Year |
Citation |
Score |
2023 |
Bhogale S, Seward C, Stubbs L, Sinha S. SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes. Biorxiv : the Preprint Server For Biology. PMID 38014229 DOI: 10.1101/2023.11.09.565900 |
0.329 |
|
2019 |
Kim J, Frey WD, Sharma K, Ghimire S, Teruyama R, Stubbs L. Allele-specific enhancer interaction at the Peg3 imprinted domain. Plos One. 14: e0224287. PMID 31639176 DOI: 10.1371/Journal.Pone.0224287 |
0.397 |
|
2019 |
Weisner PA, Chen CY, Sun Y, Yoo J, Kao WC, Zhang H, Baltz ET, Troy JM, Stubbs L. A Mouse Mutation That Dysregulates Neighboring and Genes Is Associated with Phenotypes Related to the Human AUTS2 Syndrome. G3 (Bethesda, Md.). PMID 31554716 DOI: 10.1534/G3.119.400723 |
0.434 |
|
2018 |
Negi S, Bolt CC, Zhang H, Stubbs L. An extended regulatory landscape drives Tbx18 activity in a variety of prostate-associated cell lineages. Developmental Biology. PMID 30594504 DOI: 10.1016/j.ydbio.2018.11.023 |
0.304 |
|
2018 |
Saul MC, Blatti C, Yang W, Bukhari SA, Shpigler HY, Troy JM, Seward CH, Sloofman L, Chandrasekaran S, Bell AM, Stubbs L, Robinson GE, Zhao SD, Sinha S. Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge. Genes, Brain, and Behavior. e12502. PMID 29968347 DOI: 10.1111/Gbb.12502 |
0.374 |
|
2017 |
Eidsaa M, Stubbs L, Almaas E. Comparative analysis of weighted gene co-expression networks in human and mouse. Plos One. 12: e0187611. PMID 29161290 DOI: 10.1371/Journal.Pone.0187611 |
0.325 |
|
2017 |
Saul M, Seward CH, Troy JM, Zhang H, Sloofman LG, Lu X, Weisner PA, Caetano-Anolles D, Sun H, Zhao SD, Chandrasekaran S, Sinha S, Stubbs L. Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice. Genome Research. PMID 28356321 DOI: 10.1101/Gr.214221.116 |
0.376 |
|
2016 |
Selleri L, Bartolomei MS, Bickmore WA, He L, Stubbs L, Reik W, Barsh GS. A Hox-Embedded Long Noncoding RNA: Is It All Hot Air? Plos Genetics. 12: e1006485. PMID 27977680 DOI: 10.1371/Journal.Pgen.1006485 |
0.362 |
|
2016 |
Sun Y, Zhang H, Kazemian M, Troy JM, Seward C, Lu X, Stubbs L. ZSCAN5B and primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression. Oncotarget. PMID 27732952 DOI: 10.18632/Oncotarget.12508 |
0.441 |
|
2014 |
Rittschof CC, Bukhari SA, Sloofman LG, Troy JM, Caetano-Anollés D, Cash-Ahmed A, Kent M, Lu X, Sanogo YO, Weisner PA, Zhang H, Bell AM, Ma J, Sinha S, Robinson GE, ... Stubbs L, et al. Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee. Proceedings of the National Academy of Sciences of the United States of America. 111: 17929-34. PMID 25453090 DOI: 10.1073/Pnas.1420369111 |
0.402 |
|
2014 |
Bolt CC, Elso CM, Lu X, Pan F, Kispert A, Stubbs L. A distant downstream enhancer directs essential expression of Tbx18 in urogenital tissues. Developmental Biology. 392: 483-93. PMID 24854998 DOI: 10.1016/J.Ydbio.2014.05.010 |
0.423 |
|
2014 |
Liu H, Chang LH, Sun Y, Lu X, Stubbs L. Deep vertebrate roots for mammalian zinc finger transcription factor subfamilies. Genome Biology and Evolution. 6: 510-25. PMID 24534434 DOI: 10.1093/Gbe/Evu030 |
0.515 |
|
2011 |
