Posts tagged ‘Genome editing’

Neuroscience

  1. Robie AA, Hirokawa J, Edwards AW, Umayam LA, Lee A, Phillips ML, Card GM, Korff W, Rubin GM, Simpson JH, Reiser MB, Branson K. Mapping the Neural Substrates of Behavior. Cell. 2017 Jul 13;170(2):393-406.e28. doi: 10.1016/j.cell.2017.06.032. PubMed PMID: 28709004.
  2. Smith K. How to map the circuits that define us. Nature. 2017 Aug 9;548(7666):150-152. doi: 10.1038/548150a. PubMed PMID: 28796220.

Evolution

  1. Sousa AMM, Meyer KA, Santpere G, Gulden FO, Sestan N. Evolution of the Human Nervous System Function, Structure, and Development. Cell. 2017 Jul 13;170(2):226-247. doi: 10.1016/j.cell.2017.06.036. Review. PubMed PMID: 28708995.

Genetics

  1. New concerns raised over value of genome-wide disease studies

Cell biology

  1. Biology of single cells shines a light on collaboration. Nature. 2017 Jul 5;547(7661):5. doi: 10.1038/547005a. PubMed PMID: 28682351.

Genomics

  1. Nagano T, Lubling Y, Várnai C, Dudley C, Leung W, Baran Y, Mendelson Cohen N, Wingett S, Fraser P, Tanay A. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature. 2017 Jul 5;547(7661):61-67. doi: 10.1038/nature23001. PubMed PMID: 28682332.

Molecular Biology

  1. Lin YL, Pasero P. Transcription-Replication Conflicts: Orientation Matters. Cell. 2017 Aug 10;170(4):603-604. doi: 10.1016/j.cell.2017.07.040. PubMed PMID: 28802036.

Genome editing

  1. Ma H, Marti-Gutierrez N, Park SW, Wu J, Lee Y, Suzuki K, Koski A, Ji D, Hayama T, Ahmed R, Darby H, Van Dyken C, Li Y, Kang E, Park AR, Kim D, Kim ST, Gong J, Gu Y, Xu X, Battaglia D, Krieg SA, Lee DM, Wu DH, Wolf DP, Heitner SB, Belmonte JCI, Amato P, Kim JS, Kaul S, Mitalipov S. Correction of a pathogenic gene mutation in human embryos. Nature. 2017 Aug 2. doi: 10.1038/nature23305. [Epub ahead of print] PubMed PMID: 28783728.

Genome editing

  1. Scheufele DA, Xenos MA, Howell EL, Rose KM, Brossard D, Hardy BW. U.S. attitudes on human genome editing. Science. 2017 Aug 11;357(6351):553-554. doi: 10.1126/science.aan3708. PubMed PMID: 28798120.
  2. Amitai G, Sorek R. Intracellular signaling in CRISPR-Cas defense. Science. 2017 Aug 11;357(6351):550-551. doi: 10.1126/science.aao2210. PubMed PMID: 28798118.
  3. Kazlauskiene M, Kostiuk G, Venclovas Č, Tamulaitis G, Siksnys V. A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems. Science. 2017 Aug 11;357(6351):605-609. doi: 10.1126/science.aao0100. Epub 2017 Jun 29. PubMed PMID: 28663439.

Eye

  1. Madl T. Patchy proteins form a perfect lens. Science. 2017 Aug 11;357(6351):546-547. doi: 10.1126/science.aao1456. PubMed PMID: 28798115.
  2. Cai J, Townsend JP, Dodson TC, Heiney PA, Sweeney AM. Eye patches: Protein assembly of index-gradient squid lenses. Science. 2017 Aug 11;357(6351):564-569. doi: 10.1126/science.aal2674. PubMed PMID: 28798124.

Funding

  1. Levitt M, Levitt JM. Future of fundamental discovery in US biomedical research. Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6498-6503. doi: 10.1073/pnas.1609996114. Epub 2017 Jun 5. PubMed PMID: 28584129; PubMed Central PMCID: PMC5488913.

