PUBLICATIONS
Préimpression
E Appleton, K Hong, C Rodríguez-Caycedo, Y Tanaka, A Ashkenazy-Titelman, K Bhide, C Rasmussen-Ivey, X Ambriz-Peña, N Korover, H Bai, A Quieroz, J Nelson, G Rathod, G Knox, M Morgan, N Malviya, K Zhang, B McNutt, J Kehler, A Kowalczyk, A Bow, B McLendon, B Cantarel, M James, C E. Mason, C Gray, K R. Koehler, V Pearson, B Lamm, G Church, E Hysolli, Derivation of elephant induced pluripotent stem cells, bioRxiv
F Wehbe, L Adams, S Yuen, Y-S Kim, Y Tanaka, Inferring Disease Progressive Stages in Single-Cell Transcriptomics Using Weakly-Supervised Deep Learning Approach, bioRxiv
L Masclef, O Ahmed, N Iannantuono, J Gagnon, M Gushul-Leclaire, K Boulay, B Estavoyer, M Echbicheb, M Poy, K A Boubacar, A Boubekeur, S Menggad, A Schcolnik-Cabrera, A Balsalobre, E Bonneil, P Thibault, L Hulea, Y Tanaka, F Antoine-Mallette, J Drouin, E B Affar, O-GlcNAcylation of FOXK1 orchestrates the E2F pathway and promotes oncogenesis, bioRxiv
J Jeong, J Lee, J Lim, J Shin, K Yoo, J Kim, Y Tanaka, H S Tae, L K Kim, I-H Park, J Wysolmerski, J Choi, FOXA1 is required for ErbB2 expression and luminal differentiation in HER2-positive breast cancer, bioRxiv
H Kural, U Djakbarova, B Cakir, Y Tanaka, Y Madraki, E T Chan, V A Muniz, H Qian, J Park, L R Sewanan, I-H Park, L E Niklason, C Kural, Mechano-inhibition of Endocytosis Sensitizes Cancer Cells to Fas-induced Apoptosis, bioRxiv
Articles évalues par les pairs
2024
L. Adams, M.K. Song, S Yuen, Y. Tanaka# and Y.-S. Kim#, A single-nuclei paired multiomic analysis of the human midbrain reveals age- and Parkinson's disease-associated glial changes, Nature Aging, 4(3):364-378 #Co-corresponding authors
2023
B. Patterson, B. Yang, Y. Tanaka, K.-Y. Kim, B. Cakir, Y. Xiang, J. Kim, S. Wang, I.-H. Park. (2023). Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. Science Advances, 4;9(31):eadf2245
S. P. Harrison*, R. Siller*, Y. Tanaka*, Y. Xiang, B. Patterson, H. Kempf, E. Melum, K. S. Åsrud, M. E. Cho, E. Andersen, P. M. Sandset, S. Baumgarten, F. Bonanini, D. Kurek, S. Mathapati, R. Almaas, K. Sharma, S. R. Wilson, F. S. Skottvoll, I. C. Boger, I. L. Bogen, T. A. Nyman, J. J. Wu, A. Bezrouk, D. Cizkova, J. Mokry, R. Zweigerdt, I.-H. Park, G. J. Sullivan, Scalable production of tissue-like vascularised liver organoids from human PSCs. Experimental & Molecular Medicine, 55(9):2005-2024, *Equal contribution
F. R. Kiral, B. Cakir, Y. Tanaka, J. Kim, W. S. Yang, F. Wehbe, Y.-J. Kang, M. Zhong, G. Sancer, S.-H. Lee, Y. Xiang, I.-H. Park. (2023). Generation of ventralized human thalamic organoids with thalamic reticular nucleus. Cell Stem Cell. 30(5): 677-688.
