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 number of collaborative human genetics projects, all of which constantly challenge him to develop new and more useful methods for dealing with the complexities of real data. He is studying the genetic influences on obesity, lipids, body composition, and age-related macular degeneration.  In addition, he and his colleagues are studying the effects of methylation on risk for 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 2071 Genomic Data Processing and Structures
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
2021-       Acting Chair, Department of Human Genetics

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Recent publications (from more than 219 peer-reviewed manuscripts)
Last updated July 12, 2021 - use the links above for up-to-date information.

†Graduate student; ‡Post-doctoral trainee.

 

1. 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

 

2. 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 146:671-675. PMCID: PMC7438239

 

3. 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 11:671. PMCID: PMC7332758

 

4. 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 PMCID: PMC7196816

 

5. 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 Creb 3 Regulatory Factor missense variant with body mass index and diabetes among Samoans: study protocol for the Soifua Manuia (‘Good Health’) observational cohort study. JMIR Research Protocols 9:e17329. PMCID: PMC7413272

 

6. 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

 

7. 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 33:749-758. PMCID: PMC7541432

 

8. 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

 

9. Arslanian KJ, Fidow UT, Atanoa T, Unasa-Apelu F, Naseri T, Wetzel AI, Pomer A, Duckham RL, McGarvey ST, Strayer JA, Kershaw EE, Weeks DE, Hawley NL (2021) A missense variant in CREBRF, rs373863828, is associated with fat-free mass, not fat mass in Samoan infants. Int J Obes (Lond) 45:45-55

 

10. Carlson JC, Weeks DE, Hawley NL, Sun G, Cheng H, Naseri T, Reupena MS, Tuitele J, Deka R, McGarvey ST, Minster RL (2021) Genome-wide association studies in Samoans give insight into the genetic architecture of fasting serum lipid levels. J Hum Genet 66:111-121. PMCID: PMC7785639

 

11. Heinsberg LW^‡, Ray M, Conley YP, Roberts JM, Jeyabalan A, Hubel CA, Weeks DE, Schmella MJ (2021) An Exploratory Study of Epigenetic Age in Preeclamptic and Normotensive Pregnancy Reveals Differences by Self-Reported Race but Not Pregnancy Outcome. Reprod Sci (in press)

 

12. Simon MT, Eftekharian SS, Ferdinandusse S, Tang S, Naseri T, Reupena MS, McGarvey ST, Minster RL, Weeks DE, Samoan Obesity, Lifestyle Genetic Adaptations Study Group, Nguyen DD, Lee S, Ellsworth KA, Vaz FM, Dimmock D, Pitt J, Abdenur JE (2021) ECHS1 disease in two unrelated families of Samoan descent: Common variant - rare disorder. Am J Med Genet A 185:157-167. PMCID: PMC7746601

 

13. Yan Q, Jiang Y, Huang H, Swaroop A, Chew EY, Weeks DE, Chen W, Ding Y (2021) Genome-Wide Association Studies-Based Machine Learning for Prediction of Age-Related Macular Degeneration Risk. Transl Vis Sci Technol 10:29. PMCID: PMC7900884

 

14. Treble-Barna A, Heinsberg LW^‡, Puccio AM, Shaffer JR, Okonkwo DO, Beers SR, Weeks DE, Conley YP (2021) Acute Brain-Derived Neurotrophic Factor DNA Methylation Trajectories in Cerebrospinal Fluid and Associations with Outcomes Following Severe Traumatic Brain Injury in Adults. Neurorehabil Neural Repair:15459683211028245 

Recent book chapters

1.     Yan Q, Ding Y, Weeks DE, Chen W (2021) AMD Genetics: Methods and Analyses for Association, Progression, and Prediction. Adv Exp Med Biol 1256:191-200

 

Recent preprints

1. 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  

 

2. Heinsberg LW^‡, Ray M, Conley YP, Roberts JM, Jeyabalan A, Hubel CA, Weeks DE, Schmella MJ (2020) Racial Differences in DNA Methylation-Based Age Acceleration in Preeclamptic and Normotensive Pregnancy. medRxiv [Preprint] October 02, 2020 https://doi.org/10.1101/2020.09.30.20204883   

 

