Selected Publications
  • J. Sung, S. Kim, J. J. T. Cabatbat, S. Jang, Y.-S. Jin, G. Y. Jung, N. Chia, P.-J. Kim, “Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis”, Nat. Commun. 8, 15393 (2017), Link
  • – Featured in major Korean news media
  • J.-S. Kim, D.-H. Cho, P. Heo, S.-C. Jung, M. Park, E.-J. Oh, J. Sung, P.-J. Kim, S. Lee, D.-H. Lee, S. Lee, C. H. Lee, D. Shin, Y.-S. Jin, D.-H. Kweon, "Fumarate-mediated persistence of Escherichia coli against antibiotics", Antimicrob. Agents Chemother. 60, 2232 (2016), Link
  • M. Foo, D. E. Somers, P.-J. Kim, “Kernel architecture of the genetic circuitry of the Arabidopsis circadian system”, PLOS Comput. Biol. 12, e1004748 (2016), Link
  • Y. Lee, W. Hwang, J. Jung, S. Park, J. J. T. Cabatbat, P.-J. Kim, S.-J. V. Lee, “Inverse correlation between longevity and developmental rate among wild C. elegans strains”, Aging 8, 986 (2016), Link
  • S. Kim, J. Sung, M. Foo, Y.-S. Jin, P.-J. Kim, “Uncovering the nutritional landscape of food”, PLOS ONE 10, e0118697 (2015), Link
  • – Featured in major Korean news media
  • J. Yun, P.-J. Kim, H. Jeong, “Anatomy of scientific evolution”, PLOS ONE 10, e0117388 (2015), Link
  • – Physics Today (The Dayside, “The psychohistory of scientific evolution”)
  • – MIT Technology Review (“Other Interesting arXiv Papers”)
  • M. Foo, D. E. Somers, P.-J. Kim, “System identification of the Arabidopsis plant circadian system”, J. Korean Phys. Soc. 66, 700 (2015), Link
  • J. Quarterman, S. R. Kim, P.-J. Kim, Y.-S. Jin, “Enhanced hexose fermentation by Saccharomyces cerevisiae through integration of stoichiometric modeling and genetic screening”, J. Biotechnol. 194, 48 (2015), Link
  • P.-J. Kim, “Systems biology: communication between physics and biology”, Physics and High Technology 23, 10 (2014), Link
  • – Invited review paper
  • Y. Dong, C. G. Kumar, N. Chia, P.-J. Kim, P. A. Miller, et al., “Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir”, Environ. Microbiol. 16, 1695 (2014), Link
  • – Featured in ScienceDaily, Science World Report, R&D Magazine, Astrobiology Web, Phys.org, and Technology.org
  • J. Sung, P.-J. Kim, S. Ma, C. C. Funk, A. T. Magis, Y. Wang, L. Hood, D. Geman, N. D. Price, “Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures”, PLoS Comput. Biol. 9, e1003148 (2013), Link
  • P.-J. Kim, N. D. Price, “Genetic co-occurrence network across sequenced microbes”, PLoS Comput. Biol. 7, e1002340 (2011), Link
  • S. H. Lee, P.-J. Kim, H. Jeong, “Global organization of protein complexome in the yeast Saccharomyces cerevisiae”,
    BMC Syst. Biol. 5, 126 (2011), Link
  • – Ranked as most viewed articles
  • P.-J. Kim, N. D. Price, “Macroscopic kinetic effect of cell-to-cell variation in biochemical reactions”, Phys. Rev. Lett. 104, 148103 (2010), Link
  • – Science News (“Enzymes Exposed”)
  • S. H. Lee, P.-J. Kim, Y.-Y. Ahn, H. Jeong, "Googling social interactions: Web search engine based social network construction", PLoS ONE 5, e11233 (2010), Link
  • – New Scientist (“Google tracks political allegiances”); also featured in Pocket Science
  • P.-J. Kim, D.-Y. Lee, H. Jeong, “Centralized modularity of N-linked glycosylation pathways in mammalian cells”, PLoS ONE 4, e7317 (2009), Link
  • C. B. Milne, P.-J. Kim, J. A. Eddy, N. D. Price, “Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology”, Biotechnol. J. 4, 1653 (2009), Link
  • – Highlighted in “in this issue” section
  • P.-J. Kim, D.-Y. Lee, T. Y. Kim, K. H. Lee, H. Jeong, S. Y. Lee, S. Park, “Metabolite essentiality elucidates robustness of Escherichia coli metabolism”, Proc. Natl. Acad. Sci. USA 104, 13638 (2007), Link
  • – 100+ citations
  • – Featured in major Korean news media
  • P.-J. Kim, T.-W. Ko, H. Jeong, K. J. Lee, S. K. Han, "Emergence of chaotic itinerancy in simple ecological systems", Phys. Rev. E 76, 065201(R) (2007), Link
  • P.-J. Kim, H. Jeong, "Reliability of rank order in sampled networks", Eur. Phys. J. B 55, 109 (2007), Link
  • S. H. Lee, P.-J. Kim, H. Jeong, "Statistical properties of sampled networks", Phys. Rev. E 73, 016102 (2006), Link
  • – 490+ citations
  • P.-J. Kim, H. Jeong, "Spatio-temporal dynamics in the origin of genetic information", Physica D 203, 88 (2005), Link
  • P.-J. Kim, T.-W. Ko, H. Jeong, H.-T. Moon, "Pattern formation in a two-dimensional array of oscillators with phase-shifted coupling", Phys. Rev. E 70, 065201(R) (2004), Link
Patents
  • S. Y. Lee, H. Jeong, T. Y. Kim, P.-J. Kim, K. H. Lee, "Method for screening essential metabolites in growth of microorganisms", US Patent, Registered, US 8,494,779 (July 23, 2013)
  • S. Y. Lee, H. Jeong, T. Y. Kim, P.-J. Kim, K. H. Lee, "Method for screening essential metabolites in growth of microorganisms", Korean Patent, Registered, 10-0818202 (March 25, 2008)