-
1
-
-
0033637404
-
Finding pathogenicity islands and gene transfer events in genome data
-
10.1093/bioinformatics/16.10.932, 11120683
-
Lió P, Vannucci M. Finding pathogenicity islands and gene transfer events in genome data. Bioinformatics 2000, 16:932-940. 10.1093/bioinformatics/16.10.932, 11120683.
-
(2000)
Bioinformatics
, vol.16
, pp. 932-940
-
-
Lió, P.1
Vannucci, M.2
-
2
-
-
33645429016
-
Exact Stochastic Simulation of Coupled Chemical Reactions
-
Gillespie DT. Exact Stochastic Simulation of Coupled Chemical Reactions. The Journal of Physical Chemistry 1977, 81(25):2340-2361.
-
(1977)
The Journal of Physical Chemistry
, vol.81
, Issue.25
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
3
-
-
0028874048
-
Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection
-
10.1038/373123a0, 7816094
-
Ho D, Neumann AU, Perelson AS, Chen W, Leonard JM, M M. Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 1995, 373:123-126. 10.1038/373123a0, 7816094.
-
(1995)
Nature
, vol.373
, pp. 123-126
-
-
Ho, D.1
Neumann, A.U.2
Perelson, A.S.3
Chen, W.4
Leonard, J.M.5
M, M.6
-
5
-
-
0036371443
-
Modelling viral and immune system dynamics
-
Perelson AS. Modelling viral and immune system dynamics. Nature Review Immunology 2002, 2(1):28-36.
-
(2002)
Nature Review Immunology
, vol.2
, Issue.1
, pp. 28-36
-
-
Perelson, A.S.1
-
7
-
-
34648857564
-
Modeling HIV quasispecies evolutionary dynamics
-
10.1186/1471-2148-7-S2-S5, 1963478, 17767733
-
Sguanci L, Bagnoli F, Li P. Modeling HIV quasispecies evolutionary dynamics. BMC Evolutionary Biology 2007, 7(2):S5. 10.1186/1471-2148-7-S2-S5, 1963478, 17767733.
-
(2007)
BMC Evolutionary Biology
, vol.7
, Issue.2
-
-
Sguanci, L.1
Bagnoli, F.2
Li, P.3
-
9
-
-
33748059883
-
Modeling viral coevolution. HIV multi-clonal persistence and competition dynamics
-
Bagnoli F, Lio' P, Sguanci L. Modeling viral coevolution. HIV multi-clonal persistence and competition dynamics. Physica A 2005, 366:333-346.
-
(2005)
Physica A
, vol.366
, pp. 333-346
-
-
Bagnoli, F.1
Lio', P.2
Sguanci, L.3
-
10
-
-
1942485417
-
A stochastic model of cytotoxic T cell responses
-
Chao L, Davenport MP, Forrest S, Perelson AS. A stochastic model of cytotoxic T cell responses. Journal Theoretical Biology 2004, 228:227-240.
-
(2004)
Journal Theoretical Biology
, vol.228
, pp. 227-240
-
-
Chao, L.1
Davenport, M.P.2
Forrest, S.3
Perelson, A.S.4
-
11
-
-
0030026711
-
Affinity maturation and hypermutation in a simulation of the humoral immune response
-
Celada F, Seiden PE. Affinity maturation and hypermutation in a simulation of the humoral immune response. Journal of Theoretical Biology 1996, 26:1350-1358.
-
(1996)
Journal of Theoretical Biology
, vol.26
, pp. 1350-1358
-
-
Celada, F.1
Seiden, P.E.2
-
12
-
-
0028982445
-
Towards a general function describing T cell proliferation
-
De Boer RJ, Perelson AS. Towards a general function describing T cell proliferation. European Journal of Immunology 1995, 175(4):567-576.
