Yanbin Yin
Assistant Professor
Department of Biological Sciences
Northern Illinois University
Link to faculty page
Link to lab page



  • EDUCATION AND TRAINING

  • RESEARCH INTERESTS
    • Plant cell wall biosynthesis and microbial degradation
    • Metagenomics
    • Origin and evolution of plant cell wall
    • Alternative splicing
    • Next generation sequencing
    • Evolutionary study of microbial and viral genome biology
    • Comparative and evolutionary study of important protein families
    • New genes identification and preliminary validation using in silico approaches
    • Pseudogenes and gene duplications

  • ACADEMIC SERVICES

  • PAPERS
    1. Wang S*, Yanbin Yin*, Ma Q, Tang X, Xu Y. (2012) Identification of novel cell wall related genes in Arabidopsis using biclustering coexpression analysis, BMC Plant Biology, 2012, accepted, (*equal contribution)
    2. Li G, Kollner TG, Yanbin Yin, Jiang Y, Xu Y, Gershenzon J, Pichersky E, Chen F. Acquisition of Terpene Synthase Genes through Horizontal Gene Transfer in Selaginella moellendorfii, Proc Natl Acad Sci USA, 2012, in press
    3. Mao X, Zhang H, Yanbin Yin, Xu Y. The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces, Nucleic Acids Res., 2012, doi: 10.1093/nar/gks605
    4. Blumer-Schuette SE, Giannone RJ, Zurawski1 JV, Ozdemir I, Mistry DB, Ma Q, Yanbin Yin, Xu Y, Poole FL II, Kataeva I, Adams MWW, Hamilton-Brehm SD, Elkins JG, Larimer FW, Land ML, Hauser L, Cottingham RW, Hettich RL, and Kelly RM, Caldicellulosiruptor core and pan genomes reveal determinants for non-cellulosomal thermophilic deconstruction of lignocellulose. J of Bacteriology, 2012, Aug;194(15):4015-28
    5. Yanbin Yin*, Mao X*, Yang JC, Chen X and Xu Y# dbCAN: a web resource and DataBase for automated Carbohydrate-active enzyme ANnotation (*equal contribution) Nucleic Acids Res. 40 (W1): W445-W451, 2012, DOI:10.1093/nar/GKS479
    6. Zhang, H.*, Yanbin Yin*, Olman, V. and Xu, Y. (2012) Genomic arrangement of regulons in bacterial genomes. PLoS ONE, 10.1371/journal.pone.0029496 (*equal contribution)
    7. Yanbin Yin, Huang, J., Gu, X., Bar-Peled, M., Xu, Y. (2011) Evolution of plant Nucleotide-Sugar interconversion enzymes, PLoS ONE doi10.1371/journal.pone.0027995
    8. Li*, G., Ma*, Q., Mao, X., Yanbin Yin, Zhu, X., Xu, Y. (2011) GOST: a Global Optimization Strategy for Mapping Orthologous Genes across Bacterial Genomes. Nucleic Acids Res. (accepted)
    9. A Kulkarni, MJ Pena, U Avci, K Mazumdar, B Urbanowicz, Yanbin Yin, MA. ONeill, AW Roberts, MG Hahn, Y Xu, AG Darvill, WS York (2011) The ability to synthesize 1,4-linked .-d-xylans predates the appearance of vascular plants. Glycobiology (accepted)
    10. P Dam, I Kataeva, S Yang, F Zhou, Yanbin Yin, W Chou, F L., Poole II, J Westpheling, R Hettich, R Giannone, DL. Lewis, R Kelly, H J. Gilbert, B Henrissat, Ying Xu and M. W.W. Adams (2011) Insights into Plant Biomass to Biofuel Conversion from the Genome Sequence of the Extremely Thermophilic Bacterium Caldicellulosiruptor bescii DSM 6725, Nucleic Acids Res. 39(8):3240-54 PubMed
