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maryee's library [77 articles]

Recent papers added to maryee's ordered by to_read.
  • Yeast two-hybrid contributions to interactome mapping
    Current Opinion in Biotechnology, Vol. 17, No. 4. (August 2006), pp. 387-393.
    by Jodi R Parrish, Keith D Gulyas, Jr Finley
    posted to accelerating_mapping interactome by maryee on 2007-01-04 17:14:50 as ***** along with 6 people and 2 groups dchughes eukfn nm grahamc cmor bethbromley G4ID Genetics-of-Gambling
  • Intronic sequences flanking alternatively spliced exons are conserved between human and mouse.
    Genome Res, Vol. 13, No. 7. (July 2003), pp. 1631-1637.
    by R Sorek, G Ast
    posted to no-tag by maryee on 2006-02-14 04:56:25 as ***** along with 1 person radek
  • Inferring protein interactions from experimental data by association probabilistic method.
    Proteins (4 January 2006)
    by Luonan Chen, Ling-Yun Y Wu, Yong Wang, Xiang-Sun S Zhang
    posted to interactome by maryee on 2006-02-04 22:04:35 as ***** along with 1 person phoenixzxl
  • DrugBank: a comprehensive resource for in silico drug discovery and exploration.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by DS Wishart, C Knox, AC Guo, S Shrivastava, M Hassanali, P Stothard, Z Chang, J Woolsey
    posted to no-tag by maryee on 2006-01-11 07:44:56 as ***** along with 8 people and 2 groups yaredo dansullivanblk kuhn sangeetha madhadron jdiggans massivemayhem elvinado Bioinformatics insilicodrug
  • Assessing the limits of genomic data integration for predicting protein networks.
    Genome Res, Vol. 15, No. 7. (July 2005), pp. 945-953.
    by LJ Lu, Y Xia, A Paccanaro, H Yu, M Gerstein
    posted to no-tag by maryee on 2005-12-19 21:14:39 as ***** along with 13 people and 2 groups okarsligil lfriedl balajis opheliav wnpx mbeautru eukfn grahamc nedwards brianb iris_2001 carlk phoenixzxl kdl Bioinformatics
  • Probabilistic prediction of protein-protein interactions from the protein sequences.
    Comput Biol Med (24 October 2005)
    by Arunkumar Chinnasamy, Ankush Mittal, Wing-Kin K Sung
    posted to no-tag by maryee on 2005-12-19 21:08:58 as *****
  • Assessing reliability of gene clusters from gene expression data.
    Funct Integr Genomics, Vol. 1, No. 3. (November 2000), pp. 156-173.
    by K Zhang, H Zhao
    posted to microarray treetest by maryee on 2006-12-05 22:53:27 as ****
  • Correspondence analysis of microarray time-course data in case-control design.
    J Biomed Inform, Vol. 37, No. 5. (October 2004), pp. 358-365.
    by Q Tan, K Brusgaard, TA Kruse, E Oakeley, B Hemmings, H Beck-Nielsen, L Hansen, M Gaster
    posted to microarray tb by maryee on 2006-07-14 00:17:41 as ****
  • Interactome: gateway into systems biology.
    Hum Mol Genet, Vol. 14 Spec No. 2 (15 October 2005)
    by ME Cusick, N Klitgord, M Vidal, DE Hill
    posted to interactome by maryee on 2006-02-17 16:38:24 as **** along with 8 people and 2 groups kuhn wnpx gandhih jdiggans braingrind grahamc dejori wilbur ic4 generif_paper
  • Mechanisms of alternative pre-messenger RNA splicing.
