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Members of the Lieb
lab are underlined.
Up-to-date
Pubmed search
2008
Whittle, C.M., McClinic, K.N., Ercan,
S., Zhang, X., Green, R.D., Kelly, W.G., and Lieb, J.D. (2008)
The
genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis.
PLoS Genetics.
In press
PDF Supplementary
Information
Dataset
from GEO PLoS Genetics Site
Ercan, S. and Lieb,
J.D. (2008)
Chromatin
proteins do double duty
Cell.
May 30;133(5):763-5
PDF
David S. Johnson^, Wei Li^, [42 others], Kevin Struhl*,
Richard M. Myers*, Jason D. Lieb*, and X. Shirley Liu*. (Mar
2008) ^ Co-first authors; * Co-corresponding
authors.
Systematic
evaluation of variability in ChIP-chip experiments using predefined DNA
targets
Genome
Research.
18(3):393-403
PDF Supplement Commentary in Nature Methods
2007
Voth
WP, Yu Y, Takahata S, Kretschmann
KL, Lieb JD, Parker RL, Milash B, Stillman DJ.
(Oct 2007)
Forkhead
proteins control the outcome of transcription factor binding by antiactivation. EMBO
J. 26, 4324–4334
PDF
Fang, J., Hogan, G.J., Liang, G., Lieb, J.D.,
and Zhang, Y (Jul 2007)
The
S. cerevisiae histone demethylase
Jhd1 fine-tunes the distribution of H3K36me2
Molecular and
Cellular Biology. Jul;27(13):5055-65
PDF
The ENCODE Consortium [Paul G. Giresi, Jason
D. Lieb and 305 others] (Jun 2007)
Identification
and analysis of functional elements in 1% of the human genome by the ENCODE
pilot project
Nature.
Jun 14;
447(7146):799-816.
PDF
Giresi, PG, Kim, J,
McDaniell, RM, Iyer, VR, and Lieb, JD (Jun 2007)
FAIRE (Formaldehyde Assisted Isolation of
Regulatory Elements) isolates active regulatory elements from human
chromatin.
Genome Research. Jun;17(6):877-85.
PDF Dataset from
GEO Commentary in Nature Methods
Mieczkowski, PA,
Dominska, M, Buck, MJ, Lieb,
JD, and Petes, TD (Mar 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. 104(10):3955-60.
PDF
Ercan,
S., Giresi, P.G., Whittle, C.M.,
Zhang, X., Green, R.D., and Lieb, J.D. (Mar 2007)
X-chromosome
repression by localization of the C.
elegans dosage compensation machinery to sites of transcription
initiation
Nature
Genetics. 39(3):403-408
PDF
Supplementary Information
Dataset from
GEO Nature
Genetics Site
Morris,
SA, Rao, B, Garcia, BA, Hake, SB, Diaz, RL, Shabanowitz,
J, Hunt, DF, Allis, CD, Lieb, JD, and Strahl, BD. (Mar 2007)
Identification
Of Histone H3 Lysine 36 Acetylation As A Highly Conserved Histone
Modification
Journal of Biological Chemistry. 282(10):7632-40.
PDF (Preprint) JBC Site Dataset from
GEO
Xiao T, Shibata Y, Rao B, Laribee RN, O'Rourke
R, Buck MJ, Greenblatt JF, Krogan NJ, Lieb JD, and Strahl BD. (Jan 2007)
The RNA Pol II
kinase Ctk1 regulates positioning of a 5' histone methylation boundary along
genes.
Molecular and Cellular
Biology. 27(2):721-31. PMID: 17088384
PDF Dataset from
GEO Dataset
from UNC-MD
2006
Buck, M.J. and Lieb, J.D.
(Dec 2006)
A
chromatin-mediated mechanism for specification of conditional transcription
factor targets
Nature Genetics. 38(12):1446-51.
PDF Supplementary Figures and Table
Dataset from
GEO Nature
Genetics Site
Liu, X., Lee
C.K., Granek, J.A, Clarke, N.D., and Lieb, J.D. (Dec 2006)
Whole-genome
comparison of Leu3 binding in vitro and in vivo reveals the importance of
nucleosome occupancy in target site selection
Genome Research. 16(12): 1517-1528
PDF
Dataset from
GEO Dataset
from UNC-MD
Ercan, S. and Lieb, J.D.
(Oct 2006)
New evidence that
DNA encodes its packaging.
Nature Genetics, 38(10):1104-5.
PDF
Hogan, G., Lee C.K.
and Lieb, J.D. (Sep 2006)
Cell-cycle
specified fluctuation of nucleosome occupancy at gene promoters
PLoS Genetics. 2(9):
e158
PDF (Print) PDF (Screen)
Dataset from
GEO Dataset
from UNC-MD
Giresi, P.G.,
and Lieb, J.D. (Jul 2006)
How to Find an Opening (or Lots of
Them)
Nature
Methods, 3(7)
501-502
PDF
Giresi, PG, Gupta, MG, and Lieb,
JD (Mar 2006)
Regulation of
nucleosome stability as a mediator of chromatin function.
Current Opinion in Genetics and Development.16:171–176.
