Leung Lab Blog

Retinal Development

1. Salbreux G, Barthel LK, Raymond PA, Lubensky DK. Coupling mechanical deformations and planar cell polarity to create regular patterns in the zebrafish retina. PLoS Comput Biol. 2012 Aug;8(8):e1002618. Epub 2012 Aug 23. PubMed PMID: 22936893; PubMed Central PMCID: PMC3426565.
2. Chen M, Wang K, Lin B. Development and degeneration of cone bipolar cells are  independent of cone photoreceptors in a mouse model of retinitis pigmentosa. PLoS One. 2012;7(8):e44036. Epub 2012 Aug 31. PubMed PMID: 22952865.
3. He J, Zhang G, Almeida AD, Cayouette M, Simons BD, Harris WA. How variable clones build an invariant retina. Neuron. 2012 Sep 6;75(5):786-98. PubMed PMID: 22958820.
   • Commentary: Chen Z, Li X, Desplan C. Deterministic or stochastic choices in retinal neuron specification. Neuron. 2012 Sep 6;75(5):739-42. PubMed PMID: 22958814.

Eye disease

1. Murakami Y, Matsumoto H, Roh M, Suzuki J, Hisatomi T, Ikeda Y, Miller JW, Vavvas DG. Receptor interacting protein kinase mediates necrotic cone but not rod cell death in a mouse model of inherited degeneration. Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14598-603. Epub 2012 Aug 20. PubMed PMID: 22908283.
2. Kohl S, Coppieters F, Meire F, Schaich S, Roosing S, Brennenstuhl C, Bolz S, van Genderen MM, Riemslag FC; the European Retinal Disease Consortium, Lukowski R, den Hollander AI, Cremers FP, De Baere E, Hoyng CB, Wissinger B. A Nonsense Mutation in PDE6H Causes Autosomal-Recessive Incomplete Achromatopsia. Am J Hum Genet. 2012 Sep 7;91(3):527-532. Epub 2012 Aug 16. PubMed PMID: 22901948.
3. Manzini MC, Tambunan DE, Hill RS, Yu TW, Maynard TM, Heinzen EL, Shianna KV, Stevens CR, Partlow JN, Barry BJ, Rodriguez J, Gupta VA, Al-Qudah AK, Eyaid WM, Friedman JM, Salih MA, Clark R, Moroni I, Mora M, Beggs AH, Gabriel SB, Walsh CA. Exome Sequencing and Functional Validation in Zebrafish Identify GTDC2 Mutations as a Cause of Walker-Warburg Syndrome. Am J Hum Genet. 2012 Sep 7;91(3):541-7. PubMed PMID: 22958903.

Genetics

1. Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14508-13. Epub 2012 Aug 1. PubMed PMID: 22853953.
2. Papers related to ENCODE
   • Genome Research
   1. Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res. 2012 Sep;22(9):1748-59. PubMed PMID: 22955986.
   2. Stamatoyannopoulos JA. What does our genome encode? Genome Res. 2012 Sep;22(9):1602-11. PubMed PMID: 22955972.
   3. Frazer KA. Decoding the human genome. Genome Res. 2012 Sep;22(9):1599-601. PubMed PMID: 22955971.
   1. Nature (with links to Genome Research papers)
      1. Skipper M, Dhand R, Campbell P. Presenting ENCODE. Nature. 2012 Sep6;489(7414):45. doi: 10.1038/489045a. PubMed PMID: 22955612.
      2. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. Genomics: ENCODE explained. Nature. 2012 Sep 6;489(7414):52-5. doi: 10.1038/489052a. PubMed PMID: 22955614.
      3. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome.Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. PubMed PMID: 22955616.
      4. Thurman RE, et al., The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232. PubMed PMID: 22955617.
      5. Neph S, et al., An expansive human regulatory lexicon encoded in transcription factor footprints. Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212. PubMed PMID:22955618.
      6. Gerstein MB, et al., Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245. PubMed PMID: 22955619.
      7. Djebali S, et al., Landscape of transcription in human cells. Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233. PubMed PMID: 22955620.

