Leung Lab Blog

Genetics

1. Zu Y, Tong X, Wang Z, Liu D, Pan R, Li Z, Hu Y, Luo Z, Huang P, Wu Q, Zhu Z, Zhang B, Lin S. TALEN-mediated precise genome modification by homologous recombination in zebrafish. Nat Methods. 2013 Feb 24. doi: 10.1038/nmeth.2374. [Epub ahead of print] PubMed PMID: 23435258.
2. Chang N, Sun C, Gao L, Zhu D, Xu X, Zhu X, Xiong JW, Xi JJ. Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos. Cell Res. 2013 Apr;23(4):465-72. doi: 10.1038/cr.2013.45. Epub 2013 Mar 26. PubMed PMID: 23528705; PubMed Central PMCID: PMC3616424.

Retinal development

1. Chiodini F, Matter-Sadzinski L, Rodrigues T, Skowronska-Krawczyk D, Brodier L, Schaad O, Bauer C, Ballivet M, Matter JM. A Positive Feedback Loop between ATOH7 and a Notch Effector Regulates Cell-Cycle Progression and Neurogenesis in the Retina. Cell Rep. 2013 Mar 28;3(3):796-807. doi: 10.1016/j.celrep.2013.01.035. Epub 2013 Feb 21. PubMed PMID: 23434507.

Eye diseases

1. From the Telegraph: Eye drops could treat macular degeneration. Original article in Cell Metabolism: Impaired Cholesterol Efflux in Senescent Macrophages Promotes Age-Related Macular Degeneration.
2. From the Washington Post: First U.S. artificial retina approved; device could restore some sight to blind. FDA’s news release.

Neuroscience

1. Blackiston DJ, Levin M. Ectopic eyes outside the head in Xenopus tadpoles provide sensory data for light-mediated learning. J Exp Biol. 2013 Mar 15;216(Pt 6):1031-40. doi: 10.1242/jeb.074963. PubMed PMID: 23447666.
   • Commentary: Tadpoles See with Extra Eyes
   • Very interesting article. It demonstrates how tadpole can sense light by the innervation from an ectopic eye.

Evolution

1. Feuda R, Hamilton SC, McInerney JO, Pisani D. Metazoan opsin evolution reveals a simple route to animal vision. Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18868-72. doi: 10.1073/pnas.1204609109. Epub 2012 Oct 29. PubMed PMID: 23112152; PubMed Central PMCID: PMC3503164.
   • News article:  Vision evolved 700 million years ago

Genetics

1. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science. 2013 Jan 3. [Epub ahead of print] PubMed PMID: 23287718.
2. Mali P, Yang L, Esvelt KM, Aach J, Guell M, Dicarlo JE, Norville JE, Church GM. RNA-Guided Human Genome Engineering via Cas9. Science. 2013 Jan 3. [Epub ahead of print] PubMed PMID: 23287722.
   • News coverage: Cheap, easy technique to snip DNA could revolutionize gene therapy
   • News coverage: Editing the genome with high precision

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. Nakano T, Ando S, Takata N, Kawada M, Muguruma K, Sekiguchi K, Saito K, Yonemura S, Eiraku M, Sasai Y. Self-formation of optic cups and storable stratified neural retina from human ESCs. Cell Stem Cell. 2012 Jun 14;10(6):771-85. PubMed PMID: 22704518.
2. Cyranoski D. Tissue engineering: The brainmaker. Nature. 2012 Aug 23;488(7412):444-6. doi: 10.1038/488444a. PubMed PMID: 22914148.
   • An interesting article about Dr. Sasai who leads the team to make the eye cup from human ESCs as described above and from mouse ESCs, among many other interesting discoveries!

