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RUI CHEN

TitleProfessor
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular & Human Genetics
AddressOne Baylor Plaza, 231e
Houston, 77030
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    Other Positions
    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentDepartment of Biochemistry and Molecular Pharmacology
    DivisionBiochemistry & Mol Pharmacology

    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentHuman Genome Sequencing Center
    DivisionHuman Genome Sequencing Center


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    UM1DA058229     (GIBBS, RICHARD A)May 1, 2023 - Apr 30, 2028
    NIH
    Comprehensive Somatic Variant Characterization at the HGSC
    Role: Co-Principal Investigator
    U01EY034692     (PFLUGFELDER, STEPHEN C)Sep 30, 2022 - Aug 31, 2027
    NIH
    Effects of cornea epithelial barrier disruption on the cornea trigeminal neural circuit
    Role: Co-Principal Investigator
    R01EY032768     (ZHI, DEGUI)Sep 30, 2022 - Jun 30, 2025
    NIH
    Deep-Learning-Derived Endophenotypes from Retina Images
    Role: Co-Principal Investigator
    R33NS115102     (EMBORG, MARINA)Sep 30, 2019 - May 31, 2025
    NIH
    Modeling Frontotemporal Dementia in Rhesus Macaques
    Role: Co-Principal Investigator
    R61NS115102     (EMBORG, MARINA)Sep 30, 2019 - May 31, 2021
    NIH
    Modeling Frontotemporal Dementia in Rhesus Macaques
    Role: Co-Principal Investigator
    U24EY029904     (CHEN, RUI ;ROGERS, JEFFREY A. ;STOUT, JOHN T;THOMASY, SARA MICHELLE)Sep 30, 2018 - Aug 31, 2024
    NIH
    Novel model systems for the study of cone disorders and other heritable retinal diseases
    Role: Co-Principal Investigator
    S10OD023469     (CHEN, RUI)Sep 1, 2017 - Aug 31, 2018
    NIH
    High Throughput Genomic Sequencer at BCM Core Facility
    Role: Principal Investigator
    R01EY026045     (STOUT, JOHN T)Mar 1, 2016 - Feb 28, 2022
    NIH
    Animal Models of Ocular Disease
    Role: Co-Principal Investigator
    S10OD018033     (CHEN, RUI)Jul 15, 2014 - Jul 14, 2015
    NIH
    Acquisition of the Fluidigm system to accelerate functional genomics research
    Role: Principal Investigator
    R01EY022356     (CHEN, RUI)Jun 1, 2012 - May 31, 2029
    NIH
    Molecular Basis of Human Visual System Disorders
    Role: Principal Investigator
    R01EY020540     (MARDON, GRAEME)Feb 1, 2011 - Sep 29, 2018
    NIH
    Molecular Mechanisms of Human Retinal Disease
    Role: Co-Principal Investigator
    S10RR026550     (CHEN, RUI)Jun 10, 2010 - Sep 9, 2011
    NIH
    FGI: Acquisition of an Illumina Genome Analyzer System for Functional Genomic Res
    Role: Principal Investigator
    R01EY018571     (CHEN, RUI)Dec 1, 2007 - Jul 31, 2027
    NIH
    Genetics of early onset retinal diseases
    Role: Principal Investigator
    R01EY016853     (CHEN, RUI)Aug 1, 2005 - May 31, 2011
    NIH
    Genome-wide Dissection of the Retinal Determination Network
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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. Wang M, Li Y, Wang J, Oh SH, Cao Y, Chen R. Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina. Genome Res. 2025 Apr 14; 35(4):740-754. PMID: 40050124; PMCID: PMC12047235.
      Citations: 1     Fields:    Translation:AnimalsCells
    2. Wang J, Wang M, Moshiri A, Harris RA, Raveendran M, Nguyen T, Kim S, Young L, Wang K, Wiseman R, O'Connor DH, Johnson Z, Martinez M, Montague MJ, Sayers K, Lyke M, Vallender E, Stout T, Li Y, Thomasy SM, Rogers J, Chen R. Genetic diversity of 1,845 rhesus macaques improves genetic variation interpretation and identifies disease models. Nat Commun. 2024 Jul 05; 15(1):5658. PMID: 38969634; PMCID: PMC11226599.
      Citations:    
    3. Wang J, Cheng X, Liang Q, Owen LA, Lu J, Zheng Y, Wang M, Chen S, DeAngelis MM, Li Y, Chen R. Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation. Genome Biol. 2023 11 27; 24(1):269. PMID: 38012720; PMCID: PMC10680294.
