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Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.

Friedman CE, Nguyen Q, Lukowski SW, Helfer A, Chiu HS, Miklas J, Levy S, Suo S, Han JJ, Osteil P, Peng G, Jing N, Baillie GJ, Senabouth A, Christ AN, Bruxner TJ, Murry CE, Wong ES, Ding J, Wang Y, Hudson J, Ruohola-Baker H, Bar-Joseph Z, Tam PPL, Powell JE, Palpant NJ.

Cell Stem Cell. 2018 Oct 4;23(4):586-598.e8. doi: 10.1016/j.stem.2018.09.009.


Inducible CRISPR genome editing platform in naive human embryonic stem cells reveals JARID2 function in self-renewal.

Ferreccio A, Mathieu J, Detraux D, Somasundaram L, Cavanaugh C, Sopher B, Fischer K, Bello T, M Hussein A, Levy S, Cook S, Sidhu SB, Artoni F, Palpant NJ, Reinecke H, Wang Y, Paddison P, Murry C, Jayadev S, Ware C, Ruohola-Baker H.

Cell Cycle. 2018;17(5):535-549. doi: 10.1080/15384101.2018.1442621. Epub 2018 Apr 5.


Loss of foxo rescues stem cell aging in Drosophila germ line.

Artoni F, Kreipke RE, Palmeira O, Dixon C, Goldberg Z, Ruohola-Baker H.

Elife. 2017 Sep 19;6. pii: e27842. doi: 10.7554/eLife.27842.


First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor.

Moody JD, Levy S, Mathieu J, Xing Y, Kim W, Dong C, Tempel W, Robitaille AM, Dang LT, Ferreccio A, Detraux D, Sidhu S, Zhu L, Carter L, Xu C, Valensisi C, Wang Y, Hawkins RD, Min J, Moon RT, Orkin SH, Baker D, Ruohola-Baker H.

Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10125-10130. doi: 10.1073/pnas.1706907114. Epub 2017 Sep 1.


Metabolic remodeling during the loss and acquisition of pluripotency.

Mathieu J, Ruohola-Baker H.

Development. 2017 Feb 15;144(4):541-551. doi: 10.1242/dev.128389. Review.


WNT/β-catenin signaling regulates mitochondrial activity to alter the oncogenic potential of melanoma in a PTEN-dependent manner.

Brown K, Yang P, Salvador D, Kulikauskas R, Ruohola-Baker H, Robitaille AM, Chien AJ, Moon RT, Sherwood V.

Oncogene. 2017 Jun 1;36(22):3119-3136. doi: 10.1038/onc.2016.450. Epub 2017 Jan 16.


Drosophila melanogaster as a Model of Muscle Degeneration Disorders.

Kreipke RE, Kwon YV, Shcherbata HR, Ruohola-Baker H.

Curr Top Dev Biol. 2017;121:83-109. doi: 10.1016/bs.ctdb.2016.07.003. Epub 2016 Aug 5. Review.


Wnt/β-catenin signaling promotes self-renewal and inhibits the primed state transition in naïve human embryonic stem cells.

Xu Z, Robitaille AM, Berndt JD, Davidson KC, Fischer KA, Mathieu J, Potter JC, Ruohola-Baker H, Moon RT.

Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):E6382-E6390. Epub 2016 Oct 3.


Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells.

Rahkonen N, Stubb A, Malonzo M, Edelman S, Emani MR, Närvä E, Lähdesmäki H, Ruohola-Baker H, Lahesmaa R, Lund R.

Stem Cell Res. 2016 Nov;17(3):498-503. doi: 10.1016/j.scr.2016.09.025. Epub 2016 Sep 24.


Metabolic RemodeLIN of Pluripotency.

Mathieu J, Ruohola-Baker H.

Cell Stem Cell. 2016 Jul 7;19(1):3-4. doi: 10.1016/j.stem.2016.06.016.


Metabolic remodeling in early development and cardiomyocyte maturation.

Ellen Kreipke R, Wang Y, Miklas JW, Mathieu J, Ruohola-Baker H.

Semin Cell Dev Biol. 2016 Apr;52:84-92. doi: 10.1016/j.semcdb.2016.02.004. Epub 2016 Feb 18. Review.


The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition.

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.

Nat Cell Biol. 2015 Dec;17(12):1523-35. doi: 10.1038/ncb3264. Epub 2015 Nov 16.


Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes.

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.

Proc Natl Acad Sci U S A. 2015 May 26;112(21):E2785-94. doi: 10.1073/pnas.1424042112. Epub 2015 May 11.


Tie-mediated signal from apoptotic cells protects stem cells in Drosophila melanogaster.

Xing Y, Su TT, Ruohola-Baker H.

Nat Commun. 2015 May 11;6:7058. doi: 10.1038/ncomms8058.


Tri-iodo-l-thyronine promotes the maturation of human cardiomyocytes-derived from induced pluripotent stem cells.

Yang X, Rodriguez M, Pabon L, Fischer KA, Reinecke H, Regnier M, Sniadecki NJ, Ruohola-Baker H, Murry CE.

