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Peer Reviewed Papers, Books, Chapters

Year Title Citation Authors
1. 2010 Analysis of the Basidiomycete Coprinopsis cinerea Reveals Conservation of the Core Meiotic Expression Program over Half a Billion Years of Evolution PLoS Genetics 6(9): e1001135. doi:10.1371/journal.pgen.1001135
2. 2010 The Histone H3K36 Methyltransferase MES-4 Acts Epigenetically to Transmit the Memory of Germline Gene Expression to Progeny PLoS Genetics. 2010 Sep 2;6(9). pii: e1001091. PMID: 20824077
3. 2010 Nucleoporins and transcription: new connections, new questions PLoS Genet. 2010 Feb 26;6(2):e1000861. PMID: 20195517
4. 2010 Nucleosome sequence preferences influence in vivo nucleosome organization Nature Structural and Molecular Biology Aug;17(8):918-20 PMID: 20683473
5. 2010 Allele-specific and heritable chromatin signatures in humans Hum Mol Genet. 2010 Sep 16. PMID: 20846943
6. 2010 Contributions of DNA sequence preferences to Nucleosome organization: proposed definitions and methodology Genome Biology 2010 Nov 30;11(11):140. PMID: 21118582
7. 2010 individual-specific and allele-specific chromatin signatures in humans. Science 2010 Apr 9;328(5975):235-9. PMID: 20299549
8. 2010 High nucleosome occupancy is encoded at human regulatory sequences PLoS ONE 2010 Feb 9;5(2):e9129. PMID: 20161746 PMCID: PMC2817738
9. 2010 A map of open chromatin in human pancreatic islets. Nature Genetics 2010 Mar;42(3):255-9. PMID: 20118932
10. 2010 C. elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2 Genome Biology. DOI:10.1186/gb-2010-11-12-r120
11. 2010 An assessment of histone-modification antibody quality Nature Structural and Molecular Biology 2010 Dec 5. PMID: 21131980
12. 2009 C. elegans dosage compensation: A window into mechanisms of domain-scale gene regulation Chromosome Research 17(2):215-27. PMID: 19308702
13. 2009 Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods. 2009 Mar 18. PMID: 19303047
14. 2009 Systematic identification of balanced translocation polymorphisms in Saccharomyces cerevisiae. PLoS Genetics 2009 Jun;5(6):e1000502. PMID: 19503594 PMCID: 2682701
15. 2009 Gene Expression Divergence in Yeast is Coupled to Evolution of DNA-Encoded Nucleosome Organization Nature Genetics 2009 41(4):438-45. PMID: 19252487, PMCID: 2744203
16. 2009 The DNA-encoded nucleosome organization of a eukaryotic genome Nature 2009 Mar 19;458(7236):362-6. PMID: 19092803 PMCID: PMC2658732
17. 2009 The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency PLoS ONE 2009 4(3):e4886. PMID: 19295910 PMCID: PMC2654109
18. 2009 The C. elegans dosage compensation complex propagates dynamically and independently of X-chromosome sequence Current Biology 2009 17;19(21):1777-1787. PMID:19853451 PMC2783177
19. 2009 A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae Genome Research 2009 Dec;19(12):2245-57 PMID: 19801530, PMCID: 2792181
20. 2009 The DNA-binding specificity and in vivo targets of C. elegans Nuclear Factor I Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):12049-54. PMID: 19584245 PMC: 2715542
21. 2009 Highly transcribed RNA polymerase II genes are major impediments to replication fork progression in Saccharomyces cerevisiae Molecular Cell 2009 Jun 26;34(6):722-34. PMID: 19560424, PMC Journal – In Process
22. 2009 Unlocking the secrets of the genome Nature. 2009 Jun 18;459(7249):927-30. PMID: 19560424
23. 2008 Chromatin proteins do double duty Cell. May 30;133(5):763-5
24. 2008 A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters Molecular Cell 2008 Dec 26;32(6):878-87. PMID: 19111667 PMC2743730
25. 2008 The Genomic Distribution and Function of Histone Variant HTZ-1 during C. elegans Embryogenesis PLoS Genetics 2008 4(9):e1000187. PMID 18787694 PMC2522285
26. 2008 Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets Genome Research. 2008 18(3):393-403 PMID: 18258921 PMCID: PMC2259103
27. 2007 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature. Jun 14; 447: 799-816
28. 2007 FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin Genome Research. Jun;17(6):877-85. PMID: 17179217 PMCID: PMC1891346
29. 2007 The RNA Pol II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes Molecular and Cellular Biology. Jan; 27(2):721-31 PMID: 17088384, PMC1800795
