Posts tagged ‘TALEN’

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.

Systems biology

  1. Levo M, Segal E. In pursuit of design principles of regulatory sequences. Nat Rev Genet. 2014 Jul;15(7):453-68. doi: 10.1038/nrg3684. Epub 2014 Jun 10. PubMed PMID: 24913666.
  2. Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O, Suvà ML, Regev A, Bernstein BE. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014 Jun 20;344(6190):1396-401. doi: 10.1126/science.1254257. Epub 2014 Jun 12. PubMed PMID: 24925914.

Stem cells

  1. Cattaneo E, Corbellini G. Stem cells: taking a stand against pseudoscience. Nature. 2014 Jun 19;509(7505):333-5. PubMed PMID: 24955466.
  2. Bertolotti E, Neri A, Camparini M, Macaluso C, Marigo V. Stem cells as source for retinal pigment epithelium transplantation. Prog Retin Eye Res. 2014 Jun 13. pii: S1350-9462(14)00037-8. doi: 10.1016/j.preteyeres.2014.06.002. [Epub ahead of print] Review. PubMed PMID: 24933042.
  3. Ye L, Wang J, Beyer AI, Teque F, Cradick TJ, Qi Z, Chang JC, Bao G, Muench MO, Yu J, Levy JA, Kan YW. Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5?32 mutation confers resistance to HIV infection. Proc Natl Acad Sci U S A. 2014 Jun 9. pii: 201407473. [Epub ahead of print] PubMed PMID: 24927590.
  4. Park CY, Kim J, Kweon J, Son JS, Lee JS, Yoo JE, Cho SR, Kim JH, Kim JS, Kim DW. Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs. Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9253-8. doi: 10.1073/pnas.1323941111. Epub 2014 Jun 9. PubMed PMID: 24927536.

Neuroscience

  1. Rose N. The human brain project: social and ethical challenges. Neuron. 2014 Jun 18;82(6):1212-5. doi: 10.1016/j.neuron.2014.06.001. PubMed PMID: 24945767.
  2. Cohen MA, Konkle T, Rhee JY, Nakayama K, Alvarez GA. Processing multiple visual objects is limited by overlap in neural channels. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8955-60. doi: 10.1073/pnas.1317860111. Epub 2014 Jun 2. PubMed PMID: 24889618.
  3. Prevedel R, Yoon YG, Hoffmann M, Pak N, Wetzstein G, Kato S, Schrödel T, Raskar R, Zimmer M, Boyden ES, Vaziri A. Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. Nat Methods. 2014 Jul;11(7):727-30. doi: 10.1038/nmeth.2964. Epub 2014 May 18. PubMed PMID: 24836920.

Neurobehaviour

  1. Pérez-Escudero A, Vicente-Page J, Hinz RC, Arganda S, de Polavieja GG. idTracker: tracking individuals in a group by automatic identification of unmarked animals. Nat Methods. 2014 Jul;11(7):743-8. doi: 10.1038/nmeth.2994. Epub 2014 Jun 1. PubMed PMID: 24880877.

Psychology

  1. Jung K, Shavitt S, Viswanathan M, Hilbe JM. Female hurricanes are deadlier than male hurricanes. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8782-7. doi: 10.1073/pnas.1402786111. Epub 2014 Jun 2. PubMed PMID: 24889620.

Retinal Development

  1. Laranjeiro R, Whitmore D. Transcription factors involved in retinogenesis are co-opted by the circadian clock following photoreceptor differentiation. Development. 2014 Jun 12. pii: dev.104380. [Epub ahead of print] PubMed PMID: 24924194.

Eye diseases

  1. Huber-Reggi SP, Mueller KP, Straumann D, Huang MY, Neuhauss SC. Individual Larvae of the Zebrafish Mutant belladonna Display Multiple Infantile Nystagmus-Like Waveforms that Are Influenced by Viewing Conditions. Invest Ophthalmol Vis Sci. 2014 May 27;55(6):3971-8. doi: 10.1167/iovs.13-13576. PubMed PMID: 24867578.

Zebrafish

  1. Law SH, Sargent TD. The Serine-Threonine Protein Kinase PAK4 Is Dispensable in Zebrafish: Identification of a Morpholino-Generated Pseudophenotype. PLoS One. 2014 Jun 19;9(6):e100268. doi: 10.1371/journal.pone.0100268. eCollection 2014. PubMed PMID: 24945275.

Genome editing/medicine

  1. Ye L, Wang J, Beyer AI, Teque F, Cradick TJ, Qi Z, Chang JC, Bao G, Muench MO, Yu J, Levy JA, Kan YW. Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5?32 mutation confers resistance to HIV infection. Proc Natl Acad Sci U S A. 2014 Jun 9. pii: 201407473. [Epub ahead of print] PubMed PMID: 24927590.
  2. Park CY, Kim J, Kweon J, Son JS, Lee JS, Yoo JE, Cho SR, Kim JH, Kim JS, Kim DW. Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs. Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9253-8. doi: 10.1073/pnas.1323941111. Epub 2014 Jun 9. PubMed PMID: 24927536.
  3. Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN, Xie Z, Li Y, Weiss R. CRISPR
    transcriptional repression devices and layered circuits in mammalian cells. Nat
    Methods. 2014 Jul;11(7):723-6. doi: 10.1038/nmeth.2969. Epub 2014 May 5. PubMed
    PMID: 24797424.
  4. Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK. Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells. Mol Cell. 2014 May 22;54(4):698-710. doi: 10.1016/j.molcel.2014.04.022. Epub 2014 May 15. PubMed PMID: 24837679.

