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Ruijia Wang PhD

TitleAssistant Professor
InstitutionUniversity of Massachusetts Medical School
DepartmentProgram in Molecular Medicine
AddressUniversity of Massachusetts Medical School
373 Plantation Street
Worcester MA 01605
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentProgram in Molecular Medicine


    Collapse Biography 
    Collapse education and training
    Ocean University of China, Qingdao, 37, ChinaBSBiotechnology
    Auburn University, Auburn, AL, United StatesPHDBioinformatics & Genomics

    Collapse Overview 
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    Academic Background

    Ruijia Wang received his B.S. degree in Biotechnology from the Ocean University of China in 2007, and a Ph.D. degree in Genomics and Bioinformatics from Auburn University in 2013. After graduation, he spent a short time as a Postdoctoral Fellow in the same lab at AU, and then went to Ocean University of China to complete his contractual service for two years, during which he worked on whole-genome database construction and genomic resource development for aquaculture species. Dr. Wang joined Dr. Bin Tian’s group at Rutgers New Jersey Medical School to study mechanisms and consequences of alternative polyadenylation using bioinformatic approaches from 2016 to 2019. He then joined the University of Massachusetts Medical School (UMMS) as the assistant professor, director of bioinformatics of Program in Molecular Medicine (PMM) in 2019. 

     

    Research Projects

    Bioinformatic modeling on the regulation of alternative cleavage and polyadenylation (APA).
    2016 – 2019

    APA has been increasingly recognized as an important layer mRNA processing regulator which plays an important role in disease related process, such as tumorigenesis and neurological disorder. In this ongoing research, we have studied export factor NXF1 and CPA factor PCF11, revealing gene size-based and APA-based regulatory mechanisms. We also collaborate with a UCSD team on APA regulation in acute myeloid leukemia patients

    Construction of PolyA_DB3 database and genomic evolution analysis on mammal PAS.
    2016 – 2019

    In this project, we constructed a vertebrate PAS database, PolyA_DB 3. This database contains PAS identified in several vertebrates, including humans, mouse, rat and chicken, drawn from over 100 datasets. In additions, through systematic bioinformatics analysis, we present the first comprehensive view of conserved cleavage and polyadenylation events in mammals.

    Genomic resource development in echinoderm.
    2014 – 2016

    In this project, my research mainly focusing on two aspects. 1) I involved in the creating of the first high-density genetic linkage map, whole genome assembly and annotation for echinoderms in a sea cucumber species using the whole genome sequencing and 2b-RAD-Seq technique. And 2) I analyzed transcriptome data from two echinoderm species and identified nearly 17,000 long-noncoding RNA (lncRNA). I then connected the lncRNA, mRNA and miRNA as the lncRNA-microRNA-gene trinities not only to consider their corresponding roles together, but also to construct the first coding-noncoding network in echinoderm.

     

    Identification of marker genes relevant to bacterial infectious diseases in fish.
    2012 – 2014

    We optimized Bulk segregant RNA-sequencing (BSR-seq) technology and applied it to study enteric septicemia of catfish, one of the most common and serious diseases afflicting catfish. This study demonstrated the utility and effectiveness of this novel technique and identified the candidate genomic region relevant to this disease. We also performed a series of genomic and bioinformatics analyses of the data obtained using BSR-seq, making a range of crucial discoveries concerning catfish innate immunity and resistance against bacterial infections.

     




