Andrew Scott Allen

Allen

Professor of Biostatistics & 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.

Appointments and Affiliations

  • Professor of Biostatistics & Bioinformatics
  • Director, Center for Statistical Genetics and Genomics
  • Chief, Division of Integrative Genomics
  • Member in the Duke Clinical Research Institute

Contact Information

  • Office Location: 3 Genome Ct, 1245 MSRB III, Durham, NC 27705
  • Office Phone: (919) 668-8043
  • Email Address: asallen@duke.edu
  • Websites:

Education

  • Ph.D. Emory University, 2001

Courses Taught

  • BIOSTAT 710: Statistical Genetics and Genetics Epidemiology

In the News

Representative Publications

  • Zhang, M; Gelfman, S; McCarthy, J; Harms, MB; Moreno, CAM; Goldstein, DB; Allen, AS, Incorporating external information to improve sparse signal detection in rare-variant gene-set-based analyses., Genetic Epidemiology, vol 44 no. 4 (2020), pp. 330-338 [10.1002/gepi.22283] [abs].
  • Teoh, J; Subramanian, N; Pero, ME; Bartolini, F; Amador, A; Kanber, A; Williams, D; Petri, S; Yang, M; Allen, AS; Beal, J; Haut, SR; Frankel, WN, Arfgef1 haploinsufficiency in mice alters neuronal endosome composition and decreases membrane surface postsynaptic GABAA receptors., Neurobiol Dis, vol 134 (2020) [10.1016/j.nbd.2019.104632] [abs].
  • Majoros, WH; Kim, Y-S; Barrera, A; Li, F; Wang, X; Cunningham, SJ; Johnson, GD; Guo, C; Lowe, WL; Scholtens, DM; Hayes, MG; Reddy, TE; Allen, AS, Bayesian estimation of genetic regulatory effects in high-throughput reporter assays., Bioinformatics, vol 36 no. 2 (2020), pp. 331-338 [10.1093/bioinformatics/btz545] [abs].
  • Povysil, G; Petrovski, S; Hostyk, J; Aggarwal, V; Allen, AS; Goldstein, DB, Rare-variant collapsing analyses for complex traits: guidelines and applications., Nat Rev Genet, vol 20 no. 12 (2019), pp. 747-759 [10.1038/s41576-019-0177-4] [abs].
  • Epi4K Consortium,, Quantitative analysis of phenotypic elements augments traditional electroclinical classification of common familial epilepsies., Epilepsia, vol 60 no. 11 (2019), pp. 2194-2203 [10.1111/epi.16354] [abs].
  • Edsall, LE; Berrio, A; Majoros, WH; Swain-Lenz, D; Morrow, S; Shibata, Y; Safi, A; Wray, GA; Crawford, GE; Allen, AS, Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach., Genome Biology and Evolution, vol 11 no. 10 (2019), pp. 3035-3053 [10.1093/gbe/evz218] [abs].
  • Cameron-Christie, S; Wolock, CJ; Groopman, E; Petrovski, S; Kamalakaran, S; Povysil, G; Vitsios, D; Zhang, M; Fleckner, J; March, RE; Gelfman, S; Marasa, M; Li, Y; Sanna-Cherchi, S; Kiryluk, K; Allen, AS; Fellström, BC; Haefliger, C; Platt, A; Goldstein, DB; Gharavi, AG, Exome-Based Rare-Variant Analyses in CKD., J Am Soc Nephrol, vol 30 no. 6 (2019), pp. 1109-1122 [10.1681/ASN.2018090909] [abs].
  • Li, Z; Lin, J; Sibley, AB; Truong, T; Chua, KC; Jiang, Y; McCarthy, J; Kroetz, DL; Allen, A; Owzar, K, Efficient estimation of grouped survival models., Bmc Bioinformatics, vol 20 no. 1 (2019) [10.1186/s12859-019-2899-x] [abs].
