-
1
-
-
77249123257
-
-
Treatment of Tuberculosis Guidelines: Fourth Edition. World Health Organization, 2010.
-
(2010)
World Health Organization
-
-
-
2
-
-
0036064607
-
Tuberculosis therapy: past, present and future
-
Iseman MD, Tuberculosis therapy: past, present and future. Eur Respir J Suppl. 2002;36:87s–94s. Epub 2002/08/10. 12168751.
-
(2002)
Eur Respir J Suppl
, vol.36
, pp. 87s-94s
-
-
Iseman, M.D.1
-
3
-
-
84857999389
-
A metabolic network approach for the identification and prioritization of antimicrobial drug targets
-
Chavali AK, D'Auria KM, Hewlett EL, Pearson RD, Papin JA, A metabolic network approach for the identification and prioritization of antimicrobial drug targets. Trends Microbiol. 2012;20(3):113–23. Epub 2012/02/04. S0966-842X(11)00224-1 [pii] doi: 10.1016/j.tim.2011.12.004 22300758.
-
(2012)
Trends Microbiol
, vol.20
, Issue.3
, pp. 113-123
-
-
Chavali, A.K.1
D'Auria, K.M.2
Hewlett, E.L.3
Pearson, R.D.4
Papin, J.A.5
-
4
-
-
22344449669
-
Constructing transcriptional regulatory networks
-
Blais A, Dynlacht BD, Constructing transcriptional regulatory networks. Genes Dev. 2005;19(13):1499–511. doi: 10.1101/gad.1325605 15998805.
-
(2005)
Genes Dev
, vol.19
, Issue.13
, pp. 1499-1511
-
-
Blais, A.1
Dynlacht, B.D.2
-
5
-
-
52649087274
-
Modelling and analysis of gene regulatory networks
-
Karlebach G, Shamir R, Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol. 2008;9(10):770–80. Epub 2008/09/18. nrm2503 [pii] doi: 10.1038/nrm2503 18797474.
-
(2008)
Nat Rev Mol Cell Biol
, vol.9
, Issue.10
, pp. 770-780
-
-
Karlebach, G.1
Shamir, R.2
-
6
-
-
34447523907
-
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
-
Schuetz R, Kuepfer L, Sauer U, Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol. 2007;3:119. Epub 2007/07/13. msb4100162 [pii] doi: 10.1038/msb4100162 17625511.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 119
-
-
Schuetz, R.1
Kuepfer, L.2
Sauer, U.3
-
7
-
-
44949225040
-
Context-specific metabolic networks are consistent with experiments
-
Becker SA, Palsson BO, Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol. 2008;4(5):e1000082. Epub 2008/05/17. doi: 10.1371/journal.pcbi.1000082 18483554.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.5
-
-
Becker, S.A.1
Palsson, B.O.2
-
8
-
-
79951536020
-
Functional integration of a metabolic network model and expression data without arbitrary thresholding
-
Jensen PA, Papin JA, Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics. 2011;27(4):541–7. Epub 2010/12/22. btq702 [pii] doi: 10.1093/bioinformatics/btq702 21172910.
-
(2011)
Bioinformatics
, vol.27
, Issue.4
, pp. 541-547
-
-
Jensen, P.A.1
Papin, J.A.2
-
9
-
-
51349092391
-
Network-based prediction of human tissue-specific metabolism
-
Shlomi T, Cabili MN, Herrgard MJ, Palsson BO, Ruppin E, Network-based prediction of human tissue-specific metabolism. Nat Biotechnol. 2008;26(9):1003–10. Epub 2008/08/20. nbt.1487 [pii] doi: 10.1038/nbt.1487 18711341.
-
(2008)
Nat Biotechnol
, vol.26
, Issue.9
, pp. 1003-1010
-
-
Shlomi, T.1
Cabili, M.N.2
Herrgard, M.J.3
Palsson, B.O.4
Ruppin, E.5
-
10
-
-
79951745716
-
iMAT: an integrative metabolic analysis tool
-
Zur H, Ruppin E, Shlomi T, iMAT: an integrative metabolic analysis tool. Bioinformatics. 2010;26(24):3140–2. Epub 2010/11/18. btq602 [pii] doi: 10.1093/bioinformatics/btq602 21081510.
