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COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis.

Warden CD, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, Yu H, Jove R, Yuan YC.

Nucleic Acids Res. 2019 Sep 5;47(15):8335-8336. doi: 10.1093/nar/gkz663. No abstract available.


Frequent monoallelic or skewed expression for developmental genes in CNS-derived cells and evidence for balancing selection.

Branciamore S, Valo Z, Li M, Wang J, Riggs AD, Singer-Sam J.

Proc Natl Acad Sci U S A. 2018 Oct 30;115(44):E10379-E10386. doi: 10.1073/pnas.1808652115. Epub 2018 Oct 15.


SMC1A is associated with radioresistance in prostate cancer and acts by regulating epithelial-mesenchymal transition and cancer stem-like properties.

Yadav S, Kowolik CM, Lin M, Zuro D, Hui SK, Riggs AD, Horne DA.

Mol Carcinog. 2019 Jan;58(1):113-125. doi: 10.1002/mc.22913. Epub 2018 Oct 5.


GFAP Mutations in Astrocytes Impair Oligodendrocyte Progenitor Proliferation and Myelination in an hiPSC Model of Alexander Disease.

Li L, Tian E, Chen X, Chao J, Klein J, Qu Q, Sun G, Sun G, Huang Y, Warden CD, Ye P, Feng L, Li X, Cui Q, Sultan A, Douvaras P, Fossati V, Sanjana NE, Riggs AD, Shi Y.

Cell Stem Cell. 2018 Aug 2;23(2):239-251.e6. doi: 10.1016/j.stem.2018.07.009.


Differences in silencing of mismatched targets by sliced versus diced siRNAs.

Sun G, Wang J, Huang Y, Yuan CW, Zhang K, Hu S, Chen L, Lin RJ, Yen Y, Riggs AD.

Nucleic Acids Res. 2018 Jul 27;46(13):6806-6822. doi: 10.1093/nar/gky287.


Rlip depletion prevents spontaneous neoplasia in TP53 null mice.

Awasthi S, Tompkins J, Singhal J, Riggs AD, Yadav S, Wu X, Singh S, Warden C, Liu Z, Wang J, Slavin TP, Weitzel JN, Yuan YC, Awasthi M, Srivastava SK, Awasthi YC, Singhal SS.

Proc Natl Acad Sci U S A. 2018 Apr 10;115(15):3918-3923. doi: 10.1073/pnas.1719586115. Epub 2018 Mar 23.


MHC-mismatched mixed chimerism restores peripheral tolerance of noncross-reactive autoreactive T cells in NOD mice.

Zhang M, Racine JJ, Lin Q, Liu Y, Tang S, Qin Q, Qi T, Riggs AD, Zeng D.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2329-E2337. doi: 10.1073/pnas.1720169115. Epub 2018 Feb 20.


Analysis of high-resolution 3D intrachromosomal interactions aided by Bayesian network modeling.

Zhang X, Branciamore S, Gogoshin G, Rodin AS, Riggs AD.

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):E10359-E10368. doi: 10.1073/pnas.1620425114. Epub 2017 Nov 13.


SAIC: an iterative clustering approach for analysis of single cell RNA-seq data.

Yang L, Liu J, Lu Q, Riggs AD, Wu X.

BMC Genomics. 2017 Oct 3;18(Suppl 6):689. doi: 10.1186/s12864-017-4019-5.


A Simple and Cost-Effective Approach for In Vitro Production of Sliced siRNAs as Potent Triggers for RNAi.

Sun G, Riggs AD.

Mol Ther Nucleic Acids. 2017 Sep 15;8:345-355. doi: 10.1016/j.omtn.2017.07.008. Epub 2017 Jul 13.


m6A RNA Methylation Regulates the Self-Renewal and Tumorigenesis of Glioblastoma Stem Cells.

Cui Q, Shi H, Ye P, Li L, Qu Q, Sun G, Sun G, Lu Z, Huang Y, Yang CG, Riggs AD, He C, Shi Y.

Cell Rep. 2017 Mar 14;18(11):2622-2634. doi: 10.1016/j.celrep.2017.02.059.


Small-Molecule-Based Lineage Reprogramming Creates Functional Astrocytes.

Tian E, Sun G, Sun G, Chao J, Ye P, Warden C, Riggs AD, Shi Y.

Cell Rep. 2016 Jul 19;16(3):781-92. doi: 10.1016/j.celrep.2016.06.042. Epub 2016 Jul 7.