-
(1995)
European Journal of Immunology
, vol.175
, Issue.4
, pp. 567-576
-
-
De Boer, R.J.1
Perelson, A.S.2
-
13
-
-
2342559084
-
Some scaling principles for the immune system
-
10.1046/j.0818-9641.2004.01229.x, 15061763
-
Wiegel FW, Perelson AS. Some scaling principles for the immune system. Immunology and Cell Biology 2004, 82:127-131. 10.1046/j.0818-9641.2004.01229.x, 15061763.
-
(2004)
Immunology and Cell Biology
, vol.82
, pp. 127-131
-
-
Wiegel, F.W.1
Perelson, A.S.2
-
14
-
-
0037179670
-
Cells as computation
-
10.1038/419343a, 12353013
-
Regev A, Shapiro E. Cells as computation. Nature 2002, 419:343. 10.1038/419343a, 12353013.
-
(2002)
Nature
, vol.419
, pp. 343
-
-
Regev, A.1
Shapiro, E.2
-
15
-
-
35448938139
-
Symbolic modeling of genetic regulatory networks
-
10.1142/S0219720007002850, 17636866, B
-
Mateus D, Gallois JP, Comet E. Symbolic modeling of genetic regulatory networks. Journal of Bioinformatics and Computational Biology 2007, 5(2B):627-640. 10.1142/S0219720007002850, 17636866.
-
(2007)
Journal of Bioinformatics and Computational Biology
, vol.5
, Issue.2
, pp. 627-640
-
-
Mateus, D.1
Gallois, J.P.2
Comet, E.3
-
16
-
-
57649188962
-
Analysing gene regulatory networks by both constraint programming and model-checking
-
Fromentin J, Comet JP, Le Gall P, Roux O. Analysing gene regulatory networks by both constraint programming and model-checking. Conference proceedings, IEEE Engineering in Medicine and Biology 2007, 4595-4598.
-
(2007)
Conference proceedings, IEEE Engineering in Medicine and Biology
, pp. 4595-4598
-
-
Fromentin, J.1
Comet, J.P.2
Le Gall, P.3
Roux, O.4
-
17
-
-
34548747486
-
Robustness analysis and tuning of synthetic gene networks
-
10.1093/bioinformatics/btm362, 17660209
-
Batt G, Yordanov B, Weiss R, Belta C. Robustness analysis and tuning of synthetic gene networks. Bioinformatics 2007, 23:2415-2422. 10.1093/bioinformatics/btm362, 17660209.
-
(2007)
Bioinformatics
, vol.23
, pp. 2415-2422
-
-
Batt, G.1
Yordanov, B.2
Weiss, R.3
Belta, C.4
-
18
-
-
84860513120
-
Validation of qualitative models of genetic regulatory networks by model checking. Analysis of the nutritional stress response in E. coli
-
10.1093/bioinformatics/bti1048, 15961457
-
Batt G, Ropers D, De Jong H, Geiselmann J, Mateescu R, Page M, Schneider D. Validation of qualitative models of genetic regulatory networks by model checking. Analysis of the nutritional stress response in E. coli. Bioinformatics 2005, 21(Suppl 1):i19-i28. 10.1093/bioinformatics/bti1048, 15961457.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Batt, G.1
Ropers, D.2
De Jong, H.3
Geiselmann, J.4
Mateescu, R.5
Page, M.6
Schneider, D.7
-
20
-
-
84874658228
-
The PRISM model checker
-
The PRISM model checker. , http://www.prismmodelchecker.org
-
-
-
-
21
-
-
6344237375
-
Coevolution of RANTES sensitivity and mode of CCR5 receptor use by human immunodeficiency virus type 1 of the R5 phenotype
-
10.1128/JVI.78.21.11807-11815.2004, 523262, 15479822
-
Karlsson I, Antonsson L, Shi Y, Oberg M, Karlsson A, Albert J, Olde B, Owman C, M J, Fenyo EM. Coevolution of RANTES sensitivity and mode of CCR5 receptor use by human immunodeficiency virus type 1 of the R5 phenotype. Journal of Virology 2004, 78:11807-11815. 10.1128/JVI.78.21.11807-11815.2004, 523262, 15479822.
