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Tag systems_biology [379 articles]

Recent papers classified by the tag systems_biology.
  • Network biology: understanding the cell's functional organization.
    Nat Rev Genet, Vol. 5, No. 2. (February 2004), pp. 101-113.
    by AL Barabási, ZN Oltvai
    posted to network_reconstruction systems_biology by uprock on 2006-10-30 02:14:52 as *** along with 34 people and 11 groups camster snuppepuppan dbk greg jyuh LeightonP hununu felciano mague kuhn textoris rhem1224 lfriedl balajis alexg wnpx jknabe adepace nickluscombe bundschu awooga jdiggans jeremymiller timflutre mikaelhuss gcalda grahamc fishtank jayster4 naegele Evangelia heliopais shikin hryk streptomyces spliceml dbk-lab kdl EisenLab TCR_Signaling EBI-regulation SysbioMPI-TCells GeschwindLab generif_paper GeneGo
  • Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data
    BMC Bioinformatics, Vol. 7 (03 October 2006), 426.
    by Alex Lewin, Ian C Grieve
    posted to enrichment go ontology systems_biology by uprock on 2006-10-30 02:16:30 as ** along with 6 people and 2 groups ealloza giovanni jdiggans heliopais waghsk ndiaz BioinfoCIPF GeschwindLab
  • Reconstruction of genetic circuits
    Nature, Vol. 438, No. 7067., pp. 443-448.
    by David Sprinzak, Michael B Elowitz
    posted to network regulation synthetic-biology synthetic_biology systems_biology by tuck on 2005-12-29 04:39:59 as ** along with 6 people rklancer monod jmeppley avery dbikard austin
  • Self-organization in cell biology: a brief history
    Nat Rev Mol Cell Biol, Vol. 9, No. 3. (March 2008), pp. 255-262.
    by Eric Karsenti
    posted to systems_biology by tmmurali on 2008-02-22 17:56:03 as ** along with 1 person jyuh
  • Optimization in computational systems biology
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Julio Banga
    posted to actex systems_biology by tmmurali on 2008-05-29 04:21:35 as ** along with 5 people reyez jrbanga biehl balicea phoenixzxl
  • A Systems Model of Signaling Identifies a Molecular Basis Set for Cytokine-Induced Apoptosis
    Science, Vol. 310, No. 5754. (9 December 2005), pp. 1646-1653.
    by Kevin A Janes, John G Albeck, Suzanne Gaudet, Peter K Sorger, Douglas A Lauffenburger, Michael B Yaffe
    posted to functional_linkage_network systems_biology network-legos by tmmurali on 2005-12-09 16:02:28 as **** along with 5 people and 3 groups julius j3xucite jaycopeland cdppublications cdpwebadmin SysbioMPI-TCells SorgerLab CDP
  • Molecular systems biology at the crossroads: to know less about more, or to know more about less?
    Proteome Sci, Vol. 3 (28 October 2005)
    by M Latterich
    posted to systems_biology by tmmurali on 2008-05-14 15:53:12 as ** along with 1 person and 1 group karthikram Neoscientists
  • Executable cell biology
    Nat Biotech, Vol. 25, No. 11. (November 2007), pp. 1239-1249.
    by Jasmin Fisher, Thomas A Henzinger
    posted to systems_biology by tmmurali on 2007-11-08 17:06:50 as ***** along with 10 people and 2 groups austin julius dbikard neils cjeans hpaces mircea tlandrain Doug jyuh csb_journal_club_public Centre de Recherches Interdisciplinaires
  • Systems biology: a brief overview.