2022
H. Zhang, B. Li, Q. Huang, F. López-Giráldez, Y. Tanaka, Q. Lin, S. Mehta, G. Wang, M. Graham, X. Liu, I.-H. Park, A. Eichmann, W. Min, J.H. Zhou, Mitochondrial dysfunction induces ALK5-SMAD2-mediated hypovascularization and arteriovenous malformations in mouse retinas, Nature Communications, 2022, Dec 13(1):1-21
S. Paniagua, B. Cakir, Y. Hu, F.R. Kiral, Y. Tanaka, Y. Xiang, B. Patterson, J.R. Gruen, I.-H. Park, Dyslexia associated gene, KIAA0319, regulates cell cycle during human neuroepithelium development, Front Cell Dev Biol. 2022 Aug 9;10:967147
B. Cakir*, Y. Tanaka*, F. R. Kiral, Y. Xiang, O. Dagliyan, J. Wang, M. Lee, A.M. Greaney, W.S. Yang, C. duBoulay, M.H. Kural, B. Patterson, M. Zhong, J. Kim, Y. Bai, W. Ming, L.E. Niklason, P. Patra, and I.H. Park., Expression of the transcription factor PU.1 induces the generation of microglia-like cells in human cortical organoids, Nature Communications, 2022 13: 1. *Equal contribution
2021
Y. Lim, J.E. Beane-Ebel, Y. Tanaka, B. Ning, C.R. Husted, D.C. Henderson, Y. Xiang, I.-H. Park, L.A. Farrer, H. Zhang. (2021). Exploration of alcohol use disorder-associated brain miRNA-mRNA regulatory networks. Translational Psychiatry. 11
Y. Tanaka and I-H. Park, Regional specification and complementation with non-neuroectodermal cells in human brain organoids. JMolMed, 2021 Apr;99(4):489-500.
O. Rackham, P. Cahan, N. Mah, S. Morris, J. F. Ouyang, A. L. Plant, Y. Tanaka, and C. A. Wells, Challenge for Computational Stem Cell Biology: A Discussion for the Field. Stem Cell Reports. 2021, 16(1): 3-9
J. Cho, S. Kim, H. Lee, W. Rah, H.C. Cho, N.K. Kim, S. Bae, D.H. Shin, M.G. Lee, I.H. Park, Y. Tanaka, E. Shin, H. Yi, J.W. Han, P.T.J. Hwang, H.W. Jun. H.J. Park, K. Cho, S.W. Lee, J.K. Jung, R.D. Levit, M.A. Sussman, R.P. Harvey, Y.S. Yoon, Regeneration of infarcted mouse hearts by cardiovascular tissue formed via the direct reprogramming of mouse fibroblasts. Nat Biomed Eng. 2021 Aug;5(8):880-896
N. Lin, J. Lin, Y. Tanaka, P. Sun and X. Zhou, Identification and validation of a five-lncRNA signature for predicting survival with targeted drug candidates in ovarian cancer. Bioengineered, 2021, 12 (1), 3263-3274
2020
Y. Xiang*, Y. Tanaka*, B. Patterson, S.-M. Hwang, E. Hysolli, B. Cakir, K.-Y. Kim, W. Wang, Y.-J. Kang, E. M. Clement, M. Zhong, S.-H. Lee, Y. S. Cho, P. Patra, G. J. Sullivan, S. M. Weissman, I.-H. Park, Dysregulation of BRD4 Function Underlies the Functional Abnormalities of MeCP2 Mutant Neurons, Mol. Cell, 2020, 79(1):84-98.e9
Y. Tanaka, B. Cakir, Y. Xiang, G.J. Sullivan and I.H. Park, Synthetic Analyses of Single-Cell Transcriptomes from Multiple Brain Organoids and Fetal Brain. Cell Reports, 2020, 30: 1682-1689.e3
K. Wang, H. Zhang, Y. He, Q. Jiang, Y. Tanaka, I.-H. Park, J. S Pober, W. Min, H. J. Zhou, Mural Cell-Specific Deletion of Cerebral Cavernous Malformation 3 in the Brain Induces Cerebral Cavernous Malformations. Arteriosclerosis Thrombosis and Vascular Biology, 2020, 40(9):2171-2186
2019
B. Cakir, Y. Xiang, Y. Tanaka, M. H. Kural, M. Parent, Y.J. Kang, K. Chapeton, B. Patterson, Y. Yuan, C.-S. He, M. S. B. Raredon, J. Dengelegi, K.Y. Kim, P. Sun, M. Zhong, S.-H. Lee, P. Patra, F. Hyder, L. E. Niklason, S.-H. Lee, Y.S. Yoon, and I.H. Park, Development of human brain organoids with functional vascular-like system, Nature Methods, 2019, 16: 1169-1175. .
