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Selected Publications

Office of Scientific Computing

  1. Wellman AS, Metukuri MR, Kazgan N, Xu X, Xu Q, Ren NSX, Czopik A, Shanahan MT, Kang A, Chen W, Azcarate-Peril MA, Gulati AS, Fargo DC, Guarente L, Li X. 2017. Intestinal Epithelial Sirtuin 1 Regulates Intestinal Inflammation during Aging in Mice by Altering the Intestinal Microbiota. Gastroenterology. S0016-5085, 35634-2. doi: 10.1053 [Epub ahead of print] [Abstract] 
  2. Lavender CA, Shapiro AJ, Burkholder AB, Bennett BD, Adelman K, Fargo DC. 2017. ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data. Nucleic Acids Res. 45, 5678-90. [Abstract] 
  3. Lu J, Xu Q, Ji M, Guo X, Xu X, Fargo DC, Li X. 2017. The phosphorylation status of T522 modulates tissue-specific functions of SIRT1 in energy metabolism in mice. EMBO Rep. 18, 841-57. [Abstract] 
  4. Ren NS, Ji M, Tokar EJ, Busch EL, Xu X, Lewis D, Li X, Jin A, Zhang Y, Wu WK, Huang W, Li L, Fargo DC, Keku TO, Sandler RS, Li X. 2017. Haploinsufficiency of SIRT1 Enhances Glutamine Metabolism and Promotes Cancer Development. Curr Biol. 27, 483-94. [Abstract] 
  5. Borkent M, Bennett BD, Lackford B, Bar-Nur O, Brumbaugh J, Wang L, Du Y, Fargo DC, Apostolou E, Cheloufi S, Maherali N, Elledge SJ, Hu G, Hochedlinger K. 2016. A Serial shRNA Screen for Roadblocks to Reprogramming Identifies the Protein Modifier SUMO2. Stem Cell Rep. 6, 704-16. [Abstract] 
  6. Zhou B, Wang L, Zhang S, Bennett BD, He F, Zhang Y, Xiong C, Han L, Diao L, Li P, Fargo DC, Cox AD, Hu G. 2016. INO80 governs superenhancer-mediated oncogenic transcription and tumor growth in melanoma. Genes Dev. 30, 1440-53. [Abstract] 
  7. Wang T, Santos JH, Feng J, Cahill M, Fargo DC, Shen L, Nestler EJ, Woychik RP. 2016. A novel analytical strategy to identify fusion transcripts between repetitive elements and protein coding-exons using RNA-seq. PLoS One. e0159028. [Abstract] 
  8. Bunch H, Lawney BP, Burkholder A, Ma D, Zheng X, Motola S, Fargo DC, Levine SS, Wang YE, Hu G. 2016. RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes. Genomics. 108, 64-77. [Abstract]
  9. Lavender CA, Cannady KR, Hoffman JA, Trotter KW, Gilchrist DA, Bennett BD, Burkholder AB, Burd CJ, Fargo DC, Archer TK. 2016. Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters. PLoS Genet. e1006224. [Abstract]  
  10. Zhang S, Zhou B, Wang L, Li P, Bennett BD, Snyder R, Garantziotis S, Fargo DC, Cox AD, Chen L, Hu G. 2016. INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer. Oncogene. 36, 1430-9. [Abstract]
  11. Zheng X, Yang P, Lackford B, Bennett BD, Wang L, Li H, Wang Y, Miao Y, Foley JF, Fargo DC, Jin Y, Williams CJ, Jothi R, Hu G. 2016. CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State. Stem Cell Reports. 7, 897-910. [Abstract]  
  12. Saini N, SA Roberts, LJ Klimczak, K Chan, SA Grimm, S Dai, DC Fargo, JC Boyer, WK Kaufmann, JA Taylor, E Lee, I Cortes-Ciriano, PJ Park, SH Schurman, EP Malc, PA Mieczkowski, Gordenin DA. 2016. The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts. PLoS Genet. e1006385. [Abstract] 
  13. Chan K, Roberts SA, Klimczak LJ, Sterling JF, Saini N, Malc EP, Kim J, Kwiatkowski DJ, Fargo DC, Mieczkowski PA, Getz G, Gordenin DA. 2015 An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers. Nat Genet. 47(9), 1067-72. [Abstract] 
  14. Scruggs BS, Gilchrist DA, Nechaev S, Muse GW, Burkholder A, Fargo DC, Adelman K. Mol Cell. 2015 Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin. Mol Cell 58(6):1101-12. [Abstract] 
  15. Williams LH, Fromm G, Gokey NG, Henriques T, Muse GW, Burkholder A, Fargo DC, Hu G, Adelman K. 2015 Pausing of RNA polymerase II Regulates Mammalian Developmental Potential. Mol Cell. 58(2), 311-22. [Abstract]
  16. Clausen AR, Lujan SA, Burkholder AB, Orebaugh CD, Williams JS, Clausen MF, Malc EP, Mieczkowski PA, Fargo DC, Smith DJ, Kunkel TA. 2015 Tracking DNA replication enzymology in vivo using ribonucleotides Nat Struct Mol Biol. 22(3), 185-91. [Abstract]  
  17. Wells ML, Washington OL, Hicks SN, Nobile CJ, Hartooni N, Wilson GM, Zucconi BE, Huang W, Li L, Fargo DC, Blackshear PJ. 2014 Post-transcriptional regulation of transcript abundance by a conserved member of the tristetraprolin family in Candida albicans. Mol Microbiol. 95,1036-53. [Abstract] 
  18. Lujan SA, Clausen AR, Clark AB, MacAlpine HK, MacAlpine DM, Malc EP, Mieczkowski PA, Burkholder AB, Fargo DC, Gordenin DA, Kunkel TA. 2014 Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. Genome Res. 24, 1751-64. [Abstract] 
  19. Bunch H, Zheng X, Burkholder A, Dillon ST, Motola S, Birrane G, Ebmeier CC, Levine S, Fargo D, Hu G, Taatjes DJ, Calderwood SK. 2014 TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release. Nat Struct Mol Biol. 21, 876-83. [Abstract] 