Oxidative Stress

1. Mukaigasa K, Nguyen LT, Li L, Nakajima H, Yamamoto M, Kobayashi M. Genetic Evidence of an Evolutionarily Conserved Role for Nrf2 in the Protection against Oxidative Stress. Mol Cell Biol. 2012 Sep 4. [Epub ahead of print] PubMed PMID: 22949501.

Stem cells

1. Sancho-Martinez I, Baek SH, Izpisua Belmonte JC. Lineage conversion methodologies meet the reprogramming toolbox. Nat Cell Biol. 2012 Sep 3;14(9):892-9. doi: 10.1038/ncb2567. PubMed PMID: 22945254.
2. Loh KM, Lim B. Epigenetics: Actors in the cell reprogramming drama. Nature. 2012 Aug 30;488(7413):599-600. doi: 10.1038/488599a. PubMed PMID: 22932382.

Medicine

1. Asch DA, Volpp KG. What business are we in? The emergence of health as the business of health care. N Engl J Med. 2012 Sep 6;367(10):888-9. Epub 2012 Aug 30. PubMed PMID: 22931228.
2. Fani Marvasti F, Stafford RS. From sick care to health care–reengineering prevention into the U.S. system. N Engl J Med. 2012 Sep 6;367(10):889-91. PubMed PMID: 22931257.
3. Barnes KA, Kroening-Roche JC, Comfort BW. The developing vision of primary care. N Engl J Med. 2012 Sep 6;367(10):891-3. PubMed PMID: 22931258.
4. Baker M. Doctors back circumcision. Nature. 2012 Aug 30;488(7413):568. doi: 10.1038/488568a. PubMed PMID: 22932355.
5. Nature Outlook HPV
   1. Crow JM. HPV: The global burden. Nature. 2012 Aug 30;488(7413):S2-3. doi: 10.1038/488S2a. PubMed PMID: 22932437.

Nutrition

1. Maxmen A. Calorie restriction falters in the long run. Nature. 2012 Aug 30;488(7413):569. doi: 10.1038/488569a. PubMed PMID: 22932356.

Ethics, Social and Legal Issues

1. Greenland P, Fontanarosa PB. Ending honorary authorship. Science. 2012 Aug 31;337(6098):1019. PubMed PMID: 22936744.

Stem cells

1. Chen J, Pei D. Reprogramming in suspension. Nat Methods. 2012 Apr 27;9(5):449-51. doi: 10.1038/nmeth.1989. PubMed PMID: 22543375.

Genomics

1. Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; The 1000 Genomes Project Consortium. The 1000 Genomes Project: data management and community access. Nat Methods. 2012 Apr 27;9(5):459-462. doi: 10.1038/nmeth.1974. PubMed PMID: 22543379; PubMed Central PMCID: PMC3340611.

Eye disease

1. Pearson RA, Barber AC, Rizzi M, Hippert C, Xue T, West EL, Duran Y, Smith AJ, Chuang JZ, Azam SA, Luhmann UF, Benucci A, Sung CH, Bainbridge JW, Carandini M,Yau KW, Sowden JC, Ali RR. Restoration of vision after transplantation of photoreceptors. Nature. 2012 May 3;485(7396):99-103. PubMed PMID: 22522934.

Genetic disease

1. Whalley K. Neurodevelopmental disorders: Reversing the fragile X phenotype. Nat Rev Neurosci. 2012 May 3. doi: 10.1038/nrn3255. [Epub ahead of print] PubMed PMID: 22551664.

Systems biology

1. Zhu J, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, Tu Z, Brem RB, Bumgarner RE, Schadt EE. Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation. PLoS Biol. 2012 Apr;10(4):e1001301. Epub 2012 Apr 3. PubMed PMID: 22509135; PubMed Central PMCID: PMC3317911.

