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Yan Yuan Tseng

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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. Yang TH, Syu GD, Chen CS, Chen GR, Jhong SE, Lin PH, Lin PC, Wang YC, Shah P, Tseng YY, Wu WS. BAPCP: A comprehensive and user-friendly web tool for identifying biomarkers from protein microarray technologies. Comput Methods Programs Biomed. 2024 Sep; 254:108260. PMID: 38878357.
      Citations:    Fields:    Translation:HumansCells
    2. Yang TH, Chen JC, Lee YH, Lu SY, Wu SH, Chang FY, Huang YC, Lee MH, Tseng YY, Wu WS. Identifying Human miRNA Target Sites via Learning the Interaction Patterns between miRNA and mRNA Segments. J Chem Inf Model. 2024 04 08; 64(7):2445-2453. PMID: 37903033.
      Citations: 2     Fields:    Translation:HumansAnimals
    3. Wang B, Lei X, Tian W, Perez-Rathke A, Tseng YY, Liang J. Structure-based pathogenicity relationship identifier for predicting effects of single missense variants and discovery of higher-order cancer susceptibility clusters of mutations. Brief Bioinform. 2023 07 20; 24(4). PMID: 37332013; PMCID: PMC10359089.
      Citations: 6     Fields:    Translation:Humans
    4. Yang TH, Hsu CW, Wang YX, Yu CH, Rathod J, Tseng YY, Wu WS. YMLA: A comparative platform to carry out functional enrichment analysis for multiple gene lists in yeast. Comput Biol Med. 2022 12; 151(Pt B):106314. PMID: 36455295.
      Citations: 1     Fields:    Translation:Animals
    5. Tseng YY, Sanders MA, Zhang H, Zhou L, Chou CY, Granneman JG. Structural and functional insights into ABHD5, a ligand-regulated lipase co-activator. Sci Rep. 2022 02 16; 12(1):2565. PMID: 35173175; PMCID: PMC8850477.
      Citations: 9     Fields:    Translation:HumansCells
    6. Yang TH, Shiue SC, Chen KY, Tseng YY, Wu WS. Identifying piRNA targets on mRNAs in C. elegans using a deep multi-head attention network. BMC Bioinformatics. 2021 Oct 16; 22(1):503. PMID: 34656087; PMCID: PMC8520261.
      Citations: 6     Fields:    Translation:AnimalsCells
    7. Yang TH, Chiang YH, Shiue SC, Lin PH, Yang YC, Tu KC, Tseng YY, Tseng JT, Wu WS. Cancer DEIso: An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers. Comput Struct Biotechnol J. 2021; 19:5149-5159. PMID: 34589189; PMCID: PMC8463781.
      Citations: 3     
    8. Bhattacharjee MJ, Lin JJ, Chang CY, Chiou YT, Li TN, Tai CW, Shiu TF, Chen CA, Chou CY, Chakraborty P, Tseng YY, Wang LH, Li WH. Identifying Primate ACE2 Variants That Confer Resistance to SARS-CoV-2. Mol Biol Evol. 2021 06 25; 38(7):2715-2731. PMID: 33674876; PMCID: PMC7989403.
      Citations: 18     Fields:    Translation:HumansAnimalsCells
    9. Rathod J, Yen HC, Liang B, Tseng YY, Chen CS, Wu WS. YPIBP: A repository for phosphoinositide-binding proteins in yeast. Comput Struct Biotechnol J. 2021; 19:3692-3707. PMID: 34285772; PMCID: PMC8261538.
      Citations: 1     
    10. Wu WS, Tsao YH, Shiue SC, Chen TY, Tseng YY, Tseng JT. A tool for analyzing and visualizing ribo-seq data at the isoform level. BMC Bioinformatics. 2021 May 25; 22(Suppl 10):271. PMID: 34058988; PMCID: PMC8323483.
