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Yong Kong, PhD

Senior Research Scientist; Associate Director, Bioinformatics Resource at W.M. Keck Foundation Biotechnology Laboratory

Research & Publications
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Selected Publications

Quantitative DNA Repair Biomarkers and Immune Profiling for Temozolomide and Olaparib in Metastatic Colorectal CancerCecchini M, Zhang J, Wei W, Sklar J, Lacy J, Zhong M, Kong Y, Zhao H, DiPalermo J, Devine L, Stein S, Kortmansky J, Johung K, Bindra R, LoRusso P, Schalper K. Quantitative DNA Repair Biomarkers and Immune Profiling for Temozolomide and Olaparib in Metastatic Colorectal Cancer. Cancer Research Communications 2023, 3: 1132-1139. PMID: 37387791, PMCID: PMC10305782, DOI: 10.1158/2767-9764.crc-23-0045.
Response to: Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effectTakahashi T, Stoiljkovic M, Song E, Gao X, Yasumoto Y, Kudo E, Carvalho F, Kong Y, Park A, Shanabrough M, Szigeti-Buck K, Liu Z, Kristant A, Zhang Y, Sulkowski P, Glazer P, Kaczmarek L, Horvath T, Iwasaki A. Response to: Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect. Neuron 2023, 111: 612-613. PMID: 36863323, DOI: 10.1016/j.neuron.2023.02.006.
Inflammation of the retinal pigment epithelium drives early-onset photoreceptor degeneration in Mertk-associated retinitis pigmentosaMercau M, Akalu Y, Mazzoni F, Gyimesi G, Alberto E, Kong Y, Hafler B, Finnemann S, Rothlin C, Ghosh S. Inflammation of the retinal pigment epithelium drives early-onset photoreceptor degeneration in Mertk-associated retinitis pigmentosa. Science Advances 2023, 9: eade9459. PMID: 36662852, PMCID: PMC9858494, DOI: 10.1126/sciadv.ade9459.
Gastrointestinal Microbiome Disruption and Antibiotic-Associated Diarrhea in Children Receiving Antibiotic Therapy for Community-Acquired Pneumonia.Kwon J, Kong Y, Wade M, Williams DJ, Creech CB, Evans S, Walter EB, Martin JM, Gerber JS, Newland JG, Hofto ME, Staat MA, Chambers HF, Fowler VG, Huskins WC, Pettigrew M. Gastrointestinal Microbiome Disruption and Antibiotic-Associated Diarrhea in Children Receiving Antibiotic Therapy for Community-Acquired Pneumonia. The Journal Of Infectious Diseases 2022, 226: 1109-1119. PMID: 35249113, PMCID: PMC9492313, DOI: 10.1093/infdis/jiac082.
A phase II evaluation of pembrolizumab in recurrent microsatellite instability-high (MSI-H) endometrial cancer patients with Lynch-like versus MLH-1 methylated characteristics (NCT02899793).Roque D, Bellone S, Siegel E, Buza N, Bonazzoli E, Guglielmi A, Zammataro L, Nagarkatti N, Zaidi S, Lee J, Schwartz P, Ratner E, Alexandrov L, Iwasaki A, Kong Y, Song E, Dong W, Elvin J, Choi J, Santin A. A phase II evaluation of pembrolizumab in recurrent microsatellite instability-high (MSI-H) endometrial cancer patients with Lynch-like versus MLH-1 methylated characteristics (NCT02899793). Journal Of Clinical Oncology 2021, 39: 5523-5523. DOI: 10.1200/jco.2021.39.15_suppl.5523.
Endogenous retroviruses mediate IFN-independent protection against vaginal HSV-2 infectionTokuyama M, Jayewickreme R, Mao T, Philbrick W, Kong Y, Dong H, Treger R, Rakib T, Iwasaki A. Endogenous retroviruses mediate IFN-independent protection against vaginal HSV-2 infection. The Journal Of Immunology 2021, 206: 20.39-20.39. DOI: 10.4049/jimmunol.206.supp.20.39.
Distributions of successions of arbitrary multisetsKong Y. Distributions of successions of arbitrary multisets. Communication In Statistics- Theory And Methods 2020, 51: 1693-1705. DOI: 10.1080/03610926.2020.1767137.
