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Group: BioinfoCIPF - with tag expression [73 articles]

Recent papers posted by members of the BioinfoCIPF group with tag expression
  • DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
    BMC Bioinformatics, Vol. 8 (02 November 2007), 426.
    by Brad T Sherman, Da W Huang, Qina Tan, Yongjian Guo, Stephan Bour, David Liu, Robert Stephens, Michael W Baseler, Clifford H Lane, Richard A Lempicki
    posted to database expression functional_annotation microarray by ealloza to the group BioinfoCIPF on 2007-11-05 17:30:43 as *** along with 4 people jyuh jfr barriot hpaces
  • Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer
    Bioinformatics, Vol. 23, No. 17. (1 September 2007), pp. 2273-2280.
    by Andreas Buness, Ruprecht Kuner, Markus Ruschhaupt, Annemarie Poustka, Holger Sultmann, Achim Tresch
    posted to microarray meta_analysis human expression chromosome cancer amplification algorithm aberration by ealloza to the group BioinfoCIPF on 2007-09-11 11:07:15 as read along with 2 people jfr rdiaz
  • Functional profiling and gene expression analysis of chromosomal copy number alterations.
    Bioinformation, Vol. 1, No. 10. (2007), pp. 432-435.
    by L Conde, D Montaner, J Burguet-Castell, J Tárraga, F Al-Shahrour, J Dopazo
    posted to microarray expression copy_number chromosome cgh by ealloza to the group BioinfoCIPF on 2007-08-09 12:37:48 as read along with 1 person jfr
  • GSEA-P: A desktop application for Gene Set Enrichment Analysis
    Bioinformatics (20 July 2007), btm369.
    by Aravind Subramanian, Heidi Kuehn, Joshua Gould, Pablo Tamayo, Jill P Mesirov
    posted to microarray gene_set_analysis expression applet by ealloza to the group BioinfoCIPF on 2007-08-07 10:52:49 as read along with 8 people jyuh cassj schuylrp barriot waszak dmontaner Eugene heliopais
  • Improving gene set analysis of microarray data by SAM-GS
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Irina Dinu, John Potter, Thomas Mueller, Qi Liu, Adeniyi Adewale, Gian Jhangri, Gunilla Einecke, Konrad Famulski, Philip Halloran, Yutaka Yasui
    posted to microarray gene_set_analysis expression algorithm by ealloza to the group BioinfoCIPF on 2007-07-06 10:44:14 as read along with 8 people jfr shigepong ghattem GeeSharpMinor waghsk LuigiAugugliaro heliopais renatomilani
  • MicroRNA expression alterations are linked to tumorigenesis and non-neoplastic processes in pancreatic ductal adenocarcinoma
    Oncogene, Vol. aop, No. current.
    by AE Szafranska, TS Davison, J John, T Cannon, B Sipos, A Maghnouj, E Labourier, SA Hahn, ,
    posted to microrna human expression cancer by ealloza to the group BioinfoCIPF on 2007-07-02 10:57:56 as **** along with 1 person tardigrade
  • 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 microarray gene_set_analysis expression by ealloza to the group BioinfoCIPF on 2007-06-25 13:02:28 as read along with 2 people jfr hhlee
  • Using expression arrays for copy number detection: an example from E. Coli
    BMC Bioinformatics, Vol. 8 (14 June 2007), 203.
    by Dmitriy Skvortsov, Diana Abdueva, Michael E Stitzer, Steven E Finkel, Simon Tavare
    posted to hmm expression copy_number cgh aberration by ealloza to the group BioinfoCIPF on 2007-06-25 12:50:00 as read along with 2 people and 1 group bioguru2000 shigepong Bioinformatics
  • Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways
    Genome Biology, Vol. 7 (17 October 2006), R93.
    by David M Levine, David R Haynor, John Castle, Sergey Stepaniants, Matteo Pellegrini, Mao Mao, Jason M Johnson
    posted to pathway mrna microarray gene_set_analysis gene_list_analysis expression comparison coherence coexpression by ealloza to the group BioinfoCIPF on 2007-06-04 11:07:04 as *** along with 3 people dragonrez jfr heliopais
  • Genome Expression Pathway Analysis Tool - Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context
    BMC Bioinformatics, Vol. 8 (02 June 2007), 179.
