-
1
-
-
0036500993
-
Systems biology: A brief overview
-
Kitano H (2002) Systems biology: a brief overview. Science 295:1662-1664
-
(2002)
Science
, vol.295
, pp. 1662-1664
-
-
Kitano, H.1
-
2
-
-
0036500834
-
Reverse engineering of biological complexity
-
Csete ME, Doyle JC (2002) Reverse engineering of biological complexity. Science 295:1664-1669
-
(2002)
Science
, vol.295
, pp. 1664-1669
-
-
Csete, M.E.1
Doyle, J.C.2
-
3
-
-
34247342181
-
Rules of engagement
-
Doyle J, Csete M (2007) Rules of engagement. Nature 446:860
-
(2007)
Nature
, vol.446
, pp. 860
-
-
Doyle, J.1
Csete, M.2
-
4
-
-
44649178590
-
Translational research: From benchside to bedside
-
Keramaris NC, Kanakaris NK, Tzioupis C, Kontakis G, Giannoudis PV (2008) Translational research: from benchside to bedside. Injury 39:643-650
-
(2008)
Injury
, vol.39
, pp. 643-650
-
-
Keramaris, N.C.1
Kanakaris, N.K.2
Tzioupis, C.3
Kontakis, G.4
Giannoudis, P.V.5
-
5
-
-
22244442596
-
-
Innovation or stagnation: challenge and opportunity on the critical path to new medical products
-
Food and Drug Administration (2004) Innovation or stagnation: challenge and opportunity on the critical path to new medical products. 1-38
-
(2004)
Food and Drug Administration
, pp. 1-38
-
-
-
6
-
-
84868353805
-
-
NIH roadmap for medical research: research teams
-
Anonymous (2006) NIH roadmap for medical research: research teams
-
(2006)
Anonymous
-
-
-
7
-
-
84886759411
-
-
Anonymous (2007) http://nihroadmap.nih. gov/2008initiatives.asp
-
(2007)
Anonymous
-
-
-
8
-
-
68449099540
-
-
Alberghina L, Westerhoff HV (eds Systems biology: definitions and perspectives Springer, Berlin/Heidelberg
-
Snoep JL, Westerhoff HV (2005) From isolation to integration, a systems biology approach for building the silicon cell. In: Alberghina L, Westerhoff HV (eds) Systems biology: definitions and perspectives. Springer, Berlin/Heidelberg, p 7
-
(2005)
From Isolation to Integration, A Systems Biology Approach for Building the Silicon Cell
, pp. 7
-
-
Snoep, J.L.1
Westerhoff, H.V.2
-
9
-
-
34247587012
-
Genetics. Getting closer to the whole picture
-
Sauer U, Heinemann M, Zamboni N (2007) Genetics. Getting closer to the whole picture. Science 316:550-551
-
(2007)
Science
, vol.316
, pp. 550-551
-
-
Sauer, U.1
Heinemann, M.2
Zamboni, N.3
-
11
-
-
0037251105
-
Proteomics and systems biology approaches to signal transduction in sepsis
-
Nguyen A, Yaffe MB (2003) Proteomics and systems biology approaches to signal transduction in sepsis. Crit Care Med 31:S1-S6
-
(2003)
Crit Care Med
, vol.31
-
-
Nguyen, A.1
Yaffe, M.B.2
-
12
-
-
33751101584
-
Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: A case study of an NF-kappaB signalling pathway
-
Yue H, Brown M, Knowles J, Wang H et al (2006) Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-kappaB signalling pathway. Mol Biosyst 2:640-649
-
(2006)
Mol Biosyst
, vol.2
, pp. 640-649
-
-
Yue, H.1
Brown, M.2
Knowles, J.3
Wang, H.4
-
13
-
-
33646547951
-
Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4
-
Gilchrist M, Thorsson V, Li B et al (2006) Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 441:173-178
-
(2006)
Nature
, vol.441
, pp. 173-178
-
-
Gilchrist, M.1
Thorsson, V.2
Li, B.3
-
14
-
-
31444432847
-
The influence of the signal dynamics of activated form of IKK on NF-kappaB and anti-apoptotic gene expressions: A systems biology approach
-
Park SG, Lee T, Kang HY et al (2006) The influence of the signal dynamics of activated form of IKK on NF-kappaB and anti-apoptotic gene expressions: a systems biology approach. FEBS Lett 580:822-830
-
(2006)
FEBS Lett
, vol.580
, pp. 822-830
-
-
Park, S.G.1
Lee, T.2
Kang, H.Y.3
-
15
-
-
2942678943
-
Injury research in the genomic era
-
Cobb JP, O'Keefe GE (2004) Injury research in the genomic era. Lancet 363:2076-2083
-
(2004)
Lancet
, vol.363
, pp. 2076-2083
-
-
Cobb, J.P.1
O'keefe, G.E.2
-
16
-
-
27144509163
-
A network-based analysis of systemic inflammation in humans
-
Calvano SE, Xiao W, Richards DR et al (2005) A network-based analysis of systemic inflammation in humans. Nature 437:1032-1037
-
(2005)
Nature
, vol.437
, pp. 1032-1037
-
-
Calvano, S.E.1
Xiao, W.2
Richards, D.R.3
-
17
-
-
20144387327
-
Application of genome-wide expression analysis to human health and disease
-
Cobb JP, Mindrinos MN, Miller-Graziano C et al (2005) Application of genome-wide expression analysis to human health and disease. Proc Natl Acad Sci USA 102:4801-4806
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 4801-4806
-
-
Cobb, J.P.1
Mindrinos, M.N.2
Miller-Graziano, C.3
-
18
-
-
33645765157
-
Commonality and differences in leukocyte gene expression patterns among three models of inflammation and injury
-
Brownstein BH, Logvinenko T, Lederer JA et al (2006) Commonality and differences in leukocyte gene expression patterns among three models of inflammation and injury. Physiol Genomics 24:298-309
-
(2006)
Physiol Genomics
, vol.24
, pp. 298-309
-
-
Brownstein, B.H.1
Logvinenko, T.2
Lederer, J.A.3
-
19
-
-
33750629023
-
High dynamic range characterization of the trauma patient plasma proteome
-