      Citations:    Fields:    Translation:HumansCells
    4. Choi J, Li J, Ferdous S, Liang Q, Moffitt JR, Chen R. Author Correction: Spatial organization of the mouse retina at single cell resolution by MERFISH. Nat Commun. 2023 Sep 28; 14(1):6057. PMID: 37770468; PMCID: PMC10539521.
      Citations:    Fields:    
    5. Choi J, Li J, Ferdous S, Liang Q, Moffitt JR, Chen R. Spatial organization of the mouse retina at single cell resolution by MERFISH. Nat Commun. 2023 08 15; 14(1):4929. PMID: 37582959; PMCID: PMC10427710.
      Citations: 4     Fields:    Translation:AnimalsCells
    6. Lu J, Zheng KQ, Bertrand RE, Quinlan J, Ferdous S, Srinivasan T, Oh S, Wang K, Chen R. Gene augmentation therapy to rescue degenerative photoreceptors in a Cwc27 mutant mouse model. Exp Eye Res. 2023 09; 234:109596. PMID: 37479075.
      Citations:    Fields:    Translation:AnimalsCells
    7. Lu J, Xiong K, Qian X, Choi J, Shim YK, Burnett J, Mardon G, Chen R. Spata7 is required for maintenance of the retinal connecting cilium. Sci Rep. 2022 04 02; 12(1):5575. PMID: 35368022; PMCID: PMC8976851.
      Citations:    Fields:    Translation:AnimalsCells
    8. Li DQ, Kim S, Li JM, Gao Q, Choi J, Bian F, Hu J, Zhang Y, Li J, Lu R, Li Y, Pflugfelder SC, Miao H, Chen R. Single-cell transcriptomics identifies limbal stem cell population and cell types mapping its differentiation trajectory in limbal basal epithelium of human cornea. Ocul Surf. 2021 04; 20:20-32. PMID: 33388438; PMCID: PMC8359589.
      Citations: 11     Fields:    Translation:HumansCells
    9. Bertrand RE, Wang J, Xiong KH, Thangavel C, Qian X, Ba-Abbad R, Liang Q, Carss KJ, Lucy Raymond F, Robson AG, Webster AR, Arno G, Chen R, Sim?es RT, Sampaio SAM, Porto FBO. Ceramide synthase TLCD3B is a novel gene associated with human recessive retinal dystrophy. Genet Med. 2021 03; 23(3):488-497. PMID: 33077892; PMCID: PMC7936949.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    10. Wang J, Liu H, Bertrand RE, Sarrion-Perdigones A, Gonzalez Y, Venken KJT, Chen R. A novel statistical method for interpreting the pathogenicity of rare variants. Genet Med. 2021 01; 23(1):59-68. PMID: 32884132; PMCID: PMC7796914.
      Citations: 1     Fields:    Translation:Humans
    11. Dharmat R, Kim S, Li Y, Chen R. Single-Cell Capture, RNA-seq, and Transcriptome Analysis from the Neural Retina. Methods Mol Biol. 2020; 2092:159-186. PMID: 31786788.
      Citations:    
    12. Liang Q, Dharmat R, Owen L, Shakoor A, Li Y, Kim S, Vitale A, Kim I, Morgan D, Liang S, Wu N, Chen K, DeAngelis MM, Chen R. Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling. Nat Commun. 2019 12 17; 10(1):5743. PMID: 31848347; PMCID: PMC6917696.
      Citations: 37     Fields:    Translation:HumansCells
    13. Kim S, Lowe A, Dharmat R, Lee S, Owen LA, Wang J, Shakoor A, Li Y, Morgan DJ, Hejazi AA, Cvekl A, DeAngelis MM, Zhou ZJ, Chen R, Liu W. Generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids. Proc Natl Acad Sci U S A. 2019 05 28; 116(22):10824-10833. PMID: 31072937; PMCID: PMC6561190.
      Citations: 48     Fields:    Translation:HumansCells
    14. Kean TJ, Ge Z, Li Y, Chen R, Dennis JE. Transcriptome-Wide Analysis of Human Chondrocyte Expansion on Synoviocyte Matrix. Cells. 2019 01 24; 8(2). PMID: 30678371; PMCID: PMC6406362.
      Citations: 5     Fields:    Translation:HumansCells
    15. Wang J, Zhao L, Wang X, Chen Y, Xu M, Soens ZT, Ge Z, Wang PR, Wang F, Chen R. GRIPT: a novel case-control analysis method for Mendelian disease gene discovery. Genome Biol. 2018 11 26; 19(1):203. PMID: 30477545; PMCID: PMC6258408.
