Andrew Scott Allen | Scholars@Duke

Andrew Scott 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.

Current Appointments & Affiliations

Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2015
Director, Center for Statistical Genetics and Genomics, Biostatistics & Bioinformatics, Basic Science Departments 2015
Chief, Division of Integrative Genomics, Biostatistics & Bioinformatics, Basic Science Departments 2018
Member in the Duke Clinical Research Institute, Duke Clinical Research Institute, Institutes and Centers 2002

Contact Information

3 Genome Ct, 1245 MSRB III, Durham, NC 27705
Duke Box 103854, 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
- The Duke FUNCTION Center: Pioneering the comprehensive identification of combinatorial noncoding causes of disease awarded by National Institutes of Health 2020 - 2023
- Quantifying the genetic diversity of human regulatory element activity awarded by National Institutes of Health 2019 - 2023
- Duke CTSA (TL1) awarded by National Institutes of Health 2018 - 2023
- Identifying Pathogenic Non-Coding Mutations in Rare Mendelian Disease awarded by National Institutes of Health 2019 - 2022
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Integrated Biostatistical Training for CVD Research awarded by North Carolina State University 2017 - 2021
- Genetics of Acute Rejection and Chronic Lung Allograft Dysfunction awarded by Cystic Fibrosis Foundation 2019 - 2020
- Association Tests of Rare Variants Using Sequence Reads without Calling Genotypes awarded by Emory University 2015 - 2020
- A hands-on, integrative next-generation sequencing course: design, experiment, and analysis awarded by National Institutes of Health 2016 - 2020
- Host Susceptibility to S. aureus awarded by National Institutes of Health 2012 - 2020
- Statistical/Computational Methods for Pharmacogenomics and Individualized Therapy awarded by University of North Carolina - Chapel Hill 2015 - 2020
- 1/3-Identifying regulatory mutations that influence neuropsychiatric disease awarded by Columbia University 2018 - 2019
- 1/3-Identifying regulatory mutations that influence neuropsychiatric disease awarded by Columbia University 2014 - 2019
- Duke Research Training Program for Pediatricians awarded by National Institutes of Health 2002 - 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
- Academic Articles
  - Padhi, Evin M., Tristan J. Hayeck, Zhang Cheng, Sumantra Chatterjee, Brandon J. Mannion, Marta Byrska-Bishop, Marjolaine Willems, et al. “Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism.” Hum Genomics 15, no. 1 (July 13, 2021): 44. https://doi.org/10.1186/s40246-021-00342-3.
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  - Epi25 Collaborative. Electronic address: jm4279@cumc.columbia.edu, Ruth, and Ruth Epi25 Collaborative. “Sub-genic intolerance, ClinVar, and the epilepsies: A whole-exome sequencing study of 29,165 individuals.” Am J Hum Genet 108, no. 6 (June 3, 2021): 965–82. https://doi.org/10.1016/j.ajhg.2021.04.009.
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  - Kim, Young-Sook, Graham D. Johnson, Jungkyun Seo, Alejandro Barrera, Thomas N. Cowart, William H. Majoros, Alejandro Ochoa, Andrew S. Allen, and Timothy E. Reddy. “Correcting signal biases and detecting regulatory elements in STARR-seq data.” Genome Res 31, no. 5 (May 2021): 877–89. https://doi.org/10.1101/gr.269209.120.
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  - Hwang, Hongik, Matthew J. Szucs, Lei J. Ding, Andrew Allen, Xiaobai Ren, Henny Haensgen, Fan Gao, et al. “Neurogranin, Encoded by the Schizophrenia Risk Gene NRGN, Bidirectionally Modulates Synaptic Plasticity via Calmodulin-Dependent Regulation of the Neuronal Phosphoproteome.” Biol Psychiatry 89, no. 3 (February 1, 2021): 256–69. https://doi.org/10.1016/j.biopsych.2020.07.014.
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  - Stanley, Kate E., Jessica Giordano, Vanessa Thorsten, Christie Buchovecky, Amanda Thomas, Mythily Ganapathi, Jun Liao, et al. “Casual Genetic Variants in Stillbirth.” Obstetrical & Gynecological Survey 76, no. 2 (February 2021): 79–81. https://doi.org/10.1097/01.ogx.0000733520.96334.74.
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  - Li, Fan, and Andrew S. Allen. “Secondary analysis of case-control association studies: Insights on weighting-based inference motivate a new specification test.” Stat Med 39, no. 22 (September 30, 2020): 2869–82. https://doi.org/10.1002/sim.8579.
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  - Stanley, Kate E., Jessica Giordano, Vanessa Thorsten, Christie Buchovecky, Amanda Thomas, Mythily Ganapathi, Jun Liao, et al. “Causal Genetic Variants in Stillbirth.” N Engl J Med 383, no. 12 (September 17, 2020): 1107–16. https://doi.org/10.1056/NEJMoa1908753.
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  - Zhang, Mengqi, Sahar Gelfman, Janice McCarthy, Matthew B. Harms, Cristiane A. M. Moreno, David B. Goldstein, and Andrew S. Allen. “Incorporating external information to improve sparse signal detection in rare-variant gene-set-based analyses.” Genet Epidemiol 44, no. 4 (June 2020): 330–38. https://doi.org/10.1002/gepi.22283.
