Computational Biology and Bioinformatics

29.Joshua C. Bis, Xueqiu Jian, Brian W. Kunkle, Yuning Chen, Kara L. Hamilton-Nelson, William S. Bush, William J. Salerno, …, Alzheimer's Disease Sequencing Project*, et al. 2018 (forthcoming). Whole exome sequencing study identifies novel rare and common Alzheimer's-associated variants involved in immune response and transcriptional regulation. Molecular Psychiatry. Published online Aug 14, 2018. PMID: 30108311. [*Alejandro Q Nato Jr. listed as a member of the Alzheimer's Disease Sequencing Project]

28.Rafael A. Nafikov, Alejandro Q. Nato Jr, Harkirat Sohi, Bowen Wang, Lisa Brown Andrea R. Horimoto, Badri N. Vardarajan, Sandra M. Barral, Giuseppe Tosto, Richard P. Mayeux, Timothy A. Thornton, Elizabeth Blue, and Ellen M. Wijsman. 2018 (forthcoming). Analysis of pedigree data in populations with multiple ancestries: Strategies for dealing with admixture in Caribbean Hispanic families from the ADSP. Genetic Epidemiology. Published online June 3, 2018. PMID: 29862559.

27.Badri N. Vardarajan, Sandra Barral, James Jaworski, Gary W. Beecham, Elizabeth Blue, …, for the Alzheimer's Disease Sequencing Project*. 2018. Whole genome sequencing of Caribbean Hispanic families with late-onset Alzheimer's disease. Annals of Clinical and Translational Neurology. 5(4):406-417. PMID: 29688227. PMCID: PMC5899906. [*Alejandro Q. Nato Jr. listed as a member of the Alzheimer's Disease Sequencing Project]

26.Adam C. Naj, Honghuang Lin, Badri N Vardarajan, Simon White, Daniel Lancour, Yiyi Ma, Michael Schmidt, Fangui Sun, Mariusz Butkiewicz, William S Bush, Brian W Kunkle, John S Malamon, Najaf Amin, Seung H Choi, Kara L Hamilton-Nelson, Sven van der Lee, Namrata Gupta, Daniel C Koboldt, Mohamad Saad, Bowen Wang, Alejandro Q Nato, Jr., Harkirat K Sohi, Amanda Kuzma, Li-San Wang, L. Adrienne Cupples, Cornelia van Duijn, Sudha Seshadri, Gerard D Schellenberg, Eric Boerwinkle, Josh Bis, Josée Dupuis, William J Salerno, Ellen M Wijsman, Eden R Martin, Anita L DeStefano, and Alzheimer's Disease Sequencing Project. 2018 (forthcoming). Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's Disease Sequencing Project. Genomics. Published online May 29, 2018. PMID: 29857119.

25.Elizabeth E. Blue, Joshua C. Bis, Michael O. Dorschner, Debby W. Tsuang, Sandra M. Barral, Gary Beecham, Jennifer E. Below, William S. Bush, Mariusz Butkiewicz, Carlos Cruchaga, Anita DeStefano, Lindsay A. Farrer, Alison Goate, Jonathan Haines, Jim Jaworski, Gyungah Jun, Brian Kunkle, Amanda Kuzma, Jenny J. Lee, Kathryn L. Lunetta, Yiyi Ma, Eden Martin, Adam Naj, Alejandro Q. Nato, Patrick Navas, Hiep Nguyen, Christiane Reitz, Dolly Reyes, William Salerno, Gerard D. Schellenberg, Sudha Seshadri, Harkirat Sohi, Timothy A. Thornton, Otto Valadares, Cornelia van Duijn, Badri N. Vardarajan, Li-San Wang, Eric Boerwinkle, Josée Dupuis, Margaret A. Pericak-Vance, Richard Mayeux, Ellen M. Wijsman. 2018 Genetic variation in genes underlying diverse dementias may explain a small proportion of cases in the Alzheimer's Disease Sequencing Project. Dementia and Geriatric Cognitive Disorders. 45(1-2):1-17. Epub 02/27/2018. PMID: 29486463. PMCID: PMC5971141.

24.Khalid Kunji, Ehsan Ullah, Alejandro Q. Nato, Jr., Ellen M. Wijsman, and Mohamad Saad. 2018. GIGI-Quick: A fast approach to impute missing genotypes in genome-wide association family data. Bioinformatics. 34(9): 1591-1593. PMID: 29267877. PMCID: PMC5925782.

