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Performance and Operational Evaluation of the Access Bio CareStart Rapid Antigen Test in a High-Throughput Drive-Through Community Testing Site in Massachusetts.
Published in:
Open Forum Infectious Diseases, 2021, v. 8, n. 7, p. 1, doi. 10.1093/ofid/ofab243
By:
- Pollock, Nira R;
- Tran, Kristine;
- Jacobs, Jesica R;
- Cranston, Amber E;
- Smith, Sita;
- O'Kane, Claire Y;
- Roady, Tyler J;
- Moran, Anne;
- Scarry, Alison;
- Carroll, Melissa;
- Volinsky, Leila;
- Perez, Gloria;
- Patel, Pinal;
- Gabriel, Stacey;
- Lennon, Niall J;
- Madoff, Lawrence C;
- Brown, Catherine;
- Smole, Sandra C
Publication type:
Article
A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning.
Published in:
Ecological Monographs, 2014, v. 84, n. 1, p. 3, doi. 10.1890/12-1693.1
By:
- Taylor, D. Lee;
- Hollingsworth, Teresa N.;
- McFarland, Jack W.;
- Lennon, Niall J.;
- Nusbaum, Chad;
- Ruess, Roger W.
Publication type:
Article
Endurance, Refuge, and Reemergence of Dengue Virus Type 2, Puerto Rico, 1986-2007.
Published in:
Emerging Infectious Diseases, 2011, v. 17, n. 1, p. 64, doi. 10.3201/eid1701.100961
By:
- McElroy, Kate L.;
- Santiago, Gilberto A.;
- Lennon, Niall J.;
- Birren, Bruce W.;
- Henn, Matthew R.;
- Muñoz-Jordán, Jorge L.
Publication type:
Article
Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer.
Published in:
Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00895-x
By:
- 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.
Publication type:
Article
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Published in:
Nature Biotechnology, 2014, v. 32, n. 4, p. 381, doi. 10.1038/nbt.2859
By:
- Trapnell, Cole;
- Cacchiarelli, Davide;
- Grimsby, Jonna;
- Pokharel, Prapti;
- Li, Shuqiang;
- Morse, Michael;
- Lennon, Niall J;
- Livak, Kenneth J;
- Mikkelsen, Tarjei S;
- Rinn, John L
Publication type:
Article
Whole Genome Pyrosequencing of Rare Hepatitis C Virus Genotypes Enhances Subtype Classification and Identification of Naturally Occurring Drug Resistance Variants.
Published in:
Journal of Infectious Diseases, 2013, v. 208, n. 1, p. 17, doi. 10.1093/infdis/jis679
By:
- 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.
Publication type:
Article
Reemergence and Decline of Dengue Virus Serotype 3 in Puerto Rico.
Published in:
Journal of Infectious Diseases, 2012, v. 206, n. 6, p. 893, doi. 10.1093/infdis/jis426
By:
- Santiago, Gilberto A.;
- McElroy-Horne, Kate;
- Lennon, Niall J.;
- Santiago, Luis M.;
- Birren, Bruce W.;
- Henn, Matthew R.;
- Muñoz-Jordán, Jorge L.
Publication type:
Article
Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease.
Published in:
NPJ Genomic Medicine, 2020, v. 5, n. 1, p. N.PAG, doi. 10.1038/s41525-020-00154-9
By:
- Marshall, Christian R.;
- Chowdhury, Shimul;
- Taft, Ryan J.;
- Lebo, Mathew S.;
- Buchan, Jillian G.;
- Harrison, Steven M.;
- Rowsey, Ross;
- Klee, Eric W.;
- Liu, Pengfei;
- Worthey, Elizabeth A.;
- Jobanputra, Vaidehi;
- Dimmock, David;
- Kearney, Hutton M.;
- Bick, David;
- Kulkarni, Shashikant;
- Taylor, Stacie L.;
- Belmont, John W.;
- Stavropoulos, Dimitri J.;
- Lennon, Niall J.
Publication type:
Article
Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data.
