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Li, Q., Liu, R., Lin, Z., Zhang, X., Silva, I.G., Pollock, S.D., Alvarez-Dominguez, J.R.*, and Liu, J. (2024). Cyborg islets: implanted flexible electronics reveal principles of human islet electrical maturation. bioRxiv. 2024.2003.2018.585551
Li, C., Shin, H., Bhavanasi, D., Liu, M., Yu, X., Peslak, S.A., Liu, X., Alvarez-Dominguez, J.R., Blobel, G.A., Gregory, B.D., et al. (2023). Expansion of human hematopoietic stem cells by inhibiting translation. bioRxiv. 2023.11.28.568925
Montalvo, A.P., Gruskin, Z.L., Leduc, A., Liu, M., Gao, Z., Ahn, J.H., Straubhaar, J.R., Slavov, N., and Alvarez-Dominguez, J.R.* (2023). An adult clock component links circadian rhythms to pancreatic β-cell maturation.bioRxiv. 2023.2008.2011.552890.
Pollock, S.D., Galicia-Silva, I.M., Liu, M., Gruskin, Z.L., and Alvarez-Dominguez, J.R.* (2023). Scalable generation of 3D pancreatic islet organoids from human pluripotent stem cells in suspension bioreactors.STAR Protocols. 4, 102580.
Leavens, K.F., Alvarez-Dominguez, J.R., Vo, L.T., Russ, H.A., and Parent, A.V. (2022). Stem cell-based multi-tissue platforms to model human autoimmune diabetes. Molecular Metabolism 66, 101610. PMCID: PMC9587366
Alvarez-Dominguez, J.R.*, and Melton, D.A. (2022). Cell Maturation: Hallmarks, Triggers, and Manipulation. Cell 185, 1. PMID: 34995481
Alvarez-Dominguez, J.R., Winther, S., Hansen, J.B., Lodish, H.F., and Knoll, M. (2021). An adipose lncRAP2 - Igf2bp2 complex enhances adipogenesis and energy expenditure by stabilizing target mRNAs. iScience 25, 103680
Alvarez-Dominguez, J.R.*, Donaghey, J., Rasouli, N., Kenty, J.H.R., Helman, A., Charlton, J., Straubhaar, J.R., Meissner, A., and Melton, D.A. (2020). Organoid Maturation by Circadian Entrainment. StemJournal 2, 7-13.
Highlighted in: McNamara, C. (2020). Author Q&A. StemJournal
Rasouli N., Melton, D.A., and Alvarez-Dominguez, J.R.* (2020). Purification of live stem cell-derived islet lineage intermediates. Curr Protoc Stem Cell Biol, 53, e111. PMID: 32521122
Alvarez-Dominguez, J.R., Donaghey, J., Rasouli N., Kenty, J.H.R., Helman, A., Charlton J., Straubhaar, J.R., Meissner, A., and Melton, D.A. (2019). Circadian Entrainment Triggers Maturation of Human in vitro Islets. Cell Stem Cell 26, 108-122 e110. PMID: 31839570
Highlighted in: Andersen, B., Lin, Z. (2020). Evaluation of Alvarez-Dominguez et al. Cell Stem Cell 26, 1, Stem Cell Podcast, The Stem Cell Group, Topbiopapers, Society for Research on Biological Rhythms Outreach.
Xu, D., Xu, S., Kyaw, A.M.M., Lim, Y.C., Chia, S.Y., Chee Siang, D.T., Alvarez-Dominguez, J.R., Chen, P., Leow, M.K., and Sun, L. (2017). RNA Binding Protein Ybx2 Regulates RNA Stability During Cold-Induced Brown Fat Activation. Diabetes 66, 2987-3000. PMID: 28970281
Alvarez-Dominguez, J.R.*, and Lodish, H.F. (2017). Emerging mechanisms of long noncoding RNA function during normal and malignant hematopoiesis. Blood 130, 1965-1975. PMID: 28928124
Alvarez-Dominguez, J.R.*, Knoll, M., Gromatzky, A.A., and Lodish, H.F. (2017). The Super-Enhancer-Derived alncRNA-EC7/Bloodlinc Potentiates Red Blood Cell Development in trans. Cell Reports 19, 2503–2514.
