Wang E: Cancer systems biology. Chapman & Hall/CRC mathematical and computational biology series. 2010, Boca Raton: CRC Press, 191-212.
Google Scholar
Li H, Lee Y, Chen JL, Rebman E, Li J, Lussier YA: Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. J Am Med Inform Assoc. 2012, 19: 295-305. 10.1136/amiajnl-2011-000482.
Article
PubMed
PubMed Central
Google Scholar
Suthram S, Dudley JT, Chiang AP, Chen R, Hastie TJ, Butte AJ: Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Comput Biol. 2010, 6: e1000662-10.1371/journal.pcbi.1000662.
Article
PubMed
PubMed Central
Google Scholar
Schriml LM, Arze C, Nadendla S, Chang YW, Mazaitis M, Felix V, Feng G, Kibbe WA: Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res. 2012, 40: D940-946. 10.1093/nar/gkr972.
Article
CAS
PubMed
Google Scholar
Osborne JD, Lin S, Kibbe WA, Zhu L, Danila MI, Chisholm RL: GeneRIF is a more comprehensive, current and computationally tractable source of gene-disease relationships than OMIM. Bioinformatics Core, Northwestern University Technical Report. 2007
Google Scholar
Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL: Annotating the human genome with Disease Ontology. BMC Genomics. 2009, 10 (Suppl 1): S6-10.1186/1471-2164-10-S1-S6.
Article
PubMed
PubMed Central
Google Scholar
Ideker T, Sharan R: Protein networks in disease. Genome Res. 2008, 18: 644-652. 10.1101/gr.071852.107.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL: The human disease network. Proc Natl Acad Sci USA. 2007, 104: 8685-8690. 10.1073/pnas.0701361104.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang M, Zhu C, Jacomy A, Lu LJ, Jegga AG: The orphan disease networks. Am J Hum Genet. 2011, 88: 755-766. 10.1016/j.ajhg.2011.05.006.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cortes C, Vapnik VN: Support-vector Networks. Machine Learning. 1995, 20:
Google Scholar
Dietterich TG, Lathrop RH, Lozano-Pérez T: Solving the multiple instance problem with axis-parallel rectangles. Artif Intell. 1997, 89: 31-71. 10.1016/S0004-3702(96)00034-3.
Article
Google Scholar
Liu B: Web data mining : exploring hyperlinks, contents, and usage data. 2007, Berlin ; New York: Springer
Google Scholar
Bickel PJ, Doksum KA: Mathematical statistics : basic ideas and selected topics. 2001, Upper Saddle River, N.J.: Prentice Hall, 2
Google Scholar
Quinlan JR: C4.5: Programs for Machine Learning. 1993, San Francisco, CA, USA: Morgan Kaufmann Publishers
Google Scholar
Breiman L: Bagging predictors. Machine Learning. 1996, 24: 123-140.
Google Scholar
Zadrozny B, John Langford, Naoki A: Cost-Sensitive Learning by Cost-Proportionate Example Weighting. Third IEEE International Conference on Data Mining. 2003, IEEE Computer Society, 435-
Chapter
Google Scholar
Carson MB, Langlois R, Lu H: NAPS: a residue-level nucleic acid-binding prediction server. Nucleic Acids Res. 2010, 38: W431-435. 10.1093/nar/gkq361.
Article
CAS
PubMed
PubMed Central
Google Scholar
Freund Y, Mason L: The Alternating Decision Tree Learning Algorithm. Proceedings of the Sixteenth International Conference on Machine Learning. 1999, San Francisco, CA: Morgan Kaufmann Publishers Inc., 124-133.
Google Scholar
Carson MB, Langlois R, Hui L: Mining knowledge for the methylation status of CpG islands using alternating decision trees. Engineering in Medicine and Biology Society, 2008 EMBS 2008 30th Annual International Conference of the IEEE; 20-25 Aug 2008. 2008, 3787-3790.
Google Scholar
Langlois RE, Lu H: Boosting the prediction and understanding of DNA-binding domains from sequence. Nucleic Acids Research. 2010, 38: 3149-3158. 10.1093/nar/gkq061.
Article
CAS
PubMed
PubMed Central
Google Scholar
Källberg M, Bhardwaj N, Langlois R, Lu H: A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains. Bioinformatics. 2012, 28: i431-i437. 10.1093/bioinformatics/bts409.
Article
PubMed
PubMed Central
Google Scholar
Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005, 33: D514-517.
