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2011-07-24 new articles we read this week

Sunday, July 24, 2011

Delta-Notch, signal transduction

  1. Ohata S, Aoki R, Kinoshita S, Yamaguchi M, Tsuruoka-Kinoshita S, Tanaka H, Wada H, Watabe S, Tsuboi T, Masai I, Okamoto H. Dual roles of Notch in regulation of apically restricted mitosis and apicobasal polarity of neuroepithelial cells. Neuron. 2011 Jan 27;69(2):215-30. PubMed PMID: 21262462.

Ethical, Legal and Social Issues

  1. Mismeasure for mismeasure. Nature. 2011 Jun 22;474(7352):419. doi: 10.1038/474419a. PubMed PMID: 21697903.
  2. Lewis JE, Degusta D, Meyer MR, Monge JM, Mann AE, Holloway RL. The Mismeasure of Science: Stephen Jay Gould versus Samuel George Morton on Skulls and Bias. PLoS Biol. 2011 Jun;9(6):e1001071. Epub 2011 Jun 7. PubMed PMID: 21666803; PubMedCentral PMCID: PMC3110184.
  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.

Gene regulatory network

  1. Amit R, Garcia HG, Phillips R, Fraser SE. Building enhancers from the ground up: a synthetic biology approach. Cell. 2011 Jul 8;146(1):105-18. PubMed PMID: 21729783.
  2. Frankel N, Erezyilmaz DF, McGregor AP, Wang S, Payre F, Stern DL. Morphological evolution caused by many subtle-effect substitutions in regulatory  DNA. Nature. 2011 Jun 29;474(7353):598-603. doi: 10.1038/nature10200. PubMedPMID: 21720363.
  3. Peter IS, Davidson EH. A gene regulatory network controlling the embryonic specification of endoderm. Nature. 2011 May 29;474(7353):635-9. doi: 10.1038/nature10100. PubMed PMID: 21623371.

Neurobiology

  1. Xiao T, Staub W, Robles E, Gosse NJ, Cole GJ, Baier H. Assembly of Lamina-Specific Neuronal Connections by Slit Bound to Type IV Collagen. Cell.2011 Jul 8;146(1):164-76. PubMed PMID: 21729787.

Zebrafish

  1. Lauter G, Söll I, Hauptmann G. Two-color fluorescent in situ hybridization in  the embryonic zebrafish brain using differential detection systems. BMC Dev Biol. 2011 Jul 4;11:43. PubMed PMID: 21726453.
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Fun Read

Thursday, June 16, 2011

20 Things You Didn’t Know About… 20 Things You Didn’t Know About… DNA

http://discovermagazine.com/2011/apr/20-things-you-didnt-know-about-dna

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2011-06-11 new articles we read this week

Saturday, June 11, 2011

Delta-Notch

  1. Niwa Y, Shimojo H, Isomura A, González A, Miyachi H, Kageyama R. Different types of oscillations in Notch and Fgf signaling regulate the spatiotemporal periodicity of somitogenesis. Genes Dev. 2011 Jun 1;25(11):1115-20. PubMed PMID: 21632822.

Retina

  1. Robinson R. After 40 years, retina reveals it uses positive feedback, as well as negative. PLoS Biol. 2011 May;9(5):e1001058. Epub 2011 May 3. PubMed PMID:21572905; PubMed Central PMCID: PMC3092782.

Stem cells

  1. Neuron’s Reviews on Neural Stem Cells and Neurogenesis

Gene regulatory network

  1. Peter IS, Davidson EH. A gene regulatory network controlling the embryonic specification of endoderm. Nature. 2011 May 29. [Epub ahead of print] PubMed PMID: 21623371.
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2011-06-04 new articles we read this week

Saturday, June 4, 2011

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.


 

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2011-05-29 new articles we read this week

Sunday, May 29, 2011

Eye diseases

  1. Sheffield VC, Stone EM. Genomics and the eye. N Engl J Med. 2011 May 19;364(20):1932-42. PubMed PMID: 21591945.

Regeneration

  1. Tu S, Johnson SL. Fate restriction in the growing and regenerating zebrafish fin. Dev Cell. 2011 May 17;20(5):725-32. PubMed PMID: 21571228; PubMed CentralPMCID: PMC3096007.
  2. Knopf F, Hammond C, Chekuru A, Kurth T, Hans S, Weber CW, Mahatma G, Fisher S, Brand M, Schulte-Merker S, Weidinger G. Bone Regenerates via Dedifferentiation of Osteoblasts in the Zebrafish Fin. Dev Cell. 2011 May 17;20(5):713-24. PubMedPMID: 21571227.

