Search Results - "Davuluri, Ramana V"

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome by Ji, Yanrong, Zhou, Zhihan, Liu, Han, Davuluri, Ramana V

“…Abstract Motivation Deciphering the language of non-coding DNA is one of the fundamental problems in genome research. Gene regulatory code is highly complex…”
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ADAR1 Forms a Complex with Dicer to Promote MicroRNA Processing and RNA-Induced Gene Silencing by Ota, Hiromitsu, Sakurai, Masayuki, Gupta, Ravi, Valente, Louis, Wulff, Bjorn-Erik, Ariyoshi, Kentaro, Iizasa, Hisashi, Davuluri, Ramana V., Nishikura, Kazuko

“…Adenosine deaminases acting on RNA (ADARs) are involved in RNA editing that converts adenosine residues to inosine specifically in double-stranded RNAs. In…”
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Metastatic cancers promote cachexia through ZIP14 upregulation in skeletal muscle by Wang, Gang, Biswas, Anup K., Ma, Wanchao, Kandpal, Manoj, Coker, Courtney, Grandgenett, Paul M., Hollingsworth, Michael A., Jain, Rinku, Tanji, Kurenai, Lόpez-Pintado, Sara, Borczuk, Alain, Hebert, Doreen, Jenkitkasemwong, Supak, Hojyo, Shintaro, Davuluri, Ramana V., Knutson, Mitchell D., Fukada, Toshiyuki, Acharyya, Swarnali

“…Patients with metastatic cancer experience a severe loss of skeletal muscle mass and function known as cachexia. Cachexia is associated with poor prognosis and…”
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Alternative transcription and alternative splicing in cancer by Pal, Sharmistha, Gupta, Ravi, Davuluri, Ramana V

“…In recent years, the notion of "one gene makes one protein that functions in one signaling pathway" in mammalian cells has been shown to be overly simplistic…”
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Imaging patterns predict patient survival and molecular subtype in glioblastoma via machine learning techniques by Macyszyn, Luke, Akbari, Hamed, Pisapia, Jared M, Da, Xiao, Attiah, Mark, Pigrish, Vadim, Bi, Yingtao, Pal, Sharmistha, Davuluri, Ramana V, Roccograndi, Laura, Dahmane, Nadia, Martinez-Lage, Maria, Biros, George, Wolf, Ronald L, Bilello, Michel, O'Rourke, Donald M, Davatzikos, Christos

“…MRI characteristics of brain gliomas have been used to predict clinical outcome and molecular tumor characteristics. However, previously reported imaging…”
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Genetic Predisposition to Papillary Thyroid Carcinoma: Involvement of FOXE1, TSHR, and a Novel lincRNA Gene, PTCSC2 by He, Huiling, Li, Wei, Liyanarachchi, Sandya, Jendrzejewski, Jaroslaw, Srinivas, Mukund, Davuluri, Ramana V, Nagy, Rebecca, de la Chapelle, Albert

“…Context: By genome-wide association studies, the risk allele [A] of SNP rs965513 predisposes strongly to papillary thyroid carcinoma (PTC). It is located in a…”
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polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type by Jendrzejewski, Jaroslaw, He, Huiling, Radomska, Hanna S, Li, Wei, Tomsic, Jerneja, Liyanarachchi, Sandya, Davuluri, Ramana V, Nagy, Rebecca, de la Chapelle, Albert

“…A genome-wide association study of papillary thyroid carcinoma (PTC) pinpointed two independent SNPs (rs944289 and rs965513) located in regions containing no…”
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Epigenetic priming enhances antitumor immunity in platinum-resistant ovarian cancer by Chen, Siqi, Xie, Ping, Cowan, Matthew, Huang, Hao, Cardenas, Horacio, Keathley, Russell, Tanner, Edward J, Fleming, Gini F, Moroney, John W, Pant, Alok, Akasha, Azza M, Davuluri, Ramana V, Kocherginsky, Masha, Zhang, Bin, Matei, Daniela

“…BackgroundImmune checkpoint inhibitors (ICIs) have modest activity in ovarian cancer (OC). To augment their activity, we used priming with the hypomethylating…”
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Cancer-Associated IDH1 Promotes Growth and Resistance to Targeted Therapies in the Absence of Mutation by Calvert, Andrea E., Chalastanis, Alexandra, Wu, Yongfei, Hurley, Lisa A., Kouri, Fotini M., Bi, Yingtao, Kachman, Maureen, May, Jasmine L., Bartom, Elizabeth, Hua, Youjia, Mishra, Rama K., Schiltz, Gary E., Dubrovskyi, Oleksii, Mazar, Andrew P., Peter, Marcus E., Zheng, Hongwu, James, C. David, Burant, Charles F., Chandel, Navdeep S., Davuluri, Ramana V., Horbinski, Craig, Stegh, Alexander H.

