Search Results - "Shaw, Timothy I."

C9orf72 Dipeptide Repeats Impair the Assembly, Dynamics, and Function of Membrane-Less Organelles by Lee, Kyung-Ha, Zhang, Peipei, Kim, Hong Joo, Mitrea, Diana M., Sarkar, Mohona, Freibaum, Brian D., Cika, Jaclyn, Coughlin, Maura, Messing, James, Molliex, Amandine, Maxwell, Brian A., Kim, Nam Chul, Temirov, Jamshid, Moore, Jennifer, Kolaitis, Regina-Maria, Shaw, Timothy I., Bai, Bing, Peng, Junmin, Kriwacki, Richard W., Taylor, J. Paul

“…Expansion of a hexanucleotide repeat GGGGCC (G4C2) in C9ORF72 is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia…”
Get full text

Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression by Bai, Bing, Wang, Xusheng, Li, Yuxin, Chen, Ping-Chung, Yu, Kaiwen, Dey, Kaushik Kumar, Yarbro, Jay M., Han, Xian, Lutz, Brianna M., Rao, Shuquan, Jiao, Yun, Sifford, Jeffrey M., Han, Jonghee, Wang, Minghui, Tan, Haiyan, Shaw, Timothy I., Cho, Ji-Hoon, Zhou, Suiping, Wang, Hong, Niu, Mingming, Mancieri, Ariana, Messler, Kaitlynn A., Sun, Xiaojun, Wu, Zhiping, Pagala, Vishwajeeth, High, Anthony A., Bi, Wenjian, Zhang, Hui, Chi, Hongbo, Haroutunian, Vahram, Zhang, Bin, Beach, Thomas G., Yu, Gang, Peng, Junmin

“…Alzheimer’s disease (AD) displays a long asymptomatic stage before dementia. We characterize AD stage-associated molecular networks by profiling 14,513…”
Get full text

The Noncanonical Role of ULK/ATG1 in ER-to-Golgi Trafficking Is Essential for Cellular Homeostasis by Joo, Joung Hyuck, Wang, Bo, Frankel, Elisa, Ge, Liang, Xu, Lu, Iyengar, Rekha, Li-Harms, XiuJie, Wright, Christopher, Shaw, Timothy I., Lindsten, Tullia, Green, Douglas R., Peng, Junmin, Hendershot, Linda M., Kilic, Fusun, Sze, Ji Ying, Audhya, Anjon, Kundu, Mondira

“…ULK1 and ULK2 are thought to be essential for initiating autophagy, and Ulk1/2-deficient mice die perinatally of autophagy-related defects. Therefore, we used…”
Get full text

Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression by Larson, Jon D., Kasper, Lawryn H., Paugh, Barbara S., Jin, Hongjian, Wu, Gang, Kwon, Chang-Hyuk, Fan, Yiping, Shaw, Timothy I., Silveira, André B., Qu, Chunxu, Xu, Raymond, Zhu, Xiaoyan, Zhang, Junyuan, Russell, Helen R., Peters, Jennifer L., Finkelstein, David, Xu, Beisi, Lin, Tong, Tinkle, Christopher L., Patay, Zoltan, Onar-Thomas, Arzu, Pounds, Stanley B., McKinnon, Peter J., Ellison, David W., Zhang, Jinghui, Baker, Suzanne J.

“…Diffuse intrinsic pontine gliomas (DIPGs) are incurable childhood brainstem tumors with frequent histone H3 K27M mutations and recurrent alterations in PDGFRA…”
Get full text

JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells by Li, Yuxin, Wang, Xusheng, Cho, Ji-Hoon, Shaw, Timothy I, Wu, Zhiping, Bai, Bing, Wang, Hong, Zhou, Suiping, Beach, Thomas G, Wu, Gang, Zhang, Jinghui, Peng, Junmin

“…Proteogenomics is an emerging approach to improve gene annotation and interpretation of proteomics data. Here we present JUMPg, an integrative proteogenomics…”
Get full text

