Yufeng Shen

Summary

Affiliation: Columbia University
Country: USA

Publications

  1. ncbi A hidden Markov model for copy number variant prediction from whole genome resequencing data
    Yufeng Shen
    Department of Computer Science, Columbia University, New York, NY 10027, USA
    BMC Bioinformatics 12:S4. 2011
  2. ncbi A SNP discovery method to assess variant allele probability from next-generation resequencing data
    Yufeng Shen
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 20:273-80. 2010
  3. ncbi Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association
    Yufeng Shen
    Department of Computer Science, Columbia University, New York, NY 10027, USA
    Bioinformatics 27:1995-7. 2011
  4. ncbi The complete genome of an individual by massively parallel DNA sequencing
    David A Wheeler
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 452:872-6. 2008
  5. ncbi Bos taurus genome assembly
    Yue Liu
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    BMC Genomics 10:180. 2009
  6. ncbi A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery
    Xiaohu Wang
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
    Nucleic Acids Res 36:4863-71. 2008
  7. ncbi Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing
    Yufeng Shen
    Department of Computer Science, Columbia University, New York, New York, United States of America
    PLoS ONE 3:e4012. 2008
  8. ncbi Shedding genomic light on Aristotle's lantern
    Erica Sodergren
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030, USA
    Dev Biol 300:2-8. 2006
  9. ncbi Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
  10. ncbi Variants in GATA4 are a rare cause of familial and sporadic congenital diaphragmatic hernia
    Lan Yu
    Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, 1150 St Nicholas Avenue, Room 620, New York, NY 10032, USA
    Hum Genet 132:285-92. 2013

Collaborators

Detail Information

Publications12

  1. ncbi A hidden Markov model for copy number variant prediction from whole genome resequencing data
    Yufeng Shen
    Department of Computer Science, Columbia University, New York, NY 10027, USA
    BMC Bioinformatics 12:S4. 2011
    ..While high-throughput whole genome re-sequencing provides multiple lines of evidence for detecting CNVs, computational algorithms need to be tailored for different type or size of CNVs under different experimental designs...
  2. ncbi A SNP discovery method to assess variant allele probability from next-generation resequencing data
    Yufeng Shen
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 20:273-80. 2010
    ..Validation results show that Atlas-SNP2 achieves a false-positive rate of lower than 10%, with an approximately 5% or lower false-negative rate...
  3. ncbi Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association
    Yufeng Shen
    Department of Computer Science, Columbia University, New York, NY 10027, USA
    Bioinformatics 27:1995-7. 2011
    ..Here, we describe theoretical and empirical design considerations for such sequencing studies, aimed at maximizing the power of detecting association under the constraint of study-wide cost...
  4. ncbi The complete genome of an individual by massively parallel DNA sequencing
    David A Wheeler
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 452:872-6. 2008
    ..This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'...
  5. ncbi Bos taurus genome assembly
    Yue Liu
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    BMC Genomics 10:180. 2009
    ..The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque...
  6. ncbi A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery
    Xiaohu Wang
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
    Nucleic Acids Res 36:4863-71. 2008
    ....
  7. ncbi Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing
    Yufeng Shen
    Department of Computer Science, Columbia University, New York, New York, United States of America
    PLoS ONE 3:e4012. 2008
    ..Whole-genome sequencing represents a promising approach to pinpoint chemically induced mutations in genetic model organisms, thereby short-cutting time-consuming genetic mapping efforts...
  8. ncbi Shedding genomic light on Aristotle's lantern
    Erica Sodergren
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030, USA
    Dev Biol 300:2-8. 2006
    ..Analysis of the basic deuterostome genetic complement supports the sea urchin's role as a model system for deuterostome and, by extension, chordate development...
  9. ncbi Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  10. ncbi Variants in GATA4 are a rare cause of familial and sporadic congenital diaphragmatic hernia
    Lan Yu
    Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, 1150 St Nicholas Avenue, Room 620, New York, NY 10032, USA
    Hum Genet 132:285-92. 2013
    ..848G>A; p.R283H) in a non-isolated CDH patient. In summary, GATA4 is implicated in both familial and sporadic CDH, and our data suggests that WES may be a powerful tool to discover rare variants for CDH...
  11. ncbi Genomewide pharmacogenetics of bisphosphonate-induced osteonecrosis of the jaw: the role of RBMS3
    Paola Nicoletti
    Center for Computational Biology and Bioinformatics, Columbia University Medical Center, New York, New York 10032, USA
    Oncologist 17:279-87. 2012
    ..Bisphosphonate-related osteonecrosis of the jaw (BRONJ) is a serious adverse drug reaction. We conducted a genomewide association study to search for genetic variants with a large effect size that increase the risk for BRONJ...
  12. ncbi Intrinsic flexibility and gating mechanism of the potassium channel KcsA
    Yufeng Shen
    Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 99:1949-53. 2002
    ..This series of motions leads to a dramatic enlargement of the intracellular gate without loosening up the structural integrity...