In Vitro Colony Assays for Characterizing Tri-potent Progenitor Cells Isolated from the Adult Murine Pancreas.

Tremblay JR, LeBon JM, Luo A, Quijano JC, Wedeken L, Jou K, Riggs AD, Tirrell DA, Ku HT.

J Vis Exp. 2016 Jun 10;(112). doi: 10.3791/54016.


Epigenomic profiling reveals an association between persistence of DNA methylation and metabolic memory in the DCCT/EDIC type 1 diabetes cohort.

Chen Z, Miao F, Paterson AD, Lachin JM, Zhang L, Schones DE, Wu X, Wang J, Tompkins JD, Genuth S, Braffett BH, Riggs AD; DCCT/EDIC Research Group, Natarajan R.

Proc Natl Acad Sci U S A. 2016 May 24;113(21):E3002-11. doi: 10.1073/pnas.1603712113. Epub 2016 May 9.


Mapping Human Pluripotent-to-Cardiomyocyte Differentiation: Methylomes, Transcriptomes, and Exon DNA Methylation "Memories".

Tompkins JD, Jung M, Chen CY, Lin Z, Ye J, Godatha S, Lizhar E, Wu X, Hsu D, Couture LA, Riggs AD.

EBioMedicine. 2016 Jan 19;4:74-85. doi: 10.1016/j.ebiom.2016.01.021. eCollection 2016 Feb.


The TLX-miR-219 cascade regulates neural stem cell proliferation in neurodevelopment and schizophrenia iPSC model.

Murai K, Sun G, Ye P, Tian E, Yang S, Cui Q, Sun G, Trinh D, Sun O, Hong T, Wen Z, Kalkum M, Riggs AD, Song H, Ming GL, Shi Y.

Nat Commun. 2016 Mar 11;7:10965. doi: 10.1038/ncomms10965.


Downregulation of TLX induces TET3 expression and inhibits glioblastoma stem cell self-renewal and tumorigenesis.

Cui Q, Yang S, Ye P, Tian E, Sun G, Zhou J, Sun G, Liu X, Chen C, Murai K, Zhao C, Azizian KT, Yang L, Warden C, Wu X, D'Apuzzo M, Brown C, Badie B, Peng L, Riggs AD, Rossi JJ, Shi Y.

Nat Commun. 2016 Feb 3;7:10637. doi: 10.1038/ncomms10637.


Growth factors and medium hyperglycemia induce Sox9+ ductal cell differentiation into ╬▓ cells in mice with reversal of diabetes.

Zhang M, Lin Q, Qi T, Wang T, Chen CC, Riggs AD, Zeng D.

Proc Natl Acad Sci U S A. 2016 Jan 19;113(3):650-5. doi: 10.1073/pnas.1524200113. Epub 2016 Jan 5.


Cells with surface expression of CD133highCD71low are enriched for tripotent colony-forming progenitor cells in the adult murine pancreas.

Jin L, Gao D, Feng T, Tremblay JR, Ghazalli N, Luo A, Rawson J, Quijano JC, Chai J, Wedeken L, Hsu J, LeBon J, Walker S, Shih HP, Mahdavi A, Tirrell DA, Riggs AD, Ku HT.

Stem Cell Res. 2016 Jan;16(1):40-53. doi: 10.1016/j.scr.2015.11.015. Epub 2015 Nov 30.


MHC-mismatched mixed chimerism augments thymic regulatory T-cell production and prevents relapse of EAE in mice.

Wu L, Li N, Zhang M, Xue SL, Cassady K, Lin Q, Riggs AD, Zeng D.

Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15994-9. doi: 10.1073/pnas.1521157112. Epub 2015 Dec 8.


SR4 Uncouples Mitochondrial Oxidative Phosphorylation, Modulates AMP-dependent Kinase (AMPK)-Mammalian Target of Rapamycin (mTOR) Signaling, and Inhibits Proliferation of HepG2 Hepatocarcinoma Cells.

Figarola JL, Singhal J, Tompkins JD, Rogers GW, Warden C, Horne D, Riggs AD, Awasthi S, Singhal SS.

J Biol Chem. 2015 Dec 18;290(51):30321-41. doi: 10.1074/jbc.M115.686352. Epub 2015 Nov 3.


Postnatal Pancreas of Mice Contains Tripotent Progenitors Capable of Giving Rise to Duct, Acinar, and Endocrine Cells In Vitro.

