코직 연구발표 논문들

2020

• Decoding a highly mixed Kazakh genome. Seidualy, M., Blazyte, A., Jeon, S., Bhak, Y., Jeon Y., Kim, J., . . . Bhak, J.(2020) Hum Genet.
• Whole Genome Analysis of the Red-Crowned Crane Provides Insight into Avian Longevity. Lee, H., Kim, J., Weber, J. A., Chung, O., Cho, Y. S., Jho, S., . . . Bhak, J. (2020). Mol Cells.

2019

• Brca2 abrogation engages with the alternative lengthening of telomeres via break-induced replication. Kwon, M. S., Lee, J. J., Min, J., Hwang, K., Park, S. G., Kim, E. H., . . . Lee, H. (2019). FEBS J, 286(10), 1841-1858.
• Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information. Kim, H. S., Jeon, S., Kim, C., Kim, Y. K., Cho, Y. S., Kim, J., . . . Bhak, J. (2019). Gigascience, 8(12).
• Combinatory Analysis of Cell-free and Circulating Tumor Cell DNAs Provides More Variants for Cancer Treatment. Lee, S. Y., Chae, D. K., An, J., Yoo, S., Jung, S., Chae, C. H., . . . Cho, D. H. (2019). Anticancer Res, 39(12), 6595-6602.
• Comparison of exercise electrocardiography and magnetocardiography for detection of coronary artery disease using ST-segment fluctuation score. Shin, E. S., Chung, J. H., Park, S. G., Saleh, A., Lam, Y. Y., Bhak, J., . . . Brachmann, J. (2019). Clin Hemorheol Microcirc, 73(2), 283-291.
• Depression and suicide risk prediction models using blood-derived multi-omics data. Bhak, Y., Jeong, H. O., Cho, Y. S., Jeon, S., Cho, J., Gim, J. A., . . . Lee, S. (2019). Transl Psychiatry, 9(1), 262.
• The Draft Genome of an Octocoral, Dendronephthya gigantea. Jeon, Y., Park, S. G., Lee, N., Weber, J. A., Kim, H. S., Hwang, S. J., . . . Yum, S. (2019). Genome Biol Evol, 11(3), 949-953.
• The Galleria mellonella Hologenome Supports Microbiota-Independent Metabolism of Long-Chain Hydrocarbon Beeswax. Kong, H. G., Kim, H. H., Chung, J. H., Jun, J., Lee, S., Kim, H. M., . . . Ryu, C. M. (2019). Cell Rep, 26(9), 2451-2464 e2455.
• The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation. Kim, H. M., Weber, J. A., Lee, N., Park, S. G., Cho, Y. S., Bhak, Y., . . . Yum, S. (2019). BMC Biol, 17(1), 28.
• Investigation of Hanwoo-specific structural variations using whole-genome sequencing data. Park, J., Shin, W., Mun, S., Oh, M. H., Lim, D., Oh, D. Y., . . . Han, K. (2019). Genes Genomics, 41(2), 233-240.
• Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles. Cho, Y. S., Jun, J. H., Kim, J. A., Kim, H. M., Chung, O., Kang, S. G., . . . Bhak, J. (2019). Genome Biology, 20(1), 181.
• Sequencing and analysis of the whole genome of Indian Gujarati male. Almal, S., Jeon, S., Agarwal, M., Patel, S., Patel, S., Bhak, Y., . . . Padh, H. (2019). Genomics, 111(2), 196-204.

2018

• Genomic analysis reveals secondary glioblastoma after radiotherapy in a subset of recurrent medulloblastomas. Phi, J. H., Park, A. K., Lee, S., Choi, S. A., Baek, I. P., Kim, P., . . . Kim, S. K. (2018). Acta Neuropathol, 135(6), 939-953.
• Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia. Yew, C. W., Lu, D., Deng, L., Wong, L. P., Ong, R. T., Lu, Y., . . . Hoh, B. P. (2018). Hum Genet, 137(2), 161-173.
• Grading system for periodontitis by analyzing levels of periodontal pathogens in saliva. Kim, E. H., Joo, J. Y., Lee, Y. J., Koh, J. K., Choi, J. H., Shin, Y., . . . Lee, J. Y. (2018). PLoS One, 13(11), e0200900.
• KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses. Kim, J., Weber, J. A., Jho, S., Jang, J., Jun, J., Cho, Y. S., . . . Bhak, J. (2018). Sci Rep, 8(1), 5677.
• Magnetocardiography scoring system to predict the presence of obstructive coronary artery disease. Shin, E. S., Park, S. G., Saleh, A., Lam, Y. Y., Bhak, J., Jung, F., . . . Brachmann, J. (2018). Clin Hemorheol Microcirc, 70(4), 365-373.
• Whole genome sequencing and bioinformatics analysis of two Egyptian genomes. ElHefnawi, M., Jeon, S., Bhak, Y., ElFiky, A., Horaiz, A., Jun, J., . . . Bhak, J. (2018). Gene, 668, 129-134.