    11. Kong, Y., Zhou, G., Yanbin Yin, Pattathil, S., Xu, Y., Hahn, MG. (2011) Molecular Analysis of a Family of Arabidopsis Genes Related to Galacturonosyltransferases, Plant Physiology 155(4):1791-805 PubMed
    12. Zhou, C., Yanbin Yin, Dam, P., Xu, Y. (2010) Identification of novel genes involved in plant cell wall biosynthesis by protein-protein interactions. Journal of Proteome Research 9(10):5025-37 PubMed
    13. Chou, WC., Yanbin Yin, Xu, Y. (2010) GolgiP: prediction of Golgi resident proteins in plants. Bioinformatics 26(19):2464-5 PubMed
    14. Zhao, Q., Wang, H., Yanbin Yin, Xu, Y., Chen F., Dixon DA. (2010) Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch. Proc Natl Acad Sci USA 107(32):14496-501 PubMed
    15. Yanbin Yin, Chen, H., Hahn, M., Mohnen, D., Xu, Y. (2010) Evolution and function of the plant cell wall synthesis-related Glycosyltransferase Family 8. Plant Physiology 153:1729-1746 PubMed
    16. Yanbin Yin*, Zhang H.*, Olman, V., Xu, Y. (2010) Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome. Proc Natl Acad Sci USA 107(14): 6310-6315 PubMed (*equal contribution)
    17. Gu, X., Glushka, J., Yanbin Yin, Xu, Y., Denny, T., Smith, J., Jiang, Y., Bar-Peled, M. (2010) Identification of UDP-4-keto-pentose/UDP-xylose synthase: a member of the 4,6-dehydratase & decarboxylase family in the devastating plant pathogenic bacterium Ralstonia solanacearum str. GMI1000, Journal of Biological Chemistry 285(12):9030-40 PubMed
    18. Yanbin Yin, Mohnen, D., Gelineo-Albersheim, I., Xu, Y., Hahn, M.G. (2010) Glycosyltransferases Family (GT8), in Plant Cell Wall Polysacharides: Biosysynthesis and Bioengineering: Annual Plant Review Series (2011) 41:167-212, Blackwell Publishing
    19. Escamilla-Trevino, L., Shen, H., Chen, F., Hernandez, T., Ray, T., Tang, Y., Yanbin Yin, Xu, Y., Dixon, R. (2010) Switchgrass (Panicum virgatum) possesses a divergent family of cinnamoyl CoA reductases with distinct biochemical properties. New Phytologist 185(1):143-55 PubMed
    20. Mao, F., Yanbin Yin, Zhou, F., Chou, WC, Chen, H., Zhou, C., Dam, P., and Xu, Y. (2009) pDAWG: an Integrated Database for Plant Cell-Wall Genes, Bioenergy Research 2(4):209-216
    21. Shen, H.*, Yanbin Yin*, Chen, F., Xu, Y., Dixon, R. (2009) A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production. Bioenergy Research 2(4):217-232 (*equal contribution)
    22. Yang, S., Kataeva, I., Wiegel, J., Yanbin Yin, Dam, P., Xu, Y., Westpfeling, J., Adams, MWW. (2009) Reclassification of 'Anaerocellum thermophilum' as Caldicellulosiruptor bescii strain DSM 6725T sp. nov. Int. J. Syst. Evol. Microbiol. PubMed
    23. Yanbin Yin, Huang, J., Xu, Y. (2009) The cellulose synthase superfamily in fully sequenced plants and algae. BMC Plant Biology, 9:99. BioMed|PubMed