    Annu Rev Biochem, Vol. 72 (2003), pp. 291-336.
    by DL Black
    posted to rna splicing by maryee on 2006-02-13 16:22:57 as **** along with 4 people and 1 group jknabe Cortel xico mimulus_99 WetBiology
  • Vertebrate MicroRNA Genes
    Science, Vol. 299, No. 5612. (07 March 2003), 1540.
    by Lee P Lim, Margaret E Glasner, Soraya Yekta, Christopher B Burge, David P Bartel
    posted to rna by maryee on 2006-02-13 15:13:28 as **** along with 4 people martin-novak cassj akiezun eskay
  • Evidence for the regulation of alternative splicing via complementary DNA sequence repeats.
    Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1358-1364.
    by Y Lian, HR Garner
    posted to rna splicing by maryee on 2006-02-13 14:13:06 as ****
  • From the Cover: Conserved patterns of protein interaction in multiple species.
    Proc Natl Acad Sci U S A, Vol. 102, No. 6. (8 February 2005), pp. 1974-1979.
    by R Sharan, S Suthram, RM Kelley, T Kuhn, S McCuine, P Uetz, T Sittler, RM Karp, T Ideker
    posted to no-tag by maryee on 2006-02-13 03:34:29 as **** along with 13 people and 2 groups tharris jiny sza dragonrez okarsligil balajis nuke2005 gurkanbebek koller cjeans iris_2001 maralena mdstobbe C. elegans / WormBase Bioinformatics
  • HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms.
    BMC Bioinformatics, Vol. 6 Suppl 4 (1 December 2005)
    by M Persico, A Ceol, C Gavrila, R Hoffmann, A Florio, G Cesareni
    posted to no-tag by maryee on 2006-02-03 17:20:18 as **** along with 1 person mariap3636
  • Quantitative detection of increasing HIV type 1 antibodies after seroconversion: a simple assay for detecting recent HIV infection and estimating incidence.
    AIDS Res Hum Retroviruses, Vol. 18, No. 4. (1 March 2002), pp. 295-307.
    by BS Parekh, MS Kennedy, T Dobbs, CP Pau, R Byers, T Green, DJ Hu, S Vanichseni, NL Young, K Choopanya, TD Mastro, JS McDougal
    posted to bed cdc by maryee on 2006-01-20 20:06:16 as ****
  • Do you do text?
    Bioinformatics (29 September 2005)
    by Christian Blaschke, Alexander Yeh, Evelyn Camon, Marc Colosimo, Rolf Apweiler, Lynette Hirschman, Alfonso Valencia
    posted to no-tag by maryee on 2006-01-05 23:05:47 as **** along with 2 people and 3 groups yas marcius T_lab BioinfoCIPF SGU-CIPF
  • Predicting functional gene links from phylogenetic-statistical analyses of whole genomes.
    PLoS Comput Biol, Vol. 1, No. 1. (June 2005)
    by D Barker, M Pagel
    posted to no-tag by maryee on 2005-12-19 21:16:50 as **** along with 5 people balajis arunyan bartleby pradiptaray rvosa
  • Development of human protein reference database as an initial platform for approaching systems biology in humans.
    Genome Res, Vol. 13, No. 10. (October 2003), pp. 2363-2371.
    by S Peri, JD Navarro, R Amanchy, TZ Kristiansen, CK Jonnalagadda, V Surendranath, V Niranjan, B Muthusamy, TK Gandhi, M Gronborg, N Ibarrola, N Deshpande, K Shanker, HN Shivashankar, BP Rashmi, MA Ramya, Z Zhao, KN Chandrika, N Padma, HC Harsha, AJ Yatish, MP Kavitha, M Menezes, DR Choudhury, S Suresh, N Ghosh, R Saravana, S Chandran, S Krishna, M Joy, SK Anand, V Madavan, A Joseph, GW Wong, WP Schiemann, SN Constantinescu, L Huang, R Khosravi-Far, H Steen, M Tewari, S Ghaffari, GC Blobe, CV Dang, JG Garcia, J Pevsner, ON Jensen, P Roepstorff, KS Deshpande, AM Chinnaiyan, A Hamosh, A Chakravarti, A Pandey
    posted to no-tag by maryee on 2005-12-19 20:35:30 as **** along with 2 people and 1 group miguel bundschu generif_paper
  • What are cross-validation and bootstrapping?
    posted to no-tag by maryee on 2005-11-16 19:46:11 as **** along with 1 person deysandeep
  • Conserved sequence elements associated with exon skipping.
