Reference+Material

toc Here's a page to share important papers, review articles, relevant news, etc. =A. Levine's Lectures =


 * Books**

R.Weinberg, **The Biology of Cancer**, G.S. Garland Science, 2007

S. Mukherjee, **The Emperor of All Maladies**, Scribner, 2010


 * Manuscripts**

D. Hanahan and R. Weinberg, 2011. Hallmarks of Cancer: The Next Generation, //Cell//, 144(5):646-74.

Hayflick L., and Moorhead P.S., 1961, The serial cultivation of human diploid cell strains, //Expt Cell Res//, 25, 585-621.

Hayflick L., 2000, The future of aging, //Nature//, 408(6809):267-9.

Vogelstein, B., Lane, D. and Levine, A.J. 2000. Surfing the p53 network. //Nature//, 408(6810): 307-10.

Lahav, G., Rosenfeld, N., Sigal, A., Geva-Zatorsky, N., Levine, A.J., Elowitz, M.B., and Alon, U., 2004. Dynamics of the p53-Mdm2 feedback loop in individual cells. //Nature Genetics//, 36:147-150.

Harris, S.A. and Levine, A.J., 2005. The p53 Pathway: Positive and Negative Feedback Loops. //Oncogene//, 24:2899-2908.

Hu, W., Feng, Z., Ma, L., Wagner, J., Rice, J.J., Stolovitzky, G., and Levine, A.J., 2007. A single nucleotide polymorphism in the MDM2 gene disrupts the oscillation of p53 and MDM2 levels in cells. //Cancer Research//, 67(6):2757-2765.

Atwal, G.S., Rabadán, R., Lozano, G., Strong, L., Ruijs, M., Schmidt, M., van’tVeer, L., Nevanlinna, L., Tommiska, J., Aittomaki, K., Bougeard, G., Frebourg, T., Levine, A.J., Bond,G., 2008. An Information-Theoretic Analysis of Genetics, Gender and Age in Cancer Patients. //PLoS// //One//, 3(4):1-7 (Epub ahead of print).

Puzio-Kuter, A.M., & Levine, A.J. 2009. Stem cell biology meets p53. //Nature Biotechnology//,27 (10): 914-915

Levine, A.J. and Puzio-Kuter, A., 2010. The Control of the Metabolic Switch in Cancer by Ocogenes and Tumor Suppressor Genes. //Scienc//e, 330 (6009):1340 -1344. PMID: 21127244

Mizuno, H., Spike, B.T., Wahl, G.M., Levine, A.J. Inactivation of p53 in breast cancers correlates with stem cell transcriptional signatures. //PNAS// 2010, Dec 28; 107(52):22745-50. Epub 2010 Dec 13. PMID: 21149740 PMCID: PMC3012457

Nicolau, M., Levine, A.J., and Carlsson, G. 2011 Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival. //PNAS// April 26;108 (17) :7265-70. Epub 2011 Apr 11. PMCID: PMC3084136

Markert E. K., Mizuno H., Vazquez A., Levine A. J. Molecular classification of prostate cancer using curated expression signatures. //PNAS// 2011 Dec 27; 108(52):21276 21281. Published online 2011 November 28. PMCID: PMC3248553

Aguirre-Ghiso JA. (2007)Models, mechanisms and clinical evidence for cancer dormancy. //Nat Rev Cancer// 7, 834-46.

Artandi SE, DePinho RA. (2010) Telomeres and telomerase in cancer. //Carcinogenesis// 31, 9-18.

Bierie, B., and Moses, H.L.(2006). Tumour microenvironment: TGFbeta: the molecular Jekyll and Hyde of cancer. //Nat. Rev. Cancer// 6, 506–520.

Blasco, M.A. (2005). Telomeres and human disease: ageing, cancer and beyond. //Nat. Rev. Genet//. 6//,// 611–622.

Burkhart, D.L.,and Sage, J. (2008). Cellular mechanisms of tumour suppression by the retinoblastoma gene. //Nat. Rev. Cancer// 8//,// 671–682.

Cho, R.W., and Clarke, M.F.(2008). Recent advances in cancer stem cells. //Curr. Opin. Genet. Dev//. //18,// 1–6.

Ciccia, A., and Elledge, S.J. (2010). The DNA damage response: making it safe to play with knives. Mol. //Cell// 40//,// 179–204.

