Results 31 to 40 of about 10,190 (249)

Proteogenomics connects somatic mutations to signaling in breast cancer

Nature, 2016
Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. Here we describe quantitative mass-spectrometry-based proteomic and phosphoproteomic
Philipp Mertins, D. Mani, Kelly V. Ruggles, Michael A. Gillette, Michael A. Gillette, K. Clauser, Pei Wang, Xianlong Wang, Jana W. Qiao, Song Cao, F. Petralia, Emily A. Kawaler, Filip Mundt, Filip Mundt, Karsten Krug, Zhidong Tu, Jonathan T. Lei, Michael L. Gatza, M. Wilkerson, C. Perou, V. Yellapantula, Kuan-lin Huang, ChenWei Lin, M. McLellan, Ping Yan, S. Davies, R. Townsend, S. Skates, Jing Wang, Bing Zhang, C. Kinsinger, M. Mesri, H. Rodriguez, L. Ding, A. Paulovich, D. Fenyö, M. Ellis, S. Carr   +37 more
semanticscholar   +1 more source

Proteogenomics of clear cell renal cell carcinoma response to tyrosine kinase inhibitor

Nature Communications, 2023
The tyrosine kinase inhibitor (TKI) Sunitinib is one the therapies approved for advanced renal cell carcinoma. Here, we undertake proteogenomic profiling of 115 tumors from patients with clear cell renal cell carcinoma (ccRCC) undergoing Sunitinib ...
Hailiang Zhang, Lin Bai, Xin Wu, X. Tian, Jinwen Feng, Xiaohui Wu, G. Shi, Xiaoru Pei, Jiacheng Lyu, Guojian Yang, Yang Liu, Wenhao Xu, Aihetaimujiang Anwaier, Y. Zhu, D. Cao, Fujiang Xu, Yue Wang, H. Gan, Meng Sun, Jianyuan Zhao, Y. Qu, Dingwei Ye, C. Ding   +22 more
semanticscholar   +1 more source

Proteogenomics: emergence and promise [PDF]

Cellular and Molecular Life Sciences, 2015
Proteogenomics, or the integration of proteomics with genomics and transcriptomics, is emerging as the next step towards a unified understanding of cellular functions. Looking globally and simultaneously at gene structure, RNA expression, protein synthesis and post-translational modifications have become technically feasible and offer a new perspective
Faulkner, Sam, Dun, Matthew D., Hondermarck, Hubert   +2 more
openaire   +2 more sources

Proteogenomic analysis of pancreatic cancer subtypes [PDF]

PLOS ONE, 2020
Pancreatic cancer remains a significant public health problem with an ever-rising incidence of disease. Cancers of the pancreas are characterised by various molecular aberrations, including changes in the proteomics and genomics landscape of the tumour cells.
Kafita, Doris, Nkhoma, Panji, Zulu, Mildred, Sinkala, Musalula   +3 more
openaire   +4 more sources

Proteogenomic characterization of pancreatic ductal adenocarcinoma [PDF]

Cell, 2021
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal pancreatic ductal tissues.
Liwei Cao, Chen Huang, Daniel Cui Zhou, Yingwei Hu, T. Mamie Lih, Sara R. Savage, Karsten Krug, David J. Clark, Michael Schnaubelt, Lijun Chen, Felipe da Veiga Leprevost, Rodrigo Vargas Eguez, Weiming Yang, Jianbo Pan, Bo Wen, Yongchao Dou, Wen Jiang, Yuxing Liao, Zhiao Shi, Nadezhda V. Terekhanova, Song Cao, Rita Jui-Hsien Lu, Yize Li, Ruiyang Liu, Houxiang Zhu, Peter Ronning, Yige Wu, Matthew A. Wyczalkowski, Hariharan Easwaran, Ludmila Danilova, Arvind Singh Mer, Seungyeul Yoo, Joshua M. Wang, Wenke Liu, Benjamin Haibe-Kains, Mathangi Thiagarajan, Scott D. Jewell, Galen Hostetter, Chelsea J. Newton, Qing Kay Li, Michael H. Roehrl, David Fenyö, Pei Wang, Alexey I. Nesvizhskii, D.R. Mani, Gilbert S. Omenn, Emily S. Boja, Mehdi Mesri, Ana I. Robles, Henry Rodriguez, Oliver F. Bathe, Daniel W. Chan, Ralph H. Hruban, Li Ding, Bing Zhang, Hui Zhang, Mitual Amin, Eunkyung An, Christina Ayad, Thomas Bauer, Chet Birger, Michael J. Birrer, Simina M. Boca, William Bocik, Melissa Borucki, Shuang Cai, Steven A. Carr, Sandra Cerda, Huan Chen, Steven Chen, David Chesla, Arul M. Chinnaiyan, Antonio Colaprico, Sandra Cottingham, Magdalena Derejska, Saravana M. Dhanasekaran, Marcin J. Domagalski, Brian J. Druker, Elizabeth Duffy, Maureen A. Dyer, Nathan J. Edwards, Matthew J. Ellis, Jennifer Eschbacher, Alicia Francis, Jesse Francis, Stacey Gabriel, Nikolay Gabrovski, Johanna Gardner, Gad Getz, Michael A. Gillette, Charles A. Goldthwaite, Pamela Grady, Shuai Guo, Pushpa Hariharan, Tara Hiltke, Barbara Hindenach, Katherine A. Hoadley, Jasmine Huang, Corbin D. Jones, Karen A. Ketchum, Christopher R. Kinsinger, Jennifer M. Koziak, Katarzyna Kusnierz, Tao Liu, Jiang Long, David Mallery, Sailaja Mareedu, Ronald Matteotti, Nicollette Maunganidze, Peter B. McGarvey, Parham Minoo, Oxana V. Paklina, Amanda G. Paulovich, Samuel H. Payne, Olga Potapova, Barbara Pruetz, Liqun Qi, Nancy Roche, Karin D. Rodland, Daniel C. Rohrer, Eric E. Schadt, Alexey V. Shabunin, Troy Shelton, Yvonne Shutack, Shilpi Singh, Michael Smith, Richard D. Smith, Lori J. Sokoll, James Suh, Ratna R. Thangudu, Shirley X. Tsang, Ki Sung Um, Dana R. Valley, Negin Vatanian, Wenyi Wang, George D. Wilson, Maciej Wiznerowicz, Zhen Zhang, Grace Zhao   +138 more
openaire   +2 more sources

Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum [PDF]

, 2016
BACKGROUND: Stagonospora nodorum, a fungal ascomycete in the class dothideomycetes, is a damaging pathogen of wheat. It is a model for necrotrophic fungi that cause necrotic symptoms via the interaction of multiple effector proteins with cultivar ...
Bringans, Scott, Casey, Tammy, Hane, James, Lipscombe, Richard J, Oliver, Richard Peter, Solomon, Peter S, Tan, Kar-Chun   +6 more
core   +1 more source

The plant-pathogen haustorial interface at a glance [PDF]

, 2020
Many filamentous pathogens invade plant cells through specialized hyphae called haustoria. These infection structures are enveloped by a newly synthesized plant-derived membrane called the extrahaustorial membrane (EHM).
Bozkurt, Tolga O., Kamoun, Sophien
core   +1 more source

Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis – a rich resource to identify new transcripts, proteins and to study gene regulation [PDF]

, 2016
Background: Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge.
Ahrens, Christian H., Cuklina, Jelena, Evguenieva-Hackenberg, Elena, Fischer, Hans-Martin, Förstner, Konrad U., Gelfand, Mikhail S., Goebel, Melanie, Hahn, Julia, Imakaev, Maxim, Ljubimov, Nikolay, Omasits, Ulrich, Pessi, Gabriella   +11 more
core   +12 more sources

Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies [PDF]

, 2012
[Image: see text] Proteogenomics has the potential to advance genome annotation through high quality peptide identifications derived from mass spectrometry experiments, which demonstrate a given gene or isoform is expressed and translated at the protein ...
Adamidi C., Alves G., Baerenfaller K., Baudet M., Bern M., Bindschedler L. V., Blakeley P., Boardman P. E., Borchert N., Brosch M., Brosch M., Brunner E., Castellana N. E., Chaerkady R., Ching A. T., Choi H., Choi H., Craig R., de Souza G. A., de Souza G. A., Desiere F., Edwards N. J., Elias J. E., Eng J. K., Everett L. J., Findlay G. D., Fitzgibbon M., Fukunishi Y., Gouzy J., Granholm V., Gupta N., Gupta N., Gupta N., Hall S. L., Ian M. Overton, Iseli C., Jaffe J. D., Jones A. R., Kall L., Kall L., Kall L., Kall L., Kalume D. E., Kapp E. A., Keller A., Kwon T., May P., Merrihew G. E., Nagaraj N., Nesvizhskii A. I., Paul Blakeley, Perkins D. N., Prasad T. S., Robinson M. W., Schrimpf S. P., Sevinsky J. R., Shteynberg D., Simon J. Hubbard, Stanke M., Storey J. D., Tanner S., Tanner S., Walters J. R., Wang G., Wang X., Wasmuth J. D.   +65 more
core   +1 more source

Variant biomarker discovery using mass spectrometry-based proteogenomics

Frontiers in Aging, 2023
Genomic diversity plays critical roles in risk of disease pathogenesis and diagnosis. While genomic variants—including single nucleotide variants, frameshift variants, and mis-splicing isoforms—are commonly detected at the DNA or RNA level, their ...
Luke Reilly, S. Seddighi, A. Singleton, M. Cookson, Michael E. Ward, Y. Qi   +5 more
semanticscholar   +1 more source