Ketogenic diet activates protective γδ T cell responses against influenza virus infectionGoldberg EL, Molony RD, Kudo E, Sidorov S, Kong Y, Dixit VD, Iwasaki A. Ketogenic diet activates protective γδ T cell responses against influenza virus infection. Science Immunology 2019, 4 PMID: 31732517, PMCID: PMC7189564, DOI: 10.1126/sciimmunol.aav2026.
Discovery and Contribution of Nontypeable Haemophilus influenzae NTHI1441 to Human Respiratory Epithelial Cell Invasion.Ahearn C, Kirkham C, Chaves L, Kong Y, Pettigrew M, Murphy T. Discovery and Contribution of Nontypeable Haemophilus influenzae NTHI1441 to Human Respiratory Epithelial Cell Invasion. Infection And Immunity 2019, 87 PMID: 31427451, PMCID: PMC6803334, DOI: 10.1128/iai.00462-19.
Decoupling Combinatorial Complexity: a Two-Step Approach to Distributions of RunsKong Y. Decoupling Combinatorial Complexity: a Two-Step Approach to Distributions of Runs. Methodology And Computing In Applied Probability 2018, 21: 789-803. DOI: 10.1007/s11009-018-9689-1.
Generating Function Methods for Run and Scan StatisticsKong Y. Generating Function Methods for Run and Scan Statistics. 2018, 1-19. DOI: 10.1007/978-1-4614-8414-1_56-1.
Joint distribution of rises, falls, and number of runs in random sequencesKong Y. Joint distribution of rises, falls, and number of runs in random sequences. Communication In Statistics- Theory And Methods 2018, 48: 493-499. DOI: 10.1080/03610926.2017.1414261.
IFT56 regulates vertebrate developmental patterning by maintaining IFTB complex integrity and ciliary microtubule architectureXin D, Christopher K, Zeng L, Kong Y, Weatherbee S. IFT56 regulates vertebrate developmental patterning by maintaining IFTB complex integrity and ciliary microtubule architecture. Journal Of Cell Science 2017, 130: e1.2-e1.2. DOI: 10.1242/jcs.205013.
The Adventitious Angles Problem: The Lonely Fractional Derived AngleKong Y, Zhang S. The Adventitious Angles Problem: The Lonely Fractional Derived Angle. American Mathematical Monthly 2016, 123: 814-816. DOI: 10.4169/amer.math.monthly.123.08.814.
The mth longest runs of multivariate random sequencesKong Y. The mth longest runs of multivariate random sequences. Annals Of The Institute Of Statistical Mathematics 2016, 69: 497-512. DOI: 10.1007/s10463-015-0551-8.
Number of appearances of events in random sequences: A new approach to non-overlapping runsKong Y. Number of appearances of events in random sequences: A new approach to non-overlapping runs. Communication In Statistics- Theory And Methods 2016, 45: 6765-6772. DOI: 10.1080/03610926.2014.968728.
Number of appearances of events in random sequences: a new generating function approach to Type II and Type III runsKong Y. Number of appearances of events in random sequences: a new generating function approach to Type II and Type III runs. Annals Of The Institute Of Statistical Mathematics 2015, 69: 489-495. DOI: 10.1007/s10463-015-0549-2.
Distributions of Runs RevisitedKong Y. Distributions of Runs Revisited. Communication In Statistics- Theory And Methods 2015, 44: 4663-4678. DOI: 10.1080/03610926.2013.793350.
Expression of IgA Proteases by Haemophilus influenzae in the Respiratory Tract of Adults With Chronic Obstructive Pulmonary DiseaseMurphy TF, Kirkham C, Jones MM, Sethi S, Kong Y, Pettigrew MM. Expression of IgA Proteases by Haemophilus influenzae in the Respiratory Tract of Adults With Chronic Obstructive Pulmonary Disease. The Journal Of Infectious Diseases 2015, 212: 1798-1805. PMID: 25995193, PMCID: PMC4633762, DOI: 10.1093/infdis/jiv299.
Computational Analysis in Cancer Exome SequencingEvans P, Kong Y, Krauthammer M. Computational Analysis in Cancer Exome Sequencing. 2014, 1176: 219-227. PMID: 25030931, DOI: 10.1007/978-1-4939-0992-6_18.