  • Hayeck, TJ; Stong, N; Wolock, CJ; Copeland, B; Kamalakaran, S; Goldstein, DB; Allen, AS, Improved Pathogenic Variant Localization via a Hierarchical Model of Sub-regional Intolerance., Am J Hum Genet, vol 104 no. 2 (2019), pp. 299-309 [10.1016/j.ajhg.2018.12.020] [abs].
  • Kleinstein, SE; Shea, PR; Allen, AS; Koelle, DM; Wald, A; Goldstein, DB, Genome-wide association study (GWAS) of human host factors influencing viral severity of herpes simplex virus type 2 (HSV-2)., Genes Immun, vol 20 no. 2 (2019), pp. 112-120 [10.1038/s41435-018-0013-4] [abs].
  • Qi, W; Allen, AS; Li, Y-J, Family-based association tests for rare variants with censored traits., Plos One, vol 14 no. 1 (2019) [10.1371/journal.pone.0210870] [abs].
  • Johnson, GD; Barrera, A; McDowell, IC; D'Ippolito, AM; Majoros, WH; Vockley, CM; Wang, X; Allen, AS; Reddy, TE, Human genome-wide measurement of drug-responsive regulatory activity., Nature Communications, vol 9 no. 1 (2018) [10.1038/s41467-018-07607-x] [abs].
  • Shashi, V; Magiera, MM; Klein, D; Zaki, M; Schoch, K; Rudnik-Schöneborn, S; Norman, A; Lopes Abath Neto, O; Dusl, M; Yuan, X; Bartesaghi, L; De Marco, P; Alfares, AA; Marom, R; Arold, ST; Guzmán-Vega, FJ; Pena, LD; Smith, EC; Steinlin, M; Babiker, MO; Mohassel, P; Foley, AR; Donkervoort, S; Kaur, R; Ghosh, PS; Stanley, V; Musaev, D; Nava, C; Mignot, C; Keren, B; Scala, M; Tassano, E; Picco, P; Doneda, P; Fiorillo, C; Issa, MY; Alassiri, A; Alahmad, A; Gerard, A; Liu, P; Yang, Y; Ertl-Wagner, B; Kranz, PG; Wentzensen, IM; Stucka, R; Stong, N; Allen, AS; Goldstein, DB; Undiagnosed Diseases Network, ; Schoser, B; Rösler, KM; Alfadhel, M; Capra, V; Chrast, R; Strom, TM; Kamsteeg, E-J; Bönnemann, CG; Gleeson, JG; Martini, R; Janke, C; Senderek, J, Loss of tubulin deglutamylase CCP1 causes infantile-onset neurodegeneration., The Embo Journal, vol 37 no. 23 (2018) [10.15252/embj.2018100540] [abs].
  • Lin, J; Gresham, J; Wang, T; Kim, SY; Alvarez, J; Damrauer, JS; Floyd, S; Granek, J; Allen, A; Chan, C; Xie, J; Owzar, K, bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens., Bioinformatics, vol 34 no. 20 (2018), pp. 3581-3583 [10.1093/bioinformatics/bty402] [abs].
  • Gelfman, S; Wang, Q; Lu, Y-F; Hall, D; Bostick, CD; Dhindsa, R; Halvorsen, M; McSweeney, KM; Cotterill, E; Edinburgh, T; Beaumont, MA; Frankel, WN; Petrovski, S; Allen, AS; Boland, MJ; Goldstein, DB; Eglen, SJ, meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays., Plos Computational Biology, vol 14 no. 10 (2018) [10.1371/journal.pcbi.1006506] [abs].
  • 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; Heinzen, EL, Somatic SLC35A2 variants in the brain are associated with intractable neocortical epilepsy., Annals of Neurology, vol 83 no. 6 (2018), pp. 1133-1146 [10.1002/ana.25243] [abs].
  • 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, ; Epilepsy Phenome/Genome Project,, De novo and inherited private variants in MAP1B in periventricular nodular heterotopia., Plos Genet, vol 14 no. 5 (2018) [10.1371/journal.pgen.1007281] [abs].
  • 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; Landers, JE, Genome-wide Analyses Identify KIF5A as a Novel ALS Gene., Neuron, vol 97 no. 6 (2018), pp. 1268-1283.e6 [10.1016/j.neuron.2018.02.027] [abs].
