2016
- Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Zhang, H, Liu T, Zhang Z, Payne S. et al 2016 Cell. Volume 166, Issue 3, p755–765, 28 July 2016
- Proteogenomic Analysis of Human Breast Cancer Connects Genetic Alterations to Phosphorylation. Mertins,P, Mani, DR, Ruggles, KV et al. Nature. 2016 Jun 2;534(7605):55-62. doi: 10.1038/nature18003. Epub 2016 May 25
- Effect of peptide assay library size and composition in targeted data-independent acquisition-MS analyses. Parker SJ, Venkatraman V, Van Eyk JE. Proteomics. 2016 Aug;16(15-16):2221-37. doi: 10.1002/pmic.201600007.
- Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems. Lam MP, Venkatraman V, Xing Y, Lau E, Cao Q, Ng DC, Su AI, Ge J, Van Eyk JE, Ping P. J Proteome Res. 2016 Jul 19. [Epub ahead of print]
- Initial hyperinsulinemia and subsequent β-cell dysfunction is associated with elevated palmitate levels. Staaf, J., Ubhayasekera, S.J.K.A., Sargsyan, E., Chowdhury, A., Kristinsson, H., Manell, H., Bergquist, J., Forslund, A., Bergsten, P.(2016) Pediatric Research, 80 (2), pp. 267-274.
- Early signs of disease in type 1 diabetes. Moulder, R., Lahesmaa, R.(2016) Pediatric Diabetes, 17, pp. 43-48.
- Altered plasma levels of glucagon, GLP-1 and glicentin during OGTT in adolescents with obesity and type 2 diabetes. Manell, H., Staaf, J., Manukyan, L., Kristinsson, H., Cen, J., Stenlid, R., Ciba, I., Forslund, A., Bergsten, P. (2016) Journal of Clinical Endocrinology and Metabolism, 101 (4), pp. 1181-1189.
- Proteomic Biomarker Discovery in 1000 Human Plasma Samples with Mass Spectrometry. Cominetti, O., Núñez Galindo, A., Corthésy, J., Oller Moreno, S., Irincheeva, I., Valsesia, A., Astrup, A., Saris, W.H.M., Hager, J., Kussmann, M., Dayon, L. (2016) Journal of Proteome Research, 15 (2), pp. 389-399.
- Label-free quantitation for clinical proteomics. Moulder, R., Goo, Y.A., Goodlett, D.R., Methods Mol Biol. 2016;1410:65-76. doi: 10.1007/978-1-4939-3524-6_4.
- Defining the proteome of human iris, ciliary body, retinal pigment epithelium, and choroid. Zhang P, Kirby D, Dufresne C, Chen Y, Turner R, Ferri S, Edward DP, Van Eyk JE, Semba RD. Proteomics. 2016 Apr;16(7):1146-53.
- The proteome of normal human retrobulbar optic nerve and sclera. Zhang P, Karani R, Turner RL, Dufresne C, Ferri S, Van Eyk JE, Semba RD. Proteomics. 2016 Aug 19. doi: 10.1002/pmic.201600229. [Epub ahead of print]
- A comprehensive proteomics analysis of the human iris tissue: ready to embrace postgenomics precision medicine in ophthalmology? Murthy KR, Dammalli M, Pinto SM, Murthy KB, Nirujogi RS, Madugundu AK, Dey G, Subbannayya Y, Mishra UK, Nair B, Gowda H, Prasad TS. OMICS. 2016 Sep;20(9):510-9.
- Foodomics - Novel insights in food and nutrition domains. Ferranti P, Roncada P, Scaloni A. J Proteomics. 2016 Sep 16;147:1-2. doi: 10.1016/j.jprot.2016.07.016
- Proteomics in food: Quality, safety, microbes, and allergens. Piras C, Roncada P, Rodrigues PM, Bonizzi L, Soggiu A.Proteomics. 2016 Mar;16(5):799-815. doi: 10.1002/pmic.20150036
- Comparison of analytical methods for profiling N- and O-linked glycans from cultured cell lines : HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study. Ito H, Kaji H, Togayachi A, Azadi P, Ishihara M, Geyer R, Galuska C, Geyer H, Kakehi K, Kinoshita M, Karlsson NG, Jin C, Kato K, Yagi H, Kondo S, Kawasaki N, Hashii N, Kolarich D, Stavenhagen K, Packer NH, Thaysen-Andersen M, Nakano M, Taniguchi N, Kurimoto A, Wada Y, Tajiri M, Yang P, Cao W, Li H, Rudd PM, Narimatsu H. Glycoconj J. 2016 Jun;33(3):405-15. doi: 10.1007/s10719-015-9625-3. Epub 2015 Oct 28. PMID: 26511985
- Long-term metabolic correction of Wilson's disease in a murine model by gene therapy. Murillo O, Luqui DM, Gazquez C, Martinez-Espartosa D, Navarro-Blasco I, Monreal JI, Guembe L, Moreno-Cermeño A, Corrales FJ, Prieto J, Hernandez-Alcoceba R, Gonzalez-Aseguinolaza G. J Hepatol. 2016 Feb;64(2):419-26.
