csbcbook references

[Schrodinger1944Vie] Erwin Schrödinger. Qu'est-ce que la vie? Christian Bourgois Editeur, 1986, 1944. [ bib ]
[Crick1970Central] F. Crick. Central dogma of molecular biology. Nature, 227:561-563, 1970. [ bib | .pdf | .pdf | Abstract ]
[Knudson1971Mutation] Alfred G. Knudson. Mutation and cancer: Statistical study of retinoblastoma. Proceedings of the National Academy of Sciences, 68:820-823, 1971. [ bib ]
[Elston1991Pathological] C. W. Elston and I. O. Ellis. Pathological prognostic factors in breast cancer. i. the value of histological grade in breast cancer: experience from a large study with long-term follow-up. Histopathology, 19(5):403-410, Nov 1991. [ bib | DOI | http | .pdf | Abstract ]
[Kallioniemi1992Comparative] A. Kallioniemi, O. P. Kallioniemi, D. Sudar, D. Rutovitz, J. W. Gray, F. Waldman, and D. Pinkel. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science, 258(5083):818-821, Oct 1992. [ bib | http | .pdf | Abstract ]
[Ellis1992Pathological] I. O. Ellis, M. Galea, N. Broughton, A. Locker, R. W. Blamey, and C. W. Elston. Pathological prognostic factors in breast cancer. ii. histological type. relationship with survival in a large study with long-term follow-up. Histopathology, 20(6):479-489, Jun 1992. [ bib | DOI | http | .pdf | Abstract ]
[Billerey1996Etude] C. Billerey and L. Boccon-Gibod. Etude des variations inter-pathologistes dans l'évaluation du grade et du stade des tumeurs vésicales. Progrès en Urologie, 6:49-57, 1996. [ bib | .PDF | .pdf ]
[Solinas1997Matrix] S. Solinas-Toldo, S. Lampel, S. Stilgenbauer, J. Nickolenko, A. Benner, H. Dohner, T. Cremer, and P. Lichter. Matrix-based comparative genomic hybridization: Biochips to screen for genomic imbalances. Genes Chromosomes Cancer, 20:399-407, 1997. [ bib ]
[Pinkel1998High] D. Pinkel, R. Segraves, D. Sudar, S. Clark, I. Poole, D. Kowbel, C. Collins, W. L. Kuo, C. Chen, Y. Zhai, S. H. Dairkee, B. M. Ljung, J. W. Gray, and D. G. Albertson. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet., 20(2):207-211, Oct 1998. [ bib | DOI | http | .pdf | Abstract ]
[Nakamura1998ATM] Yusuke Nakamura. ATM: the p53 booster. Nature Medicine, 4:1231-1232, 1998. [ bib ]
[Tomita1999Bioinformatics] M. Tomita, K. Hashimoto, K. Takahashi, T. S. Shimizu, Y. Matsuzaki, F. Miyoshi, K. Saito, S. Tanida, K. Yugi, J. C. Venter, and C. A. Hutchison. E-CELL: software environment for whole-cell simulation. Bioinformatics, 15(1):72-84, 1999. [ bib | DOI | arXiv | http ]
[Southern1999Molecular] Edwin Southern, Kalim Mir, and Mikhail Shchepinov. Molecular interactions on microarrays. Nat. Genet., 21:5-9, 1999. [ bib ]
[Pollack1999Genome] Jonathan R. Pollack, Charles M. Perou, Ash A. Alizadeh, Michael B. Eisen, Alexander Pergamenschikov, Cheryl F. Williams, Stefanie S. Jeffrey, David Botstein, and Patrick O. Brown. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet., 23:41-46, 1999. [ bib ]
[Perou1999Distinctive] C. M. Perou, S. S. Jeffrey, M. van de Rijn, C. A. Rees, M. B. Eisen, D. T. Ross, A. Pergamenschikov, C. F. Williams, S. X. Zhu, J. C. Lee, D. Lashkari, D. Shalon, P. O. Brown, and D. Botstein. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc. Natl. Acad. Sci. U S A, 96(16):9212-9217, Aug 1999. [ bib | DOI | http | .pdf | Abstract ]
[Golub1999Molecular] T. R. Golub, D. K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J. P. Mesirov, H. Coller, M. L. Loh, J. R. Downing, M. A. Caligiuri, C. D. Bloomfield, and E. S. Lander. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286:531-537, 1999. [ bib | DOI | http | .pdf | Abstract ]
[Bhalla1999Emergent] U. S. Bhalla and R. Iyengar. Emergent properties of networks of biological signaling pathways. Science, 283(5400):381-387, 1999. [ bib | DOI | arXiv | http | .pdf ]
[Aguda1999CellProl] B. D. Aguda and Y. Tang. The kinetic origins of the restriction point in the mammalian cell cycle. Cell Prolif, 32(5):321-35, 1999. [ bib | Abstract ]
