Google scholar


  1. Moses H. Stamboulian, Sujun Li, Yuzhen Ye. Using high abundance proteins as guides for fast and effective peptide/protein identification from metaproteomic data (paper)
  2. Tony J. Lam, Moses Stamboulian, Wontack Han, Yuzhen Ye. Pathway-based and phylogenetically adjusted quantification of metabolic interaction between microbial species (paper)


  1. Kaiyuan Liu, Sujun Li, Lei Wang, Yuzhen Ye, and Haixu Tang. Full-spectrum prediction of peptides tandem mass spectra using deep neural network. Anal. Chem. 2020, 92, 6, 4275–4283. (paper)
  2. Tony J. Lam and Yuzhen Ye. Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes. BMC Genomics 20, 567 (2019) doi:10.1186/s12864-019-5922-8. (paper)
  3. Sujun Li, Haixu Tang and Yuzhen Ye. A meta-proteogenomic approach to peptide identification incorporating assembly uncertainty and genomic variation. Molecular & Cellular Proteomics, 2019, mcp.TIR118.001233; (paper)
  4. Fatemeh Sharifi and Yuzhen Ye, MyDGR: A server for identification and characterization of diversity-generating retroelements. NAR, gkz329,, 2019 (paper; server)
  5. Wontack Han and Yuzhen Ye, A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data. PSB 2019. (paper link; software)
  6. Ursel Schuette, Jeremiah Henning, Yuzhen Ye, Anna Bowling, Fames Ford, Helene Genet, Mark Waldrop, Merritt Turetsky, Jeffrey White and James Bever. Effect of permafrost thaw on plant and soil fungal community in the boreal forest: Does fungal community change mediate plant productivity response? Journal of Ecology., 2019 (paper)
  7. Tony Lam and Yuzhen Ye, CRISPRs for strain tracking and their application to microbiota transplantation data analysis. The CRISPR journal, (paper; software)
  8. Dazhi Jiao, Wontack Han and Yuzhen Ye. Functional association prediction by community profiling. Methods, in press, 2017 (paper link; software)
  9. Quan Zhang and Yuzhen Ye. Not all predicted CRISPR-Cas systems are equal: Isolated cas genes and classes of CRISPR like elements. BMC Bioinformatics, 18:92, 2017 (paper link; companion webserver)
  10. Wontack Han, Mingjie Wang and Yuzhen Ye. A concurrent subtractive assembly approach for identification of disease associated sub-metagenomes. RECOMB 2017: Research in Computational Molecular Biology pp 18-33 (paper link; software)
  11. Haixu Tang, Sujun Li and Yuzhen Ye. A graph-centric approach for metagenome-guided peptide and protein identification in metaproteomics. PLOS Computational Biology 12 (12), e1005224 (2016) (paper link; software)
  12. Geoffrey L. House, Saliya Ekanayake, Yang Ruan, Ursel M. E. Schütte, Wittaya Kaonongbua, Geoffrey Fox, Yuzhen Ye, and James D. Bever. Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering. Appl. Environ. Microbiol, 82:4921-4930 (2016) (paper link)
  13. Sutichot Nimkulrat, Heewook Lee, Thomas G Doak, and Yuzhen Ye. Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola. Front. Microbiol. 7:852. doi: 10.3389/fmicb.2016.00852 (2016) (paper link)
  14. Yuzhen Ye and Quan Zhang. Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data. RNA, 22(7): p. 945-56 (2016) (paper link)
  15. Mingjie Wang, Thomas G. Doak and Yuzhen Ye. Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes. Genome Biology, 16:243, DOI: 10.1186/s13059-015-0804-0 (2015) (paper link | software)
  16. Yuzhen Ye and Haixu Tang. Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. Accepted to RECOMB-Seq 2015 and Bioinformatics (special issue for RECOMB-Seq); Bioinformatics, 32(7): 1001-1008. doi: 10.1093/bioinformatics/btv510 (2016) (paper link | software)
  17. Guanhui Bao, Mingjie Wang, Thomas G. Doak and Yuzhen Ye. Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota. Front. Microbiol. 6:896. doi: 10.3389/fmicb.2015.00896 (2015) (paper | see more papers in the Research Topic, From Genes to Species: Novel Insights from Metagenomics)
  18. Mingjie Wang, Haixu Tang and Yuzhen Ye. Identification and characterization of accessory genomes in bacterial species based on genome comparison and metagenomic recruitment. IEEE BIBM pp. 17-24 (2014) (Author's manuscript)
  19. Yuzhen Ye. Identification of diversity-generating retroelements in human microbiomes. Int. J. Mol. Sci. 15(8), 14234-14246; doi:10.3390/ijms150814234 (2014) (paper | software & data | see other papers in the special issue of 'Metagenomics: a Powerful Lens Viewing the Microbial World')
  20. Wazim M. Ismail, Yuzhen Ye and Haixu Tang. Gene finding in metatranscriptomic sequences. Proceeding of RECOMB Satellite Workshop on DNA sequencing (RECOMB-seq, published as a special issue in BMC Bioinformatics), BMC Bioinformatics, 15(Suppl 9):S8 (2014) (paper link | software)
  21. Zhanwen Li, Padmaja Natarajan, Yuzhen Ye, Thomas Hrabe and Adam Godzik. POSA: a user-driven, interactive multiple protein structure alignment server. Nucl. Acids Res, doi: 10.1093/nar/gku394 (2014) (paper link | server)
