Burns Lab Publications
Select Publications
2023
Sato S, Gillette M, de Santiago PR, Kuhn E, Burgess M, Doucette K, Feng Y, Mendez-Dorantes C, Ippoliti PJ, Hobday S, Mitchell MA, Doberstein K, Gysler SM, Hirsch MS, Schwartz L, Birrer MJ, Skates SJ, Burns KH, Carr SA, Drapkin R. LINE-1 ORF1p as a candidate biomarker in high grade serous ovarian carcinoma. Sci Rep. 2023 Jan 27;13(1):1537.
Kanholm T, Rentia U, Hadley M, Karlow JA, Cox OL, Diab N, Bendall ML, Dawson T, McDonald JI, Xie W, Crandall KA, Burns KH, Baylin SB, Easwaran H, Chiappinelli KB. Oncogenic transformation drives DNA methylation loss and transcriptional activation of transposable element loci. Cancer Res. 2023 Aug 1;83(15):2584-2599.
Taylor MS, Wu C, Fridy PC, Zhang SJ, Senussi Y, Wolters JC, Cajuso T, Cheng WC, Heaps JD, Miller BD, Mori K, Cohen L, Jiang H, Molloy KR, Chait BT, Goggins MG, Bhan I, Franses JW, Yang X, Taplin ME, Wang X, Christiani DC, Johnson BE, Meyerson M, Uppaluri R, Egloff AM, Denault EN, Spring LM, Wang TL, Shih IM, Fairman JE, Jung E, Arora KS, Yilmaz OH, Cohen S, Sharova T, Chi G, Norden BL, Song Y, Nieman LT, Pappas L, Parikh AR, Strickland MR, Corcoran RB, Mustelin T, Eng G, Yilmaz OH, Matulonis UA, Skates SJ, Rueda BR, Drapkin R, Klempner SJ, Deshpande V, Ting DT, Rout MP, LaCava J, Walt DR*, Burns KH*. Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker. Cancer Discov. 2023 Sep 12. doi: 10.1158/2159-8290.CD-23-0313. Epub ahead of print. PMID: 37698949.
Chu C, Lin EW, Tran A, Jin H, Ho NI, Veit A, Cortes-Ciriano I, Burns KH, Ting DT, Park PJ. The landscape of human SVA retrotransposons. Nucleic Acids Res. 2023 Oct 12:gkad821. doi: 10.1093/nar/gkad821.
Cheng KCL, Frost JM, Sánchez-Luque FJ, García-Canãdas M, Taylor D, Yang WR, Irayanar B, Sampath S, Patani H, Agger K, Helin K, Ficz G, Burns KH, Ewing A, García-Pérez JL, Branco MR. Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation. Epigenetics Chromatin. 2023 Oct 16;16(1):39.
2022
Burns, KH. Repetitive DNA in disease. Science. 2022; 376(6591): 353-354.
McKerrow W, Wang X, Mendez-Dorantes C, Mita P, Cao S, Grivainis M, Ding L, LaCava J, Burns KH, Boeke JD, Fenyö D. LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint. Proc Natl Acad Sci U S A. 2022 Feb 22;119(8):e2115999119.
Rajurkar M, Parikh AR, Solovyov A, You E, Kulkarni AS, Chu C, Xu KH, Jaicks C, Taylor MS, Wu C, Alexander KA, Good CR, Szabolcs A, Gerstberger S, Tran AV, Xu N, Ebright RY, Van Seventer EE, Vo KD, Tai EC, Lu C, Joseph-Chazan J, Raabe MJ, Nieman LT, Desai N, Arora KS, Ligorio M, Thapar V, Cohen L, Garden PM, Senussi Y, Zheng H, Allen JN, Blaszkowsky LS, Clark JW, Goyal L, Wo JY, Ryan DP, Corcoran RB, Deshpande V, Rivera MN, Aryee MJ, Hong TS, Berger SL, Walt DR, Burns KH, Park PJ, Greenbaum BD, Ting DT. Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer. Cancer Discov. 2022 Mar 23:1117.
