Dr. Daniel E Weeks, PhD

Dr. Weeks' research focuses on statistical human genetics in the area of mapping susceptibility loci involved in complex diseases. His primary interest is developing new mapping methods, which involves developing algorithms and statistics, implementing them in computer programs, and testing them on real and simulated data. In addition, he is actively involved in a large number of collaborative disease gene mapping projects, all of which constantly challenge him to develop new and more useful methods for dealing with the complexities of real data. These diseases include age-related macular degeneration, obesity, and asthma.  In addition, he and his colleagues are studying the effects of methylation on risk for childhood asthma, pre-eclampsia, on patient recovery outcomes after aneurysmal subarachnoid hemorrhage and traumatic brain injury, and on cognitive function within the context of treatment for breast cancer.

1983         B.A., summa cum laude, Biology and Mathematics, Colby College, Waterville, ME

1983-84   Graduate studies in Applied Mathematics, Rutgers University, New Brunswick, NJ
1985         M.S., Biomathematics, University of California, Los Angeles
1988         Ph.D., Biomathematics (Kenneth Lange, mentor), University of California, Los Angeles
1989-90    Postdoctoral training (Jurg Ott, mentor), Columbia University, New York, NY

Fellowships:
1982       Research Training Program, The Jackson Laboratory, Bar Harbor, ME (David E. Harrison, mentor)
1983       Summer Student Fellow, Woods Hole Oceanographic Institution, MA (Hal Caswell, mentor)
1986-87  Genetic Mechanisms Training Program, UCLA
1987-88  Systems and Integrative Biology Training Program, UCLA
1989-90  Postdoctoral Fellow with Jurg Ott, Ph.D., Columbia University

HUGEN 2070 Bioinformatics for Human Genetics
HUGEN 2080 Statistical Genetics

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1989-90   Research Scientist, New York State Psychiatric Institute
1990-96   Assistant Professor of Human Genetics (tenure-track), University of Pittsburgh
1994-98   Head of Statistical Genetics - Methods, Wellcome Trust Centre for Human Genetics, University of Oxford
1996-02   Associate Professor of Human Genetics (tenured), University of Pittsburgh
2002-03   Associate Professor of Biostatistics (joint appointment), University of Pittsburgh
2004        Acting Chair, Department of Human Genetics
2005        Acting Vice Chair, Department of Human Genetics
2002-       Professor of Human Genetics (tenured), University of Pittsburgh
2003-       Professor of Biostatistics (joint appointment), University of Pittsburgh

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Recent publications (from more than 200 peer-reviewed manuscripts)
Last updated July 11, 2019 - use the links above for up-to-date information.

†Graduate student; ‡Post-doctoral trainee.

1. Baron RV, Stickel JR, Weeks DE (2018) The Mega2R package: R tools for accessing and processing genetic data in common formats. F1000Res 7:1352. PMCID: PMC6137409.2

2. Govil M, Mukhopadhyay N, Weeks DE, Feingold E, Shaffer JR, Levy SM, Vieira AR, Slayton RL, McNeil DW, Weyant RJ, Crout RJ, Marazita ML (2018) Novel caries loci in children and adults implicated by genome-wide analysis of families. BMC Oral Health 18:98. PMCID: PMC5984765

3. Krishnan M, Major TJ, Topless RK, Dewes O, Yu L, Thompson JMD, McCowan L, de Zoysa J, Stamp LK, Dalbeth N, Harre Hindmarsh J, Rapana N, Deka R, Eng WWH, Weeks DE, Minster RL, McGarvey ST, Viali S, Naseri T, Sefuiva Reupena M, Wilcox P, Grattan D, Shepherd PR, Shelling AN, Murphy R, Merriman TR (2018) Discordant association of the CREBRF rs373863828 A allele with increased BMI and protection from type 2 diabetes in Maori and Pacific (Polynesian) people living in Aotearoa/New Zealand. Diabetologia 61:1603-1613. PMCID: PMC6434933

