Search Results - "Bekiranov, Stefan"

Quantum computing at the frontiers of biological sciences by Emani, Prashant S., Warrell, Jonathan, Anticevic, Alan, Bekiranov, Stefan, Gandal, Michael, McConnell, Michael J., Sapiro, Guillermo, Aspuru-Guzik, Alán, Baker, Justin T., Bastiani, Matteo, Murray, John D., Sotiropoulos, Stamatios N., Taylor, Jacob, Senthil, Geetha, Lehner, Thomas, Gerstein, Mark B., Harrow, Aram W.

“…Computing plays a critical role in the biological sciences but faces increasing challenges of scale and complexity. Quantum computing, a computational paradigm…”
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Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis by Alencar, Gabriel F., Owsiany, Katherine M., Karnewar, Santosh, Sukhavasi, Katyayani, Mocci, Giuseppe, Nguyen, Anh T., Williams, Corey M., Shamsuzzaman, Sohel, Mokry, Michal, Henderson, Christopher A., Haskins, Ryan, Baylis, Richard A., Finn, Aloke V., McNamara, Coleen A., Zunder, Eli R., Venkata, Vamsidhar, Pasterkamp, Gerard, Björkegren, Johan, Bekiranov, Stefan, Owens, Gary K.

“…Rupture and erosion of advanced atherosclerotic lesions with a resultant myocardial infarction or stroke are the leading worldwide cause of death. However, we…”
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Generalization Performance of Quantum Metric Learning Classifiers by Kim, Jonathan, Bekiranov, Stefan

“…Quantum computing holds great promise for a number of fields including biology and medicine. A major application in which quantum computers could yield…”
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Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective by Cherepanova, Olga A, Gomez, Delphine, Shankman, Laura S, Swiatlowska, Pamela, Williams, Jason, Sarmento, Olga F, Alencar, Gabriel F, Hess, Daniel L, Bevard, Melissa H, Greene, Elizabeth S, Murgai, Meera, Turner, Stephen D, Geng, Yong-Jian, Bekiranov, Stefan, Connelly, Jessica J, Tomilin, Alexey, Owens, Gary K

“…The pluripotency factor OCT4 is expressed in smooth muscle cells of atherosclerotic lesions in both mice and humans, and has atheroprotective effects in mice…”
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IGF1R and Src inhibition induce synergistic cytotoxicity in HNSCC through inhibition of FAK by Lehman, Christine E., Spencer, Adam, Hall, Sarah, Shaw, Jeremy J. P., Wulfkuhle, Julia, Petricoin, Emanuel F., Bekiranov, Stefan, Jameson, Mark J., Gioeli, Daniel

“…Head and neck cancer is the sixth most common cancer worldwide with a 5-year survival of only 65%. Targeting compensatory signaling pathways may improve…”
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Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human by Szlachta, Karol, Thys, Ryan G, Atkin, Naomi D, Pierce, Levi C T, Bekiranov, Stefan, Wang, Yuh-Hwa

“…Alternative DNA secondary structures can arise from single-stranded DNA when duplex DNA is unwound during DNA processes such as transcription, resulting in the…”
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Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells by Kuscu, Cem, Mammadov, Rashad, Czikora, Agnes, Unlu, Hayrunnisa, Tufan, Turan, Fischer, Natasha Lopes, Arslan, Sevki, Bekiranov, Stefan, Kanemaki, Masato, Adli, Mazhar

“…Cell-type specific gene expression programs are tightly linked to epigenetic modifications on DNA and histone proteins. Here, we used a novel CRISPR-based…”
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Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression by Xu, Xiaojiang, Hoang, Stephen, Mayo, Marty W, Bekiranov, Stefan

“…In the last decade, biochemical studies have revealed that epigenetic modifications including histone modifications, histone variants and DNA methylation form…”
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A microarray-based genetic screen for yeast chronological aging factors by Matecic, Mirela, Smith, Daniel L, Pan, Xuewen, Maqani, Nazif, Bekiranov, Stefan, Boeke, Jef D, Smith, Jeffrey S

“…Model organisms have played an important role in the elucidation of multiple genes and cellular processes that regulate aging. In this study we utilized the…”
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Associations of immune cell homing gene signatures and infiltrates of lymphocyte subsets in human melanomas: discordance with CD163+ myeloid cell infiltrates by Kwak, Minyoung, Erdag, Gulsun, Leick, Katie M, Bekiranov, Stefan, Engelhard, Victor H, Slingluff, Craig L