A Key Role for the Ubiquitin Ligase UBR4 in Myofiber Hypertrophy in Drosophila and Mice by Hunt, Liam C., Stover, Jared, Haugen, Benard, Shaw, Timothy I., Li, Yuxin, Pagala, Vishwajeeth R., Finkelstein, David, Barton, Elisabeth R., Fan, Yiping, Labelle, Myriam, Peng, Junmin, Demontis, Fabio

“…Skeletal muscle cell (myofiber) atrophy is a detrimental component of aging and cancer that primarily results from muscle protein degradation via the…”
Get full text

An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level by Liu, Xiang, Gillis, Nancy, Jiang, Chang, McCofie, Anthony, Shaw, Timothy I, Tan, Aik-Choon, Zhao, Bo, Wan, Lixin, Duckett, Derek R, Teng, Mingxiang

“…Super enhancers (SE), large genomic elements that activate transcription and drive cell identity, have been found with cancer-specific gene regulation in human…”
Get full text

Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression by Shaw, Timothy I., Wagner, Jessica, Tian, Liqing, Wickman, Elizabeth, Poudel, Suresh, Wang, Jian, Paul, Robin, Koo, Selene C., Lu, Meifen, Sheppard, Heather, Fan, Yiping, O’Neill, Francis H., Lau, Ching C., Zhou, Xin, Zhang, Jinghui, Gottschalk, Stephen

“…Immunotherapy with chimeric antigen receptor T cells for pediatric solid and brain tumors is constrained by available targetable antigens. Cancer-specific…”
Get full text

Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes by Wang, Hong, Diaz, Alexander K., Shaw, Timothy I., Li, Yuxin, Niu, Mingming, Cho, Ji-Hoon, Paugh, Barbara S., Zhang, Yang, Sifford, Jeffrey, Bai, Bing, Wu, Zhiping, Tan, Haiyan, Zhou, Suiping, Hover, Laura D., Tillman, Heather S., Shirinifard, Abbas, Thiagarajan, Suresh, Sablauer, Andras, Pagala, Vishwajeeth, High, Anthony A., Wang, Xusheng, Li, Chunliang, Baker, Suzanne J., Peng, Junmin

“…High throughput omics approaches provide an unprecedented opportunity for dissecting molecular mechanisms in cancer biology. Here we present deep profiling of…”
Get full text

Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia by Huang, Benjamin J., Smith, Jenny L., Farrar, Jason E., Wang, Yi-Cheng, Umeda, Masayuki, Ries, Rhonda E., Leonti, Amanda R., Crowgey, Erin, Furlan, Scott N., Tarlock, Katherine, Armendariz, Marcos, Liu, Yanling, Shaw, Timothy I., Wei, Lisa, Gerbing, Robert B., Cooper, Todd M., Gamis, Alan S., Aplenc, Richard, Kolb, E. Anders, Rubnitz, Jeffrey, Ma, Jing, Klco, Jeffery M., Ma, Xiaotu, Alonzo, Todd A., Triche, Timothy, Meshinchi, Soheil

“…Relapsed or refractory pediatric acute myeloid leukemia (AML) is associated with poor outcomes and relapse risk prediction approaches have not changed…”
Get full text

Metabolomic and transcriptomic analysis reveals endogenous substrates and metabolic adaptation in rats lacking Abcg2 and Abcb1a transporters by Ganguly, Samit, Finkelstein, David, Shaw, Timothy I, Michalek, Ryan D, Zorn, Kimberly M, Ekins, Sean, Yasuda, Kazuto, Fukuda, Yu, Schuetz, John D, Mukherjee, Kamalika, Schuetz, Erin G

“…Abcg2/Bcrp and Abcb1a/Pgp are xenobiotic efflux transporters limiting substrate permeability in the gastrointestinal system and brain, and increasing renal and…”
Get full text

PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing by Obermayer, Alyssa N, Chang, Darwin, Nobles, Gabrielle, Teng, Mingxiang, Tan, Aik-Choon, Wang, Xuefeng, Chen, Y Ann, Eschrich, Steven, Rodriguez, Paulo C, Grass, G Daniel, Meshinchi, Soheil, Tarhini, Ahmad, Chen, Dung-Tsa, Shaw, Timothy I

