Posts tagged ‘next-generation sequencing’

Nature’s special on “Challenges in irreproducible research”

Human Behaviour/Psychology

  1. Kramer AD, Guillory JE, Hancock JT. Experimental evidence of massive-scale emotional contagion through social networks. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8788-90. doi: 10.1073/pnas.1320040111. Epub 2014 Jun 2. PubMed PMID: 24889601.

Retinal development

  1. Hoon M, Okawa H, Della Santina L, Wong RO. Functional Architecture of the Retina: Development and Disease. Prog Retin Eye Res. 2014 Jun 28. pii: S1350-9462(14)00038-X. doi: 10.1016/j.preteyeres.2014.06.003. [Epub ahead of print] Review. PubMed PMID: 24984227.

Stem cells

  1. Ksander BR, Kolovou PE, Wilson BJ, Saab KR, Guo Q, Ma J, McGuire SP, Gregory MS, Vincent WJ, Perez VL, Cruz-Guilloty F, Kao WW, Call MK, Tucker BA, Zhan Q, Murphy GF, Lathrop KL, Alt C, Mortensen LJ, Lin CP, Zieske JD, Frank MH, Frank NY. ABCB5 is a limbal stem cell gene required for corneal development and repair. Nature. 2014 Jul 17;511(7509):353-7. doi: 10.1038/nature13426. Epub 2014 Jul 2. PubMed PMID: 25030174.
  2. Tsai SQ, Joung JK. What’s Changed with Genome Editing? Cell Stem Cell. 2014 Jul 3;15(1):3-4. doi: 10.1016/j.stem.2014.06.017. PubMed PMID: 24996161.
  3. Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Talkowski ME, Musunuru K. Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing. Cell Stem Cell. 2014 Jul 3;15(1):27-30. doi: 10.1016/j.stem.2014.04.020. PubMed PMID: 24996167; PubMed Central PMCID: PMC4082799.
  4. Smith C, Gore A, Yan W, Abalde-Atristain L, Li Z, He C, Wang Y, Brodsky RA, Zhang K, Cheng L, Ye Z. Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs. Cell Stem Cell. 2014 Jul 3;15(1):12-3. doi: 10.1016/j.stem.2014.06.011. PubMed PMID: 24996165.
  5. Suzuki K, Yu C, Qu J, Li M, Yao X, Yuan T, Goebl A, Tang S, Ren R, Aizawa E, Zhang F, Xu X, Soligalla RD, Chen F, Kim J, Kim NY, Liao HK, Benner C, Esteban CR, Jin Y, Liu GH, Li Y, Izpisua Belmonte JC. Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. Cell Stem Cell. 2014 Jul 3;15(1):31-6. doi: 10.1016/j.stem.2014.06.016. PubMed PMID: 24996168.
  6. Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K. Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1. Cell Stem Cell. 2014 Jun 5;14(6):781-95. doi: 10.1016/j.stem.2014.03.004. Epub 2014 Apr 3. PubMed PMID: 24704492.

Eye disease treatment

  1. Jepson LH, Hottowy P, Weiner GA, Dabrowski W, Litke AM, Chichilnisky EJ. High-fidelity reproduction of spatiotemporal visual signals for retinal prosthesis. Neuron. 2014 Jul 2;83(1):87-92. doi: 10.1016/j.neuron.2014.04.044. Epub 2014 Jun 5. PubMed PMID: 24910077.
    • Trenholm S, Roska B. Cell-type-specific electric stimulation for vision restoration. Neuron. 2014 Jul 2;83(1):1-2. doi: 10.1016/j.neuron.2014.06.012. PubMed PMID: 24991948.

Funding

  1. Resnick A. Systemic addiction to research funding. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):E2634. doi: 10.1073/pnas.1407369111. Epub 2014 Jun 11. PubMed PMID: 24920596.
  2. Alberts B, Kirschner MW, Tilghman S, Varmus H. Rescuing US biomedical research from its systemic flaws. Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5773-7. doi: 10.1073/pnas.1404402111. Epub 2014 Apr 14. PubMed PMID: 24733905; PubMed Central PMCID: PMC4000813.

Research Career

  1. Smaglik P. Employment: PhD overdrive. Nature. 2014 Jul 10;511(7508):255-6. PubMed PMID: 25013890.

Systems Biology

  1. Bruggner RV, Bodenmiller B, Dill DL, Tibshirani RJ, Nolan GP. Automated identification of stratifying signatures in cellular subpopulations. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):E2770-7. doi: 10.1073/pnas.1408792111. Epub 2014 Jun 16. PubMed PMID: 24979804.

Genomics/ Sequencing

  1. Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA-sequencing. Genome Biol. 2014 Jun 30;15(6):R86. [Epub ahead of print] PubMed PMID: 24981968.
  2. Tilgner H, Grubert F, Sharon D, Snyder MP. Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9869-74. doi: 10.1073/pnas.1400447111. Epub 2014 Jun
    24. PubMed PMID: 24961374.

