Publications

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

Most significant publications

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

Submitted

    2024

  1. Feng X^, Permann C, Holzinger A, Yin Y# (2024) High molecular weight DNA extraction from mucilage rich zygnematophycean green algae for long read DNA sequencing, BMC Methods, DOI: 10.1186/s44330-024-00018-z

  2. Kang C, Zhang H, Yin Y, (2024) A dual-modality complex-valued fusion method for predicting side effects of drug-drug interactions based on graph neural network, IEEE Journal of Biomedical and Health Informatics, DOI: 10.1109/JBHI.2024.3422673

  3. KhatrI M, Yin Y, Deogun J (2024) Enhancing Interpretability In Medical Image Classification By Integrating Formal Concept Analysis With Convolutional Neural Networks, Biomimetics 2024, 9(7), 421; https://doi.org/10.3390/biomimetics9070421

  4. Li M, Guo H, Wang K, Kang C, Yin Y, Zhang H (2024) AVBAE-MODFR: A novel deep learning framework of embedding and feature selection on multi-omics data for pan-cancer classification, Computers in Biology and Medicine, 2024 Jul:177:108614. doi: 10.1016/j.compbiomed.2024.108614.

  5. Zheng J, Huang L, Yi H, Yan Y, Zhang X, Akresi J, Yin Y# (2024) Carbohydrate-active enzyme annotation in microbiomes using dbCAN, https://www.biorxiv.org/content/10.1101/2024.01.10.575125v1, bioRxiv

  6. Nousias O^, Zheng J^, Li T^, Meinhardt L, Bailey B, Gutierrez O, Baruah IK, Cohen S, Zhang D, Yin Y#. (2024) Three de novo assembled wild cacao genomes from the Upper Amazon, Scientific Data, DOI : 10.1038/s41597-024-03215-1

  7. Zhan X, Yin Y and Zhang H (2024) BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework, Bioinformatics, https://doi.org/10.1093/bioinformatics/btae127

  8. Li T^, Zheng J^, Nousias O^, Meinhardt L, Goenaga R, Zhang D, Yin Y#. (2024) The cherimoya genome reveals insights into the intra-specific divergence, the evolution of Magnoliales, and a putative gene cluster for acetogenin biosynthesis, Plants, 2024, 13(5), 636; https://doi.org/10.3390/plants13050636

  9. Dexheimer S^, Shrestha N, Chapagain BS^, Bujarski J#, Yin Y# (2024) Characterization of Multivariate RNAs Encapsidated During Infection by Two Bromoviruses Based on ViReMa, Pathogens, 2024, 13(1), 96; https://doi.org/10.3390/pathogens13010096

  10. Feng X*, Zheng J*, Irisarri I*, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen J, DadrasA, Zegers J, Rieseberg TP, Ashok AD, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ben-Ari J, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J#, Yin Y# (2023), Genomes of multicellular algal sisters to land plants illuminate signaling network evolution, https://www.biorxiv.org/content/10.1101/2023.01.31.526407v1, bioRxiv, Nature Genetics, https://doi.org/10.1038/s41588-024-01737-3, highlighed at Nature Plants

    11. 2023

  11. Han M, Yin Y, Zhang H, Wang H (2023) Hierarchical Semantic Augmentation Graph Neural Network for Drug-Disease Association Prediction, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), DOI: 10.1109/BIBM58861.2023.10385961

  12. Quan X, Guo X, Zhang H, Han M, Li Z, and Yin Y (2023) Unsupervised Feature Selection by Fusing Spectral Clustering and Locality Preserving Projection, DOI: 10.1109/BIBM58861.2023.10385296

  13. Yan Y^, Zheng J^, Zhang X^, Yin Y#. (2023) dbAPIS: a database of anti-prokaryotic immune system genes, Nucleic Acids Res. 10.1093/nar/gkad932

  14. Sandesh SP, Zheng J^, Yin Y, Lorber S, Puel O, Dhingra S, Espeso EA, Calvo AM (2023) Homeobox Transcription Factor HbxA Influences Expression of over One Thousand Genes in the Model Fungus Aspergillus nidulans, PLoS ONE, 18(7): e0286271. https://doi.org/10.1371/journal.pone.0286271

  15. Han M, Li W, Zhang H, Yin Y (2023) Semantic-guided Graph Neural Network for Heterogeneous Graph Embedding (2023), Expert Systems With Applications, 232, 1 December 2023, 120810, https://doi.org/10.1016/j.eswa.2023.120810

  16. Yang B*, Khatri M*, Zheng J, Deogun J, Yin Y# (2023) Genome mining for anti-CRISPR operons using machine learning, Bioinformatics, doi:10.1093/bioinformatics/btad309

