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Transposable elements in human genetic disease.

Payer LM, Burns KH.

Nat Rev Genet. 2019 Sep 12. doi: 10.1038/s41576-019-0165-8. [Epub ahead of print] Review.


Bone Marrow Findings in Patients With Acute Promyelocytic Leukemia Treated With Arsenic Trioxide.

Miller KP, Venkataraman G, Gocke CD, Batista DA, Borowitz MJ, Burns KH, Pratz K, Duffield AS.

Am J Clin Pathol. 2019 Oct 7;152(5):675-685. doi: 10.1093/ajcp/aqz087.


Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells.

Madugundu AK, Na CH, Nirujogi RS, Renuse S, Kim KP, Burns KH, Wilks C, Langmead B, Ellis SE, Collado-Torres L, Halushka MK, Kim MS, Pandey A.

Proteomics. 2019 Aug;19(15):e1800315. doi: 10.1002/pmic.201800315. Epub 2019 Jun 26.


Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome.

Steranka JP, Tang Z, Grivainis M, Huang CRL, Payer LM, Rego FOR, Miller TLA, Galante PAF, Ramaswami S, Heguy A, Fenyö D, Boeke JD, Burns KH.

Mob DNA. 2019 Mar 8;10:8. doi: 10.1186/s13100-019-0148-5. eCollection 2019.


SQuIRE reveals locus-specific regulation of interspersed repeat expression.

Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH.

Nucleic Acids Res. 2019 Mar 18;47(5):e27. doi: 10.1093/nar/gky1301.


Long Interspersed Nuclear Element 1 Retrotransposons Become Deregulated during the Development of Ovarian Cancer Precursor Lesions.

Pisanic TR 2nd, Asaka S, Lin SF, Yen TT, Sun H, Bahadirli-Talbott A, Wang TH, Burns KH, Wang TL, Shih IM.

Am J Pathol. 2019 Mar;189(3):513-520. doi: 10.1016/j.ajpath.2018.11.005. Epub 2018 Dec 13.


The Johns Hopkins Department of Pathology Novel Organizational Model: A 25-Year-Old Ongoing Experiment.

Sanfilippo F, Burns KH, Borowitz MJ, Jackson JB, Hruban RH.

Acad Pathol. 2018 Nov 14;5:2374289518811145. doi: 10.1177/2374289518811145. eCollection 2018 Jan-Dec.


Ten things you should know about transposable elements.

Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvák Z, Levin HL, Macfarlan TS, Mager DL, Feschotte C.

Genome Biol. 2018 Nov 19;19(1):199. doi: 10.1186/s13059-018-1577-z. Review.


Alu insertion variants alter mRNA splicing.

Payer LM, Steranka JP, Ardeljan D, Walker J, Fitzgerald KC, Calabresi PA, Cooper TA, Burns KH.

Nucleic Acids Res. 2019 Jan 10;47(1):421-431. doi: 10.1093/nar/gky1086.


The Evolution of Earned, Transparent, and Quantifiable Faculty Salary Compensation: The Johns Hopkins Pathology Experience.

Burns KH, Borowitz MJ, Carroll KC, Gocke CD, Hooper JE, Amukele T, Tobian AAR, Valentine A, Kahl R, Rodas-Eral V, Boitnott JK, Jackson JB, Sanfilippo F, Hruban RH.

Acad Pathol. 2018 Jun 11;5:2374289518777463. doi: 10.1177/2374289518777463. eCollection 2018 Jan-Dec.


Systemic depletion of lymphocytes following focal radiation to the brain in a murine model.

Piotrowski AF, Nirschl TR, Velarde E, Blosser L, Ganguly S, Burns KH, Luznik L, Wong J, Drake CG, Grossman SA.

Oncoimmunology. 2018 May 9;7(7):e1445951. doi: 10.1080/2162402X.2018.1445951. eCollection 2018.


Editorial overview: Genome architecture and expression: Mobile elements at work.

Lisch D, Burns KH.

