Search Results - "Shen, John Paul"

Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls by Shen, John Paul, Ideker, Trey

“…Synthetic lethal interactions, in which the simultaneous loss of function of two genes produces a lethal phenotype, are being explored as a means to…”
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Novel Third-Generation EGFR Tyrosine Kinase Inhibitors and Strategies to Overcome Therapeutic Resistance in Lung Cancer by Murtuza, Ayesha, Bulbul, Ajaz, Shen, John Paul, Keshavarzian, Parissa, Woodward, Brian D, Lopez-Diaz, Fernando J, Lippman, Scott M, Husain, Hatim

“…EGFR-activating mutations are observed in approximately 15% to 20% of patients with non-small cell lung cancer. Tyrosine kinase inhibitors have provided an…”
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TNNGen: Automated Design of Neuromorphic Sensory Processing Units for Time-Series Clustering by Vellaisamy, Prabhu, Nair, Harideep, Ratnakaram, Vamsikrishna, Gupta, Dhruv, Paul Shen, John

“…Temporal Neural Networks (TNNs), a special class of spiking neural networks, draw inspiration from the neocortex in utilizing spike-timings for information…”
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Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions by Shen, John Paul, Zhao, Dongxin, Sasik, Roman, Luebeck, Jens, Birmingham, Amanda, Bojorquez-Gomez, Ana, Licon, Katherine, Klepper, Kristin, Pekin, Daniel, Beckett, Alex N, Sanchez, Kyle Salinas, Thomas, Alex, Kuo, Chih-Chung, Du, Dan, Roguev, Assen, Lewis, Nathan E, Chang, Aaron N, Kreisberg, Jason F, Krogan, Nevan, Qi, Lei, Ideker, Trey, Mali, Prashant

“…A library of plasmids expressing two gRNAs allows for the mapping of combinatorial genetic interactions with the CRISPR system. Results in cancer cells suggest…”
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A global transcriptional network connecting noncoding mutations to changes in tumor gene expression by Zhang, Wei, Bojorquez-Gomez, Ana, Velez, Daniel Ortiz, Xu, Guorong, Sanchez, Kyle S., Shen, John Paul, Chen, Kevin, Licon, Katherine, Melton, Collin, Olson, Katrina M., Yu, Michael Ku, Huang, Justin K., Carter, Hannah, Farley, Emma K., Snyder, Michael, Fraley, Stephanie I., Kreisberg, Jason F., Ideker, Trey

“…Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative…”
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A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy by Srivas, Rohith, Shen, John Paul, Yang, Chih Cheng, Sun, Su Ming, Li, Jianfeng, Gross, Andrew M., Jensen, James, Licon, Katherine, Bojorquez-Gomez, Ana, Klepper, Kristin, Huang, Justin, Pekin, Daniel, Xu, Jia L., Yeerna, Huwate, Sivaganesh, Vignesh, Kollenstart, Leonie, van Attikum, Haico, Aza-Blanc, Pedro, Sobol, Robert W., Ideker, Trey

“…An emerging therapeutic strategy for cancer is to induce selective lethality in a tumor by exploiting interactions between its driving mutations and specific…”
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Typing tumors using pathways selected by somatic evolution by Wang, Sheng, Ma, Jianzhu, Zhang, Wei, Shen, John Paul, Huang, Justin, Peng, Jian, Ideker, Trey

“…Many recent efforts to analyze cancer genomes involve aggregation of mutations within reference maps of molecular pathways and protein networks. Here, we find…”
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Synthesis of Eupalinilide E, a Promoter of Human Hematopoietic Stem and Progenitor Cell Expansion by Johnson, Trevor C, Chin, Matthew R, Han, Tianxu, Shen, John Paul, Rana, Tariq, Siegel, Dionicio

“…Improving the ex vivo and in vivo production of hematopoietic stem and progenitor cells (HSPCs) has the potential to address the short supply of these cells…”
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Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease by Bradner, James E., Mak, Raymond, Tanguturi, Shyam K., Mazitschek, Ralph, Haggarty, Stephen J., Ross, Kenneth, Chang, Cindy Y., Bosco, Jocelyn, West, Nathan, Morse, Elizabeth, Lin, Katherine, Shen, John Paul, Kwiatkowski, Nicholas P., Gheldof, Nele, Dekker, Job, DeAngelo, Daniel J., Carr, Steven A., Schreiber, Stuart L., Golub, Todd R., Ebert, Benjamin L.

