Publications by authors named "Birgitte B Simen"

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Notes from the Field: Early Identification of the SARS-CoV-2 Omicron BA.2.86 Variant by the Traveler-Based Genomic Surveillance Program - Dulles International Airport, August 2023.
Stephen M Bart, Andrew P Rothstein, Casandra W Philipson, Teresa C Smith, Birgitte B Simen

MMWR Morb Mortal Wkly Rep· October 2023

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Early Detection of Severe Acute Respiratory Syndrome Coronavirus 2 Variants Using Traveler-based Genomic Surveillance at 4 US Airports, September 2021-January 2022.
Renee D Wegrzyn, Grace D Appiah, Robert Morfino, Scott R Milford, Allison Taylor Walker, Birgitte B Simen

Clin Infect Dis· February 2023

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Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.
Jasmijn A Baaijens, Alessandro Zulli, Isabel M Ott, Ioanna Nika, Mart J van der Lugt, Birgitte B Simen

Genome Biol· November 2022

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Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification.
Jasmijn A Baaijens, Alessandro Zulli, Isabel M Ott, Mary E Petrone, Tara Alpert, Birgitte B Simen

medRxiv· September 2021

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Designing and Implementing NGS Tests for Inherited Disorders: A Practical Framework with Step-by-Step Guidance for Clinical Laboratories.
Avni Santani, Birgitte B Simen, Marian Briggs, Matthew Lebo, Jason D Merker

J Mol Diagn· May 2019

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A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing.
Elizabeth P St John, Birgitte B Simen, Gregory S Turenchalk, Michael S Braverman, Isabella Abbate

PLoS One· July 2016

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Validation of a next-generation-sequencing cancer panel for use in the clinical laboratory.
Birgitte B Simen, Lina Yin, Chirayu P Goswami, Kathleen O Davis, Renu Bajaj

Arch Pathol Lab Med· April 2015

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Deep sequencing of HIV-1 variants from paired plasma and cerebrospinal fluid during primary HIV infection.
Arjet Gega, Michael J Kozal, Jennifer Chiarella, Evelyn Lee, Julia Peterson, Birgitte B Simen

J Virus Erad· January 2015

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Low-frequency NNRTI-resistant HIV-1 variants and relationship to mutational load in antiretroviral-naïve subjects.
Shaili Gupta, Max Lataillade, Tassos C Kyriakides, Jennifer Chiarella, Elizabeth P St John, Birgitte B Simen

Viruses· September 2014

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An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing.
Birgitte B Simen, Michael S Braverman, Isabella Abbate, Jeroen Aerssens, Yannick Bidet

J Virol Methods· August 2014

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Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements.
Katherine J L Jackson, Yi Liu, Krishna M Roskin, Jacob Glanville, Ramona A Hoh, Birgitte B Simen

Cell Host Microbe· July 2014

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The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies.
Devin Sok, Uri Laserson, Jonathan Laserson, Yi Liu, Francois Vigneault, Birgitte B Simen

PLoS Pathog· June 2014

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High-resolution antibody dynamics of vaccine-induced immune responses.
Uri Laserson, Francois Vigneault, Daniel Gadala-Maria, Gur Yaari, Mohamed Uduman, Birgitte B Simen

Proc Natl Acad Sci U S A· April 2014

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Next generation sequencing reveals the association of DRB3*02:02 with type 1 diabetes.
Henry A Erlich, Ana Maria Valdes, Shana L McDevitt, Birgitte B Simen, Lisbeth A Blake

Diabetes· July 2013

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Therapy failure resulting from superinfection by a drug-resistant HIV variant.
Marieke Pingen, Jan L Nouwen, Sander Dinant, Jan Albert, Mattias Mild, Birgitte B Simen

Antivir Ther· June 2013

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Convergent antibody signatures in human dengue.
Poornima Parameswaran, Yi Liu, Krishna M Roskin, Katherine K L Jackson, Vaishali P Dixit, Birgitte B Simen

Cell Host Microbe· June 2013

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Assuring the quality of next-generation sequencing in clinical laboratory practice.
Amy S Gargis, Lisa Kalman, Meredith W Berry, David P Bick, David P Dimmock, Birgitte B Simen

Nat Biotechnol· November 2012

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Prevalence of low-level HIV-1 variants with reverse transcriptase mutation K65R and the effect of antiretroviral drug exposure on variant levels.
Michael J Kozal, Jennifer Chiarella, Elizabeth P St John, Elizabeth A Moreno, Birgitte B Simen

Antivir Ther· January 2012

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Use of dried-blood-spot samples and in-house assays to identify antiretroviral drug resistance in HIV-infected children in resource-constrained settings.
Carrie Ziemniak, Yohannes Mengistu, Andrea Ruff, Ya-Hui Chen, Leila Khaki, Birgitte B Simen

J Clin Microbiol· December 2011

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High-throughput sequencing of PCR products tagged with universal primers using 454 life sciences systems.
Derek Daigle, Birgitte B Simen, Pascale Pochart

Curr Protoc Mol Biol· October 2011

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Initial antibodies binding to HIV-1 gp41 in acutely infected subjects are polyreactive and highly mutated.
Hua-Xin Liao, Xi Chen, Supriya Munshaw, Ruijun Zhang, Dawn J Marshall, Birgitte B Simen

J Exp Med· October 2011

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Characterization of Mauritian cynomolgus macaque major histocompatibility complex class I haplotypes by high-resolution pyrosequencing.
Melisa L Budde, Roger W Wiseman, Julie A Karl, Bozena Hanczaruk, Birgitte B Simen

Immunogenetics· December 2010

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Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements.
Scott D Boyd, Bruno A Gaëta, Katherine J Jackson, Andrew Z Fire, Eleanor L Marshall, Birgitte B Simen

J Immunol· June 2010

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Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing.
Scott D Boyd, Eleanor L Marshall, Jason D Merker, Jay M Maniar, Lyndon N Zhang, Birgitte B Simen

Sci Transl Med· December 2009

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Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors.
Vici Varghese, Rajin Shahriar, Soo-Yon Rhee, Tommy Liu, Birgitte B Simen

J Acquir Immune Defic Syndr· November 2009

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