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snuppepuppan's library [91 articles]

Recent papers added to snuppepuppan's library.
  • Similarity metrics for ligands reflecting the similarity of the target proteins.
    J Chem Inf Comput Sci, Vol. 43, No. 2. (r 2003), pp. 391-405.
    by A Schuffenhauer, P Floersheim, P Acklin, E Jacoby
    posted to chemogenomics similarity by snuppepuppan on 2006-07-04 10:43:34 as ** along with 1 person kuhn
  • Atherosclerotic plaque macrophage transcriptional regulators are expressed in blood and modulated by tristetraprolin.
    Circ Res, Vol. 98, No. 10. (26 May 2006), pp. 1282-1289.
    by WD Patino, JG Kang, S Matoba, OY Mian, BR Gochuico, PM Hwang
    posted to atherosclerosis atherosclerosisgenes networks transcription by snuppepuppan on 2006-07-03 14:28:32 as **
  • Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes.
    Am J Hum Genet, Vol. 78, No. 6. (June 2006), pp. 1011-1025.
    by L Franke, H Bakel, L Fokkens, ED de Jong, M Egmont-Petersen, C Wijmenga
    posted to findingtargets human networks by snuppepuppan on 2006-07-03 12:25:26 as ** along with 6 people and 1 group jyuh lfriedl tabu samal mmt raiyar kdl
  • Integration of text- and data-mining using ontologies successfully selects disease gene candidates
    Nucleic Acids Research, Vol. 33, No. 5. (2005), pp. 1544-1552.
    by Nicki Tiffin, Janet F Kelso, Alan R Powell, Hong Pan, Vladimir B Bajic, Winston A Hide
    posted to disease findingtargets by snuppepuppan on 2006-07-03 12:25:15 as ** along with 2 people samal craigtalbert
  • Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades.
    DNA Res, Vol. 10, No. 1. (28 February 2003), pp. 19-25.
    by CJ Savoie, S Aburatani, S Watanabe, Y Eguchi, S Muta, S Imoto, S Miyano, S Kuhara, K Tashiro
    posted to drugdevelopment findingtargets networks by snuppepuppan on 2006-06-22 12:58:17 as **
  • A bottom-up approach to gene regulation
    Nature, Vol. 439, No. 7078. (16 February 2006), pp. 856-860.
    by Nicholas J Guido, Xiao Wang, David Adalsteinsson, David Mcmillen, Jeff Hasty, Charles R Cantor, Timothy C Elston, JJ Collins
    posted to networks transcription by snuppepuppan on 2006-06-21 10:31:26 as ** along with 14 people and 2 groups tmmurali rklancer jyuh okarsligil bayesian balicea samal madhadron balabu johncumbers mmt proulx dbikard nklee Bioinformatics SynBioSys
  • Extraction of regulatory gene/protein networks from Medline
    Bioinformatics, Vol. 22, No. 6. (15 March 2006), pp. 645-650.
    by Jasmin Saric, Lars J Jensen, Isabel Rojas, Peer Bork
    posted to networks textmining by snuppepuppan on 2006-06-19 15:41:49 as ** along with 2 people and 1 group yas zlu T_lab
  • Combination of text-mining algorithms increases the performance.
    Bioinformatics (9 June 2006)
    by Rainer Malik, Lude Franke, Arno Siebes
    posted to textmining by snuppepuppan on 2006-06-19 13:19:26 as ***** along with 7 people and 4 groups soramame_0518 irenas jyuh yas fisherp caporaso markymaypo dbk-lab T_lab biomedical-nlp ARTFL
  • Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
    Journal of Biology, Vol. 5, No. 4. (08 June 2006), 11.
    by Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Gary C Hon, Chad L Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Ho, David Botstein, Brenda Andrews, Charles Boone, Olga G Troyanskya, Trey Ideker, Kara Dolinski, Nizar N Batada, Mike Tyers
    posted to networks transcription yeast by snuppepuppan on 2006-06-19 13:18:59 as ** along with 17 people and 3 groups chasmand tmmurali lfriedl balajis wnpx nickluscombe egralla citecat noano koller grahamc iris_2001 sgoetz shikin s041629 pmendes mtruksa kdl EBI-regulation GeneGo
  • Genome-wide expression studies of atherosclerosis: critical issues in methodology, analysis, interpretation of transcriptomics data.