Behaviour

  1. Palmér T, Ek F, Enqvist O, Olsson R, Åström K, Petersson P. Action sequencing in the spontaneous swimming behavior of zebrafish larvae – implications for drug development. Sci Rep. 2017 Jun 9;7(1):3191. doi: 10.1038/s41598-017-03144-7. PubMed PMID: 28600565; PubMed Central PMCID: PMC5466685.
  2. Vliet SM, Ho TC, Volz DC. Behavioral screening of the LOPAC(1280) library in zebrafish embryos. Toxicol Appl Pharmacol. 2017 Jun 13. pii: S0041-008X(17)30267-3. doi: 10.1016/j.taap.2017.06.011. [Epub ahead of print] PubMed PMID: 28623180.

Funding

  1. Kaiser J. NIH abandons grant cap, offers new help to younger scientists. Science. 2017 Jun 16;356(6343):1108. doi: 10.1126/science.356.6343.1108. PubMed PMID: 28619891.
  2. Wahls WP. NIH’s ineffective funding policies. Science. 2017 Jun 16;356(6343):1132-1133. doi: 10.1126/science.aan6504. PubMed PMID: 28619908.

Genetics

  1. Cassels L, Barde YA. Scaling pain threshold with microRNAs. Science. 2017 Jun 16;356(6343):1124-1125. doi: 10.1126/science.aan6784. PubMed PMID: 28619901.
  2. Peng C, Li L, Zhang MD, Bengtsson Gonzales C, Parisien M, Belfer I, Usoskin D, Abdo H, Furlan A, Häring M, Lallemend F, Harkany T, Diatchenko L, Hökfelt T, Hjerling-Leffler J, Ernfors P. miR-183 cluster scales mechanical pain sensitivity by regulating basal and neuropathic pain genes. Science. 2017 Jun 16;356(6343):1168-1171. doi: 10.1126/science.aam7671. Epub 2017 Jun 1. PubMed PMID: 28572455.

Genomics

  1. Shekhar K, Lapan SW, Whitney IE, Tran NM, Macosko EZ, Kowalczyk M, Adiconis X, Levin JZ, Nemesh J, Goldman M, McCarroll SA, Cepko CL, Regev A, Sanes JR. Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics. Cell. 2016 Aug 25;166(5):1308-1323.e30. doi: 10.1016/j.cell.2016.07.054. PubMed PMID: 27565351; PubMed Central PMCID: PMC5003425.

Vision

  1. Sabbah S, Gemmer JA, Bhatia-Lin A, Manoff G, Castro G, Siegel JK, Jeffery N, Berson DM. A retinal code for motion along the gravitational and body axes. Nature. 2017 Jun 7. doi: 10.1038/nature22818. [Epub ahead of print] PubMed PMID: 28607486.
  2. Demb JB, Clark DA. Vision: These retinas are made for walkin’. Nature. 2017 Jun 7. doi: 10.1038/nature22505. [Epub ahead of print] PubMed PMID: 28607483

Genome editing

  1. Stella S, Alcón P, Montoya G. Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage. Nature. 2017 May 31. doi: 10.1038/nature22398. [Epub ahead of print] PubMed PMID: 28562584.
  2. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc Natl Acad Sci U S A. 2017 Jun 26. pii: 201707645. doi: 10.1073/pnas.1707645114. [Epub ahead of print] PubMed PMID: 28652374.
  3. Shipman SL, Nivala J, Macklis JD, Church GM. CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature. 2017 Jul 12. doi: 10.1038/nature23017. [Epub ahead of print] PubMed PMID: 28700573.

Stem cell

  1. Servick K. Stem cell approach for cataracts challenged. Science. 2017 Jun 30;356(6345):1318-1319. doi: 10.1126/science.356.6345.1318. PubMed PMID: 28663449.

Eye disease

  1. Servick K. Stem cell approach for cataracts challenged. Science. 2017 Jun 30;356(6345):1318-1319. doi: 10.1126/science.356.6345.1318. PubMed PMID: 28663449.

Ecology/Evolution

  1. Ceballos G, Ehrlich PR, Dirzo R. Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses and declines. Proc Natl Acad Sci U S A. 2017 Jul 10. pii: 201704949. doi: 10.1073/pnas.1704949114. [Epub ahead of print] PubMed PMID: 28696295.
  2. Castiglione GM, Hauser FE, Liao BS, Lujan NK, Van Nynatten A, Morrow JM, Schott RK, Bhattacharyya N, Dungan SZ, Chang BSW. Evolution of nonspectral rhodopsin function at high altitudes. Proc Natl Acad Sci U S A. 2017 Jun 22. pii: 201705765. doi: 10.1073/pnas.1705765114. [Epub ahead of print] PubMed PMID: 28642345.