Liu T, Qian WJ, Gritsenko MA et al (2006) High dynamic range characterization of the trauma patient plasma proteome. Mol Cell Proteomics 5:1899-1913
-
(2006)
Mol Cell Proteomics
, vol.5
, pp. 1899-1913
-
-
Liu, T.1
Qian, W.J.2
Gritsenko, M.A.3
-
20
-
-
33750600311
-
Strategies for plasma proteomic profiling of cancers
-
Omenn GS (2006) Strategies for plasma proteomic profiling of cancers. Proteomics 6:5662-5673
-
(2006)
Proteomics
, vol.6
, pp. 5662-5673
-
-
Omenn, G.S.1
-
21
-
-
34247853423
-
Current challenges and approaches for the synergistic use of systems biology data in the scientific community
-
Ahrens CH, Wagner U, Rehrauer HK et al (2007) Current challenges and approaches for the synergistic use of systems biology data in the scientific community. EXS 97:277-307
-
(2007)
EXS
, vol.97
, pp. 277-307
-
-
Ahrens, C.H.1
Wagner, U.2
Rehrauer, H.K.3
-
22
-
-
34247886045
-
Integrated data analysis for genomewide research
-
Steinfath M, Repsilber D, Scholz M et al (2007) Integrated data analysis for genomewide research. EXS 97:309-329
-
(2007)
EXS
, vol.97
, pp. 309-329
-
-
Steinfath, M.1
Repsilber, D.2
Scholz, M.3
-
23
-
-
34248165485
-
Genomics and proteomics: The potential role of oral diagnostics
-
Tanke HJ (2007) Genomics and proteomics: the potential role of oral diagnostics. Ann N Y Acad Sci 1098:330-334
-
(2007)
Ann N y Acad Sci
, vol.1098
, pp. 330-334
-
-
Tanke, H.J.1
-
25
-
-
34249826054
-
Challenges and rewards on the road to translational systems biology in acute illness: Four case reports from interdisciplinary teams
-
An G, Hunt CA, Clermont G, Neugebauer E, Vodovotz Y (2007) Challenges and rewards on the road to translational systems biology in acute illness: four case reports from interdisciplinary teams. J Crit Care 22:169-175
-
(2007)
J Crit Care
, vol.22
, pp. 169-175
-
-
An, G.1
Hunt, C.A.2
Clermont, G.3
Neugebauer, E.4
Vodovotz, Y.5
-
26
-
-
41849114552
-
Translational systems biology: Introduction of an engineering approach to the pathophysiology of the burn patient
-
An G, Vodovotz Y (2008) Translational systems biology: introduction of an engineering approach to the pathophysiology of the burn patient. J Burn Care Res 29:277-285
-
(2008)
J Burn Care Res
, vol.29
, pp. 277-285
-
-
An, G.1
Vodovotz, Y.2
-
27
-
-
43249089766
-
Translational systems biology of inflammation
-
Vodovotz Y, Csete M, Bartels J, Chang S, An G (2008) Translational systems biology of inflammation. PLoS Comput Biol 4:1-6
-
(2008)
PLoS Comput Biol
, vol.4
, pp. 1-6
-
-
Vodovotz, Y.1
Csete, M.2
Bartels, J.3
Chang An, S.G.4
-
28
-
-
57749172576
-
Mechanistic simulations of inflammation: Current state and future prospects
-
Vodovotz Y, Constantine G, Rubin J, Csete M, Voit EO et al (2009) Mechanistic simulations of inflammation: current state and future prospects. Math Biosci 217:1-10
-
(2009)
Math Biosci
, vol.217
, pp. 1-10
-
-
Vodovotz, Y.1
Constantine, G.2
Rubin, J.3
Csete, M.4
Voit, E.O.5
-
29
-
-
0035491584
-
Agent-based computer simulation and SIRS: Building a bridge between basic science and clinical trials
-
An G (2001) Agent-based computer simulation and SIRS: building a bridge between basic science and clinical trials. Shock 16:266-273
-
(2001)
Shock
, vol.16
, pp. 266-273
-
-
An, G.1
-
30
-
-
4744344132
-
In-silico experiments of existing and hypothetical cytokine-directed clinical trials using agent based modeling
-
An G (2004) In-silico experiments of existing and hypothetical cytokine-directed clinical trials using agent based modeling. Crit Care Med 32:2050-2060
-
(2004)
Crit Care Med
, vol.32
, pp. 2050-2060
-
-
An, G.1
-
32
-
-
4043056616
-
Silico design of clinical trials: A method coming of age
-
Clermont G, Bartels J, Kumar R, Constantine G, Vodovotz Y et al (2004) In silico design of clinical trials: a method coming of age. Crit Care Med 32:2061-2070
-
(2004)
Crit Care Med
, vol.32
, pp. 2061-2070
-
-
Clermont, G.1
Bartels, J.2
Kumar, R.3
Constantine, G.4
Vodovotz, Y.5
-
33
-
-
21744440089
-
The acute inflammatory response in diverse shock states
-
Chow CC, Clermont G, Kumar R et al (2005) The acute inflammatory response in diverse shock states. Shock 24:74-84
-
(2005)
Shock
, vol.24
, pp. 74-84
-
-
Chow, C.C.1
Clermont, G.2
Kumar, R.3
-
34
-
-
33747341838
-
Silico models of acute inflammation in animals
-
Vodovotz Y, Chow CC, Bartels J et al (2006) In silico models of acute inflammation in animals. Shock 26:235-244
-
(2006)
Shock
, vol.26
, pp. 235-244
-
-
Vodovotz, Y.1
Chow, C.C.2
Bartels, J.3
-
35
-
-
33749022785
-
Silico and in vivo approach to elucidate the inflammatory complexity of CD14-deficient mice
-
Prince JM, Levy RM, Bartels J et al (2006) In silico and in vivo approach to elucidate the inflammatory complexity of CD14-deficient mice. Mol Med 12:88-96
-
(2006)
Mol Med
, vol.12
, pp. 88-96
-
-
Prince, J.M.1
Levy, R.M.2
Bartels, J.3
-
36
-
-
33751222859
-
The role of initial trauma in the host's response to injury and hemorrhage: Insights from a comparison of mathematical simulations and hepatic transcriptomic analysis
-
Lagoa CE, Bartels J, Baratt A et al (2006) The role of initial trauma in the host's response to injury and hemorrhage: insights from a comparison of mathematical simulations and hepatic transcriptomic analysis. Shock 26:592-600
