Junhyong Kim

Junhyong Kim

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Junhyong Kim

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A lineage-resolved molecular atlas of embryogenesis at single-cell resolution.

Science 2019 Sep 5. Epub 2019 Sep 5.

Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1126/science.aax1971DOI Listing
September 2019

Understanding the kidney one cell at a time.

Kidney Int 2019 Jul 26. Epub 2019 Jul 26.

Renal, Electrolyte, and Hypertension Division, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA. Electronic address:

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http://dx.doi.org/10.1016/j.kint.2019.03.035DOI Listing
July 2019

Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons.

BMC Biol 2019 01 24;17(1). Epub 2019 Jan 24.

Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, 160 BRB II/III - 421 Curie Blvd, Philadelphia, PA, 19104-6064, USA.

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http://dx.doi.org/10.1186/s12915-019-0630-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344992PMC
January 2019

miRNA Profiling of Magnetic Nanopore-Isolated Extracellular Vesicles for the Diagnosis of Pancreatic Cancer.

Cancer Res 2018 07 7;78(13):3688-3697. Epub 2018 May 7.

Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-3703DOI Listing
July 2018

Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH.

Cell Syst 2018 Feb 14;6(2):171-179.e5. Epub 2018 Feb 14.

Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.01.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6078200PMC
February 2018

PIVOT: platform for interactive analysis and visualization of transcriptomics data.

BMC Bioinformatics 2018 01 5;19(1). Epub 2018 Jan 5.

Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1186/s12859-017-1994-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5756333PMC
January 2018

Coordination of olfactory receptor choice with guidance receptor expression and function in olfactory sensory neurons.

PLoS Genet 2018 01 31;14(1):e1007164. Epub 2018 Jan 31.

Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5809090PMC
January 2018

Single cell transcriptomics of noncoding RNAs and their cell-specificity.

Wiley Interdiscip Rev RNA 2017 11 1;8(6). Epub 2017 Aug 1.

Department of Biology, Penn Program in Single Cell Biology, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1002/wrna.1433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5675046PMC
November 2017

Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data.

Nucleic Acids Res 2017 Nov;45(19):10978-10988

Department of Statistics, University of Pennsylvania Wharton School, Philadelphia, PA 19104, USA.

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http://academic.oup.com/nar/article/45/19/10978/4210934
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http://dx.doi.org/10.1093/nar/gkx754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737676PMC
November 2017

CYCLOPS reveals human transcriptional rhythms in health and disease.

Proc Natl Acad Sci U S A 2017 05 24;114(20):5312-5317. Epub 2017 Apr 24.

Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.

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http://dx.doi.org/10.1073/pnas.1619320114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5441789PMC
May 2017

Complete fold annotation of the human proteome using a novel structural feature space.

Sci Rep 2017 04 13;7:46321. Epub 2017 Apr 13.

Genomics and Computational Biology Program, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1038/srep46321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5390313PMC
April 2017

The purinergic receptor P2X5 regulates inflammasome activity and hyper-multinucleation of murine osteoclasts.

Sci Rep 2017 03 15;7(1):196. Epub 2017 Mar 15.

Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.

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http://www.nature.com/articles/s41598-017-00139-2
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http://dx.doi.org/10.1038/s41598-017-00139-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5427844PMC
March 2017

High-resolution transcriptome analysis reveals neuropathic pain gene-expression signatures in spinal microglia after nerve injury.

Pain 2016 Apr;157(4):964-76

aPain Cognitive Function Research Center, Seoul National University, Seoul, Republic of Korea bDental Research Institute and Department of Neurobiology and Physiology, School of Dentistry, Seoul National University, Seoul, Republic of Korea cDepartment of Biology, University of Pennsylvania, Philadelphia, PA, USA dMedical Genomics Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Korea eDepartment of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA fPain Research Laboratory, Institute of Nautical Medicine, Nantong University, Nantong, Jiangsu, China gDepartment of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA hDepartment of Brain and Cognitive Sciences, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea.

