Posts tagged ‘genomics’

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.

 

Genome editing

  1. Why the CRISPR patent verdict isn’t the end of the story
  2. Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF. New CRISPR-Cas systems from uncultivated microbes. Nature. 2017 Feb 9;542(7640):237-241. doi: 10.1038/nature21059. PubMed PMID: 28005056; PubMed Central PMCID: PMC5300952.

Imaging

  1. Pan C, Cai R, Quacquarelli FP, Ghasemigharagoz A, Lourbopoulos A, Matryba P, Plesnila N, Dichgans M, Hellal F, Ertürk A. Shrinkage-mediated imaging of entire organs and organisms using uDISCO. Nat Methods. 2016 Oct;13(10):859-67. doi: 10.1038/nmeth.3964. PubMed PMID: 27548807.

Neuroscience

  1. Krakauer JW, Ghazanfar AA, Gomez-Marin A, MacIver MA, Poeppel D. Neuroscience Needs Behavior: Correcting a Reductionist Bias. Neuron. 2017 Feb 8;93(3):480-490. doi: 10.1016/j.neuron.2016.12.041. Review. PubMed PMID: 28182904.
  2. Jonas E, Kording KP. Could a Neuroscientist Understand a Microprocessor? PLoS Comput Biol. 2017 Jan 12;13(1):e1005268. doi: 10.1371/journal.pcbi.1005268. PubMed PMID: 28081141; PubMed Central PMCID: PMC5230747.

Medicine

  1. Dowdy SF. Overcoming cellular barriers for RNA therapeutics. Nat Biotechnol. 2017 Feb 27. doi: 10.1038/nbt.3802. [Epub ahead of print] PubMed PMID: 28244992.
  2. Khvorova A, Watts JK. The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol. 2017 Feb 27. doi: 10.1038/nbt.3765. [Epub ahead of print] PubMed PMID: 28244990.

Genomics

  1. Martelotto LG, Baslan T, Kendall J, Geyer FC, Burke KA, Spraggon L, Piscuoglio S, Chadalavada K, Nanjangud G, Ng CK, Moody P, D’Italia S, Rodgers L, Cox H, da Cruz Paula A, Stepansky A, Schizas M, Wen HY, King TA, Norton L, Weigelt B, Hicks JB, Reis-Filho JS. Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples. Nat Med. 2017 Feb 6. doi: 10.1038/nm.4279. [Epub ahead of print] PubMed PMID: 28165479.

Genetics

  1. Bilow M, Crespo F, Pan Z, Eskin E, Eyheramendy S. Simultaneous Modeling of Disease Status and Clinical Phenotypes to Increase Power in GWAS. Genetics. 2017 Jan 27. pii: genetics.116.198473. doi: 10.1534/genetics.116.198473. [Epub ahead of print] PubMed PMID: 28132020.

				

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.


				

Genomics

  1. Bintu L, Yong J, Antebi YE, McCue K, Kazuki Y, Uno N, Oshimura M, Elowitz MB. Dynamics of epigenetic regulation at the single-cell level. Science. 2016 Feb 12;351(6274):720-4. doi: 10.1126/science.aab2956. PubMed PMID: 26912859.
    • Commentary: Keung AJ, Khalil AS. MOLECULAR BIOLOGY. A unifying model of epigenetic regulation. Science. 2016 Feb 12;351(6274):661-2. doi: 10.1126/science.aaf1647. PubMed PMID: 26912843.
  2. Cahan P. Enabling direct fate conversion with network biology. Nat Genet. 2016 Feb 24;48(3):226-7. doi: 10.1038/ng.3516. PubMed PMID: 26906680.
  3. Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS; FANTOM Consortium, Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest AR, Hayashizaki Y, Polo JM, Gough J. A predictive computational framework for direct reprogramming between human cell types. Nat Genet. 2016 Jan 18. doi: 10.1038/ng.3487. [Epub ahead of print] PubMed PMID: 26780608.
  4. Savova V, Chun S, Sohail M, McCole RB, Witwicki R, Gai L, Lenz TL, Wu CT, Sunyaev SR, Gimelbrant AA. Genes with monoallelic expression contribute disproportionately to genetic diversity in humans. Nat Genet. 2016 Jan 25. doi: 10.1038/ng.3493. [Epub ahead of print] PubMed PMID: 26808112.
  5. Gusev A, Ko A, Shi H, Bhatia G, Chung W, Penninx BW, Jansen R, de Geus EJ, Boomsma DI, Wright FA, Sullivan PF, Nikkola E, Alvarez M, Civelek M, Lusis AJ, Lehtimäki T, Raitoharju E, Kähönen M, Seppälä I, Raitakari OT, Kuusisto J, Laakso M, Price AL, Pajukanta P, Pasaniuc B. Integrative approaches for large-scale transcriptome-wide association studies. Nat Genet. 2016 Feb 8. doi: 10.1038/ng.3506. [Epub ahead of print] PubMed PMID: 26854917.

