Yong Kong, PhD

• Melinda Pettigrew
• Shuangge Steven Ma

Information Science; Mathematical Computing

Infectious Diseases

• Length distribution of sequencing by synthesis: fixed flow cycle model.Kong Y. Length distribution of sequencing by synthesis: fixed flow cycle model. Journal Of Mathematical Biology 2013, 67: 389-410. PMID: 22689207, DOI: 10.1007/s00285-012-0556-3.
• Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma.Krauthammer M, Kong Y, Ha BH, Evans P, Bacchiocchi A, McCusker JP, Cheng E, Davis MJ, Goh G, Choi M, Ariyan S, Narayan D, Dutton-Regester K, Capatana A, Holman EC, Bosenberg M, Sznol M, Kluger HM, Brash DE, Stern DF, Materin MA, Lo RS, Mane S, Ma S, Kidd KK, Hayward NK, Lifton RP, Schlessinger J, Boggon TJ, Halaban R. Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nature Genetics 2012, 44: 1006-14. PMID: 22842228, PMCID: PMC3432702, DOI: 10.1038/ng.2359.
• Upper respiratory tract microbial communities, acute otitis media pathogens, and antibiotic use in healthy and sick children.Pettigrew MM, Laufer AS, Gent JF, Kong Y, Fennie KP, Metlay JP. Upper respiratory tract microbial communities, acute otitis media pathogens, and antibiotic use in healthy and sick children. Applied And Environmental Microbiology 2012, 78: 6262-70. PMID: 22752171, PMCID: PMC3416608, DOI: 10.1128/AEM.01051-12.
• Forward genetics uncovers Transmembrane protein 107 as a novel factor required for ciliogenesis and Sonic hedgehog signaling.Christopher KJ, Wang B, Kong Y, Weatherbee SD. Forward genetics uncovers Transmembrane protein 107 as a novel factor required for ciliogenesis and Sonic hedgehog signaling. Developmental Biology 2012, 368: 382-92. PMID: 22698544, PMCID: PMC3402655, DOI: 10.1016/j.ydbio.2012.06.008.
• Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies.Kong Y. Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics 2011, 98: 152-3. PMID: 21651976, DOI: 10.1016/j.ygeno.2011.05.009.
• Note: solution of one-dimensional self-assembly problem in multiple-component systems with correction of overcounting of non-symmetrical complexes.Kong Y. Note: solution of one-dimensional self-assembly problem in multiple-component systems with correction of overcounting of non-symmetrical complexes. The Journal Of Chemical Physics 2011, 135: 156101. PMID: 22029340, DOI: 10.1063/1.3653978.
• Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project.Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB. Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Research 2011, 39: 7058-76. PMID: 21596777, PMCID: PMC3167619, DOI: 10.1093/nar/gkr342.
• AlleleSeq: analysis of allele-specific expression and binding in a network framework.Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Molecular Systems Biology 2011, 7: 522. PMID: 21811232, PMCID: PMC3208341, DOI: 10.1038/msb.2011.54.
• Streptococcus pneumoniae serotype 6C: an intra- and interclonal complex comparison.Thomas JC, Kong Y, Sabharwal V, Pelton SI, Pettigrew MM. Streptococcus pneumoniae serotype 6C: an intra- and interclonal complex comparison. Journal Of Bacteriology 2011, 193: 3409-10. PMID: 21551297, PMCID: PMC3133277, DOI: 10.1128/JB.05079-11.
• Streptococcus pneumoniae clonal complex 199: genetic diversity and tissue-specific virulence.Thomas JC, Figueira M, Fennie KP, Laufer AS, Kong Y, Pichichero ME, Pelton SI, Pettigrew MM. Streptococcus pneumoniae clonal complex 199: genetic diversity and tissue-specific virulence. PloS One 2011, 6: e18649. PMID: 21533186, PMCID: PMC3077395, DOI: 10.1371/journal.pone.0018649.
• MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions.Garla V, Kong Y, Szpakowski S, Krauthammer M. MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions. Bioinformatics (Oxford, England) 2011, 27: 416-8. PMID: 21149339, PMCID: PMC3031033, DOI: 10.1093/bioinformatics/btq658.
• Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering.Marlatt SA, Kong Y, Cammett TJ, Korbel G, Noonan JP, Dimaio D. Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering. Protein Engineering, Design & Selection : PEDS 2011, 24: 311-20. PMID: 21149273, PMCID: PMC3038463, DOI: 10.1093/protein/gzq112.
• Microbial communities of the upper respiratory tract and otitis media in children.Laufer AS, Metlay JP, Gent JF, Fennie KP, Kong Y, Pettigrew MM. Microbial communities of the upper respiratory tract and otitis media in children. MBio 2011, 2: e00245-10. PMID: 21285435, PMCID: PMC3031303, DOI: 10.1128/mBio.00245-10.
• Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family.Murphy JW, Yuan H, Kong Y, Xiong Y, Lolis EJ. Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family. Proteins 2010, 78: 1331-7. PMID: 20077567, PMCID: PMC3021379, DOI: 10.1002/prot.22666.
