Andrew Scott Allen | Scholars@Duke

Andrew Scott Allen
Professor of Biostatistics and Bioinformatics

My research focuses on developing new statistical methods for identifying susceptibility loci involved in complex human disease. It involves a mix of genetics, statistics, and computer science and is motivated by the complexities of real data encountered in collaborative disease-gene mapping projects.

Current Appointments & Affiliations

Professor of Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2015
Member in the Duke Clinical Research Institute, Duke Clinical Research Institute, Institutes and Centers 2002

Contact Information

203 Research Drive Ste 301, 301D MSRB I, Durham, NC 27705
Duke Box 2648, Durham, NC 27710
asallen@duke.edu (919) 668-8043
Lab page

Background
Education, Training, & Certifications
- Ph.D., Emory University 2001
Duke Appointment History
- Associate Professor of Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2007 - 2015
- Assistant Professor of Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2001 - 2007
- Instructor, Temporary in the Department of Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2001
Recognition
In the News
- SEP 3, 2015
  
  School of Medicine announces new Center for Statistical Genetics and Genomics
- MAR 26, 2015 The Verge
  
  Andrew Allen quoted: The father of all humans lived 239,000 years ago
Expertise
Subject Headings
Research
Selected Grants
- Duke CTSA (KL2) awarded by National Institutes of Health 2018 - 2023
- Duke CTSA (TL1) awarded by National Institutes of Health 2018 - 2023
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- A hands-on, integrative next-generation sequencing course: design, experiment, and analysis awarded by National Institutes of Health 2016 - 2019
- Integrated Biostatistical Training for CVD Research awarded by North Carolina State University 2017 - 2019
- Host Susceptibility to S. aureus awarded by National Institutes of Health 2012 - 2019
- Statistical/Computational Methods for Pharmacogenomics and Individualized Therapy awarded by University of North Carolina - Chapel Hill 2015 - 2019
- Association Tests of Rare Variants Using Sequence Reads without Calling Genotypes awarded by Emory University 2015 - 2018
- Duke Research Training Program for Pediatricians awarded by National Institutes of Health 2002 - 2018
- 1/3-Identifying regulatory mutations that influence neuropsychiatric disease awarded by Columbia University 2014 - 2018
- Genetics of Normal Human Variation: Implications for Disease awarded by National Institutes of Health 2013 - 2017
- Subaward for Epi4k SBB Grant U01NS077303 awarded by Columbia University 2015 - 2016
- 1/3-Identifying regulatory mutations that influence neuropsychiatric disease awarded by Columbia University 2015
- 1/3-Identifying regulatory mutations that influence neuropsychiatric disease awarded by National Institutes of Health 2014
- Identifying de novo mutations causing OCD in trios by whole exome sequencing awarded by National Institutes of Health 2013 - 2014
- 1 of 2: Identification of Rare Variants of OCD awarded by National Institutes of Health 2013 - 2014
- 3 of 7 Epi4K: Gene discovery in 4,000 epilepsy genomes awarded by National Institutes of Health 2011 - 2014
- ROBUST METHODS FOR THE EFFICIENT ANALYSIS AND INTEGRATION OF DNA SEQUENCE DATA awarded by National Institutes of Health 2008 - 2013
- Prevention of Cardiovascular Complications of Pediatric SLE awarded by National Institutes of Health 2002 - 2011
- Advanced Haplotype Analyses in Coronary Artery Disease awarded by National Institutes of Health 2004 - 2010
- K24 Mid-career Clinical Investigator Award awarded by National Institutes of Health 2000 - 2007
- Implementing Research Findings for Practice Improvement awarded by National Institutes of Health 2002 - 2006
- Clinical Predictors of Antiretroviral Failure awarded by National Institutes of Health 2002 - 2004
Publications & Artistic Works
Selected Publications
- Book Sections
  - Pan, JQ, Baez-Nieto, D, Allen, A, Wang, HR, and Cottrell, JR. "Developing high-throughput assays to analyze and screen electrophysiological phenotypes." In Methods in Molecular Biology, 235-252. January 1, 2018. Full Text
- Conference Papers
  - Zhao, J, Li, D, Seo, J, Allen, AS, and Gordân, R. "Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding." May 2017. Full Text
  - Parsia, B, Alsubait, T, Leo, J, Malaisé, V, Forge, S, Gregory, M, and Allen, A. "Lifting EMMeT to OWL getting the most from SKOS." January 1, 2016. Full Text
- Journal Articles