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  - Teoh, JiaJie, Narayan Subramanian, Maria Elena Pero, Francesca Bartolini, Ariadna Amador, Ayla Kanber, Damian Williams, et al. “Arfgef1 haploinsufficiency in mice alters neuronal endosome composition and decreases membrane surface postsynaptic GABAA receptors.” Neurobiol Dis 134 (February 2020): 104632. https://doi.org/10.1016/j.nbd.2019.104632.
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  - Majoros, William H., Young-Sook Kim, Alejandro Barrera, Fan Li, Xingyan Wang, Sarah J. Cunningham, Graham D. Johnson, et al. “Bayesian estimation of genetic regulatory effects in high-throughput reporter assays.” Bioinformatics 36, no. 2 (January 15, 2020): 331–38. https://doi.org/10.1093/bioinformatics/btz545.
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  - Povysil, Gundula, Slavé Petrovski, Joseph Hostyk, Vimla Aggarwal, Andrew S. Allen, and David B. Goldstein. “Rare-variant collapsing analyses for complex traits: guidelines and applications.” Nat Rev Genet 20, no. 12 (December 2019): 747–59. https://doi.org/10.1038/s41576-019-0177-4.
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  - Epi4K Consortium, Jeffrey P. “Quantitative analysis of phenotypic elements augments traditional electroclinical classification of common familial epilepsies.” Epilepsia 60, no. 11 (November 2019): 2194–2203. https://doi.org/10.1111/epi.16354.
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  - Edsall, Lee E., Alejandro Berrio, William H. Majoros, Devjanee Swain-Lenz, Shauna Morrow, Yoichiro Shibata, Alexias Safi, Gregory A. Wray, Gregory E. Crawford, and Andrew S. Allen. “Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach.” Genome Biol Evol 11, no. 10 (October 1, 2019): 3035–53. https://doi.org/10.1093/gbe/evz218.
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  - Cameron-Christie, Sophia, Charles J. Wolock, Emily Groopman, Slavé Petrovski, Sitharthan Kamalakaran, Gundula Povysil, Dimitrios Vitsios, et al. “Exome-Based Rare-Variant Analyses in CKD.” J Am Soc Nephrol 30, no. 6 (June 2019): 1109–22. https://doi.org/10.1681/ASN.2018090909.
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  - Li, Zhiguo, Jiaxing Lin, Alexander B. Sibley, Tracy Truong, Katherina C. Chua, Yu Jiang, Janice McCarthy, Deanna L. Kroetz, Andrew Allen, and Kouros Owzar. “Efficient estimation of grouped survival models.” Bmc Bioinformatics 20, no. 1 (May 28, 2019): 269. https://doi.org/10.1186/s12859-019-2899-x.
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  - Gelfman, Sahar, Sarah Dugger, Cristiane de Araujo Martins Moreno, Zhong Ren, Charles J. Wolock, Neil A. Shneider, Hemali Phatnani, et al. “A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS.” Genome Res 29, no. 5 (May 2019): 809–18. https://doi.org/10.1101/gr.243592.118.
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  - Lu, Congyi, Xi Shi, Andrew Allen, David Baez-Nieto, Alexandria Nikish, Neville E. Sanjana, and Jen Q. Pan. “Overexpression of NEUROG2 and NEUROG1 in human embryonic stem cells produces a network of excitatory and inhibitory neurons.” Faseb J 33, no. 4 (April 2019): 5287–99. https://doi.org/10.1096/fj.201801110RR.
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  - Hayeck, Tristan J., Nicholas Stong, Charles J. Wolock, Brett Copeland, Sitharthan Kamalakaran, David B. Goldstein, and Andrew S. Allen. “Improved Pathogenic Variant Localization via a Hierarchical Model of Sub-regional Intolerance.” Am J Hum Genet 104, no. 2 (February 7, 2019): 299–309. https://doi.org/10.1016/j.ajhg.2018.12.020.
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  - Kleinstein, Sarah E., Patrick R. Shea, Andrew S. Allen, David M. Koelle, Anna Wald, and David B. Goldstein. “Genome-wide association study (GWAS) of human host factors influencing viral severity of herpes simplex virus type 2 (HSV-2).” Genes Immun 20, no. 2 (February 2019): 112–20. https://doi.org/10.1038/s41435-018-0013-4.
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  - Qi, Wenjing, Andrew S. Allen, and Yi-Ju Li. “Family-based association tests for rare variants with censored traits.” Plos One 14, no. 1 (2019): e0210870. https://doi.org/10.1371/journal.pone.0210870.
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  - Johnson, Graham D., Alejandro Barrera, Ian C. McDowell, Anthony M. D’Ippolito, William H. Majoros, Christopher M. Vockley, Xingyan Wang, Andrew S. Allen, and Timothy E. Reddy. “Human genome-wide measurement of drug-responsive regulatory activity.” Nat Commun 9, no. 1 (December 21, 2018): 5317. https://doi.org/10.1038/s41467-018-07607-x.
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  - Shashi, Vandana, Maria M. Magiera, Dennis Klein, Maha Zaki, Kelly Schoch, Sabine Rudnik-Schöneborn, Andrew Norman, et al. “Loss of tubulin deglutamylase CCP1 causes infantile-onset neurodegeneration.” Embo J 37, no. 23 (December 3, 2018). https://doi.org/10.15252/embj.2018100540.
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  - Lin, Jiaxing, Jeremy Gresham, Tongrong Wang, So Young Kim, James Alvarez, Jeffrey S. Damrauer, Scott Floyd, et al. “bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.” Bioinformatics 34, no. 20 (October 15, 2018): 3581–83. https://doi.org/10.1093/bioinformatics/bty402.
