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2011-09-17 new articles we read this week

Saturday, September 17, 2011

Synthetic biology

* a very nice review series about the potential of synthetic biology

  1. Vinson V, Pennisi E. Synthetic biology. The allure of synthetic biology. Introduction. Science. 2011 Sep 2;333(6047):1235. PubMed PMID: 21885767.
  2. Bohannon J. The life hacker. Science. 2011 Sep 2;333(6047):1236-7. PubMed PMID: 21885768.
  3. Kean S. A lab of their own. Science. 2011 Sep 2;333(6047):1240-1. PubMed PMID: 21885770.
  4. Reardon S. Visions of synthetic biology. Science. 2011 Sep 2;333(6047):1242-3. PubMed PMID: 21885771.
  5. Nandagopal N, Elowitz MB. Synthetic biology: integrated gene circuits. Science. 2011 Sep 2;333(6047):1244-8. Review. PubMed PMID: 21885772.
  6. Ruder WC, Lu T, Collins JJ. Synthetic biology moving into the clinic. Science. 2011 Sep 2;333(6047):1248-52. Review. PubMed PMID: 21885773.
  7. Xie Z, Wroblewska L, Prochazka L, Weiss R, Benenson Y. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science. 2011 Sep 2;333(6047):1307-11. PubMed PMID: 21885784.
  8. Mondragón-Palomino O, Danino T, Selimkhanov J, Tsimring L, Hasty J. Entrainment of a population of synthetic genetic oscillators. Science. 2011 Sep 2;333(6047):1315-9. PubMed PMID: 21885786.

Epigenetics

  1. Nabel CS, Kohli RM. Molecular biology. Demystifying DNA demethylation. Science. 2011 Sep 2;333(6047):1229-30. PubMed PMID: 21885763.

Delta-Notch signal transduction

  1. del Álamo D, Rouault H, Schweisguth F. Mechanism and significance of cis-inhibition in Notch signalling. Curr Biol. 2011 Jan 11;21(1):R40-7. Review. PubMed PMID: 21215938.
  2. Sprinzak D, Lakhanpal A, Lebon L, Santat LA, Fontes ME, Anderson GA, Garcia-Ojalvo J, Elowitz MB. Cis-interactions between Notch and Delta generate mutually exclusive signalling states. Nature. 2010 May 6;465(7294):86-90. Epub 2010 Apr 25. PubMed PMID: 20418862; PubMed Central PMCID: PMC2886601.
  3. Sprinzak D, Lakhanpal A, LeBon L, Garcia-Ojalvo J, Elowitz MB. Mutual inactivation of Notch receptors and ligands facilitates developmental patterning. PLoS Comput Biol. 2011 Jun;7(6):e1002069. Epub 2011 Jun 9. PubMed PMID: 21695234; PubMed Central PMCID: PMC3111533.
  4. Shaya O, Sprinzak D. From Notch signaling to fine-grained patterning: Modeling meets experiments. Curr Opin Genet Dev. 2011 Aug 19. [Epub ahead of print] PubMed PMID: 21862316.

Genomics

  1. Gabriel R, Lombardo A, Arens A, Miller JC, Genovese P, Kaeppel C, Nowrouzi A, Bartholomae CC, Wang J, Friedman G, Holmes MC, Gregory PD, Glimm H, Schmidt M, Naldini L, von Kalle C. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat Biotechnol. 2011 Aug 7;29(9):816-23. doi: 10.1038/nbt.1948. PubMed PMID: 21822255.
  2. Toung JM, Morley M, Li M, Cheung VG. RNA-sequence analysis of human B-cells. Genome Res. 2011 Jun;21(6):991-8. Epub 2011 May 2. PubMed PMID: 21536721; PubMed Central PMCID: PMC3106332.
    • An attempt to find out an appropriate coverage of gene expression by next-generation sequencing.
    • See more discussions in this blog.