[Aguda1999PNAS] B. D. Aguda. A quantitative analysis of the kinetics of the g(2) dna damage checkpoint system. Proc Natl Acad Sci U S A, 96(20):11352-7, 1999. [ bib | Abstract ]
[Aguda1999Oncogene] B. D. Aguda. Instabilities in phosphorylation-dephosphorylation cascades and cell cycle checkpoints. Oncogene, 18(18):2846-51, 1999. [ bib | Abstract ]
[Perou2000Molecular] C M. Perou, T. Sørlie, M. B. Eisen, M. van de Rijn, S. S. Jeffrey, C. A. Rees, J. R. Pollack, D. T. Ross, H. Johnsen, L. A. Akslen, O. Fluge, A. Pergamenschikov, C. Williams, S. X. Zhu, P. E. Lønning, A. L. Børresen-Dale, P. O. Brown, and D. Botstein. Molecular portraits of human breast tumours. Nature, 406(6797):747-752, Aug 2000. [ bib | DOI | http | .pdf | Abstract ]
[LevBarOr2000PNAS] R. Lev Bar-Or, R. Maya, L. A. Segel, U. Alon, A. J. Levine, and M. Oren. Generation of oscillations by the p53-mdm2 feedback loop: a theoretical and experimental study. Proc Natl Acad Sci U S A, 97(21):11250-5, 2000. [ bib | Abstract ]
[Hanahan2000hallmarks] D. Hanahan and R. A. Weinberg. The hallmarks of cancer. Cell, 100:57-70, 2000. [ bib | DOI | http | .pdf ]
[Fussenegger2000NatBio] M. Fussenegger, J. Bailey, and J. Varner. A mathematical model of caspase function in apoptosis. Nat. Biotechnol., 18:768-774, 2000. [ bib | DOI | .pdf | Abstract ]
[Alizadeh2000Distinct] A. A. Alizadeh, M. B. Eisen, R. E. Davis, C. Ma, I. S. Lossos, A. Rosenwald, J. C. Boldrick, H. Sabet, T. Tran, X. Yu, J. I. Powell, L. Yang, G. E. Marti, T. Moore, J. Hudson, L. Lu, D. B. Lewis, R. Tibshirani, G. Sherlock, W. C. Chan, T. C. Greiner, D. D. Weisenburger, J. O. Armitage, R. Warnke, R. Levy, W. Wilson, M. R. Grever, J. C. Byrd, D. Botstein, P. O. Brown, and L. M. Staudt. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403(6769):503-511, Feb 2000. [ bib | DOI | http | .pdf | Abstract ]
[Tusher2001Significance] V. G. Tusher, R. Tibshirani, and G. Chu. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA, 98(9):5116-5121, Apr 2001. [ bib | DOI | http | .pdf | Abstract ]
[Soerlie2001Gene] T. Sørlie, C. M. Perou, R. Tibshirani, T. Aas, S. Geisler, H. Johnsen, T. Hastie, M. B. Eisen, M. van de Rijn, S. S. Jeffrey, T. Thorsen, H. Quist, J. C. Matese, P. O. Brown, D. Botstein, P. Eystein Lønning, and A. L. Børresen-Dale. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad. Sci. USA, 98(19):10869-10874, Sep 2001. [ bib | DOI | http | .pdf | Abstract ]
[Vijver2002gene-expression] M. J. van de Vijver, Y. D. He, L. J. van't Veer, H. Dai, A. A. M. Hart, D. W. Voskuil, G. J. Schreiber, J. L. Peterse, C. Roberts, M. J. Marton, M. Parrish, D. Atsma, A. Witteveen, A. Glas, L. Delahaye, T. van der Velde, H. Bartelink, S. Rodenhuis, E. T. Rutgers, S. H. Friend, and R. Bernards. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med., 347(25):1999-2009, Dec 2002. [ bib | DOI | http | .pdf | Abstract ]
[Veer2002Gene] L. J. van 't Veer, H. Dai, M. J. van de Vijver, Y. D. He, A. A. M. Hart, M. Mao, H. L. Peterse, K. van der Kooy, M. J. Marton, A. T. Witteveen, G. J. Schreiber, R. M. Kerkhoven, C. Roberts, P. S. Linsley, R. Bernards, and S. H. Friend. Gene expression profiling predicts clinical outcome of breast cancers. Nature, 415(6871):530-536, Jan 2002. [ bib | DOI | http | .pdf | Abstract ]
[Turner2002Cellular] Bryan M. Turner. Cellular memory and the histone code. Cell, 111:285-291, 2002. [ bib ]
[Speybroeck2002From] L Van Speybroeck. From epigenesis to epigenetics: The case of C. H. Waddington. Annals of the New York Academy of Sciences, 981:61-81, 2002. [ bib ]
[Jablonka2002changing] A. Jablonka and M. J. Lamb. The changing concept of epigenetics. Ann N Y Acad Sci, 981:82-96, Dec 2002. [ bib | Abstract ]
[Chen2002Gene] X. Chen, S. T. Cheung, S. So, S. T. Fan, C. Barry, J. Higgins, K.-M. Lai, J. Ji, S. Dudoit, I. O L. Ng, M. Van De Rijn, D. Botstein, and P. O. Brown. Gene expression patterns in human liver cancers. Mol. Biol. Cell, 13(6):1929-1939, Jun 2002. [ bib | DOI | http | .pdf | Abstract ]
