Elucidation of functional consequences of signalling pathway interactions

[1]  Paola Lecca,et al.  Calibration of dynamic models of biological systems with KInfer , 2010, European Biophysics Journal.

[2]  Corrado Priami,et al.  BlenX4Bio - BlenX for Biologists , 2009, CMSB.

[3]  Corrado Priami,et al.  Algorithmic systems biology , 2009, CACM.

[4]  Michael B. Yaffe,et al.  Signaling Networks and Mathematics , 2008, Science Signaling.

[5]  N. Tanaka,et al.  IKK/NF-κB signaling pathway inhibits cell-cycle progression by a novel Rb-independent suppression system for E2F transcription factors , 2008, Oncogene.

[6]  Corrado Priami,et al.  The Beta Workbench: a computational tool to study the dynamics of biological systems , 2008, Briefings Bioinform..

[7]  Kenneth H. Buetow,et al.  PID: the Pathway Interaction Database , 2008, Nucleic Acids Res..

[8]  Dianne P. O'Leary,et al.  Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality , 2008, PLoS Comput. Biol..

[9]  Krin A. Kay,et al.  The implications of human metabolic network topology for disease comorbidity , 2008, Proceedings of the National Academy of Sciences.

[10]  N. Tanaka,et al.  Activated p53 induces NF-kappaB DNA binding but suppresses its transcriptional activation. , 2008, Biochemical and biophysical research communications.

[11]  Nobuyuki Tanaka,et al.  p53 regulates glucose metabolism through an IKK-NF-κB pathway and inhibits cell transformation , 2008, Nature Cell Biology.

[12]  E. Barillot,et al.  A comprehensive modular map of molecular interactions in RB/E2F pathway , 2008, Molecular systems biology.

[13]  K. Raj,et al.  Protective mechanisms of p53-p21-pRb proteins against DNA damage-induced cell death , 2008, Cell cycle.

[14]  N. Perkins,et al.  Retracted: A cell cycle regulatory network controlling NF‐κB subunit activity and function , 2007, The EMBO journal.

[15]  B. Alberts,et al.  Molecular Biology of the Cell 4th edition , 2007 .

[16]  Alvis Brazma,et al.  Current approaches to gene regulatory network modelling , 2007, BMC Bioinformatics.

[17]  Joshy George,et al.  Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. , 2007, Molecular cell.

[18]  Luonan Chen,et al.  Discovering functions and revealing mechanisms at molecular level from biological networks , 2007, Proteomics.

[19]  John J. Tyson,et al.  Irreversible cell-cycle transitions are due to systems-level feedback , 2007, Nature Cell Biology.

[20]  U. Alon.  Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.

[21]  Yi Pan,et al.  Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications , 2007 .

[22]  I. Jurisica,et al.  Unequal evolutionary conservation of human protein interactions in interologous networks , 2007, Genome Biology.

[23]  Aidong Zhang,et al.  Clustering Methods in a Protein–Protein Interaction Network , 2007 .

[24]  N. Perkins,et al.  p53 and NF-?B Crosstalk: IKKa Tips the Balance , 2007 .

[25]  Dominic Waithe,et al.  Bridging the gap between in silico and cell‐based analysis of the nuclear factor‐κB signaling pathway by in vitro studies of IKK2 , 2007, The FEBS journal.

[26]  Robert Tibshirani,et al.  Disease-specific genomic analysis: identifying the signature of pathologic biology , 2007, Bioinform..

[27]  Mark Gerstein,et al.  The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics , 2007, PLoS Comput. Biol..

[28]  K. Vousden.  Outcomes of p53 activation - spoilt for choice , 2006, Journal of Cell Science.

[29]  Sandeep Krishna,et al.  Oscillation patterns in negative feedback loops , 2006, Proceedings of the National Academy of Sciences.

[30]  N. Perkins,et al.  Regulation of p53 tumour suppressor target gene expression by the p52 NF‐κB subunit , 2006, The EMBO journal.

[31]  Peng Wang,et al.  Machine learning in bioinformatics: A brief survey and recommendations for practitioners , 2006, Comput. Biol. Medicine.

[32]  Kyu-Chul Lee,et al.  Finding the evidence for protein-protein interactions from PubMed abstracts , 2006, ISMB.

[33]  R. Milo,et al.  Oscillations and variability in the p53 system , 2006, Molecular systems biology.

[34]  Alvis Brazma,et al.  Modelling in molecular biology: describing transcription regulatory networks at different scales , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[35]  Concha Bielza,et al.  Machine Learning in Bioinformatics , 2008, Encyclopedia of Database Systems.

