Works by Kim, Junhyong

Results: 53

Machine Learning Helps Identify CHRONO as a Circadian Clock Component.

Published in:

PLoS Biology, 2014, v. 12, n. 4, p. 1, doi. 10.1371/journal.pbio.1001840

By:

Anafi, Ron C.;
Lee, Yool;
Sato, Trey K.;
Venkataraman, Anand;
Ramanathan, Chidambaram;
Kavakli, Ibrahim H.;
Hughes, Michael E.;
Baggs, Julie E.;
Growe, Jacqueline;
Liu, Andrew C.;
Kim, Junhyong;
Hogenesch, John B.

Publication type:

Article

The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer.

Published in:

PLoS Biology, 2005, v. 3, n. 10, p. 1709, doi. 10.1371/journal.pbio.0030316

By:

Fan Ge;
Li-San Wang;
Junhyong Kim

Publication type:

Article

The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer.

Published in:

PLoS Biology, 2005, v. 3, n. 8, p. 1, doi. 10.1371/journal.pbio.0030316

By:

Ge, Fan;
Wang, Li-San;
Kim, Junhyong

Publication type:

Article

Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural properties.

Published in:

Bioinformatics, 2000, v. 16, n. 9, p. 767, doi. 10.1093/bioinformatics/16.9.767

By:

Junhyong Kim;
Moriyama, Etsuko N.;
Warr, Coral G.;
Clyne, Peter J.;
Carlson, John R.

Publication type:

Article

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

Published in:

Aging Cell, 2015, v. 14, n. 3, p. 443, doi. 10.1111/acel.12323

By:

Feltzin, Virzhiniya L.;
Khaladkar, Mugdha;
Abe, Masashi;
Parisi, Michael;
Hendriks, Gert‐Jan;
Kim, Junhyong;
Bonini, Nancy M.

Publication type:

Article

CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-43158-6

By:

Lu, Youtao;
Lee, Jaehee;
Li, Jifen;
Allu, Srinivasa Rao;
Wang, Jinhui;
Kim, HyunBum;
Bullaughey, Kevin L.;
Fisher, Stephen A.;
Nordgren, C. Erik;
Rosario, Jean G.;
Anderson, Stewart A.;
Ulyanova, Alexandra V.;
Brem, Steven;
Chen, H. Isaac;
Wolf, John A.;
Grady, M. Sean;
Vinogradov, Sergei A.;
Kim, Junhyong;
Eberwine, James

Publication type:

Article

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0692-3

By:

Kyu-Tae Kim;
Hye Won Lee;
Hae-Ock Lee;
Sang Cheol Kim;
Yun Jee Seo;
Woosung Chung;
Hye Hyeon Eum;
Do-Hyun Nam;
Junhyong Kim;
Kyeung Min Joo;
Woong-Yang Park

Publication type:

Article

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

Published in:

Genome Biology, 2015, v. 16, p. 1, doi. 10.1186/s13059-015-0683-4

By:

Dueck, Hannah;
Khaladkar, Mugdha;
Tae Kyung Kim;
Spaethling, Jennifer M.;
Francis, Chantal;
Suresh, Sangita;
Fisher, Stephen A.;
Seale, Patrick;
Beck, Sheryl G.;
Bartfai, Tamas;
Kuhn, Bernhard;
Eberwine, James;
Junhyong Kim

Publication type:

Article

IVT-seq reveals extreme bias in RNA-sequencing.

Published in:

Genome Biology, 2014, v. 15, n. 6, p. 1, doi. 10.1186/gb-2014-15-6-r86

By:

Lahens, Nicholas F.;
Kavakli, Ibrahim Halil;
Ray Zhang;
Hayer, Katharina;
Black, Michael B.;
Dueck, Hannah;
Pizarro, Angel;
Junhyong Kim;
Irizarry, Rafael;
Thomas, Russell S.;
Grant, Gregory R.;
Hogenesch, John B.

