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Items: 1 to 50 of 61

1.

Mitochondrial genome diversity and evolution in Branchiopoda (Crustacea).

Luchetti A, Forni G, Skaist AM, Wheelan SJ, Mantovani B.

Zoological Lett. 2019 May 27;5:15. doi: 10.1186/s40851-019-0131-5. eCollection 2019.

2.

Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis.

Pereira GC, Sanchez L, Schaughency PM, Rubio-Roldán A, Choi JA, Planet E, Batra R, Turelli P, Trono D, Ostrow LW, Ravits J, Kazazian HH, Wheelan SJ, Heras SR, Mayer J, García-Pérez JL, Goodier JL.

Mob DNA. 2018 Dec 15;9:35. doi: 10.1186/s13100-018-0138-z. eCollection 2018.

3.

Transcriptional profiling identifies novel regulators of macrophage polarization.

Gerrick KY, Gerrick ER, Gupta A, Wheelan SJ, Yegnasubramanian S, Jaffee EM.

PLoS One. 2018 Dec 7;13(12):e0208602. doi: 10.1371/journal.pone.0208602. eCollection 2018.

4.

CMPK2 and BCL-G are associated with type 1 interferon-induced HIV restriction in humans.

El-Diwany R, Soliman M, Sugawara S, Breitwieser F, Skaist A, Coggiano C, Sangal N, Chattergoon M, Bailey JR, Siliciano RF, Blankson JN, Ray SC, Wheelan SJ, Thomas DL, Balagopal A.

Sci Adv. 2018 Aug 1;4(8):eaat0843. doi: 10.1126/sciadv.aat0843. eCollection 2018 Aug.

5.

The Terabase Search Engine: a large-scale relational database of short-read sequences.

Wilton R, Wheelan SJ, Szalay AS, Salzberg SL.

Bioinformatics. 2019 Feb 15;35(4):665-670. doi: 10.1093/bioinformatics/bty657.

PMID:
30052772
6.

ETS2 is a prostate basal cell marker and is highly expressed in prostate cancers aberrantly expressing p63.

Torres A, Alshalalfa M, Davicioni E, Gupta A, Yegnasubramanian S, Wheelan SJ, Epstein JI, De Marzo AM, Lotan TL.

Prostate. 2018 Sep;78(12):896-904. doi: 10.1002/pros.23646. Epub 2018 May 15.

PMID:
29761525
7.

A primary breast cancer with distinct foci of estrogen receptor-alpha positive and negative cells derived from the same clonal origin as revealed by whole exome sequencing.

Kyker-Snowman K, Erlanger Avigdor B, Nasim M, Cimino-Mathews A, Wheelan SJ, Argani P, Park BH.

Breast Cancer Res Treat. 2018 Jul;170(2):425-430. doi: 10.1007/s10549-018-4742-x. Epub 2018 Mar 15.

PMID:
29541976
8.

Mutational profiles of breast cancer metastases from a rapid autopsy series reveal multiple evolutionary trajectories.

Avigdor BE, Cimino-Mathews A, DeMarzo AM, Hicks JL, Shin J, Sukumar S, Fetting J, Argani P, Park BH, Wheelan SJ.

JCI Insight. 2017 Dec 21;2(24). pii: 96896. doi: 10.1172/jci.insight.96896.

9.

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.

Stavrovskaya ED, Niranjan T, Fertig EJ, Wheelan SJ, Favorov AV, Mironov AA.

Bioinformatics. 2017 Oct 15;33(20):3158-3165. doi: 10.1093/bioinformatics/btx379.

10.

Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks.

Kelley DZ, Flam EL, Izumchenko E, Danilova LV, Wulf HA, Guo T, Singman DA, Afsari B, Skaist AM, Considine M, Welch JA, Stavrovskaya E, Bishop JA, Westra WH, Khan Z, Koch WM, Sidransky D, Wheelan SJ, Califano JA, Favorov AV, Fertig EJ, Gaykalova DA.

Cancer Res. 2017 Dec 1;77(23):6538-6550. doi: 10.1158/0008-5472.CAN-17-0833. Epub 2017 Sep 25.

11.

MYC drives overexpression of telomerase RNA (hTR/TERC) in prostate cancer.

Baena-Del Valle JA, Zheng Q, Esopi DM, Rubenstein M, Hubbard GK, Moncaliano MC, Hruszkewycz A, Vaghasia A, Yegnasubramanian S, Wheelan SJ, Meeker AK, Heaphy CM, Graham MK, De Marzo AM.