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http://pdfs.journals.lww.com/pain/2016/04000/High_resolution
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http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:land
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http://dx.doi.org/10.1097/j.pain.0000000000000470DOI Listing
April 2016

Variation is function: Are single cell differences functionally important?: Testing the hypothesis that single cell variation is required for aggregate function.

Bioessays 2016 Feb 2;38(2):172-80. Epub 2015 Dec 2.

Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1002/bies.201500124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4738397PMC
February 2016

Single-cell transcriptomics and functional target validation of brown adipocytes show their complex roles in metabolic homeostasis.

FASEB J 2016 Jan 24;30(1):81-92. Epub 2015 Aug 24.

*Department of Pharmacology, Department of Genomics and Computational Biology, and Department of Cell and Developmental Biology, Perelman School of Medicine, and Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA; and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA

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http://dx.doi.org/10.1096/fj.15-273797DOI Listing
January 2016

Cellular Deconstruction: Finding Meaning in Individual Cell Variation.

Trends Cell Biol 2015 Oct;25(10):569-578

Department of Biology, Department of Computer and Information Science, School of Arts and Sciences, Program in Single Cell Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tcb.2015.07.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4584424PMC
October 2015

The exonuclease Nibbler regulates age-associated traits and modulates piRNA length in Drosophila.

Aging Cell 2015 Jun 6;14(3):443-52. Epub 2015 Mar 6.

Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1111/acel.12323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406673PMC
June 2015

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.

Genome Biol 2015 Jun 9;16:122. Epub 2015 Jun 9.

Department of Biology, School of Arts and Sciences, University of Pennsylvania, 301A/B Lynch Laboratory, 433 S University Avenue, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1186/s13059-015-0683-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480509PMC
June 2015

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

J Comput Biol 2015 May 30;22(5):377-86. Epub 2014 Dec 30.

1 Department of Computer Science, University of Texas at Austin , Austin, Texas.

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http://dx.doi.org/10.1089/cmb.2014.0156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424971PMC
May 2015

Can one hear the shape of a population history?

Theor Popul Biol 2015 03 11;100C:26-38. Epub 2014 Dec 11.

University of Melbourne, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.tpb.2014.12.002DOI Listing
March 2015

NoFold: RNA structure clustering without folding or alignment.

RNA 2014 Nov 18;20(11):1671-83. Epub 2014 Sep 18.

Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

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http://dx.doi.org/10.1261/rna.041913.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201820PMC
November 2014

Cytoplasmic intron retention, function, splicing, and the sentinel RNA hypothesis.

Wiley Interdiscip Rev RNA 2014 Mar-Apr;5(2):223-30. Epub 2013 Nov 4.

Department of Pharmacology, Perelman School of Medicine and the School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1002/wrna.1203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449146PMC
September 2014

Machine learning helps identify CHRONO as a circadian clock component.

PLoS Biol 2014 Apr 15;12(4):e1001840. Epub 2014 Apr 15.

Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America; Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1001840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988006PMC
April 2014

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue.

Nat Methods 2014 Feb 12;11(2):190-6. Epub 2014 Jan 12.

1] Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [2] PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [3].

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http://dx.doi.org/10.1038/nmeth.2804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964595PMC
February 2014

The promise of single-cell sequencing.

Nat Methods 2014 Jan;11(1):25-7

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January 2014

Dendritic glutamate receptor mRNAs show contingent local hotspot-dependent translational dynamics.

Cell Rep 2013 Oct 26;5(1):114-25. Epub 2013 Sep 26.

Department of Pharmacology, Perelman School of Medicine, Philadelphia, PA 19104-6084, USA.

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http://dx.doi.org/10.1016/j.celrep.2013.08.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901016PMC
October 2013

Pervasive antisense transcription is evolutionarily conserved in budding yeast.