“…Oncogenic mutations in two isocitrate dehydrogenase (IDH)-encoding genes (IDH1 and IDH2) have been identified in acute myelogenous leukemia, low-grade glioma,…”
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Immune landscapes associated with different glioblastoma molecular subtypes by Martinez-Lage, Maria, Lynch, Timothy M, Bi, Yingtao, Cocito, Carolina, Way, Gregory P, Pal, Sharmistha, Haller, Josephine, Yan, Rachel E, Ziober, Amy, Nguyen, Aivi, Kandpal, Manoj, O'Rourke, Donald M, Greenfield, Jeffrey P, Greene, Casey S, Davuluri, Ramana V, Dahmane, Nadia

“…Recent work has highlighted the tumor microenvironment as a central player in cancer. In particular, interactions between tumor and immune cells may help drive…”
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Single-Nucleotide Polymorphisms Inside MicroRNA Target Sites Influence Tumor Susceptibility by NICOLOSO, Milena S, HAO SUN, MANOUKIAN, Siranoush, SECRETO, Giorgio, RAVAGNANI, Fernando, XUEMEI WANG, RADICE, Paolo, CROCE, Carlo M, DAVULURI, Ramana V, CALIN, George A, SPIZZO, Riccardo, KIM, Hyunsoo, WICKRAMASINGHE, Priyankara, SHIMIZU, Masayoshi, WOJCIK, Sylwia E, FERDIN, Jana, KUNEJ, Tanja, LIANCHUN XIAO

“…Single-nucleotide polymorphisms (SNP) associated with polygenetic disorders, such as breast cancer (BC), can create, destroy, or modify microRNA (miRNA)…”
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Distinct mechanisms control genome recognition by p53 at its target genes linked to different cell fates by Farkas, Marina, Hashimoto, Hideharu, Bi, Yingtao, Davuluri, Ramana V., Resnick-Silverman, Lois, Manfredi, James J., Debler, Erik W., McMahon, Steven B.

“…The tumor suppressor p53 integrates stress response pathways by selectively engaging one of several potential transcriptomes, thereby triggering cell fate…”
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Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development by Pal, Sharmistha, Gupta, Ravi, Kim, Hyunsoo, Wickramasinghe, Priyankara, Baubet, Valérie, Showe, Louise C, Dahmane, Nadia, Davuluri, Ramana V

“…Despite our growing knowledge that many mammalian genes generate multiple transcript variants that may encode functionally distinct protein isoforms, the…”
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A role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection by Deng, Zhong, Wang, Zhuo, Stong, Nick, Plasschaert, Robert, Moczan, Aliah, Chen, Horng-Shen, Hu, Sufeng, Wikramasinghe, Priyankara, Davuluri, Ramana V, Bartolomei, Marisa S, Riethman, Harold, Lieberman, Paul M

“…The contribution of human subtelomeric DNA and chromatin organization to telomere integrity and chromosome end protection is not yet understood in molecular…”
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Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes by Liu, Xianpeng, Zhao, Bo, Sun, Limin, Bhuripanyo, Karan, Wang, Yiyang, Bi, Yingtao, Davuluri, Ramana V., Duong, Duc M., Nanavati, Dhaval, Yin, Jun, Kiyokawa, Hiroaki

“…Protein ubiquitination is mediated sequentially by ubiquitin activating enzyme E1, ubiquitin conjugating enzyme E2 and ubiquitin ligase E3. Uba1 was thought to…”
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miR-218 opposes a critical RTK-HIF pathway in mesenchymal glioblastoma by Mathew, Lijoy K., Skuli, Nicolas, Mucaj, Vera, Lee, Samuel S., Zinn, Pascal O., Sathyan, Pratheesh, Imtiyaz, Hongxia Z., Zhang, Zhongfa, Davuluri, Ramana V., Rao, Shilpa, Venneti, Sriram, Lal, Priti, Lathia, Justin D., Rich, Jeremy N., Keith, Brian, Minn, Andy J., Simon, M. Celeste

“…Glioblastoma multiforme (GBM) and the mesenchymal GBM subtype in particular are highly malignant tumors that frequently exhibit regions of severe hypoxia and…”
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AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors by Davuluri, Ramana V, Sun, Hao, Palaniswamy, Saranyan K, Matthews, Nicole, Molina, Carlos, Kurtz, Mike, Grotewold, Erich

“…The gene regulatory information is hardwired in the promoter regions formed by cis-regulatory elements that bind specific transcription factors (TFs). Hence,…”
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Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline by Stong, Nicholas, Deng, Zhong, Gupta, Ravi, Hu, Sufen, Paul, Shiela, Weiner, Amber K, Eichler, Evan E, Graves, Tina, Fronick, Catrina C, Courtney, Laura, Wilson, Richard K, Lieberman, Paul M, Davuluri, Ramana V, Riethman, Harold

“…Mapping genome-wide data to human subtelomeres has been problematic due to the incomplete assembly and challenges of low-copy repetitive DNA elements. Here, we…”
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Identification of Host-Chromosome Binding Sites and Candidate Gene Targets for Kaposi's Sarcoma-Associated Herpesvirus LANA by FANG LU, TSAI, Kevin, CHEN, Horng-Shen, WIKRAMASINGHE, Priyankara, DAVULURI, Ramana V, SHOWE, Louise, DOMSIC, John, MARMORSTEIN, Ronen, LIEBERMAN, Paul M

“…Article Usage Stats Services JVI Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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MicroRNA genes are frequently located near mouse cancer susceptibility loci by Sevignani, Cinzia, Calin, George A, Nnadi, Stephanie C, Shimizu, Masayoshi, Davuluri, Ramana V, Hyslop, Terry, Demant, Peter, Croce, Carlo M, Siracusa, Linda D

“…MicroRNAs (miRNAs) are short 19- to 24-nt RNA molecules that have been shown to regulate the expression of other genes in a variety of eukaryotic systems…”
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