Publication type:

Article

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

Published in:

Genome Biology, 2011, v. 12, n. 6, p. 1, doi. 10.1186/gb-2011-12-6-r55

By:

Simola, Daniel F.;
Junhyong Kim

Publication type:

Article

Single-mitochondrion sequencing uncovers distinct mutational patterns and heteroplasmy landscape in mouse astrocytes and neurons.

Published in:

BMC Biology, 2024, v. 22, n. 1, p. 1, doi. 10.1186/s12915-024-01953-7

By:

Kadam, Parnika S.;
Yang, Zijian;
Lu, Youtao;
Zhu, Hua;
Atiyas, Yasemin;
Shah, Nishal;
Fisher, Stephen;
Nordgren, Erik;
Kim, Junhyong;
Issadore, David;
Eberwine, James

Publication type:

Article

Phylogeny of Holothuroidea (Echinodermata) inferred from morphology.

Published in:

Zoological Journal of the Linnean Society, 2001, v. 133, n. 1, p. 63, doi. 10.1111/j.1096-3642.2001.tb00623.x

By:

KERR, ALEXANDER M.;
KIM, JUNHYONG

Publication type:

Article

Divergence of RNA localization between rat and mouse neurons reveals the potential for rapid brain evolution.

Published in:

BMC Genomics, 2014, v. 15, n. 1, p. 883, doi. 10.1186/1471-2164-15-883

By:

Francis, Chantal;
Natarajan, Shreedhar;
Lee, Miler T;
Khaladkar, Mugdha;
Buckley, Peter T;
Sul, Jai-Yoon;
Eberwine, James;
Junhyong Kim

Publication type:

Article

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

Published in:

BMC Evolutionary Biology, 2012, v. 12, n. 1, p. 153, doi. 10.1186/1471-2148-12-153

By:

Turner, Paul E.;
McBride, Robert C.;
Duffy, Siobain;
Montville, Rebecca;
Wang, Li-San;
Yang, Yul W.;
Lee, Sun Jin;
Kim, Junhyong

Publication type:

Article

Self Containment, a Property of Modular RNA Structures, Distinguishes microRNAs.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 8, p. 1, doi. 10.1371/journal.pcbi.1000150

By:

Lee, Miler T.;
Junhyong Kim

Publication type:

Article

Systematic Sampling of the Female Reproductive System for Molecular Characterization.

Published in:

Current Protocols, 2023, v. 3, n. 8, p. 1, doi. 10.1002/cpz1.848

By:

Fisher, Stephen A.;
Grijalva, Marielena;
Guo, Rong;
Johnston, Sarah A.;
Laurent, Louise C.;
Nguyen, Hieu;
Renz, John;
Rosario, Jean G.;
Rudich, Steven;
Gregory, Brian D.;
Kim, Junhyong;
O'Neill, Kathleen

Publication type:

Article

Depth-corrected multi-factor dissection of chromatin accessibility for scATAC-seq data with PACS.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-024-55580-5

By:

Miao, Zhen;
Wang, Jianqiao;
Park, Kernyu;
Kuang, Da;
Kim, Junhyong

Publication type:

Article

Challenges and emerging directions in single-cell analysis.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1218-y

By:

Guo-Cheng Yuan;
Long Cai;
Elowitz, Michael;
Enver, Tariq;
Guoping Fan;
Guoji Guo;
Irizarry, Rafael;
Kharchenko, Peter;
Junhyong Kim;
Orkin, Stuart;
Quackenbush, John;
Saadatpour, Assieh;
Schroeder, Timm;
Shivdasani, Ramesh;
Tirosh, Itay

Publication type:

Article

Evolution of gene expression in the Drosophila melanogaster subgroup.

Published in:

Nature Genetics, 2003, v. 33, n. 2, p. 138, doi. 10.1038/ng1086

By:

Rifkin, Scott A.;
Junhyong Kim;
White, Kevin P.

