230_cyto_automation.bib

@article{cyrest,
  title={CyREST: turbocharging cytoscape access for external tools via a RESTful API},
  author={Ono, Keiichiro and Muetze, Tanja and Kolishovski, Georgi and Shannon, Paul and Demchak, Barry},
  journal={F1000Research},
  volume={4},
  year={2015},
  publisher={Faculty of 1000 Ltd}
}

@article{cytoscape,
  title={Cytoscape: a software environment for integrated models of biomolecular interaction networks},
  author={Shannon, Paul and Markiel, Andrew and Ozier, Owen and Baliga, Nitin S and Wang, Jonathan T and Ramage, Daniel and Amin, Nada and Schwikowski, Benno and Ideker, Trey},
  journal={Genome research},
  volume={13},
  number={11},
  pages={2498--2504},
  year={2003},
  publisher={Cold Spring Harbor Lab}
}

@article{edgeR,
   author = {Robinson, M. D. and McCarthy, D. J. and Smyth, G. K.},
   title = {edgeR: a Bioconductor package for differential expression analysis of digital gene expression data},
   journal = {Bioinformatics},
   volume = {26},
   number = {1},
   pages = {139-40},
   ISSN = {1367-4811 (Electronic)
1367-4803 (Linking)},
   DOI = {10.1093/bioinformatics/btp616},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19910308},
   year = {2010},
   type = {Journal Article}
}

@article{GDC,
   author = {Grossman, R. L. and Heath, A. P. and Ferretti, V. and Varmus, H. E. and Lowy, D. R. and Kibbe, W. A. and Staudt, L. M.},
   title = {Toward a Shared Vision for Cancer Genomic Data},
   journal = {N Engl J Med},
   volume = {375},
   number = {12},
   pages = {1109-12},
   ISSN = {1533-4406 (Electronic)
0028-4793 (Linking)},
   DOI = {10.1056/NEJMp1607591},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/27653561},
   year = {2016},
   type = {Journal Article}
}

@article{MapSplice,
   author = {Wang, K. and Singh, D. and Zeng, Z. and Coleman, S. J. and Huang, Y. and Savich, G. L. and He, X. and Mieczkowski, P. and Grimm, S. A. and Perou, C. M. and MacLeod, J. N. and Chiang, D. Y. and Prins, J. F. and Liu, J.},
   title = {MapSplice: accurate mapping of RNA-seq reads for splice junction discovery},
   journal = {Nucleic Acids Res},
   volume = {38},
   number = {18},
   pages = {e178},
   ISSN = {1362-4962 (Electronic)
0305-1048 (Linking)},
   DOI = {10.1093/nar/gkq622},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20802226},
   year = {2010},
   type = {Journal Article}
}

@article{OV,
   author = {Verhaak, R. G. and Tamayo, P. and Yang, J. Y. and Hubbard, D. and Zhang, H. and Creighton, C. J. and Fereday, S. and Lawrence, M. and Carter, S. L. and Mermel, C. H. and Kostic, A. D. and Etemadmoghadam, D. and Saksena, G. and Cibulskis, K. and Duraisamy, S. and Levanon, K. and Sougnez, C. and Tsherniak, A. and Gomez, S. and Onofrio, R. and Gabriel, S. and Chin, L. and Zhang, N. and Spellman, P. T. and Zhang, Y. and Akbani, R. and Hoadley, K. A. and Kahn, A. and Kobel, M. and Huntsman, D. and Soslow, R. A. and Defazio, A. and Birrer, M. J. and Gray, J. W. and Weinstein, J. N. and Bowtell, D. D. and Drapkin, R. and Mesirov, J. P. and Getz, G. and Levine, D. A. and Meyerson, M. and Cancer Genome Atlas Research, Network},
   title = {Prognostically relevant gene signatures of high-grade serous ovarian carcinoma},
   journal = {J Clin Invest},
   volume = {123},
   number = {1},
   pages = {517-25},
   ISSN = {1558-8238 (Electronic)
0021-9738 (Linking)},
   DOI = {10.1172/JCI65833},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23257362},
   year = {2013},
   type = {Journal Article}
}

@article{RSEM,
   author = {Li, B. and Dewey, C. N.},
   title = {RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome},
   journal = {BMC Bioinformatics},
   volume = {12},
   pages = {323},
   ISSN = {1471-2105 (Electronic)
1471-2105 (Linking)},
   DOI = {10.1186/1471-2105-12-323},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21816040},
   year = {2011},
   type = {Journal Article}
}