    Nucleic Acids Res, Vol. 31, No. 7. (1 April 2003), pp. 1974-1983.
    by E Miriami, H Margalit, R Sperling
    posted to rna splicing by maryee on 2006-02-13 22:37:30 as ***
  • hnRNP A1 controls HIV-1 mRNA splicing through cooperative binding to intron and exon splicing silencers in the context of a conserved secondary structure.
    RNA, Vol. 8, No. 11. (November 2002), pp. 1401-1415.
    by CK Damgaard, TO Tange, J Kjems
    posted to rna splicing by maryee on 2006-02-13 22:19:37 as ***
  • Influence of RNA secondary structure on the pre-mRNA splicing process.
    Mol Cell Biol, Vol. 24, No. 24. (December 2004), pp. 10505-10514.
    by E Buratti, FE Baralle
    posted to rna splicing by maryee on 2006-02-13 21:52:28 as *** along with 1 person raylim
  • Small regulatory RNAs in mammals.
    Hum Mol Genet, Vol. 14 Spec No 1 (15 April 2005)
    by JS Mattick, IV Makunin
    posted to rna by maryee on 2006-02-13 20:04:24 as *** along with 2 people tardigrade mtagaya
  • Prediction of mammalian microRNA targets.
    Cell, Vol. 115, No. 7. (26 December 2003), pp. 787-798.
    by BP Lewis, IH Shih, MW Jones-Rhoades, DP Bartel, CB Burge
    posted to mirna rna by maryee on 2006-02-13 18:46:02 as *** along with 8 people and 2 groups giovenko jfr eckart_bindewald mortenlindow kt arcticrasta mtagaya akiezun Bioinformatics microRNA
  • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.
    Cell, Vol. 120, No. 1. (14 January 2005), pp. 15-20.
    by BP Lewis, CB Burge, DP Bartel
    posted to mirna rna by maryee on 2006-02-13 18:44:35 as *** along with 11 people and 3 groups pengchy jfr marcius eckart_bindewald tardigrade mortenlindow andersbj mtagaya heliopais Alexander_Kanitz elfar microRNA BioinfoCIPF SGU-CIPF
  • MicroRNAs: genomics, biogenesis, mechanism, and function.
    Cell, Vol. 116, No. 2. (23 January 2004), pp. 281-297.
    by DP Bartel
    posted to rna by maryee on 2006-02-13 18:42:06 as *** along with 4 people and 4 groups miguel marcius mtagaya shizhao Wikipedia Bioinformatics BioinfoCIPF SGU-CIPF
  • The small RNA world.
    J Cell Sci, Vol. 116, No. Pt 23. (1 December 2003), pp. 4689-4693.
    by EJ Finnegan, MA Matzke
    posted to rna by maryee on 2006-02-13 15:18:55 as *** along with 1 person icejiafu
  • Inferring domain-domain interactions from protein-protein interactions.
    Genome Res, Vol. 12, No. 10. (October 2002), pp. 1540-1548.
    by M Deng, S Mehta, F Sun, T Chen
    posted to no-tag by maryee on 2006-02-02 20:56:03 as *** along with 7 people opheliav wnpx neils Pao-Yang phoenixzxl carlk zdai
  • The elusive yeast interactome.
