Chromatin / DNA Shearing



Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens
Bonnie B. Blaimer, et. al., PLoS ONE 11(8):e0161531.doi:10.137

An RNF168 fragment defective for focal accumulation at DNA damage is proficient for inhibition of homologous recombination in BRCA1 deficient cells
Munoz, et. al., 2014; Nucleic Acids Research, doi: 10.1093/nar/gku421

Enhanced virome sequencing using targeted sequence capture
Wylie, et. al., 2016; Genome Research, 25: 1910-1920

Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) Using mitochondrial genome data and insight into their mitochondrial transcription
Kayal, et. al., 2015; PeerJ, 3: e1403; doi 10.7717/peerj.1403

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage
Sass, et. al., 2016; PeerJ, 4:e1584; doi 10.7717/peerj.1584

CXCL8 histone H3 acetylation is dysfunctional in airway smooth muscle in asthma: regulation by BET
Clifford, et. al., Am J Physiol Lung Cell Mol Physiol Vol. 308: L962–L972, February 2015

IƙB Kinase β (IKBKB) Mutations in Lymphomas That Constitutively Activate Canonical Nuclear Factor ƙB (NFƙB) Signaling*
Kai, et. al., Journal of Biological Chemistry Vol. 289, No. 38, pp26960-26972, September 2014

Farnesoid X receptor regulates forkhead Box O3a activation in ethanol-induced autophagy and hepatotoxicity
Manley, et. al., Redox Biology Vol. 2, pp991-1002, August 2014

Inhibition of mutant EGFR in lung cancer cells triggers SOX2-FOXO6-dependent Survival pathways
Rothenberg, et. al., eLife, 2015; 4:e06132. DOI:  10.7554/eLife.

DNA Damage Response Factors from Diverse Pathways, Including DNA Crosslink Repair, Mediate Alternative End Joining
Howard, et. al., PLOS Genetics, 11(1): e1004943, 2015; doi:10.1371/journal.pgen.1004943

KDM4A Lysine Demethylase Induces Site-Specific Copy Gain and Rereplication of Regions Amplified in Tumors
Black et.al., Cell, Volume 154, Issue 3, 541-555, 18 July 2013

Enhanced in vivo Fitness of Carbapenem-resistant oprD mutants of Pseudomonas Aeruginosa Revealed Through High-throughput Sequencing
Skurnika et al., PNAS, Volume 110 No. 51, 20747–20752, 17 December 2013

Coupling Mutagenesis and Parallel Deep Sequencing to Probe Essential Residues in a Genome or Gene
Robins et al., PNAS, Volume 110 No. 9, E848–E857, 26 February 2013

TP53 supports basal-like differentiation of mammary epithelial cells by preventing translocation of deltaNp63 into nucleoli
Munne, P.M. et.al., Nature Sci. Rep., 4, 4663; DOI: 10.1038/srep04663 (2014)

Rediscovery of an Endemic Vertebrate from the Remote Islas Revillagigedo in the Eastern Pacific Ocean: The Clarion Nightsnake Lost and Found
Mulcahy et al., PLOS ONE, Volume 9 Issue No. 5, E97682, 2 May 2015

MELK is an oncogenic kinase essential for mitotic progression in basal-like breast cancer cells Wang et al., eLife 2014; 3:e01763. DOI:10.7554/eLife.01763

SH2B1 in _-Cells Promotes Insulin Expression and Glucose Metabolism in Mice
Chen, et. al., Molecular Endocrinology, Volume 28, Issue 5, 696-705, May 2014

O-GlcNAcase expression is sensitive to changes in O-GlcNAc homeostasis
Zhang, et. al., Frontiers in Endocrinology, Volume 5, Article 206, December 2014 http://dx.doi.org/10.3389/fendo.2014.00206

Lysine Demethylase KDM4A Associates with Translation Machinery and Regulates Protein Synthesis
Van Rechem et.al., AACR Cancer Discovery 2015, Volume 5, 255-263 DOI: 10.1158/2159-8290.CD-14-1326

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
Faircloth et.al., Molecular Ecology Resources, Volume 15, 489-201, 2015


SOX4 enables oncogenic survival signals in acute lymphoblastic leukemia
Ramezani-Rad et.al., Blood Journal, Volume 121 (1), 1-9, October 2012

ZASC1 Stimulates HIV-1 Transcription Elongation by Recruiting P-TEFb and TAT to the LTR Promoter
Bruce et.al., PLOS Pathogens, Volume 9, Issue 10, 1-19, October 2013

Activation of TGF-b1 Promoter by Hepatitis C Virus-Induced AP-1 and Sp1: Role of TGF-b1 in Hepatic Stellate Cell Activation and Invasion
Presser et.al., PLOS ONE, Volume 8, Issue 2, 1-19, February 2013

Allelic Imbalance Assays to Quantify Allele-Specifi c Gene Expression and Transcription Factor Binding
Luca et.al., Pharmacogenomics: Methods and Protocols, Methods in Molecular Biology, vol. 1015, DOI 10.1007/978-1-62703-435-7_13, 201-211, (2013)

Dexamethasone Induces a Putative Repressor Complex and Chromatin Modifications in the CRH Promoter
Sharma et.al., Molecular Endocrinology, Volume 27, Issue 7, 1142-1152, July 2013

Cdk1 Regulates the Temporal Recruitment of Telomerase and Cdc13-Stn1-Ten1 Complex for Telomere Replication
Liu et.al., Molecular and Cellular Biology, Volume 34, Number 1, 57-70 , January 2014


Wnt Signaling Inhibits Adrenal Steroidogenesis by Cell-Autonomous and Non–Cell-Autonomous Mechanisms
Walczak et. al., Molecular Endocrinology, Volume 28, No. 9, pp 1471-1486; September 2014

Tissue-specific regulation of Igf2r/Airn imprinting during gastrulation
Marcho et. al., Epigenetics and Chromatin, Volume 8, No.10, 2015; DOI 10.1186/s13072-015-0003-y

Parasitology Canonical histone H2Ba and H2A.X dimerize in an opposite genomiclocalization to H2A.Z/H2B.Z dimers in Toxoplasma gondii
Bogado et.al., Molecular and Biochemical Parasitology, 197 (2014) 36-42

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia
Trimarchi et.al., Cell, Volume 158, 593-606, July 2014


The capacity of target silencing by Drosophila PIWI and piRNAs
Post et.al., Cold Spring Harbor Laboratory Press, RMA Volume 20: 1977-1986, April 2015

Chloroquine reduces osteoclastogenesis in murine osteoporosis by preventing TRAF3 degradation
Xiu et.al., Journal of Clinical Investigation, Volume 124, Issue 1, January 2014

Discontinued Models (e.g. S-4000, S-3000)

Chromatin Immunoprecipitation with Fixed Animal Tissues and Preparation for High-Throughput Sequencing
Cotney et.al., Cold Spring Harbor Laboratory Press (2015)
Cold Spring Harb Protoc; doi: 10.1101/pdb.prot084848