Search Results - "Gertz, Jason"

MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate by Ireland, Abbie S., Micinski, Alexi M., Kastner, David W., Guo, Bingqian, Wait, Sarah J., Spainhower, Kyle B., Conley, Christopher C., Chen, Opal S., Guthrie, Matthew R., Soltero, Danny, Qiao, Yi, Huang, Xiaomeng, Tarapcsák, Szabolcs, Devarakonda, Siddhartha, Chalishazar, Milind D., Gertz, Jason, Moser, Justin C., Marth, Gabor, Puri, Sonam, Witt, Benjamin L., Spike, Benjamin T., Oliver, Trudy G.

“…Small cell lung cancer (SCLC) is a neuroendocrine tumor treated clinically as a single disease with poor outcomes. Distinct SCLC molecular subtypes have been…”
Get full text

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing by Marinov, Georgi K, Williams, Brian A, McCue, Ken, Schroth, Gary P, Gertz, Jason, Myers, Richard M, Wold, Barbara J

“…Single-cell RNA-seq mammalian transcriptome studies are at an early stage in uncovering cell-to-cell variation in gene expression, transcript processing and…”
Get full text

GIGGLE: a search engine for large-scale integrated genome analysis by Layer, Ryan M, Pedersen, Brent S, DiSera, Tonya, Marth, Gabor T, Gertz, Jason, Quinlan, Aaron R

“…GIGGLE is a genome interval search engine that enables extremely fast queries of genome features from thousands of genome annotation sets. GIGGLE is a genomics…”
Get full text

Widespread plasticity in CTCF occupancy linked to DNA methylation by Wang, Hao, Maurano, Matthew T, Qu, Hongzhu, Varley, Katherine E, Gertz, Jason, Pauli, Florencia, Lee, Kristen, Canfield, Theresa, Weaver, Molly, Sandstrom, Richard, Thurman, Robert E, Kaul, Rajinder, Myers, Richard M, Stamatoyannopoulos, John A

“…CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin…”
Get full text

Analysis of combinatorial cis -regulation in synthetic and genomic promoters by Cohen, Barak A, Gertz, Jason, Siggia, Eric D

“…Transcription factor binding sites are being discovered at a rapid pace. It is now necessary to turn attention towards understanding how these sites work in…”
Get full text

MYC-Driven Small-Cell Lung Cancer is Metabolically Distinct and Vulnerable to Arginine Depletion by Chalishazar, Milind D, Wait, Sarah J, Huang, Fang, Ireland, Abbie S, Mukhopadhyay, Anandaroop, Lee, Younjee, Schuman, Sophia S, Guthrie, Matthew R, Berrett, Kristofer C, Vahrenkamp, Jeffery M, Hu, Zeping, Kudla, Marek, Modzelewska, Katarzyna, Wang, Guoying, Ingolia, Nicholas T, Gertz, Jason, Lum, David H, Cosulich, Sabina C, Bomalaski, John S, DeBerardinis, Ralph J, Oliver, Trudy G

“…Small-cell lung cancer (SCLC) has been treated clinically as a homogeneous disease, but recent discoveries suggest that SCLC is heterogeneous. Whether…”
Get full text

The Lineage-Defining Transcription Factors SOX2 and NKX2-1 Determine Lung Cancer Cell Fate and Shape the Tumor Immune Microenvironment by Mollaoglu, Gurkan, Jones, Alex, Wait, Sarah J., Mukhopadhyay, Anandaroop, Jeong, Sangmin, Arya, Rahul, Camolotto, Soledad A., Mosbruger, Timothy L., Stubben, Chris J., Conley, Christopher J., Bhutkar, Arjun, Vahrenkamp, Jeffery M., Berrett, Kristofer C., Cessna, Melissa H., Lane, Thomas E., Witt, Benjamin L., Salama, Mohamed E., Gertz, Jason, Jones, Kevin B., Snyder, Eric L., Oliver, Trudy G.

“…The major types of non-small-cell lung cancer (NSCLC)—squamous cell carcinoma and adenocarcinoma—have distinct immune microenvironments. We developed a genetic…”
Get full text

Dynamic DNA methylation across diverse human cell lines and tissues by Varley, Katherine E, Gertz, Jason, Bowling, Kevin M, Parker, Stephanie L, Reddy, Timothy E, Pauli-Behn, Florencia, Cross, Marie K, Williams, Brian A, Stamatoyannopoulos, John A, Crawford, Gregory E, Absher, Devin M, Wold, Barbara J, Myers, Richard M

“…As studies of DNA methylation increase in scope, it has become evident that methylation has a complex relationship with gene expression, plays an important…”
Get full text

Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites by Gertz, Jason, Savic, Daniel, Varley, Katherine E., Partridge, E. Christopher, Safi, Alexias, Jain, Preti, Cooper, Gregory M., Reddy, Timothy E., Crawford, Gregory E., Myers, Richard M.

“…Most human transcription factors bind a small subset of potential genomic sites and often use different subsets in different cell types. To identify mechanisms…”
Get full text

CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice by Guo, Ya, Monahan, Kevin, Wu, Haiyang, Gertz, Jason, Varley, Katherine E., Li, Wei, Myers, Richard M., Maniatis, Tom, Wu, Qiang

“…The closely linked human protocadherin (Pcdh) α, β, and γ gene clusters encode 53 distinct protein isoforms, which are expressed in a combinatorial manner to…”
Get full text

The Hypersensitive Glucocorticoid Response Specifically Regulates Period 1 and Expression of Circadian Genes by Reddy, Timothy E., Gertz, Jason, Crawford, Gregory E., Garabedian, Michael J., Myers, Richard M.

