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2015-07-12 Articles we read this week

Population Genetics

  1. Balaresque P, Poulet N, Cussat-Blanc S, Gerard P, Quintana-Murci L, Heyer E, Jobling MA. Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations. Eur J Hum Genet. 2015 Jan 14. doi: 10.1038/ejhg.2014.285. [Epub ahead of print] PubMed PMID: 25585703.


  1. Head JJ, Polly PD. Evolution of the snake body form reveals homoplasy in amniote Hox gene function. Nature. 2015 Jan 5. doi: 10.1038/nature14042. [Epub ahead of print] PubMed PMID: 25539083.
  2. Lewis SL, Maslin MA. Defining the anthropocene. Nature. 2015 Mar 12;519(7542):171-80. doi: 10.1038/nature14258. PubMed PMID: 25762280.

Research Career

  1. 10 things not enough kids know before going to college
  2. Powell K. The future of the postdoc. Nature. 2015 Apr 9;520(7546):144-7. doi: 10.1038/520144a. PubMed PMID: 25855437.
  3. Will declining funding stunt scientific discovery in the U.S.?
  4. Who Picks Up the Tab for Science?


  1. Chen F, Tillberg PW, Boyden ES. Optical imaging. Expansion microscopy. Science. 2015 Jan 30;347(6221):543-8. doi: 10.1126/science.1260088. Epub 2015 Jan 15. PubMed PMID: 25592419; PubMed Central PMCID: PMC4312537.


  1. Leinenga G, Götz J. Scanning ultrasound removes amyloid-β and restores memory in an Alzheimer’s disease mouse model. Sci Transl Med. 2015 Mar 11;7(278):278ra33. doi: 10.1126/scitranslmed.aaa2512. PubMed PMID: 25761889.
    1. New Alzheimer’s treatment fully restores memory function
  2. Kawchuk GN, Fryer J, Jaremko JL, Zeng H, Rowe L, Thompson R. Real-time visualization of joint cavitation. PLoS One. 2015 Apr 15;10(4):e0119470. doi: 10.1371/journal.pone.0119470. eCollection 2015. PubMed PMID: 25875374; PubMed Central PMCID: PMC4398549.
  3. Ganna A, Ingelsson E. 5 year mortality predictors in 498 103 UK Biobank participants: a prospective population-based study. Lancet. 2015 Jun 2. pii: S0140-6736(15)60175-1. doi: 10.1016/S0140-6736(15)60175-1. [Epub ahead of print] PubMed PMID: 26049253.


  1. Men have hands amputated and replaced with bionic ones
  2. Lab In Berkeley Accidentally Discovers Solution To Fix Color Blindness


  1. This Chemistry 3D Printer Can Synthesize Molecules From Scratch


  1. Ji X, Dadon DB, Abraham BJ, Lee TI, Jaenisch R, Bradner JE, Young RA. Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions. Proc Natl Acad Sci U S A. 2015 Mar 9. pii: 201502971. [Epub ahead of print] PubMed PMID: 25755260.
  2. Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X. Spatially resolved, highly multiplexed RNA profiling in single cells. Science. 2015 Apr 9. pii: aaa6090. PubMed PMID: 25858977.


  1. Baden T, Chagas AM, Gage G, Marzullo T, Prieto-Godino LL, Euler T. Open labware: 3-d printing your own lab equipment. PLoS Biol. 2015 Mar 20;13(3):e1002086. doi: 10.1371/journal.pbio.1002086. eCollection 2015 Mar. PubMed PMID: 25794301.


  1. Campbell PD, Chao JA, Singer RH, Marlow FL. Dynamic visualization of transcription and RNA subcellular localization in zebrafish. Development. 2015 Mar 10. pii: dev.118968. [Epub ahead of print] PubMed PMID: 25758462.
  2. Green JB, Sharpe J. Positional information and reaction-diffusion: two big ideas in developmental biology combine. Development. 2015 Apr 1;142(7):1203-1211. Review. PubMed PMID: 25804733.
  3. Wu F, Kaczynski TJ, Sethuramanujam S, Li R, Jain V, Slaughter M, Mu X. Two transcription factors, Pou4f2 and Isl1, are sufficient to specify the retinal ganglion cell fate. Proc Natl Acad Sci U S A. 2015 Mar 16. pii: 201421535. [Epub ahead of print] PubMed PMID: 25775587.
  4. Nern A, Pfeiffer BD, Rubin GM. Optimized tools for multicolor stochastic labeling reveal diverse stereotyped cell arrangements in the fly visual system.Proc Natl Acad Sci U S A. 2015 May 11. pii: 201506763. [Epub ahead of print] PubMed PMID: 25964354.


  1. Lichtman JW, Pfister H, Shavit N. The big data challenges of connectomics. Nat Neurosci. 2014 Nov;17(11):1448-54. doi: 10.1038/nn.3837. Epub 2014 Oct 28. Review. PubMed PMID: 25349911.
  2. Hayworth KJ, Xu CS, Lu Z, Knott GW, Fetter RD, Tapia JC, Lichtman JW, Hess HF.
    Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics. Nat Methods. 2015 Apr;12(4):319-22. doi: 10.1038/nmeth.3292. Epub 2015 Feb 16. PubMed PMID: 25686390; PubMed Central PMCID: PMC4382383.
  3. Madabhushi R, Gao F, Pfenning AR, Pan L, Yamakawa S, Seo J, Rueda R, Phan TX, Yamakawa H, Pao PC, Stott RT, Gjoneska E, Nott A, Cho S, Kellis M, Tsai LH. Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes. Cell. 2015 Jun 18;161(7):1592-605. doi: 10.1016/j.cell.2015.05.032. Epub 2015 Jun 4. PubMed PMID: 26052046.

Genetics/Genome Editing

  1. Yin L, Maddison LA, Li M, Kara N, LaFave MC, Varshney GK, Burgess SM, Patton JG, Chen W. Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs. Genetics. 2015 Apr 8. pii: genetics.115.176917. [Epub ahead of print] PubMed PMID: 25855067.
  2. Gonzales AP, Yeh JR. Cas9-based genome editing in zebrafish. Methods Enzymol. 2014;546:377-413. doi: 10.1016/B978-0-12-801185-0.00018-0. PubMed PMID: 25398350.
  3. Shah AN, Davey CF, Whitebirch AC, Miller AC, Moens CB. Rapid reverse genetic screening using CRISPR in zebrafish. Nat Methods. 2015 Jun;12(6):535-40. doi: 10.1038/nmeth.3360. Epub 2015 Apr 13. PubMed PMID: 25867848.
  4. Dow LE, Fisher J, O’Rourke KP, Muley A, Kastenhuber ER, Livshits G, Tschaharganeh DF, Socci ND, Lowe SW. Inducible in vivo genome editing with CRISPR-Cas9. Nat Biotechnol. 2015 Apr;33(4):390-4. doi: 10.1038/nbt.3155. Epub 2015 Feb 18. PubMed PMID: 25690852; PubMed Central PMCID: PMC4390466.