Medicine

1. Freedman ND, Park Y, Abnet CC, Hollenbeck AR, Sinha R. Association of coffee drinking with total and cause-specific mortality. N Engl J Med. 2012 May 17;366(20):1891-904. PubMed PMID: 22591295.
• The more the coffee you drink, the longer you live!
• News coverage, from Huffington Post: “Coffee Drinkers Live Longer, Claim Scientists (Although They’re Not Quite Sure Why…) “

Neuroimaging/ Connectomics

1. Wedeen VJ, Rosene DL, Wang R, Dai G, Mortazavi F, Hagmann P, Kaas JH, Tseng WY. The geometric structure of the brain fiber pathways. Science. 2012 Mar 30;335(6076):1628-34. PubMed PMID: 22461612.

Neuroscience

1. Rogulja D, Young MW. Control of sleep by cyclin A and its regulator. Science. 2012 Mar 30;335(6076):1617-21. PubMed PMID: 22461610.
2. Koch C. Newsmaker interview: Christof Koch. A vision of how mouse vision can reveal consciousness’ secrets. Interview by Yudhijit Bhattacharjee. Science. 2012 Mar 23;335(6075):1426-7. PubMed PMID: 22442452.
3. Morris RG, Takeuchi T. Neuroscience. The imaginary mind of a mouse. Science. 2012 Mar 23;335(6075):1455-6. PubMed PMID: 22442473.
4. Bardin J. Neuroscience: Making connections. Nature. 2012 Mar 21;483(7390):394-6. doi: 10.1038/483394a. PubMed PMID: 22437591.

Behaviour

1. Shohat-Ophir G, Kaun KR, Azanchi R, Heberlein U. Sexual deprivation increases ethanol intake in Drosophila. Science. 2012 Mar 16;335(6074):1351-5. PubMed PMID:22422983.
   
• Commentary: Zars T. Physiology. She said no, pass me a beer. Science. 2012 Mar 16;335(6074):1309-10. PubMed PMID: 22422968.

Philosophy of Science

1. Bodemer N, Ruggeri A. Finding a good research question, in theory. Science. 2012 Mar 23;335(6075):1439. PubMed PMID: 22442459.

Ethics, Social and Legel Issues

1. Must try harder. Nature. 2012 Mar 28;483(7391):509. doi: 10.1038/483509a.PubMed PMID: 22460859.
2. Begley CG, Ellis LM. Drug development: Raise standards for preclinical cancer research. Nature. 2012 Mar 28;483(7391):531-3. doi: 10.1038/483531a. PubMed PMID: 22460880.
3. Incidental benefits. Nature. 2012 Mar 21;483(7390):373. doi: 10.1038/483373a. PubMed PMID: 22437569.
4. Hayden EC. DNA donor rights affirmed. Nature. 2012 Mar 21;483(7390):387. doi: 10.1038/483387a. PubMed PMID: 22437587.

Systems Biology

1. Weinstein JN. Drug discovery: Cell lines battle cancer. Nature. 2012 Mar 28;483(7391):544-5. doi: 10.1038/483544a. PubMed PMID: 22460893.
2. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P Jr, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012 Mar 28;483(7391):603-7. doi: 10.1038/nature11003. PubMed PMID: 22460905.
3. Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D, Chen L, Milano RJ, Bignell GR, Tam AT, Davies H, Stevenson JA, Barthorpe S, Lutz SR, Kogera F, Lawrence K, McLaren-Douglas A, Mitropoulos X, Mironenko T, Thi H, Richardson L, Zhou W, Jewitt F, Zhang T, O’Brien P, Boisvert JL, Price S, Hur W, Yang W, Deng X, Butler A, Choi HG, Chang JW, Baselga J, Stamenkovic I, Engelman JA, Sharma SV, Delattre O, Saez-Rodriguez J, Gray NS, Settleman J, Futreal PA, Haber DA, Stratton MR, Ramaswamy S, McDermott U, Benes CH. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature. 2012 Mar 28;483(7391):570-5. doi: 10.1038/nature11005. PubMed PMID: 22460902.
4. Pujadas E, Feinberg AP. Regulated noise in the epigenetic landscape of development and disease. Cell. 2012 Mar 16;148(6):1123-31. PubMed PMID: 22424224.