“…Article Usage Stats Services MCB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
Get full text

Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner by Gertz, Jason, Reddy, Timothy E, Varley, Katherine E, Garabedian, Michael J, Myers, Richard M

“…Endogenous estrogens that are synthesized in the body impact gene regulation by activating estrogen receptors in diverse cell types. Exogenous compounds that…”
Get full text

Cooperative Dynamics of AR and ER Activity in Breast Cancer by D'Amato, Nicholas C, Gordon, Michael A, Babbs, Beatrice, Spoelstra, Nicole S, Carson Butterfield, Kiel T, Torkko, Kathleen C, Phan, Vernon T, Barton, Valerie N, Rogers, Thomas J, Sartorius, Carol A, Elias, Anthony, Gertz, Jason, Jacobsen, Britta M, Richer, Jennifer K

“…Androgen receptor (AR) is expressed in 90% of estrogen receptor alpha-positive (ER ) breast tumors, but its role in tumor growth and progression remains…”
Get full text

Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation by Gertz, Jason, Varley, Katherine E, Reddy, Timothy E, Bowling, Kevin M, Pauli, Florencia, Parker, Stephanie L, Kucera, Katerina S, Willard, Huntington F, Myers, Richard M

“…The methylation of cytosines in CpG dinucleotides is essential for cellular differentiation and the progression of many cancers, and it plays an important role…”
Get full text

Recurrent read-through fusion transcripts in breast cancer by Varley, Katherine E., Gertz, Jason, Roberts, Brian S., Davis, Nicholas S., Bowling, Kevin M., Kirby, Marie K., Nesmith, Amy S., Oliver, Patsy G., Grizzle, William E., Forero, Andres, Buchsbaum, Donald J., LoBuglio, Albert F., Myers, Richard M.

“…Read-through fusion transcripts that result from the splicing of two adjacent genes in the same coding orientation are a recently discovered type of chimeric…”
Get full text

3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression by Mortenson, Katelyn L., Dawes, Courtney, Wilson, Emily R., Patchen, Nathan E., Johnson, Hailey E., Gertz, Jason, Bailey, Swneke D., Liu, Yang, Varley, Katherine E., Zhang, Xiaoyang

“…Cancer genomes are composed of many complex structural alterations on chromosomes and extrachromosomal DNA (ecDNA), making it difficult to identify non-coding…”
Get full text

ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation by Li, Zheqi, McGinn, Olivia, Wu, Yang, Bahreini, Amir, Priedigkeit, Nolan M., Ding, Kai, Onkar, Sayali, Lampenfeld, Caleb, Sartorius, Carol A., Miller, Lori, Rosenzweig, Margaret, Cohen, Ofir, Wagle, Nikhil, Richer, Jennifer K., Muller, William J., Buluwela, Laki, Ali, Simak, Bruno, Tullia C., Vignali, Dario A. A., Fang, Yusi, Zhu, Li, Tseng, George C., Gertz, Jason, Atkinson, Jennifer M., Lee, Adrian V., Oesterreich, Steffi

“…Estrogen receptor alpha (ER/ ESR1 ) is frequently mutated in endocrine resistant ER-positive (ER+) breast cancer and linked to ligand-independent growth and…”
Get full text

Post-mortem molecular profiling of three psychiatric disorders by Ramaker, Ryne C, Bowling, Kevin M, Lasseigne, Brittany N, Hagenauer, Megan H, Hardigan, Andrew A, Davis, Nicholas S, Gertz, Jason, Cartagena, Preston M, Walsh, David M, Vawter, Marquis P, Jones, Edward G, Schatzberg, Alan F, Barchas, Jack D, Watson, Stanley J, Bunney, Blynn G, Akil, Huda, Bunney, William E, Li, Jun Z, Cooper, Sara J, Myers, Richard M

“…Psychiatric disorders are multigenic diseases with complex etiology that contribute significantly to human morbidity and mortality. Although clinically…”
Get full text

A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer by Liu, Yanli, Wu, Zhong, Zhou, Jin, Ramadurai, Dinesh K. A., Mortenson, Katelyn L., Aguilera-Jimenez, Estrella, Yan, Yifei, Yang, Xiaojun, Taylor, Alison M., Varley, Katherine E., Gertz, Jason, Choi, Peter S., Cherniack, Andrew D., Chen, Xingdong, Bass, Adam J., Bailey, Swneke D., Zhang, Xiaoyang

“…Amplification and overexpression of the SOX2 oncogene represent a hallmark of squamous cancers originating from diverse tissue types. Here, we find that…”
Get full text

IκB kinase ε (IKKε) regulates the balance between type I and type II interferon responses by Ng, Sze-Ling, Friedman, Brad A, Schmid, Sonja, Gertz, Jason, Myers, Richard M, tenOever, Benjamin R, Maniatis, Tom

“…Virus infection induces the production of type I and type II interferons (IFN-I and IFN-II), cytokines that mediate the antiviral response. IFN-I (IFN-α and…”
Get full text