    Science, Vol. 295, No. 5560. (1 March 2002), pp. 1662-1664.
    by H Kitano
    posted to systems_biology by soramame_0518 on 2008-05-09 05:22:08 as ** along with 20 people and 6 groups irenas Yanno Borelli wnpx biosv shivakumar3_14 dgront kehan cconboy mmt margaritis grahamc roland_ewald carmaus jdiezperezj maburkitt mertnuhoglu edvin lenov nsamways dbk-lab biodiversity_conservation Bioinformatics GrassBase dIEMoSIRIS MoSi-Rostock
  • On anti-portfolio effects in science and technology with application to reaction kinetics, chemical synthesis, and molecular biology
    Proceedings of the National Academy of Sciences, Vol. 104, No. 47. (20 November 2007), pp. 18398-18403.
    by Marcel O Vlad, Alexandru D Corlan, Vlad T Popa, John Ross
    posted to mathematics systems_biology by sobolevnrm on 2007-12-21 12:32:30 as read along with 1 person and 1 group RamuAnandakrishnan baker-group
  • From Pathways Databases to Network Models of Switching Behavior
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e152.
    by Baltazar D Aguda, Andrew B Goryachev
    posted to bioinformatics systems_biology by sobolevnrm on 2007-10-04 12:52:52 as read along with 5 people and 1 group balicea cjeans GustavoLacerda thomaskelder tharris baker-group
  • The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks.
    Eur J Biochem, Vol. 271, No. 14. (July 2004), pp. 2905-2922.
    by HG Holzhütter
    posted to nitric_oxide systems_biology by sobolevnrm on 2008-06-18 22:36:56 as read along with 3 people and 1 group alexg pmendes JeremyZucker baker-group
  • Controlling the rates of biochemical reactions and signaling networks by shape and volume changes
    Proceedings of the National Academy of Sciences, Vol. 105, No. 11. (18 March 2008), pp. 4099-4104.
    by L Lizana, B Bauer, O Orwar
    posted to diffusion systems_biology by sobolevnrm on 2008-05-19 11:22:52 as read along with 1 person and 1 group rmorenoe baker-group
  • Bayesian Ranking of Biochemical System Models.
    Bioinformatics (5 December 2007)
    by Vladislav Vyshemirsky, Mark A A Girolami
    posted to bioinformatics statistics systems_biology by sobolevnrm on 2008-04-24 11:32:12 as read along with 4 people and 1 group jyuh bootsy lenov keithvass baker-group
  • Robustness and modular design of the Drosophila segment polarity network
    Mol Syst Biol, Vol. 2 (12 December 2006)
    by Wenzhe Ma, Luhua Lai, Qi Ouyang, Chao Tang
    posted to systems_biology by sobolevnrm on 2007-12-20 12:21:08 as read along with 2 people and 1 group faisalm Heute baker-group
  • Toward realistic modeling of dynamic processes in cell signaling: Quantification of macromolecular crowding effects
    The Journal of Chemical Physics, Vol. 127, No. 15. (2007)
    by Jian Sun, Harel Weinstein
    posted to diffusion kinetics systems_biology by sobolevnrm on 2007-11-06 12:40:05 as read along with 1 group baker-group
  • Variable-free exploration of stochastic models: a gene regulatory network example
    (6 Nov 2006)
    by Radek Erban, Thomas A Frewen, Xiao Wang, Timothy C Elston, Ronald Coifman, Boaz Nadler, Ioannis G Kevrekidis
    posted to kinetics multiscale systems_biology by sobolevnrm on 2008-02-01 21:23:37 as ***** along with 1 person and 1 group j_vinals baker-group
  • Roles of Hemoglobin Allostery in Hypoxia-induced Metabolic Alterations in Erythrocytes: SIMULATION AND ITS VERIFICATION BY METABOLOME ANALYSIS
