Natasha I. Edman, Ashish Phal, Rachel L. Redler, Thomas Schlichthaerle, Sanjay R. Srivatsan, Devon Duron Ehnes, Ali Etemadi, Seong J. An, Andrew Favor, Zhe Li, Florian Praetorius, Max Gordon, Thomas Vincent, Silvia Marchiano, Leslie Blakely, Chuwei Lin, Wei Yang, Brian Coventry, Derrick R. Hicks, Longxing Cao, Neville Bethel, Piper Heine, Analisa Murray, Stacey Gerben, Lauren Carter, Marcos Miranda, Babak Negahdari, Sangwon Lee, Cole Trapnell, Ying Zheng, Charles E. Murry, Devin K. Schweppe, Benjamin S. Freedman, Lance Stewart, Damian C. Ekiert, Joseph Schlessinger, Jay Shendure, Gira Bhabha, Hannele Ruohola-Baker, David Baker. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Cell. 2024 Jun. doi: 10.1016/j.cell.2024.05.025. https://www.sciencedirect.com/science/article/pii/S0092867424005348
Alghadeer A, Patni AP, Li Z, Lim YC, Mathieu J, Ruohola-Baker H. Protocol for generating three-dimensional induced early ameloblasts using serum-free media and growth factors. STAR Protoc. 2024 Jun 1;5(2):103100. doi: 10.1016/j.xpro.2024.103100. Epub ahead of print. PMID: 38824640.
Keshri R, Mathieu J, Ruohola-Baker H. Fight, flight, and freeze! Cell Metab. 2023 Sep 5;35(9):1493-1495. doi: 10.1016/j.cmet.2023.08.007. PMID: 37673033.
Alghadeer A, Hanson-Drury S, Patni AP, Ehnes DD, Zhao YT, Li Z, Phal A, Vincent T, Lim YC, O’Day D, Spurrell CH, Gogate AA, Zhang H, Devi A, Wang Y, Starita L, Doherty D, Glass IA, Shendure J, Freedman BS, Baker D, Regier MC, Mathieu J, Ruohola-Baker H. Single-cell census of human tooth development enables generation of human enamel. Dev Cell. 2023 Aug 11:S1534-5807(23)00360-X. doi: 10.1016/j.devcel.2023.07.013. Epub ahead of print. PMID: 37582367.
Lutz ID, Wang S, Norn C, Courbet A, Borst AJ, Zhao YT, Dosey A, Cao L, Xu J, Leaf EM, Treichel C, Litvicov P, Li Z, Goodson AD, Rivera-Sánchez P, Bratovianu AM, Baek M, King NP, Ruohola-Baker H, Baker D. Top-down design of protein architectures with reinforcement learning. Science. 2023 Apr 21;380(6642):266-273. doi: 10.1126/science.adf6591. Epub 2023 Apr 20. PMID: 37079676.
Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An S, Favor A, Ehnes D, Li Z, Praetorius F, Gordon M, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray AN, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. bioRxiv [Preprint]. 2023 Mar 15:2023.03.14.532666. doi: 10.1101/2023.03.14.532666. PMID: 36993355; PMCID: PMC10055045.
Taslim, Tommy H., Abdiasis M. Hussein, Riya Keshri, Julien R. Ishibashi, Tung C. Chan, Bich N. Nguyen, Shuozhi Liu, Daniel Brewer, Stuart Harper, Scott Lyons, Ben Garver, Jimmy Dang, Nanditaa Balachandar, Samriddhi Jhajharia, Debra Del Castillo, Julie Mathieu, and Hannele Ruohola-Baker. 2023. “Stress-Induced Reversible Cell-Cycle Arrest Requires PRC2/PRC1-Mediated Control of Mitophagy in Drosophila Germline Stem Cells and Human IPSCs.” Stem Cell Reports 18(1):269–88. doi: 10.1016/j.stemcr.2022.11.004.
Cao, Longxing, Brian Coventry, Inna Goreshnik, Buwei Huang, William Sheffler, Joon Sung Park, Kevin M. Jude, Iva Marković, Rameshwar U. Kadam, Koen H. G. Verschueren, Kenneth Verstraete, Scott Thomas Russell Walsh, Nathaniel Bennett, Ashish Phal, Aerin Yang, Lisa Kozodoy, Michelle DeWitt, Lora Picton, Lauren Miller, Eva-Maria Strauch, Nicholas D. DeBouver, Allison Pires, Asim K. Bera, Samer Halabiya, Bradley Hammerson, Wei Yang, Steffen Bernard, Lance Stewart, Ian A. Wilson, Hannele Ruohola-Baker, Joseph Schlessinger, Sangwon Lee, Savvas N. Savvides, K. Christopher Garcia, and David Baker. 2022. “Design of Protein-Binding Proteins from the Target Structure Alone.” Nature 605(7910):551–60. doi: 10.1038/s41586-022-04654-9.
Ehnes, Devon Duron, Ammar Alghadeer, Sesha Hanson-Drury, Yan Ting Zhao, Gwen Tilmes, Julie Mathieu, and Hannele Ruohola-Baker. 2022. “Sci-Seq of Human Fetal Salivary Tissue Introduces Human Transcriptional Paradigms and a Novel Cell Population.” Frontiers in Dental Medicine 3:887057. doi: 10.3389/fdmed.2022.887057.
Hunt, Andrew C., James Brett Case, Young-Jun Park, Longxing Cao, Kejia Wu, Alexandra C. Walls, Zhuoming Liu, John E. Bowen, Hsien-Wei Yeh, Shally Saini, Louisa Helms, Yan Ting Zhao, Tien-Ying Hsiang, Tyler N. Starr, Inna Goreshnik, Lisa Kozodoy, Lauren Carter, Rashmi Ravichandran, Lydia B. Green, Wadim L. Matochko, Christy A. Thomson, Bastian Vögeli, Antje Krüger, Laura A. VanBlargan, Rita E. Chen, Baoling Ying, Adam L. Bailey, Natasha M. Kafai, Scott E. Boyken, Ajasja Ljubetič, Natasha Edman, George Ueda, Cameron M. Chow, Max Johnson, Amin Addetia, Mary-Jane Navarro, Nuttada Panpradist, Michael Jr Gale, Benjamin S. Freedman, Jesse D. Bloom, Hannele Ruohola-Baker, Sean P. J. Whelan, Lance Stewart, Michael S. Diamond, David Veesler, Michael C. Jewett, and David Baker. 2022. “Multivalent Designed Proteins Neutralize SARS-CoV-2 Variants of Concern and Confer Protection against Infection in Mice.” Science Translational Medicine 14(646):eabn1252. doi: 10.1126/scitranslmed.abn1252.
Hussein, Abdiasis M., Nanditaa Balachandar, Julie Mathieu, and Hannele Ruohola-Baker. 2022. “Molecular Regulators of Embryonic Diapause and Cancer Diapause-like State.” Cells 11(19). doi: 10.3390/cells11192929.
Levy, Shiri, Logeshwaran Somasundaram, Infencia Xavier Raj, Diego Ic-Mex, Ashish Phal, Sven Schmidt, Weng I. Ng, Daniel Mar, Justin Decarreau, Nicholas Moss, Ammar Alghadeer, Henrik Honkanen, Jay Sarthy, Nicholas Vitanza, R. David Hawkins, Julie Mathieu, Yuliang Wang, David Baker, Karol Bomsztyk, and Hannele Ruohola-Baker. 2022. “DCas9 Fusion to Computer-Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region.” Cell Reports 38(9):110457. doi: 10.1016/j.celrep.2022.110457.
Miklas, Jason W., Shiri Levy, Peter Hofsteen, Diego Ic Mex, Elisa Clark, Jeanot Muster, Aaron M. Robitaille, Gargi Sivaram, Lauren Abell, Jamie M. Goodson, Inez Pranoto, Anup Madan, Michael T. Chin, Rong Tian, Charles E. Murry, Randall T. Moon, Yuliang Wang, and Hannele Ruohola-Baker. 2022. “Amino Acid Primed MTOR Activity Is Essential for Heart Regeneration.” IScience 25(1):103574. doi: 10.1016/j.isci.2021.103574.
