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Sarah J. Wheelan, Ph.D. - Publications

Affiliations: 
2003 Johns Hopkins University, Baltimore, MD 
Area:
DNA replication
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56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Esopi D, Graham MK, Brosnan-Cashman JA, Meyers J, Vaghasia A, Gupta A, Kumar B, Haffner MC, Heaphy CM, De Marzo AM, Meeker AK, Nelson WG, Wheelan SJ, Yegnasubramanian S. Pervasive promoter hypermethylation of silenced TERT alleles in human cancers. Cellular Oncology (Dordrecht). PMID 32468444 DOI: 10.1007/S13402-020-00531-7  0.337
2020 Xu Z, Green B, Benoit N, Schatz M, Wheelan S, Cormack B. De novo genome assembly of Candida glabrata reveals cell wall protein complement and structure of dispersed tandem repeat arrays. Molecular Microbiology. PMID 32068314 DOI: 10.1111/Mmi.14488  0.386
2020 Freeman ZT, Nirschl TR, Hovelson DH, Johnston RJ, Engelhardt JJ, Selby MJ, Kochel CM, Lan RY, Zhai J, Ghasemzadeh A, Gupta A, Skaist AM, Wheelan SJ, Jiang H, Pearson AT, et al. A conserved intratumoral regulatory T cell signature identifies 4-1BB as a pan-cancer target. The Journal of Clinical Investigation. PMID 32015231 DOI: 10.1172/Jci128672  0.314
2019 Schubert AD, Channah Broner E, Agrawal N, London N, Pearson A, Gupta A, Wali N, Seiwert TY, Wheelan S, Lingen M, Macleod K, Allen H, Chatterjee A, Vassiliki S, Gaykalova D, et al. Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma. Cancer Letters. PMID 31830557 DOI: 10.1016/J.Canlet.2019.12.006  0.329
2018 Kelley DZ, Flam EL, Guo T, Danilova LV, Zamuner F, Bohrson C, Considine M, Windsor EJ, Bishop JA, Zhang C, Koch WM, Sidransky D, Westra WH, Chung CH, Califano JA, ... Wheelan S, et al. Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma. Translational Research : the Journal of Laboratory and Clinical Medicine. PMID 30118659 DOI: 10.1016/J.Trsl.2018.07.007  0.334
2018 Wilton R, Wheelan SJ, Szalay AS, Salzberg SL. The Terabase Search Engine: a large-scale relational database of short-read sequences. Bioinformatics (Oxford, England). PMID 30052772 DOI: 10.1093/Bioinformatics/Bty657  0.343
2018 Kyker-Snowman K, Erlanger Avigdor B, Nasim M, Cimino-Mathews A, Wheelan SJ, Argani P, Park BH. 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. Breast Cancer Research and Treatment. PMID 29541976 DOI: 10.1007/S10549-018-4742-X  0.304
2018 Kostadinov R, Yoo B, Farooqi MS, Kelley S, Guest E, Burke MJ, Wheelan S, Brown P. Whole Genome Bisulfite Sequencing (WGBS) Robustly Measures the Pharmacodynamic Effect of Decitabine/Vorinostat Epigenetic Treatment in Relapsed Pediatric ALL Demonstrating Potent Hypomethylation Associated with Upregulation of PRC2 and TP53 Targets Blood. 132: 918-918. DOI: 10.1182/Blood-2018-99-119206  0.355
2017 Avigdor BE, Cimino-Mathews A, DeMarzo AM, Hicks JL, Shin J, Sukumar S, Fetting J, Argani P, Park BH, Wheelan SJ. Mutational profiles of breast cancer metastases from a rapid autopsy series reveal multiple evolutionary trajectories. Jci Insight. 2. PMID 29263308 DOI: 10.1172/Jci.Insight.96896  0.326
2017 Stavrovskaya ED, Niranjan T, Fertig EJ, Wheelan SJ, Favorov AV, Mironov AA. StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data. Bioinformatics (Oxford, England). 33: 3158-3165. PMID 29028265 DOI: 10.1093/Bioinformatics/Btx379  0.34
2017 Kelley DZ, Flam E, Izumchenko E, Danilova L, Wulf HA, Guo T, Singman DA, Afsari B, Skaist A, Considine M, Stavrovskaya E, Bishop JA, Westra WH, Khan Z, Koch WM, ... ... Wheelan SJ, et al. 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. Cancer Research. PMID 28947419 DOI: 10.1158/0008-5472.Can-17-0833  0.393
2017 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. MYC drives overexpression of telomerase RNA (hTR/TERC) in prostate cancer. The Journal of Pathology. PMID 28888037 DOI: 10.1002/Path.4980  0.301