Collado, M., and Serrano, M. (2010). Senescence in tumours: evidence from mice and humans. //Nat. Rev. Cancer// 10//,// 51–57.

DeBerardinis, R.J., Lum, J.J., Hatzivassiliou, G., and Thompson, C.B.(2008). The biology of cancer: Metabolic reprogramming fuels cell growth and proliferation//. Cell Metab//. //7,// 11–20.

Esteller, M. (2007). Cancer epigenomics: DNA methylomes and histone-modification maps. //Nat. Rev. Genet.// 8, 286–298.

Evan, G., and Littlewood, T. (1998). A matter of life and cell death. //Science// 281//,// 1317–1322.

Ghebranious, N., and Donehower, L.A.(1998). Mouse models in tumor suppression. //Oncogene// 17//,// 3385–3400.Grivennikov, S.I., Greten, F.R., and Karin, M. (2010). Immunity, inflammation, and cancer. //Cell// 140//,// 883–899.

Grivennikov, S.I., Greten, F.R., and Karin, M. (2010). Immunity, inflammation, and cancer. //Cell// 140, 883–899.

Gupta, P.B., Chaffer, C.L., and Weinberg, R.A.(2009). Cancer stem cells: mirage or reality? //Nat. Med//. 15, 1010–1012.

Harper, J.W., and Elledge, S.J. (2007). The DNA damage response: Ten years after. //Mol. Cell// 28, 739–745.

Hsu, P.P., and Sabatini, D.M.(2008). Cancer cell metabolism: Warburg and beyond. //Cell// 134//,// 703–707.

Hynes, N.E., and MacDonald, G. (2009). ErbB receptors and signaling pathways in cancer. //Cancer Cell// 12, 160–170.

Ince, T.A., Richardson, A.L., Bell, G.W., Saitoh, M., Godar, S., Karnoub, A.E., Iglehart, J.D., and Weinberg, R.A. (2007). Transformation of different human breast epithelial cell types leads to distinct tumor phenotypes. //Cancer Cell// 12//,// 160–170.

Jones, P.A., and Baylin, S.B. (2007). The epigenomics of cancer. //Cell// 128//,// 683–692.

Jones, R.G., and Thompson, C.B.(2009). Tumor suppressors and cell metabolism: a recipe for cancer growth. //Genes Dev//. 23//,// 537–548.

Korkola, J., and Gray, J.W.(2010). Breast cancer genomes—form and function. //Curr. Opin. Genet. Dev.// 20, 4–14.

Lemmon, M.A., and Schlessinger, J. (2010) Cell signaling by receptor tyrosine kinases. //Cell// 141, 1117–1134.

Levine, B., and Kroemer, G. (2008). Autophagy in the pathogenesis of disease. //Cell// 132, 27–42.

Lowe, S.W., Cepero, E., and Evan, G. (2004). Intrinsic tumour suppression. //Nature// 432//,// 307–315.

Luo, J., Solimini, N.L.,and Elledge, S.J. (2009). Principles of cancer therapy: Oncogene and non-oncogene addiction. //Cell// 136//,// 823–837.

Mani, S.A., Guo, W., Liao, M.J., Eaton, E.N., Ayyanan, A., Zhou, A.Y., Brooks, M., Reinhard, F., Zhang, C.C., and Shipitsin, M., et al. (2008). The epithelial-mesenchymal transition generates cells with properties of stem cells. //Cell// 133//,// 704–715.

Massagué, J. (2008). TGFβ in cancer. //Cell// 134//,// 215–230.

Mathew, R., Karantza-Wadsworth, V., and White, E. (2007). Role of autophagy in cancer. //Nat. Rev. Cancer// 7, 961–967.

Negrini, S., Gorgoulis, V.G., and Halazonetis, T.D. (2010). Genomic instability—an evolving hallmark of cancer. //Nat. Rev. Mol. Cell Biol//. 11, 220–228.

Polyak, K., and Weinberg, R.A. (2009). Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits. //Nat. Rev. Cancer// 9//,// 265–273.

Ruoslahti, E. (2002). Specialization of tumour vasculature. //Nat. Rev. Cancer// 2, 83–90.

