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2011-03-12 new articles we read this week

Research life

  • Schwartz MA. The importance of stupidity in scientific research. J Cell Sci. 2008 Jun 1;121(Pt 11):1771. PubMed PMID: 18492790.
    • What is the difference between class room learning and research? Is being good in class room good enough to make one a research scientist?

Systems biology

  • Burrill DR, Silver PA. Synthetic circuit identifies subpopulations with sustained memory of DNA damage. Genes Dev. 2011 Mar 1;25(5):434-9. PubMed PMID: 21363961.

Genomics

  • Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 2011 Mar;21(3):447-55. Epub 2010 Nov 24. PubMed PMID: 21106904.
  • Xu W, Seok J, Mindrinos MN, Schweitzer AC, Jiang H, Wilhelmy J, Clark TA, Kapur K, Xing Y, Faham M, Storey JD, Moldawer LL, Maier RV, Tompkins RG, Wong WH, Davis RW, Xiao W; the Inflammation and Host Response to Injury Large-Scale Collaborative Research Program. Human transcriptome array for high-throughput clinical studies. Proc Natl Acad Sci U S A. 2011 Mar 1;108(9):3707-3712. Epub 2011 Feb 11. PubMed PMID: 21317363.
    • A comparative study of RNA-seq and microarrays for disease research. The authors showed that the performance of microarrays, can be more reliable than RNA-seq. That includes a higher sensitivity at the exon level for the low abundance transcripts
  • Maxmen A. Exome sequencing deciphers rare diseases. Cell. 2011 Mar 4;144(5):635-7. PubMed PMID: 21376225.
    • Whole genome sequencing helps to find the disease genes that haven’t been able to mapped.

Bioinformatics

  • Swedlow JR. Finding an image in a haystack: the case for public image repositories. Nat Cell Biol. 2011 Mar;13(3):183. PubMed PMID: 21364564.

Behaviour

  • Mathur P, Lau B, Guo S. Conditioned place preference behavior in zebrafish. Nat Protoc. 2011 Feb;6(3):338-45. Epub 2011 Feb 24. PubMed PMID: 21372814.

Retina

  • Lamba DA, Reh TA. Microarray Characterization of Human Embryonic Stem Cell-Derived Retinal Cultures. Invest Ophthalmol Vis Sci. 2011 Feb 23. [Epub ahead of print] PubMed PMID: 21345990.
  • Roberts MR, Srinivas M, Forrest D, Morreale de Escobar G, Reh TA. Making the gradient: thyroid hormone regulates cone opsin expression in the developing mouse retina. Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6218-23. Epub 2006 Apr 10. PubMed PMID: 16606843; PubMed Central PMCID: PMC1458858.

Neuroscience

  • Suzuki A, Stern SA, Bozdagi O, Huntley GW, Walker RH, Magistretti PJ, Alberini CM. Astrocyte-neuron lactate transport is required for long-term memory formation. Cell. 2011 Mar 4;144(5):810-23. PubMed PMID: 21376239.
    • Commentary Bezzi P, Volterra A. Astrocytes: powering memory. Cell. 2011 Mar 4;144(5):644-5. PubMed PMID: 21376229.
  • Anderson JR, Gallup GG. Which primates recognize themselves in mirrors? PLoSBiol. 2011 Mar;9(3):e1001024. Epub 2011 Mar 1. PubMed PMID: 21390247.

Cancer

  • Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011 Mar 4;144(5):646-74. PubMed PMID: 21376230.

Epidemiology

  • The longest longitudinal study of the same group of people starting from birth to 65 years old! Many interesting observations.
    • The generation game. Nature. 2011 Mar 3;471(7336):5. PubMed PMID: 21368778.
    • Pearson H. Epidemiology: Study of a lifetime. Nature. 2011 Mar 3;471(7336):20-4. PubMed PMID: 21368799.

Development

  • Wartlick O, Mumcu P, Kicheva A, Bittig T, Seum C, Jülicher F, González-Gaitán M. Dynamics of Dpp signaling and proliferation control. Science. 2011 Mar 4;331(6021):1154-9. PubMed PMID: 21385708.
    • Commentary: Le Goff L, Lecuit T. Developmental biology. Gradient scaling and growth. Science. 2011 Mar 4;331(6021):1141-2. PubMed PMID: 21385701.

Stem cells

  • A series of papers reveal the differences of iPS cells, suggesting more research has to be done before using these cells to treat human disease.
    • Commentary: Pera MF. Stem cells: The dark side of induced pluripotency. Nature. 2011 Mar 3;471(7336):46-7. PubMed PMID: 21368819.
    • Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O’Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, Ecker JR. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 2011 Mar 3;471(7336):68-73. Epub 2011 Feb 2. PubMed PMID: 21289626.
    • Gore A, Li Z, Fung HL, Young JE, Agarwal S, Antosiewicz-Bourget J, Canto I, Giorgetti A, Israel MA, Kiskinis E, Lee JH, Loh YH, Manos PD, Montserrat N, Panopoulos AD, Ruiz S, Wilbert ML, Yu J, Kirkness EF, Izpisua Belmonte JC, Rossi DJ, Thomson JA, Eggan K, Daley GQ, Goldstein LS, Zhang K. Somatic coding mutations in human induced pluripotent stem cells. Nature. 2011 Mar
      3;471(7336):63-7. PubMed PMID: 21368825.
    • Hussein SM, Batada NN, Vuoristo S, Ching RW, Autio R, Närvä E, Ng S, Sourour M, Hämäläinen R, Olsson C, Lundin K, Mikkola M, Trokovic R, Peitz M, Brüstle O, Bazett-Jones DP, Alitalo K, Lahesmaa R, Nagy A, Otonkoski T. Copy number variation and selection during reprogramming to pluripotency. Nature. 2011 Mar 3;471(7336):58-62. PubMed PMID: 21368824.

Structural biology

  • Spudich JA. Biochemistry. Molecular motors, beauty in complexity. Science. 2011 Mar 4;331(6021):1143-4. PubMed PMID: 21385703.

Eye

  • Veth KN, Willer JR, Collery RF, Gray MP, Willer GB, Wagner DS, Mullins MC, Udvadia AJ, Smith RS, John SW, Gregg RG, Link BA. Mutations in Zebrafish lrp2 Result in Adult-Onset Ocular Pathogenesis That Models Myopia and Other Risk Factors for Glaucoma. PLoS Genet. 2011 Feb;7(2):e1001310. Epub 2011 Feb 17. PubMed PMID: 21379331; PubMed Central PMCID: PMC3040661.
This was written by Yuk Fai Leung. Posted on Saturday, March 12, 2011, at 4:38 PM. Filed under journal watch. Bookmark the permalink. Follow comments here with the RSS feed. Both comments and trackbacks are currently closed.