Posts tagged ‘CRISPR’


  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.


  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.

Stem cells

  1. Hou P, Li Y, Zhang X, Liu C, Guan J, Li H, Zhao T, Ye J, Yang W, Liu K, Ge J, Xu J, Zhang Q, Zhao Y, Deng H. Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science. 2013 Aug 9;341(6146):651-4. doi: 10.1126/science.1239278. Epub 2013 Jul 18. PubMed PMID: 23868920.


  1. Shomrat T, Levin M. An automated training paradigm reveals long-term memory in planaria and its persistence through head regeneration. J Exp Biol. 2013 Jul 2. [Epub ahead of print] PubMed PMID: 23821717.
  2. Esposti F, Johnston J, Rosa JM, Leung KM, Lagnado L. Olfactory Stimulation Selectively Modulates the OFF Pathway in the Retina of Zebrafish. Neuron. 2013 Jul 10;79(1):97-110. doi: 10.1016/j.neuron.2013.05.001. PubMed PMID: 23849198.
    • Commentary: “Dowling JE. Olfaction and Vision Meet in the Retina. Neuron. 2013 Jul 10;79(1):1-3. doi: 10.1016/j.neuron.2013.06.024. PubMed PMID: 23849191.


  1. Endeman D, Klaassen LJ, Kamermans M. Action spectra of zebrafish cone photoreceptors. PLoS One. 2013 Jul 5;8(7):e68540. doi: 10.1371/journal.pone.0068540. Print 2013. PubMed PMID: 23861916; PubMed Central PMCID: PMC3702584.


  1. Poznik GD, Henn BM, Yee MC, Sliwerska E, Euskirchen GM, Lin AA, Snyder M, Quintana-Murci L, Kidd JM, Underhill PA, Bustamante CD. Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science. 2013 Aug 2;341(6145):562-5. doi: 10.1126/science.1237619. PubMed PMID: 23908239.
  2. Francalacci P, Morelli L, Angius A, Berutti R, Reinier F, Atzeni R, Pilu R, Busonero F, Maschio A, Zara I, Sanna D, Useli A, Urru MF, Marcelli M, Cusano R, Oppo M, Zoledziewska M, Pitzalis M, Deidda F, Porcu E, Poddie F, Kang HM, Lyons R, Tarrier B, Gresham JB, Li B, Tofanelli S, Alonso S, Dei M, Lai S, Mulas A, Whalen MB, Uzzau S, Jones C, Schlessinger D, Abecasis GR, Sanna S, Sidore C, Cucca F. Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science. 2013 Aug 2;341(6145):565-9. doi: 10.1126/science.1237947. PubMed PMID: 23908240.
  3. Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol. 2013 Jun 23. doi: 10.1038/nbt.2623. [Epub ahead of print] PubMed PMID: 23792628.


  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.


  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.


  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


  1. Kabra M, Robie AA, Rivera-Alba M, Branson S, Branson K. JAABA: interactive machine learning for automatic annotation of animal behavior. Nat Methods. 2013 Jan;10(1):64-7. doi: 10.1038/nmeth.2281. Epub 2012 Dec 2. PubMed PMID: 23202433.
  2. Koch KW. The guanylate cyclase signaling system in zebrafish photoreceptors. FEBS Lett. 2013 May 6. doi:pii: S0014-5793(13)00318-9. 10.1016/j.febslet.2013.04.023. [Epub ahead of print] PubMed PMID: 23660405.


  1. Potok ME, Nix DA, Parnell TJ, Cairns BR. Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. Cell. 2013 May 9;153(4):759-72. doi: 10.1016/j.cell.2013.04.030. PubMed PMID: 23663776.
  2. Jiang L, Zhang J, Wang JJ, Wang L, Zhang L, Li G, Yang X, Ma X, Sun X, Cai J, Zhang J, Huang X, Yu M, Wang X, Liu F, Wu CI, He C, Zhang B, Ci W, Liu J. Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos. Cell. 2013 May 9;153(4):773-84. doi: 10.1016/j.cell.2013.04.041. PubMed PMID: 23663777.
    1. Commentary for #1 & 2: Hackett JA, Surani MA. Beyond DNA: Programming and Inheritance of Parental Methylomes. Cell. 2013 May 9;153(4):737-9. doi: 10.1016/j.cell.2013.04.044. PubMed PMID: 23663772.
  3. Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R. One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering. Cell. 2013 May 9;153(4):910-8. doi: 10.1016/j.cell.2013.04.025. Epub 2013 May 2. PubMed PMID: 23643243.
  4. 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.
  5. Gerety SS, Breau MA, Sasai N, Xu Q, Briscoe J, Wilkinson DG. An inducible transgene expression system for zebrafish and chick. Development. 2013 May;140(10):2235-43. doi: 10.1242/dev.091520. PubMed PMID: 23633515.
  6. Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang TH, Lan T, Welch AJ, Juárez MJ, Simpson J, Fernández-Cortés A, Arteaga-Vázquez M, Góngora-Castillo E, Acevedo-Hernández G, Schuster SC, Himmelbauer H, Minoche AE, Xu S, Lynch M, Oropeza-Aburto A, Cervantes-Pérez SA, de Jesús Ortega-Estrada M, Cervantes-Luevano JI, Michael TP, Mockler T, Bryant D, Herrera-Estrella A, Albert VA, Herrera-Estrella L. Architecture and evolution of a minute plant genome. Nature. 2013 May 12. doi: 10.1038/nature12132. [Epub ahead of print] PubMed PMID: 23665961.


  1. Yi P, Park JS, Melton DA. Betatrophin: A Hormone that Controls Pancreatic β Cell Proliferation. Cell. 2013 May 9;153(4):747-58. doi: 10.1016/j.cell.2013.04.008. Epub 2013 Apr 25. PubMed PMID: 23623304.
  2. Mongera A, Nüsslein-Volhard C. Scales of fish arise from mesoderm. Curr Biol. 2013 May 6;23(9):R338-9. doi: 10.1016/j.cub.2013.02.056. PubMed PMID: 23660349.

Systems Biology

  1. Fisher JK, Bourniquel A, Witz G, Weiner B, Prentiss M, Kleckner N. Four-Dimensional Imaging of E. coli Nucleoid Organization and Dynamics in Living Cells. Cell. 2013 May 9;153(4):882-95. doi: 10.1016/j.cell.2013.04.006. Epub 2013 Apr 25. PubMed PMID: 23623305.

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.


  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.


  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.