    24. Kong, Y., Zhou, G., Avci, U., Gu, X., Jones, C., Yanbin Yin, Xu, Y., Hahn, M. (2009) Two poplar glycosyltransferase genes, PdGATL1.1 and PdGATL1.2, are functional orthologs to PARVUS/AtGATL1 in Arabidopsis. Molecular Plant, 2(5):1040-50PubMed
    25. Kataeva, IA, Yang, SJ, Dam, P., Poole, FL, Yanbin Yin, Zhou, F., Chou, W., Xu, Y., Goodwin, L., Sims, DR, Detter, JC, Hauser, LG, Westpheling, J., Adams, MWW. (2009) Genome Sequence of the Anaerobic, Thermophilic and Cellulolytic Bacterium. Journal of Bacteriology 191(11):3760-1. PubMed
    26. Huang, M., Sun, D., Lou Y., Yanbin Yin, et al. (2008) Analysis and Preparation of Oligonucletide Microarray of Apoptosis related Genes. Prog. Biochem. Biophys. 2008, 35(12): 1451~1460
    27. Yanbin Yin, Fischer, D. (2008) Identification and investigation of ORFans in the viral world. BMC Genomics 2008, 9:24. PubMed|BioMed (see how evolutionists and creationists argued on ORFans)
    28. Huang, M, Wang, Y., Sun, D., Zhu, H., Yanbin Yin, Zhang, W., Yang, S., Quan, L., Bai, J., Wang, S., Chen, Q., Li, S., Xu, N. (2006) Identification of genes regulated by Wnt/beta-catenin pathway and involved in apoptosis via microarray analysis. BMC Cancer 2006, 6:221. PubMed|BioMed
    29. Yanbin Yin, Fischer, D. (2006) On the origin of microbial ORFans: Quantifying the strength of the evidence for viral lateral transfer. BMC Evolutionary Biology 2006, 6:63. PubMed|BioMed (see how creationists use our paper to argue against Darwin - how ironic!)
    30. Qian, Z., Yanbin Yin, Zhang, Y., Lu, L., Li, Y., Jiang, Y. (2006) Genomic characterization of ribitol teichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication. BMC Genomics 2006, 7:74. PubMed|BioMed
    31. Yanbin Yin, Zhang, Y., Yu, P., Luo, J., Li S., Jiang, Y. (2005) Comparative study of apoptosis related genes in human, mouse and rat genomes. Acta Biochimica et Biophysica Sinica. 37(5), 341-8. PubMed
    32. Chen, Y., Zhang, Y., Yanbin Yin, Gao, G., Li, S., Jiang, Y., Gu, X. and Luo, J. (2005) SPD--a web-based secreted protein database. Nucleic Acids Res, 33 Database Issue, D169-173. PubMed
    33. Wang, B., Xu, Z., Xu, C., Yanbin Yin, Ding, W., Yu, H. (2004) A Study of Gridifying Scientific Computing Legacy Codes. Lecture Notes in Computer Science, 3251, 404 - 412. (Grid and Cooperative Computing - GCC 2004: Third International Conference, Wuhan, China, October 21-24, 2004. Proceedings) SpringerLink
    34. Zhang, Y., Yanbin Yin, Chen, Y., Gao, G., Yu, P., Luo, J. and Jiang, Y. (2003) PCAS--a precomputed proteome annotation database resource. BMC Genomics, 4, 42. PubMed
    35. Yanbin Yin, Luo, J., Jiang, Y. (2003) Advances in G-protein-coupled receptors and related bioinformatics study. Chinese Science bulletin, 48(6), 511-516. SciChina
    36. Jiang, Y., Gao, G., Fang, G., Gustafson, E.L., Laverty, M., Yanbin Yin, Zhang, Y., Luo, J., Greene, J.R., Bayne, M.L., Hedrick, J.A. and Murgolo, N.J. (2003) PepPat, a pattern-based oligopeptide homology search method and the identification of a novel tachykinin-like peptide. Mamm Genome, 14, 341-349. PubMed