Vision

  1. Ullrich-Lüter EM, Dupont S, Arboleda E, Hausen H, Arnone MI. Unique system of photoreceptors in sea urchin tube feet. Proc Natl Acad Sci U S A. 2011 May17;108(20):8367-72. Epub 2011 May 2. PubMed PMID: 21536888.
  2. Cerveny KL, Varga M, Wilson SW. Continued growth and circuit building in the anamniote visual system. Dev Neurobiol. 2011 May 11.  [Epub ahead of print] PubMed PMID: 21563317.

Behavior

  1. Rihel J, Schier AF. Behavioral screening for neuroactive drugs in zebrafish. Dev Neurobiol. 2011 May 12. [Epub ahead of print] PubMed PMID: 21567979.

Brg1

  1. Bock VL, Lyons JG, Huang XX, Jones AM, McDonald LA, Scolyer RA, Moloney FJ, Barnetson RS, Halliday GM. BRM and BRG1 subunits of the SWI/SNF chromatin remodelling complex are downregulated upon progression of benign skin lesions into invasive tumours. Br J Dermatol. 2011 Feb 24. doi: 10.1111/j.1365-2133.2011.10267.x. [Epub ahead of print] PubMed PMID: 21564052.
  2. Hasselblatt M, Gesk S, Oyen F, Rossi S, Viscardi E, Giangaspero F, Giannini C, Judkins AR, Frühwald MC, Obser T, Schneppenheim R, Siebert R, Paulus W. Nonsense Mutation and Inactivation of SMARCA4 (BRG1) in an Atypical Teratoid/Rhabdoid Tumor Showing Retained SMARCB1 (INI1) Expression. Am J Surg Pathol. 2011 Jun;35(6):933-935. PubMed PMID: 21566516.
  3. Reisman D, Glaros S, Thompson EA. The SWI/SNF complex and cancer. Oncogene. 2009 Apr 9;28(14):1653-68. Epub 2009 Feb 23. Review. PubMed PMID: 19234488.
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Wisdom from a retiring community college English teacher

Tuesday, May 24, 2011

From If the dog ate your homework, read this:

There are always excuses for not showing up, or not turning work in. I’ve heard them all. But lives built on excuses generally don’t turn out well.

Few people care whether you succeed or fail. You are not showing up to class for your teachers or even your parents. You’re not doing these assignments for anyone but yourselves.

Life has a way of getting serious with us well before some of us decide to get serious with it. By that time, it may be too late to build the life you might have wanted.

 

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How to fund research so that it generates insanely great ideas, not pretty good ones.

Saturday, May 21, 2011

An interesting article “Positive Black Swans” by Tim Harford From Slate

Still, after a few years, Capecchi had decided that Harvard was not for him. Despite great resources, inspiring colleagues and a supportive mentor in Watson, he found the Harvard environment demanded results in too much of a hurry. That was fine, if you wanted to take predictable steps along well-signposted pathways. But Capecchi felt that if you wanted to do great work, to change the world, you had to give yourself space to breathe. Harvard, he thought, had become “a bastion of short-term gratification.” Off he went instead to the University of Utah, where a brand-new department was being set up. He had spotted, in Utah, a Galapagan island on which to develop his ideas.

Mario Capecchi developed the approach for generating knock0ut mice and received the Nobel Prize in Physiology or Medicine 2007.

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2011-05-21 new articles we read this week

Saturday, May 21, 2011

Evolution

  1. Moczek AP. Evolutionary biology: the origins of novelty. Nature. 2011 May 5;473(7345):34-5. PubMed PMID: 21544136.
  2. Tena JJ, Alonso ME, de la Calle-Mustienes E, Splinter E, de Laat W, Manzanares M, Gómez-Skarmeta JL. An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation. Nat Commun. 2011;2:310. PubMed PMID: 21556064.
  3. Tirosh I, Reikhav S, Levy AA, Barkai N. A yeast hybrid provides insight into the evolution of gene expression regulation. Science. 2009 May 1;324(5927):659-62. PubMed PMID: 19407207.
  4. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M. Variation in transcription factor binding among humans. Science. 2010 Apr 9;328(5975):232-5. Epub 2010 Mar 18. PubMed PMID: 20299548; PubMed Central PMCID: PMC2938768.
  5. Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL. Genetic properties influencing the evolvability of gene expression. Science. 2007 Jul 6;317(5834):118-21. Epub 2007 May 24. PubMed PMID: 17525304.

