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    Amanda Birmingham

    TitleProgrammer Analyst 4
    SchoolUniversity of California, San Diego
    Address9500 Gilman Drive #0681
    CA La Jolla 92093
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun; 14(6):573-576. PMID: 28319113.
        View in: PubMed
      2. Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 2016 Jul; 10(7):1669-81. PMID: 26905627.
        View in: PubMed
      3. McDonald D, Birmingham A, Knight R. Context and the human microbiome. Microbiome. 2015 Nov 04; 3:52. PMID: 26530830; PMCID: PMC4632476.
      4. Anderson EM, Haupt A, Schiel JA, Chou E, Machado HB, Strezoska Ž, Lenger S, McClelland S, Birmingham A, Vermeulen A, Smith Av. Systematic analysis of CRISPR-Cas9 mismatch tolerance reveals low levels of off-target activity. J Biotechnol. 2015 Oct 10; 211:56-65. PMID: 26189696.
        View in: PubMed
      5. Barrangou R, Birmingham A, Wiemann S, Beijersbergen RL, Hornung V, Smith Av. Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference. Nucleic Acids Res. 2015 Apr 20; 43(7):3407-19. PMID: 25800748; PMCID: PMC4402539.
      6. Stombaugh J, Licon A, Strezoska Ž, Stahl J, Anderson SB, Banos M, van Brabant Smith A, Birmingham A, Vermeulen A. The Power Decoder Simulator for the Evaluation of Pooled shRNA Screen Performance. J Biomol Screen. 2015 Sep; 20(8):965-75. PMID: 25777298; PMCID: PMC4543901.
      7. Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, Zirbel CL, Laederach A. Sharing and archiving nucleic acid structure mapping data. RNA. 2011 Jul; 17(7):1204-12. PMID: 21610212; PMCID: PMC3138558.
      8. Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, Laederach A. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Stand Genomic Sci. 2011 Apr 29; 4(2):252-6. PMID: 21677862; PMCID: PMC3111981.
      9. Kwan P, Birmingham A. NoiseMaker: simulated screens for statistical assessment. Bioinformatics. 2010 Oct 01; 26(19):2484-5. PMID: 20702398; PMCID: PMC2944205.
      10. Birmingham A, Selfors LM, Forster T, Wrobel D, Kennedy CJ, Shanks E, Santoyo-Lopez J, Dunican DJ, Long A, Kelleher D, Smith Q, Beijersbergen RL, Ghazal P, Shamu CE. Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods. 2009 Aug; 6(8):569-75. PMID: 19644458; NIHMSID: NIHMS159092.
        View in: PubMed
      11. Brown JW, Birmingham A, Griffiths PE, Jossinet F, Kachouri-Lafond R, Knight R, Lang BF, Leontis N, Steger G, Stombaugh J, Westhof E. The RNA structure alignment ontology. RNA. 2009 Sep; 15(9):1623-31. PMID: 19622678; PMCID: PMC2743057.
      12. Peirce JL, Broman KW, Lu L, Chesler EJ, Zhou G, Airey DC, Birmingham A, Williams RW. Genome Reshuffling for Advanced Intercross Permutation (GRAIP): simulation and permutation for advanced intercross population analysis. PLoS One. 2008 Apr 23; 3(4):e1977. PMID: 18431467; PMCID: PMC2295257.
      13. Anderson EM, Birmingham A, Baskerville S, Reynolds A, Maksimova E, Leake D, Fedorov Y, Karpilow J, Khvorova A. Experimental validation of the importance of seed complement frequency to siRNA specificity. RNA. 2008 May; 14(5):853-61. PMID: 18367722; PMCID: PMC2327361.
      14. Birmingham A, Anderson E, Sullivan K, Reynolds A, Boese Q, Leake D, Karpilow J, Khvorova A. A protocol for designing siRNAs with high functionality and specificity. Nat Protoc. 2007; 2(9):2068-78. PMID: 17853862.
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      15. Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA. PyCogent: a toolkit for making sense from sequence. Genome Biol. 2007; 8(8):R171. PMID: 17708774; PMCID: PMC2375001.
      16. Fedorov Y, Anderson EM, Birmingham A, Reynolds A, Karpilow J, Robinson K, Leake D, Marshall WS, Khvorova A. Off-target effects by siRNA can induce toxic phenotype. RNA. 2006 Jul; 12(7):1188-96. PMID: 16682561; PMCID: PMC1484448.
      17. Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, Fedorov Y, Baskerville S, Maksimova E, Robinson K, Karpilow J, Marshall WS, Khvorova A. 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods. 2006 Mar; 3(3):199-204. PMID: 16489337.
        View in: PubMed
      18. Knight R, Birmingham A, Yarus M. BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences. RNA. 2004 Sep; 10(9):1323-36. PMID: 15317972; PMCID: PMC1370620.
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