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2010-12-26 new articles we read this week

Sunday, December 26, 2010

Medicine

  1. Barabási AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet. 2011 Jan;12(1):56-68. PubMed PMID: 21164525.
  2. Altman RB, Kroemer HK, McCarty CA, Ratain MJ, Roden D. Pharmacogenomics: will the promise be fulfilled? Nat Rev Genet. 2011 Jan;12(1):69-73. Epub 2010 Nov 30. PubMed PMID: 21116304.

Development

  1. Dahmann C, Oates AC, Brand M. Boundary formation and maintenance in tissue development. Nat Rev Genet. 2011 Jan;12(1):43-55. PubMed PMID: 21164524.

Retinal development

  1. Gomes FL, Zhang G, Carbonell F, Correa JA, Harris WA, Simons BD, Cayouette M.  Reconstruction of rat retinal progenitor cell lineages in vitro reveals a surprising degree of stochasticity in cell fate decisions. Development. 2010 Dec 9;. [Epub ahead of print]
  2. Wojciechowski R. Nature and nurture: the complex genetics of myopia and refractive error. Clin Genet. 2010 Nov 3;. [Epub ahead of print]

Delta/Notch

  1. Mahler J, Filippi A, Driever W.  DeltaA/DeltaD Regulate Multiple and Temporally Distinct Phases of Notch Signaling during Dopaminergic Neurogenesis in Zebrafish. J Neurosci. 2010 Dec 8;30(49):16621-35.

Neuroscience

  1. Redondo RL, Morris RG. Making memories last: the synaptic tagging and capture hypothesis. Nat Rev Neurosci. 2011 Jan;12(1):17-30. PubMed PMID: 21170072.

Evolution

  1. Plotkin JB, Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet. 2011 Jan;12(1):32-42. Epub 2010 Nov 23. PubMed PMID: 21102527.

Behaviour

  1. Lee A, Mathuru AS, Teh C, Kibat C, Korzh V, Penney TB, Jesuthasan S.  The Habenula Prevents Helpless Behavior in Larval Zebrafish. Curr Biol. 2010 Dec 8;. [Epub ahead of print]

Cancer

  1. Feng Y, Santoriello C, Mione M, Hurlstone A, Martin P. Live Imaging of Innate Immune Cell Sensing of Transformed Cells in Zebrafish Larvae: Parallels between Tumor Initiation and Wound Inflammation. PLoS Biol. 2010 Dec 14;8(12):e1000562. PubMed PMID: 21179501.

Systems biology

  1. Casci T. Synthetic biology: RNA device rewires cellular networks. Nat Rev Genet. 2011 Jan;12(1):4-5. Epub 2010 Dec 7. PubMed PMID: 21135865.
  2. Liu CC, Arkin AP. Cell biology. The case for RNA. Science. 2010 Nov 26;330(6008):1185-6. PubMed PMID: 21109657.
  3. Culler SJ, Hoff KG, Smolke CD. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science. 2010 Nov 26;330(6008):1251-5. PubMed PMID: 21109673.
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2010-12-19 new articles we read this week

Sunday, December 19, 2010

Retina

  1. Randlett O, Norden C, Harris WA. The vertebrate retina: A model for neuronal polarization in vivo. Dev Neurobiol. 2010 Dec 7. [Epub ahead of print] PubMed PMID: 21140403.
  2. Sedwick C. Melanopsin ganglion cells: a different way of seeing things. PLoS Biol. 2010 Dec 7;8(12):e1001003. PubMed PMID: 21151889; PubMed Central PMCID: PMC2998444.
  3. Brown TM, Gias C, Hatori M, Keding SR, Semo M, Coffey PJ, Gigg J, Piggins HD, Panda S, Lucas RJ. Melanopsin contributions to irradiance coding in the thalamo-cortical visual system. PLoS Biol. 2010 Dec 7;8(12):e1000558. PubMed PMID: 21151887; PubMed Central PMCID: PMC2998442.

Stem cells

  1. Dolgin E. Putting stem cells to the test. Nat Med. 2010 Dec;16(12):1354-7. PubMed PMID: 21135828.
  2. de Souza N. iPS cell aberrations. Nat Methods. 2010 Dec;7(12):948-9. PubMed PMID: 21166072.