    J. Biol. Chem., Vol. 282, No. 14. (6 April 2007), pp. 10731-10741.
    by Ayako Kinoshita, Kosuke Tsukada, Tomoyoshi Soga, Takako Hishiki, Yuki Ueno, Yoichi Nakayama, Masaru Tomita, Makoto Suematsu
    posted to nitric_oxide systems_biology by sobolevnrm on 2007-09-18 14:18:57 as read along with 1 group baker-group
  • Modularization of biochemical networks based on classification of Petri net t-invariants
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Eva G Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Bjorn Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch
    posted to graph_theory systems_biology by sobolevnrm on 2008-02-08 12:20:33 as read along with 3 people and 1 group bootsy maralena roys baker-group
  • Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems
    Biotechnol. Prog. (26 September 2007)
    by H Li, Y Cao, LR Petzold, DT Gillespie
    posted to kinetics mathematics systems_biology by sobolevnrm on 2007-10-02 12:42:54 as read along with 1 person and 2 groups dagmar baker-group compneur
  • A mathematical tool for exploring the dynamics of biological networks
    Proceedings of the National Academy of Sciences (21 November 2007), 0709955104.
    by Paolo E Barbano, Marina Spivak, Marc Flajolet, Angus C Nairn, Paul Greengard, Leslie Greengard
    posted to mathematics multiscale systems_biology by sobolevnrm on 2008-01-10 12:32:48 as read along with 9 people and 1 group tmmurali cjeans zwang cactus forgoston lenov sdbneuro mdramirez phoenixzxl baker-group
  • Computer Modeling of Mitochondrial Tricarboxylic Acid Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electrophysiology
    J. Biol. Chem., Vol. 282, No. 34. (24 August 2007), pp. 24525-24537.
    by Fan Wu, Feng Yang, Kalyan C Vinnakota, Daniel A Beard
    posted to systems_biology by sobolevnrm on 2007-08-22 12:25:15 as read along with 1 person and 1 group paulschlesinger baker-group
  • Towards a theory of biological robustness
    Mol Syst Biol, Vol. 3 (2007)
    by Hiroaki Kitano
    posted to systems_biology by sobolevnrm on 2007-09-25 12:30:28 as read along with 8 people and 1 group jjray dullhunk margaritis massivemayhem fishtank bootsy Ema jf76 baker-group
  • Getting Started in Probabilistic Graphical Models
    PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e252.
    by Edoardo M Airoldi
    posted to bioinformatics systems_biology by sobolevnrm on 2008-02-01 12:54:36 as read along with 12 people and 1 group jyuh balicea AbnerCYH stajich cjeans GustavoLacerda GeeSharpMinor cabbagezs nklee biehl softsimu jfr baker-group
  • Universally Sloppy Parameter Sensitivities in Systems Biology Models
    PLoS Computational Biology, Vol. 3, No. 10. (1 October 2007), e189.
    by Ryan N Gutenkunst, Joshua J Waterfall, Fergal P Casey, Kevin S Brown, Christopher R Myers, James P Sethna
    posted to systems_biology by sobolevnrm on 2007-11-09 12:12:43 as read along with 5 people and 1 group faisalm fishtank cjeans afenley entropy baker-group
  • Computational Insights on the Competing Effects of Nitric Oxide in Regulating Apoptosis
    PLoS ONE, Vol. 3, No. 5. (28 May 2008), e2249.
    by Elife Z Bagci, Yoram Vodovotz, Timothy R Billiar, Bard Ermentrout, Ivet Bahar
    posted to nitric_oxide systems_biology by sobolevnrm on 2008-07-23 12:11:10 as read along with 1 group baker-group
  • Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis
    Genome Biology, Vol. 8, No. 9. (2007)
    by Robert Kleemann, Lars Verschuren, Marjan van Erk, Yuri Nikolsky, Nicole Cnubben, Elwin Verheij, Age Smilde, Henk Hendriks, Susanne Zadelaar, Graham Smith, Valery Kaznacheev, Tatiana Nikolskaya, Anton Melnikov, Eva H Camejo, Jan van der Greef, Ben van Ommen, Teake Kooistra
    posted to genego systems_biology by shikin on 2008-05-04 13:04:56 as ** along with 2 people and 1 group aconesa vinithepooh GeneGo
  • Linking data to models: data regression
    Nature Reviews Molecular Cell Biology, Vol. 7, No. 11. (27 September 2006), pp. 813-819.
