Publications

1. Alvarez M, Benhammou JN, Darci-Maher N, French SW, Han SB, Sinsheimer JS, Agopian VG, Pisegna JR, Pajukanta P. Human liver single nucleus and single�cell RNA sequencing identify a hepatocellular carcinoma-associated cell-type affecting survival.. Genome medicine, 2022.
2. Kusters CDJ, Paul KC, Duarte Folle A, Keener AM, Bronstein JM, Bertram L, Hansen J, Horvath S, Sinsheimer JS, Lill CM, Ritz BR. Erratum to "Increased Menopausal Age Reduces the Risk of Parkinson's Disease: A Mendelian Approach".. Movement disorders : official journal of the Movement Disorder Society, 2022.
3. Ko S, German CA, Jensen A, Shen J, Wang A, Mehrotra DV, Sun YV, Sinsheimer JS, Zhou H, Zhou JJ. GWAS of longitudinal trajectories at biobank scale.. American journal of human genetics, 2022.
4. Stutz TC, Sinsheimer JS, Sehl M, Xu J. Computational tools for assessing gene therapy under branching process models of mutation.. Bulletin of mathematical biology, 2021.
5. Flores YN, Amoon AT, Su B, Velazquez-Cruz R, Ram?rez-Palacios P, Salmer?n J, Rivera-Paredez B, Sinsheimer JS, Lusis AJ, Huertas-Vazquez A, Saab S, Glenn BA, May FP, Williams KJ, Bastani R, Bensinger SJ. Serum lipids are associated with nonalcoholic fatty liver disease: a pilot case-control study in Mexico.. Lipids in health and disease, 2021.
6. Chang CC, Huang ZY, Shih SF, Luo Y, Ko A, Cui Q, Sumner J, Cavallero S, Das S, Gao W, Sinsheimer J, Bui A, Jacobs JP, Pajukanta P, Wu H, Tai YC, Li Z, Hsiai TK. Electrical impedance tomography for non-invasive identification of fatty liver infiltrate in overweight individuals.. Scientific reports, 2021.
7. Pan DZ, Miao Z, Comenho C, Rajkumar S, Koka A, Lee SHT, Alvarez M, Kaminska D, Ko A, Sinsheimer JS, Mohlke KL, Mancuso N, Mu?oz-Hernandez LL, Herrera-Hernandez M, Tusi?-Luna MT, Aguilar-Salinas C, Pietil?inen KH, Pihlajam?ki J, Laakso M, Garske KM, Pajukanta P. Correction to: Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes.. Genome medicine, 2021.
8. Miao Z, Garske KM, Pan DZ, Koka A, Kaminska D, Männistö V, Sinsheimer JS, Pihlajamäki J, Pajukanta P. Identification of 90 NAFLD GWAS loci and establishment of NAFLD PRS and causal role of NAFLD in coronary artery disease.. HGG advances, 2021.
9. Kusters CDJ, Paul KC, Duarte Folle A, Keener AM, Bronstein JM, Bertram L, Hansen J, Horvath S, Sinsheimer JS, Lill CM, Ritz BR. Increased Menopausal Age Reduces the Risk of Parkinson's Disease: A Mendelian Randomization Approach.. Movement disorders : official journal of the Movement Disorder Society, 2021.
10. Pan DZ, Miao Z, Comenho C, Rajkumar S, Koka A, Lee SHT, Alvarez M, Kaminska D, Ko A, Sinsheimer JS, Mohlke KL, Mancuso N, Mu?oz-Hernandez LL, Herrera-Hernandez M, Tusi?-Luna MT, Aguilar-Salinas C, Pietil?inen KH, Pihlajam?ki J, Laakso M, Garske KM, Pajukanta P. Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes.. Genome medicine, 2021.
11. German CA, Sinsheimer JS, Zhou J, Zhou H. WiSER: Robust and scalable estimation and inference of within-subject variances from intensive longitudinal data.. Biometrics, 2021.
12. Chu BB, Sobel EM, Wasiolek R, Ko S, Sinsheimer JS, Zhou H, Lange K. A fast Data-Driven method for genotype imputation, phasing, and local ancestry inference: MendelImpute.jl.. Bioinformatics (Oxford, England), 2021.
13. Landeros A, Ji X, Lange K, Stutz TC, Xu J, Sehl ME, Sinsheimer JS. An examination of school reopening strategies during the SARS-CoV-2 pandemic.. PloS one, 2021.
14. Ji SS, German CA, Lange K, Sinsheimer JS, Zhou H, Zhou J, Sobel EM. Modern simulation utilities for genetic analysis.. BMC bioinformatics, 2021.
15. Landeros A, Ji X, Lange K, Stutz TC, Xu J, Sehl ME, Sinsheimer JS. An examination of school reopening strategies during the SARS-CoV-2 pandemic.. medRxiv : the preprint server for health sciences, 2021.
16. Stutz TC, Landeros A, Xu J, Sinsheimer JS, Sehl M, Lange K. Stochastic simulation algorithms for Interacting Particle Systems.. PloS one, 2021.
