schwartzjmc's library 187 articles Export

	An improved algorithm for stoichiometric network analysis: theory and applications. [My Copy] Bioinformatics (Oxford, England), Vol. 21, No. 7. (1 April 2005), pp. 1203-1210. by R. Urbanczik, C. Wagner posted to em by schwartzjmc on 2009-11-06 15:05:51 as
	Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns [My Copy] Genome Research, Vol. 19, No. 10. (October 2009), pp. 1872-1883. by Christoph Kaleta, LuÃs F. de Figueiredo, Stefan Schuster posted to em by schwartzjmc on 2009-11-06 14:26:10 as along with 3 people and 1 group daveGerrard TRHvidsten fpattyn Neuroblastoma
	Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 18. (15 September 2008), pp. 2044-2050. by Markus W. Covert, Nan Xiao, Tiffany J. Chen, Jonathan R. Karr posted to logical_model fba bacteria by schwartzjmc on 2009-11-06 14:14:22 as along with 6 people pjmaybank abhishek_tiwari kalvala guhjy Ema nuin
	Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab. [My Copy] Cancer research, Vol. 69, No. 16. (15 August 2009), pp. 6713-6720. by Dana Faratian, Alexey Goltsov, Galina Lebedeva, et al.Anatoly Sorokin, Stuart Moodie, Peter Mullen, Charlene Kay, In Hwa H. Um, Simon Langdon, Igor Goryanin, David J. Harrison posted to mrc dynamic_model drug by schwartzjmc on 2009-11-04 18:50:18 as along with 3 people bertelsen ericrpaquet frohike
	A Genome-scale Metabolic Model of Arabidopsis thaliana and Some of its Properties. [My Copy] Plant physiology (15 September 2009) by Mark G. Poolman, Laurent Miguet, Lee J. Sweetlove, David A. Fell posted to plant metabolic_reconstruction arabidopsis by schwartzjmc on 2009-11-04 17:18:55 as
	Assessing the dynamics of nuclear glucocorticoid-receptor complex: adding flexibility to gene expression modeling. [My Copy] Journal of pharmacokinetics and pharmacodynamics, Vol. 34, No. 3. (June 2007), pp. 333-354. by Anasuya Hazra, Debra C. DuBois, Richard R. Almon, William J. Jusko posted to dynamic_model pharmacokinetics glucocorticoid_receptor by schwartzjmc on 2009-11-03 10:03:32 as
	Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima [My Copy] Science, Vol. 325, No. 5947. (18 September 2009), pp. 1544-1549. by Ying Zhang, Ines Thiele, Dana Weekes, et al.Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley M. Deacon, John Wooley, Scott A. Lesley, Ian A. Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik posted to metabolic_reconstruction bacteria by schwartzjmc on 2009-10-19 15:39:28 as along with 12 people venancio apocapoc eehsanipour riffraff reyez TRHvidsten flbarroso daveGerrard zwang pablocarb phoenixzxl roys
	Drug-therapy networks and the prediction of novel drug targets [My Copy] Journal of Biology, Vol. 7, No. 6. (31 July 2008), 20. by Zoltan Spiro, Istvan Kovacs, Peter Csermely posted to drug by schwartzjmc on 2009-10-15 15:07:29 as
	SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks [My Copy] BMC Systems Biology, Vol. 2, No. 1. (2008), 39. by Andreas Drager, Nadine Hassis, Jochen Supper, Adrian Schroder, Andreas Zell posted to dynamic_model software by schwartzjmc on 2009-10-04 16:23:35 as along with 2 people guhjy bootsy
	Functional cartography of complex metabolic networks [My Copy] Nature, Vol. 433, No. 7028. (24 February 2005), pp. 895-900. by Roger Guimera, Luis A. Nunes Amaral posted to topology by schwartzjmc on 2009-10-01 13:52:42 as along with 23 people and 4 groups tomt21 lawraga Scis0000002 vtraag cgaugain pdelosri cswinburne camster dbk BioGeek Borelli lfriedl balajis alexg eweaver tny wnpx cjeans kdang carlk RobMills Diego_Prada marcio streptomyces dbk-lab kdl Bioinformatics