Nowick K, Fields C, Gernat T, Caetano-Anolles D, Kholina N, Stubbs L. Gain, loss and divergence in primate zinc-finger genes: a rich resource for evolution of gene regulatory differences between species. Plos One. 6: e21553. PMID 21738707 DOI: 10.1371/Journal.Pone.0021553 |
0.516 |
|
2011 |
Stubbs L, Sun Y, Caetano-Anolles D. Function and evolution of C2H2 zinc finger arrays Sub-Cellular Biochemistry. 52: 75-94. PMID 21557079 DOI: 10.1007/978-90-481-9069-0_4 |
0.348 |
|
2010 |
Nowick K, Hamilton AT, Zhang H, Stubbs L. Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes. Molecular Biology and Evolution. 27: 2606-17. PMID 20573777 DOI: 10.1093/molbev/msq157 |
0.445 |
|
2010 |
Nowick K, Stubbs L. Lineage-specific transcription factors and the evolution of gene regulatory networks Briefings in Functional Genomics and Proteomics. 9: 65-78. PMID 20081217 DOI: 10.1093/Bfgp/Elp056 |
0.48 |
|
2009 |
Nowick K, Gernat T, Almaas E, Stubbs L. Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proceedings of the National Academy of Sciences of the United States of America. 106: 22358-63. PMID 20007773 DOI: 10.1073/Pnas.0911376106 |
0.432 |
|
2008 |
Elso C, Lu X, Morrison S, Tarver A, Thompson H, Thurkow H, Yamada NA, Stubbs L. Germline translocations in mice: unique tools for analyzing gene function and long-distance regulatory mechanisms. Journal of the National Cancer Institute. Monographs. 91-5. PMID 18648012 DOI: 10.1093/Jncimonographs/Lgn008 |
0.479 |
|
2007 |
Gordon L, Yang S, Tran-Gyamfi M, Baggott D, Christensen M, Hamilton A, Crooijmans R, Groenen M, Lucas S, Ovcharenko I, Stubbs L. Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. Genome Research. 17: 1603-13. PMID 17921355 DOI: 10.1101/Gr.6775107 |
0.515 |
|
2007 |
Aerts J, Megens HJ, Veenendaal T, Ovcharenko I, Crooijmans R, Gordon L, Stubbs L, Groenen M. Extent of linkage disequilibrium in chicken. Cytogenetic and Genome Research. 117: 338-345. PMID 17675876 DOI: 10.1159/000103196 |
0.363 |
|
2007 |
Kim J, Bergmann A, Choo JH, Stubbs L. Genomic organization and imprinting of the Peg3 domain in bovine Genomics. 90: 85-92. PMID 17509818 DOI: 10.1016/J.Ygeno.2007.03.012 |
0.48 |
|
2006 |
Kim JD, Hinz AK, Bergmann A, Huang JM, Ovcharenko I, Stubbs L, Kim J. Identification of clustered YY1 binding sites in imprinting control regions. Genome Research. 16: 901-11. PMID 16760423 DOI: 10.1101/Gr.5091406 |
0.328 |
|
2006 |
Hamilton AT, Huntley S, Tran-Gyamfi M, Baggott DM, Gordon L, Stubbs L. Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes. Genome Research. 16: 584-94. PMID 16606703 DOI: 10.1101/gr.4843906 |
0.479 |
|
2006 |
Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, Kim J, Gordon L, Branscomb E, Stubbs L. A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Research. 16: 669-77. PMID 16606702 DOI: 10.1101/Gr.4842106 |
0.545 |
|
2006 |
Choo JH, Kim JD, Chung JH, Stubbs L, Kim J. Allele-specific deposition of macroH2A1 in imprinting control regions Human Molecular Genetics. 15: 717-724. PMID 16421169 DOI: 10.1093/Hmg/Ddi485 |
0.33 |
|
2006 |
