Search Results - "White, Kevin P."

RNA-seq differential expression studies: more sequence or more replication? by Liu, Yuwen, Zhou, Jie, White, Kevin P

“…RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting…”
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Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids by Schuster, Brooke, Junkin, Michael, Kashaf, Sara Saheb, Romero-Calvo, Isabel, Kirby, Kori, Matthews, Jonathan, Weber, Christopher R., Rzhetsky, Andrey, White, Kevin P., Tay, Savaş

“…Three-dimensional (3D) cell culture technologies, such as organoids, are physiologically relevant models for basic and clinical applications. Automated…”
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Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation by Xie, Zhongyu, Zhang, Di, Chung, Dongjun, Tang, Zhanyun, Huang, He, Dai, Lunzhi, Qi, Shankang, Li, Jingya, Colak, Gozde, Chen, Yue, Xia, Chunmei, Peng, Chao, Ruan, Haibin, Kirkey, Matt, Wang, Danli, Jensen, Lindy M., Kwon, Oh Kwang, Lee, Sangkyu, Pletcher, Scott D., Tan, Minjia, Lombard, David B., White, Kevin P., Zhao, Hongyu, Li, Jia, Roeder, Robert G., Yang, Xiaoyong, Zhao, Yingming

“…Here we report the identification and verification of a β-hydroxybutyrate-derived protein modification, lysine β-hydroxybutyrylation (Kbhb), as a new type of…”
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Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas by Seiwert, Tanguy Y, Zuo, Zhixiang, Keck, Michaela K, Khattri, Arun, Pedamallu, Chandra S, Stricker, Thomas, Brown, Christopher, Pugh, Trevor J, Stojanov, Petar, Cho, Juok, Lawrence, Michael S, Getz, Gad, Brägelmann, Johannes, DeBoer, Rebecca, Weichselbaum, Ralph R, Langerman, Alexander, Portugal, Louis, Blair, Elizabeth, Stenson, Kerstin, Lingen, Mark W, Cohen, Ezra E W, Vokes, Everett E, White, Kevin P, Hammerman, Peter S

“…The genetic differences between human papilloma virus (HPV)-positive and -negative head and neck squamous cell carcinomas (HNSCC) remain largely unknown. To…”
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Functional assessment of human enhancer activities using whole-genome STARR-sequencing by Liu, Yuwen, Yu, Shan, Dhiman, Vineet K, Brunetti, Tonya, Eckart, Heather, White, Kevin P

“…Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of…”
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Genomic Antagonism between Retinoic Acid and Estrogen Signaling in Breast Cancer by Hua, Sujun, Kittler, Ralf, White, Kevin P.

“…Retinoic acid (RA) triggers antiproliferative effects in tumor cells, and therefore RA and its synthetic analogs have great potential as anticarcinogenic…”
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Integrated molecular subtyping defines a curable oligometastatic state in colorectal liver metastasis by Pitroda, Sean P., Khodarev, Nikolai N., Huang, Lei, Uppal, Abhineet, Wightman, Sean C., Ganai, Sabha, Joseph, Nora, Pitt, Jason, Brown, Miguel, Forde, Martin, Mangold, Kathy, Xue, Lai, Weber, Christopher, Segal, Jeremy P., Kadri, Sabah, Stack, Melinda E., Khan, Sajid, Paty, Philip, Kaul, Karen, Andrade, Jorge, White, Kevin P., Talamonti, Mark, Posner, Mitchell C., Hellman, Samuel, Weichselbaum, Ralph R.

“…The oligometastasis hypothesis suggests a spectrum of metastatic virulence where some metastases are limited in extent and curable with focal therapies. A…”
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A Conserved Bicycle Model for Circadian Clock Control of Membrane Excitability by Flourakis, Matthieu, Kula-Eversole, Elzbieta, Hutchison, Alan L., Han, Tae Hee, Aranda, Kimberly, Moose, Devon L., White, Kevin P., Dinner, Aaron R., Lear, Bridget C., Ren, Dejian, Diekman, Casey O., Raman, Indira M., Allada, Ravi

“…Circadian clocks regulate membrane excitability in master pacemaker neurons to control daily rhythms of sleep and wake. Here, we find that two distinctly timed…”
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Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats by Song, Se Jin, Sanders, Jon G, Delsuc, Frédéric, Metcalf, Jessica, Amato, Katherine, Taylor, Michael W, Mazel, Florent, Lutz, Holly L, Winker, Kevin, Graves, Gary R, Humphrey, Gregory, Gilbert, Jack A, Hackett, Shannon J, White, Kevin P, Skeen, Heather R, Kurtis, Sarah M, Withrow, Jack, Braile, Thomas, Miller, Matthew, McCracken, Kevin G, Maley, James M, Ezenwa, Vanessa O, Williams, Allison, Blanton, Jessica M, McKenzie, Valerie J, Knight, Rob

“…Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all…”
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Defining functional DNA elements in the human genome by Kellis, Manolis, Wold, Barbara, Snyderd, Michael P., Bernstein, Bradley E., Kundaje, Anshul, Marinov, Georgi K., Ward, Lucas D., Birney, Ewan, Crawford, Gregory E., Dekker, Job, Dunham, Ian, Elnitski, Laura L., Farnham, Peggy J., Feingold, Elise A., Gerstein, Mark, Giddings, Morgan C., Gilbert, David M., Gingeras, Thomas R., Green, Eric D., Guigo, Roderic, Hubbard, Tim, Kent, Jim, Lieb, Jason D., Myerst, Richard M., Pazin, Michael J., Ren, Bing, Stamatoyannopoulos, John A., Weng, Zhiping, White, Kevin P., Hardison, Ross C.