    by Markus Weniger, Julia C Engelmann, Joerg Schultz
    posted to webserver suite pathway microarray expression by ealloza to the group BioinfoCIPF on 2007-06-04 10:46:29 as ** along with 5 people jyuh jfr rdiaz frohike fmenolascina
  • GeneTrail--advanced gene set enrichment analysis
    Nucl. Acids Res. (25 May 2007), gkm323.
    by Christina Backes, Andreas Keller, Jan Kuentzer, Benny Kneissl, Nicole Comtesse, Yasser A Elnakady, Rolf Muller, Eckart Meese, Hans-Peter Lenhof
    posted to gene_set_analysis gene_list_analysis expression by ealloza to the group BioinfoCIPF on 2007-05-28 12:11:22 as **
  • Threshold-free high-power methods for the ontological analysis of genome-wide gene expression studies
    Genome Biology, Vol. 8 (08 May 2007), R74.
    by Bjorn Nilsson, Petra Hakansson, Mikael Johansson, Sven Nelander, Thoas Fioretos
    posted to ontology microarray gene_set_analysis expression algorithm by ealloza to the group BioinfoCIPF on 2007-05-10 15:07:53 as ** along with 1 person jfr
  • MicroRNAs as tumor suppressors
    Nature Genetics, Vol. 39, No. 5., pp. 582-583.
    by Scott M Hammond
    posted to tumor supressor microrna human expression cancer by ealloza to the group BioinfoCIPF on 2007-04-26 15:13:56 as ** along with 1 person tardigrade
  • Interpretation of microarray data in cancer
    British Journal of Cancer, Vol. aop, No. current. (06 March 2007)
    by S Michiels, S Koscielny, C Hill
    posted to validation review prediction microarray expression cancer by ealloza to the group BioinfoCIPF on 2007-04-19 15:05:07 as ** along with 4 people frohike laral jfr bioyang
  • From genes to functional classes in the study of biological systems
    BMC Bioinformatics, Vol. 8 (03 April 2007), 114.
    by Fatima Al-Shahrour, Leonardo Arbiza, Hernan Dopazo, Jaime Huerta-Cepas, Pablo Minguez, David Montaner, Joaquin Dopazo
    posted to microarray interaction gene_set_analysis expression evolution by ealloza to the group BioinfoCIPF on 2007-04-17 18:25:54 as ***** along with 6 people jfr Sharpshoot ajw Garamonfok djkt sgoetz
  • Characterization of microRNA expression levels and their biological correlates in human cancer cell lines.
    Cancer Res, Vol. 67, No. 6. (15 March 2007), pp. 2456-2468.
    by A Gaur, DA Jewell, Y Liang, D Ridzon, JH Moore, C Chen, VR Ambros, MA Israel
    posted to signature microrna human expression cancer by ealloza to the group BioinfoCIPF on 2007-04-12 11:11:07 as ** along with 2 people jfr elzodw
  • MicroRNAs and cancer
    British Journal of Surgery, Vol. 94, No. 1. (January 2007), pp. 23-30.
    by Wijnhoven, , Michael, , Watson,
    posted to review microrna microarray human expression cancer by ealloza to the group BioinfoCIPF on 2007-04-10 15:55:07 as ** along with 2 people tardigrade Garamonfok
  • Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers
    BMC Bioinformatics, Vol. 8 (06 April 2007), 118.
    by Xinan Yang, Xiao Sun
    posted to microarray meta_analysis human gene_list_analysis expression cancer by ealloza to the group BioinfoCIPF on 2007-04-10 11:16:58 as ** along with 4 people jfr shigepong ugengma srp33
  • Evidence of spatially bound gene regulation in Mus musculus: Decreased gene expression proximal to microRNA genomic location.
    Proc Natl Acad Sci U S A (12 March 2007)
    by Hidenori Inaoka, Yutaka Fukuoka, Isaac S S Kohane
    posted to regulation mus_musculus microrna gene_order expression by ealloza to the group BioinfoCIPF on 2007-03-21 11:50:34 as ** along with 4 people and 3 groups andersbj dchughes bootsy heliopais microRNA G4ID Genetics-of-Gambling
  • GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms.
    Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2618-2625.
    by M Smid, LC Dorssers
    posted to algorithm expression functional_annotation gene_set_analysis microarray sage by ealloza to the group BioinfoCIPF on 2007-03-12 15:40:07 as read
  • GOAL: automated Gene Ontology analysis of expression profiles.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by S Volinia, R Evangelisti, F Francioso, D Arcelli, M Carella, P Gasparini
    posted to algorithm expression functional_annotation gene_set_analysis microarray sage by ealloza to the group BioinfoCIPF on 2007-03-12 15:38:46 as read
  • Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression.
    Bioinformatics, Vol. 21, No. 7. (1 April 2005), pp. 1129-1137.
    by Y Ben-Shaul, H Bergman, H Soreq
    posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2007-03-12 15:36:36 as read
  • GenePattern 2.0
    Nature Genetics, Vol. 38, No. 5., pp. 500-501.
    by Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo, Jill P Mesirov
    posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2007-03-12 15:06:29 as read along with 3 people rdiaz mayercd jyuh
  • 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 algorithm expression functional_annotation gene_set_analysis microarray permutations by ealloza to the group BioinfoCIPF on 2007-03-12 15:03:34 as read along with 7 people dragonrez maryee frohike justescaped srp33 giovenko heliopais
  • Testing association of a pathway with survival using gene expression data.
    Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1950-1957.
    by JJ Goeman, J Oosting, AM Cleton-Jansen, JK Anninga, HC van Houwelingen
    posted to algorithm expression gene_set_analysis microarray survival by ealloza to the group BioinfoCIPF on 2007-03-12 14:46:06 as read
  • A global test for groups of genes: testing association with a clinical outcome.
    Bioinformatics, Vol. 20, No. 1. (1 January 2004), pp. 93-99.
    by JJ Goeman, SA van de Geer, F de Kort, HC van Houwelingen
    posted to algorithm expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2007-03-12 14:43:58 as read along with 4 people dragonrez ugengma saman_vp klo
  • Analyzing gene expression data in terms of gene sets: methodological issues.
    Bioinformatics (15 February 2007)
    by Jelle J J Goeman, Peter Bühlmann
    posted to algorithm comparison expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2007-03-12 14:39:32 as read along with 5 people and 1 group jfr shigepong heliopais jyuh diging_data BTS-PT-AS-CS
  • A gene-expression signature to predict survival in breast cancer across independent data sets
    Oncogene, Vol. aop, No. current.
    by A Naderi, AE Teschendorff, NL Barbosa-Morais, SE Pinder, AR Green, DG Powe, JFR Robertson, S Aparicio, IO Ellis, JD Brenton, C Caldas
    posted to cancer expression human microarray prediction signature by ealloza to the group BioinfoCIPF on 2007-03-05 16:10:37 as *** along with 3 people and 1 group jfr giovanni Ao_Li2007 GeschwindLab
  • Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors
    Oncogene, Vol. aop, No. current.
    by K Jong, E Marchiori, A van der Vaart, SF Chin, B Carvalho, M Tijssen, PP Eijk, P van den Ijssel, H Grabsch, P Quirke, JJ Oudejans, GA Meijer, C Caldas, B Ylstra
    posted to aberration cancer cgh chromosome cross-platform expression human meta_analysis by ealloza to the group BioinfoCIPF on 2007-03-05 16:03:07 as *** along with 2 people jfr Garamonfok
  • Enrichment or depletion of a GO category within a class of genes: which test?
    Bioinformatics (20 December 2006)
    by Isabelle Rivals, Léon Personnaz, Lieng Taing, Marie-Claude C Potier
    posted to algorithm comparison expression gene_list_analysis microarray review by ealloza to the group BioinfoCIPF on 2007-02-15 10:51:18 as ** along with 8 people and 1 group paszkows winterschlaefer jyuh grahamc capitall zhouyu yas maralena ParkinsonLab_at_MaRS
  • A network biology approach to prostate cancer
    Mol Syst Biol, Vol. 3 (13 February 2007)
    by Ayla Ergun, Carolyn A Lawrence, Michael A Kohanski, Timothy A Brennan, James J Collins
    posted to cancer expression microarray network by ealloza to the group BioinfoCIPF on 2007-02-15 10:36:15 as *** along with 5 people nolodie kentsis jfr mikaelhuss oelemento
  • FUNC: a package for detecting significant associations between gene sets and ontological annotations
    BMC Bioinformatics, Vol. 8 (06 February 2007), 41.