Retina

  1. Nelson BR, Ueki Y, Reardon S, Karl MO, Georgi S, Hartman BH, Lamba DA, Reh TA. Genome-wide analysis of müller glial differentiation reveals a requirement for notch signaling in postmitotic cells to maintain the glial fate. PLoS One. 2011;6(8):e22817. Epub 2011 Aug 2. PubMed PMID: 21829655; PubMed Central PMCID: PMC3149061.
  2. Esteve P, Sandonìs A, Ibañez C, Shimono A, Guerrero I, Bovolenta P. Secreted frizzled-related proteins are required for Wnt/{beta}-catenin signalling activation in the vertebrate optic cup. Development. 2011 Oct;138(19):4179-84. PubMed PMID: 21896628.

Eye Disease

  1. Kinori M, Pras E, Kolker A, Ferman-Attar G, Moroz I, Moisseiev J, Bandah-Rozenfeld D, Mizrahi-Meissonnier L, Sharon D, Rotenstreich Y. Enhanced S-cone function with preserved rod function: a new clinical phenotype. Mol Vis. 2011;17:2241-7. Epub 2011 Aug 18. PubMed PMID: 21897746.

Education

  1. Amsen E. Leaving the lab: career development for developmental biologists. Development. 2011 Oct;138(19):4107-9. PubMed PMID: 21896625.

Molecular Biology

  1. Proudfoot NJ. Ending the message: poly(A) signals then and now. Genes Dev. 2011 Sep 1;25(17):1770-82. PubMed PMID: 21896654.

Systems Biology

  1. Huh D, Paulsson J. Random partitioning of molecules at cell division. Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):15004-9. Epub 2011 Aug 22. PubMed PMID: 21873252.

Gene therapy

  1. Porter DL, Levine BL, Kalos M, Bagg A, June CH. Chimeric antigen receptor-modified T cells in chronic lymphoid leukemia. N Engl J Med. 2011 Aug 25;365(8):725-33. Epub 2011 Aug 10. PubMed PMID: 21830940.
  2. Kalos M, Levine BL, Porter DL, Katz S, Grupp SA, Bagg A, June CH. T cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia. Sci Transl Med. 2011 Aug 10;3(95):95ra73. PubMed PMID: 21832238.
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2011-09-10 New articles we read this week

Saturday, September 10, 2011

Genomics

  1. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT,Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011 Jul 20;475(7356):348-52. doi: 10.1038/nature10242. PubMed PMID: 21776081.
    • A new and promising way of sequencing.
  2. Chen F, Pruett-Miller SM, Huang Y, Gjoka M, Duda K, Taunton J, Collingwood TN, Frodin M, Davis GD. High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nat Methods. 2011 Jul 17;8(9):753-5. doi: 10.1038/nmeth.1653. PubMed PMID: 21765410.

Imaging

  1. Truong TV, Supatto W, Koos DS, Choi JM, Fraser SE. Deep and fast live imaging  with two-photon scanned light-sheet microscopy. Nat Methods. 2011 Jul 17;8(9):757-60. doi: 10.1038/nmeth.1652. PubMed PMID: 21765409.

Medicine

  1. Rosenbaum L. The art of doing nothing. N Engl J Med. 2011 Sep;365(9):782-5. PubMed PMID: 21879895.

Systems Biology

  1. Srivas R, Hannum G, Ruscheinski J, Ono K, Wang PL, Smoot M, Ideker T. Assembling global maps of cellular function through integrative analysis of physical and genetic networks. Nat Protoc. 2011 Aug 11;6(9):1308-23. doi: 10.1038/nprot.2011.368. PubMed PMID: 21886098.
  2. Modi SR, Camacho DM, Kohanski MA, Walker GC, Collins JJ. Functional characterization of bacterial sRNAs using a network biology approach. Proc Natl Acad Sci U S A. 2011 Aug 29. [Epub ahead of print] PubMed PMID: 21876160.
  3. Murrugarra D, Laubenbacher R. Regulatory patterns in molecular interaction networks. J Theor Biol. 2011 Aug 25. [Epub ahead of print] PubMed PMID: 21872607.

