Literature DB >> 32669682

Philosopher: a versatile toolkit for shotgun proteomics data analysis.

Felipe da Veiga Leprevost1, Sarah E Haynes1, Dmitry M Avtonomov1, Hui-Yin Chang1, Avinash K Shanmugam1,2, Dattatreya Mellacheruvu1,2, Andy T Kong1,2, Alexey I Nesvizhskii3,4.   

Abstract

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Year:  2020        PMID： 32669682      PMCID： PMC7509848          DOI： 10.1038/s41592-020-0912-y

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  27 in total

Review 1.  Cancer proteogenomics: current impact and future prospects.

Authors:  D R Mani; Karsten Krug; Bing Zhang; Shankha Satpathy; Karl R Clauser; Li Ding; Matthew Ellis; Michael A Gillette; Steven A Carr
Journal:  Nat Rev Cancer       Date:  2022-03-02       Impact factor: 60.716

2.  Inner membrane complex proteomics reveals a palmitoylation regulation critical for intraerythrocytic development of malaria parasite.

Authors:  Pengge Qian; Xu Wang; Chuan-Qi Zhong; Jiaxu Wang; Mengya Cai; Wang Nguitragool; Jian Li; Huiting Cui; Jing Yuan
Journal:  Elife       Date:  2022-07-01       Impact factor: 8.713

3.  EML2-S constitutes a new class of proteins that recognizes and regulates the dynamics of tyrosinated microtubules.

Authors:  Takashi Hotta; Thomas S McAlear; Yang Yue; Takumi Higaki; Sarah E Haynes; Alexey I Nesvizhskii; David Sept; Kristen J Verhey; Susanne Bechstedt; Ryoma Ohi
Journal:  Curr Biol       Date:  2022-08-12       Impact factor: 10.900

4.  Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Authors:  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
Journal:  Cell       Date:  2021-09-16       Impact factor: 66.850

5.  Proteogenomic analysis of cancer aneuploidy and normal tissues reveals divergent modes of gene regulation across cellular pathways.

Authors:  Pan Cheng; Xin Zhao; Lizabeth Katsnelson; Elaine M Camacho-Hernandez; Angela Mermerian; Joseph C Mays; Scott M Lippman; Reyna Edith Rosales-Alvarez; Raquel Moya; Jasmine Shwetar; Dominic Grun; David Fenyo; Teresa Davoli
Journal:  Elife       Date:  2022-09-21       Impact factor: 8.713

6.  Parthenolide Destabilizes Microtubules by Covalently Modifying Tubulin.

Authors:  Takashi Hotta; Sarah E Haynes; Teresa L Blasius; Margo Gebbie; Emily L Eberhardt; David Sept; Michael Cianfrocco; Kristen J Verhey; Alexey I Nesvizhskii; Ryoma Ohi
Journal:  Curr Biol       Date:  2021-01-21       Impact factor: 10.834

7.  Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine.

Authors:  Guo Ci Teo; Daniel A Polasky; Fengchao Yu; Alexey I Nesvizhskii
Journal:  J Proteome Res       Date:  2020-12-17       Impact factor: 4.466

8.  Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data.

Authors:  Stephen J Kiniry; Ciara E Judge; Audrey M Michel; Pavel V Baranov
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

Review 9.  Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies and Future Outlook.

Authors:  Sarah R Weber; Yuanjun Zhao; Christopher Gates; Jingqun Ma; Felipe da Veiga Leprevost; Venkatesha Basrur; Alexey I Nesvizhskii; Thomas W Gardner; Jeffrey M Sundstrom
Journal:  J Clin Med       Date:  2021-05-25       Impact factor: 4.241

10.  Transcriptome features of striated muscle aging and predictability of protein level changes.

Authors:  Yu Han; Lauren Z Li; Nikhitha L Kastury; Cody T Thomas; Maggie P Y Lam; Edward Lau
Journal:  Mol Omics       Date:  2021-10-11
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