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Mathios, Dimitrios, Johansen, Jakob Sidenius, Cristiano, Stephen, Medina, Jamie E., Phallen, Jillian, Larsen, Klaus R., Bruhm, Daniel C., Niknafs, Noushin, Ferreira, Leonardo, Adleff, Vilmos, Chiao, Jia Yuee, Leal, Alessandro, Noe, Michael, White, James R., Arun, Adith S., Hruban, Carolyn, Annapragada, Akshaya V., Jensen, Sarah Østrup, Ørntoft, Mai-Britt Worm, Madsen, Anders Husted, Carvalho, Beatriz, de Wit, Meike, Carey, Jacob, Dracopoli, Nicholas C., Maddala, Tara, Fang, Kenneth C., Hartman, Anne-Renee, Forde, Patrick M., Anagnostou, Valsamo, Brahmer, Julie R., Fijneman, Remond J. A., Nielsen, Hans Jørgen, Meijer, Gerrit A., Andersen, Claus Lindbjerg, Mellemgaard, Anders, Bojesen, Stig E., Scharpf, Robert B., Velculescu, Victor E.
Published in Nature communications (20.08.2021)
Published in Nature communications (20.08.2021)
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High grade serous ovarian carcinomas originate in the fallopian tube
Labidi-Galy, S. Intidhar, Papp, Eniko, Hallberg, Dorothy, Niknafs, Noushin, Adleff, Vilmos, Noe, Michael, Bhattacharya, Rohit, Novak, Marian, Jones, Siân, Phallen, Jillian, Hruban, Carolyn A., Hirsch, Michelle S., Lin, Douglas I., Schwartz, Lauren, Maire, Cecile L., Tille, Jean-Christophe, Bowden, Michaela, Ayhan, Ayse, Wood, Laura D., Scharpf, Robert B., Kurman, Robert, Wang, Tian-Li, Shih, Ie-Ming, Karchin, Rachel, Drapkin, Ronny, Velculescu, Victor E.
Published in Nature communications (23.10.2017)
Published in Nature communications (23.10.2017)
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Combining PARP with ATR inhibition overcomes PARP inhibitor and platinum resistance in ovarian cancer models
Kim, Hyoung, Xu, Haineng, George, Erin, Hallberg, Dorothy, Kumar, Sushil, Jagannathan, Veena, Medvedev, Sergey, Kinose, Yasuto, Devins, Kyle, Verma, Priyanka, Ly, Kevin, Wang, Yifan, Greenberg, Roger A., Schwartz, Lauren, Johnson, Neil, Scharpf, Robert B., Mills, Gordon B., Zhang, Rugang, Velculescu, Victor E., Brown, Eric J., Simpkins, Fiona
Published in Nature communications (24.07.2020)
Published in Nature communications (24.07.2020)
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Tackling the widespread and critical impact of batch effects in high-throughput data
Irizarry, Rafael A, Leek, Jeffrey T, Scharpf, Robert B, Bravo, Héctor Corrada, Simcha, David, Langmead, Benjamin, Johnson, W. Evan, Geman, Donald, Baggerly, Keith
Published in Nature reviews. Genetics (01.10.2010)
Published in Nature reviews. Genetics (01.10.2010)
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Genomic characterization of malignant progression in neoplastic pancreatic cysts
Noë, Michaël, Niknafs, Noushin, Fischer, Catherine G., Hackeng, Wenzel M., Beleva Guthrie, Violeta, Hosoda, Waki, Debeljak, Marija, Papp, Eniko, Adleff, Vilmos, White, James R., Luchini, Claudio, Pea, Antonio, Scarpa, Aldo, Butturini, Giovanni, Zamboni, Giuseppe, Castelli, Paola, Hong, Seung-Mo, Yachida, Shinichi, Hiraoka, Nobuyoshi, Gill, Anthony J., Samra, Jaswinder S., Offerhaus, G. Johan A., Hoorens, Anne, Verheij, Joanne, Jansen, Casper, Adsay, N. Volkan, Jiang, Wei, Winter, Jordan, Albores-Saavedra, Jorge, Terris, Benoit, Thompson, Elizabeth D., Roberts, Nicholas J., Hruban, Ralph H., Karchin, Rachel, Scharpf, Robert B., Brosens, Lodewijk A. A., Velculescu, Victor E., Wood, Laura D.