Drug Discovery

  1. Wang YN, Hou YY, Sun MZ, Zhang CY, Bai G, Zhao X, Feng XZ. Behavioural screening of zebrafish using neuroactive traditional Chinese medicine prescriptions and biological targets. Sci Rep. 2014 Jun 16;4:5311. doi: 10.1038/srep05311. PubMed PMID: 24931174; PubMed Central PMCID: PMC4058885.

Science Career

  1. Casadevall A, Fang FC. Causes for the persistence of impact factor mania. MBio. 2014 Mar 18;5(2):e00064-14. doi: 10.1128/mBio.00064-14. PubMed PMID: 24643863; PubMed Central PMCID: PMC3967521.

Development

  1. Nicolas M, Hassan BA. Amyloid precursor protein and neural development. Development. 2014 Jul;141(13):2543-8. doi: 10.1242/dev.108712. PubMed PMID: 24961795.
  2. Deneris ES, Hobert O. Maintenance of postmitotic neuronal cell identity. Nat Neurosci. 2014 Jul;17(7):899-907. doi: 10.1038/nn.3731. Epub 2014 Jun 15. PubMed PMID: 24929660.

Methods

  1. Hughes AJ, Spelke DP, Xu Z, Kang CC, Schaffer DV, Herr AE. Single-cell western blotting. Nat Methods. 2014 Jul;11(7):749-55. doi: 10.1038/nmeth.2992. Epub 2014  Jun 1. PubMed PMID: 24880876.

Gene regulatory network

  1. Barsi JC, Tu Q, Davidson E. General approach for in vivo recovery of cell type specific effector gene sets. Genome Res. 2014 Mar 6. [Epub ahead of print] PubMed PMID: 24604781.

Medicine

  1. Project to Improve Poor Children’s Intellect Led to Better Health, Data Show
  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.

Neuroscience

  1. Portugues R, Feierstein CE, Engert F, Orger MB. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron. 2014 Mar 19;81(6):1328-43. doi: 10.1016/j.neuron.2014.01.019. PubMed PMID: 24656252.
  2. Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger JM, Jackson AP, Knoblich JA. Cerebral organoids model human brain development and microcephaly. Nature. 2013 Sep 19;501(7467):373-9. doi: 10.1038/nature12517. Epub 2013 Aug 28. PubMed PMID: 23995685; PubMed Central
    PMCID: PMC3817409.

    • Brüstle O. Developmental neuroscience: Miniature human brains. Nature. 2013
      Sep 19;501(7467):319-20. doi: 10.1038/nature12552. Epub 2013 Aug 28. PubMed PMID: 23995687.

Genome editing

  1. Auer TO, Del Bene F. CRISPR/Cas9 and TALEN-mediated knock-in approaches in zebrafish. Methods. 2014 Apr 1. pii: S1046-2023(14)00129-7. doi: 10.1016/j.ymeth.2014.03.027. [Epub ahead of print] PubMed PMID: 24704174.
  2. Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, Wei W. High-throughput screening
    of a CRISPR/Cas9 library for functional genomics in human cells. Nature. 2014 Apr
    9. doi: 10.1038/nature13166. [Epub ahead of print] PubMed PMID: 24717434.
  3. Yin H, Xue W, Chen S, Bogorad RL, Benedetti E, Grompe M, Koteliansky V, Sharp
    PA, Jacks T, Anderson DG. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat Biotechnol. 2014 Mar 30. doi: 10.1038/nbt.2884. [Epub ahead of print] PubMed PMID: 24681508.

Stem cells

  1. Becker S, Jayaram H, Limb GA. Recent Advances towards the Clinical Application of Stem Cells for Retinal Regeneration. Cells. 2012 Oct 18;1(4):851-73. doi: 10.3390/cells1040851. PubMed PMID: 24710533.
  2. Assawachananont J et al., Transplantation of Embryonic and Induced Pluripotent Stem Cell-Derived 3D Retinal Sheets into Retinal Degenerative Mice. Stem Cell Reports. 2014; 2: 662-674.

Retinal degeneration

  1. Wasfy MM, Matsui JI, Miller J, Dowling JE, Perkins BD. myosin 7aa(-/-) mutant zebrafish show mild photoreceptor degeneration and reduced electroretinographic responses. Exp Eye Res. 2014 Apr 1. pii: S0014-4835(14)00083-9. doi: 10.1016/j.exer.2014.03.007. [Epub ahead of print] PubMed PMID: 24698764.

Retinal development

  1. Weber IP, Ramos AP, Strzyz PJ, Leung LC, Young S, Norden C. Mitotic Position and Morphology of Committed Precursor Cells in the Zebrafish Retina Adapt to Architectural Changes upon Tissue Maturation. Cell Rep. 2014 Apr 2. pii: S2211-1247(14)00192-2. doi: 10.1016/j.celrep.2014.03.014. [Epub ahead of print] PubMed PMID: 24703843.
  2. Almeida AD, Boije H, Chow RW, He J, Tham J, Suzuki SC, Harris WA. Spectrum of Fates: a new approach to the study of the developing zebrafish retina. Development. 2014 Apr 9. [Epub ahead of print] PubMed PMID: 24718991.
  3. Yoshimatsu T, Williams PR, D’Orazi FD, Suzuki SC, Fadool JM, Allison WT, Raymond PA, Wong RO. Transmission from the dominant input shapes the stereotypic ratio of photoreceptor inputs onto horizontal cells. Nat Commun. 2014 May 15;5:3699. doi: 10.1038/ncomms4699. PubMed PMID: 24832361.

Development

  1. Bianchi E, Doe B, Goulding D, Wright GJ. Juno is the egg Izumo receptor and is essential for mammalian fertilization. Nature. 2014 Apr 24;508(7497):483-7. doi: 10.1038/nature13203. Epub 2014 Apr 16. PubMed PMID: 24739963; PubMed Central PMCID: PMC3998876.

