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ptrobajo's library [138 articles]

最近录入 ptrobajo's 文献库.
  • Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
    Genome Biology, Vol. 8 (10 May 2007), R76.
    by Jason I Herschkowitz, Karl Simin, Victor J Weigman, Igor Mikaelian, Jerry Usary, Zhiyuan Hu, Karen E Rasmussen, Laundette P Jones, Shahin Assefnia, Subhashini Chandrasekharan, Michael G Backlund, Yuzhi Yin, Andrey I Khramtsov, Roy Bastein, John Quackenbush, Robert I Glazer, Powel H Brown, Jeffrey E Green, Levy Kopelovich, Priscilla A Furth, Juan P Palazzo, Olufunmilayo I Olopade, Philip S Bernard, Gary A Churchill, Terry Van Dyke, Charles M Perou
    posted to mouse microarray human cross-species cancer by ptrobajo on 2008-07-14 21:52:03 as **
  • Feature selection and molecular classification of cancer using genetic programming.
    Neoplasia, Vol. 9, No. 4. (April 2007), pp. 292-303.
    by J Yu, J Yu, AA Almal, SM Dhanasekaran, D Ghosh, WP Worzel, AM Chinnaiyan
    posted to selection programming herman genetic feature by ptrobajo on 2008-07-12 22:09:23 as ** along with 1 person jyuh
  • Zebrafish Whole-Adult-Organism Chemogenomics for Large-Scale Predictive and Discovery Chemical Biology
    PLoS Genet, Vol. 4, No. 7. (11 July 2008), e1000121.
    by Siew H Lam, Sinnakarupan Mathavan, Yan Tong, Haixia Li, Karuturi, Yilian Wu, Vinsensius B Vega, Edison T Liu, Zhiyuan Gong
    posted to zebrafish cross-species chemogenomics by ptrobajo on 2008-07-12 21:19:12 as **
  • Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    Nat Biotech, Vol. 25, No. 1. (February 2007), pp. 117-124.
    by Peng Lu, Christine Vogel, Rong Wang, Xin Yao, Edward M Marcotte
    posted to translation transcription quantitative protein expression by ptrobajo on 2008-07-12 21:18:29 as ** along with 9 people and 1 group caseybrown ihpark jyuh balabu nickluscombe aswin nicoleq dylan77 nedwards EBI-regulation
  • Derivation of stable microarray cancer-differentiating signatures using consensus scoring of multiple random sampling and gene-ranking consistency evaluation.
    Cancer Res, Vol. 67, No. 20. (15 October 2007), pp. 9996-10003.
    by ZQ Tang, LY Han, HH Lin, J Cui, J Jia, BC Low, BW Li, YZ Chen
    posted to stability signature ranking herman classification by ptrobajo on 2008-07-11 15:58:19 as ** along with 1 person jfr
  • Reliable gene signatures for microarray classification: assessment of stability and performance.
    Bioinformatics (31 July 2006)
    by Chad A A Davis, Fabian Gerick, Volker Hintermair, Caroline C C Friedel, Katrin Fundel, Robert Küffner, Ralf Zimmer
    posted to stability signature microarray herman classification by ptrobajo on 2008-07-11 15:37:21 as ** along with 5 people jfr chad_davis rdiaz efge incovoma
  • Classification based upon gene expression data: bias and precision of error rates.
    Bioinformatics (28 March 2007)
    by Ian A A Wood, Peter M M Visscher, Kerrie L L Mengersen
    posted to precision gene expression cross-validation classification bias by ptrobajo on 2008-07-11 15:33:15 as ** along with 2 people jyuh shigepong
  • A Visual Data Mining Tool that Facilitates Reconstruction of Transcription Regulatory Networks.
    PLoS ONE, Vol. 3, No. 3. (2008)
    by DC Jupiter, V Vanburen
    posted to meta-analysis gene expression correlation compendium by ptrobajo on 2008-07-11 15:12:13 as ** along with 1 person jyuh
  • Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models
    BMC Bioinformatics, Vol. 9 (24 June 2008), 292.
    by Dawei Liu, Debashis Ghosh, Xihong Lin
    posted to pathway kernel geneset by ptrobajo on 2008-07-11 14:44:27 as **
  • A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology
    Cell, Vol. 134, No. 1. (11 July 2008), pp. 112-123.