  - Heinzen, EL, O'Neill, AC, Zhu, X, Allen, AS, Bahlo, M, Chelly, J, Chen, MH, Dobyns, WB, Freytag, S, Guerrini, R, Leventer, RJ, Poduri, A, Robertson, SP, Walsh, CA, Zhang, M, Epi4K Consortium, , and Epilepsy Phenome/Genome Project, . "De novo and inherited private variants in MAP1B in periventricular nodular heterotopia." Plos Genetics 14, no. 5 (May 8, 2018): e1007281-null. Full Text
  - Winawer, MR, Griffin, NG, Samanamud, J, Baugh, EH, Rathakrishnan, D, Ramalingam, S, Zagzag, D, Schevon, CA, Dugan, P, Hegde, M, Sheth, SA, McKhann, GM, Doyle, WK, Grant, GA, Porter, BE, Mikati, MA, Muh, CR, Malone, CD, Bergin, AMR, Peters, JM, McBrian, DK, Pack, AM, Akman, CI, LaCoursiere, CM, Keever, KM, Madsen, JR, Yang, E, Lidov, HGW, Shain, C, Allen, AS, Canoll, PD, Crino, PB, Poduri, AH, and Heinzen, EL. "Somatic SLC35A2 variants in the brain are associated with intractable neocortical epilepsy." Annals of Neurology (April 20, 2018). Full Text
  - B. Sibley, A, Li, Z, Jiang, Y, Li, Y-J, Chan, C, Allen, A, and Owzar, K. "Facilitating the Calculation of the Efficient Score Using Symbolic Computing." The American Statistician 72, no. 2 (April 3, 2018): 199-205. Full Text
  - Assel, MJ, Li, F, Wang, Y, Allen, AS, Baggerly, KA, and Vickers, AJ. "Genetic Polymorphisms of CFH and ARMS2 Do Not Predict Response to Antioxidants and Zinc in Patients with Age-Related Macular Degeneration: Independent Statistical Evaluations of Data from the Age-Related Eye Disease Study." Ophthalmology 125, no. 3 (March 2018): 391-397. Full Text
  - Nicolas, A, Kenna, KP, Renton, AE, Ticozzi, N, Faghri, F, Chia, R, Dominov, JA, Kenna, BJ, Nalls, MA, Keagle, P, Rivera, AM, van Rheenen, W, Murphy, NA, van Vugt, JJFA, Geiger, JT, Van der Spek, RA, Pliner, HA, Shankaracharya, , Smith, BN, Marangi, G, Topp, SD, Abramzon, Y, Gkazi, AS, Eicher, JD, Kenna, A, ITALSGEN Consortium, , Mora, G, Calvo, A, Mazzini, L, Riva, N, Mandrioli, J, Caponnetto, C, Battistini, S, Volanti, P, La Bella, V, Conforti, FL, Borghero, G, Messina, S, Simone, IL, Trojsi, F, Salvi, F, Logullo, FO, D'Alfonso, S, Corrado, L, Capasso, M, Ferrucci, L, Genomic Translation for ALS Care (GTAC) Consortium, , Moreno, CDAM, Kamalakaran, S, Goldstein, DB, ALS Sequencing Consortium, , Gitler, AD, Harris, T, Myers, RM, NYGC ALS Consortium, , Phatnani, H, Musunuri, RL, Evani, US, Abhyankar, A, Zody, MC, Answer ALS Foundation, , Kaye, J, Finkbeiner, S, Wyman, SK, LeNail, A, Lima, L, Fraenkel, E, Svendsen, CN, Thompson, LM, Van Eyk, JE, Berry, JD, Miller, TM, Kolb, SJ, Cudkowicz, M, Baxi, E, Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium, , Benatar, M, Taylor, JP, Rampersaud, E, Wu, G, Wuu, J, SLAGEN Consortium, , Lauria, G, Verde, F, Fogh, I, Tiloca, C, Comi, GP, Sorarù, G, Cereda, C, French ALS Consortium, , Corcia, P, Laaksovirta, H, Myllykangas, L, Jansson, L, Valori, M, Ealing, J, Hamdalla, H, Rollinson, S, Pickering-Brown, S, Orrell, RW, Sidle, KC, Malaspina, A, Hardy, J, Singleton, AB, Johnson, JO, Arepalli, S, Sapp, PC, McKenna-Yasek, D, Polak, M, Asress, S, Al-Sarraj, S, King, A, Troakes, C, Vance, C, de Belleroche, J, Baas, F, Ten Asbroek, ALMA, Muñoz-Blanco, JL, Hernandez, DG, Ding, J, Gibbs, JR, Scholz, SW, Floeter, MK, Campbell, RH, Landi, F, Bowser, R, Pulst, SM, Ravits, JM, MacGowan, DJL, Kirby, J, Pioro, EP, Pamphlett, R, Broach, J, Gerhard, G, Dunckley, TL, Brady, CB, Kowall, NW, Troncoso, JC, Le Ber, I, Mouzat, K, Lumbroso, S, Heiman-Patterson, TD, Kamel, F, Van Den Bosch, L, Baloh, RH, Strom, TM, Meitinger, T, Shatunov, A, Van Eijk, KR, de Carvalho, M, Kooyman, M, Middelkoop, B, Moisse, M, McLaughlin, RL, Van Es, MA, Weber, M, Boylan, KB, Van Blitterswijk, M, Rademakers, R, Morrison, KE, Basak, AN, Mora, JS, Drory, VE, Shaw, PJ, Turner, MR, Talbot, K, Hardiman, O, Williams, KL, Fifita, JA, Nicholson, GA, Blair, IP, Rouleau, GA, Esteban-Pérez, J, García-Redondo, A, Al-Chalabi, A, Project MinE ALS Sequencing Consortium, , Rogaeva, E, Zinman, L, Ostrow, LW, Maragakis, NJ, Rothstein, JD, Simmons, Z, Cooper-Knock, J, Brice, A, Goutman, SA, Feldman, EL, Gibson, SB, Taroni, F, Ratti, A, Gellera, C, Van Damme, P, Robberecht, W, Fratta, P, Sabatelli, M, Lunetta, C, Ludolph, AC, Andersen, PM, Weishaupt, JH, Camu, W, Trojanowski, JQ, Van Deerlin, VM, Brown, RH, van den Berg, LH, Veldink, JH, Harms, MB, Glass, JD, Stone, DJ, Tienari, P, Silani, V, Chiò, A, Shaw, CE, Traynor, BJ, and Landers, JE. "Genome-wide Analyses Identify KIF5A as a Novel ALS Gene." Neuron 97, no. 6 (March 2018): 1268-1283.e6. Full Text
