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Tag pathways [287 articles]

Recent papers classified by the tag pathways.
  • Structural and functional analysis of cellular networks with CellNetAnalyzer.
    BMC Syst Biol, Vol. 1 (2007)
    by S Klamt, J Saez-Rodriguez, ED Gilles
    posted to signal pathways modelling cellular by YvesDeDeene on 2008-09-13 17:45:34 as **
  • Reactome: a knowledgebase of biological pathways.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by G Joshi-Tope, M Gillespie, I Vastrik, P D'Eustachio, E Schmidt, B de Bono, B Jassal, GR Gopinath, GR Wu, L Matthews, S Lewis, E Birney, L Stein
    posted to pathways by yggdrasil on 2008-04-21 11:15:19 as ** along with 9 people and 1 group reyez aalibes kuhn yas dullhunk duartemolha massivemayhem cerami guhjy T_lab
  • From genomics to chemical genomics: new developments in KEGG.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by M Kanehisa, S Goto, M Hattori, KF Aoki-Kinoshita, M Itoh, S Kawashima, T Katayama, M Araki, M Hirakawa
    posted to pathways by yggdrasil on 2008-04-21 11:04:28 as ** along with 14 people namunet guhjy aalibes kuhn balajis alexg eweaver tny dullhunk michC frohike incovoma sgoetz natstreet
  • The PANTHER database of protein families, subfamilies, functions and pathways.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by H Mi, B Lazareva-Ulitsky, R Loo, A Kejariwal, J Vandergriff, S Rabkin, N Guo, A Muruganujan, O Doremieux, MJ Campbell, H Kitano, PD Thomas
    posted to database domain family pathways protein subfamily by xico on 2005-12-24 16:17:33 as *** along with 3 people and 2 groups Cortel yas AlexanderPico T_lab WetBiology
  • Analysis of Signalling Pathways Using Continuous Time Markov Chains
    Transactions on Computational Systems Biology VI (2006), pp. 44-67.
    by Muffy Calder, Vladislav Vyshemirsky, David Gilbert, Richard Orton
    posted to chains checking continuous logic markov model pathways processes signalling stochastic time by ullahmukhtar on 2007-08-06 14:02:02 as ***
  • Mechanotransduction in endothelial cell migration.
    J Cell Biochem, Vol. 96, No. 6. (15 December 2005), pp. 1110-1126.
    by S Li, NF Huang, S Hsu
    posted to endothelial mechanical mechanoresponse migration molecular pathways shear by tsjipko on 2006-08-16 13:20:45 as read
  • Distinct spatial and temporal activation of caspase pathways in neurons and glial cells after excitotoxic damage to the immature rat brain.
    Journal of neuroscience research, Vol. 85, No. 16. (December 2007), pp. 3545-3556.
    by S Villapol, L Acarin, M Faiz, B Castellano, B Gonzalez
    posted to svs rat pathways neurons glia excitotoxic damage caspase by treangen on 2008-11-21 09:08:00 as **
  • Protein Folding
    Annual Review of Biochemistry, Vol. 50, No. 1. (1981), pp. 497-532.
    by MG Rossmann, P Argos
    posted to proteinfolding pathways history 1981 by toerst on 2008-09-09 17:45:04 as **
  • Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes
    Brief Bioinform, Vol. 9, No. 1. (1 January 2008), pp. 34-45.
    by Matteo Brilli, Renato Fani, Pietro Lio
    posted to bioinfpdl metabolic pathways by Tingting on 2008-05-15 06:53:32 as ** along with 2 people lylu renatomilani
  • Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses
    Science (4 September 2008), 1164368.
    by Sian Jones, Xiaosong Zhang, Williams D Parsons, Jimmy C Lin, Rebecca J Leary, Philipp Angenendt, Parminder Mankoo, Hannah Carter, Hirohiko Kamiyama, Antonio Jimeno, Seung-Mo Hong, Baojin Fu, Ming-Tseh Lin, Eric S Calhoun, Mihoko Kamiyama, Kimberly Walter, Tatiana Nikolskaya, Yuri Nikolsky, James Hartigan, Douglas R Smith, Manuel Hidalgo, Steven D Leach, Alison P Klein, Elizabeth M Jaffee, Michael Goggins, Anirban Maitra, Christine Iacobuzio-Donahue, James R Eshleman, Scott E Kern, Ralph H Hruban, Rachel Karchin, Nickolas Papadopoulos, Giovanni Parmigiani, Bert Vogelstein, Victor E Velculescu, Kenneth W Kinzler
    posted to pathways pathwayanalysis by thomaskelder on 2008-10-20 14:31:51 as ** along with 13 people and 3 groups srp33 jfr whh98 roys cmzmasek fongkoh AlexanderPico SaraNasser renatomilani brianb shikin songpku giovenko ConklinLab GeneGo Roswell Cancer Crosstalk
  • Pathway mapping tools for analysis of high content data.
