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I am a software developer and data analyst with >10 years' technical management experience. I work as a Senior Bioinformatics Engineer in the Center for Computational Biology and Bioinformatics at the University of California, San Diego. My resume is available here.

PUBLICATIONS
Peer-reviewed
  1. Barrangou, R.*, Birmingham, A.*, Wiemann, S., Beijersbergen, R., Hornung, V., & Smith, A. (In press). Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference. Nucleic Acids Research. [*Co-first authors]
  2. Stombaugh, J., Licon, A., Strezoska, Z., Stahl, J., Anderson, S.B., Banos, M., Smith, A., Birmingham, A., & Vermeulen, A. (In press). The Power Decoder simulator for the evaluation of pooled shRNA screen performance. Journal of Biomolecular Screening.
  3. Birmingham, A.*, Kaufmann, A.*, & Kozak, K.* (2014). RNAi and off-target effects. Frontiers in RNAi, Vol. 1, 3-20. [*Co-first authors]
  4. Schmidt, E.E., Banos, M.S., Smith, J.A., Birmingham, A., Boutros, M., & Shamu, C.E. Public repositories for RNAi screening data. Frontiers in RNAi, Vol. 1, 40-57.
  5. Rocca-Serra, P., Bellaousov, S., Birmingham, A., Chen, C., Cordero, P., Das, R., Davis-Neulander, L., Duncan, C. D., Halvorsen, M., Knight, R., Leontis, N. B., Mathews, D. H., Ritz, J., Stombaugh, J., Weeks, K. M., Zirbel, C. L., & Laederach, A. (2011). Sharing and archiving nucleic acid structure mapping data. RNA, 17(7), 1204-1212.
  6. Birmingham, A., Clemente, J. C., Desai, N., Gilbert, J., Gonzalez, A., Kyrpides, N., Meyer, F., Nawrocki, E., Sterk, P., Stombaugh, J., Weinberg, Z., Wendel, D., Leontis, N. B., Zirbel, C., Knight, R., & Laederach, A. (2011). Meeting report of the RNA Ontology Consortium January 8-9, 2011. Standards in Genomic Sciences, 4(2), 252.
  7. Kwan, P., & Birmingham, A. (2010). NoiseMaker: Simulated Screens for Statistical Assessment. Bioinformatics, 26(19), 2484-2485.
  8. Birmingham, A., Selfors, L. M., Forster, T., Wrobel, D., Kennedy, C. J., Shanks, E., Santoyo-Lopez, J., Dunican, D. J., Long, A., Kelleher, D., Smith, Q., Beijersbergen, R. L., Ghazal, P., & Shamu, C. E. (2009). Statistical methods for analysis of high-throughput RNA interference screens. Nature Methods, 6(8), 569-575.
  9. Brown, J. W., Birmingham, A., Griffiths, P. E., Jossinet, F., Kachouri-Lafond, R., Knight, R., Lang, B. F., Leontis, N., Steger, G., Stombaugh, J., & Westhof, E. (2009). The RNA structure alignment ontology. RNA, 15(9), 1623-1631.
  10. Anderson, E. M., Birmingham, A., Baskerville, S., Reynolds, A., Maksimova, E., Leake, D., Fedorov, Y., Karpilow, J., & Khvorova, A. (2008). Experimental validation of the importance of seed complement frequency to siRNA specificity. RNA, 14(5), 853-861.
  11. Peirce, J. L., Broman, K. W., Lu, L., Chesler, E. J., Zhou, G., Airey, D. C., Birmingham, A. E., & Williams, R. W. (2008). Genome Reshuffling for Advanced Intercross Permutation (GRAIP): simulation and permutation for advanced intercross population analysis. PLoS One, 3(4), e1977.
  12. Birmingham, A., Anderson, E., Sullivan, K., Reynolds, A., Boese, Q., Leake, D., Karpilow, J., & Khvorova, A. (2007). A protocol for designing siRNAs with high functionality and specificity. Nature Protocols, 2(9), 2068-2078.
  13. Knight, R., Maxwell, P., Birmingham, A., Carnes, J., Caporaso, J. G., Easton, B. C., Eaton, M., Hamady, M., Lindsay, H., Liu, Z., Lozupone, C., McDonald, D., Robeson, M., Sammut, R., Smit, S., Wakefield, M. J., Widmann, J., Wikman, S., Wilson, S., Ying, H., & Huttley, G. A. (2007). PyCogent: a toolkit for making sense from sequence. Genome Biology, 8(8), R171.
  14. Fedorov, Y., Anderson, E., Birmingham, A., Reynolds, A., Karpilow, J., Robinson, K., Leake, D., Marshall, W.S., & Khvorova, A. (2006). Off-target effects by siRNA can induce toxic phenotype. RNA, 12(7), 1188-1196.
  15. Birmingham, A., Anderson, E. M., Reynolds, A., Ilsley-Tyree, D., Leake, D., Fedorov, Y., Baskerville, S., Maksimova, E., Robinson, K., Karpilow, J., Marshall, W. S., & Khvorova, A. (2006). 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nature Methods, 3(3), 199-204.
  16. Birmingham, A., Anderson, E. M., Marshall, W. S., & Khvorova, A. (2005, August). Maximum sequence alignment fails to predict off-targeted gene regulation by RNAi. In Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE (pp. 233-234). IEEE.
  17. Knight, R., Birmingham, A., & Yarus, M. (2004). BayesFold: rational 2° folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences. RNA, 10(9), 1323-1336.
  18. Rebull, L. M., Makidon, R. B., Strom, S. E., Hillenbrand, L. A., Birmingham, A., Patten, B. M., Jones, B. F., Yagi, H., & Adams, Mark T. (2002). Circumstellar Disk Candidates Identified in NGC 2264. The Astronomical Journal, 123(3), 1528-1547.
  19. Rebull, L. M., Makidon, R. B., Strom, S. E., Hillenbrand, L. A., Birmingham, A., Patten, B. M., Jones, B. F., Yagi, H., & Adams, MT. (2001). Circumstellar Disk Candidates Identified in NGC 2264. Bulletin of the American Astronomical Society, 33(4), 1435.