Luo C, Lu X, Stubbs L, Kim J. Rapid evolution of a recently retroposed transcription factor YY2 in mammalian genomes Genomics. 87: 348-355. PMID 16377127 DOI: 10.1016/J.Ygeno.2005.11.001 |
0.392 |
|
2005 |
Robinson KO, Petersen AM, Morrison SN, Elso CM, Stubbs L. Two reciprocal translocations provide new clues to the high mutability of the Grid2 locus. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 16: 32-40. PMID 15674731 DOI: 10.1007/S00335-004-2423-Z |
0.402 |
|
2005 |
Herron BJ, Rao C, Liu S, Laprade L, Richardson JA, Olivieri E, Semsarian C, Millar SE, Stubbs L, Beier DR. A mutation in NFkB interacting protein 1 results in cardiomyopathy and abnormal skin development in wa3 mice. Human Molecular Genetics. 14: 667-77. PMID 15661756 DOI: 10.1093/Hmg/Ddi063 |
0.377 |
|
2005 |
Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W, Stubbs L. Evolution and functional classification of vertebrate gene deserts. Genome Research. 15: 137-45. PMID 15590943 DOI: 10.1101/Gr.3015505 |
0.441 |
|
2005 |
Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W. Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Research. 15: 184-94. PMID 15590941 DOI: 10.1101/Gr.3007205 |
0.412 |
|
2004 |
Ovcharenko I, Stubbs L, Loots GG. Interpreting mammalian evolution using Fugu genome comparisons Genomics. 84: 890-895. PMID 15475268 DOI: 10.1016/j.ygeno.2004.07.011 |
0.302 |
|
2004 |
Ovcharenko I, Nobrega MA, Loots GG, Stubbs L. ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Research. 32: W280-6. PMID 15215395 DOI: 10.1093/Nar/Gkh355 |
0.37 |
|
2004 |
Kim J, Bergmann A, Lucas S, Stone R, Stubbs L. Lineage-specific imprinting and evolution of the zinc-finger gene ZIM2 Genomics. 84: 47-58. PMID 15203203 DOI: 10.1016/J.Ygeno.2004.02.007 |
0.547 |
|
2004 |
Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, ... ... Stubbs L, et al. The DNA sequence and biology of human chromosome 19. Nature. 428: 529-35. PMID 15057824 DOI: 10.1038/Nature02399 |
0.502 |
|
2003 |
Shannon M, Hamilton AT, Gordon L, Branscomb E, Stubbs L. Differential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters. Genome Research. 13: 1097-110. PMID 12743021 DOI: 10.1101/Gr.963903 |
0.508 |
|
2003 |
Kim J, Kollhoff A, Bergmann A, Stubbs L. Methylation-sensitive binding of transcription factor YY1 to an insulator sequence within the paternally expressed imprinted gene, Peg3 Human Molecular Genetics. 12: 233-245. PMID 12554678 DOI: 10.1093/Hmg/Ddg028 |
0.434 |
|
2003 |
Stubbs L, Elso C, Loots G, Hamilton A, Ovcharenko I. Using genomic similarities and differences to interpret mouse models of human development and cancer Breast Cancer Research. 5: 38-38. DOI: 10.1186/Bcr697 |
0.479 |
|
2003 |
Wilczyński B, Hvidsten T, Kryshtafovych A, Stubbs L, Komorowski J, Fidelis K. A rule-based framework for gene regulation pathways discovery Proceedings of the 2003 Ieee Bioinformatics Conference, Csb 2003. 435-436. DOI: 10.1109/CSB.2003.1227361 |
0.358 |
|
2001 |
Kim J, Bergmann A, Wehri E, Lu X, Stubbs L. Imprinting and evolution of two Kruppel-type zinc-finger genes, ZIM3 and ZNF264, located in the PEG3/USP29 imprinted domain Genomics. 77: 91-98. PMID 11543637 DOI: 10.1006/Geno.2001.6621 |