Genetics/Synthetic biology

  1. Malyshev DA, Dhami K, Lavergne T, Chen T, Dai N, Foster JM, Corrêa IR Jr, Romesberg FE. A semi-synthetic organism with an expanded genetic alphabet. Nature. 2014 May 15;509(7500):385-8. doi: 10.1038/nature13314. Epub 2014 May 7. PubMed PMID: 24805238.
    • Commentary: Thyer R, Ellefson J. Synthetic biology: New letters for life’s alphabet. Nature. 2014 May 15;509(7500):291-2. doi: 10.1038/nature13335. Epub 2014 May 7. PubMed PMID: 24805244.

Genome editing

  1. Kim JM, Kim D, Kim S, Kim JS. Genotyping with CRISPR-Cas-derived RNA-guided endonucleases. Nat Commun. 2014 Jan 20;5:3157. doi: 10.1038/ncomms4157. PubMed PMID: 24445736.
  2. Bae S, Park J, Kim JS. Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics. 2014 Jan 24. [Epub ahead of print] PubMed PMID: 24463181.
  3. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol. 2014 Jan 26. doi: 10.1038/nbt.2808. [Epub ahead of print] PubMed PMID: 24463574.
  4. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA. Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation.
    Science. 2014 Feb 6. [Epub ahead of print] PubMed PMID: 24505130.
  5. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. 2014 Jan 29. doi: 10.1038/nature13011. [Epub ahead of print] PubMed PMID: 24476820.
  6. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O. Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Cell. 2014 Feb 12. pii: S0092-8674(14)00156-1. doi: 10.1016/j.cell.2014.02.001. [Epub ahead of print] PubMed PMID: 24529477.
  7. Niu Y, Shen B, Cui Y, Chen Y, Wang J, Wang L, Kang Y, Zhao X, Si W, Li W, Xiang AP, Zhou J, Guo X, Bi Y, Si C, Hu B, Dong G, Wang H, Zhou Z, Li T, Tan T, Pu X, Wang F, Ji S, Zhou Q, Huang X, Ji W, Sha J. Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos. Cell. 2014 Jan 30;. [Epub ahead of print]
  8. Hai T, Teng F, Guo R, Li W, Zhou Q. One-step generation of knockout pigs by zygote injection of CRISPR/Cas system. Cell Res. 2014 Jan 31;. [Epub ahead of print]
  9. Heigwer F, Kerr G, Boutros M. E-CRISP: fast CRISPR target site identification. Nat Methods. 2014 Jan 30;11(2):122-3.
  10. Nakagawa Y, Yamamoto T, Suzuki K, Araki K, Takeda N, Ohmuraya M, Sakuma T. Screening Methods to Identify TALEN-Mediated Knockout Mice. Exp Anim. 2014;63(1):79-84. PubMed PMID: 24521866.

Development

  1. Simões-Costa M, Tan-Cabugao J, Antoshechkin I, Sauka-Spengler T, Bronner ME. Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network. Genome Res. 2014 Jan 3. [Epub ahead of print] PubMed PMID: 24389048.
  2. Umulis DM, Othmer HG. Mechanisms of scaling in pattern formation. Development. 2013 Dec;140(24):4830-43. doi: 10.1242/dev.100511. Review. PubMed PMID: 24301464; PubMed Central PMCID: PMC3848184.
  3. Pauli A, Norris ML, Valen E, Chew GL, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D, Tsai SQ, Joung JK, Saghatelian A, Schier AF. Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors. Science. 2014 Jan 9. [Epub ahead of print] PubMed PMID: 24407481.
  4. Dias AS, de Almeida I, Belmonte JM, Glazier JA, Stern CD. Somites without a clock. Science. 2014 Feb 14;343(6172):791-5. doi: 10.1126/science.1247575. Epub 2014 Jan 9. PubMed PMID: 24407478.
    • Kondo S. Developmental biology. Self-organizing somites. Science. 2014 Feb 14;343(6172):736-7. doi: 10.1126/science.1250245. PubMed PMID: 24531958.

Genomics

  1. Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS. Canonical nucleosome organization at promoters forms during genome activation. Genome Res. 2014 Jan 8. [Epub ahead of print] PubMed PMID:
    24285721.

Retinal degeneration/regeneration

  1. Sherpa T, Lankford T, McGinn TE, Hunter SS, Frey RA, Sun C, Ryan M, Robison BD, Stenkamp DL. Retinal regeneration is facilitated by the presence of surviving neurons. Dev Neurobiol. 2014 Feb 1. doi: 10.1002/dneu.22167. [Epub ahead of print] PubMed PMID: 24488694.
  2. Cruz NM, Yuan Y, Leehy BD, Baid R, Kompella U, Deangelis MM, Escher P, Haider NB. Modifier genes as therapeutics: the nuclear hormone receptor rev erb alpha (nr1d1) rescues nr2e3 associated retinal disease. PLoS One. 2014;9(1):e87942.

Zebrafish

  1. Mueller KP, Neuhauss SC. Sunscreen for Fish: Co-Option of UV Light Protection for Camouflage. PLoS One. 2014 Jan 29;9(1):e87372. doi: 10.1371/journal.pone.0087372. eCollection 2014. PubMed PMID: 24489905.

Stem cells

  1. Stress-Induced Stem Cell Method Questioned

 

Stem cells

A young scientist in Japan has found a simple approach to make totipotent stem cells by lowering the pH.

Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature

Bidirectional developmental potential in reprogrammed cells with acquired pluripotency. Nature

Retina

  1. Raymond PA, Colvin SM, Jabeen Z, Nagashima M, Barthel LK, Hadidjojo J, Popova L, Pejaver VR, Lubensky DK. Patterning the cone mosaic array in zebrafish retina requires specification of ultraviolet-sensitive cones. PLoS One. 2014 Jan 21;9(1):e85325. doi: 10.1371/journal.pone.0085325. eCollection 2014 Jan 21. PubMed PMID: 24465536.
  2. Centanin L, Wittbrodt J. Retinal neurogenesis. Development. 2014 Jan;141(2):241-4. doi: 10.1242/dev.083642. PubMed PMID: 24381194.
  3. Lenkowski JR, Raymond PA. Müller glia: Stem cells for generation and regeneration of retinal neurons in teleost fish. Prog Retin Eye Res. 2014 Jan 8.  pii: S1350-9462(14)00002-0. doi: 10.1016/j.preteyeres.2013.12.007. [Epub ahead of
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Genome-editing

  1. Hruscha A, Krawitz P, Rechenberg A, Heinrich V, Hecht J, Haass C, Schmid B. Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish. Development. 2013 Dec;140(24):4982-7. doi: 10.1242/dev.099085. Epub 2013 Nov 20. PubMed PMID: 24257628.
  2. Roberts JA, Miguel-Escalada I, Slovik KJ, Walsh KT, Hadzhiev Y, Sanges R, Stupka E, Marsh EK, Balciuniene J, Balciunas D, Müller F. Targeted transgene integration overcomes variability of position effects in zebrafish. Development. 2014 Feb;141(3):715-24. doi: 10.1242/dev.100347. PubMed PMID: 24449846.
  3. Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014 Jan 3;343(6166):80-4. doi: 10.1126/science.1246981. Epub 2013 Dec 12. PubMed PMID: 24336569.
  4. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014 Jan 3;343(6166):84-7. doi: 10.1126/science.1247005. Epub 2013 Dec 12. PubMed PMID: 24336571.
  5. Wu Y, Liang D, Wang Y, Bai M, Tang W, Bao S, Yan Z, Li D, Li J. Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell. 2013 Dec 5;13(6):659-62. doi: 10.1016/j.stem.2013.10.016. PubMed PMID: 24315440.

Neuroscience

  1. Dias BG, Ressler KJ. Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat Neurosci. 2014 Jan;17(1):89-96. doi: 10.1038/nn.3594. Epub 2013 Dec 1. PubMed PMID: 24292232.

Gene therapy

  1. Maclaren RE, Groppe M, Barnard AR, Cottriall CL, Tolmachova T, Seymour L, Clark KR, During MJ, Cremers FP, Black GC, Lotery AJ, Downes SM, Webster AR, Seabra MC. Retinal gene therapy in patients with choroideremia: initial findings from a phase 1/2 clinical trial. Lancet. 2014 Jan 15. pii: S0140-6736(13)62117-0. doi: 10.1016/S0140-6736(13)62117-0. [Epub ahead of print] PubMed PMID: 24439297.

 

Neuroscience

  1. Widmann A, Schröger E. Filter effects and filter artifacts in the analysis of  electrophysiological data. Front Psychol. 2012 Jul 9;3:233. doi: 10.3389/fpsyg.2012.00233. eCollection 2012. PubMed PMID: 22787453; PubMed Central PMCID: PMC3391960.
  2. Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, Patterson PH, Mazmanian SK. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell. 2013 Dec 19;155(7):1451-63. doi: 10.1016/j.cell.2013.11.024. Epub 2013 Dec 5. PubMed PMID: 24315484.
  3. Stern P. The heavily connected brain. Connection, connection, connection… Introduction. Science. 2013 Nov 1;342(6158):577. doi: 10.1126/science.342.6158.577. PubMed PMID: 24179217.
  4. Zatorre RJ. Predispositions and plasticity in music and speech learning: neural correlates and implications. Science. 2013 Nov 1;342(6158):585-9. doi: 10.1126/science.1238414. Review. PubMed PMID: 24179219.
  5. Turk-Browne NB. Functional interactions as big data in the human brain.Science. 2013 Nov 1;342(6158):580-4. doi: 10.1126/science.1238409. Review. PubMed PMID: 24179218.
  6. DeCaen PG, Delling M, Vien TN, Clapham DE. Direct recording and molecular identification of the calcium channel of primary cilia. Nature. 2013 Dec 12;504(7479):315-8. doi: 10.1038/nature12832. PubMed PMID: 24336289.
  7. Delling M, DeCaen PG, Doerner JF, Febvay S, Clapham DE. Primary cilia are specialized calcium signalling organelles. Nature. 2013 Dec 12;504(7479):311-4. doi: 10.1038/nature12833. PubMed PMID: 24336288.