Ethics, Legal and Social Issues

  1. Trommelmans L. The challenge of regenerative medicine. Hastings Cent Rep. 2010 Nov-Dec;40(6):24-6. PubMed PMID: 21155108.

Zebrafish

  1. Mosimann C, Kaufman CK, Li P, Pugach EK, Tamplin OJ, Zon LI. Ubiquitous transgene expression and Cre-based recombination driven by the ubiquitin promoter in zebrafish. Development. 2011 Jan;138(1):169-77. PubMed PMID: 21138979.
  2. Rinkwitz S, Mourrain P, Becker TS. Zebrafish: an integrative System for Neurogenomics and Neurosciences. Prog Neurobiol. 2010 Dec 1. [Epub ahead of print] PubMed PMID: 21130139.

Genomics

  1. Algire M, Krishnakumar R, Merryman C. Megabases for kilodollars. Nat Biotechnol. 2010 Dec;28(12):1272-3. PubMed PMID: 21139611.
  2. Matzas M, Stähler PF, Kefer N, Siebelt N, Boisguérin V, Leonard JT, Keller A, Stähler CF, Häberle P, Gharizadeh B, Babrzadeh F, Church GM. High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol. 2010 Dec;28(12):1291-4. Epub 2010 Nov 28. PubMed PMID: 21113166.
  3. Kosuri S, Eroshenko N, Leproust EM, Super M, Way J, Li JB, Church GM. Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol. 2010 Dec;28(12):1295-9. Epub 2010 Nov 28. PubMed PMID: 21113165.

Developmental/ Evolutionary Genomics

  1. Prud’homme B, Gompel N. Evolutionary biology: Genomic hourglass. Nature. 2010 Dec 9;468(7325):768-9. PubMed PMID: 21150985.
  2. Kalinka AT, Varga KM, Gerrard DT, Preibisch S, Corcoran DL, Jarrells J, Ohler U, Bergman CM, Tomancak P. Gene expression divergence recapitulates the developmental hourglass model. Nature. 2010 Dec 9;468(7325):811-4. PubMed PMID: 21150996.
  3. Domazet-Lošo T, Tautz D. A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature. 2010 Dec 9;468(7325):815-8. PubMed PMID: 21150997.

Biotech Industry

  1. Hambley CJ. Catching the wave in China. Nat Biotechnol. 2010 Dec;28(12):1309-10. PubMed PMID: 21139619.

Cell Biology

  1. Picone R, Ren X, Ivanovitch KD, Clarke JD, McKendry RA, Baum B. A polarised population of dynamic microtubules mediates homeostatic length control in animal cells. PLoS Biol. 2010 Nov 16;8(11):e1000542. PubMed PMID: 21103410; PubMed Central PMCID: PMC2982804.

Systems Biology

  1. Friedman N, Schuldiner M. Genetics. The DNA damage road map. Science. 2010 Dec 3;330(6009):1327-8. PubMed PMID: 21127235.
  2. Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Rewiring of genetic networks in response to DNA damage. Science. 2010 Dec 3;330(6009):1385-9. PubMed PMID: 21127252.
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2010-12-11 articles we read this week

Saturday, December 11, 2010

Education

  1. Investing in graduate education. Nat Cell Biol. 2010 Dec;12(12):1123. PubMed PMID: 21124305.

Zebrafish

  1. Cao Z, Jensen LD, Rouhi P, Hosaka K, Länne T, Steffensen JF, Wahlberg E, Cao Y. Hypoxia-induced retinopathy model in adult zebrafish. Nat Protoc. 2010 Dec;5(12):1903-10. Epub 2010 Nov 4. PubMed PMID: 21127484.
  2. Rouhi P, Jensen LD, Cao Z, Hosaka K, Länne T, Wahlberg E, Steffensen JF, Cao Y. Hypoxia-induced metastasis model in embryonic zebrafish. Nat Protoc. 2010 Dec;5(12):1911-8. Epub 2010 Nov 4. PubMed PMID: 21127485.
  3. Lessman CA, Taylor MR, Orisme W, Carver EA. Use of Flatbed Transparency Scanners in Zebrafish Research Versatile and Economical Adjuncts to Traditional Imaging Tools for the Danio rerio Laboratory. Methods Cell Biol. 2010;100:295-322. PubMed PMID: 21111223.