3. Hindy G, Dornbos P, Chaffin MD, Liu DJ, Wang M, Aguilar-Salinas CA, Antonacci-Fulton L, Ardissino D, Arnett DK, Aslibekyan S, Atzmon G, Ballantyne CM, Barajas-Olmos F, Barzilai N, Becker LC, Bielak LF, Bis JC, Blangero J, Boerwinkle E, Bonnycastle LL, Bottinger E, Bowden DW, Bown MJ, Brody JA, Broome JG, Burtt NP, Cade BE, Centeno-Cruz F, Chan E, Chang Y-C, Chen Y-DI, Cheng C-Y, Choi WJ, Chowdhury R, Contreras-Cubas C, Córdova EJ, Correa A, Cupples LA, Curran JE, Danesh J, de Vries PS, DeFronzo RA, Doddapaneni H, Duggirala R, Dutcher SK, Ellinor PT, Emery LS, Florez JC, Fornage M, Freedman BI, Fuster V, Garay-Sevilla ME, García-Ortiz H, Germer S, Gibbs RA, Gieger C, Glaser B, Gonzalez C, Gonzalez-Villalpando ME, Graff M, Graham SE, Grarup N, Groop LC, Guo X, Gupta N, Han S, Hanis CL, Hansen T, He J, Heard-Costa NL, Hung Y-J, Hwang MY, Irvin MR, Islas-Andrade S, Jarvik GP, Kang HM, Kardia SLR, Kelly T, Kenny EE, Khan AT, Kim B-J, Kim RW, Kim YJ, Koistinen HA, Kooperberg C, Kuusisto J, Kwak SH, Laakso M, Lange LA, Lee J, Lee J, Lee S, Lehman DM, Lemaitre RN, Linneberg A, Liu J, Loos RJF, Lubitz SA, Lyssenko V, Ma RCW, Martin LW, Martínez-Hernández A, Mathias RA, McGarvey ST, McPherson R, Meigs JB, Meitinger T, Melander O, Mendoza-Caamal E, Metcalf GA, Mi X, Mohlke KL, Montasser ME, Moon J-Y, Moreno-Macías H, Morrison AC, Muzny DM, Nelson SC, Nilsson PM, O’Connell JR, Orho-Melander M, Orozco L, Palmer CNA, Palmer ND, Park CJ, Park KS, Pedersen O, Peralta JM, Peyser PA, Post WS, Preuss M, Psaty BM, Qi Q, Rao D, Redline S, Reiner AP, Revilla-Monsalve C, Rich SS, Samani N, Schunkert H, Schurmann C, Seo D, Seo J-S, Sim X, Sladek R, Small KS, So WY, Stilp AM, Sunitha SM, Tai ES, Tam CHT, Taylor KD, Teo YY, Thameem F, Tomlinson B, Tsai MY, Tuomi T, Tuomilehto J, Tusié-Luna T, van Dam RM, Vasan RS, Viaud Martinez KA, Wang FF, Wang X, Watkins H, Weeks DE, Wilson JG, Witte DR, Wong T-Y, Yanek LR, AMP-T2D-GENES, Myocardial Infarction Genetics Consortium, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, NHLBI TOPMed Lipids Working Group, Kathiresan S, Rotter JI, Boehnke M, McCarthy MI, Willer CJ, Natarajan P, Flannick JA, Khera AV, Peloso GM (2020) Rare coding variants in 35 genes associate with circulating lipid levels – a multi-ancestry analysis of 170,000 exomes. bioRxiv [Preprint] December 23, 2020: Available from: https://doi.org/10.1101/2020.12.22.423783.

 

4. Kwong AM, Blackwell TW, LeFaive J, de Andrade M, Barnard J, Barnes KC, Blangero J, Boerwinkle E, Burchard EG, Cade BE, Chasman DI, Chen H, Conomos MP, Cupples LA, Ellinor PT, Eng C, Gao Y, Guo X, Irvin MR, Kelly TN, Kim W, Kooperberg C, Lubitz SA, Mak ACY, Manichaikul AW, Mathias RA, Montasser ME, Montgomery CG, Musani S, Palmer ND, Peloso GM, Qiao D, Reiner AP, Roden DM, Shoemaker MB, Smith JA, Smith NL, Su JL, Tiwari HK, Weeks DE, Weiss ST, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Analysis Working Group, Scott LJ, Smith AV, Abecasis GR, Boehnke M, Kang HM (2020) Robust, flexible, and scalable tests for Hardy-Weinberg Equilibrium across diverse ancestries. bioRxiv [Preprint] June 25, 2020: Available from: https://doi.org/10.1101/2020.06.23.167759. 

