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Trapnell, Cole, Cacchiarelli, Davide, Grimsby, Jonna, Pokharel, Prapti, Li, Shuqiang, Morse, Michael, Lennon, Niall J, Livak, Kenneth J, Mikkelsen, Tarjei S, Rinn, John L
Published in Nature biotechnology (01.04.2014)
Published in Nature biotechnology (01.04.2014)
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Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms
Costello, Maura, Fleharty, Mark, Abreu, Justin, Farjoun, Yossi, Ferriera, Steven, Holmes, Laurie, Granger, Brian, Green, Lisa, Howd, Tom, Mason, Tamara, Vicente, Gina, Dasilva, Michael, Brodeur, Wendy, DeSmet, Timothy, Dodge, Sheila, Lennon, Niall J, Gabriel, Stacey
Published in BMC genomics (08.05.2018)
Published in BMC genomics (08.05.2018)
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Donor Clonal Hematopoiesis and Recipient Outcomes After Transplantation
Gibson, Christopher J, Kim, Haesook T, Zhao, Lin, Murdock, H Moses, Hambley, Bryan, Ogata, Alana, Madero-Marroquin, Rafael, Wang, Shiyu, Green, Lisa, Fleharty, Mark, Dougan, Tyler, Cheng, Chi-An, Blumenstiel, Brendan, Cibulskis, Carrie, Tsuji, Junko, Duran, Madeleine, Gocke, Christopher D, Antin, Joseph H, Nikiforow, Sarah, DeZern, Amy E, Chen, Yi-Bin, Ho, Vincent T, Jones, Richard J, Lennon, Niall J, Walt, David R, Ritz, Jerome, Soiffer, Robert J, Gondek, Lukasz P, Lindsley, R Coleman
Published in Journal of clinical oncology (10.01.2022)
Published in Journal of clinical oncology (10.01.2022)
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Characterizing and measuring bias in sequence data
Ross, Michael G, Russ, Carsten, Costello, Maura, Hollinger, Andrew, Lennon, Niall J, Hegarty, Ryan, Nusbaum, Chad, Jaffe, David B
Published in Genome biology (29.05.2013)
Published in Genome biology (29.05.2013)
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Dynamics of dengue disease severity determined by the interplay between viral genetics and serotype-specific immunity
OhAinle, Molly, Balmaseda, Angel, Macalalad, Alexander R, Tellez, Yolanda, Zody, Michael C, Saborío, Saira, Nuñez, Andrea, Lennon, Niall J, Birren, Bruce W, Gordon, Aubree, Henn, Matthew R, Harris, Eva
Published in Science translational medicine (21.12.2011)
Published in Science translational medicine (21.12.2011)
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Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations
Ahronian, Leanne G, Sennott, Erin M, Van Allen, Eliezer M, Wagle, Nikhil, Kwak, Eunice L, Faris, Jason E, Godfrey, Jason T, Nishimura, Koki, Lynch, Kerry D, Mermel, Craig H, Lockerman, Elizabeth L, Kalsy, Anuj, Gurski, Jr, Joseph M, Bahl, Samira, Anderka, Kristin, Green, Lisa M, Lennon, Niall J, Huynh, Tiffany G, Mino-Kenudson, Mari, Getz, Gad, Dias-Santagata, Dora, Iafrate, A John, Engelman, Jeffrey A, Garraway, Levi A, Corcoran, Ryan B
Published in Cancer discovery (01.04.2015)
Published in Cancer discovery (01.04.2015)
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De novo assembly of highly diverse viral populations
Yang, Xiao, Charlebois, Patrick, Gnerre, Sante, Coole, Matthew G, Lennon, Niall J, Levin, Joshua Z, Qu, James, Ryan, Elizabeth M, Zody, Michael C, Henn, Matthew R
Published in BMC genomics (13.09.2012)
Published in BMC genomics (13.09.2012)
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Next-generation sequencing for HLA typing of class I loci
Erlich, Rachel L, Jia, Xiaoming, Anderson, Scott, Banks, Eric, Gao, Xiaojiang, Carrington, Mary, Gupta, Namrata, DePristo, Mark A, Henn, Matthew R, Lennon, Niall J, de Bakker, Paul I W
Published in BMC genomics (18.01.2011)
Published in BMC genomics (18.01.2011)
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Whole-genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program
Venner, Eric, Muzny, Donna, Smith, Joshua D, Walker, Kimberly, Neben, Cynthia L, Lockwood, Christina M, Empey, Phillip E, Metcalf, Ginger A, Kachulis, Chris, Mian, Sana, Musick, Anjene, Rehm, Heidi L, Harrison, Steven, Gabriel, Stacey, Gibbs, Richard A, Nickerson, Deborah, Zhou, Alicia Y, Doheny, Kimberly, Ozenberger, Bradley, Topper, Scott E, Lennon, Niall J
Published in Genome medicine (28.03.2022)
Published in Genome medicine (28.03.2022)
