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List of works by Jason D Lieb

A Detailed Protocol for Formaldehyde‐Assisted Isolation of Regulatory Elements (FAIRE) ⬇️

scientific article published on January 1, 2013

A Guanosine-Centric Mechanism for RNA Chaperone Function ⬇️

scientific article published on March 7, 2013

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

scientific article

A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters

scientific article

A map of open chromatin in human pancreatic islets

scientific article

A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae

scientific article published on 2 October 2009

Allele-specific and heritable chromatin signatures in humans

scientific article published on 16 September 2010

Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses

scientific article published on 9 May 2016

An assessment of histone-modification antibody quality

scientific article

An inverse relationship to germline transcription defines centromeric chromatin in C. elegans

scientific article published on 8 April 2012

Analysis of the Basidiomycete Coprinopsis cinerea reveals conservation of the core meiotic expression program over half a billion years of evolution

scientific article published in September 2010

Broad chromosomal domains of histone modification patterns in C. elegans

scientific article

C. elegans dosage compensation: a window into mechanisms of domain-scale gene regulation

scientific article published on January 2009

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

scientific article

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

scientific article

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

scientific article

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

scientific article

Comparative analysis of metazoan chromatin organization

scientific article

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

scientific article published on 30 November 2010

Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association

scientific article published on 28 April 2015

DNA Immunoprecipitation (DIP) for the Determination of DNA-Binding Specificity

scientific article published on 01 March 2008

DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I.

scholarly article

Defining functional DNA elements in the human genome

scientific article

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster

scientific article published on 23 October 2011

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

scientific article

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

scientific article published on March 2009

Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans.

scientific article

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

scientific article published on June 13, 2013

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

scientific article published on 11 April 2012

Global analysis of the relationship between the binding of the Bas1p transcription factor and meiosis-specific double-strand DNA breaks in Saccharomyces cerevisiae

scientific article published on February 2006

H4K20me1 contributes to downregulation of X-linked genes for C. elegans dosage compensation

scientific article

Heritable individual-specific and allele-specific chromatin signatures in humans

scientific article

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans

scientific article published on 22 December 2010

High nucleosome occupancy is encoded at human regulatory sequences

scientific article

Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae

scientific article published on June 2009

How to find an opening (or lots of them)

scientific article published on 01 July 2006

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

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

scientific article published on June 21, 2012

Integral nuclear pore proteins bind to Pol III-transcribed genes and are required for Pol III transcript processing in C. elegans

scientific article published on 5 September 2013

Integrating regulatory motif discovery and genome-wide expression analysis

scholarly article

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

scientific article

Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae.

scholarly article

New evidence that DNA encodes its packaging

scientific article published on 01 October 2006

Nucleoporins and transcription: new connections, new questions

scientific article

Nucleosome dynamics define transcriptional enhancers

scientific article

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

scientific article

Nucleosome sequence preferences influence in vivo nucleosome organization

scientific article published on August 2010

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

scientific article

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

scientific article

Promoter- and RNA polymerase II-dependent hsp-16 gene association with nuclear pores in Caenorhabditis elegans

scientific article

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association

scientific article

Regulation of nucleosome stability as a mediator of chromatin function

scientific article

Regulation of the X chromosomes in Caenorhabditis elegans

scientific article published on March 2014

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

scientific article published on August 2014

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

scientific article

Single-cell ATAC-seq: strength in numbers

scientific article published on 21 August 2015

Systematic evaluation of factors influencing ChIP-seq fidelity

scientific article

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

scientific article published on 7 February 2008

Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae

scientific article

TRA-1 ChIP-seq reveals regulators of sexual differentiation and multilevel feedback in nematode sex determination

scientific article published on 17 September 2013

The C. elegans dosage compensation complex propagates dynamically and independently of X chromosome sequence

scientific article published on 22 October 2009

The DNA-encoded nucleosome organization of a eukaryotic genome

scientific article

The accessible chromatin landscape of the human genome

scientific article

The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis

scientific article

The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny.

scientific article

The open chromatin landscape of Kaposi's sarcoma-associated herpesvirus

scientific article published on 28 August 2013

The stress response factors Yap6, Cin5, Phd1, and Skn7 direct targeting of the conserved co-repressor Tup1-Ssn6 in S. cerevisiae.

scientific article

Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription

scientific article published on 10 February 2018

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

Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription.

scientific article

Unlocking the secrets of the genome

scientific article

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

scientific article published on January 19, 2012

Variation in DNA-Damage Responses to an Inhalational Carcinogen (1,3-Butadiene) in Relation to Strain-Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice

scientific article

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

scientific article published on 24 October 2013

What are super-enhancers?

scientific article

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

scientific article published on 11 February 2007

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

scientific article

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