Published in:
PLoS Computational Biology, 2012, v. 8, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002417
By:
- Macalalad, Alexander R.;
- Zody, Michael C.;
- Charlebois, Patrick;
- Lennon, Niall J.;
- Newman, Ruchi M.;
- Malboeuf, Christine M.;
- Ryan, Elizabeth M.;
- Boutwell, Christian L.;
- Power, Karen A.;
- Brackney, Doug E.;
- Pesko, Kendra N.;
- Levin, Joshua Z.;
- Ebel, Gregory D.;
- Allen, Todd M.;
- Birren, Bruce W.;
- Henn, Matthew R.
Publication type:
Article
Characterizing and measuring bias in sequence data.
Published in:
Genome Biology, 2013, v. 14, n. 5, p. 1, doi. 10.1186/gb-2013-14-5-r51
By:
- Ross, Michael G.;
- Russ, Carsten;
- Costello, Maura;
- Hollinger, Andrew;
- Lennon, Niall J.;
- Hegarty, Ryan;
- Nusbaum, Chad;
- Jaffe, David B.
Publication type:
Article
Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms.
Published in:
2018
By:
- 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
Publication type:
Abstract
Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.
Published in:
PLoS Pathogens, 2016, v. 12, n. 5, p. 1, doi. 10.1371/journal.ppat.1005619
By:
- Tully, Damien C.;
- Ogilvie, Colin B.;
- Batorsky, Rebecca E.;
- Bean, David J.;
- Power, Karen A.;
- Ghebremichael, Musie;
- Bedard, Hunter E.;
- Gladden, Adrianne D.;
- Seese, Aaron M.;
- Amero, Molly A.;
- Lane, Kimberly;
- McGrath, Graham;
- Bazner, Suzane B.;
- Tinsley, Jake;
- Lennon, Niall J.;
- Henn, Matthew R.;
- Brumme, Zabrina L.;
- Norris, Philip J.;
- Rosenberg, Eric S.;
- Mayer, Kenneth H.
Publication type:
Article
Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection.
Published in:
PLoS Pathogens, 2012, v. 8, n. 3, p. 1, doi. 10.1371/journal.ppat.1002529
By:
- Henn, Matthew R.;
- Boutwell, Christian L.;
- Charlebois, Patrick;
- Lennon, Niall J.;
- Power, Karen A.;
- Macalalad, Alexander R.;
- Berlin, Aaron M.;
- Malboeuf, Christine M.;
- Ryan, Elizabeth M.;
- Gnerre, Sante;
- Zody, Michael C.;
- Erlich, Rachel L.;
- Green, Lisa M.;
- Berical, Andrew;
- Wang, Yaoyu;
- Casali, Monica;
- Streeck, Hendrik;
- Bloom, Allyson K.;
- Dudek, Tim;
- Tully, Damien
Publication type:
Article
Endemic Dengue Associated with the Co-Circulation of Multiple Viral Lineages and Localized Density- Dependent Transmission.
Published in:
PLoS Pathogens, 2011, v. 7, n. 6, p. 1, doi. 10.1371/journal.ppat.1002064
By:
- Raghwani, Jayna;
- Rambaut, Andrew;
- Holmes, Edward C.;
- Vu Ty Hang;
- Tran Tinh Hien;
- Farrar, Jeremy;
- Wills, Bridget;
- Lennon, Niall J.;
- Birren, Bruce W.;
- Henn, Matthew R.;
- Simmons, Cameron P.
Publication type:
Article
Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans.
Published in:
Human Molecular Genetics, 2012, v. 21, n. 19, p. 4334, doi. 10.1093/hmg/dds226
By:
- McLaren, Paul J.;
- Ripke, Stephan;
- Pelak, Kimberly;
- Weintrob, Amy C.;
- Patsopoulos, Nikolaos A.;
- Jia, Xiaoming;
- Erlich, Rachel L.;
- Lennon, Niall J.;
- Kadie, Carl M.;
- Heckerman, David;
- Gupta, Namrata;
- Haas, David W.;
- Deeks, Steven G.;
- Pereyra, Florencia;
- Walker, Bruce D.;
- de Bakker, Paul I. W.
Publication type:
Article
Dynamics of Dengue Disease Severity Determined by the Interplay Between Viral Genetics and Serotype-Specific Immunity.