0.514 |
|
2001 |
Dehal P, Predki P, Olsen AS, Kobayashi A, Folta P, Lucas S, Land M, Terry A, Ecale Zhou CL, Rash S, Zhang Q, Gordon L, Kim J, Elkin C, Pollard MJ, ... ... Stubbs L, et al. Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution. Science (New York, N.Y.). 293: 104-11. PMID 11441184 DOI: 10.1126/Science.1060310 |
0.526 |
|
2001 |
Kim J, Gordon L, Dehal P, Badri H, Christensen M, Groza M, Ha C, Hammond S, Vargas M, Wehri E, Wagner M, Olsen A, Stubbs L. Homology-driven assembly of a sequence-ready mouse BAC contig map spanning regions related to the 46-Mb gene-rich euchromatic segments of human chromosome 19 Genomics. 74: 129-141. PMID 11386749 DOI: 10.1006/Geno.2001.6521 |
0.475 |
|
2001 |
Henegariu O, Artan S, Greally JM, Chen XN, Korenberg JR, Vance GH, Stubbs L, Bray-Ward P, Ward DC. Cryptic translocation identification in human and mouse using several telomeric multiplex fish (TM-FISH) strategies. Laboratory Investigation; a Journal of Technical Methods and Pathology. 81: 483-91. PMID 11304567 DOI: 10.1038/Labinvest.3780256 |
0.336 |
|
2000 |
Kim J, Bergmann A, Stubbs L. Exon sharing of a novel human zinc-finger gene, ZIM2, and paternally expressed gene 3 (PEG3) Genomics. 64: 114-118. PMID 10708526 DOI: 10.1006/Geno.1999.6112 |
0.516 |
|
1999 |
Shannon M, Lamerdin JE, Richardson L, McCutchen-Maloney SL, Hwang MH, Handel MA, Stubbs L, Thelen MP. Characterization of the mouse Xpf DNA repair gene and differential expression during spermatogenesis Genomics. 62: 427-435. PMID 10644440 DOI: 10.1006/Geno.1999.6016 |
0.504 |
|
1999 |
Rouquier S, Stubbs L, Gaillard-Sanchez I, Giorgi D. Sequence and chromosomal localization of the mouse ortholog of the human olfactory receptor gene 912-93 Mammalian Genome. 10: 1172-1174. PMID 10594242 DOI: 10.1007/s003359901185 |
0.338 |
|
1999 |
Lee BI, Shannon M, Stubbs L, Wilson DM. Expression specificity of the mouse exonuclease 1 (mExo1) gene Nucleic Acids Research. 27: 4114-4120. PMID 10497278 DOI: 10.1093/Nar/27.20.4114 |
0.487 |
|
1999 |
Walkowicz M, Ji Y, Ren X, Horsthemke B, Russell LB, Johnson D, Rinchik EM, Nicholls RD, Stubbs L. Molecular characterization of radiation- and chemically induced mutations associated with neuromuscular tremors, runting, juvenile lethality, and sperm defects in jdf2 mice. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 10: 870-8. PMID 10441737 DOI: 10.1007/S003359901106 |
0.377 |
|
1999 |
Shannon M, Stubbs L. Molecular characterization of Zfp54, a zinc-finger-containing gene that is deleted in the embryonic lethal mutation t(w18) Mammalian Genome. 10: 739-743. PMID 10384051 DOI: 10.1007/S003359901082 |
0.543 |
|
1999 |
Kim J, Lu X, Stubbs L. Zim1, a maternally expressed mouse Kruppel-type zinc-finger gene located in proximal chromosome 7 Human Molecular Genetics. 8: 847-854. PMID 10196374 DOI: 10.1093/Hmg/8.5.847 |
0.531 |
|
1999 |