-
(2006)
Shock
, vol.26
, pp. 592-600
-
-
Lagoa, C.E.1
Bartels, J.2
Baratt, A.3
-
37
-
-
27644466709
-
Dynamics of intrapulmonary bacterial growth in a murine model of repeated microaspiration
-
Ben David I, Price SE, Bortz DM et al (2005) Dynamics of intrapulmonary bacterial growth in a murine model of repeated microaspiration. Am J Respir Cell Mol Biol 33:476-482
-
(2005)
Am J Respir Cell Mol Biol
, vol.33
, pp. 476-482
-
-
Ben David, I.1
Price, S.E.2
Bortz, D.M.3
-
38
-
-
34848830242
-
Agent-based model of inflammation and wound healing: Insights into diabetic foot ulcer pathology and the role of transforming growth factor-b1
-
Mi Q, Rivière B, Clermont G et al (2007) Agent-based model of inflammation and wound healing: insights into diabetic foot ulcer pathology and the role of transforming growth factor-b1. Wound Rep Reg 15:617-682
-
(2007)
Wound Rep Reg
, vol.15
, pp. 617-682
-
-
Mi, Q.1
Rivière, B.2
Clermont, G.3
-
39
-
-
34147167183
-
A dynamical model of human immune response to influenza A virus infection
-
Hancioglu B, Swigon D, Clermont G (2007) A dynamical model of human immune response to influenza A virus infection. J Theor Biol 246:70-86
-
(2007)
J Theor Biol
, vol.246
, pp. 70-86
-
-
Hancioglu, B.1
Swigon, D.2
Clermont, G.3
-
40
-
-
37549004342
-
A mathematical simulation of the inflammatory response to anthrax infection
-
Kumar R, Chow CC, Bartels J et al (2008) A mathematical simulation of the inflammatory response to anthrax infection. Shock 29:104-111
-
(2008)
Shock
, vol.29
, pp. 104-111
-
-
Kumar, R.1
Chow, C.C.2
Bartels, J.3
-
41
-
-
38049150027
-
Complexity, emergence and pathophysiology: Using agent based computer simulation to characterize the nonadaptive inflammatory response (Manuscript # 344
-
May
-
An G, Lee I (2000) Complexity, emergence and pathophysiology: using agent based computer simulation to characterize the nonadaptive inflammatory response (Manuscript # 344). InterJournal Complex Systems: http://www.interjournal.org May
-
(2000)
InterJournal Complex Systems
-
-
An, G.1
Lee, I.2
-
42
-
-
57849158644
-
Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning
-
An G, Faeder JR (2009) Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. Math Biosci 217:53-63
-
(2009)
Math Biosci
, vol.217
, pp. 53-63
-
-
An, G.1
Faeder, J.R.2
-
43
-
-
46449119246
-
Introduction of a agent based multi-scale modular architecture for dynamic knowledge representation of acute inflammation
-
An G (2008) Introduction of a agent based multi-scale modular architecture for dynamic knowledge representation of acute inflammation. Theor Biol Med Model 5:11
-
(2008)
Theor Biol Med Model
, vol.5
, pp. 11
-
-
An, G.1
-
44
-
-
57849103868
-
A model of TLR4 signaling and tolerance using a qualitative, particle eventbased method: Introduction of spatially configured stochastic reaction chambers
-
An G (2009) A model of TLR4 signaling and tolerance using a qualitative, particle eventbased method: introduction of spatially configured stochastic reaction chambers (SCSRC). Math Biosci 217:43-52
-
(2009)
SCSRC Math Biosci
, vol.217
, pp. 43-52
-
-
An, G.1
-
46
-
-
33747106908
-
A reduced mathematical model of the acute inflammatory response: I. Derivation of model and analysis of antiinflammation
-
Reynolds A, Rubin J, Clermont G et al (2006) A reduced mathematical model of the acute inflammatory response: I. Derivation of model and analysis of antiinflammation. J Theor Biol 242:220-236
-
(2006)
J Theor Biol
, vol.242
, pp. 220-236
-
-
Reynolds, A.1
Rubin, J.2
Clermont, G.3
-
47
-
-
33747094446
-
A reduced mathematical model of the acute inflammatory response: II. Capturing scenarios of repeated endotoxin administration
-
Day J, Rubin J, Vodovotz Y et al (2006) A reduced mathematical model of the acute inflammatory response: II. Capturing scenarios of repeated endotoxin administration. J Theor Biol 242:237-256
-
(2006)
J Theor Biol
, vol.242
, pp. 237-256
-
-
Day, J.1
Rubin, J.2
Vodovotz, Y.3
-
48
-
-
33646124974
-
Bistability in apoptosis: Roles of bax Bcl-2 and mitochondrial permeability transition pores
-
Bagci EZ, Vodovotz Y, Billiar TR et al (2006) Bistability in apoptosis: roles of bax, Bcl-2 and mitochondrial permeability transition pores. Biophys J 90:1546-1559
-
(2006)
Biophys J
, vol.90
, pp. 1546-1559
-
-
Bagci, E.Z.1
Vodovotz, Y.2
Billiar, T.R.3
-
49
-
-
48449104356
-
Computational insights on the competing effects of nitric oxide in regulating apoptosis
-
Bagci EZ, Vodovotz Y, Billiar TR et al (2008) Computational insights on the competing effects of nitric oxide in regulating apoptosis. PLoS One 3:e2249
-
(2008)
PLoS One
, vol.3
-
-
Bagci, E.Z.1
Vodovotz, Y.2
Billiar, T.R.3
-
50
-
-
57749186048
-
A simple mathematical model of signaling resulting from the binding of lipopolysaccharide with Toll-like receptor 4 demonstrates inherent preconditioning behavior
-
Rivière B, Epshteyn Y, Swigon D, Vodovotz Y (2009) A simple mathematical model of signaling resulting from the binding of lipopolysaccharide with Toll-like receptor 4 demonstrates inherent preconditioning behavior. Math Biosci 217:19-26