Article
CAS
PubMed
Google Scholar
Özgür A, Vu T, Erkan G, Radev DR: Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics. 2008, 24: i277-i285. 10.1093/bioinformatics/btn182.
Article
PubMed
PubMed Central
Google Scholar
Radivojac P, Peng K, Clark WT, Peters BJ, Mohan A, Boyle SM, Mooney SD: An integrated approach to inferring gene-disease associations in humans. Proteins. 2008, 72: 1030-1037. 10.1002/prot.21989.
Article
CAS
PubMed
PubMed Central
Google Scholar
Furney SJ, Calvo B, Larranaga P, Lozano JA, Lopez-Bigas N: Prioritization of candidate cancer genes--an aid to oncogenomic studies. Nucleic Acids Res. 2008, 36: e115-10.1093/nar/gkn482.
Article
PubMed
PubMed Central
Google Scholar
Gonzalez G, Uribe JC, Tari L, Brophy C, Baral C: Mining gene-disease relationships from biomedical literature: weighting protein-protein interactions and connectivity measures. Pacific Symposium of Biocomputing (PSB). 2007, Maui, Hawaii, 28-39.
Google Scholar
Xu J, Li Y: Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics. 2006, 22: 2800-2805. 10.1093/bioinformatics/btl467.
Article
CAS
PubMed
Google Scholar
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al: Human Protein Reference Database--2009 update. Nucleic Acids Res. 2009, 37: D767-772. 10.1093/nar/gkn892.
Article
CAS
PubMed
Google Scholar
Wu X, Jiang R, Zhang MQ, Li S: Network-based global inference of human disease genes. Molecular systems biology. 2008, 4:
Google Scholar
Köhler S, Bauer S, Horn D, Robinson PN: Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet. 2008, 82: 949-958. 10.1016/j.ajhg.2008.02.013.
Article
PubMed
PubMed Central
Google Scholar
Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R: Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol. 2010, 6: e1000641-10.1371/journal.pcbi.1000641.
Article
PubMed
PubMed Central
Google Scholar
Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM: From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics. 2009, 25: i63-68. 10.1093/bioinformatics/btp193.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011, 27: 431-432. 10.1093/bioinformatics/btq675.
Article
CAS
PubMed
Google Scholar
Shimbel A: Structural parameters of communication networks. Bulletin of Mathematical Biology. 1953, 15: 501-507.
Google Scholar
Katz L: A New Status Index Derived from Sociometric Index. Psychometrika. 1953, 39-43.
Google Scholar
Brin S, Page L: The anatomy of a large-scale hypertextual Web search engine. Book The anatomy of a large-scale hypertextual Web search engine. 1998, 107-117. City
Google Scholar
Bonacich P, Lloyd P: Eigenvector-like measures of centrality for asymmetric relations. Social Networks. 2001, 23: 191-201. 10.1016/S0378-8733(01)00038-7.
Article
Google Scholar
Bonacich P: Power and Centrality: A Family of Measures. American Journal of Sociology (University of Chicago Press). 1987, 92: 1170-1182.
Google Scholar
Wang P, Yu X, Lu J: Identification and evolution of structurally dominant nodes in protein-protein interaction networks. IEEE transactions on biomedical circuits and systems. 2014, 8: 87-97.
Article
CAS
PubMed
Google Scholar
Hall M, Ian H: The WEKA Data Mining Software: An Update. SIGKDD Explorations. 2009, 11:
Google Scholar
Buntine W: Learning classification trees. Statistics and Computing. 1992, 2: 63-73. 10.1007/BF01889584.
Article
Google Scholar
Langlois RE, Lu H: Intelligible machine learning with malibu. Conf Proc IEEE Eng Med Biol Soc. 2008, 2008: 3795-3798.
PubMed
Google Scholar
Hao D, Li C: The dichotomy in degree correlation of biological networks. PLoS One. 2011, 6: e28322-10.1371/journal.pone.0028322.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Q, Wang FY, Zeng D, Wang T: Understanding crowd-powered search groups: a social network perspective. PLoS One. 2012, 7: e39749-10.1371/journal.pone.0039749.
Article
CAS
PubMed
PubMed Central
Google Scholar
Newman MEJ: Networks: An Introduction. 2010, New York, NY, USA: Oxford University Press, Inc
Book
Google Scholar
Freund Y, Schapire R: Experiments with a new boosting algorithm. Proceedings of the 13th Annual International Conference on Machine Learning. 1996, Bari, Italy, 148-156.
