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Members of the Lieb lab are underlined.
2008
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. In Press
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
Dataset from GEO Dataset from UNC-MD
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
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
Dataset from GEO Dataset from UNC-MD
Ercan,
E., 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 Dataset from
UNC-MD
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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