- Experimental setup for the identification of mitochondrial protease substrates by shotgun and top-down proteomics. Di Pierro A, Bondi H, Monti C, Pieroni L, Cilio E, Urbani A, Alberio T, Fasano M, Ronci M.EuPA Open Proteomics. 2016;11: 1-3. doi:10.1016/j.euprot.2016.02.002
- Proteomic profiling of human plasma for cancer biomarker discovery, Proteomics. Huang Z, Ma L, Huang C, Li Q, Nice EC., 2016 Aug 23. doi: 10.1002/pmic.201600240.
- Plasma Proteome Profiling to Assess Human Health and Disease, Cell Syst. Geyer PE, Kulak NA, Pichler G, Holdt LM, Teupser D, Mann M, 2016 Mar 23;2(3):185-95. doi: 10.1016/j.cels.2016.02.015
- Dual targeting of p53 and c-MYC selectively eliminates leukaemic stem cells (2016). Abraham SA, Hopcroft LE, Carrick E, Drotar ME, Dunn K, Williamson AJ, Korfi K, Baquero P, Park LE, Scott MT, Pellicano F, Pierce A, Copland M, Nourse C, Grimmond SM, Vetrie D, Whetton AD, Holyoake TL. Nature 534(7607):341-6.
2015
- Prioritizing Proteomics Assay Development for Clinical Translation. Lam MP, Venkatraman V, Cao Q, Wang D, Dincer TU, Lau E, Su AI, Xing Y, Ge J, Ping P, Van Eyk JE. 2015 Jul 14;66(2):202-4. doi: 10.1016/j.jacc.2015.04.072.
- Citrullination of myofilament proteins in heart failure. Fert-Bober J, Giles JT, Holewinski RJ, Kirk JA, Uhriqshardt H, Crowgey EL, Andrade F, Bingham CO, Park JK, Hallushka MK, KAss DA, Bathon JM, Van Eyke JE. 2015 Nov 1;108(2):232-42. doi: 10.1093/cvr/cvv185. Epub 2015 Jun 25.
2014
- C2orf62 and TTC17 Are Involved in Actin Organization and Ciliogenesis in Zebrafish and Human. Bontems F, Fish RJ, Borlat I, Lembo F, Chocu S, Chalmel F, Borg JP, Pineau C, Neerman-Arbez M, Bairoch A, Lane L. 2014 Jan 27;9(1):e86476. doi: 10.1371/journal.pone.0086476. eCollection 2014. PubMed PMID:24475127; PubMed Central PMCID: PMC3903541.
- 38 new HPP publications in 2nd annual C-HPP special issue of the Journal of Proteome Research, January 2014 and April 2014
- Proteogenomic characterization of human colon and rectal cancer. Bing Zhang, Jing Wang, Xiaojing Wang, Jing Zhu, Qi Liu, Zhiao Shi, Matthew C. Chambers, Lisa J. Zimmerman, Kent F. Shaddox, Sangtae Kim, Sherri R. Davies, Sean Wang, Pei Wang, Christopher R. Kinsinger, Robert C. Rivers, Henry Rodriguez, R. Reid Townsend, Matthew J. C. Ellis, Steven A. Carr, David L. Tabb, Robert J. Coffey, Robbert J. C. Slebos, Daniel C. Liebler & the NCI CPTAC. Nature 513, 382–387 (18 September 2014) doi:10.1038/nature13438
2013
- 48 HPP publications in 1st annual C-HPP special issue of the Journal of Proteome Research, January 2013 and June 2013
- neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects- Pascale Gaudet, Ghislaine Argoud-Puy, Isabelle Cusin, Paula Duek, Olivier Evalet, Alain Gateau, Anne Gleizes, Mario Pereira, Monique Zahn-Zabal, Catherine Zwahlen, Amos Bairoch, and Lydie Lane (2013) Journal of Proteome Research special issue 2013
- CAPER: a Chromosome-Assembled human Proteome browsER- Feifei Guo, Dan Wang, Zhongyang Liu, Liang Lu, Wei Zhang, Haiyan Sun, Hongxing Zhang, Jie Ma, Songfeng Wu, Ning Li, Ying Jiang, Weimin Zhu, Jun Qin, Ping Xu, Dong Li, and Fuchu He (2013) Journal of Proteome Research special issue 2013
- The Proteome Browser Web Portal- Robert J. A. Goode, Simon Yu, Anitha Kannan, Jeffrey H. Christiansen, Anthony Beitz, William S. Hancock, Edouard Nice, and A. Ian Smith (2013) Journal of Proteome Research special issue 2013