Ghazalli N, Mahdavi A, Feng T, Jin L, Kozlowski MT, Hsu J, Riggs AD, Tirrell DA, Ku HT.

Stem Cells Dev. 2015 Sep 1;24(17):1995-2008. doi: 10.1089/scd.2015.0007. Epub 2015 Jun 9.


Colony-forming progenitor cells in the postnatal mouse liver and pancreas give rise to morphologically distinct insulin-expressing colonies in 3D cultures.

Jin L, Feng T, Chai J, Ghazalli N, Gao D, Zerda R, Li Z, Hsu J, Mahdavi A, Tirrell DA, Riggs AD, Ku HT.

Rev Diabet Stud. 2014 Spring;11(1):35-50. doi: 10.1900/RDS.2014.11.35. Epub 2014 May 10.


Enhanced evolution by stochastically variable modification of epigenetic marks in the early embryo.

Branciamore S, Rodin AS, Riggs AD, Rodin SN.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6353-8. doi: 10.1073/pnas.1402585111. Epub 2014 Apr 14.


In vitro multilineage differentiation and self-renewal of single pancreatic colony-forming cells from adult C57BL/6 mice.

Jin L, Feng T, Zerda R, Chen CC, Riggs AD, Ku HT.

Stem Cells Dev. 2014 Apr 15;23(8):899-909. doi: 10.1089/scd.2013.0466. Epub 2014 Jan 4.


MicroRNA-26a targets ten eleven translocation enzymes and is regulated during pancreatic cell differentiation.

Fu X, Jin L, Wang X, Luo A, Hu J, Zheng X, Tsark WM, Riggs AD, Ku HT, Huang W.

Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17892-7. doi: 10.1073/pnas.1317397110. Epub 2013 Oct 10.


Regulation of adipose tissue T cell subsets by Stat3 is crucial for diet-induced obesity and insulin resistance.

Priceman SJ, Kujawski M, Shen S, Cherryholmes GA, Lee H, Zhang C, Kruper L, Mortimer J, Jove R, Riggs AD, Yu H.

Proc Natl Acad Sci U S A. 2013 Aug 6;110(32):13079-84. doi: 10.1073/pnas.1311557110. Epub 2013 Jul 22.


COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis.

Warden CD, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, Yu H, Jove R, Yuan YC.

Nucleic Acids Res. 2013 Jun;41(11):e117. doi: 10.1093/nar/gkt242. Epub 2013 Apr 17. Erratum in: Nucleic Acids Res. 2019 Sep 5;47(15):8335-8336.


Colony-forming cells in the adult mouse pancreas are expandable in Matrigel and form endocrine/acinar colonies in laminin hydrogel.

Jin L, Feng T, Shih HP, Zerda R, Luo A, Hsu J, Mahdavi A, Sander M, Tirrell DA, Riggs AD, Ku HT.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3907-12. doi: 10.1073/pnas.1301889110. Epub 2013 Feb 19.


The histone methyltransferase KMT2B is required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter.

Ladopoulos V, Hofemeister H, Hoogenkamp M, Riggs AD, Stewart AF, Bonifer C.

Mol Cell Biol. 2013 Apr;33(7):1383-93. doi: 10.1128/MCB.01721-12. Epub 2013 Jan 28.


Identification of Oct4-activating compounds that enhance reprogramming efficiency.

Li W, Tian E, Chen ZX, Sun G, Ye P, Yang S, Lu D, Xie J, Ho TV, Tsark WM, Wang C, Horne DA, Riggs AD, Yip ML, Shi Y.

Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):20853-8. doi: 10.1073/pnas.1219181110. Epub 2012 Dec 3.


Epigenetic stability, adaptability, and reversibility in human embryonic stem cells.

Tompkins JD, Hall C, Chen VC, Li AX, Wu X, Hsu D, Couture LA, Riggs AD.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12544-9. doi: 10.1073/pnas.1209620109. Epub 2012 Jul 16.


Inhibition of S-phase kinase-associated protein 2 (Skp2) reprograms and converts diabetogenic T cells to Foxp3+ regulatory T cells.

Wang D, Qin H, Du W, Shen YW, Lee WH, Riggs AD, Liu CP.

Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9493-8. doi: 10.1073/pnas.1207293109. Epub 2012 May 29.


Acetylated STAT3 is crucial for methylation of tumor-suppressor gene promoters and inhibition by resveratrol results in demethylation.

