An astronomer turned techie, I specialize in working with scientific end users and developing biology-related software applications. Currently I head the bioinformatics team for Thermo Fisher Scientific's Genomics group. My resume is available here.
PublicationsBirmingham 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.
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.
Kwan P, Birmingham A. (2010) NoiseMaker: Simulated Screens for Statistical Assessment. Bioinformatics. 2010 Aug 11.
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. (2009) Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods. 2009 Aug;6(8):569-75.
Brown JW, Birmingham A, Griffiths PE, Jossinet F, Kachouri-Lafond R, Knight R, Lang BF, Leontis N, Steger G, Stombaugh J, Westhof E. (2009) The RNA structure alignment ontology. RNA. 2009 Jul 21.
Anderson EM, 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. 2008 May;14(5):853-61.
Peirce JL, Broman KW, Lu L, Chesler EJ, Zhou G, Airey DC, Birmingham AE, Williams RW. (2008) Genome Reshuffling for Advanced Intercross Permutation (GRAIP): simulation and permutation for advanced intercross population analysis. PLoS ONE. 2008 Apr 23;3(4):e1977.
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, 2068 - 2078.
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 Biol. 2007 Aug 21;8(8):R171.
Fedorov, Y., Anderson, E., Birmingham, A., Reynolds, A., Karpilow, J., Robinson, K., Leake, D., Marshall, W.S., Khvorova, A. (2006) "Off-Targeting By siRNA Can Induce Toxic Phenotype", RNA, 2006 Jul;12(7):1188-96.
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, 2006 Mar;3(3):199-204.
Faculty of 1000 top 10 pick
Profiled in RNAi News
Knight, R., Birmingham, A., and Yarus, M. (2004) "BayesFold: Rational 2 ° Folds that Combine Thermodynamic, Covariation, and Chemical Data for Aligned RNA Sequences", RNA, 2004 Sep;10(9):1323-36.
Rebull, L.M., Makidon, R.B., Strom, S.E., Hillenbrand, L.A., Birmingham, A., Patten, Brian M., Jones, B.F., Yagi, H., and Adams, Mark T. (2002) "Circumstellar Disk Candidates Identified in NGC 2264", The Astronomical Journal, 123:1528-1547.
Book Chaptersde Zwart, I., Lozupone, C., Knight, R., Birmingham, A., Illangasekare, M., Jadhav, V., Legiewicz, M., Majerfeld, I., Widmann, J., and Yarus, M. (2005). "Artificial Selection: Finding function amongst randomized sequences" in Handbook of RNA Biochemistry. Edited by R. K. Hartmann, A. Bindereif, A. Schon, E. Westhof. Chapter 47, p 783-806.
Other PublicationsBirmingham, A. (2002) "Of Astronomical Proportions", [Product Review] Science 298:859.
Birmingham, A. (1997) "On the Star Formation History of the Rho Ophiuchus Molecular Cloud Complex." [Undergraduate Thesis] Amherst College, Amherst MA.
"Seed Enrichment in High-Throughput Screening Hits Demonstrates That miRNA-like Off-Targets Are Assay-Specific". (2011) RNA Society, 15th Annual Meeting.
"Better Than the Real Thing: In Silico Screens for Statistical Selection". (2011) RNAi Global Initiative, 10th Semiannual Meeting.
Invited Talk: "Better Than the Real Thing: In Silico Screens for Statistical Selection". (2011) The IAENG International Conference on Bioinformatics 2011, part of The International MultiConference of Engineers and Computer Scientists 2011, 6th Annual Meeting
"Automated Seed Cluster Identification in Screen Results". (2010) Weizmann Institute of Science, Rehovot, Israel
"The Hit List Mystery: Why We Need Public Data Deposition". (2010) RNAi Global Initiative, 9th Semiannual Meeting.
"Statistical Methods for RNAi Screening Analysis." (2010) International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
Invited Talk: "Computational Assessment of Screening Statistics for RNAi". (2010) Biomolecular Screening: Advanced Applications Across Academia, Government, and Industry (SBS Symposium)
"Computational Assessment of Screening Statistics". (2010) Intelligent Systems in Molecular Biology (ISMB) 2010, 18th annual meeting.
"Searching Seed-Space: Automated Seed Cluster Identification in Screen Results". (2009) RNAi Global Initiative, 8th Semiannual Meeting.
"Tomorrow, the World!: Toward World-wide Data Sharing Through NCBI". (2009) RNAi Global Initiative, 7th Semiannual Meeting.
"Rise of the Machines: Machine Learning for High Content Data Analysis". (2008) RNAi Global Initiative, 6th Semiannual Meeting.
"Predicting siRNA Off-Targets: Right Answers, Wrong Questions." (2008) Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic.
"Standardizing RNAi". (2008) RNA Ontology Consortium, 4th Annual Meeting.