J Pathol. 2018 Jan;244(1):11-24. doi: 10.1002/path.4980. Epub 2017 Nov 14.

12.

A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers.

Guo T, Sakai A, Afsari B, Considine M, Danilova L, Favorov AV, Yegnasubramanian S, Kelley DZ, Flam E, Ha PK, Khan Z, Wheelan SJ, Gutkind JS, Fertig EJ, Gaykalova DA, Califano J.

Cancer Res. 2017 Oct 1;77(19):5248-5258. doi: 10.1158/0008-5472.CAN-16-3106. Epub 2017 Jul 21.

13.

Whole-Exome Sequencing of Metaplastic Breast Carcinoma Indicates Monoclonality with Associated Ductal Carcinoma Component.

Avigdor BE, Beierl K, Gocke CD, Zabransky DJ, Cravero K, Kyker-Snowman K, Button B, Chu D, Croessmann S, Cochran RL, Connolly RM, Park BH, Wheelan SJ, Cimino-Mathews A.

Clin Cancer Res. 2017 Aug 15;23(16):4875-4884. doi: 10.1158/1078-0432.CCR-17-0108. Epub 2017 Apr 19.

14.

Intracellular HIV-1 RNA and CD4+ T-cell activation in patients starting antiretrovirals.

El-Diwany R, Breitwieser FP, Soliman M, Skaist AM, Srikrishna G, Blankson JN, Ray SC, Wheelan SJ, Thomas DL, Balagopal A.

AIDS. 2017 Jun 19;31(10):1405-1414. doi: 10.1097/QAD.0000000000001480.

15.

PTBP1 and PTBP2 Repress Nonconserved Cryptic Exons.

Ling JP, Chhabra R, Merran JD, Schaughency PM, Wheelan SJ, Corden JL, Wong PC.

Cell Rep. 2016 Sep 27;17(1):104-113. doi: 10.1016/j.celrep.2016.08.071.

16.

NUP98-PHF23 fusion is recurrent in acute myeloid leukemia and shares gene expression signature of leukemic stem cells.

Ho H, Skaist AM, Pallavajjala A, Yonescu R, Batista D, Wheelan SJ, Ning Y.

Leuk Res. 2016 Jun;45:1-7. doi: 10.1016/j.leukres.2016.03.006. Epub 2016 Mar 30.

PMID:
27060678
17.

Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma.

Rettig EM, Talbot CC Jr, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig EJ, Wheelan SJ, Marchionni L, Considine M, Ling S, Fakhry C, Papadopoulos N, Kinzler KW, Vogelstein B, Ha PK, Agrawal N.

Cancer Prev Res (Phila). 2016 Apr;9(4):265-74. doi: 10.1158/1940-6207.CAPR-15-0316. Epub 2016 Feb 9. Erratum in: Cancer Prev Res (Phila). 2018 Apr;11(4):249.

18.

ATM Kinase Is Required for Telomere Elongation in Mouse and Human Cells.

Lee SS, Bohrson C, Pike AM, Wheelan SJ, Greider CW.

Cell Rep. 2015 Nov 24;13(8):1623-32. doi: 10.1016/j.celrep.2015.10.035. Epub 2015 Nov 12.

19.

Centroacinar Cells Are Progenitors That Contribute to Endocrine Pancreas Regeneration.

Delaspre F, Beer RL, Rovira M, Huang W, Wang G, Gee S, Vitery Mdel C, Wheelan SJ, Parsons MJ.

Diabetes. 2015 Oct;64(10):3499-509. doi: 10.2337/db15-0153. Epub 2015 Jul 7.

20.

Transflip mutations produce deletions in pancreatic cancer.

Norris AL, Kamiyama H, Makohon-Moore A, Pallavajjala A, Morsberger LA, Lee K, Batista D, Iacobuzio-Donahue CA, Lin MT, Klein AP, Hruban RH, Wheelan SJ, Eshleman JR.

Genes Chromosomes Cancer. 2015 Aug;54(8):472-481. doi: 10.1002/gcc.22258. Epub 2015 May 29.

21.

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space.

Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS.

PeerJ. 2015 Mar 3;3:e808. doi: 10.7717/peerj.808. eCollection 2015.

22.

Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins.

Harr JC, Luperchio TR, Wong X, Cohen E, Wheelan SJ, Reddy KL.

J Cell Biol. 2015 Jan 5;208(1):33-52. doi: 10.1083/jcb.201405110.

23.

Familial and sporadic pancreatic cancer share the same molecular pathogenesis.

