Julie Baker, Ph.D. - Publications

Affiliations: 
Genetics Stanford University, Palo Alto, CA 

62 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T, Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh J, ... ... Baker J, et al. Genome amplification and cellular senescence are hallmarks of human placenta development. Plos Genetics. 14: e1007698. PMID 30312291 DOI: 10.1371/journal.pgen.1007698  0.56
2018 Hannibal RL, Cardoso-Moreira M, Chetty SP, Lau J, Qi Z, Gonzalez-Maldonado E, Cherry AM, Yu J, Norton ME, Baker JC. Investigating human placentation and pregnancy using first trimester chorionic villi. Placenta. 65: 65-75. PMID 29908643 DOI: 10.1016/j.placenta.2018.03.005  0.56
2017 Guernsey MW, Chuong EB, Cornelis G, Renfree MB, Baker JC. Molecular conservation of marsupial and eutherian placentation and lactation. Elife. 6. PMID 28895534 DOI: 10.7554/eLife.27450  0.56
2017 Albrecht C, Baker JC, Blundell C, Chavez SL, Carbone L, Chamley L, Hannibal RL, Illsley N, Kurre P, Laurent LC, McKenzie C, Morales-Prieto D, Pantham P, Paquette A, Powell K, et al. IFPA meeting 2016 workshop report I: Genomic communication, bioinformatics, trophoblast biology and transport systems. Placenta. PMID 28108031 DOI: 10.1016/j.placenta.2017.01.103  0.56
2017 Chang J, Baker J, Wills A. Transcriptional dynamics of tail regeneration in Xenopus tropicalis. Genesis (New York, N.Y. : 2000). PMID 28095651 DOI: 10.1002/dvg.23015  0.52
2016 Cooper DL, Medoff E, Patel N, Baker J, Pratt K, Foss F, Seropian SE, Perreault S, Wu Y. Autologous Stem Cell Mobilization in the Age of Plerixafor. Clinical Lymphoma, Myeloma & Leukemia. PMID 27245311 DOI: 10.1016/j.clml.2016.04.007  0.88
2016 Reid CD, Karra K, Chang J, Piskol R, Li Q, Li JB, Cherry JM, Baker JC. XenMine: A genomic interaction tool for the Xenopus community. Developmental Biology. PMID 27157655 DOI: 10.1016/j.ydbio.2016.02.034  0.88
2016 Zhu H, Behr B, Reddy VV, Hughes M, Pan Y, Baker J. Human Embryonic Stem Cell Lines with Lesions in FOXP3 and NF1. Plos One. 11: e0151836. PMID 26990425 DOI: 10.1371/journal.pone.0151836  0.88
2016 Hannibal RL, Baker JC. Selective Amplification of the Genome Surrounding Key Placental Genes in Trophoblast Giant Cells. Current Biology : Cb. PMID 26774788 DOI: 10.1016/j.cub.2015.11.060  0.88
2015 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, et al. H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency. Cell. 163: 1281-1286. PMID 28930648 DOI: 10.1016/j.cell.2015.10.051  0.68
2015 Spies N, Smith CL, Rodriguez JM, Baker JC, Batzoglou S, Sidow A. Constraint and divergence of global gene expression in the mammalian embryo. Elife. 4: e05538. PMID 25871848 DOI: 10.7554/eLife.05538  0.88
2015 Yoon SJ, Foley JW, Baker JC. HEB associates with PRC2 and SMAD2/3 to regulate developmental fates. Nature Communications. 6: 6546. PMID 25775035 DOI: 10.1038/ncomms7546  0.88
2015 Wills AE, Baker JC. E2a is necessary for Smad2/3-dependent transcription and the direct repression of lefty during gastrulation. Developmental Cell. 32: 345-57. PMID 25669884 DOI: 10.1016/j.devcel.2014.11.034  0.88
2014 Kwon T, Chung MI, Gupta R, Baker JC, Wallingford JB, Marcotte EM. Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement. Genomics Data. 2: 192-194. PMID 25419512 DOI: 10.1016/j.gdata.2014.06.015  0.88