Imaging

1. Small A. Faster and more versatile tools for super-resolution fluorescence microscopy. Nat Methods. 2012 Jun 28;9(7):655-6. doi: 10.1038/nmeth.2079. PubMed PMID: 22743767.
2. Weber M, Huisken J. Omnidirectional microscopy. Nat Methods. 2012 Jun 28;9(7):656-7. doi: 10.1038/nmeth.2022. PubMed PMID: 22743768.
3. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012 Jun 28;9(7):676-82. doi: 10.1038/nmeth.2019. PubMed PMID: 22743772.
4. Kankaanpää P, Paavolainen L, Tiitta S, Karjalainen M, Päivärinne J, Nieminen J, Marjomäki V, Heino J, White DJ. BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nat Methods. 2012 Jun 28;9(7):683-9.doi: 10.1038/nmeth.2047. PubMed PMID: 22743773.
5. de Chaumont F, Dallongeville S, Chenouard N, Hervé N, Pop S, Provoost T, Meas-Yedid V, Pankajakshan P, Lecomte T, Le Montagner Y, Lagache T, Dufour A, Olivo-Marin JC. Icy: an open bioimage informatics platform for extended reproducible research. Nat Methods. 2012 Jun 28;9(7):690-6. doi: 10.1038/nmeth.2075. PubMed PMID: 22743774.
6. Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE. Biological imaging software tools. Nat Methods. 2012 Jun 28;9(7):697-710. doi: 10.1038/nmeth.2084. PubMed PMID: 22743775.
7. Ronneberger O, Liu K, Rath M, Rueß D, Mueller T, Skibbe H, Drayer B, Schmidt T, Filippi A, Nitschke R, Brox T, Burkhardt H, Driever W. ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains. Nat Methods. 2012  Jun 17;9(7):735-42. doi: 10.1038/nmeth.2076. PubMed PMID: 22706672.
8. Lubeck E, Cai L. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat Methods. 2012 Jun 3;9(7):743-8. doi: 10.1038/nmeth.2069. PubMed PMID: 22660740; PubMed Central PMCID: PMC3418883.
9. Tomer R, Khairy K, Amat F, Keller PJ. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat Methods. 2012 Jun 3;9(7):755-63. doi: 10.1038/nmeth.2062. PubMed PMID: 22660741.
10. The quest for quantitative microscopy. Nat Methods. 2012 Jul;9(7):627. PubMed PMID: 22930824.
11. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012 Jul;9(7):671-5. PubMed PMID: 22930834.

Systems Biology

1. Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell. 2012 Jul 20;150(2):389-401. PubMed PMID: 22817898; PubMed Central PMCID: PMC3413483.
   • Commentary: Freddolino PL, Tavazoie S. The dawn of virtual cell biology. Cell. 2012 Jul 20;150(2):248-50. PubMed PMID: 22817888.

Genomics/Genetics

1. Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A, Wong WS, Sigurdsson G, Walters GB, Steinberg S, Helgason H, Thorleifsson G, Gudbjartsson DF, Helgason A, Magnusson OT, Thorsteinsdottir U, Stefansson K. Rate of de novo mutations and the importance of father’s age to disease risk. Nature. 2012 Aug 23;488(7412):471-5. doi: 10.1038/nature11396. PubMed PMID: 22914163.
   • A new study that shows the older the father is, the more the mutations that he will pass to the next generation!
   • News: Callaway E. Fathers bequeath more mutations as they age. Nature. 2012 Aug 23;488(7412):439. doi: 10.1038/488439a. PubMed PMID: 22914142.
   • Commentary: Kondrashov A. Genetics: The rate of human mutation. Nature. 2012 Aug 23;488(7412):467-8. doi: 10.1038/488467a. PubMed PMID: 22914161.
2. Schuster-Böckler B, Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature. 2012 Aug 23;488(7412):504-7. PubMed PMID: 22820252.

Development

1. Lefebvre JL, Kostadinov D, Chen WV, Maniatis T, Sanes JR. Protocadherins mediate dendritic self-avoidance in the mammalian nervous system. Nature. 2012 Aug 23;488(7412):517-21. PubMed PMID: 22842903; PubMed Central PMCID: PMC3427422.

Development

1. Vogel G. Reproductive biology. Potential egg stem cells reignite debate. Science. 2012 Mar 2;335(6072):1029-30. PubMed PMID: 22383817.

Scientific career

1. Mervis J. Scientific careers. Is motherhood the biggest reason for academia’s gender imbalance? Science. 2012 Mar 2;335(6072):1030-1. PubMed PMID: 22383818.