17. Bryant L, Li D, Cox SG, Marchione D, Joiner EF, Wilson K, Janssen K, Lee P, March ME, Nair D, Sherr E, Fregeau B, Wierenga KJ, Wadley A, Mancini GMS, Powell-Hamilton N, van de Kamp J, Grebe T, Dean J, Ross A, Crawford HP, Powis Z, Cho MT, Willing MC, Manwaring L, Schot R, Nava C, Afenjar A, Lessel D, Wagner M, Klopstock T, Winkelmann J, Catarino CB, Retterer K, Schuette JL, Innis JW, Pizzino A, L?ttgen S, Denecke J, Strom TM, Monaghan KG, DDD Study, Yuan ZF, Dubbs H, Bend R, Lee JA, Lyons MJ, Hoefele J, G?nthner R, Reutter H, Keren B, Radtke K, Sherbini O, Mrokse C, Helbig KL, Odent S, Cogne B, Mercier S, Bezieau S, Besnard T, Kury S, Redon R, Reinson K, Wojcik MH, ?unap K, Ilves P, Innes AM, Kernohan KD, Care4Rare Canada Consortium, Costain G, Meyn MS, Chitayat D, Zackai E, Lehman A, Kitson H, CAUSES Study, Martin MG, Martinez-Agosto JA, Undiagnosed Diseases Network, Nelson SF, Palmer CGS, Papp JC, Parker NH, Sinsheimer JS, Vilain E, Wan J, Yoon AJ, Zheng A, Brimble E, Ferrero GB, Radio FC, Carli D, Barresi S, Brusco A, Tartaglia M, Thomas JM, Umana L, Weiss MM, Gotway G, Stuurman KE, Thompson ML, McWalter K, Stumpel CTRM, Stevens SJC, Stegmann APA, Tveten K, V?llo A, Prescott T, Fagerberg C, Laulund LW, Larsen MJ, Byler M, Lebel RR, Hurst AC, Dean J, Schrier Vergano SA, Norman J, Mercimek-Andrews S, Neira J, Van Allen MI, Longo N, Sellars E, Louie RJ, Cathey SS, Brokamp E, Heron D, Snyder M, Vanderver A, Simon C, de la Cruz X, Padilla N, Crump JG, Chung W, Garcia B, Hakonarson HH, Bhoj EJ. Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients.. Science advances, 2020.
18. Crandall CJ, Diamant AL, Maglione M, Thurston RC, Sinsheimer J. Genetic Variation and Hot Flashes: A Systematic Review.. The Journal of clinical endocrinology and metabolism, 2020.
19. Hung TKW, Dong TS, Chen Z, Elashoff D, Sinsheimer JS, Jacobs JP, Lagishetty V, Vora P, Stains J, Mayer EA, Gupta A. Understanding the Heterogeneity of Obesity and the Relationship to the Brain-Gut Axis.. Nutrients, 2020.
20. Studwell CM, Kelley EG, Undiagnosed Diseases Network, Sinsheimer JS, Palmer CGS, LeBlanc K. Family genetic result communication in rare and undiagnosed disease communities: Understanding the practice.. Journal of genetic counseling, 2020.
21. Levine AJ, Soontornniyomkij V, Masliah E, Sinsheimer JS, Ji SS, Horvath S, Singer EJ, Kallianpur A, Moore DJ. Correction to: A candidate gene study of intermediate histopathological phenotypes in HIV-associated neurocognitive disorders.. Journal of neurovirology, 2020.
22. Kusters CDJ, Paul KC, Duarte Folle A, Keener AM, Bronstein JM, Dobricic V, Tysnes OB, Bertram L, Alves G, Sinsheimer JS, Lill CM, Maple-Gr?dem J, Ritz BR. Genetic risk scores and hallucinations in patients with Parkinson disease.. Neurology. Genetics, 2020.
23. Chu BB, Keys KL, German CA, Zhou H, Zhou JJ, Sobel EM, Sinsheimer JS, Lange K. Iterative hard thresholding in genome-wide association studies: Generalized linear models, prior weights, and double sparsity.. GigaScience, 2020.
24. Levine AJ, Soontornniyomkij V, Masliah E, Sinsheimer JS, Ji SS, Horvath S, Singer EJ, Kallianpur A, Moore DJ. A candidate gene study of intermediate histopathological phenotypes in HIV-associated neurocognitive disorders.. Journal of neurovirology, 2020.
25. vonHoldt BM, DeCandia AL, Heppenheimer E, Janowitz-Koch I, Shi R, Zhou H, German CA, Brzeski KE, Cassidy KA, Stahler DR, Sinsheimer JS. Heritability of interpack aggression in a wild pedigreed population of North American grey wolves.. Molecular ecology, 2020.
26. German CA, Sinsheimer JS, Klimentidis YC, Zhou H, Zhou JJ. Ordered multinomial regression for genetic association analysis of ordinal phenotypes at Biobank scale.. Genetic epidemiology, 2019.
27. Shih IF, Haan MN, Paul KC, Yu Y, Sinsheimer JS, Ritz B. The Roles of Physical Activity and Inflammation in Mortality, Cognition, and Depressive Symptoms Among Older Mexican Americans.. American journal of epidemiology, 2019.
28. Lee H, Huang AY, Wang LK, Yoon AJ, Renteria G, Eskin A, Signer RH, Dorrani N, Nieves-Rodriguez S, Wan J, Douine ED, Woods JD, Dell'Angelica EC, Fogel BL, Martin MG, Butte MJ, Parker NH, Wang RT, Shieh PB, Wong DA, Gallant N, Singh KE, Tavyev Asher YJ, Sinsheimer JS, Krakow D, Loo SK, Allard P, Papp JC, Undiagnosed Diseases Network, Palmer CGS, Martinez-Agosto JA, Nelson SF. Diagnostic utility of transcriptome sequencing for rare Mendelian diseases.. Genetics in medicine : official journal of the American College of Medical Genetics, 2019.
29. Garske KM, Pan DZ, Miao Z, Bhagat YV, Comenho C, Robles CR, Benhammou JN, Alvarez M, Ko A, Ye CJ, Pisegna JR, Mohlke KL, Sinsheimer JS, Laakso M, Pajukanta P. Reverse gene-environment interaction approach to identify variants influencing body-mass index in humans.. Nature metabolism, 2019.
30. Soontornniyomkij V, Moore DJ, Gouaux B, Soontornniyomkij B, Sinsheimer JS, Levine AJ. Associations of regional amyloid-� plaque and phospho-tau pathology with biological factors and neuropsychological functioning among HIV-infected adults.. Journal of neurovirology, 2019.
31. Zhou H, Sinsheimer JS, Bates DM, Chu BB, German CA, Ji SS, Keys KL, Kim J, Ko S, Mosher GD, Papp JC, Sobel EM, Zhai J, Zhou JJ, Lange K. OPENMENDEL: a cooperative programming project for statistical genetics.. Human genetics, 2019.
