Posts tagged ‘development’

Genome Editing

  1. Bolukbasi MF, Gupta A, Oikemus S, Derr AG, Garber M, Brodsky MH, Zhu LJ, Wolfe SA. DNA-binding-domain fusions enhance the targeting range and precision of Cas9. Nat Methods. 2015 Oct 19. doi: 10.1038/nmeth.3624. [Epub ahead of print] PubMed PMID: 26480473.
  2. Thakore PI, D’Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, Reddy TE, Crawford GE, Gersbach CA. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods. 2015 Oct 26. doi: 10.1038/nmeth.3630. [Epub ahead of print] PubMed PMID: 26501517.
  3. Nature Outlook: Genome Editing

Science Career

  1. Ma A, Mondragón RJ, Latora V. Anatomy of funded research in science. Proc Natl Acad Sci U S A. 2015 Oct 26. pii: 201513651. [Epub ahead of print] PubMed PMID: 26504240.
  2. Gould J. How to build a better PhD. Nature. 2015 Dec 2;528(7580):22-5. doi: 10.1038/528022a. PubMed PMID: 26632571.
  3. Make the most of PhDs. Nature. 2015 Dec 2;528(7580):7. doi: 10.1038/528007a. PubMed PMID: 26632550.

Neuroscience

  1. Nikolaou N, Meyer MP. Lamination Speeds the Functional Development of Visual Circuits. Neuron. 2015 Nov 18. pii: S0896-6273(15)00886-7. doi: 10.1016/j.neuron.2015.10.020. [Epub ahead of print] PubMed PMID: 26607001.

Medicine

  1. Pankow S, Bamberger C, Calzolari D, Martínez-Bartolomé S, Lavallée-Adam M, Balch WE, Yates JR 3rd. ∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis. Nature. 2015 Nov 30. doi: 10.1038/nature15729. [Epub ahead of print] PubMed PMID: 26618866.

Development

  1. Li IJ, Chang CJ, Liu SC, Abe G, Ota KG. Postembryonic staging of wild-type goldfish, with brief reference to skeletal systems. Dev Dyn. 2015 Aug 28. doi: 10.1002/dvdy.24340. [Epub ahead of print] PubMed PMID: 26316229.

Systems Biology

  1. Keren L, van Dijk D, Weingarten-Gabbay S, Davidi D, Jona G, Weinberger A, Milo R, Segal E. Noise in gene expression is coupled to growth rate. Genome Res. 2015 Dec;25(12):1893-902. doi: 10.1101/gr.191635.115. Epub 2015 Sep 9. PubMed PMID: 26355006.

Genome editing

  1. Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M, Liu Z, Doudna JA, Tjian R. Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science. 2015 Nov 13;350(6262):823-6. doi: 10.1126/science.aac6572. PubMed PMID: 26564855.
  2. Kiani S, Chavez A, Tuttle M, Hall RN, Chari R, Ter-Ovanesyan D, Qian J, Pruitt BW, Beal J, Vora S, Buchthal J, Kowal EJ, Ebrahimkhani MR, Collins JJ, Weiss R, Church G. Cas9 gRNA engineering for genome editing, activation and repression. Nat Methods. 2015 Nov;12(11):1051-4. doi: 10.1038/nmeth.3580. Epub 2015 Sep 7. PubMed PMID: 26344044.
  3. Reardon S. Leukaemia success heralds wave of gene-editing therapies. Nature. 2015 Nov 12;527(7577):146-7. doi: 10.1038/nature.2015.18737. PubMed PMID: 26560278.
  4. Mathews DJ, Lovell-Badge R, Chan S, Donovan PJ, Douglas T, Gyngell C, Harris J, Regenberg A. CRISPR: A path through the thicket. Nature. 2015 Nov 12;527(7577):159-61. doi: 10.1038/527159a. PubMed PMID: 26560284.
  5. Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015 Sep 16.
  6. Weber J, Öllinger R, Friedrich M, Ehmer U, Barenboim M, Steiger K, Heid I, Mueller S, Maresch R, Engleitner T, Gross N, Geumann U, Fu B, Segler A, Yuan D, Lange S, Strong A, de la Rosa J, Esposito I, Liu P, Cadiñanos J, Vassiliou GS, Schmid RM, Schneider G, Unger K, Yang F, Braren R, Heikenwälder M, Varela I, Saur D, Bradley A, Rad R. CRISPR/Cas9 somatic multiplex-mutagenesis for high-throughput functional cancer genomics in mice. Proc Natl Acad Sci U S A. 2015 Oct 27. pii: 201512392. [Epub ahead of print] PubMed PMID: 26508638.
  7. Carroll D, Charo RA. The societal opportunities and challenges of genome editing. Genome Biol. 2015 Nov 5;16(1):242.
  8. Ma E, Harrington LB, O’Connell MR, Zhou K, Doudna JA. Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes. Mol Cell. 2015 Nov 5;60(3):398-407.
  9. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS,
    Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F.  Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Cell. 2015 Sep 23. pii: S0092-8674(15)01200-3. doi: 10.1016/j.cell.2015.09.038. [Epub ahead of print] PubMed PMID: 26422227.
  10. Carrington B, Varshney GK, Burgess SM, Sood R. CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity. Nucleic Acids Res. 2015 Aug 7. pii: gkv802. [Epub ahead of print] PubMed PMID: 26253739.
  11. Varshney GK, Pei W, LaFave MC, Idol J, Xu L, Gallardo V, Carrington B, Bishop K, Jones M, Li M, Harper U, Huang SC, Prakash A, Chen W, Sood R, Ledin J, Burgess SM. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res. 2015 Jul;25(7):1030-42. doi: 10.1101/gr.186379.114. Epub 2015 Jun 5. PubMed PMID: 26048245; PubMed Central PMCID: PMC4484386.
  12. Bachu R, Bergareche I, Chasin LA. CRISPR-Cas targeted plasmid integration into mammalian cells via non-homologous end joining. Biotechnol Bioeng. 2015 May 5. doi: 10.1002/bit.25629. [Epub ahead of print] PubMed PMID: 25943095.