    Methods in molecular biology (Clifton, N.J.), Vol. 356 (2007), pp. 319-350.
    by S Ekins, Y Nikolsky, A Bugrim, E Kirillov, T Nikolskaya
    posted to pathwayanalysis pathways pathwaytools by thomaskelder on 2008-05-04 10:38:02 as ***** along with 2 people and 1 group shikin AlexanderPico GeneGo
  • Presenting and exploring biological pathways with PathVisio
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Martijn van Iersel, Thomas Kelder, Alexander Pico, Kristina Hanspers, Susan Coort, Bruce Conklin, Chris Evelo
    posted to pathways by thomaskelder on 2008-09-25 09:57:26 as read along with 5 people and 1 group dipenps guhjy ptrobajo AlexanderPico renatomilani ConklinLab
  • SPIKE - a database, visualization and analysis tool of cellular signaling pathways
    BMC Bioinformatics, Vol. 9 (20 February 2008), 110.
    by Ran Elkon, Rita Vesterman, Nira Amit, Igor Ulitsky, Idan Zohar, Mali Weisz, Gilad Mass, Nir Orlev, Giora Sternberg, Ran Blekhman, Jackie Assa, Yosef Shiloh, Ron Shamir
    posted to pathwayanalysis pathways by thomaskelder on 2008-02-26 10:21:29 as ***** along with 4 people guhjy renatomilani maralena AlexanderPico
  • A Global Pathway Crosstalk Network
    Bioinformatics (23 April 2008), btn200.
    by Yong Li, Pankaj Agarwal, Dilip Rajagopalan
    posted to networkanalysis pathwayanalysis pathways by thomaskelder on 2008-04-27 12:01:21 as *** along with 6 people maralena bootsy renatomilani AlexanderPico guhjy balicea
  • Multi-layered Representation for Cell Signaling Pathways
    Mol Cell Proteomics, Vol. 3, No. 10. (1 October 2004), pp. 1009-1022.
    by Eunok Paek, Jisook Park, Kong-Joo Lee
    posted to pathways by thomaskelder on 2008-05-26 13:41:50 as **
  • The public road to high-quality curated biological pathways.
    Drug discovery today (21 July 2008)
    by Michiel E E Adriaens, Magali Jaillard, Andra Waagmeester, Susan L M L Coort, Alex R R Pico, Chris T A T Evelo
    posted to pathwayanalysis pathways by thomaskelder on 2008-07-28 07:17:43 as ** along with 5 people nicklynch jfr ptrobajo AlexanderPico guhjy
  • Gene-set approach for expression pattern analysis
    Brief Bioinform (17 January 2008), bbn001.
    by Dougu Nam, Seon-Young Kim
    posted to pathwayanalysis pathways pathwaystatistics by thomaskelder on 2008-03-04 10:44:16 as ** along with 12 people ihpark ptrobajo guhjy seemu lp2 giovenko AlexanderPico heliopais tmmurali yas beete klo
  • Towards zoomable multidimensional maps of the cell
    Nature Biotechnology, Vol. 25, No. 5. (04 May 2007), pp. 547-554.
    by Zhenjun Hu, Joe Mellor, Jie Wu, Minoru Kanehisa, Joshua M Stuart, Charles Delisi
    posted to pathways by thomaskelder on 2008-05-28 19:47:49 as *** along with 10 people tmmurali kuhn cmmorel yas balajis dullhunk guhjy AlexanderPico carlk Borelli
  • Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
    Science, Vol. 292, No. 5518. (4 May 2001), pp. 929-934.
    by T Ideker, V Thorsson, JA Ranish, R Christmas, J Buhler, JK Eng, R Bumgarner, DR Goodlett, R Aebersold, L Hood
    posted to pathwayanalysis pathways systemsbiology by thomaskelder on 2008-05-13 09:58:29 as ** along with 11 people and 3 groups isimpson snuppepuppan BioGeek dragonrez bpb okarsligil opheliav wnpx gurkanbebek raiyar shikin Bioinformatics steinmetzlab GeneGo
  • Event ontology: a pathway-centric ontology for biological processes.