Norris AL, Roberts NJ, Jones S, Wheelan SJ, Papadopoulos N, Vogelstein B, Kinzler KW, Hruban RH, Klein AP, Eshleman JR.

Fam Cancer. 2015 Mar;14(1):95-103. doi: 10.1007/s10689-014-9755-y.

24.

Gibbon genome and the fast karyotype evolution of small apes.

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA.

Nature. 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679.

25.

RNA-Seq of the nucleolus reveals abundant SNORD44-derived small RNAs.

Bai B, Yegnasubramanian S, Wheelan SJ, Laiho M.

PLoS One. 2014 Sep 9;9(9):e107519. doi: 10.1371/journal.pone.0107519. eCollection 2014.

26.

Haplotype counting by next-generation sequencing for ultrasensitive human DNA detection.

Debeljak M, Freed DN, Welch JA, Haley L, Beierl K, Iglehart BS, Pallavajjala A, Gocke CD, Leffell MS, Lin MT, Pevsner J, Wheelan SJ, Eshleman JR.

J Mol Diagn. 2014 Sep;16(5):495-503. doi: 10.1016/j.jmoldx.2014.04.003. Erratum in: J Mol Diagn. 2015 Nov;17(6):749.

27.

Clinical validation of KRAS, BRAF, and EGFR mutation detection using next-generation sequencing.

Lin MT, Mosier SL, Thiess M, Beierl KF, Debeljak M, Tseng LH, Chen G, Yegnasubramanian S, Ho H, Cope L, Wheelan SJ, Gocke CD, Eshleman JR.

Am J Clin Pathol. 2014 Jun;141(6):856-66. doi: 10.1309/AJCPMWGWGO34EGOD.

28.

Analysis of BRCA2 loss of heterozygosity in tumor tissue using droplet digital polymerase chain reaction.

Cochran RL, Cravero K, Chu D, Erlanger B, Toro PV, Beaver JA, Zabransky DJ, Wong HY, Cidado J, Croessmann S, Parsons H, Kim M, Wheelan SJ, Argani P, Ho Park B.

Hum Pathol. 2014 Jul;45(7):1546-1550. doi: 10.1016/j.humpath.2014.03.013. Epub 2014 Apr 13.

29.

Cellular resolution maps of X chromosome inactivation: implications for neural development, function, and disease.

Wu H, Luo J, Yu H, Rattner A, Mo A, Wang Y, Smallwood PM, Erlanger B, Wheelan SJ, Nathans J.

Neuron. 2014 Jan 8;81(1):103-19. doi: 10.1016/j.neuron.2013.10.051.

30.

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.

31.

Genome-wide consequences of deleting any single gene.

Teng X, Dayhoff-Brannigan M, Cheng WC, Gilbert CE, Sing CN, Diny NL, Wheelan SJ, Dunham MJ, Boeke JD, Pineda FJ, Hardwick JM.

Mol Cell. 2013 Nov 21;52(4):485-94. doi: 10.1016/j.molcel.2013.09.026. Epub 2013 Nov 7.

32.

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.

33.

Telomere phenotypes in females with heterozygous mutations in the dyskeratosis congenita 1 (DKC1) gene.

Alder JK, Parry EM, Yegnasubramanian S, Wagner CL, Lieblich LM, Auerbach R, Auerbach AD, Wheelan SJ, Armanios M.

Hum Mutat. 2013 Nov;34(11):1481-5. doi: 10.1002/humu.22397. Epub 2013 Sep 11.

34.

Integrated analysis of drug-induced gene expression profiles predicts novel hERG inhibitors.

Babcock JJ, Du F, Xu K, Wheelan SJ, Li M.

PLoS One. 2013 Jul 23;8(7):e69513. doi: 10.1371/journal.pone.0069513. Print 2013.

35.

Controlled insertional mutagenesis using a LINE-1 (ORFeus) gene-trap mouse model.

O'Donnell KA, An W, Schrum CT, Wheelan SJ, Boeke JD.

Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):E2706-13. doi: 10.1073/pnas.1302504110. Epub 2013 Jul 1.

36.

piggyBac transposase tools for genome engineering.

Li X, Burnight ER, Cooney AL, Malani N, Brady T, Sander JD, Staber J, Wheelan SJ, Joung JK, McCray PB Jr, Bushman FD, Sinn PL, Craig NL.

Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):E2279-87. doi: 10.1073/pnas.1305987110. Epub 2013 May 30.

37.

A simple high-throughput technology enables gain-of-function screening of human microRNAs.