Neuroscience

  1. Chapouton P, Godinho L. Neurogenesis. Methods Cell Biol. 2010;100:72-126. PubMed PMID: 21111215.

Eye

  1. Wang JS, Kefalov VJ. The Cone-specific Visual Cycle. Prog Retin Eye Res. 2010 Nov 24. [Epub ahead of print] PubMed PMID: 21111842.
  2. Avanesov A, Malicki J. Analysis of the retina in the zebrafish model. Methods Cell Biol. 2010;100:153-204. PubMed PMID: 21111217.
  3. Perkins BD, Fadool JM. Photoreceptor Structure and Development Analyses using GFP Transgenes. Methods Cell Biol. 2010;100:205-18. PubMed PMID: 21111218.
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What a beautiful and flawless study

Sunday, December 5, 2010

Upper D. The unsuccessful self-treatment of a case of “writer’s block”. J Appl
Behav Anal. 1974 Fall;7(3):497. PubMed PMID: 16795475; PubMed Central PMCID:
PMC1311997.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1311997/pdf/jaba00061-0143a.pdf

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2010-12-04 articles we read this week

Saturday, December 4, 2010

Origin of Life

  1. Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, Oremland RS. A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. 2010 Dec 2. [Epub ahead of print] PubMed PMID: 21127214.
    • News coverage on BBC

Image analysis

  1. Shamir L, Delaney JD, Orlov N, Eckley DM, Goldberg IG. Pattern recognition software and techniques for biological image analysis. PLoS Comput Biol. 2010 Nov 24;6(11):e1000974. PubMed PMID: 21124870.
  2. Wollman R, Stuurman N. High throughput microscopy: from raw images to discoveries. J Cell Sci. 2007 Nov 1;120(Pt 21):3715-22. Review. PubMed PMID: 17959627.
  3. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006;7(10):R100. Epub 2006 Oct 31. PubMed PMID: 17076895; PubMed Central PMCID: PMC1794559.
  4. Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE. CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics. 2008 Nov 15;9:482. PubMed PMID: 19014601; PubMed Central PMCID: PMC2614436.
  5. Jones TR, Carpenter AE, Lamprecht MR, Moffat J, Silver SJ, Grenier JK, Castoreno AB, Eggert US, Root DE, Golland P, Sabatini DM. Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1826-31. Epub 2009 Feb 2.  PubMed PMID: 19188593; PubMed Central PMCID: PMC2634799.
  6. Lamprecht MR, Sabatini DM, Carpenter AE. CellProfiler: free, versatile software for automated biological image analysis. Biotechniques. 2007 Jan;42(1):71-5. PubMed PMID: 17269487.

Neuroscience

  1. Schwab ME. How hard is the CNS hardware? Nat Neurosci. 2010 Dec;13(12):1444-6. PubMed PMID: 21102566.

Retina

  1. Fischer AJ, Bongini R. Turning müller glia into neural progenitors in the retina. Mol Neurobiol. 2010 Dec;42(3):199-209. Epub 2010 Nov 20. PubMed PMID:21088932.

Genomics

  1. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010 Oct 27;11(10):R106. [Epub ahead of print] PubMed PMID: 20979621.
  2. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010 Nov 24. [Epub ahead of print] PubMed PMID: 21106759.

Brg1

  1. Watanabe T, Semba S, Yokozaki H. Regulation of PTEN expression by the SWI/SNF chromatin-remodelling protein BRG1 in human colorectal carcinoma cells. Br J Cancer. 2010 Nov 23. [Epub ahead of print] PubMed PMID: 21102582.

Physiology

  1. Ng SF, Lin RC, Laybutt DR, Barres R, Owens JA, Morris MJ. Chronic high-fat diet in fathers programs β-cell dysfunction in female rat offspring. Nature. 2010 Oct 21;467(7318):963-6. PubMed PMID: 20962845.