Publication type:

Article

Insertion variants missing in the human reference genome are widespread among human populations.

Published in:

BMC Biology, 2020, v. 18, n. 1, p. 1, doi. 10.1186/s12915-020-00894-1

By:

Lee, Young-gun;
Lee, Jin-young;
Kim, Junhyong;
Kim, Young-Joon

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2018, v. 19, p. 1, doi. 10.1186/s12859-017-1994-0

By:

Zhu, Qin;
Fisher, Stephen A.;
Dueck, Hannah;
Middleton, Sarah;
Khaladkar, Mugdha;
Kim, Junhyong

Publication type:

Article

Variation is function: Are single cell differences functionally important?

Published in:

BioEssays, 2016, v. 38, n. 2, p. 172, doi. 10.1002/bies.201500124

By:

Dueck, Hannah;
Eberwine, James;
Kim, Junhyong

Publication type:

Article

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

Published in:

PLoS Genetics, 2018, v. 14, n. 1, p. 1, doi. 10.1371/journal.pgen.1007164

By:

Dang, Puneet;
Fisher, Stephen A.;
Stefanik, Derek;
Kim, Junhyong;
Raper, Jonathan A.

Publication type:

Article

Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment.

Published in:

Science Translational Medicine, 2019, v. 11, n. 513, p. 1, doi. 10.1126/scitranslmed.aaw6419

By:

Liu, Honghai;
Zhang, Cheng-Hai;
Ammanamanchi, Niyatie;
Suresh, Sangita;
Lewarchik, Christopher;
Rao, Krithika;
Uys, Gerrida M.;
Han, Lu;
Abrial, Maryline;
Yimlamai, Dean;
Ganapathy, Balakrishnan;
Guillermier, Christelle;
Chen, Nathalie;
Khaladkar, Mugdha;
Spaethling, Jennifer;
Eberwine, James H.;
Kim, Junhyong;
Walsh, Stuart;
Choudhury, Sangita;
Little, Kathryn

Publication type:

Article

Penalized Likelihood Phylogenetic Inference: Bridging the Parsimony-Likelihood Gap.

Published in:

Systematic Biology, 2008, v. 57, n. 5, p. 665, doi. 10.1080/10635150802422274

By:

Junhyong Kim;
Sanderson, Michael J.

Publication type:

Article

Taxon Sampling Affects Inferences of Macroevolutionary Processes from Phylogenetic Trees.

Published in:

Systematic Biology, 2008, v. 57, n. 1, p. 160, doi. 10.1080/10635150701884640

By:

Heath, Tracy A.;
Zwickl, Derrick J.;
Junhyong Kim;
Hillis, David M.

Publication type:

Article

Ancestral State Estimation and Taxon Sampling Density.

Published in:

Systematic Biology, 2001, v. 50, n. 4, p. 557, doi. 10.1080/106351501750435103

By:

Salisbury, Benjamin A.;
Kim, Junhyong

Publication type:

Article

Parametric Phylogenetics?

Published in:

Systematic Biology, 2000, v. 49, n. 4, p. 817, doi. 10.1080/106351500750049860

By:

Sanderson, Michael J.;
Kim, Junhyong

Publication type:

Article

Large-Scale Phylogenies and Measuring the Performance of Phylogenetic Estimators.

Published in:

Systematic Biology, 1998, v. 47, n. 1, p. 43, doi. 10.1080/106351598261021

By:

Kim, Junhyong

Publication type:

Article

General Inconsistency Conditions for Maximum Parsimony: Effects of Branch Lengths and Increasing Numbers of Taxa.