Evolution

  1. Flajnik MF, Deschacht N, Muyldermans S. A case of convergence: why did a simple alternative to canonical antibodies arise in sharks and camels? PLoS Biol. 2011 Aug;9(8):e1001120. Epub 2011 Aug 2. PubMed PMID: 21829328; PubMed Central PMCID: PMC3149040.
  2. Reed RD, Papa R, Martin A, Hines HM, Counterman BA, Pardo-Diaz C, Jiggins CD, Chamberlain NL, Kronforst MR, Chen R, Halder G, Nijhout HF, McMillan WO. optix drives the repeated convergent evolution of butterfly wing pattern mimicry. Science. 2011 Aug 26;333(6046):1137-41. Epub 2011 Jul 21. PubMed PMID: 21778360.
    • Commentary: Carroll SB. Evolution. How great wings can look alike. Science. 2011 Aug 26;333(6046):1100-1. PubMed PMID: 21868661.

Cancer

  1. Brakenhoff RH. Cancer. Another NOTCH for cancer. Science. 2011 Aug 26;333(6046):1102-3. PubMed PMID: 21868662.
  2. Sykes SM, Lane SW, Bullinger L, Kalaitzidis D, Yusuf R, Saez B, Ferraro F, Mercier F, Singh H, Brumme KM, Acharya SS, Schöll C, Tothova Z, Attar EC, Fröhling S, Depinho RA, Armstrong SA, Gilliland DG, Scadden DT. AKT/FOXO Signaling Enforces Reversible Differentiation Blockade in Myeloid Leukemias. Cell. 2011 Sep 2;146(5):697-708. PubMed PMID: 21884932.
    • Commentary: Downing JR. A New FOXO Pathway Required for Leukemogenesis. Cell. 2011 Sep 2;146(5):669-70. PubMed PMID: 21884926.

Regeneration

  1. Smith J, Morgan JR, Zottoli SJ, Smith PJ, Buxbaum JD, Bloom OE. Regeneration in the era of functional genomics and gene network analysis. Biol Bull. 2011 Aug;221(1):18-34. PubMed PMID: 21876108.

Plant

  1. Jorgensen RA. Plant science. A window on the sophistication of plants. Science. 2011 Aug 26;333(6046):1103-4. PubMed PMID: 21868663.

Philosophy

  1. Vilela M, Danuser G. What’s wrong with correlative experiments? Nat Cell Biol. 2011 Sep 2;13(9):1011. doi: 10.1038/ncb2325. PubMed PMID: 21892139.
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2011-09-04 New articles we read this week

Sunday, September 4, 2011

The Cell Biology of the Senses

  • A good review series on the cell biology aspects of sensation published in the Journal of Cell Biology. In particular, this one is about vision.
  1. Sung CH, Chuang JZ. The cell biology of vision. J Cell Biol. 2010 Sep 20;190(6):953-63. Review. PubMed PMID: 20855501; PubMed Central PMCID: PMC3101587.

Development

  1. Luciani F, Champeval D, Herbette A, Denat L, Aylaj B, Martinozzi S, Ballotti R, Kemler R, Goding CR, De Vuyst F, Larue L, Delmas V. Biological and mathematical modeling of melanocyte development. Development. 2011 Sep;138(18):3943-54. PubMed PMID: 21862558.

Zebrafish

  1. Castranova D, Lawton A, Lawrence C, Baumann DP, Best J, Coscolla J, Doherty A, Ramos J, Hakkesteeg J, Wang C, Wilson C, Malley J, Weinstein BM. The Effect of Stocking Densities on Reproductive Performance in Laboratory Zebrafish (Danio rerio). Zebrafish. 2011 Aug 19. [Epub ahead of print] PubMed PMID: 21854208.
  2. Kaushik S, Georga I, Koumoundouros G. Growth and body composition of zebrafish (Danio rerio) larvae fed a compound feed from first feeding onward: toward implications on nutrient requirements. Zebrafish. 2011 Jun;8(2):87-95. Epub 2011 Jun 10. PubMed PMID: 21663450.
  3. Dahlbom SJ, Lagman D, Lundstedt-Enkel K, Sundström LF, Winberg S. Boldness Predicts Social Status in Zebrafish (Danio rerio). PLoS One. 2011;6(8):e23565. Epub 2011 Aug 17. PubMed PMID: 21858168; PubMed Central PMCID: PMC3157393.
  4. Bussmann J, Schulte-Merker S. Rapid BAC selection for tol2-mediated transgenesis in zebrafish. Development. 2011 Aug 24. [Epub ahead of print] PubMed PMID: 21865323.