Imaging

  1. Hildebrand DGC, Cicconet M, Torres RM, Choi W, Quan TM, Moon J, Wetzel AW, Scott Champion A, Graham BJ, Randlett O, Plummer GS, Portugues R, Bianco IH, Saalfeld S, Baden AD, Lillaney K, Burns R, Vogelstein JT, Schier AF, Lee WA, Jeong WK, Lichtman JW, Engert F. Whole-brain serial-section electron microscopy in larval zebrafish. Nature. 2017 May 18;545(7654):345-349. doi: 10.1038/nature22356. Epub 2017 May 10. PubMed PMID: 28489821.

Neuroscience

  1. Ciabatti E, González-Rueda A, Mariotti L, Morgese F, Tripodi M. Life-Long Genetic and Functional Access to Neural Circuits Using Self-Inactivating Rabies Virus. Cell. 2017 Jul 1. pii: S0092-8674(17)30697-9. doi: 10.1016/j.cell.2017.06.014. [Epub ahead of print] PubMed PMID: 28689641.

Development

  1. Kobayashi T, Zhang H, Tang WWC, Irie N, Withey S, Klisch D, Sybirna A, Dietmann S, Contreras DA, Webb R, Allegrucci C, Alberio R, Surani MA. Principles of early human development and germ cell program from conserved model systems. Nature. 2017 Jun 7. doi: 10.1038/nature22812. [Epub ahead of print] PubMed PMID: 28607482.
  2. Peter IS, Davidson EH. Assessing regulatory information in developmental gene regulatory networks. Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):5862-5869. doi: 10.1073/pnas.1610616114. PubMed PMID: 28584110.

Regeneration

  1. Laha B, Stafford BK, Huberman AD. Regenerating optic pathways from the eye to the brain. Science. 2017 Jun 9;356(6342):1031-1034. doi: 10.1126/science.aal5060. Review. PubMed PMID: 28596336.

Genomics

  1. Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D. Improved maize reference genome with single-molecule technologies. Nature. 2017 Jun 12. doi: 10.1038/nature22971. [Epub ahead of print] PubMed PMID: 28605751.

Stem cells

  1. Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature. 2017 May 10. doi: 10.1038/nature22403. [Epub ahead of print] PubMed PMID: 28489815.

Genome Editing

  1. Dong, Guo M, Wang S, Zhu Y, Wang S, Xiong Z, Yang J, Xu Z, Huang Z. Structural basis of CRISPR-SpyCas9 inhibition by an anti-CRISPR protein. Nature. 2017 Apr 27. doi: 10.1038/nature22377. [Epub ahead of print] PubMed PMID: 28448066.

Molecular Biology

  1. Pennisi E. Circular DNA throws biologists for a loop. Science. 2017 Jun 9;356(6342):996. doi: 10.1126/science.356.6342.996. PubMed PMID: 28596318.
  2. Roundtree IA, Evans ME, Pan T, He C. Dynamic RNA Modifications in Gene Expression Regulation. Cell. 2017 Jun 15;169(7):1187-1200. doi: 10.1016/j.cell.2017.05.045. Review. PubMed PMID: 28622506.

Funding

  1. Kaiser J. Data Check: Critics challenge NIH finding that bigger labs aren’t necessarily better. Science. 2017 Jun 9;356(6342):997. doi: 10.1126/science.356.6342.997. PubMed PMID: 28596319.

Genetics

  1. Boyle EA, Li YI, Pritchard JK. An Expanded View of Complex Traits: From Polygenic to Omnigenic. Cell. 2017 Jun 15;169(7):1177-1186. doi: 10.1016/j.cell.2017.05.038. Review. PubMed PMID: 28622505.
  2. Trigos AS, Pearson RB, Papenfuss AT, Goode DL. Altered interactions between unicellular and multicellular genes drive hallmarks of transformation in a diverse range of solid tumors. Proc Natl Acad Sci U S A. 2017 Jun 13;114(24):6406-6411. doi: 10.1073/pnas.1617743114. Epub 2017 May 8. PubMed PMID: 28484005.
  3. Bussey KJ, Cisneros LH, Lineweaver CH, Davies PCW. Ancestral gene regulatory networks drive cancer. Proc Natl Acad Sci U S A. 2017 Jun 13;114(24):6160-6162. doi: 10.1073/pnas.1706990114. Epub 2017 Jun 5. PubMed PMID: 28584134.