    Pac Symp Biocomput (2006), pp. 152-163.
    by T Kushida, T Takagi, KI Fukuda
    posted to pathwayontology pathways by thomaskelder on 2008-05-06 12:31:12 as ** along with 2 people and 4 groups yas jago T_lab e-maintenance Global_health_enterprise_architecture OER_Open_Educational_Resources
  • PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by H Mi, N Guo, A Kejariwal, PD Thomas
    posted to pathwaydatabase pathways by thomaskelder on 2008-05-28 12:10:11 as ** along with 4 people siebertm bootsy skumagai guhjy
  • Pathway databases.
    Ann N Y Acad Sci, Vol. 1020 (May 2004), pp. 77-91.
    by CF Schaefer
    posted to pathwaydatabases pathways by thomaskelder on 2008-05-07 12:23:35 as ***** along with 3 people and 1 group greg cantupaz AlexanderPico spliceml
  • 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 pathwaydatabases pathways by thomaskelder on 2008-05-19 10:10:38 as ** along with 5 people and 1 group balicea cjeans GustavoLacerda sobolevnrm tharris baker-group
  • Comparing classical pathways and modern networks: towards the development of an edge ontology
    Trends in Biochemical Sciences, Vol. In Press, Corrected Proof
    by Long J Lu, Andrea Sboner, Yuanpeng J Huang, Hao X Lu, Tara A Gianoulis, Kevin Y Yip, Philip M Kim, Gaetano T Montelione, Mark B Gerstein
    posted to pathwaydatabase pathways by thomaskelder on 2008-04-18 13:36:21 as ** along with 3 people kuhn andrawaagmeester lenov
  • Pathway information for systems biology.
    FEBS Lett, Vol. 579, No. 8. (21 March 2005), pp. 1815-1820.
    by MP Cary, GD Bader, C Sander
    posted to pathways by thomaskelder on 2008-05-08 09:15:40 as ** along with 3 people yaredo blackbart AlexanderPico
  • Reconstructing Signal Transduction Pathways: Challenges and Opportunities
    Annals of the New York Academy of Sciences, Vol. 1115, No. 1. (December 2007), pp. 32-50.
    by Arnold J Levine, Wenwei Hu, Zhaohui Feng, German Gil
    posted to pathwayreconstruction pathways by thomaskelder on 2008-05-04 10:33:06 as ***** along with 1 person guhjy
  • WikiPathways: Pathway Editing for the People
    PLoS Biology, Vol. 6, No. 7. (1 July 2008), e184.
    by Alexander R Pico, Thomas Kelder, Martijn P van Iersel, Kristina Hanspers, Bruce R Conklin, Chris Evelo
    posted to community database pathways social wiki by tharris on 2008-08-02 14:30:51 as ** along with 13 people and 2 groups guhjy psique ptrobajo cerami AlexanderPico thomaskelder iBartomeus renatomilani ajaymalik jarredmccaffrey laurianw dullhunk amarois ConklinLab behavior_flexibility
  • Getting started in biological pathway construction and analysis.
    PLoS computational biology, Vol. 4, No. 2. (February 2008)
    by GA Viswanathan, J Seto, S Patil, G Nudelman, SC Sealfon
    posted to bioinformatics pathways by tharris on 2008-06-02 20:09:43 as ** along with 4 people cswinburne guhjy jfr dullhunk
  • A voice region in the monkey brain
    Nature Neuroscience, Vol. 11, No. 3. (10 February 2008), pp. 367-374.
    by Christopher I Petkov, Christoph Kayser, Thomas Steudel, Kevin Whittingstall, Mark Augath, Nikos K Logothetis
    posted to auditory cortex pathways primate vocal vocalizations by tbloomf on 2008-07-31 20:29:37 as ** along with 1 person sen_cheng
  • The Neural Control of Vocalization in Mammals: A Review
    Journal of Voice, Vol. In Press, Corrected Proof
    by U Jürgens
    posted to acc auditory control cortex laryngeal learning mammals motor pathways vocal by tbloomf on 2008-07-31 20:23:44 as **
  • Species-specific calls activate homologs of Broca's and Wernicke's areas in the macaque
    Nature Neuroscience, Vol. 9, No. 8. (23 July 2006), pp. 1064-1070.