2017 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, et al. A novel functional splice variant of AKT3 defined by analysis of alternative splice expression in HPV-positive oropharyngeal cancers. Cancer Research. PMID 28733453 DOI: 10.1158/0008-5472.Can-16-3106  0.391
2017 Avigdor B, Beierl K, Gocke CD, Zabransky D, Cravero K, Kyker-Snowman K, Button B, Chu D, Croessmann S, Cochran RL, Connolly R, Park BH, Cimino-Mathews A, Wheelan SJ. Whole exome sequencing of metaplastic breast carcinoma indicates monoclonality with associated ductal carcinoma component. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 28424200 DOI: 10.1158/1078-0432.Ccr-17-0108  0.341
2017 Avigdor BE, Beierl K, Gocke CD, Zabransky DJ, Cravero K, Kyker-Snowmana K, Button B, Chu D, Croessmann S, Cochran RL, Connolly RM, Park BH, Cimino-Mathews A, Wheelan SJ. Abstract LB-278: Whole exome sequencing of metaplastic breast carcinoma indicates monoclonality with associated ductal carcinoma component Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Lb-278  0.332
2017 Kelley DZ, Flam EL, Wulf HA, Guo T, Izumchenko E, Singman DA, Danilova LV, Stavrovskaya ED, Considine M, Bishop JA, Westra WH, Khan Z, Koch WM, Sidransky D, Wheelan S, et al. Abstract 2424: The in-parallel whole-genome ChIP-Seq analysis of primary tissues, patient derived xenografts, and cancer cell lines from HPV-relative HNSCC samples Cancer Research. 77: 2424-2424. DOI: 10.1158/1538-7445.Am2017-2424  0.333
2016 Rettig EM, Talbot CC, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig E, Wheelan S, Marchionni L, Considine M, Ling S, Fakhry C, et al. Correction: Whole-genome sequencing of salivary gland adenoid cystic carcinoma (Cancer Prevention Research (2016) 9 (265-274) DOI: 10.1158/1940-6207.CAPR-15-0316) Cancer Prevention Research. 11. PMID 28642227 DOI: 10.1158/1940-6207.Capr-17-0178  0.356
2016 Ho H, Skaist AM, Pallavajjala A, Yonescu R, Batista D, Wheelan SJ, Ning Y. NUP98-PHF23 fusion is recurrent in acute myeloid leukemia and shares gene expression signature of leukemic stem cells. Leukemia Research. 45: 1-7. PMID 27060678 DOI: 10.1016/J.Leukres.2016.03.006  0.356
2016 Guo T, Gaykalova DA, Considine M, Wheelan S, Pallavajjala A, Bishop JA, Westra WH, Ideker T, Koch WM, Khan Z, Fertig EJ, Califano JA. Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma. International Journal of Cancer. PMID 26949921 DOI: 10.1002/Ijc.30081  0.369
2016 Rettig EM, Talbot C, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig E, Wheelan S, Marchionni L, Considine M, Fakhry C, Papadopoulos N, et al. Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma. Cancer Prevention Research (Philadelphia, Pa.). PMID 26862087 DOI: 10.1158/1940-6207.Capr-15-0316  0.377
2016 Valle JABD, Zheng Q, Rubenstein M, Meeker AK, Heaphy CM, Hubbard G, Bieberich CJ, Yegnasubramanian S, Esopi D, Wheelan SJ, Marzo AMD. Abstract LB-160: Human telomerase RNA component (hTR/TERC) is consistently overexpressed in prostate cancer, required for cell proliferation and is positively regulated by MYC Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Lb-160  0.333
2016 Gaykalova DA, Kelley D, Guo T, Bohrson C, Tiscareno I, Zizkova V, Considine M, Danilova L, Flam E, Bishop J, Ahn J, Merritt S, Goldsmith M, Zhang C, Koch W, ... ... Wheelan S, et al. Abstract 2880: The discovery of novel GSN alternative splicing in head and neck squamous cell carcinoma Cancer Research. 76: 2880-2880. DOI: 10.1158/1538-7445.Am2016-2880  0.373
2015 Lee SS, Bohrson C, Pike AM, Wheelan SJ, Greider CW. ATM Kinase Is Required for Telomere Elongation in Mouse and Human Cells. Cell Reports. PMID 26586427 DOI: 10.1016/J.Celrep.2015.10.035  0.305
2015 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. Transflip mutations produce deletions in pancreatic cancer. Genes, Chromosomes & Cancer. PMID 26031834 DOI: 10.1002/Gcc.22258  0.381
2015 Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS. Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space. Peerj. 3: e808. PMID 25780763 DOI: 10.7717/Peerj.808  0.336