Mol Biol Evol 2013 Feb 18;30(2):409-21. Epub 2012 Oct 18.

Department of Biology, School of Arts and Sciences, University of Pennsylvania, USA.

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http://dx.doi.org/10.1093/molbev/mss240DOI Listing
February 2013

Quantitative biology of single neurons.

J R Soc Interface 2012 Dec 22;9(77):3165-83. Epub 2012 Aug 22.

Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, 36th and Hamilton Walk, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1098/rsif.2012.0417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3481569PMC
December 2012

Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6.

BMC Evol Biol 2012 Aug 22;12:153. Epub 2012 Aug 22.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/1471-2148-12-153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495861PMC
August 2012

Transcriptome transfer provides a model for understanding the phenotype of cardiomyocytes.

Proc Natl Acad Sci U S A 2011 Jul 5;108(29):11918-23. Epub 2011 Jul 5.

Department of Pharmacology, University of Pennsylvania Medical School, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1073/pnas.1101223108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141937PMC
July 2011

Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes.

Genome Biol 2010 22;11(10):R105. Epub 2010 Oct 22.

Department of Biology, University of Pennsylvania, 433 S, University Ave, Philadelphia, PA 19104, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2010-11-10-r105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218661PMC
June 2011

Sniper: improved SNP discovery by multiply mapping deep sequenced reads.

Genome Biol 2011 Jun 20;12(6):R55. Epub 2011 Jun 20.

Department of Biology, University of Pennsylvania, 433 S, University Ave., Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1186/gb-2011-12-6-r55DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218843PMC
June 2011

RNA: state memory and mediator of cellular phenotype.

Trends Cell Biol 2010 Jun 9;20(6):311-8. Epub 2010 Apr 9.

Penn Genome Frontiers Institute, Department of Biology, University of Pennsylvania Medical School, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1016/j.tcb.2010.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892202PMC
June 2010

Dissecting the molecular mechanism of drosophila odorant receptors through activity modeling and comparative analysis.

Proteins 2010 Feb;78(2):381-99

Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1002/prot.22556DOI Listing
February 2010

Penalized likelihood phylogenetic inference: bridging the parsimony-likelihood gap.

Syst Biol 2008 Oct;57(5):665-74

Department of Biology and Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1080/10635150802422274DOI Listing
October 2008

Self containment, a property of modular RNA structures, distinguishes microRNAs.

PLoS Comput Biol 2008 Aug 22;4(8):e1000150. Epub 2008 Aug 22.

Genomics and Computational Biology Program, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2517099PMC
August 2008

Translation of sensory input into behavioral output via an olfactory system.

Neuron 2008 Jul;59(1):110-24

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1016/j.neuron.2008.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2496968PMC
July 2008

Mutational robustness and geometrical form in protein structures.

J Exp Zool B Mol Dev Evol 2008 May;310(3):216-26

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1002/jez.b.21203DOI Listing
May 2008

Transcriptional target prediction using qualitative reasoning.

Conf Proc IEEE Eng Med Biol Soc 2006 ;1:3138-41

Dept. of Biol., Univ. of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1109/IEMBS.2006.259290DOI Listing
March 2008

Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees.

Syst Biol 2008 Feb;57(1):160-6

Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1080/10635150701884640DOI Listing
February 2008

Efficient enumeration of phylogenetically informative substrings.

J Comput Biol 2007 Jul-Aug;14(6):701-23

Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1089/cmb.2007.R011DOI Listing
September 2007

Molecular evolution of Drosophila odorant receptor genes.

Mol Biol Evol 2007 May 1;24(5):1198-207. Epub 2007 Mar 1.

Penn Center for Bioinformatics, University of Pennsylvania, USA.

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http://dx.doi.org/10.1093/molbev/msm038DOI Listing
May 2007

Patterns of sequence conservation in presynaptic neural genes.