Cheng WC, Kingsbury TJ, Wheelan SJ, Civin CI.

Biotechniques. 2013 Feb;54(2):77-86. doi: 10.2144/000113991.

38.

Exploring massive, genome scale datasets with the GenometriCorr package.

Favorov A, Mularoni L, Cope LM, Medvedeva Y, Mironov AA, Makeev VJ, Wheelan SJ.

PLoS Comput Biol. 2012 May;8(5):e1002529. doi: 10.1371/journal.pcbi.1002529. Epub 2012 May 31.

39.

A Sleeping Beauty mutagenesis screen reveals a tumor suppressor role for Ncoa2/Src-2 in liver cancer.

O'Donnell KA, Keng VW, York B, Reineke EL, Seo D, Fan D, Silverstein KA, Schrum CT, Xie WR, Mularoni L, Wheelan SJ, Torbenson MS, O'Malley BW, Largaespada DA, Boeke JD.

Proc Natl Acad Sci U S A. 2012 May 22;109(21):E1377-86. doi: 10.1073/pnas.1115433109. Epub 2012 May 3.

40.

Nuclear miRNA regulates the mitochondrial genome in the heart.

Das S, Ferlito M, Kent OA, Fox-Talbot K, Wang R, Liu D, Raghavachari N, Yang Y, Wheelan SJ, Murphy E, Steenbergen C.

Circ Res. 2012 Jun 8;110(12):1596-603. doi: 10.1161/CIRCRESAHA.112.267732. Epub 2012 Apr 19.

41.

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots.

Mularoni L, Zhou Y, Bowen T, Gangadharan S, Wheelan SJ, Boeke JD.

Genome Res. 2012 Apr;22(4):693-703. doi: 10.1101/gr.129460.111. Epub 2012 Jan 4.

42.

Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1.

Creamer TJ, Darby MM, Jamonnak N, Schaughency P, Hao H, Wheelan SJ, Corden JL.

PLoS Genet. 2011 Oct;7(10):e1002329. doi: 10.1371/journal.pgen.1002329. Epub 2011 Oct 20.

43.

Establishing the baseline level of repetitive element expression in the human cortex.

Tyekucheva S, Yolken RH, McCombie WR, Parla J, Kramer M, Wheelan SJ, Sabunciyan S.

BMC Genomics. 2011 Oct 10;12:495. doi: 10.1186/1471-2164-12-495.

44.

Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis.

Niranjan TS, Adamczyk A, Bravo HC, Taub MA, Wheelan SJ, Irizarry R, Wang T.

Genome Biol. 2011 Sep 28;12(9):R93. doi: 10.1186/gb-2011-12-9-r93.

45.

Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing.

Jamonnak N, Creamer TJ, Darby MM, Schaughency P, Wheelan SJ, Corden JL.

RNA. 2011 Nov;17(11):2011-25. doi: 10.1261/rna.2840711. Epub 2011 Sep 27.

46.

Characterization of complex chromosomal rearrangements by targeted capture and next-generation sequencing.

Sobreira NL, Gnanakkan V, Walsh M, Marosy B, Wohler E, Thomas G, Hoover-Fong JE, Hamosh A, Wheelan SJ, Valle D.

Genome Res. 2011 Oct;21(10):1720-7. doi: 10.1101/gr.122986.111. Epub 2011 Sep 2.

47.

AP-1 protein induction during monopoiesis favors C/EBP: AP-1 heterodimers over C/EBP homodimerization and stimulates FosB transcription.

Hong S, Skaist AM, Wheelan SJ, Friedman AD.

J Leukoc Biol. 2011 Oct;90(4):643-51. doi: 10.1189/jlb.0111043. Epub 2011 May 4.

48.

DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo.

Gangadharan S, Mularoni L, Fain-Thornton J, Wheelan SJ, Craig NL.

Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):21966-72. doi: 10.1073/pnas.1016382107. Epub 2010 Dec 3.

49.

High frequencies of leukemia stem cells in poor-outcome childhood precursor-B acute lymphoblastic leukemias.

Morisot S, Wayne AS, Bohana-Kashtan O, Kaplan IM, Gocke CD, Hildreth R, Stetler-Stevenson M, Walker RL, Davis S, Meltzer PS, Wheelan SJ, Brown P, Jones RJ, Shultz LD, Civin CI.

Leukemia. 2010 Nov;24(11):1859-66. doi: 10.1038/leu.2010.184. Epub 2010 Aug 26.

50.

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. doi: 10.1016/j.cell.2010.05.026.

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