      Citations:    Fields:    Translation:Humans
    16. Huang J, Fu J, Fu S, Yang L, Nie K, Duan C, Cheng J, Li Y, Lv H, Chen R, Liu L, Fu J. Diagnostic value of a combination of next-generation sequencing, chorioretinal imaging and metabolic analysis: lessons from a consanguineous Chinese family with gyrate atrophy of the choroid and retina stemming from a novel OAT variant. Br J Ophthalmol. 2019 03; 103(3):428-435. PMID: 30366948.
      Citations:    
    17. Dharmat R, Eblimit A, Robichaux MA, Zhang Z, Nguyen TT, Jung SY, He F, Jain A, Li Y, Qin J, Overbeek P, Roepman R, Mardon G, Wensel TG, Chen R. SPATA7 maintains a novel photoreceptor-specific zone in the distal connecting cilium. J Cell Biol. 2018 08 06; 217(8):2851-2865. PMID: 29899041; PMCID: PMC6080925.
      Citations: 17     Fields:    Translation:AnimalsCells
    18. Eblimit A, Zaneveld SA, Liu W, Thomas K, Wang K, Li Y, Mardon G, Chen R. NMNAT1 E257K variant, associated with Leber Congenital Amaurosis (LCA9), causes a mild retinal degeneration phenotype. Exp Eye Res. 2018 08; 173:32-43. PMID: 29674119; PMCID: PMC6054811.
      Citations: 7     Fields:    Translation:AnimalsPHPublic Health
    19. Eblimit A, Agrawal SA, Thomas K, Anastassov IA, Abulikemu T, Moayedi Y, Mardon G, Chen R. Corrigendum to "Conditional loss of Spata7 in photoreceptors causes progressive retinal degeneration in mice" [Exp. Eye Res. 166 (2018) 120-130]. Exp Eye Res. 2018 06; 171:119. PMID: 29579643.
      Citations:    Fields:    
    20. Porto FBO, Jones EM, Branch J, Soens ZT, Maia IM, Sena IFG, Sampaio SAM, Sim?es RT, Chen R. Molecular Screening of 43 Brazilian Families Diagnosed with Leber Congenital Amaurosis or Early-Onset Severe Retinal Dystrophy. Genes (Basel). 2017 Nov 29; 8(12). PMID: 29186038; PMCID: PMC5748673.
      Citations:    
    21. Eblimit A, Agrawal SA, Thomas K, Anastassov IA, Abulikemu T, Moayedi Y, Mardon G, Chen R. Conditional loss of Spata7 in photoreceptors causes progressive retinal degeneration in mice. Exp Eye Res. 2018 01; 166:120-130. PMID: 29100828; PMCID: PMC5756513.
      Citations: 8     Fields:    Translation:AnimalsCells
    22. Yuan Z, Li B, Xu M, Chang EY, Li H, Yang L, Wu S, Soens ZT, Li Y, Wong LC, Lewis RA, Sui R, Chen R. The phenotypic variability of HK1-associated retinal dystrophy. Sci Rep. 2017 08 01; 7(1):7051. PMID: 28765615; PMCID: PMC5539152.
      Citations: 7     Fields:    
    23. Xu M, Xie YA, Abouzeid H, Fiorentino A, Sun Z, Lehman A, Osman IS, Dharmat R, Bapst-Wicht L, Babino D, Arno G, Zhao L, Li H, Azevedo LF, Pontikos N, Eblimit A, Kheir V, Plagnol V, Soens ZT, Yang L, Pfundt R, Allaman-Pillet N, Cheetham ME, Agrawal SA, Li H, Michaelides M, Li Y, Yuan Z, von Lintig J, Webster AR, Stoilov P, UK Inherited Retinal Dystrophy Consortium, Hardcastle AJ, Sui R, Chen R, Allikmets R, Schorderet DF, Gordon CT, Riveiro-Alvarez R, Busetto V, Lopez-Martinez MA, Hubert L, Lorda-Sanchez I, Oufadem M, Bole-Feysot C, Nitschk? P, Lyonnet S, Pinton G, Besmond C, Le Hir H, Amiel J, Ayuso C. Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies. Am J Hum Genet. 2017 Apr 06; 100(4):592-604. PMID: 28285769; PMCID: PMC5384039.
      Citations: 33     Fields:    Translation:HumansAnimals
    24. Chen Y, Zhao L, Wang Y, Cao M, Gelowani V, Xu M, Agrawal SA, Li Y, Daiger SP, Gibbs R, Wang F, Chen R. SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data. BMC Bioinformatics. 2017 Mar 03; 18(1):147. PMID: 28253855; PMCID: PMC5335817.
