Literature DB >> 27898060

OmniPath: guidelines and gateway for literature-curated signaling pathway resources.

Dénes Türei1, Tamás Korcsmáros2,3, Julio Saez-Rodriguez1,4.   

Abstract

Mesh：

Year:  2016        PMID： 27898060     DOI： 10.1038/nmeth.4077

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


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  6 in total

1.  Protein-protein interaction and pathway databases, a graphical review.

Authors:  Tomas Klingström; Dariusz Plewczynski
Journal:  Brief Bioinform       Date:  2010-09-17       Impact factor: 11.622

2.  The ConsensusPathDB interaction database: 2013 update.

Authors:  Atanas Kamburov; Ulrich Stelzl; Hans Lehrach; Ralf Herwig
Journal:  Nucleic Acids Res       Date:  2012-11-11       Impact factor: 16.971

3.  Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.

Authors:  Daniel C Kirouac; Julio Saez-Rodriguez; Jennifer Swantek; John M Burke; Douglas A Lauffenburger; Peter K Sorger
Journal:  BMC Syst Biol       Date:  2012-05-01

4.  Pathway Commons, a web resource for biological pathway data.

Authors:  Ethan G Cerami; Benjamin E Gross; Emek Demir; Igor Rodchenkov; Ozgün Babur; Nadia Anwar; Nikolaus Schultz; Gary D Bader; Chris Sander
Journal:  Nucleic Acids Res       Date:  2010-11-10       Impact factor: 16.971

5.  Pathguide: a pathway resource list.

Authors:  Gary D Bader; Michael P Cary; Chris Sander
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

6.  Literature-curated protein interaction datasets.

Authors:  Michael E Cusick; Haiyuan Yu; Alex Smolyar; Kavitha Venkatesan; Anne-Ruxandra Carvunis; Nicolas Simonis; Jean-François Rual; Heather Borick; Pascal Braun; Matija Dreze; Jean Vandenhaute; Mary Galli; Junshi Yazaki; David E Hill; Joseph R Ecker; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2009-01       Impact factor: 28.547
  6 in total
  155 in total

Review 1.  The tissue proteome in the multi-omic landscape of kidney disease.

Authors:  Markus M Rinschen; Julio Saez-Rodriguez
Journal:  Nat Rev Nephrol       Date:  2020-10-07       Impact factor: 28.314

2.  Inhibition of 3-phosphoinositide-dependent protein kinase 1 (PDK1) can revert cellular senescence in human dermal fibroblasts.

Authors:  Sugyun An; Si-Young Cho; Junsoo Kang; Soobeom Lee; Hyung-Su Kim; Dae-Jin Min; EuiDong Son; Kwang-Hyun Cho
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-23       Impact factor: 11.205

3.  Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.

Authors:  Luz Garcia-Alonso; Francesco Iorio; Angela Matchan; Nuno Fonseca; Patricia Jaaks; Gareth Peat; Miguel Pignatelli; Fiammetta Falcone; Cyril H Benes; Ian Dunham; Graham Bignell; Simon S McDade; Mathew J Garnett; Julio Saez-Rodriguez
Journal:  Cancer Res       Date:  2017-12-11       Impact factor: 12.701

4.  Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.

Authors:  Anna Niarakis; Martin Kuiper; Marek Ostaszewski; Rahuman S Malik Sheriff; Cristina Casals-Casas; Denis Thieffry; Tom C Freeman; Paul Thomas; Vasundra Touré; Vincent Noël; Gautier Stoll; Julio Saez-Rodriguez; Aurélien Naldi; Eugenia Oshurko; Ioannis Xenarios; Sylvain Soliman; Claudine Chaouiya; Tomáš Helikar; Laurence Calzone
Journal:  Brief Bioinform       Date:  2021-03-22       Impact factor: 11.622

5.  Proteogenomic Characterization of Endometrial Carcinoma.

Authors:  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
Journal:  Cell       Date:  2020-02-13       Impact factor: 41.582

6.  CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.

Authors:  L Perfetto; M L Acencio; G Bradley; G Cesareni; N Del Toro; D Fazekas; H Hermjakob; T Korcsmaros; M Kuiper; A Lægreid; P Lo Surdo; R C Lovering; S Orchard; P Porras; P D Thomas; V Touré; J Zobolas; L Licata
Journal:  Bioinformatics       Date:  2019-10-01       Impact factor: 6.937

7.  Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models.

Authors:  Federica Eduati; Victoria Doldàn-Martelli; Bertram Klinger; Thomas Cokelaer; Anja Sieber; Fiona Kogera; Mathurin Dorel; Mathew J Garnett; Nils Blüthgen; Julio Saez-Rodriguez
Journal:  Cancer Res       Date:  2017-04-05       Impact factor: 12.701

8.  FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model.

Authors:  Sascha Jung; Kartikeya Singh; Antonio Del Sol
Journal:  Brief Bioinform       Date:  2021-07-20       Impact factor: 11.622

9.  Proteomics Versus Clinical Data and Stochastic Local Search Based Feature Selection for Acute Myeloid Leukemia Patients' Classification.

Authors:  Lokmane Chebouba; Dalila Boughaci; Carito Guziolowski
Journal:  J Med Syst       Date:  2018-06-04       Impact factor: 4.460

10.  SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update.

Authors:  Luana Licata; Prisca Lo Surdo; Marta Iannuccelli; Alessandro Palma; Elisa Micarelli; Livia Perfetto; Daniele Peluso; Alberto Calderone; Luisa Castagnoli; Gianni Cesareni
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971
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