Development

  1. Aggarwal V, Dickinson RB, Lele TP. Concentration Sensing by the Moving Nucleus in Cell Fate Determination: A Computational Analysis. PLoS One. 2016 Feb 12;11(2):e0149213. doi: 10.1371/journal.pone.0149213. eCollection 2016. PubMed PMID: 26872214.
  2. Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS; FANTOM Consortium, Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest AR, Hayashizaki Y, Polo JM, Gough J. A predictive computational framework for direct reprogramming between human cell types. Nat Genet. 2016 Jan 18. doi: 10.1038/ng.3487. [Epub ahead of print] PubMed PMID: 26780608.

Molecular Biology

  1. Burgers PM, Gordenin D, Kunkel TA. Who Is Leading the Replication Fork, Pol ε or Pol δ? Mol Cell. 2016 Feb 18;61(4):492-3. doi: 10.1016/j.molcel.2016.01.017. PubMed PMID: 26895421.
  2. Johnson RE, Klassen R, Prakash L, Prakash S. Response to Burgers et al. Mol Cell. 2016 Feb 18;61(4):494-5. doi: 10.1016/j.molcel.2016.01.018. PubMed PMID: 26895422.

Funding

  1.  Vachelard J, Gambarra-Soares T, Augustini G, Riul P, Maracaja-Coutinho V. A Guide to Scientific Crowdfunding. PLoS Biol. 2016 Feb 17;14(2):e1002373. doi: 10.1371/journal.pbio.1002373. eCollection 2016 Feb. PubMed PMID: 26886064.

Genome editing

  1. Tai DJ, Ragavendran A, Manavalan P, Stortchevoi A, Seabra CM, Erdin S, Collins RL, Blumenthal I, Chen X, Shen Y, Sahin M, Zhang C, Lee C, Gusella JF, Talkowski ME. Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR. Nat Neurosci. 2016 Feb 1. doi: 10.1038/nn.4235. [Epub ahead of print] PubMed PMID: 26829649.

Behaviour

  1. Scott CA, Marsden AN, Slusarski DC. Automated, high-throughput, in vivo analysis of visual function using the zebrafish. Dev Dyn. 2016 Feb 18. doi: 10.1002/dvdy.24398. [Epub ahead of print] PubMed PMID: 26890697.

Stem cells

  1. Fatehullah A, Tan SH, Barker N. Organoids as an in vitro model of human development and disease. Nat Cell Biol. 2016 Feb 25;18(3):246-54. doi: 10.1038/ncb3312. Review. PubMed PMID: 26911908.
  2. Wang Y, Gao S. Human Naive Embryonic Stem Cells: How Full Is the Glass? Cell Stem Cell. 2016 Mar 3;18(3):301-3. doi: 10.1016/j.stem.2016.02.012. PubMed PMID: 26942847.
  3. Pastor WA, Chen D, Liu W, Kim R, Sahakyan A, Lukianchikov A, Plath K, Jacobsen SE, Clark AT. Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory. Cell Stem Cell. 2016 Mar 3;18(3):323-9. doi: 10.1016/j.stem.2016.01.019. Epub 2016 Feb 4. PubMed PMID: 26853856; PubMed Central PMCID: PMC4779431.
  4. Passier R, Orlova V, Mummery C. Complex Tissue and Disease Modeling using hiPSCs. Cell Stem Cell. 2016 Mar 3;18(3):309-21. doi: 10.1016/j.stem.2016.02.011. Review. PubMed PMID: 26942851.
  5. Orlova V, Mummery C. SnapShot: Key Advances in hiPSC Disease Modeling. Cell Stem Cell. 2016 Mar 3;18(3):422. doi: 10.1016/j.stem.2016.02.013. PubMed PMID: 26942854.
  6. Nat Rev Mol Cell Biol; Focus on: Pluripotent Stem cells

Medicine

  1. Peplow M. Synthetic biology’s first malaria drug meets market resistance. Nature. 2016 Feb 25;530(7591):389-90. doi: 10.1038/530390a. PubMed PMID: 26911755.

Genome editing

  1. Hayes RP, Xiao Y, Ding F, van Erp PB, Rajashankar K, Bailey S, Wiedenheft B, Ke A. Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli. Nature. 2016 Feb 10. doi: 10.1038/nature16995. [Epub ahead of print] PubMed PMID: 26863189.