Alleles of a Polymorphic ETV6 Binding Site in DCDC2 Confer Risk of Reading and Language ImpairmentPowers N, Eicher J, Butter F, Kong Y, Miller L, Ring S, Mann M, Gruen J. Alleles of a Polymorphic ETV6 Binding Site in DCDC2 Confer Risk of Reading and Language Impairment. American Journal Of Human Genetics 2014, 94: 798. PMCID: PMC4067563, DOI: 10.1016/j.ajhg.2014.04.001.
Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal lengthMis EK, Liem KF, Kong Y, Schwartz NB, Domowicz M, Weatherbee SD. Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal length. Developmental Biology 2013, 385: 67-82. PMID: 24161523, PMCID: PMC3895954, DOI: 10.1016/j.ydbio.2013.10.014.
Integrative Annotation of Variants from 1092 Humans: Application to Cancer GenomicsKhurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Consortium 1, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics. Science 2013, 342: 1235587. PMID: 24092746, PMCID: PMC3947637, DOI: 10.1126/science.1235587.
Forward genetics identifies Kdf1/1810019J16Rik as an essential regulator of the proliferation–differentiation decision in epidermal progenitor cellsLee S, Kong Y, Weatherbee SD. Forward genetics identifies Kdf1/1810019J16Rik as an essential regulator of the proliferation–differentiation decision in epidermal progenitor cells. Developmental Biology 2013, 383: 201-213. PMID: 24075906, PMCID: PMC3841015, DOI: 10.1016/j.ydbio.2013.09.022.
Alleles of a Polymorphic ETV6 Binding Site in DCDC2 Confer Risk of Reading and Language ImpairmentPowers NR, Eicher JD, Butter F, Kong Y, Miller LL, Ring SM, Mann M, Gruen JR. Alleles of a Polymorphic ETV6 Binding Site in DCDC2 Confer Risk of Reading and Language Impairment. American Journal Of Human Genetics 2013, 93: 19-28. PMID: 23746548, PMCID: PMC3710765, DOI: 10.1016/j.ajhg.2013.05.008.
Negligible impact of rare autoimmune-locus coding-region variants on missing heritabilityHunt KA, Mistry V, Bockett NA, Ahmad T, Ban M, Barker JN, Barrett JC, Blackburn H, Brand O, Burren O, Capon F, Compston A, Gough SC, Jostins L, Kong Y, Lee JC, Lek M, MacArthur DG, Mansfield JC, Mathew CG, Mein CA, Mirza M, Nutland S, Onengut-Gumuscu S, Papouli E, Parkes M, Rich SS, Sawcer S, Satsangi J, Simmonds MJ, Trembath RC, Walker NM, Wozniak E, Todd JA, Simpson MA, Plagnol V, van Heel DA. Negligible impact of rare autoimmune-locus coding-region variants on missing heritability. Nature 2013, 498: 232-235. PMID: 23698362, PMCID: PMC3736321, DOI: 10.1038/nature12170.
Adjusting for Background Mutation Frequency Biases Improves the Identification of Cancer Driver GenesEvans P, Avey S, Kong Y, Krauthammer M. Adjusting for Background Mutation Frequency Biases Improves the Identification of Cancer Driver Genes. IEEE Transactions On NanoBioscience 2013, 12: 150-157. PMID: 23694700, PMCID: PMC3989533, DOI: 10.1109/tnb.2013.2263391.
Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencingdel Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK. Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing. BMC Genomics 2012, 13: 649. PMID: 23171430, PMCID: PMC3526394, DOI: 10.1186/1471-2164-13-649.
Exome sequencing identifies recurrent somatic RAC1 mutations in melanomaKrauthammer M, Kong Y, Ha BH, Evans P, Bacchiocchi A, McCusker J, 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: 1006-1014. 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 ChildrenPettigrew 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: 6262-6270. PMID: 22752171, PMCID: PMC3416608, DOI: 10.1128/aem.01051-12.
Length distribution of sequencing by synthesis: fixed flow cycle modelKong Y. Length distribution of sequencing by synthesis: fixed flow cycle model. Journal Of Mathematical Biology 2012, 67: 389-410. PMID: 22689207, DOI: 10.1007/s00285-012-0556-3.