Y. Xiang*, Y. Tanaka*, B. Cakir, B. Patterson, K.Y. Kim, P. Sun, Y.J. Kang, M. Zhong, X. Liu, P. Patra, S.H. Lee, S.M. Weissman, I.H. Park, hESC-derived thalamic organoids form reciprocal projections when fused with cortical organoids. Cell Stem Cell, 2019, 24: 487-497.e7. *Equal contribution
C. Belair, S. Sim, K.Y. Kim, Y. Tanaka, I.H. Park and S.L. Wolin, The RNA exosome nuclease complex regulates human embryonic stem cell differentiation. Journal of Cell Biology, 2019, 218:2564-2582..
A.J. Rosato, X. Chen, Y. Tanaka, L.A. Farrer, H.R. Kranzler, Y.Z. Nunez, D.C. Henderson, J. Gelernter, H. Zhang, Salivary microRNAs identified by small RNA sequencing and machine learning as potential biomarkers of alcohol dependence. Epigenomics, 2019, 11: 739-749.
2018
K.Y. Kim*, Y. Tanaka*, J. Su, B. Cakir, Y. Xiang, B. Patterson, J. Ding, Y.W. Jung, J.H. Kim, E. Hysolli, H. Lee, R. Dajani, J. Kim, M. Zhong, J.H. Lee, D. D. Skalnik, J.M. Lim, G.J. Sullivan, J. Wang, I.H. Park, Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a. Nature Communications, 2018, 9: 2583. *Equal contribution
Y. Xiang, Y. Tanaka, B. Patterson, B. Cakir, K.Y. Kim, Y.S. Cho and I.H. Park, Generation and Fusion of Human Cortical and Medial Ganglionic Eminence Brain Organoids. Current Protocols in Stem Cell Biology, 2018, 47, pii: e61.
2017
Y. Xiang*, Y. Tanaka*, B. Patterson, Y.J. Kang, G. Govindaiah, N. Roselaar, B. Cakir, K.Y. Kim, A.P. Lombroso, S.M. Hwang, M. Zhong, E.G. Stanley, A.G. Elefanty, J.R. Naegele, S.H. Lee, S.M. Weissman, I.H. Park, Fusion of Regionally Specified hPSC-Derived Organoids Models Human Brain Development and Interneuron Migration. Cell Stem Cell, 2017, 21: 383-398.e7. *Equal contribution
J. Yang*, Y. Tanaka*, M. Seay, Z. Li, J. Jin, L.X. Garmire, X. Zhu, A. Taylor, W. Li, G. Euskirchen, S. Halene, Y. Kluger, M.P. Snyder, I.H. Park, X. Pan, S. M. Weissman SM. Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors. Nucleic Acids Research, 2017, 45: 1281-1296. *Equal contribution
B. Patterson, Y. Tanaka, I.H. Park, Correction to: New Advances in Human X chromosome status from a Developmental and Stem Cell Biology. Tissue Engineering and Regenerative Medicine. 2017, 15(1): 125.
B. Patterson, Y. Tanaka, I.H. Park, New Advances in Human X chromosome status from a Developmental and Stem Cell Biology. Tissue Engineering and Regenerative Medicine. 2017, 14: 643-652.
S. Lee, C. Park, J.W. Han, J.Y. Kim, K. Cho, E.J. Kim, S. Kim, S.J. Lee, S.Y. Oh, Y. Tanaka, I.H. Park, H.J. An, C.M. Shin, S. Sharma, Y.S. Yoon, Direct Reprogramming of Human Dermal Fibroblasts Into Endothelial Cells Using ER71/ETV2. Circulation Research, 2017, 120: 848-861.