    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.
    List All   |   Timeline
    1. Zhang X, Zhuo Y, Luo Q, Wu Z, Midya R, Wang Z, Song W, Wang R, Upadhyay NK, Fang Y, Kiani F, Rao M, Yang Y, Xia Q, Liu Q, Liu M, Yang JJ. An artificial spiking afferent nerve based on Mott memristors for neurorobotics. Nat Commun. 2020 Jan 02; 11(1):51. PMID: 31896758.
      View in: PubMed
    2. Wang R, Zheng D, Wei L, Ding Q, Tian B. Regulation of Intronic Polyadenylation by PCF11 Impacts mRNA Expression of Long Genes. Cell Rep. 2019 Mar 05; 26(10):2766-2778.e6. PMID: 30840896.
      View in: PubMed
    3. Chen S, Wang R, Zheng D, Zhang H, Chang X, Wang K, Li W, Fan J, Tian B, Cheng H. The mRNA Export Receptor NXF1 Coordinates Transcriptional Dynamics, Alternative Polyadenylation, and mRNA Export. Mol Cell. 2019 04 04; 74(1):118-131.e7. PMID: 30819645.
      View in: PubMed
    4. Lv J, Jiao W, Guo H, Liu P, Wang R, Zhang L, Zeng Q, Hu X, Bao Z, Wang S. HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay. Genome Res. 2018 12; 28(12):1919-1930. PMID: 30409770.
      View in: PubMed
    5. Wang R, Zheng D, Yehia G, Tian B. A compendium of conserved cleavage and polyadenylation events in mammalian genes. Genome Res. 2018 10; 28(10):1427-1441. PMID: 30143597.
      View in: PubMed
    6. Li Y, Wang R, Xun X, Wang J, Bao L, Thimmappa R, Ding J, Jiang J, Zhang L, Li T, Lv J, Mu C, Hu X, Zhang L, Liu J, Li Y, Yao L, Jiao W, Wang Y, Lian S, Zhao Z, Zhan Y, Huang X, Liao H, Wang J, Sun H, Mi X, Xia Y, Xing Q, Lu W, Osbourn A, Zhou Z, Chang Y, Bao Z, Wang S. Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation. Cell Discov. 2018; 4:29. PMID: 29951224.
      View in: PubMed
    7. Zheng D, Wang R, Ding Q, Wang T, Xie B, Wei L, Zhong Z, Tian B. Cellular stress alters 3'UTR landscape through alternative polyadenylation and isoform-specific degradation. Nat Commun. 2018 06 11; 9(1):2268. PMID: 29891946.
      View in: PubMed
    8. Wang R, Nambiar R, Zheng D, Tian B. PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes. Nucleic Acids Res. 2018 01 04; 46(D1):D315-D319. PMID: 29069441.
      View in: PubMed
    9. Wang S, Zhang J, Jiao W, Li J, Xun X, Sun Y, Guo X, Huan P, Dong B, Zhang L, Hu X, Sun X, Wang J, Zhao C, Wang Y, Wang D, Huang X, Wang R, Lv J, Li Y, Zhang Z, Liu B, Lu W, Hui Y, Liang J, Zhou Z, Hou R, Li X, Liu Y, Li H, Ning X, Lin Y, Zhao L, Xing Q, Dou J, Li Y, Mao J, Guo H, Dou H, Li T, Mu C, Jiang W, Fu Q, Fu X, Miao Y, Liu J, Yu Q, Li R, Liao H, Li X, Kong Y, Jiang Z, Chourrout D, Li R, Bao Z. Scallop genome provides insights into evolution of bilaterian karyotype and development. Nat Ecol Evol. 2017 Apr 03; 1(5):120. PMID: 28812685.
      View in: PubMed
    10. Geng X, Liu S, Yao J, Bao L, Zhang J, Li C, Wang R, Sha J, Zeng P, Zhi D, Liu Z. A Genome-Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish. G3 (Bethesda). 2016 10 13; 6(10):3389-3398. PMID: 27558670.
      View in: PubMed
    11. Mu C, Wang R, Li T, Li Y, Tian M, Jiao W, Huang X, Zhang L, Hu X, Wang S, Bao Z. Long Non-Coding RNAs (lncRNAs) of Sea Cucumber: Large-Scale Prediction, Expression Profiling, Non-Coding Network Construction, and lncRNA-microRNA-Gene Interaction Analysis of lncRNAs in Apostichopus japonicus and Holothuria glaberrima During LPS Challenge and Radial Organ Complex Regeneration. Mar Biotechnol (NY). 2016 Aug; 18(4):485-99. PMID: 27392411.
      View in: PubMed
