Śaunak Sen | Research Group

preprints

• Darnell SS, Overall RW, Guarracino A, Colonna V, Villani F, Garrison E, Isaac A, Muli P, Muriithi FM, Kabui A, Kilyungi M, Lisso F, Kibet A, Muhia B, Nijveen H, Yousefi S, Ashbrook D, Huang P, Suh GE, Umar M, Batten C, Chen H, Sen Ś, Williams RW, Prins P. Creating a biomedical knowledge base by addressing GPT inaccurate responses and benchmarking context. 2024 preprint
• Farage G, Zhao C, Choi HY, Garrett TJ, Kechris K, Elam MB, Sen Ś. Matrix Linear Models for connecting metabolite composition to individual characteristics. 2023 preprint
• Goedecke P, Nakahara A, Pope S, Madlock-Brown C, Sen S, Singarella I, Mari G, Mockus A. Social Determinants of Health as Primary Risk Factors of Hypertensive Disorders of Pregnancy: A Retrospective Cohort Study. 2024 preprint
• Yu Z, Farage G, Williams RW, Broman KW, Sen Ś. BulkLMM: Real-time genome scans for multiple quantitative traits using linear mixed models. 2023 preprint | BulkLMM.jl
• Hyeonju Kim, Gregory Farage, John T. Lovell, John K. Mckay, Thomas E. Juenger, Śaunak Sen Flexible multivariate linear mixed models for structured multiple traits bioRxiv 2020.03.27.012690. preprint | FlxQTL.jl

2024

• Bline AP, Ellis LB, Pelch KE, Lam J, Sen S, Zlatnik M, Varshavsky J. The effect of per and polyfluoroalkyl substance (PFAS) exposure on gestational diabetes mellitus and its subclinical risk factors: A systematic review and meta-analysis protocol. Environment International. 2024 Jun;188:108711. pubmed
• Crowder R, Kato-Maeda M, Schwem B, Dela Tonga A, Geocaniga-Gaviola DM, Lopez E, Valdez CL, Lim AR, Hunat N, Sedusta AG, Sacopon CA, Atienza GAM, Bulag E, Lim D, Bascuña J, Shah K, Basillio RP, Berger CA, Lopez MCDP, Sen S, Allender C, Folkerts M, Karaoz U, Brodie E, Mitarai S, Garfin AMC, Ama MC, Engelthaler DM, Cattamanchi A, Destura R. Impact of heteroresistance on treatment outcomes of people with drug-resistant TB. IJTLD OPEN. 2024 Oct 1;1(10):466–72. pubmed

2023

• Garrett TJ, Puchowicz MA, Park EA, Dong Q, Farage G, Childress R, Guingab J, Simpson CL, Sen S, Brogdon EC, Buchanan LM, Raghow R, Elam MB. Effect of statin treatment on metabolites, lipids and prostanoids in patients with Statin Associated Muscle Symptoms (SAMS). Bhatia A, editor. PLoS ONE. 2023 Dec 15;18(12):e0294498. pubmed
• Mozhui K, Kim H, Villani F, Haghani A, Sen S, Horvath S. Pleiotropic influence of DNA methylation QTLs on physiological and ageing traits. Epigenetics. 2023 Dec 31;18(1):2252631. pubmed

2022

• Sun Y, Fowke JH, Liang X, Mozhui K, Sen S, Bao W, Liu B, Snetselaar LG, Wallace RB, Shadyab AH, Saquib N, Cheng TD, Johnson KC. Changes in Dietary Intake of Methionine, Folate/Folic Acid and Vitamin B12 and Survival in Postmenopausal Women with Breast Cancer: A Prospective Cohort Study. Nutrients. 2022 Nov 10;14(22):4747. doi: 10.3390/nu14224747. pubmed
• Bou Sleiman M, Roy S, Gao AW, Sadler MC, von Alvensleben GVG, Li H, Sen S, Harrison DE, Nelson JF, Strong R, Miller RA, Kutalik Z, Williams RW, Auwerx J.Sex- and age-dependent genetics of longevity in a heterogeneous mouse population. Science. 2022 Sep 30;377(6614):eabo3191. doi: 10.1126/science.abo3191. pubmed
• Jane W. Liang, Saunak Sen. Sparse matrix linear models for structured high-throughput data. The Annals of Applied Statistics. 2022. 16(1) 169-192. preprint | MatrixLMnet.jl | supplement