Tao J, Wang Q, Mendez-Dorantes C, Burns KH, Chiarle R. Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites. Nat Commun. 2022 Jun 27;13(1):3685.
Antiochos B, Paz M, Li J, Goldman DW, Petri M, Darrah E, Cashman K, Sanz I, Burns KH, Ardeljan D, Andrade F, Rosen A. Autoantibodies targeting LINE-1-encoded ORF1p are associated with systemic lupus erythematosus diagnosis but not disease activity. Clin Exp Rheumatol. 2022 Sep;40(9):1636-1641.
2021
Payer LM, Steranka JP, Kryatova MS, Grillo G, Lupien M, Rocha PP, Burns KH. Alu insertion variants alter gene transcript levels. Genome Res. 2021 Nov 19;31(12):2236-2248.
2020
Burns, KH. Our conflict with transposable elements and its implications for human disease. Annual Review of Pathology: Mechanisms of disease. 2020; 15: 51–70.
Ardeljan D, Steranka JP, Liu C, Li Z, Taylor MS, Payer LM, Gorbounov M, Sarnecki JS, Deshpande V, Hruban RH, Boeke JD, Fenyö D, Wu PH, Smogorzewska A, Holland AJ, Burns KH. LINE-1 cellular fitness interactions reveal conflict between retrotransposition and replication. Nature Structural and Molecular Biology. 2020; 27(2): 168-178.
Goubert C, Thomas J, Payer LM, Kidd JM, Feusier J, Watkins WS, Burns KH, Jorde LB, Feschotte C. TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data. Nucleic Acids Res. 2020; 48(6): e36.
Loh JW, Ha H, Lin T, Sun N, Burns KH, Xing J. Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions. Mobile DNA. 2020; 11: 12.
Cao X, Zhang Y, Payer LM, Lords H, Steranka JP, Burns KH, Xing J. Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues. Genome Biol. 2020; 21(1): 185.
Tunbak H, Enriquez-Gasca R, Tie CHC, Gould PA, Mlcochova P, Gupta RK, Fernandes L, Holt J, van der Veen AG, Giampazolias E, Burns KH, Maillard PV, Rowe HM. The HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s. Nat Commun. 2020; 11(1): 5387.
Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH; PCAWG Structural Variation Working Group, Campbell PJ, Tubio JMC; PCAWG Consortium. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics. 2020; 52(3): 306-319.
McKerrow W, Tang Z, Steranka JP, Payer LM, Boeke JD, Keefe D, Fenyö D*, Burns KH*, Liu C*. Human Transposon Insertion Profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells. Philosophical Transactions of the Royal Society B. 2020; 375(1795): 20190335.
2019
Payer, LM, Burns KH. Transposable elements in human genetic disease. Nature Reviews Genetics. 2019; 20(12): 760-772.
Ardeljan D*, Wang X*, Oghbaie M*, Taylor MS, Husband D, Deshpande V, Steranka JP, Gorbounov M, Yang WR, Sie B, Larman HB, Jiang H, Molloy KR, Altukhov I, Li Z, McKerrow W, Fenyö D*, Burns KH*, LaCava J*. LINE-1 ORF2p Expression is Nearly Imperceptible in Human Cancers. Mobile DNA. 2019; 11: 1.
Payer LM, Steranka JP, Ardeljan D, Walker J, Fitzgerald KC, Calabresi PA, Cooper TA, Burns KH. Alu insertion variants alter mRNA splicing. Nucleic Acids Research. 2019; 47(1): 421-431.
Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH. Software for Quantifying Interspersed Repeat Elements (SQuIRE) reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Research. 2019; 47(5): e27.