Retinal Development

  1. Montana CL, Lawrence KA, Williams NL, Tran NM, Peng GH, Chen S, Corbo JC. Transcriptional regulation of neural retina leucine zipper (Nrl), a photoreceptor cell fate determinant. J Biol Chem. 2011 Aug 24. [Epub ahead of print] PubMed PMID: 21865162.
  2. Lewis A, Wilson N, Stearns G, Johnson N, Nelson R, Brockerhoff SE. Celsr3 Is Required for Normal Development of GABA Circuits in the Inner Retina. PLoS Genet. 2011 Aug;7(8):e1002239. Epub 2011 Aug 11. PubMed PMID: 21852962; PubMed Central PMCID: PMC3154962.
  3. Soto F, Bleckert A, Lewis R, Kang Y, Kerschensteiner D, Craig AM, Wong RO. Coordinated increase in inhibitory and excitatory synapses onto retinal ganglion cells during development. Neural Dev. 2011 Aug 24;6(1):31. [Epub ahead of print] PubMed PMID: 21864334.
  4. Sanuki R, Onishi A, Koike C, Muramatsu R, Watanabe S, Muranishi Y, Irie S, Uneo S, Koyasu T, Matsui R, Chérasse Y, Urade Y, Watanabe D, Kondo M, Yamashita T, Furukawa T. miR-124a is required for hippocampal axogenesis and retinal cone survival through Lhx2 suppression. Nat Neurosci. 2011 Aug 21. doi: 10.1038/nn.2897. [Epub ahead of print] PubMed PMID: 21857657.
  5. Tomlinson A, Mavromatakis YE, Struhl G. Three distinct roles for notch in Drosophila r7 photoreceptor specification. PLoS Biol. 2011 Aug;9(8):e1001132. Epub 2011 Aug 23. PubMed PMID: 21886484.

Genomics

  1. Eichler GS, Huang S, Ingber DE. Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles. Bioinformatics. 2003 Nov 22;19(17):2321-2. PubMed PMID: 14630665.

Systems Biology

  1. Pilpel Y. Noise in biological systems: pros, cons, and mechanisms of control. Methods Mol Biol. 2011;759:407-25. PubMed PMID: 21863500.

Delta-Notch Signal Transduction

  1. Wanga MM. Notch signaling and Notch signaling modifiers. Int J Biochem Cell Biol. 2011 Aug 12. [Epub ahead of print] PubMed PMID: 21854867.
  2. Wright GJ, Giudicelli F, Soza-Ried C, Hanisch A, Ariza-McNaughton L, Lewis J. DeltaC and DeltaD interact as Notch ligands in the zebrafish segmentation clock. Development. 2011 Jul;138(14):2947-56. Epub 2011 Jun 8. PubMed PMID: 21653612.

Vision

  1. Huberman AD, Niell CM. What can mice tell us about how vision works? Trends Neurosci. 2011 Aug 11. [Epub ahead of print] PubMed PMID: 21840069.

Ethics, Legal and Social Issues

  • An interesting series about funding discrimination at the NIH
  1. Tabak LA, Collins FS. Sociology. Weaving a richer tapestry in biomedical science. Science. 2011 Aug 19;333(6045):940-1. PubMed PMID: 21852476.
  2. Kaiser J. Biomedical research funding. NIH uncovers racial disparity in grant awards. Science. 2011 Aug 19;333(6045):925-6. PubMed PMID: 21852462.
  3. Price M. Biomedical research funding. A minority viewpoint. Science. 2011 Aug 19;333(6045):926. PubMed PMID: 21852463.
  4. Ginther DK, Schaffer WT, Schnell J, Masimore B, Liu F, Haak LL, Kington R. Race, ethnicity, and NIH research awards. Science. 2011 Aug 19;333(6045):1015-9. PubMed PMID: 21852498.