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  - Gelfman, Sahar, Quanli Wang, Yi-Fan Lu, Diana Hall, Christopher D. Bostick, Ryan Dhindsa, Matt Halvorsen, et al. “meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays.” Plos Comput Biol 14, no. 10 (October 2018): e1006506. https://doi.org/10.1371/journal.pcbi.1006506.
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  - Winawer, Melodie R., Nicole G. Griffin, Jorge Samanamud, Evan H. Baugh, Dinesh Rathakrishnan, Senthilmurugan Ramalingam, David Zagzag, et al. “Somatic SLC35A2 variants in the brain are associated with intractable neocortical epilepsy.” Ann Neurol 83, no. 6 (June 2018): 1133–46. https://doi.org/10.1002/ana.25243.
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  - Heinzen, Erin L., Adam C. O’Neill, Xiaolin Zhu, Andrew S. Allen, Melanie Bahlo, Jamel Chelly, Ming Hui Chen, et al. “De novo and inherited private variants in MAP1B in periventricular nodular heterotopia.” Plos Genet 14, no. 5 (May 2018): e1007281. https://doi.org/10.1371/journal.pgen.1007281.
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  - Nicolas, Aude, Kevin P. Kenna, Alan E. Renton, Nicola Ticozzi, Faraz Faghri, Ruth Chia, Janice A. Dominov, et al. “Genome-wide Analyses Identify KIF5A as a Novel ALS Gene.” Neuron 97, no. 6 (March 21, 2018): 1268-1283.e6. https://doi.org/10.1016/j.neuron.2018.02.027.
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  - Assel, Melissa J., Fan Li, Ying Wang, Andrew S. Allen, Keith A. Baggerly, and Andrew J. Vickers. “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): 391–97. https://doi.org/10.1016/j.ophtha.2017.09.008.
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  - Epilepsy Genetics Initiative, Joellen M. “De novo variants in the alternative exon 5 of SCN8A cause epileptic encephalopathy.” Genet Med 20, no. 2 (February 2018): 275–81. https://doi.org/10.1038/gim.2017.100.
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  - Sibley, Alexander, Zhiguo Li, Yu Jiang, Yi-Ju Li, Cliburn Chan, Andrew Allen, and Kouros Owzar. “Facilitating the Calculation of the Efficient Score Using Symbolic Computing.” Am Stat 72, no. 2 (2018): 199–205. https://doi.org/10.1080/00031305.2017.1392361.
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  - Zhu, Xiaolin, Raghavendra Padmanabhan, Brett Copeland, Joshua Bridgers, Zhong Ren, Sitharthan Kamalakaran, Ailbhe O’Driscoll-Collins, et al. “A case-control collapsing analysis identifies epilepsy genes implicated in trio sequencing studies focused on de novo mutations.” Plos Genet 13, no. 11 (November 2017): e1007104. https://doi.org/10.1371/journal.pgen.1007104.
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  - Acharya, Chaitanya R., Kouros Owzar, and Andrew S. Allen. “Mapping eQTL by leveraging multiple tissues and DNA methylation.” Bmc Bioinformatics 18, no. 1 (October 18, 2017): 455. https://doi.org/10.1186/s12859-017-1856-9.
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  - Griffin, Nicole G., Kenneth D. Cronin, Nicole M. Walley, Christine M. Hulette, Gerald A. Grant, Mohamad A. Mikati, Heather G. LaBreche, et al. “Somatic uniparental disomy of Chromosome 16p in hemimegalencephaly.” Cold Spring Harb Mol Case Stud 3, no. 5 (September 2017). https://doi.org/10.1101/mcs.a001735.
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  - Epi4K Consortium, Jeffrey R. “Phenotypic analysis of 303 multiplex families with common epilepsies.” Brain 140, no. 8 (August 1, 2017): 2144–56. https://doi.org/10.1093/brain/awx129.
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  - Petrovski, Slavé, Jamie L. Todd, Michael T. Durheim, Quanli Wang, Jason W. Chien, Fran L. Kelly, Courtney Frankel, et al. “An Exome Sequencing Study to Assess the Role of Rare Genetic Variation in Pulmonary Fibrosis.” Am J Respir Crit Care Med 196, no. 1 (July 1, 2017): 82–93. https://doi.org/10.1164/rccm.201610-2088OC.
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  - Epi4K Consortium, C. M. S., C. M. S. EuroEPINOMICS-RES Consortium, and C. M. S. Epilepsy Phenome Genome Project. “Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data.” Eur J Hum Genet 25, no. 7 (June 2017): 894–99. https://doi.org/10.1038/ejhg.2017.61.
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  - Guo, Cong, Ian C. McDowell, Michael Nodzenski, Denise M. Scholtens, Andrew S. Allen, William L. Lowe, and Timothy E. Reddy. “Transversions have larger regulatory effects than transitions.” Bmc Genomics 18, no. 1 (May 19, 2017): 394. https://doi.org/10.1186/s12864-017-3785-4.
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  - Majoros, William H., Michael S. Campbell, Carson Holt, Erin K. DeNardo, Doreen Ware, Andrew S. Allen, Mark Yandell, and Timothy E. Reddy. “High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.” Bioinformatics 33, no. 10 (May 15, 2017): 1437–46. https://doi.org/10.1093/bioinformatics/btw799.
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  - Cyr, D. D., A. S. Allen, G. -. J. Du, F. Ruffin, C. Adams, J. T. Thaden, S. A. Maskarinec, et al. “Evaluating genetic susceptibility to Staphylococcus aureus bacteremia in African Americans using admixture mapping.” Genes Immun 18, no. 2 (March 2017): 95–99. https://doi.org/10.1038/gene.2017.6.
