Search Results - "Mani, D"

Biotechnological advances in bioremediation of heavy metals contaminated ecosystems: an overview with special reference to phytoremediation by Mani, D, Kumar, Chitranjan

“…The ability of heavy metals bioaccumulation to cause toxicity in biological systems-human, animals, microorganisms and plants-is an important issue for…”
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Cancer proteogenomics: current impact and future prospects by Mani, D. R., Krug, Karsten, Zhang, Bing, Satpathy, Shankha, Clauser, Karl R., Ding, Li, Ellis, Matthew, Gillette, Michael A., Carr, Steven A.

“…Genomic analyses in cancer have been enormously impactful, leading to the identification of driver mutations and development of targeted therapies. But the…”
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Proteogenomics connects somatic mutations to signalling in breast cancer by Mertins, Philipp, Mani, D. R., Ruggles, Kelly V., Gillette, Michael A., Clauser, Karl R., Wang, Pei, Wang, Xianlong, Qiao, Jana W., Cao, Song, Petralia, Francesca, Kawaler, Emily, Mundt, Filip, Krug, Karsten, Tu, Zhidong, Lei, Jonathan T., Gatza, Michael L., Wilkerson, Matthew, Perou, Charles M., Yellapantula, Venkata, Huang, Kuan-lin, Lin, Chenwei, McLellan, Michael D., Yan, Ping, Davies, Sherri R., Townsend, R. Reid, Skates, Steven J., Wang, Jing, Zhang, Bing, Kinsinger, Christopher R., Mesri, Mehdi, Rodriguez, Henry, Ding, Li, Paulovich, Amanda G., Fenyö, David, Ellis, Matthew J., Carr, Steven A.

“…Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly…”
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Proteomic analyses of ECM during pancreatic ductal adenocarcinoma progression reveal different contributions by tumor and stromal cells by Tian, Chenxi, Clauser, Karl R., Öhlund, Daniel, Rickelt, Steffen, Huang, Ying, Gupta, Mala, Mani, D. R., Carr, Steven A., Tuveson, David A., Hynes, Richard O.

“…Pancreatic ductal adenocarcinoma (PDAC) has prominent extracellular matrix (ECM) that compromises treatments yet cannot be nonselectively disrupted without…”
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Prediction of high-responding peptides for targeted protein assays by mass spectrometry by Mesirov, Jill P, Carr, Steven A, Fusaro, Vincent A, Mani, D R

“…Development of sensitive mass spectrometry–based assays for complex biofluids depends on the ability to identify signature peptides that produce the strongest…”
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An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics Data by Mueller, Lukas N, Brusniak, Mi-Youn, Mani, D. R, Aebersold, Ruedi

“…Over the past decade, a series of experimental strategies for mass spectrometry based quantitative proteomics and corresponding computational methodology for…”
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Integrated proteomic analysis of post-translational modifications by serial enrichment by Mertins, Philipp, Qiao, Jana W, Patel, Jinal, Udeshi, Namrata D, Clauser, Karl R, Mani, D R, Burgess, Michael W, Gillette, Michael A, Jaffe, Jacob D, Carr, Steven A

“…A mass spectrometry–based method using serial enrichments of different post-translational modifications (SEPTM) enables high-coverage proteomic analysis of…”
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Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications by Ctortecka, Claudia, Clark, Natalie M., Boyle, Brian W., Seth, Anjali, Mani, D. R., Udeshi, Namrata D., Carr, Steven A.

“…The recent technological and computational advances in mass spectrometry-based single-cell proteomics have pushed the boundaries of sensitivity and throughput…”
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Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry by Abbatiello, Susan E, Mani, D. R, Keshishian, Hasmik, Carr, Steven A

“…Multiple reaction monitoring mass spectrometry (MRM-MS) of peptides with stable isotope-labeled internal standards (SISs) is increasingly being used to develop…”
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Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry by Mertins, Philipp, Tang, Lauren C., Krug, Karsten, Clark, David J., Gritsenko, Marina A., Chen, Lijun, Clauser, Karl R., Clauss, Therese R., Shah, Punit, Gillette, Michael A., Petyuk, Vladislav A., Thomas, Stefani N., Mani, D. R., Mundt, Filip, Moore, Ronald J., Hu, Yingwei, Zhao, Rui, Schnaubelt, Michael, Keshishian, Hasmik, Monroe, Matthew E., Zhang, Zhen, Udeshi, Namrata D., Mani, Deepak, Davies, Sherri R., Townsend, R. Reid, Chan, Daniel W., Smith, Richard D., Zhang, Hui, Liu, Tao, Carr, Steven A.