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Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia
Vu, Thi Ty Hang, Holmes, Edward C, Duong, Veasna, Nguyen, Thien Quy, Tran, Tinh Hien, Quail, Michael, Churcher, Carol, Parkhill, Julian, Cardosa, Jane, Farrar, Jeremy, Wills, Bridget, Lennon, Niall J, Birren, Bruce W, Buchy, Philippe, Henn, Matthew R, Simmons, Cameron P
Published in PLoS neglected tropical diseases (20.07.2010)
Published in PLoS neglected tropical diseases (20.07.2010)
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Genome-Wide Patterns of Intrahuman Dengue Virus Diversity Reveal Associations with Viral Phylogenetic Clade and Interhost Diversity
PARAMESWARAN, Poornima, CHARLEBOIS, Patrick, HENN, Matthew R, TELLEZ, Yolanda, NUNEZ, Andrea, RYAN, Elizabeth M, MALBOEUF, Christine M, LEVIN, Joshua Z, LENNON, Niall J, BALMASEDA, Angel, HARRIS, Eva
Published in Journal of Virology (01.08.2012)
Published in Journal of Virology (01.08.2012)
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The Early Whole-Blood Transcriptional Signature of Dengue Virus and Features Associated with Progression to Dengue Shock Syndrome in Vietnamese Children and Young Adults
LONG TRUONG HOANG, LYNN, David J, HIBBERD, Martin L, SIMMONS, Cameron P, HENN, Matt, BIRREN, Bruce W, LENNON, Niall J, PHUONG THI LE, DUONG, Kien Thi Hue, NGUYEN, Tham Thi Hong, LANH NGOC MAI, FARRAR, Jeremy J
Published in Journal of Virology (01.12.2010)
Published in Journal of Virology (01.12.2010)
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Technological considerations for genome-guided diagnosis and management of cancer
Lennon, Niall J, Adalsteinsson, Viktor A, Gabriel, Stacey B
Published in Genome medicine (26.10.2016)
Published in Genome medicine (26.10.2016)
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Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission
Raghwani, Jayna, Rambaut, Andrew, Holmes, Edward C, Hang, Vu Ty, Hien, Tran Tinh, Farrar, Jeremy, Wills, Bridget, Lennon, Niall J, Birren, Bruce W, Henn, Matthew R, Simmons, Cameron P
Published in PLoS pathogens (01.06.2011)
Published in PLoS pathogens (01.06.2011)
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Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer
Weber, Zachary T, Collier, Katharine A, Tallman, David, Forman, Juliet, Shukla, Sachet, Asad, Sarah, Rhoades, Justin, Freeman, Samuel, Parsons, Heather A, Williams, Nicole O, Barroso-Sousa, Romualdo, Stover, Elizabeth H, Mahdi, Haider, Cibulskis, Carrie, Lennon, Niall J, Ha, Gavin, Adalsteinsson, Viktor A, Tolaney, Sara M, Stover, Daniel G
Published in Genome medicine (20.05.2021)
Published in Genome medicine (20.05.2021)
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Whole Genome Pyrosequencing of Rare Hepatitis C Virus Genotypes Enhances Subtype Classification and Identification of Naturally Occurring Drug Resistance Variants
Newman, Ruchi M., Kuntzen, Thomas, Weiner, Brian, Berical, Andrew, Charlebois, Patrick, Kuiken, Carla, Murphy, Donald G., Simmonds, Peter, Bennett, Phil, Lennon, Niall J., Birren, Bruce W., Zody, Michael C., Allen, Todd M., Henn, Matthew R.
Published in The Journal of infectious diseases (01.07.2013)
Published in The Journal of infectious diseases (01.07.2013)
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High-Resolution Analysis of Intrahost Genetic Diversity in Dengue Virus Serotype 1 Infection Identifies Mixed Infections
THAI, Khoa T. D, HENN, Matthew R, FARRAR, Jeremy, ROGIER VAN DOORN, H, DE JONG, Menno D, BIRREN, Bruce W, HOLMES, Edward C, SIMMONS, Cameron P, ZODY, Michael C, TRICOU, Vianney, MINH NGUYET, Nguyen, CHARIEBOIS, Patrick, LENNON, Niaii J, GREEN, Lisa, DE VRIES, Peter J, TRAN TINH HIEN
Published in Journal of Virology (01.01.2012)
Published in Journal of Virology (01.01.2012)
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Estimating epidemiologic dynamics from cross-sectional viral load distributions
Hay, James A, Kennedy-Shaffer, Lee, Kanjilal, Sanjat, Lennon, Niall J, Gabriel, Stacey B, Lipsitch, Marc, Mina, Michael J
Published in Science (16.07.2021)
Published in Science (16.07.2021)
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