Genomics

  1. Grün D, van Oudenaarden A. Design and Analysis of Single-Cell Sequencing Experiments. Cell. 2015 Nov 5;163(4):799-810. doi: 10.1016/j.cell.2015.10.039. Review. PubMed PMID: 26544934.
  2. Duttke SH, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U. Human promoters are intrinsically directional. Mol Cell. 2015 Feb 19;57(4):674-84.
  3. Spisák S, Lawrenson K, Fu Y, Csabai I, Cottman RT, Seo JH, Haiman C, Han Y, Lenci R, Li Q, Tisza V, Szállási Z, Herbert ZT, Chabot M, Pomerantz M, Solymosi N; GAME-ON/ELLIPSE Consortium, Gayther SA, Joung JK, Freedman ML. CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants. Nat Med. 2015 Sep 23. doi: 10.1038/nm.3975. [Epub ahead of print] PubMed PMID: 26398868.
  4. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.PubMed PMID: 26432246; PubMed Central PMCID: PMC4617611.
  5. Cho MK. Preventive Genomic Sequencing in the General Population: Do PGS Fly? Am J Bioeth. 2015 Jul;15(7):1-2. doi: 10.1080/15265161.2015.1054160. PubMed PMID: 26147253.

Science Magazine Special Issue—Hunting Mutations, Targeting Disease

Statistics

  1. Lo A, Chernoff H, Zheng T, Lo SH. Why significant variables aren’t automatically good predictors. Proc Natl Acad Sci U S A. 2015 Oct 26. pii:201518285. [Epub ahead of print] PubMed PMID: 26504198.

Development

  1. Barsi JC, Tu Q, Calestani C, Davidson EH. Genome-wide assessment of differential effector gene use in embryogenesis. Development. 2015 Sep 28. pii: dev.127746. [Epub ahead of print] PubMed PMID: 26417044.
  2. Siklenka K, Erkek S, Godmann M, Lambrot R, McGraw S, Lafleur C, Cohen T, Xia J, Suderman M, Hallett M, Trasler J, Peters AH, Kimmins S. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science. 2015 Nov 6;350(6261):aab2006. doi: 10.1126/science.aab2006. Epub 2015 Oct 8. PubMed PMID: 26449473.

Stem cells

  1. Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger K. A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol. 2015 Nov;33(11):1173-1181.
  2. Firth AL, Menon T, Parker GS, Qualls SJ, Lewis BM, Ke E, Dargitz CT, Wright R, Khanna A, Gage FH, Verma IM. Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs. Cell Rep. 2015 Aug 19. pii: S2211-1247(15)00852-9. doi: 10.1016/j.celrep.2015.07.062. [Epub ahead of print] PubMed PMID: 26299960.