  - Kleinstein, SE, Shea, PR, Allen, AS, Koelle, DM, Wald, A, and Goldstein, DB. "Genome-wide association study (GWAS) of human host factors influencing viral severity of herpes simplex virus type 2 (HSV-2)." Genes and immunity (February 28, 2018). Full Text
  - Zhu, X, Padmanabhan, R, Copeland, B, Bridgers, J, Ren, Z, Kamalakaran, S, O'Driscoll-Collins, A, Berkovic, SF, Scheffer, IE, Poduri, A, Mei, D, Guerrini, R, Lowenstein, DH, Allen, AS, Heinzen, EL, and Goldstein, DB. "A case-control collapsing analysis identifies epilepsy genes implicated in trio sequencing studies focused on de novo mutations." Plos Genetics 13, no. 11 (November 29, 2017): e1007104-null. Full Text
  - Acharya, CR, Owzar, K, and Allen, AS. "Mapping eQTL by leveraging multiple tissues and DNA methylation." BMC bioinformatics 18, no. 1 (October 18, 2017): 455-. Full Text
  - Griffin, NG, Cronin, KD, Walley, NM, Hulette, CM, Grant, GA, Mikati, MA, LaBreche, HG, Rehder, CW, Allen, AS, Crino, PB, and Heinzen, EL. "Somatic uniparental disomy of Chromosome 16p in hemimegalencephaly." Cold Spring Harbor Molecular Case Studies 3, no. 5 (September 2017). Full Text
  - Epi4K Consortium, . "Phenotypic analysis of 303 multiplex families with common epilepsies." Brain : a Journal of Neurology 140, no. 8 (August 2017): 2144-2156. Full Text
  - Petrovski, S, Todd, JL, Durheim, MT, Wang, Q, Chien, JW, Kelly, FL, Frankel, C, Mebane, CM, Ren, Z, Bridgers, J, Urban, TJ, Malone, CD, Finlen Copeland, A, Brinkley, C, Allen, AS, O'Riordan, T, McHutchison, JG, Palmer, SM, and Goldstein, DB. "An Exome Sequencing Study to Assess the Role of Rare Genetic Variation in Pulmonary Fibrosis." American Journal of Respiratory and Critical Care Medicine 196, no. 1 (July 2017): 82-93. Full Text
  - Epi4K Consortium, , EuroEPINOMICS-RES Consortium, , and Epilepsy Phenome Genome Project, . "Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data." European Journal of Human Genetics 25, no. 7 (June 2017): 894-899. Full Text
  - Guo, C, McDowell, IC, Nodzenski, M, Scholtens, DM, Allen, AS, Lowe, WL, and Reddy, TE. "Transversions have larger regulatory effects than transitions." BMC genomics 18, no. 1 (May 19, 2017): 394-. Full Text
  - Majoros, WH, Campbell, MS, Holt, C, DeNardo, EK, Ware, D, Allen, AS, Yandell, M, and Reddy, TE. "High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE." Bioinformatics (Oxford, England) 33, no. 10 (May 2017): 1437-1446. Full Text
  - Cyr, DD, Allen, AS, Du, G-J, Ruffin, F, Adams, C, Thaden, JT, Maskarinec, SA, Souli, M, Guo, S, Dykxhoorn, DM, Scott, WK, and Fowler, VG. "Evaluating genetic susceptibility to Staphylococcus aureus bacteremia in African Americans using admixture mapping." Genes and immunity 18, no. 2 (March 23, 2017): 95-99. Full Text
  - Epi4K consortium, , and Epilepsy Phenome/Genome Project, . "Ultra-rare genetic variation in common epilepsies: a case-control sequencing study." The Lancet. Neurology 16, no. 2 (February 2017): 135-143. Full Text
  - Jiang, Y, Ji, Y, Sibley, AB, Li, Y-J, and Allen, AS. "Leveraging population information in family-based rare variant association analyses of quantitative traits." Genetic epidemiology 41, no. 2 (February 2017): 98-107. Full Text
  - Appenzeller, S, Balling, R, Barisic, N, Baulac, S, Caglayan, H, Craiu, D, De Jonghe, P, Depienne, C, Dimova, P, Djémié, T, Gormley, P, Guerrini, R, Helbig, I, Hjalgrim, H, Hoffman-Zacharska, D, Jähn, J, Klein, KM, Koeleman, B, Komarek, V, Krause, R, Kuhlenbäumer, G, Leguern, E, Lehesjoki, A-E, Lemke, JR, Lerche, H, Linnankivi, T, Marini, C, May, P, Møller, RS, Muhle, H, Pal, D, Palotie, A, Pendziwiat, M, Robbiano, A, Roelens, F, Rosenow, F, Selmer, K, Serratosa, JM, Sisodiya, S, Stephani, U, Sterbova, K, Striano, P, Suls, A, Talvik, T, von Spiczak, S, Weber, Y, Weckhuysen, S, Zara, F, Abou-Khalil, B, Alldredge, BK, Andermann, E, Andermann, F, Amrom, D, Bautista, JF, Berkovic, SF, Bluvstein, J, Boro, A, Cascino, G, Consalvo, D, Crumrine, P, Devinsky, O, Dlugos, D, Epstein, MP, Fiol, M, Fountain, NB, French, J, Friedman, D, Geller, EB, Glauser, T, Glynn, S, Haas, K, Haut, SR, Hayward, J, Helmers, SL, Joshi, S, Kanner, A, Kirsch, HE, Knowlton, RC, Kossoff, EH, Kuperman, R, Kuzniecky, R, Lowenstein, DH, McGuire, SM, Motika, PV, Novotny, EJ, Ottman, R, Paolicchi, JM, Parent, J, Park, K, Poduri, A, Sadleir, L, Scheffer, IE, Shellhaas, RA, Sherr, E, Shih, JJ, Singh, R, Sirven, J, Smith, MC, Sullivan, J, Thio, LL, Venkat, A, Vining, EPG, Von Allmen, GK, Weisenberg, JL, Widdess-Walsh, P, Winawer, MR, Allen, AS, Cossette, P, Delanty, N, Eichler, EE, Goldstein, DB, Han, Y, Heinzen, EL, Johnson, MR, Marson, AG, Mefford, HC, Nieh, SE, O’Brien, TJ, Petrou, S, Petrovski, S, and Ruzzo, EK. "De Novo Mutations in Synaptic Transmission Genes Including DNM1 Cause Epileptic Encephalopathies." The American Journal of Human Genetics 100, no. 1 (January 2017): 179-179. Full Text
