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jfr's library [1547 articles]

最近录入 jfr's 文献库.
  • 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 **
  • Argonaute--a database for gene regulation by mammalian microRNAs.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by P Shahi, S Loukianiouk, A Bohne-Lang, M Kenzelmann, S Küffer, S Maertens, R Eils, HJ Gröne, N Gretz, B Brors
    posted to mirna database by jfr on 2008-06-27 17:05:34 as read along with 2 people eckart_bindewald maralena
  • 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
  • MicroRNAs accurately identify cancer tissue origin.
    Nat Biotechnol (23 March 2008)
    by Nitzan Rosenfeld, Ranit Aharonov, Eti Meiri, Shai Rosenwald, Yael Spector, Merav Zepeniuk, Hila Benjamin, Norberto Shabes, Sarit Tabak, Asaf Levy, Danit Lebanony, Yaron Goren, Erez Silberschein, Nurit Targan, Alex Ben-Ari, Shlomit Gilad, Netta Sion-Vardy, Ana Tobar, Meora Feinmesser, Oleg Kharenko, Ofer Nativ, Dvora Nass, Marina Perelman, Ady Yosepovich, Bruria Shalmon, Sylvie Polak-Charcon, Eddie Fridman, Amir Avniel, Isaac Bentwich, Zvi Bentwich, Dalia Cohen, Ayelet Chajut, Iris Barshack
    posted to tissue_specificity mirna cancer by jfr on 2008-06-27 11:23:51 as read along with 7 people bootsy ealloza jyuh giovenko tmmurali jdiezperezj maralena
  • 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 **
  • 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 **
  • microRNAs exhibit high frequency genomic alterations in human cancer.
    Proc Natl Acad Sci U S A (5 June 2006)
    by Lin Zhang, Jia Huang, Nuo Yang, Joel Greshock, Molly S S Megraw, Antonis Giannakakis, Shun Liang, Tara L L Naylor, Andrea Barchetti, Michelle R R Ward, George Yao, Angelica Medina, Ann O'brien-Jenkins, Dionyssios Katsaros, Artemis Hatzigeorgiou, Phyllis A A Gimotty, Barbara L L Weber, George Coukos
    posted to mirna copy-number by jfr on 2008-06-20 11:53:33 as read along with 6 people and 2 groups maralena eckart_bindewald mtagaya cmm ealloza Garamonfok FAB-lab BioinfoCIPF
  • 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
  • Can subtle changes in gene expression be consistently detected with different microarray platforms?
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Paola Pedotti, Peter ' Hoen, Erno Vreugdenhil, Geert Schenk, Rolf Vossen, Yavuz Ariyurek, Mattias de Hollander, Rowan Kuiper, Gertjan van Ommen, Johan den Dunnen, Judith Boer, Renee de Menezes
    posted to platform_comparison genomics gene_expression by jfr on 2008-06-17 17:38:08 as ** along with 1 person heliopais
  • 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 **
  • Empirical Bayes models for multiple probe type microarrays at the probe level
    BMC Bioinformatics, Vol. 9 (20 March 2008), 156.
    by Magnus Astrand, Petter Mostad, Mats Rudemo
    posted to microarray_analysis feature_selection affy by jfr on 2008-06-17 17:00:07 as ** along with 3 people jyuh heliopais ptrobajo
  • 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 **
  • 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
  • Principles of MicroRNA-Target Recognition.
    PLoS Biol, Vol. 3, No. 3. (15 February 2005)
    by Julius Brennecke, Alexander Stark, Robert B B Russell, Stephen M M Cohen
    posted to review mirna_target by jfr on 2008-06-13 15:24:32 as ** along with 8 people and 2 groups ronnyherc rklancer tardigrade andersbj mtagaya cdawson heliopais tauberj microRNA GIG
  • 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 **
  • Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata
    Nucl. Acids Res. (11 October 2007), gkm815.
    by Jeremiah J Faith, Michael E Driscoll, Vincent A Fusaro, Elissa J Cosgrove, Boris Hayete, Frank S Juhn, Stephen J Schneider, Timothy S Gardner
    posted to gene_expression database bioinformatics affy by jfr on 2008-06-13 14:42:32 as read along with 1 person tvdbulck
  • Recommending pathway genes using a compendium of clustering solutions.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2007), pp. 379-390.
    by DM Ng, MH Woehrmann, JM Stuart
    posted to pathway consensus_clustering by jfr on 2008-06-13 14:29:38 as ***
  • Inter- and intra-combinatorial regulation by transcription factors and microRNAs
    BMC Genomics, Vol. 8 (30 October 2007), 396.
    by Yiming Zhou, John Ferguson, Joseph T Chang, Yuval Kluger
    posted to tfbs regulation mirna by jfr on 2008-06-11 09:33:33 as *** along with 4 people and 1 group heliopais bootsy eckart_bindewald maralena microRNA
  • A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 23. (5 June 2007), pp. 9758-9763.
    by RS Huang, S Duan, WK Bleibel, EO Kistner, W Zhang, TA Clark, TX Chen, AC Schweitzer, JE Blume, NJ Cox, ME Dolan
    posted to treatment snp-arrays exon_arrays cnv by jfr on 2008-06-11 09:23:54 as **
  • Comprehensive assessment of DNA copy number alterations in human prostate cancers using Affymetrix 100K SNP mapping array.
    Genes, chromosomes & cancer, Vol. 45, No. 11. (November 2006), pp. 1018-1032.
    by W Liu, B Chang, J Sauvageot, L Dimitrov, M Gielzak, T Li, G Yan, J Sun, J Sun, TS Adams, AR Turner, JW Kim, DA Meyers, SL Zheng, WB Isaacs, J Xu
    posted to snp_arrays copy-number by jfr on 2008-06-11 09:02:04 as **
  • Rapid high-resolution karyotyping with precise identification of chromosome breakpoints.
    Genes, chromosomes & cancer, Vol. 46, No. 7. (July 2007), pp. 675-683.
    by X Mao, SY James, RJ Yáñez-Muñoz, T Chaplin, G Molloy, RT Oliver, BD Young, YJ Lu
    posted to snp_arrays exon_arrays by jfr on 2008-06-11 09:00:13 as **
  • Getting started in biological pathway construction and analysis.
    PLoS computational biology, Vol. 4, No. 2. (February 2008)
    by GA Viswanathan, J Seto, S Patil, G Nudelman, SC Sealfon
    posted to plos_start by jfr on 2008-06-10 17:29:50 as ** along with 2 people tharris dullhunk
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