      Citations: 22     Fields:    Translation:Humans
    25. Arno G, Agrawal SA, Eblimit A, Bellingham J, Xu M, Wang F, Chakarova C, Parfitt DA, Lane A, Burgoyne T, Hull S, Carss KJ, Fiorentino A, Hayes MJ, Munro PM, Nicols R, Pontikos N, Holder GE, UKIRDC, Asomugha C, Raymond FL, Moore AT, Plagnol V, Michaelides M, Hardcastle AJ, Li Y, Cukras C, Webster AR, Cheetham ME, Chen R. Mutations in REEP6 Cause Autosomal-Recessive Retinitis Pigmentosa. Am J Hum Genet. 2016 Dec 01; 99(6):1305-1315. PMID: 27889058; PMCID: PMC5142109.
      Citations:    
    26. Jin M, Aibar S, Ge Z, Chen R, Aerts S, Mardon G. Identification of novel direct targets of Drosophila Sine oculis and Eyes absent by integration of genome-wide data sets. Dev Biol. 2016 07 01; 415(1):157-167. PMID: 27178668; PMCID: PMC4902760.
      Citations: 6     Fields:    Translation:AnimalsCells
    27. Xu M, Yamada T, Sun Z, Eblimit A, Lopez I, Wang F, Manya H, Xu S, Zhao L, Li Y, Kimchi A, Sharon D, Sui R, Endo T, Koenekoop RK, Chen R. Mutations in POMGNT1 cause non-syndromic retinitis pigmentosa. Hum Mol Genet. 2016 Apr 15; 25(8):1479-88. PMID: 26908613; PMCID: PMC4805308.
      Citations:    
    28. Soens ZT, Li Y, Zhao L, Eblimit A, Dharmat R, Li Y, Chen Y, Naqeeb M, Fajardo N, Lopez I, Sun Z, Koenekoop RK, Chen R. Hypomorphic mutations identified in the candidate Leber congenital amaurosis gene CLUAP1. Genet Med. 2016 10; 18(10):1044-51. PMID: 26820066; PMCID: PMC4965339.
      Citations: 16     Fields:    Translation:HumansAnimalsCells
    29. Xu M, Eblimit A, Wang J, Li J, Wang F, Zhao L, Wang X, Xiao N, Li Y, Wong LJ, Lewis RA, Chen R. ADIPOR1 Is Mutated in Syndromic Retinitis Pigmentosa. Hum Mutat. 2016 Mar; 37(3):246-9. PMID: 26662040; PMCID: PMC5383450.
      Citations: 23     Fields:    Translation:HumansAnimals
    30. Yu DH, Gadkari M, Zhou Q, Yu S, Gao N, Guan Y, Schady D, Roshan TN, Chen MH, Laritsky E, Ge Z, Wang H, Chen R, Westwater C, Bry L, Waterland RA, Moriarty C, Hwang C, Swennes AG, Moore SR, Shen L. Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome. Genome Biol. 2015 Sep 30; 16:211. PMID: 26420038; PMCID: PMC4589031.
      Citations: 54     Fields:    Translation:AnimalsCells
    31. Jiang L, Liang X, Li Y, Wang J, Zaneveld JE, Wang H, Xu S, Wang K, Wang B, Chen R, Sui R. Comprehensive molecular diagnosis of 67 Chinese Usher syndrome probands: high rate of ethnicity specific mutations in Chinese USH patients. Orphanet J Rare Dis. 2015 Sep 04; 10:110. PMID: 26338283; PMCID: PMC4559966.
      Citations:    
    32. Xu M, Yang L, Wang F, Li H, Wang X, Wang W, Ge Z, Wang K, Zhao L, Li H, Li Y, Sui R, Chen R. Mutations in human IFT140 cause non-syndromic retinal degeneration. Hum Genet. 2015 Oct; 134(10):1069-78. PMID: 26216056; PMCID: PMC4565766.
      Citations: 29     Fields:    Translation:HumansCells
    33. Sheng X, Chen X, Lei B, Chen R, Wang H, Zhang F, Rong W, Ha R, Liu Y, Zhao F, Yang P, Zhao C. Whole exome sequencing confirms the clinical diagnosis of Marfan syndrome combined with X-linked hypophosphatemia. J Transl Med. 2015 Jun 04; 13:179. PMID: 26040324; PMCID: PMC4455986.
      Citations: 1     Fields:    Translation:HumansCells
    34. Xu M, Gelowani V, Eblimit A, Wang F, Young MP, Sawyer BL, Zhao L, Jenkins G, Creel DJ, Wang K, Ge Z, Wang H, Li Y, Hartnett ME, Chen R. ATF6 Is Mutated in Early Onset Photoreceptor Degeneration With Macular Involvement. Invest Ophthalmol Vis Sci. 2015 Jun; 56(6):3889-95. PMID: 26070061; PMCID: PMC4468593.