  - Gussow, AB, Copeland, BR, Dhindsa, RS, Wang, Q, Petrovski, S, Majoros, WH, Allen, AS, and Goldstein, DB. "Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics." Plos One 12, no. 8 (January 2017): e0181604-null. Full Text
  - Andrade, A, Hope, J, Allen, A, Yorgan, V, Lipscombe, D, and Pan, JQ. "A rare schizophrenia risk variant of CACNA1I disrupts CaV3.3 channel activity." Scientific Reports 6 (October 19, 2016): 34233-null. Full Text
  - Xing, C, M McCarthy, J, Dupuis, J, Adrienne Cupples, L, B Meigs, J, Lin, X, and S Allen, A. "Robust analysis of secondary phenotypes in case-control genetic association studies." Statistics in medicine 35, no. 23 (October 2016): 4226-4237. Full Text
  - Epi4K Consortium, . "De Novo Mutations in SLC1A2 and CACNA1A Are Important Causes of Epileptic Encephalopathies." American Journal of Human Genetics 99, no. 2 (August 2016): 287-298. Full Text
  - Hildebrand, MS, Griffin, NG, Damiano, JA, Cops, EJ, Burgess, R, Ozturk, E, Jones, NC, Leventer, RJ, Freeman, JL, Harvey, AS, Sadleir, LG, Scheffer, IE, Major, H, Darbro, BW, Allen, AS, Goldstein, DB, Kerrigan, JF, Berkovic, SF, and Heinzen, EL. "Mutations of the Sonic Hedgehog Pathway Underlie Hypothalamic Hamartoma with Gelastic Epilepsy." American Journal of Human Genetics 99, no. 2 (August 2016): 423-429. Full Text
  - Acharya, CR, McCarthy, JM, Owzar, K, and Allen, AS. "Exploiting expression patterns across multiple tissues to map expression quantitative trait loci." BMC bioinformatics 17 (June 24, 2016): 257-. Full Text
  - Hu, Y-J, Liao, P, Johnston, HR, Allen, AS, and Satten, GA. "Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls." PLoS genetics 12, no. 5 (May 6, 2016): e1006040-. Full Text
  - DeLorenze, GN, Nelson, CL, Scott, WK, Allen, AS, Ray, GT, Tsai, A-L, Quesenberry, CP, and Fowler, VG. "Polymorphisms in HLA Class II Genes Are Associated With Susceptibility to Staphylococcus aureus Infection in a White Population." The Journal of infectious diseases 213, no. 5 (March 2016): 816-823. Full Text
  - Gussow, AB, Petrovski, S, Wang, Q, Allen, AS, and Goldstein, DB. "The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes." Genome Biology 17 (January 18, 2016): 9-null. Full Text
  - Shashi, V, Xie, P, Schoch, K, Goldstein, DB, Howard, TD, Berry, MN, Schwartz, CE, Cronin, K, Sliwa, S, Allen, A, and Need, AC. "The RBMX gene as a candidate for the Shashi X-linked intellectual disability syndrome." Clinical genetics 88, no. 4 (October 2015): 386-390. Full Text
  - Petrovski, S, Gussow, AB, Wang, Q, Halvorsen, M, Han, Y, Weir, WH, Allen, AS, and Goldstein, DB. "The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity." Plos Genetics 11, no. 9 (September 2, 2015): e1005492-null. Full Text
  - Jiang, Y, Han, Y, Petrovski, S, Owzar, K, Goldstein, DB, and Allen, AS. "Incorporating Functional Information in Tests of Excess De Novo Mutational Load." American Journal of Human Genetics 97, no. 2 (August 6, 2015): 272-283. Full Text
  - Jiang, Y, Han, Y, Petrovski, S, Owzar, K, Goldstein, DB, and Allen, AS. "Incorporating Functional Information in Tests of Excess De Novo Mutational Load." American Journal of Human Genetics 97, no. 2 (August 2015): 272-283. Full Text
  - Heinzen, EL, Neale, BM, Traynelis, SF, Allen, AS, and Goldstein, DB. "The genetics of neuropsychiatric diseases: looking in and beyond the exome." Annual review of neuroscience 38 (July 2015): 47-68. (Review) Full Text
  - Mccarthy, JM, Shea, PR, Goldstein, DB, and Allen, AS. "Testing for risk and protective trends in genetic analyses of HIV acquisition." Biostatistics (Oxford, England) 16, no. 2 (April 2015): 268-280. Full Text
  - Cirulli, ET, Lasseigne, BN, Petrovski, S, Sapp, PC, Dion, PA, Leblond, CS, Couthouis, J, Lu, Y-F, Wang, Q, Krueger, BJ, Ren, Z, Keebler, J, Han, Y, Levy, SE, Boone, BE, Wimbish, JR, Waite, LL, Jones, AL, Carulli, JP, Day-Williams, AG, Staropoli, JF, Xin, WW, Chesi, A, Raphael, AR, McKenna-Yasek, D, Cady, J, Vianney de Jong, JMB, Kenna, KP, Smith, BN, Topp, S, Miller, J, Gkazi, A, FALS Sequencing Consortium, , Al-Chalabi, A, van den Berg, LH, Veldink, J, Silani, V, Ticozzi, N, Shaw, CE, Baloh, RH, Appel, S, Simpson, E, Lagier-Tourenne, C, Pulst, SM, Gibson, S, Trojanowski, JQ, Elman, L, McCluskey, L, Grossman, M, Shneider, NA, Chung, WK, Ravits, JM, Glass, JD, Sims, KB, Van Deerlin, VM, Maniatis, T, Hayes, SD, Ordureau, A, Swarup, S, Landers, J, Baas, F, Allen, AS, Bedlack, RS, Harper, JW, Gitler, AD, Rouleau, GA, Brown, R, Harms, MB, Cooper, GM, Harris, T, Myers, RM, and Goldstein, DB. "Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways." Science (New York, N.Y.) 347, no. 6229 (March 2015): 1436-1441. Full Text