Ben-Sasson, Ariel J., Joseph L. Watson, William Sheffler, Matthew Camp Johnson, Alice Bittleston, Logeshwaran Somasundaram, Justin Decarreau, Fang Jiao, Jiajun Chen, Ioanna Mela, Andrew A. Drabek, Sanchez M. Jarrett, Stephen C. Blacklow, Clemens F. Kaminski, Greg L. Hura, James J. De Yoreo, Justin M. Kollman, Hannele Ruohola-Baker, Emmanuel Derivery, and David Baker. 2021a. “Author Correction: Design of Biologically Active Binary Protein 2D Materials.” Nature 591(7850):E16. doi: 10.1038/s41586-021-03331-7.
Ben-Sasson, Ariel J., Joseph L. Watson, William Sheffler, Matthew Camp Johnson, Alice Bittleston, Logeshwaran Somasundaram, Justin Decarreau, Fang Jiao, Jiajun Chen, Ioanna Mela, Andrew A. Drabek, Sanchez M. Jarrett, Stephen C. Blacklow, Clemens F. Kaminski, Greg L. Hura, James J. De Yoreo, Justin M. Kollman, Hannele Ruohola-Baker, Emmanuel Derivery, and David Baker. 2021b. “Design of Biologically Active Binary Protein 2D Materials.” Nature 589(7842):468–73. doi: 10.1038/s41586-020-03120-8.
Divine, Robby, Ha V. Dang, George Ueda, Jorge A. Fallas, Ivan Vulovic, William Sheffler, Shally Saini, Yan Ting Zhao, Infencia Xavier Raj, Peter A. Morawski, Madeleine F. Jennewein, Leah J. Homad, Yu-Hsin Wan, Marti R. Tooley, Franziska Seeger, Ali Etemadi, Mitchell L. Fahning, James Lazarovits, Alex Roederer, Alexandra C. Walls, Lance Stewart, Mohammadali Mazloomi, Neil P. King, Daniel J. Campbell, Andrew T. McGuire, Leonidas Stamatatos, Hannele Ruohola-Baker, Julie Mathieu, David Veesler, and David Baker. 2021. “Designed Proteins Assemble Antibodies into Modular Nanocages.” Science (New York, N.Y.) 372(6537). doi: 10.1126/science.abd9994.
Helms, Louisa, Silvia Marchiano, Ian B. Stanaway, Tien-Ying Hsiang, Benjamin A. Juliar, Shally Saini, Yan Ting Zhao, Akshita Khanna, Rajasree Menon, Fadhl Alakwaa, Carmen Mikacenic, Eric D. Morrell, Mark M. Wurfel, Matthias Kretzler, Jennifer L. Harder, Charles E. Murry, Jonathan Himmelfarb, Hannele Ruohola-Baker, Pavan K. Bhatraju, Michael Jr Gale, and Benjamin S. Freedman. 2021. “Cross-Validation of SARS-CoV-2 Responses in Kidney Organoids and Clinical Populations.” JCI Insight 6(24). doi: 10.1172/jci.insight.154882.
Ishibashi, Julien Roy, Riya Keshri, Tommy Henry Taslim, Daniel Kennedy Brewer, Tung Ching Chan, Scott Lyons, Anika Marie McManamen, Ashley Chen, Debra Del Castillo, and Hannele Ruohola-Baker. 2021. “Chemical Genetic Screen in Drosophila Germline Uncovers Small Molecule Drugs That Sensitize Stem Cells to Insult-Induced Apoptosis.” Cells 10(10). doi: 10.3390/cells10102771.
Zhao, Yan Ting, Jorge A. Fallas, Shally Saini, George Ueda, Logeshwaran Somasundaram, Ziben Zhou, Infencia Xavier Raj, Chunfu Xu, Lauren Carter, Samuel Wrenn, Julie Mathieu, Drew L. Sellers, David Baker, and Hannele Ruohola-Baker. 2021. “F-Domain Valency Determines Outcome of Signaling through the Angiopoietin Pathway.” EMBO Reports 22(12):e53471. doi: 10.15252/embr.202153471.
Ehnes, D. D., A. M. Hussein, C. B. Ware, J. Mathieu, and H. Ruohola-Baker. 2020. “Combinatorial Metabolism Drives the Naive to Primed Pluripotent Chromatin Landscape.” Experimental Cell Research 389(2):111913. doi: 10.1016/j.yexcr.2020.111913.
Hussein, Abdiasis M., Yuliang Wang, Julie Mathieu, Lilyana Margaretha, Chaozhong Song, Daniel C. Jones, Christopher Cavanaugh, Jason W. Miklas, Elisabeth Mahen, Megan R. Showalter, Walter L. Ruzzo, Oliver Fiehn, Carol B. Ware, C. Anthony Blau, and Hannele Ruohola-Baker. 2020. “Metabolic Control over MTOR-Dependent Diapause-like State.” Developmental Cell 52(2):236-250.e7. doi: 10.1016/j.devcel.2019.12.018.
Ishibashi, Julien Roy, Tommy Henry Taslim, and Hannele Ruohola-Baker. 2020. “Germline Stem Cell Aging in the Drosophila Ovary.” Current Opinion in Insect Science 37:57–62. doi: 10.1016/j.cois.2019.11.003.
Miklas, Jason W., Elisa Clark, Shiri Levy, Damien Detraux, Andrea Leonard, Kevin Beussman, Megan R. Showalter, Alec T. Smith, Peter Hofsteen, Xiulan Yang, Jesse Macadangdang, Tuula Manninen, Daniel Raftery, Anup Madan, Anu Suomalainen, Deok-Ho Kim, Charles E. Murry, Oliver Fiehn, Nathan J. Sniadecki, Yuliang Wang, and Hannele Ruohola-Baker. 2020. “Author Correction: TFPa/HADHA Is Required for Fatty Acid Beta-Oxidation and Cardiolipin Re-Modeling in Human Cardiomyocytes.” Nature Communications 11(1):2387. doi: 10.1038/s41467-020-16186-9.
Miklas, Jason W., and Hannele Ruohola-Baker. 2020. “Using Mitochondrial Trifunctional Protein Deficiency to Understand Maternal Health.” Journal of Cellular Signaling 1(3):97–101. doi: 10.33696/signaling.1.018.
Somasundaram, Logeshwaran, Shiri Levy, Abdiasis M. Hussein, Devon D. Ehnes, Julie Mathieu, and Hannele Ruohola-Baker. 2020. “Epigenetic Metabolites License Stem Cell States.” Current Topics in Developmental Biology 138:209–40. doi: 10.1016/bs.ctdb.2020.02.003.
Battle, Stephanie L., Naresh Doni Jayavelu, Robert N. Azad, Jennifer Hesson, Faria N. Ahmed, Eliah G. Overbey, Joseph A. Zoller, Julie Mathieu, Hannele Ruohola-Baker, Carol B. Ware, and R. David Hawkins. 2019. “Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States.” Stem Cell Reports 12(5):1129–44. doi: 10.1016/j.stemcr.2019.04.004.
Macrin, Dannie, Ammar Alghadeer, Yan Ting Zhao, Jason W. Miklas, Abdiasis M. Hussein, Damien Detraux, Aaron M. Robitaille, Anup Madan, Randall T. Moon, Yuliang Wang, Arikketh Devi, Julie Mathieu, and Hannele Ruohola-Baker. 2019. “Metabolism as an Early Predictor of DPSCs Aging.” Scientific Reports 9(1):2195. doi: 10.1038/s41598-018-37489-4.
Mathieu, J., D. Detraux, D. Kuppers, Y. Wang, C. Cavanaugh, S. Sidhu, S. Levy, A. M. Robitaille, A. Ferreccio, T. Bottorff, A. McAlister, L. Somasundaram, F. Artoni, S. Battle, R. D. Hawkins, R. T. Moon, C. B. Ware, P. J. Paddison, and H. Ruohola-Baker. 2019. “Folliculin Regulates MTORC1/2 and WNT Pathways in Early Human Pluripotency.” Nature Communications 10(1):632. doi: 10.1038/s41467-018-08020-0.
Miklas, Jason W., Elisa Clark, Shiri Levy, Damien Detraux, Andrea Leonard, Kevin Beussman, Megan R. Showalter, Alec T. Smith, Peter Hofsteen, Xiulan Yang, Jesse Macadangdang, Tuula Manninen, Daniel Raftery, Anup Madan, Anu Suomalainen, Deok-Ho Kim, Charles E. Murry, Oliver Fiehn, Nathan J. Sniadecki, Yuliang Wang, and Hannele Ruohola-Baker. 2019. “TFPa/HADHA Is Required for Fatty Acid Beta-Oxidation and Cardiolipin Re-Modeling in Human Cardiomyocytes.” Nature Communications 10(1):4671. doi: 10.1038/s41467-019-12482-1.
