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 obesity, asthma, and age-related macular degeneration.  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
HUGEN 2071 Genomic Data Processing and Structures

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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 207 peer-reviewed manuscripts)
Last updated June 15, 2020 - use the links above for up-to-date information.

†Graduate student; ‡Post-doctoral trainee.

1. 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.

2. 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

3. 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

4. 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

5. 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 (2020) A missense variant in CREBRF is associated with taller stature in Samoans. Am J Hum Biol:e23414

6. Forno E, Zhang R, Jiang Y, Kim S, Yan Q, Ren Z, Han YY, Boutaoui N, Rosser F, Weeks DE, Acosta-Perez E, Colon-Semidey A, Alvarez M, Canino G, Chen W, Celedon JC (2020) Transcriptome-wide and differential expression network analyses of childhood asthma in nasal epithelium. J Allergy Clin Immunol (in press)

7. Arockiaraj AI^†, Liu D^†, Shaffer JR, Koleck TA, Crago EA, Weeks DE, Conley YP (2020) Methylation Data Processing Protocol and Comparison of Blood and Cerebral Spinal Fluid Following Aneurysmal Subarachnoid Hemorrhage. Front Genet (in press)

8. Harris DN, Kessler MD, Shetty AC, Weeks DE, Minster RL, Browning S, Cochrane EE, Deka R, Hawley NL, Reupena MS, Naseri T, Trans-Omics for Precision Medicine Consortium, TOPMed Population Genetics Working Group, McGarvey ST, O'Connor TD (2020) Evolutionary history of modern Samoans. Proc Natl Acad Sci U S A 117:9458-9465

9. Hawley NL, Pomer A, Rivara AC, Rosenthal SL^‡, Duckham RL, Carlson JC, Naseri T, Reupena MS, Selu M, Lupematisila V, Unasa F, Vesi L, Fatu T, Unasa S, Faasalele-Savusa K, Wetzel AI, Soti-Ulberg C, Prescott AT, Siufaga G, Penaia C, To SB, LaMonica LC, Lameko V, Choy CC, Crouter SE, Redline S, Deka R, Kershaw EE, Urban Z, Minster RL, Weeks DE, McGarvey ST (2020) Exploring the paradoxical relationship of a CREBRF missense variant with body mass index and diabetes among Samoans: study protocol for the Soifua Manuia (‘Good Health’) observational cohort study. JMIR Research Protocols (in press)

10. Heinsberg LW^†, Arockiaraj AI^†, Crago EA, Ren D, Shaffer JR, Sherwood PR, Sereika SM, Weeks DE, Conley YP (2020) Genetic Variability and Trajectories of DNA Methylation May Support a Role for HAMP in Patient Outcomes After Aneurysmal Subarachnoid Hemorrhage. Neurocrit Care 32:550-563. PMCID: PMC6981002

11. Heinsberg LW^†, Alexander SA, Crago EA, Minster RL, Poloyac SM, Weeks DE, Conley YP (2020) Genetic Variability in the Iron Homeostasis Pathway and Patient Outcomes After Aneurysmal Subarachnoid Hemorrhage. Neurocrit Care (Online ahead of print)

12. Yan Q, Weeks DE, Xin H, Swaroop A, Chew EY, Huang H, Ding Y, Chen W (2020) Deep-learning-based Prediction of Late Age-Related Macular Degeneration Progression. Nat Mach Intell 2:141-150. PMCID: PMC7153739

Recent preprints

1. 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

2. 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

3. 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

4. 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 D, 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 (TOPMed) Population Genetics Working Group (2019) Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. bioRxiv: https://doi.org/10.1101/563866