2017

• Analysis of the FGF gene family provides insights into aquatic adaptation in cetaceans. Nam, K., Lee, K. W., Chung, O., Yim, H. S., Cha, S. S., Lee, S. W., . . . Jeong, J. Y. (2017). Sci Rep, 7, 40233.
• Corrigendum: An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Cho, Y. S., Kim, H., Kim, H. M., Jho, S., Jun, J., Lee, Y. J., . . . Bhak, J. (2017). Nat Commun, 8, 16168.
• Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago. Siska, V., Jones, E. R., Jeon, S., Bhak, Y., Kim, H. M., Cho, Y. S., . . . Manica, A. (2017). Sci Adv, 3(2), e1601877.
• Myotis rufoniger genome sequence and analyses: M. rufoniger's genomic feature and the decreasing effective population size of Myotis bats. Bhak, Y., Jeon, Y., Jeon, S., Chung, O., Jho, S., Jun, J., . . . Bhak, J. (2017). PLoS One, 12(7), e0180418.
• Perspectives provided by leopard and other cat genomes: how diet determined the evolutionary history of carnivores, omnivores, and herbivores. Kim, S., Cho, Y. S., Bhak, J., O'Brian, S. J., & Yeo, J. H. (2017). BMB Rep, 50(1), 3-4.

2016

• An adaptive detection method for fetal chromosomal aneuploidy using cell-free DNA from 447 Korean women. Kim, S., Jung, H., Han, S. H., Lee, S., Kwon, J., Kim, M. G., . . . Bhak, J. (2016). Bmc Medical Genomics, 9(1), 61.
• Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly. Kim, S., Cho, Y. S., Kim, H. M., Chung, O., Kim, H., Jho, S., . . . Yeo, J. H. (2016). Genome Biology, 17(1), 211.
• Comparison of two high-throughput semiconductor chip sequencing platforms in noninvasive prenatal testing for Down syndrome in early pregnancy. Kim, S., Jung, H., Han, S. H., Lee, S., Kwon, J., Kim, M. G., . . . Bhak, J. (2016). Bmc Medical Genomics, 9(1), 22.
• An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Cho, Y. S., Kim, H., Kim, H. M., Jho, S., Jun, J., Lee, Y. J., . . . Bhak, J. (2016). Nat Commun, 7, 13637.
• The genetics of an early Neolithic pastoralist from the Zagros, Iran. Gallego-Llorente, M., Connell, S., Jones, E. R., Merrett, D. C., Jeon, Y., Eriksson, A., . . . Pinhasi, R. (2016). Sci Rep, 6, 31326.
• Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. Aranda, M., Li, Y., Liew, Y. J., Baumgarten, S., Simakov, O., Wilson, M. C., . . . Voolstra, C. R. (2016). Sci Rep, 6, 39734.
• RNA-Seq analysis reveals new evidence for inflammation-related changes in aged kidney. Park, D., Kim, B. C., Kim, C. H., Choi, Y. J., Jeong, H. O., Kim, M. E., . . . Chung, H. Y. (2016). Oncotarget, 7(21), 30037-30048.
• Short-term calorie restriction ameliorates genomewide, age-related alterations in DNA methylation. Kim, C. H., Lee, E. K., Choi, Y. J., An, H. J., Jeong, H. O., Park, D., . . . Chung, H. Y. (2016). Aging Cell, 15(6), 1074-1081.

2015

• Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Gallego Llorente, M., Jones, E. R., Eriksson, A., Siska, V., Arthur, K. W., Arthur, J. W., . . . Manica, A. (2015). Science, 350(6262), 820-822.
• Characterization of cetacean Numt and its application into cetacean phylogeny. Ko, Y. J., Yang, E. C., Lee, J. H., Lee, K. W., Jeong, J. Y., Park, K., . . . Yim, H. S. (2015). Genes & Genomics, 37(12), 1061-1071.
• The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures. Chung, O., Jin, S., Cho, Y. S., Lim, J., Kim, H., Jho, S., . . . Paek, W. K. (2015). Genome Biology, 16, 215.
• Genome-wide analysis of DNA methylation before-and after exercise in the thoroughbred horse with MeDIP-Seq. Gim, J. A., Hong, C. P., Kim, D. S., Moon, J. W., Choi, Y., Eo, J., . . . Kim, H. S. (2015). Mol Cells, 38(3), 210-220.
• Genomic legacy of the African cheetah, Acinonyx jubatus. Dobrynin, P., Liu, S., Tamazian, G., Xiong, Z., Yurchenko, A. A., Krasheninnikova, K., . . . O'Brien, S. J. (2015). Genome Biology, 16, 277.
• HEpD: A database describing epigenetic differences between Thoroughbred and Jeju horses. Gim, J. A., Lee, S., Kim, D. S., Jeong, K. S., Hong, C. P., Bae, J. H., . . . Kim, H. S. (2015a). Gene, 560(1), 83-88.
• HExDB: a database for epigenetic changes occurring after horse exercise. Gim, J. A., Lee, S., Kim, D. S., Jeong, K. S., Hong, C. P., Bae, J. H., . . . Kim, H. S. (2015b). Genes & Genomics, 37(3), 287-294.
• Insights into the Evolution of Longevity from the Bowhead Whale Genome. Keane, M., Semeiks, J., Webb, A. E., Li, Y. I., Quesada, V., Craig, T., . . . de Magalhaes, J. P. (2015). Cell reports, 10(1), 112-122.
• Profiling age-related epigenetic markers of stomach adenocarcinoma in young and old subjects. Kim, B. C., Jeong, H. O., Park, D., Kim, C. H., Lee, E. K., Kim, D. H., . . . Chung, H. Y. (2015). Cancer Inform, 14, 47-54.
• SLC15A2 genomic variation is associated with the extraordinary response of sorafenib treatment: whole-genome analysis in patients with hepatocellular carcinoma. Lee, Y. S., Kim, B. H., Kim, B. C., Shin, A., Kim, J. S., Hong, S. H., . . . Park, J. W. (2015). Oncotarget, 6(18), 16449-16460.
• Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan. Ilyas, M., Kim, J. S., Cooper, J., Shin, Y. A., Kim, H. M., Cho, Y. S., . . . Bhak, J. (2015). BMC genomics, 16, 172.

