Chan:Publications

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[http://www-plb.ucdavis.edu/index.html Department of Plant Biology] at [http://www.ucdavis.edu/ UC Davis]
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[http://www-plb.ucdavis.edu/ Department of Plant Biology], [http://www.ucdavis.edu/ UC Davis] and [http://www.hhmi.org HHMI]
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Links for UC Davis papers lead to the pdf file.<br>
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Links beginning with "Image:" lead to the pdf file:<br>
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<br>
<br>
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&bull; Melters, D.P., Paliulis L.V., Korf I.F. and Chan, S.W.L.<br>
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Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis<br>
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[[:Image:2012 Daniel holocentric review Chromosome Research.pdf|Chromosome Research, published online (2012)]] [review article]<br>
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&bull; Talbert, P., 40 middle authors listed alphabetically including Chan, S.W.L., and Henikoff, S.<br>
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A unified phylogeny-based nomenclature for histone variants<br>
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[[:Image:2012 Talbert nomenclature Epigenetics and Chromatin.pdf|Epigenetics and Chromatin, 5, 7 (2012)]]
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&bull; Wijnker, E.*, van Dun, K*, de Snoo, C.B., Lelivelt, C.L., Keurentjes, J.J., Naharudin, N.S., Ravi, M., Chan, S.W., de Jong, H. and Dirks, R.<br>
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Reverse breeding in Arabidopsis generates homozygous parental lines from a heterozygous plant<br>
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[[:Image:2012 Erik reverse breeding Nature Genetics.pdf|Nature Genetics, 44, 467–470 (2012)]] (* equal contribution)<br>
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&bull; Seymour, D.K., Filiault, D., Henry, I.M., Monson-Miller, J., Ravi, M., Pang, A., Comai, L., Chan, S.W. and Maloof, J.N.<br>
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Rapid creation of Arabidopsis doubled haploid lines for quantitative trait locus mapping<br>
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[[:Image:2012 Danelle DH for QTL PNAS.pdf|PNAS, 109, 4227-4232 (2012)]]<br>
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&bull; Chan, S.W.L.<br>
&bull; Chan, S.W.L.<br>
In a battle between parental chromosomes, a failure to reload<br>
In a battle between parental chromosomes, a failure to reload<br>
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[http://www.ncbi.nlm.nih.gov/pubmed/21813763 PNAS, 108, 13361-13362 (2011)] [news and views article]<br>
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[[:Image:2011 Chan commentary PNAS.pdf|PNAS, 108, 13361-13362 (2011)]] [news and views article]<br>
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[[Image:2011 Chan commentary PNAS.pdf]]<br>
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&bull; Ravi, M., Shibata, F., Ramahi, J.S., Nagaki, K., Chen, C., Murata, M. & Chan, S.W.L.<br>
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&bull; Ravi, M., Shibata, F., Ramahi, J.S., Nagaki, K., Chen, C., Murata, M. and Chan, S.W.L.<br>
Meiosis-specific loading of the centromere-specific histone CENH3 in ''Arabidopsis thaliana''<br>
Meiosis-specific loading of the centromere-specific histone CENH3 in ''Arabidopsis thaliana''<br>
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[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002121 PLoS Genetics, 7, e1002121 (2011)]<br>
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[[:Image:2011 Ravi meiosis PLoS Genetics.pdf|PLoS Genetics, 7, e1002121 (2011)]]<br>
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[[Image:2011 Ravi meiosis PLoS Genetics.pdf]]<br>
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&bull; Marimuthu, M.P.A.*, Jolivet, S.*, Ravi, M.*, Pereira, L., Davda, J.N., Cromer, L., Wang, L., Nogué, F., Chan, S.W.L.#, Siddiqi, I.# & Mercier, R.#<br>
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&bull; Marimuthu, M.P.A.*, Jolivet, S.*, Ravi, M.*, Pereira, L., Davda, J.N., Cromer, L., Wang, L., Nogué, F., Chan, S.W.L.#, Siddiqi, I.# and Mercier, R.#<br>
Synthetic clonal reproduction through seeds<br>
Synthetic clonal reproduction through seeds<br>
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[http://www.ncbi.nlm.nih.gov/pubmed/21330535 Science, 331, 876 (2011)]<br>
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[[:Image:2011 Marimuthu cloning Science.pdf|Science, 331, 876 (2011)]], also see the [[:Image:2011 Marimuthu cloning Science SOM.pdf|Supplementary Online Material]] (* equal contribution, # corresponding authors)<br>
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(* equal contribution, # corresponding authors)<br>
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[[Image: 2011 Marimuthu cloning Science.pdf]]<br>
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[[Image: 2011 Marimuthu cloning Science SOM.pdf]]<br>
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&bull; Chan, S.W.L.<br>
&bull; Chan, S.W.L.<br>
Chromosome engineering: power tools for plant genetics<br>
Chromosome engineering: power tools for plant genetics<br>