      Citations: 29     Fields:    Translation:HumansCells
    35. Wang H, Wang X, Zou X, Xu S, Li H, Soens ZT, Wang K, Li Y, Dong F, Chen R, Sui R. Comprehensive Molecular Diagnosis of a Large Chinese Leber Congenital Amaurosis Cohort. Invest Ophthalmol Vis Sci. 2015 Jun; 56(6):3642-55. PMID: 26047050; PMCID: PMC4466882.
      Citations: 37     Fields:    Translation:Humans
    36. Mazur EC, Vasquez YM, Li X, Kommagani R, Jiang L, Chen R, Lanz RB, Kovanci E, Gibbons WE, DeMayo FJ. Progesterone receptor transcriptome and cistrome in decidualized human endometrial stromal cells. Endocrinology. 2015 Jun; 156(6):2239-53. PMID: 25781565; PMCID: PMC4430623.
      Citations: 39     Fields:    Translation:HumansCells
    37. Salvo J, Lyubasyuk V, Xu M, Wang H, Wang F, Nguyen D, Wang K, Luo H, Wen C, Shi C, Lin D, Zhang K, Chen R. Next-generation sequencing and novel variant determination in a cohort of 92 familial exudative vitreoretinopathy patients. Invest Ophthalmol Vis Sci. 2015 Feb 24; 56(3):1937-46. PMID: 25711638; PMCID: PMC4365990.
      Citations: 39     Fields:    Translation:Humans
    38. Zhong H, Chen Y, Li Y, Chen R, Mardon G. CRISPR-engineered mosaicism rapidly reveals that loss of Kcnj13 function in mice mimics human disease phenotypes. Sci Rep. 2015 Feb 10; 5:8366. PMID: 25666713; PMCID: PMC4322368.
      Citations: 56     Fields:    Translation:HumansAnimals
    39. Zhao L, Wang F, Wang H, Li Y, Alexander S, Wang K, Willoughby CE, Zaneveld JE, Jiang L, Soens ZT, Earle P, Simpson D, Silvestri G, Chen R. Next-generation sequencing-based molecular diagnosis of 82 retinitis pigmentosa probands from Northern Ireland. Hum Genet. 2015 Feb; 134(2):217-30. PMID: 25472526; PMCID: PMC4347882.
      Citations: 54     Fields:    Translation:HumansCTClinical Trials
    40. Zaneveld J, Siddiqui S, Li H, Wang X, Wang H, Wang K, Li H, Ren H, Lopez I, Dorfman A, Khan A, Wang F, Salvo J, Gelowani V, Li Y, Sui R, Koenekoop R, Chen R. Comprehensive analysis of patients with Stargardt macular dystrophy reveals new genotype-phenotype correlations and unexpected diagnostic revisions. Genet Med. 2015 Apr; 17(4):262-70. PMID: 25474345; PMCID: PMC4385427.
      Citations: 22     Fields:    Translation:Humans
    41. Wang F, Li H, Xu M, Li H, Zhao L, Yang L, Zaneveld JE, Wang K, Li Y, Sui R, Chen R. A homozygous missense mutation in NEUROD1 is associated with nonsyndromic autosomal recessive retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2014 Dec 04; 56(1):150-5. PMID: 25477324; PMCID: PMC4290556.
      Citations: 12     Fields:    Translation:Humans
    42. Jusiak B, Wang F, Karandikar UC, Kwak SJ, Wang H, Chen R, Mardon G. Genome-wide DNA binding pattern of the homeodomain transcription factor Sine oculis (So) in the developing eye of Drosophila melanogaster. Genom Data. 2014 Dec 01; 2:153-155. PMID: 25126519; PMCID: PMC4128500.
      Citations: 10     
    43. Eblimit A, Nguyen TM, Chen Y, Esteve-Rudd J, Zhong H, Letteboer S, Van Reeuwijk J, Simons DL, Ding Q, Wu KM, Li Y, Van Beersum S, Moayedi Y, Xu H, Pickard P, Wang K, Gan L, Wu SM, Williams DS, Mardon G, Roepman R, Chen R. Spata7 is a retinal ciliopathy gene critical for correct RPGRIP1 localization and protein trafficking in the retina. Hum Mol Genet. 2015 Mar 15; 24(6):1584-601. PMID: 25398945; PMCID: PMC4351378.
      Citations: 29     Fields:    Translation:HumansAnimalsCells
    44. Wang F, Wang Y, Zhang B, Zhao L, Lyubasyuk V, Wang K, Xu M, Li Y, Wu F, Wen C, Bernstein PS, Lin D, Zhu S, Wang H, Zhang K, Chen R. A missense mutation in HK1 leads to autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2014 Oct 14; 55(11):7159-64. PMID: 25316723; PMCID: PMC4224578.
