Publications

Preprint: Juric I, Fink EE, Qiu H, Desprez PE, Ravi A, Holton M, Makarov V, Almassi N, Min B, Getz G, Chan TA, Alban T, Ting AH, Lee BH.Single Cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway. bioRxiv. 2025 Feb 17:2025.02.13.638074. 

Preprint: Fink EE, Nanavaty V, Lee BH, Ting AH. Heat shock induces alternative polyadenylation through dynamic DNA methylation-regulated chromatin looping. bioRxiv. 2023 Aug 26:2023.08.25.554792.

Santo B, Fink EE, Krylova AE, Lin YC, Eltemamy M, Wee A, Wessely O, Lee BH, Ting AH. Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq. iScience. 2024 Dec 18;28(1):111628. 

Sona S, Bradley M, Ting AH. Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization. STAR Protoc. 2023 March 17;4(1). 

Qiu H, Makarov V, Bolzenius JK, Halstead A, Parker Y, Wang A, Iyer GV, Wise H, Kim D, Thayaparan V, Linder DJ, Haber GP, Ting AH, Ren B, Chan TA, Arora V, Solit DB, Lee BH. KDM6A loss triggers an epigenetic switch that disrupts urothelial differentiation and drives cell proliferation in bladder cancer. Cancer Res. 2023 Mar 15;83(6):814-829. 

Fink EE, Sona S, Lee BH, Ting AH. Processing and cryopreservation of human ureter tissues for single-cell and spatial transcriptomics assays. STAR Protoc. 2022 Dec 16;3(4):101854.

Fink EE, Sona S, Tran U, Desprez PE, Bradley M, Qiu H, Eltemamy M, Wee A, Wolkov M, Nicolas M, Min B, Haber GP, Wessely O, Lee BH, Ting AH. Single-cell and spatial mapping identify cell types and signaling networks in the human ureter. Dev Cell. 2022 Aug 8;57(15):1899-1916.e6. 

Ting AH, Lee BH. 5mC: what goes on must come off. Nat Rev Mol Cell Biol. 2022 May;23(5):306. 

Nanavaty V, Abrash EW, Hong C, Park S, Fink EE, Li Z, Sweet TJ, Bhasin JM, Singuri S, Lee BH, Hwang TH, Ting AH. DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex. Mol Cell. 2020 May 21;78(4):752-764.e6. 

Liang J, Zhou W, Sakre N, DeVecchio J, Ferrandon S, Ting AH, Bao S, Bissett I, Church J, Kalady MF. Epigenetically regulated miR-1247 functions as a novel tumour suppressor via MYCBP2 in methylator colon cancers. Br J Cancer. 2018 Nov;119(10):1267-1277. 

Do J, Kim D, Kim S, Valentin-Torres A, Dvorina N, Jang E, Nagarajavel V, DeSilva TM, Li X, Ting AH, Vignali DAA, Stohlman SA, Baldwin WM 3rd, Min B. Treg-specific IL-27Rα deletion uncovers a key role for IL-27 in Treg function to control autoimmunity. Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10190-10195. 

Sweet TJ, Ting AH. WOMEN IN CANCER THEMATIC REVIEW: Diverse functions of DNA methylation: implications for prostate cancer and beyond. Endocr Relat Cancer. 2016 Nov;23(11):T169-T178. 

Ting AH.  WOMEN IN CANCER PROFILE: Dude, where's my band? Endocr Relat Cancer. 2016 Nov;23(11):P33-P35. 

Yan H, Tang G, Wang H, Hao L, He T, Sun X, Ting AH, Deng A, Sun S. DNA methylation reactivates GAD1 expression in cancer by preventing CTCF-mediated polycomb repressive complex 2 recruitment. Oncogene. 2016 Jul 28;35(30):4020. 

Bhasin JM, Ting AH. Goldmine integrates information placing genomic ranges into meaningful biological contexts. Nucleic Acids Res. 2016 Jul 8;44(12):5550-6. 

Sadler T, Bhasin JM, Xu Y, Barnholz-Sloan J, Chen Y, Ting AH, Stylianou E. Genome-wide analysis of DNA methylation and gene expression defines molecular characteristics of Crohn's disease-associated fibrosis. Clin Epigenetics. 2016 Mar 12;8:30. 

Bhasin JM, Hu B, Ting AH. MethylAction: detecting differentially methylated regions that distinguish biological subtypes. Nucleic Acids Res. 2016 Jan 8;44(1):106-16. 

Yan H, Tang G, Wang H, Hao L, He T, Sun X, Ting AH, Deng A, Sun S. DNA methylation reactivates GAD1 expression in cancer by preventing CTCF-mediated polycomb repressive complex 2 recruitment. Oncogene. 2016 Jul 28;35(30):3995-4008. 

Bhasin JM, Lee BH, Matkin L, Taylor MG, Hu B, Xu Y, Magi-Galluzzi C, Klein EA, Ting AH. Methylome-wide Sequencing Detects DNA Hypermethylation Distinguishing Indolent from Aggressive Prostate Cancer. Cell Rep. 2015 Dec 15;13(10):2135-46. 