	Network biology: understanding the cell's functional organization. [My Copy] Nature reviews. Genetics, Vol. 5, No. 2. (February 2004), pp. 101-113. by Albert-László L. Barabási, Zoltán N. Oltvai posted to topology by schwartzjmc on 2009-10-01 13:51:53 as along with 40 people and 10 groups daforerog fastjoe23 arsyed thepogoman mtagaya camster snuppepuppan dbk greg guhjy LeightonP hununu felciano mague kuhn textoris rhem1224 lfriedl balajis alexg wnpx jknabe adepace nickluscombe bundschu awooga jdiggans jeremymiller uprock timflutre mikaelhuss gcalda grahamc fishtank jayster4 naegele Evangelia heliopais shikin hryk streptomyces dbk-lab kdl EisenLab TCR_Signaling EBI-regulation SysbioMPI-TCells GeschwindLab generif_paper GeneGo
	Network Motifs: Simple Building Blocks of Complex Networks [My Copy] Science, Vol. 298, No. 5594. (25 October 2002), pp. 824-827. by R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon posted to topology by schwartzjmc on 2009-10-01 13:51:34 as along with 69 people and 9 groups nurban balabu ocs mjoach makrehchi poirel tomhebbron arsyed vtraag sergiun fierykylin Akimasa operon dlobo daforerog chasmand wei_tang darian orahcio babakap brewbooks phoenixzxl Md_2007 mtagaya heliopais kaarsinogen galyardt cswinburne mullonc camster korakot aalibes ChaTo imouthesmp Borelli lfriedl alexg balicea tny ssb wnpx ddahlem cmm donade neveaire griota gurkanbebek jtaylor josepe iris_2001 michaelmampaey rebeccamancy karfunkel lenov Evangelia roys tfogal zibuyu maralena stefanoallesina pbull cmor renatomilani shikin carlk applesnow subhacom i-stevenson ethkim GEB Philosophy_of_Information dbk-lab Blog_and_Wiki_Research kdl FAB-lab ColDyn ADMiRes GeneGo
	Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. [My Copy] Cell, Vol. 138, No. 4. (21 August 2009), pp. 795-806. by Paola Picotti, Bernd Bodenmiller, Lukas N. Mueller, Bruno Domon, Ruedi Aebersold posted to yeast proteomics by schwartzjmc on 2009-09-09 16:21:19 as along with 2 people absterga brianb
	New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. [My Copy] Nucleic Acids Res, Vol. 32, No. 12. (2004), pp. 3581-3589. by Roland Barriot, Jérôme Poix, Alexis Groppi, et al.Aurélien Barré, Nicolas Goffard, David Sherman, Isabelle Dutour, Antoine de Daruvar posted to integration by schwartzjmc on 2009-09-04 15:46:51 as along with 1 person greg
	From minimal signed circuits to the dynamics of Boolean regulatory networks. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008), pp. i220-226. by Elisabeth Remy, Paul Ruet posted to stability regulation cycle by schwartzjmc on 2009-08-30 10:42:08 as
	Functional States of the genome-scale Escherichia coli transcriptional regulatory system. [My Copy] PLoS computational biology, Vol. 5, No. 6. (5 June 2009), e1000403. by Erwin P. Gianchandani, Andrew R. Joyce, Bernhard Ø. Palsson, Jason A. Papin posted to topology regulation bacteria by schwartzjmc on 2009-08-14 17:42:00 as along with 3 people roys TRHvidsten trfield
	Subnetwork analysis reveals dynamic features of complex (bio)chemical networks. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 49. (4 December 2007), pp. 19175-19180. by Carsten Conradi, Dietrich Flockerzi, Jörg Raisch, Jörg Stelling posted to dynamic_model topology stability em by schwartzjmc on 2009-08-14 17:03:18 as along with 3 people zwang roys mclarenv
	The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks. [My Copy] Molecular systems biology, Vol. 3 (13 November 2007) by Sergio Grimbs, Joachim Selbig, Sascha Bulik, Hermann-Georg G. Holzhütter, Ralf Steuer posted to dynamic_model topology stability regulation by schwartzjmc on 2009-08-14 16:58:47 as along with 5 people and 1 group agomez JeremyZucker cjeans zwang Ema MetabolicModeling
	A Role for Casein Kinase 2 in the Mechanism Underlying Circadian Temperature Compensation [My Copy] Cell, Vol. 137, No. 4. (15 May 2009), pp. 749-760. by Arun Mehra, Mi Shi, Christopher L. Baker, Hildur V. Colot, Jennifer J. Loros, Jay C. Dunlap posted to neurospora circadian by schwartzjmc on 2009-08-12 17:21:54 as
	Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 7. by Tobias Christensen, Ana Oliveira, Jens Nielsen posted to logical_model glycolysis regulation yeast by schwartzjmc on 2009-08-06 12:46:35 as along with 2 people ptrobajo arne
	Boolean network-based analysis of the apoptosis network: irreversible apoptosis and stable surviving. [My Copy] Journal of theoretical biology, Vol. 259, No. 4. (21 August 2009), pp. 760-769. by Zhongxing Mai, Haiyan Liu posted to logical_model apoptosis by schwartzjmc on 2009-08-06 12:35:49 as along with 1 person agonzale
	Glucose and forskolin regulate IAPP gene expression through different signal transduction pathways [My Copy] Am J Physiol Endocrinol Metab, Vol. 281, No. 5. (1 November 2001), pp. E938-945. by Wei-Qun Ding, Eileen Holicky, Laurence J. Miller posted to amylin regulation by schwartzjmc on 2009-08-06 12:30:34 as
	Group contribution method for thermodynamic analysis of complex metabolic networks. [My Copy] Biophysical journal, Vol. 95, No. 3. (1 August 2008), pp. 1487-1499. by Matthew D. Jankowski, Christopher S. Henry, Linda J. Broadbelt, Vassily Hatzimanikatis posted to metabolic_reconstruction thermodynamics by schwartzjmc on 2009-08-05 12:24:59 as along with 2 people dullhunk JeremyZucker
	Thermodynamics-Based Metabolic Flux Analysis [My Copy] Biophysical Journal, Vol. 92, No. 5. (01 March 2007), pp. 1792-1805. by C. Henry, L. Broadbelt, V. Hatzimanikatis posted to bacteria fba thermodynamics by schwartzjmc on 2009-08-05 12:23:02 as along with 5 people winterstream vpenelle BjornJohansson lylu JeremyZucker
	Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism. [My Copy] Journal of mathematical biology, Vol. 45, No. 2. (August 2002), pp. 153-181. by S. Schuster, C. Hilgetag, J. H. Woods, D. A. Fell posted to em by schwartzjmc on 2009-07-31 18:16:22 as along with 3 people and 1 group camster Borelli pmendes dbk-lab
	Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum. [My Copy] Journal of theoretical biology, Vol. 224, No. 3. (7 October 2003), pp. 313-324. by Sharon J. Wiback, Radhakrishnan Mahadevan, Bernhard Ø. Palsson posted to em by schwartzjmc on 2009-07-31 16:12:35 as
	Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. [My Copy] Trends in biotechnology, Vol. 17, No. 2. (February 1999), pp. 53-60. by S. Schuster, T. Dandekar, D. A. Fell posted to em by schwartzjmc on 2009-07-31 15:31:01 as along with 3 people and 1 group camster BragilMassoud Borelli dbk-lab
	Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans [My Copy] Journal of Theoretical Biology, Vol. 258, No. 1. (07 May 2009), pp. 71-88. by K. Sriram, Sylvain Soliman, François Fages posted to dynamic_model candida regulation stability by schwartzjmc on 2009-07-30 15:36:31 as along with 1 person balabu
	Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora. [My Copy] The EMBO journal, Vol. 28, No. 8. (22 April 2009), pp. 1029-1042. by Chen-Hui H. Chen, Carol S. Ringelberg, Robert H. Gross, Jay C. Dunlap, Jennifer J. Loros posted to circadian neurospora by schwartzjmc on 2009-07-30 15:07:11 as along with 2 people and 1 group JeremyZucker stajich Mycology
	Sloppiness, robustness, and evolvability in systems biology. [My Copy] Current opinion in biotechnology, Vol. 19, No. 4. (August 2008), pp. 389-395. by Bryan C. Daniels, Yan-Jiun J. Chen, James P. Sethna, Ryan N. Gutenkunst, Christopher R. Myers posted to circadian parameter by schwartzjmc on 2009-07-28 14:47:03 as along with 4 people PaperCollector abhishek_tiwari cjryan benjaminsb