- Qualitative and Quantitative Expression Status of the Human Chromosome 20 Genes in Cancer Tissues and the Representative Cell Lines- Quanhui Wang, Bo Wen, Guangrong Yan, Junying Wei, Liqi Xie, Shaohang Xu, Dahai Jiang, Tingyou Wang, Liang Lin, Jin Zi, Ju Zhang, Ruo Zhou, Haiyi Zhao, Zhe Ren, Nengrong Qu, Xiaomin Lou, Haidan Sun, Chaoqin Du, Chuangbin Chen, Shenyan Zhang, Fengji Tan, Youqi Xian, Zhibo Gao, Minghui He, Longyun Chen, Xiaohang Zhao, Ping Xu, Yunping Zhu, Xingfeng Yin, Huali Shen, Yang Zhang, Jing Jiang, Chengpu Zhang, Liwei Li, Cheng Chang, Jie Ma, Guoquan Yan, Jun Yao, Haojie Lu, Wantao Ying, Fan Zhong, Qing-Yu He, and Siqi Liu (2013) Journal of Proteome Research special issue 2013
- Chromosome 19 Annotations with Disease Speciation: A First Report from the Global Research Consortium- Carol L. Nilsson, Frode Berven, Frode Selheim, Huiling Liu, Joseph R. Moskal, Roger A. Kroes, Erik P. Sulman, Charles A. Conrad, Frederick F. Lang, Per E. Andrén, Anna Nilsson, Elisabet Carlsohn, Hans Lilja, Johan Malm, David Fenyö, Devipriya Subramaniyam, Xiangdong Wang, Maria Gonzales-Gonzales, Noelia Dasilva, Paula Diez, Manuel Fuentes, Ákos Végvári, Karin Sjödin, Charlotte Welinder, Thomas Laurell, Thomas E. Fehniger, Henrik Lindberg, Melinda Rezeli, Goutham Edula, Sophia Hober, and György Marko-Varga (2013) Journal of Proteome Research special issue 2013
- Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells- Victor G. Zgoda, Arthur T. Kopylov, Olga V. Tikhonova, Alexander A. Moisa, Nadezhda V. Pyndyk, Tatyana E. Farafonova, Svetlana E. Novikova, Andrey V. Lisitsa, Elena A. Ponomarenko, Ekaterina V. Poverennaya, Sergey P. Radko, Svetlana A. Khmeleva, Leonid K. Kurbatov, Aleksey D. Filimonov, Nadezhda A. Bogolyubova, Ekaterina V. Ilgisonis, Aleksey L. Chernobrovkin, Alexis S. Ivanov, Alexei E. Medvedev, Yury V. Mezentsev, Sergei A. Moshkovskii, Stanislav N. Naryzhny, Elena N. Ilina, Elena S. Kostrjukova, Dmitry G. Alexeev, Alexander V. Tyakht, Vadim M. Govorun, and Alexander I. Archakov (2013) Journal of Proteome Research special issue 2013. Presented data available: PXD000085, PXD000091, PXD000092, PXD000093
- Spanish Human Proteome Project: Dissection of Chromosome 16 - V. Segura, J. A. Medina-Aunon, E. Guruceaga, S. I. Gharbi, C. González-Tejedo, M. M. Sánchez del Pino, F. Canals, M. Fuentes, J. Ignacio Casal, S. Martínez-Bartolomé, F. Elortza, J. M. Mato, J. M. Arizmendi, J. Abian, E. Oliveira, C. Gil, F. Vivanco, F. Blanco, J. P. Albar, and F. J. Corrales (2013) Journal of Proteome Research special issue 2013. Presented datasets available: PXD000039
- GenomewidePDB, a Proteomic Database Exploring the Comprehensive Protein Parts List and Transcriptome Landscape in Human Chromosomes- Seul-Ki Jeong, Hyoung-Joo Lee, Keun Na, Jin-Young Cho, Min Jung Lee, Ja-Young Kwon, Hoguen Kim, Young-Mok Park, Jong Shin Yoo, William S. Hancock, and Young-Ki Paik (2013) Journal of Proteome Research special issue 2013
- Chromosome 11-Centric Human Proteome Analysis of Human Brain Hippocampus Tissue- Kyung-Hoon Kwon, Jin Young Kim, Se-Young Kim, Hye Kyeong Min, Hyoung-Joo Lee, In Jung Ji, Taewook Kang, Gun Wook Park, Hyun Joo An, Bonghee Lee, Rivka Ravid, Isidro Ferrer, Chun Kee Chung, Young-Ki Paik, William S. Hancock, Young Mok Park, and Jong Shin Yoo (2013) Journal of Proteome Research special issue 2013