[Alberts2002Molecular] B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. Molecular Biology of the Cell. Garland Science, Taylor & Francis Group, LLC, 2002. Fourth Edition. [ bib ]
[Wu2003Model] Z Wu, R A Irizarry, R Gentleman, F M Murillo, and F Spencer. A model based background adjustment for oligonucleotide expression arrays. Technical report, John Hopkins University, Department of Biostatistics Working Papers, Baltimore, MD, 2003. [ bib ]
[Sorlie2003Repeated] T. Sørlie, R. Tibshirani, J. Parker, T. Hastie, J.S. Marron, A. Nobel, S. Deng, H. Johnsen, R. Pesich, S. Geisler, J. Demeter, C.M. Perou, P.E. Lønning, P.O. Brown, A.L. Børresen-Dale, and D. Botstein. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc. Natl. Acad. Sci. USA, 100(14):8418-8423, Jul 2003. [ bib | DOI | http | .pdf | Abstract ]
[Mattick2003Challenging] John S. Mattick. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays, 25:930-939, 2003. [ bib ]
[Irizarry2003Exploration] R. A. Irizarry, B. Hobbs, F. Collin, Y. D. Beazer-Barclay, K. J. Antonellis, U. Scherf, and T. P. Speed. Exploration, normalization, and summaries of high density oligonucleotide array probe level datas. Biostatistics, 4(2):249-264, Apr 2003. [ bib | DOI | http | .pdf | Abstract ]
[Albertson2003Genomic] D. G. Albertson and D. Pinkel. Genomic microarrays in human genetic disease and cancer. Hum. Mol. Genet., 12 Spec No 2:R145-R152, Oct 2003. [ bib | DOI | http | .pdf | Abstract ]
[Albertson2003Chromosome] D. G. Albertson, C. Collins, F. McCormick, and J. W. Gray. Chromosome aberrations in solid tumors. Nat. Genet., 34(4):369-376, Aug 2003. [ bib | DOI | http | .pdf | Abstract ]
[Aguda2003CellCycle] B. D. Aguda and C. K. Algar. A structural analysis of the qualitative networks regulating the cell cycle and apoptosis. Cell Cycle, 2(6):538-44, 2003. [ bib | Abstract ]
[Venables2004Aberrant] Julian P. Venables. Aberrant and alternative splicing in cancer. Cancer Res., 64:7647-7654, 2004. [ bib ]
[Sherr2004Principles] Charles J. Sherr. Principles of tumor suppression. Cell, 116:235-246, 2004. [ bib ]
[Mello2004Revealing] Craig C. Mello and Darryl Conte Jr. Revealing the world of RNA interference. Nature, 43:338-342, 2004. [ bib ]
[Lahav2004NatGenet] G. Lahav, N. Rosenfeld, A. Sigal, N. Geva-Zatorsky, A. J. Levine, M. B. Elowitz, and U. Alon. Dynamics of the p53-mdm2 feedback loop in individual cells. Nat Genet, 36(2):147-50, 2004. [ bib | Abstract ]
[Ishkanian2004tiling] A. S. Ishkanian, C. A. Malloff, S. K. Watson, R. J. DeLeeuw, B. Chi, B. P. Coe, A. Snijders, D. G. Albertson, D. Pinkel, M. A. Marra, V. Ling, C. MacAulay, and W. L. Lam. A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet., 36(3):299-303, Mar 2004. [ bib | DOI | http | .pdf | Abstract ]
[Iafrate2004Detection] A. John Iafrate, Lars Feuk, Miguel N Rivera, Marc L Listewnik, Patricia K Donahoe, Ying Qi, Stephen W Scherer, and Charles Lee. Detection of large-scale variation in the human genome. Nat. Genet., 36(9):949-951, Sep 2004. [ bib | DOI | http | .pdf | Abstract ]
[Heiner2004Biosystems] M. Heiner, I. Koch, and J. Will. Model validation of biological pathways using petri nets-demonstrated for apoptosis. Biosystems, 75(1-3):15-28, 2004. [ bib | Abstract ]
[Eissing2004Bistability] T. Eissing, H. Conzelmann, E. D. Gilles, F. Allgower, E. Bullinger, and P. Scheurich. Bistability analyses of a caspase activation model for receptor-induced apoptosis. J. Biol. Chem., 279(35):36892-36897, 2004. [ bib | DOI | arXiv | http | .pdf | Abstract ]
[Cianfrocca2004Prognostic] M. Cianfrocca and L. J. Goldstein. Prognostic and predictive factors in early-stage breast cancer. Oncologist, 9(6):606-616, 2004. [ bib | DOI | http | .pdf | Abstract ]
[Bentele2004JCB] M. Bentele, I. Lavrik, M. Ulrich, S. Stosser, D. W. Heermann, H. Kalthoff, P. H. Krammer, and R. Eils. Mathematical modeling reveals threshold mechanism in cd95-induced apoptosis. J Cell Biol, 166(6):839-51, 2004. [ bib | Abstract ]