32. Chuang YH, Paul KC, Sinsheimer JS, Bronstein JM, Bordelon YM, Ritz B. Genetic variants in nicotinic receptors and smoking cessation in Parkinson's disease.. Parkinsonism & related disorders, 2019.
33. Lin LY, Chun Chang S, O'Hearn J, Hui ST, Seldin M, Gupta P, Bondar G, Deng M, Jauhiainen R, Kuusisto J, Laakso M, Sinsheimer JS, Deb A, Rau C, Ren S, Wang Y, Lusis AJ, Wang JJ, Huertas-Vazquez A. Systems Genetics Approach to Biomarker Discovery: GPNMB and Heart Failure in Mice and Humans.. G3 (Bethesda, Md.), 2018.
34. Landeros A, Stutz T, Keys KL, Alekseyenko A, Sinsheimer JS, Lange K, Sehl ME. BioSimulator.jl: Stochastic simulation in Julia.. Computer methods and programs in biomedicine, 2018.
35. Pan DZ, Garske KM, Alvarez M, Bhagat YV, Boocock J, Nikkola E, Miao Z, Raulerson CK, Cantor RM, Civelek M, Glastonbury CA, Small KS, Boehnke M, Lusis AJ, Sinsheimer JS, Mohlke KL, Laakso M, Pajukanta P, Ko A. Author Correction: Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS.. Nature communications, 2018.
36. Lake JA, Larsen J, Tran DT, Sinsheimer JS. Uncovering the Genomic Origins of Life.. Genome biology and evolution, 2018.
37. vonHoldt BM, Ji SS, Aardema ML, Stahler DR, Udell MAR, Sinsheimer JS. Activity of Genes with Functions in Human Williams-Beuren Syndrome Is Impacted by Mobile Element Insertions in the Gray Wolf Genome.. Genome biology and evolution, 2018.
38. Pan DZ, Garske KM, Alvarez M, Bhagat YV, Boocock J, Nikkola E, Miao Z, Raulerson CK, Cantor RM, Civelek M, Glastonbury CA, Small KS, Boehnke M, Lusis AJ, Sinsheimer JS, Mohlke KL, Laakso M, Pajukanta P, Ko A. Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS.. Nature communications, 2018.
39. Paul KC, Sinsheimer JS, Cockburn M, Bronstein JM, Bordelon Y, Ritz B. NFE2L2, PPARGC1a, and pesticides and Parkinson's disease risk and progression.. Mechanisms of ageing and development, 2018.
40. Gilbert PS, Wu J, Simon MW, Sinsheimer JS, Alfaro ME. Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements.. Molecular phylogenetics and evolution, 2018.
41. Palmer CGS, McConkie-Rosell A, Holm IA, LeBlanc K, Sinsheimer JS, Briere LC, Dorrani N, Herzog MR, Lincoln S, Schoch K, Spillmann RC, Brokamp E, Undiagnosed Diseases Network. Understanding Adult Participant and Parent Empowerment Prior to Evaluation in the Undiagnosed Diseases Network.. Journal of genetic counseling, 2018.
42. Bolanos R, Martinez-Maza O, Zhang ZF, Hussain S, Sehl M, Sinsheimer JS, D'Souza G, Jenkins F, Wolinsky S, Detels R. Decreased levels of the serum inflammatory biomarkers, sGP130, IL-6, sCRP and BAFF, are associated with increased likelihood of AIDS related Kaposi's sarcoma in men who have sex with men.. Cancer research frontiers, 2018.
43. Boudreault P, Wolfson A, Berman B, Venne VL, Sinsheimer JS, Palmer C. Bilingual Cancer Genetic Education Modules for the Deaf Community: Development and Evaluation of the Online Video Material.. Journal of genetic counseling, 2017.
44. Kusters CDJ, Paul KC, Guella I, Bronstein JM, Sinsheimer JS, Farrer MJ, Ritz BR. Dopamine receptors and BDNF-haplotypes predict dyskinesia in Parkinson's disease.. Parkinsonism & related disorders, 2017.
45. vonHoldt BM, Shuldiner E, Koch IJ, Kartzinel RY, Hogan A, Brubaker L, Wanser S, Stahler D, Wynne CDL, Ostrander EA, Sinsheimer JS, Udell MAR. Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs.. Science advances, 2017.
46. Paul KC, Sinsheimer JS, Cockburn M, Bronstein JM, Bordelon Y, Ritz B. Organophosphate pesticides and PON1 L55M in Parkinson's disease progression.. Environment international, 2017.
47. Lorenzo Bermejo J, Boekstegers F, González Silos R, Marcelain K, Baez Benavides P, Barahona Ponce C, Müller B, Ferreccio C, Koshiol J, Fischer C, Peil B, Sinsheimer J, Fuentes Guajardo M, Barajas O, Gonzalez-Jose R, Bedoya G, Cátira Bortolini M, Canizales-Quinteros S, Gallo C, Ruiz Linares A, Rothhammer F. Subtypes of Native American ancestry and leading causes of death: Mapuche ancestry-specific associations with gallbladder cancer risk in Chile.. PLoS genetics, 2017.
48. Crandall CJ, Manson JE, Hohensee C, Horvath S, Wactawski-Wende J, LeBlanc ES, Vitolins MZ, Nassir R, Sinsheimer JS. Association of genetic variation in the tachykinin receptor 3 locus with hot flashes and night sweats in the Women's Health Initiative Study.. Menopause (New York, N.Y.), 2017.
49. Clark MM, Chazara O, Sobel EM, Gjessing HK, Magnus P, Moffett A, Sinsheimer JS. Human Birth Weight and Reproductive Immunology: Testing for Interactions between Maternal and Offspring KIR and HLA-C Genes.. Human heredity, 2017.
50. Cybis GB, Sinsheimer JS, Bedford T, Rambaut A, Lemey P, Suchard MA. Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza.. Statistics in medicine, 2017.