Published in:
Science Translational Medicine, 2011, v. 3, n. 114, p. 1, doi. 10.1126/scitranslmed.3003084
By:
- 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
Publication type:
Article
Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations.
Published in:
Nature, 2012, v. 488, n. 7409, p. 106, doi. 10.1038/nature11329
By:
- Pugh, Trevor J.;
- Weeraratne, Shyamal Dilhan;
- Archer, Tenley C.;
- Pomeranz Krummel, Daniel A.;
- Auclair, Daniel;
- Bochicchio, James;
- Carneiro, Mauricio O.;
- Carter, Scott L.;
- Cibulskis, Kristian;
- Erlich, Rachel L.;
- Greulich, Heidi;
- Lawrence, Michael S.;
- Lennon, Niall J.;
- McKenna, Aaron;
- Meldrim, James;
- Ramos, Alex H.;
- Ross, Michael G.;
- Russ, Carsten;
- Shefler, Erica;
- Sivachenko, Andrey
Publication type:
Article
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.
Published in:
PLoS Neglected Tropical Diseases, 2010, v. 4, n. 7, p. 1, doi. 10.1371/journal.pntd.0000757
By:
- Ty Hang, Vu Thi;
- Holmes, Edward C.;
- Veasna, Duong;
- Quy, Nguyen Thien;
- Tinh Hien, Tran;
- 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.
Publication type:
Article
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.
Published in:
PLoS Neglected Tropical Diseases, 2010, v. 4, n. 7, p. 1, doi. 10.1371/journal.pntd.0000757
By:
- Vu Thi Ty Hang;
- Holmes, Edward C.;
- Veasna, Duong;
- 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.
Publication type:
Article
Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach.
Published in:
Molecular Ecology Resources, 2008, v. 8, n. 4, p. 742, doi. 10.1111/j.1755-0998.2008.02094.x
By:
- TAYLOR, D. LEE;
- BOOTH, MICHAEL G.;
- MCFARLAND, JACK W.;
- HERRIOTT, IAN C.;
- LENNON, NIALL J.;
- NUSBAUM, CHAD;
- MARR, THOMAS G.
Publication type:
Article
Cross-Sectional Assessment of SARS-CoV-2 Viral Load by Symptom Status in Massachusetts Congregate Living Facilities.
Published in:
2021
By:
- Lennon, Niall J;
- Bhattacharyya, Roby P;
- Mina, Michael J;
- Rehm, Heidi L;
- Hung, Deborah T;
- Smole, Sandra;
- Woolley, Ann;
- Lander, Eric S;
- Gabriel, Stacey B
Publication type:
journal article
De novo assembly of highly diverse viral populations.
Published in:
BMC Genomics, 2012, v. 13, n. 1, p. 475, doi. 10.1186/1471-2164-13-475
By:
- Xiao Yang;
- Charlebois, Patrick;
- Gnerre, Sante;
- Coole, Matthew G.;
- Lennon, Niall J.;
- Levin, Joshua Z.;
- Qu, James;
- Ryan, Elizabeth M.;
- Zody, Michael C.;
- Henn, Matthew R.
Publication type:
Article
Next-generation sequencing for HLA typing of class I loci.
Published in:
BMC Genomics, 2011, v. 12, n. 1, p. 42, doi. 10.1186/1471-2164-12-42
By:
- Erlich, Rachel L.;
- Xiaoming Jia;
- Anderson, Scott;
- Banks, Eric;
- Xiaojiang Gao;
- Carrington, Mary;
- Gupta, Namrata;
- DePristo, Mark A.;
- Henn, Matthew R.;
- Lennon, Niall J.;
- de Bakker, Paul I. W.
Publication type:
Article
PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.
Published in:
Bioinformatics, 2011, v. 27, n. 2, p. 266, doi. 10.1093/bioinformatics/btq624
By:
- Yu, Qing;
- Ryan, Elizabeth M.;
- Allen, Todd M.;
- Birren, Bruce W.;
- Henn, Matthew R.;
- Lennon, Niall J.
Publication type:
Article
Technological considerations for genome-guided diagnosis and management of cancer.
Published in:
Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0370-4
By:
- Lennon, Niall J.;
- Adalsteinsson, Viktor A.;
- Gabriel, Stacey B.
Publication type:
Article

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