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How to publish like a pro

Tuesday, October 19, 2010

There is an interesting article, “Publish like a pro“, in this issue of Nature that talks about how to write papers and plan your project efficiently. Several of us who are writing a manuscript of some sort are already using several tricks, including having a paper plan right at the beginning and having multiple revisions. It does not hurt to read the article and refresh your memory.

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2010-10-16 Articles we read this week

Saturday, October 16, 2010

Delta-Notch

  1. Cohen M, Georgiou M, Stevenson NL, Miodownik M, Baum B. Dynamic filopodia transmit intermittent Delta-Notch signaling to drive pattern refinement during lateral inhibition. Dev Cell. 2010 Jul 20;19(1):78-89. PubMed PMID: 20643352.

Medicine and ethics

  1. Yurkiewicz S.  The Prospects for Personalized Medicine. Hastings Cent Rep. 2010; 40:14-16.
  2. Fleck LM. Personalized Medicine’s Ragged Edge. 2010; 40:16-18.
  3. Gilbert S. Personalized Cancer Care in an Age of Anxiety. 2010; 40: 18-21.
  4. Tillinghast GW. Microarrays in the clinic. Nat Biotechnol. 2010.Aug;28(8):810-2. PubMed PMID: 20697405.
  5. Shi L, MAQC Consortium. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based  predictive models. Nat Biotechnol. 2010 Aug;28(8):827-38. Epub 2010 Jul 30. PubMed PMID: 20676074.

Systems biology

  1. Kirouac DC, Ito C, Csaszar E, Roch A, Yu M, Sykes EA, Bader GD, Zandstra PW. Dynamic interaction networks in a hierarchically organized tissue. Mol Syst Biol. 2010 Oct 5;6:417. PubMed PMID: 20924352.
  2. Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, Hasty J. A fast, robust and tunable synthetic gene oscillator. Nature. 2008 Nov 27;456(7221):516-9. Epub 2008 Oct 29. PubMed PMID: 18971928.
  3. Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M. A tunable synthetic mammalian oscillator. Nature. 2009 Jan 15;457(7227):309-12. PubMed PMID: 19148099.
  4. Cağatay T, Turcotte M, Elowitz MB, Garcia-Ojalvo J, Süel GM. Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell. 2009 Oct 30;139(3):512-22. Epub 2009 Oct 22. PubMed PMID:19853288.
  5. Bollenbach T, Kishony R. Quiet gene circuit more fragile than its noisy peer. Cell. 2009 Oct 30;139(3):460-1. PubMed PMID: 19879833.
  6. Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, Ferrell JE Jr. Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science. 2008 Jul 4;321(5885):126-9. PubMed PMID: 18599789; PubMed Central PMCID: PMC2728800.
  7. Novák B, Tyson JJ. Design principles of biochemical oscillators. Nat Rev Mol Cell Biol. 2008 Dec;9(12):981-91. Epub 2008 Oct 30. Review. PubMed PMID: 18971947; PubMed Central PMCID: PMC2796343.

Imaging

  1. Swoger J, Muzzopappa M, López-Schier H, Sharpe J. 4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies. J Biophotonics. 2010 Oct 5. [Epub ahead of print] PubMed PMID: 20925108.

Zebrafish

  1. Kim J, Wu Q, Zhang Y, Wiens KM, Huang Y, Rubin N, Shimada H, Handin RI, Chao MY, Tuan TL, Starnes VA, Lien CL. PDGF signaling is required for epicardial function and blood vessel formation in regenerating zebrafish hearts. Proc Natl Acad Sci U S A. 2010 Oct 5;107(40):17206-10. Epub 2010 Sep 21. PubMed PMID: 20858732.
  2. Dlugos CA, Brown SJ, Rabin RA. Gender differences in ethanol-induced behavioral sensitivity in zebrafish. Alcohol. 2010 Sep 28. [Epub ahead of print]PubMed PMID: 20880661.

Development

  1. Fujimoto T, Nishimura T, Goto-Kazeto R, Kawakami Y, Yamaha E, Arai K. Sexual dimorphism of gonadal structure and gene expression in germ cell-deficient loach, a teleost fish. Proc Natl Acad Sci U S A. 2010 Oct 5;107(40):17211-6. Epub 2010 Sep 20. PubMed PMID: 20855617.

Stem cells

  1. Moretti A, Bellin M, Welling A, Jung CB, Lam JT, Bott-Flügel L, Dorn T, Goedel A, Höhnke C, Hofmann F, Seyfarth M, Sinnecker D, Schömig A, Laugwitz KL.Patient-Specific Induced Pluripotent Stem-Cell Models for Long-QT Syndrome. N Engl J Med. 2010 Jul 21. [Epub ahead of print] PubMed PMID: 20660394.