2014 Gupta R, Wills A, Ucar D, Baker J. Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus. Developmental Biology. 395: 38-49. PMID 25205067 DOI: 10.1016/j.ydbio.2014.08.034  0.88
2014 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, et al. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell. 158: 673-88. PMID 25083876 DOI: 10.1016/j.cell.2014.06.027  0.88
2014 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 Genetics. 10: e1004290. PMID 24785991 DOI: 10.1371/journal.pgen.1004290  0.88
2014 Zhu H, Hu S, Baker J. JMJD5 regulates cell cycle and pluripotency in human embryonic stem cells. Stem Cells (Dayton, Ohio). 32: 2098-110. PMID 24740926 DOI: 10.1002/stem.1724  0.88
2014 Finn EH, Smith CL, Rodriguez J, Sidow A, Baker JC. Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta. Developmental Biology. 390: 80-92. PMID 24594094 DOI: 10.1016/j.ydbio.2014.02.020  0.88
2014 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. 505: 635-40. PMID 24463510 DOI: 10.1038/nature12943  0.88
2014 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. 3: e01439. PMID 24424412 DOI: 10.7554/eLife.01439  0.88
2014 Wills AE, Gupta R, Chuong E, Baker JC. Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis. Methods (San Diego, Calif.). 66: 410-21. PMID 24064036 DOI: 10.1016/j.ymeth.2013.09.010  0.88
2013 Chuong EB, Hannibal RL, Green SL, Baker JC. Evolutionary perspectives into placental biology and disease. Applied & Translational Genomics. 2: 64-69. PMID 27896057 DOI: 10.1016/j.atg.2013.07.001  0.56
2013 Chuong EB, Rumi MA, Soares MJ, Baker JC. Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nature Genetics. 45: 325-9. PMID 23396136 DOI: 10.1038/ng.2553  0.88
2013 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 Research. 23: 201-16. PMID 22960373 DOI: 10.1101/gr.141424.112  0.88
2013 Chuong EB, Hannibal RL, Green SL, Baker JC. Evolutionary perspectives into placental biology and disease Applied and Translational Genomics. 2: 64-69. DOI: 10.1016/j.atg.2013.07.001  0.88
2012 Conklin JF, Baker J, Sage J. The RB family is required for the self-renewal and survival of human embryonic stem cells. Nature Communications. 3: 1244. PMID 23212373 DOI: 10.1038/ncomms2254  0.88
2012 Oyolu C, Zakharia F, Baker J. Distinguishing human cell types based on housekeeping gene signatures. Stem Cells (Dayton, Ohio). 30: 580-4. PMID 22162332 DOI: 10.1002/stem.1009  0.88
2011 Amps K, Andrews PW, Anyfantis G, Armstrong L, Avery S, Baharvand H, Baker J, Baker D, Munoz MB, Beil S, Benvenisty N, Ben-Yosef D, Biancotti JC, Bosman A, et al. Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nature Biotechnology. 29: 1132-44. PMID 22119741 DOI: 10.1038/nbt.2051  0.88
2011 Knox K, Leuenberger D, Penn AA, Baker JC. Global hormone profiling of murine placenta reveals Secretin expression. Placenta. 32: 811-6. PMID 21944867 DOI: 10.1016/j.placenta.2011.08.013  0.88
2011 Yoon SJ, Wills AE, Chuong E, Gupta R, Baker JC. HEB and E2A function as SMAD/FOXH1 cofactors. Genes & Development. 25: 1654-61. PMID 21828274 DOI: 10.1101/gad.16800511  0.88
2011 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. Developmental Biology. 357: 492-504. PMID 21741376 DOI: 10.1016/j.ydbio.2011.06.009  0.88
