Yuzhen Ye

Summary

Affiliation: Indiana University
Country: USA

Publications

  1. pmc Identification of diversity-generating retroelements in human microbiomes
    Yuzhen Ye
    Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
    Int J Mol Sci 15:14234-46. 2014
  2. pmc Surprising complexity of the ancestral apoptosis network
    Christian M Zmasek
    Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, CA 92037, USA
    Genome Biol 8:R226. 2007
  3. pmc Novel genes dramatically alter regulatory network topology in amphioxus
    Qing Zhang
    Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, CA 92037, USA
    Genome Biol 9:R123. 2008
  4. pmc TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model
    Mallika Veeramalai
    Joint Center for Molecular Modeling, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
    BMC Bioinformatics 9:358. 2008
  5. pmc A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes
    Yuzhen Ye
    School of Informatics, Indiana University, Bloomington, IN, USA
    PLoS Comput Biol 5:e1000465. 2009
  6. ncbi request reprint An ORFome assembly approach to metagenomics sequences analysis
    Yuzhen Ye
    School of Informatics, Indiana University, Bloomington, Indiana 47408, USA
    Comput Syst Bioinformatics Conf 7:3-13. 2008
  7. pmc An ORFome assembly approach to metagenomics sequences analysis
    Yuzhen Ye
    School of Informatics, Indiana University, Bloomington, IN 47408, USA
    J Bioinform Comput Biol 7:455-71. 2009
  8. pmc RAPSearch: a fast protein similarity search tool for short reads
    Yuzhen Ye
    School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA
    BMC Bioinformatics 12:159. 2011
  9. pmc A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community
    Mingjie Wang
    School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
    J Comput Biol 19:814-25. 2012
  10. pmc Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes
    Yu Wei Wu
    School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA
    Appl Environ Microbiol 78:5288-96. 2012