Genome editing

  1. Sheridan C. First CRISPR-Cas patent opens race to stake out intellectual property. Nat Biotechnol. 2014 Jul 8;32(7):599-601. doi: 10.1038/nbt0714-599. PubMed PMID: 25004207.
  2. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol. 2014 Jul;32(7):670-6. doi: 10.1038/nbt.2889. Epub 2014 Apr 20. PubMed PMID: 24752079.
  3. Kuscu C, Arslan S, Singh R, Thorpe J, Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol. 2014 Jul;32(7):677-83. doi: 10.1038/nbt.2916. Epub 2014 May 18. PubMed PMID: 24837660.
  4. Tsai SQ, Joung JK. What’s Changed with Genome Editing? Cell Stem Cell. 2014 Jul 3;15(1):3-4. doi: 10.1016/j.stem.2014.06.017. PubMed PMID: 24996161.
  5. Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Talkowski ME, Musunuru K. Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing. Cell Stem Cell. 2014 Jul 3;15(1):27-30. doi: 10.1016/j.stem.2014.04.020. PubMed PMID: 24996167; PubMed Central PMCID: PMC4082799.
  6. Smith C, Gore A, Yan W, Abalde-Atristain L, Li Z, He C, Wang Y, Brodsky RA, Zhang K, Cheng L, Ye Z. Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs. Cell Stem Cell. 2014 Jul 3;15(1):12-3. doi: 10.1016/j.stem.2014.06.011. PubMed PMID: 24996165.
  7. Suzuki K, Yu C, Qu J, Li M, Yao X, Yuan T, Goebl A, Tang S, Ren R, Aizawa E, Zhang F, Xu X, Soligalla RD, Chen F, Kim J, Kim NY, Liao HK, Benner C, Esteban CR, Jin Y, Liu GH, Li Y, Izpisua Belmonte JC. Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. Cell Stem Cell. 2014 Jul 3;15(1):31-6. doi: 10.1016/j.stem.2014.06.016. PubMed PMID: 24996168.
  8. Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K. Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1. Cell Stem Cell. 2014 Jun 5;14(6):781-95. doi: 10.1016/j.stem.2014.03.004. Epub 2014 Apr 3. PubMed PMID: 24704492.
  9. Güell M, Yang L, Church G. Genome Editing Assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics. 2014 Jul 1. pii: btu427. [Epub ahead of print] PubMed PMID: 24990609.
  10. Spies M. Fulfilling the dream of a perfect genome editing tool. Proc Natl Acad Sci U S A. 2014 Jul 2. pii: 201408985. [Epub ahead of print] PubMed PMID: 24989506.

Genome Editing

  1. Gagnon JA, Valen E, Thyme SB, Huang P, Ahkmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF. Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs. PLoS One. 2014 May 29;9(5):e98186. doi: 10.1371/journal.pone.0098186. eCollection 2014. PubMed PMID: 24873830.
  2. Hsu PD, Lander ES, Zhang F. Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell. 2014 Jun 5;157(6):1262-1278. doi: 10.1016/j.cell.2014.05.010. Review. PubMed PMID: 24906146.
  3. Torres R, Martin MC, Garcia A, Cigudosa JC, Ramirez JC, Rodriguez-Perales S. Engineering human tumour-associated chromosomal translocations with the RNA-guided CRISPR-Cas9 system. Nat Commun. 2014 Jun 3;5:3964. doi: 10.1038/ncomms4964. PubMed PMID: 24888982.
  4. Yu C, Zhang Y, Yao S, Wei Y. A PCR Based Protocol for Detecting Indel Mutations Induced by TALENs and CRISPR/Cas9 in Zebrafish. PLoS One. 2014 Jun 5;9(6):e98282. doi: 10.1371/journal.pone.0098282. eCollection 2014. PubMed PMID: 24901507.

Sequencing

  1. Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY. Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing. N Engl J Med. 2014 Jun 4. [Epub ahead of print] PubMed PMID: 4896819.
  2. Gilissen C, Hehir-Kwa JY, Thung DT, van de Vorst M, van Bon BW, Willemsen MH, Kwint M, Janssen IM, Hoischen A, Schenck A, Leach R, Klein R, Tearle R, Bo T, Pfundt R, Yntema HG, de Vries BB, Kleefstra T, Brunner HG, Vissers LE, Veltman JA. Genome sequencing identifies major causes of severe intellectual disability. Nature. 2014 Jun 4. doi: 10.1038/nature13394. [Epub ahead of print] PubMed PMID: 24896178.

Stem cells

  1. Dunn SJ, Martello G, Yordanov B, Emmott S, Smith AG. Defining an essential transcription factor program for naïve pluripotency. Science. 2014 Jun 6;344(6188):1156-60. doi: 10.1126/science.1248882. PubMed PMID: 24904165.

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.