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[http://www.ncbi.nlm.nih.gov/pubmed/20933291 Trends in Biotechnology, 12, 605-10 (2010)] [review article]<br>
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[[:Image:2010 Chan chromosome engineering Trends Biotech.pdf|Trends in Biotechnology, 12, 605-10 (2010)]] [review article]<br>  
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[[Image:2010 Chan chromosome engineering Trends Biotech.pdf]]<br>
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&bull; Ravi, M., Kwong, P.N., Menorca, R.M.G., Valencia, J.T., Ramahi, J.S., Stewart, J.L., Tran, R.K., Sundaresan, V., Comai, L. and Chan, S.W.L.<br>
&bull; Ravi, M., Kwong, P.N., Menorca, R.M.G., Valencia, J.T., Ramahi, J.S., Stewart, J.L., Tran, R.K., Sundaresan, V., Comai, L. and Chan, S.W.L.<br>
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The rapidly evolving centromere-specific histone has stringent functional
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The rapidly evolving centromere-specific histone has stringent functional requirements in ''Arabidopsis thaliana''<br>
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requirements in ''Arabidopsis thaliana''<br>
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[[:Image:2010 Ravi cenh3 Genetics.pdf|Genetics, 186, 461–471 (2010)]]<br>  
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[http://www.ncbi.nlm.nih.gov/pubmed/20628040 Genetics, 186, 461–471 (2010)]<br>
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[[Image:2010 Ravi cenh3 Genetics.pdf]]<br>
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&bull; Ravi, M. and Chan, S.W.L.<br>
&bull; Ravi, M. and Chan, S.W.L.<br>
Haploid plants produced by centromere-mediated genome elimination<br>
Haploid plants produced by centromere-mediated genome elimination<br>
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[http://www.ncbi.nlm.nih.gov/pubmed/20336146 Nature, 464, 615-618 (2010)]<br>
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[[:Image:2010 Ravi haploids Nature.pdf|Nature, 464, 615-618 (2010)]]<br>
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[[Image:2010 Ravi haploids Nature.pdf]]<br>
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&bull; Chan, S.W.L. <br>
&bull; Chan, S.W.L. <br>
Inputs and outputs for chromatin-targeted RNAi<br>
Inputs and outputs for chromatin-targeted RNAi<br>
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[http://www.ncbi.nlm.nih.gov/pubmed/18550415 Trends in Plant Sciences 13, 383-9 (2008)] [review article]<br>
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[[:Image:2008 Chan RNAi review TiPS.pdf|Trends in Plant Sciences, 13, 383-9 (2008)]] [review article]<br>
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[[Image:2008 Chan RNAi review TiPS.pdf]]<br>
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<br>
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<b>Before UC Davis:</b><br>
<b>Before UC Davis:</b><br>
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&bull; Zhang, X.*, Yazaki, J.*, Sundaresan, A.*, Cokus, S.*, Chan, S.W.L., Chen, H., Henderson, I.R., Shinn, P., Pellegrini, M., Jacobsen, S.E., and Ecker, J.R.<br>
&bull; Zhang, X.*, Yazaki, J.*, Sundaresan, A.*, Cokus, S.*, Chan, S.W.L., Chen, H., Henderson, I.R., Shinn, P., Pellegrini, M., Jacobsen, S.E., and Ecker, J.R.<br>
Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in ''Arabidopsis''.<br>
Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in ''Arabidopsis''.<br>
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[http://www.ncbi.nlm.nih.gov/pubmed/16949657 Cell 126, 1189-1201 (2006)]
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[http://www.ncbi.nlm.nih.gov/pubmed/16949657 Cell 126, 1189-1201 (2006)] (* equal contribution)
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(* = equal contribution)
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&bull; Li, C.F., Pontes, O., El-Shami, M., Henderson, I.R., Bernatavichute, Y.V., Chan, S.W.L., Lagrange, T., Pikaard, C.S. and Jacobsen, S.E.<br>
&bull; Li, C.F., Pontes, O., El-Shami, M., Henderson, I.R., Bernatavichute, Y.V., Chan, S.W.L., Lagrange, T., Pikaard, C.S. and Jacobsen, S.E.<br>
Line 108: Line 112:
&bull; Chan, S.W.L.*, Henderson, I.R.* and Jacobsen, S.E.<br>
&bull; Chan, S.W.L.*, Henderson, I.R.* and Jacobsen, S.E.<br>
Gardening the genome: DNA methylation in ''Arabidopsis thaliana''.<br>
Gardening the genome: DNA methylation in ''Arabidopsis thaliana''.<br>
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[http://www.ncbi.nlm.nih.gov/pubmed/15861207 Nature Reviews Genetics 6, 351-360 (2005)] [review article]
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[http://www.ncbi.nlm.nih.gov/pubmed/15861207 Nature Reviews Genetics 6, 351-360 (2005)] [review article] (* = equal contribution)
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(* = equal contribution)
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&bull; Mockler, T.C., Chan, S., Sundaresan A., Chen, H., Jacobsen S.E. and Ecker, J.R.<br>
&bull; Mockler, T.C., Chan, S., Sundaresan A., Chen, H., Jacobsen S.E. and Ecker, J.R.<br>
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[http://www.ncbi.nlm.nih.gov/pubmed/12760039 Cold Spring Harbor Symposia on Quantitative Biology, 65, 253-263 (2000)]<br>
[http://www.ncbi.nlm.nih.gov/pubmed/12760039 Cold Spring Harbor Symposia on Quantitative Biology, 65, 253-263 (2000)]<br>
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Current revision