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2010-11-27 New articles we read this week

Saturday, November 27, 2010

Zebrafish

  1. Knopf F, Schnabel K, Haase C, Pfeifer K, Anastassiadis K, Weidinger G. Dually inducible TetON systems for tissue-specific conditional gene expression in zebrafish. Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):19933-19938. Epub 2010 Nov 1. PubMed PMID: 21041642.
  2. Connaughton VP. Bipolar cells in the zebrafish retina. Vis Neurosci. 2010 Nov 16:1-17. [Epub ahead of print] PubMed PMID: 21080977.
  3. Arrenberg AB, Stainier DY, Baier H, Huisken J. Optogenetic control of cardiac function. Science. 2010 Nov 12;330(6006):971-4. PubMed PMID: 21071670.

Neuroscience

  1. Yehuda R, Joëls M, Morris RG. The memory paradox. Nat Rev Neurosci. 2010 Dec;11(12):837-839. PubMed PMID: 21088685.
  2. Del Bene F, Wyart C, Robles E, Tran A, Looger L, Scott EK, Isacoff EY, Baier H. Filtering of visual information in the tectum by an identified neural circuit. Science. 2010 Oct 29;330(6004):669-73. PubMed PMID: 21030657.

Medicine

  1. D’Amato G, Liccardi G, Cecchi L, Pellegrino F, D’Amato M. Facebook: a new trigger for asthma? Lancet. 2010 Nov 20;376(9754):1740. PubMed PMID: 21093651.

Eye & Disease

  1. Parapuram SK, Cojocaru RI, Chang JR, Khanna R, Brooks M, Othman M, Zareparsi S, Khan NW, Gotoh N, Cogliati T, Swaroop A. Distinct signature of altered homeostasis in aging rod photoreceptors: implications for retinal diseases. PLoS One. 2010 Nov 8;5(11):e13885. PubMed PMID: 21079736; PubMed Central PMCID: PMC2975639.
  2. Connaughton VP. Bipolar cells in the zebrafish retina. Vis Neurosci. 2010 Nov 16:1-17. [Epub ahead of print] PubMed PMID: 21080977.
  3. Tschopp M, Takamiya M, Cerveny KL, Gestri G, Biehlmaier O, Wilson SW, Strähle U, Neuhauss SC. Funduscopy in adult zebrafish and its application to isolate mutant strains with ocular defects. PLoS One. 2010 Nov 5;5(11):e15427. PubMed PMID: 21079775; PubMed Central PMCID: PMC2974646.
  4. den Hollander AI, Biyanwila J, Kovach P, Bardakjian T, Traboulsi EI, Ragge NK, Schneider A, Malicki J. Genetic defects of GDF6 in the zebrafish out of sightmutant and in human eye developmental anomalies. BMC Genet. 2010 Nov 11;11(1):102. PubMed PMID: 21070663.
  5. Maminishkis A, Miller SS. Experimental models for study of retinal pigment epithelial physiology and pathophysiology. J Vis Exp. 2010 Nov 6;(45). pii: 2032. doi: 10.3791/2032. PubMed PMID: 21085105.

Systems biology

  1. Larsson E, Sander C, Marks D. mRNA turnover rate limits siRNA and microRNA efficacy. Mol Syst Biol. 2010 Nov 16;6:433. PubMed PMID: 21081925.
  2. Mao C, Brown CR, Falkovskaia E, Dong S, Hrabeta-Robinson E, Wenger L, Boeger H. Quantitative analysis of the transcription control mechanism. Mol Syst Biol. 2010 Nov 19;6:431. PubMed PMID: 21081924.

Funding

  1. Gross M. Britain cuts back deeply on spending. Curr Biol. 2010 Nov 9;20(21):R905-6. PubMed PMID: 21105219.
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Conrad Wolfram: Teaching kids real math with computers

Sunday, November 21, 2010

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2010-11-20 New articles we read this week

Saturday, November 20, 2010

Disease

  1. Shive HR, West RR, Embree LJ, Azuma M, Sood R, Liu P, Hickstein DD. brca2 in zebrafish ovarian development, spermatogenesis, and tumorigenesis. Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19350-5. Epub 2010 Oct 25. PubMed PMID: 20974951.
  2. Jain S, Heutink P. From single genes to gene networks: high-throughput-high-content screening for neurological disease. Neuron. 2010 Oct 21;68(2):207-17. Review. PubMed PMID: 20955929.