 

5. Ray M, Heinsberg LW^‡, Conley YP, Roberts JM, Jeyabalan A, Hubel CA, Weeks DE, Schmella MJ (2020) Utilization of Epigenome-wide DNA Methylation for Longitudinal Comparison of White Blood Cell Proportions Across Preeclamptic and Normotensive Pregnancy by Self-Reported Race. medRxiv [Preprint] September 20, 2020 https://doi.org/10.1101/2020.09.18.20197491    

 

6. Stilp AM, Emery LS, Broome JG, Buth EJ, Khan AT, Laurie CA, Wang FF, Wong Q, Chen D, D’Augustine CM, Heard-Costa NL, Hohensee CR, Johnson WC, Juarez LD, Liu J, Mutalik KM, Raffield LM, Wiggins KL, de Vries PS, Kelly TN, Kooperberg C, Natarajan P, Peloso GM, Peyser PA, Reiner AP, Arnett DK, Aslibekyan S, Barnes KC, Bielak LF, Bis JC, Cade BE, Chen M-H, Correa A, Cupples LA, de Andrade M, Ellinor PT, Fornage M, Franceschini N, Gan W, Ganesh SK, Graffelman J, Grove ML, Guo X, Hawley NL, Hsu W-L, Jackson RD, Jaquish CE, Johnson AD, Kardia SL, Kelly S, Lee J, Mathias RA, McGarvey ST, Mitchell BD, Montasser ME, Morrison AC, North KE, Nouraie SM, Oelsner EC, Pankratz N, Rich SS, Rotter JI, Smith JA, Taylor KD, Vasan RS, Weeks DE, Weiss ST, Wilson CG, Yanek LR, Psaty BM, Heckbert SR, Laurie CC (2020) A system for phenotype harmonization in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program. bioRxiv [Preprint] June 20, 2020 https://doi.org/10.1101/2020.06.18.146423  

 

7. Wessel J, Majarian TD, Highland HM, Raghavan S, Szeto MD, Hasbani NR, de Vries PS, Brody JA, Sarnowski C, DiCorpo D, Yin X, Hidalgo B, Guo X, Perry J, O’Connell JR, Lent S, Montasser ME, Cade BE, Jain D, Wang H, Wu P, Bonàs-Guarch S, D’Oliveira Albanus R, Leong A, Miguel-Escalada I, Varshney A, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Anthropometry, DIAMANTE, Kinney GL, Yanek LR, Lange L, Almeida M, Peralta JM, Aslibekyan S, Baldridge AS, Bertoni AG, Bielak LF, Bowden DW, Chen C-S, Chen Y-DI, Choi SH, Choi WJ, Darbar D, Floyd JS, Freedman BI, Goodarzi MO, Irvin R, Kalyani RR, Kelly T, Lee S, Liu C-T, Loesch D, Manson JE, Nassir R, Palmer ND, Pankow JS, Rasmussen-Torvik LJ, Reiner AP, Selvin E, Shadyab AH, Smith JA, Weeks DE, Weng L-C, Xu H, Yao J, Yoneda Z, Zhao W, Ferrer J, Mahajan A, McCarthy MI, Parker S, Alonso A, Arnett DK, Blangero J, Boerwinkle E, Cho MH, Correa A, Cupples LA, Curran JE, Duggirala R, Ellinor PT, He J, Heckbert SR, Kardia SL, Kim RW, Kooperberg C, Liu S, Lubitz SA, Mathias RA, McGarvey S, Mitchell BD, Morrison AC, Peyser PA, Psaty BM, Redline S, Roden D, Shoemaker MB, Smith NL, Taylor KD, Vasan RS, Viaud-Martinez KA, Florez JC, Wilson JG, Sladek R, Dupuis J, Rich SS, Rotter JI, Meigs JB, Manning AK (2020) Rare Non-coding Variation Identified by Large Scale Whole Genome Sequencing Reveals Unexplained Heritability of Type 2 Diabetes. medRxiv [preprint] November 16, 2020: Available from: https://doi.org/10.1101/2020.11.13.20221812.

 

8. DiCorpo D, Gaynor SM, Russell EM^‡, Westerman KE, Raffield LM, Majarian TD, Wu P, Sarnowski C, Highland HM, Jackson A, Hasbani NR, de Vries PS, Brody JA, Hidalgo B, Guo X, Perry JA, O’Connell JR, Lent S, Montasser ME, Cade BE, Jain D, Wang H, D’Oliveira Albanus R, Varshney A, Yanek LR, Lange L, Palmer ND, Almeida M, Peralta JM, Aslibekyan S, Baldridge AS, Bertoni AG, Bielak LF, Chen C-S, Chen Y-DI, Choi WJ, Goodarzi MO, Floyd JS, Irvin MR, Kalyani RR, Kelly TN, Lee S, Liu C-T, Loesch D, Manson JE, Pankow JS, Rasmussen-Torvik LJ, Reiner AP, Selvin E, Smith JA, Weeks DE, Xu H, Yao J, Zhao W, Parker S, Alonso A, Arnett DK, Blangero J, Boerwinkle E, Correa A, Cupples LA, Curran JE, Duggirala R, He J, Heckbert SR, Kardia SL, Kim RW, Kooperberg C, Liu S, Mathias RA, McGarvey ST, Mitchell BD, Morrison AC, Peyser PA, Psaty BM, Redline S, Shuldiner AR, Taylor KD, Vasan RS, Viaud-Martinez KA, Florez JC, Wilson JG, Sladek R, Rich SS, Rotter JI, Lin X, Dupuis J, Meigs JB, Wessel J, Manning AK (2021) Whole Genome Sequence Association Analysis of Fasting Glucose and Fasting Insulin Levels in Diverse Cohorts from the NHLBI TOPMed Program. medRxiv [Preprint] January 04, 2021 https://doi.org/10.1101/2020.12.31.20234310   