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  - Epi4K consortium, M Ren, and M Ren Epilepsy Phenome/Genome Project. “Ultra-rare genetic variation in common epilepsies: a case-control sequencing study.” Lancet Neurol 16, no. 2 (February 2017): 135–43. https://doi.org/10.1016/S1474-4422(16)30359-3.
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  - Jiang, Yu, Yunqi Ji, Alexander B. Sibley, Yi-Ju Li, and Andrew S. Allen. “Leveraging population information in family-based rare variant association analyses of quantitative traits.” Genet Epidemiol 41, no. 2 (February 2017): 98–107. https://doi.org/10.1002/gepi.22022.
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  - EuroEPINOMICS-RES Consortium. Electronic address: euroepinomics-RES@ua.ac.be, David B., David B. Epilepsy Phenome/Genome Project, David B. Epi4K Consortium, and David B. EuroEPINOMICS-RES Consortium. “De Novo Mutations in Synaptic Transmission Genes Including DNM1 Cause Epileptic Encephalopathies.” Am J Hum Genet 100, no. 1 (January 5, 2017): 179. https://doi.org/10.1016/j.ajhg.2016.12.012.
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  - Gussow, Ayal B., Brett R. Copeland, Ryan S. Dhindsa, Quanli Wang, Slavé Petrovski, William H. Majoros, Andrew S. Allen, and David B. Goldstein. “Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics.” Plos One 12, no. 8 (2017): e0181604. https://doi.org/10.1371/journal.pone.0181604.
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  - Xing, Chuanhua, Janice M McCarthy, Josée Dupuis, L. Adrienne Cupples, James B Meigs, Xihong Lin, and Andrew S Allen. “Robust analysis of secondary phenotypes in case-control genetic association studies.” Stat Med 35, no. 23 (October 15, 2016): 4226–37. https://doi.org/10.1002/sim.6976.
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  - Epi4K Consortium, Mark A. “De Novo Mutations in SLC1A2 and CACNA1A Are Important Causes of Epileptic Encephalopathies.” Am J Hum Genet 99, no. 2 (August 4, 2016): 287–98. https://doi.org/10.1016/j.ajhg.2016.06.003.
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  - Hildebrand, Michael S., Nicole G. Griffin, John A. Damiano, Elisa J. Cops, Rosemary Burgess, Ezgi Ozturk, Nigel C. Jones, et al. “Mutations of the Sonic Hedgehog Pathway Underlie Hypothalamic Hamartoma with Gelastic Epilepsy.” Am J Hum Genet 99, no. 2 (August 4, 2016): 423–29. https://doi.org/10.1016/j.ajhg.2016.05.031.
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  - Acharya, Chaitanya R., Janice M. McCarthy, Kouros Owzar, and Andrew S. Allen. “Exploiting expression patterns across multiple tissues to map expression quantitative trait loci.” Bmc Bioinformatics 17 (June 24, 2016): 257. https://doi.org/10.1186/s12859-016-1123-5.
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  - Hu, Yi-Juan, Peizhou Liao, H Richard Johnston, Andrew S. Allen, and Glen A. Satten. “Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls.” Plos Genet 12, no. 5 (May 2016): e1006040. https://doi.org/10.1371/journal.pgen.1006040.
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  - DeLorenze, Gerald N., Charlotte L. Nelson, William K. Scott, Andrew S. Allen, G Thomas Ray, Ai-Lin Tsai, Charles P. Quesenberry, and Vance G. Fowler. “Polymorphisms in HLA Class II Genes Are Associated With Susceptibility to Staphylococcus aureus Infection in a White Population.” J Infect Dis 213, no. 5 (March 1, 2016): 816–23. https://doi.org/10.1093/infdis/jiv483.
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  - Gussow, Ayal B., Slavé Petrovski, Quanli Wang, Andrew S. Allen, and David B. Goldstein. “The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes.” Genome Biol 17 (January 18, 2016): 9. https://doi.org/10.1186/s13059-016-0869-4.
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  - Shashi, V., P. Xie, K. Schoch, D. B. Goldstein, T. D. Howard, M. N. Berry, C. E. Schwartz, et al. “The RBMX gene as a candidate for the Shashi X-linked intellectual disability syndrome.” Clin Genet 88, no. 4 (October 2015): 386–90. https://doi.org/10.1111/cge.12511.
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  - Petrovski, Slavé, Ayal B. Gussow, Quanli Wang, Matt Halvorsen, Yujun Han, William H. Weir, Andrew S. Allen, and David B. Goldstein. “The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity.” Plos Genet 11, no. 9 (September 2015): e1005492. https://doi.org/10.1371/journal.pgen.1005492.
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  - Jiang, Yu, Yujun Han, Slavé Petrovski, Kouros Owzar, David B. Goldstein, and Andrew S. Allen. “Incorporating Functional Information in Tests of Excess De Novo Mutational Load.” Am J Hum Genet 97, no. 2 (August 6, 2015): 272–83. https://doi.org/10.1016/j.ajhg.2015.06.013.
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  - Heinzen, Erin L., Benjamin M. Neale, Stephen F. Traynelis, Andrew S. Allen, and David B. Goldstein. “The genetics of neuropsychiatric diseases: looking in and beyond the exome.” Annu Rev Neurosci 38 (July 8, 2015): 47–68. https://doi.org/10.1146/annurev-neuro-071714-034136.
