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heliopais Beobachtungsliste [1000+ articles]

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  • The need for standards, not guidelines, in biological data reporting and sharing
    Nature Biotechnology, Vol. 24, No. 11., pp. 1369-1373.
    by Lyle D Burgoon
    posted to standards comment by jfr on 2008-07-25 16:57:23 as read along with 2 people and 1 group mhucka raiyar steinmetzlab
  • Standardizing the standards.
    Mol Syst Biol, Vol. 2 (2006)
    by J Quackenbush
    posted to standards comment by jfr on 2008-07-25 16:51:57 as read along with 2 people dullhunk mhucka
  • Are we stuck in the standards?
    Nature Biotechnology, Vol. 24, No. 11., pp. 1374-1376.
    by Catherine A Ball
    posted to standards comment by jfr on 2008-07-25 16:22:27 as read along with 4 people and 3 groups dullhunk mhucka jmuhlich dagmar SorgerLab dIEMoSIRIS compneur
  • 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 tools test go by maralena on 2008-07-24 16:12:39 as ** along with 6 people and 2 groups yas jyuh ealloza grahamc capitall zhouyu BioinfoCIPF ParkinsonLab_at_MaRS
  • ArrayExpress service for reviewers/editors of DNA microarray papers
    Nature Biotechnology, Vol. 24, No. 11., pp. 1321-1322.
    by Alvis Brazma, Helen Parkinson
    posted to standards microarray_technology by jfr on 2008-07-23 18:40:18 as read along with 1 person hpiwowar
  • Lack of correct data format and comparability limits future integrative microarray research
    Nature Biotechnology, Vol. 24, No. 11., pp. 1322-1323.
    by Ola Larsson, Rickard Sandberg
    posted to standards microarray_technology by jfr on 2008-07-23 18:39:09 as read
  • Impact of microarray data quality on genomic data submissions to the FDA
    Nature Biotechnology, Vol. 24, No. 9., pp. 1105-1107.
    by Felix W Frueh
    posted to quality_control microarray_technology maqc comment by jfr on 2008-07-23 18:32:18 as read along with 3 people and 1 group giovenko giovanni cberry GeschwindLab
  • Molecular signatures predict outcomes of breast cancer.
    The New England journal of medicine, Vol. 355, No. 6. (10 August 2006), pp. 615-617.
    by JA O'Shaughnessy
    posted to comparison comment classification breast_cancer by jfr on 2008-07-23 10:01:32 as read
  • Sizing up miRNAs as cancer genes
    Nature Medicine, Vol. 11, No. 7., pp. 712-714.
    by Carlos Caldas, James D Brenton
    posted to review mirna by jfr on 2008-07-22 10:54:59 as read
  • Open software for biologists: from famine to feast
    Nature Biotechnology, Vol. 24, No. 7., pp. 801-803.
    by Dawn Field, Bela Tiwari, Tim Booth, Stewart Houten, Dan Swan, Nicolas Bertrand, Milo Thurston
    posted to software open-source by jfr on 2008-07-22 10:51:27 as read along with 1 person hpiwowar
  • Linking oncogenic pathways with therapeutic opportunities
    Nature Reviews Cancer, Vol. 6, No. 9. (17 August 2006), pp. 735-741.
    by Andrea H Bild, Anil Potti, Joseph R Nevins
    posted to therapy review pathway_analysis classification bio_signature by jfr on 2008-07-22 10:21:29 as read along with 4 people srp33 aviad_work jackjackjjj frohike
  • Gene-expression profiling in breast cancer.
    Lancet, Vol. 365, No. 9460. (5 2005), pp. 634-635.
    by TK Jenssen, E Hovig
    posted to comment breast_cancer by jfr on 2008-07-21 18:17:43 as read
  • MIAME, we have a problem.
    Trends Genet (24 December 2005)
    by Robert Shields
    posted to standards microarray_technology comment by jfr on 2008-07-21 18:15:56 as read along with 4 people hpiwowar textoris RMGraze hggr
  • Microarrays and molecular research: noise discovery?
    Lancet, Vol. 365, No. 9458. (5 February 2005), pp. 454-455.
    by JP Ioannidis
    posted to microarray_technology gene_expression comment by jfr on 2008-07-21 18:13:01 as read along with 1 person textoris
  • Individualized care for patients with cancer - a work in progress.
    The New England journal of medicine, Vol. 351, No. 27. (30 December 2004), pp. 2865-2867.
    by RC Bast, GN Hortobagyi
    posted to therapy rt-pcr comment breast_cancer by jfr on 2008-07-21 18:11:16 as read
  • Technology insight: Emerging techniques to predict response to preoperative chemotherapy in breast cancer.