  • Assel, MJ; Li, F; Wang, Y; Allen, AS; Baggerly, KA; 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, vol 125 no. 3 (2018), pp. 391-397 [10.1016/j.ophtha.2017.09.008] [abs].
  • Epilepsy Genetics Initiative,, De novo variants in the alternative exon 5 of SCN8A cause epileptic encephalopathy., Genet Med, vol 20 no. 2 (2018), pp. 275-281 [10.1038/gim.2017.100] [abs].
  • Sibley, A; Li, Z; Jiang, Y; Li, Y-J; Chan, C; Allen, A; Owzar, K, Facilitating the Calculation of the Efficient Score Using Symbolic Computing., The American Statistician, vol 72 no. 2 (2018), pp. 199-205 [10.1080/00031305.2017.1392361] [abs].
  • 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; Goldstein, DB, A case-control collapsing analysis identifies epilepsy genes implicated in trio sequencing studies focused on de novo mutations., Plos Genet, vol 13 no. 11 (2017) [10.1371/journal.pgen.1007104] [abs].
  • Acharya, CR; Owzar, K; Allen, AS, Mapping eQTL by leveraging multiple tissues and DNA methylation., Bmc Bioinformatics, vol 18 no. 1 (2017) [10.1186/s12859-017-1856-9] [abs].
  • Griffin, NG; Cronin, KD; Walley, NM; Hulette, CM; Grant, GA; Mikati, MA; LaBreche, HG; Rehder, CW; Allen, AS; Crino, PB; Heinzen, EL, Somatic uniparental disomy of Chromosome 16p in hemimegalencephaly., Cold Spring Harbor Molecular Case Studies, vol 3 no. 5 (2017) [10.1101/mcs.a001735] [abs].
  • Epi4K Consortium,, Phenotypic analysis of 303 multiplex families with common epilepsies., Brain, vol 140 no. 8 (2017), pp. 2144-2156 [10.1093/brain/awx129] [abs].
  • 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; 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, vol 196 no. 1 (2017), pp. 82-93 [10.1164/rccm.201610-2088OC] [abs].
  • Epi4K Consortium, ; EuroEPINOMICS-RES Consortium, ; Epilepsy Phenome Genome Project,, Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data., European Journal of Human Genetics : Ejhg, vol 25 no. 7 (2017), pp. 894-899 [10.1038/ejhg.2017.61] [abs].
  • Guo, C; McDowell, IC; Nodzenski, M; Scholtens, DM; Allen, AS; Lowe, WL; Reddy, TE, Transversions have larger regulatory effects than transitions., Bmc Genomics, vol 18 no. 1 (2017) [10.1186/s12864-017-3785-4] [abs].
  • Majoros, WH; Campbell, MS; Holt, C; DeNardo, EK; Ware, D; Allen, AS; Yandell, M; Reddy, TE, High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE., Bioinformatics, vol 33 no. 10 (2017), pp. 1437-1446 [10.1093/bioinformatics/btw799] [abs].
  • Cyr, DD; Allen, AS; Du, G-J; Ruffin, F; Adams, C; Thaden, JT; Maskarinec, SA; Souli, M; Guo, S; Dykxhoorn, DM; Scott, WK; Fowler, VG, Evaluating genetic susceptibility to Staphylococcus aureus bacteremia in African Americans using admixture mapping., Genes Immun, vol 18 no. 2 (2017), pp. 95-99 [10.1038/gene.2017.6] [abs].
  • Jiang, Y; Ji, Y; Sibley, AB; Li, Y-J; Allen, AS, Leveraging population information in family-based rare variant association analyses of quantitative traits., Genetic Epidemiology, vol 41 no. 2 (2017), pp. 98-107 [10.1002/gepi.22022] [abs].
  • Epi4K consortium, ; Epilepsy Phenome/Genome Project,, Ultra-rare genetic variation in common epilepsies: a case-control sequencing study., Lancet Neurol, vol 16 no. 2 (2017), pp. 135-143 [10.1016/S1474-4422(16)30359-3] [abs].