-
(2004)
Journal of Virology
, vol.78
, pp. 11807-11815
-
-
Karlsson, I.1
Antonsson, L.2
Shi, Y.3
Oberg, M.4
Karlsson, A.5
Albert, J.6
Olde, B.7
Owman, C.8
M, J.9
Fenyo, E.M.10
-
22
-
-
11444270996
-
Pathogenesis of macrophage tropic HIV
-
10.2174/1570162052772951, 15638723
-
Gorry PR, Churchill M, Crowe SM, Cunningham AL, Gabuzda D. Pathogenesis of macrophage tropic HIV. Current HIV Research 2005, 3:53-60. 10.2174/1570162052772951, 15638723.
-
(2005)
Current HIV Research
, vol.3
, pp. 53-60
-
-
Gorry, P.R.1
Churchill, M.2
Crowe, S.M.3
Cunningham, A.L.4
Gabuzda, D.5
-
23
-
-
20444395434
-
Uncoupling coreceptor usage of human immunodeficiency virus type 1 (HIV-1) from macrophage tropism reveals biological properties of CCR5-restricted HIV-1 isolates from patients with acquired immunodeficiency syndrome
-
10.1016/j.virol.2005.04.034, 15916792
-
Gray L, Sterjovski J, Churchill M, Ellery P, Nasr N, Lewin SR, Crowe SM, Wesselingh SL, Cunningham AL, Gorry PR. Uncoupling coreceptor usage of human immunodeficiency virus type 1 (HIV-1) from macrophage tropism reveals biological properties of CCR5-restricted HIV-1 isolates from patients with acquired immunodeficiency syndrome. Virology 2005, 337:384-398. 10.1016/j.virol.2005.04.034, 15916792.
-
(2005)
Virology
, vol.337
, pp. 384-398
-
-
Gray, L.1
Sterjovski, J.2
Churchill, M.3
Ellery, P.4
Nasr, N.5
Lewin, S.R.6
Crowe, S.M.7
Wesselingh, S.L.8
Cunningham, A.L.9
Gorry, P.R.10
-
24
-
-
45149132902
-
Differential effects of TNF on HIV-1 expression. R5 inhibition and implications for viral evolution
-
Pavlakis GN, Valentin A, Morrow M, Yarchoan R. Differential effects of TNF on HIV-1 expression. R5 inhibition and implications for viral evolution. Internation Conference AIDS 2004, 15:11-16.
-
(2004)
Internation Conference AIDS
, vol.15
, pp. 11-16
-
-
Pavlakis, G.N.1
Valentin, A.2
Morrow, M.3
Yarchoan, R.4
-
25
-
-
67149108220
-
Sequence variants of chemokine receptor genes and susceptibility to HIV-1 infection
-
Parczewski M, Leszczyszyn-Pynka M, M K, Adler G, Binczak-Kuleta A, Loniewska B, Boron-Kaczmarska A, Ciechanowicz A. Sequence variants of chemokine receptor genes and susceptibility to HIV-1 infection. Journal of Applied Genetics 2009, 50(2):159-166.
-
(2009)
Journal of Applied Genetics
, vol.50
, Issue.2
, pp. 159-166
-
-
Parczewski, M.1
Leszczyszyn-Pynka, M.2
M, K.3
Adler, G.4
Binczak-Kuleta, A.5
Loniewska, B.6
Boron-Kaczmarska, A.7
Ciechanowicz, A.8
-
26
-
-
33947356174
-
Modest human immunodeficiency virus coreceptor function of CXCR3 is strongly enhanced by mimicking the CXCR4 ligand binding pocket in the CXCR3 receptor
-
10.1128/JVI.01941-06, 1866035, 17251291
-
Hatse S, Huskens D, Princen K, Vermeire K, Bridger GJ, De Clercq E, Rosenkilde MM, Schwartz TW, D S. Modest human immunodeficiency virus coreceptor function of CXCR3 is strongly enhanced by mimicking the CXCR4 ligand binding pocket in the CXCR3 receptor. Journal of Virology 2007, 81(7):3632-3639. 10.1128/JVI.01941-06, 1866035, 17251291.
