Yong Kong

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc Distributions of positive signals in pyrosequencing
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, 333 Cedar Street, New Haven, CT, 06510, USA
    J Math Biol 69:39-54. 2014
  2. doi request reprint Length distribution of sequencing by synthesis: fixed flow cycle model
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, 333 Cedar Street, New Haven, CT 06510, USA
    J Math Biol 67:389-410. 2013
  3. doi request reprint Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT 06510, USA
    Genomics 98:152-3. 2011
  4. doi request reprint Statistical distributions of pyrosequencing
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut 06510, USA
    J Comput Biol 16:31-42. 2009
  5. doi request reprint Calculating complexity of large randomized libraries
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, 333 Cedar Street, New Haven, CT 06510, USA
    J Theor Biol 259:641-5. 2009
  6. doi request reprint Statistical distributions of sequencing by synthesis with probabilistic nucleotide incorporation
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut 06510, USA
    J Comput Biol 16:817-27. 2009
  7. pmc Adjusting for background mutation frequency biases improves the identification of cancer driver genes
    Perry Evans
    Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA
    IEEE Trans Nanobioscience 12:150-7. 2013
  8. pmc Forward genetics identifies Kdf1/1810019J16Rik as an essential regulator of the proliferation-differentiation decision in epidermal progenitor cells
    Sunjin Lee
    Department of Genetics, Yale University, New Haven, CT 06520, USA
    Dev Biol 383:201-13. 2013
  9. pmc Integrative annotation of variants from 1092 humans: application to cancer genomics
    Ekta Khurana
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Science 342:1235587. 2013
  10. pmc Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal length
    Emily K Mis
    Department of Genetics, Yale University, New Haven, CT 06520, United States
    Dev Biol 385:67-82. 2014