Genomics

1. Xu X, Hou Y, Yin X, Bao L, Tang A, Song L, Li F, Tsang S, Wu K, Wu H, He W, Zeng L, Xing M, Wu R, Jiang H, Liu X, Cao D, Guo G, Hu X, Gui Y, Li Z, Xie W, Sun X, Shi M, Cai Z, Wang B, Zhong M, Li J, Lu Z, Gu N, Zhang X, Goodman L, Bolund L, Wang J, Yang H, Kristiansen K, Dean M, Li Y, Wang J. Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell. 2012 Mar 2;148(5):886-95. PubMed PMID: 22385958.
2. Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, Li F, Wu K, Liang J, Shao D, Wu H, Ye X, Ye C, Wu R, Jian M, Chen Y, Xie W, Zhang R, Chen L, Liu X, Yao X, Zheng H, Yu C, Li Q, Gong Z, Mao M, Yang X, Yang L, Li J, Wang W, Lu Z, Gu N, Laurie G, Bolund L, Kristiansen K, Wang J, Yang H, Li Y, Zhang X, Wang J. Single-Cell ExomeSequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm. Cell. 2012 Mar 2;148(5):873-85. PubMed PMID: 22385957.

Systems biology

1. Angermann BR, Klauschen F, Garcia AD, Prustel T, Zhang F, Germain RN, Meier-Schellersheim M. Computational modeling of cellular signaling processes embedded into dynamic spatial contexts. Nat Methods. 2012 Jan 29;9(3):283-9. doi: 10.1038/nmeth.1861. PubMed PMID: 22286385.
• Commentary: Sneddon MW, Emonet T. Modeling cellular signaling: taking space into the computation. Nat Methods. 2012 Feb 28;9(3):239-42. doi: 10.1038/nmeth.1900. PubMed PMID: 22373909.

Imaging

1. Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR. OMERO: flexible, model-driven data management for experimental biology. Nat Methods. 2012 Feb 28;9(3):245-53. doi: 10.1038/nmeth.1896. PubMed PMID: 22373911.
2. Ragan T, Kadiri LR, Venkataraju KU, Bahlmann K, Sutin J, Taranda J, Arganda-Carreras I, Kim Y, Seung HS, Osten P. Serial two-photon tomography for automated ex vivo mouse brain imaging. Nat Methods. 2012 Jan 15;9(3):255-8. doi:  10.1038/nmeth.1854. PubMed PMID: 22245809; PubMed Central PMCID: PMC3297424

Genetics

1. Wang X, Chen X, Yang Y. Spatiotemporal control of gene expression by a light-switchable transgene system. Nat Methods. 2012 Feb 12;9(3):266-9. doi: 10.1038/nmeth.1892. PubMed PMID: 22327833.

Stem cells/ regeneration

1. Makkar RR, Smith RR, Cheng K, Malliaras K, Thomson LE, Berman D, Czer LS, Marbán L, Mendizabal A, Johnston PV, Russell SD, Schuleri KH, Lardo AC, Gerstenblith G, Marbán E. Intracoronary cardiosphere-derived cells for heart regeneration after myocardial infarction (CADUCEUS): a prospective, randomised phase 1 trial. Lancet. 2012 Feb 13. [Epub ahead of print] PubMed PMID: 22336189.
• News coverage by the BBC

Genetics/Genomics

1. MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG; 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012 Feb 17;335(6070):823-8. PubMed PMID: 22344438.
• Commentary: Quintana-Murci L. Genetics. Gene losses in the human genome. Science. 2012 Feb 17;335(6070):806-7. PubMed PMID: 22344433.

Development

1. Inaba M, Yamanaka H, Kondo S. Pigment pattern formation by contact-dependent depolarization. Science. 2012 Feb 10;335(6069):677. PubMed PMID: 22323812.

Funding

1. Mervis J. U.S. budget. Science spared brunt of ax in budget request. Science.  2012 Feb 17;335(6070):783-4. PubMed PMID: 22344417.

Academic career

1. Kaminski D, Geisler C. Survival analysis of faculty retention in science and engineering by gender. Science. 2012 Feb 17;335(6070):864-6. PubMed PMID: 22344445.

Development

1. Balaskas N, Ribeiro A, Panovska J, Dessaud E, Sasai N, Page KM, Briscoe J, Ribes V. Gene regulatory logic for reading the sonic hedgehog signaling gradient in the vertebrate neural tube. Cell. 2012 Jan 20;148(1-2):273-84. PubMed PMID: 22265416; PubMed Central PMCID: PMC3267043.
2. Lassar A. Finding MyoD with a little help from my friends. Nat Cell Biol. 2012 Feb 2;14(2):116. doi: 10.1038/ncb2421. PubMed PMID: 22298038.
• An interesting personal account of the discovery of MyoD.