51. Fejzo MS, Myhre R, Colodro-Conde L, MacGibbon KW, Sinsheimer JS, Reddy MVPL, Pajukanta P, Nyholt DR, Wright MJ, Martin NG, Engel SM, Medland SE, Magnus P, Mullin PM. Genetic analysis of hyperemesis gravidarum reveals association with intracellular calcium release channel (RYR2).. Molecular and cellular endocrinology, 2016.
52. Lee PC, Raaschou-Nielsen O, Lill CM, Bertram L, Sinsheimer JS, Hansen J, Ritz B. Gene-environment interactions linking air pollution and inflammation in Parkinson's disease.. Environmental research, 2016.
53. Gatto NM, Paul KC, Sinsheimer JS, Bronstein JM, Bordelon Y, Rausch R, Ritz B. Vitamin D receptor gene polymorphisms and cognitive decline in Parkinson's disease.. Journal of the neurological sciences, 2016.
54. Palmer CG, Boudreault P, Berman BA, Wolfson A, Duarte L, Venne VL, Sinsheimer JS. Bilingual approach to online cancer genetics education for Deaf American Sign Language users produces greater knowledge and confidence than English text only: A randomized study.. Disability and health journal, 2016.
55. Paul KC, Rausch R, Creek MM, Sinsheimer JS, Bronstein JM, Bordelon Y, Ritz B. APOE, MAPT, and COMT and Parkinson's Disease Susceptibility and Cognitive Symptom Progression.. Journal of Parkinson's disease, 2016.
56. Lake JA, Larsen J, Sarna B, de la Haba RR, Pu Y, Koo H, Zhao J, Sinsheimer JS. Rings Reconcile Genotypic and Phenotypic Evolution within the Proteobacteria.. Genome biology and evolution, 2016.
57. Chuang YH, Lill CM, Lee PC, Hansen J, Lassen CF, Bertram L, Greene N, Sinsheimer JS, Ritz B. Gene-Environment Interaction in Parkinson's Disease: Coffee, ADORA2A, and CYP1A2.. Neuroepidemiology, 2016.
58. Janowitz Koch I, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, Gnanadesikan GE, McCoy EL, Rubbi L, Stahler DR, Pellegrini M, Ostrander EA, Wayne RK, Sinsheimer JS, vonHoldt BM. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves.. Molecular ecology, 2016.
59. Lake JA, Larsen J, Sarna B, de la Haba RR, Pu Y, Koo H, Zhao J, Sinsheimer JS. Rings Reconcile Genotypic and Phenotypic Evolution within the Proteobacteria.. Genome biology and evolution, 2015.
60. Levine AJ, Soontornniyomkij V, Achim CL, Masliah E, Gelman BB, Sinsheimer JS, Singer EJ, Moore DJ. Multilevel analysis of neuropathogenesis of neurocognitive impairment in HIV.. Journal of neurovirology, 2015.
61. Clark MM, Blangero J, Dyer TD, Sobel EM, Sinsheimer JS. The Quantitative-MFG Test: A Linear Mixed Effect Model to Detect Maternal-Offspring Gene Interactions.. Annals of human genetics, 2015.
62. Narayan S, Sinsheimer JS, Paul KC, Liew Z, Cockburn M, Bronstein JM, Ritz B. Genetic variability in ABCB1, occupational pesticide exposure, and Parkinson's disease.. Environmental research, 2015.
63. Paul KC, Sinsheimer JS, Rhodes SL, Cockburn M, Bronstein J, Ritz B. Organophosphate Pesticide Exposures, Nitric Oxide Synthase Gene Variants, and Gene-Pesticide Interactions in a Case-Control Study of Parkinson's Disease, California (USA).. Environmental health perspectives, 2015.
64. Gilbert PS, Chang J, Pan C, Sobel EM, Sinsheimer JS, Faircloth BC, Alfaro ME. Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes.. Molecular phylogenetics and evolution, 2015.
65. Cybis GB, Sinsheimer JS, Bedford T, Mather AE, Lemey P, Suchard MA. ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL.. The annals of applied statistics, 2015.
66. Huertas-Vazquez A, Nelson CP, Sinsheimer JS, Reinier K, Uy-Evanado A, Teodorescu C, Ayala J, Hall AS, Gunson K, Jui J, Samani NJ, Chugh SS. Cumulative effects of common genetic variants on risk of sudden cardiac death.. International journal of cardiology. Heart & vasculature, 2015.
67. Gatto NM, Sinsheimer JS, Cockburn M, Escobedo LA, Bordelon Y, Ritz B. Vitamin D receptor gene polymorphisms and Parkinson's disease in a population with high ultraviolet radiation exposure.. Journal of the neurological sciences, 2015.
68. Rickabaugh TM, Baxter RM, Sehl M, Sinsheimer JS, Hultin PM, Hultin LE, Quach A, Mart?nez-Maza O, Horvath S, Vilain E, Jamieson BD. Acceleration of age-associated methylation patterns in HIV-1-infected adults.. PloS one, 2015.
69. Palmer CG, Boudreault P, Baldwin EE, Sinsheimer JS. Impact of genetic counseling and Connexin-26 and Connexin-30 testing on deaf identity and comprehension of genetic test results in a sample of deaf adults: a prospective, longitudinal study.. PloS one, 2014.
70. Han E, Sinsheimer JS, Novembre J. Fast and accurate site frequency spectrum estimation from low coverage sequence data.. Bioinformatics (Oxford, England), 2014.
71. Ngun TC, Ghahramani NM, Creek MM, Williams-Burris SM, Barseghyan H, Itoh Y, S?nchez FJ, McClusky R, Sinsheimer JS, Arnold AP, Vilain E. Feminized behavior and brain gene expression in a novel mouse model of Klinefelter Syndrome.. Archives of sexual behavior, 2014.