2014

• The feasibility study of non-invasive fetal trisomy 18 and 21 detection with semiconductor sequencing platform. Jeon, Y. J., Zhou, Y., Li, Y., Guo, Q., Chen, J., Quan, S., . . . Bhak, J. (2014). PLoS One, 9(10), e110240.
• Genome-wide analysis of DNA methylation patterns in horse. Lee, J. R., Hong, C. P., Moon, J. W., Jung, Y. D., Kim, D. S., Kim, T. H., . . . Kim, H. S. (2014). BMC genomics, 15, 598.
• Genomic profile analysis of diffuse-type gastric cancers. Lee, Y. S., Cho, Y. S., Lee, G. K., Lee, S., Kim, Y. W., Jho, S., . . . Lee, J. S. (2014). Genome Biology, 15(4).
• Identification and Characterization of MicroRNAs in Normal Equine Tissues by Next Generation Sequencing. Kim, M. C., Lee, S. W., Ryu, D. Y., Cui, F. J., Bhak, J., & Kim, Y. (2014). PLoS One, 9(4).
• Minke whale genome and aquatic adaptation in cetaceans. Yim, H. S., Cho, Y. S., Guang, X., Kang, S. G., Jeong, J. Y., Cha, S. S., . . . Lee, J. H. (2014). Nature Genetics, 46(1), 88-92.
• New lung cancer panel for high-throughput targeted resequencing. Kim, E. H., Lee, S., Park, J., Lee, K., Bhak, J., & Kim, B. C. (2014). Genomics Inform, 12(2), 50-57.
• PPP1R1B-STARD3 chimeric fusion transcript in human gastric cancer promotes tumorigenesis through activation of PI3K/AKT signaling. Yun, S. M., Yoon, K., Lee, S., Kim, E., Kong, S. H., Choe, J., . . . Kim, S. J. (2014). Oncogene, 33(46), 5341-5347.
• Whole-genome analysis of a patient with early-stage small-cell lung cancer. Han, J. Y., Lee, Y. S., Kim, B. C., Lee, G. K., Lee, S., Kim, E. H., . . . Bhak, J. (2014). Pharmacogenomics J, 14(6), 503-508.
• Whole genome sequence and analysis of the Marwari horse breed and its genetic origin. Jun, J., Cho, Y. S., Hu, H., Kim, H. M., Jho, S., Gadhvi, P., . . . Bhak, J. (2014). BMC genomics, 15.

2013

• Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers. Yoon, K., Lee, S., Han, T. S., Moon, S. Y., Yun, S. M., Kong, S. H., . . . Kim, S. J. (2013). Genome Research, 23(7), 1109-1117.
• The genetic basis of white tigers. Xu, X., Dong, G. X., Hu, X. S., Miao, L., Zhang, X. L., Zhang, D. L., . . . Luo, S. J. (2013). Current Biology, 23(11), 1031-1035.
• iAnn: an event sharing platform for the life sciences. Jimenez, R. C., Albar, J. P., Bhak, J., Blatter, M. C., Blicher, T., Brazas, M. D., . . . Corpas, M. (2013). Bioinformatics, 29(15), 1919-1921.
• Peeling back the evolutionary layers of molecular mechanisms responsive to exercise-stress in the skeletal muscle of the racing horse. Kim, H., Lee, T., Park, W., Lee, J. W., Kim, J., Lee, B. Y., . . . Kim, H. (2013). DNA Res, 20(3), 287-298.
• The tiger genome and comparative analysis with lion and snow leopard genomes. Cho, Y. S., Hu, L., Hou, H., Lee, H., Xu, J., Kwon, S., . . . Bhak, J. (2013). Nat Commun, 4, 2433.
• Whole genome comparison of donor and cloned dogs. Kim, H. M., Cho, Y. S., Kim, H., Jho, S., Son, B., Choi, J. Y., . . . Jang, G. (2013). Scientific reports, 3.