Curr Opin Genet Dev. 2018 Apr;49:iv-v. doi: 10.1016/j.gde.2018.05.003. No abstract available.


Familial monophasic acute transverse myelitis due to the pathogenic variant in VPS37A.

Mealy MA, Nam TS, Pardo SJ, Pardo CA, Sobreira NL, Avramopoulos D, Valle D, Burns KH, Levy M.

Neurol Genet. 2018 Jan 30;4(1):e213. doi: 10.1212/NXG.0000000000000213. eCollection 2018 Feb.


Dissection of affinity captured LINE-1 macromolecular complexes.

Taylor MS, Altukhov I, Molloy KR, Mita P, Jiang H, Adney EM, Wudzinska A, Badri S, Ischenko D, Eng G, Burns KH, Fenyö D, Chait BT, Alexeev D, Rout MP, Boeke JD, LaCava J.

Elife. 2018 Jan 8;7. pii: e30094. doi: 10.7554/eLife.30094.


Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia.

Pallavajjala A, Kim D, Li T, Ghiaur G, Jones RJ, Burns KH, Salzberg SL, Ning Y.

Leuk Lymphoma. 2018 May;59(5):1231-1238. doi: 10.1080/10428194.2017.1372577. Epub 2017 Sep 7.


Toward the human cellular microRNAome.

McCall MN, Kim MS, Adil M, Patil AH, Lu Y, Mitchell CJ, Leal-Rojas P, Xu J, Kumar M, Dawson VL, Dawson TM, Baras AS, Rosenberg AZ, Arking DE, Burns KH, Pandey A, Halushka MK.

Genome Res. 2017 Oct;27(10):1769-1781. doi: 10.1101/gr.222067.117. Epub 2017 Sep 6.


Transposable elements in cancer.

Burns KH.

Nat Rev Cancer. 2017 Jul;17(7):415-424. doi: 10.1038/nrc.2017.35. Epub 2017 Jun 9. Review.


Structural variants caused by Alu insertions are associated with risks for many human diseases.

Payer LM, Steranka JP, Yang WR, Kryatova M, Medabalimi S, Ardeljan D, Liu C, Boeke JD, Avramopoulos D, Burns KH.

Proc Natl Acad Sci U S A. 2017 May 16;114(20):E3984-E3992. doi: 10.1073/pnas.1704117114. Epub 2017 May 2.


Insertion and deletion polymorphisms of the ancient AluS family in the human genome.

Kryatova MS, Steranka JP, Burns KH, Payer LM.

Mob DNA. 2017 Apr 24;8:6. doi: 10.1186/s13100-017-0089-9. eCollection 2017.


The Human Long Interspersed Element-1 Retrotransposon: An Emerging Biomarker of Neoplasia.

Ardeljan D, Taylor MS, Ting DT, Burns KH.

Clin Chem. 2017 Apr;63(4):816-822. doi: 10.1373/clinchem.2016.257444. Epub 2017 Feb 10. Review.


Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer.

Tang Z, Steranka JP, Ma S, Grivainis M, Rodić N, Huang CR, Shih IM, Wang TL, Boeke JD, Fenyö D, Burns KH.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):E733-E740. doi: 10.1073/pnas.1619797114. Epub 2017 Jan 17.


Somatic retrotransposition is infrequent in glioblastomas.

Achanta P, Steranka JP, Tang Z, Rodić N, Sharma R, Yang WR, Ma S, Grivainis M, Huang CRL, Schneider AM, Gallia GL, Riggins GJ, Quinones-Hinojosa A, Fenyö D, Boeke JD, Burns KH.

Mob DNA. 2016 Nov 11;7:22. doi: 10.1186/s13100-016-0077-5. eCollection 2016.


A map of mobile DNA insertions in the NCI-60 human cancer cell panel.

Zampella JG, Rodić N, Yang WR, Huang CR, Welch J, Gnanakkan VP, Cornish TC, Boeke JD, Burns KH.

Mob DNA. 2016 Oct 31;7:20. eCollection 2016.


