Improved indel detection in DNA and RNA via realignment with ABRA2
Mose, Lisle E, Perou, Charles M, Parker, Joel S
Published in Bioinformatics (Oxford, England) (01.09.2019)
Published in Bioinformatics (Oxford, England) (01.09.2019)
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Journal Article
Genetic determinants of cellular addiction to DNA polymerase theta
Feng, Wanjuan, Simpson, Dennis A., Carvajal-Garcia, Juan, Price, Brandon A., Kumar, Rashmi J., Mose, Lisle E., Wood, Richard D., Rashid, Naim, Purvis, Jeremy E., Parker, Joel S., Ramsden, Dale A., Gupta, Gaorav P.
Published in Nature communications (19.09.2019)
Published in Nature communications (19.09.2019)
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Journal Article
ABRA: improved coding indel detection via assembly-based realignment
Mose, Lisle E, Wilkerson, Matthew D, Hayes, D Neil, Perou, Charles M, Parker, Joel S
Published in Bioinformatics (Oxford, England) (01.10.2014)
Published in Bioinformatics (Oxford, England) (01.10.2014)
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Journal Article
Prognostic value of B cells in cutaneous melanoma
Selitsky, Sara R, Mose, Lisle E, Smith, Christof C, Chai, Shengjie, Hoadley, Katherine A, Dittmer, Dirk P, Moschos, Stergios J, Parker, Joel S, Vincent, Benjamin G
Published in Genome medicine (28.05.2019)
Published in Genome medicine (28.05.2019)
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Journal Article
Germline Analysis from Tumor-Germline Sequencing Dyads to Identify Clinically Actionable Secondary Findings
Seifert, Bryce A, O'Daniel, Julianne M, Amin, Krunal, Marchuk, Daniel S, Patel, Nirali M, Parker, Joel S, Hoyle, Alan P, Mose, Lisle E, Marron, Andrew, Hayward, Michele C, Bizon, Christopher, Wilhelmsen, Kirk C, Evans, James P, Earp, 3rd, H Shelton, Sharpless, Norman E, Hayes, D Neil, Berg, Jonathan S
Published in Clinical cancer research (15.08.2016)
Published in Clinical cancer research (15.08.2016)
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Journal Article
Virus expression detection reveals RNA-sequencing contamination in TCGA
Selitsky, Sara R, Marron, David, Hollern, Daniel, Mose, Lisle E, Hoadley, Katherine A, Jones, Corbin, Parker, Joel S, Dittmer, Dirk P, Perou, Charles M
Published in BMC genomics (28.01.2020)
Published in BMC genomics (28.01.2020)
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Journal Article
Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer
Mose, Lisle E, Selitsky, Sara R, Bixby, Lisa M, Marron, David L, Iglesia, Michael D, Serody, Jonathan S, Perou, Charles M, Vincent, Benjamin G, Parker, Joel S
Published in Bioinformatics (Oxford, England) (15.12.2016)
Published in Bioinformatics (Oxford, England) (15.12.2016)
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Journal Article
Integrated RNA and DNA sequencing improves mutation detection in low purity tumors
Wilkerson, Matthew D, Cabanski, Christopher R, Sun, Wei, Hoadley, Katherine A, Walter, Vonn, Mose, Lisle E, Troester, Melissa A, Hammerman, Peter S, Parker, Joel S, Perou, Charles M, Hayes, D Neil
Published in Nucleic acids research (29.07.2014)
Published in Nucleic acids research (29.07.2014)
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Journal Article
SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling
Silva, Grace O, Siegel, Marni B, Mose, Lisle E, Parker, Joel S, Sun, Wei, Perou, Charles M, Chen, Mengjie
Published in Genome Biology (08.04.2017)
Published in Genome Biology (08.04.2017)
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Journal Article
Claudin-low bladder tumors are immune infiltrated and actively immune suppressed
Kardos, Jordan, Chai, Shengjie, Mose, Lisle E, Selitsky, Sara R, Krishnan, Bhavani, Saito, Ryoichi, Iglesia, Michael D, Milowsky, Matthew I, Parker, Joel S, Kim, William Y, Vincent, Benjamin G
Published in JCI insight (17.03.2016)
Published in JCI insight (17.03.2016)
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Journal Article
A P53-Independent DNA Damage Response Suppresses Oncogenic Proliferation and Genome Instability
Fagan-Solis, Katerina D., Simpson, Dennis A., Kumar, Rashmi J., Martelotto, Luciano G., Mose, Lisle E., Rashid, Naim U., Ho, Alice Y., Powell, Simon N., Wen, Y. Hannah, Parker, Joel S., Reis-Filho, Jorge S., Petrini, John H.J., Gupta, Gaorav P.