    Nature clinical practice. Oncology, Vol. 1, No. 1. (November 2004), pp. 44-50.
    by L Pusztai, L Gianni
    posted to therapy review microarray_technology gene_expression breast_cancer by jfr on 2008-07-21 18:08:40 as read
  • Getting the Noise Out of Gene Arrays
    Science, Vol. 306, No. 5696. (22 October 2004), pp. 630-631.
    by Eliot Marshall
    posted to platform_comparison microarray_technology gene_expression comment by jfr on 2008-07-21 18:07:23 as read along with 1 person cmmorel
  • Facts from text-is text mining ready to deliver?
    PLoS Biol, Vol. 3, No. 2. (February 2005)
    by D Rebholz-Schuhmann, H Kirsch, F Couto
    posted to text_mining review by jfr on 2008-07-21 18:06:01 as read along with 12 people and 3 groups snuppepuppan irenas yas dullhunk t11 onca dgront caporaso shimah78us daniel_schober dejori adoms dbk-lab T_lab biomedical-nlp
  • Trawling for genes that predict response to breast cancer adjuvant therapy.
    Journal of clinical oncology : official journal of the American Society of Clinical Oncology, Vol. 22, No. 12. (15 June 2004), pp. 2267-2269.
    by M Ellis, K Ballman
    posted to therapy comment breast_cancer by jfr on 2008-07-21 18:04:37 as read
  • Clinical proteomics: translating benchside promise into bedside reality.
    Nature reviews. Drug discovery, Vol. 1, No. 9. (September 2002), pp. 683-695.
    by EF Petricoin, KC Zoon, EC Kohn, JC Barrett, LA Liotta
    posted to review proteomics by jfr on 2008-07-21 15:19:02 as read
  • DNA microarrays in clinical cancer research.
    Current molecular medicine, Vol. 5, No. 1. (February 2005), pp. 111-120.
    by R Wadlow, S Ramaswamy
    posted to review microarray_technology by jfr on 2008-07-21 14:36:35 as read
  • In the pursuit of complexity: systems medicine in cancer biology.
    Cancer cell, Vol. 9, No. 4. (April 2006), pp. 245-247.
    by ET Liu, VA Kuznetsov, LD Miller
    posted to comment by jfr on 2008-07-21 14:32:45 as read
  • PathCluster: a framework for gene set-based hierarchical clustering.
    Bioinformatics (Oxford, England) (15 July 2008)
    by Tae-Min M Kim, Seon-Hee H Yim, Yong-Bok B Jeong, Yu-Chae C Jung, Yeun-Jun J Chung
    posted to hierarchical cluster by maralena on 2008-07-18 08:47:38 as ** along with 1 person shigepong
  • Clinical trial design for microarray predictive marker discovery and assessment.
    Ann Oncol, Vol. 15, No. 12. (December 2004), pp. 1731-1737.
    by L Pusztai, KR Hess
    posted to trial review breast_cancer by jfr on 2008-07-17 17:38:52 as ** along with 2 people and 1 group jeremymiller lauracorrigan GeschwindLab
  • Targeted cancer therapy
    Nature, Vol. 432, No. 7015. (18 November 2004), pp. 294-297.
    by Charles Sawyers
    posted to therapy review cancer by jfr on 2008-07-17 17:36:53 as read along with 2 people and 1 group Petersarkies phnk Sciences_communication_societe
  • Chipping away at the chip bias: RNA degradation in microarray analysis.
    Nat Genet, Vol. 35, No. 4. (December 2003), pp. 292-293.
    by H Auer, S Lyianarachchi, D Newsom, MI Klisovic, G Marcucci, U Marcucci, K Kornacker
    posted to rna_quality microarray_technology microarray_protocol by jfr on 2008-07-17 17:33:57 as read along with 1 person bertelsen
  • Microarray reality checks in the context of a complex disease.
    Nat Biotechnol, Vol. 22, No. 5. (May 2004), pp. 615-621.
    by GL Miklos, R Maleszka
    posted to no-tag by jfr on 2008-07-17 17:25:39 as read along with 1 person and 1 group lfriedl kdl
  • Identification of gene interactions associated with disease from gene expression data using synergy networks
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by John Watkinson, Xiaodong Wang, Tian Zheng, Dimitris Anastassiou
    posted to network interaction gene_expression by jfr on 2008-07-17 14:47:51 as *** along with 4 people balicea frohike barriot smgomez
  • Sharing and reusing gene expression profiling data in neuroscience.
    Neuroinformatics, Vol. 5, No. 3. (2007), pp. 161-175.
    by X Wan, P Pavlidis
    posted to software review gene_expression by jfr on 2008-07-17 14:42:19 as read along with 3 people klo balicea hpiwowar
  • The use of logic relationships to model colon cancer gene expression networks with mRNA microarray data.