J Mol Cell Cardiol. 2014 Jul;72:296-304. doi: 10.1016/j.yjmcc.2014.04.005. Epub 2014 Apr 13.


miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure.

Sperber H, Beem A, Shannon S, Jones R, Banik P, Chen Y, Ku S, Varani G, Yao S, Ruohola-Baker H.

RNA. 2014 May;20(5):621-31. doi: 10.1261/rna.043943.113. Epub 2014 Mar 27.


Hypoxia-inducible factors have distinct and stage-specific roles during reprogramming of human cells to pluripotency.

Mathieu J, Zhou W, Xing Y, Sperber H, Ferreccio A, Agoston Z, Kuppusamy KT, Moon RT, Ruohola-Baker H.

Cell Stem Cell. 2014 May 1;14(5):592-605. doi: 10.1016/j.stem.2014.02.012. Epub 2014 Mar 20.


Derivation of naive human embryonic stem cells.

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.

Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4484-9. doi: 10.1073/pnas.1319738111. Epub 2014 Mar 12.


Dystrophin-deficient cardiomyocytes derived from human urine: new biologic reagents for drug discovery.

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.

Stem Cell Res. 2014 Mar;12(2):467-80. doi: 10.1016/j.scr.2013.12.004. Epub 2013 Dec 23.


Molecular mechanism of sphingosine-1-phosphate action in Duchenne muscular dystrophy.

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.

Dis Model Mech. 2014 Jan;7(1):41-54. doi: 10.1242/dmm.013631. Epub 2013 Sep 25.


Increased sphingosine-1-phosphate improves muscle regeneration in acutely injured mdx mice.

Ieronimakis N, Pantoja M, Hays AL, Dosey TL, Qi J, Fischer KA, Hoofnagle AN, Sadilek M, Chamberlain JS, Ruohola-Baker H, Reyes M.

Skelet Muscle. 2013 Aug 1;3(1):20. doi: 10.1186/2044-5040-3-20.


Hypoxia induces re-entry of committed cells into pluripotency.

Mathieu J, Zhang Z, Nelson A, Lamba DA, Reh TA, Ware C, Ruohola-Baker H.

Stem Cells. 2013 Sep;31(9):1737-48. doi: 10.1002/stem.1446.


Regulation of stem cell populations by microRNAs.

Mathieu J, Ruohola-Baker H.

Adv Exp Med Biol. 2013;786:329-51. doi: 10.1007/978-94-007-6621-1_18. Review.


MicroRNA regulation and role in stem cell maintenance, cardiac differentiation and hypertrophy.

Kuppusamy KT, Sperber H, Ruohola-Baker H.

Curr Mol Med. 2013 Jun;13(5):757-64. Review.


Use of somatic mutations to quantify random contributions to mouse development.

Zhou W, Tan Y, Anderson DJ, Crist EM, Ruohola-Baker H, Salipante SJ, Horwitz MS.

BMC Genomics. 2013 Jan 18;14:39. doi: 10.1186/1471-2164-14-39.


Drosophila as a starting point for developing therapeutics for the rare disease Duchenne Muscular Dystrophy.

Pantoja M, Ruohola-Baker H.

Rare Dis. 2013 May 10;1:e24995. doi: 10.4161/rdis.24995. eCollection 2013.


Genetic elevation of sphingosine 1-phosphate suppresses dystrophic muscle phenotypes in Drosophila.

Pantoja M, Fischer KA, Ieronimakis N, Reyes M, Ruohola-Baker H.

Development. 2013 Jan 1;140(1):136-46. doi: 10.1242/dev.087791. Epub 2012 Nov 15.


HIF1α induced switch from bivalent to exclusively glycolytic metabolism during ESC-to-EpiSC/hESC transition.

Zhou W, Choi M, Margineantu D, Margaretha L, Hesson J, Cavanaugh C, Blau CA, Horwitz MS, Hockenbery D, Ware C, Ruohola-Baker H.

EMBO J. 2012 May 2;31(9):2103-16. doi: 10.1038/emboj.2012.71. Epub 2012 Mar 23.


Loss-of-Function Screen Reveals Novel Regulators Required for Drosophila Germline Stem Cell Self-Renewal.

Xing Y, Kurtz I, Thuparani M, Legard J, Ruohola-Baker H.

G3 (Bethesda). 2012 Mar;2(3):343-51. doi: 10.1534/g3.111.001651. Epub 2012 Mar 1.


Assessment of hypoxia inducible factor levels in cancer cell lines upon hypoxic induction using a novel reporter construct.

Zhou W, Dosey TL, Biechele T, Moon RT, Horwitz MS, Ruohola-Baker H.

PLoS One. 2011;6(11):e27460. doi: 10.1371/journal.pone.0027460. Epub 2011 Nov 23.


HIF induces human embryonic stem cell markers in cancer cells.

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.

Cancer Res. 2011 Jul 1;71(13):4640-52. doi: 10.1158/0008-5472.CAN-10-3320. Epub 2011 Jun 28.


Chronic hypoxia impairs muscle function in the Drosophila model of Duchenne's muscular dystrophy (DMD).

Mosqueira M, Willmann G, Ruohola-Baker H, Khurana TS.