[Tompa2005Assessing] Martin Tompa, Nan Li, Timothy L Bailey, George M Church, Bart De Moor, Eleazar Eskin, Alexander V Favorov, Martin C Frith, Yutao Fu, W James Kent, Vsevolod J Makeev, Andrei A Mironov, William Stafford Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques Van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, and Zhou Zhu. Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23:137-144, 2005. [ bib ]
[Stucki2005JTB] J. W. Stucki and H.-U. Simon. Mathematical modeling of the regulation of caspase-3 activation and degradation. Journal of Theoretical Biology, 234(1):123-131, 2005. [ bib | DOI | http | Abstract ]
[Pinkel2005Array] D. Pinkel and D. G. Albertson. Array comparative genomic hybridization and its applications in cancer. Nat. Genet., 37 Suppl:S11-S17, Jun 2005. [ bib | DOI | http | .pdf | Abstract ]
[Perkins2005Expanding] D O Perkins, C Jeffries, and P Sullivan. Expanding the 'central dogma': the regulatory role of nonprotein coding genes and implications for the genetic liability to schizophrenia. Molecular Psychiatry, 10:69-78, 2005. [ bib ]
[Ma2005PNAS] L. Ma, J. Wagner, J. J. Rice, W. Hu, A. J. Levine, and G. A. Stolovitzky. A plausible model for the digital response of p53 to dna damage. Proc Natl Acad Sci U S A, 102(40):14266-71, 2005. [ bib | Abstract ]
[Lu2005MicroRNA] J. Lu, G. Getz, E. A. Miska, E. Alvarez-Saavedra, J. Lamb, D. Peck, A. Sweet-Cordero, D. L. Ebert, R. H. Mak, A. A. Ferrando, J. R. Downing, T. Jacks, H. R. Horvitz, and T. R. Golub. Microrna expression profiles classify human cancers. Nature, 435(7043):834-838, Jun 2005. [ bib | DOI | http | .pdf | Abstract ]
[Kitano2005NatBiotechnol] H. Kitano, A. Funahashi, Y. Matsuoka, and K. Oda. Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol., 8:961-966, 2005. [ bib | DOI | Abstract ]
[Johnson2005Kinomics] S. A. Johnson and T. Hunter. Kinomics: methods for deciphering the kinome. Nat. Methods, 2(1):17-25, Jan 2005. [ bib | DOI | http | .pdf | Abstract ]
[Janoueix-Lerosey2005Preferential] Isabelle Janoueix-Lerosey, Philippe Hupé, Zofia Maciorowski, Philippe La Rosa, Gudrun Schleiermacher, Gaëlle Pierron, Stéphane Liva, Emmanuel Barillot, and Olivier Delattre. Preferential occurrence of chromosome breakpoints within early replicating regions in neuroblastoma. Cell Cycle, 4(12):1842-1846, Dec 2005. [ bib | http | .pdf | Abstract ]
[Hua2005JImmunol] F. Hua, M. G. Cornejo, M. H. Cardone, C. L. Stokes, and D. A. Lauffenburger. Effects of bcl-2 levels on fas signaling-induced caspase-3 activation: molecular genetic tests of computational model predictions. J Immunol, 175(2):985-95, 2005. [ bib | Abstract ]
[Gaudet2005MCPorteomics] S. Gaudet, K. A. Janes, J. G. Albeck, E. A. Pace, D. A. Lauffenburger, and P. K. Sorger. A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics, 4(10):1569-1590, 2005. [ bib | Abstract ]
[Davies2005Array] J. J. Davies, I. M. Wilson, and W. L. Lam. Array CGH technologies and their applications to cancer genomes. Chromosome Res., 13(3):237-248, 2005. [ bib | DOI | http | .pdf | Abstract ]
[Ciliberto2005CellCycle] A. Ciliberto, B. Novak, and J. J. Tyson. Steady states and oscillations in the p53/mdm2 network. Cell Cycle, 4(3):488-93, 2005. [ bib | Abstract ]
[Breslin2005Signal] T. Breslin, M. Krogh, C. Peterson, and C. Troein. Signal transduction pathway profiling of individual tumor samples. BMC Bioinformatics, 6:163, 2005. [ bib | DOI | http | .pdf | Abstract ]
[Ylstra2006BAC] Bauke Ylstra, Paul Van den Ijssel, Beatriz Carvalho, Ruud H Brakenhoff, and Gerrit A Meijer. BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res., 34:445-450, 2006. [ bib ]
[Soerlie2006Gene] T. Sørlie, C. M. Perou, C. Fan, S. Geisler, T. Aas, A. Nobel, G. Anker, L. A. Akslen, D. Botstein, A.-L. Børresen-Dale, and P. E. Lønning. Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer. Mol. Cancer Ther., 5(11):2914-2918, Nov 2006. [ bib | DOI | http | .pdf | Abstract ]
