Publications

Yoon SJ, Foley JW, Baker JC. HEB associates with PRC2 and SMAD2/3 to regulate developmental fatesNat Commun. 2015 Mar 16;6:6546.

Wills AE, and Baker JC. E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty. Developmental Cell. 2015 Feb 9;32(3):345-57

Gupta R, Wills AE, Ucar D, Baker JC. Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus. Dev Biol. 2014 Sep 6.

Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, Cherry JM, Brunet A. H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency. Cell. 2014 Jul 31;158(3):673-88.

Hannibal RL, Chuong EB, Rivera-Mulia JC, Gilbert DM, Valouev A, Baker JC. Copy number variation is a fundamental aspect of the placental genome. PLoS Genet. 2014 May 1;10(5):e1004290.

Zhu H, Hu S, Baker J. JMJD5 regulates cell cycle and pluripotency in human embryonic stem cells. Stem Cells. 2014 Aug;32(8):2098-110.

Finn EH, Smith CL, Rodriguez J, Sidow A, Baker JC. Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta. Dev Biol. 2014 Jun 1;390(1):80-92.

Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature. 2014 Jan 30;505(7485):635-40.

Chung MI, Kwon T, Tu F, Brooks ER, Gupta R, Meyer M, Baker JC, Marcotte EM, Wallingford JB. Coordinated genomic control of ciliogenesis and cell movement by RFX2. Elife. 2014 Jan 14:e01439.

Wills AE, Gupta R, Chuong E, Baker JC. Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis. Methods. 2014 Apr 1;66(3):410-21.

Chuong EB, Rumi MA, Soares MJ, Baker JC. Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nat Genet. 2013 Mar;45(3):325-9

Tan MH, Au KF, Yablonovitch AL, Wills AE, Chuang J, Baker JC, Wong WH, Li JB. RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. Genome Res. 2013 Jan;23(1):201-16

Knox K, Leuenberger D, Penn AA, Baker JC. Global hormone profiling of murine placenta reveals Secretin expression. Placenta. 2011 Sep 23.

Yoon SJ, Wills AE, Chuong E, Gupta R, Baker JC. HEB and E2A function as SMAD/FOXH1 cofactors. Genes Dev. 2011 Aug 1;25(15):1654-61.

Kim SW, Yoon SJ, Chuong E, Oyolu C, Wills AE, Gupta R, Baker J.Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs.  Dev Biol. 2011 Sep 15;357(2):492-504. Epub 2011 Jun 29.

Pan Y, Ouyang Z, Wong WH, Baker JC. A new FACS approach isolates hESC derived endoderm using transcription factors. PLoS One. 2011 Mar 9;6(3):e17536.

Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, Oyolu CB, Schroth GP, Absher DM, Baker JC, Myers RM. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 2009 Jun;19(6):1044-56.

Wills A, Dickinson K, Khokha M, Baker JC. Bmp signaling is necessary and sufficient for ventrolateral endoderm specification in Xenopus. Developmental Dynamics 2008 237(8): 2177-2186

Knox K, Baker JC. Genomic evolution of the placenta using co-option and duplication and divergence. Genome Res. 2008 May;18(5):695-705. Epub 2008 Mar 13.

Mitiku N, Baker JC. Genomic analysis of gastrulation and organogenesis in the mouse. Dev Cell. 2007 Dec;13(6):897-907.

Knox KS, Baker JC. Genome-wide expression profiling of placentas in the p57Kip2 model of pre-eclampsia. Mol Hum Reprod. 2007 Apr;13(4):251-63.

Fletcher, R. B., Baker, J. C., and R. M. Harland. 2006. FGF8 spliceforms mediate early mesoderm and posterior neural tissue formation in Xenopus. Development 133(9): 1703-1714.

Hufton, A., A. Vinayagam, S. Suhai, and J. C. Baker. 2006. Genomic Analysis of Xenopus Organizer Function. BMC Developmental Biology 6: 27-49.

Borchers, A., Y, Fonar, D. Frank, and J. C. Baker. 2006. XNF-ATc3 affects neural convergent extension. Development 133(9): 1745-1755.

Dickinson, K., J. Leonard, and J. C. Baker. 2006. Genomic profiling of Mixer and Sox17 targets during Xenopus endoderm development. Developmental Dynamics 235(2): 368-381.

Chiao, E., J. Leonard, K. Dickinson, and J. C. Baker. 2005. High-throughput functional screen of mouse gastrula cDNA libraries reveals new components of endoderm and mesoderm specification. Genome Research 15: 44-53.

Lu, X., A. G. M. Borchers, C. Jolicoeur, H. Rayburn, J. C. Baker, and M. Tessier-Lavigne. 2004. PTK7/CCK-4 is a novel regulator of planar cell polarity in vertebrates. Nature 430: 93-98.

Pomrehn-Myers, A., Corson, L. B., Rossant, J., and J. C. Baker. 2004.Characterization of Mouse Rsk4 as an Inhibitor of Fibroblast Growth Factor-RAS-Extracellular Signal-Regulated Kinase Signaling. Molecular and Cellular Biology 24(10): 4255-4266.

