Polynomial algebra reveals diverging roles of the unfolded protein response in endothelial cells during ischemia–reperfusion injury

[1]  R. J. Unwin,et al.  Kidney , 1969 .

[2]  A. Stephanou,et al.  Apoptosis of Endothelial Cells Precedes Myocyte Cell Apoptosis in Ischemia/Reperfusion Injury , 2001, Circulation.

[3]  F. Speleman,et al.  Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes , 2002, Genome Biology.

[4]  F. Luan Kidney transplantation from donors without a heartbeat. , 2002, The New England journal of medicine.

[5]  D. Ron,et al.  CHOP induces death by promoting protein synthesis and oxidation in the stressed endoplasmic reticulum. , 2004, Genes & development.

[6]  R. Laubenbacher,et al.  A computational algebra approach to the reverse engineering of gene regulatory networks. , 2003, Journal of theoretical biology.

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

[8]  Mark A Sussman,et al.  Hypoxic Cultured Cardiac Myocytes Activation of the Unfolded Protein Response in Infarcted Mouse Heart , 2006 .

[9]  Abdul Salam Jarrah,et al.  A Gröbner fan method for biochemical network modeling , 2007, ISSAC '07.

[10]  D. di Bernardo,et al.  How to infer gene networks from expression profiles , 2007, Molecular systems biology.

[11]  P. Walter,et al.  Signal integration in the endoplasmic reticulum unfolded protein response , 2007, Nature Reviews Molecular Cell Biology.

[12]  John Calvin Reed,et al.  Cell death and endoplasmic reticulum stress: disease relevance and therapeutic opportunities , 2008, Nature Reviews Drug Discovery.

[13]  D. di Bernardo,et al.  Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering. , 2008, Genome research.

[14]  J. Weissman,et al.  Regulated Ire1-dependent decay of messenger RNAs in mammalian cells , 2009, The Journal of cell biology.

[15]  C. Hetz,et al.  Fine-tuning of the unfolded protein response: Assembling the IRE1alpha interactome. , 2009, Molecular cell.

[16]  V. Beneš,et al.  The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. , 2009, Clinical chemistry.

[17]  Elena S. Dimitrova Estimating the Volumes of the Cones in a Gröbner Fan , 2010, Math. Comput. Sci..

[18]  Abdul Salam Jarrah,et al.  Polynomial algebra of discrete models in systems biology , 2010, Bioinform..

[19]  M. Christiaans,et al.  Kidney Transplantation From Donors After Cardiac Death: A 25-Year Experience , 2010, Transplantation.

[20]  Abdul Salam Jarrah,et al.  Probabilistic polynomial dynamical systems for reverse engineering of gene regulatory networks , 2011, EURASIP J. Bioinform. Syst. Biol..

[21]  D. Ron,et al.  Integrating the mechanisms of apoptosis induced by endoplasmic reticulum stress , 2011, Nature Cell Biology.

[22]  P. Beaune,et al.  Metabolic stress promotes renal tubular inflammation by triggering the unfolded protein response , 2011, Cell Death and Disease.

[23]  T. Eckle,et al.  Ischemia and reperfusion—from mechanism to translation , 2011, Nature Medicine.

[24]  J. Bonventre,et al.  Cellular pathophysiology of ischemic acute kidney injury. , 2011, The Journal of clinical investigation.

[25]  A. Koong,et al.  Identification of an Ire1alpha endonuclease specific inhibitor with cytotoxic activity against human multiple myeloma. , 2011, Blood.

[26]  C. Hetz The unfolded protein response: controlling cell fate decisions under ER stress and beyond , 2012, Nature Reviews Molecular Cell Biology.

[27]  R. Silverman,et al.  The molecular basis for selective inhibition of unconventional mRNA splicing by an IRE1-binding small molecule , 2012, Proceedings of the National Academy of Sciences.

[28]  R. Kaufman,et al.  The impact of the unfolded protein response on human disease , 2012, The Journal of cell biology.

[29]  Shiuan Wey,et al.  Acute Inducible Ablation of GRP78 Reveals Its Role in Hematopoietic Stem Cell Survival, Lymphogenesis and Regulation of Stress Signaling , 2012, PloS one.

[30]  J. Roselló-Catafau,et al.  IGL-1 solution reduces endoplasmic reticulum stress and apoptosis in rat liver transplantation , 2012, Cell Death and Disease.

[31]  Jun Pang,et al.  Recent development and biomedical applications of probabilistic Boolean networks , 2013, Cell Communication and Signaling.

[32]  Lisa M. Ryno,et al.  Stress-independent activation of XBP1s and/or ATF6 reveals three functionally diverse ER proteostasis environments. , 2013, Cell reports.

[33]  B. Stigler,et al.  Inferring the Topology of Gene Regulatory Networks: An Algebraic Approach to Reverse Engineering , 2013 .

[34]  Terrell L. Hodge,et al.  Mathematical Concepts and Methods in Modern Biology , 2013 .

[35]  D. Ron,et al.  Membrane lipid saturation activates endoplasmic reticulum unfolded protein response transducers through their transmembrane domains , 2013, Proceedings of the National Academy of Sciences.

[36]  R. Kaufman,et al.  ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death , 2013, Nature Cell Biology.