-
(2010)
Bioinformatics
, vol.26
, Issue.24
, pp. 3140-3142
-
-
Zur, H.1
Ruppin, E.2
Shlomi, T.3
-
11
-
-
70049110173
-
Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production
-
Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, et al. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput Biol. 2009;5(8):e1000489. Epub 2009/08/29. doi: 10.1371/journal.pcbi.1000489 19714220.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.8
-
-
Colijn, C.1
Brandes, A.2
Zucker, J.3
Lun, D.S.4
Weiner, B.5
Farhat, M.R.6
-
12
-
-
0035824029
-
Regulation of gene expression in flux balance models of metabolism
-
Covert MW, Schilling CH, Palsson B, Regulation of gene expression in flux balance models of metabolism. J Theor Biol. 2001;213(1):73–88. Epub 2001/11/16. doi: 10.1006/jtbi.2001.2405 S0022-5193(01)92405-1 [pii]. 11708855.
-
(2001)
J Theor Biol
, vol.213
, Issue.1
, pp. 73-88
-
-
Covert, M.W.1
Schilling, C.H.2
Palsson, B.3
-
13
-
-
0037008673
-
Transcriptional regulation in constraints-based metabolic models of Escherichia coli
-
Covert MW, Palsson BO, Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem. 2002;277(31):28058–64. Epub 2002/05/15. doi: 10.1074/jbc.M201691200 M201691200 [pii]. 12006566.
-
(2002)
J Biol Chem
, vol.277
, Issue.31
, pp. 28058-28064
-
-
Covert, M.W.1
Palsson, B.O.2
-
14
-
-
2342648924
-
Integrating high-throughput and computational data elucidates bacterial networks
-
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO, Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004;429(6987):92–6. Epub 2004/05/07. doi: 10.1038/nature02456 nature02456 [pii]. 15129285.
-
(2004)
Nature
, vol.429
, Issue.6987
, pp. 92-96
-
-
Covert, M.W.1
Knight, E.M.2
Reed, J.L.3
Herrgard, M.J.4
Palsson, B.O.5
-
15
-
-
34247183123
-
A genome-scale computational study of the interplay between transcriptional regulation and metabolism
-
Shlomi T, Eisenberg Y, Sharan R, Ruppin E, A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol. 2007;3:101. Epub 2007/04/18. msb4100141 [pii] doi: 10.1038/msb4100141 17437026.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 101
-
-
Shlomi, T.1
Eisenberg, Y.2
Sharan, R.3
Ruppin, E.4
-
16
-
-
78049255973
-
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
-
Chandrasekaran S, Price ND, Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2010;107(41):17845–50. Epub 2010/09/30. 1005139107 [pii] doi: 10.1073/pnas.1005139107 20876091.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, Issue.41
, pp. 17845-17850
-
-
Chandrasekaran, S.1
Price, N.D.2
-
17
-
-
34447317247
-
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets
-
Jamshidi N, Palsson BO, Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst Biol. 2007;1:26. Epub 2007/06/09. 1752-0509-1-26 [pii] doi: 10.1186/1752-0509-1-26 17555602.
-
(2007)
BMC Syst Biol
, vol.1
, pp. 26
-
-
Jamshidi, N.1
Palsson, B.O.2
-
18
-
-
55549111608
-
The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest
-
Balazsi G, Heath AP, Shi L, Gennaro ML, The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol Syst Biol. 2008;4:225. Epub 2008/11/06. msb200863 [pii] doi: 10.1038/msb.2008.63 18985025.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 225
-
-
Balazsi, G.1
Heath, A.P.2
Shi, L.3
Gennaro, M.L.4
-
19
-
-
84923112410
-
The DNA-binding network of Mycobacterium tuberculosis
-
Minch KJ, Rustad TR, Peterson EJ, Winkler J, Reiss DJ, Ma S, et al. The DNA-binding network of Mycobacterium tuberculosis. Nat Commun. 2015;6:5829. doi: 10.1038/ncomms6829 25581030; PubMed Central PMCID: PMC4301838.
-
(2015)
Nat Commun
, vol.6
, pp. 5829
-
-
Minch, K.J.1
Rustad, T.R.2
Peterson, E.J.3
Winkler, J.4
Reiss, D.J.5
Ma, S.6
-
20
-
-
34548861262
-
GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism
-
Beste DJ, Hooper T, Stewart G, Bonde B, Avignone-Rossa C, Bushell ME, et al. GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. Genome Biol. 2007;8(5):R89. Epub 2007/05/25. gb-2007-8-5-r89 [pii] doi: 10.1186/gb-2007-8-5-r89 17521419.
-
(2007)
Genome Biol
, vol.8
, Issue.5
, pp. R89
-
-
Beste, D.J.1
Hooper, T.2
Stewart, G.3
Bonde, B.4
Avignone-Rossa, C.5
Bushell, M.E.6
-
21
-
-
78549238928
-
Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis
-
Fang X, Wallqvist A, Reifman J, Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis. BMC Syst Biol. 2011;4:160. Epub 2010/11/26. 1752-0509-4-160 [pii] doi: 10.1186/1752-0509-4-160 21092312.