@article{TCGA,
   author = {International Cancer Genome, Consortium and Hudson, T. J. and Anderson, W. and Artez, A. and Barker, A. D. and Bell, C. and Bernabe, R. R. and Bhan, M. K. and Calvo, F. and Eerola, I. and Gerhard, D. S. and Guttmacher, A. and Guyer, M. and Hemsley, F. M. and Jennings, J. L. and Kerr, D. and Klatt, P. and Kolar, P. and Kusada, J. and Lane, D. P. and Laplace, F. and Youyong, L. and Nettekoven, G. and Ozenberger, B. and Peterson, J. and Rao, T. S. and Remacle, J. and Schafer, A. J. and Shibata, T. and Stratton, M. R. and Vockley, J. G. and Watanabe, K. and Yang, H. and Yuen, M. M. and Knoppers, B. M. and Bobrow, M. and Cambon-Thomsen, A. and Dressler, L. G. and Dyke, S. O. and Joly, Y. and Kato, K. and Kennedy, K. L. and Nicolas, P. and Parker, M. J. and Rial-Sebbag, E. and Romeo-Casabona, C. M. and Shaw, K. M. and Wallace, S. and Wiesner, G. L. and Zeps, N. and Lichter, P. and Biankin, A. V. and Chabannon, C. and Chin, L. and Clement, B. and de Alava, E. and Degos, F. and Ferguson, M. L. and Geary, P. and Hayes, D. N. and Hudson, T. J. and Johns, A. L. and Kasprzyk, A. and Nakagawa, H. and Penny, R. and Piris, M. A. and Sarin, R. and Scarpa, A. and Shibata, T. and van de Vijver, M. and Futreal, P. A. and Aburatani, H. and Bayes, M. and Botwell, D. D. and Campbell, P. J. and Estivill, X. and Gerhard, D. S. and Grimmond, S. M. and Gut, I. and Hirst, M. and Lopez-Otin, C. and Majumder, P. and Marra, M. and McPherson, J. D. and Nakagawa, H. and Ning, Z. and Puente, X. S. and Ruan, Y. and Shibata, T. and Stratton, M. R. and Stunnenberg, H. G. and Swerdlow, H. and Velculescu, V. E. and Wilson, R. K. and Xue, H. H. and Yang, L. and Spellman, P. T. and Bader, G. D. and Boutros, P. C. and Campbell, P. J. and others },
   title = {International network of cancer genome projects},
   journal = {Nature},
   volume = {464},
   number = {7291},
   pages = {993-8},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Linking)},
   DOI = {10.1038/nature08987},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20393554},
   year = {2010},
   type = {Journal Article}
}

@article{TCGABiolinks,
   author = {Colaprico, A. and Silva, T. C. and Olsen, C. and Garofano, L. and Cava, C. and Garolini, D. and Sabedot, T. S. and Malta, T. M. and Pagnotta, S. M. and Castiglioni, I. and Ceccarelli, M. and Bontempi, G. and Noushmehr, H.},
   title = {TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data},
   journal = {Nucleic Acids Res},
   volume = {44},
   number = {8},
   pages = {e71},
   ISSN = {1362-4962 (Electronic)
0305-1048 (Linking)},
   DOI = {10.1093/nar/gkv1507},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/26704973},
   year = {2016},
   type = {Journal Article}
}

@article{string,
  title={The STRING database in 2017: quality-controlled protein--protein association networks, made broadly accessible},
  author={Szklarczyk, Damian and Morris, John H and Cook, Helen and Kuhn, Michael and Wyder, Stefan and Simonovic, Milan and Santos, Alberto and Doncheva, Nadezhda T and Roth, Alexander and Bork, Peer and others},
  journal={Nucleic acids research},
  pages={gkw937},
  year={2016},
  publisher={Oxford University Press}
}

@article{psicquic,
  title={PSICQUIC and PSISCORE: accessing and scoring molecular interactions},
  author={Aranda, Bruno and Blankenburg, Hagen and Kerrien, Samuel and Brinkman, Fiona SL and Ceol, Arnaud and Chautard, Emilie and Dana, Jose M and De Las Rivas, Javier and Dumousseau, Marine and Galeota, Eugenia and others},
  journal={Nature methods},
  volume={8},
  number={7},
  pages={528},
  year={2011},
  publisher={Nature Publishing Group}
}