Evolution

  1. Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. Three periods of regulatory innovation during vertebrate evolution. Science. 2011 Aug 19;333(6045):1019-24. PubMed PMID: 21852499.
  2. Marshall WF. Origins of cellular geometry. BMC Biol. 2011 Aug 31;9:57. PubMed PMID: 21880160.

Education

  1. Feldon DF, Peugh J, Timmerman BE, Maher MA, Hurst M, Strickland D, Gilmore JA, Stiegelmeyer C. Graduate students’ teaching experiences improve their methodological research skills. Science. 2011 Aug 19;333(6045):1037-9. PubMed PMID: 21852504.
  2. Lorsch JR, Nichols DG. Organizing Graduate Life Sciences Education around Nodes and Connections. Cell. 2011 Aug 19;146(4):506-9. PubMed PMID: 21854978.

Cancer

  1. Gupta PB, Fillmore CM, Jiang G, Shapira SD, Tao K, Kuperwasser C, Lander ES. Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell. 2011 Aug 19;146(4):633-44. PubMed PMID: 21854987.

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2011-08-27 New articles we read this week

Saturday, August 27, 2011

Population genetics

  1. Stoneking M, Krause J. Learning about human population history from ancient and modern genomes. Nat Rev Genet. 2011 Aug 18;12(9):603-14. doi: 10.1038/nrg3029. PubMed PMID: 21850041.

Genomics

  1. Cooper GM, Shendure J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet. 2011 Aug 18;12(9):628-40. doi: 10.1038/nrg3046. PubMed PMID: 21850043.

Eye diseases

  1. Conkrite K, Sundby M, Mukai S, Thomson JM, Mu D, Hammond SM, Macpherson D. miR-17~92 cooperates with RB pathway mutations to promote retinoblastoma. Genes Dev. 2011 Aug 15;25(16):1734-45. Epub 2011 Aug 4. PubMed PMID: 21816922.

Systems biology

  1. H Koschwanez J, R Foster K, W Murray A. Sucrose utilization in budding yeast as a model for the origin of undifferentiated multicellularity. PLoS Biol. 2011 Aug;9(8):e1001122. Epub 2011 Aug 9. PubMed PMID: 21857801; PubMed Central PMCID:  PMC3153487.

Gene regulatory network

  1. Mar JC, Matigian NA, Mackay-Sim A, Mellick GD, Sue CM, Silburn PA, McGrath JJ, Quackenbush J, Wells CA. Variance of gene expression identifies altered network constraints in neurological disease. PLoS Genet. 2011 Aug;7(8):e1002207. Epub 2011 Aug 11. PubMed PMID: 21852951; PubMed Central PMCID: PMC3154954.


				

				

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2011-08-21 New articles we read this week

				
Sunday, August 21, 2011

				


Medicine


An interesting paper talking about an electronic skin that can do multiple tasks.


    

  1. Kim DH, Lu N, Ma R, Kim YS, Kim RH, Wang S, Wu J, Won SM, Tao H, Islam A, Yu KJ, Kim TI, Chowdhury R, Ying M, Xu L, Li M, Chung HJ, Keum H, McCormick M, Liu P, Zhang YW, Omenetto FG, Huang Y, Coleman T, Rogers JA. Epidermal electronics. Science. 2011 Aug 12;333(6044):838-43. PubMed PMID: 21836009.
    2. 