Vision

  1. Demb JB, Brainard DH. Vision: Neurons show their true colours. Nature. 2010 Oct 7;467(7316):670-1. PubMed PMID: 20930837.
  2. Field GD, Gauthier JL, Sher A, Greschner M, Machado TA, Jepson LH, Shlens J, Gunning DE, Mathieson K, Dabrowski W, Paninski L, Litke AM, Chichilnisky EJ.Functional connectivity in the retina at the resolution of photoreceptors. Nature. 2010 Oct 7;467(7316):673-7. PubMed PMID: 20930838; PubMed Central PMCID: PMC2953734.
  3. Satoh AK, Xia H, Yan L, Liu CH, Hardie RC, Ready DF. Arrestin translocation is stoichiometric to rhodopsin isomerization and accelerated by phototransduction in Drosophila photoreceptors. Neuron. 2010 Sep 23;67(6):997-1008. PubMed PMID: 20869596; PubMed Central PMCID: PMC2946946.

General

  1. Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R. Long noncoding RNAs with enhancer-like function in human cells. Cell. 2010 Oct 1;143(1):46-58. PubMed PMID: 20887892.
  2. Collins F. Scientists need a shorter path to research freedom. Nature. 2010 Oct 7;467(7316):635. PubMed PMID: 20930798.
  3. Ledford H. Garage biotech: Life hackers. Nature. 2010 Oct 7;467(7316):650-2. PubMed PMID: 20930820.
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Peter Hollenbeck’s interview in Current Biology

Thursday, October 14, 2010

See our neighbour’s interview here.

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Lasker Awards 2010

Tuesday, October 12, 2010

I am preparing these reading materials for my class and strongly believe that you would be interested in and benefited by reading these articles.

These are a series of articles published in this issue of Nature Medicine about this year’s Lasker Awards, the most prestigious award for biomedical research in this country.

There is an introductory article written by the Chairman of the Awards Jury, Joseph Goldstein, on the importance of the findings and a great summary of wisdom on doing great research; this is followed by the articles written by the recipients that give a personal account on the discovery process. While there is no guarantee that one will succeed by following their recipe, but there is always a lesson to learn from these good scientists. In particular, how they persisted and determined to look for an answer over many years.

Enjoy!
Fai
—

  1. Goldstein JL. How to win a Lasker? Take a close look at Bathers and Bulls. Nat Med. 2010 Oct;16(10):1091-6. PubMed PMID: 20930751.
  2. Coleman DL. A historical perspective on leptin. Nat Med. 2010Oct;16(10):1097-9. PubMed PMID: 20930752.
  3. Friedman JM. A tale of two hormones. Nat Med. 2010 Oct;16(10):1100-6. PubMedPMID: 20930753.
  4. Ferrara N. Vascular endothelial growth factor and age-related maculardegeneration: from basic science to therapy. Nat Med. 2010 Oct;16(10):1107-11.PubMed PMID: 20930754.
  5. Weatherall D. Thalassemia: the long road from the bedside through thelaboratory to the community. Nat Med. 2010 Oct;16(10):1112-5. PubMed PMID:20930755.
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2010-10-09 New articles we read this week

Saturday, October 9, 2010

Behaviour

  1. Li L. Zebrafish mutants: behavioral genetic studies of visual system defects. Dev Dyn. 2001 Aug;221(4):365-72. Review. PubMed PMID: 11500973.
  2. Orger MB, Gahtan E, Muto A, Page-McCaw P, Smear MC, Baier H. Behavioral screening assays in zebrafish. Methods Cell Biol. 2004;77:53-68. PubMed PMID: 15602905.

Cancer

  1. Feitsma H, Cuppen E. Zebrafish as a cancer model. Mol Cancer Res. 2008 May;6(5):685-94. Review. PubMed PMID: 18505914.

Gene expression

  1. Ohlsson R. Gene expression: The coherent Mediator. Nature. 2010 Sep 23;467(7314):406-7. PubMed PMID: 20864988.

Patterning

  1. Kondo S, Miura T. Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation. Science. 2010 Sep 24; 329; 1616-1620.

Evolution

  1. Burke MK, Dunham JP, Shahrestani P, Thornton KR, Rose MR, Long AD. Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature. 2010 Sep 30;467(7315):587-90. Epub 2010 Sep 15. PubMed PMID: 20844486.