"High-Throughput Screening Data Analysis Workflow". (2008) RNAi Global Initiative, 5th Semiannual Meeting.
"Computational Challenges in RNAi Gene Silencing". (2007) World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP) 2007.
"NoiseMaker: Computational Assessment of Screening Statistics". (2007) RNAi Global Initiative, 4th Semiannual Meeting.
"Analysis of a 10-Lab RNAi Pilot Screen: the Case for Standardization". (2006) RNAi Global Initiative, 2nd Semiannual Meeting.
"Predicting siRNA Off-Targets: Right Answers, Wrong Questions." (2006) University of Colorado at Denver Center for Computational Biology.
"Predicting siRNA Off-Targets: Right Answers, Wrong Questions." (2005) Bay Area RNA Club, San Francisco, December Meeting.
"Maximum Sequence Alignment Fails To Predict Off-targeted Gene Regulation By RNAi". (2004) Rocky Mountain Regional Bioinformatics Conference, 2nd Annual Meeting.
Birmingham, A., Strezoska, Z., Maksimova, E., Quinn, J., Kwan, P., Smith, A., Vermeulen, A., Howell, M., Leake, D. (2010) "Seed Enrichment in Screening Hits Demonstrates the miRNA-like Off-Targets are Assay-Specific". Mechanism and Biology of Silencing (Keystone Symposium).
Laederach, A., Bellaousov, S., Birmingham, A., Davis-Neulander, L., Leontis, N., Mathews, D., Rocca-Serra, P., Stombaugh, J., Weeks, K., Zirbel, C., Knight, R. (2010) "Standardization and Classification of Single Nucleotide Resolution Nucleic Acid Structure Mapping (SNRNASM) Experiments". RNA Society, 15th Annual Meeting.
van Brabant Smith, A., Maksimova, E., Brenton, M., Deiparine, M., Edwards, R., Kwan, P., Birmingham, A., Leake, D. (2010) "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.
van Brabant Smith, A., Deiparine, M., Maksimova, E., Brenton, M., Birmingham, A., Kwan, P., Leake, D. (2009) "Genome-Wide RNAi Screening as a Strategy for Target Identification and Validation". Society for Biomolecular Screening, 15th Annual Meeting.
Anderson, E.M.*, Birmingham, A.*, Mayer, M., Maksimova, E., Reynolds, A., Khvorova, A., Leake, D. (2008) "Context-Based miRNA Targeting Models Applied to siRNA Off-Targeting". RNA Society, 13th Annual Meeting.
Anderson, E.M.*, Birmingham, A.*, Mayer, M., Maksimova, E., Reynolds, A., Khvorova, A., Leake, D. (2008) "Context-Based miRNA Targeting Models Applied to siRNA Off-Targeting". RNAi, MicroRNA, and Non-Coding RNA (Keystone Symposium).
Sullivan, K., Hamady, M., Knight, R., Marshall, W.S., Khvorova, A., Birmingham, A. (2007) "Fast-FIND Sequence Similarity Search: An Improved Approach for siRNA Design". MicroRNAs and siRNAs: Biological Functions and Mechanisms (Keystone Symposium).
Anderson, E.M., Birmingham, A., Baskerville, S., Reynolds, A., Maksimova, E., Leake, D., Fedorov, Y., Karpilow, J., Marshall, W.S., Khvorova, A. (2007) "Low Genome-Wide 3' UTR Seed Complement Frequency is Predictive of siRNA Specificity". MicroRNAs and siRNAs: Biological Functions and Mechanisms (Keystone Symposium).
Reynolds, A., Fedorov, Y., Anderson, E., Vermeulen, A., Birmingham, A., Eklund, T., Robinson, K., Leake, D., Karpilow, J., Marshall, W., Khvorova, A. (2005) "Key Considerations for Performing RNAi in Neuronal Tissues". Society for Neuroscience, 35th Annual Meeting.
Birmingham, A., Anderson, EM., Marshall, WS., Khvorova, A. (2005) "Maximum Sequence Alignment Fails to
Predict Off-targeted Gene Regulation by RNAi". IEEE Computational Systems Bioinformatics Conference, 4th
Annual Meeting.
Awarded CSB 2005 Best Poster.
Birmingham, A., Knight, R., and Yarus, M. (2003) "BayesFold: Combining Thermodynamic, Sequence, and Chemical Data to Predict Secondary Structures for RNA Alignments". RNA Society, 8th Annual Meeting.
Rebull, L. M., Makidon, R. B., Strom, S. E., Hillenbrand, L. A., Birmingham, A., Patten, B. M., Jones, B. F., Yagi, H., and Adams, M. T. (2001) " Circumstellar Disk Candidates Identified in NGC 2264". American Astronomical Society, 199th AAS Meeting.
Birmingham, A., Eder, J., and Salter, C. (1998) "The Relation between Gas Density and Star Formation in S0 Galaxies". American Astronomical Society, 191st AAS Meeting.