References analysis of the Wikipedia article "Cancer systems biology" in the English version

doi.org

Werner, HM; Mills, GB; Ram, PT (March 2014). "Cancer Systems Biology: a peek into the future of patient care?". Nature Reviews. Clinical Oncology. 11 (3): 167–76. doi:10.1038/nrclinonc.2014.6. PMC 4321721. PMID 24492837.

Gentles, AJ; Gallahan, D (15 September 2011). "Systems biology: confronting the complexity of cancer". Cancer Research. 71 (18): 5961–4. doi:10.1158/0008-5472.CAN-11-1569. PMC 3174325. PMID 21896642.

Anderson, AR; Quaranta (2008). "Integrative mathematical oncology". Nat Rev Cancer. 8 (3): 227–234. doi:10.1038/nrc2329. PMID 18273038. S2CID 23792776.

Kreeger, PK; Lauffenburger (2010). "Cancer systems biology: A network modeling perspective". Carcinogenesis. 31 (1): 2–8. doi:10.1093/carcin/bgp261. PMC 2802670. PMID 19861649.

Huang, YW; Kuo, Stoner; Huang, Wang (2011). "An overview of epigenetics and chemoprevention". FEBS Lett. 585 (13): 2129–2136. Bibcode:2011FEBSL.585.2129H. doi:10.1016/j.febslet.2010.11.002. PMC 3071863. PMID 21056563.

Spill, Fabian; Bakal, Chris; Mak, Michael (2018). "Mechanical and Systems Biology of Cancer". Computational and Structural Biotechnology Journal. 16: 237–245. arXiv:1807.08990. Bibcode:2018arXiv180708990S. doi:10.1016/j.csbj.2018.07.002. PMC 6077126. PMID 30105089.

Lewis, NE; Abdel-Haleem, AM (2013). "The evolution of genome-scale models of cancer metabolism". Front. Physiol. 4: 237. doi:10.3389/fphys.2013.00237. PMC 3759783. PMID 24027532.

Garraway; Jänne (2012). "Circumventing cancer drug resistance in the era of personalized medicine". Cancer Discovery. 2 (3): 214–226. doi:10.1158/2159-8290.CD-12-0012. PMID 22585993.

Collins; Barker (2007). "Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies". Sci Am. 296 (3): 50–57. doi:10.1038/scientificamerican0307-50. PMID 17348159.

Pe'er, Dana; Nir Hacohen (2011). "Principles and Strategies for Developing Network Models in Cancer". Cell. 144 (6): 864–873. doi:10.1016/j.cell.2011.03.001. PMC 3082135. PMID 21414479.

Tyson, J.J.; Baumann, W.T.; Chen, C.; Verdugo, A.; Tavassoly, I.; Wang, Y.; Weiner, L.M.; Clarke, R. (2011). "Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells". Nat. Rev. Cancer. 11 (7): 523–532. doi:10.1038/nrc3081. PMC 3294292. PMID 21677677.

Tyson, D.R.; Garbett, S.P.; Frick, P.L.; Quaranta, V (2012). "Fractional proliferation: a method to deconvolve cell population dynamics from single-cell data". Nat. Methods. 9 (9): 923–928. doi:10.1038/nmeth.2138. PMC 3459330. PMID 22886092.

Traina, Tiffany A.; U. Dugan; B. Higgins; K. Kolinsky; M. Theodoulou; C. A. Hudis; Larry Norton (2010). "Optimizing Chemotherapy Dose and Schedule by Norton-Simon Mathematical Modeling". Breast Disease. 31 (1): 7–18. doi:10.3233/BD-2009-0290. PMC 3228251. PMID 20519801.

Cancer Genome Atlas Research, Network. (4 July 2013). "Comprehensive molecular characterization of clear cell renal cell carcinoma". Nature. 499 (7456): 43–9. Bibcode:2013Natur.499...43T. doi:10.1038/nature12222. PMC 3771322. PMID 23792563.