  22. Quan Zhang, Thomas G. Doak and Yuzhen Ye. Expanding the catalog of cas genes with metagenomes. Nucleic Acids Research, 42(4): 2448-2459 (2014) (paper link | data)
  23. Quan Zhang, Mina Rho, Haixu Tang, Thomas G. Doak and Yuzhen Ye. CRISPR–Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes. Genome Biology, 14:R40 (2013) (paper link)
  24. Yu-Wei Wu, Thomas G. Doak and Yuzhen Ye. The gain and loss of chromosomal integron systems in the Treponema species. BMC Evolutionary Biology, 13:16 DOI: 10.1186/1471-2148-13-16 (2013) (paper link)
  25. Dazhi Jiao, Yuzhen Ye and Haixu Tang. Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences. PLoS Comput Biol 9(3): e1002981. doi:10.1371/journal.pcbi.1002981 (2013) (paper link | software)
  26. Gregory C. Campanello, Zhen Ma, Nicholas E. Grossoehme, Alfredo J. Guerra, Brian P. Ward, Richard D. DiMarchi, Yuzhen Ye, Charles E. Dann III, and David P. Giedroc. Allosteric inhibition of a zinc-sensing transcriptional repressor: insights into the arsenic repressor (ArsR) family. J Mol Biol. 425(7):1143-57. doi: 10.1016/j.jmb.2013.01.018 (2013) (paper link)
  27. Yu-Wei Wu, Mina Rho, Thomas G. Doak and Yuzhen Ye. Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. Selected paper in the 12th European Conferences on Computational Biology (ECCB 2012); Bioinformatics, 28 (18): i363-i369 DOI: 10.1021/bi300140 (2012) (paper link)
  28. Anthony A. Fodor, Todd Z. DeSantis, Kristine M. Wylie, Jonathan H. Badger, Yuzhen Ye, Theresa Hepburn, Ping Hu, Erica Sodergren, Konstantinos Liolios, Heather Huot-Creasy, Bruce W. Birren, Ashlee M. Earl. The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing. PLoS ONE 7(7): e41294. doi:10.1371/journal.pone.0041294 (2012) (paper link)
  29. Yu-Wei Wu, Mina Rho, Thomas G. Doak, and Yuzhen Ye. Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes. Applied and Environmental Microbiology 78:5288-5296 (2012) (paper link)
  30. Susan M. Huse, Yuzhen Ye, Yanjiao Zhou, and Anthony A. Fodor. A Core Human Microbiome as Viewed Through 16S rRNA Sequence Clusters. PLoS ONE 7(6): e34242. doi:10.1371/journal.pone.0034242 (2012) (paper link)
  31. Mina Rho, Yu-Wei Wu, Haixu Tang, Thomas G. Doak, and Yuzhen Ye. Diverse CRISPRs evolving in human microbiomes. PLoS Genetics 8(6): e1002441. doi:10.1371/journal.pgen.1002441 (2012) (paper link | The Human Microbiome Project Collection | IU news | F1000)
  32. The Human Microbiome Project Consortium. Structure, function and diversity of the health human microbiome. Nature, 486, 207–214 (2012) (paper link)
  33. The Human Microbiome Project Consortium. A framework for human microbiome research. Nature, 486, 215–221 (2012) (paper link)
  34. Chul Won Lee, Dhruva K. Chakravorty, Feng-Ming James Chang, Hermes Reyes-Caballero, Yuzhen Ye, Kenneth M. Merz, Jr., and David P. Giedroc. Solution Structure of Mycobacterium tuberculosis NmtR in the Apo State: Insights into Ni(II)-Mediated Allostery. Biochemistry, 51(12):2619–2629 (2012) (paper link)
  35. Mingjie Wang, Yuzhen Ye and Haixu Tang. A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community. Journal of Computational Biology 19(6): 814-825. doi:10.1089/cmb.2012.0058 (2012) (paper link)
  36. Yongan Zhao, Haixu Tang and Yuzhen Ye. RAPSearch2: a fast and memory-efficient protein similarity search tool for next generation sequencing data. Bioinformatics 28(1):125-126 (2012) (paper link | software)
  37. Quan Zhang, Thomas G. Doak, and Yuzhen Ye. Artificial functional difference between microbial communities caused by length difference of sequencing reads. Pac Symp Biocomput. p:259-270 (2012) (paper link)
  38. Yuzhen Ye, Jeong-Hyeon Choi, and Haixu Tang. RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics, 12:159 (2011) (paper link | software)
  39. John K. Colbourne1, Michael E. Pfrender, ..., Yuzhen Ye, ..., Jeffrey L. Boore. The Ecoresponsive Genome of Daphnia pulex. Science, 331(6017)555-561 (2011) (paper link)
  40. Neethu Shah, Haixu Tang, Thomas G. Doak and Yuzhen Ye. Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Pac Symp Biocomput. p:165-76 (2011) (pubmed | paper link | software)
  41. Yuzhen Ye. Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment. The Proceedings of BIBM 2010, 153-157 (author's manuscript | software)
  42. Mina Rho, Haixu Tang and Yuzhen Ye. FragGeneScan: predicting genes in short and error-prone reads. Nucl. Acids Res., doi: 10.1093/nar/gkq747 (2011) (paper link | software)
  43. Yu-Wei Wu and Yuzhen Ye. A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. Lecture Notes in Computer Science2010, Volume 6044/2010, 535-549 (RECOMB 2010) (paper link | author's manuscript | software
    The journal version of this paper appears in J Comput Biol. 2011 Mar;18(3):523-34, which also reports the results by combing AbundanceBin and a composition-based binning algorithm.)