Detail Information

Publications28

  1. pmc Identification of diversity-generating retroelements in human microbiomes
    Yuzhen Ye
    Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
    Int J Mol Sci 15:14234-46. 2014
    ..Our study also provides functional clues for a large number of genes (reverse transcriptases and target genes) that were previously annotated as proteins of unknown functions or nonspecific functions. ..
  2. pmc Surprising complexity of the ancestral apoptosis network
    Christian M Zmasek
    Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, CA 92037, USA
    Genome Biol 8:R226. 2007
    ....
  3. pmc Novel genes dramatically alter regulatory network topology in amphioxus
    Qing Zhang
    Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, CA 92037, USA
    Genome Biol 9:R123. 2008
    ....
  4. pmc TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model
    Mallika Veeramalai
    Joint Center for Molecular Modeling, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
    BMC Bioinformatics 9:358. 2008
    ..Such intuitions could help speed up similarity searches and make it easier to understand the results of such analyses...
  5. pmc A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes
    Yuzhen Ye
    School of Informatics, Indiana University, Bloomington, IN, USA
    PLoS Comput Biol 5:e1000465. 2009
    ..Results from applying MinPath to several metagenomes indicate that the common methods used for metagenome annotation may significantly overestimate the biological pathways encoded by microbial communities...
  6. ncbi request reprint An ORFome assembly approach to metagenomics sequences analysis
    Yuzhen Ye
    School of Informatics, Indiana University, Bloomington, Indiana 47408, USA
    Comput Syst Bioinformatics Conf 7:3-13. 2008
    ..This improvement is especially useful for the metagenomic projects when the genome assembly does not work because of the low sequence coverage...
  7. pmc An ORFome assembly approach to metagenomics sequences analysis
    Yuzhen Ye
    School of Informatics, Indiana University, Bloomington, IN 47408, USA
    J Bioinform Comput Biol 7:455-71. 2009
    ..This improvement is especially useful for metagenomic projects when the genome assembly does not work because of the low sequence coverage...
  8. pmc RAPSearch: a fast protein similarity search tool for short reads
    Yuzhen Ye
    School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA
    BMC Bioinformatics 12:159. 2011
    ..Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets...
  9. pmc A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community
    Mingjie Wang
    School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
    J Comput Biol 19:814-25. 2012
    ....
  10. pmc Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes
    Yu Wei Wu
    School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA
    Appl Environ Microbiol 78:5288-96. 2012
    ..The integron gene cassette arrays found in the human microbiome are extraordinarily dynamic, with different microbial communities sharing only a small number of common genes...
  11. pmc RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
    Yongan Zhao
    School of Informatics and Computing, Indiana University, Bloomington, IN 47404, USA
    Bioinformatics 28:125-6. 2012
    ..g. 3.5X for 4-thread mode). RAPSearch2 requires up to 2G memory when running in single thread mode, or up to 3.5G memory when running in 4-thread mode...
  12. pmc The gain and loss of chromosomal integron systems in the Treponema species
    Yu Wei Wu
    School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA
    BMC Evol Biol 13:16. 2013
    ..With the recent release of many new Treponema genomes, we were able to study the distribution of chromosomal integrons in this genus...
  13. pmc Diverse CRISPRs evolving in human microbiomes
    Mina Rho
    School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
    PLoS Genet 8:e1002441. 2012
    ..This work indicates the importance of effective identification and characterization of CRISPR loci to the study of the dynamic ecology of microbiomes...
  14. pmc Allosteric inhibition of a zinc-sensing transcriptional repressor: insights into the arsenic repressor (ArsR) family
    Gregory C Campanello
    Department of Chemistry, Indiana University, Bloomington, IN 47405 7102, USA
    J Mol Biol 425:1143-57. 2013
    ....
  15. pmc Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics
    Yu Wei Wu
    School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
    Bioinformatics 28:i363-i369. 2012
    ..This further complicates annotation of metagenomic datasets, as annotation tools (such as gene predictors or similarity search tools) typically perform poorly on configs encoding short gene fragments...
  16. pmc Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences
    Dazhi Jiao
    School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
    PLoS Comput Biol 9:e1002981. 2013
    ..Source code for sampling metabolic networks is available online at http://omics.informatics.indiana.edu/mg/MetaNetSam/...
  17. ncbi request reprint Artificial functional difference between microbial communities caused by length difference of sequencing reads
    Quan Zhang
    School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
    Pac Symp Biocomput . 2012
    ....
  18. ncbi request reprint Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics
    Neethu Shah
    School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA
    Pac Symp Biocomput . 2011
    ....
  19. pmc Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes
    Mingjie Wang
    School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA
    Genome Biol 16:243. 2015
    ..Further, its application to type 2 diabetes (T2D) metagenomic datasets reveals clear signatures of the T2D gut microbiome, revealing new phylogenetic and functional features of the gut microbial communities associated with T2D. ..
  20. pmc The ecoresponsive genome of Daphnia pulex
    John K Colbourne
    Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
    Science 331:555-61. 2011
    ..Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges...
  21. pmc FragGeneScan: predicting genes in short and error-prone reads
    Mina Rho
    School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA
    Nucleic Acids Res 38:e191. 2010
    ..When applied to metagenomes, FragGeneScan recovered substantially more genes than MetaGene predicted (>90% of the genes identified by homology search), and many novel genes with no homologs in current protein sequence database...
  22. pmc A novel abundance-based algorithm for binning metagenomic sequences using l-tuples
    Yu Wei Wu
    School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA
    J Comput Biol 18:523-34. 2011
    ..g., 75 bp) or have sequencing errors. By combining AbundanceBin and a composition-based method (MetaCluster), we can achieve even higher binning accuracy. Supplementary Material is available at www.liebertonline.com/cmb ...
  23. pmc Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
    Yuzhen Ye
    School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
    Bioinformatics 32:1001-8. 2016
    ..Metagenome assemblies are far from perfect, partially explaining why metagenome assemblies are not used for the analysis of metatranscriptomic datasets...
  24. pmc Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data
    Yuzhen Ye
    School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA
    RNA 22:945-56. 2016
    ..Our study shows the promise of exploiting community RNA-seq data for investigating the transcription of CRISPR-Cas systems. ..
  25. pmc Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola
    Sutichot Nimkulrat
    School of Informatics and Computing, Indiana University, Bloomington IN, USA
    Front Microbiol 7:852. 2016
    ....
  26. pmc A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics
    Haixu Tang
    School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
    PLoS Comput Biol 12:e1005224. 2016
    ..Our tools are released as open-source software on github at https://github.com/COL-IU/Graph2Pro...
  27. pmc Expanding the catalog of cas genes with metagenomes
    Quan Zhang
    School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA, Department of Biology, Indiana University, Bloomington, IN 47405, USA and National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47408, USA
    Nucleic Acids Res 42:2448-59. 2014
    ..We further identified 24 novel Cas families; one novel family contains 20 proteins, all identified from the human microbiome datasets, illustrating the importance of metagenomics projects in expanding the diversity of cas genes. ..
  28. pmc Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery
    Chul Won Lee
    Department of Chemistry, Indiana University, Bloomington, Indiana 47405 7102, United States
    Biochemistry 51:2619-29. 2012
    ....