[Stransky2006Regional] N. Stransky, C. Vallot, F. Reyal, I. Bernard-Pierrot, S. G. Diez de Medina, R. Segraves, Y. de Rycke, P. Elvin, A. Cassidy, C. Spraggon, A. Graham, J. Southgate, B. Asselain, Y. Allory, C. C. Abbou, D. G. Albertson, J.-P. Thiery, D. K. Chopin, D. Pinkel, and F. Radvanyi. Regional copy number-independent deregulation of transcription in cancer. Nat. Genet., 38(12):1386-1396, Dec 2006. [ bib | DOI | http | .pdf | Abstract ]
[Srebrow2006Connection] A. Srebrow and A. R. Kornblihtt. The connection between splicing and cancer. J. Cell Sci., 119:2635-2641, 2006. [ bib ]
[Schumacher2006Microarray] A. Schumacher, P. Kapranov, Z. Kaminsky, J. Flanagan, A. Assadzadeh, P. Yau, C. Virtanen, N. Winegarden, J. Cheng, T. Gingeras, and A. Petronis. Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res., 34:528-542, 2006. [ bib ]
[OConnor2006BiotechnolLett] K. C. O'Connor, J. W. Muhitch, D. J. Lacks, and M. Al-Rubeai. Modeling suppression of cell death by bcl-2 over-expression in myeloma ns0 6a1 cells. Biotechnol Lett, 28(23):1919-24, 2006. [ bib | Abstract ]
[Nakabayashi2006Mathematical] J. Nakabayashi and A. Sasaki. A mathematical model for apoptosome assembly: The optimal cytochrome c/apaf-1 ratio. J. Theor. Biol., 242(2):280-287, 2006. [ bib | DOI | http | Abstract ]
[Nakabayashi2006JTB] J. Nakabayashi and A. Sasaki. A mathematical model for apoptosome assembly: The optimal cytochrome c/apaf-1 ratio. Journal of Theoretical Biology, 242(2):280 - 287, 2006. [ bib | DOI | http | Abstract ]
[Mattick2006Non] John S. Mattick and Igor V. Makunin. Non-coding RNA. Hum. Mol. Genet., 15:R17-R29, 2006. [ bib ]
[Legewie2006PLOSCompBiol] S. Legewie, N. Blathgen, and H. Herzel. Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability. PLoS Comput Biol, 2(9):e120, 09 2006. [ bib | DOI | http | Abstract ]
[Hornberg2006Cancer] J. J. Hornberg, F. J. Bruggeman, H. V. Westerhoff, and J. Lankelma. Cancer: a systems biology disease. Biosystems, 83(2-3):81-90, 2006. [ bib | DOI | http | .pdf | Abstract ]
[Hoheisel2006Microarray] J. D. Hoheisel. Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev Genet, 7(3):200-210, Mar 2006. [ bib | DOI | http | .pdf | Abstract ]
[GevaZatorsky2006MSB] N. Geva-Zatorsky, N. Rosenfeld, S. Itzkovitz, R. Milo, A. Sigal, E. Dekel, T. Yarnitzky, Y. Liron, P. Polak, G. Lahav, and U. Alon. Oscillations and variability in the p53 system. Mol Syst Biol, 2:2006 0033, 2006. [ bib | Abstract ]
[Freeman2006Copy] J. L. Freeman, G. H. Perry, L. Feuk, R. Redon, S. A. McCarroll, D. M. Altshuler, H. Aburatani, K. W. Jones, C. Tyler-Smith, M. E. Hurles, N. P. Carter, S. W. Scherer, and C. Lee. Copy number variation: new insights in genome diversity. Genome Res, 16(8):949-961, Aug 2006. [ bib | DOI | http | .pdf | Abstract ]
[Esquela-Kerscher2006Oncomirs] A. Esquela-Kerscher and F. J. Slack. Oncomirs - microRNAs with a role in cancer. Nat. Rev. Cancer, 6(4):259-269, Apr 2006. [ bib | DOI | http | .pdf | Abstract ]
[Calzone2006BIOCHAM] L. Calzone, F. Fages, and S. Soliman. BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics, 22(14):1805-1807, 2006. [ bib | DOI | arXiv | http | .pdf | Abstract ]
[Calin2006MicroRNA-cancer] G.A. Calin and C. M. Croce. MicroRNA-cancer connection: the beginning of a new tale. Cancer Res., 66(15):7390-7394, Aug 2006. [ bib | DOI | http | .pdf | Abstract ]
[Calin2006MicroRNA] G. A. Calin and C. M. Croce. MicroRNA signatures in human cancers. Nat. Rev. Cancer, 6(11):857-866, Nov 2006. [ bib | DOI | http | .pdf | Abstract ]
[Buyse2006Validation] M. Buyse, S. Loi, S. van't Veer, G. Viale, M. Delorenzi, A. M. Glas, M. Saghatchian d'Assignies, J. Bergh, R. Lidereau, P. Ellis, A. Harris, J. Bogaerts, P. Therasse, A. Floore, M. Amakrane, F. Piette, E. Rutgers, C. Sotiriou, F. Cardoso, M. J. Piccart, and T. R. A. N. S. B. I. G. Consortium. Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J. Natl. Canc. Inst., 98(17):1183-1192, Sep 2006. [ bib | DOI | http | .pdf | Abstract ]
