Yufeng Shen

Summary

Affiliation: Columbia University
Country: USA

Publications

  1. pmc 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. pmc 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
  3. pmc 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
  4. pmc Whole exome sequencing identifies de novo mutations in GATA6 associated with congenital diaphragmatic hernia
    Lan Yu
    Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
    J Med Genet 51:197-202. 2014
  5. doi request reprint 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
  6. pmc 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
  7. pmc 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
  8. ncbi request reprint 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
  9. pmc 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
  10. pmc Defining a comprehensive verotype using electronic health records for personalized medicine
    Mary Regina Boland
    Department of Biomedical Informatics, Columbia University, New York, New York, USA
    J Am Med Inform Assoc 20:e232-8. 2013

Detail Information

Publications18

  1. pmc 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. pmc 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...
  3. pmc 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...
  4. pmc Whole exome sequencing identifies de novo mutations in GATA6 associated with congenital diaphragmatic hernia
    Lan Yu
    Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
    J Med Genet 51:197-202. 2014
    ..It is characterised by herniation of abdominal viscera through an incompletely formed diaphragm. Although chromosomal anomalies and mutations in several genes have been implicated, the cause for most patients is unknown...
  5. doi request reprint 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'...
  6. pmc 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...
  7. pmc 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
    ....
  8. ncbi request reprint 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...
  9. pmc 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...
  10. pmc Defining a comprehensive verotype using electronic health records for personalized medicine
    Mary Regina Boland
    Department of Biomedical Informatics, Columbia University, New York, New York, USA
    J Am Med Inform Assoc 20:e232-8. 2013
    ....
  11. ncbi request reprint 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...
  12. pmc CANOES: detecting rare copy number variants from whole exome sequencing data
    Daniel Backenroth
    Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA JP Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY 10032, USA
    Nucleic Acids Res 42:e97. 2014
    ..g. XHMM or CoNIFER). When CANOES is used in combination with these methods, it will be possible to produce high accuracy calls, as demonstrated by a much reduced and more realistic de novo rate in results from trio data. ..
  13. pmc Whole-Exome sequencing identifies novel LEPR mutations in individuals with severe early onset obesity
    Richard Gill
    Division of Molecular Genetics Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA Department of Epidemiology, Mailman School of Public Health, Columbia University Medical Center, New York, New York, USA
    Obesity (Silver Spring) 22:576-84. 2014
    ..Despite evidence for a strong genetic contribution to susceptibility to obesity, previous efforts to discover the relevant genes using positional cloning have failed to account for most of the apparent genetic risk variance...
  14. pmc A collaborative approach to developing an electronic health record phenotyping algorithm for drug-induced liver injury
    Casey Lynnette Overby
    Department of Biomedical Informatics, Columbia University, New York, New York, USA
    J Am Med Inform Assoc 20:e243-52. 2013
    ..To describe a collaborative approach for developing an electronic health record (EHR) phenotyping algorithm for drug-induced liver injury (DILI)...
  15. pmc Position effect on FGF13 associated with X-linked congenital generalized hypertrichosis
    Gina M Destefano
    Departments of Genetics and Development, Columbia University, New York, NY, USA
    Proc Natl Acad Sci U S A 110:7790-5. 2013
    ..Taken together, our findings suggest a role for FGF13 in hair follicle growth and in the hair cycle...
  16. pmc 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...
  17. pmc 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...
  18. pmc 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...