Chan Lab

Department of Plant Biology, UC Davis and HHMI




Links for UC Davis papers lead to the pdf file.

• Melters, D.P., Paliulis L.V., Korf I.F. and Chan, S.W.L.
Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis
Chromosome Research, published online (2012) [review article]

• Talbert, P., 40 middle authors listed alphabetically including Chan, S.W.L., and Henikoff, S.
A unified phylogeny-based nomenclature for histone variants
Epigenetics and Chromatin, 5, 7 (2012)

• Wijnker, E.*, van Dun, K*, de Snoo, C.B., Lelivelt, C.L., Keurentjes, J.J., Naharudin, N.S., Ravi, M., Chan, S.W., de Jong, H. and Dirks, R.
Reverse breeding in Arabidopsis generates homozygous parental lines from a heterozygous plant
Nature Genetics, 44, 467–470 (2012) (* equal contribution)

• Seymour, D.K., Filiault, D., Henry, I.M., Monson-Miller, J., Ravi, M., Pang, A., Comai, L., Chan, S.W. and Maloof, J.N.
Rapid creation of Arabidopsis doubled haploid lines for quantitative trait locus mapping
PNAS, 109, 4227-4232 (2012)

• Chan, S.W.L.
In a battle between parental chromosomes, a failure to reload
PNAS, 108, 13361-13362 (2011) [news and views article]

• Ravi, M., Shibata, F., Ramahi, J.S., Nagaki, K., Chen, C., Murata, M. and Chan, S.W.L.
Meiosis-specific loading of the centromere-specific histone CENH3 in Arabidopsis thaliana
PLoS Genetics, 7, e1002121 (2011)

• Marimuthu, M.P.A.*, Jolivet, S.*, Ravi, M.*, Pereira, L., Davda, J.N., Cromer, L., Wang, L., Nogué, F., Chan, S.W.L.#, Siddiqi, I.# and Mercier, R.#
Synthetic clonal reproduction through seeds
Science, 331, 876 (2011), also see the Supplementary Online Material (* equal contribution, # corresponding authors)

• Chan, S.W.L.
Chromosome engineering: power tools for plant genetics
Trends in Biotechnology, 12, 605-10 (2010) [review article]

• Ravi, M., Kwong, P.N., Menorca, R.M.G., Valencia, J.T., Ramahi, J.S., Stewart, J.L., Tran, R.K., Sundaresan, V., Comai, L. and Chan, S.W.L.
The rapidly evolving centromere-specific histone has stringent functional requirements in Arabidopsis thaliana
Genetics, 186, 461–471 (2010)

