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Katherine E. Varley, Ph.D. - Publications

Affiliations: 
2009 Washington University, Saint Louis, St. Louis, MO 
Area:
Molecular Biology, Biochemistry, General
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32 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
2021 Wallace AD, Sasani TA, Swanier J, Gates BL, Greenland J, Pedersen BS, Varley KE, Quinlan AR. CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing. Plos One. 16: e0241253. PMID 33830997 DOI: 10.1371/journal.pone.0241253  0.39
2020 Conway ME, McDaniel JM, Graham JM, Guillen KP, Oliver PG, Parker SL, Yue P, Turkson J, Buchsbaum DJ, Welm BE, Myers RM, Varley KE. STAT3 and GR cooperate to drive gene expression and growth of basal-like triple-negative breast cancer. Cancer Research. PMID 32816914 DOI: 10.1158/0008-5472.Can-20-1379  0.414
2020 Stewart RL, Matynia AP, Factor RE, Varley KE. Spatially-resolved quantification of proteins in triple negative breast cancers reveals differences in the immune microenvironment associated with prognosis. Scientific Reports. 10: 6598. PMID 32313087 DOI: 10.1038/S41598-020-63539-X  0.366
2020 Martín M, Updike KL, Rodríguez-Lescure A, Calvo L, Herranz J, Martín N, Bernard PS, Varley KE. Abstract P1-10-09: The MHCII immune activation assay is prognostic for disease free survival in basal-like TNBC breast cancer patients in the GEICAM/9906 clinical trial Cancer Research. DOI: 10.1158/1538-7445.Sabcs19-P1-10-09  0.301
2019 Stewart RL, Updike KL, Factor RE, Henry NL, Boucher KM, Bernard PS, Varley KE. A multigene assay determines risk of recurrence in patients with triple-negative breast cancer. Cancer Research. PMID 31048497 DOI: 10.1158/0008-5472.Can-18-3014  0.362
2018 Giraddi RR, Chung CY, Heinz RE, Balcioglu O, Novotny M, Trejo CL, Dravis C, Hagos BM, Mehrabad EM, Rodewald LW, Hwang JY, Fan C, Lasken R, Varley KE, Perou CM, et al. Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development. Cell Reports. 24: 1653-1666.e7. PMID 30089273 DOI: 10.1016/J.Celrep.2018.07.025  0.323
2018 Guillen KP, Scherer SD, Qiao Y, Pathi SS, Graham JM, Fujita M, DeRose YS, Gertz J, Marth GT, Varley KE, Welm AL, Welm BE. Abstract LB-038: Predicting breast cancer therapy response using a patient-derived xenograft organoid screening platform Cancer Research. 78. DOI: 10.1158/1538-7445.Am2018-Lb-038  0.354
2017 Yang C, Gaffney DK, Werner TL, Jarboe EA, Gertz J, Varley KE, Peterson M, Janat-Amsbury MM. Abstract 1756: Genomic reclassification of endometrial carcinoma predicts drug response and facilitates refinement of current management based on PDX-guided efficacy outcomes Cancer Research. 77: 1756-1756. DOI: 10.1158/1538-7445.Am2017-1756  0.356
2016 McDaniel JM, Varley KE, Gertz J, Savic DS, Roberts BS, Bailey SK, Shevde LA, Ramaker RC, Lasseigne BN, Kirby MK, Newberry KM, Partridge EC, Jones AL, Boone B, Levy SE, et al. Genomic regulation of invasion by STAT3 in triple negative breast cancer. Oncotarget. PMID 28030809 DOI: 10.18632/Oncotarget.14153  0.401
2016 Forero A, Li Y, Chen D, Grizzle WE, Updike KL, Merz ND, Downs-Kelly E, Burwell TC, Vaklavas C, Buchsbaum DJ, Myers RM, LoBuglio AF, Varley KE. Expression of the MHC Class II Pathway in Triple-Negative Breast Cancer Tumor Cells is Associated with a Good Prognosis and Infiltrating Lymphocytes. Cancer Immunology Research. PMID 26980599 DOI: 10.1158/2326-6066.Cir-15-0243  0.348
2016 Yang C, Jarboe EA, Gertz J, Varley KE, Peterson CM, Janát-Amsbury MM. Abstract 648: Integrated genomic characterization of endometrial cancer tumor grafts: a step toward genomic-guided treatment Cancer Research. 76: 648-648. DOI: 10.1158/1538-7445.Am2016-648  0.405
2015 Forero-Torres A, Varley KE, Abramson VG, Li Y, Vaklavas C, Lin NU, Liu MC, Rugo HS, Nanda R, Storniolo AM, Traina TA, Patil S, Van Poznak CH, Nangia JR, Irvin WJ, et al. TBCRC 019: A Phase II Trial of Nanoparticle Albumin-Bound Paclitaxel with or without the Anti-Death Receptor 5 Monoclonal Antibody Tigatuzumab in Patients with Triple-Negative Breast Cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 21: 2722-9. PMID 25779953 DOI: 10.1158/1078-0432.Ccr-14-2780  0.32
2015 Forero-Torres A, Varley KE, Li Y, Chen D, Grizzle WE, Downs-Kelly E, Burwell TC, Buchsbaum DJ, Myers RM, LoBuglio AF. MHC II antigen presentation pathway expression in triple-negative breast cancer. Journal of Clinical Oncology. 33: 1066-1066. DOI: 10.1200/Jco.2015.33.15_Suppl.1066  0.389
