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Page 1
A travel guide to Cytoscape plugins.
Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. Saito R, et al. Nat Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6. Nat Methods. 2012. PMID: 23132118 Free PMC article.
Cytoscape app store.
Lotia S, Montojo J, Dong Y, Bader GD, Pico AR. Lotia S, et al. Bioinformatics. 2013 May 15;29(10):1350-1. doi: 10.1093/bioinformatics/btt138. Epub 2013 Apr 16. Bioinformatics. 2013. PMID: 23595664 Free PMC article.
The Cytoscape app article collection.
Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T. Pico AR, et al. F1000Res. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. eCollection 2014. F1000Res. 2014. PMID: 25580224 Free PMC article.
The Cytoscape Automation app article collection.
Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. Demchak B, et al. Among authors: pico ar. F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018. F1000Res. 2018. PMID: 29983926 Free PMC article.
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Mo… See abstract for full author list ➔ Ostaszewski M, et al. Among authors: pico ar. Mol Syst Biol. 2021 Oct;17(10):e10387. doi: 10.15252/msb.202110387. Mol Syst Biol. 2021. PMID: 34664389 Free PMC article.
The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information.
Morris JH, Soman K, Akbas RE, Zhou X, Smith B, Meng EC, Huang CC, Cerono G, Schenk G, Rizk-Jackson A, Harroud A, Sanders L, Costes SV, Bharat K, Chakraborty A, Pico AR, Mardirossian T, Keiser M, Tang A, Hardi J, Shi Y, Musen M, Israni S, Huang S, Rose PW, Nelson CA, Baranzini SE. Morris JH, et al. Among authors: pico ar. Bioinformatics. 2023 Feb 3;39(2):btad080. doi: 10.1093/bioinformatics/btad080. Bioinformatics. 2023. PMID: 36759942 Free PMC article.
Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing.
Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Helmy M, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Mee M, Oubounyt M, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sarkar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang R, Zolotareva O, Baumbach J. Maier A, et al. Among authors: pico ar. ArXiv [Preprint]. 2023 Jul 4:arXiv:2305.15453v2. ArXiv. 2023. Update in: Nucleic Acids Res. 2024 Jul 5;52(W1):W481-W488. doi: 10.1093/nar/gkae388. PMID: 37332567 Free PMC article. Updated. Preprint.
270 results