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タグ: pathway_analysis [71 articles]

Recent papers classified by the tag pathway_analysis.
  • 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 bioinformatics pathway_analysis systems by xingxu on 2007-12-27 01:10:44 as ** along with 15 people and 3 groups tmmurali dragonrez jfr gurkanbebek grahamc shigepong zwang cabbagezs cerami shikin idonaldson Pao-Yang thomaskelder heliopais AlexanderPico Bioinformatics ParkinsonLab_at_MaRS OPIG
  • Calculating the statistical significance of changes in pathway activity from gene expression data.
    Stat Appl Genet Mol Biol, Vol. 3 (2004)
    by J Rahnenführer, FS Domingues, J Maydt, T Lengauer
    posted to expression metabolism pathway_analysis statistics by xingxu on 2007-12-27 21:02:20 as ** along with 1 person dragonrez
  • Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression
    PNAS, Vol. 101, No. 25. (22 June 2004), pp. 9309-9314.
    by Daniel R Rhodes, Jianjun Yu, K Shanker, Nandan Deshpande, Radhika Varambally, Debashis Ghosh, Terrence Barrette, Akhilesh Pandey, Arul M Chinnaiyan
    posted to meta-analysis microarray pathway_analysis by srp33 on 2008-05-14 20:37:35 as ** along with 2 people and 1 group hawkeyehammer ugengma Indigene
  • Linking oncogenic pathways with therapeutic opportunities
    Nature Reviews Cancer, Vol. 6, No. 9. (17 August 2006), pp. 735-741.
    by Andrea H Bild, Anil Potti, Joseph R Nevins
    posted to microarray pathway_analysis by srp33 on 2008-05-14 04:25:32 as ** along with 4 people aviad_work jackjackjjj frohike jfr
  • From signatures to models: understanding cancer using microarrays.
    Nat Genet, Vol. 37 Suppl (June 2005)
    by E Segal, N Friedman, N Kaminski, A Regev, D Koller
    posted to meta-analysis microarray pathway_analysis by srp33 on 2008-05-14 21:02:36 as ** along with 8 people and 1 group aalibes textoris troels_marstrand wnpx nirfriedman rdiaz sampath shikin GeneGo
  • Selective integration of multiple biological data for supervised network inference
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2488-2495.
    by Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai
    posted to data_aggregation pathway_analysis by srp33 on 2008-05-30 20:39:39 as **
  • A map of human cancer signaling
    Mol Syst Biol, Vol. 3 (18 December 2007)
    by Qinghua Cui, Yun Ma, Maria Jaramillo, Hamza Bari, Arif Awan, Song Yang, Simo Zhang, Lixue Liu, Meng Lu, Maureen O'Connor-Mccourt, Enrico O Purisima, Edwin Wang
    posted to network_reconstruction pathway_analysis by srp33 on 2008-07-01 15:31:58 as ** along with 7 people jfr tmmurali ealloza cjeans Ema renatomilani frohike
  • From patterns to pathways: gene expression data analysis comes of age.
    Nat Genet, Vol. 32 Suppl (December 2002), pp. 502-508.
    by DK Slonim
    posted to microarray pathway_analysis by srp33 on 2008-05-17 16:08:33 as ** along with 4 people textoris incovoma roys klo
  • iPath: interactive exploration of biochemical pathways and networks.
    Trends in biochemical sciences, Vol. 33, No. 3. (March 2008), pp. 101-103.
    by I Letunic, T Yamada, M Kanehisa, P Bork
    posted to pathway_analysis visualization by srp33 on 2008-08-21 21:59:58 as ** along with 3 people dullhunk jyuh reyez
  • Blazing Pathways Through Genetic Mountains
    Science, Vol. 293, No. 5537. (14 September 2001), pp. 2049-2051.
    by David K Gifford
    posted to graphical_models pathway_analysis by srp33 on 2008-05-17 16:04:52 as **
  • Testing association of a pathway with survival using gene expression data
    Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1950-1957.
    by Jelle J Goeman, Jan Oosting, Anne-Marie Cleton-Jansen, Jakob K Anninga, Hans C van Houwelingen
    posted to gene_sets microarray pathway_analysis by srp33 on 2008-04-24 22:34:57 as **
  • Probabilistic discovery of overlapping cellular processes and their regulation.