	Universally sloppy parameter sensitivities in systems biology models. [My Copy] PLoS computational biology, Vol. 3, No. 10. (1 October 2007), pp. 1871-1878. by Ryan N. Gutenkunst, Joshua J. Waterfall, Fergal P. Casey, Kevin S. Brown, Christopher R. Myers, James P. Sethna posted to parameter systems_biology by schwartzjmc on 2009-07-28 14:29:58 as along with 6 people PaperCollector aheilbut jjray chad_davis csgillespie jooce
	Robust Salmonella metabolism limits possibilities for new antimicrobials [My Copy] Nature, Vol. 440, No. 7082. (16 March 2006), pp. 303-307. by Daniel Becker, Matthias Selbach, Claudia Rollenhagen, et al.Matthias Ballmaier, Thomas F. Meyer, Matthias Mann, Dirk Bumann posted to bacteria drug by schwartzjmc on 2009-07-28 14:20:27 as along with 3 people and 1 group kentsis okarsligil shung Bioinformatics
	targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. [My Copy] BMC systems biology, Vol. 2, No. 1. (2008) by Karthik Raman, Kalidas Yeturu, Nagasuma Chandra posted to bacteria drug by schwartzjmc on 2009-07-28 14:09:47 as along with 4 people and 1 group JeremyZucker shung kshameer druvus MetabolicModeling
	Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance. [My Copy] BMC microbiology, Vol. 8 (23 December 2008), 234. by K. Raman, N. Chandra posted to bacteria drug by schwartzjmc on 2009-07-28 14:09:14 as along with 1 person druvus
	Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis. [My Copy] Molecular bioSystems (29 June 2009) by Karthik Raman, Rohit Vashisht, Nagasuma Chandra posted to bacteria drug by schwartzjmc on 2009-07-28 14:08:39 as
	Robustness and fragility of Boolean models for genetic regulatory networks [My Copy] Journal of Theoretical Biology, Vol. 235, No. 3. (07 August 2005), pp. 431-449. by M. Chaves, R. Albert, E. Sontag posted to logical_model by schwartzjmc on 2009-07-28 14:00:52 as along with 1 person rklancer
	Carbon-fate maps for metabolic reactions [My Copy] Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3193-3199. by Fangping Mu, Robert F. Williams, Clifford J. Unkefer, Pat J. Unkefer, James R. Faeder, William S. Hlavacek posted to cheminformatics rule by schwartzjmc on 2009-07-27 14:34:16 as along with 1 person hryk
	An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) [My Copy] Genome Biology, Vol. 4, No. 9. (2003), R54. by Jennifer Reed, Thuy Vo, Christophe Schilling, Bernhard Palsson posted to bacteria metabolic_reconstruction by schwartzjmc on 2009-07-26 15:17:24 as along with 5 people and 2 groups csanford michaelbarton cate bjorns JeremyZucker biospec MetabolicModeling
	Distinct mechanisms act in concert to mediate cell cycle arrest. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 3. (20 January 2009), pp. 785-790. by J. E. Toettcher, A. Loewer, G. J. Ostheimer, M. B. Yaffe, B. Tidor, G. Lahav posted to dynamic_model mrc by schwartzjmc on 2009-07-24 18:14:58 as along with 1 person guhjy
	Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. [My Copy] Nature, Vol. 441, No. 7090. (11 May 2006), pp. 173-178. by Mark Gilchrist, Vesteinn Thorsson, Bin Li, et al.Alistair G. Rust, Martin Korb, Jared C. Roach, Kathleen Kennedy, Tsonwin Hai, Hamid Bolouri, Alan Aderem posted to dynamic_model mrc by schwartzjmc on 2009-07-24 18:11:37 as along with 4 people ptrobajo biozhang2001 miguel tuck
	Pulsatile Stimulation Determines Timing and Specificity of NF-kappaB-Dependent Transcription [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 242-246. by Louise Ashall, Caroline A. Horton, David E. Nelson, et al.Pawel Paszek, Claire V. Harper, Kate Sillitoe, Sheila Ryan, David G. Spiller, John F. Unitt, David S. Broomhead, Douglas B. Kell, David A. Rand, Violaine See, Michael R. H. White posted to dynamic_model mrc by schwartzjmc on 2009-07-24 18:06:21 as along with 5 people arne rbweinbe booker dullhunk kentsis