-
(2007)
Journal of Virology
, vol.81
, Issue.7
, pp. 3632-3639
-
-
Hatse, S.1
Huskens, D.2
Princen, K.3
Vermeire, K.4
Bridger, G.J.5
De Clercq, E.6
Rosenkilde, M.M.7
Schwartz, T.W.8
D, S.9
-
27
-
-
24044533505
-
HIV-1 infection initiates changes in the expression of a wide array of genes in U937 promonocytes and HUT78 T cells
-
10.1016/j.virusres.2005.04.002, 15885842
-
Wen W, Chen S, Cao Y, Zhu Y, Yamamoto Y. HIV-1 infection initiates changes in the expression of a wide array of genes in U937 promonocytes and HUT78 T cells. Virus Research 2005, 113(1):26-35. 10.1016/j.virusres.2005.04.002, 15885842.
-
(2005)
Virus Research
, vol.113
, Issue.1
, pp. 26-35
-
-
Wen, W.1
Chen, S.2
Cao, Y.3
Zhu, Y.4
Yamamoto, Y.5
-
28
-
-
65349160332
-
The interaction of monocyte chemoattractant protein-1 and tumour necrosis factor-alpha in Mycobacterium tuberculosis-induced HIV-1 replication at sites of active tuberculosis
-
10.1111/j.1365-3083.2009.02246.x, 19439012
-
Mayanja-Kizza H, Wu M, Aung H, Liu S, Luzze H, Hirsch C, Z T. The interaction of monocyte chemoattractant protein-1 and tumour necrosis factor-alpha in Mycobacterium tuberculosis-induced HIV-1 replication at sites of active tuberculosis. Scandinavian Journal of Immunology 2009, 69(6):516-520. 10.1111/j.1365-3083.2009.02246.x, 19439012.
-
(2009)
Scandinavian Journal of Immunology
, vol.69
, Issue.6
, pp. 516-520
-
-
Mayanja-Kizza, H.1
Wu, M.2
Aung, H.3
Liu, S.4
Luzze, H.5
Hirsch, C.6
Z, T.7
-
29
-
-
67650591022
-
Gene expression in HIV-1/Mycobacterium tuberculosis co-infected macrophages is dominated by M. tuberculosis
-
10.1016/j.tube.2009.05.003, 19520608
-
Maddocks S, Scandurra GM, Nourse C, Bye C, Williams RB, Slobedman B, Cunningham AL, J BW. Gene expression in HIV-1/Mycobacterium tuberculosis co-infected macrophages is dominated by M. tuberculosis. Tuberculosis (Edinb) 2009, 89(4):285-293. 10.1016/j.tube.2009.05.003, 19520608.
-
(2009)
Tuberculosis (Edinb)
, vol.89
, Issue.4
, pp. 285-293
-
-
Maddocks, S.1
Scandurra, G.M.2
Nourse, C.3
Bye, C.4
Williams, R.B.5
Slobedman, B.6
Cunningham, A.L.7
J, B.W.8
-
30
-
-
33746032518
-
Gene expression profiling of human macrophages at late time of infection with Mycobacterium tuberculosis
-
1782319, 16895554
-
Volpe E, Cappelli G, Grassi M, Martino A, Serafino A, Colizzi V, Sanarico N, Mariani F. Gene expression profiling of human macrophages at late time of infection with Mycobacterium tuberculosis. Immunology 2006, 118(4):449-460. 1782319, 16895554.
-
(2006)
Immunology
, vol.118
, Issue.4
, pp. 449-460
-
-
Volpe, E.1
Cappelli, G.2
Grassi, M.3
Martino, A.4
Serafino, A.5
Colizzi, V.6
Sanarico, N.7
Mariani, F.8
-
31
-
-
0037383455
-
Tumor necrosis factor alpha (TNF-alpha)-induced RANTES chemokine expression via activation of NF-kappaB and p38 MAP kinase. roles of TNF-alpha in alcoholic liver diseases
-
10.1016/S0168-8278(02)00456-7, 12663241
-
Hirano F, Komura K, Fukawa E, Makino I. Tumor necrosis factor alpha (TNF-alpha)-induced RANTES chemokine expression via activation of NF-kappaB and p38 MAP kinase. roles of TNF-alpha in alcoholic liver diseases. Journal of Hepatology 2003, 38(4):483-489. 10.1016/S0168-8278(02)00456-7, 12663241.