2015 Harr JC, Luperchio TR, Wong X, Cohen E, Wheelan SJ, Reddy KL. Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins. The Journal of Cell Biology. 208: 33-52. PMID 25559185 DOI: 10.1083/Jcb.201405110  0.332
2015 Norris AL, Roberts NJ, Jones S, Wheelan SJ, Papadopoulos N, Vogelstein B, Kinzler KW, Hruban RH, Klein AP, Eshleman JR. Familial and sporadic pancreatic cancer share the same molecular pathogenesis. Familial Cancer. 14: 95-103. PMID 25240578 DOI: 10.1007/S10689-014-9755-Y  0.368
2015 Debeljak M, Freed DN, Welch JA, Haley L, Beierl K, Iglehart BS, Pallavajjala A, Gocke CD, Leffell MS, Lin M, Wood LD, Pevsner J, Wheelan SJ, Eshleman JR. Abstract 4270: NGS based microhaplotype counting for ultrasensitive human DNA detection Cancer Research. 75: 4270-4270. DOI: 10.1158/1538-7445.Am2015-4270  0.346
2014 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, ... ... Wheelan SJ, et al. Gibbon genome and the fast karyotype evolution of small apes. Nature. 513: 195-201. PMID 25209798 DOI: 10.1038/Nature13679  0.362
2014 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. Haplotype counting by next-generation sequencing for ultrasensitive human DNA detection. The Journal of Molecular Diagnostics : Jmd. 16: 495-503. PMID 25132481 DOI: 10.1016/J.Jmoldx.2014.04.003  0.307
2014 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. Clinical validation of KRAS, BRAF, and EGFR mutation detection using next-generation sequencing. American Journal of Clinical Pathology. 141: 856-66. PMID 24838331 DOI: 10.1309/Ajcpmwgwgo34Egod  0.363
2014 Cochran RL, Cravero K, Chu D, Erlanger B, Toro PV, Beaver JA, Zabransky DJ, Wong HY, Cidado J, Croessmann S, Parsons HA, Kim M, Wheelan SJ, Argani P, Park BH. Analysis of BRCA2 loss of heterozygosity in tumor tissue using droplet digital polymerase chain reaction. Human Pathology. 45: 1546-50. PMID 24824029 DOI: 10.1016/J.Humpath.2014.03.013  0.304
2013 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. 14: 869. PMID 24325565 DOI: 10.1186/1471-2164-14-869  0.379
2013 Teng X, Dayhoff-Brannigan M, Cheng WC, Gilbert CE, Sing CN, Diny NL, Wheelan SJ, Dunham MJ, Boeke JD, Pineda FJ, Hardwick JM. Genome-wide consequences of deleting any single gene. Molecular Cell. 52: 485-94. PMID 24211263 DOI: 10.1016/J.Molcel.2013.09.026  0.386
2013 O'Donnell KA, An W, Schrum CT, Wheelan SJ, Boeke JD. Controlled insertional mutagenesis using a LINE-1 (ORFeus) gene-trap mouse model. Proceedings of the National Academy of Sciences of the United States of America. 110: E2706-13. PMID 23818630 DOI: 10.1073/Pnas.1302504110  0.333
2013 Li X, Burnight ER, Cooney AL, Malani N, Brady T, Sander JD, Staber J, Wheelan SJ, Joung JK, McCray PB, Bushman FD, Sinn PL, Craig NL. piggyBac transposase tools for genome engineering. Proceedings of the National Academy of Sciences of the United States of America. 110: E2279-87. PMID 23723351 DOI: 10.1073/Pnas.1305987110  0.369
2013 Behera V, Budman J, Dria S, Morgan M, Velliquette D, Bekbolysnov D, Skaist A, Wheelan S. Impact Of Rad50 On Telomere Recombination Mechanisms In Primary Bone Marrow and B-Cell Lymphomas Lacking Telomerase Blood. 122: 3807-3807. DOI: 10.1182/Blood.V122.21.3807.3807  0.312
2012 Solyom S, Ewing AD, Rahrmann EP, Doucet T, Nelson HH, Burns MB, Harris RS, Sigmon DF, Casella A, Erlanger B, Wheelan S, Upton KR, Shukla R, Faulkner GJ, Largaespada DA, et al. Extensive somatic L1 retrotransposition in colorectal tumors. Genome Research. 22: 2328-38. PMID 22968929 DOI: 10.1101/Gr.145235.112  0.338
2012 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. A Sleeping Beauty mutagenesis screen reveals a tumor suppressor role for Ncoa2/Src-2 in liver cancer. Proceedings of the National Academy of Sciences of the United States of America. 109: E1377-86. PMID 22556267 DOI: 10.1073/Pnas.1115433109  0.321
2012 Mularoni L, Zhou Y, Bowen T, Gangadharan S, Wheelan SJ, Boeke JD. Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots. Genome Research. 22: 693-703. PMID 22219510 DOI: 10.1101/Gr.129460.111  0.355