-
(2011)
BMC Syst Biol
, vol.4
, pp. 160
-
-
Fang, X.1
Wallqvist, A.2
Reifman, J.3
-
22
-
-
84949292421
-
-
Kalapanulak S, High quality genome-scale metabolic network reconstruction of Mycobacterium tuberculosis and comparison with human metabolic network: application for drug targets identification. Edinburgh: University of Edinburgh; 2009.
-
(2009)
Edinburgh
-
-
Kalapanulak, S.1
-
23
-
-
84895458423
-
Systems-based approaches to probing metabolic variation within the Mycobacterium tuberculosis complex
-
Lofthouse EK, Wheeler PR, Beste DJ, Khatri BL, Wu H, Mendum TA, et al. Systems-based approaches to probing metabolic variation within the Mycobacterium tuberculosis complex. PLoS One. 2013;8(9):e75913. Epub 2013/10/08. doi: 10.1371/journal.pone.0075913 PONE-D-13-19042 [pii]. 24098743.
-
(2013)
PLoS One
, vol.8
, Issue.9
-
-
Lofthouse, E.K.1
Wheeler, P.R.2
Beste, D.J.3
Khatri, B.L.4
Wu, H.5
Mendum, T.A.6
-
24
-
-
77955712976
-
TB database 2010: overview and update
-
Galagan JE, Sisk P, Stolte C, Weiner B, Koehrsen M, Wymore F, et al. TB database 2010: overview and update. Tuberculosis (Edinb). 2010;90(4):225–35. Epub 2010/05/22. S1472-9792(10)00041-7 [pii] doi: 10.1016/j.tube.2010.03.010 20488753.
-
(2010)
Tuberculosis (Edinb)
, vol.90
, Issue.4
, pp. 225-235
-
-
Galagan, J.E.1
Sisk, P.2
Stolte, C.3
Weiner, B.4
Koehrsen, M.5
Wymore, F.6
-
25
-
-
58149182735
-
TB database: an integrated platform for tuberculosis research
-
Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, et al. TB database: an integrated platform for tuberculosis research. Nucleic Acids Res. 2009;37(Database issue):D499–508. doi: 10.1093/nar/gkn652 18835847; PubMed Central PMCID: PMC2686437.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.Database issue
, pp. D499-D508
-
-
Reddy, T.B.1
Riley, R.2
Wymore, F.3
Montgomery, P.4
DeCaprio, D.5
Engels, R.6
-
26
-
-
84965191948
-
Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network
-
Rustad TR, Minch KJ, Ma S, Winkler JK, Hobbs S, Hickey M, et al. Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network. Genome Biol. 2014;15(11):502. doi: 10.1186/PREACCEPT-1701638048134699 25380655; PubMed Central PMCID: PMC4249609.
-
(2014)
Genome Biol
, vol.15
, Issue.11
, pp. 502
-
-
Rustad, T.R.1
Minch, K.J.2
Ma, S.3
Winkler, J.K.4
Hobbs, S.5
Hickey, M.6
-
27
-
-
80053459692
-
High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism
-
Griffin JE, Gawronski JD, Dejesus MA, Ioerger TR, Akerley BJ, Sassetti CM, High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism. PLoS Pathog. 2011;7(9):e1002251. Epub 2011/10/08. doi: 10.1371/journal.ppat.1002251 PPATHOGENS-D-11-00689 [pii]. 21980284.
-
(2011)
PLoS Pathog
, vol.7
, Issue.9
-
-
Griffin, J.E.1
Gawronski, J.D.2
Dejesus, M.A.3
Ioerger, T.R.4
Akerley, B.J.5
Sassetti, C.M.6
-
28
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
-
Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc. 2011;6(9):1290–307. Epub 2011/09/03. nprot.2011.308 [pii] doi: 10.1038/nprot.2011.308 21886097.
-
(2011)
Nat Protoc
, vol.6
, Issue.9
, pp. 1290-1307
-
-
Schellenberger, J.1
Que, R.2
Fleming, R.M.3
Thiele, I.4
Orth, J.D.5
Feist, A.M.6
-
29
-
-
84884505005
-
Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis
-
Ioerger TR, O'Malley T, Liao R, Guinn KM, Hickey MJ, Mohaideen N, et al. Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis. PLoS One. 2013;8(9):e75245. doi: 10.1371/journal.pone.0075245 24086479; PubMed Central PMCID: PMC3781026.
