Junhyong Kim - Publications

Biology University of Pennsylvania, Philadelphia, PA, United States 

49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Eberwine J, Kim J. Cellular Deconstruction: Finding Meaning in Individual Cell Variation. Trends in Cell Biology. 25: 569-578. PMID 26410403 DOI: 10.1016/J.Tcb.2015.07.004  1
2015 Spaethling JM, Sanchez-Alavez M, Lee J, Xia FC, Dueck H, Wang W, Fisher SA, Sul JY, Seale P, Kim J, Bartfai T, Eberwine J. Single-cell transcriptomics and functional target validation of brown adipocytes show their complex roles in metabolic homeostasis. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. PMID 26304220 DOI: 10.1096/Fj.15-273797  1
2015 Kim KT, Lee HW, Lee HO, Kim SC, Seo YJ, Chung W, Eum HH, Nam DH, Kim J, Joo KM, Park WY. Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. Genome Biology. 16: 127. PMID 26084335 DOI: 10.1186/S13059-015-0692-3  1
2015 Dueck H, Khaladkar M, Kim TK, Spaethling JM, Francis C, Suresh S, Fisher SA, Seale P, Beck SG, Bartfai T, Kuhn B, Eberwine J, Kim J. Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. Genome Biology. 16: 122. PMID 26056000 DOI: 10.1186/S13059-015-0683-4  1
2015 Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 377-86. PMID 25549288 DOI: 10.1089/Cmb.2014.0156  1
2014 Kim J, Mossel E, Rácz MZ, Ross N. Can one hear the shape of a population history? Theoretical Population Biology. 100: 26-38. PMID 25498195 DOI: 10.1016/J.Tpb.2014.12.002  1
2014 Middleton SA, Kim J. NoFold: RNA structure clustering without folding or alignment. Rna (New York, N.Y.). 20: 1671-83. PMID 25234928 DOI: 10.1261/Rna.041913.113  1
2014 Lovatt D, Ruble BK, Lee J, Dueck H, Kim TK, Fisher S, Francis C, Spaethling JM, Wolf JA, Grady MS, Ulyanova AV, Yeldell SB, Griepenburg JC, Buckley PT, Kim J, et al. Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. Nature Methods. 11: 190-6. PMID 24412976 DOI: 10.1038/Nmeth.2804  0.36
2013 Khaladkar M, Buckley PT, Lee MT, Francis C, Eghbal MM, Chuong T, Suresh S, Kuhn B, Eberwine J, Kim J. Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons. Plos One. 8: e76194. PMID 24098440 DOI: 10.1371/Journal.Pone.0076194  1
2013 Goodman AJ, Daugharthy ER, Kim J. Pervasive antisense transcription is evolutionarily conserved in budding yeast. Molecular Biology and Evolution. 30: 409-21. PMID 23079418 DOI: 10.1093/Molbev/Mss240  1
2012 Eberwine J, Lovatt D, Buckley P, Dueck H, Francis C, Kim TK, Lee J, Lee M, Miyashiro K, Morris J, Peritz T, Schochet T, Spaethling J, Sul JY, Kim J. Quantitative biology of single neurons. Journal of the Royal Society, Interface / the Royal Society. 9: 3165-83. PMID 22915636 DOI: 10.1098/Rsif.2012.0417  1
2012 Turner PE, McBride RC, Duffy S, Montville R, Wang LS, Yang YW, Lee SJ, Kim J. Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6. Bmc Evolutionary Biology. 12: 153. PMID 22913547 DOI: 10.1186/1471-2148-12-153  1
2011 Kim TK, Sul JY, Peternko NB, Lee JH, Lee M, Patel VV, Kim J, Eberwine JH. Transcriptome transfer provides a model for understanding the phenotype of cardiomyocytes. Proceedings of the National Academy of Sciences of the United States of America. 108: 11918-23. PMID 21730152 DOI: 10.1073/Pnas.1101223108  1
2011 Simola DF, Kim J. Sniper: improved SNP discovery by multiply mapping deep sequenced reads. Genome Biology. 12: R55. PMID 21689413 DOI: 10.1186/Gb-2011-12-6-R55  1
2011 Buckley PT, Lee MT, Sul JY, Miyashiro KY, Bell TJ, Fisher SA, Kim J, Eberwine J. Cytoplasmic intron sequence-retaining transcripts can be dendritically targeted via ID element retrotransposons. Neuron. 69: 877-84. PMID 21382548 DOI: 10.1016/J.Neuron.2011.02.028  1