  - Jiang, Y, McCarthy, JM, and Allen, AS. "Testing the effect of rare compound-heterozygous and recessive mutations in case--parent sequencing studies." Genetic epidemiology 39, no. 3 (March 2015): 166-172. Full Text
  - Jiang, Y, Mccarthy, JM, and Allen, AS. "Testing the Effect of Rare Compound-Heterozygous and Recessive Mutations in Case-Parent Sequencing Studies." Genetic Epidemiology 39, no. 3 (January 1, 2015): 166-172. Full Text
  - EuroEPINOMICS-RES Consortium, , Epilepsy Phenome/Genome Project, , and Epi4K Consortium, . "De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies." American journal of human genetics 95, no. 4 (October 2014): 360-370. Full Text
  - Tan, R, Wang, Y, Kleinstein, SE, Liu, Y, Zhu, X, Guo, H, Jiang, Q, Allen, AS, and Zhu, M. "An evaluation of copy number variation detection tools from whole-exome sequencing data." Human Mutation 35, no. 7 (July 2014): 899-907. Full Text
  - Jiang, Y, Satten, GA, Han, Y, Epstein, MP, Heinzen, EL, Goldstein, DB, and Allen, AS. "Utilizing population controls in rare-variant case-parent association tests." American Journal of Human Genetics 94, no. 6 (June 5, 2014): 845-853. Full Text
  - Nelson, CL, Pelak, K, Podgoreanu, MV, Ahn, SH, Scott, WK, Allen, AS, Cowell, LG, Rude, TH, Zhang, Y, Tong, A, Ruffin, F, Sharma-Kuinkel, BK, and Fowler, VG. "A genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting." Bmc Infectious Diseases 14 (February 13, 2014): 83-null. Full Text Open Access Copy
  - Satten, GA, Allen, AS, Ikeda, M, Mulle, JG, and Warren, ST. "Robust regression analysis of copy number variation data based on a univariate score." PloS one 9, no. 2 (January 2014): e86272-. Full Text
  - Epi4K Consortium, , Epilepsy Phenome/Genome Project, , Allen, AS, Berkovic, SF, Cossette, P, Delanty, N, Dlugos, D, Eichler, EE, Epstein, MP, Glauser, T, Goldstein, DB, Han, Y, Heinzen, EL, Hitomi, Y, Howell, KB, Johnson, MR, Kuzniecky, R, Lowenstein, DH, Lu, Y-F, Madou, MRZ, Marson, AG, Mefford, HC, Esmaeeli Nieh, S, O'Brien, TJ, Ottman, R, Petrovski, S, Poduri, A, Ruzzo, EK, Scheffer, IE, Sherr, EH, Yuskaitis, CJ, Abou-Khalil, B, Alldredge, BK, Bautista, JF, Boro, A, Cascino, GD, Consalvo, D, Crumrine, P, Devinsky, O, Fiol, M, Fountain, NB, French, J, Friedman, D, Geller, EB, Glynn, S, Haut, SR, Hayward, J, Helmers, SL, Joshi, S, Kanner, A, Kirsch, HE, Knowlton, RC, Kossoff, EH, Kuperman, R, McGuire, SM, Motika, PV, Novotny, EJ, Paolicchi, JM, Parent, JM, Park, K, Shellhaas, RA, Shih, JJ, Singh, R, Sirven, J, Smith, MC, Sullivan, J, Lin Thio, L, Venkat, A, Vining, EPG, Von Allmen, GK, Weisenberg, JL, Widdess-Walsh, P, and Winawer, MR. "De novo mutations in epileptic encephalopathies." Nature 501, no. 7466 (September 2013): 217-221. Full Text
  - Goldstein, DB, Allen, A, Keebler, J, Margulies, EH, Petrou, S, Petrovski, S, and Sunyaev, S. "Sequencing studies in human genetics: design and interpretation." Nature Reviews. Genetics 14, no. 7 (July 2013): 460-470. (Review) Full Text
  - Hooper, SR, Curtiss, K, Schoch, K, Keshavan, MS, Allen, A, and Shashi, V. "A longitudinal examination of the psychoeducational, neurocognitive, and psychiatric functioning in children with 22q11.2 deletion syndrome." Res Dev Disabil 34, no. 5 (May 2013): 1758-1769. Full Text Link to Item
  - Long, N, Dickson, SP, Maia, JM, Kim, HS, Zhu, Q, and Allen, AS. "Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression." PLoS Computational Biology 9, no. 6 (2013). Full Text
  - Petrovski, S, Wang, Q, Heinzen, EL, Allen, AS, and Goldstein, DB. "Genic intolerance to functional variation and the interpretation of personal genomes." Plos Genetics 9, no. 8 (January 2013): e1003709-null. Full Text
  - Epstein, MP, Duncan, R, Jiang, Y, Conneely, KN, Allen, AS, and Satten, GA. "A permutation procedure to correct for confounders in case-control studies, including tests of rare variation." American Journal of Human Genetics 91, no. 2 (August 2012): 215-223. Full Text
  - Johnson, NV, Ahn, SH, Deshmukh, H, Levin, MK, Nelson, CL, Scott, WK, Allen, A, Fowler, VG, and Cowell, LG. "Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus." G3 (Bethesda, Md.) 2, no. 6 (June 2012): 693-700. Full Text Open Access Copy
