Amanda Birmingham

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Rob KnightWolfe Family Chair at Rady Children's; Director, Center for Microbiome Innovation; Professor, UCSDVerifisert e-postadresse på ucsd.edu
Anastasia KhvorovaUMASS Medical SchoolVerifisert e-postadresse på umassmed.edu
Catherine LozuponeAssociate Professor of Medicine, University of Colorado, DenverVerifisert e-postadresse på ucdenver.edu
Angela ReynoldsBio-TechneVerifisert e-postadresse på bio-techne.com
Antonio GonzálezProgrammer Analyst, UC San DiegoVerifisert e-postadresse på ucsd.edu
Yuriy FedorovCase Western Reserve UniversityVerifisert e-postadresse på case.edu
Zhenjiang Zech Xustate key lab of food science and resources, nuVerifisert e-postadresse på ucsd.edu
Yoshiki Vázquez-BaezaBiomeSenseVerifisert e-postadresse på biomesense.com
Jesse RR ZaneveldAssociate Professor, Division of Biological Sciences, University of Washington, BothellVerifisert e-postadresse på uw.edu
Kyle BittingerUniversity of PennsylvaniaVerifisert e-postadresse på mail.med.upenn.edu
Trey IdekerUniversity of California San DiegoVerifisert e-postadresse på ucsd.edu
Prashant MaliProfessor, Bioengineering Department, UCSDVerifisert e-postadresse på ucsd.edu
Jens LuebeckUniversity of California San DiegoVerifisert e-postadresse på ucsd.edu
Daniel McDonaldAmerican Gut, Knight Lab, Department of Pediatrics, UCSDVerifisert e-postadresse på ucsd.edu
Kathleen Fisch, Ph.D.University of California, San Diego, Department of Obstetrics, Gynecology & Reproductive SciencesVerifisert e-postadresse på ucsd.edu
Roderick BeijersbergenThe Netherlands Cancer InstituteVerifisert e-postadresse på nki.nl
Javier Santoyo-LopezEdinburgh GenomicsVerifisert e-postadresse på ed.ac.uk
Dara J. DunicanDublin City UniversityVerifisert e-postadresse på dcu.ie
John Paul ShenAssistant Professor, University of Texas MD Anderson Cancer CenterVerifisert e-postadresse på alum.mit.edu
Caroline E. ShamuHarvard Medical SchoolVerifisert e-postadresse på hms.harvard.edu

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Amanda Birmingham

Senior Bioinformatics Programmer; University of California, San Diego

Verifisert e-postadresse på ucsd.edu

Bioinformatics microbiome cloud computing RNAi high-throughput screening


Tittel Sorter etter sitater Sorter etter år Sorter etter tittel	Sitert av Sitert av	År
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	1985	2017
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	1211	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	1063	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	719	2016
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	691	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	686	2006
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	387	2017
[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	346*	2021
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	342	2020
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	285	2007
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	235	2007
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	210	2015
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	199	2015
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	196	2021
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	186	2008
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	172*	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	143	2002
Context and the human microbiome D McDonald, A Birmingham, R Knight Microbiome 3 (1), 1-8, 2015	100	2015
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	99	2018
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	55	2017

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