Retinal Regeneration

1. Qin Z, Kidd AR 3rd, Thomas JL, Poss KD, Hyde DR, Raymond PA, Thummel R. FGF signaling regulates rod photoreceptor cell maintenance and regeneration in zebrafish. Exp Eye Res. 2011 Nov;93(5):726-34. Epub 2011 Sep 17. PubMed PMID: 21945172; PubMed Central PMCID: PMC3243491.
2. Hochmann S, Kaslin J, Hans S, Weber A, Machate A, Geffarth M, Funk RH, Brand M. Fgf Signaling is Required for Photoreceptor Maintenance in the Adult Zebrafish Retina. PLoS One. 2012;7(1):e30365. Epub 2012 Jan 26. PubMed PMID: 22291943; PubMed Central PMCID: PMC3266925.

Genetics

1. Visscher PM, Brown MA, McCarthy MI, Yang J. Five Years of GWAS Discovery. Am J Hum Genet. 2012 Jan 13;90(1):7-24. PubMed PMID: 22243964.

Genomics

1. Baker M. Structural variation: the genome’s hidden architecture. Nat Methods. 2012 Jan 30;9(2):133-7. doi: 10.1038/nmeth.1858. PubMed PMID: 22290183.
2. Xiong Q, Ancona N, Hauser ER, Mukherjee S, Furey TS. Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome Res. 2012 Feb;22(2):386-97. Epub 2011 Sep 22. PubMed PMID: 21940837.

Imaging

1. Cox S, Rosten E, Monypenny J, Jovanovic-Talisman T, Burnette DT, Lippincott-Schwartz J, Jones GE, Heintzmann R. Bayesian localization microscopy reveals nanoscale podosome dynamics. Nat Methods. 2011 Dec 4;9(2):195-200. doi: 10.1038/nmeth.1812. PubMed PMID: 22138825.
• Commentary: Lidke KA. Super resolution for common probes and common microscopes. Nat Methods. 2012 Jan 30;9(2):139-41. doi: 10.1038/nmeth.1863. PubMed PMID: 22290184.
• This looks like an interesting article that talks about how to use common fluorescent setup for super-resolution imaging.
2. Xu K, Babcock HP, Zhuang X. Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. Nat Methods. 2012 Jan 8;9(2):185-8. doi: 10.1038/nmeth.1841. PubMed PMID: 22231642.

Gene Regulatory Network

1. Damle SS, Davidson EH. Synthetic in vivo validation of gene network circuitry. Proc Natl Acad Sci U S A. 2012 Jan 11. [Epub ahead of print] PubMed PMID: 22238426.
2. Weaver J. New signaling chemicals spur worms to seek company. PLoS Biol. 2012 Jan;10(1):e1001240. Epub 2012 Jan 10. PubMed PMID: 22253575; PubMed Central PMCID: PMC3254651.
3. Gross L. Built-in Timer Delays Differentiation. PLoS Biol. 2012 Jan;10(1):e1001254. Epub 2012 Jan 31. PubMed PMID: 22303284.
4. van Dijk AD, van Mourik S, van Ham RC. Mutational robustness of gene regulatory networks. PLoS One. 2012;7(1):e30591. Epub 2012 Jan 25. PubMed PMID: 22295094; PubMed Central PMCID: PMC3266278.

Ageing

1. Heidinger BJ, Blount JD, Boner W, Griffiths K, Metcalfe NB, Monaghan P. Telomere length in early life predicts lifespan. Proc Natl Acad Sci U S A. 2012 Jan 9. [Epub ahead of print] PubMed PMID: 22232671.

Brg1

1. Curtis CD, Griffin CT. The chromatin-remodeling enzymes BRG1 and CHD4 antagonistically regulate vascular Wnt signaling. Mol Cell Biol. 2012 Jan 30. [Epub ahead of print] PubMed PMID: 22290435.

Funding

1. Macilwain C. Funding in 2012: “great recession” starts to bite. Cell. 2012 Jan 20;148(1-2):14-6. PubMed PMID: 22265395.

