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2016-03-28 new articles we read this week

Monday, March 28, 2016

Zebrafish

  1. Adatto I, Krug L, Zon LI. The Red Light District and Its Effects on Zebrafish Reproduction. Zebrafish. 2016 Mar 15. [Epub ahead of print] PubMed PMID: 26978703.
  2. Brocal I, White RJ, Dooley CM, Carruthers SN, Clark R, Hall A, Busch-Nentwich EM, Stemple DL, Kettleborough RN. Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafish. BMC Genomics. 2016 Mar 24;17(1):259. doi: 10.1186/s12864-016-2563-z. PubMed PMID: 27009152.
  3. Hoshijima K, Jurynec MJ, Grunwald DJ. Precise Editing of the Zebrafish Genome Made Simple and Efficient. Dev Cell. 2016 Mar 21;36(6):654-67. doi: 10.1016/j.devcel.2016.02.015. PubMed PMID: 27003937.
  4. Varshney GK, Zhang S, Pei W, Adomako-Ankomah A, Fohtung J, Schaffer K, Carrington B, Maskeri A, Slevin C, Wolfsberg T, Ledin J, Sood R, Burgess SM. CRISPRz: a database of zebrafish validated sgRNAs. Nucleic Acids Res. 2016 Jan 4;44(D1):D822-6. doi: 10.1093/nar/gkv998. Epub 2015 Oct 4. PubMed PMID: 26438539; PubMed Central PMCID: PMC4702947.

Retina

  1. Mullally M, Albrecht C, Horton M, Laboissonniere LA, Goetz JJ, Chowdhury R, Manning A, Wester AK, Bose Q, Trimarchi JM. Expression Profiling of Developing Zebrafish Retinal Cells. Zebrafish. 2016 Mar 16. [Epub ahead of print] PubMed PMID: 26982811.

Disease

  1. Roy DS, Arons A, Mitchell TI, Pignatelli M, Ryan TJ, Tonegawa S. Memory retrieval by activating engram cells in mouse models of early Alzheimer’s disease. Nature. 2016 Mar 16. doi: 10.1038/nature17172. [Epub ahead of print] PubMed PMID: 26982728.

Molecular Biology

  1. Louder RK, He Y, López-Blanco JR, Fang J, Chacón P, Nogales E. Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. Nature. 2016 Mar 23. doi: 10.1038/nature17394. [Epub ahead of print] PubMed PMID: 27007846.

Cell Biology

  1. Norris DP, Jackson PK. Cell biology: Calcium contradictions in cilia. Nature. 2016 Mar 23. doi: 10.1038/nature17313. [Epub ahead of print] PubMed PMID: 27007852.

Systems Biology

  1. Hashimoto M, Nozoe T, Nakaoka H, Okura R, Akiyoshi S, Kaneko K, Kussell E, Wakamoto Y. Noise-driven growth rate gain in clonal cellular populations. Proc Natl Acad Sci U S A. 2016 Mar 7. pii: 201519412. [Epub ahead of print] PubMed PMID: 26951676.
  2. Davidi D, Noor E, Liebermeister W, Bar-Even A, Flamholz A, Tummler K, Barenholz U, Goldenfeld M, Shlomi T, Milo R. Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements. Proc Natl Acad Sci U S A. 2016 Mar 7. pii: 201514240. [Epub ahead of print] PubMed PMID: 26951675.

Genome editing

  1. Hoshijima K, Jurynec MJ, Grunwald DJ. Precise Editing of the Zebrafish Genome Made Simple and Efficient. Dev Cell. 2016 Mar 21;36(6):654-67. doi: 10.1016/j.devcel.2016.02.015. PubMed PMID: 27003937.
  2. Varshney GK, Zhang S, Pei W, Adomako-Ankomah A, Fohtung J, Schaffer K, Carrington B, Maskeri A, Slevin C, Wolfsberg T, Ledin J, Sood R, Burgess SM. CRISPRz: a database of zebrafish validated sgRNAs. Nucleic Acids Res. 2016 Jan 4;44(D1):D822-6. doi: 10.1093/nar/gkv998. Epub 2015 Oct 4. PubMed PMID: 26438539; PubMed Central PMCID: PMC4702947.