Non-peer-reviewed
  1. de Zwart, I., Lozupone, C., Knight, R., Birmingham, A., Illangasekare, M., Jadhav, V., Legiewicz, M., Majerfeld, I., Widmann, J., & Yarus, M. (2005). Artificial Selection: Finding Function amongst Randomized Sequences. Handbook of RNA Biochemistry, 783-806.
  2. Birmingham, A. (2002). Of Astronomical Proportions, Science, 298(5594), 859. [Product review].
  3. Birmingham, A. (1997). On the Star Formation History of the Rho Ophiuchus Molecular Cloud Complex. [Undergraduate thesis, Amherst College, Amherst, MA].

PATENTS
  1. Kelley, M., Birmingham, A., Karpilow, J., Khvorova, A., & Sullivan, K. "Micro-RNA scaffolds, non-naturally occurring micro-RNAs, and methods for optimizing non-naturally occurring micro-RNAs".
    • US Patent 8,841,267
    • European Patent 2,155,911
  2. Kelley, M., Birmingham, A., Karpilow, J., Khvorova, A., & Sullivan, K. "Micro-RNA scaffolds and non-naturally occurring micro-RNAs".
    • European Patent 2,160,477
    • Chinese Patent 2,687,336

PRESENTATIONS AT PROFESSIONAL MEETINGS
Talks
2014 "Targeting and Off-targeting of Long Non-coding RNAs by siRNAs". RNAi Global Initiative, 16th Meeting.
2014 "Riding the Data Wave: Analysis of High-Throughput RNAi Screens". RNAi Global Initiative, 16th Meeting.
2014 "Targeting and Off-targeting of Long Non-coding RNAs by siRNAs". Long Noncoding RNAs: Marching Toward Mechanism (Keystone Symposium).
2013 "Methods for Analysis of High-Throughput RNAi Screens". RNA, MicroRNAs & Single Cell Biology, 10th Meeting.
2013 "Riding the Data Wave: Analysis of High-Throughput RNAi Screens". RNAi Global Initiative, 15th Meeting.
2012 "High-Throughput Screening Data Analysis Workflow". RNAi Global Initiative, 14th Meeting.
2011 "Seed Enrichment in High-Throughput Screening Hits Demonstrates That miRNA-like Off- Targets Are Assay-Specific". RNA Society, 15th Annual Meeting.
2011 "Better Than the Real Thing: In Silico Screens for Statistical Selection". RNAi Global Initiative, 12th Meeting.
2011 Invited Talk: "Better Than the Real Thing: In Silico Screens for Statistical Selection". The IAENG International Conference on Bioinformatics 2011, part of The International MultiConference of Engineers and Computer Scientists 2011, 6th Annual Meeting.
2010 "The Hit List Mystery: Why We Need Public Data Deposition". RNAi Global Initiative, 11th Meeting.
2010 Invited Talk: "Computational Assessment of Screening Statistics for RNAi". Biomolecular Screening: Advanced Applications Across Academia, Government, and Industry (SBS Symposium).
2010 "Computational Assessment of Screening Statistics". Intelligent Systems in Molecular Biology (ISMB) 2010, 18th Annual Meeting.
2010 "Pathway Analysis Guidelines Project". RNAi Global Initiative, 10th Meeting.
2009 "Searching Seed-Space: Automated Seed Cluster Identification in Screen Results". RNAi Global Initiative, 9th Meeting.
2009 "Tomorrow, the World!: Toward World-wide Data Sharing Through NCBI". RNAi Global Initiative, 8th Meeting.
2008 "Rise of the Machines: Machine Learning for High Content Data Analysis". RNAi Global Initiative, 7th Meeting.
2008 "Standardizing RNAi". RNA Ontology Consortium, 4th Annual Meeting.
2008 "Preparing for Pathway Analysis: A Case Study". RNAi Global Initiative, 5th Meeting.
2007 "Computational Challenges in RNAi Gene Silencing". World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP) 2007.
2007 "NoiseMaker: Computational Assessment of Screening Statistics". RNAi Global Initiative, 4th Meeting.
2006 "New Sequence Offering: Making the Most of the Collection". RNAi Global Initiative, 3rd Meeting.
2006 "Analysis of a 10-Lab RNAi Pilot Screen: the Case for Standardization". RNAi Global Initiative, 2nd Meeting.
2004 "Maximum Sequence Alignment Fails To Predict Off-targeted Gene Regulation By RNAi". Rocky Mountain Regional Bioinformatics Conference, 2nd Annual Meeting.

