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2011-06-04 new articles we read this week

Gene regulatory network

  1. Walhout AJ. What does biologically meaningful mean? A perspective on generegulatory network validation. Genome Biol. 2011 Apr 11;12(4):109. [Epub ahead ofprint] PubMed PMID: 21489330.
  2. Su WL, Kleinhanz RR, Schadt EE. Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques. Mol Syst Biol. 2011 May 24;7:490. PubMed PMID: 21613979.
  3. Yu H, Tardivo L, Tam S, Weiner E, Gebreab F, Fan C, Svrzikapa N, Hirozane-Kishikawa T, Rietman E, Yang X, Sahalie J, Salehi-Ashtiani K, Hao T, Cusick ME, Hill DE, Roth FP, Braun P, Vidal M. Next-generation sequencing to generate interactome datasets. Nat Methods. 2011 Apr 24. [Epub ahead of print] PubMed PMID: 21516116.
  4. Emmert-Streib F, Glazko GV. Pathway analysis of expression data: deciphering functional building blocks of complex diseases. PLoS Comput Biol. 2011 May;7(5):e1002053. Epub 2011 May 26. PubMed PMID: 21637797.

Systems Biology

  1. Oswald A, Oates AC. Control of endogenous gene expression timing by introns.Genome Biol. 2011 Mar 29;12(3):107. [Epub ahead of print] PubMed PMID: 21463534.
  2. Pourquié O. Vertebrate segmentation: from cyclic gene networks to scoliosis. Cell. 2011 May 27;145(5):650-63. PubMed PMID: 21620133

Retina

  1. Nevin LM, Xiao T, Staub W, Baier H. Topoisomerase II{beta} is required for lamina-specific targeting of retinal ganglion cell axons and dendrites.Development. 2011 Jun;138(12):2457-65. PubMed PMID: 21610027.

Development

  1. Pottin K, Hinaux H, Rétaux S. Restoring eye size in Astyanax mexicanus blind cavefish embryos through modulation of the Shh and Fgf8 forebrain organisingcentres. Development. 2011 Jun;138(12):2467-76. PubMed PMID: 21610028.

Delta-Notch

  1. Acosta H, López SL, Revinski DR, Carrasco AE. Notch destabilises maternal {beta}-catenin and restricts dorsal-anterior development in Xenopus. Development.2011 Jun;138(12):2567-79. PubMed PMID: 21610033.

Eye disease

  1. Zhang T, Zhang N, Baehr W, Fu Y. Cone opsin determines the time course of cone photoreceptor degeneration in Leber congenital amaurosis. Proc Natl Acad Sci U S A. 2011 May 24;108(21):8879-84. Epub 2011 May 9. PubMed PMID: 21555576.

Neurobiology

  1. Park M, Watanabe S, Poon VY, Ou CY, Jorgensen EM, Shen K. CYY-1/Cyclin Y and CDK-5 Differentially Regulate Synapse Elimination and Formation for RewiringNeural Circuits. Neuron. 2011 May 26;70(4):742-57. PubMed PMID: 21609829.
  2. Wolf L, Goldberg C, Manor N, Sharan R, Ruppin E. Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity. PLoS Comput Biol. 2011 May;7(5):e1002040. Epub 2011 May 5. PubMed PMID: 21573208; PubMed Central PMCID:  PMC3088660.

Imaging

  1. Shu X, Lev-Ram V, Deerinck TJ, Qi Y, Ramko EB, Davidson MW, Jin Y, Ellisman MH, Tsien RY. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. PLoS Biol. 2011 Apr;9(4):e1001041. Epub 2011 Apr 5. PubMed PMID: 21483721; PubMed Central PMCID:  PMC3071375.
  2. Jones SA, Shim SH, He J, Zhuang X. Fast, three-dimensional super-resolution imaging of live cells. Nat Methods. 2011 May 8. [Epub ahead of print] PubMed PMID: 21552254.
  3. Peravali R, Gehrig J, Giselbrecht S, Lütjohann DS, Hadzhiev Y, Müller F, Liebel U. Automated feature detection and imaging for high-resolution screening of zebrafish embryos. Biotechniques. 2011 May;50(5):319-24. PubMed PMID: 21548893.

Genomics

  1. Richard H, Schulz MH, Sultan M, Nürnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, Lehrach H, Vingron M, Haas SA, Yaspo ML. Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res. 2010 Jun;38(10):e112. Epub 2010 Feb 11. PubMed PMID: 20150413; PubMed CentralPMCID: PMC2879520.
  2. Baker M. Microarrays, megasynthesis. Nat Methods. 2011 Jun;8(6):457-60. PubMed PMID: 21623349.

Zebrafish

  1. Clark KJ, Balciunas D, Pogoda HM, Ding Y, Westcot SE, Bedell VM, Greenwood TM, Urban MD, Skuster KJ, Petzold AM, Ni J, Nielsen AL, Patowary A, Scaria V, Sivasubbu S, Xu X, Hammerschmidt M, Ekker SC. In vivo protein trapping produces a functional expression codex of the vertebrate proteome. Nat Methods. 2011 May 8.  [Epub ahead of print] PubMed PMID: 21552255.
    • Mullins MC. All-in-one live: genes trapped, tagged and conditionally broken. Nat Methods. 2011 Jun;8(6):466-7. PubMed PMID: 21623352.

Stem cells

  1. Hayden EC. Stem cells: The growing pains of pluripotency. Nature. 2011 May 19;473(7347):272-4. PubMed PMID: 21593837.


 

This was written by Yuk Fai Leung. Posted on Saturday, June 4, 2011, at 1:02 PM. Filed under journal watch. Bookmark the permalink. Follow comments here with the RSS feed. Both comments and trackbacks are currently closed.