Amanda Birmingham
Amanda Birmingham
Senior Bioinformatics Engineer; University of California, San Diego
Verified email at
Cited by
Cited by
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
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
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
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
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
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
Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions
JP Shen, D Zhao, R Sasik, J Luebeck, A Birmingham, ...
Nature methods, 2017
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
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
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
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
Circumstellar Disk Candidates Identified in NGC 2264
LM Rebull, RB Makidon, SE Strom, LA Hillenbrand, A Birmingham, ...
The Astronomical Journal 123 (3), 1528, 2002
Circumstellar Disk Candidates Identified in NGC 2264
LM Rebull, RB Makidon, SE Strom, LA Hillenbrand, A Birmingham, ...
Bulletin of the American Astronomical Society 33, 1435, 2001
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
Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data
SJ Weiss, Z Xu, A Amir, S Peddada, K Bittinger, A Gonzalez, C Lozupone, ...
PeerJ PrePrints, 2015
Context and the human microbiome
D McDonald, A Birmingham, R Knight
Microbiome 3 (1), 1-8, 2015
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
BayesFold: rational 2 folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences
R Knight, A Birmingham, M Yarus
Rna 10 (9), 1323-1336, 2004
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
The RNA structure alignment ontology
JW Brown, A Birmingham, PE Griffiths, F Jossinet, R Kachouri-Lafond, ...
RNA 15 (9), 1623-1631, 2009
The system can't perform the operation now. Try again later.
Articles 1–20