“…Abstract Background Immune cells in the tumor microenvironment have prognostic value. In preclinical models, recruitment and infiltration of these cells…”
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A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure by Li, Mingguang, Fine, Ryan D, Dinda, Manikarna, Bekiranov, Stefan, Smith, Jeffrey S

“…The NAD+-dependent histone deacetylase Sir2 was originally identified in Saccharomyces cerevisiae as a silencing factor for HML and HMR, the heterochromatic…”
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NF-κB regulates mesenchymal transition for the induction of non-small cell lung cancer initiating cells by Kumar, Manish, Allison, David F, Baranova, Natalya N, Wamsley, J Jacob, Katz, Adam J, Bekiranov, Stefan, Jones, David R, Mayo, Marty W

“…The epithelial-to-mesenchymal transition (EMT) is a de-differentiation process that has been implicated in metastasis and the generation of cancer initiating…”
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Measuring Chromatin Interaction Dynamics on the Second Time Scale at Single-Copy Genes by Poorey, Kunal, Viswanathan, Ramya, Carver, Melissa N., Karpova, Tatiana S., Cirimotich, Shana M., McNally, James G., Bekiranov, Stefan, Auble, David T.

“…The chromatin immunoprecipitation (ChIP) assay is widely used to capture interactions between chromatin and regulatory proteins, but it is unknown how stable…”
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Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins by Mesner, Larry D, Valsakumar, Veena, Cieslik, Marcin, Pickin, Rebecca, Hamlin, Joyce L, Bekiranov, Stefan

“…We have devised a method for isolating virtually pure and comprehensive libraries of restriction fragments that contained replication initiation sites…”
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COCOA: coordinate covariation analysis of epigenetic heterogeneity by Lawson, John T., Smith, Jason P., Bekiranov, Stefan, Garrett-Bakelman, Francine E., Sheffield, Nathan C.

“…Abstract A key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate…”
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Genomic and evolutionary portraits of disease relapse in acute myeloid leukemia by Rapaport, Franck, Neelamraju, Yaseswini, Baslan, Timour, Hassane, Duane, Gruszczynska, Agata, Robert de Massy, Marc, Farnoud, Noushin, Haddox, Samuel, Lee, Tak, Medina-Martinez, Juan, Sheridan, Caroline, Thurmond, Alexis, Becker, Michael, Bekiranov, Stefan, Carroll, Martin, Moses Murdock, Heardly, Valk, Peter J. M., Bullinger, Lars, D’Andrea, Richard, Lowe, Scott W., Neuberg, Donna, Levine, Ross L., Melnick, Ari, Garrett-Bakelman, Francine E.

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Tolerogenic properties of lymphatic endothelial cells are controlled by the lymph node microenvironment by Cohen, Jarish N, Tewalt, Eric F, Rouhani, Sherin J, Buonomo, Erica L, Bruce, Amber N, Xu, Xiaojiang, Bekiranov, Stefan, Fu, Yang-Xin, Engelhard, Victor H

“…Peripheral self-tolerance eliminates lymphocytes specific for tissue-specific antigens not encountered in the thymus. Recently, we demonstrated that lymphatic…”
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Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution by Cheng, Jill, Kapranov, Philipp, Drenkow, Jorg, Dike, Sujit, Brubaker, Shane, Patel, Sandeep, Long, Jeffrey, Stern, David, Tammana, Hari, Helt, Gregg, Sementchenko, Victor, Piccolboni, Antonio, Bekiranov, Stefan, Bailey, Dione K., Ganesh, Madhavan, Ghosh, Srinka, Bell, Ian, Gerhard, Daniela S., Gingeras, Thomas R.

“…Sites of transcription of polyadenylated and nonpolyadenylated RNAs for 10 human chromosomes were mapped at 5-base pair resolution in eight cell lines…”
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Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse by Bernstein, Bradley E., Kamal, Michael, Lindblad-Toh, Kerstin, Bekiranov, Stefan, Bailey, Dione K., Huebert, Dana J., McMahon, Scott, Karlsson, Elinor K., Kulbokas, Edward J., Gingeras, Thomas R., Schreiber, Stuart L., Lander, Eric S.

“…We mapped histone H3 lysine 4 di- and trimethylation and lysine 9/14 acetylation across the nonrepetitive portions of human chromosomes 21 and 22 and compared…”
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Combinatorial epigenetic patterns as quantitative predictors of chromatin biology by Cieślik, Marcin, Bekiranov, Stefan

“…Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is the most widely used method for characterizing the epigenetic states of chromatin on a…”
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