  - Epstein, MP, Duncan, R, Broadaway, KA, He, M, Allen, AS, and Satten, GA. "Stratification-score matching improves correction for confounding by population stratification in case-control association studies." Genetic epidemiology 36, no. 3 (2012): 195-205. Full Text
  - Xing, C, Satten, GA, and Allen, AS. "A weighted accumulation test for associating rare genetic variation with quantitative phenotypes." Bmc Proceedings 5 Suppl 9 (November 29, 2011): S6-null. Full Text
  - Ge, D, Ruzzo, EK, Shianna, KV, He, M, Pelak, K, Heinzen, EL, Need, AC, Cirulli, ET, Maia, JM, Dickson, SP, Zhu, M, Singh, A, Allen, AS, and Goldstein, DB. "SVA: software for annotating and visualizing sequenced human genomes." Bioinformatics 27, no. 14 (July 15, 2011): 1998-2000. Full Text Link to Item
  - Allen, AS, and Satten, GA. "Control for confounding in case-control studies using the stratification score, a retrospective balancing score." American Journal of Epidemiology 173, no. 7 (April 2011): 752-760. Full Text
  - Zhang, L, Connelly, JJ, Peppel, K, Brian, L, Shah, SH, Nelson, S, Crosslin, DR, Wang, T, Allen, A, Kraus, WE, Gregory, SG, Hauser, ER, and Freedman, NJ. "Aging-related atherosclerosis is exacerbated by arterial expression of tumor necrosis factor receptor-1: evidence from mouse models and human association studies." Hum Mol Genet 19, no. 14 (July 15, 2010): 2754-2766. Full Text Link to Item
  - Laje, G, Cannon, DM, Allen, AS, Klaver, JM, Peck, SA, Liu, X, Manji, HK, Drevets, WC, and McMahon, FJ. "Genetic variation in HTR2A influences serotonin transporter binding potential as measured using PET and [11C]DASB." The International Journal of Neuropsychopharmacology 13, no. 6 (July 2010): 715-724. Full Text
  - Allen, AS, and Satten, GA. "SNPs in CAST are associated with Parkinson disease: a confirmation study." Am J Med Genet B Neuropsychiatr Genet 153B, no. 4 (June 5, 2010): 973-979. Full Text Link to Item
  - Allen, A, Epstein, MP, and Satten, GA. "Score-based adjustment for confounding by population stratification in genetic association studies." Genetic Epidemiology 34, no. 5 (2010): 383-385. Full Text
  - Allen, AS, Satten, GA, Bray, SL, Dudbridge, F, and Epstein, MP. "Fast and robust association tests for untyped SNPs in case-control studies." Hum Hered 70, no. 3 (2010): 167-176. Full Text Link to Item
  - He, M, and Allen, A. "Testing gene-treatment interactions in pharmacogenetic studies." Journal of Biopharmaceutical Statistics 20, no. 2 (2010): 301-314. Full Text
  - Laje, G, Cannon, DM, Allen, AS, Klaver, JM, Peck, SA, Liu, X, Manji, HK, Drevets, WC, and McMahon, FJ. "Genetic variation in HTR2A influences serotonin transporter binding potential as measured using PET and [11C]DASB." The international journal of neuropsychopharmacology / official scientific journal of the Collegium Internationale Neuropsychopharmacologicum (CINP) (January 2010): 1-10. (Academic Article)
  - Allen, AS, and Satten, GA. "Genome-wide association analysis of rheumatoid arthritis data via haplotype sharing. (Published online)" BMC Proc 3 Suppl 7 (December 15, 2009): S30-. Link to Item
  - Sarasua, SM, Collins, JS, Williamson, DM, Satten, GA, and Allen, AS. "Effect of population stratification on the identification of significant single-nucleotide polymorphisms in genome-wide association studies. (Published online)" BMC Proc 3 Suppl 7 (December 15, 2009): S13-. Link to Item
  - Allen, AS, and Satten, GA. "A novel haplotype-sharing approach for genome-wide case-control association studies implicates the calpastatin gene in Parkinson's disease." Genet Epidemiol 33, no. 8 (December 2009): 657-667. Full Text Link to Item
  - Laje, G, Allen, AS, Akula, N, Manji, H, John Rush, A, and McMahon, FJ. "Genome-wide association study of suicidal ideation emerging during citalopram treatment of depressed outpatients." Pharmacogenetics and Genomics 19, no. 9 (September 2009): 666-674. Full Text
  - Liu, Y, Li, Y-J, Satten, GA, Allen, AS, and Tzeng, J-Y. "A regression-based association test for case-control studies that uses inferred ancestral haplotype similarity." Ann Hum Genet 73, no. Pt 5 (September 2009): 520-526. Full Text Link to Item
  - Levesque, MC, Hauswirth, DW, Mervin-Blake, S, Fernandez, CA, Patch, KB, Alexander, KM, Allgood, S, McNair, PD, Allen, AS, and Sundy, JS. "Determinants of exhaled nitric oxide levels in healthy, nonsmoking African American adults." J Allergy Clin Immunol 121, no. 2 (February 2008): 396-402.e3. Full Text Link to Item
