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Riyan Cheng

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InstitutionUniversity of Chicago
AddressChicago IL 60637
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Chen D, Chitre AS, Nguyen KH, Cohen K, Peng B, Ziegler KS, Okamoto F, Lin B, Johnson BB, Sanches TM, Cheng R, Polesskaya O, Palmer AA, Chen D, Chitre AS, Nguyen KH, Cohen KA, Peng BF, Ziegler KS, Okamoto F, Lin B, Johnson BB, Sanches TM, Cheng R, Polesskaya O, Palmer AA. A cost-effective, high-throughput, highly accurate genotyping method for outbred populations. G3 (Bethesda). 2025 Feb 05; 15(2). PMID: 39670731; PMCID: PMC11797033.
      Citations:    Fields:    
    2. Chen D, Chitre AS, Nguyen KH, Cohen K, Peng B, Ziegler KS, Okamoto F, Lin B, Johnson BB, Sanches TM, Cheng R, Polesskaya O, Palmer AA. A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations. bioRxiv. 2024 Jul 18. PMID: 39071405; PMCID: PMC11275765.
      Citations:    
    3. Polesskaya O, Boussaty E, Cheng R, Lamonte O, Zhou T, Du E, Sanches TM, Nguyen KM, Okamoto M, Palmer AA, Friedman R. Genome-wide association study for age-related hearing loss in CFW mice. bioRxiv. 2024 Jun 10. PMID: 38915500; PMCID: PMC11195089.
      Citations:    
    4. King CP, Chitre AS, Leal-Gutiérrez JD, Tripi JA, Hughson AR, Horvath AP, Lamparelli AC, George A, Martin C, Pierre CLS, Sanches T, Bimschleger HV, Gao J, Cheng R, Nguyen KM, Holl KL, Polesskaya O, Ishiwari K, Chen H, Woods LCS, Palmer AA, Robinson TE, Flagel SB, Meyer PJ. Genomic Loci Influencing Cue-Reactivity in Heterogeneous Stock Rats. bioRxiv. 2024 Apr 03. PMID: 38559127; PMCID: PMC10980002.
      Citations:    
    5. Xu J, Casanave R, Chitre AS, Wang Q, Nguyen KM, Blake C, Wagle M, Cheng R, Polesskaya O, Palmer AA, Guo S. Causal Genetic Loci for a Motivated Behavior Spectrum Harbor Psychiatric Risk Genes. bioRxiv. 2023 Sep 06. PMID: 37732200; PMCID: PMC10508786.
      Citations:    
    6. Wright SN, Leger BS, Rosenthal SB, Liu SN, Jia T, Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Garcia Martinez A, George A, Gileta AF, Han W, Netzley AH, King CP, Lamparelli A, Martin C, St Pierre CL, Wang T, Bimschleger H, Richards J, Ishiwari K, Chen H, Flagel SB, Meyer P, Robinson TE, Solberg Woods LC, Kreisberg JF, Ideker T, Palmer AA. Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks. Cell Rep. 2023 08 29; 42(8):112873. PMID: 37527041; PMCID: PMC10546330.
      Citations: 5     Fields:    Translation:HumansAnimals
    7. Chitre AS, Polesskaya O, Munro D, Cheng R, Mohammadi P, Gao J, Bimschleger H, Martinez AG, Gileta AF, Horvath A, Hughson A, Ishiwari K, King CP, Lamparelli A, Versaggi CL, Tripi JA, Richards JB, Wang T, Chen H, Meyer P, Robinson TE, Solberg Woods LC, Palmer AA, Holl K, George AM, Han W, Martin CD, St Pierre CL, Flagel SB. An exponential increase in QTL detection with an increased sample size. Genetics. 2023 05 26; 224(2). PMID: 36974931; PMCID: PMC10213487.
      Citations:    Fields:    Translation:HumansAnimals
    8. Fowler S, Wang T, Munro D, Kumar A, Chitre AS, Hollingsworth TJ, Garcia Martinez A, St Pierre CL, Bimschleger H, Gao J, Cheng R, Mohammadi P, Chen H, Palmer AA, Polesskaya O, Jablonski MM. Genome-wide association study finds multiple loci associated with intraocular pressure in HS rats. Front Genet. 2022; 13:1029058. PMID: 36793389; PMCID: PMC9922724.