2012

• De novo transcriptome sequencing of Momordica cochinchinensis to identify genes involved in the carotenoid biosynthesis. Hyun, T. K., Rim, Y., Jang, H. J., Kim, C. H., Park, J., Kumar, R., . . . Kim, J. Y. (2012). Plant Mol Biol, 79(4-5), 413-427.
• Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion. Xu, S. H., Pugach, I., Stoneking, M., Kayser, M., Jin, L., & Consortium, H. P.-A. S. (2012). Proceedings of the National Academy of Sciences of the United States of America, 109(12), 4574-4579.
• Low budget analysis of Direct-To-Consumer genomic testing familial data. Glusman, G., Cariaso, M., Jimenez, R., Swan, D., Greshake, B., Bhak, J., . . . Corpas, M. (2012). F1000Res, 1, 3.
• MetaBase--the wiki-database of biological databases. Bolser, D. M., Chibon, P. Y., Palopoli, N., Gong, S., Jacob, D., Del Angel, V. D., . . . Bhak, J. (2012). Nucleic Acids Res, 40(Database issue), D1250-1254.
• A public resource facilitating clinical use of genomes. Ball, M. P., Thakuria, J. V., Zaranek, A. W., Clegg, T., Rosenbaum, A. M., Wu, X. D., . . . Church, G. M. (2012). Proceedings of the National Academy of Sciences of the United States of America, 109(30), 11920-11927.
• Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq. Park, K. D., Park, J., Ko, J., Kim, B. C., Kim, H. S., Ahn, K., . . . Cho, B. W. (2012). BMC genomics, 13.

2011

• BetaDock: shape-priority docking method based on beta-complex. Kim, D. S., Kim, C. M., Won, C. I., Kim, J. K., Ryu, J., Cho, Y., . . . Bhak, J. (2011). J Biomol Struct Dyn, 29(1), 219-242.
• Gene expression pattern in transmitochondrial cytoplasmic hybrid cells harboring type 2 diabetes-associated mitochondrial DNA haplogroups. Hwang, S., Kwak, S. H., Bhak, J., Kang, H. S., Lee, Y. R., Koo, B. K., . . . Cho, Y. M. (2011). PLoS One, 6(7), e22116.
• Identification of close relatives in the HUGO Pan-Asian SNP database. Yang, X., Xu, S., Consortium, H. P.-A. S., & Indian Genome Variation, C. (2011). PLoS One, 6(12), e29502.
• Liverome: a curated database of liver cancer-related gene signatures with self-contained context information. Lee, L., Wang, K., Li, G., Xie, Z., Wang, Y., Xu, J., . . . Hwang, S. (2011). BMC genomics, 12 Suppl 3, S3.
• Mutational hotspots in the mitochondrial genome of lung cancer. Choi, S. J., Kim, S. H., Kang, H. Y., Lee, J., Bhak, J. H., Sohn, I., . . . Kim, J. (2011). Biochem Biophys Res Commun, 407(1), 23-27.
• PanSNPdb: the Pan-Asian SNP genotyping database. Ngamphiw, C., Assawamakin, A., Xu, S., Shaw, P. J., Yang, J. O., Ghang, H., . . . Consortium, H. P.-A. S. (2011). PLoS One, 6(6), e21451.
• Population genetic structure of peninsular Malaysia Malay sub-ethnic groups. Hatin, W. I., Nur-Shafawati, A. R., Zahri, M. K., Xu, S., Jin, L., Tan, S. G., . . . Consortium, H. P.-A. S. (2011). PLoS One, 6(4), e18312.

2010

• Alpha-glucosidase folding during urea denaturation: enzyme kinetics and computational prediction. Wu, X. Q., Wang, J., Lu, Z. R., Tang, H. M., Park, D., Oh, S. H., . . . Zou, F. (2010). Appl Biochem Biotechnol, 160(5), 1341-1355.
• Differential evolutionary rates of neuronal transcriptome in Aplysia kurodai and Aplysia californica as a tool for gene mining. Choi, S. L., Lee, Y. S., Rim, Y. S., Kim, T. H., Moroz, L. L., Kandel, E. R., . . . Kaang, B. K. (2010). J Neurogenet, 24(2), 75-82.
• The effect of trifluoroethanol on tyrosinase activity and conformation: inhibition kinetics and computational simulations. Lu, Z. R., Shi, L., Wang, J., Park, D., Bhak, J., Yang, J. M., . . . Zou, F. (2010). Appl Biochem Biotechnol, 160(7), 1896-1908.
• Gene flow between the Korean peninsula and its neighboring countries. Jung, J., Kang, H., Cho, Y. S., Oh, J. H., Ryu, M. H., Chung, H. W., . . . Kim, H. L. (2010). PLoS One, 5(7), e11855.
• Kinetics of Zn(2+)-induced brain type creatine kinase unfolding and aggregation. Mu, H., Lu, Z. R., Park, D., Kim, B. C., Bhak, J., Zou, F., . . . Zhou, H. M. (2010). Appl Biochem Biotechnol, 160(5), 1309-1320.
• PDBWiki: added value through community annotation of the Protein Data Bank. Stehr, H., Duarte, J. M., Lappe, M., Bhak, J., & Bolser, D. M. (2010). Database (Oxford), 2010, baq009.
• A proposal for the revision of molecular boundary typology. Kim, D. S., Won, C. I., & Bhak, J. (2010). J Biomol Struct Dyn, 28(2), 277-288.
• Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. Florez, A. F., Park, D., Bhak, J., Kim, B. C., Kuchinsky, A., Morris, J. H., . . . Muskus, C. (2010). BMC Bioinformatics, 11, 484.
• Sphericity of a protein via the beta-complex. Kim, D. S., Kim, J. K., Won, C. I., Kim, C. M., Park, J. Y., & Bhak, J. (2010). J Mol Graph Model, 28(7), 636-649.
• Structural analysis and inhibitory kinetics of brain type creatine kinase by sodium dodecyl sulfate. Lu, Z. R., Oh, S. H., Zhou, S. S., Zou, H. C., Park, D., Park, S. J., . . . Zou, F. (2010). Appl Biochem Biotechnol, 160(3), 831-842.
• Systematic cyanobacterial membrane proteome analysis by combining acid hydrolysis and digestive enzymes with nano-liquid chromatography-Fourier transform mass spectrometry. Kwon, J., Oh, J., Park, C., Cho, K., Kim, S. I., Kim, S., . . . Choi, J. S. (2010). J Chromatogr A, 1217(3), 285-293.
• Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Kim, M. Y., Lee, S., Van, K., Kim, T. H., Jeong, S. C., Choi, I. Y., . . . Lee, S. H. (2010). Proc Natl Acad Sci U S A, 107(51), 22032-22037.