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  - Mccarthy, Janice M., Patrick R. Shea, David B. Goldstein, and Andrew S. Allen. “Testing for risk and protective trends in genetic analyses of HIV acquisition.” Biostatistics 16, no. 2 (April 2015): 268–80. https://doi.org/10.1093/biostatistics/kxu044.
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  - Cirulli, Elizabeth T., Brittany N. Lasseigne, Slavé Petrovski, Peter C. Sapp, Patrick A. Dion, Claire S. Leblond, Julien Couthouis, et al. “Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways.” Science 347, no. 6229 (March 27, 2015): 1436–41. https://doi.org/10.1126/science.aaa3650.
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  - Jiang, Yu, Janice M. McCarthy, and Andrew S. Allen. “Testing the effect of rare compound-heterozygous and recessive mutations in case--parent sequencing studies.” Genet Epidemiol 39, no. 3 (March 2015): 166–72. https://doi.org/10.1002/gepi.21885.
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  - “De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies.” Am J Hum Genet 95, no. 4 (October 2, 2014): 360–70. https://doi.org/10.1016/j.ajhg.2014.08.013.
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  - Tan, Renjie, Yadong Wang, Sarah E. Kleinstein, Yongzhuang Liu, Xiaolin Zhu, Hongzhe Guo, Qinghua Jiang, Andrew S. Allen, and Mingfu Zhu. “An evaluation of copy number variation detection tools from whole-exome sequencing data.” Hum Mutat 35, no. 7 (July 2014): 899–907. https://doi.org/10.1002/humu.22537.
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  - Nelson, Charlotte L., Kimberly Pelak, Mihai V. Podgoreanu, Sun Hee Ahn, William K. Scott, Andrew S. Allen, Lindsay G. Cowell, et al. “A genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting.” Bmc Infect Dis 14 (February 13, 2014): 83. https://doi.org/10.1186/1471-2334-14-83.
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  - Satten, Glen A., Andrew S. Allen, Morna Ikeda, Jennifer G. Mulle, and Stephen T. Warren. “Robust regression analysis of copy number variation data based on a univariate score.” Plos One 9, no. 2 (2014): e86272. https://doi.org/10.1371/journal.pone.0086272.
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  - Epi4K Consortium, Melodie R., Melodie R. Epilepsy Phenome/Genome Project, Andrew S. Allen, Samuel F. Berkovic, Patrick Cossette, Norman Delanty, Dennis Dlugos, et al. “De novo mutations in epileptic encephalopathies.” Nature 501, no. 7466 (September 12, 2013): 217–21. https://doi.org/10.1038/nature12439.
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  - Goldstein, David B., Andrew Allen, Jonathan Keebler, Elliott H. Margulies, Steven Petrou, Slavé Petrovski, and Shamil Sunyaev. “Sequencing studies in human genetics: design and interpretation.” Nat Rev Genet 14, no. 7 (July 2013): 460–70. https://doi.org/10.1038/nrg3455.
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  - Hooper, Stephen R., Kathleen Curtiss, Kelly Schoch, Matcheri S. Keshavan, Andrew Allen, and Vandana Shashi. “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): 1758–69. https://doi.org/10.1016/j.ridd.2012.12.003.
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  - Long, Nanye, Samuel P. Dickson, Jessica M. Maia, Hee Shin Kim, Qianqian Zhu, and Andrew S. Allen. “Leveraging prior information to detect causal variants via multi-variant regression.” Plos Comput Biol 9, no. 6 (2013): e1003093. https://doi.org/10.1371/journal.pcbi.1003093.
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  - Petrovski, Slavé, Quanli Wang, Erin L. Heinzen, Andrew S. Allen, and David B. Goldstein. “Genic intolerance to functional variation and the interpretation of personal genomes.” Plos Genet 9, no. 8 (2013): e1003709. https://doi.org/10.1371/journal.pgen.1003709.
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  - Epstein, Michael P., Richard Duncan, Yunxuan Jiang, Karen N. Conneely, Andrew S. Allen, and Glen A. Satten. “A permutation procedure to correct for confounders in case-control studies, including tests of rare variation.” Am J Hum Genet 91, no. 2 (August 10, 2012): 215–23. https://doi.org/10.1016/j.ajhg.2012.06.004.
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  - Johnson, Nicole V., Sun Hee Ahn, Hitesh Deshmukh, Mikhail K. Levin, Charlotte L. Nelson, William K. Scott, Andrew Allen, Vance G. Fowler, and Lindsay G. Cowell. “Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus.” G3 (Bethesda) 2, no. 6 (June 2012): 693–700. https://doi.org/10.1534/g3.112.002501.
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  - Epstein, Michael P., Richard Duncan, K Alaine Broadaway, Min He, Andrew S. Allen, and Glen A. Satten. “Stratification-score matching improves correction for confounding by population stratification in case-control association studies.” Genet Epidemiol 36, no. 3 (April 2012): 195–205. https://doi.org/10.1002/gepi.21611.
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  - Xing, Chuanhua, Glen A. Satten, and Andrew S. Allen. “A weighted accumulation test for associating rare genetic variation with quantitative phenotypes.” Bmc Proc 5 Suppl 9 (November 29, 2011): S6. https://doi.org/10.1186/1753-6561-5-S9-S6.
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  - Ge, Dongliang, Elizabeth K. Ruzzo, Kevin V. Shianna, Min He, Kimberly Pelak, Erin L. Heinzen, Anna C. Need, et al. “SVA: software for annotating and visualizing sequenced human genomes.” Bioinformatics 27, no. 14 (July 15, 2011): 1998–2000. https://doi.org/10.1093/bioinformatics/btr317.