Published in Nature communications (14.08.2020)
Published in Nature communications (14.08.2020)
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Detecting antibody reactivities in Phage ImmunoPrecipitation Sequencing data
Chen, Athena, Kammers, Kai, Larman, H Benjamin, Scharpf, Robert B, Ruczinski, Ingo
Published in BMC genomics (15.09.2022)
Published in BMC genomics (15.09.2022)
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Early Noninvasive Detection of Response to Targeted Therapy in Non-Small Cell Lung Cancer
Phallen, Jillian, Leal, Alessandro, Woodward, Brian D, Forde, Patrick M, Naidoo, Jarushka, Marrone, Kristen A, Brahmer, Julie R, Fiksel, Jacob, Medina, Jamie E, Cristiano, Stephen, Palsgrove, Doreen N, Gocke, Christopher D, Bruhm, Daniel C, Keshavarzian, Parissa, Adleff, Vilmos, Weihe, Elizabeth, Anagnostou, Valsamo, Scharpf, Robert B, Velculescu, Victor E, Husain, Hatim
Published in Cancer research (Chicago, Ill.) (15.03.2019)
Published in Cancer research (Chicago, Ill.) (15.03.2019)
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Single-molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer
Bruhm, Daniel C., Mathios, Dimitrios, Foda, Zachariah H., Annapragada, Akshaya V., Medina, Jamie E., Adleff, Vilmos, Chiao, Elaine Jiayuee, Ferreira, Leonardo, Cristiano, Stephen, White, James R., Mazzilli, Sarah A., Billatos, Ehab, Spira, Avrum, Zaidi, Ali H., Mueller, Jeffrey, Kim, Amy K., Anagnostou, Valsamo, Phallen, Jillian, Scharpf, Robert B., Velculescu, Victor E.
Published in Nature genetics (01.08.2023)
Published in Nature genetics (01.08.2023)
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DNA methylation and gene expression as determinants of genome-wide cell-free DNA fragmentation
Noë, Michaël, Mathios, Dimitrios, Annapragada, Akshaya V., Koul, Shashikant, Foda, Zacharia H., Medina, Jamie E., Cristiano, Stephen, Cherry, Christopher, Bruhm, Daniel C., Niknafs, Noushin, Adleff, Vilmos, Ferreira, Leonardo, Easwaran, Hari, Baylin, Stephen, Phallen, Jillian, Scharpf, Robert B., Velculescu, Victor E.