    Arterioscler Thromb Vasc Biol, Vol. 26, No. 6. (June 2006), pp. 1226-1235.
    by AP Bijnens, E Lutgens, T Ayoubi, J Kuiper, AJ Horrevoets, MJ Daemen
    posted to atherosclerosis networks by snuppepuppan on 2006-06-19 13:18:46 as *****
  • Transcriptome network component analysis with limited microarray data.
    Bioinformatics (9 June 2006)
    by Simon J J Galbraith, Linh M M Tran, James C C Liao
    posted to networks transcription yeast by snuppepuppan on 2006-06-19 13:18:24 as ** along with 3 people and 1 group mariakmejia jyuh kengg Plantandetc
  • The genetics of variation in gene expression.
    Nat Genet, Vol. 32 Suppl (December 2002), pp. 522-525.
    by VG Cheung, RS Spielman
    posted to genevariation by snuppepuppan on 2005-12-21 12:21:43 as ** along with 3 people and 1 group adepace jo_davies annacarina07 EisenLab
  • Genetic analysis of genome-wide variation in human gene expression.
    Nature, Vol. 430, No. 7001. (12 August 2004), pp. 743-747.
    by M Morley, CM Molony, TM Weber, JL Devlin, KG Ewens, RS Spielman, VG Cheung
    posted to genevariation by snuppepuppan on 2005-12-21 12:19:44 as ** along with 9 people and 1 group caseybrown kentsis RMGraze adepace qfwills vplagnol nagendraproj jo_davies mimulus_99 EisenLab
  • Innovation: Can cell systems biology rescue drug discovery?
    Nature Reviews Drug Discovery, Vol. 4, No. 6. (01 June 2005), pp. 461-467.
    by Eugene C Butcher
    posted to findingtargets by snuppepuppan on 2005-12-20 14:50:37 as ** along with 2 people kuhn eweaver
  • Systems modeling: a pathway to drug discovery.
    Curr Opin Chem Biol, Vol. 9, No. 4. (August 2005), pp. 400-406.
    by P Rajasethupathy, SJ Vayttaden, US Bhalla
    posted to findingtargets networks by snuppepuppan on 2005-12-20 14:50:17 as ** along with 4 people kuhn wnpx mmt jdiggans
  • Using bioinformatics for drug target identification from the genome.
    Am J Pharmacogenomics, Vol. 5, No. 6. (2005), pp. 387-396.
    by Z Jiang, Y Zhou
    posted to findingtargets networks pharmacogenomics by snuppepuppan on 2005-12-20 14:50:02 as **
  • Drug target pharmacogenomics: an overview.
    Am J Pharmacogenomics, Vol. 1, No. 4. (2001), pp. 271-281.
    by JA Johnson
    posted to findingtargets pharmacogenomics by snuppepuppan on 2005-12-20 14:46:35 as **
  • Use of gene networks for identifying and validating drug targets.
    J Bioinform Comput Biol, Vol. 1, No. 3. (October 2003), pp. 459-474.
    by S Imoto, CJ Savoie, S Aburatani, S Kim, K Tashiro, S Kuhara, S Miyano
    posted to findingtargets networks by snuppepuppan on 2005-12-20 14:43:47 as ** along with 1 person wnpx
  • Identifying drug active pathways from gene networks estimated by gene expression data.
    Genome Inform Ser Workshop Genome Inform, Vol. 16, No. 1. (2005), pp. 182-191.
    by Y Tamada, S Imoto, K Tashiro, S Kuhara, S Miyano
    posted to findingtargets networks by snuppepuppan on 2005-12-20 14:42:49 as ** along with 2 people abhik wnpx
  • Systematic intervention of transcription for identifying network response to disease and cellular phenotypes.
    Bioinformatics (8 November 2005)
    by Huai Li, Ming Zhan
    posted to findingtargets networks by snuppepuppan on 2005-12-20 14:41:28 as ** along with 2 people abhik wnpx
  • SYSTEMS BIOLOGY: Less Is More in Modeling Large Genetic Networks
    Science, Vol. 310, No. 5747. (21 October 2005), pp. 449-451.
    by Stefan Bornholdt
    posted to modeling networks by snuppepuppan on 2005-10-23 09:48:34 as ** along with 6 people and 1 group eldan jmeppley balajis wnpx biosv fishtank Bioinformatics
  • Genomic profiles and predictive biological networks in oxidant-induced atherogenesis.