    by Khuloud Jaqaman, Gaudenz Danuser
    posted to nature_sysbio_08 systems_biology by shikin on 2008-05-04 12:29:10 as *** along with 5 people and 3 groups jxl nickluscombe glyg rahulthadani cdpwebadmin EC EBI-regulation GeneGo
  • T1DBase, a community web-based resource for type 1 diabetes research.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by LJ Smink, EM Helton, BC Healy, CC Cavnor, AC Lam, D Flamez, OS Burren, Y Wang, GE Dolman, DB Burdick, VH Everett, G Glusman, D Laneri, L Rowen, H Schuilenburg, NM Walker, J Mychaleckyj, LS Wicker, DL Eizirik, JA Todd, N Goodman
    posted to diabetes systems_biology by shikin on 2007-10-23 19:33:39 as read along with 1 person massivemayhem
  • A new approach to decoding life: systems biology.
    Annu Rev Genomics Hum Genet, Vol. 2 (2001), pp. 343-372.
    by T Ideker, T Galitski, L Hood
    posted to genomics ideker systems_biology by shikin on 2007-10-18 16:18:10 as **** along with 6 people and 1 group okarsligil wnpx biosv mangtronix lh1 cerca Bioinformatics
  • A novel method for generation of signature networks as biomarkers from complex high throughput data.
    Toxicol Lett, Vol. 158, No. 1. (28 July 2005), pp. 20-29.
    by Y Nikolsky, S Ekins, T Nikolskaya, A Bugrim
    posted to genego systems_biology by shikin on 2008-02-18 14:46:29 as **
  • A novel method for visualizing nuclear hormone receptor networks relevant to drug metabolism.
    Drug metabolism and disposition: the biological fate of chemicals, Vol. 33, No. 3. (March 2005), pp. 474-481.
    by S Ekins, E Kirillov, EA Rakhmatulin, T Nikolskaya
    posted to genego network systems_biology toxicology by shikin on 2008-05-04 13:19:07 as ** along with 1 group GeneGo
  • Gene Expression Profiling in Lung Tissues from Mice Exposed to Cigarette Smoke, Lipopolysaccharide, or Smoke Plus Lipopolysaccharide by Inhalation
    Inhalation Toxicology, Vol. 18, No. 8. (July 2006), pp. 555-568.
    by Meng, , Gideon, , Harbo, , Renne, , Lee, , Brys, , Jones,
    posted to genego systems_biology by shikin on 2008-02-18 15:00:48 as **
  • Functional network analysis of the transcriptomes of mesenchymal stem cells derived from amniotic fluid, amniotic membrane, cord blood, and bone marrow.
    Stem Cells, Vol. 25, No. 10. (October 2007), pp. 2511-2523.
    by MS Tsai, SM Hwang, KD Chen, YS Lee, LW Hsu, YJ Chang, CN Wang, HH Peng, YL Chang, AS Chao, SD Chang, KD Lee, TH Wang, HS Wang, YK Soong
    posted to functional_analysis genomics pathway-analysis systems_biology by shikin on 2008-01-09 17:43:16 as read
  • Different signaling pathways in the livers of patients with chronic hepatitis B or chronic hepatitis C.
    Hepatology, Vol. 44, No. 5. (November 2006), pp. 1122-1138.
    by M Honda, T Yamashita, T Ueda, H Takatori, R Nishino, S Kaneko
    posted to genego systems_biology by shikin on 2008-02-18 14:32:53 as **
  • Predicting synthetic rescues in metabolic networks
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Adilson E Motter, Natali Gulbahce, Eivind Almaas, Albert-Laszlo Barabasi
    posted to metabolomics systems_biology by shikin on 2008-02-15 15:10:07 as read along with 9 people kentsis zwang bootsy biomcgary cabbagezs westoll shung debasis tmmurali
  • notes A systems biology approach for pathway level analysis
    Genome Res. (4 September 2007), gr.6202607.
    by Sorin Draghici, Purvesh Khatri, Adi L Tarca, Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, Roberto Romero
    posted to genomics pathway-analysis systems_biology by shikin on 2007-12-14 13:22:26 as read along with 15 people and 3 groups tmmurali dragonrez jfr gurkanbebek grahamc shigepong zwang cabbagezs cerami xingxu idonaldson Pao-Yang thomaskelder heliopais AlexanderPico Bioinformatics ParkinsonLab_at_MaRS OPIG
  • The Genomic Landscapes of Human Breast and Colorectal Cancers.