Ji Y, Walkowicz MJ, Buiting K, Johnson DK, Tarvin RE, Rinchik EM, Horsthemke B, Stubbs L, Nicholls RD. The ancestral gene for transcribed, low-copy repeats in the Prader-Willi/Angelman region encodes a large protein implicated in protein trafficking, which is deficient in mice with neuromuscular and spermiogenic abnormalities. Human Molecular Genetics. 8: 533-42. PMID 9949213 DOI: 10.1093/Hmg/8.3.533 |
0.5 |
|
1998 |
Shannon M, Kim J, Ashworth L, Branscomb E, Stubbs L. Tandem zinc-finger gene families in mammals: Insights and unanswered questions Mitochondrial Dna. 8: 303-315. PMID 10993601 DOI: 10.3109/10425179809034075 |
0.383 |
|
1998 |
Gabriel JM, Gray TA, Stubbs L, Saitoh S, Ohta T, Nicholls RD. Structure and function correlations at the imprinted mouse Snrpn locus Mammalian Genome. 9: 788-793. PMID 9745031 DOI: 10.1007/s003359900868 |
0.41 |
|
1998 |
Shannon M, Stubbs L. Analysis of homologous XRCC1-linked zinc-finger gene families in human and mouse: Evidence for orthologous genes Genomics. 49: 112-121. PMID 9570955 DOI: 10.1006/geno.1998.5230 |
0.455 |
|
1998 |
Carver EA, Issel-Tarver L, Rine J, Olsen AS, Stubbs L. Location of mouse and human genes corresponding to conserved canine olfactory receptor gene subfamilies. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 9: 349-54. PMID 9545490 DOI: 10.1007/S003359900768 |
0.408 |
|
1998 |
Geisler JG, Stubbs LJ, Wasserman WW, Mucenski ML. Molecular cloning of a novel mouse gene with predominant muscle and neural expression Mammalian Genome. 9: 274-282. PMID 9530622 DOI: 10.1007/s003359900748 |
0.458 |
|
1997 |
Stubbs L, Carver EA, Cacheiro NLA, Shelby M, Generoso W. Generation and characterization of heritable reciprocal translocations in mice Methods: a Companion to Methods in Enzymology. 13: 397-408. PMID 9480784 DOI: 10.1006/Meth.1997.0546 |
0.462 |
|
1997 |
Carver EA, Stubbs L. Zooming in on the human-mouse comparative map: Genome conservation re-examined on a high-resolution scale Genome Research. 7: 1123-1137. PMID 9414318 |
0.328 |
|
1997 |
Kirn J, Park YS, Chung JH, Stubbs L. The gene encoding sepiapterin reductase is located in central mouse chromosome 6 Mammalian Genome. 8: 942. PMID 9383299 DOI: 10.1007/S003359900631 |
0.472 |
|
1997 |
Lin HH, Stubbs LJ, Mucenski ML. Identification and characterization of a seven transmembrane hormone receptor using differential display Genomics. 41: 301-308. PMID 9169125 DOI: 10.1006/geno.1997.4674 |
0.408 |
|
1997 |
Kim J, Ashworth L, Branscomb E, Stubbs L. The human homolog of a mouse-imprinted gene, Peg3, maps to a zinc finger gene-rich region of human chromosome 19q13.4 Genome Research. 7: 532-540. PMID 9149948 DOI: 10.1101/Gr.7.5.532 |
0.542 |
|
1997 |
Doyle J, Ren X, Lennon G, Stubbs L. Mutations in the Cacnl1a4 calcium channel gene are associated with seizures, cerebellar degeneration, and ataxia in tottering and leaner mutant mice. Mammalian Genome. 8: 113-120. PMID 9060410 DOI: 10.1007/S003359900369 |
0.429 |
|
1996 |
Mohrenweiser H, Olsen A, Archibald A, Beattie C, Burmeister M, Lamerdin J, Lennon G, Stewart E, Stubbs L, Weber JL, Johnson K. Report an abstracts of the third international workshop on human chromosome 19 mapping 1996. Cytogenetics and Cell Genetics. 74: 161-86. PMID 8941368 DOI: 10.1159/000134408 |