2021

• Krukowski R, Johnson B, Kim H, Sen S, Homsi R. A Pragmatic Intervention Using Financial Incentives for Pregnancy Weight Management: Feasibility Randomized Controlled Trial. JMIR Form Res. 2021 Dec 24;5(12):e30578. doi: 10.2196/30578. pubmed
• Baessler A, Smith PJ, Brolin TJ, Neel RT, Sen S, Zhu R, Bernholt D, Azar FM, Throckmorton TW. Routman HD, Namdari S, Gulotta LV, Throckmorton TW. Preoperative opioid usage predicts markedly inferior outcomes two years after reverse total shoulder arthroplasty. J Shoulder Elbow Surg. pubmed
• Trotter C, Kim H, Farage G, Prins P, Williams RW, Broman KW, Sen Ś. Speeding up eQTL scans in the BXD population using GPUs. G3 (Bethesda). 2021 Aug 16:jkab254. pubmed | LiteQTL.jl | supplementary info
• Roy S, Sleiman MB, Jha P, Ingels JF, Chapman CJ, McCarty MS, Ziebarth JD, Hook M, Sun A, Zhao W, Huang J, Neuner SM, Wilmott LA, Shapaker TM, Centeno AG, Ashbrook DG, Mulligan MK, Kaczorowski CC, Makowski L, Cui Y, Read RW, Miller RA, Mozhui K, Williams EG, Sen S, Lu L, Auwerx J, Williams RW. Gene-by-environmental modulation of longevity and weight gain in the murine BXD family Nat Metab. 2021 Sep;3(9):1217-1227. pubmed
• Baessler AM, Brolin TJ, Azar FM, Sen S, Chang M, Zmistowski BM, Routman HD, Namdari S, Gulotta LV, Throckmorton TW. Development and Validation of a Predictive Model for Outcomes in Shoulder Arthroplasty: A Multicenter Analysis of over 2000 Patients. J Shoulder Elbow Surg. 2021 Jul 17:S1058-2746(21)00544-9. pubmed
• Farage G, Simmons C, Kocak M, Klesges RC, Talcott GW, Richey P, Hare M, Johnson KC, Sen S, Krukowski R. JMIR Mhealth Uhealth. 2021 Jul 14;9(7):e18741. doi: 10.2196/18741. Assessing the Contribution of Self-Monitoring Through a Commercial Weight Loss App: Mediation and Predictive Modeling Study. pubmed | supplementary info
• Mao M, Popli T, Jeanne M, Hoff K, Sen S, Gould DB. Dis Model Mech. 2021 Apr 1;14(4):dmm048231 Identification of fibronectin 1 as a candidate genetic modifier in a Col4a1 mutant mouse model of Gould syndrome. pubmed
• Varshavsky JR, Robinson JF, Zhou Y, Puckett KA, Kwan E, Buarpung S, Aburajab R, Gaw SL, Sen S, Gao S, Smith SC, Park JS, Zakharevich I, Gerona RR, Fisher SJ, Woodruff TJ. Organophosphate Flame Retardants, Highly Fluorinated Chemicals, and Biomarkers of Placental Development and Disease During Mid-Gestation. Toxicol Sci. 2021 May 27;181(2):215-228. pubmed
• Olney AM, Smith J, Sen S, Thomas F, Unwin HJT. Estimating the Effect of Social Distancing Interventions on COVID-19 in the United States. Am J Epidemiol. 2021 Jan 7:kwaa293. pubmed

2020

• Krukowski R, Kim H, Stansbury M, Li Q, Sen S, Farage G, West D. Importance of Multiple Reinforcing Comments and Areas for Change in Optimizing Dietary and Exercise Self-Monitoring Feedback in Behavioral Weight Loss Programs: Factorial Design. J Med Internet Res. 2020 Nov 23;22(11):e18104. doi: 10.2196/18104. pubmed
• Varshavsky JR, Sen S, Robinson JF, Smith SC, Frankenfield J, Wang Y, Yeh G, Park JS, Fisher SJ, Woodruff TJ. Racial/ethnic and geographic differences in polybrominated diphenyl ether (PBDE) levels across maternal, placental, and fetal tissues during mid-gestation. Sci Rep. 2020 Jul 22;10(1):12247. doi: 10.1038/s41598-020-69067-y. pubmed
• Varshavsky JR, Robinson JF, Zhou Y, Puckett KA, Kwan E, Buarpung S, Aburajab R, Gaw SL, Sen S, Smith SC, Frankenfield J, Park JS, Fisher SJ, Woodruff TJ. Association of polybrominated diphenyl ether (PBDE) levels with biomarkers of placental development and disease during mid-gestation. Environ Health. 2020 Jun 3;19(1):61. doi: 10.1186/s12940-020-00617-7. pubmed

2019

• Liang JW, Nichols RJ, Sen Ś. Matrix Linear Models for High-Throughput Chemical Genetic Screens. Genetics. 2019 Aug;212(4):1063-1073. doi: 10.1534/genetics.119.302299. pubmed
• Broman KW, Gatti DM, Svenson KL, Sen Ś, Churchill GA. Cleaning Genotype Data from Diversity Outbred Mice. G3 (Bethesda). 2019 May 7;9(5):1571-1579. doi: 10.1534/g3.119.400165. pubmed
• Hernandez-Pacheco N, Farzan N, Francis B, Karimi L, Repnik K, Vijverberg SJ, Soares P, Schieck M, Gorenjak M, Forno E, Eng C, Oh SS, Pérez-Méndez L, Berce V, Tavendale R, Samedy LA, Hunstman S, Hu D, Meade K, Farber HJ, Avila PC, Serebrisky D, Thyne SM, Brigino-Buenaventura E, Rodriguez-Cintron W, Sen S, Kumar R, Lenoir M, Rodriguez-Santana JR, Celedón JC, Mukhopadhyay S, Potočnik U, Pirmohamed M, Verhamme KM, Kabesch M, Palmer CNA, Hawcutt DB, Flores C, Maitland-van der Zee AH, Burchard EG, Pino-Yanes M. Genome-wide association study of inhaled corticosteroid response in admixed children with asthma. Clin Exp Allergy. 2019 Jun;49(6):789-798. doi: 10.1111/cea.13354. pubmed
• Thakur N, Borrell LN, Ye M, Oh SS, Eng C, Meade K, Avila PC, Farber HJ, Serebrisky D, Brigino-Buenaventura E, Rodriguez-Cintron W, Kumar R, Bibbins-Domingo K, Thyne S, Sen S, Rodriguez-Santana JR, Burchard EG. Acculturation is associated with asthma burden and pulmonary function in Latino youth: The GALA II study. J Allergy Clin Immunol. 2019 May;143(5):1914-1922. doi: 10.1016/j.jaci.2018.12.1015. pubmed
• Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA. R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations. Genetics. 2019 Feb;211(2):495-502. | pubmed

