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heliopais's 关注列表 [1000+ articles]

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  • Coherent Coupling of Feedback Loops: A Design Principle of Cell Signaling Networks.
    Bioinformatics (Oxford, England) (2 July 2008)
    by Yung-Keun K Kwon, Kwang-Hyun H Cho
    posted to signaling principle network loop feedback by maralena on 2008-07-09 08:04:36 as ** along with 1 person bootsy
  • Identifying gene-disease associations using centrality on a literature mined gene-interaction network
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i277-285.
    by Arzucan Ozgur, Thuy Vu, Gunes Erkan, Dragomir R Radev
    posted to network literature interaction gene disease by maralena on 2008-07-02 09:06:36 as **
  • The mechanism of micro-RNA-mediated translation repression is determined by the promoter of the target gene
    Proceedings of the National Academy of Sciences (25 June 2008), 0800650105.
    by Yi W Kong, Ian G Cannell, Cornelia H de Moor, Kirsti Hill, Paul G Garside, Tiffany L Hamilton, Hedda A Meijer, Helen C Dobbyn, Mark Stoneley, Keith A Spriggs, Anne E Willis, Martin Bushell
    posted to repression promoter microrna mechanism by maralena on 2008-06-28 13:40:02 as ** along with 1 person bootsy
  • BioGraphE: high-performance bionetwork analysis using the Biological Graph Environment
    BMC Bioinformatics, Vol. 9, No. Suppl 6. (2008)
    by George Chin, Daniel Chavarria, Grant Nakamura, Heidi Sofia
    posted to network graph by maralena on 2008-06-28 13:39:49 as ** along with 1 person jyuh
  • wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data.
    Nucleic acids research, Vol. 36, No. 7. (April 2008)
    by P Cahan, LE Godfrey, PS Eis, TA Richmond, RR Selzer, M Brent, HL McLeod, TJ Ley, TA Graubert
    posted to methodology copy-number cnv array-cgh by jfr on 2008-06-27 17:08:57 as **
  • Genomic analysis of epithelial ovarian cancer.
    Cell research, Vol. 18, No. 5. (May 2008), pp. 538-548.
    by J Farley, LL Ozbun, MJ Birrer
    posted to review ovarian_cancer by jfr on 2008-06-27 14:27:50 as **
  • Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions.
    Nucleic Acids Res (16 March 2008)
    by Katleen De Preter, Roland Barriot, Frank Speleman, Jo Vandesompele, Yves Moreau
    posted to gene_set_analysis gene_expression by jfr on 2008-06-27 13:29:10 as *** along with 3 people and 1 group tmmurali frohike bootsy Bioinformatics
  • Real-time quantification of microRNAs by stem-loop RT-PCR.
    Nucleic Acids Res, Vol. 33, No. 20. (2005)
    by C Chen, DA Ridzon, AJ Broomer, Z Zhou, DH Lee, JT Nguyen, M Barbisin, NL Xu, VR Mahuvakar, MR Andersen, KQ Lao, KJ Livak, KJ Guegler
    posted to tech rt-pcr mirna by jfr on 2008-06-27 13:26:48 as read along with 2 people and 1 group imouthesmp cdawson GIG
  • The minimum information about a genome sequence (MIGS) specification
    Nat Biotech, Vol. 26, No. 5. (May 2008), pp. 541-547.