    J Comput Biol, Vol. 12, No. 7. (September 2005), pp. 909-927.
    by A Battle, E Segal, D Koller
    posted to gene_sets microarray pathway_analysis by srp33 on 2008-07-31 22:59:20 as ** along with 2 people nirfriedman roys
  • Discovering statistically significant pathways in expression profiling studies.
    Proc Natl Acad Sci U S A, Vol. 102, No. 38. (20 September 2005), pp. 13544-13549.
    by L Tian, SA Greenberg, SW Kong, J Altschuler, IS Kohane, PJ Park
    posted to gene_sets microarray pathway_analysis by srp33 on 2008-04-28 15:19:41 as ** along with 7 people and 1 group dragonrez maryee ealloza frohike justescaped giovenko heliopais BioinfoCIPF
  • Integrating biomedical knowledge to model pathways of prostate cancer progression.
    Cell cycle (Georgetown, Tex.), Vol. 6, No. 10. (May 2007), pp. 1177-1187.
    by DS Morris, SA Tomlins, DR Rhodes, R Mehra, RB Shah, AM Chinnaiyan
    posted to drug_discovery pathway_analysis by srp33 on 2008-05-14 20:59:48 as **
  • Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality.
    PLoS computational biology, Vol. 4, No. 8. (August 2008)
    by E Zotenko, J Mestre, DP O'Leary, TM Przytycka
    posted to pathway_analysis hub_genes by srp33 on 2008-09-04 22:50:09 as ** along with 5 people and 1 group maralena cabbagesofdoom shikin cerca tmmurali GeneGo
  • Reconstructing pathways in large genetic networks from genetic perturbations.
    J Comput Biol, Vol. 11, No. 1. (2004), pp. 53-60.
    by A Wagner
    posted to network_reconstruction pathway_analysis by srp33 on 2008-05-15 21:31:40 as ** along with 2 people and 1 group greg cantupaz spliceml
  • Meta-Analysis of Microarrays: Interstudy Validation of Gene Expression Profiles Reveals Pathway Dysregulation in Prostate Cancer
    Cancer Res, Vol. 62, No. 15. (1 August 2002), pp. 4427-4433.
    by Daniel R Rhodes, Terrence R Barrette, Mark A Rubin, Debashis Ghosh, Arul M Chinnaiyan
    posted to meta-analysis microarray pathway_analysis by srp33 on 2008-05-14 20:34:37 as ** along with 4 people and 1 group hawkeyehammer ugengma waghsk kengg Indigene
  • Using process diagrams for the graphical representation of biological networks
    Nature Biotechnology, Vol. 23, No. 8. (04 August 2005), pp. 961-966.
    by Hiroaki Kitano, Akira Funahashi, Yukiko Matsuoka, Kanae Oda
    posted to graphical_models pathway_analysis by srp33 on 2008-05-17 16:06:34 as ** along with 6 people dullhunk massivemayhem maralena pmendes csanford lenov
  • Integrating high-throughput and computational data elucidates bacterial networks.
    Nature, Vol. 429, No. 6987. (6 May 2004), pp. 92-96.
    by MW Covert, EM Knight, JL Reed, MJ Herrgard, BO Palsson
    posted to data_aggregation pathway_analysis visualization by srp33 on 2008-08-01 18:23:51 as ** along with 6 people and 2 groups Retchless lfriedl RMGraze alexg raiyar JeremyZucker kdl steinmetzlab
  • VisANT: an integrative framework for networks in systems biology
    Brief Bioinform (7 May 2008), bbn020.
