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. Science, 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

BMC Bioinformatics 2006 Margolin copy.pdf

Proceedings of the National Academy of Sciences 2010 Marbach.pdf

7F21E74B-ED13-4DB5-BAA0-CCFFAE7FD5FA copy.pdf

Network Centrality Indices

Bioinformatics 2009 Scardoni.pdf

Integrating Large-scale Data Sets

IET Syst. Biol. 2010 Montefusco.pdf

IET Syst. Biol. 2007 Cosentino.pdf

Identifying/interrogating critical subcircuits (switches)

J. Comput. Biol. 2012 Cosentino.pdf

Testing network functions by cis-regulatory analysis

Science 2007 Smith.pdf

Proceedings of the National Academy of Sciences 2008 Smith.pdf

Proceedings of the National Academy of Sciences 2009 Smith.pdf

Vazquez's talk


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


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. "Hallmarks of Cancer" (2000): Hanahan and Weinberg, Cell Vol 100, 57-70

2. "Hallmarks of Cancer": The Next Generation" (2011): Hanahan and Weinberg, Cell Vol 144, 646-674

3. "Tumor Metastasis: Molecular Insights and Evolving Paradigms" (2011): Vatsalyan and Weinberg, Cell Vol 147, 275-292.

4. Gyan's notes on 1 and 2 above:

Eshel Ben-Jacob's lecture July 5