-
(2003)
Journal of Hepatology
, vol.38
, Issue.4
, pp. 483-489
-
-
Hirano, F.1
Komura, K.2
Fukawa, E.3
Makino, I.4
-
32
-
-
67651240219
-
HIV-1 replication is differentially regulated by distinct clinical strains of Mycobacterium tuberculosis
-
10.1371/journal.pone.0006116, 2699470, 19568431
-
Ranjbar S, Boshoff HI, Mulder A, Siddiqi N, Rubin EJ, Goldfeld AE. HIV-1 replication is differentially regulated by distinct clinical strains of Mycobacterium tuberculosis. PLoS One 2009, 4(7):e6116. 10.1371/journal.pone.0006116, 2699470, 19568431.
-
(2009)
PLoS One
, vol.4
, Issue.7
-
-
Ranjbar, S.1
Boshoff, H.I.2
Mulder, A.3
Siddiqi, N.4
Rubin, E.J.5
Goldfeld, A.E.6
-
33
-
-
0036148120
-
Human immunodeficiency virus type 1 (HIV-1) quasispecies at the sites of Mycobacterium tuberculosis infection contribute to systemic HIV-1 heterogeneity
-
10.1128/JVI.76.4.1697-1706.2002, 135892, 11799165
-
Collins KR, Quinones-Mateu ME, Wu M, Luzze H, Johnson JL, Hirsch C, Toossi Z, Arts EJ. Human immunodeficiency virus type 1 (HIV-1) quasispecies at the sites of Mycobacterium tuberculosis infection contribute to systemic HIV-1 heterogeneity. Journal of Virology 2002, 76(4):1697-1706. 10.1128/JVI.76.4.1697-1706.2002, 135892, 11799165.
-
(2002)
Journal of Virology
, vol.76
, Issue.4
, pp. 1697-1706
-
-
Collins, K.R.1
Quinones-Mateu, M.E.2
Wu, M.3
Luzze, H.4
Johnson, J.L.5
Hirsch, C.6
Toossi, Z.7
Arts, E.J.8
-
34
-
-
33750294583
-
Stochastic Modelling for Systems Biology
-
CRC press
-
Wilkinson D. Stochastic Modelling for Systems Biology. 2006, CRC press.
-
(2006)
-
-
Wilkinson, D.1
-
35
-
-
33748961351
-
Stochastic processes in physics and in chemistry
-
Elsevier, Amsterdam
-
Van-Kampen NG. Stochastic processes in physics and in chemistry. 1992, Elsevier, Amsterdam.
-
(1992)
-
-
Van-Kampen, N.G.1
-
36
-
-
0036204115
-
Stocks. Stochastic kinetic simulations of biochemical system with Gillespie algorithm
-
10.1093/bioinformatics/18.3.470, 11934747
-
Kierzek AM. Stocks. Stochastic kinetic simulations of biochemical system with Gillespie algorithm. Bioinformatics 2002, 18:470-481. 10.1093/bioinformatics/18.3.470, 11934747.
-
(2002)
Bioinformatics
, vol.18
, pp. 470-481
-
-
Kierzek, A.M.1
-
37
-
-
0029967721
-
HIV-1 Dynamics in Vivo. Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time
-
10.1126/science.271.5255.1582, 8599114
-
Perelson AS, Neumann AU, Markowitz M, Leonard JM, Ho DD. HIV-1 Dynamics in Vivo. Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time. Science 1996, 271:1582-1586. 10.1126/science.271.5255.1582, 8599114.