2018

• Gignoux CR, Torgerson DG, Pino-Yanes M, Uricchio LH, Galanter J, Roth LA, Eng C, Hu D, Nguyen EA, Huntsman S, Mathias RA, Kumar R, Rodriguez-Santana J, Thakur N, Oh SS, McGarry M, Moreno-Estrada A, Sandoval K, Winkler CA, Seibold MA, Padhukasahasram B, Conti DV, Farber HJ, Avila P, Brigino-Buenaventura E, Lenoir M, Meade K, Serebrisky D, Borrell LN, Rodriguez-Cintron W, Thyne S, Joubert BR, Romieu I, Levin AM, Sienra-Monge JJ, Del Rio-Navarro BE, Gan W, Raby BA, Weiss ST, Bleecker E, Meyers DA, Martinez FJ, Gauderman WJ, Gilliland F, London SJ, Bustamante CD, Nicolae DL, Ober C, Sen S, Barnes K, Williams LK, Hernandez RD, Burchard EG. An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos. J Allergy Clin Immunol. 2018 Sep 7. pii: S0091-6749(18)31274-0. | pubmed
• Neophytou AM, Oh SS, White MJ, Mak ACY, Hu D, Huntsman S, Eng C, Serebrisky D, Borrell LN, Farber HJ, Meade K, Davis A, Avila PC, Thyne SM, Rodríguez-Cintrón W, Rodríguez-Santana JR, Kumar R, Brigino-Buenaventura E, Sen S, Lenoir MA, Williams LK, Benowitz NL, Balmes JR, Eisen EA, Burchard EG. Secondhand smoke exposure and asthma outcomes among African-American and Latino children with asthma. Thorax. 2018 Nov;73(11):1041-1048. | pubmed
• Mak ACY, White MJ, Eckalbar WL, Szpiech ZA, Oh SS, Pino-Yanes M, Hu D, Goddard P, Huntsman S, Galanter J, Wu AC, Himes BE, Germer S, Vogel JM, Bunting KL, Eng C, Salazar S, Keys KL, Liberto J, Nuckton TJ, Nguyen TA, Torgerson DG, Kwok PY, Levin AM, Celedón JC, Forno E, Hakonarson H, Sleiman PM, Dahlin A, Tantisira KG, Weiss ST, Serebrisky D, Brigino-Buenaventura E, Farber HJ, Meade K, Lenoir MA, Avila PC, Sen S, Thyne SM, Rodriguez-Cintron W, Winkler CA, Moreno-Estrada A, Sandoval K, Rodriguez-Santana JR, Kumar R, Williams LK, Ahituv N, Ziv E, Seibold MA, Darnell RB, Zaitlen N, Hernandez RD, Burchard EG; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium. Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Am J Respir Crit Care Med. 2018 Jun 15;197(12):1552-1564. | pubmed

2017

• Lam J, Lanphear BP, Bellinger D, Axelrad DA, McPartland J, Sutton P, Davidson L, Daniels N, Sen S, Woodruff TJ. Developmental PBDE Exposure and IQ/ADHD in Childhood: A Systematic Review and Meta-analysis. Environ Health Perspect. 2017 Aug 3;125(8):086001. | pubmed
• Vesterinen HM, Morello-Frosch R, Sen S, Zeise L, Woodruff TJ. Cumulative effects of prenatal-exposure to exogenous chemicals and psychosocial stress on fetal growth: Systematic-review of the human and animal evidence. PLoS One. 2017 Jul 12;12(7):e0176331. | pubmed
• Hernandez-Pacheco N, Flores C, Alonso S, Eng C, Mak AC, Hunstman S, Hu D, White MJ, Oh SS, Meade K, Farber HJ, Avila PC, Serebrisky D, Thyne SM, Brigino-Buenaventura E, Rodriguez-Cintron W, Sen S, Kumar R, Lenoir M, Rodriguez-Santana JR, Burchard EG, Pino-Yanes M. Identification of a novel locus associated with skin colour in African-admixed populations. Sci Rep. 2017 Mar 16;7:44548. | pubmed
• Oh SS, Du R, Zeiger AM, McGarry ME, Hu D, Thakur N, Pino-Yanes M, Galanter JM, Eng C, Nishimura KK, Huntsman S, Farber HJ, Meade K, Avila P, Serebrisky D, Bibbins-Domingo K, Lenoir MA, Ford JG, Brigino-Buenaventura E, Rodriguez-Cintron W, Thyne SM, Sen S, Rodriguez-Santana JR, Williams K, Kumar R, Burchard EG. Breastfeeding associated with higher lung function in African American youths with asthma. J Asthma. 2017 Oct;54(8):856-865. | pubmed
• Thakur N, Barcelo NE, Borrell LN, Singh S, Eng C, Davis A, Meade K, LeNoir MA, Avila PC, Farber HJ, Serebrisky D, Brigino-Buenaventura E, Rodriguez-Cintron W, Thyne S, Rodriguez-Santana JR, Sen S, Bibbins-Domingo K, Burchard EG. Perceived Discrimination Associated With Asthma and Related Outcomes in Minority Youth: The GALA II and SAGE II Studies. Chest. 2017 Apr;151(4):804-812. | pubmed