30. 2007 Forkhead proteins control the outcome of transcription factor binding by antiactivation EMBO Journal. 2007 26, 4324–4334 PMID: 17898805, PMC2034669
31. 2007 Identification Of Histone H3 Lysine 36 Acetylation As A Highly Conserved Histone Modification Journal of Biological Chemistry. Mar 9;282(10):7632-40. PMID: 17189264, PMCID: 2811852
32. 2007 Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae Proc Natl Acad Sci U S A. Mar; 104(10):3955-60. PMID: 17360459, PMCID: 1805699
33. 2007 X-chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation Nature Genetics. Mar;39(3):403-408 PMID: 17293863 PMC2753834
34. 2006 Global analysis of the relationship between the binding of the Bas1p transcription factor and meiosis-specific double-strand DNA breaks in Saccharomyces cerevisiae Molecular and Cellular Biology. 26(3):1014-27. PMID: 16428454, PMCID: 1347019
35. 2006 Applying whole-genome studies of epigenetic regulation to study human disease Cytogenetic and Genome Research. 114(1):1-15. PMC2734277
36. 2006 Regulation of nucleosome stability as a mediator of chromatin function. Current Opinion in Genetics and Development.16:171–176
37. 2006 How to Find an Opening (or Lots of Them) Nature Methods. 3(7) 501-502
38. 2006 New evidence that DNA encodes its packaging Nature Genetics. 38(10):1104-5
39. 2006 Cell-cycle specified fluctuation of nucleosome occupancy at gene promoters PLoS Genetics. Sep; 2(9): e158 PMID: 17002501, PMCID: 1570381
40. 2006 Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection Genome Research. Dec; 16(12): 1517-1528 PMID: 17053089, PMCID: 1665635
41. 2006 A chromatin-mediated mechanism for specification of conditional transcription factor targets Nature Genetics. Dec; 38(12):1446-51. PMID: 17099712, PMC2756100
42. 2005 ChIPOTle: A User-Friendly Tool For The Analysis Of ChIP-chip Data Genome Biology. 6(11): R97. PMID: 16277752, PMCID: 1297653
43. 2005 Dimethylation of Histone H3 at Lysine 36 Demarcates Regulatory and Non-Regulatory Chromatin Genome-wide Molecular and Cellular Biology. 25(21):9447-59. PMID: 16227595 PMCID: 1265832
44. 2005 Control of Transcription through Intragenic Patterns of Nucleosome Composition Cell. Dec 29;123(7):1187-90.
45. 2005 DIP-chip: Rapid and accurate determination of DNA binding specificity Genome Research. 15(3): 421-427 PMID: 15710749, PMCID: 551568
46. 2005 Out With the Old, In With the New Nature Genetics. 37(10):1024-5.
47. 2004 ChIP-chip: Considerations for the Design, Analysis, and Application of Genome-wide Chromatin Immunoprecipitation Experiments Genomics. 83(3):349-360
48. 2004 Evidence for nucleosome depletion at active regulatory regions genome-wide Nature Genetics. 36(8): 900-905.
49. 2004 Progress and Challenges in Profiling the Dynamics of Chromatin and Transcription Factor Binding with DNA Microarrays Current Opinion in Genetics and Development. 14:697–705
50. 2003 Genome-wide Mapping of Protein-DNA Interactions by Chromatin Immunoprecipitation and DNA Microarray Hybridization Chapter 8 of Functional Genomics: Methods and Protocols. pp. 99-110. Humana Press. Edited by Michael J. Brownstein and Arkady B. Khodursky
51. 2003 Genomewide Demarcation of RNA Polymerase II Transcription Units Revealed by Physical Fractionation of Chromatin Proc Natl Acad Sci U S A. 100(11): 6364-6369. PMC164452
52. 2003 Integrating Regulatory Motif Discovery and Genome-wide Expression Analysis Proc Natl Acad Sci U S A. 100(6): 3339-3344. PMC152294
53. 2002 A Molecular Link between Gene-Specific and Chromosome-Wide Transcriptional Repression Genes and Development 16(7):796-805. PMC186330
54. 2001 Promoter-Specific Binding of Rap1 Revealed by Genome-wide Maps of Protein-DNA Association Nature Genetics 28(4):327-334
55. 2000 The Caenorhabditis elegans Dosage Compensation Machinery is Recruited to X-Chromosome DNA Attached to an Autosome Genetics 156: 1603-1621 PMC1461385
56. 1998 MIX-1: An Essential Component of the C. elegans Mitotic Machinery that Executes X-Chromosome Dosage Compensation Cell 92(2): 265-277
57. 1996 DPY-26, a link between dosage compensation and meiotic chromosome segregation in the nematode Science 274: 1732-1736
58. 1996 Sex-specific assembly of a dosage compensation complex on the nematode X chromosome Science 274: 1736-1739

4th Annual Pharma R&D Asia Congress
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