Lieb, Jason: search on Z-Library

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1

The DNA-encoded nucleosome organization of a eukaryotic genome

Kaplan, Noam, Moore, Irene K., Fondufe-Mittendorf, Yvonne, Gossett, Andrea J., Tillo, Desiree, Field, Yair, LeProust, Emily M., Hughes, Timothy R., Lieb, Jason D., Widom, Jonathan

Journal:

Year:

2008

Language:

english

File:

PDF, 578 KB

english, 2008

2

A Split Personality for Nucleosomes

McKay, Daniel J., Lieb, Jason D.

Journal:

Year:

2014

Language:

english

File:

PDF, 214 KB

english, 2014

3

What are super-enhancers?

Pott, Sebastian, Lieb, Jason D

Journal:

Nature Genetics

Year:

2014

Language:

english

File:

PDF, 641 KB

english, 2014

4

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis

Osborne Nishimura, Erin, Zhang, Jay C., Werts, Adam D., Goldstein, Bob, Lieb, Jason D., Mango, Susan E.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.79 MB

english, 2015

5

Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans

Jeffers, Tess E, Lieb, Jason D

Journal:

Genome Research

Year:

2016

Language:

english

File:

PDF, 5.36 MB

english, 2016

6

Phosphorylated Lamin A/C in the Nuclear Interior Binds Active Enhancers Associated with Abnormal Transcription in Progeria

Ikegami, Kohta, Secchia, Stefano, Almakki, Omar, Lieb, Jason D., Moskowitz, Ivan P.

Journal:

Developmental Cell

Year:

2020

Language:

english

File:

PDF, 6.16 MB

english, 2020

7

C. elegansdosage compensation: A window into mechanisms of domain-scale gene regulation

Sevinc Ercan, Jason D. Lieb

Journal:

Chromosome Research

Year:

2009

Language:

english

File:

PDF, 264 KB

english, 2009

8

Unlocking the secrets of the genome

Celniker, Susan E., Dillon, Laura A. L., Gerstein, Mark B., Gunsalus, Kristin C., Henikoff, Steven, Karpen, Gary H., Kellis, Manolis, Lai, Eric C., Lieb, Jason D., MacAlpine, David M.

Journal:

Year:

2009

Language:

english

File:

PDF, 1.03 MB

english, 2009

9

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization

Field, Yair, Fondufe-Mittendorf, Yvonne, Moore, Irene K, Mieczkowski, Piotr, Kaplan, Noam, Lubling, Yaniv, Lieb, Jason D, Widom, Jonathan, Segal, Eran

Journal:

Nature Genetics

Year:

2009

Language:

english

File:

PDF, 880 KB

english, 2009

10

New evidence that DNA encodes its packaging

Ercan, Sevinc, Lieb, Jason D.

Journal:

Nature Genetics

Year:

2006

Language:

english

File:

PDF, 246 KB

english, 2006

11

Out with the old, in with the new

Journal:

Nature Genetics

Year:

2005

Language:

english

File:

PDF, 320 KB

english, 2005

12

Evidence for nucleosome depletion at active regulatory regions genome-wide

Lee, Cheol-Koo, Shibata, Yoichiro, Rao, Bhargavi, Strahl, Brian D, Lieb, Jason D

Journal:

Nature Genetics

Year:

2004

Language:

english

File:

PDF, 963 KB

english, 2004

13

A chromatin-mediated mechanism for specification of conditional transcription factor targets

Buck, Michael J, Lieb, Jason D

Journal:

Nature Genetics

Year:

2006

Language:

english

File:

PDF, 588 KB

english, 2006

14

X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation

Ercan, Sevinc, Giresi, Paul G, Whittle, Christina M, Zhang, Xinmin, Green, Roland D, Lieb, Jason D

Journal:

Nature Genetics

Year:

2007

Language:

english

File:

PDF, 716 KB

english, 2007

15

How to find an opening (or lots of them)

Giresi, Paul G, Lieb, Jason D

Journal:

Year:

2006

Language:

english

File:

PDF, 529 KB

english, 2006

16

Nucleosome sequence preferences influence in vivo nucleosome organization

Kaplan, Noam, Moore, Irene, Fondufe-Mittendorf, Yvonne, Gossett, Andrea J, Tillo, Desiree, Field, Yair, Hughes, Timothy R, Lieb, Jason D, Widom, Jonathan, Segal, Eran

Journal:

Nature Structural and Molecular Biology

Year:

2010

Language:

english

File:

PDF, 321 KB

english, 2010

17

Forkhead proteins control the outcome of transcription factor binding by antiactivation

Voth, Warren P, Yu, Yaxin, Takahata, Shinya, Kretschmann, Kelsi L, Lieb, Jason D, Parker, Rebecca L, Milash, Brett, Stillman, David J

Journal:

The EMBO Journal

Year:

2007

Language:

english

File:

PDF, 1.20 MB

english, 2007

18

Tuning gene expression with nucleosome-disfavoring sequences

Palpant, Timothy, Lieb, Jason

Journal:

Nature Genetics

Year:

2012

Language:

english

File:

PDF, 2.03 MB

english, 2012

19

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

Lickwar, Colin R., Mueller, Florian, Hanlon, Sean E., McNally, James G., Lieb, Jason D.