    by David J Pagliarini, Sarah E Calvo, Betty Chang, Sunil A Sheth, Scott B Vafai, Shao-En Ong, Geoffrey A Walford, Canny Sugiana, Avihu Boneh, William K Chen, David E Hill, Marc Vidal, James G Evans, David R Thorburn, Steven A Carr, Vamsi K Mootha
    posted to protein nazanin mitochondrial localization by ptrobajo on 2008-07-11 11:21:38 as ** along with 1 person neils
  • An Integrated Approach for the Analysis of Biological Pathways using Mixed Models
    PLoS Genet, Vol. 4, No. 7. (4 July 2008), e1000115.
    by Lily Wang, Bing Zhang, Russell D Wolfinger, Xi Chen
    posted to test pathway model mixed geneset by ptrobajo on 2008-07-07 19:46:11 as ** along with 1 person aviad_work
  • Mining co-regulated gene profiles for the detection of functional associations in gene expression data.
    Bioinformatics (30 May 2007)
    by Attila Gyenesei, Ulrich Wagner, Simon Barkow-Oesterreicher, Etzard Stolte, Ralph Schlapbach
    posted to network itemset gene expression dragan by ptrobajo on 2008-07-03 15:53:18 as ** along with 2 people isimpson shigepong
  • Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis.
    Proteomics, Vol. 7, No. 6. (March 2007), pp. 900-909.
    by S Okamoto, Y Yamanishi, S Ehira, S Kawashima, K Tonomura, M Kanehisa
    posted to proteomics missing miranda kernel genes by ptrobajo on 2008-07-03 14:49:04 as **
  • Using the information embedded in the testing sample to break the limits caused by the small sample size in microarray-based classification
    BMC Bioinformatics, Vol. 9 (14 June 2008), 280.
    by Manli Zhu, Aleix M Martinez
    posted to size semi-supervised sample lda classification by ptrobajo on 2008-07-03 12:55:46 as **
  • Classification in the presence of class noise using a probabilistic Kernel Fisher method
    Pattern Recogn., Vol. 40, No. 12. (December 2007), pp. 3349-3357.
    by Yunlei Li, Lodewyk FA Wessels, Dick de Ridder, Marcel JT Reinders
    posted to pipeline noise kernel emiel classification by ptrobajo on 2008-07-01 15:59:27 as **
  • Fasting induces changes in peripheral blood mononuclear cell gene expression profiles related to increases in fatty acid beta-oxidation: functional role of peroxisome proliferator activated receptor alpha in human peripheral blood mononuclear cells.
    The American journal of clinical nutrition, Vol. 86, No. 5. (November 2007), pp. 1515-1523.
    by M Bouwens, LA Afman, M Müller
    posted to ppar monocyte milka mice fasting by ptrobajo on 2008-07-01 12:57:10 as **
  • TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure.
    Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006)
    by BT Alako, D Rainey, H Nijveen, JA Leunissen
    posted to protein phylogeny peroxisome domain by ptrobajo on 2008-07-01 12:27:01 as **
  • Mass spectrometry proteomic diagnosis: enacting the double cross-validatory paradigm.
    Journal of computational biology : a journal of computational molecular cell biology, Vol. 13, No. 9. (November 2006), pp. 1591-1605.
    by BJ Mertens, ME De Noo, RA Tollenaar, AM Deelder
    posted to spectrometry seldi mass cross-validation classification by ptrobajo on 2008-07-01 12:26:09 as **
  • A statistical framework for genomic data fusion.
    Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2626-2635.
    by GR Lanckriet, T De Bie, N Cristianini, MI Jordan, WS Noble
    posted to protein nazanin kernel integration function by ptrobajo on 2008-06-27 09:56:04 as ** along with 5 people carlk tmmurali jfr mbeautru nedwards
  • Proteomics Characterization of Mouse Kidney Peroxisomes by Tandem Mass Spectrometry and Protein Correlation Profiling
    Mol Cell Proteomics, Vol. 6, No. 12. (1 December 2007), pp. 2045-2057.
    by Sebastian Wiese, Thomas Gronemeyer, Rob Ofman, Markus Kunze, Claudia P Grou, Jose A Almeida, Martin Eisenacher, Christian Stephan, Heiko Hayen, Lukas Schollenberger, Thomas Korosec, Hans R Waterham, Wolfgang Schliebs, Ralf Erdmann, Johannes Berger, Helmut E Meyer, Wilhelm Just, Jorge E Azevedo, Ronald J Wanders, Bettina Warscheid
    posted to spectrometry peroxisome nazanin mouse mass by ptrobajo on 2008-06-27 09:49:15 as **
  • Identifying novel peroxisomal proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by John Hawkins, Donna Mahony, Stefan Maetschke, Mark Wakabayashi, Rohan D Teasdale, Mikael Bodén
    posted to pts1 protein peroxisome nazanin localization by ptrobajo on 2008-06-27 09:47:40 as ** along with 1 person viktor21614
  • Peroxisome targeting signal 1: Is it really a simple tripeptide?
    Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1763, No. 12. (December 2006), pp. 1565-1573.
    by Cecile Brocard, Andreas Hartig
    posted to pts1 protein peroxisome nazanin localization by ptrobajo on 2008-06-27 09:44:15 as ** along with 2 people fhaenel viktor21614
  • PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease
    Nucleic Acids Research, Vol. 35, No. Supplement 1. (January 2007), pp. D815-D822.
    by Schluter, Agatha, Fourcade, Stephane, Domenech-Estevez, Enric, Gabaldon, Toni, Huerta-Cepas, Jaime, Berthommier, Guillaume, Ripp, Raymond, Wanders, JA Ronald, Poch, Olivier, Pujol, Aurora
    posted to peroxisome nazanin database by ptrobajo on 2008-06-27 09:43:06 as **
  • Locating proteins in the cell using TargetP, SignalP and related tools.
    Nat Protoc, Vol. 2, No. 4. (2007), pp. 953-971.
    by O Emanuelsson, S Brunak, G von Heijne, H Nielsen
    posted to tool protein nazanin localization by ptrobajo on 2008-06-27 09:24:15 as ** along with 1 person jyuh
  • MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition.
    Bioinformatics (Oxford, England), Vol. 22, No. 10. (15 May 2006), pp. 1158-1165.
    by A Höglund, P Dönnes, T Blum, HW Adolph, O Kohlbacher
    posted to svm protein nazanin localization integration by ptrobajo on 2008-06-27 09:18:54 as **
  • In silico prediction of the peroxisomal proteome in fungi, plants and animals.
    Journal of molecular biology, Vol. 330, No. 2. (4 July 2003), pp. 443-456.
    by O Emanuelsson, A Elofsson, G von Heijne, S Cristóbal
    posted to pts1 protein peroxisome nazanin localization by ptrobajo on 2008-06-27 09:16:18 as **
  • Systematic identification of human mitochondrial disease genes through integrative genomics
    Nature Genetics, Vol. 38, No. 5. (02 April 2006), pp. 576-582.
    by Sarah Calvo, Mohit Jain, Xiaohui Xie, Sunil A Sheth, Betty Chang, Olga A Goldberger, Antonella Spinazzola, Massimo Zeviani, Steven A Carr, Vamsi K Mootha
    posted to protein nazanin mitochondrial localization integration by ptrobajo on 2008-06-27 09:14:29 as ** along with 4 people and 1 group kentsis balicea nirfriedman raiyar steinmetzlab
  • Age-related subproteomic analysis of mouse liver and kidney peroxisomes
    Proteome Science, Vol. 5 (27 November 2007), 19.
    by Jia Mi, Itsaso Garcia-Arcos, Ruben Alvarez, Susana Cristobal
    posted to tissue-specific spectrometry proteomics peroxisome mouse mass by ptrobajo on 2008-06-24 23:04:57 as **
  • Inferring causal relationships among different histone modifications and gene expression
    Genome Res. (18 June 2008), gr.073080.107.
    by Hong Yu, Shanshan Zhu, Bing Zhou, Huiling Xue, Jing-Dong J Han
    posted to network modifications histone gene expression deep-sequencing bayesian by ptrobajo on 2008-06-22 21:46:20 as ** along with 5 people sharmapank bcondon bootsy rschulz fpattyn
  • Thematic review series: Systems Biology Approaches to Metabolic and Cardiovascular Disorders. Reverse engineering gene networks to identify key drivers of complex disease phenotypes
    J. Lipid Res., Vol. 47, No. 12. (1 December 2006), pp. 2601-2613.
    by Eric E Schadt, Pek Y Lum
    posted to systems networks metabolic integration biology by ptrobajo on 2008-06-20 14:01:57 as ** along with 3 people and 1 group jfr giovanni jo_davies GeschwindLab
  • Mapping the Genetic Architecture of Gene Expression in Human Liver.