72. Anastasopoulos E, Coleman AL, Wilson MR, Sinsheimer JS, Yu F, Katafigiotis S, Founti P, Salonikiou A, Pappas T, Koskosas A, Katopodi T, Lambropoulos A, Topouzis F. Association of LOXL1 polymorphisms with pseudoexfoliation, glaucoma, intraocular pressure, and systemic diseases in a Greek population. The Thessaloniki eye study.. Investigative ophthalmology & visual science, 2014.
73. Ko A, Cantor RM, Weissglas-Volkov D, Nikkola E, Reddy PM, Sinsheimer JS, Pasaniuc B, Brown R, Alvarez M, Rodriguez A, Rodriguez-Guillen R, Bautista IC, Arellano-Campos O, Mu?oz-Hern?ndez LL, Salomaa V, Kaprio J, Jula A, Jauhiainen M, Heli?vaara M, Raitakari O, Lehtim?ki T, Eriksson JG, Perola M, Lohmueller KE, Matikainen N, Taskinen MR, Rodriguez-Torres M, Riba L, Tusie-Luna T, Aguilar-Salinas CA, Pajukanta P. Amerindian-specific regions under positive selection harbour new lipid variants in Latinos.. Nature communications, 2014.
74. Arboleda VA, Fleming A, Barseghyan H, D?lot E, Sinsheimer JS, Vilain E. Regulation of sex determination in mice by a non-coding genomic region.. Genetics, 2014.
75. Levine AJ, Reynolds S, Cox C, Miller EN, Sinsheimer JS, Becker JT, Martin E, Sacktor N, Neuropsychology Working Group of the Multicenter AIDS Cohort Study. The longitudinal and interactive effects of HIV status, stimulant use, and host genotype upon neurocognitive functioning.. Journal of neurovirology, 2014.
76. Lange K, Papp JC, Sinsheimer JS, Sobel EM. Next Generation Statistical Genetics: Modeling, Penalization, and Optimization in High-Dimensional Data.. Annual review of statistics and its application, 2014.
77. Han E, Sinsheimer JS, Novembre J. Characterizing bias in population genetic inferences from low-coverage sequencing data.. Molecular biology and evolution, 2013.
78. Kobayashi Y, Boudreault P, Hill K, Sinsheimer JS, Palmer CG. Using a social marketing framework to evaluate recruitment of a prospective study of genetic counseling and testing for the deaf community.. BMC medical research methodology, 2013.
79. Rhodes SL, Buchanan DD, Ahmed I, Taylor KD, Loriot MA, Sinsheimer JS, Bronstein JM, Elbaz A, Mellick GD, Rotter JI, Ritz B. Pooled analysis of iron-related genes in Parkinson's disease: association with transferrin.. Neurobiology of disease, 2013.
80. Narayan S, Liew Z, Paul K, Lee PC, Sinsheimer JS, Bronstein JM, Ritz B. Household organophosphorus pesticide use and Parkinson's disease.. International journal of epidemiology, 2013.
81. Rhodes SL, Fitzmaurice AG, Cockburn M, Bronstein JM, Sinsheimer JS, Ritz B. Pesticides that inhibit the ubiquitin-proteasome system: effect measure modification by genetic variation in SKP1 in Parkinson?s disease.. Environmental research, 2013.
82. Panos SE, Hinkin CH, Singer EJ, Thames AD, Patel SM, Sinsheimer JS, Del Re AC, Gelman BB, Morgello S, Moore DJ, Levine AJ. Apolipoprotein-E genotype and human immunodeficiency virus-associated neurocognitive disorder: the modulating effects of older age and disease severity.. Neurobehavioral HIV medicine, 2013.
83. Lange K, Papp JC, Sinsheimer JS, Sripracha R, Zhou H, Sobel EM. Mendel: the Swiss army knife of genetic analysis programs.. Bioinformatics (Oxford, England), 2013.
84. Lee PC, Rhodes SL, Sinsheimer JS, Bronstein J, Ritz B. Functional paraoxonase 1 variants modify the risk of Parkinson's disease due to organophosphate exposure.. Environment international, 2013.
85. Weissglas-Volkov D, Aguilar-Salinas CA, Nikkola E, Deere KA, Cruz-Bautista I, Arellano-Campos O, Mu?oz-Hernandez LL, Gomez-Munguia L, Ordo?ez-S?nchez ML, Reddy PM, Lusis AJ, Matikainen N, Taskinen MR, Riba L, Cantor RM, Sinsheimer JS, Tusie-Luna T, Pajukanta P. Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.. Journal of medical genetics, 2013.
86. Palmer CG, Boudreault P, Baldwin EE, Fox M, Deignan JL, Kobayashi Y, Sininger Y, Grody W, Sinsheimer JS. Deaf genetic testing and psychological well-being in deaf adults.. Journal of genetic counseling, 2013.
87. Cybis GB, Sinsheimer JS, Lemey P, Suchard MA. Graph hierarchies for phylogeography.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2013.
88. Lake JA, Sinsheimer JS. The deep roots of the rings of life.. Genome biology and evolution, 2013.
89. Riley L, Zhou H, Lange K, Sinsheimer JS, Sehl ME. Determining duration of HER2-targeted therapy using stem cell extinction models.. PloS one, 2012.
90. Reddy MV, Iatan I, Weissglas-Volkov D, Nikkola E, Haas BE, Juvonen M, Ruel I, Ruel MJ, Sinsheimer JS, Genest J, Pajukanta P. Exome sequencing identifies 2 rare variants for low high-density lipoprotein cholesterol in an extended family.. Circulation. Cardiovascular genetics, 2012.
91. Anastasopoulos E, Kakoulidou A, Coleman AL, Sinsheimer JS, Wilson MR, Yu F, Salonikiou A, Koskosas A, Pappas T, Founti P, Lambropoulos A, Topouzis F. Association of sequence variation in the CX3CR1 gene with geographic atrophy age-related macular degeneration in a Greek population.. Current eye research, 2012.