Lee H, Zhang P, Herrmann A, Yang C, Xin H, Wang Z, Hoon DS, Forman SJ, Jove R, Riggs AD, Yu H.

Proc Natl Acad Sci U S A. 2012 May 15;109(20):7765-9. doi: 10.1073/pnas.1205132109. Epub 2012 Apr 30.


DNA methylation biomarkers for lung cancer.

Rauch TA, Wang Z, Wu X, Kernstine KH, Riggs AD, Pfeifer GP.

Tumour Biol. 2012 Apr;33(2):287-96. doi: 10.1007/s13277-011-0282-2. Epub 2011 Dec 6.


Recurrent meningitis associated with frontal sinus tuber encephalocele in a patient with tuberous sclerosis.

Elbabaa SK, Riggs AD, Saad AG.

J Neurosurg Pediatr. 2011 Jul;8(1):103-6. doi: 10.3171/2011.4.PEDS10308.


DNA methylation and demethylation in mammals.

Chen ZX, Riggs AD.

J Biol Chem. 2011 May 27;286(21):18347-53. doi: 10.1074/jbc.R110.205286. Epub 2011 Mar 24. Review.


Killer cell Ig-like receptor (KIR) 3DL1 down-regulation enhances inhibition of type 1 diabetes by autoantigen-specific regulatory T cells.

Qin H, Wang Z, Du W, Lee WH, Wu X, Riggs AD, Liu CP.

Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):2016-21. doi: 10.1073/pnas.1019082108. Epub 2011 Jan 18.


CpG island clusters and pro-epigenetic selection for CpGs in protein-coding exons of HOX and other transcription factors.

Branciamore S, Chen ZX, Riggs AD, Rodin SN.

Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15485-90. doi: 10.1073/pnas.1010506107. Epub 2010 Aug 17.


CRM1 mediates nuclear-cytoplasmic shuttling of mature microRNAs.

Castanotto D, Lingeman R, Riggs AD, Rossi JJ.

Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21655-9. doi: 10.1073/pnas.0912384106. Epub 2009 Dec 2.


A human B cell methylome at 100-base pair resolution.

Rauch TA, Wu X, Zhong X, Riggs AD, Pfeifer GP.

Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):671-8. doi: 10.1073/pnas.0812399106. Epub 2009 Jan 12.


Methylation of polycomb target genes in intestinal cancer is mediated by inflammation.

Hahn MA, Hahn T, Lee DH, Esworthy RS, Kim BW, Riggs AD, Chu FF, Pfeifer GP.

Cancer Res. 2008 Dec 15;68(24):10280-9. doi: 10.1158/0008-5472.CAN-08-1957.


Analysis of RNA structure and RNA-protein interactions in mammalian cells by use of terminal transferase-dependent PCR.

Chen HH, Lebon J, Riggs AD.

Methods Mol Biol. 2008;488:319-41. doi: 10.1007/978-1-60327-475-3_21.


X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations.

Shen Y, Matsuno Y, Fouse SD, Rao N, Root S, Xu R, Pellegrini M, Riggs AD, Fan G.

Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4709-14. doi: 10.1073/pnas.0712018105. Epub 2008 Mar 13.


PAP-LMPCR for improved, allele-specific footprinting and automated chromatin fine structure analysis.

Ingram R, Gao C, Lebon J, Liu Q, Mayoral RJ, Sommer SS, Hoogenkamp M, Riggs AD, Bonifer C.

Nucleic Acids Res. 2008 Feb;36(3):e19. doi: 10.1093/nar/gkm1159. Epub 2008 Jan 21.


High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer.

Rauch TA, Zhong X, Wu X, Wang M, Kernstine KH, Wang Z, Riggs AD, Pfeifer GP.

Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):252-7. Epub 2007 Dec 27.


Methylated-CpG island recovery assay-assisted microarrays for cancer diagnosis.

Pfeifer GP, Wang Z, Riggs AD, Rauch TA.

Expert Opin Med Diagn. 2007 Sep;1(1):99-108. doi: 10.1517/17530059.1.1.99.


Riggs AD Co-Editor-in-Chief.

Riggs AD.

Biosci Trends. 2007 Aug;1(1):2. No abstract available.


Nucleotide excision repair eliminates unique DNA-protein cross-links from mammalian cells.

Baker DJ, Wuenschell G, Xia L, Termini J, Bates SE, Riggs AD, O'Connor TR.

J Biol Chem. 2007 Aug 3;282(31):22592-604. Epub 2007 May 16.

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