      Citations: 11     Fields:    Translation:Humans
    45. Haelterman NA, Jiang L, Li Y, Bayat V, Sandoval H, Ugur B, Tan KL, Zhang K, Bei D, Xiong B, Charng WL, Busby T, Jawaid A, David G, Jaiswal M, Venken KJ, Yamamoto S, Chen R, Bellen HJ. Large-scale identification of chemically induced mutations in Drosophila melanogaster. Genome Res. 2014 Oct; 24(10):1707-18. PMID: 25258387; PMCID: PMC4199363.
      Citations: 40     Fields:    Translation:AnimalsCells
    46. Yamamoto S, Jaiswal M, Charng WL, Gambin T, Karaca E, Mirzaa G, Wiszniewski W, Sandoval H, Haelterman NA, Xiong B, Zhang K, Bayat V, David G, Li T, Chen K, Gala U, Harel T, Pehlivan D, Penney S, Vissers LELM, de Ligt J, Jhangiani SN, Xie Y, Tsang SH, Parman Y, Sivaci M, Battaloglu E, Muzny D, Wan YW, Liu Z, Lin-Moore AT, Clark RD, Curry CJ, Link N, Schulze KL, Boerwinkle E, Dobyns WB, Allikmets R, Gibbs RA, Chen R, Lupski JR, Wangler MF, Bellen HJ. A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases. Cell. 2014 Sep 25; 159(1):200-214. PMID: 25259927; PMCID: PMC4298142.
      Citations: 168     Fields:    Translation:HumansAnimalsCells
    47. Bejar R, Lord A, Stevenson K, Bar-Natan M, Zaneveld J, Wang H, Caughey B, Stojanov P, Getz G, Garcia-Manero G, Kantarjian H, Chen R, Stone RM, Neuberg D, Steensma DP, Ebert BL, P?rez-Ladaga A. TET2 mutations predict response to hypomethylating agents in myelodysplastic syndrome patients. Blood. 2014 Oct 23; 124(17):2705-12. PMID: 25224413; PMCID: PMC4208285.
      Citations: 229     Fields:    Translation:HumansAnimalsCells
    48. Tao J, Jiang MM, Jiang L, Salvo JS, Zeng HC, Dawson B, Bertin TK, Rao PH, Chen R, Donehower LA, Gannon F, Lee BH. Notch activation as a driver of osteogenic sarcoma. Cancer Cell. 2014 Sep 08; 26(3):390-401. PMID: 25203324; PMCID: PMC4159617.
      Citations: 59     Fields:    Translation:HumansAnimalsCells
    49. Karandikar UC, Jin M, Jusiak B, Kwak S, Chen R, Mardon G. Drosophila eyes absent is required for normal cone and pigment cell development. PLoS One. 2014; 9(7):e102143. PMID: 25057928; PMCID: PMC4109927.
      Citations: 12     Fields:    Translation:AnimalsCells
    50. Sun D, Luo M, Jeong M, Rodriguez B, Xia Z, Hannah R, Wang H, Le T, Faull KF, Chen R, Gu H, Bock C, Meissner A, Darlington GJ, Li W, Goodell MA, G?ttgens B. Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. Cell Stem Cell. 2014 May 01; 14(5):673-88. PMID: 24792119; PMCID: PMC4070311.
      Citations: 256     Fields:    Translation:AnimalsCells
    51. Jusiak B, Karandikar UC, Kwak SJ, Wang F, Wang H, Chen R, Mardon G. Regulation of Drosophila eye development by the transcription factor Sine oculis. PLoS One. 2014; 9(2):e89695. PMID: 24586968; PMCID: PMC3934907.
      Citations: 19     Fields:    Translation:Animals
    52. Kunde-Ramamoorthy G, Coarfa C, Laritsky E, Kessler NJ, Harris RA, Xu M, Chen R, Shen L, Milosavljevic A, Waterland RA. Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing. Nucleic Acids Res. 2014 Apr; 42(6):e43. PMID: 24391148; PMCID: PMC3973287.
      Citations: 29     Fields:    Translation:HumansCells
    53. Jeong M, Sun D, Luo M, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim SB, Yang L, Ko M, Chen R, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W, Goodell MA, G?ttgens B. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat Genet. 2014 Jan; 46(1):17-23. PMID: 24270360; PMCID: PMC3920905.