Published in Cell reports (Cambridge) (04.02.2020)
Published in Cell reports (Cambridge) (04.02.2020)
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Journal Article
Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality
Selitsky, Sara R, Marron, David, Mose, Lisle E, Parker, Joel S, Dittmer, Dirk P
Published in mSystems (01.09.2018)
Published in mSystems (01.09.2018)
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Journal Article
Rad18 mediates specific mutational signatures and shapes the genomic landscape of carcinogen-induced tumors in vivo
Lou, Jitong, Yang, Yang, Gu, Qisheng, Price, Brandon A, Qiu, Yuheng, Fedoriw, Yuri, Desai, Siddhi, Mose, Lisle E, Chen, Brian, Tateishi, Satoshi, Parker, Joel S, Vaziri, Cyrus, Wu, Di
Published in NAR cancer (01.03.2021)
Published in NAR cancer (01.03.2021)
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Journal Article
Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer
Ciriello, Giovanni, Gatza, Michael L., Wilkerson, Matthew D., Rhie, Suhn K., Pastore, Alessandro, McLellan, Michael, Bowlby, Reanne, Lester, Susan C., Tse, Gary M.K., Chen, Yunn-Yi, Jensen, Kristin, Johnson, Nicole B., Mills, Gordon B., Robertson, Gordon, Benz, Christopher, Sander, Chris, Hoadley, Katherine A., King, Tari A., Akbani, Rehan, Auman, J. Todd, Balasundaram, Miruna, Barr, Thomas, Beck, Andrew, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Cherniack, Andrew D., Chin, Lynda, Davidsen, Tanja, Demchok, John A., Dennison, Jennifer B., Ding, Li, Ferguson, Martin L., Gabriel, Stacey B., Gao, JianJiong, Gastier-Foster, Julie M., Gatza, Michael L., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Gibson, William J., Hayes, D. Neil, Heiman, David I., Hoadley, Katherine A., Holbrook, Andrea, Hoyle, Alan P., Hu, Hai, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J.M., Ju, Zhenlin, Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lin, Pei, Liu, Jia, Liu, Wenbin, Maglinte, Dennis T., Mardis, Elaine, Marra, Marco A., McAllister, Cynthia, McLellan, Michael, Meng, Shaowu, Mills, Gordon B., Mose, Lisle E., Mungall, Andrew J., Naresh, Rashi, Noble, Michael S., Olopade, Olufunmilayo, Perou, Charles M., Saksena, Gordon, Schumacher, Steven E., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Sander, Chris, Sheth, Margi, Shi, Yan, Shih, Juliann, Shelley, Carl Simon, Simons, Janae V., Sofia, Heidi J., Sougnez, Carrie, Sun, Charlie, Van Den Berg, David J., Wan, Yunhu, Wang, Zhining, Wise, Lisa, Wiznerowicz, Maciej, Wu, Junyuan, Yang, Liming, Yau, Christina, Zack, Travis I., Zhang, Hailei, Zhang, Jiashan, Perou, Charles M.
Published in Cell (08.10.2015)
Published in Cell (08.10.2015)
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Journal Article
Abstract 1678: Accurate detection of expressed variation in RNA-seq
Mose, Lisle E., Marron, David, Parker, Joel S.
Published in Cancer research (Chicago, Ill.) (01.07.2019)
Published in Cancer research (Chicago, Ill.) (01.07.2019)
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Journal Article
Abstract 3592: Improved indel detection in RNA-seq data via assembly based re-alignment reveals expressed Epidermal Growth Factor Receptor indels in Lung Adenocarcinoma
Mose, Lisle E., Hayes, D. Neil, Perou, Charles M., Parker, Joel S.
Published in Cancer research (Chicago, Ill.) (01.07.2017)
Published in Cancer research (Chicago, Ill.) (01.07.2017)
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Journal Article
Abstract P4-05-03: Mutational analysis of triple-negative breast cancer (TNBC): CALGB 40603 (Alliance)
Hoadley, Katherine A, Powell, Bradford C., Kanavy, Dona, Marron, David, Mose, Lisle E., Hyslop, Terry, Berry, Donald A., Hahn, Olwen, Tolaney, Sara M., Sikov, William M., Perou, Charles M., Carey, Lisa A.
Published in Cancer research (Chicago, Ill.) (15.02.2020)
Published in Cancer research (Chicago, Ill.) (15.02.2020)
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Journal Article
Abstract 5120: The novel claudin-low molecular subtype of high-grade urothelial bladder cancer is highly immunogenic yet immunosuppressed
Vincent, Benjamin G., Kim, William, Kardos, Jordan, Chai, Shengjie, Parker, Joel, Mose, Lisle, Selitsky, Sara, Iglesia, Michael, Milowsky, Matthew
Published in Cancer research (Chicago, Ill.) (15.07.2016)
Published in Cancer research (Chicago, Ill.) (15.07.2016)
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Journal Article