    by Zhenjun Hu, Evan S Snitkin, Charles Delisi
    posted to pathway_analysis visualization by srp33 on 2008-08-05 15:19:15 as ** along with 5 people and 1 group sameetmehta bootsy maralena jyuh maoxizeng Bioinformatics
  • cPath: open source software for collecting, storing, and querying biological pathways
    BMC Bioinformatics, Vol. 7 (13 November 2006), 497.
    by Ethan G Cerami, Gary D Bader, Benjamin Gross, Chris Sander
    posted to pathway_analysis by srp33 on 2008-08-05 00:01:29 as ** along with 6 people and 2 groups jfr dquest carmaus bootsy cerami AlexanderPico dIEMoSIRIS MoSi-Rostock
  • Integrative analysis of the cancer transcriptome.
    Nat Genet, Vol. 37 Suppl (June 2005)
    by DR Rhodes, AM Chinnaiyan
    posted to meta-analysis pathway_analysis by srp33 on 2008-05-14 20:43:01 as ** along with 5 people and 2 groups aalibes textoris ealloza shikin waghsk BioinfoCIPF GeneGo
  • BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network
    Bioinformatics, Vol. 22, No. 23. (1 December 2006), pp. 2952-2954.
    by Chen, Xiaohui, Chen, Ming, Ning, Kaida
    posted to bayesian_networks microarray pathway_analysis by srp33 on 2008-05-22 15:51:27 as ** along with 1 person jhatrimatri
  • From the Cover: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    PNAS, Vol. 102, No. 43. (25 October 2005), pp. 15545-15550.
    by Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander, Jill P Mesirov
    posted to gene_sets microarray pathway_analysis by srp33 on 2008-05-14 04:29:25 as ** along with 22 people and 4 groups dragonrez jfr balajis maryee xwbcn hpiwowar aviad_work ealloza jdiggans jeremymiller frohike hawkeyehammer schuylrp natstreet heliopais shikin waghsk roys ellakat ihpark sgoetz AbnerCYH Bioinformatics BioinfoCIPF GeschwindLab Indigene
  • Molecular concepts analysis links tumors, pathways, mechanisms, and drugs.
    Neoplasia, Vol. 9, No. 5. (May 2007), pp. 443-454.
    by DR Rhodes, S Kalyana-Sundaram, SA Tomlins, V Mahavisno, N Kasper, R Varambally, TR Barrette, D Ghosh, S Varambally, AM Chinnaiyan
    posted to gene_sets pathway_analysis by srp33 on 2008-05-21 19:54:13 as ** along with 2 people jfr waghsk
  • Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks.
    BMC Bioinformatics, Vol. 6 (2005)
    by CJ Wolfe, IS Kohane, AJ Butte
    posted to microarray pathway_analysis by srp33 on 2008-07-28 17:49:24 as ** along with 3 people balajis maryee dragonrez
  • Oncogenic pathway signatures in human cancers as a guide to targeted therapies
    Nature (06 November 2005)
    by Andrea H Bild, Guang Yao, Jeffrey T Chang, Quanli Wang, Anil Potti, Dawn Chasse, Mary-Beth Joshi, David Harpole, Johnathan M Lancaster, Andrew Berchuck, John A Olson, Jeffrey R Marks, Holly K Dressman, Mike West, Joseph R Nevins
    posted to microarray pathway_analysis by srp33 on 2008-05-14 04:24:32 as ** along with 11 people Yanno jyuh kentsis mfenner ajeffs tuck maryee eckart_bindewald frohike Ao_Li2007 waghsk
  • Disease gene explorer: display disease gene dependency by combining Bayesian networks with clustering
    Computational Systems Bioinformatics Conference, 2004. CSB 2004. Proceedings. 2004 IEEE (2004), pp. 574-575.
    by Qian Diao, We Hu, Hao Zhong, Juntao Li, Feng Xue, Tao Wang, Yimin Zhang
    posted to bayesian_networks clustering pathway_analysis by srp33 on 2008-08-01 00:18:38 as **
  • PathExpress: a web-based tool to identify relevant pathways in gene expression data
    Nucl. Acids Res. (22 June 2007), gkm261.