23.D. T. Truong, L. D. Shriberg, S. D. Smith, K. L. Chapman, A. R. Scheer-Cohen, M. M. C. DeMille, A. K. Adams, A. Q. Nato, E. M. Wijsman, J. D. Eicher, and J. R. Gruen. 2016. Multipoint genome-wide linkage scan for nonword repetition further supports chromosome 13q as a locus for verbal trait disorders in a multigenerational family. Human Genetics. 135(12):1329-1341. Accepted 07/22/2016. Epub 08/17/2016. PMID: 27535846. PMCID: PMC5065602.

22.Elizabeth M. Blue, Lisa A. Brown, Matthew P. Conomos, Jennifer Kirk, Alejandro Q. Nato, Alice B. Popejoy, Jesse D. Raffa, J. Ranola, Timothy A. Thornton, and Ellen M. Wijsman. 2016. Estimation of relationships between subjects and phenotypes in admixed families. BMC Proceedings. 10(Suppl 7):357-362. Accepted 02/24/2015. PMID: 27980662. PMCID: PMC5133521.

21.Mohamad Saad, Alejandro Q. Nato, Fiona L. Grimson, Steven M. Lewis, Elizabeth M. Blue, Elizabeth A. Thompson, and Ellen M. Wijsman. 2016. Population- and pedigree-based imputation and identity by descent estimation in admixed family data. BMC Proceedings. 10(Suppl 7):295-301. Accepted 01/26/2015. PMID: 27980652. PMCID: PMC5133511.

20.Beate Peter, Ellen M. Wijsman, Alejandro Q. Nato, Jr., UW Center for Mendelian Genomics, Mark M. Matsushita, Kathy L. Chapman, Ian B. Stanaway, John Wolff, Kaori Oda, Virginia B. Gabo, and Wendy H. Raskind. 2016. Genetic candidate variants in two multigenerational families with childhood apraxia of speech. PLoS One. 11(4):e0153864. Accepted 04/12/2016. Epub 04/27/2016. PMID: 27120335. PMCID: PMC4847873. [Abstract]

19.Alejandro Q. Nato, Jr., Nicola H. Chapman, Harkirat K. Sohi, Hiep D. Nguyen, Zoran Brkanac, and Ellen M. Wijsman. 2015. PBAP: A pipeline for family-based quality control of pedigree structures and dense genetic marker data. Bioinformatics. 31(23):3790-3798. Accepted 07/25/2015. Epub 07/30/2015. PMID: 26231429. PMCID: PMC4668752. [Abstract]

18.Nicola H Chapman, Alejandro Q. Nato, Jr., Raphael Bernier, Katy Ankeman, Harkirat K. Sohi, Jeff Munson, Ashok Patowary, Marilyn Archer, Elizabeth M Blue, Sara J Webb, Hilary Coon, Wendy H Raskind, Zoran Brkanac and Ellen M Wijsman. 2015. Whole exome sequencing in extended families with autism spectrum disorder implicates four candidate genes. Human Genetics. 134(10):10655-1068. Accepted 07/24/2015. Epub 07/24/2015. PMID: 26204995. PMCID: PMC4578871. [Abstract]

17.Bo Li, Paul G. Matteson, Myka F. Ababon, Alejandro Q. Nato, Jr., Yong Lin, Vikas Nanda, Tara C. Matise, and James H. Millonig. 2015. The orphan GPCR, Gpr161, regulates the retinoic acid and canonical Wnt pathways during neurulation. Developmental Biology. 402(1):17-31. Accepted 02/10/2015. Epub 03/06/2015. PMID: 25753732. [Abstract]

16.Adam E. Locke, Bratali Kahali, Sonja I. Berndt, Anne E. Justice, Tune H. Pers, Felix R. Day, …, The PAGE Consortium*, et al. 2015. Genetic studies of body mass index yield new insights for obesity biology. Nature. 518(7538):197-206. Accepted 12/23/2014. Epub 02/11/2015. PMID: 25673413. PMCID: PMC4382211. [Abstract] [*Andrew Nato listed as a member of the PAGE Consortium]

15.Dmitry Shungin, Thomas W. Winkler, Damien C. Croteau-Chonka, Teresa Ferreira, Adam E. Locke, Reedik Mägi, …, The PAGE Consortium*, et al. 2015. New genetic loci link adipose and insulin biology to body fat distribution. Nature. 518(7538):187-196. Accepted 12/02/2014. Epub 02/11/2015. PMID: 25673412. PMCID: PMC4338562. [Abstract] [*Andrew Nato listed as a member of The PAGE Consortium]