Pisanic TR 2nd, Asaka S, Lin SF, Yen TT, Sun H, Bahadirli-Talbott A, Wang TH, Burns KH, Wang TL, Shih IM. LINE-1 retrotransposons become deregulated during the development of ovarian cancer precursor lesions. American Journal of Pathology. 2019; 189(3): 513-520.
Steranka JP, Tang Z, Grivainis M, Huang CRL, Rego FOR, Miller TLA, Galante PAF, Ramaswami S, Heguy A, Fenyö D, Boeke JD, Burns KH. Transposon Insertion Profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome. Mobile DNA. 2019; 10:8.
2018
Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvák Z, Levin HL, Macfarlan TS, Mager DL, Feschotte C. Ten things you should know about transposable elements. Genome Biology; 19(1): 199.
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. Dissection of affinity captured LINE-1 macromolecular complexes. Elife. 2018;7. e30094.
2017
Ardeljan D, Taylor MS, Ting DT, Burns KH. The Human Long Interspersed Element-1 Retrotransposon: An Emerging Biomarker of Neoplasia. Clinical Chemistry. 2017; 63(4): 816-822.
Burns KH. Transposable elements in cancer. Nature Reviews Cancer. 2017; 17(7): 415-424.
Kryatova MS, Steranka JP, Burns KH*, Payer LM*. Insertion and deletion polymorphisms of the ancient AluS family in the human genome. Mobile DNA. 2017; 8: 6.
Tang Z, Steranka JP, Ma S, Grivainis M, Rodić N, Huang CR, Shih IM, Wang TL, Boeke JD*, Fenyö D*, Burns KH*. Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer. Proceedings of the National Academy of Sciences USA. 2017; 114(5): E733-E740.
Payer LM, Steranka JP, Yang WR, Kryatova M, Medabalimi S, Ardeljan D, Liu C, Boeke JD, Avramopoulos D, Burns KH. Structural variants caused by Alu insertions are associated with risks for many human diseases. Proceedings of the National Academy of Sciences USA. 2017; 114(20): E3984-E3992.
2016
Sharma R, Rodić N, Burns KH*, Taylor MS*. Immunodetection of Human LINE-1 Expression in Cultured Cells and Human Tissues. Methods in Molecular Biology. 2016; 1400: 261-280.
Taylor MS, LaCava J, Dai L, Mita P, Burns KH, Rout MP, Boeke JD. Characterization of L1-Ribonucleoprotein Particles. Methods in Molecular Biology. 2016; 1400:311-338.
Criscione SW, Theodosakis N, Micevic G, Cornish TC, Burns KH, Neretti N, Rodić N. Genome-wide characterization of human L1 antisense promoter-driven transcripts. BMC Genomics. 2016; 17: 463.
Doucet-O'Hare TT, Sharma R, Rodić N, Anders RA, Burns KH, Kazazian HH Jr. Somatically Acquired LINE-1 Insertions in Normal Esophagus Undergo Clonal Expansion in Esophageal Squamous Cell Carcinoma. Human Mutation. 2016; 37(9): 942-954.
Zampella JG, Rodić N, Yang WR, Huang CR, Welch J, Gnanakkan VP, Cornish TC, Boeke JD, Burns KH. A map of mobile DNA insertions in the NCI-60 human cancer cell panel. Mobile DNA. 2016; 7:20.
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. Somatic retrotransposition is infrequent in glioblastomas. Mobile DNA. 2016; 7: 22.
2015
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. Proceedings of the National Academy of Sciences USA. 2015; 112(35): e4894-4900.
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. Nature Medicine. 2015; 21(9): 1060-1064.
2014
Halper-Stromberg E, Steranka J, Burns KH, Irizarry RA. Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinformatics. 2014; 30(11): 1514-1521.
Rodić N, Sharma R, Zampella J, Hruban RH, Iacobuzio-Donahue CA, Maitra A, Torbenson MS, Shih IM, Kurman RJ, Montgomery EA, Gabrielson E, Netto GJ, Lotan TL, DeMarzo 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. American Journal of Pathology. 2014; 184(5): 1280-1286.