Siebenthall, Kyle T., Chris P. Miller, Jeff D. Vierstra, Julie Mathieu, Maria Tretiakova, Alex Reynolds, Richard Sandstrom, Eric Rynes, Eric Haugen, Audra Johnson, Jemma Nelson, Daniel Bates, Morgan Diegel, Douglass Dunn, Mark Frerker, Michael Buckley, Rajinder Kaul, Ying Zheng, Jonathan Himmelfarb, Hannele Ruohola-Baker, and Shreeram Akilesh. 2019. “Integrated Epigenomic Profiling Reveals Endogenous Retrovirus Reactivation in Renal Cell Carcinoma.” EBioMedicine 41:427–42. doi: 10.1016/j.ebiom.2019.01.063.
Wang, Yuliang, Abdiasis M. Hussein, Logeshwaran Somasundaram, Rithika Sankar, Damien Detraux, Julie Mathieu, and Hannele Ruohola-Baker. 2019. “MicroRNAs Regulating Human and Mouse Naïve Pluripotency.” International Journal of Molecular Sciences 20(23). doi: 10.3390/ijms20235864.
Yang, Xiulan, Marita L. Rodriguez, Andrea Leonard, Lihua Sun, Karin A. Fischer, Yuliang Wang, Julia Ritterhoff, Limei Zhao, Stephen C. Jr Kolwicz, Lil Pabon, Hans Reinecke, Nathan J. Sniadecki, Rong Tian, Hannele Ruohola-Baker, Haodong Xu, and Charles E. Murry. 2019. “Fatty Acids Enhance the Maturation of Cardiomyocytes Derived from Human Pluripotent Stem Cells.” Stem Cell Reports 13(4):657–68. doi: 10.1016/j.stemcr.2019.08.013.
Ferreccio, Amy, Julie Mathieu, Damien Detraux, Logeshwaran Somasundaram, Christopher Cavanaugh, Bryce Sopher, Karin Fischer, Thomas Bello, Abdiasis M Hussein, Shiri Levy, Savannah Cook, Sonia B. Sidhu, Filippo Artoni, Nathan J. Palpant, Hans Reinecke, Yuliang Wang, Patrick Paddison, Charles Murry, Suman Jayadev, Carol Ware, and Hannele Ruohola-Baker. 2018. “Inducible CRISPR Genome Editing Platform in Naive Human Embryonic Stem Cells Reveals JARID2 Function in Self-Renewal.” Cell Cycle (Georgetown, Tex.) 17(5):535–49. doi: 10.1080/15384101.2018.1442621.
Friedman, Clayton E., Quan Nguyen, Samuel W. Lukowski, Abbigail Helfer, Han Sheng Chiu, Jason Miklas, Shiri Levy, Shengbao Suo, Jing-Dong Jackie Han, Pierre Osteil, Guangdun Peng, Naihe Jing, Greg J. Baillie, Anne Senabouth, Angelika N. Christ, Timothy J. Bruxner, Charles E. Murry, Emily S. Wong, Jun Ding, Yuliang Wang, James Hudson, Hannele Ruohola-Baker, Ziv Bar-Joseph, Patrick P. L. Tam, Joseph E. Powell, and Nathan J. Palpant. 2018. “Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.” Cell Stem Cell 23(4):586-598.e8. doi: 10.1016/j.stem.2018.09.009.
Artoni, Filippo, Rebecca E. Kreipke, Ondina Palmeira, Connor Dixon, Zachary Goldberg, and Hannele Ruohola-Baker. 2017. “Loss of Foxo Rescues Stem Cell Aging in Drosophila Germ Line.” ELife 6. doi: 10.7554/eLife.27842.
Brown, K., P. Yang, D. Salvador, R. Kulikauskas, H. Ruohola-Baker, A. M. Robitaille, A. J. Chien, R. T. Moon, and V. Sherwood. 2017. “WNT/β-Catenin Signaling Regulates Mitochondrial Activity to Alter the Oncogenic Potential of Melanoma in a PTEN-Dependent Manner.” Oncogene 36(22):3119–36. doi: 10.1038/onc.2016.450.
Kreipke, R. E., Y. V. Kwon, H. R. Shcherbata, and H. Ruohola-Baker. 2017. “Drosophila Melanogaster as a Model of Muscle Degeneration Disorders.” Current Topics in Developmental Biology 121:83–109. doi: 10.1016/bs.ctdb.2016.07.003.
Mathieu, Julie, and Hannele Ruohola-Baker. 2017. “Metabolic Remodeling during the Loss and Acquisition of Pluripotency.” Development (Cambridge, England) 144(4):541–51. doi: 10.1242/dev.128389.
Moody, James D., Shiri Levy, Julie Mathieu, Yalan Xing, Woojin Kim, Cheng Dong, Wolfram Tempel, Aaron M. Robitaille, Luke T. Dang, Amy Ferreccio, Damien Detraux, Sonia Sidhu, Licheng Zhu, Lauren Carter, Chao Xu, Cristina Valensisi, Yuliang Wang, R. David Hawkins, Jinrong Min, Randall T. Moon, Stuart H. Orkin, David Baker, and Hannele Ruohola-Baker. 2017. “First Critical Repressive H3K27me3 Marks in Embryonic Stem Cells Identified Using Designed Protein Inhibitor.” Proceedings of the National Academy of Sciences of the United States of America 114(38):10125–30. doi: 10.1073/pnas.1706907114.
Ellen Kreipke, Rebecca, Yuliang Wang, Jason Wayne Miklas, Julie Mathieu, and Hannele Ruohola-Baker. 2016. “Metabolic Remodeling in Early Development and Cardiomyocyte Maturation.” Seminars in Cell & Developmental Biology 52:84–92. doi: 10.1016/j.semcdb.2016.02.004.
Mathieu, Julie, and Hannele Ruohola-Baker. 2016. “Metabolic RemodeLIN of Pluripotency.” Cell Stem Cell 19(1):3–4. doi: 10.1016/j.stem.2016.06.016.
Rahkonen, Nelly, Aki Stubb, Maia Malonzo, Sanna Edelman, Maheswara Reddy Emani, Elisa Närvä, Harri Lähdesmäki, Hannele Ruohola-Baker, Riitta Lahesmaa, and Riikka Lund. 2016. “Mature Let-7 MiRNAs Fine Tune Expression of LIN28B in Pluripotent Human Embryonic Stem Cells.” Stem Cell Research 17(3):498–503. doi: 10.1016/j.scr.2016.09.025.
Xu, Zhuojin, Aaron M. Robitaille, Jason D. Berndt, Kathryn C. Davidson, Karin A. Fischer, Julie Mathieu, Jennifer C. Potter, Hannele Ruohola-Baker, and Randall T. Moon. 2016. “Wnt/β-Catenin Signaling Promotes Self-Renewal and Inhibits the Primed State Transition in Naïve Human Embryonic Stem Cells.” Proceedings of the National Academy of Sciences of the United States of America 113(42):E6382–90. doi: 10.1073/pnas.1613849113.
Sperber H, Mathieu J, Wang Y, Ferreccio A, Hesson J, Xu Z, Fischer KA, Devi A, Detraux D, Gu H, Battle SL, Showalter M, Valensisi C, Bielas JH, Ericson NG, Margaretha L, Robitaille AM, Margineantu D, Fiehn O, Hockenbery D, Blau CA, Raftery D, Margolin AA, Hawkins RD, Moon RT, Ware CB, Ruohola-Baker H. The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition. Nat Cell Biol. 2015 Dec;17(12):1523-35. doi: 10.1038/ncb3264. Epub 2015 Nov 16.PMID:26571212
Kuppusamy KT, Jones DC, Sperber H, Madan A, Fischer KA, Rodriguez ML, Pabon L, Zhu WZ, Tulloch NL, Yang X, Sniadecki NJ, Laflamme MA, Ruzzo WL, Murry CE, Ruohola-Baker H. Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes. Proc Natl Acad Sci U S A. 2015 May 26;112(21):E2785-94. doi: 10.1073/pnas.1424042112. Epub 2015 May 11. PubMed 25964336
Xing Y, Su TT, Ruohola-Baker H. Tie-mediated signal from apoptotic cells protects stem cells in Drosophila melanogaster. Nature Communications. 2015 May 11;6:7058. doi: 10.1038/ncomms8058. PubMed 25959206
Yang X, Rodriguez M, Pabon L, Fischer KA, Reinecke H, Regnier M, Sniadecki NJ, Ruohola-Baker H, Murry CE. Tri-iodo-l-thyronine promotes the maturation of human cardiomyocytes-derived from induced pluripotent stem cells. Journal of molecular and cellular cardiology. Published:2014 Vol 72. PubMed 24735830.