14.Andrew R. Wood, Tonu Esko, Jian Yang, Sailaja Vedantam, Tune H Pers, Stefan Gustafsson, …, The PAGE Consortium*, et al. 2015. Defining the role of common variation in the genomic and biological architecture of adult human height. Nature. 46(11):1173-1186. Accepted 08/29/2014. Epub 10/5/2014. PMID: 25282103. PMCID: PMC4250049. [Abstract] [*Andrew Nato listed as a member of The PAGE Consortium]

13.Anthony Musolf, Alejandro Q. Nato, Jr., Douglas Londono, Lisheng Zhou, Tara C. Matise, and Derek Gordon. 2014. Mapping genes with longitudinal phenotypes via Bayesian posterior probabilities. BMC Proceedings. 8(Suppl 1):S81. Accepted 03/21/2013. Epub 06/17/2014. PMID: 25519410. PMCID: PMC4143622. [Abstract]

12.Logan Dumitrescu, Cara L. Carty, Nora Franceschini, Lucia A. Hindorff, Shelley A. Cole, Petra Bůžková, Fredrick R. Schumacher, Charles B. Eaton, Robert J. Goodloe, David J. Duggan, Jeff Haessler, Barbara Cochran, Brian E. Henderson, Iona Cheng, Karen C. Johnson, Chris S. Carlson, Shelly-Anne Love, Kristin Brown-Gentry, Alejandro Q. Nato, Miguel Quibrera, Ralph Shohet, José Luis Ambite, Lynne R. Wilkens, Loïc Le Marchand, Christopher A. Haiman, Steven Buyske, Charles Kooperberg, Kari E. North, Myriam Fornage, and Dana C. Crawford. 2013. No evidence of interaction between known lipid-associated genetic variants and smoking in the multi-ethnic PAGE population. Human Genetics. 132(12):1427-31. Accepted 08/29/2013. Epub 10/08/2013. PMID: 24100633. PMCID: PMC3895337. [Abstract]

11.Megan D. Fesinmeyer, James B. Meigs, Kari E. North, Fredrick R Schumacher, Petra Bůžková, Nora Franceschini, Jeffrey Haessler, Robert Goodloe, Kylee L. Spencer, V. Saroja Voruganti, Barbara V. Howard, Rebecca Jackson, Laurence N. Kolonel, Simin Liu, JoAnn E. Manson, Kristine R. Monroe, Kenneth Mukamal, Holli H. Dilks, Sarah A. Pendergrass, Andrew Nato, Peggy Wan, Lynne R. Wilkens, Loic Le Marchand, José Luis Ambite, Steven Buyske, Jose C. Florez, Dana C. Crawford, Lucia A. Hindorff, Christopher A. Haiman, Ulrike Peters, and James S. Pankow. 2013. Genetic variants associated with fasting glucose and insulin concentrations in an ethnically diverse population: results from the Population Architecture using Genomics and Epidemiology (PAGE) Study. BMC Medical Genetics. 14:98. Accepted 09/10/2013. Epub 09/25/2013. PMID: 24063630. PMCID: PMC3849560. [Abstract]

10.Christopher S. Carlson, Tara C. Matise, Kari E. North, Christopher A. Haiman, Megan D. Fesinmeyer, Steven Buyske, Fredrick R. Schumacher, Ulrike Peters, Nora Franceschini, Marylyn D. Ritchie, David J. Duggan, Kylee L. Spencer, Logan Dumitrescu, Charles B. Eaton, Fridtjof Thomas, Alicia Young, Cara Carty, Gerardo Heiss, Loic Le Marchand, Dana C. Crawford, Lucia A. Hindorff, Charles L. Kooperberg, PAGE Consortium*. 2015. Generalization and Dilution of Association Results from European GWAS in Populations of Non-European Ancestry: The PAGE Study. PLoS Biology. 11(9):e1001661. Accepted 08/08/2013. Epub 09/17/2013. PMID: 24068893. PMCID: PMC3775722. [Abstract] [*Andrew Nato listed as a member of the PAGE Consortium]