2013
Rodić N, Burns KH. Long interspersed element-1 (L1): passenger or driver in human neoplasms? PLoS Genetics. 2013; 9(3): e1003402.
Babatz T, Burns KH. Mobile DNA and human genetic disease. Current Opinion in Genetics and Development. 2013; 23(3): 264-270.
Gnanakkan VP, Jaffe AE, Dai L, Fu Jie, Wheelan SJ, Levitsky HI, Boeke JD*, Burns KH*. TE-array – A high throughput tool for studying transposon transcription. BMC Genomics. 2013; 14(1): 869.
Rodić N, Zampella J, Cornish TC, Wheelan S, Burns KH. Translocation junctions in TCF3-PBX1 acute lymphoblastic leukemia/lymphoma cluster near transposable elements. Mobile DNA. 2013; 4(1): 22.
Taylor MS, LaCava J, Mita P, Molloy K, Huang C, Li D, Adney E, Jiang H, Burns KH, Chait B, Rout M, Boeke J, Dai L. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell. 2013; 155(5): 1034-1048.
2012
Burns KH, Boeke JD. Human Transposon Tectonics. Cell. 2012; 149(4): 740-752.
Huang CRL, Burns KH, Boeke JD. Active transposition in genomes. Annual Reviews in Genetics. 2012; (46): 651-675.
2010
Huang CRL, Schneider AM, Lu Y, Niranjan T, Shen P, Valle D, Civin CI, Costello JF, Wang T, Wheelan SJ, Ji HK, Boeke JD*, Burns KH*. Mobile interspersed repeats are major structural variants in the human genome. Cell. 2010; 141(7): 1171-1182.
O'Donnell KA, Burns KH. Mobilizing diversity: transposable element insertions in genetic variation and disease. Mobile DNA. 2010; 1(1): 21.
2023
Sato S, Gillette M, de Santiago PR, Kuhn E, Burgess M, Doucette K, Feng Y, Mendez-Dorantes C, Ippoliti PJ, Hobday S, Mitchell MA, Doberstein K, Gysler SM, Hirsch MS, Schwartz L, Birrer MJ, Skates SJ, Burns KH, Carr SA, Drapkin R. LINE-1 ORF1p as a candidate biomarker in high grade serous ovarian carcinoma. Sci Rep. 2023 Jan 27;13(1):1537.
Kanholm T, Rentia U, Hadley M, Karlow JA, Cox OL, Diab N, Bendall ML, Dawson T, McDonald JI, Xie W, Crandall KA, Burns KH, Baylin SB, Easwaran H, Chiappinelli KB. Oncogenic transformation drives DNA methylation loss and transcriptional activation of transposable element loci. Cancer Res. 2023 Aug 1;83(15):2584-2599.
Taylor MS, Wu C, Fridy PC, Zhang SJ, Senussi Y, Wolters JC, Cajuso T, Cheng WC, Heaps JD, Miller BD, Mori K, Cohen L, Jiang H, Molloy KR, Chait BT, Goggins MG, Bhan I, Franses JW, Yang X, Taplin ME, Wang X, Christiani DC, Johnson BE, Meyerson M, Uppaluri R, Egloff AM, Denault EN, Spring LM, Wang TL, Shih IM, Fairman JE, Jung E, Arora KS, Yilmaz OH, Cohen S, Sharova T, Chi G, Norden BL, Song Y, Nieman LT, Pappas L, Parikh AR, Strickland MR, Corcoran RB, Mustelin T, Eng G, Yilmaz OH, Matulonis UA, Skates SJ, Rueda BR, Drapkin R, Klempner SJ, Deshpande V, Ting DT, Rout MP, LaCava J, Walt DR*, Burns KH*. Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker. Cancer Discov. 2023 Sep 12. doi: 10.1158/2159-8290.CD-23-0313. Epub ahead of print. PMID: 37698949.
