Results 11 to 20 of about 10,190 (249)

Integrative Proteogenomics Using ProteomeGenerator2.

Journal of Proteome Research, 2023
Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms.
Nathaniel Kwok, Zita E H Aretz, Sumiko Takao, Zheng Ser, P. Cifani, A. Kentsis   +5 more
semanticscholar   +4 more sources

Deep Proteogenomics of a Photosynthetic Cyanobacterium

Journal of Proteome Research, 2023
Cyanobacteria, the evolutionary ancestors of plant chloroplasts, contribute substantially to the Earth’s biogeochemical cycles and are of great interest for a sustainable economy. Knowledge of protein expression is the key to understanding cyanobacterial
Philipp Spät, Vanessa Krauspe, W. Hess, Boris Maček, N. Nalpas   +4 more
semanticscholar   +4 more sources

Bacterial riboproteogenomics : the era of N-terminal proteoform existence revealed [PDF]

, 2020
With the rapid increase in the number of sequenced prokaryotic genomes, relying on automated gene annotation became a necessity. Multiple lines of evidence, however, suggest that current bacterial genome annotations may contain inconsistencies and are ...
Fijalkowska, Daria, Fijalkowski, Igor, Van Damme, Petra, Willems, Patrick   +3 more
core   +2 more sources

Mass Spectrometry–Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine

Annual Review of Pharmacology and Toxicology, 2023
Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis ...
Sunil K Joshi, P. Piehowski, T. Liu, Sara J C Gosline, Jason E McDermott, Brian J Druker, E. Traer, Jeffrey W Tyner, A. Agarwal, Cristina E Tognon, Karin D Rodland   +10 more
semanticscholar   +1 more source

Proteogenomic Characterization of Endometrial Carcinoma [PDF]

Cell, 2020
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences of perturbations to the p53 and Wnt/β-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and
Yongchao Dou, Emily A. Kawaler, Daniel Cui Zhou, Marina A. Gritsenko, Chen Huang, Lili Blumenberg, Alla Karpova, Vladislav A. Petyuk, Sara R. Savage, Shankha Satpathy, Wenke Liu, Yige Wu, Chia-Feng Tsai, Bo Wen, Zhi Li, Song Cao, Jamie Moon, Zhiao Shi, MacIntosh Cornwell, Matthew A. Wyczalkowski, Rosalie K. Chu, Suhas Vasaikar, Hua Zhou, Qingsong Gao, Ronald J. Moore, Kai Li, Sunantha Sethuraman, Matthew E. Monroe, Rui Zhao, David Heiman, Karsten Krug, Karl Clauser, Ramani Kothadia, Yosef Maruvka, Alexander R. Pico, Amanda E. Oliphant, Emily L. Hoskins, Samuel L. Pugh, Sean J.I. Beecroft, David W. Adams, Jonathan C. Jarman, Andy Kong, Hui-Yin Chang, Boris Reva, Yuxing Liao, Dmitry Rykunov, Antonio Colaprico, Xi Steven Chen, Andrzej Czekański, Marcin Jędryka, Rafał Matkowski, Maciej Wiznerowicz, Tara Hiltke, Emily Boja, Christopher R. Kinsinger, Mehdi Mesri, Ana I. Robles, Henry Rodriguez, David Mutch, Katherine Fuh, Matthew J. Ellis, Deborah DeLair, Mathangi Thiagarajan, D.R. Mani, Gad Getz, Michael Noble, Alexey I. Nesvizhskii, Pei Wang, Matthew L. Anderson, Douglas A. Levine, Richard D. Smith, Samuel H. Payne, Kelly V. Ruggles, Karin D. Rodland, Li Ding, Bing Zhang, Tao Liu, David Fenyö, Anupriya Agarwal, Meenakshi Anurag, Dmitry Avtonomov, Chet Birger, Michael J. Birrer, Simina M. Boca, William E. Bocik, Uma Borate, Melissa Borucki, Meghan C. Burke, Shuang Cai, Anna Calinawan, Steven A. Carr, Sonya Carter, Patricia Castro, Sandra Cerda, Michelle Chaikin, Daniel W. Chan, Doug Chan, Alyssa Charamut, Feng Chen, Jin Chen, Lijun Chen, Lin S. Chen, David Chesla, Milan G. Chheda, Arul M. Chinnaiyan, Shrabanti Chowdhury, Marcin P. Cieslik, David J. Clark, Sandra Cottingham, Houston Culpepper, Jacob Day, Stephanie De Young, Emek Demir, Saravana Mohan Dhanasekaran, Rajiv Dhir, Marcin J. Domagalski, Peter Dottino, Brian Druker, Elizabeth Duffy, Maureen Dyer, Nathan J. Edwards, Robert Edwards, Kim Elburn, Jayson B. Field, Alicia Francis, Stacey Gabriel, Yifat Geffen, Daniel Geiszler, Michael A. Gillette, Andrew K. Godwin, Pamela Grady, Linda Hannick, Pushpa Hariharan, Sue Hilsenbeck, Barbara Hindenach, Katherine A. Hoadley, Runyu Hong, Galen Hostetter, James J. Hsieh, Yingwei Hu, Michael M. Ittmann, Eric Jaehnig, Scott D. Jewell, Jiayi Ji, Corbin D. Jones, Renee Karabon, Karen A. Ketchum, Munziba Khan, Beom-Jun Kim, Azra Krek, Tanya Krubit, Chandan Kumar-Sinha, Felipe D. Leprevost, Michael Lewis, Qing Kay Li, Yize Li, Hongwei Liu, Jan Lubinski, Weiping Ma, Rashna Madan, Ewa Malc, Anna Malovannaya, Sailaja Mareedu, Sanford P. Markey, Annette Marrero-Oliveras, John Martignetti, Jason McDermott, Peter B. McGarvey, John McGee, Piotr Mieczkowski, Francesmary Modugno, Rebecca Montgomery, Chelsea J. Newton, Gilbert S. Omenn, Amanda G. Paulovich, Amy M. Perou, Francesca Petralia, Paul Piehowski, Larisa Polonskaya, Liqun Qi, Shannon Richey, Karna Robinson, Nancy Roche, Daniel C. Rohrer, Eric E. Schadt, Michael Schnaubelt, Yan Shi, Tara Skelly, Lori J. Sokoll, Xiaoyu Song, Stephen E. Stein, James Suh, Donghui Tan, Darlene Tansil, Guo Ci Teo, Ratna R. Thangudu, Cristina Tognon, Elie Traer, Jeffrey Tyner, Ki Sung Um, Liang-Bo Wang   +200 more
openaire   +4 more sources