Published in Nature communications (06.08.2024)
Published in Nature communications (06.08.2024)
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Cell-free DNA approaches for cancer early detection and interception
Medina, Jamie E, Dracopoli, Nicholas C, Bach, Peter B, Lau, Anna, Scharpf, Robert B, Meijer, Gerrit A, Andersen, Claus Lindbjerg, Velculescu, Victor E
Published in Journal for immunotherapy of cancer (01.09.2023)
Published in Journal for immunotherapy of cancer (01.09.2023)
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Pre-processing Agilent microarray data
Zahurak, Marianna, Parmigiani, Giovanni, Yu, Wayne, Scharpf, Robert B, Berman, David, Schaeffer, Edward, Shabbeer, Shabana, Cope, Leslie
Published in BMC bioinformatics (01.05.2007)
Published in BMC bioinformatics (01.05.2007)
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Using the R Package crlmm for Genotyping and Copy Number Estimation
Scharpf, Robert B, Irizarry, Rafael A, Ritchie, Matthew E, Carvalho, Benilton, Ruczinski, Ingo
Published in Journal of statistical software (01.05.2011)
Published in Journal of statistical software (01.05.2011)
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CRISPR-Cas9 for selective targeting of somatic mutations in pancreatic cancers
Teh, Selina Shiqing K, Bowland, Kirsten, Halper-Stromberg, Eitan, Kotwal, Akhil, Bennett, Alexis, Skaist, Alyza, Tang, Jacqueline, Cai, Fidel, Macoretta, Antonella, Liang, Hong, Kamiyama, Hirohiko, Wheelan, Sarah, Lin, Ming-Tseh, Hruban, Ralph H, Hung, Chien-Fu, Goldstein, Michael, Scharpf, Robert B, Roberts, Nicholas J, Eshleman, James R
Published in NAR cancer (19.06.2024)
Published in NAR cancer (19.06.2024)
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NDRG1 links p53 with proliferation-mediated centrosome homeostasis and genome stability
Croessmann, Sarah, Wong, Hong Yuen, Zabransky, Daniel J, Chu, David, Mendonca, Janet, Sharma, Anup, Mohseni, Morassa, Rosen, D Marc, Scharpf, Robert B, Cidado, Justin, Cochran, Rory L, Parsons, Heather A, Dalton, W Brian, Erlanger, Bracha, Button, Berry, Cravero, Karen, Kyker-Snowman, Kelly, Beaver, Julia A, Kachhap, Sushant, Hurley, Paula J, Lauring, Josh, Park, Ben Ho
Published in Proceedings of the National Academy of Sciences - PNAS (15.09.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (15.09.2015)
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Bayesian copy number detection and association in large-scale studies
Cristiano, Stephen, McKean, David, Carey, Jacob, Bracci, Paige, Brennan, Paul, Chou, Michael, Du, Mengmeng, Gallinger, Steven, Goggins, Michael G, Hassan, Manal M, Hung, Rayjean J, Kurtz, Robert C, Li, Donghui, Lu, Lingeng, Neale, Rachel, Olson, Sara, Petersen, Gloria, Rabe, Kari G, Fu, Jack, Risch, Harvey, Rosner, Gary L, Ruczinski, Ingo, Klein, Alison P, Scharpf, Robert B
Published in BMC cancer (07.09.2020)
Published in BMC cancer (07.09.2020)
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Genome-Wide Association of Copy Number Polymorphisms and Kidney Function
Li, Man, Carey, Jacob, Cristiano, Stephen, Susztak, Katalin, Coresh, Josef, Boerwinkle, Eric, Kao, Wen Hong L, Beaty, Terri H, Köttgen, Anna, Scharpf, Robert B
Published in PloS one (30.01.2017)
Published in PloS one (30.01.2017)
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H2Bub1 loss is an early contributor to clear cell ovarian cancer progression
Ferrari, Adam J, Rawat, Priyanka, Rendulich, Hannah S, Annapragada, Akshaya V, Kinose, Yasuto, Zhang, Xiaoming, Devins, Kyle, Budina, Anna, Scharpf, Robert B, Mitchell, Marilyn A, Tanyi, Janos L, Morgan, Mark A, Schwartz, Lauren E, Soong, T Rinda, Velculescu, Victor E, Drapkin, Ronny
Published in JCI insight (22.06.2023)
Published in JCI insight (22.06.2023)
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Hemizygous Deletion on Chromosome 3p26.1 Is Associated with Heavy Smoking among African American Subjects in the COPDGene Study
Begum, Ferdouse, Ruczinski, Ingo, Hokanson, John E, Lutz, Sharon M, Parker, Margaret M, Cho, Michael H, Hetmanski, Jacqueline B, Scharpf, Robert B, Crapo, James D, Silverman, Edwin K, Beaty, Terri H
Published in PloS one (06.10.2016)
Published in PloS one (06.10.2016)
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