				

				

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A good development in scientific publishing

				
Tuesday, March 22, 2016

				


Several interesting and good discussions on publishing life science articles on BioRxiv, a preprint server based on the arXiv model:


From the New York Times: “Handful of Biologists Went Rogue and Published Directly to Internet“.


From Mike Eisen’s blog.


				

				

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2016-03-21 new articles we read this week

				
Monday, March 21, 2016

				


Eye diseases


    

  1. Lin H, Ouyang H, Zhu J, Huang S, Liu Z, Chen S, Cao G, Li G, Signer RA, Xu Y, Chung C, Zhang Y, Lin D, Patel S, Wu F, Cai H, Hou J, Wen C, Jafari M, Liu X, Luo L, Zhu J, Qiu A, Hou R, Chen B, Chen J, Granet D, Heichel C, Shang F, Li X, Krawczyk M, Skowronska-Krawczyk D, Wang Y, Shi W, Chen D, Zhong Z, Zhong S, Zhang L, Chen S, Morrison SJ, Maas RL, Zhang K, Liu Y. Lens regeneration using endogenous stem cells with gain of visual function. Nature. 2016 Mar 9. doi: 10.1038/nature17181. [Epub ahead of print] PubMed PMID: 26958831. News release: Stem Cells Regenerate Human Lens After Cataract Surgery, Restoring Vision
    2. 

  2. Hayashi R, Ishikawa Y, Sasamoto Y, Katori R, Nomura N, Ichikawa T, Araki S, Soma T, Kawasaki S, Sekiguchi K, Quantock AJ, Tsujikawa M, Nishida K. Co-ordinated ocular development from human iPS cells and recovery of corneal function. Nature. 2016 Mar 9. doi: 10.1038/nature17000. [Epub ahead of print] PubMed PMID: 26958835.
    3. 



Stem cells


    

  1. Sridhar A, Ohlemacher SK, Langer KB, Meyer JS. Robust Differentiation of mRNA-Reprogrammed Human Induced Pluripotent Stem Cells Toward a Retinal Lineage. Stem Cells Transl Med. 2016 Mar 1. pii: sctm.2015-0093. [Epub ahead of print] PubMed PMID: 26933039.
    2. 

  2. Sagi I, Chia G, Golan-Lev T, Peretz M, Weissbein U, Sui L, Sauer MV, Yanuka O, Egli D, Benvenisty N. Derivation and differentiation of haploid human embryonic stem cells. Nature. 2016 Mar 16. doi: 10.1038/nature17408. [Epub ahead of print] PubMed PMID: 26982723.
    3. 



Development


    

  1. Pueschel R, Coraggio F, Meister P. From single genes to entire genomes: the search for a function of nuclear organization. Development. 2016 Mar 15;143(6):910-23. doi: 10.1242/dev.129007. Review. PubMed PMID: 26980791.
    2. 

  2. Salomon DR. A CRISPR Way to Block PERVs – Engineering Organs for Transplantation. N Engl J Med. 2016 Mar 17;374(11):1089-1091. PubMed PMID: 26981939.
    3. 



Neuroscience 


    

  1. Mullins C, Fishell G, Tsien RW. Unifying Views of Autism Spectrum Disorders: A Consideration of Autoregulatory Feedback Loops. Neuron. 2016 Mar 16;89(6):1131-56. doi: 10.1016/j.neuron.2016.02.017. Review. PubMed PMID: 26985722.
    2. 

  2. Hazen JL, Faust GG, Rodriguez AR, Ferguson WC, Shumilina S, Clark RA, Boland MJ, Martin G, Chubukov P, Tsunemoto RK, Torkamani A, Kupriyanov S, Hall IM, Baldwin KK. The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning. Neuron. 2016 Mar 16;89(6):1223-36. doi: 10.1016/j.neuron.2016.02.004. Epub 2016 Mar 3. PubMed PMID: 26948891; PubMed Central PMCID: PMC4795965.
    3. 