Systems Biology

  1. Green RA, Kao HL, Audhya A, Arur S, Mayers JR, Fridolfsson HN, Schulman M, Schloissnig S, Niessen S, Laband K, Wang S, Starr DA, Hyman AA, Schedl T, Desai A, Piano F, Gunsalus KC, Oegema K. A High-Resolution C. elegans Essential Gene Network Based on Phenotypic Profiling of a Complex Tissue. Cell. 2011 Apr29;145(3):470-82. PubMed PMID: 21529718; PubMed Central PMCID: PMC3086541.
  2. Liu YY, Slotine JJ, Barabási AL. Controllability of complex networks. Nature. 2011 May 12;473(7346):167-73. PubMed PMID: 21562557.
    • Commentary: Egerstedt M. Complex networks: Degrees of control. Nature. 2011 May 12;473(7346):158-9. PubMed PMID: 21562550.

Genomics

  1. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9. Epub 2011 Mar 23. PubMed PMID: 21441907; PubMed Central PMCID: PMC3088773.
  2. Tasic B, Hippenmeyer S, Wang C, Gamboa M, Zong H, Chen-Tsai Y, Luo L. From the Cover: Site-specific integrase-mediated transgenesis in mice via pronuclear injection. Proc Natl Acad Sci U S A. 2011 May 10;108(19):7902-7. Epub 2011 Apr 4. PubMed PMID: 21464299.

Stem cells

  1. Rao M. Keeping things simple. Nat Methods. 2011 May;8(5):389-90. PubMed PMID: 21527929.
  2. Kim J, Efe JA, Zhu S, Talantova M, Yuan X, Wang S, Lipton SA, Zhang K, Ding S. Direct reprogramming of mouse fibroblasts to neural progenitors. Proc Natl Acad Sci U S A. 2011 May 10;108(19):7838-43. Epub 2011 Apr 26. PubMed PMID: 21521790.
  3. Brennand KJ, Simone A, Jou J, Gelboin-Burkhart C, Tran N, Sangar S, Li Y, Mu Y, Chen G, Yu D, McCarthy S, Sebat J, Gage FH. Modelling schizophrenia using human induced pluripotent stem cells. Nature. 2011 May 12;473(7346):221-5. Epub 2011 Apr 13. PubMed PMID: 21490598.

Development

  1. Quillien A, Blanco-Sanchez B, Halluin C, Moore JC, Lawson ND, Blader P, Cau E. BMP signaling orchestrates photoreceptor specification in the zebrafish pineal gland in collaboration with Notch. Development. 2011 Jun;138(11):2293-302. PubMed PMID: 21558377.
  2. Clanton JA, Shestopalov I, Chen J, Gamse JT. Lineage labeling of zebrafish cells with laser uncagable fluorescein dextran. J Vis Exp. 2011 Apr 28;(50). pii: 2672. doi: 10.3791/2672. PubMed PMID: 21559005.
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2011-05-14 new articles we read this week

Saturday, May 14, 2011

Genomics/ next-generation sequencing

  1. Anders S, Huber W. Differential expression analysis for sequence count data.Genome Biol. 2010;11(10):R106. Epub 2010 Oct 27. PubMed PMID: 20979621.
  2. Gresham D, Boer VM, Caudy A, Ziv N, Brandt NJ, Storey JD, Botstein D. System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae. Genetics. 2011 Jan;187(1):299-317. Epub2010 Oct 13. PubMed PMID: 20944018; PubMed Central PMCID: PMC3018308.
  3. Inaki K, Hillmer AM, Ukil L, Yao F, Woo XY, Vardy LA, Zawack KF, Lee CW, Ariyaratne PN, Chan YS, Desai KV, Bergh J, Hall P, Putti TC, Ong WL, Shahab A, Cacheux-Rataboul V, Karuturi RK, Sung WK, Ruan X, Bourque G, Ruan Y, Liu ET. Transcriptional consequences of genomic structural aberrations in breast cancer.  Genome Res. 2011 May;21(5):676-87. Epub 2011 Apr 5. PubMed PMID: 21467264.