-
(2009)
Math Biosci
, vol.217
, pp. 19-26
-
-
Rivière, B.1
Epshteyn, Y.2
Swigon, D.3
Vodovotz, Y.4
-
51
-
-
47849114337
-
An ensemble of models of the acute inflammatory response to bacterial lipopolysaccharide in rats: Results from parameter space reduction
-
Daun S, Rubin J, Vodovotz Y et al (2008) An ensemble of models of the acute inflammatory response to bacterial lipopolysaccharide in rats: results from parameter space reduction. J Theor Biol 253:843-853
-
(2008)
J Theor Biol
, vol.253
, pp. 843-853
-
-
Daun, S.1
Rubin, J.2
Vodovotz, Y.3
-
52
-
-
67749139592
-
Mathematical modeling of post-hemorrhage inflammation in mice: Studies using a novel, computer-controlled, closed-loop hemorrhage apparatus
-
Torres A, Bentley T, Bartels J et al (2008) Mathematical modeling of post-hemorrhage inflammation in mice: studies using a novel, computer-controlled, closed-loop hemorrhage apparatus. Shock 32:172-178
-
(2008)
Shock
, vol.32
, pp. 172-178
-
-
Torres, A.1
Bentley, T.2
Bartels, J.3
-
53
-
-
0027415226
-
Cellular automata approaches to biological modeling
-
Ermentrout GB, Edelstein-Keshet L (1993) Cellular automata approaches to biological modeling. J Theor Biol 160:97-133
-
(1993)
J Theor Biol
, vol.160
, pp. 97-133
-
-
Ermentrout, G.B.1
Edelstein-Keshet, L.2
-
55
-
-
36849055522
-
Onedimensional elastic continuum model of epithelial wound healing
-
Mi Q, Riviere B, Cetin S et al (2007) Onedimensional elastic continuum model of epithelial wound healing. Biophys J 93:3745-3752
-
(2007)
Biophys J
, vol.93
, pp. 3745-3752
-
-
Mi, Q.1
Riviere, B.2
Cetin, S.3
-
56
-
-
10244219918
-
BioNetGen: Software for rulebased modeling of signal transduction based on the interactions of molecular domains
-
Blinov ML, Faeder JR, Goldstein B, Hlavacek WS (2004) BioNetGen: software for rulebased modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 20:3289-3291
-
(2004)
Bioinformatics
, vol.20
, pp. 3289-3291
-
-
Blinov, M.L.1
Faeder, J.R.2
Goldstein, B.3
Hlavacek, W.S.4
-
57
-
-
84934434959
-
BioNetGen: A tool for formal knowledge representation of intracellular pathways
-
Faeder JR, Hlavacek WS, An G (2007) BioNetGen: a tool for formal knowledge representation of intracellular pathways. Shock 27(S1):S31
-
(2007)
Shock
, vol.27
, Issue.1
-
-
Faeder, J.R.1
Hlavacek An, W.S.G.2
-
59
-
-
0025275951
-
Pulmonary capillary dynamics and fluid distribution after burn and inhalation injury
-
Roa L, Gomez-Cia T, Cantero A (1990) Pulmonary capillary dynamics and fluid distribution after burn and inhalation injury. Burns 16:25-35
-
(1990)
Burns
, vol.16
, pp. 25-35
-
-
Roa, L.1
Gomez-Cia, T.2
Cantero, A.3
-
60
-
-
0030969159
-
Fluid resuscitation following a burn injury: Implications of a mathematical model of microvascular exchange
-
Bert J, Gyenge C, Bowen B et al (1997) Fluid resuscitation following a burn injury: implications of a mathematical model of microvascular exchange. Burns 23:93-105
-
(1997)
Burns
, vol.23
, pp. 93-105
-
-
Bert, J.1
Gyenge, C.2
Bowen, B.3
-
61
-
-
4544238686
-
Quantitative dynamics of in vivo bone marrow neutrophil production and egress in response to injury and infection
-
Rosinski M, Yarmush ML, Berthiaume F (2004) Quantitative dynamics of in vivo bone marrow neutrophil production and egress in response to injury and infection. Ann Biomed Eng 32:1108-1119
-
(2004)
Ann Biomed Eng
, vol.32
, pp. 1108-1119
-
-
Rosinski, M.1
Yarmush, M.L.2
Berthiaume, F.3
-
62
-
-
33846935020
-
The establishment of the mathematical model of the 2nd degree burn injury of human tissues and its application
-
Feng Q, Zhao-Yan H, Zheng-Kang Z, Li-Xing S (2005) The establishment of the mathematical model of the 2nd degree burn injury of human tissues and its application. Conf Proc IEEE Eng Med Biol Soc 3:2918-2921
-
(2005)
Conf Proc IEEE Eng Med Biol Soc
, vol.3
, pp. 2918-2921
-
-
Feng, Q.1
Zhao-Yan, H.2
Zheng-Kang, Z.3
Li-Xing, S.4
-
63
-
-
27944438859
-
Modeling thermal burns due to airbag deployment
-
Mercer GN, Sidhu HS (2005) Modeling thermal burns due to airbag deployment. Burns 31:977-980
-
(2005)
Burns
, vol.31
, pp. 977-980
-
-
Mercer, G.N.1
Sidhu, H.S.2
-
64
-
-
33646079394
-
Theoretical evaluation of burns to the human respiratory tract due to inhalation of hot gas in the early stage of fires
-
Lv YG, Liu J, Zhang J (2006) Theoretical evaluation of burns to the human respiratory tract due to inhalation of hot gas in the early stage of fires. Burns 32:436-446
-
(2006)
Burns
, vol.32
, pp. 436-446
-
-
Lv, Y.G.1
Liu, J.2
Zhang, J.3
-
65
-
-
33846487889
-
Mathematical modelling of aerosolised skin grafts incorporating keratinocyte clonal subtypes
-
Denman PK, McElwain DL, Harkin DG, Upton Z (2007) Mathematical modelling of aerosolised skin grafts incorporating keratinocyte clonal subtypes. Bull Math Biol 69:157-179
-
(2007)
Bull Math Biol
, vol.69
, pp. 157-179
-
-
Denman, P.K.1
McElwain, D.L.2
Harkin, D.G.3
Upton, Z.4
-
66
-
-
1642462948
-
Computational physiology and the Physiome Project
-
Crampin EJ, Halstead M, Hunter P et al (2004) Computational physiology and the Physiome Project. Exp Physiol 89:1-26
-
(2004)
Exp Physiol