Published in:

Systematic Biology, 1996, v. 45, n. 3, p. 363, doi. 10.1093/sysbio/45.3.363

By:

Kim, Junhyong

Publication type:

Article

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

Published in:

Nature Methods, 2014, v. 11, n. 2, p. 190, doi. 10.1038/nmeth.2804

By:

Lovatt, Ditte;
Ruble, Brittani K;
Lee, Jaehee;
Dueck, Hannah;
Kim, Tae Kyung;
Fisher, Stephen;
Francis, Chantal;
Spaethling, Jennifer M;
Wolf, John A;
Grady, M Sean;
Ulyanova, Alexandra V;
Yeldell, Sean B;
Griepenburg, Julianne C;
Buckley, Peter T;
Kim, Junhyong;
Sul, Jai-Yoon;
Dmochowski, Ivan J;
Eberwine, James

Publication type:

Article

The promise of single-cell sequencing.

Published in:

Nature Methods, 2014, v. 11, n. 1, p. 25, doi. 10.1038/nmeth.2769

By:

Eberwine, James;
Sul, Jai-Yoon;
Bartfai, Tamas;
Kim, Junhyong

Publication type:

Article

Single cell phototransfection of mRNAs encoding SARS-CoV2 spike and nucleocapsid into human astrocytes results in RNA dependent translation interference.

Published in:

Frontiers in Drug Delivery, 2024, p. 1, doi. 10.3389/fddev.2024.1359700

By:

Hyun-Bum Kim;
Brosseau, Quentin;
Radzio, Julia;
Jinhui Wang;
Hiromi Muramatsu;
Da Kuang;
Grady, M. Sean;
Chen, H. Isaac;
Wolf, John A.;
Ulyanova, Alexandra V.;
Bartfai, Tamas;
Junhyong Kim;
Pardi, Norbert;
Jai-Yoon Sul;
Arratia, Paulo;
Eberwine, James

Publication type:

Article

Pervasive Antisense Transcription Is Evolutionarily Conserved in Budding Yeast.

Published in:

Molecular Biology & Evolution, 2013, v. 30, n. 2, p. 409, doi. 10.1093/molbev/mss240

By:

Goodman, Aaron J.;
Daugharthy, Evan R.;
Kim, Junhyong

Publication type:

Article

Molecular Evolution of Drosophila Odorant Receptor Genes.

Published in:

Molecular Biology & Evolution, 2007, v. 24, n. 5, p. 1198, doi. 10.1093/molbev/msm038

By:

Guo, Sheng;
Kim, Junhyong

Publication type:

Article

Phylogenetic Reconstruction of Vertebrate Hox Cluster Duplications.

Published in:

Molecular Biology & Evolution, 1997, v. 14, n. 8, p. 843, doi. 10.1093/oxfordjournals.molbev.a025825

By:

Bailey, Wendy J.;
Junhyong Kim;
Wagner, Günter P.;
Ruddle, Frank H.

Publication type:

Article

Molecular Phylogeny of Coral-Reef Sea Cucumbers (Holothuriidae: Aspidochirotida) Based on 16S Mitochondrial Ribosomal DNA Sequence.

Published in:

Marine Biotechnology, 2005, v. 7, n. 1, p. 53, doi. 10.1007/s10126-004-0019-y

By:

Kerr, Alexander M.;
Janies, Daniel A.;
Clouse, Ronald M.;
Samyn, Yves;
Kuszak, Jeni;
Kim, Junhyong

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2017, v. 45, n. 19, p. 10978, doi. 10.1093/nar/gkx754

By:

Cheng Jia;
Yu Hu;
Kelly, Derek;
Junhyong Kim;
Mingyao Li;
Zhang, Nancy R.

Publication type:

Article

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

Published in:

Nature, 2005, v. 438, n. 7065, p. 220, doi. 10.1038/nature04114

By:

Rifkin, Scott A.;
Houle, David;
Junhyong Kim;
White, Kevin P.

Publication type:

Article

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

Published in:

Scientific Reports, 2017, p. 46321, doi. 10.1038/srep46321

By:

Middleton, Sarah A.;
Illuminati, Joseph;
Kim, Junhyong

Publication type:

Article

A study on the restoration method of friction, wear and fatigue performance of remanufactured crankshaft.