    by Dawn Field, George Garrity, Tanya Gray, Norman Morrison, Jeremy Selengut, Peter Sterk, Tatiana Tatusova, Nicholas Thomson, Michael J Allen, Samuel V Angiuoli, Michael Ashburner, Nelson Axelrod, Sandra Baldauf, Stuart Ballard, Jeffrey Boore, Guy Cochrane, James Cole, Peter Dawyndt, Paul De Vos, Claude Depamphilis, Robert Edwards, Nadeem Faruque, Robert Feldman, Jack Gilbert, Paul Gilna, Frank O Glockner, Philip Goldstein, Robert Guralnick, Dan Haft, David Hancock, Henning Hermjakob, Christiane Hertz-Fowler, Phil Hugenholtz, Ian Joint, Leonid Kagan, Matthew Kane, Jessie Kennedy, George Kowalchuk, Renzo Kottmann, Eugene Kolker, Saul Kravitz, Nikos Kyrpides, Jim Leebens-Mack, Suzanna E Lewis, Kelvin Li, Allyson L Lister, Phillip Lord, Natalia Maltsev, Victor Markowitz, Jennifer Martiny, Barbara Methe, Ilene Mizrachi, Richard Moxon, Karen Nelson, Julian Parkhill, Lita Proctor, Owen White, Susanna-Assunta Sansone, Andrew Spiers, Robert Stevens, Paul Swift, Chris Taylor, Yoshio Tateno, Adrian Tett, Sarah Turner, David Ussery, Bob Vaughan, Naomi Ward, Trish Whetzel, Ingio San Gil, Gareth Wilson, Anil Wipat
    posted to standards sequencing genomics by jfr on 2008-06-27 11:22:35 as * along with 5 people tharris jyuh jamselem dullhunk neils
  • Discovering microRNAs from deep sequencing data using miRDeep
    Nature Biotechnology, Vol. 26, No. 4., pp. 407-415.
    by Marc R Friedländer, Wei Chen, Catherine Adamidi, Jonas Maaskola, Ralf Einspanier, Signe Knespel, Nikolaus Rajewsky
    posted to mirna deep_sequencing by jfr on 2008-06-27 09:11:18 as **** along with 3 people and 1 group stajich tmmurali giovanni Berkeley Mycology
  • Small is beautiful: microRNAs and breast cancer-where are we now?
    The Journal of pathology, Vol. 215, No. 3. (July 2008), pp. 214-221.
    by E Verghese, A Hanby, V Speirs, T Hughes
    posted to review mirna breast_cancer by jfr on 2008-06-27 09:09:35 as **
  • An activity-regulated microRNA controls dendritic plasticity by down-regulating p250GAP.
    Proceedings of the National Academy of Sciences of the United States of America (24 June 2008)
    by Gary A A Wayman, Monika Davare, Hideaki Ando, Dale Fortin, Olga Varlamova, Hai-Ying M Y Cheng, Daniel Marks, Karl Obrietan, Thomas R R Soderling, Richard H H Goodman, Soren Impey
    posted to p250gap mir-132 microrna by maralena on 2008-06-27 08:27:44 as **
  • MethCancerDB [ndash] aberrant DNA methylation in human cancer
    British Journal of Cancer, Vol. aop, No. current. (05 February 2008)
    by M Lauss, I Visne, A Weinhaeusel, K Vierlinger, C Noehammer, A Kriegner
    posted to methylation database by jfr on 2008-06-20 16:47:56 as **
  • MicroRNA Expression and Identification of Putative miRNA Targets in Ovarian Cancer
    PLoS ONE, Vol. 3, No. 6. (18 June 2008), e2436.
    by Neetu Dahiya, Cheryl A Sherman-Baust, Tian-Li Wang, Ben Davidson, Ie-Ming Shih, Yongqing Zhang, William Wood, Kevin G Becker, Patrice J Morin
    posted to target microrna expression cancer by maralena on 2008-06-19 08:06:37 as ** along with 1 person ealloza
  • Inducible expression of microRNA-194 is regulated by HNF-1alpha during intestinal epithelial cell differentiation.
    RNA (New York, N.Y.) (20 May 2008)
    by Kimihiro Hino, Kiichiro Tsuchiya, Taro Fukao, Kotaro Kiga, Ryuichi Okamoto, Takanori Kanai, Mamoru Watanabe
    posted to mir-194 microrna hnf1 differentiation by maralena on 2008-06-19 08:03:59 as ** along with 1 person bootsy
  • A novel noncoding RNA processed by Drosha is restricted to nucleus in mouse
    RNA, Vol. 14, No. 7. (1 July 2008), pp. 1399-1410.
    by Gayatri Ganesan, Satyanarayana M Rao
    posted to nucleus ncrna mouse drosha by maralena on 2008-06-19 08:03:15 as **
  • The 3'-UTR mediates the cellular localization of an mRNA encoding a short plasma membrane protein
    RNA, Vol. 14, No. 7. (1 July 2008), pp. 1352-1365.