    12. Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Wang R, Zhang Y, Zhou T, Zeng Q, Fu Q, Gao S, Li N, Koren S, Jiang Y, Zimin A, Xu P, Phillippy AM, Geng X, Song L, Sun F, Li C, Wang X, Chen A, Jin Y, Yuan Z, Yang Y, Tan S, Peatman E, Lu J, Qin Z, Dunham R, Li Z, Sonstegard T, Feng J, Danzmann RG, Schroeder S, Scheffler B, Duke MV, Ballard L, Kucuktas H, Kaltenboeck L, Liu H, Armbruster J, Xie Y, Kirby ML, Tian Y, Flanagan ME, Mu W, Waldbieser GC. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nat Commun. 2016 06 02; 7:11757. PMID: 27249958.
      View in: PubMed
    13. Xing Q, Yu Q, Dou H, Wang J, Li R, Ning X, Wang R, Wang S, Zhang L, Hu X, Bao Z. Genome-wide identification, characterization and expression analyses of two TNFRs in Yesso scallop (Patinopecten yessoensis) provide insight into the disparity of responses to bacterial infections and heat stress in bivalves. Fish Shellfish Immunol. 2016 May; 52:44-56. PMID: 26988286.
      View in: PubMed
    14. Chen A, Wang R, Liu S, Peatman E, Sun L, Bao L, Jiang C, Li C, Li Y, Zeng Q, Liu Z. Ribosomal protein genes are highly enriched among genes with allele-specific expression in the interspecific F1 hybrid catfish. Mol Genet Genomics. 2016 Jun; 291(3):1083-93. PMID: 26747053.
      View in: PubMed
    15. Li X, Wang R, Xun X, Jiao W, Zhang M, Wang S, Wang S, Zhang L, Huang X, Hu X, Bao Z. The Rho GTPase Family Genes in Bivalvia Genomes: Sequence, Evolution and Expression Analysis. PLoS One. 2015; 10(12):e0143932. PMID: 26633655.
      View in: PubMed
    16. Tian M, Li Y, Jing J, Mu C, Du H, Dou J, Mao J, Li X, Jiao W, Wang Y, Hu X, Wang S, Wang R, Bao Z. Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus. Sci Rep. 2015 Oct 06; 5:14852. PMID: 26439740.
      View in: PubMed
    17. Wang J, Wang R, Wang S, Zhang M, Ma X, Liu P, Zhang M, Hu X, Zhang L, Wang S, Bao Z. Genome-wide identification and characterization of TRAF genes in the Yesso scallop (Patinopecten yessoensis) and their distinct expression patterns in response to bacterial challenge. Fish Shellfish Immunol. 2015 Nov; 47(1):545-55. PMID: 26434715.
      View in: PubMed
    18. Ning X, Wang R, Li X, Wang S, Zhang M, Xing Q, Sun Y, Wang S, Zhang L, Hu X, Bao Z. Genome-wide identification and characterization of five MyD88 duplication genes in Yesso scallop (Patinopecten yessoensis) and expression changes in response to bacterial challenge. Fish Shellfish Immunol. 2015 Oct; 46(2):181-91. PMID: 26115632.
      View in: PubMed
    19. Zou J, Wang R, Li R, Kong Y, Wang J, Ning X, Zhang L, Wang S, Hu X, Bao Z. The genome-wide identification of mitogen-activated protein kinase kinase (MKK) genes in Yesso scallop Patinopecten yessoensis and their expression responses to bacteria challenges. Fish Shellfish Immunol. 2015 Aug; 45(2):901-11. PMID: 26067168.
      View in: PubMed
    20. Li R, Zhang R, Zhang L, Zou J, Xing Q, Dou H, Hu X, Zhang L, Wang R, Bao Z. Characterizations and expression analyses of NF-?B and Rel genes in the Yesso scallop (Patinopecten yessoensis) suggest specific response patterns against Gram-negative infection in bivalves. Fish Shellfish Immunol. 2015 Jun; 44(2):611-21. PMID: 25842178.
      View in: PubMed
    21. Geng X, Sha J, Liu S, Bao L, Zhang J, Wang R, Yao J, Li C, Feng J, Sun F, Sun L, Jiang C, Zhang Y, Chen A, Dunham R, Zhi D, Liu Z. A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for columnaris disease resistance. BMC Genomics. 2015 Mar 17; 16:196. PMID: 25888203.
