Publications

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

Most significant publications

[P]: plant bioinformatics; [M]: microbial evolutionary genomics


Submitted

  1. Cao H^, Shimura Y, Steffen MM, Li G, Ma Q, Masanobu K, Yin Y# (2016) Harmful cyanobacterial blooms are driven by superior resource-utilizing metabolic capabilities revealed by comparative genomics and transcriptomics, submitted

  2. Fitzek E^, Balazic R+, Yin Y# (2016) Bioinformatics analysis of plant cell wall evolution. Invited chapter for "The plant cell wall: Methods and protocols. 2nd edition", Methods in Molecular Biology, submitted


    2017

  1. Huang L, Zhang H, Wu P, Entwistle S+, Li X^, Yohe T+, Yi H, Yang Z, Yin Y# (2017) dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation, Nucleic Acids Res. database issue 2018, accepted

  2. Yang X, ..., Fitzek E^, ... Yin Y, ..., Tuskan GA (2016) Kalanchoe genome reveals convergent evolution of crassulacean acid metabolism, Nature Communications, accepted

  3. Jiang X, Quan X, Zhang H, Zhan D, Yin Y (2017) Disease-related Gene Module Detection Based on A Multi-label Propagation Clustering Algorithm, PLoS One. 2017 May 19;12(5):e0178006

  4. Huo L, Zhang H, Huo X, Yang Y^, Li X^, Yin Y# (2017) pHMM-tree: Phylogeny of Profile Hidden Markov Models, Bioinformatics, 2017 Apr 1;33(7):1093-1095, doi:10.1093/bioinformatics/btw779


  5. 2016

  6. 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

  7. 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.

  8. Ekstrom A+, Yin Y# (2016) ORFanFinder: automated identification of taxonomically restricted orphan genes, Bioinformatics, pii: btw122, doi:10.1093/bioinformatics/btw122

  9. 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.


  10. 2015

  11. 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

  12. 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]

  13. 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]

  14. 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

  15. 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

  16. 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


  17. 2014

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

  19. 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. 2014 Aug 5. pii: S0031-9422(14)00278-7. doi: 10.1016/j.phytochem.2014.07.008

  20. 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

  21. Zhou C, Ma Q, Mao X, Yin Y#, Xu Y# (2014) New Insights Revealed through Comparative Genomic Analysis of 40 Clostridium Genomes, Bioenergy Research,7:1481-1492, doi: 10.1007/s12155-014-9486-9

  22. 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

  23. Cao H^, Yin Y# (2014) Rapid evolution of cellulosome modules by comparative analyses of five Clostridiales genomes. Bioenergy Research, 7:1369-1381, DOI 10.1007/s12155-014-9474-0

  24. 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]

  25. 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

  26. 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


  27. 2013

  28. 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: http://f1000.com/prime/718148808]

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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 J. 2013 Apr;74(1):160-73. doi: 10.1111/tpj.12104


  34. 2012

  35. 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

  36. Li G, Köllner TG, Yin Y, Jiang Y, Xu Y, Gershenzon J, Pichersky E, Chen F. Nonseed plant Selaginella moellendorffii has both seed plant and microbial types of terpene synthases, Proc Natl Acad Sci USA, 2012, Sep 4; 109(36):14711-5 [selected by Faculty 1000: http://f1000.com/717957718, listed as must read]

  37. Blumer-Schuette SE, Giannone RJ, Zurawski1 JV, Ozdemir I, Mistry DB, Ma Q, Yin Y, 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 Bacteriol. 2012 Aug;194(15):4015-28. Epub 2012 May 25.

  38. Mao X, Zhang H, Yin Y, Xu Y. The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces, Nucleic Acids Res., 2012 Sep 1;40(17):8210-8.

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

  40. 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.

  41. Kulkarni AR, Peña MJ, Avci U, Mazumder K, Urbanowicz BR, Pattathil S, Yin Y, O'Neill MA, Roberts AW, Hahn MG, Xu Y, Darvill AG, York WS. The ability of land plants to synthesize glucuronoxylans predates the evolution of tracheophytes. Glycobiology. 2012 Mar;22(3):439-51. Epub 2011 Nov 2. PubMed PMID: 22048859.


  42. 2011

  43. 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.

  44. 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

  45. Li G, Ma Q, Mao X, Yin Y, Zhu X, Xu Y. Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes. Nucleic Acids Res. 2011 Dec;39(22):e150. Epub 2011 Sep 29. PubMed PMID: 21965536; PubMed Central PMCID: PMC3239196.

  46. Kong Y, Zhou G, Yin Y, Xu Y, Pattathil S, Hahn MG. Molecular analysis of a family of Arabidopsis genes related to galacturonosyltransferases. Plant Physiol. 2011 Apr;155(4):1791-805. Epub 2011 Feb 7. PubMed PMID: 21300919; PubMed Central PMCID: PMC3091093.

  47. Dam P, Kataeva I, Yang SJ, Zhou F, Yin Y, Chou W, Poole FL 2nd, Westpheling J, Hettich R, Giannone R, Lewis DL, Kelly R, Gilbert HJ, Henrissat B, Xu Y, Adams MW. Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. Nucleic Acids Res. 2011 Apr;39(8):3240-54. Epub 2011 Jan 11. PubMed PMID: 21227922; PubMed Central PMCID: PMC3082886.


  48. 2010

  49. 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. [cited 12 times]

  50. 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. [cited 2 times]

  51. 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.

  52. Zhou C, Yin Y, Dam P, Xu Y. Identification of novel proteins involved in plant cell-wall synthesis based on protein-protein interaction data. J Proteome Res. 2010 Oct 1;9(10):5025-37. PubMed PMID: 20687615.