      Citations: 3     
    9. Chitre AS, Hebda-Bauer EK, Blandino P, Bimschleger H, Nguyen KM, Maras P, Li F, Ozel AB, Pan Y, Polesskaya O, Cheng R, Flagel SB, Watson SJ, Li J, Akil H, Palmer AA. Genome-wide association study in a rat model of temperament identifies multiple loci for exploratory locomotion and anxiety-like traits. Front Genet. 2022; 13:1003074. PMID: 36712851; PMCID: PMC9873817.
      Citations: 9     
    10. Han L, Liu H, Kang G, Zhang M, Cheng R. Editorial: Statistical methods, computing, and resources for genome-wide association studies, Volume II. Front Genet. 2022; 13:1040022. PMID: 36338957; PMCID: PMC9633282.
      Citations:    
    11. Gunturkun MH, Wang T, Chitre AS, Garcia Martinez A, Holl K, St Pierre C, Bimschleger H, Gao J, Cheng R, Polesskaya O, Solberg Woods LC, Palmer AA, Chen H. Genome-Wide Association Study on Three Behaviors Tested in an Open Field in Heterogeneous Stock Rats Identifies Multiple Loci Implicated in Psychiatric Disorders. Front Psychiatry. 2022; 13:790566. PMID: 35237186; PMCID: PMC8882588.
      Citations: 7     
    12. Liu H, Han L, Kang G, Zhang M, Cheng R. Editorial: Statistical Methods, Computing and Resources for Genome-Wide Association Studies. Front Genet. 2021; 12:714894. PMID: 34422016; PMCID: PMC8376476.
      Citations:    
    13. Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Bimschleger H, Garcia Martinez A, George T, Gileta AF, Han W, Horvath A, Hughson A, Ishiwari K, King CP, Lamparelli A, Versaggi CL, Martin C, St Pierre CL, Tripi JA, Wang T, Chen H, Flagel SB, Meyer P, Richards J, Robinson TE, Palmer AA, Solberg Woods LC. Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose. Obesity (Silver Spring). 2020 10; 28(10):1964-1973. PMID: 32860487; PMCID: PMC7511439.
      Citations: 43     Fields:    Translation:Animals
    14. Zhou X, St Pierre CL, Gonzales NM, Zou J, Cheng R, Chitre AS, Sokoloff G, Palmer AA. Genome-Wide Association Study in Two Cohorts from a Multi-generational Mouse Advanced Intercross Line Highlights the Difficulty of Replication Due to Study-Specific Heterogeneity. G3 (Bethesda). 2020 03 05; 10(3):951-965. PMID: 31974095; PMCID: PMC7056977.
      Citations: 4     Fields:    Translation:Animals
    15. Hernandez Cordero AI, Gonzales NM, Parker CC, Sokoloff G, Vandenbergh DJ, Cheng R, Abney M, Skol A, Douglas A, Palmer AA, Gregory JS, Lionikas A. Genome-wide Associations Reveal Human-Mouse Genetic Convergence and Modifiers of Myogenesis, CPNE1 and STC2. Am J Hum Genet. 2020 Jan 02; 106(1):138. PMID: 31901248; PMCID: PMC7042490.
      Citations: 2     Fields:    
    16. Hernandez Cordero AI, Gonzales NM, Parker CC, Sokolof G, Vandenbergh DJ, Cheng R, Abney M, Sko A, Douglas A, Palmer AA, Gregory JS, Lionikas A. Genome-wide Associations Reveal Human-Mouse Genetic Convergence and Modifiers of Myogenesis, CPNE1 and STC2. Am J Hum Genet. 2019 12 05; 105(6):1222-1236. PMID: 31761296; PMCID: PMC6904802.
      Citations: 29     Fields:    Translation:HumansAnimals
    17. Rungrat T, Almonte AA, Cheng R, Gollan PJ, Stuart T, Aro EM, Borevitz JO, Pogson B, Wilson PB. A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in Arabidopsis thaliana. Plant Direct. 2019 May; 3(5):e00138. PMID: 31276082; PMCID: PMC6603398.