Medicine

  1. Cooke M. Science for Physicians. Science. 2010 Sep 24; 329; 1573.

Gene regulatory network & Systems biology

  1. Acar M, et al., A General Mechanism for Network-Dosage Compensation in Gene Circuits. Science. 2010 Sep 24; 329; 1656-1660.
  2. Young NM, Chong HJ, Hu D, Hallgrímsson B, Marcucio RS. Quantitative analyses link modulation of sonic hedgehog signaling to continuous variation in facial growth and shape. Development. 2010 Oct;137(20):3405-9. Epub 2010 Sep 8. PubMed PMID: 20826528.
  3. Toettcher JE, Mock C, Batchelor E, Loewer A, Lahav G. A synthetic-natural hybrid oscillator in human cells. Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):17047-52. Epub 2010 Sep 13. PubMed PMID: 20837528.
  4. Bandyopadhyay et al., A human MAP kinase interactome. Nat. Method. 2010; 7:801-805.
  5. Neems D, Kosak ST. Turning down the volume on transcriptional noise. Nat Cell Biol. 2010 Oct;12(10):929-31. PubMed PMID: 20885421.
  6. Giacomantonio CE, Goodhill GJ. A Boolean model of the gene regulatory network underlying Mammalian cortical area development. PLoS Comput Biol. 2010 Sep 16;6(9). pii: e1000936. PubMed PMID: 20862356; PubMed Central PMCID: PMC2940723.
  7. Stormo GD, Zhao Y. Determining the specificity of protein-DNA interactions. Nat Rev Genet. 2010 Sep 28. [Epub ahead of print] PubMed PMID: 20877328.
  8. Alon U. Network motifs: theory and experimental approaches. Nat Rev Genet. 2007 Jun;8(6):450-61. Review. PubMed PMID: 17510665.

Retina

  1. Allison WT, Barthel LK, Skebo KM, Takechi M, Kawamura S, Raymond PA. Ontogeny of cone photoreceptor mosaics in zebrafish. J Comp Neurol. 2010 Oct 15;518(20):4182-95. PubMed PMID: 20878782.

Delta-Notch signal transduction

  1. Matsuda M, Chitnis AB. Atoh1a expression must be restricted by Notch signaling for effective morphogenesis of the posterior lateral line primordium in zebrafish. Development. 2010 Oct;137(20):3477-87. PubMed PMID: 20876657.
  2. Milán M, Cohen SM.  Notch signaling: filopodia dynamics confer robustness. Curr Biol. 2010 Sep 28;20(18):R802-4. PMID: 20869605 [PubMed – in process]
  3. Del Debbio CB, Balasubramanian S, Parameswaran S, Chaudhuri A, Qiu F, Ahmad I. Notch and Wnt signaling mediated rod photoreceptor regeneration by Müller cells in adult mammalian retina. PLoS One. 2010 Aug 26;5(8):e12425. PubMed PMID: 20865053; PubMed Central PMCID: PMC2928741.

Research funding

  1. Powell K. Research funding: Making the cut. Nature. 2010 Sep 23;467(7314):383-5. PubMed PMID: 20864969.

Research ethics

  1. Cyranoski D. Brawl in Beijing. Nature. 2010 Sep 30;467(7315):511. PubMed PMID: 20881985.
  2. Maher B. Research integrity: Sabotage! Nature. 2010 Sep 30;467(7315):516-8. PubMed PMID: 20881988.
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The Nobel Prize in Chemistry 2010

Thursday, October 7, 2010

The Nobel Prize in Chemistry 2010 was awarded to Richard F. Heck, Ei-ichi Negishi, Akira Suzuki “for palladium-catalyzed cross couplings in organic synthesis”. And Ei-ichi Negishi is in the Department of Chemistry at our institute, i.e Purdue!

Richard F. Heck. Photo: University of Delaware, USA

Ei-ichi Negishi. Photo: Purdue University, USA

Akira Suzuki. Photo: Hokkaido University, Japan

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The Nobel Prize in Physiology or Medicine 2010

Monday, October 4, 2010

The Nobel Prize in Physiology or Medicine 2010 was awarded to Robert G. Edwards “for the development of in vitro fertilization”.