    by Ricardo Gil-Da-Costa, Alex Martin, Marco A Lopes, Monica Muñoz, Jonathan B Fritz, Allen R Braun
    posted to pathways primates recognition vocal by tbloomf on 2008-07-31 22:40:11 as **
  • Microcircuitry of the direct and indirect pathways of the basal ganglia
    Neuroscience, Vol. 86, No. 2. (September 1998), pp. 353-387.
    by Y Smith, MD Bevan, E Shink, JP Bolam
    posted to basalganglia pathways by stain on 2006-06-06 02:22:01 as ** along with 1 person awooga
  • Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families
    Science, Vol. 286, No. 5438. (08 October 1999), pp. 295-299.
    by Steve W Lockless, Rama Ranganathan
    posted to conserved interactions long-range pathways by sriram_s on 2006-03-24 23:11:33 as *** along with 15 people and 5 groups stevanspringer Einat marcius eckart_bindewald analogAI dgront caporaso choonpeng Haggan rabio mottonen zambujo mingzhi bethbromley ca3295 structural_bioinformatics FAB-lab biomedical-nlp BioinfoCIPF SGU-CIPF
  • Pathways to the analysis of microarray data
    Trends in Biotechnology, Vol. 23, No. 8. (August 2005), pp. 429-435.
    by Keira R Curtis, Matej Oresic, Antonio Vidal-Puig
    posted to networks pathways by snuppepuppan on 2005-08-01 09:18:01 as **** along with 8 people and 2 groups AlexanderPico jfr saman_vp textoris Ayest tardigrade ealloza heliopais ConklinLab BioinfoCIPF
  • Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'
    Nature Genetics, Vol. 37, No. 3. (13 February 2005), pp. 225-232.
    by Leonid Bystrykh, Ellen Weersing, Bert Dontje, Sue Sutton, Mathew T Pletcher, Tim Wiltshire, Andrew I Su, Edo Vellenga, Jintao Wang, Kenneth F Manly, Lu Lu, Elissa J Chesler, Rudi Alberts, Ritsert C Jansen, Robert W Williams, Michael P Cooke, Gerald d de Haan
    posted to human pathways by snuppepuppan on 2005-03-23 11:54:14 as ** along with 4 people kentsis fisherp caseybrown hplatero
  • Validation and refinement of gene-regulatory pathways on a network of physical interactions.
    Genome Biol, Vol. 6, No. 7. (2005)
    by CH Yeang, HC Mak, S McCuine, C Workman, T Jaakkola, T Ideker
    posted to networks pathways by snuppepuppan on 2005-07-19 09:24:49 as **** along with 14 people and 1 group kaarsinogen isimpson hplatero abhik tmmurali textoris wnpx noano koller ccr cdppublications AlexanderPico carlk jago CDP
  • Reconstruction of cellular signalling networks and analysis of their properties
    Nature Reviews Molecular Cell Biology, Vol. 6, No. 2. (01 February 2005), pp. 99-111.
    by Jason A Papin, Tony Hunter, Bernhard O Palsson, Shankar Subramaniam
    posted to networks pathways by snuppepuppan on 2005-07-19 08:57:43 as ** along with 8 people and 5 groups camster rklancer textoris rhem1224 rubendrr iris_2001 arne maralena dbk-lab TCR_Signaling cytoskeleton-and-afm SysbioMPI-TCells dIEMoSIRIS
  • Pathway analysis of coronary atherosclerosis.
    Physiol Genomics (7 June 2005)
    by Jennifer Y Y King, Rossella Ferrara, Raymond Tabibiazar, Joshua M M Spin, Mary M M Chen, Allan Kuchinsky, Aditya Vailaya, Robert Kincaid, Anya Tsalenko, David Xing-Fei X Deng, Andrew Connolly, Peng Zhang, Eugene Yang, Clifton Watt, Zohar Yakhini, Amir Ben-Dor, Annette Adler, Laurakay Bruhn, Philip Tsao, Thomas Quertermous, Euan A A Ashley
    posted to atherosclerosis networks pathways by snuppepuppan on 2005-07-19 09:21:02 as *****
  • Phenotype characterisation using integrated gene transcript, protein and metabolite profiling.
