| Year |
Citation |
Score |
| 2019 |
Ransick A, Lindström NO, Liu J, Zhu Q, Guo JJ, Alvarado GF, Kim AD, Black HG, Kim J, McMahon AP. Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney. Developmental Cell. 51: 399-413.e7. PMID 31689386 DOI: 10.1016/J.Devcel.2019.10.005 |
0.306 |
|
| 2019 |
Park J, Liu CL, Kim J, Susztak K. Understanding the kidney one cell at a time. Kidney International. PMID 31492507 DOI: 10.1016/J.Kint.2019.03.035 |
0.337 |
|
| 2019 |
Packer JS, Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI. A lineage-resolved molecular atlas of embryogenesis at single-cell resolution. Science (New York, N.Y.). PMID 31488706 DOI: 10.1126/Science.Aax1971 |
0.3 |
|
| 2019 |
Huss DJ, Saias S, Hamamah S, Singh JM, Wang J, Dave M, Kim J, Eberwine J, Lansford R. Avian Primordial Germ Cells Contribute to and Interact With the Extracellular Matrix During Early Migration. Frontiers in Cell and Developmental Biology. 7: 35. PMID 30984757 DOI: 10.3389/Fcell.2019.00035 |
0.32 |
|
| 2018 |
Torre E, Dueck H, Shaffer S, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A. Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. Cell Systems. PMID 29454938 DOI: 10.1016/J.Cels.2018.01.014 |
0.387 |
|
| 2018 |
Dang P, Fisher SA, Stefanik D, Kim J, Raper JA. Coordination of olfactory receptor choice with guidance receptor expression and function in olfactory sensory neurons. Plos Genetics. 14: e1007164. PMID 29385124 DOI: 10.1371/Journal.Pgen.1007164 |
0.328 |
|
| 2017 |
Morris J, Na YJ, Zhu H, Lee JH, Giang H, Ulyanova AV, Baltuch GH, Brem S, Chen HI, Kung DK, Lucas TH, O'Rourke DM, Wolf JA, Grady MS, Sul JY, ... Kim J, et al. Pervasive within-Mitochondrion Single-Nucleotide Variant Heteroplasmy as Revealed by Single-Mitochondrion Sequencing. Cell Reports. 21: 2706-2713. PMID 29212019 DOI: 10.1016/J.Celrep.2017.11.031 |
0.634 |
|
| 2017 |
Jia C, Hu Y, Kelly D, Kim J, Li M, Zhang NR. Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data. Nucleic Acids Research. PMID 29036714 DOI: 10.1093/Nar/Gkx754 |
0.378 |
|
| 2017 |
Gawronski KAB, Kim J. Single cell transcriptomics of noncoding RNAs and their cell-specificity. Wiley Interdisciplinary Reviews. Rna. PMID 28762653 DOI: 10.1002/Wrna.1433 |
0.368 |
|
| 2017 |
Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biology. 18: 84. PMID 28482897 DOI: 10.1186/S13059-017-1218-Y |
0.315 |
|
| 2017 |
Anafi RC, Francey LJ, Hogenesch JB, Kim J. CYCLOPS reveals human transcriptional rhythms in health and disease. Proceedings of the National Academy of Sciences of the United States of America. PMID 28439010 DOI: 10.1073/Pnas.1619320114 |
0.347 |
|
| 2017 |
Middleton SA, Illuminati J, Kim J. Complete fold annotation of the human proteome using a novel structural feature space. Scientific Reports. 7: 46321. PMID 28406174 DOI: 10.1038/Srep46321 |
0.304 |
|
| 2016 |
Dueck HR, Ai R, Camarena A, Ding B, Dominguez R, Evgrafov OV, Fan JB, Fisher SA, Herstein JS, Kim TK, Kim JM, Lin MY, Liu R, Mack WJ, McGroty S, ... ... Kim J, et al. Assessing characteristics of RNA amplification methods for single cell RNA sequencing. Bmc Genomics. 17: 966. PMID 27881084 DOI: 10.1186/S12864-016-3300-3 |
0.306 |
|
| 2015 |
Dueck H, Eberwine J, Kim J. Variation is function: Are single cell differences functionally important?: Testing the hypothesis that single cell variation is required for aggregate function. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. PMID 26625861 DOI: 10.1002/Bies.201500124 |
0.312 |
|
| 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 |
0.335 |
|
| 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 |
0.309 |
|
| 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 |
0.321 |
|
| 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 |
0.409 |
|
| 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 |
0.519 |
|
| 2014 |
Francis C, Natarajan S, Lee MT, Khaladkar M, Buckley PT, Sul JY, Eberwine J, Kim J. Divergence of RNA localization between rat and mouse neurons reveals the potential for rapid brain evolution. Bmc Genomics. 15: 883. PMID 25301173 DOI: 10.1186/1471-2164-15-883 |
0.587 |
|
| 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 |
0.376 |
|
| 2014 |
Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA sequencing. Genome Biology. 15: R86. PMID 24981968 DOI: 10.1186/Gb-2014-15-6-R86 |
0.322 |
|
| 2014 |
Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe J, Liu AC, Kim J, Hogenesch JB. Machine learning helps identify CHRONO as a circadian clock component. Plos Biology. 12: e1001840. PMID 24737000 DOI: 10.1371/Journal.Pbio.1001840 |
0.35 |
|
| 2014 |
Eberwine J, Sul JY, Bartfai T, Kim J. The promise of single-cell sequencing. Nature Methods. 11: 25-7. PMID 24524134 DOI: 10.1038/Nmeth.2769 |
0.334 |
|
| 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 |
0.324 |
|
| 2014 |
Buckley PT, Khaladkar M, Kim J, Eberwine J. Cytoplasmic intron retention, function, splicing, and the sentinel RNA hypothesis. Wiley Interdisciplinary Reviews. Rna. 5: 223-30. PMID 24190870 DOI: 10.1002/Wrna.1203 |
0.375 |
|
| 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 |
0.596 |
|
| 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 |
0.365 |
|
| 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 |
0.552 |
|
| 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 |
0.323 |
|
| 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 |
0.6 |
|
| 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 |
0.748 |
|
| 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 |
0.581 |
|
| 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 |
0.555 |
|
| 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 |
0.76 |
|
| 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 |
0.344 |
|
| 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 |
0.406 |
|
| 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 |
0.624 |
|
| 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 |
0.585 |
|
| 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 |
0.549 |
|
| 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 |
0.738 |
|
| 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 |
0.348 |
|
| 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 |
0.548 |
|
| 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 |
0.657 |
|
| 2005 |
Rifkin SA, Houle D, Kim J, White KP. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature. 438: 220-3. PMID 16281035 DOI: 10.1038/Nature04114 |
0.715 |
|
| 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 |
0.575 |
|
| 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 |
0.601 |
|
| 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 |
0.695 |
|
| 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 |
0.36 |
|
| 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 |
0.378 |
|
| 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 |
0.689 |
|
| 2003 |
Rifkin SA, Kim J, White KP. Evolution of gene expression in the Drosophila melanogaster subgroup. Nature Genetics. 33: 138-44. PMID 12548287 DOI: 10.1038/Ng1086 |
0.718 |
|
| 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 |
0.737 |
|
| 2002 |
Rifkin SA, Kim J. Geometry of gene expression dynamics. Bioinformatics (Oxford, England). 18: 1176-83. PMID 12217909 DOI: 10.1093/Bioinformatics/18.9.1176 |
0.669 |
|
| 2001 |
Kim J. Descartes' fly: The geometry of genomic annotation Functional and Integrative Genomics. 1: 241-249. PMID 11793243 DOI: 10.1007/S101420000025 |
0.351 |
|
| 2001 |
Kim J. Macro-evolution of the hairy enhancer in Drosophila species Journal of Experimental Zoology. 291: 175-185. PMID 11479916 DOI: 10.1002/Jez.1067 |
0.337 |
|
| 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 |
0.337 |
|
| 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 |
0.588 |
|
| 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 |
0.682 |
|
| 2000 |
Kim J. Slicing hyperdimensional oranges: The geometry of phylogenetic estimation Molecular Phylogenetics and Evolution. 17: 58-75. PMID 11020305 DOI: 10.1006/Mpev.2000.0816 |
0.322 |
|
| 1999 |
Kerr AM, Kim J. Bi-penta-bi-decaradial symmetry: A review of evolutionary and developmental trends in holothuroidea (echinodermata) The Journal of Experimental Zoology. 285: 93-103. PMID 10440720 DOI: 10.1002/(Sici)1097-010X(19990815)285:2<93::Aid-Jez1>3.0.Co;2-9 |
0.606 |
|
| 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 |
0.343 |
|
| Show low-probability matches. |