    by Kay Prufer, Bjoern Muetzel, Hong-Hai Do, Gunter Weiss, Philipp Khaitovich, Erhard Rahm, Svante Paabo, Michael Lachmann, Wolfgang Enard
    posted to microarray gene_set_analysis gene_list_analysis expression algorithm by ealloza to the group BioinfoCIPF on 2007-02-12 18:00:00 as read along with 4 people leechuck cap1 heliopais ndiaz
  • Extensions to gene set enrichment
    Bioinformatics, Vol. 23, No. 3. (1 February 2007), pp. 306-313.
    by Zhen Jiang, Robert Gentleman
    posted to microarray gene_set_analysis expression algorithm by ealloza to the group BioinfoCIPF on 2007-02-05 10:58:15 as ***** along with 5 people djkt waghsk heliopais giovenko magusina
  • Discovering tightly regulated and differentially expressed gene sets in whole genome expression data.
    Bioinformatics, Vol. 23, No. 2. (15 January 2007)
    by C Ye, E Eskin
    posted to microarray gene_set_analysis functional_annotation expression algorithm by ealloza to the group BioinfoCIPF on 2007-01-24 12:44:19 as read along with 2 people and 1 group shigepong MrBrownShoes NBI
  • Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas
    BMC Bioinformatics, Vol. 7 (01 December 2006), 526.
    by Federico E Turkheimer, Federico Roncaroli, Benoit Hennuy, Christian Herens, Minh Nguyen, Didier Martin, Annick Evrard, Vincent Bours, Jacques Boniver, Manuel Deprez
    posted to microarray human expression chromosome cancer algorithm by ealloza to the group BioinfoCIPF on 2006-12-12 15:34:11 as *** along with 2 people jfr shigepong
  • A multivariate approach for integrating genome-wide expression data and biological knowledge
    Bioinformatics, Vol. 22, No. 19. (1 October 2006), pp. 2373-2380.
    by Sek W Kong, William T Pu, Peter J Park
    posted to algorithm expression gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-12-12 15:32:02 as read along with 2 people jfr aconesa
  • The role of microRNA genes in papillary thyroid carcinoma.
    Proc Natl Acad Sci U S A, Vol. 102, No. 52. (27 December 2005), pp. 19075-19080.
    by H He, K Jazdzewski, W Li, S Liyanarachchi, R Nagy, S Volinia, GA Calin, CG Liu, K Franssila, S Suster, RT Kloos, CM Croce, A de la Chapelle
    posted to cancer expression human microarray microrna by ealloza to the group BioinfoCIPF on 2006-11-29 14:31:26 as read along with 1 person textoris
  • Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    Bioinformatics, Vol. 22, No. 13. (1 July 2006), pp. 1600-1607.
    by Alexa, Adrian, Rahnenfuhrer, Jorg, Lengauer, Thomas
    posted to algorithm expression microarray ontology by ealloza to the group BioinfoCIPF on 2006-11-27 10:41:02 as read along with 3 people and 1 group yas sgoetz marck T_lab
  • Meta-Analysis of Differentiating Mouse Embryonic Stem Cell Gene Expression Kinetics Reveals Early Change of a Small Gene Set
    PLoS Computational Biology, Vol. 2, No. 11. (1 November 2006), e158.
    by Clive H Glover, Michael Marin, Connie J Eaves, Cheryl D Helgason, James M Piret, Jennifer Bryan
    posted to expression meta_analysis microarray signature stem_cell by ealloza to the group BioinfoCIPF on 2006-11-27 10:38:02 as read along with 1 person jfr
  • Are microRNAs located in genomic regions associated with cancer?
    British Journal of Cancer, Vol. aop, No. current. (26 September 2006)
    by P Lamy, CL Andersen, L Dyrskjot, N Torring, T Orntoft, C Wiuf
    posted to cancer copy_number expression human microrna by ealloza to the group BioinfoCIPF on 2006-11-16 09:55:14 as read along with 3 people and 1 group jfr andersbj Garamonfok microRNA
  • A scalable method for integration and functional analysis of multiple microarray data sets.