    by Adi Loya, Lilach Pnueli, Yahav Yosefzon, Ydo Wexler, Michal Ziv-Ukelson, Yoav Arava
    posted to mrna 3utr by maralena on 2008-06-19 08:02:47 as **
  • Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
    Nature genetics (15 June 2008)
    by Jun Zhu, Bin Zhang, Erin N N Smith, Becky Drees, Rachel B B Brem, Leonid Kruglyak, Roger E E Bumgarner, Eric E E Schadt
    posted to yeast regulatory network by maralena on 2008-06-18 07:59:09 as ** along with 9 people caseybrown djkt marck roys jyuh realzhang kengg tmmurali ptrobajo
  • Imbalance between pSmad3 and Notch induces CDK inhibitors in old muscle stem cells
    Nature (15 June 2008)
    by Morgan E Carlson, Michael Hsu, Irina M Conboy
    posted to stemcell smad notch muscle by maralena on 2008-06-18 07:58:48 as **
  • Genome-wide promoter analysis uncovers portions of the cancer methylome.
    Cancer research, Vol. 68, No. 8. (15 April 2008), pp. 2661-2670.
    by MO Hoque, MS Kim, KL Ostrow, J Liu, GB Wisman, HL Park, ML Poeta, C Jeronimo, R Henrique, A Lendvai, E Schuuring, S Begum, E Rosenbaum, M Ongenaert, K Yamashita, J Califano, W Westra, AG van der Zee, W Van Criekinge, D Sidransky
    posted to methylation by jfr on 2008-06-17 18:00:18 as ***
  • A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets
    Nucl. Acids Res. (1 April 2008), gkn133.
    by Hairong Wei, Pei F Kuan, Shulan Tian, Chuhu Yang, Jeff Nie, Srikumar Sengupta, Victor Ruotti, Gudrun A Jonsdottir, Sunduz Keles, James A Thomson, Ron Stewart
    posted to nimble by jfr on 2008-06-17 17:59:26 as ** along with 1 person magusina
  • The MGED Ontology: a resource for semantics-based description of microarray experiments
    Bioinformatics, Vol. 22, No. 7. (1 April 2006), pp. 866-873.
    by Patricia L Whetzel, Helen Parkinson, Helen C Causton, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Laurence Game, Mervi Heiskanen, Norman Morrison, Philippe Rocca-Serra, Susanna-Assunta Sansone, Chris Taylor, Joseph White, Christian J Stoeckert
    posted to standards ontology microarray_technology by jfr on 2008-06-17 17:57:55 as read along with 2 people shikin dansullivanblk
  • Expression profiling with RNA from formalin-fixed, paraffin-embedded material.
    BMC medical genomics, Vol. 1 (2008)
    by A Oberli, V Popovici, M Delorenzi, A Baltzer, J Antonov, S Matthey, S Aebi, HJ Altermatt, R Jaggi
    posted to microarray_technology ffpe by jfr on 2008-06-17 17:51:33 as ** along with 1 person jyuh
  • miR-Q: a novel quantitative RT-PCR approach for the expression profiling of small RNA molecules such as miRNAs in a complex sample
    BMC Molecular Biology, Vol. 9 (10 April 2008), 34.
    by Soroush Sharbati-Tehrani, Barbara Kutz-Lohroff, Ramona Bergbauer, Jutta Scholven, Ralf Einspanier
    posted to tech rt-pcr mirna by jfr on 2008-06-17 17:49:38 as **
  • Bayesian biclustering of gene expression data
    BMC Genomics, Vol. 9, No. Suppl 1. (2008)
    by Jiajun Gu, Jun Liu
    posted to clustering by jfr on 2008-06-17 17:47:30 as * along with 3 people bertelsen tvdbulck yangc
  • Efficient non-unique probes selection algorithms for DNA microarray.
    BMC genomics, Vol. 9 Suppl 1 (2008)
    by P Deng, MT Thai, Q Ma, W Wu
    posted to probe_design microarray_technology by jfr on 2008-06-17 17:43:14 as *
  • A software framework for microarray and gene expression object model (MAGE-OM) array design annotation
    BMC Genomics, Vol. 9 (20 March 2008), 133.
    by Matloob Qureshi, Alasdair Ivens
    posted to standards software microarray_technology by jfr on 2008-06-17 17:39:57 as * along with 1 person dansullivanblk
  • Ontology-based, Tissue MicroArray oriented, image centered tissue bank.