, vol.89
, pp. 1-26
-
-
Crampin, E.J.1
Halstead, M.2
Hunter, P.3
-
67
-
-
33645985742
-
Agent based model of cell culture epithelial barrier function: Using computer simulation in conjunction with a basic science model
-
An G (2004) Agent based model of cell culture epithelial barrier function: using computer simulation in conjunction with a basic science model. Shock 21(Suppl 2):S13
-
(2004)
Shock
, vol.21
, Issue.13 SUPPL. 2
-
-
An, G.1
-
69
-
-
33645982172
-
In-silico unification of different basic science models of gut epithelial barrier function using agent based modeling
-
An G, Feinman R, Xu D, Deitch E (2004) In-silico unification of different basic science models of gut epithelial barrier function using agent based modeling. Crit Care Med 32:A95
-
(2004)
Crit Care Med
, vol.32
-
-
An, G.1
Feinman, R.2
Xu, D.3
Deitch, E.4
-
70
-
-
84857762971
-
Multi-hierarchical agent-based modeling of the inflammatory aspects of the gut
-
An G (2005) Multi-hierarchical agent-based modeling of the inflammatory aspects of the gut. J Crit Care 20:383
-
(2005)
J Crit Care
, vol.20
, pp. 383
-
-
An, G.1
-
71
-
-
41849128360
-
Agent based models of pulmonary epithelial barrier function
-
An G (2006) Agent based models of pulmonary epithelial barrier function. Proc Am Thorac Soc 3:A309
-
(2006)
Proc Am Thorac Soc
, vol.3
-
-
An, G.1
-
72
-
-
34249821557
-
Computer simulations of multiple organ failure secondary to shock and sepsis with a multi-tissue, endothelial level agent based model
-
An G (2004) Computer simulations of multiple organ failure secondary to shock and sepsis with a multi-tissue, endothelial level agent based model. Shock 21S2:66
-
(2004)
Shock 21S2
, vol.66
-
-
An, G.1
-
73
-
-
0033787566
-
Metabolic networks: A signal-oriented approach to cellular models
-
Lengeler JW (2000) Metabolic networks: a signal-oriented approach to cellular models. Biol Chem 381:911-920
-
(2000)
Biol Chem
, vol.381
, pp. 911-920
-
-
Lengeler, J.W.1
-
74
-
-
0036837507
-
Mathematical modelling for the new millenium: Medicine by numbers
-
Smye SW, Clayton RH (2002) Mathematical modelling for the new millenium: medicine by numbers. Med Eng Phys 24:565-574
-
(2002)
Med Eng Phys
, vol.24
, pp. 565-574
-
-
Smye, S.W.1
Clayton, R.H.2
-
75
-
-
2942588906
-
Mathematical and computational models of immune-receptor signalling
-
Goldstein B, Faeder JR et al (2004) Mathematical and computational models of immune-receptor signalling. Nat Rev Immunol 4:445-456
-
(2004)
Nat Rev Immunol
, vol.4
, pp. 445-456
-
-
Goldstein, B.1
Faeder, J.R.2
-
77
-
-
20344368797
-
Making waves: Pattern formation by a cellsurface- associated signal
-
Stevens A, Sogaard-Andersen L (2005) Making waves: pattern formation by a cellsurface- associated signal. Trends Microbiol 13:249-252
-
(2005)
Trends Microbiol
, vol.13
, pp. 249-252
-
-
Stevens, A.1
Sogaard-Andersen, L.2
-
79
-
-
3142781475
-
CNplot: Visualizing pre-clustered networks
-
Batada NN (2004) CNplot: visualizing pre-clustered networks. Bioinformatics 20:1455-1456
-
(2004)
Bioinformatics
, vol.20
, pp. 1455-1456
-
-
Batada, N.N.1
-
80
-
-
13444309633
-
ProViz: Protein interaction visualization and exploration
-
Iragne F, Nikolski M et al (2005) ProViz: protein interaction visualization and exploration. Bioinformatics 21:272-274
-
(2005)
Bioinformatics
, vol.21
, pp. 272-274
-
-
Iragne, F.1
Nikolski, M.2
-
81
-
-
33645832196
-
PIANA: Protein interactions and network analysis
-
Aragues R, Jaeggi D, Oliva B (2006) PIANA: protein interactions and network analysis. Bioinformatics 22:1015-1017
-
(2006)
Bioinformatics
, vol.22
, pp. 1015-1017
-
-
Aragues, R.1
Jaeggi, D.2
Oliva, B.3
-
82
-
-
33645151090
-
PathSys: Integrating molecular interaction graphs for systems biology
-
Baitaluk M, Qian X et al (2006) PathSys: integrating molecular interaction graphs for systems biology. BMC Bioinform 7:55
-
(2006)
BMC Bioinform
, vol.7
, pp. 55
-
-
Baitaluk, M.1
Qian, X.2
-
83
-
-
33646203362
-
WebCell: A webbased environment for kinetic modeling and dynamic simulation of cellular networks
-
Lee DY, Yun C et al (2006) WebCell: a webbased environment for kinetic modeling and dynamic simulation of cellular networks. Bioinformatics 22:1150-1151
-
(2006)
Bioinformatics
, vol.22
, pp. 1150-1151
-
-
Lee, D.Y.1
Yun, C.2
-
84
-
-
33847253388
-
From bytes to bedside: Data integration and computational biology for translational cancer research
-
Mathew JP, Taylor BS et al (2007) From bytes to bedside: data integration and computational biology for translational cancer research. PLoS Comput Biol 3:e12
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Mathew, J.P.1
Taylor, B.S.2
-
85
-
-
84934436266
-
Crossing levels of biological organization: Agent based modeling of genomic/proteomic data
-
An G (2007) Crossing levels of biological organization: agent based modeling of genomic/proteomic data. Inflamm Res 56(Suppl 2):s208-s209
-
(2007)
Inflamm Res
, vol.56 SUPPL. 2
-
-
An, G.1
-
86
-
-
33645957683
-
Concepts for developing a collaborative in silico model of the acute inflammatory response using agent-based modeling
-