Forward genetics uncovers Transmembrane protein 107 as a novel factor required for ciliogenesis and Sonic hedgehog signalingChristopher 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: 382-392. PMID: 22698544, PMCID: PMC3402655, DOI: 10.1016/j.ydbio.2012.06.008.
Note: Solution of one-dimensional self-assembly problem in multiple-component systems with correction of overcounting of non-symmetrical complexesKong 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.
The Expectation of Sample Central MomentsKong Y. The Expectation of Sample Central Moments. The American Statistician 2011, 65: 198-199. DOI: 10.1198/tast.2011.11041.
Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologiesKong Y. Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics 2011, 98: 152-153. PMID: 21651976, DOI: 10.1016/j.ygeno.2011.05.009.
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes ProjectMu 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: 7058-7076. PMID: 21596777, PMCID: PMC3167619, DOI: 10.1093/nar/gkr342.
Streptococcus pneumoniae Serotype 6C: an Intra- and Interclonal Complex ComparisonThomas JC, Kong Y, Sabharwal V, Pelton SI, Pettigrew MM. Streptococcus pneumoniae Serotype 6C: an Intra- and Interclonal Complex Comparison. Journal Of Bacteriology 2011, 193: 3409-3410. PMID: 21551297, PMCID: PMC3133277, DOI: 10.1128/jb.05079-11.
Streptococcus pneumoniae Clonal Complex 199: Genetic Diversity and Tissue-Specific VirulenceThomas 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.
Microbial Communities of the Upper Respiratory Tract and Otitis Media in ChildrenLaufer 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.
AlleleSeq: analysis of allele‐specific expression and binding in a network frameworkRozowsky 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: 522-522. PMID: 21811232, PMCID: PMC3208341, DOI: 10.1038/msb.2011.54.
MU2A—reconciling the genome and transcriptome to determine the effects of base substitutionsGarla V, Kong Y, Szpakowski S, Krauthammer M. MU2A—reconciling the genome and transcriptome to determine the effects of base substitutions. Bioinformatics 2010, 27: 416-418. PMID: 21149339, PMCID: PMC3031033, DOI: 10.1093/bioinformatics/btq658.
Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineeringMarlatt 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 And Selection 2010, 24: 311-320. PMID: 21149273, PMCID: PMC3038463, DOI: 10.1093/protein/gzq112.
Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine familyMurphy JW, Yuan H, Kong Y, Xiong Y, Lolis EJ. Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family. Proteins Structure Function And Bioinformatics 2010, 78: 1331-1337. PMID: 20077567, PMCID: PMC3021379, DOI: 10.1002/prot.22666.
Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural VariantsDu 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.
Statistical Distributions of Sequencing by Synthesis with Probabilistic Nucleotide IncorporationKong Y. Statistical Distributions of Sequencing by Synthesis with Probabilistic Nucleotide Incorporation. Journal Of Computational Biology 2009, 16: 817-827. PMID: 19522665, DOI: 10.1089/cmb.2008.0215.
Calculating complexity of large randomized librariesKong Y. Calculating complexity of large randomized libraries. Journal Of Theoretical Biology 2009, 259: 641-645. PMID: 19376134, DOI: 10.1016/j.jtbi.2009.04.008.
Statistical Distributions of PyrosequencingKong Y. Statistical Distributions of Pyrosequencing. Journal Of Computational Biology 2009, 16: 31-42. PMID: 19072582, DOI: 10.1089/cmb.2008.0106.
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*. Journal Of Biological Chemistry 2008, 283: 19511-19520. PMID: 18482985, PMCID: PMC2443660, DOI: 10.1074/jbc.m801074200.
Keck Foundation Biotechnology Resource Laboratory, Yale University.Stone KL, Bjornson RD, Blasko GG, Bruce C, Cofrancesco R, Carriero NJ, Colangelo CM, Crawford JK, Crawford JM, daSilva NC, Deluca JD, Elliott JI, Elliott MM, Flory PJ, Folta-Stogniew EJ, Gulcicek E, Kong Y, Lam TT, Lee JY, Lin A, LoPresti MB, Mane SM, McMurray WJ, Tikhonova IR, Westman S, Williams NA, Wu TL, Hongyu Z, Williams KR. Keck Foundation Biotechnology Resource Laboratory, Yale University. The Yale Journal Of Biology And Medicine 2007, 80: 195-211. PMID: 18449392, PMCID: PMC2347368.