Genomics

  1. Shen SQ, Myers CA, Hughes AE, Byrne LC, Flannery JG, Corbo JC. Massively parallel cis-regulatory analysis in the mammalian central nervous system. Genome Res. 2016 Feb;26(2):238-55. doi: 10.1101/gr.193789.115. Epub 2015 Nov 17. PubMed PMID: 26576614.
  2. Quick J, et al., . Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016 Feb 3. doi: 10.1038/nature16996. [Epub ahead of print] PubMed PMID: 26840485.

Neuroscience

  1. Ishiko N, Huberman AD. Life goes by: a visual circuit signals perceptual-motor mismatch. Nat Neurosci. 2016 Jan 27;19(2):177-9. doi: 10.1038/nn.4233. PubMed PMID: 26814584.
  2. Tasic B, Menon V, Nguyen TN, Kim TK, Jarsky T, Yao Z, Levi B, Gray LT, Sorensen SA, Dolbeare T, Bertagnolli D, Goldy J, Shapovalova N, Parry S, Lee C, Smith K, Bernard A, Madisen L, Sunkin SM, Hawrylycz M, Koch C, Zeng H. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nat Neurosci. 2016 Feb;19(2):335-46. doi: 10.1038/nn.4216. Epub 2016 Jan 4. PubMed PMID: 26727548.
  3. Chen HH, Arlotta P. Seq-ing the cortex one neuron at a time. Nat Neurosci. 2016 Jan 27;19(2):179-81. doi: 10.1038/nn.4230. PubMed PMID: 26814585.
  4. Johnson MR, Shkura K, Langley SR, Delahaye-Duriez A, Srivastava P, Hill WD, Rackham OJ, Davies G, Harris SE, Moreno-Moral A, Rotival M, Speed D, Petrovski S, Katz A, Hayward C, Porteous DJ, Smith BH, Padmanabhan S, Hocking LJ, Starr JM, Liewald DC, Visconti A, Falchi M, Bottolo L, Rossetti T, Danis B, Mazzuferi M, Foerch P, Grote A, Helmstaedter C, Becker AJ, Kaminski RM, Deary IJ, Petretto E. Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease. Nat Neurosci. 2016 Feb;19(2):223-32. doi: 10.1038/nn.4205. Epub 2015 Dec 21. PubMed PMID: 26691832.
  5. Yoshimatsu T, D’Orazi FD, Gamlin CR, Suzuki SC, Suli A, Kimelman D, Raible DW, Wong RO. Presynaptic partner selection during retinal circuit reassembly varies with timing of neuronal regeneration in vivo. Nat Commun. 2016 Feb 3;7:10590. doi: 10.1038/ncomms10590. PubMed PMID: 26838932.
  6. Hoffman EJ, Turner KJ, Fernandez JM, Cifuentes D, Ghosh M, Ijaz S, Jain RA, Kubo F, Bill BR, Baier H, Granato M, Barresi MJ, Wilson SW, Rihel J, State MW, Giraldez AJ. Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2. Neuron. 2016 Jan 27. pii: S0896-6273(15)01167-8. doi: 10.1016/j.neuron.2015.12.039. [Epub ahead of print] PubMed PMID: 26833134.

Development

  1. Rister J, Razzaq A, Boodram P, Desai N, Tsanis C, Chen H, Jukam D, Desplan C. Single-base pair differences in a shared motif determine differential Rhodopsin expression. Science. 2015 Dec 4;350(6265):1258-61. doi: 10.1126/science.aab3417. PubMed PMID: 26785491.

Genome editing

  1. Farasat I, Salis HM. A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation. PLoS Comput Biol. 2016 Jan 29;12(1):e1004724. doi: 10.1371/journal.pcbi.1004724. eCollection 2016 Jan. PubMed PMID: 26824432.
  2.  Song J, Yang D, Xu J, Zhu T, Chen YE, Zhang J. RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency. Nat Commun. 2016 Jan 28;7:10548. doi: 10.1038/ncomms10548. PubMed PMID: 26817820.
  3. Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K, Thompson AJ, Nogales E, Doudna JA. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Science. 2016 Jan 14. pii: aad8282. [Epub ahead of print] PubMed PMID: 26841432.
  4.  Jusiak B, Cleto S, Perez-Piñera P, Lu TK. Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology. Trends Biotechnol. 2016 Jan 22. pii: S0167-7799(15)00274-7. doi: 10.1016/j.tibtech.2015.12.014. [Epub ahead of print] Review. PubMed PMID: 26809780.