Photo: Sheikh Hamdan Bin Rashid Al Maktoum Award for Medical Sciences

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2010-10-02 new articles we read this week

Saturday, October 2, 2010

Systems biology, gene regulatory network & development

  1. Huang S, Eichler G, Bar-Yam Y, Ingber DE. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys Rev Lett. 2005 Apr 1;94(12):128701. Epub 2005 Apr 1. PubMed PMID: 15903968.
  2. Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature. 2008 May 22;453(7194):544-7. PubMed PMID: 18497826.
  3. Bar-Yam Y, Harmon D, de Bivort B. Systems biology. Attractors and democratic dynamics. Science. 2009 Feb 20;323(5917):1016-7. PubMed PMID: 19229023.
  4. Brock A, Chang H, Huang S. Non-genetic heterogeneity–a mutation-independent driving force for the somatic evolution of tumours. Nat Rev Genet. 2009 May;10(5):336-42. PubMed PMID: 19337290.

Delta-Notch & cancer

  1. Pancewicz J, Taylor JM, Datta A, Baydoun HH, Waldmann TA, Hermine O, Nicot C. Notch signaling contributes to proliferation and tumor formation of human T-cell leukemia virus type 1-associated adult T-cell leukemia. Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16619-24. Epub 2010 Sep 7. PubMed PMID: 20823234.
  2. Schouwey K, Aydin IT, Radtke F, Beermann F. RBP-Jκ-dependent Notch signaling enhances retinal pigment epithelial cell proliferation in transgenic mice. Oncogene. 2010 Sep 20. [Epub ahead of print] PubMed PMID: 20856205.

Neuroscience

  1. Portales-Casamar E, Swanson DJ, Liu L, Leeuw CN, Banks KG, Ho Sui SJ, FultonDL, Ali J, Amirabbasi M, Arenillas DJ, Babyak N, Black SF, Bonaguro RJ, Brauer E, Candido TR, Castellarin M, Chen J, Chen Y, Cheng JC, Chopra V, Docking TR, Dreolini L, D’Souza CA, Flynn EK, Glenn R, Hatakka K, Hearty TG, Imanian B, Jiang S, Khorasan-Zadeh S, Komljenovic I, Laprise S, Liao NY, Lim JS, Lithwick S, Liu F, Liu J, Lu M, McConechy M, McLeod AJ, Milisavljevic M, Mis J, O’Connor K, Palma B, Palmquist DL, Schmouth JF, Swanson MI, Tam B, Ticoll A, Turner JL, Varhol R, Vermeulen J, Watkins RF, Wilson G, Wong BK, Wong SH, Wong TY, Yang GS, Ypsilanti AR, Jones SJ, Holt RA, Goldowitz D, Wasserman WW, Simpson EM. A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16589-94. Epub 2010 Aug 31. PubMed PMID: 20807748.

Genomics

  1. Listgarten J, Kadie C, Schadt EE, Heckerman D. Correction for hidden confounders in the genetic analysis of gene expression. Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16465-70. Epub 2010 Sep 1. PubMed PMID: 20810919.
  2. Hohm T, Zitzler E. A hierarchical approach to model parameter optimization for developmental systems. Biosystems. 2010 Sep 21. [Epub ahead of print] PubMed PMID: 20851739.
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The 2010 Ig Nobel Prize

Friday, October 1, 2010

Have your ever seen a Nobel laureate putting a bra on his face? Well… you can see three.

It is the time of the year for Ig Nobel Prize again….. 😉

Charles Krupa / AP

Nobel laureates Roy Glauber (Physics, 2005), Sheldon Glashow (Physics, 1979) and James Muller (Peace, 1985) demonstrate how bra cups that can be converted to emergency gas masks during the 2010 Ig Nobel Prize ceremony at Harvard. The bra-mask invention won one of the not-completely-serious scientific prizes in 2009. Charles Krupa / AP

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2010-9-29

Wednesday, September 29, 2010

John F. Rawlsa, Eve M. Mellgrena and Stephen L. Johnson1, a. How the Zebrafish Gets Its Stripes. Developmental Biology
Volume 240, Issue 2, 15 December 2001, Pages 301-314.

Kelsh RN, Schmid B, Eisen JS.  Genetic Analysis of Melanophore Development in Zebrafish Embryos. Developmental Biology
Volume 225, Issue 2, 15 September 2000, Pages 277-293.

Lee Y, Nachtrab G, Klinsawat PW, Hami D, Poss KD.   Ras controls menalocyte expansion during zebrafish fin stripe regeneration. Dis Model Mech. 2010 Jul-Aug;3(7-8):496-503. Epub 2010 May 18.

Johnson SL, Rawls JF.  Zebrafish kit mutation reveals primary and secondary regulation of melanocyte development during fin stripe regeneration. Development 127, 3715-3724 (2000).

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