      Citations: 3     Fields:    Translation:HumansCells
    11. Wu WS, Wang LJ, Yen HC, Tseng YY. YQFC: a web tool to compare quantitative biological features between two yeast gene lists. Database (Oxford). 2020 01 01; 2020. PMID: 33186464; PMCID: PMC7805433.
      Citations: 1     Fields:    Translation:Animals
    12. Lei X, Wang B, Perez-Rathke A, Tian W, Chou CY, Tseng YY, Liang J. Predicting Oncogenic Missense Mutations. IEEE EMBS Int Conf Biomed Health Inform. 2019 May; 2019. PMID: 35261984; PMCID: PMC8901086.
      Citations:    
    13. Lin JJ, Bhattacharjee MJ, Yu CP, Tseng YY, Li WH. Many human RNA viruses show extraordinarily stringent selective constraints on protein evolution. Proc Natl Acad Sci U S A. 2019 09 17; 116(38):19009-19018. PMID: 31484772; PMCID: PMC6754614.
      Citations: 29     Fields:    Translation:HumansAnimalsCells
    14. Rathod J, Tu HP, Chang YI, Chu YH, Tseng YY, Jean JS, Wu WS. YARG: A repository for arsenic-related genes in yeast. PLoS One. 2018; 13(7):e0201204. PMID: 30048518; PMCID: PMC6062094.
      Citations: 4     Fields:    Translation:Animals
    15. Yu K, Lung PY, Zhao T, Zhao P, Tseng YY, Zhang J. Automatic extraction of protein-protein interactions using grammatical relationship graph. BMC Med Inform Decis Mak. 2018 07 23; 18(Suppl 2):42. PMID: 30066644; PMCID: PMC6069288.
      Citations: 12     Fields:    
    16. Wu WS, Tu HP, Chu YH, Nordling TEM, Tseng YY, Liaw HJ. YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast. Database (Oxford). 2018 01 01; 2018. PMID: 30371756; PMCID: PMC6204766.
      Citations: 1     Fields:    Translation:AnimalsCells
    17. Wu WS, Jiang YX, Chang JW, Chu YH, Chiu YH, Tsao YH, Nordling TEM, Tseng YY, Tseng JT. HRPDviewer: human ribosome profiling data viewer. Database (Oxford). 2018 01 01; 2018. PMID: 30010738; PMCID: PMC6041748.
      Citations: 7     Fields:    Translation:HumansCells
    18. Dai X, Thiagarajan D, Fang J, Shen J, Annam NP, Yang Z, Jiang H, Ju D, Xie Y, Zhang K, Tseng YY, Yang Z, Rishi AK, Li HJ, Yang M, Li L. SM22a suppresses cytokine-induced inflammation and the transcription of NF-?B inducing kinase (Nik) by modulating SRF transcriptional activity in vascular smooth muscle cells. PLoS One. 2017; 12(12):e0190191. PMID: 29284006; PMCID: PMC5746259.
      Citations: 6     Fields:    Translation:AnimalsCells
    19. Sanders MA, Zhang H, Mladenovic L, Tseng YY, Granneman JG. Molecular Basis of ABHD5 Lipolysis Activation. Sci Rep. 2017 02 17; 7:42589. PMID: 28211464; PMCID: PMC5314347.
      Citations: 27     Fields:    Translation:AnimalsCells
    20. Wu WS, Chen PH, Chen TT, Tseng YY. YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules. Database (Oxford). 2017 01 01; 2017. PMID: 29220473; PMCID: PMC5691354.
      Citations: 2     Fields:    Translation:Animals
    21. Tseng YY, Li WH. PSC: protein surface classification. Nucleic Acids Res. 2012 Jul; 40(Web Server issue):W435-9. PMID: 22669905; PMCID: PMC3394246.
      Citations: 4     Fields:    Translation:HumansCells
    22. Tseng YY, Li WH. Classification of protein functional surfaces using structural characteristics. Proc Natl Acad Sci U S A. 2012 Jan 24; 109(4):1170-5. PMID: 22238424; PMCID: PMC3268291.
