 10.1242/jcs.099697 ID - Huang2012 ER - TY - JOUR AU - Ishii, H. AU - Saitoh, M. AU - Sakamoto, K. AU - Kondo, T. AU - Katoh, R. PY - 2014 DA - 2014// TI - Epithelial splicing regulatory protein 1 (ESRP1) and 2 (ESRP2) suppress cancer cell motility via different mechanisms JO - J Bio Chem VL - 289 UR - https://doi.org/10.1074/jbc.M114.589432 DO - 10.1074/jbc.M114.589432 ID - Ishii2014 ER - TY - STD TI - Bebee TW, Park JW, Sheridan KI, Warzecha CC, Cieply BW, Rohacek AM, et al. The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development. elife. 2015;4. https://doi.org/10.7554/eLife.08954. ID - ref39 ER - TY - JOUR AU - Barbosa-Morais, N. L. AU - Irimia, M. AU - Pan, Q. AU - Xiong, H. Y. AU - Gueroussov, S. AU - Lee, L. J. PY - 2012 DA - 2012// TI - The evolutionary landscape of alternative splicing in vertebrate species JO - Science VL - 338 UR - https://doi.org/10.1126/science.1230612 DO - 10.1126/science.1230612 ID - Barbosa-Morais2012 ER - TY - JOUR AU - Yeo, G. W. AU - Nostrand, E. AU - Holste, D. AU - Poggio, T. AU - Burge, C. B. PY - 2005 DA - 2005// TI - Identification and analysis of alternative splicing events conserved in human and mouse JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0409742102 DO - 10.1073/pnas.0409742102 ID - Yeo2005 ER - TY - JOUR AU - Szklarczyk, D. AU - Franceschini, A. AU - Wyder, S. AU - Forslund, K. AU - Heller, D. AU - Huerta-Cepas, J. PY - 2015 DA - 2015// TI - STRING v10: protein-protein interaction networks, integrated over the tree of life JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1003 DO - 10.1093/nar/gku1003 ID - Szklarczyk2015 ER - TY - JOUR AU - Kanitz, A. AU - Gypas, F. AU - Gruber, A. J. AU - Gruber, A. R. AU - Martin, G. AU - Zavolan, M. PY - 2015 DA - 2015// TI - Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0702-5 DO - 10.1186/s13059-015-0702-5 ID - Kanitz2015 ER - TY - JOUR AU - Thomson, J. A. AU - Itskovitz-Eldor, J. AU - Shapiro, S. S. AU - Waknitz, M. A. AU - Swiergiel, J. J. AU - Marshall, V. S. PY - 1998 DA - 1998// TI - Embryonic stem cell lines derived from human blastocysts JO - Science VL - 282 UR - https://doi.org/10.1126/science.282.5391.1145 DO - 10.1126/science.282.5391.1145 ID - Thomson1998 ER - TY - JOUR AU - Takahashi, K. AU - Yamanaka, S. PY - 2006 DA - 2006// TI - Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors JO - Cell VL - 126 UR - https://doi.org/10.1016/j.cell.2006.07.024 DO - 10.1016/j.cell.2006.07.024 ID - Takahashi2006 ER - TY - JOUR AU - Takahashi, K. AU - Tanabe, K. AU - Ohnuki, M. AU - Narita, M. AU - Ichisaka, T. AU - Tomoda, K. PY - 2007 DA - 2007// TI - Induction of pluripotent stem cells from adult human fibroblasts by defined factors JO - Cell VL - 131 UR - https://doi.org/10.1016/j.cell.2007.11.019 DO - 10.1016/j.cell.2007.11.019 ID - Takahashi2007 ER - TY - JOUR AU - Scudellari, M. PY - 2016 DA - 2016// TI - How iPS cells changed the world JO - Nature VL - 534 UR - https://doi.org/10.1038/534310a DO - 10.1038/534310a ID - Scudellari2016 ER - TY - JOUR AU - Avior, Y. AU - Sagi, I. AU - Benvenisty, N. PY - 2016 DA - 2016// TI - Pluripotent stem cells in disease modelling and drug discovery JO - Nat Rev Mol Cell Biol. VL - 17 UR - https://doi.org/10.1038/nrm.2015.27 DO - 10.1038/nrm.2015.27 ID - Avior2016 ER - TY - JOUR AU - Takagi, R. AU - Ishimaru, J. AU - Sugawara, A. AU - Koh-ei, T. AU - Ishida, K. AU - Ogawa, M. PY - 2016 DA - 2016// TI - Bioengineering a 3D integumentary organ system from iPS cells using an in vivo transplantation model JO - Sci Adv VL - 2 UR - https://doi.org/10.1126/sciadv.1500887 DO - 10.1126/sciadv.1500887 ID - Takagi2016 ER - TY - JOUR AU - Qian, X. AU - Nguyen, H. N. AU - Song, M. M. AU - Hadiono, C. AU - Ogden, S. C. AU - Hammack, C. PY - 2016 DA - 2016// TI - Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure JO - Cell VL - 165 UR - https://doi.org/10.1016/j.cell.2016.04.032 DO - 10.1016/j.cell.2016.04.032 ID - Qian2016 ER - TY - JOUR AU - Bershteyn, M. AU - Nowakowski, T. J. AU - Pollen, A. A. AU - Lullo, E. AU - Nene, A. AU - Wynshaw-Boris, A. PY - 2017 DA - 2017// TI - Human iPSC-Derived Cerebral Organoids Model Cellular Features of Lissencephaly and Reveal Prolonged Mitosis of Outer Radial Glia JO - Cell Stem Cell VL - 20 UR - https://doi.org/10.1016/j.stem.2016.12.007 DO - 10.1016/j.stem.2016.12.007 ID - Bershteyn2017 ER - TY - JOUR AU - Kamao, H. AU - Hiroyuki, K. AU - Michiko, M. AU - Satoshi, O. AU - Noriko, S. AU - Akiko, S. PY - 2014 DA - 2014// TI - Characterization of human induced pluripotent stem cell-derived retinal pigment epithelium cell sheets aiming for clinical application JO - Stem Cell Rep VL - 2 UR - https://doi.org/10.1016/j.stemcr.2013.12.007 DO - 10.1016/j.stemcr.2013.12.007 ID - Kamao2014 ER - TY - JOUR AU - Trounson, A. AU - DeWitt, N. D. PY - 2016 DA - 2016// TI - Pluripotent stem cells progressing to the clinic JO - Nat Rev Mol Cell Biol VL - 17 UR - https://doi.org/10.1038/nrm.2016.10 DO - 10.1038/nrm.2016.10 ID - Trounson2016 ER - TY - JOUR AU - Cyranoski, D. PY - 2014 DA - 2014// TI - Stem cells: the black box of reprogramming JO - Nature VL - 516 UR - https://doi.org/10.1038/516162a DO - 10.1038/516162a ID - Cyranoski2014 ER - TY - JOUR AU - Silva, J. AU - Barrandon, O. AU - Nichols, J. AU - Kawaguchi, J. AU - Theunissen, T. W. AU - Smith, A. PY - 2008 DA - 2008// TI - Promotion of reprogramming to ground state pluripotency by signal inhibition JO - PLoS Biol VL - 6 UR - https://doi.org/10.1371/journal.pbio.0060253 DO - 10.1371/journal.pbio.0060253 ID - Silva2008 ER - TY - JOUR AU - Esteban, M. A. AU - Wang, T. AU - Qin, B. AU - Yang, J. AU - Qin, D. AU - Cai, J. PY - 2010 DA - 2010// TI - Vitamin C enhances the generation of mouse and human induced pluripotent stem cells JO - Cell Stem Cell VL - 6 UR - https://doi.org/10.1016/j.stem.2009.12.001 DO - 10.1016/j.stem.2009.12.001 ID - Esteban2010 ER - TY - JOUR AU - Wang, T. AU - Chen, K. AU - Zeng, X. AU - Yang, J. AU - Wu, Y. AU - Shi, X. PY - 2011 DA - 2011// TI - The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner JO - Cell Stem Cell VL - 9 UR - https://doi.org/10.1016/j.stem.2011.10.005 DO - 10.1016/j.stem.2011.10.005 ID - Wang2011 ER - TY - JOUR AU - Chen, J. AU - Guo, L. AU - Zhang, L. AU - Wu, H. AU - Yang, J. AU - Liu, H. PY - 2013 DA - 2013// TI - Vitamin C modulates TET1 function during somatic cell reprogramming JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2807 DO - 10.1038/ng.2807 ID - Chen2013 ER - TY - JOUR AU - Subramanyam, D. AU - Lamouille, S. AU - Judson, R. L. AU - Liu, J. Y. AU - Bucay, N. AU - Derynck, R. PY - 2011 DA - 2011// TI - Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells JO - Nat Biotechnol VL - 29 UR - https://doi.org/10.1038/nbt.1862 DO - 10.1038/nbt.1862 ID - Subramanyam2011 ER - TY - JOUR AU - Sinkkonen, L. AU - Hugenschmidt, T. AU - Berninger, P. AU - Gaidatzis, D. AU - Mohn, F. AU - Artus-Revel, C. G. PY - 2008 DA - 2008// TI - MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells JO - Nat Struct Mol Biol VL - 15 UR - https://doi.org/10.1038/nsmb.1391 DO - 10.1038/nsmb.1391 ID - Sinkkonen2008 ER - TY - JOUR AU - Benetti, R. AU - Gonzalo, S. AU - Jaco, I. AU - Muñoz, P. AU - Gonzalez, S. AU - Schoeftner, S. PY - 2008 DA - 2008// TI - A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases JO - Nat Struct Mol Biol VL - 15 UR - https://doi.org/10.1038/nsmb.1399 DO - 10.1038/nsmb.1399 ID - Benetti2008 ER - TY - JOUR AU - Gruber, A. J. AU - Grandy, W. A. AU - Balwierz, P. J. AU - Dimitrova, Y. A. AU - Pachkov, M. AU - Ciaudo, C. PY - 2014 DA - 2014// TI - Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku544 DO - 10.1093/nar/gku544 ID - Gruber2014 ER - TY - JOUR AU - Gruber, A. J. AU - Zavolan, M. PY - 2013 DA - 2013// TI - Modulation of epigenetic regulators and cell fate decisions by miRNAs JO - Epigenomics VL - 5 UR - https://doi.org/10.2217/epi.13.65 DO - 10.2217/epi.13.65 ID - Gruber2013 ER - TY - JOUR AU - Atlasi, Y. AU - Mowla, S. J. AU - Ziaee, S. A. M. AU - Gokhale, P. J. AU - Andrews, P. W. PY - 2008 DA - 2008// TI - OCT4 spliced variants are differentially expressed in human pluripotent and nonpluripotent cells JO - Stem Cells VL - 26 UR - https://doi.org/10.1634/stemcells.2008-0530 DO - 10.1634/stemcells.2008-0530 ID - Atlasi2008 ER - TY - JOUR AU - Das, S. AU - Jena, S. AU - Levasseur, D. N. PY - 2011 DA - 2011// TI - Alternative splicing produces Nanog protein variants with different capacities for self-renewal and pluripotency in embryonic stem cells JO - J Biol Chem VL - 286 UR - https://doi.org/10.1074/jbc.M111.290189 DO - 10.1074/jbc.M111.290189 ID - Das2011 ER - TY - JOUR AU - Toh, C. -. X. D. AU - Chan, J. -. W. AU - Chong, Z. -. S. AU - Wang, H. F. AU - Guo, H. C. AU - Satapathy, S. PY - 2016 DA - 2016// TI - RNAi reveals phase-specific global regulators of human somatic cell reprogramming JO - Cell Rep VL - 15 UR - https://doi.org/10.1016/j.celrep.2016.05.049 DO - 10.1016/j.celrep.2016.05.049 ID - Toh2016 ER - TY - JOUR AU - Gabut, M. AU - Samavarchi-Tehrani, P. AU - Wang, X. AU - Slobodeniuc, V. AU - O’Hanlon, D. AU - Sung, H. -. K. PY - 2011 DA - 2011// TI - An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming JO - Cell VL - 147 UR - https://doi.org/10.1016/j.cell.2011.08.023 DO - 10.1016/j.cell.2011.08.023 ID - Gabut2011 ER - TY - JOUR AU - Nichols, J. AU - Smith, A. PY - 2009 DA - 2009// TI - Naive and primed pluripotent states JO - Cell Stem Cell VL - 4 UR - https://doi.org/10.1016/j.stem.2009.05.015 DO - 10.1016/j.stem.2009.05.015 ID - Nichols2009 ER - TY - JOUR AU - Barrett, T. AU - Wilhite, S. E. AU - Ledoux, P. AU - Evangelista, C. AU - Kim, I. F. AU - Tomashevsky, M. PY - 2013 DA - 2013// TI - NCBI GEO: archive for functional genomics data sets--update JO - Nucleic Acids Res VL - 41 ID - Barrett2013 ER - TY - JOUR AU - Yates, A. AU - Akanni, W. AU - Amode, M. R. AU - Barrell, D. AU - Billis, K. AU - Carvalho-Silva, D. PY - 2016 DA - 2016// TI - Ensembl 2016 JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1157 DO - 10.1093/nar/gkv1157 ID - Yates2016 ER - TY - STD TI - SRA Tools. Github. https://github.com/ncbi/sra-tools. Accessed 12 June 2017. UR - https://github.com/ncbi/sra-tools ID - ref71 ER - TY - JOUR AU - Weinstein, J. N. AU - Collisson, E. A. AU - Mills, G. B. AU - Shaw, K. R. M. AU - Ozenberger, B. A. AU - Ellrott, K. PY - 2013 DA - 2013// TI - The cancer genome atlas pan-cancer analysis project JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2764 DO - 10.1038/ng.2764 ID - Weinstein2013 ER - TY - STD TI - FireBrowse. Broad Institute of MIT and Harvard. http://firebrowse.org/. doi:https://doi.org/10.7908/C11G0KM9. Accessed: 30 Nov 2017. UR - http://firebrowse.org ID - ref73 ER - TY - JOUR AU - Dobin, A. AU - Davis, C. A. AU - Schlesinger, F. AU - Drenkow, J. AU - Zaleski, C. AU - Jha, S. PY - 2013 DA - 2013// TI - STAR: ultrafast universal RNA-seq aligner JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts635 DO - 10.1093/bioinformatics/bts635 ID - Dobin2013 ER - TY - JOUR AU - Bray, N. L. AU - Pimentel, H. AU - Melsted, P. AU - Pachter, L. PY - 2016 DA - 2016// TI - Near-optimal probabilistic RNA-seq quantification JO - Nat Biotechnol VL - 34 UR - https://doi.org/10.1038/nbt.3519 DO - 10.1038/nbt.3519 ID - Bray2016 ER - TY - JOUR AU - Alamancos, G. P. AU - Pagès, A. AU - Trincado, J. L. AU - Bellora, N. AU - Eyras, E. PY - 2015 DA - 2015// TI - Leveraging transcript quantification for fast computation of alternative splicing profiles JO - RNA VL - 21 UR - https://doi.org/10.1261/rna.051557.115 DO - 10.1261/rna.051557.115 ID - Alamancos2015 ER - TY - JOUR AU - Martin, M. PY - 2011 DA - 2011// TI - Cutadapt removes adapter sequences from high-throughput sequencing reads JO - EMBnet j VL - 17 UR - https://doi.org/10.14806/ej.17.1.200 DO - 10.14806/ej.17.1.200 ID - Martin2011 ER - TY - JOUR AU - Ovaska, K. AU - Laakso, M. AU - Haapa-Paananen, S. AU - Louhimo, R. AU - Chen, P. AU - Aittomäki, V. PY - 2010 DA - 2010// TI - Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme JO - Genome Med VL - 2 UR - https://doi.org/10.1186/gm186 DO - 10.1186/gm186 ID - Ovaska2010 ER - TY - STD TI - Kanitz A, Syed AP, Kaji K, Zavolan M. Conserved regulation of RNA processing in somatic cell reprogramming – supplementary data; 2018. https://doi.org/10.5281/zenodo.1193699. ID - ref79 ER - TY - JOUR AU - Soneson, C. AU - Love, M. I. AU - Robinson, M. D. PY - 2015 DA - 2015// TI - Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences JO - F1000Res VL - 4 UR - https://doi.org/10.12688/f1000research.7563.1 DO - 10.12688/f1000research.7563.1 ID - Soneson2015 ER - TY - JOUR AU - Robinson, M. D. AU - McCarthy, D. J. AU - Smyth, G. K. PY - 2010 DA - 2010// TI - edgeR: a Bioconductor package for differential expression analysis of digital gene expression data JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp616 DO - 10.1093/bioinformatics/btp616 ID - Robinson2010 ER - TY - JOUR AU - Bauer, S. AU - Grossmann, S. AU - Vingron, M. AU - Robinson, P. N. PY - 2008 DA - 2008// TI - Ontologizer 2.0—a multifunctional tool for GO term enrichment analysis and data exploration JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn250 DO - 10.1093/bioinformatics/btn250 ID - Bauer2008 ER - TY - JOUR PY - 2015 DA - 2015// TI - Gene Ontology Consortium: going forward JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1179 DO - 10.1093/nar/gku1179 ID - ref83 ER - TY - JOUR AU - Kinsella, R. J. AU - Kähäri, A. AU - Haider, S. AU - Zamora, J. AU - Proctor, G. AU - Spudich, G. PY - 2011 DA - 2011// TI - Ensembl BioMarts: a hub for data retrieval across taxonomic space JO - Database VL - 2011 UR - https://doi.org/10.1093/database/bar030 DO - 10.1093/database/bar030 ID - Kinsella2011 ER - TY - JOUR AU - Trincado, J. L. AU - Entizne, J. C. AU - Hysenaj, G. AU - Singh, B. AU - Skalic, M. AU - Elliott, D. J. PY - 2018 DA - 2018// TI - SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions JO - Genome Biol VL - 19 UR - https://doi.org/10.1186/s13059-018-1417-1 DO - 10.1186/s13059-018-1417-1 ID - Trincado2018 ER - TY - STD TI - Kanitz A, Syed AP, Kaji K, Zavolan M. Conserved regulation of RNA processing in somatic cell reprogramming – code repository. GitHub. https://github.com/zavolanlab/SplicingReprogramming. Accessed 7 Feb 2018. UR - https://github.com/zavolanlab/SplicingReprogramming ID - ref86 ER - TY - JOUR AU - Chantzoura, E. AU - Skylaki, S. AU - Menendez, S. AU - Kim, S. -. I. AU - Johnsson, A. AU - Linnarsson, S. PY - 2015 DA - 2015// TI - Reprogramming roadblocks are system dependent JO - Stem Cell Rep VL - 5 UR - https://doi.org/10.1016/j.stemcr.2015.07.007 DO - 10.1016/j.stemcr.2015.07.007 ID - Chantzoura2015 ER - TY - JOUR AU - Maeda, M. AU - Johnson, K. R. AU - Wheelock, M. J. PY - 2005 DA - 2005// TI - Cadherin switching: essential for behavioral but not morphological changes during an epithelium-to-mesenchyme transition JO - J Cell Sci VL - 118 UR - https://doi.org/10.1242/jcs.01634 DO - 10.1242/jcs.01634 ID - Maeda2005 ER - TY - JOUR AU - Livak, K. J. AU - Schmittgen, T. D. PY - 2001 DA - 2001// TI - Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method JO - Methods VL - 25 UR - https://doi.org/10.1006/meth.2001.1262 DO - 10.1006/meth.2001.1262 ID - Livak2001 ER - TY - JOUR AU - Mittal, N. AU - Guimaraes, J. C. AU - Gross, T. AU - Schmidt, A. AU - Vina-Vilaseca, A. AU - Nedialkova, D. D. PY - 2017 DA - 2017// TI - The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan JO - Nat Commun VL - 8 UR - https://doi.org/10.1038/s41467-017-00539-y DO - 10.1038/s41467-017-00539-y ID - Mittal2017 ER - TY - STD TI - sciCORE - Center for Scientific Computing. University of Basel. https://scicore.unibas.ch/. Accessed 7 Feb 2018. UR - https://scicore.unibas.ch ID - ref91 ER - TY - STD TI - The Cancer Genome Atlas. National Cancer Institute. https://cancergenome.nih.gov/. Accessed 7 Feb 2018. UR - https://cancergenome.nih.gov/ ID - ref92 ER - TY - JOUR AU - Wang, M. AU - Zhao, Y. AU - Zhang, B. PY - 2015 DA - 2015// TI - Efficient test and visualization of multi-set intersections JO - Sci Rep VL - 5 UR - https://doi.org/10.1038/srep16923 DO - 10.1038/srep16923 ID - Wang2015 ER - TY - JOUR AU - Bibel, M. AU - Richter, J. AU - Lacroix, E. AU - Barde, Y. -. A. PY - 2007 DA - 2007// TI - Generation of a defined and uniform population of CNS progenitors and neurons from mouse embryonic stem cells JO - Nat Protoc VL - 2 UR - https://doi.org/10.1038/nprot.2007.147 DO - 10.1038/nprot.2007.147 ID - Bibel2007 ER - TY - JOUR AU - Chang, G. AU - Gao, S. AU - Hou, X. AU - Xu, Z. AU - Liu, Y. AU - Kang, L. PY - 2014 DA - 