    BMC bioinformatics, Vol. 9 Suppl 4 (2008)
    by F Viti, I Merelli, A Caprera, B Lazzari, A Stella, L Milanesi
    posted to tma software by jfr on 2008-06-17 17:31:22 as ** along with 1 person jyuh
  • A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays
    BMC Bioinformatics, Vol. 9 (14 April 2008), 194.
    by Huanying Ge, Chao Cheng, Lei M Li
    posted to normalization low_level affy by jfr on 2008-06-17 17:25:42 as **
  • MPDA: Microarray pooled DNA analyzer
    BMC Bioinformatics, Vol. 9 (15 April 2008), 196.
    by Hsin-Chou Yang, Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice LT Yu, Mitchell B Diccianni, Jer-Yuan Wu, Yuan-Tsong Chen, Cathy SJ Fann
    posted to pooling by jfr on 2008-06-17 17:22:51 as ** along with 1 person jyuh
  • ParaKMeans: Implementation of a parallelized K-means algorithm suitable for general laboratory use.
    BMC Bioinformatics, Vol. 9 (16 April 2008), 200.
    by Piotr Kraj, Ashok Sharma, Nikhil Garge, Robert Podolsky, Richard A Mcindoe
    posted to software clustering by jfr on 2008-06-17 17:21:32 as ** along with 1 person and 1 group laughcry BioInfPDL
  • M-BISON: microarray-based integration of data sources using networks
    BMC Bioinformatics, Vol. 9 (25 April 2008), 214.
    by Bernie J Daigle, Russ B Altman
    posted to microarray_analysis feature_selection by jfr on 2008-06-17 17:20:37 as ** along with 2 people jyuh frohike
  • Automating dChip: toward reproducible sharing of microarray data analysis
    BMC Bioinformatics, Vol. 9 (08 May 2008), 231.
    by Cheng Li
    posted to reproducible_research microarray_analysis by jfr on 2008-06-17 17:18:00 as *** along with 1 person jyuh
  • Multidimensional scaling for large genomic data sets
    BMC Bioinformatics, Vol. 9 (04 April 2008), 179.
    by Jengnan Tzeng, Henry H Lu, Wen-Hsiung Li
    posted to genomics class_discovery by jfr on 2008-06-17 17:01:49 as **
  • Microarray data mining using landmark gene-guided clustering
    BMC Bioinformatics, Vol. 9 (11 February 2008), 92.
    by Pankaj Chopra, Jaewoo Kang, Jiong Yang, Hyungjun Cho, Heenam S Kim, Min-Goo Lee
    posted to microarray_analysis clustering by jfr on 2008-06-17 16:55:08 as ** along with 1 person jyuh
  • A comparison of Affymetrix gene expression arrays
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Mark Robinson, Terence Speed
    posted to exon_arrays affy by jfr on 2008-06-17 16:52:18 as read along with 2 people hpaces waszak
  • Unequal group variances in microarray data analyses.
    Bioinformatics (14 March 2008)
    by Meaza Demissie, Barbara Mascialino, Stefano Calza, Yudi Pawitan
    posted to microarray_analysis feature_selection fdr by jfr on 2008-06-17 16:44:57 as *** along with 3 people aviad_work jyuh shigepong
  • Chromosomal breakpoints in primary colon cancer cluster at sites of structural variants in the genome.
    Cancer research, Vol. 68, No. 5. (1 March 2008), pp. 1284-1295.
    by J Camps, M Grade, QT Nguyen, P Hörmann, S Becker, AB Hummon, V Rodriguez, S Chandrasekharappa, Y Chen, MJ Difilippantonio, H Becker, BM Ghadimi, T Ried
    posted to copy-number colon_cancer by jfr on 2008-06-17 16:43:30 as read
  • Fast Network Component Analysis (FastNCA) for gene regulatory network reconstruction from microarray data.