An G (2006) Concepts for developing a collaborative in silico model of the acute inflammatory response using agent-based modeling. J Crit Care 21:105-110
-
(2006)
J Crit Care
, vol.21
, pp. 105-110
-
-
An, G.1
-
89
-
-
4644335402
-
Systems biology, proteomics, and the future of health care: Toward predictive, preventative, and personalized medicine
-
Weston AD, Hood L (2004) Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res 3:179-196
-
(2004)
J Proteome Res
, vol.3
, pp. 179-196
-
-
Weston, A.D.1
Hood, L.2
-
90
-
-
34249778602
-
Mathematical model predicting outcomes of sepsis patients treated with Xigris(R): ENHANCE trial
-
Chang S, Baratt A et al (2006) Mathematical model predicting outcomes of sepsis patients treated with Xigris(R): ENHANCE trial. Shock 25:70-71
-
(2006)
Shock
, vol.25
, pp. 70-71
-
-
Chang, S.1
Baratt, A.2
-
91
-
-
0036598961
-
Inflammation. 1: Its role in the healing of acute wounds
-
Hart J (2002) Inflammation. 1: its role in the healing of acute wounds. J Wound Care 11:205-209
-
(2002)
J Wound Care
, vol.11
, pp. 205-209
-
-
Hart, J.1
-
92
-
-
0036635809
-
Inflammation. 2: Its role in the healing of chronic wounds
-
Hart J (2002) Inflammation. 2: its role in the healing of chronic wounds. J Wound Care 11:245-249
-
(2002)
J Wound Care
, vol.11
, pp. 245-249
-
-
Hart, J.1
-
93
-
-
0042838281
-
Inflammatory mediators as essential elements in bone remodeling
-
Goldring SR (2003) Inflammatory mediators as essential elements in bone remodeling. Calcif Tissue Int 73:97-100
-
(2003)
Calcif Tissue Int
, vol.73
, pp. 97-100
-
-
Goldring, S.R.1
-
94
-
-
2942731600
-
The role of biomechanics and inflammation in cartilage injury and repair
-
Guilak F, Fermor B et al (2004) The role of biomechanics and inflammation in cartilage injury and repair. Clin Orthop 423:17-26
-
(2004)
Clin Orthop
, vol.423
, pp. 17-26
-
-
Guilak, F.1
Fermor, B.2
-
95
-
-
4444300866
-
Inflammation, damage repair, immune cells, and liver fibrosis: Specific or nonspecific, this is the question
-
Ramadori G, Saile B (2004) Inflammation, damage repair, immune cells, and liver fibrosis: specific or nonspecific, this is the question. Gastroenterology 127:997-1000
-
(2004)
Gastroenterology
, vol.127
, pp. 997-1000
-
-
Ramadori, G.1
Saile, B.2
-
96
-
-
2542421285
-
Wound healing and inflammation: Embryos reveal the way to perfect repair
-
Redd MJ, Cooper L et al (2004) Wound healing and inflammation: embryos reveal the way to perfect repair. Philos Trans R Soc Lond B Biol Sci 359:777-784
-
(2004)
Philos Trans R Soc Lond B Biol Sci
, vol.359
, pp. 777-784
-
-
Redd, M.J.1
Cooper, L.2
-
97
-
-
2542478053
-
Wound healing: An overview of acute, fibrotic and delayed healing
-
Diegelmann RF, Evans MC (2004) Wound healing: an overview of acute, fibrotic and delayed healing. Front Biosci 9:283-289
-
(2004)
Front Biosci
, vol.9
, pp. 283-289
-
-
Diegelmann, R.F.1
Evans, M.C.2
-
98
-
-
45449124064
-
Mechanochemical models for generating biological pattern and form in development
-
Murray JD, Maini PK, Tranquillo R (1988) Mechanochemical models for generating biological pattern and form in development. Phys Rep 171:59-84
-
(1988)
Phys Rep
, vol.171
, pp. 59-84
-
-
Murray, J.D.1
Maini, P.K.2
Tranquillo, R.3
-
100
-
-
0025074095
-
Models of epidermal wound healing
-
Sherratt JA, Murray JD (1990) Models of epidermal wound healing. Proc Biol Sci 241:29-36
-
(1990)
Proc Biol Sci
, vol.241
, pp. 29-36
-
-
Sherratt, J.A.1
Murray, J.D.2
-
101
-
-
0026799246
-
Model of fibroblast-driven wound contraction: Inflammation-mediation
-
Continuum
-
Tranquillo RT, Murray JD (1992) Continuum model of fibroblast-driven wound contraction: inflammation-mediation. J Theor Biol 158:135-172
-
(1992)
J Theor Biol
, vol.158
, pp. 135-172
-
-
Tranquillo, R.T.1
Murray, J.D.2
-
102
-
-
0027491019
-
Mechanistic model of wound contraction
-
Tranquillo RT, Murray JD (1993) Mechanistic model of wound contraction. J Surg Res 55:233-247
-
(1993)
J Surg Res
, vol.55
, pp. 233-247
-
-
Tranquillo, R.T.1
Murray, J.D.2
-
103
-
-
0009920219
-
A mathematical model for dermal wound healing: Wound contraction and scar formation [dissertation]
-
Cook J (1995) A mathematical model for dermal wound healing: wound contraction and scar formation [dissertation]. University of Washington, Seattle
-
(1995)
University of Washington Seattle
-
-
Cook, J.1
-
104
-
-
0029584674
-
A mechanochemical model for adult dermal wound contraction and the permanence of the contracted tissue displacement profile
-
Olsen L, Sherratt JA, Maini PK (1995) A mechanochemical model for adult dermal wound contraction and the permanence of the contracted tissue displacement profile. J Theor Biol 177:113-128
-
(1995)
J Theor Biol
, vol.177
, pp. 113-128
-
-
Olsen, L.1
Sherratt, J.A.2
Maini, P.K.3
-
105
-
-
0034798578
-
Modeling the effects of transforming growth factor-beta on extracellular matrix alignment in dermal wound repair
-
Dallon JC, Sherratt JA, Maini PK (2001) Modeling the effects of transforming growth factor-beta on extracellular matrix alignment in dermal wound repair. Wound Repair Regen 9:278-286
-
(2001)
Wound Repair Regen
, vol.9
, pp. 278-286
-
-
Dallon, J.C.1
Sherratt, J.A.2
Maini, P.K.3