Chu C, Lin EW, Tran A, Jin H, Ho NI, Veit A, Cortes-Ciriano I, Burns KH, Ting DT, Park PJ. The landscape of human SVA retrotransposons. Nucleic Acids Res. 2023 Oct 12:gkad821. doi: 10.1093/nar/gkad821.
Cheng KCL, Frost JM, Sánchez-Luque FJ, García-Canãdas M, Taylor D, Yang WR, Irayanar B, Sampath S, Patani H, Agger K, Helin K, Ficz G, Burns KH, Ewing A, García-Pérez JL, Branco MR. Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation. Epigenetics Chromatin. 2023 Oct 16;16(1):39.
2022
Burns, KH. Repetitive DNA in disease. Science. 2022; 376(6591): 353-354.
McKerrow W, Wang X, Mendez-Dorantes C, Mita P, Cao S, Grivainis M, Ding L, LaCava J, Burns KH, Boeke JD, Fenyö D. LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint. Proc Natl Acad Sci U S A. 2022 Feb 22;119(8):e2115999119.
Rajurkar M, Parikh AR, Solovyov A, You E, Kulkarni AS, Chu C, Xu KH, Jaicks C, Taylor MS, Wu C, Alexander KA, Good CR, Szabolcs A, Gerstberger S, Tran AV, Xu N, Ebright RY, Van Seventer EE, Vo KD, Tai EC, Lu C, Joseph-Chazan J, Raabe MJ, Nieman LT, Desai N, Arora KS, Ligorio M, Thapar V, Cohen L, Garden PM, Senussi Y, Zheng H, Allen JN, Blaszkowsky LS, Clark JW, Goyal L, Wo JY, Ryan DP, Corcoran RB, Deshpande V, Rivera MN, Aryee MJ, Hong TS, Berger SL, Walt DR, Burns KH, Park PJ, Greenbaum BD, Ting DT. Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer. Cancer Discov. 2022 Mar 23:1117.
Tao J, Wang Q, Mendez-Dorantes C, Burns KH, Chiarle R. Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites. Nat Commun. 2022 Jun 27;13(1):3685.
Antiochos B, Paz M, Li J, Goldman DW, Petri M, Darrah E, Cashman K, Sanz I, Burns KH, Ardeljan D, Andrade F, Rosen A. Autoantibodies targeting LINE-1-encoded ORF1p are associated with systemic lupus erythematosus diagnosis but not disease activity. Clin Exp Rheumatol. 2022 Sep;40(9):1636-1641.
2021
Payer LM, Steranka JP, Kryatova MS, Grillo G, Lupien M, Rocha PP, Burns KH. Alu insertion variants alter gene transcript levels. Genome Res. 2021 Nov 19;31(12):2236-2248.
2020
Burns, KH. Our conflict with transposable elements and its implications for human disease. Annual Review of Pathology: Mechanisms of disease. 2020; 15: 51–70.
Ardeljan D, Steranka JP, Liu C, Li Z, Taylor MS, Payer LM, Gorbounov M, Sarnecki JS, Deshpande V, Hruban RH, Boeke JD, Fenyö D, Wu PH, Smogorzewska A, Holland AJ, Burns KH. LINE-1 cellular fitness interactions reveal conflict between retrotransposition and replication. Nature Structural and Molecular Biology. 2020; 27(2): 168-178.
Goubert C, Thomas J, Payer LM, Kidd JM, Feusier J, Watkins WS, Burns KH, Jorde LB, Feschotte C. TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data. Nucleic Acids Res. 2020; 48(6): e36.
Loh JW, Ha H, Lin T, Sun N, Burns KH, Xing J. Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions. Mobile DNA. 2020; 11: 12.
Cao X, Zhang Y, Payer LM, Lords H, Steranka JP, Burns KH, Xing J. Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues. Genome Biol. 2020; 21(1): 185.