Highlighted: Espinosa, J.M. (2017). On the Origin of lncRNAs: Missing Link Found. Trends Genet 33, 660-662. PMID: 28636939
Alvarez-Dominguez, J.R.*, Zhang, X., and Hu, W. (2017). Widespread and dynamic translational control of red blood cell development. Blood 129, 619-629. PMID: 27899360
Highlighted in: Warren, A.J. (2017). Decoding erythropoiesis. Blood 129, 544-545. DOI: 10.1182/blood-2016-12-755538
Atianand, M.K., Hu, W., Satpathy, A.T., Shen, Y., Ricci, E.P., Alvarez-Dominguez, J.R., Bhatta, A., Schattgen, S.A., McGowan, J.D., Blin, J., et al. (2016). A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation. Cell 165, 1672-1685 PMID: 27315481.
Highlighted in: Lu, C. (2016). Curb Your Inflammation. Cell 165, 1553-1555, Science Daily, and Newswise. DOI: 10.1016/j.cell.2016.06.013
Alvarez-Dominguez, J.R.*, and Lodish, H.F. (2016). Unravelling of the role of long noncoding RNAs in haematopoiesis. ISBT Science Series 11, 188- 195.
Russell, M.R., Penikis, A., Oldridge, D.A., Alvarez-Dominguez, J.R., McDaniel, L., Diamond, M., Padovan, O., Raman, P., Li, Y., Wei, J.S., et al. (2015). CASC15-S Is a Tumor Suppressor lncRNA at the 6p22 Neuroblastoma Susceptibility Locus. Cancer Research 75, 3155-3166.
PMID: 26100672
Amosova, O., Alvarez-Dominguez, J.R.*, and Fresco, J.R. (2015). Why the DNA self-depurination mechanism operates in HB-beta but not in beta- globin paralogs HB-delta, HB-varepsilon1, HB-gamma1 and HB-gamma2. Mutation Research 778, 11-17 PMID: 26042536.
Alvarez-Dominguez, J.R., Bai, Z., Xu, D., Yuan, B., Lo, K.A., Yoon, M.J., Lim, Y.C., Knoll, M., Slavov, N., Chen, S., et al. (2015). De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development. Cell Metabolism 21, 764-776. Highlighted in: Futurity (2015). RNA catalogue reveals key to brown fat. PMID: 25921091
Smith, J., Alvarez-Dominguez, J.R., Kline, N., Huynh, N., Geisler, S., Hu, W., Coller, J., and Baker, K.E. (2014). Translation of small open reading frames within unannotated RNA transcripts in Saccharomyces cerevisiae. Cell Reports 7, 1858-1866. PMID: 24931603
Alvarez-Dominguez, J.R., Hu, W., Gromatzky, A.A., and Lodish, H.F. (2014). Long noncoding RNAs during normal and malignant hematopoiesis. Int J Hematol 99, 531-541. PMID: 24609766
Alvarez-Dominguez, J.R., Hu, W., Yuan, B., Shi, J., Park, S.S., Gromatzky, A.A., van Oudenaarden, A., and Lodish, H.F. (2014). Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation. Blood 123, 570-581. PMID: 24200680
Highlighted in: Gallagher, P.G. (2014). Long noncoding RNAs in erythropoiesis. Blood 123, 465-466. Coetzer, T. (2014). Red Cells, RNA, and Regulation: The Plot Thickens. The Hematologist 11, 10 DOI: 10.1182/blood-2013-10-530683
Caudy, A.A., Guan, Y., Jia, Y., Hansen, C., DeSevo, C., Hayes, A.P., Agee, J., Alvarez-Dominguez, J.R., Arellano, H., Barrett, D., et al. (2013). A new system for comparative functional genomics of Saccharomyces yeasts. Genetics 195, 275-287. PMID: 23852385
Alvarez-Dominguez, J.R.*, Amosova, O., Fresco, J.R. (2013). Self-catalytic DNA depurination underlies human beta-globin gene mutations at codon 6 that cause anemias and thalassemias. J Biol Chem 288, 11581-11589. PMID: 23457306
Hu, W., Alvarez-Dominguez, J.R., and Lodish, H.F. (2012). Regulation of mammalian cell differentiation by long non-coding RNAs. EMBO Rep 13, 971- 983. PMID: 23070366
Book chapters
Alvarez-Dominguez, J.R., Hu, W., and Lodish, H.F. (2013). Regulation of Eukaryotic Cell Differentiation by Long Noncoding RNAs. Molecular Biology of Long Non-coding RNAs, 15-67. (New York: Springer Science).
Fresco, J.R., Amosova, O., Wei, P., Alvarez-Dominguez, J.R., Glumcher, D., and Torres, R. (2011). Site-Specific Self-Catalyzed DNA Depurination, the Basis of a Spontaneous Mutagenic Mechanism of Wide Evolutionary Significance. Evolutionary Biology: Concepts, Biodiversity, Macroevolution and Genome Evolution, 3-19. (Springer-Verlag Berlin).