  17. Zheng J*, Ge Q*, Yan Y, Zhang X, Huang L, Yin Y# (2023) dbCAN3: automated carbohydrate-active enzyme and substrate annotation, Nucleic Acids Res., doi:10.1093/nar/gkad328

    18. 2022

  18. Huang W, Zhang H, Li Z, and Yin Y (2022) Mutual Information Estimation-Based Disentangled Representation Network for Medical Image Fusion, IEEE International Conference on Bioinformatics and Biomedicine 2022 (IEEE BIBM 2022), Las Vegas, NV, USA, 2022 pp. 991-998. doi: 10.1109/BIBM55620.2022.9995221, selected for Best Student Paper Award

  19. Yang B^, Zheng J^, Yin Y# (2022) AcaFinder: genome mining of anti-CRISPR associated genes in bacteria and phages, mSystems, doi:10.1128/msystems.00817-22, https://www.biorxiv.org/content/10.1101/2022.08.29.505781v1.abstract

  20. Zheng J^, Hu B^, Zhang X^, Ge Q^, Yan Y^, Piyush V^, Huang L, Yin Y# (2022) dbCAN-seq update: CAZyme gene clusters and substates in microbiomes, Nucleic Acids Res., doi:10.1093/nar/gkac1068

  21. Wei H, Li Y, Yan J, Peng S, Wei S, Yin Y, Li K, Cheng X (2022) Root cell wall remodeling: a way for exopolysaccharides to mitigate cadmium toxicity in rice seedling, accepted, Journal of Hazardous Materials

  22. Li W, Zhang H, Li M, Han M, Yin Y (2022) MGEGFP: a multi-view graph embedding method for gene function prediction based on adaptive estimation with GCN, Briefings in Bioinformatics 2022 Aug 10:bbac333. doi: 10.1093/bib/bbac333

  23. Li T^, Yin Y# (2022) Critical assessment of pan-genomics of metagenome-assembled genomes, bioRxiv, doi: https://doi.org/10.1101/2022.01.13.476228, Briefings in Bioinformatics 2022, doi: 10.1093/bib/bbac413

    24. 2021

  24. Zheng J^, Meinhardt L, Goenaga R, Matsumoto T, Zhang D, Yin Y# (2021) The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes, Horticulture Research, 2022 Feb 11;9:uhac014. doi: 10.1093/hr/uhac014.

  25. Wang X, Wang J, Huang S, Zhang H, Yin Y. HDMC: a novel deep learning based framework for removing batch effects in single-cell RNA-seq data, Bioinformatics, 2021, doi:10.1093/bioinformatics/btab821

  26. Zheng B^, He Y+, Zhang P+, Huo YX, Yin Y# (2021) Polyphenol utilization proteins in human gut microbiome, Applied and Environmental Microbiology, https://doi.org/10.1128/AEM.01851-21

  27. Kang C, Zhang H, Liu Z, Huang S, Yin Y (2021) LR-GNN: a graph neural network based on link representation for predicting molecular associations, Briefings in Bioinformatics, 2021, DOI: 10.1093/bib/bbab513

  28. Jin C, Shi Z, Zhang H, and Yin Y (2021) Predicting lncRNA–protein interactions based on graph autoencoders and collaborative training. IEEE International Conference on Bioinformatics and Biomedicine 2021 (IEEE BIBM 2021)

  29. Li W, Zhang H, Zhao Q, Liu, J and Yin Y (2021) Adversarial Dual-Channel Variational Graph Autoencoder for Synthetic Lethality Prediction in Human Cancers. IEEE International Conference on Bioinformatics and Biomedicine 2021 (IEEE BIBM 2021)

  30. Cheng X*, Yang B^*, Zheng J^, Wei H, Feng X^ and Yin Y# (2021) Cadmium stress triggers significant metabolic reprogramming in Enterococcus faecium CX 2-6, Computational and Structural Biotechnology Journal, https://doi.org/10.1016/j.csbj.2021.10.021

  31. Shi Z, Zhang H, Jin C, Quan X, Yin Y (2021) A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations. BMC Bioinformatics. 2021 Mar 21;22(1):136. doi: 10.1186/s12859-021-04073-z.