- Proteome Atlas of Human Chromosome 8 and Its Multiple 8p Deficiencies in Tumorigenesis of the Stomach, Colon, and Liver- Yang Zhang, Guoquan Yan, Linhui Zhai, Shaohang Xu, Huali Shen, Jun Yao, Feifei Wu, Liqi Xie, Hailin Tang, Hongxiu Yu, Mingqi Liu, Pengyuan Yang, Ping Xu, Chengpu Zhang, Liwei Li, Cheng Chang, Ning Li, Songfeng Wu, Yunping Zhu, Quanhui Wang, Bo Wen, Liang Lin, Yinzhu Wang, Guiyan Zheng, Lanping Zhou, Haojie Lu, Siqi Liu, Fuchu He, and Fan Zhong (2013) Journal of Proteome Research special issue 2013
- First Proteomic Exploration of Protein-Encoding Genes on Chromosome 1 in Human Liver, Stomach, and Colon - Songfeng Wu, Ning Li, Jie Ma, Huali Shen, Dahai Jiang, Cheng Chang, Chengpu Zhang, Liwei Li, Hongxing Zhang, Jing Jiang, Zhongwei Xu, Lingyan Ping, Tao Chen, Wei Zhang, Tao Zhang, Xiaohua Xing, Tailong Yi, Yanchang Li, Fengxu Fan, Xiaoqian Li, Fan Zhong, Quanhui Wang, Yang Zhang, Bo Wen, Guoquan Yan, Liang Lin, Jun Yao, Zhilong Lin, Feifei Wu, Liqi Xie, Hongxiu Yu, Mingqi Liu, Haojie Lu, Hong Mu, Dong Li, Weimin Zhu, Bei Zhen, Xiaohong Qian, Jun Qin, Siqi Liu, Pengyuan Yang, Yunping Zhu, Ping Xu, and Fuchu He (2013) Journal of Proteome Research special issue 2013
- Integrated View of the Human Chromosome X-centric Proteome Project - Tadashi Yamamoto, Keiichi Nakayama, Hisashi Hirano, Takeshi Tomonaga, Yasushi Ishihama, Tetsushi Yamada, Tadashi Kondo, Yoshio Kodera, Yuichi Sato, Norie Araki, Hiroshi Mamitsuka, and Naoki Goshima (2013) Journal of Proteome Research special issue 2013
- A Chromosome-centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17- Suli Liu, Hogune Im, Amos Bairoch, Massimo Cristofanilli, Rui Chen, Eric W. Deutsch, Stephen Dalton, David Fenyo, Susan Fanayan, Chris Gates, Pascale Gaudet, Marina Hincapie, Samir Hanash, Hoguen Kim, Seul-Ki Jeong, Emma Lundberg, George Mias, Rajasree Menon, Zhaomei Mu, Edouard Nice, Young-Ki Paik, Mathias Uhlen, Lance Wells, Shiaw-Lin Wu, Fangfei Yan, Fan Zhang, Yue Zhang, Michael Snyder, Gilbert S. Omenn, Ronald C. Beavis, and William S. Hancock (2013) Journal of Proteome Research special issue 2013
- Decoding the Disease-Associated Proteins Encoded in the Human Chromosome 4 - Lien-Chin Chen, Mei-Ying Liu, Yung-Chin Hsiao, Wai-Kok Choong, Hsin-Yi Wu, Wen-Lian Hsu, Pao-Chi Liao, Ting-Yi Sung, Shih-Feng Tsai, Jau-Song Yu, and Yu-Ju Chen (2013) Journal of Proteome Research special issue 2013
- A Fresh Look at the Male-specific Region of the Human Y Chromosome- Zohreh Jangravi, Mehdi Alikhani, Babak Arefnezhad, Mehdi Sharifi Tabar, Sara Taleahmad, Razieh Karamzadeh, Mahdieh Jadaliha, Seyed Ahmad Mousavi, Diba Ahmadi Rastegar, Pouria Parsamatin, Haghighat Vakilian, Shahab Mirshahvaladi, Marjan Sabbaghian, Anahita Mohseni Meybodi, Mehdi Mirzaei, Maryam Shahhoseini, Marzieh Ebrahimi, Abbas Piryaei, Ali Akbar Moosavi-Movahedi, Paul A. Haynes, Ann K. Goodchild, Mohammad Hossein Nasr-Esfahani, Esmaiel Jabbari, Hossein Baharvand, Mohammad Ali Sedighi Gilani, Hamid Gourabi, and Ghasem Hosseini Salekdeh (2013) Journal of Proteome Research special issue 2013
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