Literature DB >> 34040252

PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis.

D R Mani1, Myranda Maynard2, Ramani Kothadia2, Karsten Krug2, Karen E Christianson2, David Heiman3, Karl R Clauser2, Chet Birger3, Gad Getz3,4,5, Steven A Carr2.   

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Year:  2021        PMID: 34040252      PMCID: PMC8791030          DOI: 10.1038/s41592-021-01176-6

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


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  10 in total

1.  A Curated Resource for Phosphosite-specific Signature Analysis.

Authors:  Karsten Krug; Philipp Mertins; Bin Zhang; Peter Hornbeck; Rajesh Raju; Rushdy Ahmad; Matthew Szucs; Filip Mundt; Dominique Forestier; Judit Jane-Valbuena; Hasmik Keshishian; Michael A Gillette; Pablo Tamayo; Jill P Mesirov; Jacob D Jaffe; Steven A Carr; D R Mani
Journal:  Mol Cell Proteomics       Date:  2018-12-18       Impact factor: 5.911

2.  Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma.

Authors:  Michael A Gillette; Shankha Satpathy; Song Cao; Saravana M Dhanasekaran; Suhas V Vasaikar; Karsten Krug; Francesca Petralia; Yize Li; Wen-Wei Liang; Boris Reva; Azra Krek; Jiayi Ji; Xiaoyu Song; Wenke Liu; Runyu Hong; Lijun Yao; Lili Blumenberg; Sara R Savage; Michael C Wendl; Bo Wen; Kai Li; Lauren C Tang; Melanie A MacMullan; Shayan C Avanessian; M Harry Kane; Chelsea J Newton; MacIntosh Cornwell; Ramani B Kothadia; Weiping Ma; Seungyeul Yoo; Rahul Mannan; Pankaj Vats; Chandan Kumar-Sinha; Emily A Kawaler; Tatiana Omelchenko; Antonio Colaprico; Yifat Geffen; Yosef E Maruvka; Felipe da Veiga Leprevost; Maciej Wiznerowicz; Zeynep H Gümüş; Rajwanth R Veluswamy; Galen Hostetter; David I Heiman; Matthew A Wyczalkowski; Tara Hiltke; Mehdi Mesri; Christopher R Kinsinger; Emily S Boja; Gilbert S Omenn; Arul M Chinnaiyan; Henry Rodriguez; Qing Kay Li; Scott D Jewell; Mathangi Thiagarajan; Gad Getz; Bing Zhang; David Fenyö; Kelly V Ruggles; Marcin P Cieslik; Ana I Robles; Karl R Clauser; Ramaswamy Govindan; Pei Wang; Alexey I Nesvizhskii; Li Ding; D R Mani; Steven A Carr
Journal:  Cell       Date:  2020-07-09       Impact factor: 41.582

3.  Proteogenomic characterization of human colon and rectal cancer.

Authors:  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
Journal:  Nature       Date:  2014-07-20       Impact factor: 49.962

4.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

5.  Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.

Authors:  Karsten Krug; Eric J Jaehnig; Shankha Satpathy; Lili Blumenberg; Alla Karpova; Meenakshi Anurag; George Miles; Philipp Mertins; Yifat Geffen; Lauren C Tang; David I Heiman; Song Cao; Yosef E Maruvka; Jonathan T Lei; Chen Huang; Ramani B Kothadia; Antonio Colaprico; Chet Birger; Jarey Wang; Yongchao Dou; Bo Wen; Zhiao Shi; Yuxing Liao; Maciej Wiznerowicz; Matthew A Wyczalkowski; Xi Steven Chen; Jacob J Kennedy; Amanda G Paulovich; Mathangi Thiagarajan; Christopher R Kinsinger; Tara Hiltke; Emily S Boja; Mehdi Mesri; Ana I Robles; Henry Rodriguez; Thomas F Westbrook; Li Ding; Gad Getz; Karl R Clauser; David Fenyö; Kelly V Ruggles; Bing Zhang; D R Mani; Steven A Carr; Matthew J Ellis; Michael A Gillette
Journal:  Cell       Date:  2020-11-18       Impact factor: 41.582