Regeneration

  1. Ueki Y, Wilken MS, Cox KE, Chipman L, Jorstad N, Sternhagen K, Simic M, Ullom K, Nakafuku M, Reh TA. Transgenic expression of the proneural transcription factor Ascl1 in Müller glia stimulates retinal regeneration in young mice. Proc Natl Acad Sci U S A. 2015 Oct 19. pii: 201510595. [Epub ahead of print] PubMed PMID: 26483457.

Retina/Photoreceptor

  1. Taylor SM, Alvarez-Delfin K, Saade CJ, Thomas JL, Thummel R, Fadool JM, Hitchcock PF. The bHLH Transcription Factor NeuroD Governs  Photoreceptor Genesis and Regeneration Through Delta-Notch Signaling. Invest Ophthalmol Vis Sci. 2015 Nov 1;56(12):7496-7515.
  2. Hernández-Bejarano M, Gestri G, Spawls L, Nieto-López F, Picker A, Tada M, Brand M, Bovolenta P, Wilson SW, Cavodeassi F. Opposing Shh and Fgf signals initiate nasotemporal patterning of the retina. Development. 2015 Oct 1. pii: dev.125120. [Epub ahead of print] PubMed PMID: 26428010.
  3. Tsujimura T, Masuda R, Ashino R, Kawamura S. Spatially differentiated
    expression of quadruplicated green-sensitive RH2 opsin genes in zebrafish is determined by proximal regulatory regions and gene order to the locus control region. BMC Genet. 2015 Nov 4;16(1):130.
  4. Boije H, Rulands S, Dudczig S, Simons BD, Harris WA. The Independent
    Probabilistic Firing of Transcription Factors: A Paradigm for Clonal Variability in the Zebrafish Retina. Dev Cell. 2015 Sep 2. pii: S1534-5807(15)00525-0.
  5. Chow RW, Almeida AD, Randlett O, Norden C, Harris WA. Inhibitory neuron migration and IPL formation in the developing zebrafish retina. Development. 2015 Jun 26. pii: dev.122473. [Epub ahead of print] PubMed PMID: 26116662.
  6. Ogawa Y, Shiraki T, Kojima D, Fukada Y. Homeobox transcription factor Six7 governs expression of green opsin genes in zebrafish. Proc Biol Sci. 2015 Aug 7;282(1812). pii: 20150659. doi: 10.1098/rspb.2015.0659. PubMed PMID: 26180064.

Eye disease

  1. Zhao L, Chen XJ, Zhu J, Xi YB, Yang X, Hu LD, Ouyang H, Patel SH, Jin X, Lin D, Wu F, Flagg K, Cai H, Li G, Cao G, Lin Y, Chen D, Wen C, Chung C, Wang Y, Qiu A, Yeh E, Wang W, Hu X, Grob S, Abagyan R, Su Z, Tjondro HC, Zhao XJ, Luo H, Hou R, Perry JJ, Gao W, Kozak I, Granet D, Li Y, Sun X, Wang J, Zhang L, Liu Y, Yan YB, Zhang K. Lanosterol reverses protein aggregation in cataracts. Nature. 2015 Jul 30;523(7562):607-11. doi: 10.1038/nature14650. Epub 2015 Jul 22. Erratum in:  Nature. 2015 Oct 22;526(7574):595. PubMed PMID: 26200341.
  2. Makley LN, McMenimen KA, DeVree BT, Goldman JW, McGlasson BN, Rajagopal P, Dunyak BM, McQuade TJ, Thompson AD, Sunahara R, Klevit RE, Andley UP, Gestwicki JE. Pharmacological chaperone for α-crystallin partially restores transparency in cataract models. Science. 2015 Nov 6;350(6261):674-7. doi: 10.1126/science.aac9145. PubMed PMID: 26542570.
  3. Commentary: Quinlan RA. DRUG DISCOVERY. A new dawn for cataracts. Science. 2015 Nov 6;350(6261):636-7. doi: 10.1126/science.aad6303. PubMed PMID: 26542559.

Zebrafish

  1. Xu C, Volkery S, Siekmann AF. Intubation-based anesthesia for long-term time-lapse imaging of adult zebrafish. Nat Protoc. 2015 Dec;10(12):2064-2073.
  2. Pauli A, Montague TG, Lennox KA, Behlke MA, Schier AF. Antisense Oligonucleotide-Mediated Transcript Knockdown in Zebrafish. PLoS One. 2015 Oct 5;10(10):e0139504. doi: 10.1371/journal.pone.0139504. eCollection 2015. PubMed PMID: 26436892; PubMed Central PMCID: PMC4593562.

