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Photo of Yanbin YinYanbin Yin

assiociate professor

Research Interests

We are generally interested in using bioinformatics approaches to analyze different types of biological omics data such as sequence, structure, expression and pathway data, in order to gain a better understanding of the function and evolution of biological molecules at the systems biology level.

Plant cell walls: 

Plant cell walls (the main component of plant biomass / dry materials) are composed of the most abundant biopolymers in nature (cellulose, hemicellulose and lignin), and represent the most promising renewable resource for producing biofuels and biomaterials. Using bioinformatics techniques, we study genomics, transcriptomics, epigenomics, metabolomics data of model plants and focus on the proteins (mostly enzymes) involved in plant cell wall synthesis and modification, with the goal to derive new hypothesis/insights into their functions and to understand how plant cell walls have evolved.

Carbohydrate active enzymes (CAZymes): 

CAZymes are responsible for the synthesis, degradation, modification and recognition of all carbohydrates on Earth. They are also the most important enzymes used for biomass formation and degradation to produce biofuels. We identify these enzymes in plants, algae, microbes and environmental metagenomes and do comparative analysis.

Database and web servers: 

We maintain the web resource dbCAN, dedicated to functional domain-based CAZyme annotation for newly sequenced genomes/metagenomes. We also build bioinformatics tools, servers and databases for other important industrial enzymes

Evolutionary genomics: 

We look into ncRNAs, small RNAs, microRNAs, intrinsic disordered proteins and ORFans in plant, microbial genomes and metagenomes to understand their evolution and function.

 Photo of Yanbin Yin Lab

For more information, see our lab webpage at: http://cys.bios.niu.edu/

Representative Publications

Corresponding authors, ^NIU grad students/postdoc,
+Undergraduate student, * co-first authors

Huo L, Zhang H, Huo X, Yang Y^, Li X^, Yin Y# (2016) pHMM-tree: Phylogeny of Profile Hidden Markov Models, Bioinformatics, doi:10.1093/bioinformatics/btw779

Wysocki W, Riuz-Sanches E, Yin Y, Duvall M (2016) The floral transcriptomes of four bamboo species (Bambusoideae; Poaceae): support for common ancestry among woody bamboos, BMC Genomics, 17:384, DOI: 10.1186/s12864-016-2707-1

Yu J, Wu G, Jurick WM, Jr, Gaskins VL, Yin Y, Yin G, Bennett JW, Shelton DR. (2016) Genome sequence of Penicillium solitum RS1, which causes postharvest apple decay. Genome Announc 4(3):e00363-16. doi:10.1128/genomeA.00363-16.

Ekstrom A+, Yin Y# (2016) ORFanFinder: automated identification of taxonomically restricted orphan genes, Bioinformatics, 2016 Jul 1;32(13):2053-5. doi: 10.1093/bioinformatics/btw122

Hu L, Taujale R^, Song J, Guo J, Yin Y# (2016) Draft genome sequence of Talaromyces verruculosus ("Penicillium verruculosum") strain TS63-9, a fungus with great potential for industrial production of polysaccharide-degrading enzymes, Journal of Biotechnology, 2016 Feb 10;219:5-6. doi: 10.1016/j.jbiotec.2015.12.017.

Yang X, Leeben-Mack J, Chen F, Yin Y (2015) Plant Comparative and Functional Genomics, International Journal of Genomics, 2015:924369. doi: 10.1155/2015/924369

Nguyen M+, Ekstrom A+, Li X^ and Yin Y# (2015) HGT-Finder: a new tool for horizontal gene transfer finding and application to Aspergillus genomes, Toxins, 7(10):4035-4053; doi:10.3390/toxins7104035 [highly accessed article]

Cary JW*, Han Z*, Yin Y*, Lohmar JM, Shantappa S, Harris-Coward PY, Mack B, Ehrlich KC, Wei Q, Arroyo-Manzanares N, Uka V, Vanhaecke L, Bhatnagar D, Yu J, Nierman WC, Johns MA, Sorensen D+, Shen H^, De Saeger S, Diana Di Mavungu J, Calvo AM. (2015) Transcriptome analysis of Aspergillus flavus reveals veA-dependent regulation of secondary metabolite gene clusters, including the novel aflavarin cluster. Eukaryot Cell 14:983-997. doi:10.1128/EC.00092-15. [Articles of Significant Interest Selected from This Issue by the Editors]

Taujale R^, Yin Y# (2015) Glycosyltransferase family 43 is also found in early eukaryotes and has three subfamilies in Charophycean green algae, PLoS ONE, doi:10.1371/journal.pone.0128409

