Yuzhen Ye

Summary

Affiliation: Indiana University
Country: USA

Publications

  1. ncbi 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
  2. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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 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. ncbi 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. ncbi 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
  9. ncbi 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
  10. ncbi 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

Research Grants

  1. Fragment assembly and metabolic/species diversity analysis for Human microbiome p
    Yuzhen Ye; Fiscal Year: 2010

Detail Information

Publications11

  1. ncbi 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
    ....
  2. ncbi 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
    ....
  3. ncbi 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
    ..burnham.org/TOPS/ CONCLUSION: TOPS++FATCAT provides FATCAT accuracy and insights into protein structural changes at a speed comparable to sequence alignments, opening up a possibility of interactive protein structure similarity searches...
  4. ncbi 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...
  5. ncbi 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 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. ncbi 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. ncbi 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...
  9. ncbi 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...
  10. ncbi 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 ...
  11. ncbi 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
    ..5G memory when running in 4-thread mode. Availability and implementation: Implemented in C++, the source code is freely available for download at the RAPSearch2 website: http://omics.informatics.indiana.edu/mg/RAPSearch2/...

Research Grants3

  1. Fragment assembly and metabolic/species diversity analysis for Human microbiome p
    Yuzhen Ye; Fiscal Year: 2010
    ....