    Appl Bioinformatics, Vol. 3, No. 4. (2004), pp. 205-217.
    by M Oresic, CB Clish, EJ Davidov, E Verheij, J Vogels, LM Havekes, E Neumann, A Adourian, S Naylor, J van der Greef, T Plasterer
    posted to networks pathways by snuppepuppan on 2005-09-13 13:51:31 as **
  • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
    Nucleic acids research (25 November 2008)
    by Da Wei W Huang, Brad T T Sherman, Richard A A Lempicki
    posted to pathways gene-lists analysis by sjcockell on 2008-11-28 13:45:48 as ** along with 3 people pengchy phoenixzxl guhjy
  • The evolution of signalling pathways in animal development
    Nat Rev Genet, Vol. 4, No. 1. (January 2003), pp. 39-49.
    by Andre Pires-Dasilva, Ralf J Sommer
    posted to devo evo pathways review signalling by signalduplication on 2007-11-02 17:23:23 as **
  • Psidin Is Required in Drosophila Blood Cells for Both Phagocytic Degradation and Immune Activation of the Fat Body
    Current Biology, Vol. 17, No. 1. (9 January 2007), pp. 67-72.
    by Catherine A Brennan, Joseph R Delaney, David S Schneider, Kathryn V Anderson
    posted to psidin phagocytosis pathways innate_immunity hemocytes drosophila by shuzhens on 2008-09-16 21:39:04 as *****
  • Pathogen recognition and signalling in the Drosophila innate immune response
    Immunobiology, Vol. 211, No. 4. (2 June 2006), pp. 251-261.
    by Lihui Wang, Petros Ligoxygakis
    posted to drosophila innate_immunity pathways review by shuzhens on 2008-08-27 16:09:23 as **
  • Rudra Interrupts Receptor Signaling Complexes to Negatively Regulate the IMD Pathway
    PLoS Pathog, Vol. 4, No. 8. (2008), e1000120.
    by Kamna Aggarwal, Florentina Rus, Christie Vriesema-Magnuson, Deniz Ertürk-Hasdemir, Nicholas Paquette, Neal Silverman
    posted to toll pathways innate_immunity imd drosophila by shuzhens on 2008-09-02 21:25:34 as **
  • Down-regulation of NF-kappaB target genes by the AP-1 and STAT complex during the innate immune response in Drosophila.
    PLoS biology, Vol. 5, No. 9. (September 2007)
    by LK Kim, UY Choi, HS Cho, JS Lee, WB Lee, J Kim, K Jeong, J Shim, J Kim-Ha, YJ Kim
    posted to pathways insect innate_immunity immune_suppression imd drosophila by shuzhens on 2008-09-16 20:59:57 as *****
  • From A to B in free energy space
    The Journal of Chemical Physics, Vol. 126, No. 5. (2007)
    by Davide Branduardi, Francesco L Gervasio, Michele Parrinello
    posted to pathways free-energy alaninedipeptide by ruvido on 2007-02-08 13:04:33 as ** along with 3 people loison kdesmond Diego_Prada
  • Structural and functional investigation of a putative archaeal selenocysteine synthase.
    Biochemistry, Vol. 44, No. 40. (11 October 2005), pp. 13315-13327.
    by JT Kaiser, K Gromadski, M Rother, H Engelhardt, MV Rodnina, MC Wahl
    posted to amino-acids archaea pathways rareaa structure selenocysteine by rsandie on 2007-12-11 20:10:30 as **
  • Biosynthesis of Selenocysteine on Its tRNA in Eukaryotes
    PLoS Biology, Vol. 5, No. 1. (1 January 2007), e4.
    by Xue-Ming Xu, Bradley A Carlson, Heiko Mix, Yan Zhang, Kazima Saira, Richard S Glass, Marla J Berry, Vadim N Gladyshev, Dolph L Hatfield
    posted to eukaryote pathways rareaa trna selenocysteine by rsandie on 2007-12-11 20:08:02 as ***
  • A search engine to identify pathway genes from expression data on multiple organisms
    BMC Systems Biology, Vol. 1, No. 1. (2007)
    by Chunnuan Chen, Matthew Weirauch, Corey Powell, Alexander Zambon, Joshua Stuart
    posted to expression pathways search by rsandie on 2007-05-07 16:20:55 as ** along with 6 people and 1 group tharris guhjy tmmurali jfr waszak AlexanderPico C. elegans / WormBase
  • The koniocellular pathway in primate vision.
    Annu Rev Neurosci, Vol. 23 (2000), pp. 127-153.
    by SH Hendry, RC Reid
    posted to pathways s-cone by rknight15 on 2007-12-31 14:41:50 as ** along with 3 people and 1 group sylvain_chevallier alexstorer marcbernot eslab
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