    by Nicolas Goffard, Georg Weiller
    posted to database pathway_analysis by jfr on 2007-12-04 11:58:45 as * along with 3 people and 1 group jyuh ealloza AlexanderPico BioinfoCIPF
  • 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 pathway_analysis by jfr on 2007-09-07 13:09:18 as ** along with 5 people jyuh tmmurali rsandie waszak AlexanderPico
  • Pathway Analysis of Microarray Data via Regression
    Journal of Computational Biology, Vol. 0, No. 0. (0), pp. 1-9.
    by AJ Adewale, I Dinu, JD Potter, Q Liu, Y Yasui
    posted to pathway_analysis by jfr on 2008-05-14 11:50:02 as ** along with 6 people tmmurali csgillespie huali heliopais jyuh AlexanderPico
  • Mining pathway signatures from microarray data and relevant biological knowledge.
    J Biomed Inform, Vol. 40, No. 6. (December 2007), pp. 698-706.
    by E Panteris, S Swift, A Payne, X Liu
    posted to pathway_analysis by jfr on 2007-11-26 10:17:08 as ** along with 2 people jyuh AlexanderPico
  • Reactome: a knowledgebase of biological pathways and processes
    Genome Biology, Vol. 8 (16 March 2007), R39.
    by Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Geeta Joshi-Tope, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein
    posted to bioinformatics pathway_analysis by jfr on 2007-07-31 16:29:35 as ** along with 6 people jyuh dragonrez balajis raiyar toshiaki_katayama AlexanderPico
  • Reverse engineering of regulatory networks in human B cells.
    Nat Genet (20 March 2005)
    by Katia Basso, Adam A A Margolin, Gustavo Stolovitzky, Ulf Klein, Riccardo Dalla-Favera, Andrea Califano
    posted to pathway_analysis by jfr on 2007-03-23 14:36:56 as read along with 8 people snuppepuppan kentsis dragonrez wnpx raiyar naegele heliopais lylu
  • The use of logic relationships to model colon cancer gene expression networks with mRNA microarray data.
    Journal of biomedical informatics, Vol. 41, No. 4. (August 2008), pp. 530-543.
    by X Ruan, J Wang, H Li, RE Perozzi, EF Perozzi
    posted to colon_cancer gene_expression network pathway_analysis progression by jfr on 2008-07-17 14:36:18 as read along with 1 person balicea
  • Pathway recognition and augmentation by computational analysis of microarray expression data.
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 233-241.
    by BA Novak, AN Jain
    posted to systems_biology pathway_analysis methodology by jfr on 2007-01-12 14:00:46 as ** along with 1 person AlexanderPico
  • Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases.
    Bioinformatics (28 June 2007)
    by Duccio Cavalieri, Cinzia Castagnini, Simona Toti, Karolina Maciag, Thomas Kelder, Luca Gambineri, Samuele Angioli, Piero Dolara
    posted to pathway_analysis software by jfr on 2007-09-05 11:41:12 as * along with 6 people jyuh tmmurali aviad_work waszak AlexanderPico thomaskelder
  • Nonparametric pathway-based regression models for analysis of genomic data.
    Biostatistics (13 June 2006)
    by Zhi Wei, Hongzhe Li
    posted to breast_cancer classification pathway_analysis by jfr on 2007-01-08 12:08:40 as **** along with 3 people macavity1g waghsk ptrobajo
  • Modeling Cancer Progression via Pathway Dependencies.
    PLoS Comput Biol, Vol. 4, No. 2. (15 February 2008)
    by Elena J J Edelman, Justin Guinney, Jen-Tsan T Chi, Phillip G G Febbo, Sayan Mukherjee
    posted to model pathway_analysis progression by jfr on 2008-08-05 17:40:00 as **** along with 1 person bootsy
  • Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation.