  20. Davis CF, et al. (with Gordenin DA, Roberts SA, Klimczak LJ, Fargo D). 2014 The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma. Cancer Cell. 26, 319-30 [Abstract] 
  21. Tang S, Huang G, Fan W, Chen Y, Ward JM, Xu X, Xu Q, Kang A, McBurney MW, Fargo DC, Hu G, Baumgart-Vogt E, Zhao Y, Li X. 2014 SIRT1-Mediated Deacetylation of CRABPII Regulates Cellular Retinoic Acid Signaling and Modulates Embryonic Stem Cell Differentiation. Mol Cell. 55, 843-55. [Abstract] 
  22. Wang L, Du Y, Ward JM, Shimbo T, Lackford B, Zheng X, Miao Y, Zhou B, Han L, Fargo DC, Jothi R, Williams CJ, Wade PA, Hu G. 2014 INO80 Facilitates Pluripotency Gene Activation in Embryonic Stem Cell Self-Renewal, Reprogramming, and Blastocyst Development. Cell Stem Cell. 14, 575–591. [Abstract] 
  23. Hewitt SC, Li L, Grimm SA, Winuthayanon W, Hamilton KJ, Pockette B, Rubel CA, Pedersen LC, Fargo D, Lanz RB, Demayo FJ, Schütz G, Korach KS. 2014 Unexpected Hormone Response Motif Activity of Female Estrogen Receptor α DNA Binding Deficient Mouse. Mol Endocrinol. 28, 899-911. [Abstract] 
  24. Weinstein JN, et al. (with Gordenin DA, Fargo D, Klimczak LJ, Roberts SA). 2014 Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 20, 315-22. [Abstract]
  25. Wang L, Miao YL, Zheng X, Lackford B, Zhou B, Han L, Yao C, Ward JM, Burkholder A, Lipchina I, Fargo DC, Hochedlinger K, Shi Y, Williams CJ, Hu G. 2013 The THO complex regulates pluripotency gene mRNA export and controls embryonic stem cell self-renewal and somatic cell reprogramming. Cell Stem Cell. 13, 676-90. [Abstract]  
  26. Henriques T, Gilchrist DA, Nechaev S, Bern M, Muse GW, Burkholder A, Fargo DC, Adelman K. 2013 Stable Pausing by RNA Polymerase II Provides an Opportunity to Target and Integrate Regulatory Signals. Mol Cell. 52, 517-28. [Abstract] 
  27. Huang W, Loganantharaj R, Schroeder B, Fargo D, Li L. 2013 PAVIS: a tool for Peak Annotation and Visualization. Bioinformatics. 29, 3097-9. [Abstract] 
  28. Lai WS, Stumpo DJ, Kennington EA, Burkholder AB, Ward JM, Fargo D, Blackshear PJ. 2013 Life without TTP: apparent absence of an important anti-inflammatory protein in birds. Am J Physiol Regul Integr Comp Physiol. 305, 689-700. [Abstract] 
  29. Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D, Stojanov P, Kiezun A, Kryukov GV, Carter SL, Saksena G, Harris S, Shah RR, Resnick MA, Getz G, Gordenin DA. 2013 An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat Genet. 45, 970-6. [Abstract] 
  30. Core LJ, Waterfall JJ, Gilchrist DA, Fargo DC, Kwak H, Adelman K, Lis JT. 2012 Defining the status of RNA polymerase at promoters. Cell Rep. 2:1025-35. [Abstract] 
  31. Wells ML, Huang W, Li L, Gerrish KE, Fargo DC, Ozsolak F, Blackshear PJ. 2012 Posttranscriptional regulation of cell-cell interaction protein-encoding transcripts by Zfs1p in Schizosaccharomyces pombe. Mol Cell Biol. 32, 4206-14. [Abstract] 
  32. Gilchrist DA, Fromm G, Dos Santos G, Pham LN, McDaniel IE, Burkholder A, Fargo DC, Adelman K. 2012 Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks. Genes Dev. 26, 933-44. [Abstract] 
  33. Hewitt SC, Li L, Grimm SA, Chen Y, Liu L, Li Y, Bushel PR, Fargo D, Korach KS. 2012 Research Resource: Whole-Genome Estrogen Receptor α Binding in Mouse Uterine Tissue Revealed by ChIP-Seq. Mol Endocrinol. 26, 887-98. [Abstract] 
  34. Saha RN, Wissink EM, Bailey ER, Zhao M, Fargo DC, Hwang JY, Daigle KR, Fenn JD, Adelman K, Dudek SM. 2011 Rapid activity-induced transcription of Arc and other IEGs relies on poised RNA polymerase II. Nat Neurosci. 14, 848-56. [Abstract] 
  35. Colaneri A, Staffa N, Fargo DC, Gao Y, Wang T, Peddada SD, Birnbaumer L. 2011 Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome. Proc Natl Acad Sci U S A. 108, 9715-20. [Abstract] 
  36. Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K. 2010 Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell. 143, 540-51. [Abstract] 
  37. Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, Burns C, Canbäck B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigó R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kües U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng Q, Zolan ME, Pukkila PJ 2010 Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci U S A. 107, 11889-94. [Abstract] 
  38. Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K. 2010 Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science. 327, 335-8. [Abstract] 
  39. Gilchrist DA, Fargo DC, Adelman K. 2009 Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation. Methods. 4, 398-408. [Abstract]