Research Career

  1. Jackson ST. Going where the science matters. Science. 2015 Oct
    30;350(6260):594. doi: 10.1126/science.350.6260.594. PubMed PMID: 26516284.

Medicine

  1. Henao-Restrepo AM, Longini IM, Egger M, Dean NE, Edmunds WJ, Camacho A, Carroll MW, Doumbia M, Draguez B, Duraffour S, Enwere G, Grais R, Gunther S, Hossmann S, Kondé MK, Kone S, Kuisma E, Levine MM, Mandal S, Norheim G, Riveros X, Soumah A, Trelle S, Vicari AS, Watson CH, Kéïta S, Kieny MP, Røttingen JA. Efficacy and effectiveness of an rVSV-vectored vaccine expressing Ebola surface glycoprotein: interim results from the Guinea ring vaccination cluster-randomised trial. Lancet. 2015 Aug 29;386(9996):857-66. doi: 10.1016/S0140-6736(15)61117-5. Epub 2015 Aug 3. PubMed PMID: 26248676.

Population Genetics

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

Evolution

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

Research Career

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

Imaging

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

Medicine

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

Medicine/Prosthetics

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

Chemistry

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

Genomics

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

General

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

Development

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

Neuroscience

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

Genetics/Genome Editing

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

Cancer

  1. Tomasetti C, Vogelstein B. Cancer etiology. Variation in cancer risk among tissues can be explained by the number of stem cell divisions. Science. 2015 Jan 2;347(6217):78-81. doi: 10.1126/science.1260825. PubMed PMID: 25554788.

Zebrafish

  1. Kok FO, Shin M, Ni CW, Gupta A, Grosse AS, van Impel A, Kirchmaier BC, Peterson-Maduro J, Kourkoulis G, Male I, DeSantis DF, Sheppard-Tindell S, Ebarasi L, Betsholtz C, Schulte-Merker S, Wolfe SA, Lawson ND. Reverse Genetic Screening Reveals Poor Correlation between Morpholino-Induced and Mutant Phenotypes in Zebrafish. Dev Cell. 2015 Jan 12;32(1):97-108. doi: 10.1016/j.devcel.2014.11.018. Epub 2014 Dec 18. PubMed PMID: 25533206.

Imaging

  1. Callaway E. Blown-up brains reveal nanoscale details. Nature. 2015 Jan 15;517(7534):254. doi: 10.1038/nature.2015.16667. PubMed PMID: 25592513.

Genetics

  1. Gurdasani D, Carstensen T, Tekola-Ayele F, Pagani L, Tachmazidou I, Hatzikotoulas K, Karthikeyan S, Iles L, Pollard MO, Choudhury A, Ritchie GR, Xue Y, Asimit J, Nsubuga RN, Young EH, Pomilla C, Kivinen K, Rockett K, Kamali A, Doumatey AP, Asiki G, Seeley J, Sisay-Joof F, Jallow M, Tollman S, Mekonnen E, Ekong R, Oljira T, Bradman N, Bojang K, Ramsay M, Adeyemo A, Bekele E, Motala A, Norris SA, Pirie F, Kaleebu P, Kwiatkowski D, Tyler-Smith C, Rotimi C, Zeggini E, Sandhu MS. The African Genome Variation Project shapes medical genetics in Africa. Nature. 2015 Jan 15;517(7534):327-32. doi: 10.1038/nature13997. Epub 2014 Dec 3. PubMed PMID: 25470054; PubMed Central PMCID: PMC4297536.
  2. Jens M, Rajewsky N. Competition between target sites of regulators shapes post-transcriptional gene regulation. Nat Rev Genet. 2015 Feb;16(2):113-26. doi: 10.1038/nrg3853. Epub 2014 Dec 9. PubMed PMID: 25488579.
  3. Ritchie MD, Holzinger ER, Li R, Pendergrass SA, Kim D. Methods of integrating data to uncover genotype-phenotype interactions. Nat Rev Genet. 2015 Feb;16(2):85-97. doi: 10.1038/nrg3868. Epub 2015 Jan 13. PubMed PMID: 25582081.

Genome-editing

  1. Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA. Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds. Cell. 2015 Jan 15;160(1-2):339-50. doi: 10.1016/j.cell.2014.11.052. Epub 2014 Dec 18. PubMed PMID: 25533786; PubMed Central PMCID: PMC4297522.

