JUNHYONG contact KIM

Summary

Affiliation: University of Pennsylvania
Country: USA

Publications

  1. pmc Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons
    Mugdha Khaladkar
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 8:e76194. 2013
  2. pmc Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6
    Paul E Turner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    BMC Evol Biol 12:153. 2012
  3. pmc The cobweb of life revealed by genome-scale estimates of horizontal gene transfer
    Fan Ge
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    PLoS Biol 3:e316. 2005
  4. pmc Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes
    Daniel F Simola
    Department of Biology, University of Pennsylvania, 433 S, University Ave, Philadelphia, PA 19104, USA
    Genome Biol 11:R105. 2010
  5. pmc Patterns of sequence conservation in presynaptic neural genes
    Dexter Hadley
    Penn Center for Bioinformatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Biol 7:R105. 2006
  6. pmc Estimating genomic coexpression networks using first-order conditional independence
    Paul M Magwene
    Department of Biology, University of Pennsylvania, 415 S University Avenue, Philadelphia, PA 19104, USA
    Genome Biol 5:R100. 2004
  7. pmc Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling
    Timothy E Gookin
    Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    Genome Biol 9:R120. 2008
  8. pmc RNA: state memory and mediator of cellular phenotype
    Junhyong Kim
    Penn Genome Frontiers Institute, Department of Biology, University of Pennsylvania Medical School, University of Pennsylvania, Philadelphia, PA 19104, USA
    Trends Cell Biol 20:311-8. 2010
  9. pmc Sniper: improved SNP discovery by multiply mapping deep sequenced reads
    Daniel F Simola
    Department of Biology, University of Pennsylvania, 433 S, University Ave, Philadelphia, PA 19104, USA
    Genome Biol 12:R55. 2011
  10. doi request reprint Penalized likelihood phylogenetic inference: bridging the parsimony-likelihood gap
    Junhyong Kim
    Department of Biology and Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    Syst Biol 57:665-74. 2008

Research Grants

  1. Single-cell comparative genomics of the neuron
    Junhyong Kim; Fiscal Year: 2009
  2. Comparative Approaches to Bio-knowledge Discovery
    Junhyong Kim; Fiscal Year: 2005
  3. Single-cell comparative genomics of the neuron
    JUNHYONG contact KIM; Fiscal Year: 2010

Collaborators

  • Li San Wang
  • Mugdha Khaladkar
  • Daniel F Simola
  • Michael J Sanderson
  • Timothy E Gookin
  • Stanislav Angelov
  • Sridhar Hannenhalli
  • Paul Sniegowski
  • David Meaney
  • Paul M Magwene
  • Alexander M Kerr
  • D M Hillis
  • Derrick J Zwickl
  • Miler T Lee
  • Paul E Turner
  • Jai Yoon Sul
  • Tracy A Heath
  • Sheng Guo
  • Dexter Hadley
  • Fan Ge
  • Matthew E Roth
  • Scott A Rifkin
  • James Aspnes
  • Siobain Duffy
  • Robert C McBride
  • Yul W Yang
  • Rebecca Montville
  • Sun Jin Lee
  • Chia wen K Wu
  • Minsun Kim
  • Peter Buckley
  • Vijay Kumar
  • Tiina Peritz
  • James Eberwine
  • Tae Kyung Kim
  • Fanyi Zeng
  • David J Cappelleri
  • Jeanine Jochems
  • Margaret Maronski
  • Lyle Ungar
  • Maja Bucan
  • Tara Murphy
  • Otto Valladares
  • Carol D Graham
  • Anton Tevelev
  • Craig E Parman
  • David M Kranz
  • Anthony Valerio
  • Paul M Lizardi
  • Li Feng
  • Jason P Affourtit
  • Martin J Mattessich
  • Kevin J McConnell
  • Debasish Raha
  • Brent Orr
  • Chris Michaelson
  • Lisa Guccione
  • Cesar E Guerra
  • Paul J Schaffer
  • Kevin R Piper
  • Conrad Halling
  • Rixin Wang
  • Clotilde Perbost
  • Michelle Lacey
  • Jane S Merkel
  • Jennifer Lane
  • Joseph C Kaufman
  • Ji Liao
  • Baoge Ying
  • Darin R Latimer
  • Barbara Jedrzkiewicz
  • Gino Intrieri
  • Jonathan Hnath
  • Harish Krishnaswamy
  • Lorri Guccione
  • Brenda Zolla
  • Stephen W Powell
  • Jayashree Hariharan
  • Maura J Ford
  • Kevin P White
  • Julia Hartling
  • Ming Yang Kao
  • Gauri Shah