    Physiol Genomics, Vol. 13, No. 3. (13 May 2003), pp. 263-275.
    by CD Johnson, Y Balagurunathan, KP Lu, M Tadesse, MH Falahatpisheh, RJ Carroll, ER Dougherty, CA Afshari, KS Ramos
    posted to atherosclerosis networks by snuppepuppan on 2005-09-14 07:53:12 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 **
  • A probabilistic view of gene function.
    Nat Genet, Vol. 36, No. 6. (June 2004), pp. 559-564.
    by AG Fraser, EM Marcotte
    posted to networks textmining by snuppepuppan on 2005-09-13 13:00:54 as ** along with 9 people and 1 group ziquje lfriedl opheliav wnpx samal grahamc massivemayhem bootsy vietanh0 kdl
  • 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 5 people and 1 group textoris Ayest tardigrade ealloza heliopais BioinfoCIPF
  • Transcriptional profiling of in vitro smooth muscle cell differentiation identifies specific patterns of gene and pathway activation.
    Physiol Genomics, Vol. 19, No. 3. (17 November 2004), pp. 292-302.
    by JM Spin, S Nallamshetty, R Tabibiazar, EA Ashley, JY King, M Chen, PS Tsao, T Quertermous
    posted to atherosclerosisgenes mouse by snuppepuppan on 2005-07-19 09:32:08 as **
  • Mouse strain-specific differences in vascular wall gene expression and their relationship to vascular disease.
    Arterioscler Thromb Vasc Biol, Vol. 25, No. 2. (February 2005), pp. 302-308.
    by R Tabibiazar, RA Wagner, JM Spin, EA Ashley, B Narasimhan, EM Rubin, B Efron, PS Tsao, R Tibshirani, T Quertermous
    posted to atherosclerosis atherosclerosisgenes mouse by snuppepuppan on 2005-07-19 09:31:30 as **
  • Use of high throughput genomic tools for the study of endothelial cell biology.
    Lymphat Res Biol, Vol. 1, No. 2. (2003), pp. 133-145.
    by R Tabibiazar, T Quertermous
    posted to atherosclerosis atherosclerosisgenes by snuppepuppan on 2005-07-19 09:30:13 as ***
  • Identification of endothelial cell genes by combined database mining and microarray analysis.
    Physiol Genomics, Vol. 13, No. 3. (13 May 2003), pp. 249-262.
    by M Ho, E Yang, G Matcuk, D Deng, N Sampas, A Tsalenko, R Tabibiazar, Y Zhang, M Chen, S Talbi, YD Ho, J Wang, PS Tsao, A Ben-Dor, Z Yakhini, L Bruhn, T Quertermous
    posted to atherosclerosis atherosclerosisgenes by snuppepuppan on 2005-07-19 09:29:35 as ****
  • An architecture for biological information extraction and representation.
    Bioinformatics, Vol. 21, No. 4. (15 February 2005), pp. 430-438.
    by A Vailaya, P Bluvas, R Kincaid, A Kuchinsky, M Creech, A Adler
    posted to abstracts textmining by snuppepuppan on 2005-07-19 09:27:52 as *** along with 3 people and 2 groups irenas yas samal dbk-lab T_lab
  • 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 11 people and 1 group jago carlk AlexanderPico abhik tmmurali textoris wnpx noano koller ccr cdppublications CDP
  • Identifying Novel Genes for Atherosclerosis through Mouse-Human Comparative Genetics.
    Am J Hum Genet, Vol. 77, No. 1. (July 2005), pp. 1-16.
    by X Wang, N Ishimori, R Korstanje, J Rollins, B Paigen
    posted to atherosclerosis by snuppepuppan on 2005-07-19 09:23:11 as ****
  • 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 *****
  • Differential network expression during drug and stress response.
    Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2898-2905.
    by L Cabusora, E Sutton, A Fulmer, CV Forst
    posted to drugdevelopment pags by snuppepuppan on 2005-07-19 09:15:45 as **
  • An integrated approach for inference and mechanistic modeling for advancing drug development
    FEBS Letters, Vol. 579, No. 8. (21 March 2005), pp. 1878-1883.
    by Sergej V Aksenov, Bruce Church, Anjali Dhiman, Anna Georgieva, Ramesh Sarangapani, Gabriel Helmlinger, Iya G Khalil
    posted to drugdevelopment modeling pags by snuppepuppan on 2005-07-19 08:59:36 as ** along with 2 people mdimmic Borelli
  • 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
  • Text Mining Biomedical Literature for Discovering Gene-to-Gene Relationships: A Comparative Study of Algorithms
    IEEE/ACM Trans. Comput. Biol. Bioinformatics, Vol. 2, No. 1. (January 2005), pp. 62-76.
    by Ying Liu, Shamkant B Navathe, Jorge Civera, Venu Dasigi, Ashwin Ram, Brian J Ciliax, Ray Dingledine
    posted to networks textmining by snuppepuppan on 2005-07-19 08:54:36 as ** along with 2 people and 1 group zhengzhong yas T_lab
  • Effect of sampling on topology predictions of protein-protein interaction networks
    Nature Biotechnology, Vol. 23, No. 7. (07 July 2005), pp. 839-844.
    by Jing-Dong J Han, Denis Dupuy, Nicolas Bertin, Michael E Cusick, Marc Vidal
    posted to networks powerlaw by snuppepuppan on 2005-07-19 08:47:02 as ** along with 11 people carlk paolomarcatili kuhn rabbat gurkanbebek koller eukfn mikaelhuss grahamc cjeans iris_2001
  • Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.
    BMC Bioinformatics, Vol. 6, No. 1. (7 June 2005)
    by James W Cooper, Aaron Kershenbaum
    posted to networks textmining by snuppepuppan on 2005-06-17 10:40:16 as ** along with 3 people satre pggm chad_davis
  • GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.
    Bioinformatics, Vol. 17 Suppl 1 (2001)
    by C Friedman, P Kra, H Yu, M Krauthammer, A Rzhetsky
    posted to fulltext networks textmining by snuppepuppan on 2005-04-14 08:35:20 as ** along with 4 people and 2 groups irenas yas johnkork dejori dbk-lab T_lab
  • Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data.
    Proc Natl Acad Sci U S A, Vol. 101, No. 9. (2 March 2004), pp. 2981-2986.
    by A Tanay, R Sharan, M Kupiec, R Shamir
    posted to integratingdata modules networks by snuppepuppan on 2005-03-31 08:53:10 as ** along with 6 people and 1 group ellakat carlk dragonrez lfriedl balajis natstreet kdl
  • Multilevel modeling and inference of transcription regulation.
    J Comput Biol, Vol. 11, No. 2-3. (2004), pp. 357-375.
    by A Tanay, R Shamir
    posted to integratingdata modeling networks by snuppepuppan on 2005-03-31 08:52:38 as ** along with 1 person koller
  • Computational expansion of genetic networks.
    Bioinformatics, Vol. 17 Suppl 1 (2001)
    by A Tanay, R Shamir
    posted to expansion networks by snuppepuppan on 2005-03-31 08:52:08 as ** along with 2 people carlk dragonrez
  • Content-rich biological network constructed by mining PubMed abstracts.
    BMC Bioinformatics, Vol. 5, No. 1. (8 October 2004)
    by H Chen, BM Sharp
    posted to networks textmining by snuppepuppan on 2005-03-30 15:45:47 as ** along with 7 people and 2 groups irenas Enro BioGeek fisherp jeremymiller daniel_schober adoms dbk-lab GeschwindLab
  • Bioinformatic analysis of autism positional candidate genes using biological databases and computational gene network prediction.
    Genes Brain Behav, Vol. 2, No. 5. (October 2003), pp. 303-320.
    by AL Yonan, AA Palmer, KC Smith, I Feldman, HK Lee, JM Yonan, SG Fischer, P Pavlidis, TC Gilliam
    posted to disease networks textmining by snuppepuppan on 2005-03-30 15:12:21 as ** along with 2 people BioGeek kschiess
  • BioRAT: extracting biological information from full-length papers.
    Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 3206-3213.
    by DP Corney, BF Buxton, WB Langdon, DT Jones
    posted to fulltext textmining by snuppepuppan on 2005-03-30 15:03:58 as *** along with 9 people and 5 groups satre sobolevnrm camster irenas Enro jyuh A_Olympia helliontroy massivemayhem baker-group Philosophy_of_Information dbk-lab Blog_and_Wiki_Research biomedical-nlp
  • Application of genome-wide expression analysis to human health and disease.
    Proc Natl Acad Sci U S A (21 March 2005)
    by J Perren P Cobb, Michael N N Mindrinos, Carol Miller-Graziano, Steve E E Calvano, Henry V V Baker, Wenzhong Xiao, Krzysztof Laudanski, Bernard H H Brownstein, Constance M M Elson, Douglas L L Hayden, David N N Herndon, Stephen F F Lowry, Ronald V V Maier, David A A Schoenfeld, Lyle L L Moldawer, Ronald W W Davis, Ronald G G Tompkins, Henry V V Baker, Paul Bankey, Timothy Billiar, Bernard H H Brownstein, Steve E E Calvano, David Camp, Irshad Chaudry, J Perren P Cobb, Ronald W W Davis, Constance M M Elson, Bradley Freeman, Richard Gamelli, Nicole Gibran, Brian Harbrecht, Douglas L L Hayden, Wyrta Heagy, David Heimbach, David N N Herndon, Jureta Horton, John Hunt, Krzysztof Laudanski, James Lederer, Stephen F F Lowry, Ronald V V Maier, John Mannick, Bruce McKinley, Carol Miller-Graziano, Michael N N Mindrinos, Joseph Minei, Lyle L L Moldawer, Ernest Moore, Frederick Moore, Robert Munford, Avery Nathens, Grant O'keefe, Gary Purdue, Laurence Rahme, Daniel Remick, Matthew Sailors, David A A Schoenfeld, Michael Shapiro, Geoffrey Silver, Richard Smith, Gregory Stephanopoulos, Gary Stormo, Ronald G G Tompkins, Mehmet Toner, Shaw Warren, Michael West, Steven Wolfe, Wenzhong Xiao, Vernon Young
    posted to disease genevariation human by snuppepuppan on 2005-03-30 07:39:48 as ** along with 4 people and 1 group kentsis textoris jfr mgaldzic CHIP
  • Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks
    Nature Biotechnology, Vol. 23, No. 3. (04 March 2005), pp. 377-383.
    by Diego d di Bernardo, Michael J Thompson, Timothy S Gardner, Sarah E Chobot, Erin L Eastwood, Andrew P Wojtovich, Sean J Elliott, Scott E Schaus, James J Collins
    posted to networks pags by snuppepuppan on 2005-03-29 07:33:01 as ***** along with 6 people and 2 groups rklancer kentsis mjt rhem1224 balajis jayster4 TCR_Signaling SysbioMPI-TCells
  • Interaction network containing conserved and essential protein complexes in Escherichia coli
    Nature, Vol. 433, No. 7025. (03 February 2005), pp. 531-537.
    by Gareth Butland, Jose M Peregrin-Alvarez, Joyce Li, Wehong Yang, Xiaochun Yang, Veronica Canadien, Andrei Starostine, Dawn Richards, Bryan Beattie, Nevan Krogan, Michael Davey, John Parkinson, Jack Greenblatt, Andrew Emili
    posted to ecoli networks protein by snuppepuppan on 2005-03-29 07:29:46 as ** along with 6 people karbak bjorns balajis BarrosH gcalda discreteonyxorb
  • Systematic discovery of regulatory motifs in human promoters and 3[prime] UTRs by comparison of several mammals
    Nature, Vol. aop, No. current. (27 February 2005)
    by Xiaohui Xie, Jun Lu, EJ Kulbokas, Todd R Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric S Lander, Manolis Kellis
    posted to regulation transcription by snuppepuppan on 2005-03-29 07:27:23 as ** along with 22 people and 4 groups mariakmejia BioGeek briann jtextori tmmurali okarsligil jfr balajis lyongu eckart_bindewald mtagaya adepace fisherp nickluscombe panetebrother smiddha franklin oscarluoinau heliopais ale emptyhb maralena Bioinformatics EisenLab microRNA EBI-regulation
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