2014// TI - High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells JO - Cell Res VL - 24 UR - https://doi.org/10.1038/cr.2013.173 DO - 10.1038/cr.2013.173 ID - Chang2014 ER - TY - JOUR AU - Hou, P. AU - Li, Y. AU - Zhang, X. AU - Liu, C. AU - Guan, J. AU - Li, H. PY - 2013 DA - 2013// TI - Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds JO - Science VL - 341 UR - https://doi.org/10.1126/science.1239278 DO - 10.1126/science.1239278 ID - Hou2013 ER - TY - JOUR AU - Guo, S. AU - Zi, X. AU - Schulz, V. P. AU - Cheng, J. AU - Zhong, M. AU - Koochaki, S. H. J. PY - 2014 DA - 2014// TI - Nonstochastic reprogramming from a privileged somatic cell state JO - Cell VL - 156 UR - https://doi.org/10.1016/j.cell.2014.01.020 DO - 10.1016/j.cell.2014.01.020 ID - Guo2014 ER - TY - JOUR AU - Ma, H. AU - Morey, R. AU - O’Neil, R. C. AU - He, Y. AU - Daughtry, B. AU - Schultz, M. D. PY - 2014 DA - 2014// TI - Abnormalities in human pluripotent cells due to reprogramming mechanisms JO - Nature VL - 511 UR - https://doi.org/10.1038/nature13551 DO - 10.1038/nature13551 ID - Ma2014 ER - TY - JOUR AU - Carter, A. C. AU - Davis-Dusenbery, B. N. AU - Koszka, K. AU - Ichida, J. K. AU - Eggan, K. PY - 2014 DA - 2014// TI - Nanog-independent reprogramming to iPSCs with canonical factors JO - Stem Cell Rep VL - 2 UR - https://doi.org/10.1016/j.stemcr.2013.12.010 DO - 10.1016/j.stemcr.2013.12.010 ID - Carter2014 ER - TY - JOUR AU - Huang, K. AU - Zhang, X. AU - Shi, J. AU - Yao, M. AU - Lin, J. AU - Li, J. PY - 2015 DA - 2015// TI - Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells JO - Sci Rep VL - 5 UR - https://doi.org/10.1038/srep17691 DO - 10.1038/srep17691 ID - Huang2015 ER - TY - JOUR AU - Gallego Romero, I. AU - Pavlovic, B. J. AU - Hernando-Herraez, I. AU - Zhou, X. AU - Ward, M. C. AU - Banovich, N. E. PY - 2015 DA - 2015// TI - A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics JO - elife VL - 4 UR - https://doi.org/10.7554/eLife.07103 DO - 10.7554/eLife.07103 ID - Gallego Romero2015 ER - TY - JOUR AU - Bermejo-Álvarez, P. AU - Ramos-Ibeas, P. AU - Park, K. E. AU - Powell, A. P. AU - Vansandt, L. AU - Derek, B. PY - 2015 DA - 2015// TI - Tet-mediated imprinting erasure in H19 locus following reprogramming of spermatogonial stem cells to induced pluripotent stem cells JO - Sci Rep VL - 5 UR - https://doi.org/10.1038/srep13691 DO - 10.1038/srep13691 ID - Bermejo-Álvarez2015 ER - TY - JOUR AU - Maza, I. AU - Caspi, I. AU - Zviran, A. AU - Chomsky, E. AU - Rais, Y. AU - Viukov, S. PY - 2015 DA - 2015// TI - Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors JO - Nat Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3270 DO - 10.1038/nbt.3270 ID - Maza2015 ER - TY - JOUR AU - Choi, J. AU - Lee, S. AU - Mallard, W. AU - Clement, K. AU - Tagliazucchi, G. M. AU - Lim, H. PY - 2015 DA - 2015// TI - A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs JO - Nat Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3388 DO - 10.1038/nbt.3388 ID - Choi2015 ER - TY - JOUR AU - Zhao, Y. AU - Zhao, T. AU - Guan, J. AU - Zhang, X. AU - Fu, Y. AU - Ye, J. PY - 2015 DA - 2015// TI - A XEN-like state bridges somatic cells to pluripotency during chemical reprogramming JO - Cell VL - 163 UR - https://doi.org/10.1016/j.cell.2015.11.017 DO - 10.1016/j.cell.2015.11.017 ID - Zhao2015 ER -