“…Here we present an optimized workflow for global proteome and phosphoproteome analysis of tissues or cell lines that uses isobaric tags (TMT (tandem mass…”
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Methods, Tools and Current Perspectives in Proteogenomics by Ruggles, Kelly V., Krug, Karsten, Wang, Xiaojing, Clauser, Karl R., Wang, Jing, Payne, Samuel H., Fenyö, David, Zhang, Bing, Mani, D.R.

“…With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics, i.e. the…”
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Proteogenomic characterization of pancreatic ductal adenocarcinoma by Cao, Liwei, Huang, Chen, Cui Zhou, Daniel, Hu, Yingwei, Savage, Sara R., Krug, Karsten, Schnaubelt, Michael, Eguez, Rodrigo Vargas, Yang, Weiming, Pan, Jianbo, Wen, Bo, Jiang, Wen, Liao, Yuxing, Terekhanova, Nadezhda V., Cao, Song, Lu, Rita Jui-Hsien, Liu, Ruiyang, Zhu, Houxiang, Wu, Yige, Easwaran, Hariharan, Yoo, Seungyeul, Liu, Wenke, Haibe-Kains, Benjamin, Thiagarajan, Mathangi, Jewell, Scott D., Hostetter, Galen, Li, Qing Kay, Fenyö, David, Wang, Pei, Mani, D.R., Omenn, Gilbert S., Boja, Emily S., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Chan, Daniel W., Hruban, Ralph H., Ding, Li, Zhang, Hui, Amin, Mitual, An, Eunkyung, Bauer, Thomas, Birger, Chet, Birrer, Michael J., Bocik, William, Borucki, Melissa, Carr, Steven A., Cerda, Sandra, Chen, Huan, Chen, Steven, Chesla, David, Chinnaiyan, Arul M., Colaprico, Antonio, Cottingham, Sandra, Derejska, Magdalena, Dhanasekaran, Saravana M., Domagalski, Marcin J., Edwards, Nathan J., Francis, Alicia, Francis, Jesse, Gabriel, Stacey, Gabrovski, Nikolay, Gardner, Johanna, Getz, Gad, Goldthwaite, Charles A., Grady, Pamela, Guo, Shuai, Hariharan, Pushpa, Hindenach, Barbara, Hoadley, Katherine A., Jones, Corbin D., Ketchum, Karen A., Kinsinger, Christopher R., Kusnierz, Katarzyna, Mallery, David, Matteotti, Ronald, McGarvey, Peter B., Minoo, Parham, Paklina, Oxana V., Paulovich, Amanda G., Payne, Samuel H., Potapova, Olga, Qi, Liqun, Roche, Nancy, Rodland, Karin D., Rohrer, Daniel C., Shabunin, Alexey V., Shelton, Troy, Shutack, Yvonne, Singh, Shilpi, Smith, Michael, Smith, Richard D., Sokoll, Lori J., Suh, James, Thangudu, Ratna R., Valley, Dana R., Wang, Wenyi, Wilson, George D., Wiznerowicz, Maciej, Zhang, Zhen

“…Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations…”
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Evaluation of caries arresting potential of silver diamine fluoride and sodium fluoride varnish in primary molars: A randomized controlled trial by Mani Prakash, D, Vinay, C, Uloopi, K, RojaRamya, Kakarla, Penmatsa, Chaitanya, Chandana, N

“…Background: Caries management in the modern era has shifted away from the traditional surgical method toward a medical paradigm, which often includes fluoride…”
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iTRAQ Labeling is Superior to mTRAQ for Quantitative Global Proteomics and Phosphoproteomics by Mertins, Philipp, Udeshi, Namrata D., Clauser, Karl R., Mani, DR, Patel, Jinal, Ong, Shao-en, Jaffe, Jacob D., Carr, Steven A.