2016
E. Hysolli*, Y. Tanaka*, J. Su, K.-Y. Kim, T. Zhong, R. Janknecht, X.L. Zhou, L. Geng, C. Qiu, X. Pan, Y.W. Jung, J. Cheng, J. Lu, M. Zhong, S.M. Weissman, I.H. Park, Regulation of the DNA Methylation Landscape in Human Somatic Cell Reprogramming by the miR-29 Family. Stem Cell Reports, 2016, 7: 43-54. *Equal contribution
2015
Y. Tanaka*, E. Hysolli*, J. Su, Y. Xiang, K.-Y. Kim, M. Zhong, Y. Li, K. Heydari, G. Euskirchen, M.P. Snyder, X. Pan, S.M. Weissman, I.-H. Park, Transcriptome Signature and Regulation in Human Somatic Cell Reprogramming. Stem Cell Reports, 2015, 4: 1125-39. *Equal contribution
C.B. Greer, Y. Tanaka, Y.J. Kim, P. Xie, M.Q. Zhang, I.-H. Park, T.H. Kim, Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery. Cell Reports, 2015, 13: 1444-55.
2014
Y. Tanaka*, K.-Y. Kim*, M. Zhong, X. Pan, S. M. Weissman and I.-H. Park, Transcriptional regulation in pluripotent stem cells by methyl CpG-binding protein 2 (MeCP2). Human Molecular Genetics, 2014, 23: 1045-55. *Equal contribution
K.-Y. Kim, E. Hysolli, Y. Tanaka, B. Wang, Y.-W. Jung, X. Pan, S. M. Weissman, and I.-H. Park, X Chromosome of Female Cells Shows Dynamic Changes in Status during Human Somatic Cell Reprogramming. Stem Cell Reports, 2014, 2:896-909.
2013
X. Pan, R.E. Rurrett*, H. Zhu*, Y. Tanaka*, Y. Li, X. Zi, S.L. Marjani, G. Euskirchen, C. Ma, R.H. Lamotte, I.-H. Park, M.P. Snyder, C.E. Mason and S.M. Weissman, Two methods for full-length RNA sequencing for low quantities of cells and single cells. PNAS, 2013, 110: 594-9 *Equal contribution
2012
Y. Tanaka, L. Chung and I.-H. Park, Impact of Retrotransposons in Pluripotent Stem Cells. Molecules and Cells, 2012, 34: 509-16.
N. Ohkura, M. Hamaguchi, H. Morikawa, K. Sugimura, A. Tanaka, Y. Ito, M. Osaki, Y. Tanaka, R. Yamashita, N. Nakano, J. Huehn, H. J. Fehling, T. Sparwasser, K. Nakai, and S. Sakaguchi, T Cell Receptor Stimulation-Induced Epigenetic Changes and Foxp3 Expression Are Independent and Complementary Events Required for Treg Cell Development. Immunity, 2012, 37: 785-99.
Y.-W. Jung, E. Hysolli, K.-Y. Kim, Y. Tanaka and I.-H. Park, Human induced pluripotent stem cells and neurodegenerative disease: prospects for novel therapies. Current Opinions in Neurology, 2012, 25: 125-30.
E. Hysolli,Y.-W. Jung, Y. Tanaka, K.-Y. Kim and I.-H. Park, The lesser known story of X-chromosome reactivation. Cell Cycle, 2012, 11: 229-35.
2011
R. Yamashita, N. P Sathira, A. Kanai, K. Tanimoto, T. Arauchi, Y. Tanaka, S. Hashimoto, S. Sugano, K. Nakai, and Y. Suzuki, Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Research, 2011, 21: 775-89.
2010
Y. Tanaka, I. Yoshimura and K. Nakai, Positional Variations among Heterogeneous Nucleosome Maps Give Dynamical Information on Chromatin. Chromosoma, 2010, 119: 391-404.
Y. Tanaka, R. Yamashita, Y. Suzuki and K. Nakai, Effects of Alu elements on global nucleosome positioning in the human genome, BMC Genomics, 2010, 11:309.
T. Satoh, O. Takeuchi, A. Vandenbon, K. Yasuda, Y. Tanaka, Y. Kumagai, T. Miyake, K. Matsushita, T. Okazaki, T. Saitoh, K. Honma, T. Matsuyama, K. Yui, T. Tsujimura, D. M. Standley, K. Nakanishi, K. Nakai and S. Akira The JMJD3-IRF4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nature Immunology, 2010, 11: 936-4
2009
Y. Tanaka and K. Nakai, An assessment of prediction algorithms for nucleosome positioning. Genome Informatics, 2009, 23: 169-78