Collaborators

Detail Information

Publications23

  1. pmc Distributions of positive signals in pyrosequencing
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, 333 Cedar Street, New Haven, CT, 06510, USA
    J Math Biol 69:39-54. 2014
    ..The statistical distributions will be useful for instrument and software development for pyrosequencing and other related platforms. ..
  2. doi request reprint Length distribution of sequencing by synthesis: fixed flow cycle model
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, 333 Cedar Street, New Haven, CT 06510, USA
    J Math Biol 67:389-410. 2013
    ..Unlike the previous model, the new model yields the probability distribution for the sequence length. Explicit closed form formulas are derived for the mean and variance of the distribution. ..
  3. doi request reprint Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT 06510, USA
    Genomics 98:152-3. 2011
    ..Btrim is a versatile stand-alone tool that can be used as the first step in virtually all next-generation sequence analysis pipelines. The program is available at http://graphics.med.yale.edu/trim/...
  4. doi request reprint Statistical distributions of pyrosequencing
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut 06510, USA
    J Comput Biol 16:31-42. 2009
    ..In both cases, the distributions can be approximated accurately by normal distributions with the same mean and variance. The statistical distributions will be useful for instrument and software development for pyrosequencing platforms...
  5. doi request reprint Calculating complexity of large randomized libraries
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, 333 Cedar Street, New Haven, CT 06510, USA
    J Theor Biol 259:641-5. 2009
    ..The more skewed the ratio, the larger the library size is needed to obtain the same expected number of unique sequences. The program is freely available at http://graphics.med.yale.edu/cgi-bin/lib_comp.pl...
  6. doi request reprint Statistical distributions of sequencing by synthesis with probabilistic nucleotide incorporation
    Yong Kong
    Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut 06510, USA
    J Comput Biol 16:817-27. 2009
    ..The results are also generalized to handle sequence context dependent incorporation. The statistical distributions will be useful for instrument and software development for sequencing by synthesis platforms...
  7. pmc Adjusting for background mutation frequency biases improves the identification of cancer driver genes
    Perry Evans
    Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA
    IEEE Trans Nanobioscience 12:150-7. 2013
    ..In conclusion, the use of the gene-specific synonymous mutation frequency is well suited for assessing a gene's non-synonymous mutation burden...
  8. pmc Forward genetics identifies Kdf1/1810019J16Rik as an essential regulator of the proliferation-differentiation decision in epidermal progenitor cells
    Sunjin Lee
    Department of Genetics, Yale University, New Haven, CT 06520, USA
    Dev Biol 383:201-13. 2013
    ....
  9. pmc Integrative annotation of variants from 1092 humans: application to cancer genomics
    Ekta Khurana
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Science 342:1235587. 2013
    ..g., certain deletions and enhancers). On the basis of these patterns, we developed a computational tool (FunSeq), whose application to ~90 cancer genomes reveals nearly a hundred candidate noncoding drivers. ..
  10. pmc Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal length
    Emily K Mis
    Department of Genetics, Yale University, New Haven, CT 06520, United States
    Dev Biol 385:67-82. 2014
    ..The pug mutant serves as a novel model for mammalian dwarfism and identifies a key role for proteoglycan modification in the initiation of chondrocyte maturation. ..
  11. pmc Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project
    Xinmeng Jasmine Mu
    Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, W M Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT 06520, USA
    Nucleic Acids Res 39:7058-76. 2011
    ....
  12. ncbi request reprint Computational analysis in cancer exome sequencing
    Perry Evans
    Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
    Methods Mol Biol 1176:219-27. 2014
    ..We further describe analytical methods to generate lists of driver genes with more mutational events than expected by chance. ..
  13. pmc Alleles of a polymorphic ETV6 binding site in DCDC2 confer risk of reading and language impairment
    Natalie R Powers
    Department of Genetics, Yale University, 464 Congress Avenue, Suite 243, New Haven, CT 06520, USA
    Am J Hum Genet 93:19-28. 2013
    ..On the basis of these data, we propose a new name for BV677278: "READ1" or "regulatory element associated with dyslexia 1." ..
  14. pmc Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma
    Michael Krauthammer
    Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
    Nat Genet 44:1006-14. 2012
    ..These findings raise the possibility that pharmacological inhibition of downstream effectors of RAC1 signaling could be of therapeutic benefit...
  15. pmc AlleleSeq: analysis of allele-specific expression and binding in a network framework
    Joel Rozowsky
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Mol Syst Biol 7:522. 2011
    ..Furthermore, we investigate the coordination between ASE and ASB from multiple transcription factors events using a regulatory network framework. Correlation analyses and network motifs show mostly coordinated ASB and ASE...
  16. pmc Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants
    Jiang Du
    Department of Computer Science, Yale University, New Haven, Connecticut, USA
    PLoS Comput Biol 5:e1000432. 2009
    ..Our strategy should facilitate the sequencing of human genomes at maximum accuracy and low cost...
  17. ncbi request reprint Rare SF3B1 R625 mutations in cutaneous melanoma
    Yong Kong
    aDepartment of Molecular Biophysics and Biochemistry bW M Keck Foundation Biotechnology Resource Laboratory cDepartment of Pathology dDepartment of Dermatology, Yale University, School of Medicine, New Haven, Connecticut, USA
    Melanoma Res 24:332-4. 2014
    ..The results were validated by Sanger sequencing. We conclude that SF3B1 R625 mutation does occur in cutaneous melanoma, although with a low frequency (∼1%). ..
  18. pmc Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing
    Florencia del Viso
    Department of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
    BMC Genomics 13:649. 2012
    ..To facilitate cloning of X. tropicalis mutants identified in forward genetic screens, we sought to combine bulk segregant analysis and exome sequencing into a single step...
  19. pmc MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions
    Vijay Garla
    Department of Biological and Biomedical Sciences, Interdepartmental Program in Computational Biology and Bioinformatics, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520, USA
    Bioinformatics 27:416-8. 2011
    ..The MU2A web service is available at http://krauthammerlab.med.yale.edu/mu2a. We have released MU2A as open source, available at http://code.google.com/p/mu2a/...
  20. pmc Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering
    Sara A Marlatt
    Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520 8005, USA
    Protein Eng Des Sel 24:311-20. 2011
    ..These findings suggest that deep sequencing can be used to determine the quality and content of other libraries with randomized segments and to follow individual sequences during selection...
  21. pmc Substrate discrimination among mitogen-activated protein kinases through distinct docking sequence motifs
    Douglas L Sheridan
    Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    J Biol Chem 283:19511-20. 2008
    ..Variations in DEF site sequence requirements provide one possible mechanism for encoding complex target specificity among MAPK isoforms...
  22. pmc Keck Foundation Biotechnology Resource Laboratory, Yale University
    Kathryn L Stone
    Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut, USA
    Yale J Biol Med 80:195-211. 2007
  23. ncbi request reprint A note on the quantitative properties of McGhee-von Hippel model
    Yong Kong
    CuraGen Corporation, 555 Long Wharf Drive, New Haven, CT 06511, USA
    Biophys Chem 95:1-6. 2002
    ....