Sperber H, Beem A, Shannon S, Jones R, Banik P, Chen Y, Ku S, Varani G, Yao S, Ruohola-Baker H. miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure. RNA (New York, N.Y.). Published:2014 Vol 20(5). PubMed 24677349.
Mathieu J, Zhou W, Xing Y, Sperber H, Ferreccio A, Agoston Z, Kuppusamy KT, Moon RT, Ruohola-Baker H. Hypoxia-inducible factors have distinct and stage-specific roles during reprogramming of human cells to pluripotency. Cell stem cell. Published:2014 Vol 14(5). PubMed 24656769.
Ware CB, Nelson AM, Mecham B, Hesson J, Zhou W, Jonlin EC, Jimenez-Caliani AJ, Deng X, Cavanaugh C, Cook S, Tesar PJ, Okada J, Margaretha L, Sperber H, Choi M, Blau CA, Treuting PM, Hawkins RD, Cirulli V, Ruohola-Baker H. Derivation of naive human embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America. Published:2014 Vol 111(12). PubMed24623855.
Guan X, Mack DL, Moreno CM, Strande JL, Mathieu J, Shi Y, Markert CD, Wang Z, Liu G, Lawlor MW, Moorefield EC, Jones TN, Fugate JA, Furth ME, Murry CE, Ruohola-Baker H, Zhang Y, Santana LF, Childers MK. Dystrophin-deficient cardiomyocytes derived from human urine: new biologic reagents for drug discovery. Stem cell research. Published:2014 Vol 12(2). PubMed 24434629.
Nguyen-Tran DH, Hait NC, Sperber H, Qi J, Fischer K, Ieronimakis N, Pantoja M, Hays A, Allegood J, Reyes M, Spiegel S, Ruohola-Baker H. Molecular mechanism of sphingosine-1-phosphate action in Duchenne muscular dystrophy. Disease models & mechanisms. Published:2014 Vol 7(1). PubMed 24077965.
Ieronimakis N, Pantoja M, Hays AL, Dosey TL, Qi J, Fischer KA, Hoofnagle AN, Sadilek M, Chamberlain JS, Ruohola-Baker H, Reyes M. Increased sphingosine-1-phosphate improves muscle regeneration in acutely injured mdx mice. Skeletal muscle. Published:2013 Vol 3(1). PubMed 23915702.
Mathieu J, Zhang Z, Nelson A, Lamba DA, Reh TA, Ware C, Ruohola-Baker H. Hypoxia induces re-entry of committed cells into pluripotency. Stem cells (Dayton, Ohio). Published:2013 Vol 31(9). PubMed 23765801.
Mathieu J, Ruohola-Baker H. Regulation of stem cell populations by microRNAs. Advances in experimental medicine and biology. Published:2013 Vol 786. PubMed 23696365.
Kuppusamy KT, Sperber H, Ruohola-Baker H. MicroRNA regulation and role in stem cell maintenance, cardiac differentiation and hypertrophy. Current molecular medicine. Published:2013 Vol 13(5). PubMed 23642057.
Zhou W, Tan Y, Anderson DJ, Crist EM, Ruohola-Baker H, Salipante SJ, Horwitz MS. Use of somatic mutations to quantify random contributions to mouse development. BMC genomics. Published:2013 Vol 14. PubMed 23327737.
Pantoja M, Ruohola-Baker H. Drosophila as a starting point for developing therapeutics for the rare disease Duchenne Muscular Dystrophy. Rare diseases (Austin, Tex.). Published:2013 Vol 1. PubMed25002997.
Pantoja M, Fischer KA, Ieronimakis N, Reyes M, Ruohola-Baker H. Genetic elevation of sphingosine 1-phosphate suppresses dystrophic muscle phenotypes in Drosophila. Development (Cambridge, England). Published:2013 Vol 140(1). PubMed 23154413.
Zhou W, Choi M, Margineantu D, Margaretha L, Hesson J, Cavanaugh C, Blau CA, Horwitz MS, Hockenbery D, Ware C, Ruohola-Baker H. HIF1α induced switch from bivalent to exclusively glycolytic metabolism during ESC-to-EpiSC/hESC transition. The EMBO journal. Published:2012 Vol 31(9). PubMed 22446391.
Xing Y, Kurtz I, Thuparani M, Legard J, Ruohola-Baker H. Loss-of-Function Screen Reveals Novel Regulators Required for Drosophila Germline Stem Cell Self-Renewal. G3 (Bethesda, Md.). Published:2012 Vol 2(3). PubMed 22413088.
Zhou W, Dosey TL, Biechele T, Moon RT, Horwitz MS, Ruohola-Baker H. Assessment of hypoxia inducible factor levels in cancer cell lines upon hypoxic induction using a novel reporter construct. PloS one. Published:2011 Vol 6(11). PubMed 22132102.
Mathieu J, Zhang Z, Zhou W, Wang AJ, Heddleston JM, Pinna CM, Hubaud A, Stadler B, Choi M, Bar M, Tewari M, Liu A, Vessella R, Rostomily R, Born D, Horwitz M, Ware C, Blau CA, Cleary MA, Rich JN, Ruohola-Baker H. HIF induces human embryonic stem cell markers in cancer cells. Cancer research. Published:2011 Vol 71(13). PubMed 21712410.
Mosqueira M, Willmann G, Ruohola-Baker H, Khurana TS. Chronic hypoxia impairs muscle function in the Drosophila model of Duchenne’s muscular dystrophy (DMD). PloS one. Published:2010 Vol 5(10). PubMed 20975992.
Vêncio EF, Pascal LE, Page LS, Denyer G, Wang AJ, Ruohola-Baker H, Zhang S, Wang K, Galas DJ, Liu AY. Embryonal carcinoma cell induction of miRNA and mRNA changes in co-cultured prostate stromal fibromuscular cells. Journal of cellular physiology. Published:2011 Vol 226(6). PubMed 20945389.
Chan K, Ruohola-Baker H. Assessing in vivo microRNA function in the germline stem cells of the Drosophila ovary. Methods in molecular biology (Clifton, N.J.). Published:2010 Vol 650. PubMed 20686953.
Zhan Y, Melian NY, Pantoja M, Haines N, Ruohola-Baker H, Bourque CW, Rao Y, Carbonetto S. Dystroglycan and mitochondrial ribosomal protein L34 regulate differentiation in the Drosophila eye. PloS one. Published:2010 Vol 5(5). PubMed 20463973.
Stadler B, Ivanovska I, Mehta K, Song S, Nelson A, Tan Y, Mathieu J, Darby C, Blau CA, Ware C, Peters G, Miller DG, Shen L, Cleary MA, Ruohola-Baker H. Characterization of microRNAs involved in embryonic stem cell states. Stem cells and development. Published:2010 Vol 19(7). PubMed 20128659.
Qi J, Yu JY, Shcherbata HR, Mathieu J, Wang AJ, Seal S, Zhou W, Stadler BM, Bourgin D, Wang L, Nelson A, Ware C, Raymond C, Lim LP, Magnus J, Ivanovska I, Diaz R, Ball A, Cleary MA, Ruohola-Baker H. microRNAs regulate human embryonic stem cell division. Cell cycle (Georgetown, Tex.). Published:2009 Vol 8(22). PubMed 19823043.
Reynolds SH, Ruohola-Baker H. PIWI goes solo in the soma. Developmental cell. Published:2009 Vol 16(5). PubMed 19460338.
Yu JY, Reynolds SH, Hatfield SD, Shcherbata HR, Fischer KA, Ward EJ, Long D, Ding Y, Ruohola-Baker H. Dicer-1-dependent Dacapo suppression acts downstream of Insulin receptor in regulating cell division of Drosophila germline stem cells. Development (Cambridge, England). Published:2009 Vol 136(9). PubMed 19336466.