  • INVITED/CONTRIBUTED TALKS
    • dbCAN: a web resource and database for CAZy annotation, BESC (BioEnergy Science Center) Retreat, Chattanooga, Tennessee, July 18-21, 2011
    • Constraints of biological processes on the bacterial genome arrangement, Bioinformatics Interest group in Department of Biostatistics and Bioinformatics, Emory University, November 19, 2010
    • Bioinformatics study of plant cell wall biosynthesis, Integrative BioSystems Institute, Georgia Tech, October 27, 2010
    • Evolution and Functions of Plant Cell Walls Biosynthesis-Related Enzyme Families, Department of Biochemistry and Molecular Biology, UGA, October 18, 2010
    • Evolution and Function of Glycosyltransferase Family 8, BESC Science Retreat, Asheville, North Carolina, June 21-23, 2010
    • Evolution and Function of Glycosyltransferase Family 8, CCRC, UGA, December 11, 2009
    • Computational study of the plant GT8 genes: insight about their origin and function, BESC Science Retreat, Chattanooga, Tennessee, December 1-3, 2008

  • CONFERENCE POSTERS
    • Yin, Y., Mao, X., Yang, JC, Chen, X. and Xu, Y. (2011) dbCAN: a web resource and database for CAZy annotation. BioEnergy Science Center 5th retreat
    • Zhang, J., Lee Y-C, Torres-Jerez, I., Wang, M., Yanbin Yin, Chou, WC., He, J., Shen, H., Xu, Y., Saha, M., Tang, Y., Dixon, R., Udvardi, M. (2011) A gene index and gene expression atlas for gene discovery and characterization in switchgrass. BioEnergy Science Center 5th retreat
    • Escamilla-Trevino, L., Shen, H., Hernandez, T., Yanbin Yin, Xu, Y., Dixon, R. (2011) Relationship between the biosynthesis of lignin and chlorogenic acid in switchgrass, BioEnergy Science Center 5th retreat
    • Srivastava AC, Yanbin Yin, Ma J, Lindquist E, Xu Y, Blancaflor EB, Tang Y (2011) Identifying Novel Transcripts Involved In Secondary Cell Wall From Vascular Tissues Of Switchgrass (Panicum virgatum L. cv Alamo) Using Genomics Tools. Plant & Animal Genomes XIX Conference
    • Escamilla-Trevino, L., Shen, H., Chen, F., Hernandez, T., Tang, Y., Yanbin Yin, Xu, Y., Dixon, R. (2010) Characterizing switchgrass genes encoding monolignol biosynthesis pathway enzymes. BioEnergy Science Center 4th retreat
    • Zhang, J., Lee Y-C, Torres-Jerez, I., Worley, E., Yang, J., Wang, M., He, J., Pennacchio, C., Lindquist, E., Yanbin Yin, Xu, Y., Saha, M., Tang, Y., Dixon, R., (2010) Development of resources for switchgrass functional genomics. BioEnergy Science Center 4th retreat
    • Srivastava, A.C., Ma, J., Yanbin Yin, Ray, T., Xu, Y., Blancaflor, E., Tang, Y. (2010) Laser capture microdissection (LCM) of swithgrass vascular bundles leads to the identification of potential recalcitrance genes. BioEnergy Science Center 4th retreat
    • Wang, S., Yanbin Yin, Ma, Q., Tang, X., Xu, Y. (2010) Identification and characterization of plant cell-wall related proteins through co-expression analyses. BioEnergy Science Center 4th retreat
    • Yanbin Yin, Chou, WC., Xu, Y. (2010) The carbohydrate active enzyme space in nature: sub-classification and survey in metagenomes. BioEnergy Science Center 4th retreat
    • Chou, WC, Yanbin Yin, Xu, Y. (2010) Evolutionary study of transport from the ER to the Golgi. BioEnergy Science Center 4th retreat
    • Shen, H.*, Yanbin Yin*, Chen, F., Xu, Y., Dixon, R. (2010) A systematic prediction of NAC transcription factors for improving biomass yield and quality in relation to lignocellulosic bioenergy production. 32nd Symposium on Biotechnology for Fuels and Chemicals