Journal:

Year:

2012

Language:

english

File:

PDF, 2.57 MB

english, 2012

20

The C. elegans Dosage Compensation Complex Propagates Dynamically and Independently of X Chromosome Sequence

Sevinç Ercan, Lindsay L. Dick, Jason D. Lieb

Journal:

Current Biology

Year:

2009

Language:

english

File:

PDF, 2.18 MB

english, 2009

21

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

Simon, Jeremy M, Giresi, Paul G, Davis, Ian J, Lieb, Jason D

Journal:

Nature Protocols

Year:

2012

Language:

english

File:

PDF, 848 KB

english, 2012

22

Control of Transcription through Intragenic Patterns of Nucleosome Composition

Jason D. Lieb, Neil D. Clarke

Journal:

Year:

2005

Language:

english

File:

PDF, 572 KB

english, 2005

23

Chromatin Proteins Do Double Duty

Sevinc Ercan, Jason D. Lieb

Journal:

Year:

2008

Language:

english

File:

PDF, 296 KB

english, 2008

24

Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays

Sean E Hanlon, Jason D Lieb

Journal:

Current Opinion in Genetics & Development

Year:

2004

Language:

english

File:

PDF, 728 KB

english, 2004

25

Regulation of nucleosome stability as a mediator of chromatin function

Paul G Giresi, Mayetri Gupta, Jason D Lieb

Journal:

Current Opinion in Genetics & Development

Year:

2006

Language:

english

File:

PDF, 210 KB

english, 2006

26

Highly Transcribed RNA Polymerase II Genes Are Impediments to Replication Fork Progression in Saccharomyces cerevisiae

Anna Azvolinsky, Paul G. Giresi, Jason D. Lieb, Virginia A. Zakian

Journal:

Year:

2009

Language:

english

File:

PDF, 1.73 MB

english, 2009

27

Identification of direct targets of the Caenorhabditis elegans global sexual regulator TRA-1 by chromatin immunoprecipitation

Matthew R. Berkseth, Kohta Ikegami, Jason D. Lieb, David Zarkower

Journal:

Developmental Biology

Year:

2010

Language:

english

File:

PDF, 132 KB

english, 2010

28

ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments

Michael J Buck, Jason D Lieb

Journal:

Year:

2004

Language:

english

File:

PDF, 766 KB

english, 2004

29

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)

Paul G. Giresi, Jason D. Lieb

Journal:

Year:

2009

Language:

english

File:

PDF, 612 KB

english, 2009

30

MIX-1: An Essential Component of the C. elegans Mitotic Machinery Executes X Chromosome Dosage Compensation

Jason D Lieb, Michael R Albrecht, Pao-Tien Chuang, Barbara J Meyer

Journal:

Year:

1998

Language:

english

File:

PDF, 19.03 MB

english, 1998

31

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

Naim U Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, Jason D Lieb

Journal:

Year:

2011

Language:

english

File:

PDF, 1.57 MB

english, 2011

32

10.1038/ng569

Lieb, Jason D., Liu, Xiaole, Botstein, David, Brown, Patrick O.

Journal:

Nature Genetics

Year:

2001

Language:

english

File:

PDF, 675 KB

english, 2001

33

Genome-wide measurement of protein-DNA binding dynamics using competition ChIP

Lickwar, Colin R, Mueller, Florian, Lieb, Jason D

Journal:

Bioentrepreneur

Year:

2013

Language:

english

File:

PDF, 1.63 MB

english, 2013

34

Caenorhabditis eleganschromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2

Kohta Ikegami, Thea A Egelhofer, Susan Strome, Jason D Lieb

Journal:

Year:

2010

Language:

english

File:

PDF, 1.90 MB

english, 2010

35

ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data

Michael J Buck, Andrew B Nobel, Jason D Lieb

Journal:

Year:

2005

Language:

english

File:

PDF, 341 KB

english, 2005

36

Integral Nuclear Pore Proteins Bind to Pol III-Transcribed Genes and Are Required for Pol III Transcript Processing in C. elegans

Ikegami, Kohta, Lieb, Jason D.