Yatsenko AS, Kucherenko MM, Pantoja M, Fischer KA, Madeoy J, Deng WM, Schneider M, Baumgartner S, Akey J, Shcherbata HR, Ruohola-Baker H. The conserved WW-domain binding sites in Dystroglycan C-terminus are essential but partially redundant for Dystroglycan function. BMC developmental biology. Published:2009 Vol 9. PubMed 19250553.
Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM, Ruzzo WL, Ware C, Radich JP, Gentleman R, Ruohola-Baker H, Tewari M. MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem cells (Dayton, Ohio). Published:2008 Vol 26(10). PubMed 18583537.
Kucherenko MM, Pantoja M, Yatsenko AS, Shcherbata HR, Fischer KA, Maksymiv DV, Chernyk YI, Ruohola-Baker H. Genetic modifier screens reveal new components that interact with the Drosophila dystroglycan-dystrophin complex. PloS one. Published:2008 Vol 3(6). PubMed 18545683.
Stadler BM, Ruohola-Baker H. Small RNAs: keeping stem cells in line. Cell. Published:2008 Vol 132(4). PubMed 18295575.
Shcherbata HR, Ward EJ, Fischer KA, Yu JY, Reynolds SH, Chen CH, Xu P, Hay BA, Ruohola-Baker H. Stage-specific differences in the requirements for germline stem cell maintenance in the Drosophila ovary. Cell stem cell. Published:2007 Vol 1(6). PubMed 18213359.
Hatfield S, Ruohola-Baker H. microRNA and stem cell function. Cell and tissue research. Published:2008 Vol 331(1). PubMed 17987317.
Yatsenko AS, Gray EE, Shcherbata HR, Patterson LB, Sood VD, Kucherenko MM, Baker D, Ruohola-Baker H. A putative Src homology 3 domain binding motif but not the C-terminal dystrophin WW domain binding motif is required for dystroglycan function in cellular polarity in Drosophila. The Journal of biological chemistry. Published:2007 Vol 282(20). PubMed 17355978.
Shcherbata HR, Yatsenko AS, Patterson L, Sood VD, Nudel U, Yaffe D, Baker D, Ruohola-Baker H. Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy. The EMBO journal. Published:2007 Vol 26(2). PubMed 17215867.
Ward EJ, Shcherbata HR, Reynolds SH, Fischer KA, Hatfield SD, Ruohola-Baker H. Stem cells signal to the niche through the Notch pathway in the Drosophila ovary. Current biology : CB. Published:2006 Vol 16(23). PubMed 17070683.
Ward EJ, Zhou X, Riddiford LM, Berg CA, Ruohola-Baker H. Border of Notch activity establishes a boundary between the two dorsal appendage tube cell types. Developmental biology. Published:2006 Vol 297(2). PubMed 16828735.
Jordan KC, Schaeffer V, Fischer KA, Gray EE, Ruohola-Baker H. Notch signaling through tramtrack bypasses the mitosis promoting activity of the JNK pathway in the mitotic-to-endocycle transition of Drosophila follicle cells. BMC developmental biology. Published:2006 Vol 6. PubMed 16542414.
Shcherbata HR, Hatfield S, Ward EJ, Reynolds S, Fischer KA, Ruohola-Baker H. The MicroRNA pathway plays a regulatory role in stem cell division. Cell cycle (Georgetown, Tex.). Published:2006 Vol 5(2). PubMed 16357538.
Hatfield SD, Shcherbata HR, Fischer KA, Nakahara K, Carthew RW, Ruohola-Baker H. Stem cell division is regulated by the microRNA pathway. Nature. Published:2005 Vol 435(7044). PubMed 15944714.
Althauser C, Jordan KC, Deng WM, Ruohola-Baker H. Fringe-dependent notch activation and tramtrack function are required for specification of the polar cells in Drosophila oogenesis. Developmental dynamics : an official publication of the American Association of Anatomists. Published:2005 Vol 232(4). PubMed 15765546.
Jordan KC, Hatfield SD, Tworoger M, Ward EJ, Fischer KA, Bowers S, Ruohola-Baker H. Genome wide analysis of transcript levels after perturbation of the EGFR pathway in the Drosophila ovary. Developmental dynamics : an official publication of the American Association of Anatomists. Published:2005 Vol 232(3). PubMed15704171.
Shcherbata HR, Althauser C, Findley SD, Ruohola-Baker H. The mitotic-to-endocycle switch in Drosophila follicle cells is executed by Notch-dependent regulation of G1/S, G2/M and M/G1 cell-cycle transitions. Development (Cambridge, England). Published:2004 Vol 131(13). PubMed 15175253.
Schaeffer V, Althauser C, Shcherbata HR, Deng WM, Ruohola-Baker H. Notch-dependent Fizzy-related/Hec1/Cdh1 expression is required for the mitotic-to-endocycle transition in Drosophila follicle cells. Current biology : CB. Published:2004 Vol 14(7). PubMed 15062106.
Findley SD, Tamanaha M, Clegg NJ, Ruohola-Baker H. Maelstrom, a Drosophila spindle-class gene, encodes a protein that colocalizes with Vasa and RDE1/AGO1 homolog, Aubergine, in nuage. Development (Cambridge, England). Published:2003 Vol 130(5). PubMed 12538514.
Deng WM, Schneider M, Frock R, Castillejo-Lopez C, Gaman EA, Baumgartner S, Ruohola-Baker H. Dystroglycan is required for polarizing the epithelial cells and the oocyte in Drosophila. Development (Cambridge, England). Published:2003 Vol 130(1). PubMed 12441301.
Deng WM, Althauser C, Ruohola-Baker H. Notch-Delta signaling induces a transition from mitotic cell cycle to endocycle in Drosophila follicle cells. Development (Cambridge, England). Published:2001 Vol 128(23). PubMed 11731454.
Clegg NJ, Findley SD, Mahowald AP, Ruohola-Baker H. Maelstrom is required to position the MTOC in stage 2-6 Drosophila oocytes. Development genes and evolution. Published:2001 Vol 211(1). PubMed11277405.
Keller Larkin M, Deng WM, Holder K, Tworoger M, Clegg N, Ruohola-Baker H. Role of Notch pathway in terminal follicle cell differentiation during Drosophila oogenesis. Development genes and evolution. Published:1999 Vol 209(5). PubMed 11252183.
Deng WM, Ruohola-Baker H. Laminin A is required for follicle cell-oocyte signaling that leads to establishment of the anterior-posterior axis in Drosophila. Current biology : CB. Published:2000 Vol 10(11). PubMed 10837250.
Jordan KC, Clegg NJ, Blasi JA, Morimoto AM, Sen J, Stein D, McNeill H, Deng WM, Tworoger M, Ruohola-Baker H. The homeobox gene mirror links EGF signalling to embryonic dorso-ventral axis formation through notch activation. Nature genetics. Published:2000 Vol 24(4). PubMed 10742112.
Bryant Z, Subrahmanyan L, Tworoger M, LaTray L, Liu CR, Li MJ, van den Engh G, Ruohola-Baker H. Characterization of differentially expressed genes in purified Drosophila follicle cells: toward a general strategy for cell type-specific developmental analysis. Proceedings of the National Academy of Sciences of the United States of America. Published:1999 Vol 96(10). PubMed 10318923.
Tworoger M, Larkin MK, Bryant Z, Ruohola-Baker H. Mosaic analysis in the drosophila ovary reveals a common hedgehog-inducible precursor stage for stalk and polar cells. Genetics. Published:1999 Vol 151(2). PubMed 9927465.
Clegg NJ, Frost DM, Larkin MK, Subrahmanyan L, Bryant Z, Ruohola-Baker H. maelstrom is required for an early step in the establishment of Drosophila oocyte polarity: posterior localization of grk mRNA. Development (Cambridge, England). Published:1997 Vol 124(22). PubMed 9409682.
Morimoto AM, Jordan KC, Tietze K, Britton JS, O’Neill EM, Ruohola-Baker H. Pointed, an ETS domain transcription factor, negatively regulates the EGF receptor pathway in Drosophila oogenesis. Development (Cambridge, England). Published:1996 Vol 122(12). PubMed 9012496.