Lack of TERT Promoter Mutations in Human B-Cell Non-Hodgkin Lymphoma.

Lam G, Xian RR, Li Y, Burns KH, Beemon KL.

Genes (Basel). 2016 Oct 25;7(11). pii: E93.


Tumor-Infiltrating Macrophages in Post-Transplant, Relapsed Classical Hodgkin Lymphoma Are Donor-Derived.

Crane GM, Samols MA, Morsberger LA, Yonescu R, Thiess ML, Batista DA, Ning Y, Burns KH, Vuica-Ross M, Borowitz MJ, Gocke CD, Ambinder RF, Duffield AS.

PLoS One. 2016 Sep 29;11(9):e0163559. doi: 10.1371/journal.pone.0163559. eCollection 2016.


Meeting Report: The Role of the Mobilome in Cancer.

Ardeljan D, Taylor MS, Burns KH, Boeke JD, Espey MG, Woodhouse EC, Howcroft TK.

Cancer Res. 2016 Aug 1;76(15):4316-9. doi: 10.1158/0008-5472.CAN-15-3421. Epub 2016 Jul 18.


Somatically Acquired LINE-1 Insertions in Normal Esophagus Undergo Clonal Expansion in Esophageal Squamous Cell Carcinoma.

Doucet-O'Hare TT, Sharma R, Rodić N, Anders RA, Burns KH, Kazazian HH Jr.

Hum Mutat. 2016 Sep;37(9):942-54. doi: 10.1002/humu.23027. Epub 2016 Jul 13.


Genome-wide characterization of human L1 antisense promoter-driven transcripts.

Criscione SW, Theodosakis N, Micevic G, Cornish TC, Burns KH, Neretti N, Rodić N.

BMC Genomics. 2016 Jun 14;17:463. doi: 10.1186/s12864-016-2800-5.


Characterization of L1-Ribonucleoprotein Particles.

Taylor MS, LaCava J, Dai L, Mita P, Burns KH, Rout MP, Boeke JD.

Methods Mol Biol. 2016;1400:311-38. doi: 10.1007/978-1-4939-3372-3_20.


Immunodetection of Human LINE-1 Expression in Cultured Cells and Human Tissues.

Sharma R, Rodić N, Burns KH, Taylor MS.

Methods Mol Biol. 2016;1400:261-80. doi: 10.1007/978-1-4939-3372-3_17.


A robust nonlinear tissue-component discrimination method for computational pathology.

Sarnecki JS, Burns KH, Wood LD, Waters KM, Hruban RH, Wirtz D, Wu PH.

Lab Invest. 2016 Apr;96(4):450-8. doi: 10.1038/labinvest.2015.162. Epub 2016 Jan 18.


LINE-1 expression and retrotransposition in Barrett's esophagus and esophageal carcinoma.

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.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):E4894-900. doi: 10.1073/pnas.1502474112. Epub 2015 Aug 17. Erratum in: Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):E104.


Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma.

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.

Nat Med. 2015 Sep;21(9):1060-4. doi: 10.1038/nm.3919. Epub 2015 Aug 10.


Diagnostic utility of 5-hydroxymethylcytosine immunohistochemistry in melanocytic proliferations.

Rodić N, Zampella J, Sharma R, Burns KH, Taube JM.

J Cutan Pathol. 2015 Nov;42(11):807-14. doi: 10.1111/cup.12564. Epub 2015 Sep 2.


Primary effusion lymphoma presenting as a cutaneous intravascular lymphoma.

Crane GM, Xian RR, Burns KH, Borowitz MJ, Duffield AS, Taube JM.

J Cutan Pathol. 2014 Dec;41(12):928-35. doi: 10.1111/cup.12405. Epub 2014 Dec 8.


Long interspersed element-1 protein expression is a hallmark of many human cancers.

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.

Am J Pathol. 2014 May;184(5):1280-6. doi: 10.1016/j.ajpath.2014.01.007. Epub 2014 Mar 6.