Cancer Genome Atlas Research, Network.; Kandoth, C; Schultz, N; Cherniack, AD; Akbani, R; Liu, Y; Shen, H; Robertson, AG; Pashtan, I; Shen, R; Benz, CC; Yau, C; Laird, PW; Ding, L; Zhang, W; Mills, GB; Kucherlapati, R; Mardis, ER; Levine, DA (2 May 2013). "Integrated genomic characterization of endometrial carcinoma". Nature. 497 (7447): 67–73. Bibcode:2013Natur.497...67T. doi:10.1038/nature12113. PMC 3704730. PMID 23636398.

Sumazin, P; Yang, X; Chiu, HS; Chung, WJ; Iyer, A; Llobet-Navas, D; Rajbhandari, P; Bansal, M; Guarnieri, P; Silva, J; Califano, A (14 October 2011). "An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma". Cell. 147 (2): 370–81. doi:10.1016/j.cell.2011.09.041. PMC 3214599. PMID 22000015.

Tentner, AR; Lee, MJ; Ostheimer, GJ; Samson, LD; Lauffenburger, DA; Yaffe, MB (31 January 2012). "Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress". Molecular Systems Biology. 8: 568. doi:10.1038/msb.2012.1. PMC 3296916. PMID 22294094.

Bozic, I; Antal, T; Ohtsuki, H; Carter, H; Kim, D; Chen, S; Karchin, R; Kinzler, KW; Vogelstein, B; Nowak, MA (26 October 2010). "Accumulation of driver and passenger mutations during tumor progression". Proceedings of the National Academy of Sciences of the United States of America. 107 (43): 18545–50. arXiv:0912.1627. Bibcode:2010PNAS..10718545B. doi:10.1073/pnas.1010978107. PMC 2972991. PMID 20876136.

Greenman, C; Stephens, P; Smith, R; Dalgliesh, GL; Hunter, C; Bignell, G; Davies, H; Teague, J; Butler, A; Stevens, C; Edkins, S; O'Meara, S; Vastrik, I; Schmidt, EE; Avis, T; Barthorpe, S; Bhamra, G; Buck, G; Choudhury, B; Clements, J; Cole, J; Dicks, E; Forbes, S; Gray, K; Halliday, K; Harrison, R; Hills, K; Hinton, J; Jenkinson, A; Jones, D; Menzies, A; Mironenko, T; Perry, J; Raine, K; Richardson, D; Shepherd, R; Small, A; Tofts, C; Varian, J; Webb, T; West, S; Widaa, S; Yates, A; Cahill, DP; Louis, DN; Goldstraw, P; Nicholson, AG; Brasseur, F; Looijenga, L; Weber, BL; Chiew, YE; DeFazio, A; Greaves, MF; Green, AR; Campbell, P; Birney, E; Easton, DF; Chenevix-Trench, G; Tan, MH; Khoo, SK; Teh, BT; Yuen, ST; Leung, SY; Wooster, R; Futreal, PA; Stratton, MR (8 March 2007). "Patterns of somatic mutation in human cancer genomes". Nature. 446 (7132): 153–8. Bibcode:2007Natur.446..153G. doi:10.1038/nature05610. PMC 2712719. PMID 17344846.

Benson, DA; Clark, K; Karsch-Mizrachi, I; Lipman, DJ; Ostell, J; Sayers, EW (January 2014). "GenBank". Nucleic Acids Research. 42 (Database issue): D32–7. doi:10.1093/nar/gkt1030. PMC 3965104. PMID 24217914.

Kodama, Y; Mashima, J; Kosuge, T; Katayama, T; Fujisawa, T; Kaminuma, E; Ogasawara, O; Okubo, K; Takagi, T; Nakamura, Y (January 2015). "The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data". Nucleic Acids Research. 43 (Database issue): D18–22. doi:10.1093/nar/gku1120. PMC 4383935. PMID 25477381.