Larkin MK, Holder K, Yost C, Giniger E, Ruohola-Baker H. Expression of constitutively active Notch arrests follicle cells at a precursor stage during Drosophila oogenesis and disrupts the anterior-posterior axis of the oocyte. Development (Cambridge, England). Published:1996 Vol 122(11). PubMed 8951079.
Clark I, Giniger E, Ruohola-Baker H, Jan LY, Jan YN. Transient posterior localization of a kinesin fusion protein reflects anteroposterior polarity of the Drosophila oocyte. Current biology : CB. Published:1994 Vol 4(4). PubMed 7922338.
Ruohola-Baker H, Jan LY, Jan YN. The role of gene cassettes in axis formation during Drosophila oogenesis. Trends in genetics : TIG. Published:1994 Vol 10(3). PubMed 8178370.
Ruohola-Baker H, Grell E, Chou TB, Baker D, Jan LY, Jan YN. Spatially localized rhomboid is required for establishment of the dorsal-ventral axis in Drosophila oogenesis. Cell. Published:1993 Vol 73(5). PubMed 8500182.
Ferro-Novick S, Newman AP, Groesch M, Ruohola H, Rossi G, Graf J, Shim J. An analysis of BET1, BET2, and BOS1. Three factors mediating ER to Golgi transport in yeast. Cell biophysics. Published: Vol 19(1-3). PubMed 1726885.
Ruohola H, Bremer KA, Baker D, Swedlow JR, Jan LY, Jan YN. Role of neurogenic genes in establishment of follicle cell fate and oocyte polarity during oogenesis in Drosophila. Cell. Published:1991 Vol 66(3). PubMed 1907889.
Groesch ME, Ruohola H, Bacon R, Rossi G, Ferro-Novick S. Isolation of a functional vesicular intermediate that mediates ER to Golgi transport in yeast. The Journal of cell biology. Published:1990 Vol 111(1). PubMed 2195039.
Bacon RA, Salminen A, Ruohola H, Novick P, Ferro-Novick S. The GTP-binding protein Ypt1 is required for transport in vitro: the Golgi apparatus is defective in ypt1 mutants. The Journal of cell biology. Published:1989 Vol 109(3). PubMed 2504726.
Walworth NC, Goud B, Ruohola H, Novick PJ. Fractionation of yeast organelles. Methods in cell biology. Published:1989 Vol 31. PubMed2674627.
Ruohola H, Kabcenell AK, Ferro-Novick S. Reconstitution of transport from the ER to the Golgi complex in yeast using microsomes and permeabilized yeast cells. Methods in cell biology. Published:1989 Vol 31. PubMed 2674624.
Ruohola H, Kabcenell AK, Ferro-Novick S. Reconstitution of protein transport from the endoplasmic reticulum to the Golgi complex in yeast: the acceptor Golgi compartment is defective in the sec23 mutant. The Journal of cell biology. Published:1988 Vol 107(4). PubMed3049622.
Ruohola H, Baker SM, Parker R, Platt T. Orientation-dependent function of a short CYC1 DNA fragment in directing mRNA 3′ end formation in yeast. Proceedings of the National Academy of Sciences of the United States of America. Published:1988 Vol 85(14). PubMed2839828.
Ruohola H, Ferro-Novick S. Sec53, a protein required for an early step in secretory protein processing and transport in yeast, interacts with the cytoplasmic surface of the endoplasmic reticulum. Proceedings of the National Academy of Sciences of the United States of America. Published:1987 Vol 84(23). PubMed 3317409.
Nikula P, Ruohola H, Alhonen-Hongisto L, Janne J. Carnitine prevents the early mitochondrial damage induced by methylglyoxal bis(guanylhydrazone) in L1210 leukaemia cells. The Biochemical journal. Published:1985 Vol 228(2). PubMed 3837667.
Seppanen P, Ruohola H, Janne J. Ethylglyoxal bis(guanylhydrazone) as an inhibitor of polyamine biosynthesis in L1210 leukemia cells. Biochimica et biophysica acta. Published:1984 Vol 803(4). PubMed6322861.
Kuppusamy KT, Jones DC, Sperber H, Madan A, Fischer KA, Rodriguez ML, Pabon L, Zhu WZ, Tulloch NL, Yang X, Sniadecki NJ, Laflamme MA, Ruzzo WL, Murry CE, Ruohola-Baker H. Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes. Proc Natl Acad Sci U S A. 2015 May 26;112(21):E2785-94. doi: 10.1073/pnas.1424042112. Epub 2015 May 11. PubMed 25964336
Xing Y, Su TT, Ruohola-Baker H. Tie-mediated signal from apoptotic cells protects stem cells in Drosophila melanogaster. Nature Communications. 2015 May 11;6:7058. doi: 10.1038/ncomms8058. PubMed 25959206
Yang X, Rodriguez M, Pabon L, Fischer KA, Reinecke H, Regnier M, Sniadecki NJ, Ruohola-Baker H, Murry CE. Tri-iodo-l-thyronine promotes the maturation of human cardiomyocytes-derived from induced pluripotent stem cells. Journal of molecular and cellular cardiology. Published:2014 Vol 72. PubMed 24735830.
Sperber H, Beem A, Shannon S, Jones R, Banik P, Chen Y, Ku S, Varani G, Yao S, Ruohola-Baker H. miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure. RNA (New York, N.Y.). Published:2014 Vol 20(5). PubMed 24677349.
Mathieu J, Zhou W, Xing Y, Sperber H, Ferreccio A, Agoston Z, Kuppusamy KT, Moon RT, Ruohola-Baker H. Hypoxia-inducible factors have distinct and stage-specific roles during reprogramming of human cells to pluripotency. Cell stem cell. Published:2014 Vol 14(5). PubMed 24656769.
Ware CB, Nelson AM, Mecham B, Hesson J, Zhou W, Jonlin EC, Jimenez-Caliani AJ, Deng X, Cavanaugh C, Cook S, Tesar PJ, Okada J, Margaretha L, Sperber H, Choi M, Blau CA, Treuting PM, Hawkins RD, Cirulli V, Ruohola-Baker H. Derivation of naive human embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America. Published:2014 Vol 111(12). PubMed24623855.
Guan X, Mack DL, Moreno CM, Strande JL, Mathieu J, Shi Y, Markert CD, Wang Z, Liu G, Lawlor MW, Moorefield EC, Jones TN, Fugate JA, Furth ME, Murry CE, Ruohola-Baker H, Zhang Y, Santana LF, Childers MK. Dystrophin-deficient cardiomyocytes derived from human urine: new biologic reagents for drug discovery. Stem cell research. Published:2014 Vol 12(2). PubMed 24434629.
Nguyen-Tran DH, Hait NC, Sperber H, Qi J, Fischer K, Ieronimakis N, Pantoja M, Hays A, Allegood J, Reyes M, Spiegel S, Ruohola-Baker H. Molecular mechanism of sphingosine-1-phosphate action in Duchenne muscular dystrophy. Disease models & mechanisms. Published:2014 Vol 7(1). PubMed 24077965.
Ieronimakis N, Pantoja M, Hays AL, Dosey TL, Qi J, Fischer KA, Hoofnagle AN, Sadilek M, Chamberlain JS, Ruohola-Baker H, Reyes M. Increased sphingosine-1-phosphate improves muscle regeneration in acutely injured mdx mice. Skeletal muscle. Published:2013 Vol 3(1). PubMed 23915702.
Mathieu J, Zhang Z, Nelson A, Lamba DA, Reh TA, Ware C, Ruohola-Baker H. Hypoxia induces re-entry of committed cells into pluripotency. Stem cells (Dayton, Ohio). Published:2013 Vol 31(9). PubMed 23765801.
Mathieu J, Ruohola-Baker H. Regulation of stem cell populations by microRNAs. Advances in experimental medicine and biology. Published:2013 Vol 786. PubMed 23696365.
Kuppusamy KT, Sperber H, Ruohola-Baker H. MicroRNA regulation and role in stem cell maintenance, cardiac differentiation and hypertrophy. Current molecular medicine. Published:2013 Vol 13(5). PubMed 23642057.
Zhou W, Tan Y, Anderson DJ, Crist EM, Ruohola-Baker H, Salipante SJ, Horwitz MS. Use of somatic mutations to quantify random contributions to mouse development. BMC genomics. Published:2013 Vol 14. PubMed 23327737.