Visualization and probability-based scoring of structural variants within repetitive sequences.

Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA.

Bioinformatics. 2014 Jun 1;30(11):1514-21. doi: 10.1093/bioinformatics/btu054. Epub 2014 Feb 4.


TE-array--a high throughput tool to study transposon transcription.

Gnanakkan VP, Jaffe AE, Dai L, Fu J, Wheelan SJ, Levitsky HI, Boeke JD, Burns KH.

BMC Genomics. 2013 Dec 10;14:869. doi: 10.1186/1471-2164-14-869.


Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition.

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.

Cell. 2013 Nov 21;155(5):1034-48. doi: 10.1016/j.cell.2013.10.021.


Translocation junctions in TCF3-PBX1 acute lymphoblastic leukemia/lymphoma cluster near transposable elements.

Rodić N, Zampella JG, Cornish TC, Wheelan SJ, Burns KH.

Mob DNA. 2013 Oct 17;4(1):22. doi: 10.1186/1759-8753-4-22.


Software-automated counting of Ki-67 proliferation index correlates with pathologic grade and disease progression of follicular lymphomas.

Samols MA, Smith NE, Gerber JM, Vuica-Ross M, Gocke CD, Burns KH, Borowitz MJ, Cornish TC, Duffield AS.

Am J Clin Pathol. 2013 Oct;140(4):579-87. doi: 10.1309/AJCPTMA1F6LWYTQV.


Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies.

Halper-Stromberg E, Steranka J, Giraldo-Castillo N, Fuller T, Desiderio S, Burns KH.

BMC Genomics. 2013 Aug 19;14:565. doi: 10.1186/1471-2164-14-565.


Parent-reported outcomes of comprehensive care for children with medical complexity.

Kuo DZ, Robbins JM, Lyle RE, Barrett KW, Burns KH, Casey PH.

Fam Syst Health. 2013 Jun;31(2):132-41. doi: 10.1037/a0032341.


Infection of Xenotransplanted Human Cell Lines by Murine Retroviruses: A Lesson Brought Back to Light by XMRV.

Hempel HA, Burns KH, De Marzo AM, Sfanos KS.

Front Oncol. 2013 Jun 17;3:156. doi: 10.3389/fonc.2013.00156. eCollection 2013.


Targeted pathologic evaluation of bone marrow donors identifies previously undiagnosed marrow abnormalities.

Tilson MP, Jones RJ, Sexauer A, Griffin CA, Morsberger LA, Batista DA, Small D, Burns KH, Gocke CD, Vuica-Ross M, Borowitz MJ, Duffield AS.

Biol Blood Marrow Transplant. 2013 Aug;19(8):1254-9. doi: 10.1016/j.bbmt.2013.05.022. Epub 2013 Jun 13.


Long interspersed element-1 (LINE-1): passenger or driver in human neoplasms?

Rodić N, Burns KH.

PLoS Genet. 2013 Mar;9(3):e1003402. doi: 10.1371/journal.pgen.1003402. Epub 2013 Mar 28. Review.


Functional impact of the human mobilome.

Babatz TD, Burns KH.

Curr Opin Genet Dev. 2013 Jun;23(3):264-70. doi: 10.1016/j.gde.2013.02.007. Epub 2013 Mar 22. Review.


The impact of chorioamnionitis on neurodevelopmental outcomes at 3, 8 and 18 years in low-birthweight preterm infants.

Burns SA, Lyle RE, Casey PH, Burns KH, Barrett KW, Whiteside-Mansell L.

J Perinatol. 2013 Jul;33(7):548-52. doi: 10.1038/jp.2012.160. Epub 2013 Jan 10.


Blastic transformation of mantle cell lymphoma.

Kasamon YL, Burns KH.

Blood. 2012 Sep 20;120(12):2359. No abstract available.


Active transposition in genomes.

Huang CR, Burns KH, Boeke JD.

Annu Rev Genet. 2012;46:651-75. doi: 10.1146/annurev-genet-110711-155616. Review.

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