[Bagci2006BiophysJ] E. Z. Bagci, Y. Vodovotz, T. R. Billiar, G. B. Ermentrout, and I. Bahar. Bistability in apoptosis: roles of bax, bcl-2, and mitochondrial permeability transition pores. Biophys J, 90(5):1546-59, 2006. [ bib | Abstract ]
[Frigola2006Epigenetic] J. Frigola, J. Song, C. Stirzaker, R. A. Hinshelwood, M. A. Peinado, and S. J. Clark. Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat. Genet., 38(5):540-549, May 2006. [ bib | DOI | http | .pdf | Abstract ]
[Weinberg2007Biology] R A Weinberg. The biology of cancer. Garland Science, Taylor & Francis Group, LLC, 2007. [ bib ]
[Vaidya2007Breast] Jayant S Vaidya. Breast cancer: an artistic view. The Lancet Oncology, 8:583-585, 2007. [ bib ]
[Npg2007DNA] Nature Publishing Group. DNA Technologies - Milestones timeline. Nature Milestones, 2007. http://www.nature.com/milestones/miledna/timeline.html. [ bib ]
[Mitelman2007Impact] F. Mitelman, B. Johansson, and F. Mertens. The impact of translocations and gene fusions on cancer causation. Nat. Rev. Cancer, 7:233-245, 2007. [ bib ]
[Miller2007Expression] L.D. Miller and E.T. Liu. Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine. Breast Cancer Res., 9:206, 2007. [ bib | DOI | http | .pdf | Abstract ]
[Loenning2007Breast] P. E. Lønning. Breast cancer prognostication and prediction: are we making progress? Ann. Oncol., 18 Suppl 8:viii3-viii7, Sep 2007. [ bib | DOI | http | .pdf | Abstract ]
[Li2007JBiosci] C. Li, Q. W. Ge, M. Nakata, H. Matsuno, and S. Miyano. Modelling and simulation of signal transductions in an apoptosis pathway by using timed petri nets. J Biosci, 32(1):113-27, 2007. [ bib | Abstract ]
[Lavrik2007JBC] I. N. Lavrik, A. Golks, D. Riess, M. Bentele, R. Eils, and P. H. Krammer. Analysis of cd95 threshold signaling: triggering of cd95 (fas/apo-1) at low concentrations primarily results in survival signaling. J Biol Chem, 282(18):13664-71, 2007. [ bib | Abstract ]
[Hudis2007Trastuzumab] C.A. Hudis. Trastuzumab-mechanism of action and use in clinical practice. N. Engl. J. Med., 357(1):39-51, Jul 2007. [ bib | DOI | http | .pdf ]
[Esteller2007Cancer] M. Esteller. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat. Rev. Genet., 8(4):286-298, Apr 2007. [ bib | DOI | http | .pdf | Abstract ]
[Eissing2007Responsea] T. Eissing, S. Waldherr, F. Allgower, P. Scheurich, and E. Bullinger. Response to bistability in apoptosis: Roles of bax, bcl-2, and mitochondrial permeability transition pores. Biophys. J., 92(9):3332-3334, 2007. [ bib | DOI | http ]
[Eissing2007Response] T. Eissing, S. Waldherr, F. Allgower, P. Scheurich, and E. Bullinger. Response to bistability in apoptosis: Roles of bax, bcl-2, and mitochondrial permeability transition pores. Biophysical Journal, 92(9):3332 - 3334, 2007. [ bib | DOI | http | .pdf ]
[Cowell2007application] J.K. Cowell and L. Hawthorn. The application of microarray technology to the analysis of the cancer genome. Curr. Mol. Med., 7(1):103-120, Feb 2007. [ bib | Abstract ]
[Choi2007Coupled] H.-S. Choi, S. Han, H. Yokota, and K.-H. Cho. Coupled positive feedbacks provoke slow induction plus fast switching in apoptosis. FEBS Letters, 581(14):2684 - 2690, 2007. [ bib | DOI | http | .pdf | Abstract ]
[Chen2007FEBS] C. Chen, J. Cui, W. Zhang, and P. Shen. Robustness analysis identifies the plausible model of the bcl-2 apoptotic switch. FEBS Lett, 581(26):5143-50, 2007. [ bib | Abstract ]
[Chen2007BiophysJ] C. Chen, J. Cui, H. Lu, R. Wang, S. Zhang, and P. Shen. Modeling of the role of a bax-activation switch in the mitochondrial apoptosis decision. Biophys J, 92(12):4304-15, 2007. [ bib | Abstract ]
[Aouba2007Les] A. Aouba, F. Péquignot, A. Le Toullec, and E. Jougla. Les causes médicales de décès en France en 2004 et leur évolution 1980-2004. Bulletin épidémiologique hebdomadaire, 35-36:308-314, 2007. [ bib | .pdf | .pdf ]
