Johns Hopkins Pathology

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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 2. pii: 201704117. doi: 10.1073/pnas.1704117114.

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 Feb 10. pii: clinchem.2016.257444. doi: 10.1373/clinchem.2016.257444.

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 17. pii: 201619797. doi: 10.1073/pnas.1619797114.

Somatic retrotransposition is infrequent in glioblastomas.
Achanta P, Steranka JP, Tang Z, Rodić N, Sharma R, Yang WR, Ma S, Grivainis M, Huang CR, Schneider AM, Gallia GL, Riggins GJ, Quinones-Hinojosa A, Fenyö D, Boeke JD, Burns KH.
Mob DNA. 2016 Nov 11;7:22.

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.

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.

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 Jun 20. doi: 10.1002/humu.23027.

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(1):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 Jan 18. doi: 10.1038/labinvest.2015.162.

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

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 Aug 10. doi: 10.1038/nm.3919.

Diagnostic utility of 5-hydroxymethylcytosine immunohistochemistry in melanocytic proliferations.
Rodić N, Zampella J, Sharma R, Burns KH, Taube JM.
J Cutan Pathol. 2015 Aug 4. doi: 10.1111/cup.12564

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 IM, 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 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 Feb 21.

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.

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.

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.

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.

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.

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

Functional impact of the human mobilome.
Babatz TD, Burns KH.
Curr Opin Genet Dev. 2013 Jun;23(3):264-70

Long interspersed element-1 (LINE-1): passenger or driver in human neoplasms?
Rodić N, Burns KH.
PLoS Genet. 2013 Mar;9(3):e1003402.

Active transposition in genomes.
Huang CR, Burns KH, Boeke JD.
Annu Rev Genet. 2012;46:651-75

Genetics of mammalian reproduction: modeling the end of the germline.
Matzuk MM, Burns KH.
Annu Rev Physiol. 2012;74:503-28.

Blastic transformation of mantle cell lymphoma.
Kasamon YL, Burns KH.
Blood. 2012 Sep 20;120(12):2359.

Human transposon tectonics.
Burns KH, Boeke JD.
Cell. 2012 May 11;149(4):740-52

Flow cytometric findings in hemophagocytic lymphohistiocytosis.
McCall CM, Mudali S, Arceci RJ, Small D, Fuller S, Gocke CD, Vuica-Ross M, Burns KH, Borowitz MJ, Duffield AS.
Am J Clin Pathol. 2012 May;137(5):786-94.

Clinical and pathologic features of secondary acute promyelocytic leukemia.
Duffield AS, Aoki J, Levis M, Cowan K, Gocke CD, Burns KH, Borowitz MJ, Vuica-Ross M.
Am J Clin Pathol. 2012 Mar;137(3):395-402.

Massively parallel rare disease genetics.
Burns KH, Chakravarti A.
Genome Med. 2011 May 30;3(5):29.

Mobilizing diversity: transposable element insertions in genetic variation and disease.
O’Donnell KA, Burns KH.
Mob DNA. 2010 Sep 2;1(1):21.

Mobile interspersed repeats are major structural variants in the human genome.
Huang CR, Schneider AM, Lu Y, Niranjan T, Shen P, Robinson MA, Steranka JP, Valle D, Civin CI, Wang T, Wheelan SJ, Ji H, Boeke JD, Burns KH.
Cell. 2010 Jun 25;141(7):1171-82.

Roles of retrotransposons in benign and malignant hematologic disease.
Schneider AM, Duffield AS, Symer DE, Burns KH.
Cellscience. 2009 Oct 27;6(2):121-145.

GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline.
Ma L, Buchold GM, Greenbaum MP, Roy A, Burns KH, Zhu H, Han DY, Harris RA, Coarfa C, Gunaratne PH, Yan W, Matzuk MM.
PLoS Genet. 2009 Sep;5(9):e1000635.

Great exaptations.
Burns KH, Boeke JD.
J Biol. 2008;7(2):5.

Hematological manifestations of nephropathic cystinosis.
Emadi A, Burns KH, Confer B, Borowitz MJ, Streiff MB.
Acta Haematol. 2008;119(3):169-72.

A descent into the nuage: the maelstrom of transposon control.
O’Donnell KA, Burns KH, Boeke JD.
Dev Cell. 2008 Aug;15(2):179-81.