    Journal of biomedical informatics, Vol. 41, No. 4. (August 2008), pp. 530-543.
    by X Ruan, J Wang, H Li, RE Perozzi, EF Perozzi
    posted to progression pathway_analysis network gene_expression colon_cancer by jfr on 2008-07-17 14:36:18 as read along with 1 person balicea
  • ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays
    Bioinformatics, Vol. 24, No. 6. (15 March 2008), pp. 768-774.
    by Guillem Rigaill, Philippe Hupe, Anna Almeida, Philippe La Rosa, Jean-Philippe Meyniel, Charles Decraene, Emmanuel Barillot
    posted to software snp-arrays copy-number by jfr on 2008-07-17 14:22:20 as ** along with 1 person djkt
  • An improved method for detecting and delineating genomic regions with altered gene expression in cancer
    Genome Biology, Vol. 9, No. 1. (2008)
    by Bjorn Nilsson, Mikael Johansson, Anders Heyden, Sven Nelander, Thoas Fioretos
    posted to integration gene_expression copy-number by jfr on 2008-07-17 14:18:14 as ** along with 3 people natstreet barriot ptrobajo
  • Identification and validation of colorectal neoplasia-specific methylation markers for accurate classification of disease.
    Molecular cancer research : MCR, Vol. 5, No. 2. (February 2007), pp. 153-163.
    by F Model, N Osborn, D Ahlquist, R Gruetzmann, B Molnar, F Sipos, O Galamb, C Pilarsky, HD Saeger, Z Tulassay, K Hale, S Mooney, J Lograsso, P Adorjan, R Lesche, A Dessauer, J Kleiber, B Porstmann, A Sledziewski, C Lofton-Day
    posted to methylation colon_cancer by jfr on 2008-07-17 14:10:19 as **
  • Cross-generation and cross-laboratory predictions of Affymetrix microarrays by rank-based methods.
    Journal of biomedical informatics, Vol. 41, No. 4. (August 2008), pp. 570-579.
    by HC Liu, CY Chen, YT Liu, CB Chu, DC Liang, LY Shih, CJ Lin
    posted to platform_comparison meta-analysis by jfr on 2008-07-17 14:05:53 as **
  • Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production.
    The Journal of cell biology, Vol. 182, No. 1. (14 July 2008), pp. 61-76.
    by JM Pawlicki, JA Steitz
    posted to transcription primary microrna by maralena on 2008-07-17 10:27:00 as **
  • Functional organisation of Escherichia coli transcriptional regulatory network
    Journal of Molecular Biology, Vol. 381, No. 1. (1 August 2008), pp. 238-247.
    by Agustino Martínez-Antonio, Sarath C Janga, Denis Thieffry
    posted to transcription regulatory network ecoli by maralena on 2008-07-17 10:24:47 as ** along with 1 person jjray
  • Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes
    Genome Res. (9 July 2008), gr.078246.108.
    by Jeffrey G Reid, Francis C Lynn, Ankur K Nagaraja, Rafal B Drabek, Donna M Muzny, Chad A Shaw, Michelle K Weiss, Arash O Naghavi, Mahjabeen F Khan, Huifeng Zhu, Gemunu H Gunaratne, David B Corry, Jonathan N Miller, Michael S German, Richard A Gibbs, Martin M Matzuk, Preethi H Gunaratne
    posted to mouse microrna let-7 by maralena on 2008-07-14 08:04:52 as ** along with 1 person bootsy
  • MicroRNA regulation and the variability of human cortical gene expression.
    Nucleic acids research (10 July 2008)
    by Rui Zhang, Bing Su
    posted to regulation microrna human gene expression by maralena on 2008-07-14 08:04:29 as ** along with 1 person bootsy
  • Regulation of microRNA expression: the hypoxic component.
    Cell cycle (Georgetown, Tex.), Vol. 6, No. 12. (15 June 2007), pp. 1426-1431.
    by R Kulshreshtha, M Ferracin, M Negrini, GA Calin, RV Davuluri, M Ivan
    posted to mirna_target mirna_regulation mirna by jfr on 2008-07-10 17:25:44 as ***
  • A susceptibility gene set for early onset colorectal cancer that integrates diverse signaling pathways: implication for tumorigenesis.
    Clinical cancer research : an official journal of the American Association for Cancer Research, Vol. 13, No. 4. (15 February 2007), pp. 1107-1114.
    by Y Hong, KS Ho, KW Eu, PY Cheah
    posted to gene_expression colon_cancer by jfr on 2008-07-10 17:19:34 as ***
  • A segmental maximum a posteriori approach to genome-wide copy number profiling.