2011 Cooper DL, Pratt K, Baker J, Medoff E, Conkling-Walsh A, Foss F, Snyder E, Yen W, Seropian SE. Late afternoon dosing of plerixafor for stem cell mobilization: a practical solution. Clinical Lymphoma, Myeloma & Leukemia. 11: 267-72. PMID 21658654 DOI: 10.1016/j.clml.2011.03.014  0.88
2011 Pan Y, Ouyang Z, Wong WH, Baker JC. A new FACS approach isolates hESC derived endoderm using transcription factors. Plos One. 6: e17536. PMID 21408072 DOI: 10.1371/journal.pone.0017536  0.88
2009 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 Research. 19: 1044-56. PMID 19273619 DOI: 10.1101/gr.088773.108  0.88
2009 Cho NJ, Elazar M, Xiong A, Lee W, Chiao E, Baker J, Frank CW, Glenn JS. Viral infection of human progenitor and liver-derived cells encapsulated in three-dimensional PEG-based hydrogel. Biomedical Materials (Bristol, England). 4: 011001. PMID 18981544 DOI: 10.1088/1748-6041/25/1/011001  0.88
2008 Wills A, Dickinson K, Khokha M, Baker JC. Bmp signaling is necessary and sufficient for ventrolateral endoderm specification in Xenopus. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 237: 2177-86. PMID 18651654 DOI: 10.1002/dvdy.21631  0.88
2008 Chiao E, Elazar M, Xing Y, Xiong A, Kmet M, Millan MT, Glenn JS, Wong WH, Baker J. Isolation and transcriptional profiling of purified hepatic cells derived from human embryonic stem cells. Stem Cells (Dayton, Ohio). 26: 2032-41. PMID 18535157 DOI: 10.1634/stemcells.2007-0964  0.88
2008 Chiao E, Kmet M, Behr B, Baker J. Derivation of human embryonic stem cells in standard and chemically defined conditions. Methods in Cell Biology. 86: 1-14. PMID 18442641 DOI: 10.1016/S0091-679X(08)00001-0  0.88
2008 Knox K, Baker JC. Genomic evolution of the placenta using co-option and duplication and divergence. Genome Research. 18: 695-705. PMID 18340042 DOI: 10.1101/gr.071407.107  0.88
2007 Mitiku N, Baker JC. Genomic analysis of gastrulation and organogenesis in the mouse. Developmental Cell. 13: 897-907. PMID 18061570 DOI: 10.1016/j.devcel.2007.10.004  0.88
2007 Knox KS, Baker JC. Genome-wide expression profiling of placentas in the p57Kip2 model of pre-eclampsia. Molecular Human Reproduction. 13: 251-63. PMID 17289831 DOI: 10.1093/molehr/gal116  0.88
2006 Hufton AL, Vinayagam A, Suhai S, Baker JC. Genomic analysis of Xenopus organizer function. Bmc Developmental Biology. 6: 27. PMID 16756679 DOI: 10.1186/1471-213X-6-27  0.88
2006 Borchers A, Fonar Y, Frank D, Baker JC. XNF-ATc3 affects neural convergent extension. Development (Cambridge, England). 133: 1745-55. PMID 16571629 DOI: 10.1242/dev.02343  0.88
2006 Fletcher RB, Baker JC, Harland RM. FGF8 spliceforms mediate early mesoderm and posterior neural tissue formation in Xenopus. Development (Cambridge, England). 133: 1703-14. PMID 16554360 DOI: 10.1242/dev.02342  0.88
2006 Dickinson K, Leonard J, Baker JC. Genomic profiling of mixer and Sox17beta targets during Xenopus endoderm development. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 235: 368-81. PMID 16278889 DOI: 10.1002/dvdy.20636  0.88
2005 Chiao E, Leonard J, Dickinson K, Baker JC. High-throughput functional screen of mouse gastrula cDNA libraries reveals new components of endoderm and mesoderm specification. Genome Research. 15: 44-53. PMID 15632089 DOI: 10.1101/gr.2993405  0.88