    PLoS biology, Vol. 6, No. 5. (6 May 2008)
    by Eric E E Schadt, Cliona Molony, Eugene Chudin, Ke Hao, Xia Yang, Pek Y Y Lum, Andrew Kasarskis, Bin Zhang, Susanna Wang, Christine Suver, Jun Zhu, Joshua Millstein, Solveig Sieberts, John Lamb, Debraj Guhathakurta, Jonathan Derry, John D D Storey, Iliana Avila-Campillo, Mark J J Kruger, Jason M M Johnson, Carol A A Rohl, Atila van Nas, Margarete Mehrabian, Thomas A A Drake, Aldons J J Lusis, Ryan C C Smith, F Peter P Guengerich, Stephen C C Strom, Erin Schuetz, Thomas H H Rushmore, Roger Ulrich
    posted to snp network microarray liver integration expression association by ptrobajo on 2008-06-20 13:59:33 as ** along with 5 people semrich caseybrown ddunbar vplagnol Schmidtc
  • 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 snp protein-protein network integration heterogeneous expression by ptrobajo on 2008-06-18 14:02:08 as ** along with 9 people caseybrown djkt marck roys jyuh realzhang kengg tmmurali maralena
  • Use and misuse of the gene ontology annotations.
    Nature reviews. Genetics (13 May 2008)
    by Seung Yon Rhee, Valerie Wood, Kara Dolinski, Sorin Draghici
    posted to ontology gene education annotation by ptrobajo on 2008-06-18 13:56:11 as ** along with 18 people and 1 group marck capitall realzhang gjuggler A_Olympia fpattyn cmzmasek djkt renatomilani giovenko tmmurali cabbagesofdoom RamuAnandakrishnan roys carlk mariakmejia aheilbut jyuh logics of knowledge
  • Quantitative evidence for conserved longevity pathways between divergent eukaryotic species
    Genome Res., Vol. 18, No. 4. (1 April 2008), pp. 564-570.
    by Erica D Smith, Mitsuhiro Tsuchiya, Lindsay A Fox, Nick Dang, Di Hu, Emily O Kerr, Elijah D Johnston, Bie N Tchao, Diana N Pak, Linnea K Welton, Daniel E Promislow, James H Thomas, Matt Kaeberlein, Brian K Kennedy
    posted to pathways cross-species age by ptrobajo on 2008-06-18 13:49:43 as ** along with 2 people wilbur tmmurali
  • Protein networks in disease
    Genome Res., Vol. 18, No. 4. (1 April 2008), pp. 644-652.
    by Trey Ideker, Roded Sharan
    posted to review protein network geneset disease by ptrobajo on 2008-06-18 13:49:12 as ** along with 19 people zwang balicea raiyar jfr brianb paolomarcatili thomaskelder gracio schuylrp jyuh tmmurali Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl
  • Spike-in validation of an Illumina-specific variance stabilizing transformation
    BMC Research Notes, Vol. 1, 18.
    by Mark J Dunning, Matthew E Ritchie, Nuno L Barbosa-Morais, Simon Tavare, Andy G Lynch
    posted to vst spike-in microarray illumina by ptrobajo on 2008-06-18 13:48:46 as **
  • Transcript mapping with high-density oligonucleotide tiling arrays
    Bioinformatics, Vol. 22, No. 16. (15 August 2006), pp. 1963-1970.
    by Wolfgang Huber, Joern Toedling, Lars M Steinmetz
    posted to tiling oligo niek microarray by ptrobajo on 2008-06-18 13:45:46 as ** along with 2 people johncumbers jtaylor
  • Network-based global inference of human disease genes
    Mol Syst Biol, Vol. 4 (6 May 2008)
    by Xuebing Wu, Rui Jiang, Michael Q Zhang, Shao Li
    posted to prioritization network heterogeneous gene disease by ptrobajo on 2008-06-18 13:44:28 as ** along with 6 people Borelli bootsy maralena zwang jyuh biomcgary
  • On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation
    Biology Direct, Vol. 3 (03 June 2008), 23.
    by Wing-Cheong Wong, Marie Loh, Frank Eisenhaber
    posted to microarray illumina analysis by ptrobajo on 2008-06-18 13:38:15 as **
  • Gene-expression of metastasized versus non-metastasized primary head and neck squamous cell carcinomas: a pathway-based analysis
    BMC Cancer, Vol. 8 (10 June 2008), 168.