“…The worldwide burden of sickle cell disease is enormous, with over 200,000 infants born with the disease each year in Africa alone. Induction of fetal…”
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Survival improvement for patients with metastatic colorectal cancer over twenty years by Zeineddine, Fadl A., Zeineddine, Mohammad A., Yousef, Abdelrahman, Gu, Yue, Chowdhury, Saikat, Dasari, Arvind, Huey, Ryan W., Johnson, Benny, Kee, Bryan, Lee, Michael S., Morelli, Maria Pia, Morris, Van K., Overman, Michael J., Parseghian, Christine, Raghav, Kanwal, Willis, Jason, Wolff, Robert A., Kawaguchi, Yoshikuni, Vauthey, Jean-Nicolas, Sun, Ryan, Kopetz, Scott, Shen, John Paul

“…Over the past two decades of successive clinical trials in metastatic colorectal cancer (CRC), the median overall survival of both control and experimental…”
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Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate by Licon, Katherine, Shen, John Paul, Munson, Brenton P, Michaca, Manuel, Fassino, Cole, Fassino, Luke, Kreisberg, Jason F, Ideker, Trey

“…Systematic measurements of genetic interactions have been used to classify gene functions and to categorize genes into protein complexes, functional pathways…”
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Lamotrigine-induced hemophagocytic lymphohistiocytosis with Takotsubo cardiomyopathy: a case report by Zhou, Jenny Y, Martinez, Jordan A, Shen, John Paul

“…Hemophagocytic lymphohistiocytosis is a rare hematological syndrome characterized by excessive and uncontrolled activation of the immune system. The often…”
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ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer by Choueiri, Michel B, Shen, John Paul, Gross, Andrew M, Huang, Justin K, Ideker, Trey, Fanta, Paul

“…In patients with metastatic colon cancer, response to first line chemotherapy is a strong predictor of overall survival (OS). Currently, oncologists lack…”
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Unsupervised Clustering of Time Series Signals Using Neuromorphic Energy-Efficient Temporal Neural Networks by Chaudhari, Shreyas, Nair, Harideep, Moura, Jose M. F., Paul Shen, John

“…Unsupervised time series clustering is a challenging problem with diverse industrial applications such as anomaly detection, bio-wearables, etc. These…”
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The Provocative Roles of Platelets in Liver Disease and Cancer by Kanikarla Marie, Preeti, Fowlkes, Natalie W, Afshar-Kharghan, Vahid, Martch, Stephanie L, Sorokin, Alexey, Shen, John Paul, Morris, Van K, Dasari, Arvind, You, Nancy, Sood, Anil K, Overman, Michael J, Kopetz, Scott, Menter, David George

“…Both platelets and the liver play important roles in the processes of coagulation and innate immunity. Platelet responses at the site of an injury are rapid;…”
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Corrigendum: SemNet: Learning semantic attributes for human activity recognition with deep belief networks by Venkatachalam, Shanmuga, Nair, Harideep, Zeng, Ming, Tan, Cathy Shunwen, Mengshoel, Ole J, Shen, John Paul

“…[This corrects the article DOI: 10.3389/fdata.2022.879389.]…”
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Impact of KRAS mutations and co-mutations on clinical outcomes in pancreatic ductal adenocarcinoma by Yousef, Abdelrahman, Yousef, Mahmoud, Chowdhury, Saikat, Abdilleh, Kawther, Knafl, Mark, Edelkamp, Paul, Alfaro-Munoz, Kristin, Chacko, Ray, Peterson, Jennifer, Smaglo, Brandon G., Wolff, Robert A., Pant, Shubham, Lee, Michael S., Willis, Jason, Overman, Michael, Doss, Sudheer, Matrisian, Lynn, Hurd, Mark W., Snyder, Rebecca, Katz, Matthew H. G., Wang, Huamin, Maitra, Anirban, Shen, John Paul, Zhao, Dan

“…The relevance of KRAS mutation alleles to clinical outcome remains inconclusive in pancreatic adenocarcinoma (PDAC). We conducted a retrospective study of 803…”
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SemNet: Learning semantic attributes for human activity recognition with deep belief networks by Venkatachalam, Shanmuga, Nair, Harideep, Zeng, Ming, Tan, Cathy Shunwen, Mengshoel, Ole J, Shen, John Paul

“…Human Activity Recognition (HAR) is a prominent application in mobile computing and Internet of Things (IoT) that aims to detect human activities based on…”
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Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF‐PU.1‐DPP4 Axis by Wang, Lihua, Wang, Ergang, Prado Balcazar, Jorge, Wu, Zhenzhen, Xiang, Kun, Wang, Yi, Huang, Qiang, Negrete, Marcos, Chen, Kai‐Yuan, Li, Wei, Fu, Yujie, Dohlman, Anders, Mines, Robert, Zhang, Liwen, Kobayashi, Yoshihiko, Chen, Tianyi, Shi, Guizhi, Shen, John Paul, Kopetz, Scott, Tata, Purushothama Rao, Moreno, Victor, Gersbach, Charles, Crawford, Gregory, Hsu, David, Huang, Emina, Bu, Pengcheng, Shen, Xiling

“…Colorectal cancer (CRC) metastasizes mainly to the liver, which accounts for the majority of CRC‐related deaths. Here it is shown that metastatic cells undergo…”
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Regarding Blood‐Based Next‐Generation Sequencing Analysis of Appendiceal Cancers by Shen, John Paul

“…This letter to the editor questions whether liquid next‐generation sequencing is a reasonable substitute for tissue next‐generation sequencing for all forms of…”
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