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  - Allen, Andrew S., and Glen A. Satten. “Control for confounding in case-control studies using the stratification score, a retrospective balancing score.” Am J Epidemiol 173, no. 7 (April 1, 2011): 752–60. https://doi.org/10.1093/aje/kwq406.
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  - Zhang, Lisheng, Jessica J. Connelly, Karsten Peppel, Leigh Brian, Svati H. Shah, Sarah Nelson, David R. Crosslin, et al. “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): 2754–66. https://doi.org/10.1093/hmg/ddq172.
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  - Allen, Andrew, Michael P. Epstein, and Glen A. Satten. “Score-based adjustment for confounding by population stratification in genetic association studies.” Genet Epidemiol 34, no. 5 (July 2010): 383–85. https://doi.org/10.1002/gepi.20487.
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  - Laje, Gonzalo, Dara M. Cannon, Andrew S. Allen, Jackie M. Klaver, Summer A. Peck, Xinmin Liu, Husseini K. Manji, Wayne C. Drevets, and Francis J. McMahon. “Genetic variation in HTR2A influences serotonin transporter binding potential as measured using PET and [11C]DASB.” Int J Neuropsychopharmacol 13, no. 6 (July 2010): 715–24. https://doi.org/10.1017/S1461145709991027.
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  - Allen, Andrew S., and Glen A. Satten. “SNPs in CAST are associated with Parkinson disease: a confirmation study.” Am J Med Genet B Neuropsychiatr Genet 153B, no. 4 (June 5, 2010): 973–79. https://doi.org/10.1002/ajmg.b.31061.
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  - He, Min, and Andrew Allen. “Testing gene-treatment interactions in pharmacogenetic studies.” J Biopharm Stat 20, no. 2 (March 2010): 301–14. https://doi.org/10.1080/10543400903572761.
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  - Allen, Andrew S., Glen A. Satten, Sarah L. Bray, Frank Dudbridge, and Michael P. Epstein. “Fast and robust association tests for untyped SNPs in case-control studies.” Hum Hered 70, no. 3 (2010): 167–76. https://doi.org/10.1159/000308456.
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  - Laje, G., D. M. Cannon, A. S. Allen, J. M. Klaver, S. A. Peck, X. Liu, H. K. Manji, W. C. Drevets, and F. J. McMahon. “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.
  - Allen, Andrew S., and Glen A. Satten. “Genome-wide association analysis of rheumatoid arthritis data via haplotype sharing.” Bmc Proc 3 Suppl 7 (December 15, 2009): S30. https://doi.org/10.1186/1753-6561-3-s7-s30.
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  - Sarasua, Sara M., Julianne S. Collins, Dhelia M. Williamson, Glen A. Satten, and Andrew S. Allen. “Effect of population stratification on the identification of significant single-nucleotide polymorphisms in genome-wide association studies.” Bmc Proc 3 Suppl 7 (December 15, 2009): S13. https://doi.org/10.1186/1753-6561-3-s7-s13.
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  - Allen, Andrew S., and Glen A. Satten. “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): 657–67. https://doi.org/10.1002/gepi.20417.
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  - Laje, Gonzalo, Andrew S. Allen, Nirmala Akula, Husseini Manji, A. John Rush, and Francis J. McMahon. “Genome-wide association study of suicidal ideation emerging during citalopram treatment of depressed outpatients.” Pharmacogenet Genomics 19, no. 9 (September 2009): 666–74. https://doi.org/10.1097/FPC.0b013e32832e4bcd.
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  - Liu, Youfang, Yi-Ju Li, Glen A. Satten, Andrew S. Allen, and Jung-Ying Tzeng. “A regression-based association test for case-control studies that uses inferred ancestral haplotype similarity.” Ann Hum Genet 73, no. Pt 5 (September 2009): 520–26. https://doi.org/10.1111/j.1469-1809.2009.00536.x.
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  - Allen, A. S. “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 (August 27, 2008): 183. https://doi.org/10.1007/978-3-540-79450-9_17.
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  - Levesque, Marc C., David W. Hauswirth, Sabrena Mervin-Blake, Carolyn A. Fernandez, Kistie B. Patch, Katie M. Alexander, Sallie Allgood, Patrice D. McNair, Andrew S. Allen, and John S. Sundy. “Determinants of exhaled nitric oxide levels in healthy, nonsmoking African American adults.” J Allergy Clin Immunol 121, no. 2 (February 2008): 396-402.e3. https://doi.org/10.1016/j.jaci.2007.09.031.
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  - Allen, Andrew S., and Glen A. Satten. “Robust estimation and testing of haplotype effects in case-control studies.” Genet Epidemiol 32, no. 1 (January 2008): 29–40. https://doi.org/10.1002/gepi.20259.
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  - Epstein, M. P., A. S. Allen, and G. A. Satten. “Response to Lee et al.” American Journal of Human Genetics 82, no. 2 (2008): 526–28. https://doi.org/10.1016/j.ajhg.2007.11.010.
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  - Epstein, Michael P., Andrew S. Allen, and Glen A. Satten. “A simple and improved correction for population stratification in case-control studies.” Am J Hum Genet 80, no. 5 (May 2007): 921–30. https://doi.org/10.1086/516842.