  - Levesque, MC, Hauswirth, DW, Mervin-Blake, S, Fernandez, CA, Patch, KB, Alexander, KM, Allgood, S, McNair, PD, Allen, AS, and Sundy, JS. "Determinants of exhaled nitric oxide levels in healthy, nonsmoking African American adults." JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY 121, no. 2 (February 2008): 396-402. Full Text Link to Item
  - Allen, AS, and Satten, GA. "Robust estimation and testing of haplotype effects in case-control studies." Genet Epidemiol 32, no. 1 (January 2008): 29-40. Full Text Link to Item
  - Allen, AS. "Invited keynote talk: Haplotype sharing for genome-wide case-control association studies." Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4983 LNBI (2008): 183--. Full Text
  - Epstein, MP, Allen, AS, and Satten, GA. "Response to Lee et al." American Journal of Human Genetics 82, no. 2 (2008): 526-528. Full Text
  - Epstein, MP, Allen, AS, and Satten, GA. "A simple and improved correction for population stratification in case-control studies." American Journal of Human Genetics 80, no. 5 (May 2007): 921-930. Full Text
  - Allen, AS, and Satten, GA. "Inference on haplotype/disease association using parent-affected-child data: the projection conditional on parental haplotypes method." Genet Epidemiol 31, no. 3 (April 2007): 211-223. Full Text Link to Item
  - Allen, AS, and Satten, GA. "Statistical models for haplotype sharing in case-parent trio data." Hum Hered 64, no. 1 (2007): 35-44. Full Text Link to Item
  - Allen, AS, and Satten, GA. "Association mapping via a class of haplotype-sharing statistics." BMC Proc 1 Suppl 1 (2007): S123-. Link to Item
  - Kwee, LC, Epstein, MP, Manatunga, AK, Duncan, R, Allen, AS, and Satten, GA. "Simple methods for assessing haplotype-environment interactions in case-only and case-control studies." Genetic Epidemiology 31, no. 1 (January 2007): 75-90. Full Text
  - de Andrade, M, Allen, AS, Brinza, D, Cheng, R, Da, Y, de Vries, AR, Ewhida, A, Feng, Z, Jung, H, Hsieh, H-J, Köhler, K, Liu, Y, Liu-Mares, W, Luan, J, Marquard, V, Nolte, IM, Oh, S, Platt, A, Qin, X, Yoo, YJ, Yuan, A, Tian, X, and Won, S. "Summary of contributions to GAW15 Group 13: candidate gene association studies." Genet Epidemiol 31 Suppl 1 (2007): S110-S117. (Review) Full Text Link to Item
  - Lyles, RH, Allen, AS, Dana Flanders, W, Kupper, LL, and Christensen, DL. "Inference for case-control studies when exposure status is both informatively missing and misclassified." Statistics in Medicine 25, no. 23 (December 2006): 4065-4080. Full Text
  - Allen, AS, Martin, ER, Qin, X, and Li, Y-J. "Genetic association tests based on ranks (GATOR) for quantitative traits with and without censoring." Genetic Epidemiology 30, no. 3 (April 2006): 248-258. Full Text
  - Satten, GA, Allen, AS, and Epstein, MR. "Likelihood-based inference on haplotype effects in genetic association studies - Comment." JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION 101, no. 473 (March 2006): 107-108. Full Text Link to Item
  - Sabatti, C, Satten, GA, Allen, AS, Epstein, MP, Chatterjee, N, Spinka, C, Chen, J, Carroll, RJ, Tzeng, J-Y, Roeder, K, Li, H, Lin, DY, and Zeng, D. "Journal of the American Statistical Association: Comment." Journal of the American Statistical Association 101, no. 473 (2006): 104-118. Full Text
  - Allen, AS, and Satten, GA. "Robust testing of haplotype/disease association." Bmc Genetics 6 Suppl 1 (December 30, 2005): S69-null. Full Text
  - Li, Y-J, Martin, ER, Zhang, L, and Allen, AS. "Application of a rank-based genetic association test to age-at-onset data from the Collaborative Study on the Genetics of Alcoholism study." Bmc Genetics 6 Suppl 1 (December 30, 2005): S53-null. Full Text Open Access Copy
  - Hedayati, SS, Grambow, SC, Szczech, LA, Stechuchak, KM, Allen, AS, and Bosworth, HB. "Physician-diagnosed depression as a correlate of hospitalizations in patients receiving long-term hemodialysis." Am J Kidney Dis 46, no. 4 (October 2005): 642-649. Full Text Link to Item
  - Anstrom, KJ, Weinfurt, KP, and Allen, AS. "Estimating causal effects in randomized studies with imperfect adherence: Conceptual and statistical foundations." (August 21, 2005): 453-474. (Chapter) Full Text
  - Donahue, MP, and Allen, AS. "Genetic association studies in cardiology." Am Heart J 149, no. 6 (June 2005): 964-970. (Review) Full Text Link to Item
  - Allen, AS, Satten, GA, and Tsiatis, AA. "Locally-efficient robust estimation of haplotype-disease association in family-based studies." Biometrika 92, no. 3 (2005): 559-571. Full Text