Evolution

  1. Cindrova-Davies T, Jauniaux E, Elliot MG, Gong S, Burton GJ, Charnock-Jones DS. RNA-seq reveals conservation of function among the yolk sacs of human, mouse, and chicken. Proc Natl Acad Sci U S A. 2017 Jun 13;114(24):E4753-E4761. doi: 10.1073/pnas.1702560114. Epub 2017 May 30. PubMed PMID: 28559354.

 

Stem cells

  1. Mandai M, Watanabe A, Kurimoto Y, Hirami Y, Morinaga C, Daimon T, Fujihara M, Akimaru H, Sakai N, Shibata Y, Terada M, Nomiya Y, Tanishima S, Nakamura M, Kamao H, Sugita S, Onishi A, Ito T, Fujita K, Kawamata S, Go MJ, Shinohara C, Hata KI, Sawada M, Yamamoto M, Ohta S, Ohara Y, Yoshida K, Kuwahara J, Kitano Y, Amano N, Umekage M, Kitaoka F, Tanaka A, Okada C, Takasu N, Ogawa S, Yamanaka S, Takahashi M. Autologous Induced Stem-Cell-Derived Retinal Cells for Macular Degeneration. N Engl J Med. 2017 Mar 16;376(11):1038-1046. doi: 10.1056/NEJMoa1608368. PubMed PMID: 28296613.
  2. Merkle FT, Ghosh S, Kamitaki N, Mitchell J, Avior Y, Mello C, Kashin S, Mekhoubad S, Ilic D, Charlton M, Saphier G, Handsaker RE, Genovese G, Bar S, Benvenisty N, McCarroll SA, Eggan K. Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature. 2017 May 11;545(7653):229-233. doi: 10.1038/nature22312. Epub 2017 Apr 26. PubMed PMID: 28445466; PubMed Central PMCID: PMC5427175.

Genome-editing

  1. Yu W, Mookherjee S, Chaitankar V, Hiriyanna S, Kim JW, Brooks M, Ataeijannati Y, Sun X, Dong L, Li T, Swaroop A, Wu Z. Nrl knockdown by AAV-delivered CRISPR/Cas9 prevents retinal degeneration in mice. Nat Commun. 2017 Mar 14;8:14716. doi: 10.1038/ncomms14716. PubMed PMID: 28291770.
  2. Schaefer KA, Wu WH, Colgan DF, Tsang SH, Bassuk AG, Mahajan VB. Unexpected mutations after CRISPR-Cas9 editing in vivo. Nat Methods. 2017 May 30;14(6):547-548. doi: 10.1038/nmeth.4293. PubMed PMID: 28557981.

Scientific Career

  1. Barnett A. Comment: Research needs more competence, less ‘excellence’. Nature. 2017 Mar 22;543(7646):S29. doi: 10.1038/543S29a. PubMed PMID: 28328912.

Development

  1. Lefrançais E, Ortiz-Muñoz G, Caudrillier A, Mallavia B, Liu F, Sayah DM, Thornton EE, Headley MB, David T, Coughlin SR, Krummel MF, Leavitt AD, Passegué E, Looney MR. The lung is a site of platelet biogenesis and a reservoir for haematopoietic progenitors. Nature. 2017 Apr 6;544(7648):105-109. doi: 10.1038/nature21706. Epub 2017 Mar 22. PubMed PMID: 28329764.

Genomics

  1. Stevens TJ, Lando D, Basu S, Atkinson LP, Cao Y, Lee SF, Leeb M, Wohlfahrt KJ, Boucher W, O’Shaughnessy-Kirwan A, Cramard J, Faure AJ, Ralser M, Blanco E, Morey L, Sansó M, Palayret MG, Lehner B, Di Croce L, Wutz A, Hendrich B, Klenerman D, Laue ED. 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature. 2017 Apr 6;544(7648):59-64. doi: 10.1038/nature21429. Epub 2017 Mar 13. PubMed PMID: 28289288; PubMed Central PMCID: PMC5385134.