Asymptotics of the monomer-dimer model on two-dimensional semi-infinite latticesKong Y. Asymptotics of the monomer-dimer model on two-dimensional semi-infinite lattices. Physical Review E 2007, 75: 051123. PMID: 17677038, DOI: 10.1103/physreve.75.051123.
Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology SearchKong Y. Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search. Journal Of Computational Biology 2007, 14: 238-254. PMID: 17456017, DOI: 10.1089/cmb.2006.0008.
Monomer-dimer model in two-dimensional rectangular lattices with fixed dimer densityKong Y. Monomer-dimer model in two-dimensional rectangular lattices with fixed dimer density. Physical Review E 2006, 74: 061102. PMID: 17280033, DOI: 10.1103/physreve.74.061102.
Distribution of Runs and Longest RunsKong Y. Distribution of Runs and Longest Runs. Journal Of The American Statistical Association 2006, 101: 1253-1263. DOI: 10.1198/016214505000001401.
Logarithmic corrections in the free energy of monomer-dimer model on plane lattices with free boundariesKong Y. Logarithmic corrections in the free energy of monomer-dimer model on plane lattices with free boundaries. Physical Review E 2006, 74: 011102. PMID: 16907056, DOI: 10.1103/physreve.74.011102.
Packing dimers on (2p+1)×(2q+1) latticesKong Y. Packing dimers on (2p+1)×(2q+1) lattices. Physical Review E 2006, 73: 016106. PMID: 16486215, DOI: 10.1103/physreve.73.016106.
Extension of Goulden–Jackson cluster method on pattern occurrences in random sequences and comparison with Régnier–Szpankowski methodKong Y. Extension of Goulden–Jackson cluster method on pattern occurrences in random sequences and comparison with Régnier–Szpankowski method. The Journal Of Difference Equations And Applications 2005, 11: 1265-1271. DOI: 10.1080/10236190500376326.
MicroRNA: Biological and Computational PerspectiveKong Y, Han J. 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*. Journal Of Biological Chemistry 2004, 279: 42826-42835. PMID: 15284231, DOI: 10.1074/jbc.m406529200.
A Protein Interaction Map of Drosophila melanogasterGiot 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 2003, 302: 1727-1736. PMID: 14605208, DOI: 10.1126/science.1090289.
A note on the quantitative properties of McGhee–von Hippel modelKong 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.
A Simple Method for Evaluating Partition Functions of Linear PolymersKong Y. A Simple Method for Evaluating Partition Functions of Linear Polymers. The Journal Of Physical Chemistry B 2001, 105: 10111-10114. DOI: 10.1021/jp011758n.
General recurrence theory of ligand binding on a three-dimensional latticeKong Y. General recurrence theory of ligand binding on a three-dimensional lattice. The Journal Of Chemical Physics 1999, 111: 4790-4799. DOI: 10.1063/1.479242.
Ligand binding on ladder latticesKong Y. Ligand binding on ladder lattices. Biophysical Chemistry 1999, 81: 7-21. PMID: 17030328, DOI: 10.1016/s0301-4622(99)00078-2.
A Summation Identity: 10575Yu X, Holzsager R, Prasad M, Zeilberger D, Kong Y, Steelman J. A Summation Identity: 10575. American Mathematical Monthly 1999, 106: 266. DOI: 10.2307/2589694.
Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphatesLi 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 1998, 7: 1116-1123. PMID: 9605316, PMCID: PMC2144016, DOI: 10.1002/pro.5560070505.
Calculation of the reaction field due to off-center point multipolesKong Y, Ponder J. Calculation of the reaction field due to off-center point multipoles. The Journal Of Chemical Physics 1997, 107: 481-492. DOI: 10.1063/1.474409.
Theory of multivalent binding in one and two-dimensional latticesDi Cera E, Kong Y. Theory of multivalent binding in one and two-dimensional lattices. Biophysical Chemistry 1996, 61: 107-124. PMID: 17023370, DOI: 10.1016/s0301-4622(96)02178-3.

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