Cao H^, Ekstrom A+, Yin Y# (2015) Plant carbohydrate active enzyme (CAZyme) repertoires: a comparative study, invited book chapter for "Advances in the Understanding of Biological Sciences using Next Generation Sequencing (NGS) Approaches", Springer publishing, 10.1007/978-3-319-17157-9_8, p115-134

Cui J, Yin Y, Ma Q, Wang G, Olman V, Zhang Y, Chou WC, Hong CS, Zhang C, Cao S, Mao X, Li Y, Qin S, Zhao S, Jiang J, Hastings P, Li F, Xu Y. (2015) Comprehensive Characterization of the Genomic Alterations in Human Gastric Cancer. Int J Cancer. 2014 Nov 24. doi: 10.1002/ijc.29352

Ekstrom A+, Taujale R^, McGinn N+, Yin Y# (2014) PlantCAZyme: a database for plant carbohydrate-active enzymes, Database (Oxford), DOI: 10.1093/database/bau079, PMID: 25125445 [Undergraduate Research and Artistry Day award of NIU]

Cao H^, Yin Y# (2014) Rapid evolution of cellulosome modules by comparative analyses of five Clostridiales genomes. Bioenergy Research, DOI 10.1007/s12155-014-9474-0

Yin Y#, Johns MA, Cao H^, Rupani M^ (2014) A survey of the genomes and transcriptomes of diverse plants and algae reveals new insights into the evolution and function of the cellulose synthase superfamily, BMC Genomics, 15:260, DOI: 10.1186/1471-2164-15-260 [highly accessed article], PMID: 24708035

Cao H^, Shimura Y, Masanobu K, Yin Y# (2014) Draft genome sequence of the toxic bloom-forming cyanobacterium Aphanizomenon flos-aquae NIES-81. Genome Announc. 2(1):e00044-14. doi:10.1128/genomeA.00044-14, PMID: 24526634

Zhou C, Ma Q, Mao X, Yin Y#, Xu Y# (2014) New Insights Revealed through Comparative Genomic Analysis of 40 Clostridium Genomes, Bioenergy Research, doi: 10.1007/s12155-014-9486-9

Zhao Q, Zeng Y, Yin Y, Pu Y, Jackson LA, Engle NL, Martin MZ, Tschaplinski TJ, Ding SY, Ragauskas AJ, Dixon RA (2014) Pinoresinol reductase 1 impacts lignin distribution during secondary cell wall biosynthesis in Arabidopsis, Phytochemistry, pii: S0031-9422(14)00278-7. doi: 10.1016/j.phytochem.2014.07.008, PMID: 25107662

Yu J, Jurick WM, Cao H^, Yin Y, Gaskins VL, Losada L, Zafar N, Kim M, Bennett JW, Nierman WC (2014) Draft genome sequence of Penicillium expansum (R19) that causes postharvest decay of apple fruit. Genome Announcements, 2(3):e00635-14. doi:10.1128/genomeA.00635-14, PMID: 24948776

Zhou C, Mao F, Yin Y, Huang J, Gogarten JP, et al. (2014) AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees. PLoS ONE 9(6): e98844. doi:10.1371/journal.pone.0098844, PMID: 24892935

Escamilla-Trevino L, Shen H, Hernandez T, Yin Y, Xu Y, and Dixon RA (2014) Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.) Plant Mol Biol. 2014 Mar;84(4-5):565-76. doi: 10.1007/s11103-013-0152-y. Epub 2013 Nov 5

Zhao Q, Nakashima Q, Chen F, Yin Y, Yun J, Shao H, Wang X, and Dixon RA (2013) LACCASE is necessary and non-redundant with PEROXIDASE for lignin polymerization during vascular development in Arabidopsis thaliana. Plant Cell, 2013 Oct;25(10):3976-87. doi: 10.1105/tpc.113.117770 [selected by Faculty 1000: https://www.ncbi.nlm.nih.gov/pubmed/24143805

Liu J, Duan X, Sun J, Yin Y, Li G, Wang L, Liu B (2013) Bi-factor Analysis Based on Noise-reduction (BIFANR): A New Algorithm for Detecting Coevolving Amino Acid Sites in Proteins. Plos ONE, 2013 Nov 20;8(11):e79764. doi: 10.1371/journal.pone.0079764

Ma Q, Liu B, Zhou C, Yin Y, Li G, Xu Y (2013) An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale. Bioinformatics. 2013 Sep 15;29(18):2261-8

Yin Y# (2013) Databases for bioenergy-related enzymes. Chapter 6 of Bioenergy Research: Advances & Applications, Elsevier Publishing, edited by Gupta VJ et al., 95-107