    by Erik F Hensen, Maria J De Herdt, Jelle J Goeman, Jan Oosting, Vincent THBM Smit, Cees J Cornelisse, Robert
    posted to roepman pathway geneset by ptrobajo on 2008-06-18 13:34:42 as **
  • Context-Specific Metabolic Networks Are Consistent with Experiments
    PLoS Comput Biol, Vol. 4, No. 5. (16 May 2008), e1000082.
    by Scott A Becker, Bernhard O Palsson
    posted to network miranda metabolism context-specific by ptrobajo on 2008-06-18 13:29:15 as ** along with 1 person roys
  • Divergence of canonical danger signals: The genome-level expression patterns of human mononuclear cells subjected to heat shock or lipopolysaccharide
    BMC Immunology, Vol. 9 (30 May 2008), 24.
    by Hector R Wong, Kelli Odoms, Bhuvaneswari Sakthivel
    posted to stimulation stephan monocytes microarray lps by ptrobajo on 2008-06-18 13:16:33 as **
  • A modular approach for integrative analysis of large-scale gene-expression and drug-response data
    Nature Biotechnology, Vol. 26, No. 5. (08 May 2008), pp. 531-539.
    by Zoltán Kutalik, Jacques S Beckmann, Sven Bergmann
    posted to module interaction gene expression drug by ptrobajo on 2008-06-18 12:53:05 as ** along with 3 people oelemento stringertheory tmmurali
  • eQED: an efficient method for interpreting eQTL associations using protein networks
    Mol Syst Biol, Vol. 4 (4 March 2008)
    by Silpa Suthram, Andreas Beyer, Richard M Karp, Yonina Eldar, Trey Ideker
    posted to qtl protein network by ptrobajo on 2008-06-18 12:45:58 as ** along with 6 people jyuh thomaskelder caseybrown zwang biomcgary jo_davies
  • GraphWeb: mining heterogeneous biological networks for gene modules with functional significance.
    Nucleic acids research (6 May 2008)
    by Jüri Reimand, Laur Tooming, Hedi Peterson, Priit Adler, Jaak Vilo
    posted to networks modules miranda graph by ptrobajo on 2008-06-18 12:44:34 as ** along with 4 people jyuh shigepong maralena pinney
  • Exploiting the pathway structure of metabolism to reveal high-order epistasis.
    BMC systems biology, Vol. 2 (2008)
    by M Imielinski, C Belta
    posted to pathway metabolism knockout epistasis by ptrobajo on 2008-06-18 12:35:46 as **
  • Hierarchical structure and the prediction of missing links in networks
    Nature, Vol. 453, No. 7191., pp. 98-101.
    by Aaron Clauset, Cristopher Moore, MEJ Newman
    posted to random network missing miranda hierarchical graph by ptrobajo on 2008-06-18 12:30:34 as ** along with 35 people sen_cheng jjray rds Borelli apwesolowski dpf cmmorel fbaroni balicea cmor kengg pbull jago Ema gtgt15 hryk nedwards i-stevenson pinney elsantosneto markusd eyliu craigwilson06 jyuh margaritis gagliol bryanhughes akshat tmmurali cactus AbnerCYH tny briordan deanmalmgren soramame_0518
  • The Innate Immune Database (IIDB)
    BMC Immunology, Vol. 9 (05 March 2008), 7.
    by Martin Korb, Aistair G Rust, Vesteinn Thorsson, Christophe Battail, Bin Li, Daehee Hwang, Kathleen A Kennedy, Jared Roach, Carrie M Rosenberger, Mark Gilchrist, Daniel Zak, Carrie Johnson, Bruz Marzolf, Alan Aderem, Ilya Shmulevich, Hamid Bolouri
    posted to toll-like immunology immunity database by ptrobajo on 2008-06-18 12:22:59 as **
  • A gene sets approach for identifying prognostic gene signatures for outcome prediction
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Seon Y Kim, Yong S Kim
    posted to signature geneset classification by ptrobajo on 2008-06-18 12:07:57 as ** along with 2 people srp33 barriot
  • A new pairwise kernel for biological network inference with support vector machines.
    BMC bioinformatics, Vol. 8 Suppl 10 (2007)
    by JP Vert, J Qiu, WS Noble
    posted to svm supervised network miranda kernel by ptrobajo on 2008-06-18 11:07:56 as **
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