2011 Tyekucheva S, Yolken RH, McCombie WR, Parla J, Kramer M, Wheelan SJ, Sabunciyan S. Establishing the baseline level of repetitive element expression in the human cortex. Bmc Genomics. 12: 495. PMID 21985647 DOI: 10.1186/1471-2164-12-495  0.346
2011 Niranjan TS, Adamczyk A, Bravo HC, Taub MA, Wheelan SJ, Irizarry R, Wang T. Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis. Genome Biology. 12: R93. PMID 21955804 DOI: 10.1186/Gb-2011-12-9-R93  0.322
2010 Gangadharan S, Mularoni L, Fain-Thornton J, Wheelan SJ, Craig NL. DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo Proceedings of the National Academy of Sciences of the United States of America. 107: 21966-21972. PMID 21131571 DOI: 10.1073/Pnas.1016382107  0.38
2010 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. Mobile interspersed repeats are major structural variants in the human genome. Cell. 141: 1171-82. PMID 20602999 DOI: 10.1016/J.Cell.2010.05.026  0.379
2010 Lin M, Tseng L, Kamiyama H, Kamiyama M, Lim P, Hidalgo M, Wheelan S, Eshleman JR. Quantifying the relative amount of mouse and human DNA in cancer xenografts using species-specific variation in gene length. Biotechniques. 48: 211-218. PMID 20359302 DOI: 10.2144/000113363  0.405
2010 Lin M, Tseng L, Kamiyama H, Kamiyama M, Lim P, Wheelan S, Eshleman J. Abstract 2210: Quantification of the relative amount of mouse and human DNA in cancer xenografts using species-specific gene length variations Cancer Research. 70: 2210-2210. DOI: 10.1158/1538-7445.Am10-2210  0.406
2008 Wheelan SJ, Martínez Murillo F, Boeke JD. The incredible shrinking world of DNA microarrays. Molecular Biosystems. 4: 726-32. PMID 18563246 DOI: 10.1039/B706237K  0.365
2006 Wheelan SJ, Scheifele LZ, Martínez-Murillo F, Irizarry RA, Boeke JD. Transposon insertion site profiling chip (TIP-chip). Proceedings of the National Academy of Sciences of the United States of America. 103: 17632-7. PMID 17101968 DOI: 10.1073/Pnas.0605450103  0.362
2006 Wheelan SJ, Martínez-Murillo F, Irizarry RA, Boeke JD. Stacking the deck: double-tiled DNA microarrays. Nature Methods. 3: 903-7. PMID 17060914 DOI: 10.1038/Nmeth951  0.342
2006 Richardson SM, Wheelan SJ, Yarrington RM, Boeke JD. GeneDesign: rapid, automated design of multikilobase synthetic genes. Genome Research. 16: 550-6. PMID 16481661 DOI: 10.1101/Gr.4431306  0.356
2005 Wheelan SJ, Aizawa Y, Han JS, Boeke JD. Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution. Genome Research. 15: 1073-8. PMID 16024818 DOI: 10.1101/Gr.3688905  0.346
2003 Marth G, Schuler G, Yeh R, Davenport R, Agarwala R, Church D, Wheelan S, Baker J, Ward M, Kholodov M, Phan L, Czabarka E, Murvai J, Cutler D, Wooding S, et al. Sequence variations in the public human genome data reflect a bottlenecked population history. Proceedings of the National Academy of Sciences of the United States of America. 100: 376-81. PMID 12502794 DOI: 10.1073/Pnas.222673099  0.368
2001 Wheelan SJ, Church DM, Ostell JM. Spidey: a tool for mRNA-to-genomic alignments. Genome Research. 11: 1952-7. PMID 11691860 DOI: 10.1101/Gr.195301  0.398
2000 Onyango P, Miller W, Lehoczky J, Leung CT, Birren B, Wheelan S, Dewar K, Feinberg AP. Sequence and comparative analysis of the mouse 1-megabase region orthologous to the human 11p15 imprinted domain. Genome Research. 10: 1697-710. PMID 11076855 DOI: 10.1101/Gr.161800  0.404
2000 Wheelan SJ, Makalowski W. Genome research: the second decade. A report on the XI Cold Spring Harbor Laboratory Meeting on Genome Mapping and Sequencing, May 13-17, 1998, Cold Spring Harbor, NY. Computational Biology and Chemistry. 24: 125-127. PMID 10642884 DOI: 10.1016/S0097-8485(00)80011-X  0.341
1999 Wheelan SJ, Boguski MS, Duret L, Maka?owski W. Human and nematode orthologs--lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans. Gene. 238: 163-70. PMID 10570994 DOI: 10.1016/S0378-1119(99)00298-X  0.338
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