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Tag pathway_analysis [85 articles]

Recent papers classified by the tag pathway_analysis.
  • 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
  • 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 17 people and 3 groups ptrobajo pengchy tmmurali dragonrez jfr gurkanbebek grahamc shigepong zwang cabbagezs cerami shikin idonaldson Pao-Yang thomaskelder heliopais AlexanderPico Bioinformatics ParkinsonLab_at_MaRS OPIG
  • 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
  • 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
  • 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 **
  • 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 5 people frohike 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 guhjy reyez
  • 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 3 people guhjy pengchy jhatrimatri
  • 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 8 people shikin jfr tmmurali ealloza cjeans Ema renatomilani frohike
  • Discovering Combinations of Genomic Aberrations Associated With Cancer
    Journal of the American Statistical Association (December 2002), pp. 931-942.
    by MA Newton
    posted to pathway_analysis genomic_aberrations copy_number_variation bayesian_statistics by srp33 on 2008-10-20 22:57:56 as **
  • 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 5 people huiminC ptrobajo oelemento jfr 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 **
  • 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
  • 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
  • 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 3 people ptrobajo nirfriedman roys
  • 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 9 people and 1 group cswinburne aalibes textoris troels_marstrand wnpx nirfriedman rdiaz sampath shikin GeneGo
  • 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 **
  • 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 guhjy kentsis mfenner ajeffs tuck maryee eckart_bindewald frohike Ao_Li2007 waghsk
  • 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 24 people and 4 groups idonaldson ihpark chrisamiller dragonrez jfr balajis maryee xwbcn hpiwowar aviad_work ealloza jdiggans jeremymiller frohike hawkeyehammer schuylrp natstreet heliopais shikin waghsk roys ellakat sgoetz AbnerCYH Bioinformatics BioinfoCIPF GeschwindLab Indigene
  • 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
  • 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 **
  • PIK3CA Cooperates with Other Phosphatidylinositol 3'-Kinase Pathway Mutations to Effect Oncogenic Transformation
    Cancer Res, Vol. 68, No. 19. (1 October 2008), pp. 8127-8136.
    by Katsutoshi Oda, Jennifer Okada, Luika Timmerman, Pablo Rodriguez-Viciana, David Stokoe, Keiko Shoji, Yuji Taketani, Hiroyuki Kuramoto, Zachary A Knight, Kevan M Shokat, Frank Mccormick
    posted to somatic_mutations pathway_analysis mutual_exclusivity by srp33 on 2008-10-23 15:54:57 as **
  • 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 6 people and 2 groups cswinburne aalibes textoris ealloza shikin waghsk BioinfoCIPF GeneGo
  • 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
  • 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 9 people and 1 group kaarsinogen jfr aramata jmjimenez maralena cabbagesofdoom shikin cerca tmmurali GeneGo
  • 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 7 people and 1 group druvus jfr sameetmehta bootsy maralena guhjy maoxizeng Bioinformatics
  • 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 7 people lflorez dullhunk massivemayhem maralena pmendes csanford lenov
  • 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 ** along with 1 person winterschlaefer
  • 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
  • Building pathway clusters from Random Forests classification using class votes
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Herbert Pang, Hongyu Zhao
    posted to clustering network pathway_analysis by jfr on 2008-04-29 15:40:12 as **** along with 4 people xtizon thomaskelder guhjy AlexanderPico
  • Identification of key processes underlying cancer phenotypes using biologic pathway analysis.
    PLoS ONE, Vol. 2, No. 5. (2007)
    by S Efroni, CF Schaefer, KH Buetow
    posted to pathway_analysis by jfr on 2007-11-23 14:53:43 as ** along with 6 people cswinburne ptrobajo dragonrez AlexanderPico daed thomaskelder
  • 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 guhjy ealloza AlexanderPico BioinfoCIPF
  • GenMAPP 2: New Features and Resources for Pathway Analysis
    BMC Bioinformatics, Vol. 8 (24 June 2007), 217.
    by Nathan Salomonis, Kristina Hanspers, Alexander C Zambon, Karen Vranizan, Steven C Lawlor, Kam D Dahlquist, Scott W Doniger, Joshua M Stuart, Bruce R Conklin, Alexander R Pico
    posted to pathway_analysis software by jfr on 2007-12-05 10:36:36 as * along with 2 people and 1 group thomaskelder AlexanderPico ConklinLab
  • Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer
    BMC Cancer, Vol. 7 (25 September 2007), 182.
    by Jack X Yu, Anieta M Sieuwerts, Yi Zhang, John WM Martens, Marcel Smid, Jan GM Klijn, Yixin Wang, John A Foekens
    posted to prognosis pathway_analysis gene_set_analysis breast_cancer by jfr on 2008-09-04 10:39:43 as *** along with 2 people and 1 group Zephyrus ealloza BioinfoCIPF
  • 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 guhjy AlexanderPico
  • Systematic reconstruction of TRANSPATH data into Cell System Markup Language
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, Satoru Miyano
    posted to systems_biology software pathway_analysis by jfr on 2008-09-24 13:49:23 as ** along with 4 people guhjy reyez bootsy JeremyZucker
  • 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
  • Extending pathways based on gene lists using InterPro domain signatures
    BMC Bioinformatics, Vol. 9 (04 January 2008), 3.
    by Florian Hahne, Alexander Mehrle, Dorit Arlt, Annemarie Poustka, Stefan Wiemann, Tim Beissbarth
    posted to pathway_analysis gene_set_analysis bioconductor annotation by jfr on 2008-11-28 14:01:46 as ** along with 5 people and 1 group ealloza frohike renatomilani guhjy AlexanderPico Bioinformatics
  • PathCase: Pathways Database System
    Bioinformatics (26 August 2008), btn459.
    by B Elliott, M Kirac, A Cakmak, G Yavas, S Mayes, E Cheng, Y Wang, C Gupta, G Ozsoyoglu, ZM Ozsoyoglu
    posted to software pathway_analysis by jfr on 2008-11-10 15:22:08 as ** along with 10 people and 2 groups AlexanderPico Zephyrus ptrobajo druvus mdstobbe dullhunk guhjy aconesa renatomilani thomaskelder ConklinLab Roswell Cancer Crosstalk
  • 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
  • Inferring differentiation pathways from gene expression.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
    by IG Costa, S Roepcke, C Hafemeister, A Schliep
    posted to pathway_analysis gene_set_analysis by jfr on 2008-09-26 10:56:15 as ** along with 1 person guhjy
  • 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 guhjy tmmurali aviad_work waszak AlexanderPico thomaskelder
  • Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Wei Jiang, Xia Li, Shaoqi Rao, Lihong Wang, Lei Du, Chuanxing Li, Chao Wu, Hongzhi Wang, Yadong Wang, Baofeng Yang
    posted to pathway_analysis pathway network il8 eno1 colon_cancer by jfr on 2008-11-26 11:07:34 as read along with 1 person frohike
  • 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
  • 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
  • Pathway analysis reveals functional convergence of gene expression profiles in breast cancer.
    BMC medical genomics, Vol. 1 (2008)
    by R Shen, AM Chinnaiyan, D Ghosh
    posted to prognosis pathway_analysis breast_cancer by jfr on 2008-11-03 15:00:27 as ** along with 2 people and 3 groups songpku Zephyrus Roswell Cancer Crosstalk BCDC Lab Notebook Breast Cancer Reading Club
  • 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 guhjy 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 guhjy AlexanderPico
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