Posters
2014 Haupt, A., Anderson, A., Strezoska, Ž., Machado, H., McClelland, S., Mayer, M., Rocker, A., Vermeulen, A., Birmingham, A., Kelley, M., & Smith, A. "Cas9 driven by an optimal promoter improves gene editing in eukaryotic cell lines when paired with synthetic crRNA and tracrRNA". Discovery On-Target, 12th Annual Meeting.
2014 Mayer, M., McClelland, S., Anderson, S., van Brabant Smith, A., Vermeulen, A., & Birmingham, A. "Targeting and Off-targeting of Long Non-coding RNAs by siRNAs". RNA Silencing (Keystone Symposium).
2014 Licon, A., Strezoska, Z., Stombaugh, J., Banos, M., Stahl, J., Anderson, S.B., Leake, D., van Brabant Smith, A., Birmingham, A., & Vermeulen, A. "Power Decoder-A Simulator for the Evaluation of Pooled shRNA Screen Performance". RNA Silencing (Keystone Symposium).
2012 Rocca-Serra, P., Bellaousov, S., Birmingham, A., Chen, C., Cordero, P., Das, R., Davis- Neulander, L., Duncan, C., Halvorsen, M., Knight, R., Leontis, N., Mathews, D., Ritz, J., Stombaugh, J., Weeks, K., Zirbel, C., & Laederach, A. "Sharing and Archiving Nucleic Acid Structure Mapping Data". RNA Society, 17th Annual Meeting.
2010 Birmingham, A., Strezoska, Z., Maksimova, E., Quinn, J., Kwan, P., Smith, A., Vermeulen, A., Howell, M., & Leake, D. "Seed Enrichment in Screening Hits Demonstrates the miRNA-like Off-Targets are Assay-Specific". Mechanism and Biology of Silencing (Keystone Symposium).
2010 Laederach, A., Bellaousov, S., Birmingham, A., Davis-Neulander, L., Leontis, N., Mathews, D., Rocca-Serra, P., Stombaugh, J., Weeks, K., Zirbel, C., & Knight, R. "Standardization and Classification of Single Nucleotide Resolution Nucleic Acid Structure Mapping (SNRNASM) Experiments". RNA Society, 15th Annual Meeting.
2010 van Brabant Smith, A., Maksimova, E., Brenton, M., Deiparine, M., Edwards, R., Kwan, P., Birmingham, A., & Leake, D. "Strategies for Improving RNAi Screening Success: Using a Ubiquitin-EGFP Assay to Identify Druggable Genes Required for Proteasome Function". Society for Biomolecular Screening, 16th Annual Meeting.
2009 van Brabant Smith, A., Deiparine, M., Maksimova, E., Brenton, M., Birmingham, A., Kwan, P., & Leake, D. "Genome-Wide RNAi Screening as a Strategy for Target Identification and Validation". Society for Biomolecular Screening, 15th Annual Meeting.
2008 Anderson, E.M.*, Birmingham, A.*, Mayer, M., Maksimova, E., Reynolds, A., Khvorova, A., & Leake, D. "Context-Based miRNA Targeting Models Applied to siRNA Off-Targeting". RNA Society, 13th Annual Meeting. [*Co-first-authors]
2008 Anderson, E.M.*, Birmingham, A.*, Mayer, M., Maksimova, E., Reynolds, A., Khvorova, A., & Leake, D. "Context-Based miRNA Targeting Models Applied to siRNA Off-Targeting". RNAi, MicroRNA, and Non-Coding RNA (Keystone Symposium). [*Co-first-authors]
2007 Sullivan, K., Hamady, M., Knight, R., Marshall, W. S., Khvorova, A., & Birmingham, A. "Fast- FIND Sequence Similarity Search: An Improved Approach for siRNA Design". MicroRNAs and siRNAs: Biological Functions and Mechanisms (Keystone Symposium).