Eye Disease

  1. Linder B, Dill H, Hirmer A, Brocher J, Lee GP, Mathavan S, Bolz HJ, Winkler C, Laggerbauer B, Fischer U. Systemic splicing factor deficiency causes tissue-specific defects: A zebrafish model for Retinitis pigmentosa. Hum Mol Genet. 2010 Nov 3. [Epub ahead of print] PubMed PMID: 21051334.

Development

  1. Lek M, Dias JM, Marklund U, Uhde CW, Kurdija S, Lei Q, Sussel L, Rubenstein JL, Matise MP, Arnold HH, Jessell TM, Ericson J. A homeodomain feedback circuit underlies step-function interpretation of a Shh morphogen gradient during ventral neural patterning. Development. 2010 Dec;137(23):4051-60. PubMed PMID: 21062862.
  2. Green AA, Kennaway JR, Hanna AI, Bangham JA, Coen E. Genetic Control of Organ Shape and Tissue Polarity. PLoS Biol. 2010 Nov 9;8(11):e1000537. PubMed PMID: 21085690.
  3. Cui ML, Copsey L, Green AA, Bangham JA, Coen E. Quantitative Control of Organ Shape by Combinatorial Gene Activity. PLoS Biol. 2010 Nov 9;8(11):e1000538. PubMed PMID: 21085695.

Eye Development

  1. Billings NA, Emerson MM, Cepko CL. Analysis of Thyroid Response Element Activity during Retinal Development. PLoS One. 2010 Oct 29;5(10):e13739. PubMed PMID: 21060789; PubMed Central PMCID: PMC2966421.
  2. Phillips MJ, Otteson DC. Differential expression of neuronal genes in Muller glia in two- and three-dimensional cultures. Invest Ophthalmol Vis Sci. 2010 Nov 4. [Epub ahead of print] PubMed PMID: 21051699.

Stem Cells

  1. Hanna JH, Saha K, Jaenisch R. Pluripotency and cellular reprogramming: facts, hypotheses, unresolved issues. Cell. 2010 Nov 12;143(4):508-25. PubMed PMID: 21074044.
  2. Marchetto MC, Carromeu C, Acab A, Yu D, Yeo GW, Mu Y, Chen G, Gage FH, Muotri AR. A model for neural development and treatment of rett syndrome using humaninduced pluripotent stem cells. Cell. 2010 Nov 12;143(4):527-39. PubMed PMID: 21074045.

Zebrafish

  1. Newman M, Lardelli M. A hyperactive sleeping beauty transposase enhances transgenesis in zebrafish embryos. BMC Res Notes. 2010 Nov 4;3(1):282. [Epub ahead of print] PubMed PMID: 21050486.

Genomics

  1. Wyart M, Botstein D, Wingreen NS. Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data. PLoS Comput Biol. 2010 Nov 4;6(11):e1000979. PubMed PMID: 21079668; PubMed Central PMCID: PMC2973809.

Systems Biology

  1. Lehner B. Conflict between Noise and Plasticity in Yeast. PLoS Genet. 2010 Nov 4;6(11):e1001185. PubMed PMID: 21079670; PubMed Central PMCID: PMC2973811.
  2. Li J, Yuan Z, Zhang Z. The cellular robustness by genetic redundancy in budding yeast. PLoS Genet. 2010 Nov 4;6(11):e1001187. PubMed PMID: 21079672; PubMed Central PMCID: PMC2973813.

Ethics, Society and Legal Issues

  1. Johnson DG. The role of ethics in science and engineering. Trends Biotechnol. 2010 Sep 9. [Epub ahead of print] PubMed PMID: 20832883.
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Interesting article on the evolution of the heart.

Thursday, November 18, 2010

Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature 461, 95-98 (3 September 2009). It also has some really nice photos. Enjoy!

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RSA Animate – Drive: The surprising truth about what motivates us

Sunday, November 14, 2010

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