2016

• Cho SH, Min JY, Kim DY, Oh SS, Torgerson DR, Pino-Yanes M, Hu D, Sen S, Huntsman S, Eng C, Farber HJ, Rodriguez-Cintron W, Rodriguez-Santana JR, Serebrisky D, Thyne SM, Borrell LN, Williams LK, DuPont W, Seibold MA, Burchard EG, Avila PC, Kumar R. Association of a PAI-1 Gene Polymorphism and Early Life Infections with Asthma Risk, Exacerbations, and Reduced Lung Function. PLoS One. 2016 Aug 24;11(8):e0157848. | pubmed
• Nishimura KK, Iwanaga K, Oh SS, Pino-Yanes M, Eng C, Keswani A, Roth LA, Nguyen EA, Thyne SM, Farber HJ, Serebrisky D, Meade K, LeNoir MA, Rodriguez-Cintron W, Borrell LN, Bibbins-Domingo K, Lurmann F, Sen Ś, Rodriguez-Santana JR, Brigino-Buenaventura E, Avila PC, Balmes JR, Kumar R, Burchard EG. Early-life ozone exposure associated with asthma without sensitization in Latino children. J Allergy Clin Immunol. 2016 Dec;138(6):1703-1706.e1. | pubmed
• Suskind AM, Jin C, Cooperberg MR, Finlayson E, Boscardin WJ, Sen S, Walter LC. Preoperative Frailty Is Associated With Discharge to Skilled or Assisted Living Facilities After Urologic Procedures of Varying Complexity. Urology. 2016 Nov;97:25-32. | pubmed
• Fishbein AB, Lee TA, Cai M, Oh SS, Eng C, Hu D, Huntsman S, Farber HJ, Serebrisky D, Silverberg J, Williams LK, Seibold MA, Sen S, Borrell LN, Avila P, Rodriguez-Cintron W, Rodriguez-Santana JR, Burchard EG, Kumar R. Sensitization to mouse and cockroach allergens and asthma morbidity in urban minority youth: Genes-environments and Admixture in Latino American (GALA-II) and Study of African-Americans, Asthma, Genes, and Environments (SAGE-II). Ann Allergy Asthma Immunol. 2016 Jul;117(1):43-49.e1. | pubmed
• Johnson PI, Koustas E, Vesterinen HM, Sutton P, Atchley DS, Kim AN, Campbell M, Donald JM, Sen S, Bero L, Zeise L, Woodruff TJ. Application of the Navigation Guide systematic review methodology to the evidence for developmental and reproductive toxicity of triclosan. Environ Int. 2016 Jul-Aug;92-93:716-28. | pubmed
• Neophytou AM, White MJ, Oh SS, Thakur N, Galanter JM, Nishimura KK, Pino-Yanes M, Torgerson DG, Gignoux CR, Eng C, Nguyen EA, Hu D, Mak AC, Kumar R, Seibold MA, Davis A, Farber HJ, Meade K, Avila PC, Serebrisky D, Lenoir MA, Brigino-Buenaventura E, Rodriguez-Cintron W, Bibbins-Domingo K, Thyne SM, Williams LK, Sen S, Gilliland FD, Gauderman WJ, Rodriguez-Santana JR, Lurmann F, Balmes JR, Eisen EA, Burchard EG.Air Pollution and Lung Function in Minority Youth with Asthma in the GALA II & SAGE II Studies. Am J Respir Crit Care Med. 2016 Jan 6. | pubmed
• Suskind AM, Walter LC, Jin C, Boscardin J, Sen S, Cooperberg MR, Finlayson E. The impact of Frailty on complications in patients undergoing common urologic procedures; a study from the American College of Surgeons National Surgical Quality Improvement Database. BJU International. doi: 10.1111/bju.13399 | pubmed
• Lai JC, Dodge JL, Sen S, Covinsky K, Feng S. Functional decline in patients with cirrhosis awaiting liver transplantation: Results from the functional assessment in liver transplantation (FrAILT) study. Hepatology. 2016 Feb;63(2):574-80. | pubmed

2015

• Shah AD, Schmidt H, Sen S, Shlipak MG, Kanaya AM. The association between body composition and cystatn C in South Asicnas: results from the MASALA study. Obesity Research and Clinical Practice. Mar-Apr 2015;9(2):180-3.| pubmed
• Broman KW, Keller MP, Broman AT, Kendziorski C, Yandell BS, Sen S, Attie AD. Identification and Correction of Sample Mix-Ups in Expression Genetic Data: A Case Study. G3 (Bethesda). 2015 Aug 19. | pubmed
• Lovell JT, Mullen JL, Lowry DB, Awole K, Richards JH, Sen S, Verslues PE, Juenger TE, McKay JK. Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana. Plant Cell. 2015 Apr; 27(4):969-83. | pubmed
• McGarry ME, Castellanos E, Thakur N, Oh SS, Eng C, Davis A, Meade K, LeNoir MA, Avila PC, Farber HJ, Serebrisky D, Brigino-Buenaventura E, Rodriguez-Cintron W, Kumar R, Bibbins-Domingo K, Thyne SM, Sen S, Rodriguez-Santana JR, Borrell LN, Burchard EG. Obesity and Bronchodilator Response in African-American and Hispanic Children and Adolescents with Asthma. Chest. 2015 Mar 5. | pubmed
• Pino-Yanes M, Thakur N, Gignoux CR, Galanter JM, Roth LA, Eng C, Nishimura KK, Oh SS, Vora H, Huntsman S, Nguyen EA, Hu D, Drake KA, Conti DV, Moreno-Estrada A, Sandoval K, Winkler CA, Borrell LN, Lurmann F, Islam TS, Davis A, Farber HJ, Meade K, Avila PC, Serebrisky D, Bibbins-Domingo K, Lenoir MA, Ford JG, Brigino-Buenaventura E, Rodriguez-Cintron W, Thyne SM, Sen S, Rodriguez-Santana JR, Bustamante CD, Williams LK, Gilliland FD, Gauderman WJ, Kumar R, Torgerson DG, Burchard EG. "Genetic ancestry influences asthma susceptibility and lung function among Latinos," Journal of Allergy and Clinical Immunology. 2015 Jan; 135(1):228-35. | pubmed | journal

2014

• Lam J, Koustas E, Sutton P, Johnson PI, Atchley DS, Sen S, Robinson KA, Axelrad DA, Woodruff TJ. "The Navigation Guide-Evidence-Based Medicine Meets Environmental Health: Integration of Animal and Human Evidence for PFOA Effects on Fetal Growth," Environmental Health Perspectives. 2014 Oct; 122:1040–1051. | pubmed | journal
• Johnson PI, Sutton P, Atchley DS, Koustas E, Lam J, Sen S, Robinson KA, Axelrad DA, Woodruff TJ. The Navigation Guide-Evidence-Based Medicine Meets Environmental Health: Systematic Review of Human Evidence for PFOA Effects on Fetal Growth. Environmental Health Perspectives. 2014 Oct; 122:1028–1039. | pubmed | journal
• Koustas E, Lam J, Sutton P, Johnson PI, Atchley DS, Sen S, Robinson KA, Axelrad DA, Woodruff TJ. The Navigation Guide-Evidence-Based Medicine Meets Environmental Health: Systematic Review of Nonhuman Evidence for PFOA Effects on Fetal Growth. Environmental Health Perspectives. 2014 Oct; 122:1015–1027. | pubmed | journal
• Rubinstein ML, Rait MA, Sen S, Shiffman S. Characteristics of adolescent intermittent and daily smokers. Addict Behav. 2014 Sep; 39(9):1337-41. | pubmed | journal
• Thakur N, Martin M, Castellanos E, Oh SS, Roth LA, Eng C, Brigino-Buenaventura E, Davis A, Meade K, Lenoir MA, Farber HJ, Thyne S, Sen S, Bibbins-Domingo K, Borrell LN, Burchard EG. Socioeconomic Status and Asthma Control in African American Youth in SAGE II. Journal of Asthma. 2014 Mar 21. | pubmed
• Galanter JM, Gignoux CR, Torgerson DG, Roth LA, Eng C, Oh SS, Nguyen EA, Drake KA, Huntsman S, Hu D, Sen S, Davis A, Farber HJ, Avila PC, Brigino-Buenaventura E, Lenoir MA, Meade K, Serebrisky D, Borrell LN, Rodríguez-Cintrón W, Estrada AM, Mendoza KS, Winkler CA, Klitz W, Romieu I, London SJ, Gilliland F, Martinez F, Bustamante C, Williams LK, Kumar R, Rodríguez-Santana JR, Burchard EG. Genome-wide association study and admixture mapping identify different asthma-associated loci in Latinos: The Genes-environments & Admixture in Latino Americans study. The Journal of Allergy and Clnical Immunology. 2014 Jan 7. | pubmed | journal