Genetics

  1. Korf I. Genomics: the state of the art in RNA-seq analysis. Nat Methods. 2013 Nov 26;10(12):1165-6. doi: 10.1038/nmeth.2735. PubMed PMID: 24296473.
  2. Steijger T, Abril JF, Engström PG, Kokocinski F; RGASP Consortium, Abril JF, Akerman M, Alioto T, Ambrosini G, Antonarakis SE, Behr J, Bertone P, Bohnert R, Bucher P, Cloonan N, Derrien T, Djebali S, Du J, Dudoit S, Engström PG, Gerstein M, Gingeras TR, Gonzalez D, Grimmond SM, Guigó R, Habegger L, Harrow J, Hubbard TJ, Iseli C, Jean G, Kahles A, Kokocinski F, Lagarde J, Leng J, Lefebvre G, Lewis S, Mortazavi A, Niermann P, Rätsch G, Reymond A, Ribeca P, Richard H, Rougemont J, Rozowsky J, Sammeth M, Sboner A, Schulz MH, Searle SM, Solorzano ND, Solovyev V, Stanke M, Steijger T, Stevenson BJ, Stockinger H, Valsesia A, Weese D, White S, Wold BJ, Wu J, Wu TD, Zeller G, Zerbino D, Zhang MQ, Hubbard TJ, Guigó R, Harrow J, Bertone P. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods. 2013 Dec;10(12):1177-84. doi: 10.1038/nmeth.2714. Epub 2013 Nov 3. PubMed PMID: 24185837; PubMed Central PMCID: PMC3851240.
  3. Engström PG, Steijger T, Sipos B, Grant GR, Kahles A; RGASP Consortium, Alioto T, Behr J, Bertone P, Bohnert R, Campagna D, Davis CA, Dobin A, Engström PG, Gingeras TR, Goldman N, Grant GR, Guigó R, Harrow J, Hubbard TJ, Jean G, Kahles A, Kosarev P, Li S, Liu J, Mason CE, Molodtsov V, Ning Z, Ponstingl H, Prins JF, Rätsch G, Ribeca P, Seledtsov I, Sipos B, Solovyev V, Steijger T, Valle G, Vitulo N, Wang K, Wu TD, Zeller G, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P. Systematic evaluation of spliced alignment programs for RNA-seq data.  Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3. PubMed PMID: 24185836.
  4. Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke HA, Young RA. Super-enhancers in the control of cell identity and disease. Cell. 2013 Nov 7;155(4):934-47. doi: 10.1016/j.cell.2013.09.053. Epub 2013 Oct 10. PubMed PMID: 24119843; PubMed Central PMCID: PMC3841062.
  5. Collins FS, Hamburg MA. First FDA authorization for next-generation sequencer. N Engl J Med. 2013 Dec 19;369(25):2369-71. doi: 10.1056/NEJMp1314561. Epub 2013 Nov 19. PubMed PMID: 24251383.

Imaging

  1. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B. Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System. Cell. 2013 Dec 19;155(7):1479-91. doi: 10.1016/j.cell.2013.12.001. PubMed PMID: 24360272.
  2. Ma H, Reyes-Gutierrez P, Pederson T. Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors. Proc Natl Acad Sci U S A. 2013 Dec 9. [Epub ahead of print] PubMed PMID: 24324157.
  3. Elia N, Ott C, Lippincott-Schwartz J. Incisive imaging and computation for cellular mysteries: lessons from abscission. Cell. 2013 Dec 5;155(6):1220-31. doi: 10.1016/j.cell.2013.11.011. PubMed PMID: 24315094.
  4. Marx V. Is super-resolution microscopy right for you? Nat Methods. 2013 Nov 26;10(12):1157-63. doi: 10.1038/nmeth.2756. PubMed PMID: 24296472.

Genome editing

  1. Auer TO, Duroure K, De Cian A, Concordet JP, Del Bene F. Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair. Genome Res. 2013 Dec 2. [Epub ahead of print] PubMed PMID: 24179142.
  2. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013 Nov;8(11):2281-308. doi: 10.1038/nprot.2013.143. Epub 2013 Oct 24. PubMed PMID: 24157548.
  3. Cradick TJ, Fine EJ, Antico CJ, Bao G. CRISPR/Cas9 systems targeting ß-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res. 2013 Nov 1;41(20):9584-92. doi: 10.1093/nar/gkt714. Epub 2013 Aug 11. PubMed PMID: 23939622; PubMed Central PMCID: PMC3814385.
  4. 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 Apr;10(4):329-31. doi: 10.1038/nmeth.2374. Epub 2013 Feb 24. PubMed PMID: 23435258.

Gene regulatory network

  1. Fuxman Bass JI, Diallo A, Nelson J, Soto JM, Myers CL, Walhout AJ. Using networks to measure similarity between genes: association index selection. Nat Methods. 2013 Nov 26;10(12):1169-76. doi: 10.1038/nmeth.2728. PubMed PMID:24296474.

Genomics/Systems biology

  1. Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20338-43. doi: 10.1073/pnas.1307797110. Epub 2013 Nov 25. PubMed PMID: 24277855.
  2. Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, Mulawadi FH, Sung WK, Nicolis S, Ahituv N, Ruan Y, Wei CL. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature. 2013 Dec 12;504(7479):306-10. doi: 10.1038/nature12716. Epub 2013 Nov 10. PubMed PMID: 24213634.
  3. Markson JS, Piechura JR, Puszynska AM, O’Shea EK. Circadian Control of Global Gene Expression by the Cyanobacterial Master Regulator RpaA. Cell. 2013 Dec 5;155(6):1396-408. doi: 10.1016/j.cell.2013.11.005. PubMed PMID: 24315105.

Zebrafish

  1. Xu C, Tabebordbar M, Iovino S, Ciarlo C, Liu J, Castiglioni A, Price E, Liu M, Barton ER, Kahn CR, Wagers AJ, Zon LI. A Zebrafish Embryo Culture System Defines Factors that Promote Vertebrate Myogenesis across Species. Cell. 2013 Nov 7;155(4):909-21. doi: 10.1016/j.cell.2013.10.023. PubMed PMID: 24209627.
  2. Wilkinson RN, Elworthy S, Ingham PW, van Eeden FJ. A method for high-throughput PCR-based genotyping of larval zebrafish tail biopsies. Biotechniques. 2013 Dec;55(6):314-6. doi: 10.2144/000114116. PubMed PMID: 24344681.
  3. Maaswinkel H, Zhu L, Weng W. Using an Automated 3D-tracking System to Record Individual and Shoals of Adult Zebrafish. J Vis Exp. 2013 Dec 5;(82). doi: 10.3791/50681. PubMed PMID: 24336189.

Evolution

  1. Williams TA, Foster PG, Cox CJ, Embley TM. An archaeal origin of eukaryotes supports only two primary domains of life. Nature. 2013 Dec 12;504(7479):231-6. doi: 10.1038/nature12779. PubMed PMID: 24336283.