    Genome Biol, Vol. 7, No. 6. (2006)
    by J Goll, P Uetz
    posted to accelerating_mapping interactome by maryee on 2006-11-21 19:51:26 as ** along with 3 people eukfn Evangelia chad_davis
  • A Crossed Random Effects Model for Unbalanced Data with Applications in Cross-Sectional and Longitudinal Research
    Journal of Educational Statistics, Vol. 18, No. 4. (1993), pp. 321-349.
    by Stephen W Raudenbush
    posted to mixedeffectsmodel by maryee on 2006-10-25 00:11:34 as **
  • Learning to predict protein-protein interactions from protein sequences.
    Bioinformatics, Vol. 19, No. 15. (12 October 2003), pp. 1875-1881.
    by SM Gomez, WS Noble, A Rzhetsky
    posted to interactome by maryee on 2006-10-18 15:21:14 as ** along with 4 people grahamc cjeans wilbur Pao-Yang
  • Correlated sequence-signatures as markers of protein-protein interaction.
    J Mol Biol, Vol. 311, No. 4. (24 August 2001), pp. 681-692.
    by E Sprinzak, H Margalit
    posted to interactome by maryee on 2006-10-17 04:19:38 as ** along with 9 people bicko chad_davis dyermd grahamc cjeans lilith wilbur Rhys phoenixzxl
  • Pvclust: an R package for assessing the uncertainty in hierarchical clustering.
    Bioinformatics, Vol. 22, No. 12. (15 June 2006), pp. 1540-1542.
    by R Suzuki, H Shimodaira
    posted to microarray treetest by maryee on 2006-09-08 18:12:05 as ** along with 8 people druvus jfr wnpx josepe ghattem elfar quianominorleo briordan
  • A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules
    Science, Vol. 302, No. 5643. (10 October 2003), pp. 249-255.
    by Joshua M Stuart, Eran Segal, Daphne Koller, Stuart K Kim
    posted to microarray treetest by maryee on 2006-09-08 16:45:30 as ** along with 18 people and 7 groups pengchy nolodie jeremymiller tharris dragonrez textoris lfriedl balajis nuke2005 tardigrade opheliav wnpx neveaire macle raylim lp2 karfunkel vertikalist C. elegans / WormBase kdl Biostatistics Computational-Genomics Bioinformatics Neuroscience BTS-PT-AS-CS
  • Coexpression analysis of human genes across many microarray data sets.
    Genome Res, Vol. 14, No. 6. (June 2004), pp. 1085-1094.
    by HK Lee, AK Hsu, J Sajdak, J Qin, P Pavlidis
    posted to microarray treetest by maryee on 2006-09-08 16:43:50 as ** along with 14 people and 2 groups pengchy jiny gpalidwor giovanni jeremymiller hawkeyehammer grahamc macavity1g raylim sgoetz wilbur jo_davies nedwards dragonrez GeschwindLab Indigene
  • A systematic statistical linear modeling approach to oligonucleotide array experiments
    Mathematical Biosciences, Vol. 176, No. 1. (March 2002), pp. 35-51.
    by Tzu-Ming Chu, Bruce Weir, Russ Wolfinger
    posted to microarray treetest by maryee on 2006-09-08 01:10:21 as ** along with 2 people gabe_rosser bertelsen
  • Assessing Gene Significance from cDNA Microarray Expression Data via Mixed Models
    J Comput Biol., Vol. 8, No. 6. (2001), pp. 625-637.
    by Wolfinger
    posted to microarray treetest by maryee on 2006-09-08 01:08:27 as **
  • Application of a priori established gene sets to discover biologically important differential expression in microarray data
    PNAS, Vol. 102, No. 43. (25 October 2005), pp. 15278-15279.
    by Andrea Bild, Phillip G Febbo
    posted to microarray treetest by maryee on 2006-08-22 06:09:26 as ** along with 3 people and 1 group ealloza jdiggans srp33 BioinfoCIPF
  • Linear models and empirical bayes methods for assessing differential expression in microarray experiments.