“…Pathway-level survival analysis offers the opportunity to examine molecular pathways and immune signatures that influence patient outcomes. However, available…”
Get full text

The landscape of coding RNA editing events in pediatric cancer by Wen, Ji, Rusch, Michael, Brady, Samuel W, Shao, Ying, Edmonson, Michael N, Shaw, Timothy I, Powers, Brent B, Tian, Liqing, Easton, John, Mullighan, Charles G, Gruber, Tanja, Ellison, David, Zhang, Jinghui

“…RNA editing leads to post-transcriptional variation in protein sequences and has important biological implications. We sought to elucidate the landscape of RNA…”
Get full text

Isotope Labeling-Assisted Evaluation of Hydrophilic and Hydrophobic Liquid Chromatograph–Mass Spectrometry for Metabolomics Profiling by Xie, Boer, Wang, Yuanyuan, Jones, Drew R, Dey, Kaushik Kumar, Wang, Xusheng, Li, Yuxin, Cho, Ji-Hoon, Shaw, Timothy I, Tan, Haiyan, Peng, Junmin

“…High throughput untargeted metabolomics usually relies on complementary liquid chromatography–mass spectrometry (LC-MS) methods to expand the coverage of…”
Get full text

The Noncanonical Role of ULK/ATG1 in ER-to-Golgi Trafficking Is Essential for Cellular Homeostasis by Joo, Joung Hyuck, Wang, Bo, Frankel, Elisa, Ge, Liang, Xu, Lu, Iyengar, Rekha, Li-Harms, XiuJie, Wright, Christopher, Shaw, Timothy I., Lindsten, Tullia, Green, Douglas R., Peng, Junmin, Hendershot, Linda M., Kilic, Fusun, Sze, Ji Ying, Audhya, Anjon, Kundu, Mondira

Get full text

Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients by Shaw, Timothy I, Zhao, Bi, Li, Yuxin, Wang, Hong, Wang, Liang, Manley, Brandon, Stewart, Paul A, Karolak, Aleksandra

“…Cancer-specific alternatively spliced events (ASE) play a role in cancer pathogenesis and can be targeted by immunotherapy, oligonucleotide therapy, and small…”
Get full text

Transcriptome sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis) by Shaw, Timothy I, Srivastava, Anuj, Chou, Wen-Chi, Liu, Liang, Hawkinson, Ann, Glenn, Travis C, Adams, Rick, Schountz, Tony

“…The Jamaican fruit bat (Artibeus jamaicensis) is one of the most common bats in the tropical Americas. It is thought to be a potential reservoir host of…”
Get full text

Rapid Microbiome Changes in Freshly Deposited Cow Feces under Field Conditions by Wong, Kelvin, Shaw, Timothy I, Oladeinde, Adelumola, Glenn, Travis C, Oakley, Brian, Molina, Marirosa

“…Although development of next generation sequencing (NGS) has substantially improved our understanding of the microbial ecology of animal feces, previous…”
Get full text

Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL) by Shaw, Timothy I., Dong, Li, Tian, Liqing, Qian, Chenxi, Liu, Yu, Ju, Bensheng, High, Anthony, Kavdia, Kanisha, Pagala, Vishwajeeth R., Shaner, Bridget, Pei, Deqing, Easton, John, Janke, Laura J., Porter, Shaina N., Ma, Xiaotu, Cheng, Cheng, Pruett-Miller, Shondra M., Choi, John, Yu, Jiyang, Peng, Junmin, Gu, Wei, Look, A. Thomas, Downing, James R., Zhang, Jinghui

“…USP7, which encodes a deubiquitylating enzyme, is among the most frequently mutated genes in pediatric T-ALL, with somatic heterozygous loss-of-function…”
Get full text

DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets by Obermayer, Alyssa, Dong, Li, Hu, Qianqian, Golden, Michael, Noble, Jerald D, Rodriguez, Paulo, Robinson, Timothy J, Teng, Mingxiang, Tan, Aik-Choon, Shaw, Timothy I

“…High-throughput transcriptomic and proteomic analyses are now routinely applied to study cancer biology. However, complex omics integration remains challenging…”
Get full text