Li, C., Shin, H., Bhavanasi, D., Liu, M., Yu, X., Peslak, S.A., Liu, X., Alvarez-Dominguez, J.R., Blobel, G.A., Gregory, B.D., et al. (2023). Expansion of human hematopoietic stem cells by inhibiting translation. bioRxiv. 2023.11.28.568925
Montalvo, A.P., Gruskin, Z.L., Leduc, A., Liu, M., Gao, Z., Ahn, J.H., Straubhaar, J.R., Slavov, N., and Alvarez-Dominguez, J.R.* (2023). An adult clock component links circadian rhythms to pancreatic β-cell maturation.bioRxiv. 2023.2008.2011.552890.
Pollock, S.D., Galicia-Silva, I.M., Liu, M., Gruskin, Z.L., and Alvarez-Dominguez, J.R.* (2023). Scalable generation of 3D pancreatic islet organoids from human pluripotent stem cells in suspension bioreactors.STAR Protocols. 4, 102580.
Leavens, K.F., Alvarez-Dominguez, J.R., Vo, L.T., Russ, H.A., and Parent, A.V. (2022). Stem cell-based multi-tissue platforms to model human autoimmune diabetes. Molecular Metabolism 66, 101610. PMCID: PMC9587366
Alvarez-Dominguez, J.R.*, and Melton, D.A. (2022). Cell Maturation: Hallmarks, Triggers, and Manipulation. Cell 185, 1. PMID: 34995481
Alvarez-Dominguez, J.R., Winther, S., Hansen, J.B., Lodish, H.F., and Knoll, M. (2021). An adipose lncRAP2 - Igf2bp2 complex enhances adipogenesis and energy expenditure by stabilizing target mRNAs. iScience 25, 103680
Alvarez-Dominguez, J.R.*, Donaghey, J., Rasouli, N., Kenty, J.H.R., Helman, A., Charlton, J., Straubhaar, J.R., Meissner, A., and Melton, D.A. (2020). Organoid Maturation by Circadian Entrainment. StemJournal 2, 7-13.
Highlighted in: McNamara, C. (2020). Author Q&A. StemJournal
Rasouli N., Melton, D.A., and Alvarez-Dominguez, J.R.* (2020). Purification of live stem cell-derived islet lineage intermediates. Curr Protoc Stem Cell Biol, 53, e111. PMID: 32521122
Alvarez-Dominguez, J.R., Donaghey, J., Rasouli N., Kenty, J.H.R., Helman, A., Charlton J., Straubhaar, J.R., Meissner, A., and Melton, D.A. (2019). Circadian Entrainment Triggers Maturation of Human in vitro Islets. Cell Stem Cell 26, 108-122 e110. PMID: 31839570
Highlighted in: Andersen, B., Lin, Z. (2020). Evaluation of Alvarez-Dominguez et al. Cell Stem Cell 26, 1, Stem Cell Podcast, The Stem Cell Group, Topbiopapers, Society for Research on Biological Rhythms Outreach.
Xu, D., Xu, S., Kyaw, A.M.M., Lim, Y.C., Chia, S.Y., Chee Siang, D.T., Alvarez-Dominguez, J.R., Chen, P., Leow, M.K., and Sun, L. (2017). RNA Binding Protein Ybx2 Regulates RNA Stability During Cold-Induced Brown Fat Activation. Diabetes 66, 2987-3000. PMID: 28970281
Alvarez-Dominguez, J.R.*, and Lodish, H.F. (2017). Emerging mechanisms of long noncoding RNA function during normal and malignant hematopoiesis. Blood 130, 1965-1975. PMID: 28928124
Alvarez-Dominguez, J.R.*, Knoll, M., Gromatzky, A.A., and Lodish, H.F. (2017). The Super-Enhancer-Derived alncRNA-EC7/Bloodlinc Potentiates Red Blood Cell Development in trans. Cell Reports 19, 2503–2514.
Highlighted: Espinosa, J.M. (2017). On the Origin of lncRNAs: Missing Link Found. Trends Genet 33, 660-662. PMID: 28636939
Alvarez-Dominguez, J.R.*, Zhang, X., and Hu, W. (2017). Widespread and dynamic translational control of red blood cell development. Blood 129, 619-629. PMID: 27899360
Highlighted in: Warren, A.J. (2017). Decoding erythropoiesis. Blood 129, 544-545. DOI: 10.1182/blood-2016-12-755538
Atianand, M.K., Hu, W., Satpathy, A.T., Shen, Y., Ricci, E.P., Alvarez-Dominguez, J.R., Bhatta, A., Schattgen, S.A., McGowan, J.D., Blin, J., et al. (2016). A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation. Cell 165, 1672-1685 PMID: 27315481.