Detail Information

Publications22

  1. pmc Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons
    Mugdha Khaladkar
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 8:e76194. 2013
    ..We also speculate that release of CIRT sequences prior to translation may form RNA-based signals within the cell potentially comprising a novel class of signaling pathways. ..
  2. pmc Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6
    Paul E Turner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    BMC Evol Biol 12:153. 2012
    ..The resulting tree yielded 32 clones at the tips and internal nodes; these strains were fully sequenced and measured for phenotypic changes in selected traits (fitness on original and novel hosts)...
  3. pmc The cobweb of life revealed by genome-scale estimates of horizontal gene transfer
    Fan Ge
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    PLoS Biol 3:e316. 2005
    ..We propose that HGT events, even when relatively common, still leave the treelike history of phylogenies intact, much like cobwebs hanging from tree branches...
  4. pmc Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes
    Daniel F Simola
    Department of Biology, University of Pennsylvania, 433 S, University Ave, Philadelphia, PA 19104, USA
    Genome Biol 11:R105. 2010
    ..Here, we examined transcriptome evolution in the dynamical context of the budding yeast cell-division cycle, to investigate the extent of divergence in expression timing and the regulatory architecture underlying timing evolution...
  5. pmc Patterns of sequence conservation in presynaptic neural genes
    Dexter Hadley
    Penn Center for Bioinformatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Biol 7:R105. 2006
    ..Because synaptic function is evolutionarily conserved, we reasoned that functional sequences of genes and related genomic elements known to play important roles in neurotransmitter release would also be conserved...
  6. pmc Estimating genomic coexpression networks using first-order conditional independence
    Paul M Magwene
    Department of Biology, University of Pennsylvania, 415 S University Avenue, Philadelphia, PA 19104, USA
    Genome Biol 5:R100. 2004
    ..We apply this algorithm to our coexpression network model and show that subgraphs found using this approach correspond to particular biological processes or contain representatives of distinct gene families...
  7. pmc Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling
    Timothy E Gookin
    Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    Genome Biol 9:R120. 2008
    ....
  8. pmc RNA: state memory and mediator of cellular phenotype
    Junhyong Kim
    Penn Genome Frontiers Institute, Department of Biology, University of Pennsylvania Medical School, University of Pennsylvania, Philadelphia, PA 19104, USA
    Trends Cell Biol 20:311-8. 2010
    ..We argue that the quantitative state of RNA can be likened to a state memory, that when transferred between cells, alters the phenotype in a predictable manner...
  9. pmc Sniper: improved SNP discovery by multiply mapping deep sequenced reads
    Daniel F Simola
    Department of Biology, University of Pennsylvania, 433 S, University Ave, Philadelphia, PA 19104, USA
    Genome Biol 12:R55. 2011
    ..An implementation of Sniper is freely available at http://kim.bio.upenn.edu/software/sniper.shtml...
  10. doi request reprint Penalized likelihood phylogenetic inference: bridging the parsimony-likelihood gap
    Junhyong Kim
    Department of Biology and Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    Syst Biol 57:665-74. 2008
    ..Furthermore, using the appropriate penalty function, the complexity of the underlying models can be partitioned into separately controlled classes allowing flexible control of model complexity...
  11. ncbi request reprint Efficient enumeration of phylogenetically informative substrings
    Stanislav Angelov
    Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, USA
    J Comput Biol 14:701-23. 2007
    ..Finally, we use our tag enumeration algorithm to analyze a phylogeny containing 57 whole microbial genomes. We find tags for all nodes in the phylogeny except the root for which we find generalized tag sets...
  12. pmc Self containment, a property of modular RNA structures, distinguishes microRNAs
    Miler T Lee
    Genomics and Computational Biology Program, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
    PLoS Comput Biol 4:e1000150. 2008