2009

• BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources. Lim, J., Kim, S. Y., Kim, S., Eo, H. S., Kim, C. B., Paek, W. K., . . . Bhak, J. (2009). BMC genomics, 10 Suppl 3, S8.
• COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System. Jho, S., Kim, B. C., Ghang, H., Kim, J. H., Park, D., Kim, H. M., . . . Bhak, J. (2009). BMC genomics, 10 Suppl 3, S35.
• DNA microarray analyses and interactomic predictions for atopic dermatitis. Lu, Z. R., Kim, W. S., Cho, I. H., Park, D., Bhak, J., Shi, L., . . . Zou, F. (2009). J Dermatol Sci, 55(2), 123-125.
• Dysregulated genes of extrinsic type of atopic dermatitis: 34K microarray and interactomic analyses. Lu, Z. R., Park, T. H., Lee, E. S., Kim, K. J., Park, D., Kim, B. C., . . . Yang, J. M. (2009). J Dermatol Sci, 53(2), 146-150.
• The effects of acrylamide on brain creatine kinase: inhibition kinetics and computational docking simulation. Lu, Z. R., Zou, H. C., Park, S. J., Park, D., Shi, L., Oh, S. H., . . . Zou, F. (2009). Int J Biol Macromol, 44(2), 128-132.
• The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Ahn, S. M., Kim, T. H., Lee, S., Kim, D., Ghang, H., Kim, D. S., . . . Kim, S. J. (2009). Genome Res, 19(9), 1622-1629.
• Gevab: a prototype genome variation analysis browsing server. Kim, W. Y., Kim, S. Y., Kim, T. H., Ahn, S. M., Byun, H. N., Kim, D., . . . Bhak, J. (2009). BMC Bioinformatics, 10 Suppl 15, S3.
• The Korean Bird Information System (KBIS) through open and public participation. Paik, I. H., Lim, J., Chun, B. S., Jin, S. D., Yu, J. P., Lee, J. W., . . . Paek, W. K. (2009). BMC Bioinformatics, 10 Suppl 15, S11.
• Mapping human genetic diversity in Asia. Consortium, H. P.-A. S., Abdulla, M. A., Ahmed, I., Assawamakin, A., Bhak, J., Brahmachari, S. K., . . . Indian Genome Variation, C. (2009). Science, 326(5959), 1541-1545.
• MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. Reja, R., Venkatakrishnan, A. J., Lee, J., Kim, B. C., Ryu, J. W., Gong, S., . . . Park, D. (2009). BMC genomics, 10 Suppl 3, S20.
• MitoVariome: a variome database of human mitochondrial DNA. Lee, Y. S., Kim, W. Y., Ji, M., Kim, J. H., & Bhak, J. (2009). BMC genomics, 10 Suppl 3, S12.
• PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs. Yang, J. O., Kim, W. Y., Jeong, S. Y., Oh, J. H., Jho, S., Bhak, J., & Kim, N. S. (2009). BMC genomics, 10 Suppl 3, S32.
• Planning the human variome project: the Spain report. Kaput, J., Cotton, R. G., Hardman, L., Watson, M., Al Aqeel, A. I., Al-Aama, J. Y., . . . Contributors to the Human Variome Project Planning, M. (2009). Human Mutation, 30(4), 496-510.
• Profiling the dysregulated genes of keratinocytes in atopic dermatitis patients: cDNA microarray and interactomic analyses. Lu, Z. R., Park, D., Lee, K. A., Ryu, J. W., Bhak, J., Shi, L., . . . Yang, J. M. (2009). J Dermatol Sci, 54(2), 126-129.
• PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. Park, S. J., Choi, J. S., Kim, B. C., Jho, S. W., Ryu, J. W., Park, D., . . . Kim, S. I. (2009). BMC genomics, 10 Suppl 3, S18.
• ssSNPTarget: genome-wide splice-site Single Nucleotide Polymorphism database. Yang, J. O., Kim, W. Y., & Bhak, J. (2009). Human Mutation, 30(12), E1010-1020.
• Transcriptome and protein domain analyses in Aplysia nervous system with evolutionary implications. Lee, Y. S., Kim, T. H., Choi, S. L., Lee, S., Bhak, J., & Kaang, B. K. (2009). Commun Integr Biol, 2(4), 321-323.