-
106
-
-
0036332895
-
Theoretical models of wound healing: Past successes and future challenges
-
Sherratt JA, Dallon JC (2002) Theoretical models of wound healing: past successes and future challenges. C R Biol 325:557-564
-
(2002)
C R Biol
, vol.325
, pp. 557-564
-
-
Sherratt, J.A.1
Dallon, J.C.2
-
107
-
-
4544247005
-
Agent-based computational modeling of epithelial cell monolayers: Predicting the effect of exogenous calcium concentration on the rate of wound closure
-
Walker DC, Hill G et al (2004) Agent-based computational modeling of epithelial cell monolayers: predicting the effect of exogenous calcium concentration on the rate of wound closure. IEEE Trans Nanobioscience 3:153-163
-
(2004)
IEEE Trans Nanobioscience
, vol.3
, pp. 153-163
-
-
Walker, D.C.1
Hill, G.2
-
108
-
-
4444350085
-
The epitheliome: Agent-based modelling of the social behaviour of cells
-
Walker DC, Southgate J et al (2004) The epitheliome: agent-based modelling of the social behaviour of cells. Biosystems 76:89-100
-
(2004)
Biosystems
, vol.76
, pp. 89-100
-
-
Walker, D.C.1
Southgate, J.2
-
109
-
-
33847274571
-
Mathematical modeling in NEC - A new look at an ongoing problem
-
Upperman JS, Lugo B et al (2007) Mathematical modeling in NEC - a new look at an ongoing problem. J Pediatr Surg 42:445-453
-
(2007)
J Pediatr Surg
, vol.42
, pp. 445-453
-
-
Upperman, J.S.1
Lugo, B.2
-
110
-
-
17644413577
-
Disordered enterocyte signaling and intestinal barrier dysfunction in the pathogenesis of necrotizing enterocolitis
-
Hackam DJ, Upperman JS et al (2005) Disordered enterocyte signaling and intestinal barrier dysfunction in the pathogenesis of necrotizing enterocolitis. Semin Pediatr Surg 14:49-57
-
(2005)
Semin Pediatr Surg
, vol.14
, pp. 49-57
-
-
Hackam, D.J.1
Upperman, J.S.2
-
111
-
-
50949091234
-
A patientspecific in silico model of inflammation and healing tested in acute vocal fold injury
-
Li NYK, Verdolini K et al (2008) A patientspecific in silico model of inflammation and healing tested in acute vocal fold injury. PLoS ONE 3:e2789
-
(2008)
PLoS ONE
, vol.3
-
-
Nyk, L.1
Verdolini, K.2
-
113
-
-
0037066427
-
The danger model: A renewed sense of self
-
Matzinger P (2002) The danger model: a renewed sense of self. Science 296:301-305
-
(2002)
Science
, vol.296
, pp. 301-305
-
-
Matzinger, P.1
-
114
-
-
33750312909
-
Emerging paradigm: Toll-like receptor 4-sentinel for the detection of tissue damage
-
Mollen KP, Anand RJ et al (2006) Emerging paradigm: toll-like receptor 4-sentinel for the detection of tissue damage. Shock 26:430-437
-
(2006)
Shock
, vol.26
, pp. 430-437
-
-
Mollen, K.P.1
Anand, R.J.2
-
115
-
-
20244373939
-
The nuclear factor HMGB1 mediates hepatic injury after murine liver ischemia-reperfusion
-
Tsung A, Sahai R et al (2005) The nuclear factor HMGB1 mediates hepatic injury after murine liver ischemia-reperfusion. J Exp Med 201:1135-1143
-
(2005)
J Exp Med
, vol.201
, pp. 1135-1143
-
-
Tsung, A.1
Sahai, R.2
-
116
-
-
33744932946
-
Cutting edge: High-mobility group box 1 preconditioning protects against liver ischemia-reperfusion injury
-
Izuishi K, Tsung A et al (2006) Cutting edge: high-mobility group box 1 preconditioning protects against liver ischemia-reperfusion injury. J Immunol 176:7154-7158
-
(2006)
J Immunol
, vol.176
, pp. 7154-7158
-
-
Izuishi, K.1
Tsung, A.2
-
117
-
-
33749019109
-
Anti-HMGB1 neutralizing antibody ameliorates gut barrier dysfunction and improves survival after hemorrhagic shock
-
Yang R, Harada T et al (2006) Anti-HMGB1 neutralizing antibody ameliorates gut barrier dysfunction and improves survival after hemorrhagic shock. Mol Med 12:105-114
-
(2006)
Mol Med
, vol.12
, pp. 105-114
-
-
Yang, R.1
Harada, T.2
-
118
-
-
33845869847
-
Increasing numbers of hepatic dendritic cells promote HMGB1-mediated ischemia-reperfusion injury
-
Tsung A, Zheng N et al (2007) Increasing numbers of hepatic dendritic cells promote HMGB1-mediated ischemia-reperfusion injury. J Leukoc Biol 81:119-128
-
(2007)
J Leukoc Biol
, vol.81
, pp. 119-128
-
-
Tsung, A.1
Zheng, N.2
-
119
-
-
34248228729
-
Hemorrhagic shock induces NAD(P)H oxidase activation in neutrophils: Role of HMGB1-TLR4 signaling
-
Fan J, Li Y et al (2007) Hemorrhagic shock induces NAD(P)H oxidase activation in neutrophils: role of HMGB1-TLR4 signaling. J Immunol 178:6573-6580
-
(2007)
J Immunol
, vol.178
, pp. 6573-6580
-
-
Fan, J.1
Li, Y.2
-
120
-
-
36548999695
-
HMGB1 release induced by liver ischemia involves Toll-like receptor 4 dependent reactive oxygen species production and calcium-mediated signaling
-
Tsung A, Klune JR et al (2007) HMGB1 release induced by liver ischemia involves Toll-like receptor 4 dependent reactive oxygen species production and calcium-mediated signaling. J Exp Med 204:2913-2923
-
(2007)
J Exp Med
, vol.204
, pp. 2913-2923
-
-
Tsung, A.1
Klune, J.R.2
-
121
-
-
48149096398
-
HMGB1: Endogenous danger signaling
-
Klune JR, Dhupar R et al (2008) HMGB1: endogenous danger signaling. Mol Med 14:476-484
-
(2008)
Mol Med
, vol.14
, pp. 476-484
-
-
Klune, J.R.1
Dhupar, R.2
-
122
-
-
43349095360
-
HMGB1 preconditioning therapeutic application for a danger signal?