    Bioinformatics (Oxford, England) (9 April 2008)
    by Chunqi Chang, Zhi Ding, Yeung Sam S Hung, Peter Chin Wan C Fung
    posted to network by jfr on 2008-06-17 16:42:35 as ** along with 3 people AbnerCYH roys jyuh
  • Visualizing chromosomes as transcriptome correlation maps: evidence of chromosomal domains containing co-expressed genes--a study of 130 invasive ductal breast carcinomas.
    Cancer research, Vol. 65, No. 4. (15 February 2005), pp. 1376-1383.
    by F Reyal, N Stransky, I Bernard-Pierrot, A Vincent-Salomon, Y de Rycke, P Elvin, A Cassidy, A Graham, C Spraggon, Y Désille, A Fourquet, C Nos, P Pouillart, H Magdelénat, D Stoppa-Lyonnet, J Couturier, B Sigal-Zafrani, B Asselain, X Sastre-Garau, O Delattre, JP Thiery, F Radvanyi
    posted to integration gene_expression copy-number breast_cancer by jfr on 2008-06-17 12:04:03 as ***
  • Comprehensive high-throughput arrays for relative methylation (CHARM).
    Genome research, Vol. 18, No. 5. (May 2008), pp. 780-790.
    by RA Irizarry, C Ladd-Acosta, B Carvalho, H Wu, SA Brandenburg, JA Jeddeloh, B Wen, AP Feinberg
    posted to methylation by jfr on 2008-06-17 11:56:53 as ** along with 1 person jyuh
  • Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines.
    Genome research, Vol. 18, No. 5. (May 2008), pp. 791-801.
    by YJ Shann, C Cheng, CH Chiao, DT Chen, PH Li, MT Hsu
    posted to methylation by jfr on 2008-06-17 11:55:48 as **
  • Discovering functional interaction patterns in protein-protein interaction networks
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Mehmet Turanalp, Tolga Can
    posted to ppi network interaction by maralena on 2008-06-16 08:23:23 as ** along with 2 people renatomilani Tingting
  • SMAD proteins control DROSHA-mediated microRNA maturation
    Nature (11 June 2008)
    by Brandi N Davis, Aaron C Hilyard, Giorgio Lagna, Akiko Hata
    posted to smad mir-21 microna drosha by maralena on 2008-06-16 08:22:04 as **
  • affyGG: Computational protocols for genetical genomics with Affymetrix arrays
    Bioinformatics (16 December 2007), btm614.
    by Rudi Alberts, Gonzalo Vera, Ritsert C Jansen
    posted to software qtl affy by jfr on 2008-06-13 16:44:49 as ** along with 2 people djkt giovanni
  • Current Status of Prognostic Profiling in Breast Cancer
    Oncologist, Vol. 13, No. 4. (1 April 2008), pp. 350-360.
    by Lajos Pusztai
    posted to review prognostic breast_cancer by jfr on 2008-06-13 16:35:57 as read along with 1 person jo_davies
  • Systematic reviews in health care: Systematic reviews of evaluations of prognostic variables
    BMJ, Vol. 323, No. 7306. (28 July 2001), pp. 224-228.
    by Douglas G Altman
    posted to review meta-analysis by jfr on 2008-06-13 16:28:34 as **
  • Microarrays--planning your experiment.
    Methods in molecular medicine, Vol. 141 (2008), pp. 71-85.
    by JY Yang
    posted to microarray_technology experiment_design by jfr on 2008-06-13 16:23:19 as ** along with 1 person balicea
  • The methodology used to measure differential gene expression affects the outcome.
    Journal of biomolecular techniques : JBT, Vol. 18, No. 5. (December 2007), pp. 321-330.
    by Y Ding, L Xu, BD Jovanovic, IB Helenowski, DL Kelly, WJ Catalona, XJ Yang, M Pins, RC Bergan
    posted to platform_comparison by jfr on 2008-06-13 15:19:02 as **
  • Exon-based mapping of microarray probes: recovering differential gene expression signal in underpowered hypoxia experiment.
    Molecular and cellular probes, Vol. 21, No. 2. (April 2007), pp. 134-139.
    by DN Grigoryev, SF Ma, LA Shimoda, RA Johns, B Lee, JG Garcia
    posted to exon_arrays by jfr on 2008-06-13 15:16:25 as **
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