Publications

Published:

  1. Mitchell PS, Young JM, Emerman M, Malik HS. Evolutionary Analyses Suggest a Function of MxB Immunity Proteins Beyond Lentivirus Restriction. PLoS Pathog. 2015 Dec 10;11(12):e1005304. PMCID: PMC4687636.
  2. Boeke JD, Fenyo D. Much Ado about Zero. Cell. 2015 Oct 22;163(3):534-5. PubMed PMID: 26496595.
  3. Ewing AD, Gacita A, Wood LD Ma F, Xing D, Kim M-S, Manda SS, Gabriela Abril  G, Pereira G, Makohon-Moore A, Looijenga LHJ, Gillis AJM, Hruban  RH, Anders RA, Romans KE,Pandey A, Iacobuzio-Donahue CA, Vogelstein B, Kinzler KW, Kazazian HH Jr.*, Solyom S*. Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution. Genome Research, 2015 Oct;25 (10):1536-45. PMCID: PMC4579339 (*corresponding authors)
  4. Rodić N, Steranka JP, Makohon-Moore A, Moyer A, Shen P, Sharma R, Kohutek ZA, Huang CR, Ahn D, Mita P, Taylor MS, Barker NJ, Hruban RH, Iacobuzio-Donahue CA,
    Boeke JD, Burns KH. Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma. Nat Med. 2015; Sep;21(9): 1060-4. PubMed PMID: 26259033.
  5. Doucet-O'Hare TT, Rodić N, Sharma R, Darbari I, Abril G, Choi JA, Young Ahn J, Cheng Y, Anders RA, Burns KH, Meltzer SJ, Kazazian HH Jr. LINE-1 expression and
    retrotransposition in Barrett's esophagus and esophageal carcinoma
    . Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):E4894-900. PMCID: PMC4568228.
  6. Grandi, F.C., Rosser, J.M., Newkirk, S.J., Yin, J., Jiang, X., Xing, Z., Whitmore, L., Bashir, S., Ivics, Z., Izsvák, Z., Ye, P., Yu, Y.E. & An, W. Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites. Genome Research. 2015. Aug; 25: 1135-1146. PMCID: PMC4509998
  7. McLaughlin RN Jr, Malik HS. LINE-1 Retroelements Get ZAPped! PLoS Genet. 2015 Jul 16; 11(7): e1005364. doi: 10.1371/journal.pgen.1005364. eCollection 2015 Jul. PubMed PMID: 26182081. PMCID: PMC4504689.
  8. LaCava, J., Molloy, K. R., Taylor, M. S., Domanski, M., Chait, B. T., & Rout, M. P. (2015). Affinity proteomics to study endogenous protein complexes: Pointers, pitfalls, preferences and perspectives. BioTechniques, 2015 Mar 1; 58(3), 103–119. doi:10.2144/000114262. PMCID: PMC4465938
  9. Gorbunova V, Boeke JD, Helfand SL, Sedivy JM. Human Genomics. Sleeping dogs of the genome. Science. 2014 Dec 5;346(6214):1187-8. PMCID: PMC4312280
  10. McLaughlin R, Young J, Yang L, Wichman H, Malik H. Positive selection and multiple losses of the LINE-1-derived L1TD1 gene in mammals suggest a dual role in genome defense and pluripotency. PLoS Genetics, 2014 Sep 11;10(9): e1004531. PMCID: PMC4161310
  11. Belfort M, Marraffini L, Macfarlan T, Boeke J, Slotkin K, Malik H, Maquat L. Mobile DNA: an evolving field. 2014 Mob DNA. Jun 5;5:16. PMCID: PMC4046146.
  12. Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA. Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinformatics. 2014  Jun 1;30(11):1514-21. PMCID: PMC4029030.
  13. Dai L, LaCava J, Taylor MS, Boeke JD. Expression and detection of LINE-1 ORF-encoded proteins. 2014 Mob Genet Elements. May 22;4:e29319. eCollection 2014. PMCID: PMC4091050.
  14. Rodić N, Sharma R, Sharma R, Zampella J, Dai L, Taylor MS, Hruban RH, Iacobuzio-Donahue CA, Maitra A, Torbenson MS, Goggins M, Shih IeM, Duffield AS, Montgomery EA, Gabrielson E, Netto GJ, Lotan TL, De Marzo AM, Westra W, Binder ZA, Orr BA, Gallia GL, Eberhart CG, Boeke JD, Harris CR, Burns KH. Long interspersed element-1 protein expression is a hallmark of many human cancers. Am J Pathol. 2014 May;184:1280-6. PMCID: PMC4005969
  15. Shimizu A, Nakatani Y, Nakamura T, Jinno-Oue A, Ishikawa O, Boeke JD, Takeuchi Y, Hoshino H. Characterisation of cytoplasmic DNA complementary to non-retroviral RNA viruses in human cells. Sci Rep. 2014 May 30;4:5074. doi: 10.1038/srep05074. PMCID: PMC4038843.
  16. Daugherty MD, Young JM, Kerns JA, Malik HS. Rapid evolution of PARP genes suggests a broad role for ADP-ribosylation in host-virus conflicts. PLoS Genet.
    2014 May 29;10(5):e1004403. doi: 10.1371/journal.pgen.1004403. eCollection 2014. PMCID: PMC4038475.
  17. Gnanakkan VP, Jaffe AE, Dai L, Fu J, Wheelan SJ, Levitsky HI, Boeke JD, Burns KH. TE-array--a high throughput tool to study transposon transcription. BMC
    Genomics. 2013 Dec 10;14:869. doi: 10.1186/1471-2164-14-869. PMCID: PMC3878892.
  18. Taylor MS, Lacava J, Mita P, Molloy KR, Huang CR, Li D, Adney EM, Jiang H, Burns KH, Chait BT, Rout MP, Boeke JD, Dai L. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell 2013 Nov 21;155(5):1034-48. doi: 10.1016/j.cell.2013.10.021; PMCID: PMC3904357 
  19. Terasaki N, Goodier JL, Cheung LE, Wang YJ, Kajikawa M, Kazazian HH Jr, Okada N. In vitro screening for compounds that enhance human L1 mobilization. PLoS One 2013 Sep 11;8(9):e74629. PMCID: PMC3770661
  20. Zhao K, Du J, Han X, Goodier JL, Li P, Zhou X, Wei W, Evans SL, Li L, Zhang W, Cheung LE, Wang G, Kazazian HH Jr, and Yu XF. Modulation of LINE-1 and Alu/SVA retrotransposition by Aicardi-Goutières syndrome-related SAMHD1. Cell Rep. 2013 Sep 26; 1108-15. PMCID: PMC3988314
  21. Mita P, Boeke JD. How retrotransposons shape genome regulation.  Current Opinions in Genetics and Development, 2016 Apr;37:90-100. PMCID: PMC4914423

In Press:

4 chapters in press for a Methods in Molecular Biology book on "Retrotransposons and Transposons"  Editor : Jose Luis García Pérez

Submitted:

McLaughlin RN Jr, Gable JT, Wittkopp C, Emerman M, Malik HS. Conservation and innovation of APOBEC3A restriction functions during primate evolution. Mol Biol Evol 2016.

Doucet-Ohare TT, Reema Sharmac, Nemanja Rodic, Robert A. Anders, Kathleen H. Burns, and Haig H. Kazazian Jr.  Frequent sub-clonal LINE-1 insertions in normal esophagus expand in subsequent esophageal squamous cell carcinoma. Oncogene 2016.