  - Anstrom, KJ, Reed, SD, Allen, AS, Glendenning, GA, and Schulman, KA. "Long-term survival estimates for imatinib versus interferon-alpha plus low-dose cytarabine for patients with newly diagnosed chronic-phase chronic myeloid leukemia." Cancer 101, no. 11 (December 1, 2004): 2584-2592. Full Text Link to Item
  - Rampersaud, E, Allen, A, Li, Y-J, Shao, Y, Bass, M, Haynes, C, Ashley-Koch, A, Martin, ER, Schmidt, S, and Hauser, ER. "Adjusting for covariates on a slippery slope: linkage analysis of change over time." Bmc Genetics 4 Suppl 1 (December 31, 2004): S50-null. Full Text
  - Alexander, TH, Ortiz, GM, Wellons, MF, Allen, A, Grace, EJ, Schweighardt, B, Brancato, J, Sandberg, JK, Furlan, SN, Miralles, GD, Nixon, DF, and Bartlett, JA. "Changes in CD4+ T-cell differentiation phenotype during structured treatment interruption in patients with chronic HIV-1 infection." J Acquir Immune Defic Syndr 34, no. 5 (December 15, 2003): 475-481. Link to Item
  - Griffith, TF, Chua, BSY, Allen, AS, Klassen, PS, Reddan, DN, and Szczech, LA. "Characteristics of treated hypertension in incident hemodialysis and peritoneal dialysis patients." Am J Kidney Dis 42, no. 6 (December 2003): 1260-1269. Link to Item
  - Hauser, ER, and Allen, AS. "Where the rubber meets the road in pharmacogenetics: assessment of gene-environment interactions." Am Heart J 146, no. 6 (December 2003): 929-931. Full Text Link to Item
  - Kandzari, DE, Labinaz, M, Cantor, WJ, Madan, M, Gallup, DS, Hasselblad, V, Joseph, D, Allen, A, Green, C, Hidinger, KG, Krucoff, MW, Christenson, RH, Harrington, RA, and Tcheng, JE. "Reduction of myocardial ischemic injury following coronary intervention (the MC-1 to Eliminate Necrosis and Damage trial)." Am J Cardiol 92, no. 6 (September 15, 2003): 660-664. Link to Item
  - Hasselblad, V, and Allen, AS. "Power calculations for large multi-arm placebo-controlled studies of dichotomous outcomes." Stat Med 22, no. 12 (June 30, 2003): 1943-1954. Full Text Link to Item
  - Allen, AS, Rathouz, PJ, and Satten, GA. "Informative missingness in genetic association studies: case-parent designs." Am J Hum Genet 72, no. 3 (March 2003): 671-680. Full Text Link to Item
  - Lyles, RH, and Allen, AS. "Missing data in the 2 x 2 table: patterns and likelihood-based analysis for cross-sectional studies with supplemental sampling." Stat Med 22, no. 4 (February 28, 2003): 517-534. Full Text Link to Item
  - Allen, AS, Collins, JS, Rathouz, PJ, Selander, CL, and Satten, GA. "Bootstrap calibration of TRANSMIT for informative missingness of parental genotype data." Bmc Genetics 4 Suppl 1 (January 2003): S39-null. Full Text
  - Allen, AS, and Barnhart, HX. "Joint models for toxicology studies with dose-dependent number of implantations." Risk Anal 22, no. 6 (December 2002): 1165-1173. Link to Item
  - Lyles, RH, and Allen, AS. "Estimating crude or common odds ratios in case-control studies with informatively missing exposure data." Am J Epidemiol 155, no. 3 (February 1, 2002): 274-281. Link to Item
  - Dunlop, AL, Allen, AS, and Frank, E. "Involving the male partner for interpreting the basal body temperature graph." Obstet Gynecol 98, no. 1 (July 2001): 133-138. Link to Item
  - Lindeman, RD, Romero, LJ, Allen, AS, Liang, HC, Baumgartner, RN, Koehler, KM, and Garry, PJ. "Alcohol consumption is negatively associated with the prevalence of coronary heart disease in the New Mexico Elder Health Survey." J Am Geriatr Soc 47, no. 4 (April 1999): 396-401. Link to Item
  - Lindeman, RD, Romero, LJ, Hundley, R, Allen, AS, Liang, HC, Baumgartner, RN, Koehler, KM, Schade, DS, and Garry, PJ. "Prevalences of type 2 diabetes, the insulin resistance syndrome, and coronary heart disease in an elderly, biethnic population." Diabetes Care 21, no. 6 (June 1998): 959-966. Link to Item
  - Romero, LJ, Lindeman, RD, Hundley, R, Koehler, KM, Baumgartner, RN, Allen, AS, Schade, DS, LaRue, A, Ortiz, IE, and Garry, PJ. "Outcome of recruitment and report on participation rate in the New Mexico Elder Health Survey." Ethn Dis 8, no. 3 (1998): 350-359. Link to Item
  - Romero, LJ, Lindeman, RD, Koehler, KM, and Allen, A. "Influence of ethnicity on advance directives and end-of-life decisions [5]." Journal of the American Medical Association 277, no. 4 (1997): 298-299.
Teaching & Mentoring
Recent Courses
- BIOSTAT 902: Missing Data Analysis: Theory and Application 2018
- BIOSTAT 710: Statistical Genetics and Genetics Epidemiology 2017

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