2013

• Thakur N, Oh SS, Nguyen EA, Martin M, Roth LA, Galanter J, Gignoux CR, Eng C, Davis A, Meade K, Lenoir MA, Avila PC, Farber HJ, Serebrisky D, Brigino-Buenaventura E, Rodriguez-Cintron W, Kumar R, Williams LK, Bibbins-Domingo K, Thyne S, Sen S, Rodriguez-Santana JR, Borrell LN, Burchard EG. Socioeconomic Status and Childhood Asthma in Urban Minority Youths. The GALA II and SAGE II Studies. American Journal of Respiratory and Critical Care Medicine. 2013 Nov 15; 188(10):1202-9. | pubmed | journal
• Gerona RR, Woodruff TJ, Dickenson CA, Pan J, Schwartz JM, Sen S, Friesen MW, Fujimoto VY, Hunt PA. Bisphenol-A (BPA), BPA Glucuronide, and BPA Sulfate in Midgestation Umbilical Cord Serum in a Northern and Central California Population. Environmental Science and Technology 2013 Nov 5; 47(21):12477-85. | pubmed | journal
• Fletcher RS, Mullen JL, Yoder S, Bauerle WL, Reuning G, Sen S, Meyer E, Juenger TE, McKay JK. Development of a next-generation NIL library in Arabidopsis thaliana for dissecting complex traits. BMC Genomics. 2013; 14:655. | pubmed | journal
• Lowry DB, Logan TL, Santuari L, Hardtke CS, Richards JH, DeRose-Wilson LJ, McKay JK, Sen S, Juenger TE. Expression quantitative trait locus mapping across water availability environments reveals contrasting associations with genomic features in Arabidopsis. Plant Cell. 2013 Sep; 25(9):3266-79. | pubmed | journal
• Drake KA, Torgerson DG, Gignoux CR, Galanter JM, Roth LA, Huntsman S, Eng C, Oh SS, Yee SW, Lin L, Bustamante CD, Moreno-Estrada A, Sandoval K, Davis A, Borrell LN, Farber HJ, Kumar R, Avila PC, Brigino-Buenaventura E, Chapela R, Ford JG, Lenoir MA, Lurmann F, Meade K, Serebrisky D, Thyne S, Rodríguez-Cintrón W, Sen S, Rodríguez-Santana JR, Hernandez RD, Giacomini KM, Burchard EG. A genome-wide association study of bronchodilator response in Latinos implicates rare variants. The Journal of Allergy and Clnical Immunology. 2014 Feb; 133(2):370-378.e15. | pubmed | journal
• Nishimura KK, Galanter JM, Roth LA, Oh SS, Thakur N, Nguyen EA, Thyne S, Farber HJ, Serebrisky D, Kumar R, Brigino-Buenaventura E, Davis A, LeNoir MA, Meade K, Rodriguez-Cintron W, Avila PC, Borrell LN, Bibbins-Domingo K, Rodriguez-Santana JR, Sen S, Lurmann F, Balmes JR, Burchard EG. Early-life air pollution and asthma risk in minority children. The GALA II and SAGE II studies. American Journal of Respiratory and Crtical Care Medicine. 2013 Aug 1; 188(3):309-18. | pubmed | journal
• Lovell JT, Juenger TE, Michaels SD, Lasky JR, Platt A, Richards JH, Yu X, Easlon HM, Sen S, McKay JK. Pleiotropy of FRIGIDA enhances the potential for multivariate adaptation. Proceedings of the Royal Society B. 2013 Jul 22; 280(1763):20131043. | pubmed | journal
• Jones-Davis DM, Yang M, Rider E, Osbun NC, da Gente GJ, Li J, Katz AM, Weber MD, Sen S, Crawley J, Sherr EH. Quantitative trait loci for interhemispheric commissure development and social behaviors in the BTBR T? tf/J mouse model of autism. PLoS One. 2013; 8(4):e61829. | pubmed | journal
• Borrell LN, Nguyen EA, Roth LA, Oh SS, Tcheurekdjian H, Sen S, Davis A, Farber HJ, Avila PC, Brigino-Buenaventura E, Lenoir MA, Lurmann F, Meade K, Serebrisky D, Rodriguez-Cintron W, Kumar R, Rodriguez-Santana JR, Thyne SM, Burchard EG. Childhood obesity and asthma control in the GALA II and SAGE II studies. American Journal of Respiratory and Crtical Care Medicine. 2013 Apr 1; 187(7):697-702. | pubmed | journal
• Rubinstein ML, Shiffman S, Moscicki AB, Rait MA, Sen S, Benowitz NL. Nicotine metabolism and addiction among adolescent smokers. Addiction. 2013 Feb; 108(2):406-12. | pubmed | journal