Pantoja M, Ruohola-Baker H. Drosophila as a starting point for developing therapeutics for the rare disease Duchenne Muscular Dystrophy. Rare diseases (Austin, Tex.). Published:2013 Vol 1. PubMed25002997.
Pantoja M, Fischer KA, Ieronimakis N, Reyes M, Ruohola-Baker H. Genetic elevation of sphingosine 1-phosphate suppresses dystrophic muscle phenotypes in Drosophila. Development (Cambridge, England). Published:2013 Vol 140(1). PubMed 23154413.
Zhou W, Choi M, Margineantu D, Margaretha L, Hesson J, Cavanaugh C, Blau CA, Horwitz MS, Hockenbery D, Ware C, Ruohola-Baker H. HIF1α induced switch from bivalent to exclusively glycolytic metabolism during ESC-to-EpiSC/hESC transition. The EMBO journal. Published:2012 Vol 31(9). PubMed 22446391.
Xing Y, Kurtz I, Thuparani M, Legard J, Ruohola-Baker H. Loss-of-Function Screen Reveals Novel Regulators Required for Drosophila Germline Stem Cell Self-Renewal. G3 (Bethesda, Md.). Published:2012 Vol 2(3). PubMed 22413088.
Zhou W, Dosey TL, Biechele T, Moon RT, Horwitz MS, Ruohola-Baker H. Assessment of hypoxia inducible factor levels in cancer cell lines upon hypoxic induction using a novel reporter construct. PloS one. Published:2011 Vol 6(11). PubMed 22132102.
Mathieu J, Zhang Z, Zhou W, Wang AJ, Heddleston JM, Pinna CM, Hubaud A, Stadler B, Choi M, Bar M, Tewari M, Liu A, Vessella R, Rostomily R, Born D, Horwitz M, Ware C, Blau CA, Cleary MA, Rich JN, Ruohola-Baker H. HIF induces human embryonic stem cell markers in cancer cells. Cancer research. Published:2011 Vol 71(13). PubMed 21712410.
Mosqueira M, Willmann G, Ruohola-Baker H, Khurana TS. Chronic hypoxia impairs muscle function in the Drosophila model of Duchenne’s muscular dystrophy (DMD). PloS one. Published:2010 Vol 5(10). PubMed 20975992.
Vêncio EF, Pascal LE, Page LS, Denyer G, Wang AJ, Ruohola-Baker H, Zhang S, Wang K, Galas DJ, Liu AY. Embryonal carcinoma cell induction of miRNA and mRNA changes in co-cultured prostate stromal fibromuscular cells. Journal of cellular physiology. Published:2011 Vol 226(6). PubMed 20945389.
Chan K, Ruohola-Baker H. Assessing in vivo microRNA function in the germline stem cells of the Drosophila ovary. Methods in molecular biology (Clifton, N.J.). Published:2010 Vol 650. PubMed 20686953.
Zhan Y, Melian NY, Pantoja M, Haines N, Ruohola-Baker H, Bourque CW, Rao Y, Carbonetto S. Dystroglycan and mitochondrial ribosomal protein L34 regulate differentiation in the Drosophila eye. PloS one. Published:2010 Vol 5(5). PubMed 20463973.
Stadler B, Ivanovska I, Mehta K, Song S, Nelson A, Tan Y, Mathieu J, Darby C, Blau CA, Ware C, Peters G, Miller DG, Shen L, Cleary MA, Ruohola-Baker H. Characterization of microRNAs involved in embryonic stem cell states. Stem cells and development. Published:2010 Vol 19(7). PubMed 20128659.
Qi J, Yu JY, Shcherbata HR, Mathieu J, Wang AJ, Seal S, Zhou W, Stadler BM, Bourgin D, Wang L, Nelson A, Ware C, Raymond C, Lim LP, Magnus J, Ivanovska I, Diaz R, Ball A, Cleary MA, Ruohola-Baker H. microRNAs regulate human embryonic stem cell division. Cell cycle (Georgetown, Tex.). Published:2009 Vol 8(22). PubMed 19823043.
Reynolds SH, Ruohola-Baker H. PIWI goes solo in the soma. Developmental cell. Published:2009 Vol 16(5). PubMed 19460338.
Yu JY, Reynolds SH, Hatfield SD, Shcherbata HR, Fischer KA, Ward EJ, Long D, Ding Y, Ruohola-Baker H. Dicer-1-dependent Dacapo suppression acts downstream of Insulin receptor in regulating cell division of Drosophila germline stem cells. Development (Cambridge, England). Published:2009 Vol 136(9). PubMed 19336466.
Yatsenko AS, Kucherenko MM, Pantoja M, Fischer KA, Madeoy J, Deng WM, Schneider M, Baumgartner S, Akey J, Shcherbata HR, Ruohola-Baker H. The conserved WW-domain binding sites in Dystroglycan C-terminus are essential but partially redundant for Dystroglycan function. BMC developmental biology. Published:2009 Vol 9. PubMed 19250553.
Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM, Ruzzo WL, Ware C, Radich JP, Gentleman R, Ruohola-Baker H, Tewari M. MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem cells (Dayton, Ohio). Published:2008 Vol 26(10). PubMed 18583537.
Kucherenko MM, Pantoja M, Yatsenko AS, Shcherbata HR, Fischer KA, Maksymiv DV, Chernyk YI, Ruohola-Baker H. Genetic modifier screens reveal new components that interact with the Drosophila dystroglycan-dystrophin complex. PloS one. Published:2008 Vol 3(6). PubMed 18545683.
Stadler BM, Ruohola-Baker H. Small RNAs: keeping stem cells in line. Cell. Published:2008 Vol 132(4). PubMed 18295575.
Shcherbata HR, Ward EJ, Fischer KA, Yu JY, Reynolds SH, Chen CH, Xu P, Hay BA, Ruohola-Baker H. Stage-specific differences in the requirements for germline stem cell maintenance in the Drosophila ovary. Cell stem cell. Published:2007 Vol 1(6). PubMed 18213359.
Hatfield S, Ruohola-Baker H. microRNA and stem cell function. Cell and tissue research. Published:2008 Vol 331(1). PubMed 17987317.
Yatsenko AS, Gray EE, Shcherbata HR, Patterson LB, Sood VD, Kucherenko MM, Baker D, Ruohola-Baker H. A putative Src homology 3 domain binding motif but not the C-terminal dystrophin WW domain binding motif is required for dystroglycan function in cellular polarity in Drosophila. The Journal of biological chemistry. Published:2007 Vol 282(20). PubMed 17355978.
Shcherbata HR, Yatsenko AS, Patterson L, Sood VD, Nudel U, Yaffe D, Baker D, Ruohola-Baker H. Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy. The EMBO journal. Published:2007 Vol 26(2). PubMed 17215867.
Ward EJ, Shcherbata HR, Reynolds SH, Fischer KA, Hatfield SD, Ruohola-Baker H. Stem cells signal to the niche through the Notch pathway in the Drosophila ovary. Current biology : CB. Published:2006 Vol 16(23). PubMed 17070683.
Ward EJ, Zhou X, Riddiford LM, Berg CA, Ruohola-Baker H. Border of Notch activity establishes a boundary between the two dorsal appendage tube cell types. Developmental biology. Published:2006 Vol 297(2). PubMed 16828735.
Jordan KC, Schaeffer V, Fischer KA, Gray EE, Ruohola-Baker H. Notch signaling through tramtrack bypasses the mitosis promoting activity of the JNK pathway in the mitotic-to-endocycle transition of Drosophila follicle cells. BMC developmental biology. Published:2006 Vol 6. PubMed 16542414.
Shcherbata HR, Hatfield S, Ward EJ, Reynolds S, Fischer KA, Ruohola-Baker H. The MicroRNA pathway plays a regulatory role in stem cell division. Cell cycle (Georgetown, Tex.). Published:2006 Vol 5(2). PubMed 16357538.
Hatfield SD, Shcherbata HR, Fischer KA, Nakahara K, Carthew RW, Ruohola-Baker H. Stem cell division is regulated by the microRNA pathway. Nature. Published:2005 Vol 435(7044). PubMed 15944714.
Althauser C, Jordan KC, Deng WM, Ruohola-Baker H. Fringe-dependent notch activation and tramtrack function are required for specification of the polar cells in Drosophila oogenesis. Developmental dynamics : an official publication of the American Association of Anatomists. Published:2005 Vol 232(4). PubMed 15765546.