Mathematics 


    

  1. Castelvecchi D. Fermat’s last theorem earns Andrew Wiles the Abel Prize. Nature. 2016 Mar 17;531(7594):287. doi: 10.1038/nature.2016.19552. PubMed PMID: 26983518.
    2. 



				

				

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Menna participated in the Lafayette Regional Science & Engineering Fair!

				
Monday, March 14, 2016

				


Menna Hassan participated in the Lafayette Regional Science & Engineering Fair and won two awards: (1) a bronze medal under the Animal Science category in the Seniors division, and (2) a blue ribbon. Congratulations! By winning the latter award, she is ranked in the top ten students of the Fair and has been invited to participate in the State Science Fair. She conducted her zebrafish research under the supervision of Prahatha Venkatraman, a graduate student in the laboratory and a Schlumberger Foundation Faculty for Future Fellow.


Menna and her poster!


Menna and Prahatha


 


				

				

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TEDxSantaMonica – Kurt Schwengel – Occupy Kindergarten

				
Saturday, March 12, 2016

				


A good wake-up call to the people who are obsessed in creating standards for education and reform curriculum, at all levels. Learn from the good teachers, and do more what they are already doing. 




				

				

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2016-03-07 new articles we read this week

				
Wednesday, March 9, 2016

				


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. 

  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. 

  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. 

  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. 

  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.
    6. 



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. 

  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.
    3. 



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. 

  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.
    3. 



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. 
    2. 



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.
    

    2. 



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. 
    2. 



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. 

  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. 

  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. 

  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. 

  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. 

  6. Nat Rev Mol Cell Biol; Focus on: Pluripotent Stem cells
    7. 



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.
    2. 



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.
    2. 



				

				

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Cheap visual aid for people with poor vision

				
Sunday, February 28, 2016

				


I have just come across an interesting approach to help patients with poor vision–using a smartphone app designed for augmenting vision with google cardboard.


I first came across this approach through this youtube video. It shows how the approach helped a lady who suffered from Stargardt’s disease and could not see well for eight years.




After using the app and google cardboard, she seemed to see much better and was so excited by the experience. I find this interesting because many of my friends and relatives suffered from poor vision. They can potentially see better through this simple and cheap approach. I am going to set this up for my parents soon and see if that helps them see better!


 


				

				

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2016-02-22 new articles we read this week

				
Monday, February 22, 2016

				


Genetics


    

  1. Gage SH, Davey Smith G, Ware JJ, Flint J, Munafò MR. G = E: What GWAS Can Tell Us about the Environment. PLoS Genet. 2016 Feb 11;12(2):e1005765. doi: 10.1371/journal.pgen.1005765. eCollection 2016 Feb. PubMed PMID: 26866486.
    2. 

  2. Murray A. Salvador Luria and Max Delbrück on Random Mutation and Fluctuation Tests. Genetics. 2016 Feb;202(2):367-8. doi: 10.1534/genetics.115.186163. PubMed PMID: 26869479. 
    3. 



Neuroscience


    

  1. A Zebrafish Genetic Screen Identifies Neuromedin U as a Regulator of Sleep/Wake States Zebrafish Reel in Phenotypic Suppressors of Autism Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2
    2. 

  2. Carr F. Reward: A separate sweet circuit. Nat Rev Neurosci. 2016 Feb 11. doi: 10.1038/nrn.2016.19. [Epub ahead of print] PubMed PMID: 26865014.
    3. 



Evolution


    

  1. Fox D. What sparked the Cambrian explosion? Nature. 2016 Feb 18;530(7590):268-70. doi: 10.1038/530268a. PubMed PMID: 26887475.
    2. 

  2. McGowan KA, Barsh GS. How the zebrafish got its stripes. Elife. 2016 Feb 15;5. pii: e14239. doi: 10.7554/eLife.14239. PubMed PMID: 26880558.
    3. 



Scientific publication


    

  1. Callaway E, Powell K. Biologists urged to hug a preprint. Nature. 2016 Feb 18;530(7590):265. doi: 10.1038/530265a. PubMed PMID: 26887471.
    2. 