Development

  1. Singh AP, Nüsslein-Volhard C. Zebrafish Stripes as a Model for Vertebrate Colour Pattern Formation. Curr Biol. 2015 Jan 19;25(2):R81-R92. doi: 10.1016/j.cub.2014.11.013. Review. PubMed PMID: 25602311.
  2. Hiscock TW, Megason SG. Mathematically guided approaches to distinguish models of periodic patterning. Development. 2015 Feb 1;142(3):409-419. Review. PubMed PMID: 25605777; PubMed Central PMCID: PMC4302999.

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
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  3. Yin H, Xue W, Chen S, Bogorad RL, Benedetti E, Grompe M, Koteliansky V, Sharp
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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.
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  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.
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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.
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  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:
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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

 

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.

Neuroscience

  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.

Genetics

  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.

Development

  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.

Science special section - Forces in Development

  1. Purnell BA. Forces in development. Forceful thinking. Introduction. Science. 2012 Oct 12;338(6104):209. doi: 10.1126/science.338.6104.209. PubMed PMID: 23066070.
  2. Kicheva A, Cohen M, Briscoe J. Developmental pattern formation: insights from physics and biology. Science. 2012 Oct 12;338(6104):210-2. doi: 10.1126/science.1225182. Review. PubMed PMID: 23066071.
  3. Furusawa C, Kaneko K. A dynamical-systems view of stem cell biology. Science.  2012 Oct 12;338(6104):215-7. doi: 10.1126/science.1224311. Review. PubMed PMID: 23066073.
  4. Newman SA. Physico-genetic determinants in the evolution of development. Science. 2012 Oct 12;338(6104):217-9. doi: 10.1126/science.1222003. PubMed PMID: 23066074.
  5. Behrndt M, Salbreux G, Campinho P, Hauschild R, Oswald F, Roensch J, Grill SW, Heisenberg CP. Forces driving epithelial spreading in zebrafish gastrulation. Science. 2012 Oct 12;338(6104):257-60. doi: 10.1126/science.1224143. PubMed PMID: 23066079.

Visual sciences

  1. Hardie RC, Franze K. Photomechanical responses in Drosophila photoreceptors. Science. 2012 Oct 12;338(6104):260-3. doi: 10.1126/science.1222376. PubMed PMID: 23066080.

Neural behaviour

  1. Fernandes AM, Fero K, Arrenberg AB, Bergeron SA, Driever W, Burgess HA. Deep Brain Photoreceptors Control Light-Seeking Behavior in Zebrafish Larvae. Curr Biol. 2012 Sep 18. pii: S0960-9822(12)00944-X. doi: 10.1016/j.cub.2012.08.016. [Epub ahead of print] PubMed PMID: 23000151.

Retinal development

  1. Xiang M. Intrinsic control of mammalian retinogenesis. Cell Mol Life Sci. 2012 Oct 12. [Epub ahead of print] PubMed PMID: 23064704.

Eye diseases

  1. Sahly I, Dufour E, Schietroma C, Michel V, Bahloul A, Perfettini I, Pepermans E, Estivalet A, Carette D, Aghaie A, Ebermann I, Lelli A, Iribarne M, Hardelin JP, Weil D, Sahel JA, El-Amraoui A, Petit C. Localization of Usher 1 proteins to the photoreceptor calyceal processes, which are absent from mice. J Cell Biol. 2012 Oct 15;199(2):381-99. doi: 10.1083/jcb.201202012. Epub 2012 Oct 8. PubMed PMID: 23045546; PubMed Central PMCID: PMC3471240.

Medicine

  1. Krogsbøll LT, Jørgensen KJ, Grønhøj Larsen C, Gøtzsche PC. General health checks in adults for reducing morbidity and mortality from disease. Cochrane Database Syst Rev. 2012 Oct 17;10:CD009009. doi: 10.1002/14651858.CD009009.pub2. PubMed PMID: 23076952.

Stem cells

  1. Nakano T, Ando S, Takata N, Kawada M, Muguruma K, Sekiguchi K, Saito K, Yonemura S, Eiraku M, Sasai Y. Self-formation of optic cups and storable stratified neural retina from human ESCs. Cell Stem Cell. 2012 Jun 14;10(6):771-85. PubMed PMID: 22704518.
  2. Cyranoski D. Tissue engineering: The brainmaker. Nature. 2012 Aug 23;488(7412):444-6. doi: 10.1038/488444a. PubMed PMID: 22914148.
    • An interesting article about Dr. Sasai who leads the team to make the eye cup from human ESCs as described above and from mouse ESCs, among many other interesting discoveries!