0.328 |
|
1996 |
Stubbs L, Carver E, Ashworth L, Lopez-Molina L. Location of the DBP transcription factor gene in human and mouse Mammalian Genome. 7: 65-67. PMID 8903733 DOI: 10.1007/S003359900016 |
0.361 |
|
1996 |
Stubbs L, Chittenden L, Chakrabarti A, Onaivi E. The gene encoding the central cannabinoid receptor is located in proximal mouse Chromosome 4 Mammalian Genome. 7: 165-166. PMID 8835542 |
0.337 |
|
1996 |
Lamerdin JE, Stilwagen SA, Ramirez MH, Stubbs L, Carrano AV. Sequence analysis of the ERCC2 gene regions in human, mouse, and hamster reveals three linked genes Genomics. 34: 399-409. PMID 8786141 DOI: 10.1006/Geno.1996.0303 |
0.532 |
|
1996 |
Doyle J, Hellevuo K, Stubbs L. The gene encoding adenylyl cyclase VII is located in central mouse Chromosome 8 Mammalian Genome. 7: 320-321. PMID 8661708 |
0.386 |
|
1996 |
Onaivi ES, Chakrabani A, McDuffie I, Chitlenden LR, Stubbs L, Chaudhuri G. Genes encoding marijuana receptors and their chromosomal localization Faseb Journal. 10. |
0.428 |
|
1994 |
Lai F, Stubbs L, Artzt K. Molecular Analysis of Mouse Rab11b: A New Type of Mammalian YPT/Rab Protein Genomics. 22: 610-616. PMID 8001972 DOI: 10.1006/Geno.1994.1434 |
0.495 |
|
1994 |
Lai F, Stubbs L, Lehrach H, Huang Y, Yeom Y, Artzt K. Genomic Organization and Expressed Sequences of the Mouse Extended H-2K Region Genomics. 23: 338-343. PMID 7835882 DOI: 10.1006/Geno.1994.1509 |
0.381 |
|
1994 |
Stubbs L, Rinchik EM, Goldberg E, Rudy B, Handel MA, Johnson D. Clustering of Six Human 11p15 Gene Homologs within a 500-kb Interval of Proximal Mouse Chromosome 7 Genomics. 24: 324-332. PMID 7698755 DOI: 10.1006/Geno.1994.1623 |
0.404 |
|
1993 |
Michaud EJ, Bultman SJ, Stubbs LJ, Woychik RP. The embryonic lethality of homozygous lethal yellow mice AylAy] is associated with the disruption of a novel RNA-binding protein Genes and Development. 7: 1203-1213. PMID 8319910 DOI: 10.1101/Gad.7.7A.1203 |
0.417 |
|
1991 |
Cheah KS, Au PK, Lau ET, Little PF, Stubbs L. The mouse Col2a-1 gene is highly conserved and is linked to Int-1 on chromosome 15. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 1: 171-83. PMID 1797232 DOI: 10.1007/BF00351064 |
0.415 |
|
1990 |
Stubbs L, Kraus J, Lehrach H. The α-A-crystallin and cystathionine β-synthase genes are physically very closely linked in proximal mouse chromosome 17 Genomics. 7: 284-288. PMID 2347594 DOI: 10.1016/0888-7543(90)90553-7 |
0.363 |
|
1990 |
Stubbs L, Poustka A, Baron A, Lehrach H, Lonai P, Duboule D. The murine genes Hox-5.1 and Hox-4.1 belong to the same HOX complex on chromosome 2. Genomics. 7: 422-7. PMID 1973141 DOI: 10.1016/0888-7543(90)90177-V |
0.418 |
|
1987 |
Rappold GA, Stubbs L, Labeit S, Crkvenjakov RB, Lehrach H. Identification of a testis-specific gene from the mouse t-complex next to a CpG-rich island Embo Journal. 6: 1975-1980. PMID 3653077 |
0.376 |
|
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