The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells von Trapnell, Cole, Cacchiarelli, Davide, Grimsby, Jonna, Pokharel, Prapti, Li, Shuqiang, Morse, Michael, Lennon, Niall J, Livak, Kenneth J, Mikkelsen, Tarjei S, Rinn, John L

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Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms von 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

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A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning von Taylor, D. Lee, Hollingsworth, Teresa N., Mcfarland, Jack W., Lennon, Niall J., Nusbaum, Chad, Ruess, Roger W.

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Donor Clonal Hematopoiesis and Recipient Outcomes After Transplantation von 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

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Characterizing and measuring bias in sequence data von Ross, Michael G, Russ, Carsten, Costello, Maura, Hollinger, Andrew, Lennon, Niall J, Hegarty, Ryan, Nusbaum, Chad, Jaffe, David B

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De novo assembly of highly diverse viral populations von 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

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Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations von 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

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Next-generation sequencing for HLA typing of class I loci von 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

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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 von 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

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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 von 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

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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 von 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

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Genome-Wide Patterns of Intrahuman Dengue Virus Diversity Reveal Associations with Viral Phylogenetic Clade and Interhost Diversity von 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

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Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission von 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

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Estimating epidemiologic dynamics from cross-sectional viral load distributions von Hay, James A, Kennedy-Shaffer, Lee, Kanjilal, Sanjat, Lennon, Niall J, Gabriel, Stacey B, Lipsitch, Marc, Mina, Michael J

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Dysferlin Interacts with Annexins A1 and A2 and Mediates Sarcolemmal Wound-healing von Lennon, Niall J., Kho, Alvin, Bacskai, Brian J., Perlmutter, Sarah L., Hyman, Bradley T., Brown, Robert H.

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Technological considerations for genome-guided diagnosis and management of cancer von Lennon, Niall J, Adalsteinsson, Viktor A, Gabriel, Stacey B

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Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing von Taylor, D Lee, Walters, William A, Lennon, Niall J, Bochicchio, James, Krohn, Andrew, Caporaso, J Gregory, Pennanen, Taina

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Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer von 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

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High-Resolution Analysis of Intrahost Genetic Diversity in Dengue Virus Serotype 1 Infection Identifies Mixed Infections von 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

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Whole Genome Pyrosequencing of Rare Hepatitis C Virus Genotypes Enhances Subtype Classification and Identification of Naturally Occurring Drug Resistance Variants von 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.

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