Eye diseases, glaucoma

  1. Williams PA, Harder JM, Foxworth NE, Cochran KE, Philip VM, Porciatti V, Smithies O, John SW. Vitamin B(3) modulates mitochondrial vulnerability and prevents glaucoma in aged mice. Science. 2017 Feb 17;355(6326):756-760. doi: 10.1126/science.aal0092. PubMed PMID: 28209901; PubMed Central PMCID: PMC5408298.
    • Crowston J, Trounce I. Relief for retinal neurons under pressure. Science. 2017 Feb 17;355(6326):688-689. doi: 10.1126/science.aam7935. PubMed PMID: 28209856.

Retina

  1. Wang J, O’Sullivan ML, Mukherjee D, Puñal VM, Farsiu S, Kay JN. Anatomy and spatial organization of Müller glia in mouse retina. J Comp Neurol. 2017 Jun 1;525(8):1759-1777. doi: 10.1002/cne.24153. Epub 2017 Mar 7. PubMed PMID: 27997986.
  2. Xiang L, Chen XJ, Wu KC, Zhang CJ, Zhou GH, Lv JN, Sun LF, Cheng FF, Cai XB, Jin ZB. miR-183/96 plays a pivotal regulatory role in mouse photoreceptor maturation and maintenance. Proc Natl Acad Sci U S A. 2017 May 30. pii: 201618757. doi: 10.1073/pnas.1618757114. [Epub ahead of print] PubMed PMID: 28559309.
  3. Fan J, Jia L, Li Y, Ebrahim S, May-Simera H, Wood A, Morell RJ, Liu P, Lei J,  Kachar B, Belluscio L, Qian H, Li T, Li W, Wistow G, Dong L. Maturation arrest in early postnatal sensory receptors by deletion of the miR-183/96/182 cluster in mouse. Proc Natl Acad Sci U S A. 2017 May 23;114(21):E4271-E4280. doi: 10.1073/pnas.1619442114. Epub 2017 May 8. PubMed PMID: 28484004; PubMed Central PMCID: PMC5448201.

Genetics

  1. Yang J, Jin ZB, Chen J, Huang XF, Li XM, Liang YB, Mao JY, Chen X, Zheng Z, Bakshi A, Zheng DD, Zheng MQ, Wray NR, Visscher PM, Lu F, Qu J. Genetic signatures of high-altitude adaptation in Tibetans. Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):4189-4194. doi: 10.1073/pnas.1617042114. Epub 2017 Apr 3. PubMed PMID: 28373541; PubMed Central PMCID: PMC5402460.
  2. Jin ZB, Wu J, Huang XF, Feng CY, Cai XB, Mao JY, Xiang L, Wu KC, Xiao X, Kloss BA, Li Z, Liu Z, Huang S, Shen M, Cheng FF, Cheng XW, Zheng ZL, Chen X, Zhuang W, Zhang Q, Young TL, Xie T, Lu F, Qu J. Trio-based exome sequencing arrests de novo mutations in early-onset high myopia. Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):4219-4224. doi: 10.1073/pnas.1615970114. Epub 2017 Apr 3. PubMed PMID: 28373534; PubMed Central PMCID: PMC5402409.

 

Neuroscience

  1. Dresler M, Shirer WR, Konrad BN, Müller NC, Wagner IC, Fernández G, Czisch M, Greicius MD. Mnemonic Training Reshapes Brain Networks to Support Superior Memory. Neuron. 2017 Mar 8;93(5):1227-1235.e6. doi: 10.1016/j.neuron.2017.02.003. PubMed PMID: 28279356.
  2. Burton CE, Zhou Y, Bai Q, Burton EA. Spectral properties of the zebrafish visual motor response. Neurosci Lett. 2017 Mar 3. pii: S0304-3940(17)30204-5. doi: 10.1016/j.neulet.2017.03.002. [Epub ahead of print] PubMed PMID: 28267562.

Genome editing

  1. Tang L, Zeng Y, Du H, Gong M, Peng J, Zhang B, Lei M, Zhao F, Wang W, Li X, Liu J. CRISPR/Cas9-mediated gene editing in human zygotes using Cas9 protein. Mol Genet Genomics. 2017 Mar 1. doi: 10.1007/s00438-017-1299-z. [Epub ahead of print] PubMed PMID: 28251317.
  2. Hohmann S. Editor’s comment on “CRISPR/Cas9-mediated gene editing in human zygotes using Cas9 protein”. Mol Genet Genomics. 2017 Mar 1. doi: 10.1007/s00438-017-1300-x. [Epub ahead of print] PubMed PMID: 28251316.