  44. John C. Wooley and Yuzhen Ye. Metagenomics: facts and artifacts, and computational challenges. Journal of Computer Science and Technology, 25(1):71-81 (2010) (paper link | NIH public access)
  45. Yuzhen Ye and Thomas G. Doak. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Computational Biology, 5(8): e1000465 (2009) (paper link | software)
  46. Yuzhen Ye and Haixu Tang. An ORFome assembly approach to metagenomics sequences analysis. J Bioinform Comput Biol, 7(3):455-71 (2009) (paper link | NIH public access | an older version in the Proceedings of CSB 2008)
  47. Mallika Veeramalai, Yuzhen Ye and Adam Godzik. TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinformatics, 9:358 (2008) (paper link)
  48. Linda Z. Holland, Ricard Albalat, .., Yuzhen Ye, .., Peter W.H. Holland. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Research, 18:1100-1111 (2008) (paper link)
  49. Qing Zhang, Christian M. Zmasek, Larry J. Dishaw, M. Gail Mueller, Yuzhen Ye, Gary W. Litman and Adam Godzik. Novel genes dramatically alter regulatory network topology in amphioxus. Genome Biology, 9:R123 (2008) (paper link)
  50. Christian M. Zmasek, Qing Zhang, Yuzhen Ye and Adam Godzik. Surprising complexity of the ancestral apoptosis network, Genome Biology, 8:R226 (2007) (paper link)
  51. Marc Awobuluyi, Jin Yang, Yuzhen Ye, Jon E Chatterton, Adam Godzik, Stuart A Lipton, and Dongxian Zhang. Subunit-specific roles of gycine-binding domains in activation of NR1/NR3 N-methyl-D-aspartate receptors. Molecular Pharmacology, 71(1):112-122 (2007) (paper link)
  52. Yuzhen Ye, Zhanwen Li and Adam Godzik. Modeling and analyzing three-dimensional structures of Human disease proteins. Proceedings of Pacific Symposium on Biocomputing, 11:439-450 (2006) PDF supplementary material
  53. Zhanwen Li, Yuzhen Ye and Adam Godzik. Flexible Structural Neighborhood: a database of protein structural similarities and alignments. Nucleic Acids Research, 34(Database issue):D277-80 (2006) paper link server
  54. Ross Overbeek, Tadhg Begley, et al. Yuzhen Ye, Olga Zagnitko, and Veronika Vonstein. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research, 33: 5691-5702 (2005) paper link
  55. Yuzhen Ye and Adam Godzik. Multiple flexible structure alignment using partial order graphs. Bioinformatics, 21(10):2362-2369 (2005) PubMed color figures 4-6 server
  56. Yuzhen Ye, Andrei Osterman, Ross Overbeek and Adam Godzik. Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics, 21 Suppl 1:i478-i486 (ISMB 2005) PubMed (check out the supplementary material at this link)
  57. Yuzhen Ye and Adam Godzik. Database searching by flexible protein structure alignment. Protein Science, 13(7):1841-1850 (2004) PubMed Server
  58. Yuzhen Ye and Adam Godzik. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acid Research, 32:W582-585 (2004) PubMed Server
  59. Iddo Friedberg, Lukasz Jaroszewski, Yuzhen Ye and Adam Godzik. The interplay of fold recognition and experimental structure determination in structural genomics. Current Opinion in Structural Biology, 14(3):307-12 (2004) PubMed
  60. Yuzhen Ye and Adam Godzik. Comparative analysis of domain organization: a graph theory approach to comparison of domain distribution in genomes. Genome Research, 14:343-353 (2004) PubMed Server
  61. Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski and Adam Godzik.Integrated web service for improving alignment quality based on segments comparison. BMC Bioinformatics, 5(1):98 (2003) PubMed
  62. Yuzhen Ye and Adam Godzik. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19(suppl.2):ii246-ii255 (2003) PubMed