Ma Q*, Yin Y*, Schell M, Li G, Xu Y (2013) Elucidation of the Dynamic Supercoil Structures of folded E. coli Chromosome: a computational approach, Nucleic Acids Research, 2013 Jun 1;41(11):5594-5603. Epub 2013 Apr 17

Zhang JY, Lee YC, Torres-Jerez I, Wang M, Yin Y, Chou WC, He J, Shen H, Srivastava AC, Pennacchio C, Lindquist E, Grimwood J, Schmutz J, Xu Y, Sharma M, Sharma R, Bartley LE, Ronald PC, Saha MC, Dixon RA, Tang Y, Udvardi MK (2013) Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.). Plant Journal. 2013 Apr;74(1):160-73. doi: 10.1111/tpj.12104

Li G, Köllner TG, Yin Y, 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)

 Wang S*, Yin Y*, Ma Q, Tang X, Xu Y. Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis. BMC Plant Biology, 2012, 12:138

Yin Y*, Mao X*, Yang JC, Chen X and Xu Y. dbCAN: a web resource for automated carbohydrate-active enzyme annotationNucleic Acids Res. 2012 Jul;40(Web Server issue):W445-51 [selected by DOE's Bioenergy Science Centers as one of the Key Advances for Biofuels Production]

Zhang H*, Yin Y*, Olman V, Xu Y. Genomic arrangement of regulons in bacterial genomes. PLoS One. 2012;7(1):e29496. Epub 2012 Jan 3. PubMed PMID: 22235300; PubMed Central PMCID: PMC3250446.

Yin Y, Huang J, Gu X, Bar-Peled M, Xu Y. Evolution of plant nucleotide-sugar interconversion enzymes. PLoS One. 2011;6(11):e27995. Epub 2011 Nov 18. PubMed PMID: 22125650; PubMed Central PMCID: PMC3220709.

Yin Y, Mohnen D, Xu Y, Hahn M Glycosyltransferase Family 8 (GT8). Book chapter of “Plant Cell Wall Polysaccharides: Biosynthesis and Bioengineering”; Annual Plant Review series (Blackwell), 2011;41:167-212 

Yin Y, Chen H, Hahn MG, Mohnen D, Xu Y. Evolution and function of the plant cell wall synthesis-related glycosyltransferase family 8. Plant Physiol. 2010 Aug;153(4):1729-46. Epub 2010 Jun 3. PubMed PMID: 20522722; PubMed Central MCID: PMC2923890.

Yin Y*, Zhang H*, Olman V, Xu Y. Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome. Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6310-5. Epub 2010 Mar 22. PubMed PMID: 20308592; PubMed Central PMCID: PMC2851940.

Chou WC, Yin Y, Xu Y. GolgiP: prediction of Golgi-resident proteins in plants. Bioinformatics. 2010 Oct 1;26(19):2464-5. Epub 2010 Aug 23. PubMed PMID: 20733061; PubMed Central PMCID: PMC2944200.

Zhao Q, Wang H, Yin Y, Xu Y, Chen F, Dixon RA. Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch. Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14496-501. Epub 2010 Jul 26. PubMed PMID: 20660755; PubMed Central PMCID: PMC2922545.

Yin Y, Huang J, Xu Y. The cellulose synthase superfamily in fully sequenced plants and algae. BMC Plant Biol. 2009 Jul 31;9:99. PubMed PMID: 19646250; PubMed Central PMCID: PMC3091534.

Shen H*, Yin Y*, Chen F, Xu Y, Dixon R. A bioinformatic analysis of NAC genes for plant cell wall development in relation to lignocellulosic bioenergy production. Bioenergy Research 2009;2(4):217-232

Yin Y, Fischer D. Identification and investigation of ORFans in the viral world. BMC Genomics. 2008 Jan 19;9:24. PubMed PMID: 18205946; PubMed Central PMCID: PMC2245933.

Yin Y, Fischer D. On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer. BMC Evol Biol. 2006 Aug 16;6:63. PubMed PMID: 16914045; PubMed Central PMCID: PMC1559721.

 

Curriculum Vitae

Degrees

Postdoc and research scientist in Bioinformatics, 2005-2012, University of Georgia, University at Buffalo (SUNY)

Ph.D. in Biology (Bioinformatics), 2005, Peking University, China

B.S. in Biochemistry, 2000, Yantai University, China

Field of Interest: Bioinformatics and Evolutionary Genomics

Contact

Professor Yanbin Yin
Email
: yyin@niu.edu
Office:
MO 325A
Phone: (815) 753-8963
Lab: MO 429
Phone: (815) 753-3405

Yanbin Yin Lab Website

Current Funding:
NIH: 1R15GM114706