      Citations: 12     
    18. Wilson PB, Streich JC, Murray KD, Eichten SR, Cheng R, Aitken NC, Spokas K, Warthmann N, Gordon SP, Accession Contributors, Vogel JP, Borevitz JO. Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate. Genetics. 2019 01; 211(1):317-331. PMID: 30446522; PMCID: PMC6325704.
      Citations: 8     Fields:    Translation:Animals
    19. Cheng R, Doerge RW, Borevitz J. Novel Resampling Improves Statistical Power for Multiple-Trait QTL Mapping. G3 (Bethesda). 2017 03 10; 7(3):813-822. PMID: 28064191; PMCID: PMC5345711.
      Citations: 3     Fields:    
    20. Rungrat T, Awlia M, Brown T, Cheng R, Sirault X, Fajkus J, Trtilek M, Furbank B, Badger M, Tester M, Pogson BJ, Borevitz JO, Wilson P. Using Phenomic Analysis of Photosynthetic Function for Abiotic Stress Response Gene Discovery. Arabidopsis Book. 2016; 14:e0185. PMID: 27695390; PMCID: PMC5042155.
      Citations: 21     
    21. Yazdani N, Parker CC, Shen Y, Reed ER, Guido MA, Kole LA, Kirkpatrick SL, Lim JE, Sokoloff G, Cheng R, Johnson WE, Palmer AA, Bryant CD. Hnrnph1 Is A Quantitative Trait Gene for Methamphetamine Sensitivity. PLoS Genet. 2015 Dec; 11(12):e1005713. PMID: 26658939; PMCID: PMC4675533.
      Citations: 31     Fields:    Translation:HumansAnimalsCells
    22. Gatti DM, Svenson KL, Shabalin A, Wu LY, Valdar W, Simecek P, Goodwin N, Cheng R, Pomp D, Palmer A, Chesler EJ, Broman KW, Churchill GA. Quantitative trait locus mapping methods for diversity outbred mice. G3 (Bethesda). 2014 Sep 18; 4(9):1623-33. PMID: 25237114; PMCID: PMC4169154.
      Citations: 135     Fields:    Translation:AnimalsCells
    23. Carbonetto P, Cheng R, Gyekis JP, Parker CC, Blizard DA, Palmer AA, Lionikas A. Discovery and refinement of muscle weight QTLs in B6 × D2 advanced intercross mice. Physiol Genomics. 2014 Aug 15; 46(16):571-82. PMID: 24963006; PMCID: PMC4137148.
      Citations: 8     Fields:    Translation:AnimalsCells
    24. Brown TB, Cheng R, Sirault XR, Rungrat T, Murray KD, Trtilek M, Furbank RT, Badger M, Pogson BJ, Borevitz JO. TraitCapture: genomic and environment modelling of plant phenomic data. Curr Opin Plant Biol. 2014 Apr; 18:73-9. PMID: 24646691.
      Citations: 22     Fields:    Translation:Animals
    25. Li Y, Cheng R, Spokas KA, Palmer AA, Borevitz JO. Genetic variation for life history sensitivity to seasonal warming in Arabidopsis thaliana. Genetics. 2014 Feb; 196(2):569-77. PMID: 24281156; PMCID: PMC3914627.
      Citations: 21     Fields:    Translation:Animals
    26. Cheng R, Parker CC, Abney M, Palmer AA. Practical considerations regarding the use of genotype and pedigree data to model relatedness in the context of genome-wide association studies. G3 (Bethesda). 2013 Oct 03; 3(10):1861-7. PMID: 23979941; PMCID: PMC3789811.
      Citations: 38     Fields:    Translation:HumansAnimals
    27. Cheng R, Borevitz J, Doerge RW. Selecting informative traits for multivariate quantitative trait locus mapping helps to gain optimal power. Genetics. 2013 Nov; 195(3):683-91. PMID: 23979571; PMCID: PMC3813856.
      Citations: 3     Fields:    Translation:Animals
    28. Cheng R, Palmer AA. A simulation study of permutation, bootstrap, and gene dropping for assessing statistical significance in the case of unequal relatedness. Genetics. 2013 Mar; 193(3):1015-8. PMID: 23267053; PMCID: PMC3583989.