4. Liu X, Hong X, Tsai HJ, Mestan KK, Shi M, Kefi A, Hao K, Chen Q, Wang G, Caruso D, Geng H, Gao Y, He J, Kumar R, Wang H, Yu Y, Bartell T, Tan XD, Schleimer RP, Weeks DE, Pongracic JA, Wang X (2018) Genome-wide association study of maternal genetic effects and parent-of-origin effects on food allergy. Medicine (Baltimore) 97:e0043. PMCID: PMC5851764

5. Ozbek U^†, Lin HM, Lin Y, Weeks DE, Chen W, Shaffer JR, Purcell SM, Feingold E (2018) Statistics for X-chromosome associations. Genet Epidemiol 42:539-550. PMCID: PMC6394852

6. Yan Q, Ding Y, Liu Y, Sun T, Fritsche LG, Clemons T, Ratnapriya R, Klein ML, Cook RJ, Liu Y, Fan R, Wei L, Abecasis GR, Swaroop A, Chew EY, Group AR, Weeks DE, Chen W (2018) Genome-wide analysis of disease progression in age-related macular degeneration. Hum Mol Genet 27:929-940. PMCID: PMC6059197

7. Biedrzycki RJ^†, Sier AE^†, Liu D^†, Dreikorn EN^†, Weeks DE (2019) Spinning convincing stories for both true and false association signals. Genet Epidemiol 43:356-364.

8. Chiu CY, Yuan F, Zhang BS, Yuan A, Li X, Fang HB, Lange K, Weeks DE, Wilson AF, Bailey-Wilson JE, Musolf AM, Stambolian D, Lakhal-Chaieb ML, Cook RJ, McMahon FJ, Amos CI, Xiong M, Fan R (2019) Linear mixed models for association analysis of quantitative traits with next-generation sequencing data. Genet Epidemiol 43:189-206. PMCID: PMC6375753

9. Forno E, Wang T, Qi C, Yan Q, Xu CJ, Boutaoui N, Han YY, Weeks DE, Jiang Y, Rosser F, Vonk JM, Brouwer S, Acosta-Perez E, Colon-Semidey A, Alvarez M, Canino G, Koppelman GH, Chen W, Celedon JC (2019) DNA methylation in nasal epithelium, atopy, and atopic asthma in children: a genome-wide study. Lancet Respir Med 7:336-346. PMCID: PMC6441380

10. Grassmann F, Kiel C, den Hollander AI, Weeks DE, Lotery A, Cipriani V, Weber BHF, International Age-related Macular Degeneration Genomics C (2019) Y chromosome mosaicism is associated with age-related macular degeneration. Eur J Hum Genet 27:36-41. PMCID: PMC6303255

11. Heinsberg LW^†, Arockiaraj AI^†, Crago EA, Ren D, Shaffer JR, Sherwood PR, Sereika SM, Weeks DE, Conley YP (2019) Genetic variability and trajectories of DNA methylation may support a role for HAMP in patient outcomes after aneurysmal subarachnoid hemorrhage. Neurocritical Care:in press

Recent preprints

1. Forno E, Wang T, Qi C, Yan Q, Xu C-J, boutaoui N, Han Y-Y, Weeks D, Jiang Y, Rosser F, Vonk J, Brouwer S, Acosta-Perez E, Colon-Semidey A, Alvarez M, Canino G, Koppelman G, Chen W, Celedón J (2018) A Genome-wide Study of DNA Methylation in Nasal Epithelium and Atopy and Atopic Asthma in Children. SSRN: https://ssrn.com/abstract=3276045

2. Krishnan M, Major TJ, Topless RK, Dewes O, Yu L, Thompson JM, McCowan L, Zoysa Jd, Stamp LK, Dalbeth N, Hindmarsh JH, Rapana N, Deka R, Eng WWH, Weeks DE, Minster RL, McGarvey ST, Viali Si, Naseri T, Reupena Ma, Wilcox P, Grattan D, Shepherd PR, Shelling AN, Murphy R, Merriman TR (2018) Discordant association of the CREBRF rs373863828 minor allele with increased body mass index and protection from type 2 diabetes in Māori and Pacific (Polynesian) people living in Aotearoa. New Zealand. bioRxiv: https://doi.org/10.1101/188110