  • EuroEPINOMICS-RES Consortium. Electronic address: euroepinomics-RES@ua.ac.be, ; Epilepsy Phenome/Genome Project, ; Epi4K Consortium, ; EuroEPINOMICS-RES Consortium,, De Novo Mutations in Synaptic Transmission Genes Including DNM1 Cause Epileptic Encephalopathies., Am J Hum Genet, vol 100 no. 1 (2017) [10.1016/j.ajhg.2016.12.012] [abs].
  • Gussow, AB; Copeland, BR; Dhindsa, RS; Wang, Q; Petrovski, S; Majoros, WH; Allen, AS; Goldstein, DB, Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics., Plos One, vol 12 no. 8 (2017) [10.1371/journal.pone.0181604] [abs].
  • Xing, C; M McCarthy, J; Dupuis, J; Adrienne Cupples, L; B Meigs, J; Lin, X; S Allen, A, Robust analysis of secondary phenotypes in case-control genetic association studies., Stat Med, vol 35 no. 23 (2016), pp. 4226-4237 [10.1002/sim.6976] [abs].
  • 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; Heinzen, EL, Mutations of the Sonic Hedgehog Pathway Underlie Hypothalamic Hamartoma with Gelastic Epilepsy., Am J Hum Genet, vol 99 no. 2 (2016), pp. 423-429 [10.1016/j.ajhg.2016.05.031] [abs].
  • Epi4K Consortium,, De Novo Mutations in SLC1A2 and CACNA1A Are Important Causes of Epileptic Encephalopathies., Am J Hum Genet, vol 99 no. 2 (2016), pp. 287-298 [10.1016/j.ajhg.2016.06.003] [abs].
  • Acharya, CR; McCarthy, JM; Owzar, K; Allen, AS, Exploiting expression patterns across multiple tissues to map expression quantitative trait loci., Bmc Bioinformatics, vol 17 (2016) [10.1186/s12859-016-1123-5] [abs].
  • Hu, Y-J; Liao, P; Johnston, HR; Allen, AS; Satten, GA, Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls., Plos Genet, vol 12 no. 5 (2016) [10.1371/journal.pgen.1006040] [abs].
  • DeLorenze, GN; Nelson, CL; Scott, WK; Allen, AS; Ray, GT; Tsai, A-L; Quesenberry, CP; Fowler, VG, Polymorphisms in HLA Class II Genes Are Associated With Susceptibility to Staphylococcus aureus Infection in a White Population., J Infect Dis, vol 213 no. 5 (2016), pp. 816-823 [10.1093/infdis/jiv483] [abs].
  • Gussow, AB; Petrovski, S; Wang, Q; Allen, AS; Goldstein, DB, The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes., Genome Biology, vol 17 (2016) [10.1186/s13059-016-0869-4] [abs].
  • Shashi, V; Xie, P; Schoch, K; Goldstein, DB; Howard, TD; Berry, MN; Schwartz, CE; Cronin, K; Sliwa, S; Allen, A; Need, AC, The RBMX gene as a candidate for the Shashi X-linked intellectual disability syndrome., Clin Genet, vol 88 no. 4 (2015), pp. 386-390 [10.1111/cge.12511] [abs].
  • Petrovski, S; Gussow, AB; Wang, Q; Halvorsen, M; Han, Y; Weir, WH; Allen, AS; Goldstein, DB, The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity., Plos Genet, vol 11 no. 9 (2015) [10.1371/journal.pgen.1005492] [abs].
  • Jiang, Y; Han, Y; Petrovski, S; Owzar, K; Goldstein, DB; Allen, AS, Incorporating Functional Information in Tests of Excess De Novo Mutational Load., Am J Hum Genet, vol 97 no. 2 (2015), pp. 272-283 [10.1016/j.ajhg.2015.06.013] [abs].
  • Heinzen, EL; Neale, BM; Traynelis, SF; Allen, AS; Goldstein, DB, The genetics of neuropsychiatric diseases: looking in and beyond the exome., Annu Rev Neurosci, vol 38 (2015), pp. 47-68 [10.1146/annurev-neuro-071714-034136] [abs].