“…Labeling of primary amines on peptides with reagents containing stable isotopes is a commonly used technique in quantitative mass spectrometry. Isobaric…”
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A proteogenomic portrait of lung squamous cell carcinoma by Satpathy, Shankha, Krug, Karsten, Jean Beltran, Pierre M, Savage, Sara R, Petralia, Francesca, Kumar-Sinha, Chandan, Dou, Yongchao, Reva, Boris, Kane, M Harry, Avanessian, Shayan C, Vasaikar, Suhas V, Krek, Azra, Lei, Jonathan T, Jaehnig, Eric J, Omelchenko, Tatiana, Geffen, Yifat, Bergstrom, Erik J, Stathias, Vasileios, Christianson, Karen E, Heiman, David I, Cieslik, Marcin P, Cao, Song, Song, Xiaoyu, Ji, Jiayi, Liu, Wenke, Li, Kai, Wen, Bo, Li, Yize, Gümüş, Zeynep H, Selvan, Myvizhi Esai, Soundararajan, Rama, Visal, Tanvi H, Raso, Maria G, Parra, Edwin Roger, Babur, Özgün, Vats, Pankaj, Anand, Shankara, Schraink, Tobias, Cornwell, MacIntosh, Rodrigues, Fernanda Martins, Zhu, Houxiang, Mo, Chia-Kuei, Zhang, Yuping, da Veiga Leprevost, Felipe, Huang, Chen, Chinnaiyan, Arul M, Wyczalkowski, Matthew A, Omenn, Gilbert S, Newton, Chelsea J, Schurer, Stephan, Ruggles, Kelly V, Fenyö, David, Jewell, Scott D, Thiagarajan, Mathangi, Mesri, Mehdi, Rodriguez, Henry, Mani, Sendurai A, Udeshi, Namrata D, Getz, Gad, Suh, James, Li, Qing Kay, Hostetter, Galen, Paik, Paul K, Dhanasekaran, Saravana M, Govindan, Ramaswamy, Ding, Li, Robles, Ana I, Clauser, Karl R, Nesvizhskii, Alexey I, Wang, Pei, Carr, Steven A, Zhang, Bing, Mani, D R, Gillette, Michael A

“…Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC,…”
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Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS by Krönke, Jan, Fink, Emma C., Hollenbach, Paul W., MacBeth, Kyle J., Hurst, Slater N., Udeshi, Namrata D., Chamberlain, Philip P., Mani, D. R., Man, Hon Wah, Gandhi, Anita K., Svinkina, Tanya, Schneider, Rebekka K., McConkey, Marie, Järås, Marcus, Griffiths, Elizabeth, Wetzler, Meir, Bullinger, Lars, Cathers, Brian E., Carr, Steven A., Chopra, Rajesh, Ebert, Benjamin L.

“…Lenalidomide is a highly effective treatment for myelodysplastic syndrome (MDS) with deletion of chromosome 5q (del(5q)). Here, we demonstrate that…”
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Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2 by Greulich, Heidi, Kaplan, Bethany, Mertins, Philipp, Chen, Tzu-Hsiu, Tanaka, Kumiko E, Yun, Cai-Hong, Zhang, Xiaohong, Lee, Se-Hoon, Cho, Jeonghee, Ambrogio, Lauren, Liao, Rachel, Imielinski, Marcin, Banerji, Shantanu, Berger, Alice H, Lawrence, Michael S, Zhang, Jinghui, Pho, Nam H, Walker, Sarah R, Winckler, Wendy, Getz, Gad, Frank, David, Hahn, William C, Eck, Michael J, Mani, D. R, Jaffe, Jacob D, Carr, Steven A, Wong, Kwok-Kin, Meyerson, Matthew

“…We assessed somatic alleles of six receptor tyrosine kinase genes mutated in lung adenocarcinoma for oncogenic activity. Five of these genes failed to score in…”
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Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression by Naba, Alexandra, Clauser, Karl R., Mani, D. R., Carr, Steven A., Hynes, Richard O.

“…The angiogenic switch, the time at which a tumor becomes vascularized, is a critical step in tumor progression. Indeed, without blood supply, tumors will fail…”
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The Parkinson’s disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability by Hallacli, Erinc, Kayatekin, Can, Nazeen, Sumaiya, Wang, Xiou H., Sheinkopf, Zoe, Sathyakumar, Shubhangi, Sarkar, Souvarish, Jiang, Xin, Dong, Xianjun, Di Maio, Roberto, Wang, Wen, Keeney, Matthew T., Felsky, Daniel, Sandoe, Jackson, Vahdatshoar, Aazam, Udeshi, Namrata D., Mani, D.R., Carr, Steven A., Lindquist, Susan, De Jager, Philip L., Bartel, David P., Myers, Chad L., Greenamyre, J. Timothy, Feany, Mel B., Sunyaev, Shamil R., Chung, Chee Yeun, Khurana, Vikram

“…Alpha-synuclein (αS) is a conformationally plastic protein that reversibly binds to cellular membranes. It aggregates and is genetically linked to Parkinson’s…”
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Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury by Keshishian, Hasmik, Burgess, Michael W., Gillette, Michael A., Mertins, Philipp, Clauser, Karl R., Mani, D.R., Kuhn, Eric W., Farrell, Laurie A., Gerszten, Robert E., Carr, Steven A.

“…We have developed a novel plasma protein analysis platform with optimized sample preparation, chromatography, and MS analysis protocols. The workflow, which…”
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