Imaging

  1. Small A. Faster and more versatile tools for super-resolution fluorescence microscopy. Nat Methods. 2012 Jun 28;9(7):655-6. doi: 10.1038/nmeth.2079. PubMed PMID: 22743767.
  2. Weber M, Huisken J. Omnidirectional microscopy. Nat Methods. 2012 Jun 28;9(7):656-7. doi: 10.1038/nmeth.2022. PubMed PMID: 22743768.
  3. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012 Jun 28;9(7):676-82. doi: 10.1038/nmeth.2019. PubMed PMID: 22743772.
  4. Kankaanpää P, Paavolainen L, Tiitta S, Karjalainen M, Päivärinne J, Nieminen J, Marjomäki V, Heino J, White DJ. BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nat Methods. 2012 Jun 28;9(7):683-9.doi: 10.1038/nmeth.2047. PubMed PMID: 22743773.
  5. de Chaumont F, Dallongeville S, Chenouard N, Hervé N, Pop S, Provoost T, Meas-Yedid V, Pankajakshan P, Lecomte T, Le Montagner Y, Lagache T, Dufour A, Olivo-Marin JC. Icy: an open bioimage informatics platform for extended reproducible research. Nat Methods. 2012 Jun 28;9(7):690-6. doi: 10.1038/nmeth.2075. PubMed PMID: 22743774.
  6. Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE. Biological imaging software tools. Nat Methods. 2012 Jun 28;9(7):697-710. doi: 10.1038/nmeth.2084. PubMed PMID: 22743775.
  7. Ronneberger O, Liu K, Rath M, Rueß D, Mueller T, Skibbe H, Drayer B, Schmidt T, Filippi A, Nitschke R, Brox T, Burkhardt H, Driever W. ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains. Nat Methods. 2012  Jun 17;9(7):735-42. doi: 10.1038/nmeth.2076. PubMed PMID: 22706672.
  8. Lubeck E, Cai L. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat Methods. 2012 Jun 3;9(7):743-8. doi: 10.1038/nmeth.2069. PubMed PMID: 22660740; PubMed Central PMCID: PMC3418883.
  9. Tomer R, Khairy K, Amat F, Keller PJ. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat Methods. 2012 Jun 3;9(7):755-63. doi: 10.1038/nmeth.2062. PubMed PMID: 22660741.
  10. The quest for quantitative microscopy. Nat Methods. 2012 Jul;9(7):627. PubMed PMID: 22930824.
  11. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012 Jul;9(7):671-5. PubMed PMID: 22930834.

Systems Biology

  1. Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell. 2012 Jul 20;150(2):389-401. PubMed PMID: 22817898; PubMed Central PMCID: PMC3413483.
    • Commentary: Freddolino PL, Tavazoie S. The dawn of virtual cell biology. Cell. 2012 Jul 20;150(2):248-50. PubMed PMID: 22817888.

Genomics/Genetics

  1. Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A, Wong WS, Sigurdsson G, Walters GB, Steinberg S, Helgason H, Thorleifsson G, Gudbjartsson DF, Helgason A, Magnusson OT, Thorsteinsdottir U, Stefansson K. Rate of de novo mutations and the importance of father’s age to disease risk. Nature. 2012 Aug 23;488(7412):471-5. doi: 10.1038/nature11396. PubMed PMID: 22914163.
    • A new study that shows the older the father is, the more the mutations that he will pass to the next generation!
    • News: Callaway E. Fathers bequeath more mutations as they age. Nature. 2012 Aug 23;488(7412):439. doi: 10.1038/488439a. PubMed PMID: 22914142.
    • Commentary: Kondrashov A. Genetics: The rate of human mutation. Nature. 2012 Aug 23;488(7412):467-8. doi: 10.1038/488467a. PubMed PMID: 22914161.
  2. Schuster-Böckler B, Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature. 2012 Aug 23;488(7412):504-7. PubMed PMID: 22820252.

Development

  1. Lefebvre JL, Kostadinov D, Chen WV, Maniatis T, Sanes JR. Protocadherins mediate dendritic self-avoidance in the mammalian nervous system. Nature. 2012 Aug 23;488(7412):517-21. PubMed PMID: 22842903; PubMed Central PMCID: PMC3427422.