  • Mccarthy, JM; Shea, PR; Goldstein, DB; Allen, AS, Testing for risk and protective trends in genetic analyses of HIV acquisition., Biostatistics, vol 16 no. 2 (2015), pp. 268-280 [10.1093/biostatistics/kxu044] [abs].
  • 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; Goldstein, DB, Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways., Science, vol 347 no. 6229 (2015), pp. 1436-1441 [10.1126/science.aaa3650] [abs].
  • Jiang, Y; McCarthy, JM; Allen, AS, Testing the effect of rare compound-heterozygous and recessive mutations in case--parent sequencing studies., Genetic Epidemiology, vol 39 no. 3 (2015), pp. 166-172 [10.1002/gepi.21885] [abs].
  • , De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies., Am J Hum Genet, vol 95 no. 4 (2014), pp. 360-370 [10.1016/j.ajhg.2014.08.013] [abs].
  • Tan, R; Wang, Y; Kleinstein, SE; Liu, Y; Zhu, X; Guo, H; Jiang, Q; Allen, AS; Zhu, M, An evaluation of copy number variation detection tools from whole-exome sequencing data., Hum Mutat, vol 35 no. 7 (2014), pp. 899-907 [10.1002/humu.22537] [abs].
  • Satten, GA; Allen, AS; Ikeda, M; Mulle, JG; Warren, ST, Robust regression analysis of copy number variation data based on a univariate score., Plos One, vol 9 no. 2 (2014) [10.1371/journal.pone.0086272] [abs].
  • 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; Winawer, MR, De novo mutations in epileptic encephalopathies., Nature, vol 501 no. 7466 (2013), pp. 217-221 [10.1038/nature12439] [abs].
  • Goldstein, DB; Allen, A; Keebler, J; Margulies, EH; Petrou, S; Petrovski, S; Sunyaev, S, Sequencing studies in human genetics: design and interpretation., Nat Rev Genet, vol 14 no. 7 (2013), pp. 460-470 [10.1038/nrg3455] [abs].
  • Hooper, SR; Curtiss, K; Schoch, K; Keshavan, MS; Allen, A; Shashi, V, A longitudinal examination of the psychoeducational, neurocognitive, and psychiatric functioning in children with 22q11.2 deletion syndrome., Res Dev Disabil, vol 34 no. 5 (2013), pp. 1758-1769 [10.1016/j.ridd.2012.12.003] [abs].
  • Long, N; Dickson, SP; Maia, JM; Kim, HS; Zhu, Q; Allen, AS, Leveraging prior information to detect causal variants via multi-variant regression., Plos Computational Biology, vol 9 no. 6 (2013) [10.1371/journal.pcbi.1003093] [abs].
  • Petrovski, S; Wang, Q; Heinzen, EL; Allen, AS; Goldstein, DB, Genic intolerance to functional variation and the interpretation of personal genomes., Plos Genet, vol 9 no. 8 (2013) [10.1371/journal.pgen.1003709] [abs].
  • Epstein, MP; Duncan, R; Jiang, Y; Conneely, KN; Allen, AS; Satten, GA, A permutation procedure to correct for confounders in case-control studies, including tests of rare variation., Am J Hum Genet, vol 91 no. 2 (2012), pp. 215-223 [10.1016/j.ajhg.2012.06.004] [abs].
  • Johnson, NV; Ahn, SH; Deshmukh, H; Levin, MK; Nelson, CL; Scott, WK; Allen, A; Fowler, VG; Cowell, LG, Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus., G3 (Bethesda, Md.), vol 2 no. 6 (2012), pp. 693-700 [10.1534/g3.112.002501] [abs].
  • Epstein, MP; Duncan, R; Broadaway, KA; He, M; Allen, AS; Satten, GA, Stratification-score matching improves correction for confounding by population stratification in case-control association studies., Genetic Epidemiology, vol 36 no. 3 (2012), pp. 195-205 [10.1002/gepi.21611] [abs].