    Bioinformatics (28 March 2007)
    by Daniel Kemp, N R R Nirmala, Joseph D D Szustakowski
    posted to gene_set_analysis pathway_analysis by jfr on 2007-09-07 11:44:27 as ** along with 2 people and 1 group ealloza hhlee BioinfoCIPF
  • Group additive regression models for genomic data analysis.
    Biostatistics (18 May 2007)
    by Yihui Luan, Hongzhe Li
    posted to pathway_analysis by jfr on 2007-11-23 15:12:28 as ** along with 1 person ptrobajo
  • KEGGanim: pathway animations for high-throughput data.
    Bioinformatics (1 December 2007)
    by Priit Adler, Jüri Reimand, Jürgen Jänes, Raivo Kolde, Hedi Peterson, Jaak Vilo
    posted to pathway_analysis software by jfr on 2008-04-09 15:05:49 as read along with 4 people jyuh dullhunk renatomilani AlexanderPico
  • Bioinformatics applications for pathway analysis of microarray data.
    Curr Opin Biotechnol (18 January 2008)
    by Thomas Werner
    posted to pathway_analysis review by jfr on 2008-04-28 15:53:23 as ** along with 2 people jyuh AlexanderPico
  • An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer.
    BMC genomics, Vol. 9 Suppl 1 (2008)
    by M Xu, MC Kao, J Nunez-Iglesias, JR Nevins, M West, XJ Zhou
    posted to pathway_analysis integration breast_cancer by jfr on 2008-09-04 11:05:25 as *****
  • Computational exploration of the activated pathways associated with DNA damage response in breast cancer.
    Proteins, Vol. 65, No. 1. (1 October 2006), pp. 103-110.
    by L Wen, W Li, M Sobel, JA Feng
    posted to breast_cancer dna_damage pathway_analysis by jfr on 2007-03-01 10:30:10 as *** along with 1 person macavity1g
  • Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer.
    Cancer Res, Vol. 67, No. 21. (1 November 2007), pp. 10296-10303.
    by SR Setlur, TE Royce, A Sboner, JM Mosquera, F Demichelis, MD Hofer, KD Mertz, M Gerstein, MA Rubin
    posted to integration pathway_analysis meta-analysis by jfr on 2008-02-04 09:52:11 as *** along with 2 people oelemento dragonrez
  • VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by Z Hu, DM Ng, T Yamada, C Chen, S Kawashima, J Mellor, B Linghu, M Kanehisa, JM Stuart, C DeLisi
    posted to database pathway_analysis by jfr on 2007-12-04 12:02:00 as ** along with 1 person AlexanderPico
  • Topology-based cancer classification and related pathway mining using microarray data.
    Nucleic Acids Res, Vol. 34, No. 14. (2006), pp. 4069-4080.
    by CC Liu, WS Chen, CC Lin, HC Liu, HY Chen, PC Yang, PC Chang, JJ Chen
    posted to bioinformatics classification pathway_analysis by jfr on 2006-11-08 10:03:24 as **
  • Pathway analysis using random forests classification and regression.
    Bioinformatics (29 June 2006)
    by Herbert Pang, Aiping Lin, Matthew Holford, Bradley E E Enerson, Bin Lu, Michael P P Lawton, Eugenia Floyd, Hongyu Zhao
    posted to pathway_analysis classification by jfr on 2007-01-10 09:44:37 as *** along with 5 people and 2 groups tabu ealloza giovanni ptrobajo AlexanderPico BioinfoCIPF GeschwindLab
  • Evaluation of biological pathways involved in chemotherapy response in breast cancer
    Breast Cancer Research, Vol. 10 (29 April 2008), R37.
    by Attila Tordai, Jing Wang, Fabrice Andre, Cornelia Liedtke, Kai Yan, Christos Sotiriou, Gabriel N Hortobagyi, Fraser W Symmans, Lajos Pusztai
    posted to therapy pathway_analysis breast_cancer by jfr on 2008-09-04 14:36:41 as read
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