PGNneo: A Proteogenomics-Based Neoantigen Prediction Pipeline in Noncoding Regions

Cells, 2023
The development of a neoantigen-based personalized vaccine has promise in the hunt for cancer immunotherapy. The challenge in neoantigen vaccine design is the need to rapidly and accurately identify, in patients, those neoantigens with vaccine potential.
Xiaoxiu Tan, Linfeng Xu, Xingxing Jian, Ouyang Jian, Bo Hu, Xinrong Yang, Tao Wang, Lu Xie   +7 more
semanticscholar   +1 more source

The Proteogenomic Mapping Tool [PDF]

BMC Bioinformatics, 2011
Abstract Background High-throughput mass spectrometry (MS) proteomics data is increasingly being used to complement traditional structural genome annotation methods. To keep pace with the high speed of experimental data generation and to aid in structural genome annotation, experimentally observed peptides need to be ...
Sanders, William S., Wang, Nan, Bridges, Susan M., Malone, Brandon M., Dandass, Yoginder S., McCarthy, Fiona M., Nanduri, Bindu, Lawrence, Mark L., Burgess, Shane C.   +8 more
openaire   +3 more sources

Enhanced protein isoform characterization through long-read proteogenomics

Genome Biology, 2022
The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic analysis relies on ...
Rachel M. Miller, B. Jordan, Madison M. Mehlferber, Erin D. Jeffery, C. Chatzipantsiou, Simi Kaur, R. Millikin, Yunxiang Dai, S. Tiberi, P. Castaldi, M. Shortreed, C. J. Luckey, A. Conesa, Lloyd M. Smith, Anne Deslattes Mays, Gloria M. Sheynkman   +15 more
semanticscholar   +1 more source

Proteogenomics in cerebrospinal fluid and plasma reveals new biological fingerprint of cerebral small vessel disease [PDF]

Alzheimers Dement
Caro I, Western D, Okada Y, Jager P, Duperron M, Sargurupremraj M, Seshadri S, Tregouët D, Cruchaga C, Debette S.   +9 more
europepmc   +3 more sources

Proteogenomic characterization of hepatocellular carcinoma [PDF]

, 2021
SUMMARYWe performed a proteogenomic analysis of hepatocellular carcinomas (HCCs) across clinical stages and etiologies. We identified pathways differentially regulated on the genomic, transcriptomic, proteomic and phosphoproteomic levels. These pathways are involved in the organization of cellular components, cell cycle control, signaling pathways ...
Charlotte K Y Ng, Eva Dazert, Tuyana Boldanova, Mairene Coto-Llerena, Sandro Nuciforo, Caner Ercan, Aleksei Suslov, Marie-Anne Meier, Thomas Bock, Alexander Schmidt, Sylvia Ketterer, Xueya Wang, Stefan Wieland, Matthias S Matter, Marco Colombi, Salvatore Piscuoglio, Luigi M Terracciano, Michael N Hall, Markus H Heim   +18 more
openaire   +3 more sources