  • Xing, C; Satten, GA; Allen, AS, A weighted accumulation test for associating rare genetic variation with quantitative phenotypes., Bmc Proceedings, vol 5 Suppl 9 (2011) [10.1186/1753-6561-5-S9-S6] [abs].
  • 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; Goldstein, DB, SVA: software for annotating and visualizing sequenced human genomes., Bioinformatics, vol 27 no. 14 (2011), pp. 1998-2000 [10.1093/bioinformatics/btr317] [abs].
  • Allen, AS; Satten, GA, Control for confounding in case-control studies using the stratification score, a retrospective balancing score., American Journal of Epidemiology, vol 173 no. 7 (2011), pp. 752-760 [10.1093/aje/kwq406] [abs].
  • Zhang, L; Connelly, JJ; Peppel, K; Brian, L; Shah, SH; Nelson, S; Crosslin, DR; Wang, T; Allen, A; Kraus, WE; Gregory, SG; Hauser, ER; 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, vol 19 no. 14 (2010), pp. 2754-2766 [10.1093/hmg/ddq172] [abs].
  • Laje, G; Cannon, DM; Allen, AS; Klaver, JM; Peck, SA; Liu, X; Manji, HK; Drevets, WC; McMahon, FJ, Genetic variation in HTR2A influences serotonin transporter binding potential as measured using PET and [11C]DASB., The International Journal of Neuropsychopharmacology, vol 13 no. 6 (2010), pp. 715-724 [10.1017/S1461145709991027] [abs].
  • Allen, A; Epstein, MP; Satten, GA, Score-based adjustment for confounding by population stratification in genetic association studies., Genetic Epidemiology, vol 34 no. 5 (2010), pp. 383-385 [10.1002/gepi.20487] [abs].
  • Allen, AS; Satten, GA, SNPs in CAST are associated with Parkinson disease: a confirmation study., Am J Med Genet B Neuropsychiatr Genet, vol 153B no. 4 (2010), pp. 973-979 [10.1002/ajmg.b.31061] [abs].
  • He, M; Allen, A, Testing gene-treatment interactions in pharmacogenetic studies., J Biopharm Stat, vol 20 no. 2 (2010), pp. 301-314 [10.1080/10543400903572761] [abs].
  • Laje, G; Cannon, DM; Allen, AS; Klaver, JM; Peck, SA; Liu, X; Manji, HK; Drevets, WC; McMahon, FJ, Genetic variation in HTR2A influences serotonin transporter binding potential as measured using PET and [11C]DASB., The International Journal of Neuropsychopharmacology (2010), pp. 1-10 [abs].
  • Allen, AS; Satten, GA; Bray, SL; Dudbridge, F; Epstein, MP, Fast and robust association tests for untyped SNPs in case-control studies., Hum Hered, vol 70 no. 3 (2010), pp. 167-176 [10.1159/000308456] [abs].
  • Allen, AS; Satten, GA, Genome-wide association analysis of rheumatoid arthritis data via haplotype sharing., Bmc Proceedings, vol 3 Suppl 7 (2009) [10.1186/1753-6561-3-s7-s30] [abs].
  • Sarasua, SM; Collins, JS; Williamson, DM; Satten, GA; Allen, AS, Effect of population stratification on the identification of significant single-nucleotide polymorphisms in genome-wide association studies., Bmc Proceedings, vol 3 Suppl 7 (2009) [10.1186/1753-6561-3-s7-s13] [abs].
  • Allen, AS; Satten, GA, A novel haplotype-sharing approach for genome-wide case-control association studies implicates the calpastatin gene in Parkinson's disease., Genetic Epidemiology, vol 33 no. 8 (2009), pp. 657-667 [10.1002/gepi.20417] [abs].
  • Laje, G; Allen, AS; Akula, N; Manji, H; John Rush, A; McMahon, FJ, Genome-wide association study of suicidal ideation emerging during citalopram treatment of depressed outpatients., Pharmacogenetics and Genomics, vol 19 no. 9 (2009), pp. 666-674 [10.1097/FPC.0b013e32832e4bcd] [abs].