PLoS One. 2010 Oct 20;5(10):e13450. doi: 10.1371/journal.pone.0013450.


Embryonal carcinoma cell induction of miRNA and mRNA changes in co-cultured prostate stromal fibromuscular cells.

Vêncio EF, Pascal LE, Page LS, Denyer G, Wang AJ, Ruohola-Baker H, Zhang S, Wang K, Galas DJ, Liu AY.

J Cell Physiol. 2011 Jun;226(6):1479-88. doi: 10.1002/jcp.22464.


Assessing in vivo microRNA function in the germline stem cells of the Drosophila ovary.

Chan K, Ruohola-Baker H.

Methods Mol Biol. 2010;650:201-12. doi: 10.1007/978-1-60761-769-3_15.


The role of microRNAs in germline differentiation.

Reynolds S, Ruohola-Baker H.

StemBook [Internet]. Cambridge (MA): Harvard Stem Cell Institute; 2008-.
2008 Sep 15.


Dystroglycan and mitochondrial ribosomal protein L34 regulate differentiation in the Drosophila eye.

Zhan Y, Melian NY, Pantoja M, Haines N, Ruohola-Baker H, Bourque CW, Rao Y, Carbonetto S.

PLoS One. 2010 May 5;5(5):e10488. doi: 10.1371/journal.pone.0010488.


Characterization of microRNAs involved in embryonic stem cell states.

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.

Stem Cells Dev. 2010 Jul;19(7):935-50. doi: 10.1089/scd.2009.0426.


microRNAs regulate human embryonic stem cell division.

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.

Cell Cycle. 2009 Nov 15;8(22):3729-41. Epub 2009 Nov 10.


PIWI goes solo in the soma.

Reynolds SH, Ruohola-Baker H.

Dev Cell. 2009 May;16(5):627-8. doi: 10.1016/j.devcel.2009.05.004.


Dicer-1-dependent Dacapo suppression acts downstream of Insulin receptor in regulating cell division of Drosophila germline stem cells.

Yu JY, Reynolds SH, Hatfield SD, Shcherbata HR, Fischer KA, Ward EJ, Long D, Ding Y, Ruohola-Baker H.

Development. 2009 May;136(9):1497-507. doi: 10.1242/dev.025999. Epub 2009 Mar 31.


The conserved WW-domain binding sites in Dystroglycan C-terminus are essential but partially redundant for Dystroglycan function.

Yatsenko AS, Kucherenko MM, Pantoja M, Fischer KA, Madeoy J, Deng WM, Schneider M, Baumgartner S, Akey J, Shcherbata HR, Ruohola-Baker H.

BMC Dev Biol. 2009 Feb 27;9:18. doi: 10.1186/1471-213X-9-18.


MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.

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.

Stem Cells. 2008 Oct;26(10):2496-505. doi: 10.1634/stemcells.2008-0356. Epub 2008 Jun 26.


Genetic modifier screens reveal new components that interact with the Drosophila dystroglycan-dystrophin complex.

Kucherenko MM, Pantoja M, Yatsenko AS, Shcherbata HR, Fischer KA, Maksymiv DV, Chernyk YI, Ruohola-Baker H.

PLoS One. 2008 Jun 11;3(6):e2418. doi: 10.1371/journal.pone.0002418.


Small RNAs: keeping stem cells in line.

Stadler BM, Ruohola-Baker H.

Cell. 2008 Feb 22;132(4):563-6. doi: 10.1016/j.cell.2008.02.005. Review.


Stage-specific differences in the requirements for germline stem cell maintenance in the Drosophila ovary.

Shcherbata HR, Ward EJ, Fischer KA, Yu JY, Reynolds SH, Chen CH, Xu P, Hay BA, Ruohola-Baker H.

Cell Stem Cell. 2007 Dec 13;1(6):698-709. doi: 10.1016/j.stem.2007.11.007.


microRNA and stem cell function.

Hatfield S, Ruohola-Baker H.

Cell Tissue Res. 2008 Jan;331(1):57-66. Epub 2007 Nov 7. Review.


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.

Yatsenko AS, Gray EE, Shcherbata HR, Patterson LB, Sood VD, Kucherenko MM, Baker D, Ruohola-Baker H.

J Biol Chem. 2007 May 18;282(20):15159-69. Epub 2007 Mar 12.


Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy.

Shcherbata HR, Yatsenko AS, Patterson L, Sood VD, Nudel U, Yaffe D, Baker D, Ruohola-Baker H.

EMBO J. 2007 Jan 24;26(2):481-93. Epub 2007 Jan 11.


Stem cells signal to the niche through the Notch pathway in the Drosophila ovary.

Ward EJ, Shcherbata HR, Reynolds SH, Fischer KA, Hatfield SD, Ruohola-Baker H.

Curr Biol. 2006 Dec 5;16(23):2352-8. Epub 2006 Nov 2.


Border of Notch activity establishes a boundary between the two dorsal appendage tube cell types.

Ward EJ, Zhou X, Riddiford LM, Berg CA, Ruohola-Baker H.

Dev Biol. 2006 Sep 15;297(2):461-70. Epub 2006 May 24.

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