ELSI

  1. Williams WM, Ceci SJ. National hiring experiments reveal 2:1 faculty preference for women on STEM tenure track. Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):5360-5. doi: 10.1073/pnas.1418878112. PubMed PMID: 25870272; PubMed Central PMCID: PMC4418903.

Genome editing

  1. Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe-Molina P, Monel B, Schumann K, Yu H, Krupzcak KM, Garcia-Beltran W, Piechocka-Trocha A, Krogan NJ, Marson A, Sabatini DM, Lander ES, Hacohen N, Walker BD. A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Nat Genet. 2017 Feb;49(2):193-203. doi: 10.1038/ng.3741. PubMed PMID: 27992415.
    • Commentary: Tsui CK, Gupta A, Bassik MC. Finding host targets for HIV therapy. Nat Genet. 2017 Jan 31;49(2):175-176. doi: 10.1038/ng.3777. PubMed PMID: 28138150.
  2. Bengtsson NE, Hall JK, Odom GL, Phelps MP, Andrus CR, Hawkins RD, Hauschka SD, Chamberlain JR, Chamberlain JS. Muscle-specific CRISPR/Cas9 dystrophin gene editing ameliorates pathophysiology in a mouse model for Duchenne muscular dystrophy. Nat Commun. 2017 Feb 14;8:14454. doi: 10.1038/ncomms14454. PubMed PMID: 28195574.

Disease

  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.

Genomics

  1. Li X, Xiong X, Yi C. Epitranscriptome sequencing technologies: decoding RNA modifications. Nat Methods. 2016 Dec 29;14(1):23-31. doi: 10.1038/nmeth.4110. PubMed PMID: 28032622.
  2. Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016 Dec 15;167(7):1867-1882.e21. doi: 10.1016/j.cell.2016.11.048. PubMed PMID: 27984733.
  3. Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016 Dec 15;167(7):1853-1866.e17. doi: 10.1016/j.cell.2016.11.038. PubMed PMID: 27984732; PubMed Central PMCID: PMC5181115.
  4. Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, Salame TM, Tanay A, van Oudenaarden A, Amit I. Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq. Cell. 2016 Dec 15;167(7):1883-1896.e15. doi: 10.1016/j.cell.2016.11.039. PubMed PMID: 27984734.

RNA

  1. Rivas E, Clements J, Eddy SR. A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs. Nat Methods. 2017 Jan;14(1):45-48. doi: 10.1038/nmeth.4066. PubMed PMID: 27819659.

Cell cycle

  1. Swaffer MP, Jones AW, Flynn HR, Snijders AP, Nurse P. CDK Substrate Phosphorylation and Ordering the Cell Cycle. Cell. 2016 Dec 15;167(7):1750-1761.e16. doi: 10.1016/j.cell.2016.11.034. PubMed PMID: 27984725; PubMed Central PMCID: PMC5161751.

Genome Editing

  1. Pawluk A, Amrani N, Zhang Y, Garcia B, Hidalgo-Reyes Y, Lee J, Edraki A, Shah M, Sontheimer EJ, Maxwell KL, Davidson AR. Naturally Occurring Off-Switches for CRISPR-Cas9. Cell. 2016 Dec 15;167(7):1829-1838.e9. doi: 10.1016/j.cell.2016.11.017. PubMed PMID: 27984730.
  2. Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016 Dec 15;167(7):1867-1882.e21. doi: 10.1016/j.cell.2016.11.048. PubMed PMID: 27984733.
  3. Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016 Dec 15;167(7):1853-1866.e17. doi: 10.1016/j.cell.2016.11.038. PubMed PMID: 27984732; PubMed Central PMCID: PMC5181115.
  4. Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, Salame TM, Tanay A, van Oudenaarden A, Amit I. Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq. Cell. 2016 Dec 15;167(7):1883-1896.e15. doi: 10.1016/j.cell.2016.11.039. PubMed PMID: 27984734.
  5. Sheridan C. CRISPR therapeutics push into human testing. Nat Biotechnol. 2017 Jan 10;35(1):3-5. doi: 10.1038/nbt0117-3. PubMed PMID: 28072788.

Zebrafish

  1. Reade A, Motta-Mena LB, Gardner KH, Stainier DY, Weiner OD, Woo S. TAEL: A zebrafish-optimized optogenetic gene expression system with fine spatial and temporal control. Development. 2016 Dec 19. pii: dev.139238. [Epub ahead of print] PubMed PMID: 27993986.