 

9. Hawley NL, Duckham RL, Carlson JC, Naseri T, Reupena MS, Lameko V, Pomer A, Wetzel A, Selu M, Lupematisila V, Unasa F, Vesi L, Fatu T, Unasa S, Faasalele-Savusa K, Viali S, Rivara AC, Russell EM^‡, Deka R, Kershaw EE, Minster RL, Weeks DE, McGarvey ST (2021) The association of CREBRF variant rs373863828 with body composition in adult Samoans. medRxiv [preprint] February 12, 2021 https://doi.org/10.1101/2021.02.11.21251582   

 

10. Kanshana JS, Mattila PE, Ewing MC, Wood AN, Schoiswohl G, Meyer AC, Kowalski A, Rosenthal SL, Gingras S, Kaufman BA, Lu R, Weeks DE, McGarvey ST, Minster RL, Hawley NL, Kershaw EE (2021) A murine model of the human CREBRF^R457Q obesity-risk variant does not influence energy or glucose homeostasis in response to nutritional stress. bioRxiv [Preprint] May 06, 2021 https://doi.org/10.1101/2021.05.06.442909   

 

11. Nakao T, Bick AG, Taub MA, Zekavat SM, Uddin MM, Niroula A, Carty CL, Lane J, Honigberg MC, Weinstock JS, Pampana A, Gibson CJ, Griffin GK, Clarke SL, Bhattacharya R, Assimes TL, Emery LS, Stilp AM, Wong Q, Broome J, Laurie CA, Khan AT, Smith AV, Blackwell TW, Yoneda ZT, Peralta JM, Bowden DW, Irvin MR, Boorgula M, Zhao W, Yanek LR, Wiggins KL, Hixson JE, Gu CC, Peloso GM, Roden DM, Reupena MaS, Hwu C-M, DeMeo DL, North KE, Kelly S, Musani SK, Bis JC, Lloyd-Jones DM, Johnsen JM, Preuss M, Tracy RP, Peyser PA, Qiao D, Desai P, Curran JE, Freedman BI, Tiwari HK, Chavan S, Smith JA, Smith NL, Kelly TN, Hildalgo B, Cupples LA, Weeks DE, Hawley NL, Minster RL, The Samoan Obesity, Lifestyle and Genetic Adaptations Study (OLaGA) Group, Deka R, Naseri TT, de las Fuentes L, Raffield LM, Tracy RP, Morrison AC, Vries PS, Ballantyne CM, Kenny EE, Rich SS, Whitsel EA, Cho MH, Shoemaker MB, Pace BS, Blangero J, Palmer ND, Mitchell BD, Shuldiner AR, Barnes KC, Redline S, Kardia SLR, Abecasis GR, Becker LC, Heckbert SR, He J, Post W, Arnett DK, Vasan RS, Darbar D, Weiss ST, McGarvey ST, de Andrade M, Chen Y-DI, Kaplan RC, Meyers DA, Custer BS, Correa A, Psaty BM, Fornage M, Manson JE, Boerwinkle E, Konkle BA, Loos RJF, Rotter JI, Silverman EK, Kooperberg C, Jaiswal S, Libby P, Ellinor PT, Pankratz N, Ebert BL, Reiner AP, Mathias RA, Do R, NHLBI Trans-Omics in Precision Medicine (TOPMed) Consortium, Natarajan P (2021) Bidirectional Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of intermediate potential. medRxiv [preprint] March 1, 2021 Available from: https://doi.org/10.1101/2021.02.26.21252199 

 

12. Russell EM^‡, Carlson JC, Krishnan M, Hawley NL, Sun G, Cheng H, Naseri T, Sefuiva Reupena Ma, Viali Si, Tuitele J, Major TJ, Miljkovic I, Merriman TR, Deka R, Weeks DE, McGarvey ST, Minster RL (2021) CREBRF missense variant rs373863828 has both direct and indirect effects on type 2 diabetes and fasting glucose in Polynesians living in Samoa and Aotearoa New Zealand. medRxiv [Preprint] February 19, 2021 https://doi.org/10.1101/2021.02.15.21251768