2008

• Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries. Sangket, U., Phongdara, A., Chotigeat, W., Nathan, D., Kim, W. Y., Bhak, J., . . . Tan, T. W. (2008). Bioinformatics, 24(2), 299-301.
• Cyanobacterial hybrid kinase Sll0043 regulates phototaxis by suppressing pilin and twitching motility protein. Shin, B. J., Oh, J., Kang, S., Chung, Y. H., Park, Y. M., Kim, Y. H., . . . Choi, J. S. (2008). J Microbiol, 46(3), 300-308.
• The effect of histidine residue modification on tyrosinase activity and conformation: inhibition kinetics and computational prediction. Guo, L., Lu, Z. R., Park, D., Oh, S. H., Shi, L., Park, S. J., . . . Zou, F. (2008). J Biomol Struct Dyn, 26(3), 395-402.
• Identification of gene-related Korean patents and construction of a database server for Korean patent sequences. Lee, B., Kim, S.-K., Kim, T., Kim, S. S., Ryu, G. C., & Bhak, J. (2008). Biotechnology and Bioprocess Engineering, 13(2), 248.
• An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases. Yang, J. O., Hwang, S., Oh, J., Bhak, J., & Sohn, T. K. (2008). BMC Bioinformatics, 9 Suppl 12, S19.
• An integrated Korean biodiversity and genetic information retrieval system. Lim, J., Bhak, J., Oh, H. M., Kim, C. B., Park, Y. H., & Paek, W. K. (2008). BMC Bioinformatics, 9 Suppl 12, S24.
• MassNet: a functional annotation service for protein mass spectrometry data. Park, D., Kim, B. C., Cho, S. W., Park, S. J., Choi, J. S., Kim, S. I., . . . Lee, S. (2008). Nucleic Acids Res, 36(Web Server issue), W491-495.
• Personal genomics, bioinformatics, and variomics. Bhak, J., Ghang, H., Reja, R., & Kim, S.-S. (2008). Genomics & Informatics, 6(4), 161-165.
• Pocket extraction on proteins via the Voronoi diagram of spheres. Kim, D., Cho, C. H., Cho, Y., Ryu, J., Bhak, J., & Kim, D. S. (2008). J Mol Graph Model, 26(7), 1104-1112.
• Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. Kim, J. G., Park, D., Kim, B. C., Cho, S. W., Kim, Y. T., Park, Y. J., . . . Bhak, J. (2008). BMC Bioinformatics, 9, 41.
• Prediction and evaluation of protein-protein interaction in keratinocyte differentiation. Yoon, H. K., Sohn, K. C., Lee, J. S., Kim, Y. J., Bhak, J., Yang, J. M., . . . Lee, J. H. (2008). Biochem Biophys Res Commun, 377(2), 662-667.
• Proteomic approaches to the analysis of atopic dermatitis and new insights from interactomics. Park, Y. D., Park, D., Bhak, J., & Yang, J. M. (2008). Proteomics Clin Appl, 2(3), 290-300.
• SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions. Kim, B. C., Kim, W. Y., Park, D., Chung, W. H., Shin, K. S., & Bhak, J. (2008). BMC Bioinformatics, 9 Suppl 1, S2.
• Structural Bioinformatics Analysis of Disease-related Mutations. Park, S.-J., Oh, S.-H., Park, D.-U., & Bhak, J. (2008). Genomics & Informatics, 6(3), 142-146.
• SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. Kim, W. Y., Kang, S., Kim, B. C., Oh, J., Cho, S., Bhak, J., & Choi, J. S. (2008). BMC Bioinformatics, 9 Suppl 1, S20.
• Transcriptome analysis and identification of regulators for long-term plasticity in Aplysia kurodai. Lee, Y. S., Choi, S. L., Kim, T. H., Lee, J. A., Kim, H. K., Kim, H., . . . Kaang, B. K. (2008). Proc Natl Acad Sci U S A, 105(47), 18602-18607.