• Statistical distributions of sequencing by synthesis with probabilistic nucleotide incorporation.Kong Y. Statistical distributions of sequencing by synthesis with probabilistic nucleotide incorporation. Journal Of Computational Biology : A Journal Of Computational Molecular Cell Biology 2009, 16: 817-27. PMID: 19522665, DOI: 10.1089/cmb.2008.0215.
• Statistical distributions of pyrosequencing.Kong Y. Statistical distributions of pyrosequencing. Journal Of Computational Biology : A Journal Of Computational Molecular Cell Biology 2009, 16: 31-42. PMID: 19072582, DOI: 10.1089/cmb.2008.0106.
• Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants. PLoS Computational Biology 2009, 5: e1000432. PMID: 19593373, PMCID: PMC2700963, DOI: 10.1371/journal.pcbi.1000432.
• Substrate discrimination among mitogen-activated protein kinases through distinct docking sequence motifs.Sheridan DL, Kong Y, Parker SA, Dalby KN, Turk BE. Substrate discrimination among mitogen-activated protein kinases through distinct docking sequence motifs. The Journal Of Biological Chemistry 2008, 283: 19511-20. PMID: 18482985, PMCID: PMC2443660, DOI: 10.1074/jbc.M801074200.
• Calculating complexity of large randomized libraries.Kong Y. Calculating complexity of large randomized libraries. Journal Of Theoretical Biology 2009, 259: 641-5. PMID: 19376134, DOI: 10.1016/j.jtbi.2009.04.008.
• Generalized correlation functions and their applications in selection of optimal multiple spaced seeds for homology search.Kong Y. Generalized correlation functions and their applications in selection of optimal multiple spaced seeds for homology search. Journal Of Computational Biology : A Journal Of Computational Molecular Cell Biology 2007, 14: 238-54. PMID: 17456017, DOI: 10.1089/cmb.2006.0008.
• Asymptotics of the monomer-dimer model on two-dimensional semi-infinite lattices.Kong Y. Asymptotics of the monomer-dimer model on two-dimensional semi-infinite lattices. Physical Review. E, Statistical, Nonlinear, And Soft Matter Physics 2007, 75: 051123. PMID: 17677038, DOI: 10.1103/PhysRevE.75.051123.
• Monomer-dimer model in two-dimensional rectangular lattices with fixed dimer density.Kong Y. Monomer-dimer model in two-dimensional rectangular lattices with fixed dimer density. Physical Review. E, Statistical, Nonlinear, And Soft Matter Physics 2006, 74: 061102. PMID: 17280033, DOI: 10.1103/PhysRevE.74.061102.
• Logarithmic corrections in the free energy of monomer-dimer model on plane lattices with free boundaries.Kong Y. Logarithmic corrections in the free energy of monomer-dimer model on plane lattices with free boundaries. Physical Review. E, Statistical, Nonlinear, And Soft Matter Physics 2006, 74: 011102. PMID: 16907056, DOI: 10.1103/PhysRevE.74.011102.
• Packing dimers on (2p+1) x (2q+1) lattices.Kong Y. Packing dimers on (2p+1) x (2q+1) lattices. Physical Review. E, Statistical, Nonlinear, And Soft Matter Physics 2006, 73: 016106. PMID: 16486215, DOI: 10.1103/PhysRevE.73.016106.
• MicroRNA: biological and computational perspective.Kong Y, Han JH. MicroRNA: biological and computational perspective. Genomics, Proteomics & Bioinformatics 2005, 3: 62-72. PMID: 16393143, PMCID: PMC5172550, DOI: 10.1016/s1672-0229(05)03011-1.
• Fluorescence anisotropy studies on the Ku-DNA interaction: anion and cation effects.Arosio D, Costantini S, Kong Y, Vindigni A. Fluorescence anisotropy studies on the Ku-DNA interaction: anion and cation effects. The Journal Of Biological Chemistry 2004, 279: 42826-35. PMID: 15284231, DOI: 10.1074/jbc.M406529200.
• A protein interaction map of Drosophila melanogaster.Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM. A protein interaction map of Drosophila melanogaster. Science (New York, N.Y.) 2003, 302: 1727-36. PMID: 14605208, DOI: 10.1126/science.1090289.
• A note on the quantitative properties of McGhee-von Hippel model.Kong Y. A note on the quantitative properties of McGhee-von Hippel model. Biophysical Chemistry 2002, 95: 1-6. PMID: 11880169, DOI: 10.1016/s0301-4622(01)00234-4.
• Ligand binding on ladder lattices.Kong Y. Ligand binding on ladder lattices. Biophysical Chemistry 1999, 81: 7-21. PMID: 17030328.
• Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates.Li Y, Kong Y, Korolev S, Waksman G. Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates. Protein Science : A Publication Of The Protein Society 1998, 7: 1116-23. PMID: 9605316, PMCID: PMC2144016, DOI: 10.1002/pro.5560070505.
• Theory of multivalent binding in one and two-dimensional lattices.Di Cera E, Kong Y. Theory of multivalent binding in one and two-dimensional lattices. Biophysical Chemistry 1996, 61: 107-24. PMID: 17023370.