Shay, J.W., and Wright, W.E. (2000). Hayflick, his limit, and cellular ageing. //Nat. Rev. Mol. Cell Biol//. 1, 72–76.

Sherr, C.J., and McCormick, F. (2002). The RB and p53 pathways in cancer. //Cancer Cell// 2, 103–112.

Soda, Y., Marumoto, T., Friedmann-Morvinski, D., Soda, M., Liu, F., Michiue, H., Pastorino, S., Yang, M., Hoffman, R.M., Kesari, S., et al. (2011). Feature Article: Transdifferentiation of glioblastoma cells into vascular endothelial cells. //Proc. Natl. Acad. Sci.// //USA//, Published online January 24, 2011.

Vander Heiden, M.G., Cantley, L.C., and Thompson, C.B. (2009). Understanding the Warburg effect: the metabolic requirements of cell proliferation. //Science// 324//,// 1029–1033.

Warburg, O. (1956). On respiratory impairment in cancer cells. //Science// 124//,// 269–270.

Warburg, O.H. (1930). The Metabolism of Tumours: Investigations from the Kaiser Wilhelm Institute for Biology, Berlin-Dahlem. (London, UK: Arnold Constable).

Yuan, T.L., and Cantley, L.C. (2008). PI3K pathway alterations in cancer: variations on a theme. //Oncogene// //27,// 5497–5510.

=Joel Smith's Talk=


 * Network Inference**








 * Network Centrality Indices**




 * Integrating Large-scale Data Sets**






 * Identifying/interrogating critical subcircuits (switches)**


 * [[file:cancer12/J. Comput. Biol. 2012 Cosentino.pdf|J. Comput. Biol. 2012 Cosentino.pdf]]**


 * Testing network functions by cis-regulatory analysis**


 * [[file:cancer12/Science 2007 Smith.pdf|Science 2007 Smith.pdf]]**


 * [[file:cancer12/Proceedings of the National Academy of Sciences 2008 Smith.pdf|Proceedings of the National Academy of Sciences 2008 Smith.pdf]]**


 * [[file:cancer12/Proceedings of the National Academy of Sciences 2009 Smith.pdf|Proceedings of the National Academy of Sciences 2009 Smith.pdf]]**

=**Vazquez's talk**=

**Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation**
 * Warburg O. On the Origin of Cancer Cells.**

Glycolysis does not necessarily reflects cellular anoxia
 * Glycolysis is independent of oxygenation state in stimulated human skeletal muscle in vivo**
 * Shaking up glycolysis: Sustained, high lactate flux during aerobic rattling**

The Warburg effect as a consequence of intracellular crowding


 * Total cell protein concentration as an evolutionary constraint on the metabolic control distribution in cells**
 * Catabolic efficiency of aerobic glycolysis: The Warburg effect revisited**
 * Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the warburg effect**
 * Serine Biosynthesis with One Carbon Catabolism and the Glycine Cleavage System Represents a Novel Pathway for ATP Generation**

The lactate switch in muscle metabolism


 * Plasma lactate accumulation and distance running performance**
 * Molecular Crowding Defines a Common Origin for the Warburg Effect in Proliferating Cells and the Lactate Threshold in Muscle Physiology**

The acetate switch in E. coli


 * Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity**
 * Impact of the solvent capacity constraint on E. coli metabolism**

Optimal cell density


 * Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects**
 * Optimal macromolecular density in the cell**

=**Gyan Bhanot and Herbie Levine's chalk talk on 6/29 on Hallmarks of Cancer I and II and other papers**=


 * 1. [[file:Hallmarks_of_Cancer.pdf|"Hallmarks of Cancer"]] (2000): Hanahan and Weinberg, Cell Vol 100, 57-70**


 * 2. [[file:Hallmarks_of_Cancer_II.pdf|"]]Hallmarks of Cancer": The Next Generation" (2011): Hanahan and Weinberg, Cell Vol 144, 646-674**


 * 3. [[file:Weinberg_3.pdf|"Tumor Metastasis: Molecular Insights and Evolving Paradigms" ]](2011): Vatsalyan and Weinberg, Cell Vol 147, 275-292.**


 * 4. [[file:GB_Chalk_talk_KITP_29_Jun_2012.pdf|Gyan's notes on 1 and 2 above:]]**


 * Eshel Ben-Jacob's lecture July 5**