  32. Peterson D^, Li T^, Calvo AM, Yin Y# (2021) Categorization of orthologous gene clusters in 92 Ascomycota genomes reveals functions important for phytopathogenicity, Journal of Fungi, 2021, 7(5), 337; https://doi.org/10.3390/jof7050337

  33. Zheng J^, Meinhardt L, Goenaga R, Zhang D, Yin Y# (2021) The chromosome-level genome of dragon fruit reveals whole genome duplication and chromosomal co-localization of betacyanin biosynthetic genes, Horticulture Research, 8, 63 (2021). https://doi.org/10.1038/s41438-021-00501-6

  34. Feng X^, Holzinger A, Permann C, Anderson C, Yin Y# (2021) Characterization of two Zygnema strains (Zygnema circumcarinatum SAG 698-1a and SAG 698-1b) and a rapid method to estimate nuclear genome size of Zygnematophycean green algae, Frontiers in Plant Science, 2021 Feb 10;12:610381, 10.3389/fpls.2021.610381

  35. Li W, Zhao Q, Zhang H, Quan X, Xu J, and Yin Y (2021) Bayesian Multi-scale Convolutional Neural Network for Motif Occupancy Identification, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 293-298, doi: 10.1109/BIBM49941.2020.9313556

    36. 2020

  36. Huang L^*, Yang B^*, Yi H^, Asif A, Wang J, Lithgow T, Zhang H, Minhas F, Yin Y# (2020) AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses, Nucleic Acids Res., 10.1093/nar/gkaa857

  37. Ausland C^, Zheng J^, Yi H^, Yang B^, Li T^, Feng X^, Zheng B^, Yin Y#. (2020) dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates, Nucleic Acids Res., 10.1093/nar/gkaa742

  38. Fitzek E.^, Balazic R.+, Yin Y#. (2020) Bioinformatics Analysis of Plant Cell Wall Evolution. In: Popper Z. (eds) The Plant Cell Wall. Methods in Molecular Biology, vol 2149. Humana, New York, NY, https://doi.org/10.1007/978-1-0716-0621-6_27

  39. Cao H^, Shimura Y, Steffen MM, Yang Z, Lu J, Joel A, Jenkins L, Kawachi M, Yin Y#, Garcia-Pichel F#. (2020). The trait repertoire enabling cyanobacteria to bloom assessed through comparative genomic complexity and metatranscriptomics. mBio 11:e01155-20. https://doi.org/10.1128/mBio.01155-20.

  40. Wang X, Yi H, Wang J, Zhan D, Yin Y, Zhang H (2020) GDASC: A GPU parallel based web server for detecting hidden batch factors, Bioinformatics, 2020 May 9:btaa427. doi: 10.1093/bioinformatics/btaa427

  41. Yi H^, Huang L^, Yang B^, Zhang H, Yin Y# (2020) AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses, Nucleic Acids Res., doi:10.1093/nar/gkaa351

  42. Orton L^, Fitzek E^, Feng X^, Grayburn SW, Mower JP, Liu K, Zhang C, Duvall MR, Yin Y# (2020) Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution, Journal of Experimental Botany, 2020 Mar 24. pii: eraa149. doi: 10.1093/jxb/eraa149.

  43. Becker B, Feng X^, Yin Y, Holzinger A (2020) Desiccation tolerance in streptophyte algae and the algae to land plant transition: Evolution of LEA and MIP protein families within the Viridiplantae, Journal of Experimental Botany, 2020 Feb 28. pii: eraa105. doi: 10.1093/jxb/eraa105

    44. 2019

  44. Su X, Xu J, Yin Y, Quan X, Zhang H (2019) Antimicrobial Peptide Identification Using Multi-scale Convolutional Network, BMC Bioinformatics 20, 730 (2019). https://doi.org/10.1186/s12859-019-3327-y

  45. Xu J, Zhang H, Zheng J^, Dovoedo P^, Yin Y# (2019) eCAMI: simultaneous classification and motif identification for enzyme annotation, Bioinformatics, doi:10.1093/bioinformatics/btz908

  46. Li W, Yin Y, Quan X, Zhang H (2019) Gene Expression Value Prediction Based on XGBoost Algorithm, Frontiers in Genetics, doi: 10.3389/fgene.2019.01077

  47. Satterlee T, Entwistle S, Yin Y, Cary J, Lebar M, Losada L, Calvo A (2019) rmtA-Dependent Transcriptome and its Role in Secondary Metabolism, Environmental Stress, and Virulence in Aspergillus flavus, G3: Genes Genomes Genetics, g3. doi.org/10.1534/g3.119.400777

  48. Yin Y#, Yang B^, Entwistle S^ (2019) Bioinformatics identification of anti-CRISPR loci using homology, guilt-by-association, and CRISPR self-targeting spacer approaches, mSystems, doi:10.1128/mSystems.00455-19

  49. Fitzek E^, Orton F^, Entwistle S^, Grayburn SW, Ausland C^, Duvall DR, Yin Y# (2019) Cell wall enzymes in Zygnema circumcarinatum UTEX 1559 respond to osmotic stress in a plant-like fashion, Frontiers in Plant Science, doi: 10.3389/fpls.2019.00732

  50. Han W, Fan X, Teng L, Kaczurowski M, Zhang X, Xu D, Yin Y, Ye X (2018), Classification, Evolution and Function of putative Xylosyltransferases from Algae, Protoplasma. 2019 Apr 3. doi: 10.1007/s00709-019-01358-2.