2005 Pula G, Crosby D, Baker J, Poole AW. Functional interaction of protein kinase Calpha with the tyrosine kinases Syk and Src in human platelets. The Journal of Biological Chemistry. 280: 7194-205. PMID 15583006 DOI: 10.1074/jbc.M409212200  0.88
2004 Baker J, Griggs RK, Falati S, Poole AW. GPIb potentiates GPVI-induced responses in human platelets. Platelets. 15: 207-14. PMID 15203711 DOI: 10.1080/09537100410001701010  0.88
2004 Myers AP, Corson LB, Rossant J, Baker JC. Characterization of mouse Rsk4 as an inhibitor of fibroblast growth factor-RAS-extracellular signal-regulated kinase signaling. Molecular and Cellular Biology. 24: 4255-66. PMID 15121846 DOI: 10.1128/MCB.24.10.4255-4266.2004  0.88
2003 DeYoung RA, Baker JC, Cado D, Winoto A. The orphan steroid receptor Nur77 family member Nor-1 is essential for early mouse embryogenesis. The Journal of Biological Chemistry. 278: 47104-9. PMID 13129926 DOI: 10.1074/jbc.M307496200  0.88
2002 Borchers AG, Hufton AL, Eldridge AG, Jackson PK, Harland RM, Baker JC. The E3 ubiquitin ligase GREUL1 anteriorizes ectoderm during Xenopus development. Developmental Biology. 251: 395-408. PMID 12435366 DOI: 10.1006/dbio.2002.0814  0.88
2000 Tabata S, Kaneko T, Nakamura Y, Kotani H, Kato T, Asamizu E, Miyajima N, Sasamoto S, Kimura T, Hosouchi T, Kawashima K, Kohara M, Matsumoto M, Matsuno A, Muraki A, ... ... Baker J, et al. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature. 408: 823-6. PMID 11130714 DOI: 10.1038/35048507  0.88
1999 Baker JC, Beddington RS, Harland RM. Wnt signaling in Xenopus embryos inhibits bmp4 expression and activates neural development. Genes & Development. 13: 3149-59. PMID 10601040 DOI: 10.1101/gad.13.23.3149  0.88
1999 Das P, Inoue H, Baker JC, Beppu H, Kawabata M, Harland RM, Miyazono K, Padgett RW. Drosophila dSmad2 and Atr-I transmit activin/TGFbeta signals. Genes to Cells : Devoted to Molecular & Cellular Mechanisms. 4: 123-34. PMID 10320478  0.88
1997 Baker JC, Harland RM. From receptor to nucleus: the Smad pathway. Current Opinion in Genetics & Development. 7: 467-73. PMID 9309176 DOI: 10.1016/S0959-437X(97)80072-X  0.88
1996 Baker J, Hardy MP, Zhou J, Bondy C, Lupu F, Bellvé AR, Efstratiadis A. Effects of an Igf1 gene null mutation on mouse reproduction. Molecular Endocrinology (Baltimore, Md.). 10: 903-18. PMID 8813730 DOI: 10.1210/mend.10.7.8813730  0.88
1996 Baker JC, Harland RM. A novel mesoderm inducer, Madr2, functions in the activin signal transduction pathway. Genes & Development. 10: 1880-9. PMID 8756346  0.88
1996 Liu F, Hata A, Baker JC, Doody J, Cárcamo J, Harland RM, Massagué J. A human Mad protein acting as a BMP-regulated transcriptional activator. Nature. 381: 620-3. PMID 8637600 DOI: 10.1038/381620a0  0.88
1993 Baker J, Liu JP, Robertson EJ, Efstratiadis A. Role of insulin-like growth factors in embryonic and postnatal growth. Cell. 75: 73-82. PMID 8402902  0.88
1993 Liu JP, Baker J, Perkins AS, Robertson EJ, Efstratiadis A. Mice carrying null mutations of the genes encoding insulin-like growth factor I (Igf-1) and type 1 IGF receptor (Igf1r). Cell. 75: 59-72. PMID 8402901 DOI: 10.1016/0092-8674(93)90679-K  0.88
1991 Baker J, Limberger R, Schneider SJ, Campbell A. Recombination and modular exchange in the genesis of new lambdoid phages New Biologist. 3: 297-308. PMID 1715186  0.88
Show low-probability matches.