“…With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and…”
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A Nondegenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk by Blair, David R., Lyttle, Christopher S., Mortensen, Jonathan M., Bearden, Charles F., Jensen, Anders Boeck, Khiabanian, Hossein, Melamed, Rachel, Rabadan, Raul, Bernstam, Elmer V., Brunak, Søren, Jensen, Lars Juhl, Nicolae, Dan, Shah, Nigam H., Grossman, Robert L., Cox, Nancy J., White, Kevin P., Rzhetsky, Andrey

“…Although countless highly penetrant variants have been associated with Mendelian disorders, the genetic etiologies underlying complex diseases remain largely…”
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Integration of temporal and spatial patterning generates neural diversity by Erclik, Ted, Li, Xin, Courgeon, Maximilien, Bertet, Claire, Chen, Zhenqing, Baumert, Ryan, Ng, June, Koo, Clara, Arain, Urfa, Behnia, Rudy, Del Valle Rodriguez, Alberto, Senderowicz, Lionel, Negre, Nicolas, White, Kevin P., Desplan, Claude

“…In the Drosophila optic lobes, 800 retinotopically organized columns in the medulla act as functional units for processing visual information. The medulla…”
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Integrative analysis of head and neck cancer identifies two biologically distinct HPV and three non-HPV subtypes by Keck, Michaela K, Zuo, Zhixiang, Khattri, Arun, Stricker, Thomas P, Brown, Christopher D, Imanguli, Matin, Rieke, Damian, Endhardt, Katharina, Fang, Petra, Brägelmann, Johannes, DeBoer, Rebecca, El-Dinali, Mohamed, Aktolga, Serdal, Lei, Zhengdeng, Tan, Patrick, Rozen, Steve G, Salgia, Ravi, Weichselbaum, Ralph R, Lingen, Mark W, Story, Michael D, Ang, K Kian, Cohen, Ezra E W, White, Kevin P, Vokes, Everett E, Seiwert, Tanguy Y

“…Current classification of head and neck squamous cell carcinomas (HNSCC) based on anatomic site and stage fails to capture biologic heterogeneity or adequately…”
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Systematic identification of regulatory variants associated with cancer risk by Liu, Song, Liu, Yuwen, Zhang, Qin, Wu, Jiayu, Liang, Junbo, Yu, Shan, Wei, Gong-Hong, White, Kevin P, Wang, Xiaoyue

“…Most cancer risk-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) are noncoding and it is challenging to…”
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Infectious vaccine-derived rubella viruses emerge, persist, and evolve in cutaneous granulomas of children with primary immunodeficiencies by Perelygina, Ludmila, Chen, Min-Hsin, Suppiah, Suganthi, Adebayo, Adebola, Abernathy, Emily, Dorsey, Morna, Bercovitch, Lionel, Paris, Kenneth, White, Kevin P, Krol, Alfons, Dhossche, Julie, Torshin, Ivan Y, Saini, Natalie, Klimczak, Leszek J, Gordenin, Dmitry A, Zharkikh, Andrey, Plotkin, Stanley, Sullivan, Kathleen E, Icenogle, Joseph

“…Rubella viruses (RV) have been found in an association with granulomas in children with primary immune deficiencies (PID). Here, we report the recovery and…”
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STARRPeaker: uniform processing and accurate identification of STARR-seq active regions by Lee, Donghoon, Shi, Manman, Moran, Jennifer, Wall, Martha, Zhang, Jing, Liu, Jason, Fitzgerald, Dominic, Kyono, Yasuhiro, Ma, Lijia, White, Kevin P, Gerstein, Mark

“…STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and…”
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Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia by Bryois, Julien, Garrett, Melanie E., Song, Lingyun, Safi, Alexias, Giusti-Rodriguez, Paola, Johnson, Graham D., Shieh, Annie W., Buil, Alfonso, Fullard, John F., Roussos, Panos, Sklar, Pamela, Akbarian, Schahram, Haroutunian, Vahram, Stockmeier, Craig A., Wray, Gregory A., White, Kevin P., Liu, Chunyu, Reddy, Timothy E., Ashley-Koch, Allison, Sullivan, Patrick F., Crawford, Gregory E.

“…Schizophrenia genome-wide association studies have identified >150 regions of the genome associated with disease risk, yet there is little evidence that coding…”
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Su(H)-Mediated Repression Positions Gene Boundaries along the Dorsal-Ventral Axis of Drosophila Embryos by Ozdemir, Anil, Ma, Lijia, White, Kevin P., Stathopoulos, Angelike

“…In Drosophila embryos, a nuclear gradient of the Dorsal (Dl) transcription factor directs differential gene expression along the dorsoventral (DV) axis,…”
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Genome-wide Association of Yorkie with Chromatin and Chromatin-Remodeling Complexes by Oh, Hyangyee, Slattery, Matthew, Ma, Lijia, Crofts, Alex, White, Kevin P., Mann, Richard S., Irvine, Kenneth D.

“…The Hippo pathway regulates growth through the transcriptional coactivator Yorkie, but how Yorkie promotes transcription remains poorly understood. We address…”
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A comprehensive map of insulator elements for the Drosophila genome by Nègre, Nicolas, Brown, Christopher D, Shah, Parantu K, Kheradpour, Pouya, Morrison, Carolyn A, Henikoff, Jorja G, Feng, Xin, Ahmad, Kami, Russell, Steven, White, Robert A H, Stein, Lincoln, Henikoff, Steven, Kellis, Manolis, White, Kevin P

“…Insulators are DNA sequences that control the interactions among genomic regulatory elements and act as chromatin boundaries. A thorough understanding of their…”
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