-
(2013)
PLoS One
, vol.8
, Issue.9
-
-
Ioerger, T.R.1
O'Malley, T.2
Liao, R.3
Guinn, K.M.4
Hickey, M.J.5
Mohaideen, N.6
-
30
-
-
43049182981
-
The enduring hypoxic response of Mycobacterium tuberculosis
-
Rustad TR, Harrell MI, Liao R, Sherman DR, The enduring hypoxic response of Mycobacterium tuberculosis. PLoS One. 2008;3(1):e1502. Epub 2008/01/31. doi: 10.1371/journal.pone.0001502 18231589.
-
(2008)
PLoS One
, vol.3
, Issue.1
-
-
Rustad, T.R.1
Harrell, M.I.2
Liao, R.3
Sherman, D.R.4
-
31
-
-
0030903133
-
Microplate alamar blue assay versus BACTEC 460 system for high-throughput screening of compounds against Mycobacterium tuberculosis and Mycobacterium avium
-
Collins L, Franzblau SG, Microplate alamar blue assay versus BACTEC 460 system for high-throughput screening of compounds against Mycobacterium tuberculosis and Mycobacterium avium. Antimicrob Agents Chemother. 1997;41(5):1004–9. 9145860; PubMed Central PMCID: PMC163841.
-
(1997)
Antimicrob Agents Chemother
, vol.41
, Issue.5
, pp. 1004-1009
-
-
Collins, L.1
Franzblau, S.G.2
-
32
-
-
34347258175
-
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
-
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ, Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc. 2007;2(3):727–38. Epub 2007/04/05. nprot.2007.99 [pii] doi: 10.1038/nprot.2007.99 17406635.
-
(2007)
Nat Protoc
, vol.2
, Issue.3
, pp. 727-738
-
-
Becker, S.A.1
Feist, A.M.2
Mo, M.L.3
Hannum, G.4
Palsson, B.O.5
Herrgard, M.J.6
-
33
-
-
0016772212
-
Comparison of the predicted and observed secondary structure of T4 phage lysozyme
-
Matthews BW, Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochimica et biophysica acta. 1975;405(2):442–51. 1180967.
-
(1975)
Biochimica et biophysica acta
, vol.405
, Issue.2
, pp. 442-451
-
-
Matthews, B.W.1
-
34
-
-
77950292485
-
Attenuation of Mycobacterium tuberculosis functionally disrupted in a fatty acyl-coenzyme A synthetase gene fadD5
-
Dunphy KY, Senaratne RH, Masuzawa M, Kendall LV, Riley LW, Attenuation of Mycobacterium tuberculosis functionally disrupted in a fatty acyl-coenzyme A synthetase gene fadD5. J Infect Dis. 2010;201(8):1232–9. Epub 2010/03/11. doi: 10.1086/651452 20214478.
-
(2010)
J Infect Dis
, vol.201
, Issue.8
, pp. 1232-1239
-
-
Dunphy, K.Y.1
Senaratne, R.H.2
Masuzawa, M.3
Kendall, L.V.4
Riley, L.W.5
-
35
-
-
0037214410
-
Growth of mycobacteria on carbon monoxide and methanol
-
Park SW, Hwang EH, Park H, Kim JA, Heo J, Lee KH, et al. Growth of mycobacteria on carbon monoxide and methanol. J Bacteriol. 2003;185(1):142–7. Epub 2002/12/18. 12486050.
-
(2003)
J Bacteriol
, vol.185
, Issue.1
, pp. 142-147
-
-
Park, S.W.1
Hwang, E.H.2
Park, H.3
Kim, J.A.4
Heo, J.5
Lee, K.H.6
-
36
-
-
34547731308
-
Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase
-
Yang X, Dubnau E, Smith I, Sampson NS, Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry. 2007;46(31):9058–67. Epub 2007/07/17. doi: 10.1021/bi700688x 17630785.
-
(2007)
Biochemistry
, vol.46
, Issue.31
, pp. 9058-9067
-
-
Yang, X.1
Dubnau, E.2
Smith, I.3
Sampson, N.S.4
-
37
-
-
54749140927
-
Laboratory maintenance of Mycobacterium tuberculosis
-
Larsen MH, Biermann K, Jacobs WR, JrLaboratory maintenance of Mycobacterium tuberculosis. Curr Protoc Microbiol. 2007;Chapter 10:Unit 10A 1. Epub 2008/09/05. 18770602.
-
(2007)
Curr Protoc Microbiol
, vol.Chapter 10
, Issue.Unit 10A
, pp. 1
-
-
Larsen, M.H.1
Biermann, K.2
Jacobs, W.R.3
|