2014 Varley KE, Gertz J, Roberts BS, Davis NS, Bowling KM, Kirby MK, Nesmith AS, Oliver PG, Grizzle WE, Forero A, Buchsbaum DJ, LoBuglio AF, Myers RM. Recurrent read-through fusion transcripts in breast cancer. Breast Cancer Research and Treatment. 146: 287-97. PMID 24929677 DOI: 10.1007/S10549-014-3019-2  0.384
2013 Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM. Distinct properties of cell-type-specific and shared transcription factor binding sites. Molecular Cell. 52: 25-36. PMID 24076218 DOI: 10.1016/J.Molcel.2013.08.037  0.348
2013 Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Badoo M, Crain CM, Song L, Crawford GE, Myers RM, Lacey M, Ehrlich M. Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics : Official Journal of the Dna Methylation Society. 8: 317-32. PMID 23417056 DOI: 10.4161/Epi.23989  0.349
2013 Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE, Absher DM, Wold BJ, Myers RM. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Research. 23: 555-67. PMID 23325432 DOI: 10.1101/Gr.147942.112  0.423
2013 Forero A, Santos JD, Bowen K, Jones C, Varley K, Nabell L, Carpenter J, Falkson C, Krontiras H, Caterinicchia V, O'Malley J, Li Y, LoBuglio A, Myers R, Saleh M. Abstract P1-15-02: Long term follow-up of the neo-adjuvant pilot trial evaluating activity of letrozole in combination with bevacizumab in post-menopausal women with newly diagnosed estrogen and/or progesterone receptor positive primary breast cancer Cancer Research. 73. DOI: 10.1158/0008-5472.Sabcs13-P1-15-02  0.333
2012 Guo Y, Monahan K, Wu H, Gertz J, Varley KE, Li W, Myers RM, Maniatis T, Wu Q. CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice. Proceedings of the National Academy of Sciences of the United States of America. 109: 21081-6. PMID 23204437 DOI: 10.1073/Pnas.1219280110  0.342
2012 Gertz J, Reddy TE, Varley KE, Garabedian MJ, Myers RM. Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner. Genome Research. 22: 2153-62. PMID 23019147 DOI: 10.1101/Gr.135681.111  0.354
2012 Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, Stamatoyannopoulos JA. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Research. 22: 1680-8. PMID 22955980 DOI: 10.1101/Gr.136101.111  0.436
2012 Reyes A, Sandoval A, Cubillos-Ruiz A, Varley KE, Hernández-Neuta I, Samper S, Martín C, García MJ, Ritacco V, López L, Robledo J, Zambrano MM, Mitra RD, Del Portillo P. IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes. Bmc Genomics. 13: 249. PMID 22703188 DOI: 10.1186/1471-2164-13-249  0.577
2012 Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L, Crawford GE, Wold B, Willard HF, Myers RM. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Research. 22: 860-9. PMID 22300769 DOI: 10.1101/Gr.131201.111  0.42
2012 Gertz J, Varley KE, Davis NS, Baas BJ, Goryshin IY, Vaidyanathan R, Kuersten S, Myers RM. Transposase mediated construction of RNA-seq libraries. Genome Research. 22: 134-41. PMID 22128135 DOI: 10.1101/Gr.127373.111  0.302
2012 Spayd KJ, Vasenkova I, Shvetsova T, Bachmeyer RC, Myers RM, Moore DT, Varley KE. Abstract LB-412: TargetRich cancer gene panels: targeted next generation sequencing in cancer samples Cancer Research. 72. DOI: 10.1158/1538-7445.Am2012-Lb-412  0.513
2011 Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, Kucera KS, Willard HF, Myers RM. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. Plos Genetics. 7: e1002228. PMID 21852959 DOI: 10.1371/Journal.Pgen.1002228  0.433
2010 Varley KE, Mitra RD. Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Research. 20: 1279-87. PMID 20627893 DOI: 10.1101/Gr.101212.109  0.679
2009 Varley KE, Mitra RD. Nested Patch PCR for highly multiplexed amplification of genomic loci. Cold Spring Harbor Protocols. 2009: pdb.prot5252. PMID 20147217 DOI: 10.1101/Pdb.Prot5252  0.626
2009 Varley KE, Mutch DG, Edmonston TB, Goodfellow PJ, Mitra RD. Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing. Nucleic Acids Research. 37: 4603-12. PMID 19494183 DOI: 10.1093/Nar/Gkp457  0.604
2009 Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD. Quantification of rare allelic variants from pooled genomic DNA. Nature Methods. 6: 263-5. PMID 19252504 DOI: 10.1038/Nmeth.1307  0.622
2008 Varley KE, Mitra RD. Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes. Genome Research. 18: 1844-50. PMID 18849522 DOI: 10.1101/Gr.078204.108  0.646
2007 Zhao G, Chang KY, Varley K, Stormo GD. Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach. Plos One. 2: e262. PMID 17327921 DOI: 10.1371/Journal.Pone.0000262  0.404
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