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Items: 23

1.

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.

Rougny A, Touré V, Moodie S, Balaur I, Czauderna T, Borlinghaus H, Dogrusoz U, Mazein A, Dräger A, Blinov ML, Villéger A, Haw R, Demir E, Mi H, Sorokin A, Schreiber F, Luna A.

J Integr Bioinform. 2019 Jun 13;16(2). pii: /j/jib.2019.16.issue-2/jib-2019-0022/jib-2019-0022.xml. doi: 10.1515/jib-2019-0022.

PMID:
31199769
2.

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.

Mazein A, Ostaszewski M, Kuperstein I, Watterson S, Le Novère N, Lefaudeux D, De Meulder B, Pellet J, Balaur I, Saqi M, Nogueira MM, He F, Parton A, Lemonnier N, Gawron P, Gebel S, Hainaut P, Ollert M, Dogrusoz U, Barillot E, Zinovyev A, Schneider R, Balling R, Auffray C.

NPJ Syst Biol Appl. 2018 Jun 2;4:21. doi: 10.1038/s41540-018-0059-y. eCollection 2018.

3.

Efficient methods and readily customizable libraries for managing complexity of large networks.

Dogrusoz U, Karacelik A, Safarli I, Balci H, Dervishi L, Siper MC.

PLoS One. 2018 May 29;13(5):e0197238. doi: 10.1371/journal.pone.0197238. eCollection 2018.

4.

Community-driven roadmap for integrated disease maps.

Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming RMT, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R.

Brief Bioinform. 2019 Mar 25;20(2):659-670. doi: 10.1093/bib/bby024.

5.

Oncogenic Signaling Pathways in The Cancer Genome Atlas.

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M; Cancer Genome Atlas Research Network, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N.

Cell. 2018 Apr 5;173(2):321-337.e10. doi: 10.1016/j.cell.2018.03.035.

6.

PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data.

Bahceci I, Dogrusoz U, La KC, Babur Ö, Gao J, Schultz N.

Bioinformatics. 2017 Jul 15;33(14):2238-2240. doi: 10.1093/bioinformatics/btx149.

7.

An algorithm for automated layout of process description maps drawn in SBGN.

Genc B, Dogrusoz U.

Bioinformatics. 2016 Jan 1;32(1):77-84. doi: 10.1093/bioinformatics/btv516. Epub 2015 Sep 10.

8.

SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.

Sari M, Bahceci I, Dogrusoz U, Sumer SO, Aksoy BA, Babur Ö, Demir E.

PLoS One. 2015 Jun 1;10(6):e0128985. doi: 10.1371/journal.pone.0128985. eCollection 2015.

9.

Integrating biological pathways and genomic profiles with ChiBE 2.

Babur Ö, Dogrusoz U, Çakır M, Aksoy BA, Schultz N, Sander C, Demir E.

BMC Genomics. 2014 Aug 3;15:642. doi: 10.1186/1471-2164-15-642.

10.

CiSE: a circular spring embedder layout algorithm.

Dogrusoz U, Belviranli ME, Dilek A.

IEEE Trans Vis Comput Graph. 2013 Jun;19(6):953-66. doi: 10.1109/TVCG.2012.178.

PMID:
23559509
11.

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.

Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N.

Sci Signal. 2013 Apr 2;6(269):pl1. doi: 10.1126/scisignal.2004088.

12.

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.

Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N.

Cancer Discov. 2012 May;2(5):401-4. doi: 10.1158/2159-8290.CD-12-0095. Erratum in: Cancer Discov. 2012 Oct;2(10):960.

13.

Software support for SBGN maps: SBGN-ML and LibSBGN.

van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F.

Bioinformatics. 2012 Aug 1;28(15):2016-21. Epub 2012 May 10.

14.

The BioPAX community standard for pathway data sharing.

Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD.

Nat Biotechnol. 2010 Sep;28(9):935-42. doi: 10.1038/nbt.1666. Epub 2010 Sep 9. Erratum in: Nat Biotechnol. 2010 Dec;28(12):1308. Nat Biotechnol. 2012 Apr;30(4):365. Reubenacker, Oliver [corrected to Ruebenacker, Oliver].

15.

Discovering modulators of gene expression.

Babur O, Demir E, Gönen M, Sander C, Dogrusoz U.

Nucleic Acids Res. 2010 Sep;38(17):5648-56. doi: 10.1093/nar/gkq287. Epub 2010 May 13.

16.

VISIBIOweb: visualization and layout services for BioPAX pathway models.

Dilek A, Belviranli ME, Dogrusoz U.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W150-4. doi: 10.1093/nar/gkq352. Epub 2010 May 11.

17.

ChiBE: interactive visualization and manipulation of BioPAX pathway models.

Babur O, Dogrusoz U, Demir E, Sander C.

Bioinformatics. 2010 Feb 1;26(3):429-31. doi: 10.1093/bioinformatics/btp665. Epub 2009 Dec 9.

18.

Algorithms for effective querying of compound graph-based pathway databases.

Dogrusoz U, Cetintas A, Demir E, Babur O.

BMC Bioinformatics. 2009 Nov 16;10:376. doi: 10.1186/1471-2105-10-376.

19.

The Systems Biology Graphical Notation.

Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H.

Nat Biotechnol. 2009 Aug;27(8):735-41. doi: 10.1038/nbt.1558. Epub 2009 Aug 7. Erratum in: Nat Biotechnol. 2009 Sep;27(9):864.

PMID:
19668183
20.

PATIKAmad: putting microarray data into pathway context.

Babur O, Colak R, Demir E, Dogrusoz U.

Proteomics. 2008 Jun;8(11):2196-8. doi: 10.1002/pmic.200700769.

PMID:
18452226
21.

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

Dogrusoz U, Erson EZ, Giral E, Demir E, Babur O, Cetintas A, Colak R.

Bioinformatics. 2006 Feb 1;22(3):374-5. Epub 2005 Nov 15.

PMID:
16287939
22.

An ontology for collaborative construction and analysis of cellular pathways.

Demir E, Babur O, Dogrusoz U, Gursoy A, Ayaz A, Gulesir G, Nisanci G, Cetin-Atalay R.

Bioinformatics. 2004 Feb 12;20(3):349-56.

PMID:
14960461
23.

PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.

Demir E, Babur O, Dogrusoz U, Gursoy A, Nisanci G, Cetin-Atalay R, Ozturk M.

Bioinformatics. 2002 Jul;18(7):996-1003.

PMID:
12117798

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