2012

• Choudhry S, Deshpande A, Qiao L, Beckman K, Sen S, Baskin LS. Genome-wide DNA methylation profiling of CpG islands in hypospadias. Journal of Urology. 2012 Oct; 188(4 Suppl):1450-5. | pubmed | journal
• Broman KW, Kim S, Sen S, Ané C, Payseur BA. Mapping quantitative trait loci onto a phylogenetic tree. Genetics. 2012 Sep; 192(1):267-79. | pubmed | journal
• Aldrich MC, Kumar R, Colangelo LA, Williams LK, Sen S, Kritchevsky SB, Meibohm B, Galanter J, Hu D, Gignoux CR, Liu Y, Harris TB, Ziv E, Zmuda J, Garcia M, Leak TS, Foreman MG, Smith LJ, Fornage M, Liu K, Burchard EG. Genetic ancestry-smoking interactions and lung function in African Americans: a cohort study. PLoS One. 2012; 7(6):e39541. | pubmed | journal
• Oh SS, Tcheurekdjian H, Roth LA, Nguyen EA, Sen S, Galanter JM, Davis A, Farber HJ, Gilliland FD, Kumar R, Avila PC, Brigino-Buenaventura E, Chapela R, Ford JG, LeNoir MA, Lurmann F, Meade K, Serebrisky D, Thyne S, Rodriguez-Cintron W, Rodriguez-Santana JR, Williams LK, Borrell LN, Burchard EG. Effect of secondhand smoke on asthma control among black and Latino children. J Allergy Clin Immunol. 2012 Jun; 129(6):1478-83.e7. | pubmed | journal
• King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S, Broman KW, Long AD, Macdonald SJ. Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Research. 2012 Aug; 22(8):1558-66. | pubmed | journal
• Des Marais DL, McKay JK, Richards JH, Sen S, Wayne T, Juenger TE. Physiological genomics of response to soil drying in diverse Arabidopsis accessions. Plant Cell. 2012 Mar; 24(3):893-914. | pubmed | journal

2011

• Xiong H, Capurso D, Sen S, Segal MR. Sequence-based classification using discriminatory motif feature selection. PLoS One. 2011; 6(11):e27382. | pubmed | journal
• Xiong H, Goulding EH, Carlson EJ, Tecott LH, McCulloch CE, Sen S. A flexible estimating equations approach for mapping function-valued traits. Genetics. 2011 Sep; 189(1):305-16. | pubmed | journal
• Galanter JM, Torgerson D, Gignoux CR, Sen S, Roth LA, Via M, Aldrich MC, Eng C, Huntsman S, Rodriguez-Santana J, Rodriguez-Cintrón W, Chapela R, Ford JG, Burchard EG. Cosmopolitan and ethnic-specific replication of genetic risk factors for asthma in 2 Latino populations. J Allergy Clin Immunol. 2011 Jul; 128(1):37-43.e12. | pubmed | journal
• Breyer BN, Sen S, Aaronson DS, Stoller ML, Erickson BA, Eisenberg ML. Use of Google Insights for Search to track seasonal and geographic kidney stone incidence in the United States. Urology. 2011 Aug; 78(2):267-71. | pubmed | journal
• Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA. (2011) "Phenotypic landscape of a bacterial cell," Cell, 144(1):143-56. | pubmed | journal

2010

• Kumar R, Seibold MA, Aldrich MC, Williams LK, Reiner AP, Colangelo L, Galanter J, Gignoux C, Hu D, Sen S, Choudhry S, Peterson EL, Rodriguez-Santana J, Rodriguez-Cintron W, Nalls MA, Leak TS, O'Meara E, Meibohm B, Kritchevsky SB, Li R, Harris TB, Nickerson DA, Fornage M, Enright P, Ziv E, Smith LJ, Liu K, Burchard EG (2010) "Genetic ancestry in lung-function predictions," New England Journal of Medicine, 363(4):321-30. | pubmed | journal
• Juenger TE, Sen S, Bray E, Stahl E, Wayne T, McKay J, Richards JH (2010) "Exploring genetic and expression differences between physiologically extreme ecotypes: comparative genomic hybridization and gene expression studies of Kas-1 and Tsu-1 accessions of Arabidopsis thaliana," Plant Cell and Environment 33(8):1268-84. | pubmed | journal
• Shah S, Sanford UR, Vargas JC, Xu H, Groen A, Paulusma CC, Grenert JP, Pawlikowska L, Sen S, Elferink RP, Bull LN (2010), "Strain background modifies phenotypes in the ATP8B1-deficient mouse," PLoS ONE, 5:e8984. | pubmed | journal
• Via M, De Giacomo A, Corvol H, Eng C, Seibold MA, Gillett C, Galanter J, Sen S, Tcheurekdjian H, Chapela R, Rodríguez-Santana JR, Rodríguez-Cintrón W, Thyne S, Avila PC, Choudhry S, González Burchard E(2010) "The role of LTA4H and ALOX5AP genes in the risk for asthma in Latinos," Clinical & Experimental Allergy, 40:582-589. | pubmed | journal

2009

• Asgari MM, Bertenthal D, Sen S, Sahay A, Chren MM (2009) "Patient satisfaction after treatment of nonmelanoma skin cancer," Dermatological Surgery, 35:1041-1049. | pubmed | journal
• Tanaka Y, Zaman MS, Majid S, Liu J, Kawakami K, Shiina H, Tokizane T, Dahiya AV, Sen S, Nakajima K (2009) "Polymorphisms of MLH1 in benign prostatic hyperplasia and sporadic prostate cancer," | pubmed | journal Biochemical and Biophysical Research Communications, 383:440-444.
• Sen S, Johannes F, and Broman KW (2009) "Selective genotyping and phenotyping strategies in a complex trait context," Genetics,181:1613-1626. | pubmed | journal
• Manichaikul A, Moon JY, Sen S, Yandell BS, Broman KW (2009) "A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis," Genetics, 181:1077-1086. | pubmed | journal
• Vittinghoff E, Sen S, McCulloch CE (2009) "Sample size calculations for evaluating mediation," Statistics in Medicine, 28:541-557. | pubmed | journal
• Yaffe K, Lindquist K, Sen S, Cauley JA, Ferrell RE, Penninx B, Harris T, Li R, Cummings SR (2009) "Estrogen receptor genotype and risk of cognitive impairment in elders: Findings from the Health ABC study," Neurobiology of Aging, 30:607-614. | pubmed | journal