92. Sinsheimer JS, Little RJ, Lake JA. Rooting gene trees without outgroups: EP rooting.. Genome biology and evolution, 2012.
93. Tom JA, Sinsheimer JS, Suchard MA. Does history repeat itself? Wavelets and the phylodynamics of influenza A.. Molecular biology and evolution, 2011.
94. Zhou JJ, Ghazalpour A, Sobel EM, Sinsheimer JS, Lange K. Quantitative trait Loci association mapping by imputation of strain origins in multifounder crosses.. Genetics, 2011.
95. Deere KA, Grether GF, Sun A, Sinsheimer JS. Female mate preference explains countergradient variation in the sexual coloration of guppies (Poecilia reticulata).. Proceedings. Biological sciences, 2011.
96. Levine AJ, Sinsheimer JS, Bilder R, Shapshak P, Singer EJ. Functional polymorphisms in dopamine-related genes: effect on neurocognitive functioning in HIV+ adults.. Journal of clinical and experimental neuropsychology, 2011.
97. Childs EJ, Sobel EM, Palmer CG, Sinsheimer JS. Detection of intergenerational genetic effects with application to HLA-B matching as a risk factor for schizophrenia.. Human heredity, 2011.
98. Sehl M, Zhou H, Sinsheimer JS, Lange KL. Extinction models for cancer stem cell therapy.. Mathematical biosciences, 2011.
99. Sinsheimer J. "Statistics 101"--a primer for the genetics of complex human disease.. Cold Spring Harbor protocols, 2011.
100. Baldwin EE, Boudreault P, Fox M, Sinsheimer JS, Palmer CG. Effect of pre-test genetic counseling for deaf adults on knowledge of genetic testing.. Journal of genetic counseling, 2011.
101. Weissglas-Volkov D, Calkin AC, Tusie-Luna T, Sinsheimer JS, Zelcer N, Riba L, Tino AM, Ordo?ez-S?nchez ML, Cruz-Bautista I, Aguilar-Salinas CA, Tontonoz P, Pajukanta P. The N342S MYLIP polymorphism is associated with high total cholesterol and increased LDL receptor degradation in humans.. The Journal of clinical investigation, 2011.
102. Bocklandt S, Lin W, Sehl ME, S?nchez FJ, Sinsheimer JS, Horvath S, Vilain E. Epigenetic predictor of age.. PloS one, 2011.
103. Ghazalpour A, Bennett B, Petyuk VA, Orozco L, Hagopian R, Mungrue IN, Farber CR, Sinsheimer J, Kang HM, Furlotte N, Park CC, Wen PZ, Brewer H, Weitz K, Camp DG, Pan C, Yordanova R, Neuhaus I, Tilford C, Siemers N, Gargalovic P, Eskin E, Kirchgessner T, Smith DJ, Smith RD, Lusis AJ. Comparative analysis of proteome and transcriptome variation in mouse.. PLoS genetics, 2011.
104. Suwanwela J, Lee J, Lin A, Ucer TC, Devlin H, Sinsheimer J, Garrett NR, Nishimura I. A genetic association study of single nucleotide polymorphisms in FGFR1OP2/wit3.0 and long-term atrophy of edentulous mandible.. PloS one, 2011.
105. Rhodes SL, Sinsheimer JS, Bordelon Y, Bronstein JM, Ritz B. Replication of GWAS associations for GAK and MAPT in Parkinson's disease.. Annals of human genetics, 2010.
106. Zhou H, Sehl ME, Sinsheimer JS, Lange K. Association screening of common and rare genetic variants by penalized regression.. Bioinformatics (Oxford, England), 2010.
107. Sinsheimer JS, Elston RC, Fu WJ. Gene-gene interaction in maternal and perinatal research.. Journal of biomedicine & biotechnology, 2010.
108. Childs EJ, Palmer CG, Lange K, Sinsheimer JS. Modeling maternal-offspring gene-gene interactions: the extended-MFG test.. Genetic epidemiology, 2010.
109. Boudreault P, Baldwin EE, Fox M, Dutton L, Tullis L, Linden J, Kobayashi Y, Zhou J, Sinsheimer JS, Sininger Y, Grody WW, Palmer CG. Deaf adults' reasons for genetic testing depend on cultural affiliation: results from a prospective, longitudinal genetic counseling and testing study.. Journal of deaf studies and deaf education, 2010.
110. van Nas A, Ingram-Drake L, Sinsheimer JS, Wang SS, Schadt EE, Drake T, Lusis AJ. Expression quantitative trait loci: replication, tissue- and sex-specificity in mice.. Genetics, 2010.
111. Cantor RM, Lange K, Sinsheimer JS. Prioritizing GWAS results: A review of statistical methods and recommendations for their application.. American journal of human genetics, 2010.
112. Tom JA, Sinsheimer JS, Suchard MA. Reuse, Recycle, Reweigh: Combating Influenza through Efficient Sequential Bayesian Computation for Massive Data.. The annals of applied statistics, 2010.
113. Sehl ME, Sinsheimer JS, Zhou H, Lange KL. Differential destruction of stem cells: implications for targeted cancer stem cell therapy.. Cancer research, 2009.
114. Weissglas-Volkov D, Aguilar-Salinas CA, Sinsheimer JS, Riba L, Huertas-Vazquez A, Ordo?ez-S?nchez ML, Rodriguez-Guillen R, Cantor RM, Tusie-Luna T, Pajukanta P. Investigation of variants identified in caucasian genome-wide association studies for plasma high-density lipoprotein cholesterol and triglycerides levels in Mexican dyslipidemic study samples.. Circulation. Cardiovascular genetics, 2009.
115. Weissglas-Volkov D, Plaisier CL, Huertas-Vazquez A, Cruz-Bautista I, Riaño-Barros D, Herrera-Hernandez M, Riba L, Cantor RM, Sinsheimer JS, Aguilar-Salinas CA, Tusie-Luna T, Pajukanta P. Identification of two common variants contributing to serum apolipoprotein B levels in Mexicans.. Arteriosclerosis, thrombosis, and vascular biology, 2009.
