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Amanda Birmingham
Amanda Birmingham
Senior Bioinformatics Programmer; University of California, San Diego
Verified email at ucsd.edu
Title
Cited by
Cited by
Year
Normalization and microbial differential abundance strategies depend upon data characteristics
S Weiss, ZZ Xu, S Peddada, A Amir, K Bittinger, A Gonzalez, C Lozupone, ...
Microbiome 5 (1), 1-18, 2017
17972017
3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets
A Birmingham, EM Anderson, A Reynolds, D Ilsley-Tyree, D Leake, ...
Nature methods 3 (3), 199-204, 2006
11752006
Adipose Tissue Macrophage-Derived Exosomal miRNAs Can Modulate In Vivo and In Vitro Insulin Sensitivity
W Ying, M Riopel, G Bandyopadhyay, Y Dong, A Birmingham, JB Seo, ...
Cell 171 (2), 372-384. e12, 2017
9402017
Statistical methods for analysis of high-throughput RNA interference screens
A Birmingham, LM Selfors, T Forster, D Wrobel, CJ Kennedy, E Shanks, ...
Nature Methods 6 (8), 569-575, 2009
6732009
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
S Weiss, W Van Treuren, C Lozupone, K Faust, J Friedman, Y Deng, ...
The ISME journal 10 (7), 1669-1681, 2016
6632016
Off-target effects by siRNA can induce toxic phenotype
Y Fedorov, EM Anderson, A Birmingham, A Reynolds, J Karpilow, ...
Rna 12 (7), 1188-1196, 2006
6552006
Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions
JP Shen, D Zhao, R Sasik, J Luebeck, A Birmingham, ...
Nature methods 14 (6), 573-576, 2017
3582017
A protocol for designing siRNAs with high functionality and specificity
A Birmingham, E Anderson, K Sullivan, A Reynolds, Q Boese, D Leake, ...
Nature protocols 2 (9), 2068-2078, 2007
2672007
QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data
M Estaki, L Jiang, NA Bokulich, D McDonald, A González, T Kosciolek, ...
Current Protocols in Bioinformatics 70 (1), e100, 2020
2582020
[Preprint] Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission
S Karthikeyan, JI Levy, P De Hoff, G Humphrey, A Birmingham, K Jepsen, ...
medRxiv, 2021
235*2021
PyCogent: a toolkit for making sense from sequence
R Knight, P Maxwell, A Birmingham, J Carnes, JG Caporaso, BC Easton, ...
Genome biology 8 (8), 1-16, 2007
2242007
Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference
R Barrangou, A Birmingham, S Wiemann, RL Beijersbergen, V Hornung, ...
Nucleic acids research 43 (7), 3407-3419, 2015
1952015
Resurgence of SARS-CoV-2 infection in a highly vaccinated health system workforce
J Keehner, LE Horton, NJ Binkin, LC Laurent, ...
New England Journal of Medicine 385 (14), 1330-1332, 2021
1902021
Systematic analysis of CRISPR–Cas9 mismatch tolerance reveals low levels of off-target activity
EM Anderson, A Haupt, JA Schiel, E Chou, HB Machado, Ž Strezoska, ...
Journal of biotechnology 211, 56-65, 2015
1852015
Experimental validation of the importance of seed complement frequency to siRNA specificity
EM Anderson, A Birmingham, S Baskerville, A Reynolds, E Maksimova, ...
Rna 14 (5), 853-861, 2008
1812008
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks
A Rule, A Birmingham, C Zuniga, I Altintas, SC Huang, R Knight, ...
PLoS computational biology 15 (7), 2019
152*2019
Circumstellar disk candidates identified in NGC 2264
LM Rebull, RB Makidon, SE Strom, LA Hillenbrand, A Birmingham, ...
The Astronomical Journal 123 (3), 1528, 2002
1442002
Context and the human microbiome
D McDonald, A Birmingham, R Knight
Microbiome 3 (1), 1-8, 2015
962015
Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis
D Zhao, MG Badur, J Luebeck, JH Magaña, A Birmingham, R Sasik, ...
Molecular cell 69 (4), 699-708. e7, 2018
932018
HIV-1 TAT protein enhances sensitization to methamphetamine by affecting dopaminergic function
JP Kesby, JA Najera, B Romoli, Y Fang, L Basova, A Birmingham, ...
Brain, behavior, and immunity 65, 210-221, 2017
482017
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