  • Liu, Y; Li, Y-J; Satten, GA; Allen, AS; Tzeng, J-Y, A regression-based association test for case-control studies that uses inferred ancestral haplotype similarity., Ann Hum Genet, vol 73 no. Pt 5 (2009), pp. 520-526 [10.1111/j.1469-1809.2009.00536.x] [abs].
  • Levesque, MC; Hauswirth, DW; Mervin-Blake, S; Fernandez, CA; Patch, KB; Alexander, KM; Allgood, S; McNair, PD; Allen, AS; Sundy, JS, Determinants of exhaled nitric oxide levels in healthy, nonsmoking African American adults., The Journal of Allergy and Clinical Immunology, vol 121 no. 2 (2008), pp. 396-402.e3 [10.1016/j.jaci.2007.09.031] [abs].
  • Allen, AS; Satten, GA, Robust estimation and testing of haplotype effects in case-control studies., Genetic Epidemiology, vol 32 no. 1 (2008), pp. 29-40 [10.1002/gepi.20259] [abs].
  • Epstein, MP; Allen, AS; Satten, GA, Response to Lee et al., American Journal of Human Genetics, vol 82 no. 2 (2008), pp. 526-528 [10.1016/j.ajhg.2007.11.010] [abs].
  • Epstein, MP; Allen, AS; Satten, GA, A simple and improved correction for population stratification in case-control studies., American Journal of Human Genetics, vol 80 no. 5 (2007), pp. 921-930 [10.1086/516842] [abs].
  • Allen, AS; Satten, GA, Inference on haplotype/disease association using parent-affected-child data: the projection conditional on parental haplotypes method., Genetic Epidemiology, vol 31 no. 3 (2007), pp. 211-223 [10.1002/gepi.20203] [abs].
  • Kwee, LC; Epstein, MP; Manatunga, AK; Duncan, R; Allen, AS; Satten, GA, Simple methods for assessing haplotype-environment interactions in case-only and case-control studies., Genetic Epidemiology, vol 31 no. 1 (2007), pp. 75-90 [10.1002/gepi.20192] [abs].
  • Allen, AS; Satten, GA, Statistical models for haplotype sharing in case-parent trio data., Human Heredity, vol 64 no. 1 (2007), pp. 35-44 [10.1159/000101421] [abs].
  • 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; Won, S, Summary of contributions to GAW15 Group 13: candidate gene association studies., Genetic Epidemiology, vol 31 Suppl 1 (2007), pp. S110-S117 [10.1002/gepi.20287] [abs].
  • Allen, AS; Satten, GA, Association mapping via a class of haplotype-sharing statistics., Bmc Proceedings, vol 1 Suppl 1 (2007) [10.1186/1753-6561-1-s1-s123] [abs].
  • Lyles, RH; Allen, AS; Dana Flanders, W; Kupper, LL; Christensen, DL, Inference for case-control studies when exposure status is both informatively missing and misclassified., Statistics in Medicine, vol 25 no. 23 (2006), pp. 4065-4080 [10.1002/sim.2500] [abs].
  • Allen, AS; Martin, ER; Qin, X; Li, Y-J, Genetic association tests based on ranks (GATOR) for quantitative traits with and without censoring., Genetic Epidemiology, vol 30 no. 3 (2006), pp. 248-258 [10.1002/gepi.20141] [abs].
  • Allen, AS; Satten, GA, Robust testing of haplotype/disease association., Bmc Genetics, vol 6 Suppl 1 (2005) [10.1186/1471-2156-6-S1-S69] [abs].
  • Li, Y-J; Martin, ER; Zhang, L; 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, vol 6 Suppl 1 (2005) [10.1186/1471-2156-6-S1-S53] [abs].
  • Hedayati, SS; Grambow, SC; Szczech, LA; Stechuchak, KM; Allen, AS; Bosworth, HB, Physician-diagnosed depression as a correlate of hospitalizations in patients receiving long-term hemodialysis., Am J Kidney Dis, vol 46 no. 4 (2005), pp. 642-649 [10.1053/j.ajkd.2005.07.002] [abs].