[36]  Edward E Allen,et al.  Algebraic dependency models of protein signal transduction networks from time-series data. , 2006, Journal of theoretical biology.

[37]  D S Broomhead,et al.  Synergistic control of oscillations in the NF-kappaB signalling pathway. , 2005, Systems biology.

[38]  John Jeremy Rice,et al.  A plausible model for the digital response of p53 to DNA damage. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[39]  D B Kell,et al.  Metabolomics, machine learning and modelling: towards an understanding of the language of cells. , 2005, Biochemical Society transactions.

[40]  G. Casari,et al.  From molecular networks to qualitative cell behavior , 2005, FEBS letters.

[41]  Galit Lahav,et al.  The Strength of Indecisiveness: Oscillatory Behavior for Better Cell Fate Determination , 2004, Science's STKE.

[42]  Lincoln Stein,et al.  Reactome: a knowledgebase of biological pathways , 2004, Nucleic Acids Res..

[43]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..

[44]  James R. Johnson,et al.  Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression , 2004, Science.

[45]  Julien Gagneur,et al.  Modular decomposition of protein-protein interaction networks , 2004, Genome Biology.

[46]  B. Andrews,et al.  Protein-protein interaction affinity plays a crucial role in controlling the Sho1p-mediated signal transduction pathway in yeast. , 2004, Molecular cell.

[47]  David S. Broomhead,et al.  Sensitivity analysis of parameters controlling oscillatory signalling in the NF-/sub K/Bpathway: the roles of IKK and I/sub K/B/sub alpha/ , 2004 .

[48]  N. Dyson,et al.  Molecular mechanisms of E2F-dependent activation and pRB-mediated repression , 2004, Journal of Cell Science.

[49]  David J Harrison,et al.  Additive effect of p53, p21 and Rb deletion in triple knockout primary hepatocytes , 2004, Oncogene.

[50]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[51]  U. Alon,et al.  Dynamics of the p53-Mdm2 feedback loop in individual cells , 2004, Nature Genetics.

[52]  R. Milo,et al.  Topological generalizations of network motifs. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[53]  Michael Lappe,et al.  From gene networks to gene function. , 2003, Genome research.

[54]  I. Verma,et al.  IκB Kinase-Independent IκBα Degradation Pathway: Functional NF-κB Activity and Implications for Cancer Therapy , 2003, Molecular and Cellular Biology.

[55]  P. Robbins,et al.  The role of the transcription factor DP in apoptosis , 2003, Apoptosis.

[56]  L. Mirny,et al.  Protein complexes and functional modules in molecular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[57]  A. Goldbeter.  Computational approaches to cellular rhythms , 2002, Nature.

[58]  A. Hoffmann,et al.  The I (cid:1) B –NF-(cid:1) B Signaling Module: Temporal Control and Selective Gene Activation , 2022 .

[59]  Martin Steffen,et al.  Automated modelling of signal transduction networks , 2002, BMC Bioinformatics.

[60]  P. Brazhnik,et al.  Gene networks: how to put the function in genomics. , 2002, Trends in biotechnology.

[61]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[62]  A. Leonardi,et al.  Association of the Adaptor TANK with the IκB Kinase (IKK) Regulator NEMO Connects IKK Complexes with IKKε and TBK1 Kinases* , 2002, The Journal of Biological Chemistry.

[63]  G. Wahl,et al.  p53 stabilization is decreased upon NFκB activation , 2002 .

[64]  Beom Jun Kim,et al.  Path finding strategies in scale-free networks. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[65]  N. Dyson,et al.  Functional antagonism between E2F family members. , 2001, Genes & development.

[66]  K. Vousden,et al.  E2F-1 induced apoptosis , 2001, Apoptosis.

[67]  S. Strogatz.  Exploring complex networks , 2001, Nature.

[68]  Chris Albanese,et al.  NF-κB and cell-cycle regulation: the cyclin connection , 2001 .

[69]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[70]  G. Dotto,et al.  p21(WAF1/Cip1): more than a break to the cell cycle? , 2000, Biochimica et biophysica acta.

[71]  K. Vousden,et al.  E2F-1 potentiates cell death by blocking antiapoptotic signaling pathways. , 1999, Molecular cell.

[72]  A. Barabasi,et al.  Emergence of Scaling in Random Networks , 1999 .

[73]  Christian Kaltschmidt,et al.  Repression of NF-κB impairs HeLa cell proliferation by functional interference with cell cycle checkpoint regulators , 1999, Oncogene.