2007

• Biological Object Downloader (BOD) Service for Easy Download and Management of Biological Databases. Park, D.-U., Lee, J.-W., Yoon, G.-S., Gong, S.-S., & Bhak, J. (2007). Genomics & Informatics, 5(4), 196-199.
• CONSORF: a consensus prediction system for prokaryotic coding sequences. Kang, S., Yang, S. J., Kim, S., & Bhak, J. (2007). Bioinformatics, 23(22), 3088-3090.
• Genomic distribution of simple sequence repeats in Brassica rapa. Hong, C. P., Piao, Z. Y., Kang, T. W., Batley, J., Yang, T. J., Hur, Y. K., . . . Lim, Y. P. (2007). Mol Cells, 23(3), 349-356.
• GS2PATH: a web-based integrated analysis tool for finding functional relationships using gene ontology and biochemical pathway data. Yang, J. O., Charny, P., Lee, B., Kim, S., Bhak, J., & Woo, H. G. (2007). Bioinformation, 2(5), 194-196.
• Impact of transcriptional properties on essentiality and evolutionary rate. Choi, J. K., Kim, S. C., Seo, J., Kim, S., & Bhak, J. (2007). Genetics, 175(1), 199-206.
• Multi-resolution protein model.Kim, D.-S., Lee, B., Won, C.-I., Kim, D., Ryu, J., Cho, Y., . . . Bhak, J. (2007). Paper presented at the International Conference on Computational Science and Its Applications.

2006

• BioCC: an openfree hypertext bio community cluster for biology. Gong, S.-S., Kim, T.-H., Oh, J.-S., Kwon, J.-K., Cho, S.-A., Bolser, D., & Bhak, J. (2006). Genomics & Informatics, 4(3), 125-128.
• Developmental rate and ploidy of embryos produced by nuclear transfer with different activation treatments in cattle. Bhak, J. S., Lee, S. L., Ock, S. A., Mohana Kumar, B., Choe, S. Y., & Rho, G. J. (2006). Anim Reprod Sci, 92(1-2), 37-49.
• Functional annotation and analysis of Korean patented biological sequences using bioinformatics. Lee, B. W., Kim, T. H., Kim, S. K., Kim, S. S., Ryu, G. C., & Bhak, J. (2006). Mol Cells, 21(2), 269-275.
• Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. Lee, S., Lee, B., Jang, I., Kim, S., & Bhak, J. (2006). Nucleic Acids Res, 34(Web Server issue), W99-103.
• Parameter selection of pocket extraction algorithm using interaction interface. Kim, C.-M., Won, C.-I., Ryu, J., Cho, C.-H., Bhak, J., & Kim, D.-S. (2006). Journal of Zhejiang University-Science A, 7(9), 1492-1499.
• Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Yang, T. J., Kim, J. S., Kwon, S. J., Lim, K. B., Choi, B. S., Kim, J. A., . . . Park, B. S. (2006). Plant Cell, 18(6), 1339-1347.

2005

• Architecture of basic building blocks in protein and domain structural interaction networks. Moon, H. S., Bhak, J., Lee, K. H., & Lee, D. (2005). Bioinformatics, 21(8), 1479-1486.
• BioCovi: A Visualization Service for Comparative Genomics Analysis. Lee, J., Park, D., & Bhak, J. (2005). Genomics Inform, 3(2), 52.
• BioSubroutine: an Open Web Server for Bioinformatics Algorithms and Subroutines. Lee, J., Kim, H., Lee, W., Chung, D., & Bhak, J. (2005). Genomics & Informatics, 3(1), 35-38.
• Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map). Park, D., Lee, S., Bolser, D., Schroeder, M., Lappe, M., Oh, D., & Bhak, J. (2005). Bioinformatics, 21(15), 3234-3240.
• Euclidean Voronoi diagrams of 3D spheres and applications to protein structure analysis. Kim, D.-S., Cho, Y., Kim, D., Kim, S., Bhak, J., & Lee, S.-H. (2005). Japan Journal of Industrial and Applied Mathematics, 22(2), 251.
• HExDB: Human EXon DataBase for Alternative Splicing Pattern Analysis and predicted human gene number. Park¹, J., Lee¹, M., Kim, T. H., & Bhak, J. (2005). Genomics & Informatics, 3(3), 112-117.
• A protein domain interaction interface database: InterPare. Gong, S., Park, C., Choi, H., Ko, J., Jang, I., Lee, J., . . . Bhak, J. (2005). BMC Bioinformatics, 6, 207.
• PSIbase: a database of Protein Structural Interactome map (PSIMAP). Gong, S., Yoon, G., Jang, I., Bolser, D., Dafas, P., Schroeder, M., . . . Bhak, J. (2005). Bioinformatics, 21(10), 2541-2543.

2004

• The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions. An, H. J., Lee, D., Lee, K. H., & Bhak, J. (2004). BMC genomics, 5(1), 97.
• The Atom of Evolution. Bhak, J., Bolser, D., Park, D., Cho, Y., Yoo, K., Lee, S., . . . Huston, M. (2004). Genomics & Informatics, 2(4), 167-173.
• High Correlation between Alu Elements and the Conversion of 3'UTR of mRNAs Processed Pseudogenes. An, H. J., Na, D., Lee, D., Lee, K. H., & Bhak, J. (2004). Genomics & Informatics, 2(2), 86-91.
• HPID: the Human Protein Interaction Database. Han, K., Park, B., Kim, H., Hong, J., & Park, J. (2004). Bioinformatics, 20(15), 2466-2470.
• Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Kim, W. K., Bolser, D. M., & Park, J. H. (2004). Bioinformatics, 20(7), 1138-1150.
• Using convex hulls to extract interaction interfaces from known structures. Dafas, P., Bolser, D., Gomoluch, J., Park, J., & Schroeder, M. (2004). Bioinformatics, 20(10), 1486-1490.