    Bioinformatics (Oxford, England), Vol. 24, No. 6. (15 March 2008), pp. 751-758.
    by R Andersson, CE Bruder, A Piotrowski, U Menzel, H Nord, J Sandgren, TR Hvidsten, T Diaz de Ståhl, JP Dumanski, J Komorowski
    posted to segmentation bioinformatics bioconductor array-cgh by jfr on 2008-07-10 17:15:08 as ***
  • Multimarker phenotype predicts adverse survival in patients with lymph node-negative colorectal cancer.
    Cancer, Vol. 112, No. 3. (1 February 2008), pp. 495-502.
    by I Zlobec, P Minoo, D Baumhoer, K Baker, L Terracciano, JR Jass, A Lugli
    posted to stageii markers immunohistochemistry colon_cancer by jfr on 2008-07-10 17:08:43 as **
  • A genome-wide map of aberrantly expressed chromosomal islands in colorectal cancer
    Molecular Cancer, Vol. 5 (18 September 2006), 37.
    by Eike Staub, Joern Groene, Detlev Mennerich, Stefan Roepcke, Irina Klaman, Bernd Hinzmann, Esmeralda Castanos-Velez, Benno Mann, Christian Pilarsky, Thomas Brummendorf, Birgit Weber, Heinz-Johannes Buhr, Andre Rosenthal
    posted to gene_expression copy-number colon_cancer by jfr on 2008-07-10 17:06:51 as read along with 2 people rdiaz cpnP
  • Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data.
    Nucleic acids research, Vol. 36, No. 2. (February 2008)
    by C Klijn, H Holstege, J de Ridder, X Liu, M Reinders, J Jonkers, L Wessels
    posted to breast_cancer bioinformatics array-cgh by jfr on 2008-07-10 17:03:13 as ****
  • Single nucleotide polymorphism array analysis of chromosomal instability patterns discriminates rectal adenomas from carcinomas
    The Journal of Pathology, Vol. 9999, No. 9999. (2007), n/a.
    by EH Lips, EJ de Graaf, RAEM Tollenaar, R van Eijk, J Oosting, K Szuhai, T Karsten, Y Nanya, S Ogawa, CJ van de Velde, PHC Eilers, Tom van Wezel, H Morreau
    posted to snp-arrays progression cin by jfr on 2008-07-10 16:50:12 as read along with 1 person cpnP
  • Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer
    BMC Genomics, Vol. 8 (20 February 2007), 53.
    by Judith N Kloth, Jan Oosting, Tom van Wezel, Karoly Szuhai, Jeroen Knijnenburg, Arko Gorter, Gemma G Kenter, Gert J Fleuren, Ekaterina S Jordanova
    posted to snp-arrays loh array-cgh by jfr on 2008-07-10 16:47:56 as **
  • Array CGH identifies distinct DNA copy number profiles of oncogenes and tumor suppressor genes in chromosomal- and microsatellite-unstable sporadic colorectal carcinomas
    Journal of Molecular Medicine, Vol. 85, No. 3. (March 2007), pp. 289-300.
    by Lassmann, Silke, Weis, Roland, Makowiec, Frank, Roth, Jasmine, Danciu, Mihai, Hopt, Ulrich, Werner, Martin
    posted to colon_cancer array-cgh by jfr on 2008-07-10 16:40:46 as **
  • Common and distinct genomic events in sporadic colorectal cancer and diverse cancer types.
    Cancer research, Vol. 67, No. 22. (15 November 2007), pp. 10736-10743.
    by ES Martin, G Tonon, R Sinha, Y Xiao, B Feng, AC Kimmelman, A Protopopov, E Ivanova, C Brennan, K Montgomery, R Kucherlapati, G Bailey, M Redston, L Chin, RA DePinho
    posted to colon_cancer array-cgh by jfr on 2008-07-10 16:38:40 as read
  • Computational Methods for the Analysis of Array Comparative Genomic Hybridization.
    Cancer informatics, Vol. 2 (2006), pp. 48-58.
    by Raj Chari, William W W Lockwood, Wan L L Lam
    posted to snp-arrays review array-cgh by jfr on 2008-07-10 16:34:36 as read
  • Comprehensive analysis of loss of heterozygosity events in glioblastoma using the 100K SNP mapping arrays and comparison with copy number abnormalities defined by BAC array comparative genomic hybridization.
    Genes, chromosomes & cancer, Vol. 47, No. 3. (March 2008), pp. 221-237.
    by KC Lo, D Bailey, T Burkhardt, P Gardina, Y Turpaz, JK Cowell
    posted to snp-arrays loh array-cgh by jfr on 2008-07-10 16:29:17 as **
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