      Citations: 164     Fields:    Translation:HumansAnimalsCells
    54. Zhou Q, Zhang T, Jemc JC, Chen Y, Chen R, Rebay I, Pignoni F. Onset of atonal expression in Drosophila retinal progenitors involves redundant and synergistic contributions of Ey/Pax6 and So binding sites within two distant enhancers. Dev Biol. 2014 Feb 01; 386(1):152-64. PMID: 24247006; PMCID: PMC5223736.
      Citations: 11     Fields:    Translation:AnimalsCells
    55. Wang F, Wang H, Tuan HF, Nguyen DH, Sun V, Keser V, Bowne SJ, Sullivan LS, Luo H, Zhao L, Wang X, Zaneveld JE, Salvo JS, Siddiqui S, Mao L, Wheaton DK, Birch DG, Branham KE, Heckenlively JR, Wen C, Flagg K, Ferreyra H, Pei J, Khan A, Ren H, Wang K, Lopez I, Qamar R, Zenteno JC, Ayala-Ramirez R, Buentello-Volante B, Fu Q, Simpson DA, Li Y, Sui R, Silvestri G, Daiger SP, Koenekoop RK, Zhang K, Chen R. Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. Hum Genet. 2014 Mar; 133(3):331-45. PMID: 24154662; PMCID: PMC3945441.
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    56. Wang X, Wang H, Sun V, Tuan HF, Keser V, Wang K, Ren H, Lopez I, Zaneveld JE, Siddiqui S, Bowles S, Khan A, Salvo J, Jacobson SG, Iannaccone A, Wang F, Birch D, Heckenlively JR, Fishman GA, Traboulsi EI, Li Y, Wheaton D, Koenekoop RK, Chen R. Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing. J Med Genet. 2013 Oct; 50(10):674-88. PMID: 23847139; PMCID: PMC3932025.
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    57. Li Y, Jiang Y, Chen Y, Karandikar U, Hoffman K, Chattopadhyay A, Mardon G, Chen R. optix functions as a link between the retinal determination network and the dpp pathway to control morphogenetic furrow progression in Drosophila. Dev Biol. 2013 Sep 01; 381(1):50-61. PMID: 23792115; PMCID: PMC3742619.
      Citations: 8     Fields:    Translation:AnimalsCells
    58. Nasser W, Santhanam B, Miranda ER, Parikh A, Juneja K, Rot G, Dinh C, Chen R, Zupan B, Shaulsky G, Kuspa A. Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions. Curr Biol. 2013 May 20; 23(10):862-72. PMID: 23664307; PMCID: PMC3914002.
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    59. Haase Gilbert E, Kwak SJ, Chen R, Mardon G. Drosophila signal peptidase complex member Spase12 is required for development and cell differentiation. PLoS One. 2013; 8(4):e60908. PMID: 23573290; PMCID: PMC3616019.
      Citations: 3     Fields:    Translation:Animals
    60. Huang Z, Chen K, Zhang J, Li Y, Wang H, Cui D, Tang J, Liu Y, Shi X, Li W, Liu D, Chen R, Sucgang RS, Pan X. A functional variomics tool for discovering drug-resistance genes and drug targets. Cell Rep. 2013 Feb 21; 3(2):577-85. PMID: 23416056; PMCID: PMC3594652.
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    61. Zaneveld J, Wang F, Wang X, Chen R. Dawn of ocular gene therapy: implications for molecular diagnosis in retinal disease. Sci China Life Sci. 2013 Feb; 56(2):125-33. PMID: 23393028; PMCID: PMC3567286.
      Citations: 4     Fields:    Translation:HumansAnimals
    62. Jusiak B, Abulimiti A, Haelterman N, Chen R, Mardon G. MAPK target sites of eyes absent are not required for eye development or survival in Drosophila. PLoS One. 2012; 7(12):e50776. PMID: 23251383; PMCID: PMC3520925.
      Citations: 7     Fields:    Translation:AnimalsCells
    63. Kriel A, Bittner AN, Kim SH, Liu K, Tehranchi AK, Zou WY, Rendon S, Chen R, Tu BP, Wang JD. Direct regulation of GTP homeostasis by (p)ppGpp: a critical component of viability and stress resistance. Mol Cell. 2012 Oct 26; 48(2):231-41. PMID: 22981860; PMCID: PMC3483369.
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    64. Wang H, Chen X, Dudinsky L, Patenia C, Chen Y, Li Y, Wei Y, Abboud EB, Al-Rajhi AA, Lewis RA, Lupski JR, Mardon G, Gibbs RA, Perkins BD, Chen R. Exome capture sequencing identifies a novel mutation in BBS4. Mol Vis. 2011; 17:3529-40. PMID: 22219648; PMCID: PMC3250376.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    65. Wang X, Wang H, Cao M, Li Z, Chen X, Patenia C, Gore A, Abboud EB, Al-Rajhi AA, Lewis RA, Lupski JR, Mardon G, Zhang K, Muzny D, Gibbs RA, Chen R. Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with Leber congenital amaurosis. Hum Mutat. 2011 Dec; 32(12):1450-9. PMID: 21901789; PMCID: PMC3943164.