9.Logan Dumitrescu, Cara L. Carty, Nora Franceschini, Lucia A. Hindorff, Shelley A. Cole, Petra Bůžková, Fredrick R. Schumacher, Charles B. Eaton, Robert J. Goodloe, David J. Duggan, Jeff Haessler, Barbara Cochran, Brian E. Henderson, Iona Cheng, Karen C. Johnson, Chris S. Carlson, Shelly-Anne Love, Kristin Brown-Gentry, Alejandro Q. Nato, Miguel Quibrera, Garnet Anderson, Ralph Shohet, José Luis Ambite, Lynne R. Wilkens, Loïc Le Marchand, Christopher A. Haiman, Steven Buyske, Charles Kooperberg, Kari E. North, Myriam Fornage, and Dana C. Crawford. 2013. Post genome-wide association study challenges for lipid traits: describing age as a modifier of gene-lipid associations in the Population Architecture using Genomics and Epidemiology (PAGE) study. Annals of Human Genetics. Accepted 04/01/2013. Epub 06/28/2013. PMID: 23808484. PMCID: PMC3796061. [Abstract]

8.Lili Zhang, Nora Franceschini, Petra Buzkova, Christina L. Wassel, Mary J. Roman, Kari E. North, Dana C. Crawford, Jonathan Boston, Kristin D. Brown-Gentry, Shelley A. Cole, Ewa Deelman, Robert Goodloe, Gerardo Heiss, Nancy S. Jenny, Neal W. Jorgensen, Tara C. Matise, Bob E. McClellan, Jr., Alejandro Q. Nato, Jr., Marylyn D. Ritchie, Sarah Wilson, and WH Linda Kao. 2013. Lack of associations of ten candidate coronary heart disease risk genetic variants and subclinical atherosclerosis in four U.S. populations: the Population Architecture using Genomics and Epidemiology (PAGE) Study Atherosclerosis. 228(2):390-9. Accepted 03/13/2013. Epub 03/13/2013. PMID: 23587283. PMCID: PMC3717342. [Abstract]

7.Wonkuk Kim, Douglas Londono, Lisheng Zhou, Jinchuan Xing, Alejandro Q. Nato, Jr., Anthony M. Musolf, Tara C. Matise, Stephen J. Finch, and Derek Gordon. 2012. Single-variant and multi-variant tests for genetic association with next generation sequencing that are robust to sequencing error Human Heredity.74(3-4):172-83. Epub 03/13/2013. Accepted 01/04/2013. PMID: 23594495. PMCID: PMC3863939. [Abstract]

6.Makoto K. Shimada, Karuna Panchapakesan, Sarah Tishkoff, Alejandro Q. Nato, Jr., and Jody Hey. 2007. Divergent haplotypes and human history as revealed in a worldwide survey of X-linked DNA sequence variation. Mol Biol Evol. 24(3):687-698. (Adv Access: 14 Dec 2006). PMID: 17175528. [PDF]

5.Elmer-Rico E. Mojica, Alejandro Q. Nato, Jr., Maria Edlyn T. Ambas, Chitho P. Feliciano, Maria Leonora D.L. Francisco, and Custer C. Deocaris. 2005. Application of irradiation as pretreatment method in the production of fermented fish paste. J Appl Sci Res. 1(1): 90-94. [PDF]

4.Teresa Yulo-Nazarea, Alejandro Q. Nato, Jr., Eliza B. Enriquez, Lorna Jean H. Palad, Fe M. dela Cruz, Teofilo Y. Garcia, Antonio A. Asada, Jr., and Maria Lucia C. Cobar. 2004. Radiological surveillance of the former U.S. Base: Poro Point, San Fernando City, La Union. Philipp Nucl J. 14:40-47.[PDF]

3.Custer C. Deocaris, Maria Cereza R. Velasco, Earl Louis Sempio, Alejandro Q. Nato, Jr., and Apolinario D. Nazarea. 2002. An evolutionary perspective on the possible involvement of plasminogen in the pathology of bovine spongiform encelopathy. Phil J Vet Anim Sci.28(2):58-68. [PDF]

2.Alejandro Q. Nato, Jr., Eliza B. Enriquez, Ariel T. Ortiz, and Custer C. Deocaris. 2001. Putative bioindicator of ¹³⁷Cs in Perna viridis. Philipp Nucl J. 13:77-79.[PDF]

1.Teresa Yulo-Nazarea, Ma. Lucia C. Cobar, Alejandro Q. Nato, Jr., and Apolinario D. Nazarea. 2001. Somatic mutation in peripheral blood lymphocytes among Metro Manila residents: Indicator of exposure to environmental pollution. Philipp Nucl J. 13:11-22.[PDF]