Cunningham, F; Amode, MR; Barrell, D; Beal, K; Billis, K; Brent, S; Carvalho-Silva, D; Clapham, P; Coates, G; Fitzgerald, S; Gil, L; Girón, CG; Gordon, L; Hourlier, T; Hunt, SE; Janacek, SH; Johnson, N; Juettemann, T; Kähäri, AK; Keenan, S; Martin, FJ; Maurel, T; McLaren, W; Murphy, DN; Nag, R; Overduin, B; Parker, A; Patricio, M; Perry, E; Pignatelli, M; Riat, HS; Sheppard, D; Taylor, K; Thormann, A; Vullo, A; Wilder, SP; Zadissa, A; Aken, BL; Birney, E; Harrow, J; Kinsella, R; Muffato, M; Ruffier, M; Searle, SM; Spudich, G; Trevanion, SJ; Yates, A; Zerbino, DR; Flicek, P (January 2015). "Ensembl 2015". Nucleic Acids Research. 43 (Database issue): D662–9. doi:10.1093/nar/gku1010. PMC 4383879. PMID 25352552.

Edgar, R; Domrachev, M; Lash, AE (1 January 2002). "Gene Expression Omnibus: NCBI gene expression and hybridization array data repository". Nucleic Acids Research. 30 (1): 207–10. doi:10.1093/nar/30.1.207. PMC 99122. PMID 11752295.

Petryszak, R; Burdett, T; Fiorelli, B; Fonseca, NA; Gonzalez-Porta, M; Hastings, E; Huber, W; Jupp, S; Keays, M; Kryvych, N; McMurry, J; Marioni, JC; Malone, J; Megy, K; Rustici, G; Tang, AY; Taubert, J; Williams, E; Mannion, O; Parkinson, HE; Brazma, A (January 2014). "Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments". Nucleic Acids Research. 42 (Database issue): D926–32. doi:10.1093/nar/gkt1270. PMC 3964963. PMID 24304889.

Uhlen, M; Oksvold, P; Fagerberg, L; Lundberg, E; Jonasson, K; Forsberg, M; Zwahlen, M; Kampf, C; Wester, K; Hober, S; Wernerus, H; Björling, L; Ponten, F (December 2010). "Towards a knowledge-based Human Protein Atlas". Nature Biotechnology. 28 (12): 1248–50. doi:10.1038/nbt1210-1248. PMID 21139605. S2CID 26688909.

Li, JH; Liu, S; Zhou, H; Qu, LH; Yang, JH (January 2014). "starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data". Nucleic Acids Research. 42 (Database issue): D92–7. doi:10.1093/nar/gkt1248. PMC 3964941. PMID 24297251.

Keshava Prasad, TS; Goel, R; Kandasamy, K; Keerthikumar, S; Kumar, S; Mathivanan, S; Telikicherla, D; Raju, R; Shafreen, B; Venugopal, A; Balakrishnan, L; Marimuthu, A; Banerjee, S; Somanathan, DS; Sebastian, A; Rani, S; Ray, S; Harrys Kishore, CJ; Kanth, S; Ahmed, M; Kashyap, MK; Mohmood, R; Ramachandra, YL; Krishna, V; Rahiman, BA; Mohan, S; Ranganathan, P; Ramabadran, S; Chaerkady, R; Pandey, A (January 2009). "Human Protein Reference Database--2009 update". Nucleic Acids Research. 37 (Database issue): D767–72. doi:10.1093/nar/gkn892. PMC 2686490. PMID 18988627.

Chatr-Aryamontri, A; Breitkreutz, BJ; Oughtred, R; Boucher, L; Heinicke, S; Chen, D; Stark, C; Breitkreutz, A; Kolas, N; O'Donnell, L; Reguly, T; Nixon, J; Ramage, L; Winter, A; Sellam, A; Chang, C; Hirschman, J; Theesfeld, C; Rust, J; Livstone, MS; Dolinski, K; Tyers, M (January 2015). "The BioGRID interaction database: 2015 update". Nucleic Acids Research. 43 (Database issue): D470–8. doi:10.1093/nar/gku1204. PMC 4383984. PMID 25428363.

Carro, MS; Lim, WK; Alvarez, MJ; Bollo, RJ; Zhao, X; Snyder, EY; Sulman, EP; Anne, SL; Doetsch, F; Colman, H; Lasorella, A; Aldape, K; Califano, A; Iavarone, A (21 January 2010). "The transcriptional network for mesenchymal transformation of brain tumours". Nature. 463 (7279): 318–25. Bibcode:2010Natur.463..318C. doi:10.1038/nature08712. PMC 4011561. PMID 20032975.