      

    • Commentary: Ma Z. Materials science. An electronic second skin. Science. 2011 Aug 12;333(6044):830-1. PubMed PMID: 21836004.
      • 

    



Genomics


    

  1. Gonzalez-Roca E, Garcia-Albéniz X, Rodriguez-Mulero S, Gomis RR, Kornacker K,  Auer H. Accurate expression profiling of very small cell populations. PLoS One. 2010 Dec 28;5(12):e14418. PubMed PMID: 21203435; PubMed Central PMCID:
    
PMC3010985.
    2. 



Disease Gene Mapping


    

  1. Ozgül RK, Siemiatkowska AM, Yücel D, Myers CA, Collin RW, Zonneveld MN, Beryozkin A, Banin E, Hoyng CB, van den Born LI; The European Retinal Disease Consortium, Bose R, Shen W, Sharon D, Cremers FP, Klevering BJ, den Hollander AI, Corbo JC. Exome Sequencing and cis-Regulatory Mapping Identify Mutations in MAK, a Gene Encoding a Regulator of Ciliary Length, as a Cause of Retinitis Pigmentosa. Am J Hum Genet. 2011 Aug 12;89(2):253-264. PubMed PMID: 21835304.
    2. 



Genetics


    

  • This is a series of papers about TALENs (Transcription Activator-Like Effector Nucleases), a new way of gene disruption that can potentially replace ZFNS (Zinc Finger Nucleases).
    

    • 



    

  1. Move over ZFNs. Nat Biotechnol. 2011 Aug 5;29(8):681-4. doi: 10.1038/nbt.1935. PubMed PMID: 21822235.
    2. 

  2. Tesson L, Usal C, Ménoret S, Leung E, Niles BJ, Remy S, Santiago Y, Vincent AI, Meng X, Zhang L, Gregory PD, Anegon I, Cost GJ. Knockout rats generated by embryo microinjection of TALENs. Nat Biotechnol. 2011 Aug 5;29(8):695-6. doi: 10.1038/nbt.1940. PubMed PMID: 21822240.
    3. 

  3. Sander JD, Cade L, Khayter C, Reyon D, Peterson RT, Joung JK, Yeh JR. Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat Biotechnol. 2011 Aug 5;29(8):697-8. doi: 10.1038/nbt.1934. PubMed PMID: 21822241; PubMed Central PMCID: PMC3154023.
    4. 

  4. Huang P, Xiao A, Zhou M, Zhu Z, Lin S, Zhang B. Heritable gene targeting in zebrafish using customized TALENs. Nat Biotechnol. 2011 Aug 5;29(8):699-700. doi: 10.1038/nbt.1939. PubMed PMID: 21822242.
    5. 

  5. Hockemeyer D, Wang H, Kiani S, Lai CS, Gao Q, Cassady JP, Cost GJ, Zhang L, Santiago Y, Miller JC, Zeitler B, Cherone JM, Meng X, Hinkley SJ, Rebar EJ, Gregory PD, Urnov FD, Jaenisch R. Genetic engineering of human pluripotent cells  using TALE nucleases. Nat Biotechnol. 2011 Jul 7;29(8):731-4. doi: 10.1038/nbt.1927. PubMed PMID: 21738127; PubMed Central PMCID: PMC3152587.
    6. 



Delta-Notch Signal Transduction


    

  1. Andersson ER, Sandberg R, Lendahl U. Notch signaling: simplicity in design, versatility in function. Development. 2011 Sep;138(17):3593-612. PubMed PMID: 21828089.
    2. 

  2. Tossell K, Kiecker C, Wizenmann A, Lang E, Irving C. Notch signalling stabilises boundary formation at the midbrain-hindbrain organiser. Development. 2011 Sep;138(17):3745-57. Epub 2011 Jul 27. PubMed PMID: 21795283.
    3. 



Gene regulatory network


    

  1. Karczewski KJ, Tatonetti NP, Landt SG, Yang X, Slifer T, Altman RB, Snyder M.  Cooperative transcription factor associations discovered using regulatory variation. Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13353-8. Epub 2011 Jul 26. PubMed PMID: 21828005.
    2. 