Jordan KC, Hatfield SD, Tworoger M, Ward EJ, Fischer KA, Bowers S, Ruohola-Baker H. Genome wide analysis of transcript levels after perturbation of the EGFR pathway in the Drosophila ovary. Developmental dynamics : an official publication of the American Association of Anatomists. Published:2005 Vol 232(3). PubMed15704171.
Shcherbata HR, Althauser C, Findley SD, Ruohola-Baker H. The mitotic-to-endocycle switch in Drosophila follicle cells is executed by Notch-dependent regulation of G1/S, G2/M and M/G1 cell-cycle transitions. Development (Cambridge, England). Published:2004 Vol 131(13). PubMed 15175253.
Schaeffer V, Althauser C, Shcherbata HR, Deng WM, Ruohola-Baker H. Notch-dependent Fizzy-related/Hec1/Cdh1 expression is required for the mitotic-to-endocycle transition in Drosophila follicle cells. Current biology : CB. Published:2004 Vol 14(7). PubMed 15062106.
Findley SD, Tamanaha M, Clegg NJ, Ruohola-Baker H. Maelstrom, a Drosophila spindle-class gene, encodes a protein that colocalizes with Vasa and RDE1/AGO1 homolog, Aubergine, in nuage. Development (Cambridge, England). Published:2003 Vol 130(5). PubMed 12538514.
Deng WM, Schneider M, Frock R, Castillejo-Lopez C, Gaman EA, Baumgartner S, Ruohola-Baker H. Dystroglycan is required for polarizing the epithelial cells and the oocyte in Drosophila. Development (Cambridge, England). Published:2003 Vol 130(1). PubMed 12441301.
Deng WM, Althauser C, Ruohola-Baker H. Notch-Delta signaling induces a transition from mitotic cell cycle to endocycle in Drosophila follicle cells. Development (Cambridge, England). Published:2001 Vol 128(23). PubMed 11731454.
Clegg NJ, Findley SD, Mahowald AP, Ruohola-Baker H. Maelstrom is required to position the MTOC in stage 2-6 Drosophila oocytes. Development genes and evolution. Published:2001 Vol 211(1). PubMed11277405.
Keller Larkin M, Deng WM, Holder K, Tworoger M, Clegg N, Ruohola-Baker H. Role of Notch pathway in terminal follicle cell differentiation during Drosophila oogenesis. Development genes and evolution. Published:1999 Vol 209(5). PubMed 11252183.
Deng WM, Ruohola-Baker H. Laminin A is required for follicle cell-oocyte signaling that leads to establishment of the anterior-posterior axis in Drosophila. Current biology : CB. Published:2000 Vol 10(11). PubMed 10837250.
Jordan KC, Clegg NJ, Blasi JA, Morimoto AM, Sen J, Stein D, McNeill H, Deng WM, Tworoger M, Ruohola-Baker H. The homeobox gene mirror links EGF signalling to embryonic dorso-ventral axis formation through notch activation. Nature genetics. Published:2000 Vol 24(4). PubMed 10742112.
Bryant Z, Subrahmanyan L, Tworoger M, LaTray L, Liu CR, Li MJ, van den Engh G, Ruohola-Baker H. Characterization of differentially expressed genes in purified Drosophila follicle cells: toward a general strategy for cell type-specific developmental analysis. Proceedings of the National Academy of Sciences of the United States of America. Published:1999 Vol 96(10). PubMed 10318923.
Tworoger M, Larkin MK, Bryant Z, Ruohola-Baker H. Mosaic analysis in the drosophila ovary reveals a common hedgehog-inducible precursor stage for stalk and polar cells. Genetics. Published:1999 Vol 151(2). PubMed 9927465.
Clegg NJ, Frost DM, Larkin MK, Subrahmanyan L, Bryant Z, Ruohola-Baker H. maelstrom is required for an early step in the establishment of Drosophila oocyte polarity: posterior localization of grk mRNA. Development (Cambridge, England). Published:1997 Vol 124(22). PubMed 9409682.
Morimoto AM, Jordan KC, Tietze K, Britton JS, O’Neill EM, Ruohola-Baker H. Pointed, an ETS domain transcription factor, negatively regulates the EGF receptor pathway in Drosophila oogenesis. Development (Cambridge, England). Published:1996 Vol 122(12). PubMed 9012496.
Larkin MK, Holder K, Yost C, Giniger E, Ruohola-Baker H. Expression of constitutively active Notch arrests follicle cells at a precursor stage during Drosophila oogenesis and disrupts the anterior-posterior axis of the oocyte. Development (Cambridge, England). Published:1996 Vol 122(11). PubMed 8951079.
Clark I, Giniger E, Ruohola-Baker H, Jan LY, Jan YN. Transient posterior localization of a kinesin fusion protein reflects anteroposterior polarity of the Drosophila oocyte. Current biology : CB. Published:1994 Vol 4(4). PubMed 7922338.
Ruohola-Baker H, Jan LY, Jan YN. The role of gene cassettes in axis formation during Drosophila oogenesis. Trends in genetics : TIG. Published:1994 Vol 10(3). PubMed 8178370.
Ruohola-Baker H, Grell E, Chou TB, Baker D, Jan LY, Jan YN. Spatially localized rhomboid is required for establishment of the dorsal-ventral axis in Drosophila oogenesis. Cell. Published:1993 Vol 73(5). PubMed 8500182.
Ferro-Novick S, Newman AP, Groesch M, Ruohola H, Rossi G, Graf J, Shim J. An analysis of BET1, BET2, and BOS1. Three factors mediating ER to Golgi transport in yeast. Cell biophysics. Published: Vol 19(1-3). PubMed 1726885.
Ruohola H, Bremer KA, Baker D, Swedlow JR, Jan LY, Jan YN. Role of neurogenic genes in establishment of follicle cell fate and oocyte polarity during oogenesis in Drosophila. Cell. Published:1991 Vol 66(3). PubMed 1907889.
Groesch ME, Ruohola H, Bacon R, Rossi G, Ferro-Novick S. Isolation of a functional vesicular intermediate that mediates ER to Golgi transport in yeast. The Journal of cell biology. Published:1990 Vol 111(1). PubMed 2195039.
Bacon RA, Salminen A, Ruohola H, Novick P, Ferro-Novick S. The GTP-binding protein Ypt1 is required for transport in vitro: the Golgi apparatus is defective in ypt1 mutants. The Journal of cell biology. Published:1989 Vol 109(3). PubMed 2504726.
Walworth NC, Goud B, Ruohola H, Novick PJ. Fractionation of yeast organelles. Methods in cell biology. Published:1989 Vol 31. PubMed2674627.
Ruohola H, Kabcenell AK, Ferro-Novick S. Reconstitution of transport from the ER to the Golgi complex in yeast using microsomes and permeabilized yeast cells. Methods in cell biology. Published:1989 Vol 31. PubMed 2674624.
Ruohola H, Kabcenell AK, Ferro-Novick S. Reconstitution of protein transport from the endoplasmic reticulum to the Golgi complex in yeast: the acceptor Golgi compartment is defective in the sec23 mutant. The Journal of cell biology. Published:1988 Vol 107(4). PubMed3049622.
Ruohola H, Baker SM, Parker R, Platt T. Orientation-dependent function of a short CYC1 DNA fragment in directing mRNA 3′ end formation in yeast. Proceedings of the National Academy of Sciences of the United States of America. Published:1988 Vol 85(14). PubMed2839828.
Ruohola H, Ferro-Novick S. Sec53, a protein required for an early step in secretory protein processing and transport in yeast, interacts with the cytoplasmic surface of the endoplasmic reticulum. Proceedings of the National Academy of Sciences of the United States of America. Published:1987 Vol 84(23). PubMed 3317409.
Nikula P, Ruohola H, Alhonen-Hongisto L, Janne J. Carnitine prevents the early mitochondrial damage induced by methylglyoxal bis(guanylhydrazone) in L1210 leukaemia cells. The Biochemical journal. Published:1985 Vol 228(2). PubMed 3837667.
Seppanen P, Ruohola H, Janne J. Ethylglyoxal bis(guanylhydrazone) as an inhibitor of polyamine biosynthesis in L1210 leukemia cells. Biochimica et biophysica acta. Published:1984 Vol 803(4). PubMed6322861.