Development

  1. Kearns NA, Genga RM, Enuameh MS, Garber M, Wolfe SA, Maehr R. Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development. 2014 Jan;141(1):219-23. doi: 10.1242/dev.103341. PubMed PMID: 24346702.
  2. Koyanagi-Aoi M, Ohnuki M, Takahashi K, Okita K, Noma H, Sawamura Y, Teramoto I, Narita M, Sato Y, Ichisaka T, Amano N, Watanabe A, Morizane A, Yamada Y, Sato T, Takahashi J, Yamanaka S. Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells. Proc Natl Acad Sci U S A. 2013 Nov 20. [Epub ahead of print] PubMed PMID: 24259714.
  3. Plouhinec JL, Zakin L, Moriyama Y, De Robertis EM. Chordin forms a self-organizing morphogen gradient in the extracellular space between ectoderm and mesoderm in the Xenopus embryo. Proc Natl Acad Sci U S A. 2013 Nov 27. [Epub ahead of print] PubMed PMID: 24284174.
  4. Tan L, Zong C, Xie XS. Rare event of histone demethylation can initiate singular gene expression of olfactory receptors. Proc Natl Acad Sci U S A. 2013 Dec 16. [Epub ahead of print] PubMed PMID: 24344257.

Retina

  1. Weber A, Hochmann S, Cimalla P, Gärtner M, Kuscha V, Hans S, Geffarth M, Kaslin J, Koch E, Brand M. Characterization of light lesion paradigms and optical coherence tomography as tools to study adult retina regeneration in zebrafish. PLoS One. 2013 Nov 26;8(11):e80483. doi: 10.1371/journal.pone.0080483. PubMed PMID: 24303018; PubMed Central PMCID: PMC3841302.

Funding

  1. Mervis J, Malakoff D. Science funding. U.S. budget deal offers researchers some sequester relief. Science. 2013 Dec 20;342(6165):1426-7. doi: 10.1126/science.342.6165.1426. PubMed PMID: 24357280.

Medicine

  1. Johnson SC, Yanos ME, Kayser EB, Quintana A, Sangesland M, Castanza A, Uhde L, Hui J, Wall VZ, Gagnidze A, Oh K, Wasko BM, Ramos FJ, Palmiter RD, Rabinovitch PS, Morgan PG, Sedensky MM, Kaeberlein M. mTOR inhibition alleviates mitochondrial disease in a mouse model of Leigh syndrome. Science. 2013 Dec 20;342(6165):1524-8. doi: 10.1126/science.1244360. Epub 2013 Nov 14. PubMed PMID: 24231806.
    • Vafai SB, Mootha VK. Medicine. A common pathway for a rare disease? Science. 2013 Dec 20;342(6165):1453-4. doi: 10.1126/science.1248449. PubMed PMID: 24357304.

Biochemistry

  1. Xie XS. Biochemistry. Enzyme kinetics, past and present. Science. 2013 Dec 20;342(6165):1457-9. doi: 10.1126/science.1248859. PubMed PMID: 24357307.

Genetics

  1. Xiao A, Wang Z, Hu Y, Wu Y, Luo Z, Yang Z, Zu Y, Li W, Huang P, Tong X, Zhu Z, Lin S, Zhang B. Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Res. 2013 Aug 1;41(14):e141.doi: 10.1093/nar/gkt464. Epub 2013 Jun 6. PubMed PMID: 23748566; PubMed Central PMCID: PMC3737551.
  2. Wei C, Liu J, Yu Z, Zhang B, Gao G, Jiao R. TALEN or Cas9 – rapid, efficient and specific choices for genome modifications. J Genet Genomics. 2013 Jun 20;40(6):281-9. doi: 10.1016/j.jgg.2013.03.013. Epub 2013 Apr 12. PubMed PMID: 23790627. 
  3. Gaj T, Gersbach CA, Barbas CF 3rd. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013 Jul;31(7):397-405. doi: 10.1016/j.tibtech.2013.04.004. Epub 2013 May 9. PubMed PMID: 23664777; PubMed Central PMCID: PMC3694601.
  4. Ochiai H, Fujita K, Suzuki K, Nishikawa M, Shibata T, Sakamoto N, Yamamoto T. Targeted mutagenesis in the sea urchin embryo using zinc-finger nucleases. Genes Cells. 2010 Aug;15(8):875-85. doi: 10.1111/j.1365-2443.2010.01425.x. Epub 2010 Jul 2. PubMed PMID: 20604805.
    • SSA assay
  5. Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol. 2013 Aug 11. doi: 10.1038/nbt.2673. [Epub ahead of print] PubMed PMID: 23934178.
  6. Bruder CE, Piotrowski A, Gijsbers AA, Andersson R, Erickson S, Diaz de Ståhl T, Menzel U, Sandgren J, von Tell D, Poplawski A, Crowley M, Crasto C, Partridge EC, Tiwari H, Allison DB, Komorowski J, van Ommen GJ, Boomsma DI, Pedersen NL, den Dunnen JT, Wirdefeldt K, Dumanski JP. Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. Am J Hum Genet. 2008 Mar;82(3):763-71. doi: 10.1016/j.ajhg.2007.12.011. Epub 2008 Feb 14. PubMed PMID: 18304490; PubMed Central PMCID: PMC2427204.
  7. Narlikar GJ, Sundaramoorthy R, Owen-Hughes T. Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes. Cell. 2013 Aug 1;154(3):490-503. doi: 10.1016/j.cell.2013.07.011. PubMed PMID: 23911317.