Irx


    

  1. Zhang SS, Kim KH, Rosen A, Smyth JW, Sakuma R, Delgado-Olguín P, Davis M, Chi NC, Puviindran V, Gaborit N, Sukonnik T, Wylie JN, Brand-Arzamendi K, Farman GP, Kim J, Rose RA, Marsden PA, Zhu Y, Zhou YQ, Miquerol L, Henkelman RM, Stainier DY, Shaw RM, Hui CC, Bruneau BG, Backx PH. Iroquois homeobox gene 3 establishes fast conduction in the cardiac His-Purkinje network. Proc Natl Acad Sci U S A. 2011 Aug 8. [Epub ahead of print] PubMed PMID: 21825130.
    2. 



Eye disease


    

  1.  Nelson BR, Ueki Y, Reardon S, Karl MO, Georgi S, Hartman BH, Lamba DA, Reh TA. Genome-wide analysis of müller glial differentiation reveals a requirement for notch signaling in postmitotic cells to maintain the glial fate. PLoS One. 2011;6(8):e22817. Epub 2011 Aug 2. PubMed PMID: 21829655.
    2. 



Regeneration


    

  1. Bermingham-McDonogh O, Reh TA. Regulated reprogramming in the regeneration of  sensory receptor cells. Neuron. 2011 Aug 11;71(3):389-405. PubMed PMID: 21835338.
    2. 



				

				

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Great stories about adaptation in your career/life

				
Sunday, August 14, 2011

				


I have recently read these interesting articles about people who can adapt a drastic change in career/life. There seems to be a good lesson to learn, even for our everyday routine work.


Pulling off the ultimate career makeover


Job security has gone the way of the three-martini lunch. You can’t become bulletproof, but you can reinvent yourself. How five gutsy professionals turned job setbacks into satisfying, sustainable careers.





				

				

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2011-08-06 Articles we read this week

				
Sunday, August 7, 2011

				


Retinal development


    

  1. Brzezinski JA 4th, Kim EJ, Johnson JE, Reh TA. Ascl1 expression defines a subpopulation of lineage-restricted progenitors in the mammalian retina.Development. 2011 Aug;138(16):3519-31. Epub 2011 Jul 19. PubMed PMID: 21771810.
    2. 

  2. Ford KJ, Feller MB. Assembly and disassembly of a retinal cholinergic network.Vis Neurosci. 2011 Jul 26:1-11. [Epub ahead of print] PubMed PMID: 21787461.
    3. 



Development


    

  1. Schwank G, Dalessi S, Yang SF, Yagi R, de Lachapelle AM, Affolter M, Bergmann S, Basler K. Formation of the long range dpp morphogen gradient. PLoS Biol. 2011 Jul;9(7):e1001111. Epub 2011 Jul 26. PubMed PMID: 21814489.
    2. 

  2. Wu G, Liu N, Rittelmeyer I, Sharma AD, Sgodda M, Zaehres H, Bleidißel M, Greber B, Gentile L, Han DW, Rudolph C, Steinemann D, Schambach A, Ott M, Schöler HR, Cantz T. Generation of Healthy Mice from Gene-Corrected Disease-Specific Induced Pluripotent Stem Cells. PLoS Biol. 2011 Jul;9(7):e1001099. Epub 2011 Jul 12. PubMed PMID: 21765802; PubMed Central PMCID: PMC3134447.
    3. 



Genetics


    

  1. Montgomery SB, Lappalainen T, Gutierrez-Arcelus M, Dermitzakis ET. Rare and common regulatory variation in population-scale sequenced human genomes. PLoS Genet. 2011 Jul;7(7):e1002144. Epub 2011 Jul 21. PubMed PMID: 21811411.
    2. 



				

				

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Academic Irony is

				
Monday, August 1, 2011

				


… after spending years of effort to get into the American research circle to have access to better resources, and find out your library requested two articles that you don’t have local subscription from your home institution through interlibrary loan.