      View in: PubMed
    22. Zhang R, Li R, Wang J, Wang S, Zhang M, Hu X, Zhang L, Wang S, Wang R, Bao Z. Identification, characterization and expression profiling of the Tollip gene in Yesso scallop (Patinopecten yessoensis). Genes Genet Syst. 2015; 90(2):99-108. PMID: 26399769.
      View in: PubMed
    23. Li Y, Liu S, Qin Z, Waldbieser G, Wang R, Sun L, Bao L, Danzmann RG, Dunham R, Liu Z. Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish. DNA Res. 2015 Feb; 22(1):39-52. PMID: 25428894.
      View in: PubMed
    24. Sun L, Liu S, Wang R, Jiang Y, Zhang Y, Zhang J, Bao L, Kaltenboeck L, Dunham R, Waldbieser G, Liu Z. Identification and analysis of genome-wide SNPs provide insight into signatures of selection and domestication in channel catfish (Ictalurus punctatus). PLoS One. 2014; 9(10):e109666. PMID: 25313648.
      View in: PubMed
    25. Sun L, Liu S, Wang R, Li C, Zhang J, Liu Z. Pathogen recognition receptors in channel catfish: IV. Identification, phylogeny and expression analysis of peptidoglycan recognition proteins. Dev Comp Immunol. 2014 Oct; 46(2):291-9. PMID: 24814805.
      View in: PubMed
    26. Zhang J, Yao J, Wang R, Zhang Y, Liu S, Sun L, Jiang Y, Feng J, Liu N, Nelson D, Waldbieser G, Liu Z. The cytochrome P450 genes of channel catfish: their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq data sets. Biochim Biophys Acta. 2014 Sep; 1840(9):2813-28. PMID: 24780645.
      View in: PubMed
    27. Yao J, Li C, Zhang J, Liu S, Feng J, Wang R, Li Y, Jiang C, Song L, Chen A, Liu Z. Expression of nitric oxide synthase (NOS) genes in channel catfish is highly regulated and time dependent after bacterial challenges. Dev Comp Immunol. 2014 Jul; 45(1):74-86. PMID: 24560653.
      View in: PubMed
    28. Wang R, Zhang Y, Liu S, Li C, Sun L, Bao L, Feng J, Liu Z. Analysis of 52 Rab GTPases from channel catfish and their involvement in immune responses after bacterial infections. Dev Comp Immunol. 2014 Jul; 45(1):21-34. PMID: 24513270.
      View in: PubMed
    29. Wang R, Sun L, Bao L, Zhang J, Jiang Y, Yao J, Song L, Feng J, Liu S, Liu Z. Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish. BMC Genomics. 2013 Dec 30; 14:929. PMID: 24373586.
      View in: PubMed
    30. Feng J, Liu S, Wang X, Wang R, Zhang J, Jiang Y, Li C, Kaltenboeck L, Li J, Liu Z. Channel catfish hemoglobin genes: identification, phylogenetic and syntenic analysis, and specific induction in response to heat stress. Comp Biochem Physiol Part D Genomics Proteomics. 2014 Mar; 9:11-22. PMID: 24334243.
      View in: PubMed
    31. Wang R, Feng J, Li C, Liu S, Zhang Y, Liu Z. Four lysozymes (one c-type and three g-type) in catfish are drastically but differentially induced after bacterial infection. Fish Shellfish Immunol. 2013 Jul; 35(1):136-45. PMID: 23639933.
      View in: PubMed
    32. Li C, Wang R, Su B, Luo Y, Terhune J, Beck B, Peatman E. Evasion of mucosal defenses during Aeromonas hydrophila infection of channel catfish (Ictalurus punctatus) skin. Dev Comp Immunol. 2013 Apr; 39(4):447-55. PMID: 23219904.
      View in: PubMed
    33. Li C, Zhang Y, Wang R, Lu J, Nandi S, Mohanty S, Terhune J, Liu Z, Peatman E. RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. Fish Shellfish Immunol. 2012 May; 32(5):816-27. PMID: 22366064.
      View in: PubMed
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