Retinal Development

1. Kwan KM, Otsuna H, Kidokoro H, Carney KR, Saijoh Y, Chien CB. A complex choreography of cell movements shapes the vertebrate eye. Development. 2012 Jan;139(2):359-72. PubMed PMID: 22186726.
2. Morgan JL, Soto F, Wong RO, Kerschensteiner D. Development of cell type-specific connectivity patterns of converging excitatory axons in the retina. Neuron. 2011 Sep 22;71(6):1014-21. Epub 2011 Sep 21. PubMed PMID: 21943599; PubMed Central PMCID: PMC3184549.

Stem cells

1. Salero E, Blenkinsop TA, Corneo B, Harris A, Rabin D, Stern JH, Temple S. Adult Human RPE Can Be Activated into a Multipotent Stem Cell that Produces Mesenchymal Derivatives. Cell Stem Cell. 2012 Jan 6;10(1):88-95. PubMed PMID: 22226358.
• Commentary: Trounson A, Grieshammer U. Chimeric Primates: Embryonic Stem Cells Need Not Apply. Cell. 2012 Jan 4. [Epub ahead of print] PubMed PMID: 22225613.
2. Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods. 2011 Sep 11;8(10):821-7. doi: 10.1038/nmeth.1699. PubMed PMID: 21983960.

Genetics

1. Zhang F, Vierock J, Yizhar O, Fenno LE, Tsunoda S, Kianianmomeni A, Prigge M, Berndt A, Cushman J, Polle J, Magnuson J, Hegemann P, Deisseroth K. The microbial opsin family of optogenetic tools. Cell. 2011 Dec 23;147(7):1446-57. PubMed PMID: 22196724.
2. McMahon MA, Rahdar M, Porteus M. Gene editing: not just for translation anymore. Nat Methods. 2011 Dec 28;9(1):28-31. doi: 10.1038/nmeth.1811. PubMed PMID: 22205513.
3. Zhao S, Ting JT, Atallah HE, Qiu L, Tan J, Gloss B, Augustine GJ, Deisseroth K, Luo M, Graybiel AM, Feng G. Cell  type–specific channelrhodopsin-2 transgenic mice for optogenetic dissection of neural circuitry function. Nat Methods. 2011 Sep;8(9):745-52. PubMed PMID: 21985008; PubMed Central PMCID: PMC3191888.

Genomics

1. Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol. 2011 Dec 25;30(1):90-8. doi: 10.1038/nbt.2057. PubMed PMID: 22198700.
• Commentary: Misteli T. Parallel genome universes. Nat Biotechnol. 2012 Jan 9;30(1):55-6. doi: 10.1038/nbt.2085. PubMed PMID: 22231096.
2. Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O’Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2011 Dec  18;30(1):78-82. doi: 10.1038/nbt.2065. PubMed PMID: 22178993.
3. Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol. 2011 Nov 13;30(1):99-104. doi: 10.1038/nbt.2024. PubMed PMID: 22081020.

Systems Biology

1. Young JW, Locke JC, Altinok A, Rosenfeld N, Bacarian T, Swain PS, Mjolsness E, Elowitz MB. Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nat Protoc. 2011 Dec 15;7(1):80-8. doi: 10.1038/nprot.2011.432. PubMed PMID: 22179594.
2. Dutkowski J, Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 2011 Sep;7(9):e1002180. Epub 2011 Sep 29. PubMed PMID: 21980275; PubMed Central PMCID: PMC3182870.

Neuroscience

1. Kralj JM, Douglass AD, Hochbaum DR, Maclaurin D, Cohen AE. Optical recording of action potentials in mammalian neurons using a microbial rhodopsin. Nat Methods. 2011 Nov 27;9(1):90-5. doi: 10.1038/nmeth.1782. PubMed PMID: 22120467; PubMed Central PMCID: PMC3248630.
• Commentary: Looger LL. Running in reverse: rhodopsins sense voltage. Nat Methods. 2011 Dec 28;9(1):43-4. doi: 10.1038/nmeth.1817. PubMed PMID: 22205516.
2. Pan YA, Choy M, Prober DA, Schier AF. Robo2 determines subtype-specific axonal projections of trigeminal sensory neurons. Development. 2012 Feb;139(3):591-600. Epub 2011 Dec 21. PubMed PMID: 22190641; PubMed Central PMCID: PMC3252355.
3. Nishimoto S, Vu AT, Naselaris T, Benjamini Y, Yu B, Gallant JL. Reconstructing visual experiences from brain activity evoked by natural movies. Curr Biol. 2011 Oct 11;21(19):1641-6. Epub 2011 Sep 22. PubMed PMID: 21945275.
4. Cavallari N, Frigato E, Vallone D, Fröhlich N, Lopez-Olmeda JF, Foà A, Berti R, Sánchez-Vázquez FJ, Bertolucci C, Foulkes NS. A blind circadian clock in cavefish reveals that opsins mediate peripheral clock photoreception. PLoS Biol. 2011 Sep;9(9):e1001142. Epub 2011 Sep 6. PubMed PMID: 21909239; PubMed Central PMCID: PMC3167789.