DeYoung, A. R, J. C. Baker, D. Cado, and A. Winoto. 2003. The orphan steroid receptor Nur77 family member Nor-1 is essential for   early mouse embryogenesis. Journal of Cell Biology 278(47): 47104-47109.

Borchers, A. G. M., A. L. Hufton, A. G. Eldridge, P. K. J. Jackson, R. M. Harland, and J. C. Baker. 2002. The E3 ubiquitin ligase GREUL1 anteriorizes ectoderm during Xenopus development. Developmental Biology 251(2):395-408.

Baker, J. C., R. S. Beddington and R. M. Harland. 1999. Wnt signaling in Xenopus embryos inhibits bmp4 expression and activates neural development. Genes and Development 13(23): 3149-3159.

Das, P., H. Inoue, J. C. Baker, H. Beppu, M. Kawabata, R. M. Harland, K. Miyazono, R. W. Padgett. 1999. Drosophila dSmad2 and Atr-I transmit activin/TGFbeta signals. Genes Cells 4(2): 123-134.

Baker, J. C. and R. M. Harland. 1997. From receptor to nucleus: the Smad pathway. Current Opinion in Genetics and Development 7(4): 467-473.

Baker, J., M. P. Hardy, J. Zhou, C. Bondy, F. Lupu, A. Bellve, and A. Efstratiadis. 1996. Effects of an Igf-1 gene null mutation on mouse reproduction. Molecular Endocrinology 10: 903-918.

Liu, F., A. Hata, J. C. Baker, J. Doody, J. Carcamo, R. M. Harland and J. Massague. 1996. A human Mad protein acting as a BMP-regulated transcriptional activator. Nature 381: 620-623.

Baker, J. C. and R. M. Harland. 1996. A novel mesoderm inducer, Madr2, functions in the activin signal transduction pathway. Genes and Development 10(15): 1880-1889.

Liu, J. P., J. Baker, A. S. Perkins, E. J. Robertson, and A. Efstratiadis. 1993. Mice encoding null mutations of the genes encoding insulin-like growth factor I and type 1 IGF receptor. Cell 75: 59-72.

Baker, J., J. P. Liu, E. J. Robertson, and A. Efstratiadis. 1993. Role of insulin-like growth factors in embryonic and postnatal growth. Cell 75: 73-82.

Thompson, E. W., J. C. Baker, S. A. Kamoss and W. H. Anderson. 1991.The severity of diabetes is a major determinant of myocardial damage in the rat. Proc. Soc. Exp. Biol. Med. 196 (2): 230-233.

Clicking on the images below will direct you to the paper of interest.

 

JMJD5 is essential for human embryonic stem cell (hESC) identity. Depletion of JMJD5 led to loss of distinct colonies and enlarged flattened cell morphology. Infection of hESCs with GFP-marked lentivirus carrying control vector, shJMJD5-A, and shJMJD5-B.
JMJD5 is essential for human embryonic stem cell (hESC) identity. Depletion of JMJD5 led to loss of distinct colonies and enlarged flattened cell morphology.
Infection of hESCs with GFP-marked lentivirus carrying control vector, shJMJD5-A, and shJMJD5-B.

 

 

 

 

 

 

Core TSC transcription factors bind RLTR13D5 copies
Heat map of all 608 RLTR13D5 copies. Rows represent 10-kb windows centered on an individual copy, and the ChIP enrichment signal from each experiment is shown in each column. Elements are sorted by average H3K4me1 signal across the 10-kb window.

 

 

 

 

 

Genome-wide expression profiling of the fetal and maternal placenta: Samples were taken at nine stages throughout placental development, and dissected into placental and decidual portions. The data set includes biological triplicates for placenta samples at e8.5, e9.0, e10.5, e12.0, e15.0, and e17.0, biological duplicates for placenta samples at e13.5, e19.0, and P0, and biological duplicates for decidual samples at e8.5, e9.0, e10.5, e12.0, e15.0, e17.0, e19.0, and P0.
Genome-wide expression profiling of the fetal and maternal placenta: Samples were taken at nine stages throughout placental development, and dissected into placental and decidual portions. The data set includes biological triplicates for placenta samples at e8.5, e9.0, e10.5, e12.0, e15.0, and e17.0, biological duplicates for placenta samples at e13.5, e19.0, and P0, and biological duplicates for decidual samples at e8.5, e9.0, e10.5, e12.0, e15.0, e17.0, e19.0, and P0.

 

 

 

Positive clones that cause inhibition of mesoderm or endoderm in whole embryos:
Positive clones that cause inhibition of mesoderm or endoderm in whole embryos: Gastrulating Xenopus embryos expressing positive clones were analyzed for the expression of Xbra (A,C,E,G,I,K), a combination of edd and Xsox17β (B,D,F) or edd alone (H,J,L). Identities of clones are listed at left and include Lefty2 (C,D), geminin (E,F), cyclin F (G,H), Cks2 (I,J), and D7Ssb2 (K,L). (A,B) Uninjected controls. Concentrations of injected mRNAs are as follows: Lefty2 (A,B: 1 ng), geminin (C,D: 400 pg), cyclin F (G,H: 200 pg), Cks2 (I,J: 200 pg), and D7Ssb2 (K: 10 ng; L: 500 pg).