Al-Harbi S, Choudhary GS, Ebron JS, Hill BT, Vivekanathan N, Ting AH, Radivoyevitch T, Smith MR, Shukla GC, Almasan A. miR-377-dependent BCL-xL regulation drives chemotherapeutic resistance in B-cell lymphoid malignancies. Mol Cancer. 2015 Nov 4;14:185. 

Hu K, Ting AH, Li J. BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data. BMC Bioinformatics. 2015 Jul 11;16:220. doi: 10.1186/s12859-015-0649-2. 

Kim JG, Kim TO, Bae JH, Shim JW, Kang MJ, Yang K, Ting AH, Yi JM. Epigenetically regulated MIR941 and MIR1247 target gastric cancer cell growth and migration. Epigenetics. 2014 Jul;9(7):1018-30. doi: 10.4161/epi.29007. 

Hu B, Ji Y, Xu Y, Ting AH. Screening for SNPs with Allele-Specific Methylation based on Next-Generation Sequencing Data. Stat Biosci. 2013 May;5(1):179-197. 

Lee BH, Taylor MG, Robinet P, Smith JD, Schweitzer J, Sehayek E, Falzarano SM, Magi-Galluzzi C, Klein EA, Ting AH. Dysregulation of cholesterol homeostasis in human prostate cancer through loss of ABCA1. Cancer Res. 2013 Feb 1;73(3):1211-8. 

Ginsberg MR, Rubin RA, Falcone T, Ting AH, Natowicz MR. Brain transcriptional and epigenetic associations with autism. PLoS One. 2012;7(9):e44736. 

Naguib M, Bie B, Ting AH. Fundamental concepts of epigenetics for consideration in anesthesiology. Curr Opin Anaesthesiol. 2012 Aug;25(4):434-43. 

Xu Y, Hu B, Choi AJ, Gopalan B, Lee BH, Kalady MF, Church JM, Ting AH. Unique DNA methylome profiles in CpG island methylator phenotype colon cancers. Genome Res. 2012 Feb;22(2):283-91. 

Yan H, Choi AJ, Lee BH, Ting AH. Identification and functional analysis of epigenetically silenced microRNAs in colorectal cancer cells. PLoS One. 2011;6(6):e20628. 

Messick CA, Church JM, Liu X, Ting AH, Kalady MF. Stage III colorectal cancer: molecular disparity between primary cancers and lymph node metastases. Ann Surg Oncol. 2010 Feb;17(2):425-31. 

Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res. 2010 Jan;38(2):391-9. 

Ting AH, Suzuki H, Cope L, Schuebel KE, Lee BH, Toyota M, Imai K, Shinomura Y, Tokino T, Baylin SB. A requirement for DICER to maintain full promoter CpG island hypermethylation in human cancer cells. Cancer Res. 2008 Apr 15;68(8):2570-5. 

Winter JM, Ting AH, Vilardell F, Gallmeier E, Baylin SB, Hruban RH, Kern SE, Iacobuzio-Donahue CA. Absence of E-cadherin expression distinguishes noncohesive from cohesive pancreatic cancer. Clin Cancer Res. 2008 Jan 15;14(2):412-8. 

Schuebel KE, Chen W, Cope L, Glöckner SC, Suzuki H, Yi JM, Chan TA, Van Neste L, Van Criekinge W, van den Bosch S, van Engeland M, Ting AH, Jair K, Yu W, Toyota M, Imai K, Ahuja N, Herman JG, Baylin SB. Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genet. 2007 Sep;3(9):1709-23. 

Ting AH, McGarvey KM, Baylin SB. The cancer epigenome--components and functional correlates. Genes Dev. 2006 Dec 1;20(23):3215-31. 

Jair KW, Bachman KE, Suzuki H, Ting AH, Rhee I, Yen RW, Baylin SB, Schuebel KE. De novo CpG island methylation in human cancer cells. Cancer Res. 2006 Jan 15;66(2):682-92. 

Ting AH, Jair KW, Schuebel KE, Baylin SB. Differential requirement for DNA methyltransferase 1 in maintaining human cancer cell gene promoter hypermethylation. Cancer Res. 2006 Jan 15;66(2):729-35. 

Ting AH, Schuebel KE, Herman JG, Baylin SB. Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat Genet. 2005 Aug;37(8):906-10. 

Ting AH, Jair KW, Suzuki H, Yen RW, Baylin SB, Schuebel KE. Mammalian DNA methyltransferase 1: inspiration for new directions. Cell Cycle. 2004 Aug;3(8):1024-6. 

Ting AH, Jair KW, Suzuki H, Yen RW, Baylin SB, Schuebel KE. CpG island hypermethylation is maintained in human colorectal cancer cells after RNAi-mediated depletion of DNMT1. Nat Genet. 2004 Jun;36(6):582-4.