    Science (11 October 2007)
    by Laura D D Wood, D Williams W Parsons, Siân Jones, Jimmy Lin, Tobias Sjöblom, Rebecca J J Leary, Dong Shen, Simina M M Boca, Thomas Barber, Janine Ptak, Natalie Silliman, Steve Szabo, Zoltan Dezso, Vadim Ustyanksky, Tatiana Nikolskaya, Yuri Nikolsky, Rachel Karchin, Paul A A Wilson, Joshua S S Kaminker, Zemin Zhang, Randal Croshaw, Joseph Willis, Dawn Dawson, Michail Shipitsin, James K V K Willson, Saraswati Sukumar, Kornelia Polyak, Ben Ho H Park, Charit L L Pethiyagoda, P V Krishna V Pant, Dennis G G Ballinger, Andrew B B Sparks, James Hartigan, Douglas R R Smith, Erick Suh, Nickolas Papadopoulos, Phillip Buckhaults, Sanford D D Markowitz, Giovanni Parmigiani, Kenneth W W Kinzler, Victor E E Velculescu, Bert Vogelstein
    posted to cancer genego systems_biology by shikin on 2008-02-18 14:19:27 as ** along with 14 people and 1 group jyuh tmmurali jfr rdiaz eisei ramensky massivemayhem bioyang cabbagezs xingxu renatomilani gwenknight cerami srp33 VUMCGenomics
  • Molecular definition of breast tumor heterogeneity.
    Cancer Cell, Vol. 11, No. 3. (March 2007), pp. 259-273.
    by M Shipitsin, LL Campbell, P Argani, S Weremowicz, N Bloushtain-Qimron, J Yao, T Nikolskaya, T Serebryiskaya, R Beroukhim, M Hu, MK Halushka, S Sukumar, LM Parker, KS Anderson, LN Harris, JE Garber, AL Richardson, SJ Schnitt, Y Nikolsky, RS Gelman, K Polyak
    posted to cancer genego systems_biology by shikin on 2008-02-18 14:20:35 as ** along with 2 people jyuh jfr
  • notes Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases
    BMC Bioinformatics, Vol. 8 (04 October 2007), 372.
    by Seth I Berger, Jeremy M Posner, Avi Ma'ayan
    posted to network systems_biology by shikin on 2008-04-15 08:14:04 as read along with 2 people and 1 group jyuh jfr GeneGo
  • notes The large-scale organization of metabolic networks.
    Nature, Vol. 407, No. 6804. (5 October 2000), pp. 651-654.
    by H Jeong, B Tombor, R Albert, ZN Oltvai, AL Barabási
    posted to metabolomics network systems_biology thesis by shikin on 2008-05-04 17:10:53 as ** along with 22 people and 2 groups camster snuppepuppan jpmague mague alexisgallagher bjorns Borelli shivaram lfriedl cmmorel alexg Shirakawa ddahlem gcalda grahamc jrbanga karfunkel Evangelia shung pmendes stefanoallesina dylanwalker dbk-lab kdl
  • The properties of high-dimensional data spaces: implications for exploring gene and protein expression data
    Nat Rev Cancer, Vol. 8, No. 1. (January 2008), pp. 37-49.
    by Robert Clarke, Habtom W Ressom, Antai Wang, Jianhua Xuan, Minetta C Liu, Edmund A Gehan, Yue Wang
    posted to genomics systems_biology by shikin on 2008-01-09 16:22:05 as read along with 9 people and 1 group jfr jyuh tmmurali dwf frohike cjeans nedwards blackm0k brianb Bioinformatics
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
    Nature, Vol. 447, No. 7146. (14 June 2007), pp. 799-816.
    by
    posted to genomics systems_biology by shikin on 2008-04-17 18:27:01 as ** along with 10 people and 2 groups jyuh jfr chad_davis kengg olympos blobbybirdman fpattyn yevishere elfar eskay Bioinformatics UH - Computational Biology
  • Application of transcriptional and biological network analyses in mouse germ-cell transcriptomes.