116. Levine AJ, Singer EJ, Sinsheimer JS, Hinkin CH, Papp J, Dandekar S, Giovanelli A, Shapshak P. CCL3 genotype and current depression increase risk of HIV-associated dementia.. Neurobehavioral HIV medicine, 2009.
117. Bonneaud C, Sinsheimer JS, Richard M, Chastel O, Sorci G. Mhc polymorphisms fail to explain the heritability of phytohaemagglutinin-induced skin swelling in a wild passerine.. Biology letters, 2009.
118. Meex SJ, Weissglas-Volkov D, van der Kallen CJ, Thuerauf DJ, van Greevenbroek MM, Schalkwijk CG, Stehouwer CD, Feskens EJ, Heldens L, Ayoubi TA, Hofker MH, Wouters BG, Vlietinck R, Sinsheimer JS, Taskinen MR, Kuusisto J, Laakso M, de Bruin TW, Pajukanta P, Glembotski CC. The ATF6-Met[67]Val substitution is associated with increased plasma cholesterol levels.. Arteriosclerosis, thrombosis, and vascular biology, 2009.
119. Sinsheimer J. Statistical genetic approaches for mapping ophthalmic trait and disease genes.. American journal of ophthalmology, 2009.
120. Crandall CJ, Sehl ME, Crawford SL, Gold EB, Habel LA, Butler LM, Sowers MR, Greendale GA, Sinsheimer JS. Sex steroid metabolism polymorphisms and mammographic density in pre- and early perimenopausal women.. Breast cancer research : BCR, 2009.
121. Zhou JJ, Lange K, Papp JC, Sinsheimer JS. A heterozygote-homozygote test of Hardy-Weinberg equilibrium.. European journal of human genetics : EJHG, 2009.
122. Sehl ME, Langer LR, Papp JC, Kwan L, Seldon JL, Arellano G, Reiss J, Reed EF, Dandekar S, Korin Y, Sinsheimer JS, Zhang ZF, Ganz PA. Associations between single nucleotide polymorphisms in double-stranded DNA repair pathway genes and familial breast cancer.. Clinical cancer research : an official journal of the American Association for Cancer Research, 2009.
123. Plaisier CL, Kyttälä M, Weissglas-Volkov D, Sinsheimer JS, Huertas-Vazquez A, Riba L, Ramírez-Jiménez S, de Bruin TW, Tusié-Luna T, Aouizerat BE, Pullinger CR, Malloy MJ, Kane JP, Cruz-Bautista I, Herrera MF, Aguilar-Salinas C, Kuusisto J, Laakso M, Taskinen MR, van der Kallen CJ, Pajukanta P. Galanin preproprotein is associated with elevated plasma triglycerides.. Arteriosclerosis, thrombosis, and vascular biology, 2008.
124. Bauman LE, Sinsheimer JS, Sobel EM, Lange K. Mixed effects models for quantitative trait loci mapping with inbred strains.. Genetics, 2008.
125. Palmer CG, Mallery E, Turunen JA, Hsieh HJ, Peltonen L, Lonnqvist J, Woodward JA, Sinsheimer JS. Effect of Rhesus D incompatibility on schizophrenia depends on offspring sex.. Schizophrenia research, 2008.
126. Nikolova G, Sinsheimer JS, Eicher EM, Vilain E. The chromosome 11 region from strain 129 provides protection from sex reversal in XYPOS mice.. Genetics, 2008.
127. Lee YC, Morgenstern H, Greenland S, Tashkin DP, Papp J, Sinsheimer J, Cao W, Hashibe M, You NC, Mao JT, Cozen W, Mack TM, Zhang ZF. A case-control study of the association of the polymorphisms and haplotypes of DNA ligase I with lung and upper-aerodigestive-tract cancers.. International journal of cancer, 2008.
128. Seitzman RL, Mahajan VB, Mangione C, Cauley JA, Ensrud KE, Stone KL, Cummings SR, Hochberg MC, Hillier TA, Sinsheimer JS, Yu F, Coleman AL, Study of Osteoporotic Fractures Research Group. Estrogen receptor alpha and matrix metalloproteinase 2 polymorphisms and age-related maculopathy in older women.. American journal of epidemiology, 2008.
129. Sinsheimer JS, Plaisier CL, Huertas-Vazquez A, Aguilar-Salinas C, Tusie-Luna T, Pajukanta P, Lange K. Estimating ethnic admixture from pedigree data.. American journal of human genetics, 2008.
130. Hsieh HJ, Palmer CG, Harney S, Chen HW, Bauman L, Brown MA, Sinsheimer JS. Using the maternal-fetal genotype incompatibility test to assess non-inherited maternal HLA-DRB1 antigen coding alleles as rheumatoid arthritis risk factors.. BMC proceedings, 2007.
131. Lee JC, Weissglas-Volkov D, Kyttälä M, Sinsheimer JS, Jokiaho A, de Bruin TW, Lusis AJ, Brennan ML, van Greevenbroek MM, van der Kallen CJ, Hazen SL, Pajukanta P. USF1 contributes to high serum lipid levels in Dutch FCHL families and U.S. whites with coronary artery disease.. Arteriosclerosis, thrombosis, and vascular biology, 2007.
132. Wahner AD, Sinsheimer JS, Bronstein JM, Ritz B. Inflammatory cytokine gene polymorphisms and increased risk of Parkinson disease.. Archives of neurology, 2007.
133. Loughlin J, Meulenbelt I, Min J, Mustafa Z, Sinsheimer JS, Carr A, Slagboom PE. Genetic association analysis of RHOB and TXNDC3 in osteoarthritis.. American journal of human genetics, 2007.
134. Hsieh HJ, Palmer CG, Sinsheimer JS. Allowing for missing data at highly polymorphic genes when testing for maternal, offspring and maternal-fetal genotype incompatibility effects.. Human heredity, 2006.