[Aguda2007PLOSCompBiol] B. D. Aguda and A. B. Goryachev. From pathways databases to network models of switching behavior. PLoS Comput Biol, 3(9):1674-8, 2007. [ bib ]
[Coe2007Resolving] B. P. Coe, B. Ylstra, B. Carvalho, G. A. Meijer, C. Macaulay, and W. L. Lam. Resolving the resolution of array CGH. Genomics, 89(5):647-653, May 2007. [ bib | DOI | http | .pdf | Abstract ]
[Zinovyev2008Bioinformatics] A. Zinovyev, E. Viara, L. Calzone, and E. Barillot. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics, 24(6):876-877, 2008. [ bib | DOI | arXiv | http | Abstract ]
[Watanabe2008Endogenous] T. Watanabe, Y. Totoki, A. Toyoda, M. Kaneda, S. Kuramochi-Miyagawa, Y. Obata, H. Chiba, Y. Kohara, T. Kono, T. Nakano, M.A. Surani, Y. Sakaki, and H. Sasaki. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature, 453:539-543, 2008. [ bib ]
[Vermeulen2008Cancer] L. Vermeulen, M.R. Sprick, K. Kemper, G. Stassi, and J.P. Medema. Cancer stem cells - old concepts, new insights. Cell Death and Differentiation, 15:947-58, 2008. [ bib ]
[Stratton2008Emerging] M.R. Stratton and N. Rahman. The emerging landscape of breast cancer susceptibility. Nat. Genet., 40:17-22, 2008. [ bib ]
[Shann2008Genome] Y.J. Shann, C. Cheng, C.H. Chiao, D.T. Chen, P.H. Li, and M.T. Hsu. Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines. Genome Res., 18:791-801, 2008. [ bib ]
[Schones2008Genome] Dustin E. Schones and Keji Zhao. Genome-wide approaches to studying chromatin modifications. Nat. Rev. Genet., 9:179-191, 2008. [ bib ]
[Sawyers2008cancer] C. L. Sawyers. The cancer biomarker problem. Nature, 452(7187):548-552, Apr 2008. [ bib | DOI | http | .pdf | Abstract ]
[Satzinger2008Theodor] Helga Satzinger. Theodor and Marcella Boveri: chromosomes and cytoplasm in heredity and development. Nat. Rev. Genet., 9:231-238, 2008. [ bib ]
[Rusk2008Primer] Nicole Rusk and Veronique Kiermer. Primer: Sequencing - the next generation. Nat. Methods, 5:15, 2008. [ bib ]
[Reinders2008Genome] Jon Reinders, Celine Delucinge Vivier, Gregory Theiler, Didier Chollet, Patrick Descombes, and Jerzy Paszkowski. Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Genome Res., 18:469-76, 2008. [ bib ]
[Lowery2008MicroRNAs] A. J. Lowery, N. Miller, R. E. McNeill, and M. J. Kerin. MicroRNAs as prognostic indicators and therapeutic targets: potential effect on breast cancer management. Clin. Cancer Res., 14(2):360-365, Jan 2008. [ bib | DOI | http | .pdf | Abstract ]
[Kim2008Insights] Eddo Kim, Amir Goren, and Gil Ast. Insights into the connection between cancer and alternative splicing. Trends Genet., 24:7-10, 2008. [ bib ]
[Kallioniemi2008CGH] A. Kallioniemi. CGH microarrays and cancer. Curr Opin Biotechnol, 19(1):36-40, Feb 2008. [ bib | DOI | http | .pdf | Abstract ]
[Han2008Apoptosis] L. Han, Y. Zhao, and X. Jia. Mathematical modeling identified c-flip as an apoptotic switch in death receptor induced apoptosis. Apoptosis, 13(10):1198-204, 2008. [ bib | Abstract ]
[Galluzzi2008Cell] L. Galluzzi and G. Kroemer. Necroptosis: A specialized pathway of programmed necrosis. Cell, 135(7):1161-1163, 2008. doi: DOI: 10.1016/j.cell.2008.12.004. [ bib ]
[Finetti2008Sixteen-kinase] P. Finetti, N. Cervera, E. Charafe-Jauffret, C. Chabannon, C. Charpin, M. Chaffanet, J. Jacquemier, P. Viens, D. Birnbaum, and F. Bertucci. Sixteen-kinase gene expression identifies luminal breast cancers with poor prognosis. Cancer Res., 68(3):767-776, Feb 2008. [ bib | DOI | http | .pdf | Abstract ]
[Filipowicz2008Mechanisms] W. Filipowicz, S. N. Bhattacharyya, and N. Sonenberg. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet., 9(2):102-114, Feb 2008. [ bib | DOI | http | .pdf | Abstract ]
[Fabbri2008MicroRNAs] M. Fabbri, C. M. Croce, and G. A. Calin. MicroRNAs. Cancer J., 14(1):1-6, 2008. [ bib | DOI | http | Abstract ]
[Esteller2008Epigenetics] M. Esteller. Epigenetics in cancer. N. Engl. J. Med., 358(11):1148-1159, Mar 2008. [ bib | DOI | http | .pdf ]