    ..Analysis of self containment will be important for both annotation and design of functional RNAs. A Python implementation and Web interface to calculate the self-containment index are available at http://kim.bio.upenn.edu/software/...
  13. ncbi request reprint Transcriptional target prediction using qualitative reasoning
    Li San Wang
    Dept of Biol, Univ of Pennsylvania, Philadelphia, PA 19104, USA
    Conf Proc IEEE Eng Med Biol Soc 1:3138-41. 2006
    ..Our new algorithm performed comparably to published approaches and allowed rapid analysis of complex, multiple gene selection criteria...
  14. ncbi request reprint Molecular evolution of Drosophila odorant receptor genes
    Sheng Guo
    Penn Center for Bioinformatics, University of Pennsylvania, USA
    Mol Biol Evol 24:1198-207. 2007
    ..This repertoire has been largely maintained in the current species, whereas lineage-specific gene duplication seems to have led to additional specialization in some species in response to specific ecological conditions...
  15. pmc Transcriptome transfer produces a predictable cellular phenotype
    Jai Yoon Sul
    Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 106:7624-9. 2009
    ..The host-cell phenotypic changes develop over many weeks and are persistent. We call this process of RNA-induced phenotype changes, transcriptome-induced phenotype remodeling...
  16. ncbi request reprint Reconstructing the temporal ordering of biological samples using microarray data
    Paul M Magwene
    Department of Ecology and Evolutionary Biology, Yale University School of Medicine, New Haven, CT, USA
    Bioinformatics 19:842-50. 2003
    ..Methods are needed that can utilize multi-dimensional data, such as those resulting from DNA microarray experiments, in order to reconstruct time series from unordered or poorly ordered sets of observations...
  17. doi request reprint Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees
    Tracy A Heath
    Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, Texas 78712, USA
    Syst Biol 57:160-6. 2008
  18. ncbi request reprint A combinatorial toolbox for protein sequence design and landscape analysis in the grand canonical model
    James Aspnes
    Department of Computer Science, Yale University, New Haven, CT 06520 8285, USA
    J Comput Biol 9:721-41. 2002
    ..We have further used the algorithms to analyze 3D structures drawn from the Protein Data Bank and have discovered some novel relationships between such native 3D structures and the Grand Canonical model...
  19. ncbi request reprint Evolution of gene expression in the Drosophila melanogaster subgroup
    Scott A Rifkin
    Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, Connecticut 06520 8106, USA
    Nat Genet 33:138-44. 2003
    ..Our results demonstrate extensive evolution of developmental gene expression among closely related species...
  20. ncbi request reprint Expression profiling using a hexamer-based universal microarray
    Matthew E Roth
    Agilix Corporation, 2 Church Street South, New Haven, Connecticut 06519, USA
    Nat Biotechnol 22:418-26. 2004
    ..The technology was also used to demonstrate expression profiling from a hybrid organism in a proof-of-concept experiment where a T-cell receptor gene was expressed in yeast...
  21. ncbi request reprint Molecular phylogeny of coral-reef sea cucumbers (Holothuriidae: Aspidochirotida) based on 16S mitochondrial ribosomal DNA sequence
    Alexander M Kerr
    Department of Ecology and Evolutionary Biology, Osborn Zo├Âlogical Laboratories, Yale University, New Haven, CT 06520, U S A
    Mar Biotechnol (NY) 7:53-60. 2005
    ..Cuvierian tubules, defensive organs unique to numerous members of Holothuriidae, were probably present before the initial radiation of the family, but the reconstruction is ambiguous as to their ancestral function...
  22. ncbi request reprint Gene discovery by e-genetics: Drosophila odor and taste receptors
    Junhyong Kim
    Department of Molecular, Cellular and Developmental Biology, Yale University, P O Box 208103, New Haven, CT 06520 8103, USA
    J Cell Sci 115:1107-12. 2002
    ..Modification of the algorithm should allow identification of other classes of multitransmembrane-domain protein...

Research Grants3

  1. Single-cell comparative genomics of the neuron
    Junhyong Kim; Fiscal Year: 2009
    ....
  2. Comparative Approaches to Bio-knowledge Discovery
    Junhyong Kim; Fiscal Year: 2005
    ..An existing PhD level training program in biomedical computing will be supplemented to provide research experience for undergraduates and masters students. ..
  3. Single-cell comparative genomics of the neuron
    JUNHYONG contact KIM; Fiscal Year: 2010
    ....