Google Scholar
Broomhead DS, Lowe D: Multivariable functional interpolation and adaptive networks. Complex Systems. 1988, 2: 321-355.
Google Scholar
Rappaport N, Nativ N, Stelzer G, Twik M, Guan-Golan Y, Stein TI, Bahir I, Belinky F, Morrey CP, Safran M, Lancet D: MalaCards: an integrated compendium for diseases and their annotation. Database : the journal of biological databases and curation. 2013, 2013: bat018-
Article
PubMed
Google Scholar
Stelzer G, Dalah I, Stein TI, Satanower Y, Rosen N, Nativ N, Oz-Levi D, Olender T, Belinky F, Bahir I, et al: In-silico human genomics with GeneCards. Human genomics. 2011, 5: 709-717. 10.1186/1479-7364-5-6-709.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yoon JW, Jun HS: Autoimmune destruction of pancreatic beta cells. American journal of therapeutics. 2005, 12: 580-591. 10.1097/01.mjt.0000178767.67857.63.
Article
PubMed
Google Scholar
Amiel J, Rio M, de Pontual L, Redon R, Malan V, Boddaert N, Plouin P, Carter NP, Lyonnet S, Munnich A, Colleaux L: Mutations in TCF4, encoding a class I basic helix-loop-helix transcription factor, are responsible for Pitt-Hopkins syndrome, a severe epileptic encephalopathy associated with autonomic dysfunction. Am J Hum Genet. 2007, 80: 988-993. 10.1086/515582.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bastian M. HS, Jacomy M: Gephi: an open source software for exploring and manipulating networks. International AAAI Conference on Weblogs and Social Media. 2009
Google Scholar
Blondel VD, Guillaume , Jean-Loup , Lambiotte , Renaud , Lefebvre , Etienne : Fast unfolding of communities in large networks. Journal of Statistical Mechanics: Theory and Experiment. 2008, 10: 1000-
Google Scholar
Amir A, Barua M, McKnight NC, Cheng S, Yuan X, Balk SP: A direct beta-catenin-independent interaction between androgen receptor and T cell factor 4. J Biol Chem. 2003, 278: 30828-30834. 10.1074/jbc.M301208200.
Article
CAS
PubMed
Google Scholar
Cochrane DR, Bernales S, Jacobsen BM, Cittelly DM, Howe EN, NC DA, Spoelstra NS, Edgerton SM, Jean A, Guerrero J, et al: Role of the Androgen Receptor in Breast Cancer and Preclinical Analysis of Enzalutamide. Breast cancer research : BCR. 2014, 16: R7-10.1186/bcr3599.
Article
PubMed
PubMed Central
Google Scholar
Garay J, Park BH: Androgen receptor as a targeted therapy for breast cancer. Am J Cancer Res. 2012, 2: 434-445.
CAS
PubMed
PubMed Central
Google Scholar
Ravindranath A, Yuen HF, Chan KK, Grills C, Fennell DA, Lappin TR, El-Tanani M: Wnt-beta-catenin-Tcf-4 signalling-modulated invasiveness is dependent on osteopontin expression in breast cancer. British journal of cancer. 2011, 105: 542-551. 10.1038/bjc.2011.269.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang F, Herrington M, Larsson J, Permert J: The relationship between diabetes and pancreatic cancer. Mol Cancer. 2003, 2: 4-10.1186/1476-4598-2-4.
Article
PubMed
PubMed Central
Google Scholar
Anand P, Kunnumakkara AB, Sundaram C, Harikumar KB, Tharakan ST, Lai OS, Sung B, Aggarwal BB: Cancer is a preventable disease that requires major lifestyle changes. Pharm Res. 2008, 25: 2097-2116. 10.1007/s11095-008-9661-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kushi LH, Byers T, Doyle C, Bandera EV, McCullough M, McTiernan A, Gansler T, Andrews KS, Thun MJ: American Cancer Society Guidelines on Nutrition and Physical Activity for cancer prevention: reducing the risk of cancer with healthy food choices and physical activity. CA Cancer J Clin. 2006, 56: 254-281. 10.3322/canjclin.56.5.254. quiz 313-254
Article
PubMed
Google Scholar
Taubes G: Cancer research. Unraveling the obesity-cancer connection. Science. 2012, 335 (28): 30-22.
Google Scholar