-
(1996)
Science
, vol.271
, pp. 1582-1586
-
-
Perelson, A.S.1
Neumann, A.U.2
Markowitz, M.3
Leonard, J.M.4
Ho, D.D.5
-
38
-
-
34249725570
-
Predictive modeling of signaling crosstalk during C. elegans vulval development
-
10.1371/journal.pcbi.0030092, 1868774,1868774, 17511512
-
Fisher J, Piterman N, Hajnal A, Henzinger TA. Predictive modeling of signaling crosstalk during C. elegans vulval development. PLoS Computational Biology 2007, 3(5):e92. 10.1371/journal.pcbi.0030092, 1868774,1868774, 17511512.
-
(2007)
PLoS Computational Biology
, vol.3
, Issue.5
-
-
Fisher, J.1
Piterman, N.2
Hajnal, A.3
Henzinger, T.A.4
-
39
-
-
84941709469
-
Model checking continuous time Markov chains
-
Aziz A, Sanwal K, Singhal V, Brayton R. Model checking continuous time Markov chains. ACM Transactions on Computational Logic 2000, 1(1):162-170.
-
(2000)
ACM Transactions on Computational Logic
, vol.1
, Issue.1
, pp. 162-170
-
-
Aziz, A.1
Sanwal, K.2
Singhal, V.3
Brayton, R.4
-
40
-
-
0042349303
-
Model-checking algorithms for continuous-time Markov chains
-
Baier C, Haverkort B, Hermanns H, Katoen JP. Model-checking algorithms for continuous-time Markov chains. IEEE Transactions on Software Engineering 2003, 29(6):524-541.
-
(2003)
IEEE Transactions on Software Engineering
, vol.29
, Issue.6
, pp. 524-541
-
-
Baier, C.1
Haverkort, B.2
Hermanns, H.3
Katoen, J.P.4
-
41
-
-
75149130603
-
Quantitative Verification Techniques for Biological Processes
-
Algorithmic Bioprocesses, Springer, Condon A, Harel D, Kok J, Salomaa A, Winfree E
-
Kwiatkowska M, Norman G, Parker D. Quantitative Verification Techniques for Biological Processes. 2009, Algorithmic Bioprocesses, Springer, Condon A, Harel D, Kok J, Salomaa A, Winfree E.
-
(2009)
-
-
Kwiatkowska, M.1
Norman, G.2
Parker, D.3
-
42
-
-
0034632830
-
Evolvability of an RNA virus determined by its mutational neighborhood
-
10.1038/35020564, 10949302
-
Bruch CL, Chao L. Evolvability of an RNA virus determined by its mutational neighborhood. Nature 2000, 406:625-628. 10.1038/35020564, 10949302.
-
(2000)
Nature
, vol.406
, pp. 625-628
-
-
Bruch, C.L.1
Chao, L.2
-
43
-
-
33645768069
-
Inefficient Cytotoxic T Lymphocyte Mediated Killing of HIV-1 Infected Cells In Vivo
-
10.1371/journal.pbio.0040090, 1395353,1395353, 16515366
-
Asquith B, Edwards CTT, Lipsitch M, McLean AR. Inefficient Cytotoxic T Lymphocyte Mediated Killing of HIV-1 Infected Cells In Vivo. PLOS Biology 2006, 4(4):e90. 10.1371/journal.pbio.0040090, 1395353,1395353, 16515366.
-
(2006)
PLOS Biology
, vol.4
, Issue.4
-
-
Asquith, B.1
Edwards, C.T.T.2
Lipsitch, M.3
McLean, A.R.4
-
44
-
-
48249088137
-
Dynamics of Immune escape during HIV/SIV Infection
-
10.1371/journal.pcbi.1000103, 2423483, 18636096
-
Althaus CL, Be Boer RJ. Dynamics of Immune escape during HIV/SIV Infection. PLOS Computational Biology 2008, 4(7):e1000103. 10.1371/journal.pcbi.1000103, 2423483, 18636096.
-
(2008)
PLOS Computational Biology
, vol.4
, Issue.7
-
-
Althaus, C.L.1
Be Boer, R.J.2
|