2003

• Biological network evolution hypothesis applied to protein structural interactome. Bolser, D. M., & Park, J. H. (2003). Genomics & Informatics, 1(1), 7-19.
• Challenges and New Approaches in Genomics and Bioinformatics. Park, J. H., & Han, K. S. (2003). Genomics & Informatics, 1(1), 1-6.
• Different activation treatments for successful development of bovine oocytes following intracytoplasmic sperm injection. Ock, S. A., Bhak, J. S., Balasubramanian, S., Lee, H. J., Choe, S. Y., & Rho, G. J. (2003). Zygote, 11(1), 69-76.
• Predicting protein interactions in human by homologous interactions in yeast.Kim, H., Park, J., & Han, K. (2003). Paper presented at the Pacific-Asia Conference on Knowledge Discovery and Data Mining.
• Visualisation and graph-theoretic analysis of a large-scale protein structural interactome. Bolser, D., Dafas, P., Harrington, R., Park, J., & Schroeder, M. (2003). BMC Bioinformatics, 4, 45.
• Visualization and analysis of protein interactions. Ju, B. H., Park, B., Park, J. H., & Han, K. (2003). Bioinformatics, 19(2), 317-318.

2002

• InterViewer: Dynamic visualization of protein-protein interactions.Han, K., Ju, B.-H., & Park, J. H. (2002). Paper presented at the International Symposium on Graph Drawing.
• Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair. Kim, W. K., Park, J., & Suh, J. K. (2002). Genome Inform, 13, 42-50.
• Protein Interactions in the Whole Human Genome. Han, K., Park, B., Kim, H., Kim, H.-J., & Park, J. (2002). Genome Informatics, 13, 318-319.
• Sequence similarity between stereocilin and otoancorin points to a unified mechanism for mechanotransduction in the mammalian inner ear. Jovine, L., Park, J., & Wassarman, P. M. (2002). BMC cell biology, 3(1), 28.

2001

• Conservation of protein interaction network in evolution. Park, J., & Bolser, D. (2001). Genome Inform, 12, 135-140.
• A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Dietmann, S., Park, J., Notredame, C., Heger, A., Lappe, M., & Holm, L. (2001). Nucleic Acids Res, 29(1), 55-57.
• Generating protein interaction maps from incomplete data: application to fold assignment. Lappe, M., Park, J., Niggemann, O., & Holm, L. (2001). Bioinformatics, 17 Suppl 1, S149-156.
• An Integrated Bioinformatic Search Server: Sequences, Structure, Interaction, and Function of Proteins (SSIF) Server. Lee, J.-H., Koh, I. S., & Park, J. (2001). Genome Informatics, 12, 480-481.
• Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. Park, J., Lappe, M., & Teichmann, S. A. (2001). J Mol Biol, 307(3), 929-938.
• PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. Qian, J., Stenger, B., Wilson, C. A., Lin, J., Jansen, R., Teichmann, S. A., . . . Gerstein, M. (2001). Nucleic Acids Res, 29(8), 1750-1764.
• Protein classification comparison server. Park, J.-H., Ryu, S.-R., Kim, C., Koh, I. S., & Park, J. (2001). Genome Informatics, 12, 350-351.

2000

• DaliLite workbench for protein structure comparison. Holm, L., & Park, J. (2000). Bioinformatics, 16(6), 566-567.
• Estimating the significance of sequence order in protein secondary structure and prediction. Park, J., Dietmann, S., Heger, A., & Holm, L. (2000). Bioinformatics, 16(11), 978-987.
• Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Teichmann, S. A., Chothia, C., Church, G. M., & Park, J. (2000). Bioinformatics, 16(2), 117-124.
• RSDB: representative protein sequence databases have high information content. Park, J., Holm, L., Heger, A., & Chothia, C. (2000). Bioinformatics, 16(5), 458-464.
• Sequence search algorithm assessment and testing toolkit (SAT). Park, J., Holm, L., & Chothia, C. (2000). Bioinformatics, 16(2), 104-110.

1998

• DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Park, J., & Teichmann, S. A. (1998). Bioinformatics, 14(2), 144-150.
• Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T., & Chothia, C. (1998). Journal of molecular biology, 284(4), 1201-1210.
• Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Teichmann, S. A., Park, J., & Chothia, C. (1998). Proc Natl Acad Sci U S A, 95(25), 14658-14663.

1997

• Intermediate sequences increase the detection of homology between sequences. Park, J., Teichmann, S. A., Hubbard, T., & Chothia, C. (1997). J Mol Biol, 273(1), 349-354.

1996

• Protein structure prediction: playing the fold. Hubbard, T., Park, J., Lahm, A., Leplae, R., & Tramontano, A. (1996). Trends Biochem Sci, 21(8), 279-281.

• Update on protein structure prediction: results of the 1995 IRBM workshop. Hubbard, T., & Tramontano, A. (1996). Fold Des, 1(3), R55-63.

1995

• Fold recognition and ab initio structure predictions using hidden Markov models and beta-strand pair potentials. Hubbard, T. J., & Park, J. (1995). Proteins, 23(3), 398-402.