Eye disease

1. Zhang J, Benavente CA, McEvoy J, Flores-Otero J, Ding L, Chen X, Ulyanov A, Wu G, Wilson M, Wang J, Brennan R, Rusch M, Manning AL, Ma J, Easton J, Shurtleff S, Mullighan C, Pounds S, Mukatira S, Gupta P, Neale G, Zhao D, Lu C, Fulton RS, Fulton LL, Hong X, Dooling DJ, Ochoa K, Naeve C, Dyson NJ, Mardis ER, Bahrami A, Ellison D, Wilson RK, Downing JR, Dyer MA. A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature. 2012 Jan 11;481(7381):329-34. doi: 10.1038/nature10733. PubMed PMID: 22237022; PubMed Central PMCID: PMC3289956.

Medicine

1. Vaidyanathan G. Redefining clinical trials: the age of personalized medicine.  Cell. 2012 Mar 16;148(6):1079-80. PubMed PMID: 22424218.

Stem cells

1. Cherry AB, Daley GQ. Reprogramming Cellular Identity for Regenerative Medicine. Cell. 2012 Mar 16;148(6):1110-1122. Epub 2012 Mar 15. PubMed PMID: 22424223.

Career

1. Perkel JM Ph D. Run your lab on dollars a day! Biotechniques. 2012 Mar;52(3):141-143. PubMed PMID: 22401545.
2. Blow N Ph D. Reflections on the modern lab. Biotechniques. 2012 Mar;52(3):145-147. PubMed PMID: 22401546.

Delta-Notch

1. Luo H, Jin K, Xie Z, Qiu F, Li S, Zou M, Cai L, Hozumi K, Shima DT, Xiang M. Forkhead box N4 (Foxn4) activates Dll4-Notch signaling to suppress photoreceptor cell fates of early retinal progenitors. Proc Natl Acad Sci U S A. 2012 Feb 8. [Epub ahead of print] PubMed PMID: 22323600.

Stem Cells

1. Robinton DA, Daley GQ. The promise of induced pluripotent stem cells in research and therapy. Nature. 2012 Jan 18;481(7381):295-305. doi: 10.1038/nature10761. PubMed PMID: 22258608.

Imaging

1. Miller EW, Lin JY, Frady EP, Steinbach PA, Kristan WB Jr, Tsien RY. Optically monitoring voltage in neurons by photo-induced electron transfer through molecular wires. Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2114-9. Epub 2012 Jan 24. PubMed PMID: 22308458.

Eye Disease

1. Beltran WA, Cideciyan AV, Lewin AS, Iwabe S, Khanna H, Sumaroka A, Chiodo VA, Fajardo DS, Román AJ, Deng WT, Swider M, Alemán TS, Boye SL, Genini S, Swaroop A, Hauswirth WW, Jacobson SG, Aguirre GD. Gene therapy rescues photoreceptor blindness in dogs and paves the way for treating human X-linked retinitis pigmentosa. Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2132-7. Epub 2012 Jan 23. PubMed PMID: 22308428.

Genomics

1. Kaiser J. Cell biology. Donation spurs a cell observatory–and bigger plans. Science. 2012 Feb 3;335(6068):514. PubMed PMID: 22301289.
2. Normile D. Genomics. China’s sequencing powerhouse comes of age. Science. 2012 Feb 3;335(6068):516-9. PubMed PMID: 22301291.
3. Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science. 2012 Feb 3;335(6068):552-7. Epub 2011 Dec 22. PubMed PMID: 22194413.
4. Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science. 2012 Feb 3;335(6068):587-90. PubMed PMID: 22301318.

Medical Research

*These two articles point out the problems of using animal models for research if the goal is to extract translational values and how mouse model, the gold standard for disease research, can actually be a poor reference standard because of the ways we want to standardize the biological tool for testing.

1. Lynch VJ. Use with caution: developmental systems divergence and potential pitfalls of animal models. Yale J Biol Med. 2009 Jun;82(2):53-66. Review. PubMed PMID: 19562005; PubMed Central PMCID: PMC2701150.
2. Martin B, Ji S, Maudsley S, Mattson MP. “Control” laboratory rodents are metabolically morbid: why it matters. Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6127-33. Epub 2010 Mar 1. PubMed PMID: 20194732; PubMed Central PMCID: PMC2852022.