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  - Allen, Andrew S., and Glen A. Satten. “Inference on haplotype/disease association using parent-affected-child data: the projection conditional on parental haplotypes method.” Genet Epidemiol 31, no. 3 (April 2007): 211–23. https://doi.org/10.1002/gepi.20203.
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  - Allen, Andrew S., and Glen A. Satten. “Statistical models for haplotype sharing in case-parent trio data.” Hum Hered 64, no. 1 (2007): 35–44. https://doi.org/10.1159/000101421.
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  - Allen, Andrew S., and Glen A. Satten. “Association mapping via a class of haplotype-sharing statistics.” Bmc Proc 1 Suppl 1 (2007): S123. https://doi.org/10.1186/1753-6561-1-s1-s123.
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  - Andrade, Mariza de, Andrew S. Allen, Dimitru Brinza, Rong Cheng, Yang Da, André R. de Vries, Adel Ewhida, et al. “Summary of contributions to GAW15 Group 13: candidate gene association studies.” Genet Epidemiol 31 Suppl 1 (2007): S110–17. https://doi.org/10.1002/gepi.20287.
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  - Kwee, L. C., M. P. Epstein, A. K. Manatunga, R. Duncan, A. S. Allen, and G. A. Satten. “Simple methods for assessing haplotype-environment interactions in case-only and case-control studies.” Genet Epidemiol 31, no. 1 (January 2007): 75–90. https://doi.org/10.1002/gepi.20192.
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  - Lyles, Robert H., Andrew S. Allen, W. Dana Flanders, Lawrence L. Kupper, and Deborah L. Christensen. “Inference for case-control studies when exposure status is both informatively missing and misclassified.” Stat Med 25, no. 23 (December 15, 2006): 4065–80. https://doi.org/10.1002/sim.2500.
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  - Allen, Andrew S., Eden R. Martin, Xuejun Qin, and Yi-Ju Li. “Genetic association tests based on ranks (GATOR) for quantitative traits with and without censoring.” Genet Epidemiol 30, no. 3 (April 2006): 248–58. https://doi.org/10.1002/gepi.20141.
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  - Sabatti, C., G. A. Satten, A. S. Allen, M. P. Epstein, N. Chatterjee, C. Spinka, J. Chen, et al. “Journal of the American Statistical Association: Comment.” Journal of the American Statistical Association 101, no. 473 (March 1, 2006): 104–18. https://doi.org/10.1198/016214505000000817.
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  - Satten, G. A., A. S. Allen, and M. P. Epstein. “Comment.” Journal of the American Statistical Association 101, no. 473 (March 1, 2006): 107–8. https://doi.org/10.1198/016214505000000826.
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  - Allen, Andrew S., and Glen A. Satten. “Robust testing of haplotype/disease association.” Bmc Genet 6 Suppl 1 (December 30, 2005): S69. https://doi.org/10.1186/1471-2156-6-S1-S69.
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  - Li, Yi-Ju, Eden R. Martin, Ling Zhang, and Andrew S. Allen. “Application of a rank-based genetic association test to age-at-onset data from the Collaborative Study on the Genetics of Alcoholism study.” Bmc Genet 6 Suppl 1 (December 30, 2005): S53. https://doi.org/10.1186/1471-2156-6-S1-S53.
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  - Hedayati, S Susan, Steven C. Grambow, Lynda A. Szczech, Karen M. Stechuchak, Andrew S. Allen, and Hayden B. Bosworth. “Physician-diagnosed depression as a correlate of hospitalizations in patients receiving long-term hemodialysis.” Am J Kidney Dis 46, no. 4 (October 2005): 642–49. https://doi.org/10.1053/j.ajkd.2005.07.002.
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  - Allen, A. S., G. A. Satten, and A. A. Tsiatis. “Locally-efficient robust estimation of haplotype-disease association in family-based studies.” Biometrika 92, no. 3 (September 1, 2005): 559–71. https://doi.org/10.1093/biomet/92.3.559.
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  - Matchar, D. B., M. B. Patwardhan, and G. P. Samsa. “Improving adherence with clinical guidelines,” August 21, 2005, 475–89. https://doi.org/10.4324/9781410615626.
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  - Donahue, Mark P., and Andrew S. Allen. “Genetic association studies in cardiology.” Am Heart J 149, no. 6 (June 2005): 964–70. https://doi.org/10.1016/j.ahj.2005.03.011.
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  - Anstrom, Kevin J., Shelby D. Reed, Andrew S. Allen, G Alastair Glendenning, and Kevin A. Schulman. “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): 2584–92. https://doi.org/10.1002/cncr.20674.
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  - Allen, Andrew S., Julianne S. Collins, Paul J. Rathouz, Craig L. Selander, and Glen A. Satten. “Bootstrap calibration of TRANSMIT for informative missingness of parental genotype data.” Bmc Genet 4 Suppl 1 (December 31, 2003): S39. https://doi.org/10.1186/1471-2156-4-S1-S39.
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  - Rampersaud, Evadnie, Andrew Allen, Yi-Ju Li, Yujun Shao, Meredyth Bass, Carol Haynes, Allison Ashley-Koch, Eden R. Martin, Silke Schmidt, and Elizabeth R. Hauser. “Adjusting for covariates on a slippery slope: linkage analysis of change over time.” Bmc Genet 4 Suppl 1 (December 31, 2003): S50. https://doi.org/10.1186/1471-2156-4-S1-S50.
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  - Alexander, Thomas H., Gabriel M. Ortiz, Melissa F. Wellons, Andrew Allen, Edward J. Grace, Becky Schweighardt, Jason Brancato, et al. “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): 475–81. https://doi.org/10.1097/00126334-200312150-00005.