2007 Wiemann, S., Argo, S., Mehrle, A., Hahne, F., Hermjakob, H., Apweiler, R., Arlt, S., Bielke, W., Birmingham, A., Boese, Q., Bork, P., Buchholz, F., Cai, X., Camon, C., Carninci, P., Chanda, S., Chen, Z., Cusick, M., Echeverri, C., Eils, J., Eils, R., Frank, R., Fraser, A., Girod, A., Haedrich, B., Hannus, M., Harris, M., Hayashizaki, Y., Hide, W., Hofmann, O., Huber, P., Hyman, A., Kallioniemi, O., Khvorova, A., Koski, L., Kraybill, B., LaBaer, J., Landegren, U., Lawerenz, C., Lehrach, H., Liu, F., Majety, M., Mathey-Prevot, B., Mills, G., Nomura, N., The OBI working group, Perrimon, N., Pizarro, A., Poustka, A., Quackenbush, J., Rosenfelder, H., Sahin, O., Salehi-Ashtiani, K., Sasse, F., Sauermann, M., Schimmer, A., Schmidt, C., Selfors, L., Shamu, C., Sönnichsen, B., Taylor, C., Temple, G., Vidal, M., & Wrobel, D. "The MIACA minimum information guideline for cellular assays and systems biology". HUGO's 12th Human Genome Meeting.
2007 Anderson, E.M., Birmingham, A., Baskerville, S., Reynolds, A., Maksimova, E., Leake, D., Fedorov, Y., Karpilow, J., Marshall, W. S., & Khvorova, A. "Low Genome-Wide 3' UTR Seed Complement Frequency is Predictive of siRNA Specificity". MicroRNAs and siRNAs: Biological Functions and Mechanisms (Keystone Symposium).
2005 Reynolds, A., Fedorov, Y., Anderson, E., Vermeulen, A., Birmingham, A., Eklund, T., Robinson, K., Leake, D., Karpilow, J., Marshall, W., & Khvorova, A. "Key Considerations for Performing RNAi in Neuronal Tissues". Society for Neuroscience, 35th Annual Meeting.
2005 Birmingham, A., Anderson, E. M., Marshall, W. S., & Khvorova, A. "Maximum Sequence Alignment Fails to Predict Off-targeted Gene Regulation by RNAi". IEEE Computational Systems Bioinformatics Conference, 4th Annual Meeting.
2003 Birmingham, A., Knight, R., & Yarus, M. "BayesFold: Combining Thermodynamic, Sequence, and Chemical Data to Predict Secondary Structures for RNA Alignments". RNA Society, 8th Annual Meeting.
2001 Rebull, L. M., Makidon, R. B., Strom, S. E., Hillenbrand, L. A., Birmingham, A., Patten, B. M., Jones, B. F., Yagi, H., & Adams, M. T. " Circumstellar Disk Candidates Identified in NGC 2264". American Astronomical Society, 199th AAS Meeting.
1998 Birmingham, A., Eder, J., and Salter, C. "The Relation between Gas Density and Star Formation in S0 Galaxies". American Astronomical Society, 191st AAS Meeting.


RESEARCH SEMINARS
2014 University of Colorado at Boulder Bioinformatics Supergroup, Boulder, CO
2010 Weizmann Institute of Science, Rehovot, Israel
2010 International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
2008 Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
2006 University of Colorado at Denver Center for Computational Biology, Denver, CO
2005 Bay Area RNA Club, San Francisco, CA


PEER REVIEW
Refereed papers submitted to the journals

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