PDF
Mieczkowski PA,
Dominska M, Buck MJ, Gerton JL, Lieb JD,
and Petes TD (Mar 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.
PDF
Dataset from
GEO Dataset
from UNC-MD
Lieb, JD,
Beck, S, Bulyk, ML, Farnham, P, Hattori, N, Henikoff, S, Liu, XS, Okumura, K,
Shiota, K, Ushiijima, T,
and Greally, JM (Jan 2006)
Applying
whole-genome studies of epigenetic regulation to study human disease
Cytogenetic and Genome Research,
114(1):1-15.
PDF
2005
Lieb, JD and Clarke, ND
(Dec 2005)
Control of
Transcription through Intragenic Patterns of Nucleosome Composition
Cell, Dec 29;123(7):1187-90.
PDF
Rao,
B., Shibata, Y., Strahl, B.D. and Lieb,
J.D. (Nov 2005)
Dimethylation of Histone H3 at Lysine 36 Demarcates Regulatory
and Non-Regulatory Chromatin Genome-wide
Molecular and Cellular
Biology. 25(21):9447-59.
PDF Web Supplement
Dataset from
GEO Dataset
from UNC-MD
Buck, MJ, Noble A.B., and Lieb,
JD (Oct 2005)
ChIPOTle: A
User-Friendly Tool For The Analysis Of ChIP-chip Data
Genome Biology. 6(11): R97
PDF Web
Supplement Software (excel version) Perl version
Lieb
JD. (Oct 2005)
Out with the old, in with the new.
Nature
Genetics. 37(10):1024-5.
PDF
Liu, X., Noll, D.M., Lieb, J.D., and Clarke, N.D.
(Mar 2005)
DIP-chip: Rapid and accurate determination of DNA
binding specificity.
Genome
Research. 15(3):
421-427
PDF Web Supplement News Piece
Dataset from
GEO Dataset
from UNC-MD
2004
Hanlon,
S.E.
and Lieb, J.D. (Dec
2004)
Progress and challenges in profiling the
dynamics of chromatin and transcription factor binding with DNA microarrays.
Current Opinion in Genetics &
Development.
14(6):697-705.
PDF
Lee C.K., Shibata Y., Rao B., Strahl B.D., Lieb
J.D. (Aug 2004)
Evidence for
nucleosome depletion at active regulatory regions genome-wide.
Nature Genetics. 36(8): 900-905.
PDF Web
Supplement Press Release
Dataset from
GEO Dataset
from UNC-MD
Buck, M. J. and Lieb, J.D. (Mar 2004)
ChIP-chip:
Considerations for the Design, Analysis, and Application of Genome-wide
Chromatin Immunoprecipitation Experiments
Genomics. 83(3):349-360.
PDF Accompanying Editorial
2003
Nagy, P.L., Cleary, M. Brown, P.O., and Lieb, J.D. (May 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.
PDF Web Supplement Press
Release
Dataset
from GEO Dataset
from UNC-MD
Conlon, E.M, Liu, X. S., Lieb, J.D., and Liu, J.S. (Mar 2003)
Integrating
Regulatory Motif Discovery and Genome-wide Expression Analysis.
Proc Natl Acad Sci U S A. 100(6):
3339-3344.
PDF
Lieb, J. D. (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.
PDF (Uncorrected
Proof)
Pre-UNC (2002 and earlier)
Chu, D.S., Dawes, H.E., Lieb, J.D., Chan, R.C., Kuo, A.F.,
and Meyer, B.J. (2002).
A Molecular Link
between Gene-Specific and Chromosome-Wide Transcriptional Repression.
Genes and
Development
16(7): 796-805.
PDF
Perspective (PDF)
Lieb, J.D., Liu, X., Botstein, D.,
and Brown, P.O. (2001).
Promoter-Specific
Binding of Rap1 Revealed by Genome-wide Maps of Protein-DNA Association.
Nature Genetics 28(4): 327-33
PDF
News and Views (PDF) Web Supplement Dataset from
GEO Dataset
from SMD
Lieb, J.D., de Solorzano, C.O., Rodriguez, E.G.,
Jones, A., Angelo, M., Lockett,
S., and Meyer, B.J. (2000)
The Caenorhabditis elegans Dosage
Compensation Machinery is Recruited to X-Chromosome
DNA Attached to an Autosome.
Genetics 156:
1603-1621
PDF Web Supplement
Lieb, J.D., Albrecht, M., Chuang, P.-T., and Meyer,
B.J. (1998).
MIX-1: An Essential
Component of the C. elegans Mitotic
Machinery that Executes X-Chromosome Dosage Compensation.
Cell 92(2):
265-277
PDF (19 Mb) Full Text (Cell HTML)
Lieb, J.D., Capowski, E.E., Meneely, P. and Meyer, B.J. (1996).
DPY-26, a link
between dosage compensation and meiotic chromosome segregation in the
nematode.
Science 274: 1732-1736
PDF (B&W) Full Text (HTML) News and Views (PDF)
Chuang, P.-T., Lieb, J.D. and Meyer, B.J. (1996).
Sex-specific
assembly of a dosage compensation complex on the nematode X chromosome.
Science 274: 1736-1739
PDF (B&W) Full Text
(HTML) News and Views (PDF)
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