3. Harris DN, Kessler MD, Shetty AC, Weeks DE, Minster RL, Browning S, Cochrane EE, Deka R, Hawley NL, Reupena MaS, Naseri T, Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Population Genetics Working Group, McGarvey ST, O’Connor TD (2019) Evolutionary Genomics of Samoans. SSRN: http://dx.doi.org/10.2139/ssrn.3329885

4. Carlson JC, Weeks DE, Hawley NL, Gao G, Cheng H, Naseri T, Reupena MS, Deka R, McGarvey ST, Minster RL (2019) Genome-wide association studies in Samoans give insight into the genetic architecture of fasting serum lipid levels. bioRxiv: https://doi.org/10.1101/411546

5. Taliun D, Harris D, Kessler M, Carlson J, Szpiech Z, Torres R, Taliun SG, Corvelo A, Gogarten S, Kang HM, Pitsillides A, LeFaive J, Lee S-B, Tian X, Browning B, Das S, Emde A-K, Clarke W, Loesch D, Shetty A, Blackwell T, Wong Q, Aguet F, Albert C, Alonso A, Ardlie K, Aslibekyan S, Auer P, Barnard J, Barr G, Becker L, Beer R, Benjamin E, Bielak L, Blangero J, Boehnke M, Bowden D, Brody J, Burchard E, Cade B, Casella J, Chalazan B, Chen Y-DI, Cho M, Choi SH, Chung M, Clish C, Correa A, Curran J, Custer B, Darbar D, Daya M, Andrade Md, DeMeo D, Dutcher S, Ellinor P, Emery L, Fatkin D, Forer L, Fornage M, Franceschini N, Fuchsberger C, Fullerton S, Germer S, Gladwin M, Gottlieb D, Guo X, Hall M, He J, Heard-Costa N, Heckbert S, Irvin M, Johnsen J, Johnson A, Kardia SLR, Kelly T, Kelly S, Kenny E, Kiel D, Klemmer R, Konkle B, Kooperberg C, Köttgen A, Lange L, Lasky-Su J, Levy D, Lin X, Lin K-H, Liu C, Loos RJF, Garman L, Gerszten R, Lubitz S, Lunetta K, Mak ACY, Manichaikul A, Manning A, Mathias R, McManus D, McGarvey S, Meigs J, Meyers D, Mikulla J, Minear M, Mitchell B, Mohanty S, Montasser M, Montgomery C, Morrison A, Murabito J, Natale A, Natarajan P, Nelson S, North K, O’Connell J, Palmer N, Pankratz N, Peloso G, Peyser P, Post W, Psaty B, Rao DC, Redline S, Reiner A, Roden D, Rotter J, Ruczinski I, Sarnowski C, Schoenherr S, Seo J-S, Seshadri S, Sheehan V, Shoemaker B, Smith A, Smith N, Smith J, Sotoodehnia N, Stilp A, Tang W, Taylor K, Telen M, Thornton T, Tracy R, Berg DVD, Vasan R, Viaud-Martinez K, Vrieze S, Weeks DE, Weir B, Weiss S, Weng L-C, Willer C, Zhang Y, Zhao X, Arnett D, Ashley-Koch A, Barnes K, Boerwinkle E, Gabriel S, Gibbs R, Rice K, Rich S, Silverman E, Qasba P, Gan W, Papanicolaou G, Nickerson D, Browning S, Zody M, Zöllner S, Wilson J, Cupples A, Laurie C, Jaquish C, Hernandez R, O’Connor T, Abecasis G, Trans-Omics for Precision Medicine Program TPGWG (2019) Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. bioRxiv: https://doi.org/10.1101/563866

6. Carlson JC, Rosenthal SL, Russell EM, Hawley NL, Sun G, Cheng H, Naseri T, Reupena MS, Tuitele J, Deka R, McGarvey ST, Weeks DE, Minster RL (2019) A missense variant in CREBRF is associated with taller stature in Samoans. bioRxiv: https://doi.org/10.1101/690586