    Genomics, Vol. 88, No. 1. (July 2006), pp. 18-33.
    by TL Lee, D Alba, V Baxendale, OM Rennert, WY Chan
    posted to genego systems_biology by shikin on 2008-02-18 14:38:28 as **
  • Early prediction of drug metabolism and toxicity: systems biology approach and modeling.
    Drug Discov Today, Vol. 9, No. 3. (1 February 2004), pp. 127-135.
    by A Bugrim, T Nikolskaya, Y Nikolsky
    posted to genego systems_biology toxicology by shikin on 2008-02-18 15:30:46 as ** along with 1 person kuhn
  • Transcriptional networks in plasmacytoid dendritic cells stimulated with synthetic TLR 7 agonists
    BMC Immunology, Vol. 8 (12 October 2007), 26.
    by Woubalem Birmachu, Raymond M Gleason, Barbara J Bulbulian, Christie L Riter, John P Vasilakos, Kenneth E Lipson, Yuri Nikolsky
    posted to genego systems_biology by shikin on 2008-02-18 14:42:56 as **
  • Identification of the Proliferation/Differentiation Switch in the Cellular Network of Multicellular Organisms
    PLoS Computational Biology, Vol. 2, No. 11. (1 November 2006), e145.
    by Kai Xia, Huiling Xue, Dong Dong, Shanshan Zhu, Jiamu Wang, Qingpeng Zhang, Lei Hou, Hua Chen, Ran Tao, Zheng Huang, Zheng Fu, Ye-Guang Chen, Jing-Dong J Han
    posted to gene_expression network systems_biology by shikin on 2008-04-15 07:49:08 as *** along with 3 people and 2 groups dolhuis mingzhi carlk SNE GeneGo
  • Comparative assessment of large-scale data sets of protein-protein interactions.
    Nature, Vol. 417, No. 6887. (23 May 2002), pp. 399-403.
    by C von Mering, R Krause, B Snel, M Cornell, SG Oliver, S Fields, P Bork
    posted to ppi systems_biology by shikin on 2008-04-17 12:38:49 as ** along with 21 people and 6 groups camster barry dragonrez bicko lfriedl chad_davis alexg j3xucite bundschu yeastyboy ruvido raiyar grahamc iris_2001 cmor shu Evangelia Pao-Yang carlk cerca ethkim dbk-lab structural_bioinformatics kdl Bioinformatics generif_paper GeneGo
  • Overlapping gene expression profiles of model compounds provide opportunities for immunotoxicity screening.
    Toxicol Appl Pharmacol, Vol. 226, No. 1. (1 January 2008), pp. 46-59.
    by KA Baken, JL Pennings, MJ Jonker, MM Schaap, A de Vries, H van Steeg, TM Breit, H van Loveren
    posted to genego systems_biology toxicology by shikin on 2008-02-18 15:25:59 as **
  • Integrating physical and genetic maps: from genomes to interaction networks
    Nature Reviews Genetics, Vol. 8, No. 9., pp. 699-710.
    by Andreas Beyer, Sourav Bandyopadhyay, Trey Ideker
    posted to ideker systems_biology by shikin on 2007-10-23 19:42:59 as ** along with 10 people and 3 groups jyuh balicea dchughes sebastien_vigneau grahamc joepickrell zwang lh1 cdeane carlk Bioinformatics G4ID Genetics-of-Gambling
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