@article{ndex,
  title={NDEx 2.0: A Clearinghouse for Research on Cancer Pathways},
  author={Pratt, Dexter and Chen, Jing and Pillich, Rudolf and Rynkov, Vladimir and Gary, Aaron and Demchak, Barry and Ideker, Trey},
  journal={Cancer research},
  volume={77},
  number={21},
  pages={e58--e61},
  year={2017},
  publisher={AACR}
}

@article{genemania,
  title={GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function},
  author={Mostafavi, Sara and Ray, Debajyoti and Warde-Farley, David and Grouios, Chris and Morris, Quaid},
  journal={Genome biology},
  volume={9},
  number={1},
  pages={S4},
  year={2008},
  publisher={BioMed Central}
}

@article{wgcna,
  title={WGCNA: an R package for weighted correlation network analysis},
  author={Langfelder, Peter and Horvath, Steve},
  journal={BMC bioinformatics},
  volume={9},
  number={1},
  pages={559},
  year={2008},
  publisher={BioMed Central}
}

@article{amatreader,
  title={aMatReader: Importing adjacency matrices via Cytoscape Automation},
  author={Settle, Brett and Otasek, David and Morris, John H and Demchak, Barry},
  journal={F1000Research},
  volume={7},
  year={2018}
}

@article{gprofiler,
  title={g: Profiler—a web server for functional interpretation of gene lists (2016 update)},
  author={Reimand, J{\"u}ri and Arak, Tambet and Adler, Priit and Kolberg, Liis and Reisberg, Sulev and Peterson, Hedi and Vilo, Jaak},
  journal={Nucleic acids research},
  volume={44},
  number={W1},
  pages={W83--W89},
  year={2016},
  publisher={Oxford University Press}
}

@article{biopax,
  title={The BioPAX community standard for pathway data sharing},
  author={Demir, Emek and Cary, Michael P and Paley, Suzanne and Fukuda, Ken and Lemer, Christian and Vastrik, Imre and Wu, Guanming and D'eustachio, Peter and Schaefer, Carl and Luciano, Joanne and others},
  journal={Nature biotechnology},
  volume={28},
  number={9},
  pages={935},
  year={2010},
  publisher={Nature Publishing Group}
}

@article{paxtoolsr,
  title={PaxtoolsR: pathway analysis in R using Pathway Commons},
  author={Luna, Augustin and Babur, {\"O}zg{\"u}n and Aksoy, B{\"u}lent Arman and Demir, Emek and Sander, Chris},
  journal={Bioinformatics},
  volume={32},
  number={8},
  pages={1262--1264},
  year={2015},
  publisher={Oxford University Press}
}

@article{enrichmentmap,
  title={Enrichment map: a network-based method for gene-set enrichment visualization and interpretation},
  author={Merico, Daniele and Isserlin, Ruth and Stueker, Oliver and Emili, Andrew and Bader, Gary D},
  journal={PloS one},
  volume={5},
  number={11},
  pages={e13984},
  year={2010},
  publisher={Public Library of Science}
}

@article{autoannotate,
  title={AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations},
  author={Kucera, Mike and Isserlin, Ruth and Arkhangorodsky, Arkady and Bader, Gary D},
  journal={F1000Research},
  volume={5},
  year={2016},
  publisher={Faculty of 1000 Ltd}
}

@article{wordcloud,
  title={WordCloud: a Cytoscape plugin to create a visual semantic summary of networks},
  author={Oesper, Layla and Merico, Daniele and Isserlin, Ruth and Bader, Gary D},
  journal={Source code for biology and medicine},
  volume={6},
  number={1},
  pages={7},
  year={2011},
  publisher={BioMed Central}
}

@article{clustermaker,
  title={clusterMaker: a multi-algorithm clustering plugin for Cytoscape},
  author={Morris, John H and Apeltsin, Leonard and Newman, Aaron M and Baumbach, Jan and Wittkop, Tobias and Su, Gang and Bader, Gary D and Ferrin, Thomas E},
  journal={BMC bioinformatics},
  volume={12},
  number={1},
  pages={436},
  year={2011},
  publisher={BioMed Central}
}