2010 Bell TJ, Miyashiro KY, Sul JY, Buckley PT, Lee MT, McCullough R, Jochems J, Kim J, Cantor CR, Parsons TD, Eberwine JH. Intron retention facilitates splice variant diversity in calcium-activated big potassium channel populations. Proceedings of the National Academy of Sciences of the United States of America. 107: 21152-7. PMID 21078998 DOI: 10.1073/Pnas.1015264107  1
2010 Simola DF, Francis C, Sniegowski PD, Kim J. Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes. Genome Biology. 11: R105. PMID 20969771 DOI: 10.1186/Gb-2010-11-10-R105  1
2010 Kim J, Eberwine J. RNA: state memory and mediator of cellular phenotype. Trends in Cell Biology. 20: 311-8. PMID 20382532 DOI: 10.1016/J.Tcb.2010.03.003  1
2010 Guo S, Kim J. Dissecting the molecular mechanism of drosophila odorant receptors through activity modeling and comparative analysis. Proteins. 78: 381-99. PMID 19714770 DOI: 10.1002/Prot.22556  1
2009 Bucan M, Abrahams BS, Wang K, Glessner JT, Herman EI, Sonnenblick LI, Alvarez Retuerto AI, Imielinski M, Hadley D, Bradfield JP, Kim C, Gidaya NB, Lindquist I, Hutman T, Sigman M, ... ... Kim J, et al. Genome-wide analyses of exonic copy number variants in a family-based study point to novel autism susceptibility genes. Plos Genetics. 5: e1000536. PMID 19557195 DOI: 10.1371/Journal.Pgen.1000536  1
2009 Sul JY, Wu CW, Zeng F, Jochems J, Lee MT, Kim TK, Peritz T, Buckley P, Cappelleri DJ, Maronski M, Kim M, Kumar V, Meaney D, Kim J, Eberwine J. Transcriptome transfer produces a predictable cellular phenotype. Proceedings of the National Academy of Sciences of the United States of America. 106: 7624-9. PMID 19380745 DOI: 10.1073/Pnas.0902161106  1
2008 Kim J, Sanderson MJ. Penalized likelihood phylogenetic inference: bridging the parsimony-likelihood gap. Systematic Biology. 57: 665-74. PMID 18853355 DOI: 10.1080/10635150802422274  1
2008 Lee MT, Kim J. Self containment, a property of modular RNA structures, distinguishes microRNAs. Plos Computational Biology. 4: e1000150. PMID 18725951 DOI: 10.1371/Journal.Pcbi.1000150  1
2008 Gookin TE, Kim J, Assmann SM. Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling. Genome Biology. 9: R120. PMID 18671868 DOI: 10.1186/Gb-2008-9-7-R120  1
2008 Kreher SA, Mathew D, Kim J, Carlson JR. Translation of sensory input into behavioral output via an olfactory system. Neuron. 59: 110-24. PMID 18614033 DOI: 10.1016/J.Neuron.2008.06.010  1
2008 Heath TA, Zwickl DJ, Kim J, Hillis DM. Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Systematic Biology. 57: 160-6. PMID 18300029 DOI: 10.1080/10635150701884640  1
2008 Hartling J, Kim J. Mutational robustness and geometrical form in protein structures. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 310: 216-26. PMID 17973270 DOI: 10.1002/Jez.B.21203  1
2007 Angelov S, Harb B, Kannan S, Khanna S, Kim J. Efficient enumeration of phylogenetically informative substrings. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 701-23. PMID 17691889 DOI: 10.1089/Cmb.2007.R011  1
2007 Guo S, Kim J. Molecular evolution of Drosophila odorant receptor genes. Molecular Biology and Evolution. 24: 1198-207. PMID 17331958 DOI: 10.1093/Molbev/Msm038  1
2006 Wang LS, Wagner D, Kwon CS, Su Y, Kim J. Transcriptional target prediction using qualitative reasoning. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 1: 3138-41. PMID 17947008 DOI: 10.1109/IEMBS.2006.259290  1
2006 Hadley D, Murphy T, Valladares O, Hannenhalli S, Ungar L, Kim J, Bućan M. Patterns of sequence conservation in presynaptic neural genes. Genome Biology. 7: R105. PMID 17096848 DOI: 10.1186/Gb-2006-7-11-R105  1