    Stat Appl Genet Mol Biol, Vol. 3, No. 1. (2004)
    by GK Smyth
    posted to microarray by maryee on 2006-07-17 00:56:34 as ** along with 8 people giovenko RMGraze mayercd justescaped ugengma heliopais jyuh talponer
  • Use of within-array replicate spots for assessing differential expression in microarray experiments.
    Bioinformatics (18 January 2005)
    by Gordon K K Smyth, Joëlle Michaud, Hamish S S Scott
    posted to microarray by maryee on 2006-07-17 00:54:55 as ** along with 2 people mdimmic Dax42
  • A new closed multiple testing procedure for hierarchical families of hypotheses
    Journal of Statistical Planning and Inference, Vol. 46, No. 3. (15 August 1995), pp. 265-275.
    by Dror M Rom, Burt Holland
    posted to microarray by maryee on 2006-06-15 01:40:04 as **
  • The Control of the False Discovery Rate in Multiple Testing under Dependency
    Annals of Statistics (2001)
    by Y Benjamini, D Yekutieli
    posted to microarray by maryee on 2006-06-15 01:27:15 as **
  • Identifying differentially expressed genes using false discovery rate controlling procedures.
    Bioinformatics, Vol. 19, No. 3. (12 February 2003), pp. 368-375.
    by A Reiner, D Yekutieli, Y Benjamini
    posted to microarray by maryee on 2006-06-15 01:25:35 as ** along with 3 people RMGraze talponer shikin
  • Markov modelling of immunological and virological states in HIV-1 infected patients.
    Biom J, Vol. 47, No. 6. (December 2005), pp. 834-846.
    by E Mathieu, P Loup, P Dellamonica, JP Daures
    posted to hai by maryee on 2006-06-14 20:24:21 as **
  • notes Microarray analysis and tumor classification.
    N Engl J Med, Vol. 354, No. 23. (8 June 2006), pp. 2463-2472.
    by J Quackenbush
    posted to microarray by maryee on 2006-06-14 15:22:26 as ** along with 2 people and 1 group jeremymiller frohike GeschwindLab
  • Clustering microarray gene expression data using weighted Chinese restaurant process.
    Bioinformatics (9 June 2006)
    by Zhaohui Qin
    posted to microarray by maryee on 2006-06-14 15:21:23 as ** along with 3 people jfr archroad bayes
  • Visualization methods for statistical analysis of microarray clusters.
    BMC Bioinformatics, Vol. 6 (2005)
    by MA Hibbs, NC Dirksen, K Li, OG Troyanskaya
    posted to microarray by maryee on 2006-06-14 15:19:49 as ** along with 5 people jyuh jfr smbaxtersf waszak ndiaz
  • Towards precise classification of cancers based on robust gene functional expression profiles
    BMC Bioinformatics, Vol. 6, No. 1. (2005)
    by Zheng Guo, Tianwen Zhang, Xia Li, Qi Wang, Jianzhen Xu, Hui Yu, Jing Zhu, Haiyun Wang, Chenguang Wang, Eric Topol, Qing Wang, Shaoqi Rao
    posted to microarray by maryee on 2006-06-14 15:11:37 as ** along with 3 people jfr eckart_bindewald macavity1g
  • Mathematical modeling of the interrelationship of CD4 lymphocyte count and viral load changes induced by the protease inhibitor indinavir.
    Antimicrob Agents Chemother, Vol. 42, No. 2. (February 1998), pp. 358-361.
    by GL Drusano, DS Stein
    posted to hai by maryee on 2006-06-13 04:32:04 as **
  • Cost-effectiveness of screening for HIV in the era of highly active antiretroviral therapy.
    N Engl J Med, Vol. 352, No. 6. (10 February 2005), pp. 570-585.
    by GD Sanders, AM Bayoumi, V Sundaram, SP Bilir, CP Neukermans, CE Rydzak, LR Douglass, LC Lazzeroni, M Holodniy, DK Owens
    posted to hai by maryee on 2006-06-07 18:08:14 as **
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