Journal:

Year:

2013

Language:

english

File:

PDF, 3.71 MB

english, 2013

37

Genome-wide analysis links emerin to neuromuscular junction activity inCaenorhabditis elegans

González-Aguilera, Cristina, Ikegami, Kohta, Ayuso, Cristina, de Luis, Alberto, Íñiguez, María, Cabello, Juan, Lieb, Jason D, Askjaer, Peter

Journal:

Year:

2014

Language:

english

File:

PDF, 1.26 MB

english, 2014

38

A Common Set of DNA Regulatory Elements Shapes Drosophila Appendages

McKay, Daniel J., Lieb, Jason D.

Journal:

Developmental Cell

Year:

2013

Language:

english

File:

PDF, 3.57 MB

english, 2013

39

Tu1927 Genetically Driven Chromatin Organization Identifies Regulatory SNPs Associated With Crohn's Disease

Weiser, Matthew, Raulerson, Chelsea, Robinson, Adam, Gipson, Gregory, Sujino, Tomohisa, Takeuchi, Osamu, Kobayashi, Taku, Herfarth, Hans H., Sartor, Ryan B., McGovern, Dermot P., Lieb, Jason D., Furey

Journal:

Gastroenterology

Year:

2014

Language:

english

File:

PDF, 51 KB

english, 2014

40

Addendum: Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

Simon, Jeremy M, Giresi, Paul G, Davis, Ian J, Lieb, Jason D

Journal:

Nature Protocols

Year:

2014

Language:

english

File:

PDF, 118 KB

english, 2014

41

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology

Noam Kaplan,Timothy R Hughes,Jason D Lieb,Jonathan Widom,Eran Segal

Journal:

Year:

2010

Language:

english

File:

PDF, 596 KB

english, 2010

42

Quality Indicators Common to All GI Endoscopic Procedures

Rizk, Maged K, Sawhney, Mandeep S, Cohen, Jonathan, Pike, Irving M, Adler, Douglas G, Dominitz, Jason A, Lieb, John G, Lieberman, David A, Park, Walter G, Shaheen, Nicholas J, Wani, Sachin

Journal:

American Journal of Gastroenterology

Year:

2015

Language:

english

File:

PDF, 331 KB

english, 2015

43

Quality indicators common to all GI endoscopic procedures

Rizk, Maged K., Sawhney, Mandeep S., Cohen, Jonathan, Pike, Irving M., Adler, Douglas G., Dominitz, Jason A., Lieb, John G., Lieberman, David A., Park, Walter G., Shaheen, Nicholas J., Wani, Sachin

Journal:

Gastrointestinal Endoscopy

Year:

2015

Language:

english

File:

PDF, 572 KB

english, 2015

44

Interrogating the Function of Metazoan Histones using Engineered Gene Clusters

McKay, Daniel J., Klusza, Stephen, Penke, Taylor J.R., Meers, Michael P., Curry, Kaitlin P., McDaniel, Stephen L., Malek, Pamela Y., Cooper, Stephen W., Tatomer, Deirdre C., Lieb, Jason D., Strahl, Br

Journal:

Developmental Cell

Year:

2015

Language:

english

File:

PDF, 4.28 MB

english, 2015

45

STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer

Fleming, Joseph D, Giresi, Paul G, Lindahl-Allen, Marianne, Krall, Elsa B, Lieb, Jason D, Struhl, Kevin

Journal:

Epigenetics & Chromatin

Year:

2015

Language:

english

File:

PDF, 1.98 MB

english, 2015

46

Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

Hu, Jinchuan, Adar, Sheera, Selby, Christopher P., Lieb, Jason D., Sancar, Aziz

Journal:

Genes & Development

Year:

2015

Language:

english

File:

PDF, 3.27 MB

english, 2015

47

GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters

Fuda, Nicholas J., Guertin, Michael J., Sharma, Sumeet, Danko, Charles G., Martins, André L., Siepel, Adam, Lis, John T., Lieb, Jason D.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.24 MB

english, 2015

48

Cell Cycle–Specified Fluctuation of Nucleosome Occupancy at Gene Promoters

Hogan, Gregory J., Lee, Cheol-Koo, Lieb, Jason D.

Journal:

Year:

2006

Language:

english

File:

PDF, 3.09 MB

english, 2006

49

Replication and Active Demethylation Represent Partially Overlapping Mechanisms for Erasure of H3K4me3 in Budding Yeast

Radman-Livaja, Marta, Liu, Chih Long, Friedman, Nir, Schreiber, Stuart L., Rando, Oliver J., Lieb, Jason D.

Journal:

Year:

2010

Language:

english

File:

PDF, 1.86 MB

english, 2010

50

In Vivo Effects of Histone H3 Depletion on Nucleosome Occupancy and Position in Saccharomyces cerevisiae

Gossett, Andrea J., Lieb, Jason D., Rando, Oliver J.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.60 MB

english, 2012