      Citations: 11     Fields:    Translation:Cells
    23. Tseng YY, Li WH. Evolutionary approach to predicting the binding site residues of a protein from its primary sequence. Proc Natl Acad Sci U S A. 2011 Mar 29; 108(13):5313-8. PMID: 21402946; PMCID: PMC3069214.
      Citations: 9     Fields:    Translation:Cells
    24. Adamian L, Tseng YY, Muni NJ, Feng F, Qian H, Pepperberg DR, Liang J, Gussin HA. Structural model of rho1 GABAC receptor based on evolutionary analysis: Testing of predicted protein-protein interactions involved in receptor assembly and function. Protein Sci. 2009 Nov; 18(11):2371-83. PMID: 19768800; PMCID: PMC2788291.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    25. Tseng YY, Chen ZJ, Li WH. fPOP: footprinting functional pockets of proteins by comparative spatial patterns. Nucleic Acids Res. 2010 Jan; 38(Database issue):D288-95. PMID: 19880384; PMCID: PMC2808891.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    26. Tseng YY, Li WH. Identification of protein functional surfaces by the concept of a split pocket. Proteins. 2009 Sep; 76(4):959-76. PMID: 19326458.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    27. Tseng YY, Dupree C, Chen ZJ, Li WH. SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns. Nucleic Acids Res. 2009 Jul; 37(Web Server issue):W384-9. PMID: 19406922; PMCID: PMC2703984.
      Citations: 17     Fields:    Translation:HumansCells
    28. Liang J, Tseng YY, Dundas J, Binkowski TA, Joachimiak A, Ouyang Z, Adamian L. Chapter 4. Predicting and characterizing protein functions through matching geometric and evolutionary patterns of binding surfaces. Adv Protein Chem Struct Biol. 2008; 75:107-41. PMID: 20731991; PMCID: PMC2882714.
      Citations: 3     Fields:    Translation:Cells
    29. Tseng YY, Dundas J, Liang J. Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. J Mol Biol. 2009 Mar 27; 387(2):451-64. PMID: 19154742; PMCID: PMC2670802.
      Citations: 37     Fields:    Translation:HumansCells
    30. Tseng YY, Liang J. Predicting enzyme functional surfaces and locating key residues automatically from structures. Ann Biomed Eng. 2007 Jun; 35(6):1037-42. PMID: 17294116.
      Citations: 9     Fields:    Translation:Cells
    31. Adamian L, Ouyang Z, Tseng YY, Liang J. Evolutionary patterns of retinal-binding pockets of type I rhodopsins and their functions. Photochem Photobiol. 2006 Nov-Dec; 82(6):1426-35. PMID: 16922602.
      Citations: 6     Fields:    Translation:Cells
    32. Tseng YY, Liang J. Automated method for predicting enzyme functional surfaces and locating key residues with accuracy and specificity. Conf Proc IEEE Eng Med Biol Soc. 2006; 2006:4552-5. PMID: 17947099.
      Citations: 1     Fields:    Translation:Cells
    33. Tseng YY, Liang J. Estimation of amino acid residue substitution rates at local spatial regions and application in protein function inference: a Bayesian Monte Carlo approach. Mol Biol Evol. 2006 Feb; 23(2):421-36. PMID: 16251508.
      Citations: 45     Fields:    Translation:Cells
    34. Tseng YY, Liang J. Are residues in a protein folding nucleus evolutionarily conserved? J Mol Biol. 2004 Jan 23; 335(4):869-80. PMID: 14698285.
      Citations: 14     Fields:    Translation:Cells
    35. Stitziel NO, Binkowski TA, Tseng YY, Kasif S, Liang J. topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D520-2. PMID: 14681472; PMCID: PMC308838.
      Citations: 49     Fields:    Translation:HumansCells
    36. Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, Liang J. Structural location of disease-associated single-nucleotide polymorphisms. J Mol Biol. 2003 Apr 11; 327(5):1021-30. PMID: 12662927.
      Citations: 32     Fields:    Translation:Humans
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