  63. Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, and Adam Godzik. A segment alignment approach to protein comparison. Bioinformatics, 19(6):742-749 (2003) PubMed
  64. Tong Liu, Ana Rojas, Yuzhen Ye and Adam Godzik. Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family. Protein Science, 12(9):1872-1881 (2003) PubMed
  65. Yuzhen Ye, Hao Fei and Dafu Ding. Rational redesign of inhibitors of furin/kexin processing protease. Acta Biochimica et Biophysica Sinica, 33(5):504-512 (2001) PubMed
  66. Hao Fei, Mingjuan Luo, Yuzhen Ye, Dafu Ding and Chengwu Chi. The inhibitory activities of recombinant eglin C mutants on kexin and furin, using site-directed mutagenesis and molecular modeling. Acta Biochimica et Biophysica Sinica, 33(6):591-599 (2001) PubMed
  67. Qing Zhang, Yuzhen Ye and Dafu Ding. Structural basis of functional specificity of steroid receptors. Acta Biophysica sinica, 17(4): 685-694 (2001)
  68. Yuzhen Ye, Tao Xie and Dafu Ding. Protein functional-group 3D motif and its applications. Chinese Science Bulletin, 45(22):2044-2051 (2000) PDF
  69. Sheng Yang, He Huang, Shiyun Li, Yuzhen Ye, Lin Wan, Fengwen Zhang and Zhongyi Yuan. Enhancing penicillin G acylase stability by site-directed mutagenesis. Acta Biochimica et Biophysica Sinica, 32(6):581-585 (2000) PubMed
  70. Yuzhen Ye and Dafu Ding. Construction of protein scaffold database and its applications to functional protein design. Acta Biophysica Sinica, 15(4):751-757 (1999)
  71. Yuzhen Ye, Haixu Tang and Dafu Ding. Engineering novel functional proteins: grafting active sites into natural scaffolds. Acta Biochimica et Biophysica Sinica, 31(3):303-308 (1999) PubMed
  72. Yuzhen Ye, Haixu Tang and Dafu Ding. Predicting the solvated structures of protein mutants by self-consistent ensemble optimization. Acta Biophysica Sinica (1998), 14(2):311-317
  73. Haixu Tang, Yuzhen Ye and Dafu Ding. Flexible docking of proteins and "drug-like" ligands. Acta Biochimica et Biophysica Sinica, 30(6):623-630 (1998) PubMed
  74. Yuzhen Ye, Haixu Tang and Dafu Ding. Design of protein cores by screening combinatorial sequence library. Acta Biochimica et Biophysica Sinica, 30(5):525-529 (1998) PubMed

Book chapters:

  1. Fatemeh sharifi and Yuzhen ye. From gene annotation to function prediction for metagenomics. In "Methods in Molecular Biology", volume 1611, pp27-34 (edited by Daisuke Kihara) (link)
  2. Yuzhen Ye and Thomas G. Doak, A Parsimony Approach to Biological Pathway Reconstruction/Inference for Metagenomes. In "Handbook of Molecular Microbial Ecology I" (edited by Frans J. de Bruijn; Wiley-blackwell), 453-460 (2011)
  3. Yuzhen Ye and Haixu Tang, Dynamic programming algorithms for sequence and structure comparison. In "Bioinformatics Algorithms: Techniques and Applications" (edited by Ion Mandoiu and Alexander Zelikovsky; Wiley Press), 9-27 (2008) google book
  4. John C. Wooley and Yuzhen Ye. A historical perspective and overview of protein structure prediction. In "Computational methods for protein structure prediction" (edited by Ying Xu, Dong Xu and Jie Liang; Spinger), 1-43 (2007) link

Online articles:

  1. Yuzhen Ye. CRISPRs in the Human Microbiome. In "Encyclopedia of Metagenomics" (edited by Karen E. Nelson)
  2. Yuzhen Ye. FragGeneScan: predicting genes in short and error-prone reads. In "Encyclopedia of Metagenomics" (edited by Karen E. Nelson)
  3. Yuzhen Ye. Metabolic and Species Diversity Analysis for Metagenomics. In "Encyclopedia of Metagenomics" (edited by Karen E. Nelson)
  4. Yuzhen Ye. AbundanceBin, Metagenomic Sequencing. In "Encyclopedia of Metagenomics" (edited by Karen E. Nelson)