Literature DB >> 28486446

Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis.

Jinwen Feng1,2, Chen Ding1,3, Naiqi Qiu1,2, Xiaotian Ni1,2, Dongdong Zhan1,2, Wanlin Liu1, Xia Xia1, Peng Li2, Bingxin Lu2, Qi Zhao4, Peng Nie4, Lei Song1, Quan Zhou1, Mi Lai1, Gaigai Guo1, Weimin Zhu1, Jian Ren4, Tieliu Shi2, Jun Qin1,3.   

Abstract

Mesh：

Year:  2017        PMID： 28486446     DOI： 10.1038/nbt.3825

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  22 in total

1.  The human genome browser at UCSC.

Authors:  W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal:  Genome Res       Date:  2002-06       Impact factor: 9.043

2.  Trans-proteomic pipeline: a pipeline for proteomic analysis.

Authors:  Patrick G A Pedrioli
Journal:  Methods Mol Biol       Date:  2010

3.  iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.

Authors:  David Shteynberg; Eric W Deutsch; Henry Lam; Jimmy K Eng; Zhi Sun; Natalie Tasman; Luis Mendoza; Robert L Moritz; Ruedi Aebersold; Alexey I Nesvizhskii
Journal:  Mol Cell Proteomics       Date:  2011-08-29       Impact factor: 5.911

4.  PeptideShaker enables reanalysis of MS-derived proteomics data sets.

Authors:  Marc Vaudel; Julia M Burkhart; René P Zahedi; Eystein Oveland; Frode S Berven; Albert Sickmann; Lennart Martens; Harald Barsnes
Journal:  Nat Biotechnol       Date:  2015-01       Impact factor: 54.908

5.  Mass-spectrometry-based draft of the human proteome.

Authors:  Mathias Wilhelm; Judith Schlegl; Hannes Hahne; Amin Moghaddas Gholami; Marcus Lieberenz; Mikhail M Savitski; Emanuel Ziegler; Lars Butzmann; Siegfried Gessulat; Harald Marx; Toby Mathieson; Simone Lemeer; Karsten Schnatbaum; Ulf Reimer; Holger Wenschuh; Martin Mollenhauer; Julia Slotta-Huspenina; Joos-Hendrik Boese; Marcus Bantscheff; Anja Gerstmair; Franz Faerber; Bernhard Kuster
Journal:  Nature       Date:  2014-05-29       Impact factor: 49.962

6.  OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.

Authors:  Hannes L Röst; George Rosenberger; Pedro Navarro; Ludovic Gillet; Saša M Miladinović; Olga T Schubert; Witold Wolski; Ben C Collins; Johan Malmström; Lars Malmström; Ruedi Aebersold
Journal:  Nat Biotechnol       Date:  2014-03       Impact factor: 54.908

7.  System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap.

Authors:  Nagarjuna Nagaraj; Nils Alexander Kulak; Juergen Cox; Nadin Neuhauser; Korbinian Mayr; Ole Hoerning; Ole Vorm; Matthias Mann
Journal:  Mol Cell Proteomics       Date:  2011-10-20       Impact factor: 5.911

8.  A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.

Authors:  Jesper V Olsen; Jae C Schwartz; Jens Griep-Raming; Michael L Nielsen; Eugen Damoc; Eduard Denisov; Oliver Lange; Philip Remes; Dennis Taylor; Maurizio Splendore; Eloy R Wouters; Michael Senko; Alexander Makarov; Matthias Mann; Stevan Horning
Journal:  Mol Cell Proteomics       Date:  2009-10-14       Impact factor: 5.911

9.  CellNet: network biology applied to stem cell engineering.

Authors:  Patrick Cahan; Hu Li; Samantha A Morris; Edroaldo Lummertz da Rocha; George Q Daley; James J Collins
Journal:  Cell       Date:  2014-08-14       Impact factor: 41.582

10.  Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.

Authors:  Pratik D Jagtap; James E Johnson; Getiria Onsongo; Fredrik W Sadler; Kevin Murray; Yuanbo Wang; Gloria M Shenykman; Sricharan Bandhakavi; Lloyd M Smith; Timothy J Griffin
Journal:  J Proteome Res       Date:  2014-10-23       Impact factor: 4.466
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  19 in total

1.  Urinary protein biomarker panel predicts esophageal squamous carcinoma from control cases and other tumors.

Authors:  Linlin Ji; Jianping Wang; Bo Yang; Jianping Zhu; Yini Wang; Jiaqi Jiao; Kai Zhu; Min Zhang; Liqiang Zhai; Tongqing Gong; Changqing Sun; Jun Qin; Guangshun Wang
Journal:  Esophagus       Date:  2022-07-06       Impact factor: 3.671

2.  Proteomic characterization of gastric cancer response to chemotherapy and targeted therapy reveals new therapeutic strategies.