6.  A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

Authors:  Aravind Subramanian; Rajiv Narayan; Steven M Corsello; David D Peck; Ted E Natoli; Xiaodong Lu; Joshua Gould; John F Davis; Andrew A Tubelli; Jacob K Asiedu; David L Lahr; Jodi E Hirschman; Zihan Liu; Melanie Donahue; Bina Julian; Mariya Khan; David Wadden; Ian C Smith; Daniel Lam; Arthur Liberzon; Courtney Toder; Mukta Bagul; Marek Orzechowski; Oana M Enache; Federica Piccioni; Sarah A Johnson; Nicholas J Lyons; Alice H Berger; Alykhan F Shamji; Angela N Brooks; Anita Vrcic; Corey Flynn; Jacqueline Rosains; David Y Takeda; Roger Hu; Desiree Davison; Justin Lamb; Kristin Ardlie; Larson Hogstrom; Peyton Greenside; Nathanael S Gray; Paul A Clemons; Serena Silver; Xiaoyun Wu; Wen-Ning Zhao; Willis Read-Button; Xiaohua Wu; Stephen J Haggarty; Lucienne V Ronco; Jesse S Boehm; Stuart L Schreiber; John G Doench; Joshua A Bittker; David E Root; Bang Wong; Todd R Golub
Journal:  Cell       Date:  2017-11-30       Impact factor: 41.582

7.  Inferring tumour purity and stromal and immune cell admixture from expression data.

Authors:  Kosuke Yoshihara; Maria Shahmoradgoli; Emmanuel Martínez; Rahulsimham Vegesna; Hoon Kim; Wandaliz Torres-Garcia; Victor Treviño; Hui Shen; Peter W Laird; Douglas A Levine; Scott L Carter; Gad Getz; Katherine Stemke-Hale; Gordon B Mills; Roel G W Verhaak
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

8.  xCell: digitally portraying the tissue cellular heterogeneity landscape.

Authors:  Dvir Aran; Zicheng Hu; Atul J Butte
Journal:  Genome Biol       Date:  2017-11-15       Impact factor: 13.583

9.  BlackSheep: A Bioconductor and Bioconda Package for Differential Extreme Value Analysis.

Authors:  Lili Blumenberg; Emily A Kawaler; MacIntosh Cornwell; Shaleigh Smith; Kelly V Ruggles; David Fenyö
Journal:  J Proteome Res       Date:  2021-06-24       Impact factor: 5.370

10.  Proteogenomics connects somatic mutations to signalling in breast cancer.

Authors:  Philipp Mertins; D R Mani; Kelly V Ruggles; Michael A Gillette; Karl R Clauser; Pei Wang; Xianlong Wang; Jana W Qiao; Song Cao; Francesca Petralia; Emily Kawaler; Filip Mundt; Karsten Krug; Zhidong Tu; Jonathan T Lei; Michael L Gatza; Matthew Wilkerson; Charles M Perou; Venkata Yellapantula; Kuan-lin Huang; Chenwei Lin; Michael D McLellan; Ping Yan; Sherri R Davies; R Reid Townsend; Steven J Skates; Jing Wang; Bing Zhang; Christopher R Kinsinger; Mehdi Mesri; Henry Rodriguez; Li Ding; Amanda G Paulovich; David Fenyö; Matthew J Ellis; Steven A Carr
Journal:  Nature       Date:  2016-05-25       Impact factor: 49.962

  10 in total
  3 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.  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

3.  A proteogenomic portrait of lung squamous cell carcinoma.

Authors:  Shankha Satpathy; Karsten Krug; Pierre M Jean Beltran; Sara R Savage; Francesca Petralia; Chandan Kumar-Sinha; Yongchao Dou; Boris Reva; M Harry Kane; Shayan C Avanessian; Suhas V Vasaikar; Azra Krek; Jonathan T Lei; Eric J Jaehnig; Tatiana Omelchenko; Yifat Geffen; Erik J Bergstrom; Vasileios Stathias; Karen E Christianson; David I Heiman; Marcin P Cieslik; Song Cao; Xiaoyu Song; Jiayi Ji; Wenke Liu; Kai Li; Bo Wen; Yize Li; Zeynep H Gümüş; Myvizhi Esai Selvan; Rama Soundararajan; Tanvi H Visal; Maria G Raso; Edwin Roger Parra; Özgün Babur; Pankaj Vats; Shankara Anand; Tobias Schraink; MacIntosh Cornwell; Fernanda Martins Rodrigues; Houxiang Zhu; Chia-Kuei Mo; Yuping Zhang; Felipe da Veiga Leprevost; Chen Huang; Arul M Chinnaiyan; Matthew A Wyczalkowski; Gilbert S Omenn; Chelsea J Newton; Stephan Schurer; Kelly V Ruggles; David Fenyö; Scott D Jewell; Mathangi Thiagarajan; Mehdi Mesri; Henry Rodriguez; Sendurai A Mani; Namrata D Udeshi; Gad Getz; James Suh; Qing Kay Li; Galen Hostetter; Paul K Paik; Saravana M Dhanasekaran; Ramaswamy Govindan; Li Ding; Ana I Robles; Karl R Clauser; Alexey I Nesvizhskii; Pei Wang; Steven A Carr; Bing Zhang; D R Mani; Michael A Gillette
Journal:  Cell       Date:  2021-08-05       Impact factor: 66.850

  3 in total

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