      Citations: 32     Fields:    Translation:Humans
    66. Malovannaya A, Lanz RB, Jung SY, Bulynko Y, Le NT, Chan DW, Ding C, Shi Y, Yucer N, Krenciute G, Kim BJ, Li C, Chen R, Li W, Wang Y, O'Malley BW, Qin J. Analysis of the human endogenous coregulator complexome. Cell. 2011 May 27; 145(5):787-99. PMID: 21620140; PMCID: PMC3131083.
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    67. Yang D, Xiong Y, Kim H, He Q, Li Y, Chen R, Songyang Z. Human telomeric proteins occupy selective interstitial sites. Cell Res. 2011 Jul; 21(7):1013-27. PMID: 21423278; PMCID: PMC3193500.
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    68. Xi Y, Yao J, Chen R, Li W, He X. Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation. Genome Res. 2011 May; 21(5):718-24. PMID: 21363969; PMCID: PMC3083088.
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    69. Daines B, Wang H, Wang L, Li Y, Han Y, Emmert D, Gelbart W, Wang X, Li W, Gibbs R, Chen R. The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res. 2011 Feb; 21(2):315-24. PMID: 21177959; PMCID: PMC3032934.
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    70. Wiszniewski W, Lewis RA, Stockton DW, Peng J, Mardon G, Chen R, Lupski JR. Potential involvement of more than one locus in trait manifestation for individuals with Leber congenital amaurosis. Hum Genet. 2011 Mar; 129(3):319-27. PMID: 21153841; PMCID: PMC3625363.
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    71. Kim BJ, Li Y, Zhang J, Xi Y, Li Y, Yang T, Jung SY, Pan X, Chen R, Li W, Wang Y, Qin J. Genome-wide reinforcement of cohesin binding at pre-existing cohesin sites in response to ionizing radiation in human cells. J Biol Chem. 2010 Jul 23; 285(30):22784-92. PMID: 20501661; PMCID: PMC2906269.
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    72. Wang H, Chattopadhyay A, Li Z, Daines B, Li Y, Gao C, Gibbs R, Zhang K, Chen R. Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Res. 2010 Jul; 20(7):981-8. PMID: 20472684; PMCID: PMC2892099.
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    73. Parikh A, Miranda ER, Katoh-Kurasawa M, Fuller D, Rot G, Zagar L, Curk T, Sucgang R, Chen R, Zupan B, Loomis WF, Kuspa A, Shaulsky G. Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biol. 2010; 11(3):R35. PMID: 20236529; PMCID: PMC2864575.
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    74. Daines B, Wang H, Li Y, Han Y, Gibbs R, Chen R. High-throughput multiplex sequencing to discover copy number variants in Drosophila. Genetics. 2009 Aug; 182(4):935-41. PMID: 19528327; PMCID: PMC2728881.
      Citations: 14     Fields:    Translation:Animals
    75. Wang H, den Hollander AI, Moayedi Y, Abulimiti A, Li Y, Collin RW, Hoyng CB, Lopez I, Abboud EB, Al-Rajhi AA, Bray M, Lewis RA, Lupski JR, Mardon G, Koenekoop RK, Chen R. Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa. Am J Hum Genet. 2009 Mar; 84(3):380-7. PMID: 19268277; PMCID: PMC2668010.
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    76. Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs R, Wang JD, Chen R. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet. 2008 Aug 01; 4(8):e1000139. PMID: 18670626; PMCID: PMC2474695.
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      Citations: 6     Fields:    Translation:AnimalsCells
    88. Pappu KS, Chen R, Middlebrooks BW, Woo C, Heberlein U, Mardon G. Mechanism of hedgehog signaling during Drosophila eye development. Development. 2003 Jul; 130(13):3053-62. PMID: 12756186.
      Citations: 36     Fields:    Translation:AnimalsCells
    89. Chen R, Bouck JB, Weinstock GM, Gibbs RA. Comparing vertebrate whole-genome shotgun reads to the human genome. Genome Res. 2001 Nov; 11(11):1807-16. PMID: 11691844; PMCID: PMC311156.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    90. Cai WW, Chen R, Gibbs RA, Bradley A. A clone-array pooled shotgun strategy for sequencing large genomes. Genome Res. 2001 Oct; 11(10):1619-23. PMID: 11591638.
      Citations: 22     Fields:    Translation:HumansAnimals
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