  2. Powell K. Does it take too long to publish research? Nature. 2016 Feb 11;530(7589):148-51. doi: 10.1038/530148a. PubMed PMID: 26863966. 
    3. 



Development


    

  1. Webb AB, Lengyel IM, Jörg DJ, Valentin G, Jülicher F, Morelli LG, Oates AC. Persistence, period and precision of autonomous cellular oscillators from the zebrafish segmentation clock. Elife. 2016 Feb 16;5. pii: e08438. doi: 10.7554/eLife.08438. [Epub ahead of print] PubMed PMID: 26880542.
    2. 



Genome editing


    

  1. Nyerges Á, Csörgő B, Nagy I, Bálint B, Bihari P, Lázár V, Apjok G, Umenhoffer K, Bogos B, Pósfai G, Pál C. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species. Proc Natl Acad Sci U S A. 2016 Feb 16. pii: 201520040. [Epub ahead of print] PubMed PMID: 26884157.
    2. 

  2. Wong AS, Choi GC, Cui CH, Pregernig G, Milani P, Adam M, Perli SD, Kazer SW, Gaillard A, Hermann M, Shalek AK, Fraenkel E, Lu TK. Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM. Proc Natl Acad Sci U S A. 2016 Feb 10. pii: 201517883. [Epub ahead of print] PubMed PMID: 26864203.
    3. 

  3. Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O. Structure and Engineering of Francisella novicida Cas9. Cell. 2016 Feb 10. pii: S0092-8674(16)30053-8. doi: 10.1016/j.cell.2016.01.039. [Epub ahead of print] PubMed PMID: 26875867.
    4. 

  4. Orkin SH. Recent advances in globin research using genome-wide association studies and gene editing. Ann N Y Acad Sci. 2016 Feb 11. doi: 10.1111/nyas.13001. [Epub ahead of print] PubMed PMID: 26866328.
    5. 





				

				

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2016-02-15 new articles we read this week

				
Monday, February 15, 2016

				


Scientific publishing


    

  1. Gibney E. Open journals that piggyback on arXiv gather momentum. Nature. 2016 Feb 4;530(7588):117-8. PubMed PMID: 26854297.
    2. 



Genome editing


    

  1. Wu B, Luo L, Gao XJ. Cas9-triggered chain ablation of cas9 as a gene drive brake. Nat Biotechnol. 2016 Feb 5;34(2):137-8. doi: 10.1038/nbt.3444. PubMed PMID: 26849513.
    2. 

  2. Alphey L. Can CRISPR-Cas9 gene drives curb malaria? Nat Biotechnol. 2016 Feb 5;34(2):149-50. doi: 10.1038/nbt.3473. PubMed PMID: 26849518.
    3. 

  3. Rajagopal N, Srinivasan S, Kooshesh K, Guo Y, Edwards MD, Banerjee B, Syed T, Emons BJ, Gifford DK, Sherwood RI. High-throughput mapping of regulatory DNA. Nat Biotechnol. 2016 Feb;34(2):167-74. doi: 10.1038/nbt.3468. Epub 2016 Jan 25. PubMed PMID: 26807528.
    4. 

  4. Korkmaz G, Lopes R, Ugalde AP, Nevedomskaya E, Han R, Myacheva K, Zwart W, Elkon R, Agami R. Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9. Nat Biotechnol. 2016 Feb;34(2):192-8. doi: 10.1038/nbt.3450. Epub 2016 Jan 11. PubMed PMID: 26751173.
    5. 

  5. Zhou Y, Wei W. Mapping regulatory elements. Nat Biotechnol. 2016 Feb 5;34(2):151-2. doi: 10.1038/nbt.3477. PubMed PMID: 26849519.
    6. 

  6. Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J, Root DE. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016 Feb;34(2):184-91. doi: 10.1038/nbt.3437. Epub 2016 Jan 18. PubMed PMID: 26780180; PubMed Central PMCID: PMC4744125.
    7. 

  7. 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; PubMed Central PMCID: PMC4732943.
    8. 