Stem Cells

  1. Mandai M, Fujii M, Hashiguchi T, Sunagawa GA, Ito S, Sun J, Kaneko J, Sho J, Yamada C, Takahashi M. iPSC-Derived Retina Transplants Improve Vision in rd1 End-Stage Retinal-Degeneration Mice. Stem Cell Reports. 2017 Jan 10;8(1):69-83. doi: 10.1016/j.stemcr.2016.12.008. PubMed PMID: 28076757.

				

Genome editing

  1. Braun CJ, Bruno PM, Horlbeck MA, Gilbert LA, Weissman JS, Hemann MT. Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation. Proc Natl Acad Sci U S A. 2016 Jun 20. pii: 201600582. [Epub ahead of print] PubMed PMID: 27325776.

Regeneration

  1. Neves J, Zhu J, Sousa-Victor P, Konjikusic M, Riley R, Chew S, Qi Y, Jasper H, Lamba DA. Immune modulation by MANF promotes tissue repair and regenerative success in the retina. Science. 2016 Jul 1;353(6294):aaf3646. doi: 10.1126/science.aaf3646. PubMed PMID: 27365452.

Genomics

  1. Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea PI, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 2016 Jul 1;353(6294):78-82. doi: 10.1126/science.aaf2403. PubMed PMID: 27365449.
  2. Wu J, Huang B, Chen H, Yin Q, Liu Y, Xiang Y, Zhang B, Liu B, Wang Q, Xia W, Li W, Li Y, Ma J, Peng X, Zheng H, Ming J, Zhang W, Zhang J, Tian G, Xu F, Chang Z, Na J, Yang X, Xie W. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016 Jun 15;534(7609):652-657. doi: 10.1038/nature18606. [Epub ahead of print] PubMed PMID: 27309802.

Development

  1. Wu J, Huang B, Chen H, Yin Q, Liu Y, Xiang Y, Zhang B, Liu B, Wang Q, Xia W, Li W, Li Y, Ma J, Peng X, Zheng H, Ming J, Zhang W, Zhang J, Tian G, Xu F, Chang Z, Na J, Yang X, Xie W. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016 Jun 15;534(7609):652-657. doi: 10.1038/nature18606. [Epub ahead of print] PubMed PMID: 27309802.

Funding

  1. von Hippel T, von Hippel C. To apply or not to apply: a survey analysis of grant writing costs and benefits. PLoS One. 2015 Mar 4;10(3):e0118494. doi: 10.1371/journal.pone.0118494. eCollection 2015. PubMed PMID: 25738742; PubMed Central PMCID: PMC4349454.

				

Development

  1. Baxendale S, Whitfield TT. Methods to study the development, anatomy, and function of the zebrafish inner ear across the life course. Methods Cell Biol. 2016;134:165-209. doi: 10.1016/bs.mcb.2016.02.007. Epub 2016 Mar 9. PubMed PMID: 27312494.
  2. Simoes-Costa M, Bronner ME. Reprogramming of avian neural crest axial identity and cell fate. Science. 2016 Jun 24;352(6293):1570-3. doi: 10.1126/science.aaf2729. PubMed PMID: 27339986.

Genetics

  1. Birney E, Smith GD, Greally JM. Epigenome-wide Association Studies and the Interpretation of Disease -Omics. PLoS Genet. 2016 Jun 23;12(6):e1006105. doi: 10.1371/journal.pgen.1006105. eCollection 2016 Jun. Review. PubMed PMID: 27336614.

Molecular Biology

  1. Ellefson JW, Gollihar J, Shroff R, Shivram H, Iyer VR, Ellington AD. Synthetic evolutionary origin of a proofreading reverse transcriptase. Science. 2016 Jun 24;352(6293):1590-3. doi: 10.1126/science.aaf5409. PubMed PMID: 27339990.

Genome Editing

  1. Feng Y, Chen C, Han Y, Chen Z, Lu X, Liang F, Li S, Qin W, Lin S. Expanding CRISPR/Cas9 Genome Editing Capacity in Zebrafish Using SaCas9. G3 (Bethesda). 2016 Jun 17. pii: g3.116.031914. doi: 10.1534/g3.116.031914. [Epub ahead of print] PubMed PMID: 27317783.