Tunbak H, Enriquez-Gasca R, Tie CHC, Gould PA, Mlcochova P, Gupta RK, Fernandes L, Holt J, van der Veen AG, Giampazolias E, Burns KH, Maillard PV, Rowe HM. The HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s. Nat Commun. 2020; 11(1): 5387.
Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH; PCAWG Structural Variation Working Group, Campbell PJ, Tubio JMC; PCAWG Consortium. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics. 2020; 52(3): 306-319.
McKerrow W, Tang Z, Steranka JP, Payer LM, Boeke JD, Keefe D, Fenyö D*, Burns KH*, Liu C*. Human Transposon Insertion Profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells. Philosophical Transactions of the Royal Society B. 2020; 375(1795): 20190335.
2019
Payer, LM, Burns KH. Transposable elements in human genetic disease. Nature Reviews Genetics. 2019; 20(12): 760-772.
Ardeljan D*, Wang X*, Oghbaie M*, Taylor MS, Husband D, Deshpande V, Steranka JP, Gorbounov M, Yang WR, Sie B, Larman HB, Jiang H, Molloy KR, Altukhov I, Li Z, McKerrow W, Fenyö D*, Burns KH*, LaCava J*. LINE-1 ORF2p Expression is Nearly Imperceptible in Human Cancers. Mobile DNA. 2019; 11: 1.
Payer LM, Steranka JP, Ardeljan D, Walker J, Fitzgerald KC, Calabresi PA, Cooper TA, Burns KH. Alu insertion variants alter mRNA splicing. Nucleic Acids Research. 2019; 47(1): 421-431.
Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH. Software for Quantifying Interspersed Repeat Elements (SQuIRE) reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Research. 2019; 47(5): e27.
Pisanic TR 2nd, Asaka S, Lin SF, Yen TT, Sun H, Bahadirli-Talbott A, Wang TH, Burns KH, Wang TL, Shih IM. LINE-1 retrotransposons become deregulated during the development of ovarian cancer precursor lesions. American Journal of Pathology. 2019; 189(3): 513-520.
Steranka JP, Tang Z, Grivainis M, Huang CRL, Rego FOR, Miller TLA, Galante PAF, Ramaswami S, Heguy A, Fenyö D, Boeke JD, Burns KH. Transposon Insertion Profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome. Mobile DNA. 2019; 10:8.
2018
Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvák Z, Levin HL, Macfarlan TS, Mager DL, Feschotte C. Ten things you should know about transposable elements. Genome Biology; 19(1): 199.
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. Dissection of affinity captured LINE-1 macromolecular complexes. Elife. 2018;7. e30094.
2017
Ardeljan D, Taylor MS, Ting DT, Burns KH. The Human Long Interspersed Element-1 Retrotransposon: An Emerging Biomarker of Neoplasia. Clinical Chemistry. 2017; 63(4): 816-822.
Burns KH. Transposable elements in cancer. Nature Reviews Cancer. 2017; 17(7): 415-424.
Kryatova MS, Steranka JP, Burns KH*, Payer LM*. Insertion and deletion polymorphisms of the ancient AluS family in the human genome. Mobile DNA. 2017; 8: 6.
Tang Z, Steranka JP, Ma S, Grivainis M, Rodić N, Huang CR, Shih IM, Wang TL, Boeke JD*, Fenyö D*, Burns KH*. Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer. Proceedings of the National Academy of Sciences USA. 2017; 114(5): E733-E740.
Payer LM, Steranka JP, Yang WR, Kryatova M, Medabalimi S, Ardeljan D, Liu C, Boeke JD, Avramopoulos D, Burns KH. Structural variants caused by Alu insertions are associated with risks for many human diseases. Proceedings of the National Academy of Sciences USA. 2017; 114(20): E3984-E3992.