Genome Biol 2006 ;7(11):R105

Penn Center for Bioinformatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1186/gb-2006-7-11-r105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794582PMC
March 2007

Molecular phylogeny of coral-reef sea cucumbers (Holothuriidae: Aspidochirotida) based on 16S mitochondrial ribosomal DNA sequence.

Mar Biotechnol (NY) 2005 Jan-Feb;7(1):53-60. Epub 2004 Dec 30.

Department of Ecology and Evolutionary Biology, Osborn Zoölogical Laboratories, Yale University, New Haven, CT 06520, U.S.A.

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http://dx.doi.org/10.1007/s10126-004-0019-yDOI Listing
February 2006

A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression.

Nature 2005 Nov;438(7065):220-3

Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, Connecticut 06520-8106, USA.

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http://dx.doi.org/10.1038/nature04114DOI Listing
November 2005

Estimating genomic coexpression networks using first-order conditional independence.

Genome Biol 2004 30;5(12):R100. Epub 2004 Nov 30.

Department of Biology, University of Pennsylvania, 415 S University Avenue, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1186/gb-2004-5-12-r100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545795PMC
October 2005

The cobweb of life revealed by genome-scale estimates of horizontal gene transfer.

PLoS Biol 2005 Oct 30;3(10):e316. Epub 2005 Aug 30.

Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1371/journal.pbio.0030316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1233574PMC
October 2005

A combinatorial toolbox for protein sequence design and landscape analysis in the grand canonical model.

J Comput Biol 2002 ;9(5):721-41

Department of Computer Science, Yale University, New Haven, CT 06520-8285, USA.

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http://dx.doi.org/10.1089/106652702761034154DOI Listing
May 2003

Reconstructing the temporal ordering of biological samples using microarray data.

Bioinformatics 2003 May;19(7):842-50

Department of Ecology and Evolutionary Biology, Yale University School of Medicine, New Haven, CT, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg081DOI Listing
May 2003

Unwrapping glial biology: Gcm target genes regulating glial development, diversification, and function.

Neuron 2003 May;38(4):567-80

Institutes of Neuroscience and Molecular Biology, University of Oregon, Eugene, OR 97403, USA.

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http://www.pbrc.hawaii.edu/~danh/Neurodiversity/Fall%202011/
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http://dx.doi.org/10.1016/s0896-6273(03)00289-7DOI Listing
May 2003

Evolution of gene expression in the Drosophila melanogaster subgroup.

Nat Genet 2003 Feb 27;33(2):138-44. Epub 2003 Jan 27.

Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, Connecticut 06520-8106, USA.

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http://dx.doi.org/10.1038/ng1086DOI Listing
February 2003

Gene discovery by e-genetics: Drosophila odor and taste receptors.

J Cell Sci 2002 Mar;115(Pt 6):1107-12

Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA.

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March 2002

THE ACCURACY OF PHYLOGENETIC ESTIMATION USING THE NEIGHBOR-JOINING METHOD.

Evolution 1993 Apr;47(2):471-486

Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, NY, 11794, USA.

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http://dx.doi.org/10.1111/j.1558-5646.1993.tb02107.xDOI Listing
April 1993

ACCURACY OF ESTIMATED PHYLOGENIES: EFFECTS OF TREE TOPOLOGY AND EVOLUTIONARY MODEL.

Evolution 1990 Sep;44(6):1671-1684

Department of Ecology and Evolution, State University of New York, Stony Brook, NY, 11794, USA.

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http://dx.doi.org/10.1111/j.1558-5646.1990.tb03855.xDOI Listing
September 1990

ACCURACY OF PHYLOGENETIC-ESTIMATION METHODS UNDER UNEQUAL EVOLUTIONARY RATES.

Evolution 1988 May;42(3):596-602

Department of Ecology and Evolution, State University of New York, Stony Brook, NY, 11794.

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http://dx.doi.org/10.1111/j.1558-5646.1988.tb04163.xDOI Listing
May 1988