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2012-09-03 new articles we read this week

Stem cells

  1. Nakano T, Ando S, Takata N, Kawada M, Muguruma K, Sekiguchi K, Saito K, Yonemura S, Eiraku M, Sasai Y. Self-formation of optic cups and storable stratified neural retina from human ESCs. Cell Stem Cell. 2012 Jun 14;10(6):771-85. PubMed PMID: 22704518.
  2. Cyranoski D. Tissue engineering: The brainmaker. Nature. 2012 Aug 23;488(7412):444-6. doi: 10.1038/488444a. PubMed PMID: 22914148.
    • An interesting article about Dr. Sasai who leads the team to make the eye cup from human ESCs as described above and from mouse ESCs, among many other interesting discoveries!


  1. Small A. Faster and more versatile tools for super-resolution fluorescence microscopy. Nat Methods. 2012 Jun 28;9(7):655-6. doi: 10.1038/nmeth.2079. PubMed PMID: 22743767.
  2. Weber M, Huisken J. Omnidirectional microscopy. Nat Methods. 2012 Jun 28;9(7):656-7. doi: 10.1038/nmeth.2022. PubMed PMID: 22743768.
  3. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012 Jun 28;9(7):676-82. doi: 10.1038/nmeth.2019. PubMed PMID: 22743772.
  4. Kankaanpää P, Paavolainen L, Tiitta S, Karjalainen M, Päivärinne J, Nieminen J, Marjomäki V, Heino J, White DJ. BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nat Methods. 2012 Jun 28;9(7):683-9.doi: 10.1038/nmeth.2047. PubMed PMID: 22743773.
  5. de Chaumont F, Dallongeville S, Chenouard N, Hervé N, Pop S, Provoost T, Meas-Yedid V, Pankajakshan P, Lecomte T, Le Montagner Y, Lagache T, Dufour A, Olivo-Marin JC. Icy: an open bioimage informatics platform for extended reproducible research. Nat Methods. 2012 Jun 28;9(7):690-6. doi: 10.1038/nmeth.2075. PubMed PMID: 22743774.
  6. Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE. Biological imaging software tools. Nat Methods. 2012 Jun 28;9(7):697-710. doi: 10.1038/nmeth.2084. PubMed PMID: 22743775.
  7. Ronneberger O, Liu K, Rath M, Rueß D, Mueller T, Skibbe H, Drayer B, Schmidt T, Filippi A, Nitschke R, Brox T, Burkhardt H, Driever W. ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains. Nat Methods. 2012  Jun 17;9(7):735-42. doi: 10.1038/nmeth.2076. PubMed PMID: 22706672.
  8. Lubeck E, Cai L. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat Methods. 2012 Jun 3;9(7):743-8. doi: 10.1038/nmeth.2069. PubMed PMID: 22660740; PubMed Central PMCID: PMC3418883.
  9. Tomer R, Khairy K, Amat F, Keller PJ. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat Methods. 2012 Jun 3;9(7):755-63. doi: 10.1038/nmeth.2062. PubMed PMID: 22660741.
  10. The quest for quantitative microscopy. Nat Methods. 2012 Jul;9(7):627. PubMed PMID: 22930824.
  11. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012 Jul;9(7):671-5. PubMed PMID: 22930834.

Systems Biology

  1. Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell. 2012 Jul 20;150(2):389-401. PubMed PMID: 22817898; PubMed Central PMCID: PMC3413483.
    • Commentary: Freddolino PL, Tavazoie S. The dawn of virtual cell biology. Cell. 2012 Jul 20;150(2):248-50. PubMed PMID: 22817888.


  1. Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A, Wong WS, Sigurdsson G, Walters GB, Steinberg S, Helgason H, Thorleifsson G, Gudbjartsson DF, Helgason A, Magnusson OT, Thorsteinsdottir U, Stefansson K. Rate of de novo mutations and the importance of father’s age to disease risk. Nature. 2012 Aug 23;488(7412):471-5. doi: 10.1038/nature11396. PubMed PMID: 22914163.
    • A new study that shows the older the father is, the more the mutations that he will pass to the next generation!
    • News: Callaway E. Fathers bequeath more mutations as they age. Nature. 2012 Aug 23;488(7412):439. doi: 10.1038/488439a. PubMed PMID: 22914142.
    • Commentary: Kondrashov A. Genetics: The rate of human mutation. Nature. 2012 Aug 23;488(7412):467-8. doi: 10.1038/488467a. PubMed PMID: 22914161.
  2. Schuster-Böckler B, Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature. 2012 Aug 23;488(7412):504-7. PubMed PMID: 22820252.


  1. Lefebvre JL, Kostadinov D, Chen WV, Maniatis T, Sanes JR. Protocadherins mediate dendritic self-avoidance in the mammalian nervous system. Nature. 2012 Aug 23;488(7412):517-21. PubMed PMID: 22842903; PubMed Central PMCID: PMC3427422.