				

				

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Journal club – “The value of hypothesis-driven research”

				
Saturday, July 30, 2011

				


These days many cherish “hypothesis-driven” research and trash everything that is observational, exploratory and non-translational. And yet the hypothesis in many research is “post-research” hypothesis. The “hypothesis” itself is also often generated for the sake of having an hypothesis; the essence of the research can still be exploratory.


So when funding is getting scarce and the pressure of coming up with beautiful hypothesis is mounting, one must ask what the value of hypothesis-driven research is. Is it the only way to get important findings? Is it delivering more than other “inferior” approaches?


As I am thinking about these questions and situation all the time, I am leading a journal club in the lab on 8/1 and trying to discuss the philosophical aspects of this with my lab members. And I want to write this down and have a record before we do so. We will read a few articles:


    

  1. Pisani E. Has the internet changed science? Prospect 2010; 177:54 [pdf]
    2. 

  2. Kell DB, Oliver SG. Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays. 2004 Jan;26(1):99-105. PubMed PMID: 14696046.
    3. 

  3. Ioannidis JP. Why most published research findings are false. PLoS Med.  2005 Aug;2(8):e124. Epub 2005 Aug 30. PubMed PMID: 16060722; PubMed  Central PMCID: PMC1182327.
    4. 



and discuss a few questions, in addition to the ones I have above:


    

  1.  Are data mining or descriptive research useless?
    2. 

  2. What are the downsides of doing “hypothesis-driven research”?
    3. 

  3. Are we/funding agencies/authorities doing the society a favor by  insisting scientists to have a hypothesis/justification attached to a  research idea? how about research that has translational value (i.e.  curing disease)? or technical value (e.g. developing a cheaper and faster way to sequence human genome?)
    4. 

  4. Is/Can there a balance between different scientific research  approaches?
    5. 





				

				

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2011-07-30 new articles we read this week

				
Saturday, July 30, 2011

				


Animal model


    

  1. Aitman TJ, Boone C, Churchill GA, Hengartner MO, Mackay TF, Stemple DL. The future of model organisms in human disease research. Nat Rev Genet. 2011 Jul18;12(8):575-82. doi: 10.1038/nrg3047. PubMed PMID: 21765459.
    2. 

  2. Thomas JL, Vihtelic TS, Dendekker AD, Willer G, Luo X, Murphy TR, Gregg RG, Hyde DR, Thummel R. The loss of vacuolar protein sorting 11 (vps11) causes retinal pathogenesis in a vertebrate model of syndromic albinism. Invest Ophthalmol Vis Sci. 2011 May 27. [Epub ahead of print] PubMed PMID: 21622697.
    3. 



Systems biology


    

  1. Garcia HG, Phillips R. Quantitative dissection of the simple repression input-output function. Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):12173-8.Epub 2011 Jul 5. PubMed PMID: 21730194.
    2. 

  2. Schmidt A, Beck M, Malmström J, Lam H, Claassen M, Campbell D, Aebersold R. Absolute quantification of microbial proteomes at different states by directed mass spectrometry. Mol Syst Biol. 2011 Jul 19;7:510. doi: 10.1038/msb.2011.37. PubMed PMID: 21772258.
    3. 

  3. Dahan O, Gingold H, Pilpel Y. Regulatory mechanisms and networks couple the different phases of gene expression. Trends Genet. 2011 Jul 13. [Epub ahead of print] PubMed PMID: 21763027.
    4. 



Retinal development


    

  1. Brzezinski JA 4th, Kim EJ, Johnson JE, Reh TA. Ascl1 expression defines a subpopulation of lineage-restricted progenitors in the mammalian retina.Development. 2011 Jul 19. [Epub ahead of print] PubMed PMID: 21771810.
    2. 



Ethics, Legal and Social Issues


    

  1. Dresser R. Families and forensic DNA profiles. Hastings Cent Rep. 2011 May-Jun;41(3):11-2. PubMed PMID: 21678805.
    2. 

  2. Nelson L, Ashby B. Rethinking the ethics of physician participation in lethal injection execution. Hastings Cent Rep. 2011 May-Jun;41(3):28-37. PubMed PMID: 21678813.
    3. 



				

				

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