[74]  N. Perkins,et al.  Transcriptional Cross Talk between NF-κB and p53 , 1999, Molecular and Cellular Biology.

[75]  Kevin Ryan,et al.  The alternative product from the human CDKN2A locus, p14ARF, participates in a regulatory feedback loop with p53 and MDM2 , 1998, The EMBO journal.

[76]  F. Zindy,et al.  Functional and physical interactions of the ARF tumor suppressor with p53 and Mdm2. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[77]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[78]  Ken Chen,et al.  The Ink4a Tumor Suppressor Gene Product, p19Arf, Interacts with MDM2 and Neutralizes MDM2's Inhibition of p53 , 1998, Cell.

[79]  Donald E. Knuth,et al.  The Art of Computer Programming, Volume I: Fundamental Algorithms, 2nd Edition , 1997 .

[80]  A. Goldbeter.  A model for circadian oscillations in the Drosophila period protein (PER) , 1995, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[81]  S. Pfeffer,et al.  Molecular Biology of the Cell , 2021, Biophysics for Beginners.

[82]  E. Kay,et al.  Introductory Graph Theory , 1978 .

[83]  Leonard M. Freeman,et al.  A set of measures of centrality based upon betweenness , 1977 .

[84]  M. Karin,et al.  Is NF-kappaB a good target for cancer therapy? Hopes and pitfalls. , 2009 .

[85]  Michael Karin,et al.  Is NF-κB a good target for cancer therapy? Hopes and pitfalls , 2009, Nature Reviews Drug Discovery.

[86]  Corrado Priami,et al.  Algorithmic Systems Biology: An Opportunity for Computer Science , 2008 .

[87]  N. Perkins,et al.  p53 and NF-kappaB crosstalk: IKKalpha tips the balance. , 2007, Molecular cell.

[88]  N. Perkins,et al.  Integrating cell-signalling pathways with NF-kappaB and IKK function. , 2007, Nature reviews. Molecular cell biology.

[89]  N. Perkins,et al.  Integrating cell-signalling pathways with NF-κB and IKK function , 2007, Nature Reviews Molecular Cell Biology.

[90]  N. Perkins,et al.  Regulation of NF-kappaB function. , 2006, Biochemical Society symposium.

[91]  B. Baguley,et al.  Do negative feedback oscillations drive variations in the length of the tumor cell division cycle? , 2005, Oncology research.

[92]  Hannu Toivonen,et al.  Data Mining In Bioinformatics , 2005 .

[93]  See-Kiong Ng,et al.  Discovering Protein-protein Interactions , 2004, J. Bioinform. Comput. Biol..

[94]  D B Kell,et al.  Oscillations in NF-kappaB signaling control the dynamics of gene expression. , 2004, Science.

[95]  D. Broomhead,et al.  Sensitivity analysis of parameters controlling oscillatory signalling in the NFk B pathway : the roles of IKK and I k B a , 2004 .

[96]  Uri Alon,et al.  Topological generalizations of network motifs. Phys Rev E 70:031909 , 2004 .

[97]  Upinder S Bhalla,et al.  Understanding complex signaling networks through models and metaphors. , 2003, Progress in biophysics and molecular biology.

[98]  Jeffrey M. Trimarchi,et al.  Transcription: Sibling rivalry in the E2F family , 2002, Nature Reviews Molecular Cell Biology.

[99]  A. Leonardi,et al.  Association of the adaptor TANK with the I kappa B kinase (IKK) regulator NEMO connects IKK complexes with IKK epsilon and TBK1 kinases. , 2002, The Journal of biological chemistry.

[100]  A. Hoffmann,et al.  The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. , 2002, Science.

[101]  G. Wahl,et al.  p53 stabilization is decreased upon NFkappaB activation: a role for NFkappaB in acquisition of resistance to chemotherapy. , 2002, Cancer cell.

[102]  C. Albanese,et al.  NF-kappaB and cell-cycle regulation: the cyclin connection. , 2001, Cytokine & growth factor reviews.

[103]  Ronald L. Rivest,et al.  Introduction to Algorithms, Second Edition , 2001 .

[104]  N. Perkins,et al.  Transcriptional cross talk between NF-kappaB and p53. , 1999, Molecular and cellular biology.

[105]  M J May,et al.  NF-kappa B and Rel proteins: evolutionarily conserved mediators of immune responses. , 1998, Annual review of immunology.

[106]  Frank Harary,et al.  Graph Theory , 2016 .