• Ravi, M. and Chan, S.W.L.
Haploid plants produced by centromere-mediated genome elimination
Nature, 464, 615-618 (2010)

• Chan, S.W.L.
Inputs and outputs for chromatin-targeted RNAi
Trends in Plant Sciences, 13, 383-9 (2008) [review article]

Before UC Davis:

• Greenberg, M.V.C., Ausin, I., Chan, S.W.L, Cokus, S.J., Cuperus, J.T., Feng, S., Law, J.A., Chu, C., Pellegrini, M., Carrington, J.C. and Jacobsen, S.E.
Identification of genes required for de novo DNA methylation in Arabidopsis
Epigenetics, 6, 344-355 (2011)

• Henderson, I.R., Chan, S.R., Cao, X., Johnson, L. and Jacobsen, S.E.
Accurate sodium bisulfite sequencing in plants
Epigenetics, 5, 47-49 (2010)

• Chan, S.W.L., Zhang, X.Y., Bernatavichute, Y.V. and Jacobsen, S.E.
Two-step recruitment of RNA-directed DNA methylation to tandem repeats.
PLoS Biology 4 No. 11 e363 (2006)

• Peng P., Chan, S.W.L., Shah, G.A. and Jacobsen, S.E.
Increased outcrossing in hothead mutants.
Nature 443, E8 (2006)

• Zhang, X.*, Yazaki, J.*, Sundaresan, A.*, Cokus, S.*, Chan, S.W.L., Chen, H., Henderson, I.R., Shinn, P., Pellegrini, M., Jacobsen, S.E., and Ecker, J.R.
Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis.
Cell 126, 1189-1201 (2006) (* equal contribution)

• Li, C.F., Pontes, O., El-Shami, M., Henderson, I.R., Bernatavichute, Y.V., Chan, S.W.L., Lagrange, T., Pikaard, C.S. and Jacobsen, S.E.
An ARGONAUTE4-containing nuclear processing center co-localized with Cajal bodies in Arabidopsis thaliana.
Cell 126, 93-106 (2006)

• Chan, S.W.L., Henderson, I.R., Zhang, X.Y., Chien, J.S.C., Shah, G. and Jacobsen, S.E.
RNAi, DRD1 and Histone Methylation Actively Target Developmentally Important Non-CG DNA Methylation in Arabidopsis.
PLoS Genetics 2, No. 6 e83 (2006)

• Chan, S.W.L.*, Henderson, I.R.* and Jacobsen, S.E.
Gardening the genome: DNA methylation in Arabidopsis thaliana.
Nature Reviews Genetics 6, 351-360 (2005) [review article] (* = equal contribution)

• Mockler, T.C., Chan, S., Sundaresan A., Chen, H., Jacobsen S.E. and Ecker, J.R.
Applications of DNA tiling arrays for whole-genome analysis.
Genomics 85, 1-15 (2005) [review article]

• Morris, K.V., Chan, S.W.L., Jacobsen, S.E. and Looney, D.J.
siRNA-induced transcriptional gene silencing in human cells.
Science 305, 1289-1292 (2004)

• Chan, S.W.L., Zilberman D., Xie, Z., Johansen, L.K., Carrington, J.C. and Jacobsen, S.E.
RNA silencing genes control de novo DNA methylation.
Science 303, 1336 (2004)

• Chan, S.R.W.L. and Blackburn, E.H.
Telomeres and telomerase.
Phil. Trans. R. Soc. Lond. B 359, 109-121 (2004)

• Chan, S.W.L. and Blackburn, E.H.
Telomerase and ATM/Tel1p protect telomeres from non-homologous end-joining.
Molecular Cell 11, 1379-1387 (2003)

• Chan, S.W.L. and Blackburn, E.H.
New ways not to make ends meet: telomerase, DNA damage proteins and heterochromatin.
Oncogene 21, 553-563 (2002) [review article]

• Chan, S.W.L., Chang, J., Prescott, J. and Blackburn, E.H.
Altering telomere structure allows telomerase to act in yeast lacking ATM kinases.
Current Biology 11, 1240-1250 (2001)

• Blackburn, E.H., Chan, S., Chang, J., Fulton, T.B., Krauskopf, A., McEachern, M., Prescott, J., Roy, J., Smith, C. and Wang, H.
Molecular manifestations and molecular determinants of telomere capping.
Cold Spring Harbor Symposia on Quantitative Biology, 65, 253-263 (2000)

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