Neuroscience 


    

  1. Fuzik J, Zeisel A, Máté Z, Calvigioni D, Yanagawa Y, Szabó G, Linnarsson S, Harkany T. Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes. Nat Biotechnol. 2016 Feb;34(2):175-83. doi: 10.1038/nbt.3443. Epub 2015 Dec 21. PubMed PMID: 26689544.
    2. 

  2. Cadwell CR, Palasantza A, Jiang X, Berens P, Deng Q, Yilmaz M, Reimer J, Shen S, Bethge M, Tolias KF, Sandberg R, Tolias AS. Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq. Nat Biotechnol. 2016 Feb;34(2):199-203. doi: 10.1038/nbt.3445. Epub 2015 Dec 21. PubMed PMID: 26689543.
    3. 



Disease


    

  1. Mlakar J, Korva M, Tul N, Popović M, Poljšak-Prijatelj M, Mraz J, Kolenc M, Resman Rus K, Vesnaver Vipotnik T, Fabjan Vodušek V, Vizjak A, Pižem J, Petrovec M, Avšič Županc T. Zika Virus Associated with Microcephaly. N Engl J Med. 2016 Feb 10. [Epub ahead of print] PubMed PMID: 26862926. 
    2. 



ESLI


    

  1. Baker M. Biotech giant publishes failures to confirm high-profile science. Nature. 2016 Feb 11;530(7589):141. doi: 10.1038/nature.2016.19269. PubMed PMID: 26863961.
    2. 



Stem cells


    

  1. Chakradhar S. An eye to the future: Researchers debate best path for stem cell-derived therapies. Nat Med. 2016 Feb 4;22(2):116-9. doi: 10.1038/nm0216-116. PubMed PMID: 26845400.
    2. 

  2. Scognamiglio R, Cabezas-Wallscheid N, Thier MC, Altamura S, Reyes A, Prendergast ÁM, Baumgärtner D, Carnevalli LS, Atzberger A, Haas S, von Paleske L, Boroviak T, Wörsdörfer P, Essers MA, Kloz U, Eisenman RN, Edenhofer F, Bertone P, Huber W, van der Hoeven F, Smith A, Trumpp A. Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause. Cell. 2016 Feb 11;164(4):668-80. doi: 10.1016/j.cell.2015.12.033. PubMed PMID: 26871632.
    3. 



Systems Biology 


    

  1. Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Cell. 2016 Feb 11;164(4):805-17. doi: 10.1016/j.cell.2016.01.029. PubMed PMID: 26871637.
    2. 

  2. Morsut L, Roybal KT, Xiong X, Gordley RM, Coyle SM, Thomson M, Lim WA. Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors. Cell. 2016 Feb 11;164(4):780-91. doi: 10.1016/j.cell.2016.01.012. Epub 2016 Jan 28. PubMed PMID: 26830878; PubMed Central PMCID: PMC4752866.
    3. 

  3. Tsiairis CD, Aulehla A. Self-Organization of Embryonic Genetic Oscillators into Spatiotemporal Wave Patterns. Cell. 2016 Feb 11;164(4):656-67. doi: 10.1016/j.cell.2016.01.028. PubMed PMID: 26871631.
    4. 

  4. Sylwestrak EL, Rajasethupathy P, Wright MA, Jaffe A, Deisseroth K. Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution. Cell. 2016 Feb 11;164(4):792-804. doi: 10.1016/j.cell.2016.01.038. PubMed PMID: 26871636.
    5. 



Development 


    

  1. Tsiairis CD, Aulehla A. Self-Organization of Embryonic Genetic Oscillators into Spatiotemporal Wave Patterns. Cell. 2016 Feb 11;164(4):656-67. doi: 10.1016/j.cell.2016.01.028. PubMed PMID: 26871631.
    2. 



				

				

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2016-02-08 new articles we read this week

				
Monday, February 8, 2016

				


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. 

  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.
    3. 



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. 

  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. 

  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. 

  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. 

  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. 

  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.
    7. 



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.
    2. 



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. 

  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. 

  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. 

  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.
    5. 



				

				

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