Huang, SS; Clarke, DC; Gosline, SJ; Labadorf, A; Chouinard, CR; Gordon, W; Lauffenburger, DA; Fraenkel, E (2013). "Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling". PLOS Computational Biology. 9 (2): e1002887. Bibcode:2013PLSCB...9E2887H. doi:10.1371/journal.pcbi.1002887. PMC 3567149. PMID 23408876.

Pascal, J; Bearer, EL; Wang, Z; Koay, EJ; Curley, SA; Cristini, V (27 August 2013). "Mechanistic patient-specific predictive correlation of tumor drug response with microenvironment and perfusion measurements". Proceedings of the National Academy of Sciences of the United States of America. 110 (35): 14266–71. Bibcode:2013PNAS..11014266P. doi:10.1073/pnas.1300619110. PMC 3761643. PMID 23940372.

Hill, SM; Lu, Y; Molina, J; Heiser, LM; Spellman, PT; Speed, TP; Gray, JW; Mills, GB; Mukherjee, S (1 November 2012). "Bayesian inference of signaling network topology in a cancer cell line". Bioinformatics. 28 (21): 2804–10. doi:10.1093/bioinformatics/bts514. PMC 3476330. PMID 22923301.

Mills, GB (February 2012). "An emerging toolkit for targeted cancer therapies". Genome Research. 22 (2): 177–82. doi:10.1101/gr.136044.111. PMC 3266025. PMID 22301131.

Metzcar, John; Wang, Yafei; Heiland, Randy; Macklin, Paul (2019-02-04). "A Review of Cell-Based Computational Modeling in Cancer Biology". JCO Clinical Cancer Informatics. 3 (3): 1–13. doi:10.1200/CCI.18.00069. PMC 6584763. PMID 30715927.

Schoeberl, B; Kudla, A; Masson, K; Kalra, A; Curley, M; Finn, G; Pace, E; Harms, B; Kim, J; Kearns, J; Fulgham, A; Burenkova, O; Grantcharova, V; Yarar, D; Paragas, V; Fitzgerald, J; Wainszelbaum, M; West, K; Mathews, S; Nering, R; Adiwijaya, B; Garcia, G; Kubasek, B; Moyo, V; Czibere, A; Nielsen, UB; MacBeath, G (2017). "Systems biology driving drug development: from design to the clinical testing of the anti-ErbB3 antibody seribantumab (MM-121)". npj Systems Biology and Applications. 3: 16034. doi:10.1038/npjsba.2016.34. PMC 5516865. PMID 28725482.

Wang, Z; Deisboeck, TS (February 2014). "Mathematical modeling in cancer drug discovery". Drug Discovery Today. 19 (2): 145–50. doi:10.1016/j.drudis.2013.06.015. PMID 23831857.

Bekkal Brikci, F; Clairambault, J; Ribba, B; Perthame, B (July 2008). "An age-and-cyclin-structured cell population model for healthy and tumoral tissues". Journal of Mathematical Biology. 57 (1): 91–110. doi:10.1007/s00285-007-0147-x. PMID 18064465. S2CID 31756481.

Yankeelov, TE; Abramson, RG; Quarles, CC (November 2014). "Quantitative multimodality imaging in cancer research and therapy". Nature Reviews. Clinical Oncology. 11 (11): 670–80. doi:10.1038/nrclinonc.2014.134. PMC 4909117. PMID 25113842.

Gentles; Gallahan (2011). "Systems biology: confronting the complexity of cancer". Cancer Res. 71 (18): 5961–5964. doi:10.1158/0008-5472.CAN-11-1569. PMC 3174325. PMID 21896642.

harvard.edu

ui.adsabs.harvard.edu

nih.gov

pubmed.ncbi.nlm.nih.gov

Anderson, AR; Quaranta (2008). "Integrative mathematical oncology". Nat Rev Cancer. 8 (3): 227–234. doi:10.1038/nrc2329. PMID 18273038. S2CID 23792776.