135. Nikolova G, Lee H, Berkovitz S, Nelson S, Sinsheimer J, Vilain E, Rodríguez LV. Sequence variant in the laminin gamma1 (LAMC1) gene associated with familial pelvic organ prolapse.. Human genetics, 2006.
136. Kim S, Kim Y, Liang T, Sinsheimer JS, Chow SA. A high-throughput method for cloning and sequencing human immunodeficiency virus type 1 integration sites.. Journal of virology, 2006.
137. Palmer CG, Hsieh HJ, Reed EF, Lonnqvist J, Peltonen L, Woodward JA, Sinsheimer JS. HLA-B maternal-fetal genotype matching increases risk of schizophrenia.. American journal of human genetics, 2006.
138. Hsieh HJ, Palmer CG, Harney S, Newton JL, Wordsworth P, Brown MA, Sinsheimer JS. The v-MFG test: investigating maternal, offspring and maternal-fetal genetic incompatibility effects on disease and viability.. Genetic epidemiology, 2006.
139. Chapman K, Carr A, Loughlin J, Sinsheimer JS. Presence of a primary hip osteoarthritis susceptibility locus on chromosome 6: comment on the article by Meenagh et al.. Arthritis and rheumatism, 2006.
140. Mustafa Z, Dowling B, Chapman K, Sinsheimer JS, Carr A, Loughlin J. Investigating the aspartic acid (D) repeat of asporin as a risk factor for osteoarthritis in a UK Caucasian population.. Arthritis and rheumatism, 2005.
141. Suchard MA, Weiss RE, Sinsheimer JS. Models for estimating bayes factors with applications to phylogeny and tests of monophyly.. Biometrics, 2005.
142. Kraft P, Hsieh HJ, Cordell HJ, Sinsheimer J. A conditional-on-exchangeable-parental-genotypes likelihood that remains unbiased at the causal locus under multiple-affected-sibling ascertainment.. Genetic epidemiology, 2005.
143. Lange K, Sinsheimer JS, Sobel E. Association testing with Mendel.. Genetic epidemiology, 2005.
144. Minassian SL, Palmer CG, Sinsheimer JS. An exact maternal-fetal genotype incompatibility (MFG) test.. Genetic epidemiology, 2005.
145. Fang G, Kuiken C, Weiser B, Rowland-Jones S, Plummer F, Chen CH, Kaul R, Anzala AO, Bwayo J, Kimani J, Philpott SM, Kitchen C, Sinsheimer JS, Gaschen B, Lang D, Shi B, Kemal KS, Rostron T, Brunner C, Beddows S, Sattenau Q, Paxinos E, Oyugi J, Burger H. Long-term survivors in Nairobi: complete HIV-1 RNA sequences and immunogenetic associations.. The Journal of infectious diseases, 2004.
146. Mar R, Pajukanta P, Allayee H, Groenendijk M, Dallinga-Thie G, Krauss RM, Sinsheimer JS, Cantor RM, de Bruin TW, Lusis AJ. Association of the APOLIPOPROTEIN A1/C3/A4/A5 gene cluster with triglyceride levels and LDL particle size in familial combined hyperlipidemia.. Circulation research, 2004.
147. Kraft P, Palmer CG, Woodward AJ, Turunen JA, Minassian S, Paunio T, Lönnqvist J, Peltonen L, Sinsheimer JS. RHD maternal-fetal genotype incompatibility and schizophrenia: extending the MFG test to include multiple siblings and birth order.. European journal of human genetics : EJHG, 2004.
148. Pajukanta P, Lilja HE, Sinsheimer JS, Cantor RM, Lusis AJ, Gentile M, Duan XJ, Soro-Paavonen A, Naukkarinen J, Saarela J, Laakso M, Ehnholm C, Taskinen MR, Peltonen L. Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1).. Nature genetics, 2004.
149. Lange K, Sinsheimer JS. The pedigree trimming problem.. Human heredity, 2004.
150. Suchard MA, Kitchen CM, Sinsheimer JS, Weiss RE. Hierarchical phylogenetic models for analyzing multipartite sequence data.. Systematic biology, 2003.
151. Duncan EL, Cardon LR, Sinsheimer JS, Wass JA, Brown MA. Site and gender specificity of inheritance of bone mineral density.. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research, 2003.
152. Suchard MA, Weiss RE, Sinsheimer JS. Testing a molecular clock without an outgroup: derivations of induced priors on branch-length restrictions in a Bayesian framework.. Systematic biology, 2003.
153. Sinsheimer JS, Suchard MA, Dorman KS, Fang F, Weiss RE. Are you my mother? Bayesian phylogenetic inference of recombination among putative parental strains.. Applied bioinformatics, 2003.
154. Sinsheimer JS, Palmer CG, Woodward JA. Detecting genotype combinations that increase risk for disease: maternal-fetal genotype incompatibility test.. Genetic epidemiology, 2003.
155. Palmer CG, Turunen JA, Sinsheimer JS, Minassian S, Paunio T, Lönnqvist J, Peltonen L, Woodward JA. RHD maternal-fetal genotype incompatibility increases schizophrenia susceptibility.. American journal of human genetics, 2002.
156. Suchard MA, Weiss RE, Dorman KS, Sinsheimer JS. Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage.. Systematic biology, 2002.
157. Schadt EE, Sinsheimer JS, Lange K. Applications of codon and rate variation models in molecular phylogeny.. Molecular biology and evolution, 2002.
158. Auranen M, Vanhala R, Varilo T, Ayers K, Kempas E, Ylisaukko-Oja T, Sinsheimer JS, Peltonen L, Järvelä I. A genomewide screen for autism-spectrum disorders: evidence for a major susceptibility locus on chromosome 3q25-27.. American journal of human genetics, 2002.
159. Dorman KS, Kaplan AH, Sinsheimer JS. Bootstrap confidence levels for HIV-1 recombination.. Journal of molecular evolution, 2002.