2016
Sharma R, Rodić N, Burns KH*, Taylor MS*. Immunodetection of Human LINE-1 Expression in Cultured Cells and Human Tissues. Methods in Molecular Biology. 2016; 1400: 261-280.
Taylor MS, LaCava J, Dai L, Mita P, Burns KH, Rout MP, Boeke JD. Characterization of L1-Ribonucleoprotein Particles. Methods in Molecular Biology. 2016; 1400:311-338.
Criscione SW, Theodosakis N, Micevic G, Cornish TC, Burns KH, Neretti N, Rodić N. Genome-wide characterization of human L1 antisense promoter-driven transcripts. BMC Genomics. 2016; 17: 463.
Doucet-O'Hare TT, Sharma R, Rodić N, Anders RA, Burns KH, Kazazian HH Jr. Somatically Acquired LINE-1 Insertions in Normal Esophagus Undergo Clonal Expansion in Esophageal Squamous Cell Carcinoma. Human Mutation. 2016; 37(9): 942-954.
Zampella JG, Rodić N, Yang WR, Huang CR, Welch J, Gnanakkan VP, Cornish TC, Boeke JD, Burns KH. A map of mobile DNA insertions in the NCI-60 human cancer cell panel. Mobile DNA. 2016; 7:20.
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. Somatic retrotransposition is infrequent in glioblastomas. Mobile DNA. 2016; 7: 22.
2015
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. Proceedings of the National Academy of Sciences USA. 2015; 112(35): e4894-4900.
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. Nature Medicine. 2015; 21(9): 1060-1064.
2014
Halper-Stromberg E, Steranka J, Burns KH, Irizarry RA. Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinformatics. 2014; 30(11): 1514-1521.
Rodić N, Sharma R, Zampella J, Hruban RH, Iacobuzio-Donahue CA, Maitra A, Torbenson MS, Shih IM, Kurman RJ, Montgomery EA, Gabrielson E, Netto GJ, Lotan TL, DeMarzo 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. American Journal of Pathology. 2014; 184(5): 1280-1286.
2013
Rodić N, Burns KH. Long interspersed element-1 (L1): passenger or driver in human neoplasms? PLoS Genetics. 2013; 9(3): e1003402.
Babatz T, Burns KH. Mobile DNA and human genetic disease. Current Opinion in Genetics and Development. 2013; 23(3): 264-270.
Gnanakkan VP, Jaffe AE, Dai L, Fu Jie, Wheelan SJ, Levitsky HI, Boeke JD*, Burns KH*. TE-array – A high throughput tool for studying transposon transcription. BMC Genomics. 2013; 14(1): 869.
Rodić N, Zampella J, Cornish TC, Wheelan S, Burns KH. Translocation junctions in TCF3-PBX1 acute lymphoblastic leukemia/lymphoma cluster near transposable elements. Mobile DNA. 2013; 4(1): 22.
Taylor MS, LaCava J, Mita P, Molloy K, Huang C, Li D, Adney E, Jiang H, Burns KH, Chait B, Rout M, Boeke J, Dai L. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell. 2013; 155(5): 1034-1048.
2012
Burns KH, Boeke JD. Human Transposon Tectonics. Cell. 2012; 149(4): 740-752.
Huang CRL, Burns KH, Boeke JD. Active transposition in genomes. Annual Reviews in Genetics. 2012; (46): 651-675.
2010
Huang CRL, Schneider AM, Lu Y, Niranjan T, Shen P, Valle D, Civin CI, Costello JF, Wang T, Wheelan SJ, Ji HK, Boeke JD*, Burns KH*. Mobile interspersed repeats are major structural variants in the human genome. Cell. 2010; 141(7): 1171-1182.
O'Donnell KA, Burns KH. Mobilizing diversity: transposable element insertions in genetic variation and disease. Mobile DNA. 2010; 1(1): 21.
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©2020 Burns Lab at Dana-Farber Cancer Institute
©2020 Burns Lab at Dana-Farber Cancer Institute