Genomics

1. Tariq MA, Kim HJ, Jejelowo O, Pourmand N. Whole-transcriptome RNAseq analysis from minute amount of total RNA. Nucleic Acids Res. 2011 Oct 1;39(18):e120. Epub 2011 Jul 6. PubMed PMID: 21737426; PubMed Central PMCID: PMC3185437.
2. Compeau PE, Pevzner PA, Tesler G. How to apply de Bruijn graphs to genome assembly. Nat Biotechnol. 2011 Nov 8;29(11):987-91. doi: 10.1038/nbt.2023. PubMed PMID: 22068540.
3. Ala-Korpela M, Kangas AJ, Inouye M. Genome-wide association studies and systems biology: together at last. Trends Genet. 2011 Oct 20. [Epub ahead of print] PubMed PMID: 22018481.

Regeneration

1. Kroehne V, Freudenreich D, Hans S, Kaslin J, Brand M. Regeneration of the adult zebrafish brain from neurogenic radial glia-type progenitors. Development.  2011 Nov;138(22):4831-41. Epub 2011 Oct 17. PubMed PMID: 22007133.

Disease/Evolution

1. Cusack BP, Arndt PF, Duret L, Roest Crollius H. Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes. PLoS Genet. 2011 Oct;7(10):e1002276. Epub 2011 Oct 13. PubMed PMID: 22022272; PubMed Central PMCID: PMC3192821.
• Commentary: Wilke CO. Transcriptional robustness complements nonsense-mediated decay in humans. PLoS Genet. 2011 Oct;7(10):e1002296. Epub 2011 Oct 13. PubMed PMID:22022274; PubMed Central PMCID: PMC3192817.
2. Shelly T, McInnis D. Road test for genetically modified mosquitoes. Nat Biotechnol. 2011 Nov 8;29(11):984-5. doi: 10.1038/nbt.2025. PubMed PMID: 22068534.

Eye Disease

1. Johnson LV, Forest DL, Banna CD, Radeke CM, Maloney MA, Hu J, Spencer CN, Walker AM, Tsie MS, Bok D, Radeke MJ, Anderson DH. Cell culture model that mimics drusen formation and triggers complement activation associated with age-related macular degeneration. Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18277-82. Epub 2011 Oct 3. PubMed PMID: 21969589.
2. Jiang L, Zhang H, Dizhoor AM, Boye SE, Hauswirth WW, Frederick JM, Baehr W. Long-term RNA interference gene therapy in a dominant retinitis pigmentosa mouse model. Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18476-81. Epub 2011 Oct 31. PubMed PMID: 22042849.

Evolution

1. Liu R, Ochman H. Stepwise formation of the bacterial flagellar system. Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7116-21. Epub 2007 Apr 16. Erratum in: Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11507. PubMed PMID: 17438286; PubMed Central PMCID: PMC1852327.

Systems biology

1. Navlakha S, Bar-Joseph Z. Algorithms in nature: the convergence of systems biology and computational thinking. Mol Syst Biol. 2011 Nov 8;7:546. doi: 10.1038/msb.2011.78. PubMed PMID: 22068329.
2. Ala-Korpela M, Kangas AJ, Inouye M. Genome-wide association studies and systems biology: together at last. Trends Genet. 2011 Oct 20. [Epub ahead of print] PubMed PMID: 22018481.
3. Cheong R, Rhee A, Wang CJ, Nemenman I, Levchenko A. Information transduction capacity of noisy biochemical signaling networks. Science. 2011 Oct 21;334(6054):354-8. Epub 2011 Sep 15. PubMed PMID: 21921160.

Biotech business

1. Francisco M. Third-quarter biotech job picture. Nat Biotechnol. 2011 Nov 8;29(11):1052. doi: 10.1038/nbt.2037. PubMed PMID: 22068542.