      Citations: 35     Fields:    Translation:Humans
    29. Bryant CD, Guido MA, Kole LA, Cheng R. The heritability of oxycodone reward and concomitant phenotypes in a LG/J?×?SM/J mouse advanced intercross line. Addict Biol. 2014 Jul; 19(4):552-61. PMID: 23231598; PMCID: PMC4300855.
      Citations: 7     Fields:    Translation:Animals
    30. Bryant CD, Kole LA, Guido MA, Cheng R, Palmer AA. Methamphetamine-induced conditioned place preference in LG/J and SM/J mouse strains and an F45/F46 advanced intercross line. Front Genet. 2012; 3:126. PMID: 22798962; PMCID: PMC3393886.
      Citations: 8     
    31. Bartnikas TB, Parker CC, Cheng R, Campagna DR, Lim JE, Palmer AA, Fleming MD. QTLs for murine red blood cell parameters in LG/J and SM/J F(2) and advanced intercross lines. Mamm Genome. 2012 Jun; 23(5-6):356-66. PMID: 22322356; PMCID: PMC3358495.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    32. Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, Chesler EJ, Palmer AA, McMillan L, Churchill GA. High-resolution genetic mapping using the Mouse Diversity outbred population. Genetics. 2012 Feb; 190(2):437-47. PMID: 22345611; PMCID: PMC3276626.
      Citations: 302     Fields:    Translation:Animals
    33. Parker CC, Sokoloff G, Cheng R, Palmer AA. Genome-wide association for fear conditioning in an advanced intercross mouse line. Behav Genet. 2012 May; 42(3):437-48. PMID: 22237917; PMCID: PMC3351497.
      Citations: 23     Fields:    Translation:Animals
    34. Parker CC, Cheng R, Sokoloff G, Palmer AA. Genome-wide association for methamphetamine sensitivity in an advanced intercross mouse line. Genes Brain Behav. 2012 Feb; 11(1):52-61. PMID: 22032291; PMCID: PMC3368015.
      Citations: 23     Fields:    Translation:Animals
    35. Cheng R, Abney M, Palmer AA, Skol AD. QTLRel: an R package for genome-wide association studies in which relatedness is a concern. BMC Genet. 2011 Jul 27; 12:66. PMID: 21794153; PMCID: PMC3160955.
      Citations: 49     Fields:    Translation:Humans
    36. Parker CC, Cheng R, Sokoloff G, Lim JE, Skol AD, Abney M, Palmer AA. Fine-mapping alleles for body weight in LG/J × SM/J F2 and F(34) advanced intercross lines. Mamm Genome. 2011 Oct; 22(9-10):563-71. PMID: 21761260; PMCID: PMC3308133.
      Citations: 21     Fields:    Translation:Animals
    37. Cheng R, Schmitt AO, Yang H, de Villena FP, Palmer AA, Brockmann GA, Kärst S. Genetic determinants for intramuscular fat content and water-holding capacity in mice selected for high muscle mass. Mamm Genome. 2011 Oct; 22(9-10):530-43. PMID: 21732194; PMCID: PMC3318964.
      Citations: 10     Fields:    Translation:Animals
    38. Samocha KE, Lim JE, Cheng R, Sokoloff G, Palmer AA. Fine mapping of QTL for prepulse inhibition in LG/J and SM/J mice using F(2) and advanced intercross lines. Genes Brain Behav. 2010 Oct; 9(7):759-67. PMID: 20597988; PMCID: PMC3749925.
      Citations: 24     Fields:    Translation:Animals
    39. Cheng R, Lim JE, Samocha KE, Sokoloff G, Abney M, Skol AD, Palmer AA. Genome-wide association studies and the problem of relatedness among advanced intercross lines and other highly recombinant populations. Genetics. 2010 Jul; 185(3):1033-44. PMID: 20439773; PMCID: PMC2907190.
      Citations: 71     Fields:    Translation:HumansAnimalsCells
    40. Bogdan M, Frommlet F, Biecek P, Cheng R, Ghosh JK, Doerge RW. Extending the modified bayesian information criterion (mBIC) to dense markers and multiple interval mapping. Biometrics. 2008 Dec; 64(4):1162-9. PMID: 18266892.
      Citations: 5     Fields:    
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