2005 Ge F, Wang LS, Kim J. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. Plos Biology. 3: e316. PMID 16122348 DOI: 10.1371/Journal.Pbio.0030316  1
2005 Kerr AM, Janies DA, Clouse RM, Samyn Y, Kuszak J, Kim J. Molecular phylogeny of coral-reef sea cucumbers (Holothuriidae: Aspidochirotida) based on 16S mitochondrial ribosomal DNA sequence. Marine Biotechnology (New York, N.Y.). 7: 53-60. PMID 15997365 DOI: 10.1007/S10126-004-0019-Y  1
2005 Kim J, Jonassen I. Guest editorial: WABI special section part II Ieee/Acm Transactions On Computational Biology and Bioinformatics. 2: 1. DOI: 10.1109/Tcbb.2004.42  1
2004 Magwene PM, Kim J. Estimating genomic coexpression networks using first-order conditional independence. Genome Biology. 5: R100. PMID 15575966 DOI: 10.1186/Gb-2004-5-12-R100  1
2004 Roth ME, Feng L, McConnell KJ, Schaffer PJ, Guerra CE, Affourtit JP, Piper KR, Guccione L, Hariharan J, Ford MJ, Powell SW, Krishnaswamy H, Lane J, Guccione L, Intrieri G, ... ... Kim J, et al. Expression profiling using a hexamer-based universal microarray. Nature Biotechnology. 22: 418-26. PMID 15024387 DOI: 10.1038/Nbt948  1
2004 Kim J, Jonassen I. Guest editorial: WABI special section part 1 Ieee/Acm Transactions On Computational Biology and Bioinformatics. 1: 137. DOI: 10.1109/TCBB.2004.42  1
2004 Angelov S, Harb B, Kannan S, Khanna S, Kim J, Wang LS. Genome identification and classification by short oligo arrays Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3240: 400-411.  1
2003 Freeman MR, Delrow J, Kim J, Johnson E, Doe CQ. Unwrapping glial biology: Gcm target genes regulating glial development, diversification, and function. Neuron. 38: 567-80. PMID 12765609 DOI: 10.1016/S0896-6273(03)00289-7  1
2003 Magwene PM, Lizardi P, Kim J. Reconstructing the temporal ordering of biological samples using microarray data. Bioinformatics (Oxford, England). 19: 842-50. PMID 12724294 DOI: 10.1093/Bioinformatics/Btg081  1
2002 Aspnes J, Hartling J, Kao MY, Kim J, Shah G. A combinatorial toolbox for protein sequence design and landscape analysis in the grand canonical model. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 721-41. PMID 12487760 DOI: 10.1089/106652702761034154  1
2002 Kim J, Carlson JR. Gene discovery by e-genetics: Drosophila odor and taste receptors. Journal of Cell Science. 115: 1107-12. PMID 11884511  1
2002 Kim J. Computers are from mars, organisms are from venus Computer. 35: 25-32+9. DOI: 10.1109/Mc.2002.1016898  1
2001 Warr C, Clyne P, de Bruyne M, Kim J, Carlson JR. Olfaction in Drosophila: coding, genetics and e-genetics. Chemical Senses. 26: 201-6. PMID 11238252 DOI: 10.1093/Chemse/26.2.201  1
2001 Kerr AM, Kim J. Phylogeny of Holothuroidea (Echinodermata) inferred from morphology Zoological Journal of the Linnean Society. 133: 63-81. DOI: 10.1111/J.1096-3642.2001.Tb00623.X  1
2000 Rifkin SA, Atteson K, Kim J. Constraint structure analysis of gene expression. Functional & Integrative Genomics. 1: 174-85. PMID 11793235 DOI: 10.1007/S101420000018  1
2000 Kim J, Moriyama EN, Warr CG, Clyne PJ, Carlson JR. Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural properties. Bioinformatics (Oxford, England). 16: 767-75. PMID 11108699  1
1999 Clyne PJ, Warr CG, Freeman MR, Lessing D, Kim J, Carlson JR. A novel family of divergent seven-transmembrane proteins: candidate odorant receptors in Drosophila. Neuron. 22: 327-38. PMID 10069338 DOI: 10.1016/S0896-6273(00)81093-4  1
1993 Kim J. Improving the accuracy of phylogenetic estimation by combining different methods Systematic Biology. 42: 331-340. DOI: 10.1093/Sysbio/42.3.331  1
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