[Cui2008Two] J. Cui, C. Chen, H. Lu, T. Sun, and P. Shen. Two independent positive feedbacks and bistability in the bcl-2 apoptotic switch. PLoS ONE, 3(1):e1469, 01 2008. [ bib | DOI | http | .pdf | Abstract ]
[Croce2008Oncogenes] C. M. Croce. Oncogenes and cancer. N. Engl. J. Med., 358(5):502-511, Jan 2008. [ bib | DOI | http | .pdf ]
[Chin2008Translating] L. Chin and J. W. Gray. Translating insights from the cancer genome into clinical practice. Nature, 452(7187):553-563, Apr 2008. [ bib | DOI | http | .pdf | Abstract ]
[Chi2008year] K. R. Chi. The year of sequencing. Nat. Methods, 5(1):11-14, Jan 2008. [ bib | DOI | http | .pdf | Abstract ]
[Chen2008Mapping] Wei Chen, Vera Kalscheuer, Andreas Tzschach, Corinna Menzel, Reinhard Ullmann, Marcel Holger Schulz, Fikret Erdogan, Na Li, Zofia Kijas, Ger Arkesteijn, Isidora Lopez Pajares, Margret Goetz-Sothmann, Uwe Heinrich, Imma Rost, Andreas Dufke, Ute Grasshoff, Birgitta Glaeser, Martin Vingron, and H. Hilger Ropers. Mapping translocation breakpoints by next-generation sequencing. Genome Res., 18(7):1143-1149, Jul 2008. [ bib | DOI | http | .pdf | Abstract ]
[Calzone2008comprehensive] L. Calzone, A. Gelay, A. Zinovyev, F. Radvanyi, and E. Barillot. A comprehensive modular map of molecular interactions in RB/E2F pathway. Mol. Syst. Biol., 4:173, 2008. [ bib | DOI | http | .pdf | Abstract ]
[Blow2008DNA] N. Blow. DNA sequencing: generation next-next. Nat. Meth., 5(3):267-274, 2008. [ bib | DOI | http | .pdf | Abstract ]
[Bagci2008PLOS1] E. Z. Bagci, Y. Vodovotz, T. R. Billiar, B. Ermentrout, and I. Bahar. Computational insights on the competing effects of nitric oxide in regulating apoptosis. PLoS One, 3(5):e2249, 2008. [ bib | Abstract ]
[Aguilera2008Genome] A. Aguilera and B. Gómez-González. Genome instability: a mechanistic view of its causes and consequences. Nat. Rev. Genet., 9(3):204-217, Mar 2008. [ bib | DOI | http | .pdf | Abstract ]
[Veer2008Enabling] L. J. van't Veer and R. Bernards. Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature, 452(7187):564-570, Apr 2008. [ bib | DOI | http | .pdf | Abstract ]
[Tournier2009JTB] L. Tournier and M. Chaves. Uncovering operational interactions in genetic networks using asynchronous boolean dynamics. Journal of Theoretical Biology, 260(2):196-209, 2009. [ bib | DOI | http | Abstract ]
[Rehm2009Dynamics] M. Rehm, H. J. Huber, C. T. Hellwig, S. Anguissola, H. Dussmann, and J. H. M. Prehn. Dynamics of outer mitochondrial membrane permeabilization during apoptosis. Cell Death Differ., 16:613-623, 2009. [ bib | .html ]
[Rehm2009CellDeathDiff] M. Rehm, H. J. Huber, C. T. Hellwig, S. Anguissola, H. Dussmann, and J. H. M. Prehn. Dynamics of outer mitochondrial membrane permeabilization during apoptosis. Cell Death and Differentiation, 16:613 - 623, 2009. [ bib | .html ]
[Philippi2009BMCSysBio] N. Philippi, D. Walter, R. Schlatter, K. Ferreira, M. Ederer, O. Sawodny, J. Timmer, C. Borner, and T. Dandekar. Modeling system states in liver cells: survival, apoptosis and their modifications in response to viral infection. BMC Syst Biol, 3:97, 2009. [ bib | Abstract ]
[Li2009BriefBioinform] C. Li, M. Courtot, N. Le Novere, and C. Laibe. Biomodels.net web services, a free and integrated toolkit for computational modelling software. Brief Bioinform, 2009. [ bib | Abstract ]
[Declercq2009RIP] W. Declercq, T. Vanden Berghe, and P. Vandenabeele. RIP kinases at the crossroads of cell death and survival. Cell, 138(2):229-232, 2009. [ bib | DOI | http | .pdf ]
[Cianfrocca2009New] M. Cianfrocca and W. Gradishar. New molecular classifications of breast cancer. CA Cancer J. Clin., 59(5):303-313, 2009. [ bib | DOI | http | .pdf | Abstract ]
[Croce2009Causes] Carlo M. Croce. Causes and consequences of microRNA dysregulation in cancer. Nat Rev Genet, 10(10):704-714, October 2009. [ bib | DOI | http | .pdf ]

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