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2014-07-20 new articles we read this week

Nature’s special on “Challenges in irreproducible research”

Human Behaviour/Psychology

  1. Kramer AD, Guillory JE, Hancock JT. Experimental evidence of massive-scale emotional contagion through social networks. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8788-90. doi: 10.1073/pnas.1320040111. Epub 2014 Jun 2. PubMed PMID: 24889601.

Retinal development

  1. Hoon M, Okawa H, Della Santina L, Wong RO. Functional Architecture of the Retina: Development and Disease. Prog Retin Eye Res. 2014 Jun 28. pii: S1350-9462(14)00038-X. doi: 10.1016/j.preteyeres.2014.06.003. [Epub ahead of print] Review. PubMed PMID: 24984227.

Stem cells

  1. Ksander BR, Kolovou PE, Wilson BJ, Saab KR, Guo Q, Ma J, McGuire SP, Gregory MS, Vincent WJ, Perez VL, Cruz-Guilloty F, Kao WW, Call MK, Tucker BA, Zhan Q, Murphy GF, Lathrop KL, Alt C, Mortensen LJ, Lin CP, Zieske JD, Frank MH, Frank NY. ABCB5 is a limbal stem cell gene required for corneal development and repair. Nature. 2014 Jul 17;511(7509):353-7. doi: 10.1038/nature13426. Epub 2014 Jul 2. PubMed PMID: 25030174.
  2. Tsai SQ, Joung JK. What’s Changed with Genome Editing? Cell Stem Cell. 2014 Jul 3;15(1):3-4. doi: 10.1016/j.stem.2014.06.017. PubMed PMID: 24996161.
  3. Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Talkowski ME, Musunuru K. Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing. Cell Stem Cell. 2014 Jul 3;15(1):27-30. doi: 10.1016/j.stem.2014.04.020. PubMed PMID: 24996167; PubMed Central PMCID: PMC4082799.
  4. Smith C, Gore A, Yan W, Abalde-Atristain L, Li Z, He C, Wang Y, Brodsky RA, Zhang K, Cheng L, Ye Z. Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs. Cell Stem Cell. 2014 Jul 3;15(1):12-3. doi: 10.1016/j.stem.2014.06.011. PubMed PMID: 24996165.
  5. Suzuki K, Yu C, Qu J, Li M, Yao X, Yuan T, Goebl A, Tang S, Ren R, Aizawa E, Zhang F, Xu X, Soligalla RD, Chen F, Kim J, Kim NY, Liao HK, Benner C, Esteban CR, Jin Y, Liu GH, Li Y, Izpisua Belmonte JC. Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. Cell Stem Cell. 2014 Jul 3;15(1):31-6. doi: 10.1016/j.stem.2014.06.016. PubMed PMID: 24996168.
  6. Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K. Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1. Cell Stem Cell. 2014 Jun 5;14(6):781-95. doi: 10.1016/j.stem.2014.03.004. Epub 2014 Apr 3. PubMed PMID: 24704492.

Eye disease treatment

  1. Jepson LH, Hottowy P, Weiner GA, Dabrowski W, Litke AM, Chichilnisky EJ. High-fidelity reproduction of spatiotemporal visual signals for retinal prosthesis. Neuron. 2014 Jul 2;83(1):87-92. doi: 10.1016/j.neuron.2014.04.044. Epub 2014 Jun 5. PubMed PMID: 24910077.
    • Trenholm S, Roska B. Cell-type-specific electric stimulation for vision restoration. Neuron. 2014 Jul 2;83(1):1-2. doi: 10.1016/j.neuron.2014.06.012. PubMed PMID: 24991948.

Funding

  1. Resnick A. Systemic addiction to research funding. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):E2634. doi: 10.1073/pnas.1407369111. Epub 2014 Jun 11. PubMed PMID: 24920596.
  2. Alberts B, Kirschner MW, Tilghman S, Varmus H. Rescuing US biomedical research from its systemic flaws. Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5773-7. doi: 10.1073/pnas.1404402111. Epub 2014 Apr 14. PubMed PMID: 24733905; PubMed Central PMCID: PMC4000813.