2008

• McKay JK, Richards JH, Nemali KS, Sen S, Mitchell-Olds T, Boles S, Stahl EA, Wayne T, Juenger TE (2008) "Genetics of drought adaptation in Arabidopsis thaliana II: QTL analysis of a new mapping population, Kas-1xTsu-1," Evolution, 62:3014-3026. | pubmed | journal
• Wetmore JB, Lovett DH, Hung AM, Cook-Wiens G, Mahnken JD, Sen S, Johansen KL (2008) "Associations of interleukin-6, C-reactive protein and serum amyloid A with mortality in haemodialysis patients," Nephrology, 13:593-600. | pubmed | journal
• Seibold MA, Wang B, Eng C, Kumar G, Beckman KB, Sen S, Choudhry S, Meade K, Lenoir M, Watson HG, Thyne S, Williams LK, Kumar R, Weiss KB, Grammer LC, Avila PC, Schleimer RP, Burchard EG, Brenner R (2008) "An African-specific functional polymorphism in KCNMB1 shows sex-specific association with asthma severity," Human Molecular Genetics, 17:2681-2690. | pubmed | journal
• Ku T-S, Kane CJ, Sen S, Henderson WG, Dudley RA, Cason BA (2008) "Effects of hospital procedure volume and resident training on clinical outcomes and resource use in radical retropubic prostatectomy surgery in the Department of Veterans Affairs," Journal of Urology, 179:272-278. | pubmed | journal

2007

• Manichaikul A, Palmer AA, Sen S, Broman KW (2007) "Significance thresholds for quantitative trait locus mapping under selective genotyping," Genetics, 177:1963-1966. | pubmed | journal
• Folayan M, Owotade F, Adejuyigbe E, Sen S, Lawal B, Ndukwe K (2007) "The timing of eruption of the primary dentition in Nigerian children," American Journal of Physical Anthropology, 134:443-448. | pubmed | journal
• Chen T, Bertenthal D, Sahay A, Sen S, Chren MM (2007) "Predictors of skin-related quality of life after treatment of cutaneous basal cell carcinoma and squamous cell carcinoma," Archives of Dermatology, 143:1386-1392. | pubmed | journal
• Moody-Ayers S, Lindquist K, Sen S, Covinsky KE (2007) "Childhood Social and Economic Well-Being and Health in Older Age," American Journal of Epidemiology, 166:1059-1067. | pubmed | journal
• Cascio M, Xing Y, Gong D, Popovich J, Eger EI, Sen S, Peltz G, Sonner JM (2007) "Mouse chromosome 7 harbors a quantitative trait locus for isoflurane minimum alveolar concentration," Anesthesia and Analgesia, 105:381-385. | pubmed | journal
• Chren MM, Sahay AP, Bertenthal D, Sen S, Landefeld CS (2007) "Quality-of-life outcomes of treatments for cutaneous basal cell carcinoma and squamous cell carcinoma," Journal of Investigative Dermatology, 127:1351-57. | pubmed | journal
• Satagopan JM, Sen S, Churchill GA (2007) "Sequential quantitative trait locus mapping in experimental crosses," Statistical Applications in Genetics and Molecular Biology, 6:Article12. | pubmed | journal
• Sen S, Satagopan JM, Broman, KW, and Churchill GA (2007) "R/qtlDesign: Inbred line cross experimental design," Mammalian Genome, 18:87-93. | pubmed | journal
• Rodriguez RA, Sen S, Mehta K, Moody-Ayers S, Bacchetti P, O'Hare AM (2007) "Geography Matters: Residential segregation by race and outcomes among metropolitan dialysis patients and facilities," Annals of Internal Medicine, 146:493-501. | pubmed | journal
• Seal KH, Bertenthal D, Miner CR, Sen S, Marmar C (2007) "Bringing the war back home: Mental health disorders among 103,788 US veterans returning from Iraq and Afghanistan seen at VA facilities," Archives of Internal Medicine, 167:476-482. | pubmed | journal
• Holroyd-Leduc JM, Sen S, Bertenthal D, Sands LP, Palmer RM, Kresevic DM, Covinsky KE, Landefeld CS (2007) "The relationship of indwelling urinary catheters to death, length of hospital stay, functional decline, and nursing home admission in hospitalized older medical patients," Journal of the American Geriatric Society, 55:227-233. | pubmed | journal
• Steinman MA, Rosenthal GE, Landefeld CS, Bertenthal D, Sen S, Kaboli PJ (2007) "Conflicts and Concordance Between Measures of Medication Prescribing Quality," Medical Care, 45:95-99. | pubmed | journal