  53. 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.

  54. Gu X, Glushka J, Yin Y, Xu Y, Denny T, Smith J, Jiang Y, Bar-Peled M. Identification of a bifunctional UDP-4-keto-pentose/UDP-xylose synthase in the plant pathogenic bacterium Ralstonia solanacearum strain GMI1000, a distinct member of the 4,6-dehydratase and decarboxylase family. J Biol Chem. 2010 Mar 19;285(12):9030-40. Epub 2010 Jan 29. PubMed PMID: 20118241; PubMed Central PMCID: PMC2838324.

  55. Yang SJ, Kataeva I, Wiegel J, Yin Y, Dam P, Xu Y, Westpheling J, Adams MW. Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. nov. Int J Syst Evol Microbiol. 2010 Sep;60(Pt9):2011-5. Epub 2009 Oct 2. PubMed PMID: 19801388.


  56. 2009

  57. 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. [cited 21 times]

  58. 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; [cited 11 times]

  59. Escamilla-Treviño LL, Shen H, Uppalapati SR, Ray T, Tang Y, Hernandez T, Yin Y, Xu Y, Dixon RA. Switchgrass (Panicum virgatum) possesses a divergent family of cinnamoyl CoA reductases with distinct biochemical properties. New Phytol. 2010 Jan;185(1):143-55. Epub 2009 Sep 15. PubMed PMID: 19761442.

  60. Mao F, Yin Y, Zhou F, Chou WC, Chen H, Zhou C, Dam P, Xu Y. Computational annotation of plant and algae genomes with an emphasis on cell wall biosynthesis. Bioenergy Research 2009;2(4): 209-216

  61. Kong Y, Zhou G, Avci U, Gu X, Jones C, Yin Y, Xu Y, Hahn MG. Two poplar glycosyltransferase genes, PdGATL1.1 and PdGATL1.2, are functional orthologs to PARVUS/AtGATL1 in Arabidopsis. Mol Plant. 2009 Sep;2(5):1040-50. Epub 2009 Aug 24. PubMed PMID: 19825678.

  62. Kataeva IA, Yang SJ, Dam P, Poole FL 2nd, Yin Y, Zhou F, Chou WC, Xu Y, Goodwin L, Sims DR, Detter JC, Hauser LJ, Westpheling J, Adams MW. Genome sequence of the anaerobic, thermophilic, and cellulolytic bacterium "Anaerocellum thermophilum" DSM 6725. J Bacteriol. 2009 Jun;191(11):3760-1. Epub 2009 Apr 3. PubMed PMID: 19346307; PubMed Central PMCID: PMC2681903.


  63. 2006-2008

  64. 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. [cited 18 times]

  65. Huang ML, Sun DC, Lou YX, Yin Y, Li CY, Zhang Y, Gao G, Wang SQ, Bo XC, Wei LP, Li SG. Analysis and Preparation of Oligonucletide Microarray of Apoptosis related Genes. Prog. Biochem. Biophys. 2008, 35(12): 1451~1460

  66. 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. [cited 25 times]

  67. Qian Z, Yin Y, Zhang Y, Lu L, Li Y, Jiang Y. Genomic characterization of ribitol eichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication. BMC Genomics. 2006 Apr 5;7:74. PubMed PMID: 16595020; PubMed Central PMCID: PMC1458327.

  68. Huang M, Wang Y, Sun D, Zhu H, Yin Y, Zhang W, Yang S, Quan L, Bai J, Wang S, Chen Q, Li S, Xu N. Identification of genes regulated by Wnt/beta-catenin pathway and involved in apoptosis via microarray analysis. BMC Cancer. 2006 Sep 7;6:221. PubMed PMID: 16959035; PubMed Central PMCID: PMC1574340


  69. 2005 and earlier

  70. Chen Y, Zhang Y, Yin Y, Gao G, Li S, Jiang Y, Gu X, Luo J. SPD--a web-based secreted protein database. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D169-73. PubMed MID: 15608170; PubMed Central PMCID: PMC540047.

  71. Yin Y, Zhang Y, Yu P, Luo JC, Jiang Y, Li SG. Comparative study of apoptosis-related gene loci in human, mouse and rat genomes. Acta Biochim Biophys Sin. 2005 May;37(5):341-8. PubMed PMID: 15880263.

  72. Wang B, Xu Z, Xu C, Yin Y, Ding W, Yu H. A Study of Gridifying Scientific Computing Legacy Codes. Lecture Notes in Computer Science, 2004;3251, 404 - 412.

  73. Zhang Y, Yin Y, Chen Y, Gao G, Yu P, Luo J, Jiang Y. PCAS--a precomputed proteome annotation database resource. BMC Genomics. 2003 Nov 1;4(1):42. PubMed PMID: 14594458; PubMed Central PMCID: PMC293463.

  74. Yin Y, Luo J, Jiang Y. Advances in G-protein-coupled receptors and related bioinformatics study. Chinese Science bulletin, 2003;48(6) 511-516.

  75. Jiang Y, Gao G, Fang G, Gustafson EL, Laverty M, Yin Y, Zhang Y, Luo J, Greene JR, Bayne ML, Hedrick JA, Murgolo NJ. PepPat, a pattern-based oligopeptide homology search method and the identification of a novel tachykinin-like peptide. Mamm Genome. 2003 May;14(5):341-9. Erratum in: Mamm Genome. 2003 Aug;14(8):580. PubMed MID: 12856286.

* co-first authors, # corresponding authors