Cell cycle

  1. Jonas K, Liu J, Chien P, Laub MT. Proteotoxic Stress Induces a Cell-Cycle Arrest by Stimulating Lon to Degrade the Replication Initiator DnaA. Cell. 2013 Aug 1;154(3):623-36. doi: 10.1016/j.cell.2013.06.034. PubMed PMID: 23911325; PubMed Central PMCID: PMC3749246.

 Disease gene mapping and sequencing

  1. Brunham LR, Hayden MR. Hunting human disease genes: lessons from the past, challenges for the future. Hum Genet. 2013 Jun;132(6):603-17. doi: 10.1007/s00439-013-1286-3. Epub 2013 Mar 17. Review. PubMed PMID: 23504071; PubMed Central PMCID: PMC3654184.
  2. Shendure J, Lieberman Aiden E. The expanding scope of DNA sequencing. Nat Biotechnol. 2012 Nov;30(11):1084-94. doi: 10.1038/nbt.2421. Epub 2012 Nov 8. Review. PubMed PMID: 23138308.
  3. Gilissen C, Hoischen A, Brunner HG, Veltman JA. Disease gene identification strategies for exome sequencing. Eur J Hum Genet. 2012 May;20(5):490-7. doi: 10.1038/ejhg.2011.258. Epub 2012 Jan 18. Review. PubMed PMID: 22258526; PubMed Central PMCID: PMC3330229.
  4. Ku CS, Cooper DN, Polychronakos C, Naidoo N, Wu M, Soong R. Exome sequencing: dual role as a discovery and diagnostic tool. Ann Neurol. 2012 Jan;71(1):5-14. doi: 10.1002/ana.22647. Review. PubMed PMID: 22275248.
  5. Goldstein DB, Allen A, Keebler J, Margulies EH, Petrou S, Petrovski S, Sunyaev S. Sequencing studies in human genetics: design and interpretation. Nat Rev Genet. 2013 Jul;14(7):460-70. doi: 10.1038/nrg3455. Epub 2013 Jun 11. PubMed PMID: 23752795.
  6. Cirulli ET, Goldstein DB. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet. 2010 Jun;11(6):415-25. doi: 10.1038/nrg2779. Review. PubMed PMID: 20479773.
  7. Rehm HL. Disease-targeted sequencing: a cornerstone in the clinic. Nat Rev Genet. 2013 Apr;14(4):295-300. doi: 10.1038/nrg3463. Epub 2013 Mar 12. PubMed PMID: 23478348.
  8. Gulsuner S, Walsh T, Watts AC, Lee MK, Thornton AM, Casadei S, Rippey C, Shahin H; Consortium on the Genetics of Schizophrenia (COGS); PAARTNERS Study Group, Nimgaonkar VL, Go RC, Savage RM, Swerdlow NR, Gur RE, Braff DL, King MC, McClellan JM. Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network. Cell. 2013 Aug 1;154(3):518-29. doi: 10.1016/j.cell.2013.06.049. PubMed PMID: 23911319.

Alzheimer’s Disease

  1. Mullard A. Sting of Alzheimer’s failures offset by upcoming prevention trials. Nat Rev Drug Discov. 2012 Sep;11(9):657-60. doi: 10.1038/nrd3842. PubMed PMID: 22935790.
  2. Aisen PS, Vellas B, Hampel H. Moving towards early clinical trials for amyloid-targeted therapy in Alzheimer’s disease. Nat Rev Drug Discov. 2013 Apr;12(4):324. doi: 10.1038/nrd3842-c1. Epub 2013 Mar 15. PubMed PMID: 23493086.
  3. Doody RS, Raman R, Farlow M, Iwatsubo T, Vellas B, Joffe S, Kieburtz K, He F, Sun X, Thomas RG, Aisen PS; Alzheimer’s Disease Cooperative Study SteeringCommittee, Siemers E, Sethuraman G, Mohs R; Semagacestat Study Group. A phase 3 trial of semagacestat for treatment of Alzheimer’s disease. N Engl J Med. 2013 Jul 25;369(4):341-50. doi: 10.1056/NEJMoa1210951. PubMed PMID: 23883379.
  4. Mullard A. Sting of Alzheimer’s failures offset by upcoming prevention trials. Nat Rev Drug Discov. 2012 Sep;11(9):657-60. doi: 10.1038/nrd3842. PubMed PMID: 22935790.
  5. Jonsson T, Atwal JK, Steinberg S, Snaedal J, Jonsson PV, Bjornsson S, Stefansson H, Sulem P, Gudbjartsson D, Maloney J, Hoyte K, Gustafson A, Liu Y, Lu Y, Bhangale T, Graham RR, Huttenlocher J, Bjornsdottir G, Andreassen OA, Jönsson EG, Palotie A, Behrens TW, Magnusson OT, Kong A, Thorsteinsdottir U, Watts RJ, Stefansson K. A mutation in APP protects against Alzheimer’s disease and age-related cognitive decline. Nature. 2012 Aug 2;488(7409):96-9. doi: 10.1038/nature11283. PubMed PMID: 22801501.

Retinal development

  1. Suzuki SC, Bleckert A, Williams PR, Takechi M, Kawamura S, Wong RO. Cone photoreceptor types in zebrafish are generated by symmetric terminal divisions of dedicated precursors. Proc Natl Acad Sci U S A. 2013 Aug 26. [Epub ahead of print] PubMed PMID: 23980162.

Zebrafish

  1. Vignet C, Bégout ML, Péan S, Lyphout L, Leguay D, Cousin X. Systematic Screening of Behavioral Responses in Two Zebrafish Strains. Zebrafish. 2013 Jun 5. [Epub ahead of print] PubMed PMID: 23738739.