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  - Griffith, Todd F., Benjamin S. Y. Chua, Andrew S. Allen, Preston S. Klassen, Donal N. Reddan, and Lynda A. Szczech. “Characteristics of treated hypertension in incident hemodialysis and peritoneal dialysis patients.” Am J Kidney Dis 42, no. 6 (December 2003): 1260–69. https://doi.org/10.1053/j.ajkd.2003.08.028.
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  - Hauser, Elizabeth R., and Andrew S. Allen. “Where the rubber meets the road in pharmacogenetics: assessment of gene-environment interactions.” Am Heart J 146, no. 6 (December 2003): 929–31. https://doi.org/10.1016/S0002-8703(03)00502-7.
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  - Kandzari, David E., Marino Labinaz, Warren J. Cantor, Mina Madan, Dianne S. Gallup, Vic Hasselblad, Diane Joseph, et al. “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): 660–64. https://doi.org/10.1016/s0002-9149(03)00818-x.
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  - Hasselblad, Vic, and Andrew S. Allen. “Power calculations for large multi-arm placebo-controlled studies of dichotomous outcomes.” Stat Med 22, no. 12 (June 30, 2003): 1943–54. https://doi.org/10.1002/sim.1427.
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  - Allen, Andrew S., Paul J. Rathouz, and Glen A. Satten. “Informative missingness in genetic association studies: case-parent designs.” Am J Hum Genet 72, no. 3 (March 2003): 671–80. https://doi.org/10.1086/368276.
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  - Lyles, Robert H., and Andrew S. Allen. “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): 517–34. https://doi.org/10.1002/sim.1348.
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  - Allen, Andrew S., and Huiman X. Barnhart. “Joint models for toxicology studies with dose-dependent number of implantations.” Risk Anal 22, no. 6 (December 2002): 1165–73. https://doi.org/10.1111/1539-6924.00280.
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  - Lyles, Robert H., and Andrew S. Allen. “Estimating crude or common odds ratios in case-control studies with informatively missing exposure data.” Am J Epidemiol 155, no. 3 (February 1, 2002): 274–81. https://doi.org/10.1093/aje/155.3.274.
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  - Dunlop, A. L., A. S. Allen, and E. Frank. “Involving the male partner for interpreting the basal body temperature graph.” Obstet Gynecol 98, no. 1 (July 2001): 133–38. https://doi.org/10.1016/s0029-7844(01)01399-0.
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  - Lindeman, R. D., L. J. Romero, A. S. Allen, H. C. Liang, R. N. Baumgartner, K. M. Koehler, and P. J. Garry. “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. https://doi.org/10.1111/j.1532-5415.1999.tb07229.x.
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  - Lindeman, R. D., L. J. Romero, R. Hundley, A. S. Allen, H. C. Liang, R. N. Baumgartner, K. M. Koehler, D. S. Schade, and P. J. Garry. “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): 959–66. https://doi.org/10.2337/diacare.21.6.959.
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  - Romero, L. J., R. D. Lindeman, R. Hundley, K. M. Koehler, R. N. Baumgartner, A. S. Allen, D. S. Schade, A. LaRue, I. E. Ortiz, and P. J. Garry. “Outcome of recruitment and report on participation rate in the New Mexico Elder Health Survey.” Ethn Dis 8, no. 3 (1998): 350–59.
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  - Romero, L. J., R. D. Lindeman, K. M. Koehler, and A. Allen. “Influence of ethnicity on advance directives and end-of-life decisions.” Jama 277, no. 4 (January 22, 1997): 298–99.
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- Book Sections
  - Pan, Jen Q., David Baez-Nieto, Andrew Allen, Hao-Ran Wang, and Jeffrey R. Cottrell. “Developing High-Throughput Assays to Analyze and Screen Electrophysiological Phenotypes.,” 1787:235–52, 2018. https://doi.org/10.1007/978-1-4939-7847-2_18.
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  - Gonzalez, J. M., and J. W. Williams. “The effects of clinical depression and depressive symptoms on treatment adherence.” In Patient Treatment Adherence: Concepts, Interventions, and Measurement, 275–305, 2005. https://doi.org/10.4324/9781410615626.
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- Conference Papers
  - Li, Yi-Ju, Wenjing Qi, Michael A. Schmidt, Xuejun Qin, Susan H. Slifer, Andrew S. Allen, X Raymond Gao, and Eden R. Martin. “FamRVC Program for Family-based Rare Variant Association Tests for Censored Traits and its Applications to Age-at-onset of Alzheimer's Disease.” In Genetic Epidemiology, 43:892–892, 2019.
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  - Zhang, Mengqi, Sahar Gelfman, David B. Goldstein, and Andrew S. Allen. “Incorporating prior information into set-based analyses using higher criticism statistics with an application to amyotrophic lateral sclerosis.” In Genetic Epidemiology, 42:747–747. WILEY, 2018.
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  - Zhao, Jingkang, Dongshunyi Li, Jungkyun Seo, Andrew S. Allen, and Raluca Gordân. “Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding.” In Res Comput Mol Biol, 10229:336–52, 2017. https://doi.org/10.1007/978-3-319-56970-3_21.
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  - Parsia, B., T. Alsubait, J. Leo, V. Malaisé, S. Forge, M. Gregory, and A. Allen. “Lifting EMMeT to OWL getting the most from SKOS.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 9557:69–80, 2016. https://doi.org/10.1007/978-3-319-33245-1_7.
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