Behaviour

  1. Peeters BW, Moeskops M, Veenvliet AR. Color Preference in Danio rerio: Effects of Age and Anxiolytic Treatments. Zebrafish. 2016 Aug;13(4):330-4. doi: 10.1089/zeb.2015.1150. PubMed PMID: 27333080.

Stem cells

  1. Clevers H. Modeling Development and Disease with Organoids. Cell. 2016 Jun 16;165(7):1586-97. doi: 10.1016/j.cell.2016.05.082. Review. PubMed PMID: 27315476.

Retina

  1. Malicki J, Pooranachandran N, Nikolaev A, Fang X, Avanesov A. Analysis of the retina in the zebrafish model. Methods Cell Biol. 2016;134:257-334. doi: 10.1016/bs.mcb.2016.04.017. Epub 2016 Jun 2. PubMed PMID: 27312496.
  2. Kim JW, Yang HJ, Oel AP, Brooks MJ, Jia L, Plachetzki DC, Li W, Allison WT, Swaroop A. Recruitment of Rod Photoreceptors from Short-Wavelength-Sensitive Cones during the Evolution of Nocturnal Vision in Mammals. Dev Cell. 2016 Jun 20;37(6):520-32. doi: 10.1016/j.devcel.2016.05.023. PubMed PMID: 27326930; PubMed Central PMCID: PMC4918105.


				

Retinal development

  1. Tian C, Zou S, Hu B. Extraocular Source of Oligodendrocytes Contribute to Retinal Myelination and Optokinetic Responses in Zebrafish. Invest Ophthalmol Vis Sci. 2016 Apr 1;57(4):2129-38. doi: 10.1167/iovs.15-17675. PubMed PMID: 27100159.
  2. Riesenberg AN, Brown NL. Cell autonomous and nonautonomous requirements for Delltalike1 during early mouse retinal neurogenesis. Dev Dyn. 2016 Jun;245(6):631-40. doi: 10.1002/dvdy.24402. Epub 2016 Apr 4. PubMed PMID: 26947267; PubMed Central PMCID: PMC4873400.

Scientific Career

  1. Mervis J. BEHIND THE NUMBERS. ‘Employment crisis’ for new Ph.D.s is an illusion. Science. 2016 May 20;352(6288):880. doi: 10.1126/science.352.6288.880. PubMed PMID: 27199396.

Evolution

  1. Karnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, Novák L, Žárský V, Barlow LD, Herman EK, Soukal P, Hroudová M, Doležal P, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Vlček Č, Hampl V. A Eukaryote without a Mitochondrial Organelle. Curr Biol. 2016 May 23;26(10):1274-84. doi: 10.1016/j.cub.2016.03.053. Epub 2016 May 12. PubMed PMID: 27185558.

Visual behaviour

  1. Orger MB. The Cellular Organization of Zebrafish Visuomotor Circuits. Curr Biol. 2016 May 9;26(9):R377-85. doi: 10.1016/j.cub.2016.03.054. Review. PubMed PMID: 27166700.
  2. Currie SP, Doherty GH, Sillar KT. Deep-brain photoreception links luminance detection to motor output in Xenopus frog tadpoles. Proc Natl Acad Sci U S A. 2016 May 24;113(21):6053-8. doi: 10.1073/pnas.1515516113. Epub 2016 May 10. PubMed PMID: 27166423.

Scientific publishing

  1. Berg JM, Bhalla N, Bourne PE, Chalfie M, Drubin DG, Fraser JS, Greider CW, Hendricks M, Jones C, Kiley R, King S, Kirschner MW, Krumholz HM, Lehmann R, Leptin M, Pulverer B, Rosenzweig B, Spiro JE, Stebbins M, Strasser C, Swaminathan S, Turner P, Vale RD, VijayRaghavan K, Wolberger C. SCIENTIFIC COMMUNITY. Preprints for the life sciences. Science. 2016 May 20;352(6288):899-901. doi: 10.1126/science.aaf9133. PubMed PMID: 27199406.
  2. Sarewitz D. The pressure to publish pushes down quality. Nature. 2016 May 11;533(7602):147. doi: 10.1038/533147a. PubMed PMID: 27172010.

Genome editing

  1. Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016 Jun 2. pii: aaf5573. [Epub ahead of print] PubMed PMID: 27256883.