Neuroscience

  1. Cai D, Cohen KB, Luo T, Lichtman JW, Sanes JR. Improved tools for the Brainbow toolbox. Nat Methods. 2013 May 5;10(6):540-7. doi: 10.1038/nmeth.2450. Epub 2013 May 5. PubMed PMID: 23817127.
  2. Pan YA, Freundlich T, Weissman TA, Schoppik D, Wang XC, Zimmerman S, Ciruna B, Sanes JR, Lichtman JW, Schier AF. Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish. Development. 2013 Jul;140(13):2835-46. doi: 10.1242/dev.094631. PubMed PMID: 23757414; PubMed Central PMCID: PMC3678346.
    1. Blog post by the first author: Red fish, blue fish, Brainbow fish!

Eye disease

  1. Berger W, Kloeckener-Gruissem B, Neidhardt J. The molecular basis of human retinal and vitreoretinal diseases. Prog Retin Eye Res. 2010 Sep;29(5):335-75. doi: 10.1016/j.preteyeres.2010.03.004. Epub 2010 Mar 31. Review. PubMed PMID: 20362068.
  2. Dalkara D, Byrne LC, Klimczak RR, Visel M, Yin L, Merigan WH, Flannery JG, Schaffer DV. In vivo-directed evolution of a new adeno-associated virus for therapeutic outer retinal gene delivery from the vitreous. Sci Transl Med. 2013 Jun 12;5(189):189ra76. doi: 10.1126/scitranslmed.3005708. PubMed PMID: 23761039.
    1. News coverage: Genes Get in Your Eye.

Genetics

  1. A collection of seminal papers on CRISPR-CAS
    1. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013 Feb 28;152(5):1173-83. doi: 10.1016/j.cell.2013.02.022. PubMed PMID: 23452860; PubMed Central PMCID:PMC3664290.
    2. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012 Aug 17;337(6096):816-21. doi: 10.1126/science.1225829. Epub 2012 Jun 28. PubMed PMID: 22745249.
    3. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010 Jan 8;327(5962):167-70. doi: 10.1126/science.1179555. Review. PubMed PMID: 20056882.
    4. Sampson TR, Saroj SD, Llewellyn AC, Tzeng YL, Weiss DS. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature. 2013 May 9;497(7448):254-7. doi: 10.1038/nature12048. Epub 2013 Apr 14. PubMed PMID: 23584588; PubMed Central PMCID: PMC3651764.
  2. Ma AC, Lee HB, Clark KJ, Ekker SC. High Efficiency In Vivo Genome Engineering with a Simplified 15-RVD GoldyTALEN Design. PLoS One. 2013 May 29;8(5):e65259.doi: 10.1371/journal.pone.0065259. Print 2013. PubMed PMID: 23734242.
  3. Lim S, Wang Y, Yu X, Huang Y, Featherstone MS, Sampath K. A simple strategy for heritable chromosomal deletions in zebrafish via the combinatorial action of  targeting nucleases. Genome Biol. 2013 Jul 1;14(7):R69. [Epub ahead of print] PubMed PMID: 23815890.

Funding

  1. Fortin JM, Currie DJ. Big Science vs. Little Science: How Scientific Impact Scales with Funding. PLoS One. 2013 Jun 19;8(6):e65263. Print 2013. PubMed PMID: 23840323; PubMed Central PMCID: PMC3686789.

Philosophy of science

  1. Biesecker LG. Hypothesis-generating research and predictive medicine. Genome Res. 2013 Jul;23(7):1051-3. doi: 10.1101/gr.157826.113. PubMed PMID: 23817045; PubMed Central PMCID: PMC3698497.

Stem cells

  1. Tachibana M, Amato P, Sparman M, Gutierrez NM, Tippner-Hedges R, Ma H, Kang E, Fulati A, Lee HS, Sritanaudomchai H, Masterson K, Larson J, Eaton D, Sadler-Fredd K, Battaglia D, Lee D, Wu D, Jensen J, Patton P, Gokhale S, Stouffer RL, Wolf D,  Mitalipov S. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell. 2013 Jun 6;153(6):1228-38. doi: 10.1016/j.cell.2013.05.006. Epub 2013 May 15. PubMed PMID: 23683578
    1. News coverage: Scientists create human embryos to make stem cells

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.

 

Gene Therapy/Retinal degeneration

  1. Cideciyan AV, Jacobson SG, Beltran WA, Sumaroka A, Swider M, Iwabe S, Roman AJ, Olivares MB, Schwartz SB, Komáromy AM, Hauswirth WW, Aguirre GD. Human retinal gene therapy for Leber congenital amaurosis shows advancing retinal degeneration despite enduring visual improvement. Proc Natl Acad Sci U S A. 2013 Jan 22. [Epub ahead of print] PubMed PMID: 23341635.

Neuroscience

  1. Muto A, Ohkura M, Abe G, Nakai J, Kawakami K. Real-Time Visualization of Neuronal Activity during Perception. Curr Biol. 2013 Jan 29. doi:pii: S0960-9822(13)00002-X. 10.1016/j.cub.2012.12.040. [Epub ahead of print] PubMed PMID: 23375894.

Genetics

  1. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol. 2013 Jan 29. doi: 10.1038/nbt.2501. [Epub ahead of print] PubMed PMID: 23360964.
  2. Bedell VM, Wang Y, Campbell JM, Poshusta TL, Starker CG, Krug RG 2nd, Tan W, Penheiter SG, Ma AC, Leung AY, Fahrenkrug SC, Carlson DF, Voytas DF, Clark KJ, Essner JJ, Ekker SC. In vivo genome editing using a high-efficiency TALEN system. Nature. 2012 Nov 1;491(7422):114-8. doi: 10.1038/nature11537. Epub 2012 Sep 23. PubMed PMID: 23000899; PubMed Central PMCID: PMC3491146.