    Bioinformatics (27 September 2006)
    by Curtis Huttenhower, Matt Hibbs, Chad Myers, Olga G G Troyanskaya
    posted to platform microarray meta_analysis functional_annotation expression bayes by ealloza to the group BioinfoCIPF on 2006-11-06 16:44:34 as read along with 1 person macavity1g
  • Genetics of global gene expression
    Nature Reviews Genetics, Vol. 7, No. 11., pp. 862-872.
    by Matthew V Rockman, Leonid Kruglyak
    posted to expression microarray review by ealloza to the group BioinfoCIPF on 2006-10-19 11:30:26 as *** along with 16 people and 9 groups dpollard tardigrade balicea dchughes nickluscombe neveaire aswin qfwills giovanni mlovell grahamc lp2 emarker natstreet mimulus_99 jyuh Biostatistics Computational-Genomics Bioinformatics EisenLab Neuroscience G4ID EBI-regulation GeschwindLab Genetics-of-Gambling
  • 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 ontology microarray gene_list_analysis functional_annotation expression composite by ealloza to the group BioinfoCIPF on 2006-10-05 11:24:23 as read along with 6 people and 1 group giovanni jdiggans uprock heliopais waghsk ndiaz GeschwindLab
  • A rapid method for microarray cross platform comparisons using gene expression signatures.
    Mol Cell Probes (10 August 2006)
    by Chris Cheadle, Kevin G G Becker, Yoon S S Cho-Chung, Maria Nesterova, Tonya Watkins, William Wood, Vinayakumar Prabhu, Kathleen C C Barnes
    posted to comparison expression gene_set_analysis microarray platform by ealloza to the group BioinfoCIPF on 2006-09-22 14:42:20 as read along with 4 people jyuh jfr neveaire jdiggans
  • OrderedList--a bioconductor package for detecting similarity in ordered gene lists
    Bioinformatics, Vol. 22, No. 18. (15 September 2006), pp. 2315-2316.
    by Claudio Lottaz, Xinan Yang, Stefanie Scheid, Rainer Spang
    posted to comparison expression gene_list_analysis microarray by ealloza to the group BioinfoCIPF on 2006-09-07 12:23:44 as read along with 2 people ima jdiggans
  • ADGO: analysis of differentially expressed gene sets using composite GO annotation
    Bioinformatics, Vol. 22, No. 18. (15 September 2006), pp. 2249-2253.
    by Dougu Nam, Sang-Bae Kim, Seon-Kyu Kim, Sungjin Yang, Seon-Young Kim, In-Sun Chu
    posted to composite expression functional_annotation gene_set_analysis microarray by ealloza to the group BioinfoCIPF on 2006-09-07 12:19:17 as read along with 2 people jdiggans heliopais
  • To permute or not to permute
    Bioinformatics, Vol. 22, No. 18. (15 September 2006), pp. 2244-2248.
    by Yifan Huang, Haiyan Xu, Violeta Calian, Jason C Hsu
    posted to error_rate expression permutations by ealloza to the group BioinfoCIPF on 2006-09-07 12:11:36 as read along with 2 people jyuh jdiggans
  • 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 random_forest prediction microarray gene_set_analysis gene_list_analysis expression classification algorithm by ealloza to the group BioinfoCIPF on 2006-09-01 17:05:13 as read along with 5 people and 1 group jfr tabu giovanni ptrobajo AlexanderPico GeschwindLab
  • A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers
    Nature Genetics, Vol. 38, No. 9. (20 August 2006), pp. 1043-1048.
    by Scott L Carter, Aron C Eklund, Isaac S Kohane, Lyndsay N Harris, Zoltan Szallasi
    posted to aberration cancer expression instability microarray prediction signature by ealloza to the group BioinfoCIPF on 2006-08-30 10:22:41 as read along with 3 people jfr tuck cpnP
  • Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data.
    Bioinformatics, Vol. 20, No. 13. (1 September 2004), pp. 2156-2158.
    by R Pandey, RK Guru, DW Mount
    posted to expression functional_annotation gene_set_analysis microarray pathway visualisation by ealloza to the group BioinfoCIPF on 2006-08-23 14:47:23 as read along with 2 people dragonrez tardigrade
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