	From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation. [My Copy] Trends in genetics : TIG, Vol. 25, No. 3. (18 March 2009), pp. 111-119. by V. Mustonen, M. Lässig posted to adaptation thermodynamics by schwartzjmc on 2009-07-16 12:03:21 as along with 2 people djkt JustinCrocker
	From Plant Traits to Plant Communities: A Statistical Mechanistic Approach to Biodiversity [My Copy] Science, Vol. 314, No. 5800. (3 November 2006), pp. 812-814. by Bill Shipley, Denis Vile, Eric Garnier posted to adaptation neutral_theory by schwartzjmc on 2009-07-16 11:58:42 as along with 6 people and 2 groups anphony JLMC liucun mullonc cmm JLM Savage Lab, UCLA FAB-lab
	Neutral theory (communication arising): The stability of forest biodiversity [My Copy] Nature, Vol. 427, No. 6976. (19 February 2004), pp. 696-696. by Igor Volkov, Jayanth R. Banavar, Amos Maritan, Stephen P. Hubbell posted to adaptation neutral_theory by schwartzjmc on 2009-07-16 11:56:15 as
	Regulation of metabolic networks by small molecule metabolites [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (13 March 2007), 88. by Alex Gutteridge, Minoru Kanehisa, Susumu Goto posted to database regulation by schwartzjmc on 2009-07-15 15:57:31 as along with 3 people and 1 group marodoc aswin shung Bioinformatics
	Towards Kinetic Modeling of Global Metabolic Networks: Methylobacterium extorquens AM1 Growth as Validation [My Copy] Chinese Journal of Biotechnology, Vol. 24, No. 6. (June 2008), pp. 980-994. by P. Ao, L. Lee, M. Lidstrom, L. Yin, X. Zhu posted to dynamic_model bacteria by schwartzjmc on 2009-07-15 12:23:13 as
	Genetic modification of flux for flux prediction of mutants [My Copy] Bioinformatics, Vol. 25, No. 13. (1 July 2009), pp. 1702-1708. by Quanyu Zhao, Hiroyuki Kurata posted to em flux by schwartzjmc on 2009-07-14 18:06:12 as
	A Logical Model Provides Insights into T Cell Receptor Signaling [My Copy] PLoS Comput Biol, Vol. 3, No. 8. (24 August 2007), e163. by Julio Saez-Rodriguez, Luca Simeoni, Jonathan A. Lindquist, et al.Rebecca Hemenway, Ursula Bommhardt, Boerge Arndt, Utz-Uwe Haus, Robert Weismantel, Ernst D. Gilles, Steffen Klamt, Burkhart Schraven posted to logical_model regulation by schwartzjmc on 2009-07-14 17:28:43 as along with 1 person hannahrajasingh
	Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 12. (12 August 2004), pp. 1877-1886. by E. Sontag, A. Kiyatkin, B. N. Kholodenko posted to logical_model dynamic_model microarray by schwartzjmc on 2009-07-14 15:52:33 as along with 5 people and 3 groups camster dbk mrm wnpx smgomez streptomyces dbk-lab GomezLab
	Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks [My Copy] PLoS Comput Biol, Vol. 4, No. 5. (23 May 2008), e1000086. by Jong Min Lee, Erwin P. Gianchandani, James A. Eddy, Jason A. Papin posted to dynamic_model fba regulation by schwartzjmc on 2009-07-14 15:30:50 as along with 9 people abhishek_tiwari raik guhjy Borelli nolodie bootsy roys lymxz Ema

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metabolic_reconstruction	26
dynamic_model	25
yeast	24
bacteria	22
regulation	20
em	19
thermodynamics	19
topology	17
drug	11
cycle	10
fba	10
logical_model	9
arabidopsis	8
cheminformatics	8
flux	7
database	5
kudriavzevii	5
metabolomics	5
software	5
stability	5
systems_biology	5
glycolysis	4
integration	4
mca	4
microarray	4
modularity	4
mrc	4
plant	4
scope	4
adaptation	3
circadian	3
human	3
neurospora	2
neutral_theory	2
parameter	2
stoichiometry	2
string_comparison	2
tree	2
amylin	1
apoptosis	1
camp	1
candida	1
environment	1
evolution	1
gene_duplication	1
glucocorticoid_receptor	1
isozyme	1
kegg	1
metacyc	1
mouse	1
pharmacokinetics	1
proteomics	1
pubchem	1
rule	1
sequencing	1
sucrose	1
translation	1
visualisation	1

schwartzjmc's library 187 articles Export

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