Kreeger, PK; Lauffenburger (2010). "Cancer systems biology: A network modeling perspective". Carcinogenesis. 31 (1): 2–8. doi:10.1093/carcin/bgp261. PMC 2802670. PMID 19861649.

Lewis, NE; Abdel-Haleem, AM (2013). "The evolution of genome-scale models of cancer metabolism". Front. Physiol. 4: 237. doi:10.3389/fphys.2013.00237. PMC 3759783. PMID 24027532.

Garraway; Jänne (2012). "Circumventing cancer drug resistance in the era of personalized medicine". Cancer Discovery. 2 (3): 214–226. doi:10.1158/2159-8290.CD-12-0012. PMID 22585993.

Pe'er, Dana; Nir Hacohen (2011). "Principles and Strategies for Developing Network Models in Cancer". Cell. 144 (6): 864–873. doi:10.1016/j.cell.2011.03.001. PMC 3082135. PMID 21414479.

Mills, GB (February 2012). "An emerging toolkit for targeted cancer therapies". Genome Research. 22 (2): 177–82. doi:10.1101/gr.136044.111. PMC 3266025. PMID 22301131.

Wang, Z; Deisboeck, TS (February 2014). "Mathematical modeling in cancer drug discovery". Drug Discovery Today. 19 (2): 145–50. doi:10.1016/j.drudis.2013.06.015. PMID 23831857.

Gentles; Gallahan (2011). "Systems biology: confronting the complexity of cancer". Cancer Res. 71 (18): 5961–5964. doi:10.1158/0008-5472.CAN-11-1569. PMC 3174325. PMID 21896642.

ncbi.nlm.nih.gov

Kreeger, PK; Lauffenburger (2010). "Cancer systems biology: A network modeling perspective". Carcinogenesis. 31 (1): 2–8. doi:10.1093/carcin/bgp261. PMC 2802670. PMID 19861649.

Lewis, NE; Abdel-Haleem, AM (2013). "The evolution of genome-scale models of cancer metabolism". Front. Physiol. 4: 237. doi:10.3389/fphys.2013.00237. PMC 3759783. PMID 24027532.

Pe'er, Dana; Nir Hacohen (2011). "Principles and Strategies for Developing Network Models in Cancer". Cell. 144 (6): 864–873. doi:10.1016/j.cell.2011.03.001. PMC 3082135. PMID 21414479.

"Home - dbGaP - NCBI". www.ncbi.nlm.nih.gov.

"dbSNP Home Page". www.ncbi.nlm.nih.gov.

Mills, GB (February 2012). "An emerging toolkit for targeted cancer therapies". Genome Research. 22 (2): 177–82. doi:10.1101/gr.136044.111. PMC 3266025. PMID 22301131.

Gentles; Gallahan (2011). "Systems biology: confronting the complexity of cancer". Cancer Res. 71 (18): 5961–5964. doi:10.1158/0008-5472.CAN-11-1569. PMC 3174325. PMID 21896642.

cancergenome.nih.gov

"The Cancer Genome Atlas Home Page". The Cancer Genome Atlas - National Cancer Institute. 2018-06-13.

semanticscholar.org

api.semanticscholar.org

Anderson, AR; Quaranta (2008). "Integrative mathematical oncology". Nat Rev Cancer. 8 (3): 227–234. doi:10.1038/nrc2329. PMID 18273038. S2CID 23792776.

Cancer systems biology (English Wikipedia)

arxiv.org

doi.org

ebi.ac.uk

encodeproject.org

gene-regulation.com

genereg.net

jaspar.genereg.net

genome.jp

harvard.edu

ui.adsabs.harvard.edu

hmdb.ca

nctu.edu.tw

mirtarbase.mbc.nctu.edu.tw

nih.gov

pubmed.ncbi.nlm.nih.gov

ncbi.nlm.nih.gov

cancergenome.nih.gov

phosphosite.org

reactome.org

semanticscholar.org

api.semanticscholar.org

thegpm.org

gpmdb.thegpm.org