Authors:  Yan Li; Chen Xu; Bing Wang; Fujiang Xu; Fahan Ma; Yuanyuan Qu; Dongxian Jiang; Kai Li; Jinwen Feng; Sha Tian; Xiaohui Wu; Yunzhi Wang; Yang Liu; Zhaoyu Qin; Yalan Liu; Jing Qin; Qi Song; Xiaolei Zhang; Akesu Sujie; Jie Huang; Tianshu Liu; Kuntang Shen; Jian-Yuan Zhao; Yingyong Hou; Chen Ding
Journal:  Nat Commun       Date:  2022-09-29       Impact factor: 17.694

3.  Integrated proteogenomic characterization of urothelial carcinoma of the bladder.

Authors:  Ning Xu; Zhenmei Yao; Guoguo Shang; Dingwei Ye; Haixing Wang; Hailiang Zhang; Yuanyuan Qu; Jun Hou; Fujiang Xu; Yunzhi Wang; Zhaoyu Qin; Jiajun Zhu; Fan Zhang; Jinwen Feng; Sha Tian; Yang Liu; Jianyuan Zhao; Jianming Guo; Yingyong Hou; Chen Ding
Journal:  J Hematol Oncol       Date:  2022-06-03       Impact factor: 23.168

4.  Tumor-associated antigen Prame targets tumor suppressor p14/ARF for degradation as the  receptor protein of CRL2Prame complex.

Authors:  Wenjuan Zhang; Lihui Li; Lili Cai; Yupei Liang; Junfeng Xu; Yue Liu; Lisha Zhou; Chen Ding; Yanmei Zhang; Hu Zhao; Jun Qin; Zhimin Shao; Wenyi Wei; Lijun Jia
Journal:  Cell Death Differ       Date:  2021-01-27       Impact factor: 15.828

5.  Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

Authors:  Eric W Deutsch; Sandra Orchard; Pierre-Alain Binz; Wout Bittremieux; Martin Eisenacher; Henning Hermjakob; Shin Kawano; Henry Lam; Gerhard Mayer; Gerben Menschaert; Yasset Perez-Riverol; Reza M Salek; David L Tabb; Stefan Tenzer; Juan Antonio Vizcaíno; Mathias Walzer; Andrew R Jones
Journal:  J Proteome Res       Date:  2017-09-15       Impact factor: 4.466

6.  -Omics biomarker identification pipeline for translational medicine.

Authors:  Laura Bravo-Merodio; John A Williams; Georgios V Gkoutos; Animesh Acharjee
Journal:  J Transl Med       Date:  2019-05-14       Impact factor: 5.531

7.  Proteomics provides individualized options of precision medicine for patients with gastric cancer.

Authors:  Wenwen Huang; Dongdong Zhan; Yazhuo Li; Nairen Zheng; Xin Wei; Bin Bai; Kecheng Zhang; Mingwei Liu; Xuefei Zhao; Xiaotian Ni; Xia Xia; Jinwen Shi; Cheng Zhang; Zhihao Lu; Jiafu Ji; Juan Wang; Shiqi Wang; Gang Ji; Jipeng Li; Yongzhan Nie; Wenquan Liang; Xiaosong Wu; Jianxin Cui; Yongsheng Meng; Feilin Cao; Tieliu Shi; Weimin Zhu; Yi Wang; Lin Chen; Qingchuan Zhao; Hongwei Wang; Lin Shen; Jun Qin
Journal:  Sci China Life Sci       Date:  2021-07-09       Impact factor: 6.038

8.  Blood molecular markers associated with COVID-19 immunopathology and multi-organ damage.

Authors:  Yan-Mei Chen; Yuanting Zheng; Ying Yu; Yunzhi Wang; Qingxia Huang; Feng Qian; Lei Sun; Zhi-Gang Song; Ziyin Chen; Jinwen Feng; Yanpeng An; Jingcheng Yang; Zhenqiang Su; Shanyue Sun; Fahui Dai; Qinsheng Chen; Qinwei Lu; Pengcheng Li; Yun Ling; Zhong Yang; Huiru Tang; Leming Shi; Li Jin; Edward C Holmes; Chen Ding; Tong-Yu Zhu; Yong-Zhen Zhang
Journal:  EMBO J       Date:  2020-12-14       Impact factor: 14.012

9.  A region-resolved mucosa proteome of the human stomach.

Authors:  Xiaotian Ni; Zhaoli Tan; Chen Ding; Chunchao Zhang; Lan Song; Shuai Yang; Mingwei Liu; Ru Jia; Chuanhua Zhao; Lei Song; Wanlin Liu; Quan Zhou; Tongqing Gong; Xianju Li; Yanhong Tai; Weimin Zhu; Tieliu Shi; Yi Wang; Jianming Xu; Bei Zhen; Jun Qin
Journal:  Nat Commun       Date:  2019-01-03       Impact factor: 14.919

10.  Phosphoproteomics Enables Molecular Subtyping and Nomination of Kinase Candidates for Individual Patients of Diffuse-Type Gastric Cancer.

Authors:  Mengsha Tong; Chunyu Yu; Jinwen Shi; Wenwen Huang; Sai Ge; Mingwei Liu; Lei Song; Dongdong Zhan; Xia Xia; Wanlin Liu; Jinwen Feng; Wenhao Shi; Jiafu Ji; Jing Gao; Tieliu Shi; Weimin Zhu; Chen Ding; Yi Wang; Fuchu He; Lin Shen; Tingting Li; Jun Qin
Journal:  iScience       Date:  2019-11-06
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