Research Career

  1. Smaglik P. Employment: PhD overdrive. Nature. 2014 Jul 10;511(7508):255-6. PubMed PMID: 25013890.

Systems Biology

  1. Bruggner RV, Bodenmiller B, Dill DL, Tibshirani RJ, Nolan GP. Automated identification of stratifying signatures in cellular subpopulations. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):E2770-7. doi: 10.1073/pnas.1408792111. Epub 2014 Jun 16. PubMed PMID: 24979804.

Genomics/ Sequencing

  1. Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA-sequencing. Genome Biol. 2014 Jun 30;15(6):R86. [Epub ahead of print] PubMed PMID: 24981968.
  2. Tilgner H, Grubert F, Sharon D, Snyder MP. Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9869-74. doi: 10.1073/pnas.1400447111. Epub 2014 Jun
    24. PubMed PMID: 24961374.

Genome editing

  1. Sheridan C. First CRISPR-Cas patent opens race to stake out intellectual property. Nat Biotechnol. 2014 Jul 8;32(7):599-601. doi: 10.1038/nbt0714-599. PubMed PMID: 25004207.
  2. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol. 2014 Jul;32(7):670-6. doi: 10.1038/nbt.2889. Epub 2014 Apr 20. PubMed PMID: 24752079.
  3. Kuscu C, Arslan S, Singh R, Thorpe J, Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol. 2014 Jul;32(7):677-83. doi: 10.1038/nbt.2916. Epub 2014 May 18. PubMed PMID: 24837660.
  4. Tsai SQ, Joung JK. What’s Changed with Genome Editing? Cell Stem Cell. 2014 Jul 3;15(1):3-4. doi: 10.1016/j.stem.2014.06.017. PubMed PMID: 24996161.
  5. Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Talkowski ME, Musunuru K. Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing. Cell Stem Cell. 2014 Jul 3;15(1):27-30. doi: 10.1016/j.stem.2014.04.020. PubMed PMID: 24996167; PubMed Central PMCID: PMC4082799.
  6. Smith C, Gore A, Yan W, Abalde-Atristain L, Li Z, He C, Wang Y, Brodsky RA, Zhang K, Cheng L, Ye Z. Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs. Cell Stem Cell. 2014 Jul 3;15(1):12-3. doi: 10.1016/j.stem.2014.06.011. PubMed PMID: 24996165.
  7. Suzuki K, Yu C, Qu J, Li M, Yao X, Yuan T, Goebl A, Tang S, Ren R, Aizawa E, Zhang F, Xu X, Soligalla RD, Chen F, Kim J, Kim NY, Liao HK, Benner C, Esteban CR, Jin Y, Liu GH, Li Y, Izpisua Belmonte JC. Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. Cell Stem Cell. 2014 Jul 3;15(1):31-6. doi: 10.1016/j.stem.2014.06.016. PubMed PMID: 24996168.
  8. Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K. Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1. Cell Stem Cell. 2014 Jun 5;14(6):781-95. doi: 10.1016/j.stem.2014.03.004. Epub 2014 Apr 3. PubMed PMID: 24704492.
  9. Güell M, Yang L, Church G. Genome Editing Assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics. 2014 Jul 1. pii: btu427. [Epub ahead of print] PubMed PMID: 24990609.
  10. Spies M. Fulfilling the dream of a perfect genome editing tool. Proc Natl Acad Sci U S A. 2014 Jul 2. pii: 201408985. [Epub ahead of print] PubMed PMID: 24989506.
This was written by Yuk Fai Leung. Posted on Sunday, July 20, 2014, at 6:25 PM. Filed under Fai's sharing, journal watch. Tagged , , , , , , , , , , , , , , . Bookmark the permalink. Follow comments here with the RSS feed. Both comments and trackbacks are currently closed.