Published in:

Journal of Mechanical Science & Technology, 2013, v. 27, n. 10, p. 3047, doi. 10.1007/s12206-013-0824-1

By:

Tominaga, Yasutoshi;
Kim, Jinsoo;
Pyun, Youngsik;
Kayumov, Ravil;
Kim, Junhyong;
Woo, Juha

Publication type:

Article

Subcellular RNA Sequencing Reveals Broad Presence of Cytoplasmic Intron-Sequence Retaining Transcripts in Mouse and Rat Neurons.

Published in:

PLoS ONE, 2013, v. 8, n. 10, p. 1, doi. 10.1371/journal.pone.0076194

By:

Khaladkar, Mugdha;
Buckley, Peter T.;
Lee, Miler T.;
Francis, Chantal;
Eghbal, Mitra M.;
Chuong, Tina;
Suresh, Sangita;
Kuhn, Bernhard;
Eberwine, James;
Kim, Junhyong

Publication type:

Article

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

Published in:

Proteins, 2010, v. 78, n. 2, p. 381, doi. 10.1002/prot.22556

By:

Guo, Sheng;
Kim, Junhyong

Publication type:

Article

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

Published in:

BMC Biology, 2019, v. 17, n. 1, p. 1, doi. 10.1186/s12915-019-0630-z

By:

Middleton, Sarah A.;
Eberwine, James;
Kim, Junhyong

Publication type:

Article

Transcriptional profiling of dental sensory and proprioceptive trigeminal neurons using single-cell RNA sequencing.

Published in:

International Journal of Oral Science, 2023, v. 15, n. 1, p. 1, doi. 10.1038/s41368-023-00246-z

By:

Lee, Pa Reum;
Kim, Jihoon;
Rossi, Heather Lynn;
Chung, Sena;
Han, Seung Yub;
Kim, Junhyong;
Oh, Seog Bae

Publication type:

Article

Testing for Regional Differences in Means: Distinguishing Inherent from Spurious Spatial Autocorrelation by Restricted Randomization.

Published in:

Geographical Analysis, 1993, v. 25, n. 3, p. 199, doi. 10.1111/j.1538-4632.1993.tb00291.x

By:

Sokal, Robert R.;
Oden, Neal L.;
Thomson, Barbara A.;
Kim, Junhyong

Publication type:

Article

IgSF11 regulates osteoclast differentiation through association with the scaffold protein PSD-95.

Published in:

Bone Research, 2020, v. 8, n. 1, p. 1, doi. 10.1038/s41413-019-0080-9

By:

Kim, Hyunsoo;
Takegahara, Noriko;
Walsh, Matthew C.;
Middleton, Sarah A.;
Yu, Jiyeon;
Shirakawa, Jumpei;
Ueda, Jun;
Fujihara, Yoshitaka;
Ikawa, Masahito;
Ishii, Masaru;
Kim, Junhyong;
Choi, Yongwon

Publication type:

Article

Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-22266-1

By:

Miao, Zhen;
Balzer, Michael S.;
Ma, Ziyuan;
Liu, Hongbo;
Wu, Junnan;
Shrestha, Rojesh;
Aranyi, Tamas;
Kwan, Amy;
Kondo, Ayano;
Pontoglio, Marco;
Kim, Junhyong;
Li, Mingyao;
Kaestner, Klaus H.;
Susztak, Katalin

Publication type:

Article

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

Published in:

Wiley Interdisciplinary Reviews: RNA, 2017, v. 8, n. 6, p. n/a, doi. 10.1002/wrna.1433

By:

Gawronski, Katerina A.B.;
Kim, Junhyong

Publication type:

Article

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

Published in:

Wiley Interdisciplinary Reviews: RNA, 2014, v. 5, n. 2, p. 223, doi. 10.1002/wrna.1203

By:

Buckley, Peter T.;
Khaladkar, Mugdha;
Kim, Junhyong;
Eberwine, James

Publication type:

Article