  51. Entwistle S, Li X, Yin Y# (2018) Orphan genes shared by pathogenic genomes are more associated with bacterial pathogenicity, mSystems, 4(1). pii: e00290-18, doi:10.1128/mSystems.00290-18

    52. 2018

  52. Cary J, Entwistle S, Satterlee T, Mack B, Gilbert M, Chang P, Scharfenstein L, Yin Y, Calvo A (2018) The transcriptional regulator Hbx1 affects the expression of thousands of genes in the aflatoxin-producing fungus Aspergillus flavus, G3: Genes Genomes Genetics, g3. 200870.2018

  53. Wu G, Jurick W, Yin G, Yu J, Peng H, Gaskins V, Yin Y, Hua S, Peter K, Bennett J (2018) Penicillium expansum and Penicillium solitum comparative genomics yields new insights into phylogeny and candidate genes involved in postharvest apple-fungus interactions, Peer J, DOI:10.7287/peerj.preprints.27430v1

  54. Lyu Q*, Zhang K, Zhu Q, Li Z, Liu Y, Fitzek E^, Yohe Y+, Zhao L, Li W, Liu T, Yin Y, Liu W (2018), Structural and biochemical characterization of a multidomain alginate lyase reveals a novel role of CBM32 in CAZymes., Biochim Biophys Acta. 2018 Jun 1;1862(9):1862-1869.

  55. Driscoll CB, Meyer KA, Šulčius S, Brown NM, Dick GJ, Cao H^, Gasiūnas G, Timinskas A, Yin Y, Landry ZC, Otten TG, Davis TW, Watson SB, Dreher TW (2018), A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales, Harmful Algae, Volume 77, July 2018, Pages 93–107

  56. Zhang H*, Yohe T*+, Huang L, Entwistle S^, Wu P, Yang Z, Busk P, Xu Y, Yin Y# (2018) dbCAN2: a meta server for automated carbohydrate-active enzyme annotation, Nucleic Acids Res. Web server issue 2018, doi:10.1093/nar/gky418

  57. Han W, Ibarra G, Gupta M, Yin Y, Elsawa S (2018), Elevated Expression of GLI3 in Germinal Center Diffuse Large B Cell Lymphoma, Leukemia and Lymphoma, 2018 Feb 21:1-3. doi: 10.1080/10428194.2018.1439169

    58. 2017

  58. 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, 46 (D1), D516-D521, doi:10.1093/nar/gkx894

  59. Yang X, ..., Fitzek E^, ... Yin Y, ..., Tuskan GA (2017) The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism, Nature Communications 8:1899, doi:10.1038/s41467-017-01491-7

  60. Jiang X, Zhang H, Quan X, Yin Y (2017) A Heterogeneous Networks Fusion Algorithm Based on Local Topological Information for Neurodegenerative Disease, Current Bioinformatics 12 (5), 387-397

  61. 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

  62. 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

    63. 2016

  63. 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

  64. 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.

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

  66. 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.

    67. 2015

  67. 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

  68. 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]

  69. 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]

  70. 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

  71. 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

  72. 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

    73. 2014

  73. 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]

  74. 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

  75. 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

  76. 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

  77. 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

  78. 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

  79. 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]

  80. 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

  81. 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

    82. 2013

  82. 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]; ESI Highly Cited (Top 1%) Paper in Plant & Animal Science field

  83. 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

  84. 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

  85. 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

  86. 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

  87. 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

    88. 2012

  88. 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

  89. 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]

  90. 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.

  91. 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.

  92. 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]

  93. 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.

  94. 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.

    95. 2011

  95. 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.

  96. 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

  97. 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.

  98. 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.

  99. 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.

    100. 2010

  100. 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]

  101. 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]

  102. 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.

  103. 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.

  104. 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.

  105. 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.

  106. 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.

    107. 2009

  107. 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]

  108. 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]

  109. 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.

  110. 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

  111. 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.

  112. 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.

    113. 2006-2008

  113. 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]

  114. 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

  115. 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]

  116. 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.

  117. 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

    118. 2005 and earlier

  118. 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.

  119. 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.

  120. 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.

  121. 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.

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

  123. 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