Vision

1. Kingdom FA. Binocular vision: the eyes add and subtract. Curr Biol. 2012 Jan 10;22(1):R22-4. PubMed PMID: 22240475.

Education

1. Vanderford NL. Broadening PhD curricula. Nat Biotechnol. 2012 Jan 9;30(1):113-4. doi: 10.1038/nbt.2091. PubMed PMID: 22231111.

Medical Research

1. Reed JC, White EL, Aubé J, Lindsley C, Li M, Sklar L, Schreiber S. The NIH’s role in accelerating translational sciences. Nat Biotechnol. 2012 Jan 9;30(1):16-9. doi: 10.1038/nbt.2087. PubMed PMID: 22231085.
2. Hudson KL. Genomics, health care, and society. N Engl J Med. 2011 Sep 15;365(11):1033-41. Review. PubMed PMID: 21916641.
3. Devi S. Lasker Foundation honours malaria researcher. Lancet. 2011 Sep 24;378(9797):1129. PubMed PMID: 21969956.

Zebrafish

1. Thummel R, Bailey TJ, Hyde DR. <em>In vivo</em> Electroporation of Morpholinos into the Adult Zebrafish Retina. J Vis Exp. 2011 Dec 27;(58). pii: 3603. doi: 10.3791/3603. PubMed PMID: 22231802.
2. Lawrence C. Advances in zebrafish husbandry and management. Methods Cell Biol. 2011;104:429-51. Review. PubMed PMID: 21924176.

Evolution

1. Pearlman SM, Serber Z, Ferrell JE Jr. A mechanism for the evolution of phosphorylation sites. Cell. 2011 Nov 11;147(4):934-46. PubMed PMID: 22078888; PubMed Central PMCID: PMC3220604.

Development

1. Lander AD. Pattern, growth, and control. Cell. 2011 Mar 18;144(6):955-69. Review. PubMed PMID: 21414486; PubMed Central PMCID: PMC3128888.
2. Braendle C, Felix MA. The other side of phenotypic plasticity: a developmental system that generates an invariant phenotype despite environmental variation. J Biosci. 2009 Oct;34(4):543-51. Review. PubMed PMID: 19920340.
3. Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D. The dynamic architecture of Hox gene clusters. Science. 2011 Oct 14;334(6053):222-5. PubMed PMID: 21998387.

Genomics

1. Sadeh R, Allis CD. Genome-wide “Re”-Modeling of Nucleosome Positions. Cell. 2011 Oct 14;147(2):263-6. PubMed PMID: 22000006.
2. Lupski JR, Belmont JW, Boerwinkle E, Gibbs RA. Clan genomics and the complex architecture of human disease. Cell. 2011 Sep 30;147(1):32-43. PubMed PMID: 21962505.
3. Raychaudhuri S. Mapping rare and common causal alleles for complex human diseases. Cell. 2011 Sep 30;147(1):57-69. PubMed PMID: 21962507; PubMed Central PMCID: PMC3198013.

Genetics

1. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011 Oct 14;147(2):358-69. PubMed PMID: 22000014.

Funding

1. Mervis J. Peer review. Beyond the data. Science. 2011 Oct 14;334(6053):169-71. PubMed PMID: 21998363.

Systems biology

1. Liu C, Fu X, Liu L, Ren X, Chau CK, Li S, Xiang L, Zeng H, Chen G, Tang LH, Lenz P, Cui X, Huang W, Hwa T, Huang JD. Sequential establishment of stripe patterns in an expanding cell population. Science. 2011 Oct 14;334(6053):238-41.  PubMed PMID: 21998392.

Medical research

1. Novarino G, Akizu N, Gleeson JG. Modeling human disease in humans: the ciliopathies. Cell. 2011 Sep 30;147(1):70-9. PubMed PMID: 21962508.