5. Bick A, Weinstock J, Nandakumar S, Fulco C, Leventhal M, Bao E, Nasser J, Zekavat S, Szeto M, Laurie C, Taub M, Mitchell B, Barnes K, Moscati A, Fornage M, Redline S, Psaty B, Silverman E, Weiss S, Palmer N, Vasan R, Burchard E, Kardia SLR, He J, Kaplan R, Smith N, Arnett D, Schwartz D, Correa A, de Andrade M, Guo X, Konkle B, Custer B, Peralta J, Gui H, Meyers D, McGarvey S, Chen IY-D, Shoemaker B, Peyser P, Broome J, Gogarten S, Wang FF, Wong Q, Montasser M, Daya M, Kenny E, North K, Launer L, Cade B, Bis J, Cho M, Lasky-Su J, Bowden D, Cupples A, Mak ACY, Becker L, Smith J, Kelly T, Aslibekyan S, Heckbert S, Tiwari H, Yang I, Heit J, Lubitz S, Rich S, Johnsen J, Curran J, Wenzel S, Weeks D, Rao D, Darbar D, Moon J-Y, Tracy R, Buth E, Rafaels N, Loos RJF, Hou L, Lee J, Kachroo P, Freedman B, Levy D, Bielak L, Hixson J, Floyd J, Whitsel E, Ellinor P, Irvin M, Fingerlin T, Raffield L, Armasu S, Rotter J, Wheeler M, Sabino E, Blangero J, Williams K, Levy B, Sheu WH-H, Roden D, Boerwinkle E, Manson J, Mathias R, Desai P, Taylor K, Johnson A, Auer P, Kooperberg C, Laurie C, Blackwell T, Smith A, Zhao H, Lange E, Lange L, Wilson J, Lander E, Engreitz J, Ebert B, Reiner A, Sankaran V, Jaiswal S, Abecasis G, Natarajan P, Kathiresan S, NHLBI Trans-Omics for Precision Medicine Consortium (2019) Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes. bioRxiv: https://doi.org/10.1101/782748

6. Taub M, Weinstock J, Iyer K, Yanek L, Conomos M, Brody J, Keramati A, Laurie C, Arvanitis M, Smith A, Lane J, Becker L, Bis J, Blangero J, Bleecker E, Burchard E, Celedon J, Chang YP, Custer B, Darbar D, de las Fuentes L, DeMeo D, Freedman B, Garrett M, Gladwin M, Heckbert S, Hidalgo B, Ingram C, Irvin M, Craig Johnson W, Kaab S, Launer L, Lee J, Liu S, Moscati A, North K, Peyser P, Rafaels N, Raffield L, Weeks D, Wheeler M, Keoki Williams L, Zhao W, Armanios M, Aslibekyan S, Auer P, Bowden D, Cade B, Yii-Der Chen I, Cho M, Cupples A, Curran J, Daya M, Deka R, Guo X, Hou L, Hwang S-J, Johnsen J, Kenny E, Levin A, Liu C, Minster R, Nouraie M, Sabino E, Smith J, Smith N, Lasky Su J, Telen M, Tiwari H, Tracy R, White M, Zhang Y, Wiggins K, Weiss S, Vasan R, Taylor K, Sinner M, Silverman E, Benjamin Shoemaker M, Sheu WHH, Rotter J, Redline S, Psaty B, Peralta J, Palmer N, Loos RJF, Montgomery C, Mitchell B, Meyers D, McGarvey S, Mak ACY, Kumar R, Kooperberg C, Konkle B, Kelly S, Kardia SLR, Kaplan R, He J, Gui H, Fornage M, Ellinor P, de Andrade M, Correa A, Boerwinkle E, Barnes K, Ashley-Koch A, Arnett D, Albert C, Laurie C, Abecasis G, Aviv A, Nickerson D, Wilson J, Rich S, Levy D, Battle A, Blackwell T, Ruczinski I, Thornton T, O’Connell J, Perry J, Pankratz N, Reiner A, Mathias R, NHLBI Trans-Omics for Precision Medicine Consortium, TOPMed Hematology Hemostasis Working Group, TOPMed Structural Variation Working Group (2019) Novel genetic determinants of telomere length from a multi-ethnic analysis of 75,000 whole genome sequences in TOPMed. bioRxiv: https://doi.org/10.1101/749010

7. Yan Q, Jiang Y, Huang H, Swaroop A, Chew E, Weeks D, Chen W, Ding Y (2019) GWAS-based Machine Learning for Prediction of Age-Related Macular Degeneration Risk. medRxiv: https://doi.org/10.1101/19006155

8. Yan Q, Weeks D, Xin H, Huang H, Swaroop A, Chew E, Ding Y, Chen W (2019) Deep-learning-based Prediction of Late Age-Related Macular Degeneration Progression. medRxiv, https://doi.org/10.1101/19006171

9. Arockiaraj A, Liu D, Shaffer J, Koleck T, Crago E, Weeks D, Conley Y (2020) Methylation Data Processing Protocol & Comparison of Blood and Cerebral Spinal Fluid Following Aneurysmal Subarachnoid Hemorrhage. bioRxiv: https://doi.org/10.1101/2020.03.24.005264