Gene mapping

  1. Chakravarti A. Genomic contributions to Mendelian disease. Genome Res. 2011 May;21(5):643-4. PubMed PMID: 21536725.
  2. Erlich Y, Edvardson S, Hodges E, Zenvirt S, Thekkat P, Shaag A, Dor T, Hannon GJ, Elpeleg O. Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Res. 2011 May;21(5):658-64. Epub 2011 Apr 12. PubMed PMID: 21487076.
  3. Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DC, Nazareth L, Bainbridge M, Dinh H, Jing C, Wheeler DA, McGuire AL, Zhang F, Stankiewicz P, Halperin JJ, Yang C, Gehman C, Guo D, Irikat RK, Tom W, Fantin NJ, Muzny DM, Gibbs RA. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med. 2010 Apr 1;362(13):1181-91. Epub 2010 Mar 10. PubMed PMID: 20220177.
  4. Musunuru K, Pirruccello JP, Do R, Peloso GM, Guiducci C, Sougnez C, Garimella KV, Fisher S, Abreu J, Barry AJ, Fennell T, Banks E, Ambrogio L, Cibulskis K, Kernytsky A, Gonzalez E, Rudzicz N, Engert JC, DePristo MA, Daly MJ, Cohen JC, Hobbs HH, Altshuler D, Schonfeld G, Gabriel SB, Yue P, Kathiresan S. Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. N Engl J Med. 2010 Dec 2;363(23):2220-7. Epub 2010 Oct 13. PubMed PMID: 20942659; PubMed Central PMCID: PMC3008575.

Systems Biology/ gene regulatory network

  1. Macneil L, Walhout AJ. Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res. 2011 Feb 4. [Epub ahead of print] PubMed PMID: 21324878.
  2. Hakim O, Sung MH, Voss TC, Splinter E, John S, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, de Laat W, Hager GL. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 2011 May;21(5):697-706. Epub 2011 Apr 6. PubMed PMID: 21471403.

Stem cells

  1. Focus on stem cells. Nat Cell Biol. 2011 May;13(5):489. PubMed PMID: 21540843.
  2. Ng HH, Surani MA. The transcriptional and signalling networks of pluripotency. Nat Cell Biol. 2011 May;13(5):490-6. PubMed PMID: 21540844.
  3. Wu SM, Hochedlinger K. Harnessing the potential of induced pluripotent stem cells for regenerative medicine. Nat Cell Biol. 2011 May;13(5):497-505. PubMed PMID: 21540845.
  4. Jones DL, Rando TA. Emerging models and paradigms for stem cell ageing. NatCell Biol. 2011 May;13(5):506-12. PubMed PMID: 21540846.
  5. Fuchs E, Horsley V. Ferreting out stem cells from their niches. Nat Cell Biol.2011 May;13(5):513-8. PubMed PMID: 21540847.
  6. Barrero MJ, Izpisua Belmonte JC. iPS cells forgive but do not forget. Nat CellBiol. 2011 May;13(5):523-5. PubMed PMID: 21540851.
  7. Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol. 2011 May;13(5):541-9. Epub 2011 Apr 17. PubMedPMID: 21499256.

Eye disease

  1. Shu X, Zeng Z, Gautier P, Lennon A, Gakovic M, Cheetham ME, Patton EE, Wright AF. Knockdown of the Zebrafish Ortholog of the Retinitis Pigmentosa 2 (RP2) Gene Results in Retinal Degeneration. Invest Ophthalmol Vis Sci. 2011 May5;52(6):2960-6. Print 2011. PubMed PMID: 21282572.
  2. Pinazo-Durán MD, Pons-Vázquez S, Gallego-Pinazo R, Galbis Estrada C, Zanón-Moreno V, Vila Bou V, Sanz Solana P. Thyroid hormone deficiency disrupts rat eye neurodevelopment. Brain Res. 2011 Apr 9. [Epub ahead of print] PubMedPMID: 21529787.

Zebrafish

  1. Nava SS, An S, Hamil T. Visual detection of UV cues by adult zebrafish (Danio rerio). J Vis. 2011 May 4;11(6). pii: 2. doi: 10.1167/11.6.2. Print 2011. PubMed PMID: 21543523.
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Common Faults in Human Thought

Thursday, May 12, 2011

I just come across these two excellent articles that point out many wrong ideas that we can have in life. Interestingly, I find most are also our attitude towards scientific research. Try not to do that.

Top 10 Common Faults in Human Thought

10 More Common Faults in Human Thought

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