    • Escamilla-Trevino, L., Shen, H., Chen, F., Hernandez, T., Tang, Y., Yanbin Yin, Xu, Y., Dixon, R. (2010) Characterizing switchgrass genes encoding monolignol biosynthesis pathway enzymes. 32nd Symposium on Biotechnology for Fuels and Chemicals
    • Yanbin Yin, Chou, WC., Xu Y. (2010) Application of Phylogenomic Techniques in Studying Glycosyltransferase and Glycoside Hydrolase Families. Genomic Science 2010 Awardee Workshop VIII and Knowledgebase Workshop
    • Yanbin Yin, Chou, WC., Xu, Y. (2009) Phylogenetic sub-classification of CAZy families and application in identification of novel glycosyl hydrolases in the environmental metagenomes. BioEnergy Science Center 3rd retreat
    • Yanbin Yin, Gu, X., Bar-Peled, M., Xu, Y. (2009) Phylogenetic study of NDP-sugar interconversion enzymes: evolutionary relatedness and origin. BioEnergy Science Center 3rd retreat
    • Kong, Y., Zhou, G., Avci, U., Gu, X., Jones, C., Yanbin Yin, Xu, Y., Hahn, M. Two poplar glycosyltransferase genes, PdGATL1.1 and PdGATL1.2, are functional orthologs to PARVUS/AtGATL1 in Arabidopsis. BioEnergy Science Center 3rd retreat
    • Gu, X., Wages, C., Yanbin Yin, Xu, Y., Amor, J., Bar-Peled. M. (2009) Characterization of UDP-Xylose Synthase Like (UXSL) Enzymes in Pathogenic Bacteria. BioEnergy Science Center 3rd retreat
    • Biswal, A., Yanbin Yin, Xu, Y., Mohnen, D. (2009) Identifying recalcitrance genes target among PL1 and GT77 family. BioEnergy Science Center 3rd retreat
    • Kulkarni, A., Urbanowicz, B., Pena, M., Yanbin Yin, Xu, Y., York, W. (2009) Phylogenetic study of Xylan biosynthesis genes. BioEnergy Science Center 3rd retreat
    • Yang, S., Kataeva, I., Yanbin Yin, Dam, P., Xu, Y., Westpfeling, J., Adams, MWW. (2009) Reclassification of 'Anaerocellum thermophilum' DSM 6725 as Caldicellulosiruptor bescii comb. nov., and emended description of the genus Caldicellulosiruptor. BioEnergy Science Center 3rd retreat
    • Yanbin Yin, Chen, H., Cantwell, B., Jouline, I., Hahn, M., Mohnen, D., Xu Y. (2009) The plant cell wall biosynthesis related Galacturonosyltransferase (GAUT) and GAUT like (GATL) genes have a different origin than the other Glycosyltransferase family 8 genes. Genomics:GTL Awardee Workshop VII.
    • Yanbin Yin, Huang J., Xu Y. (2008) The cellulose synthase superfamily in fully sequenced plants and algae. CSB2008.
    • Yanbin Yin, Fischer, D. (2007) Identification and investigation of ORFans in the viral world. SMBE 2007.
    • Yanbin Yin, Fischer, D. (2006) On the origin of microbial ORFans: Quantifying the strength of the evidence for viral lateral transfer. ISMB 2006.
    • Yanbin Yin, Chen, Y., Luo, J., Gu, X., Jiang, Y. (2002) Mining for novel G-protein coupled receptors based on similarity search. The 2nd Chinese conference on Bioinformatics, 38.
    • Jiang, Y., Gao, G., Fang G., Yanbin Yin, Luo, J., Greene, J., Bayne, M., Murgolo, N. (2002) PepPat: a pattern based oligopeptide homology search algorithm. The 2nd Chinese conference on Bioinformatics, 37.
    • Zhang, Y., Yanbin Yin, Yu, P., Luo, J., Gu, X., Jiang, Y. (2002) Classifying IPI based on protein folding features and conserved domains. The 2nd Chinese conference on Bioinformatics, 36.

  • RESEARCH LINKS

  • MISCELLANEOUS

Dobzhansky, Th.
1973.
"Nothing in Biology Makes Sense Except in the Light of Evolution"
The American Biology Teacher 35: (March): 125-129.

Counters
Since 09/2006