2006

• Broman KW, Sen S, Owens SE, Manichaikul A, Southard-Smith EM, Churchill GA (2006) "The X chromosome in quantitative trait locus mapping," Genetics, 174:2151-2158. | pubmed | journal
• O'Hare AM, Bertenthal D, Covinsky KE, Landefeld CS, Sen S, Mehta K, Steinman MA, Borzecki A, Walter LC (2006) "Mortality risk stratification in chronic kidney disease: One size for all ages?" Journal of the American Society of Nephrology, 7:846-853. | pubmed | journal
• O'Hare AM, Bertenthal D, Sidawy AN, Shlipak MG, Sen S, Chren MM (2006) "Renal insufficiency and use of revascularization among a national cohort of men with advanced lower extremity peripheral arterial disease," Clinical Journal of the American Society of Nephrology, 1:297-304. | pubmed | journal
• Ruo B, Bertenthal D, Sen S, Bittner V, Ireland CC, Hlatky MA (2006) "Self-rated health among women with coronary disease: Depression is as important as recent cardiovascular events," American Heart Journal, 152:Article921.e1. | pubmed | journal
• Steinman MA, Landefeld CS, Rosenthal GE, Berthenthal D, Sen S, Kaboli PJ (2006) "Polypharmacy and prescribing quality in older people," Journal of the American Geriatric Society 54:1516-1523. | pubmed | journal
• Manichaikul A, Dupuis J, Sen S, Broman KW (2006) "Poor performance of bootstrap confidence intervals for the location of a quantitative trait locus," Genetics, 174:481-489. | pubmed | journal
• Wetmore JB, Johansen KL, Sen S, Hung AM, Lovett DH (2006) "An angiotensin converting enzyme haplotype predicts survival in patients with end stage renal disease," Human Genetics, 120:201-210. | pubmed | journal
• Hoopes RR, Middleton FA, Sen S, Hueber PA, Reid R, Bushinsky DA, Scheinman SJ (2006) "Isolation and confirmation of calcium excretion QTL on chromosome 1 in GHS congenic rats", Journal of the American Society of Nephrology, 17:1292-1304. | pubmed | journal

2005

• Collin GB, Maddatu TP, Sen S, and Naggert JK (2005) "Genetic modifiers interact with Cpefat to affect body weight, adiposity, and hyperglycemia," Physiological Genomics, 22:182-190. | pubmed | journal
• Juenger TE, McKay JK, Hausmann N, Keurentjes J, Sen S, Stowe KA, Dawson TE, Simms EL, Richards JH (2005) "Identification and characterization of QTL underlying whole-plant physiology in Arabidopsis thaliana: &delta13C, stomatal conductance, and transpiration efficiency," Plant, Cell, and the Environment, 28:697-708. | journal
• Wetmore JB, Hung AM, Lovett DH, Sen S, Quershy O, Johansen KL (2005) "Interleukin-1 gene cluster polymorphisms predict risk of ESRD," Kidney International, 68:278-284. | pubmed | journal
• Sen S, Satagopan JM, and Churchill GA (2005) "Quantitative trait locus study design from an information perspective," Genetics, 170:447-464. | pubmed | journal
• Juenger TE, Sen S, Stowe KA, Simms EL (2005) "Epistasis and genotype-environment interaction for quantitative trait loci affecting flowering time in Arabidopsis thaliana," Genetica, 123:87-105. | pubmed | journal
• O'Hare AM, Bertenthal D, Shlipak MG, Sen S, Chren MM (2005) "Impact of renal insufficiency on mortality in advanced lower extremity peripheral arterial disease," Journal of the American Society of Nephrology,16:514-519. | pubmed | journal
• Hausmann N, Juenger TE, Sen S, Stowe KA, Dawson TE, Simms EL (2005) "Quantitative trait loci (QTL) affecting &delta13C and response to differential water availability in Arabidopsis thaliana," Evolution, 59:81-96. | pubmed | journal

2004

• Lustig RH, Sen S, Soberman JE, Velasquez-Mieyer PA (2004) "Obesity, leptin resistance, and the effects of insulin reduction," International Journal of Obesity, 28:1344-1348. | pubmed | journal
• Korstanje R, Eriksson P, Samnegard A, Olsson PG, Forsman-Semb K, Sen S, Churchill GA, Rollins J, Harris S, Hamsten A, Paigen B (2004) "Locating Ath8, a locus for murine atherosclerosis susceptibility and testing several of its candidate genes in mice and humans," Atherosclerosis, 177:443-50. | pubmed | journal
• Bouxsein ML, Uchiyama T, Rosen CJ, Schultz KL, Donahue LR, Turner CH, Sen S, Churchill GA, Muller R, Beamer WG (2004) "Mapping quantitative trait loci for vertebral trabecular bone volume fraction and microarchitecture in mice," Journal of Bone and Mineral Research, 19:587-99. | pubmed | journal

2003

• Hoopes RR, Reid R, Sen S, Szpirer C, Dixon P, Pannet A, Thakker RV, Bushinsky DA, Scheinman SJ. (2003) "Quantitative trait loci for hypercalciuria in a rat model of kidney stone disease," Journal of the American Society of Nephrology,14:1844-1850. | pubmed | journal
• Broman KW, Wu H, Sen S, Churchill GA (2003) "R/qtl: QTL mapping in experimental crosses," Bioinformatics,19:889-890. | pubmed | journal | website

2002

• Ormoneit D and Sen S (2002), "Kernel-based reinforcement learning," Machine Learning; 49:161-178. | journal

2001

• Sen S and Churchill GA (2001), "A statistical framework for quantitative trait mapping"; Genetics; 159:371-387. | pubmed | journal
• Kim JH, Sen S, Avery CS, Simpson EM, Churchill GA, Nishina PM, and Naggert JK (2001), "Genetic analysis of a new mouse model for non-insulin-dependent diabetes"; Genomics; 74:273-286. | pubmed | journal
• Beamer WG, Shultz KL, Donahue LR, Churchill GA, Sen S, Wergedal JR, Baylink DJ, and Rosen CJ (2001), "Quantitative trait loci for femoral and lumbar vertebral bone mineral density in C57BL/6J and C3H/HeJ inbred strains of mice"; Journal of Bone and Mineral Research; 16:1195-1206. | pubmed | journal

1999

• Dighe A and Sen S (1999), "Information content in B->VV decays and the angular moments method," Physical Review D; 59:074002. | journal

1995

• Vijayakumar S, Quadri F, Sen S, Vaida F, Ignacio L, Weichselbaum R (1995) "Measurement of Weekly Prostate Specific Antigen Levels in Patients Receiving Pelvic Radiotherapy for Nonprostatic Malignancies," International Journal of Radiation Oncology and Biological Physics, 32:189-195. | pubmed | journal

A guide to QTL mapping with R/qtl
Karl W. Broman and Śaunak Sen
Springer, 2009

The book is a practical guide to the analysis of crosses between inbred strains using the software R/qtl.

If you are looking for places to drink beer, you might want to look at my note on Memphis brewpubs.