-
Klune JR, Billiar TR, Tsung A (2008) HMGB1 preconditioning: therapeutic application for a danger signal? J Leukoc Biol 83:558-563
-
(2008)
J Leukoc Biol
, vol.83
, pp. 558-563
-
-
Klune, J.R.1
Billiar, T.R.2
Tsung, A.3
-
123
-
-
55549133613
-
Preconditioning with high mobility group box 1 (HMGB1) induces lipopolysaccharide (LPS) tolerance
-
Aneja RK, Tsung A, Sjodin H, Gefter JV, Delude RL et al (2008) Preconditioning with high mobility group box 1 (HMGB1) induces lipopolysaccharide (LPS) tolerance. J Leukoc Biol 84(5):1326-1334
-
(2008)
J Leukoc Biol
, vol.84
, Issue.5
, pp. 1326-1334
-
-
Aneja, R.K.1
Tsung, A.2
Sjodin, H.3
Gefter, J.V.4
Delude, R.L.5
-
124
-
-
0034698830
-
High mobility group 1 protein (HMG-1) stimulates proinflammatory cytokine synthesis in human monocytes
-
Andersson U, Wang H, Palmblad K, Aveberger AC, Bloom O et al (2000) High mobility group 1 protein (HMG-1) stimulates proinflammatory cytokine synthesis in human monocytes. J Exp Med 192:565-570
-
(2000)
J Exp Med
, vol.192
, pp. 565-570
-
-
Andersson, U.1
Wang, H.2
Palmblad, K.3
Aveberger, A.C.4
Bloom, O.5
-
125
-
-
34447643247
-
HMGB1 modulates inflammatory responses in LPS-activated macrophages
-
El GM (2007) HMGB1 modulates inflammatory responses in LPS-activated macrophages. Inflamm Res 56:162-167
-
(2007)
Inflamm Res
, vol.56
, pp. 162-167
-
-
El, G.M.1
-
126
-
-
28544446736
-
Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection
-
Dunbar SA (2006) Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection. Clin Chim Acta 363:71-82
-
(2006)
Clin Chim Acta
, vol.363
, pp. 71-82
-
-
Dunbar, S.A.1
-
127
-
-
48249151773
-
A simple, rapid, and convenient Luminex-compatible method of tissue isolation
-
Barclay D, Zamora R, Torres A, Namas R, Steed D et al (2008) A simple, rapid, and convenient Luminex-compatible method of tissue isolation. J Clin Lab Anal 22:278-281
-
(2008)
J Clin Lab Anal
, vol.22
, pp. 278-281
-
-
Barclay, D.1
Zamora, R.2
Torres, A.3
Namas, R.4
Steed, D.5
-
128
-
-
58149262632
-
Local exposure of bone components to injured soft tissue induces Toll-like-receptor-4 dependent systemic inflammation with acute lung injury
-
Kobbe P, Kaczorowski D, Vodovotz Y, Tzioupis C, Mollen KP et al (2008) Local exposure of bone components to injured soft tissue induces Toll-like-receptor-4 dependent systemic inflammation with acute lung injury. Shock 30:686-691
-
(2008)
Shock
, vol.30
, pp. 686-691
-
-
Kobbe, P.1
Kaczorowski, D.2
Vodovotz, Y.3
Tzioupis, C.4
Mollen, K.P.5
-
129
-
-
51549112628
-
Patterns of cytokine release and evolution of remote organ dysfunction after bilateral femur fracture
-
Kobbe P, Vodovotz Y, Kaczorowski D, Mollen KP, Billiar TR et al (2008) Patterns of cytokine release and evolution of remote organ dysfunction after bilateral femur fracture. Shock 30:43-47
-
(2008)
Shock
, vol.30
, pp. 43-47
-
-
Kobbe, P.1
Vodovotz, Y.2
Kaczorowski, D.3
Mollen, K.P.4
Billiar, T.R.5
-
130
-
-
28844441230
-
A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis
-
Janes KA, Albeck JG, Gaudet S, Sorger PK, Lauffenburger DA et al (2005) A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310:1646-1653
-
(2005)
Science
, vol.310
, pp. 1646-1653
-
-
Janes, K.A.1
Albeck, J.G.2
Gaudet, S.3
Sorger, P.K.4
Lauffenburger, D.A.5
-
131
-
-
17244380380
-
A survey of current work in biomedical text mining
-
Cohen AM, Hersh WR (2005) A survey of current work in biomedical text mining. Brief Bioinform 6:57-71
-
(2005)
Brief Bioinform
, vol.6
, pp. 57-71
-
-
Cohen, A.M.1
Hersh, W.R.2
-
132
-
-
27744487007
-
Text mining and ontologies in biomedicine: Making sense of raw text
-
Spasic I, Ananiadou S, McNaught J, Kumar A (2005) Text mining and ontologies in biomedicine: making sense of raw text. Brief Bioinform 6:239-251
-
(2005)
Brief Bioinform
, vol.6
, pp. 239-251
-
-
Spasic, I.1
Ananiadou, S.2
McNaught, J.3
Kumar, A.4
-
133
-
-
5644230749
-
Through a glass darkly: The brave new world of in silico modeling
-
Marshall JC (2004) Through a glass darkly: the brave new world of in silico modeling. Crit Care Med 32:2157-2159
-
(2004)
Crit Care Med
, vol.32
, pp. 2157-2159
-
-
Marshall, J.C.1
|