  • Donahue, MP; Allen, AS, Genetic association studies in cardiology., American Heart Journal, vol 149 no. 6 (2005), pp. 964-970 [10.1016/j.ahj.2005.03.011] [abs].
  • Anstrom, KJ; Reed, SD; Allen, AS; Glendenning, GA; 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, vol 101 no. 11 (2004), pp. 2584-2592 [10.1002/cncr.20674] [abs].
  • Allen, AS; Collins, JS; Rathouz, PJ; Selander, CL; Satten, GA, Bootstrap calibration of TRANSMIT for informative missingness of parental genotype data., Bmc Genetics, vol 4 Suppl 1 (2003) [10.1186/1471-2156-4-S1-S39] [abs].
  • Griffith, TF; Chua, BSY; Allen, AS; Klassen, PS; Reddan, DN; Szczech, LA, Characteristics of treated hypertension in incident hemodialysis and peritoneal dialysis patients., Am J Kidney Dis, vol 42 no. 6 (2003), pp. 1260-1269 [10.1053/j.ajkd.2003.08.028] [abs].
  • Hauser, ER; Allen, AS, Where the rubber meets the road in pharmacogenetics: assessment of gene-environment interactions., American Heart Journal, vol 146 no. 6 (2003), pp. 929-931 [10.1016/S0002-8703(03)00502-7] [abs].
  • Hasselblad, V; Allen, AS, Power calculations for large multi-arm placebo-controlled studies of dichotomous outcomes., Statistics in Medicine, vol 22 no. 12 (2003), pp. 1943-1954 [10.1002/sim.1427] [abs].
  • Allen, AS; Rathouz, PJ; Satten, GA, Informative missingness in genetic association studies: case-parent designs., American Journal of Human Genetics, vol 72 no. 3 (2003), pp. 671-680 [10.1086/368276] [abs].
  • Lyles, RH; Allen, AS, Missing data in the 2 x 2 table: patterns and likelihood-based analysis for cross-sectional studies with supplemental sampling., Statistics in Medicine, vol 22 no. 4 (2003), pp. 517-534 [10.1002/sim.1348] [abs].
  • Allen, AS; Barnhart, HX, Joint models for toxicology studies with dose-dependent number of implantations., Risk Analysis : an Official Publication of the Society for Risk Analysis, vol 22 no. 6 (2002), pp. 1165-1173 [10.1111/1539-6924.00280] [abs].
  • Lyles, RH; Allen, AS, Estimating crude or common odds ratios in case-control studies with informatively missing exposure data., American Journal of Epidemiology, vol 155 no. 3 (2002), pp. 274-281 [10.1093/aje/155.3.274] [abs].
  • Dunlop, AL; Allen, AS; Frank, E, Involving the male partner for interpreting the basal body temperature graph., Obstetrics and Gynecology, vol 98 no. 1 (2001), pp. 133-138 [10.1016/s0029-7844(01)01399-0] [abs].
  • Lindeman, RD; Romero, LJ; Allen, AS; Liang, HC; Baumgartner, RN; Koehler, KM; Garry, PJ, Alcohol consumption is negatively associated with the prevalence of coronary heart disease in the New Mexico Elder Health Survey., Journal of the American Geriatrics Society, vol 47 no. 4 (1999), pp. 396-401 [10.1111/j.1532-5415.1999.tb07229.x] [abs].
  • Lindeman, RD; Romero, LJ; Hundley, R; Allen, AS; Liang, HC; Baumgartner, RN; Koehler, KM; Schade, DS; Garry, PJ, Prevalences of type 2 diabetes, the insulin resistance syndrome, and coronary heart disease in an elderly, biethnic population., Diabetes Care, vol 21 no. 6 (1998), pp. 959-966 [10.2337/diacare.21.6.959] [abs].
  • Romero, LJ; Lindeman, RD; Hundley, R; Koehler, KM; Baumgartner, RN; Allen, AS; Schade, DS; LaRue, A; Ortiz, IE; Garry, PJ, Outcome of recruitment and report on participation rate in the New Mexico Elder Health Survey., Ethnicity & Disease, vol 8 no. 3 (1998), pp. 350-359 [abs].