Highlighted in: Lu, C. (2016). Curb Your Inflammation. Cell 165, 1553-1555, Science Daily, and Newswise. DOI: 10.1016/j.cell.2016.06.013
Alvarez-Dominguez, J.R.*, and Lodish, H.F. (2016). Unravelling of the role of long noncoding RNAs in haematopoiesis. ISBT Science Series 11, 188- 195.
Russell, M.R., Penikis, A., Oldridge, D.A., Alvarez-Dominguez, J.R., McDaniel, L., Diamond, M., Padovan, O., Raman, P., Li, Y., Wei, J.S., et al. (2015). CASC15-S Is a Tumor Suppressor lncRNA at the 6p22 Neuroblastoma Susceptibility Locus. Cancer Research 75, 3155-3166.
PMID: 26100672
Amosova, O., Alvarez-Dominguez, J.R.*, and Fresco, J.R. (2015). Why the DNA self-depurination mechanism operates in HB-beta but not in beta- globin paralogs HB-delta, HB-varepsilon1, HB-gamma1 and HB-gamma2. Mutation Research 778, 11-17 PMID: 26042536.
Alvarez-Dominguez, J.R., Bai, Z., Xu, D., Yuan, B., Lo, K.A., Yoon, M.J., Lim, Y.C., Knoll, M., Slavov, N., Chen, S., et al. (2015). De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development. Cell Metabolism 21, 764-776. Highlighted in: Futurity (2015). RNA catalogue reveals key to brown fat. PMID: 25921091
Smith, J., Alvarez-Dominguez, J.R., Kline, N., Huynh, N., Geisler, S., Hu, W., Coller, J., and Baker, K.E. (2014). Translation of small open reading frames within unannotated RNA transcripts in Saccharomyces cerevisiae. Cell Reports 7, 1858-1866. PMID: 24931603
Alvarez-Dominguez, J.R., Hu, W., Gromatzky, A.A., and Lodish, H.F. (2014). Long noncoding RNAs during normal and malignant hematopoiesis. Int J Hematol 99, 531-541. PMID: 24609766
Alvarez-Dominguez, J.R., Hu, W., Yuan, B., Shi, J., Park, S.S., Gromatzky, A.A., van Oudenaarden, A., and Lodish, H.F. (2014). Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation. Blood 123, 570-581. PMID: 24200680
Highlighted in: Gallagher, P.G. (2014). Long noncoding RNAs in erythropoiesis. Blood 123, 465-466. Coetzer, T. (2014). Red Cells, RNA, and Regulation: The Plot Thickens. The Hematologist 11, 10 DOI: 10.1182/blood-2013-10-530683
Caudy, A.A., Guan, Y., Jia, Y., Hansen, C., DeSevo, C., Hayes, A.P., Agee, J., Alvarez-Dominguez, J.R., Arellano, H., Barrett, D., et al. (2013). A new system for comparative functional genomics of Saccharomyces yeasts. Genetics 195, 275-287. PMID: 23852385
Alvarez-Dominguez, J.R.*, Amosova, O., Fresco, J.R. (2013). Self-catalytic DNA depurination underlies human beta-globin gene mutations at codon 6 that cause anemias and thalassemias. J Biol Chem 288, 11581-11589. PMID: 23457306
Hu, W., Alvarez-Dominguez, J.R., and Lodish, H.F. (2012). Regulation of mammalian cell differentiation by long non-coding RNAs. EMBO Rep 13, 971- 983. PMID: 23070366
Book chapters
Alvarez-Dominguez, J.R., Hu, W., and Lodish, H.F. (2013). Regulation of Eukaryotic Cell Differentiation by Long Noncoding RNAs. Molecular Biology of Long Non-coding RNAs, 15-67. (New York: Springer Science).
Fresco, J.R., Amosova, O., Wei, P., Alvarez-Dominguez, J.R., Glumcher, D., and Torres, R. (2011). Site-Specific Self-Catalyzed DNA Depurination, the Basis of a Spontaneous Mutagenic Mechanism of Wide Evolutionary Significance. Evolutionary Biology: Concepts, Biodiversity, Macroevolution and Genome Evolution, 3-19. (Springer-Verlag Berlin).