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A Biologist’s Mother’s Day Song

Sunday, May 8, 2011

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2011-05-08 new articles we read this week

Sunday, May 8, 2011

Genomics

  1. Nagano T, Fraser P. No-Nonsense Functions for Long Noncoding RNAs. Cell. 2011 Apr 15;145(2):178-81. PubMed PMID: 21496640.
  2. Mak HC. John storey. Nat Biotechnol. 2011 Apr;29(4):331-3. PubMed PMID: 21478851.
    • A nice discussion by John Storey on the challenges of normalization and analysis of next generation sequencing data for RNA-Seq.

Systems biology

  1. Oleksiuk O, Jakovljevic V, Vladimirov N, Carvalho R, Paster E, Ryu WS, Meir Y, Wingreen NS, Kollmann M, Sourjik V. Thermal robustness of signaling in bacterial
    chemotaxis. Cell. 2011 Apr 15;145(2):312-21. PubMed PMID: 21496648.

Development

  1. McKay R. Developmental biology: Remarkable role for the placenta. Nature. 2011 Apr 21;472(7343):298-9. PubMed PMID: 21512563.

Funding

  1. Samuel Reich E, Semeniuk I, Tollefson J, Wadman M. US budget a taste ofbattles to come. Nature. 2011 Apr 21;472(7343):267-9. PubMed PMID: 21512542.

Reviewing

  1. Ploegh H. End the wasteful tyranny of reviewer experiments. Nature. 2011 Apr 28;472(7344):391. PubMed PMID: 21525890.

Ethical, Legal and Social Issues

  1. Dugdale LS, Ridenour AA. Making sense of the Roman Catholic directive to extend life indefinitely. Hastings Cent Rep. 2011 Mar-Apr;41(2):28-9. PubMed PMID: 21495514.
  2. Rennie S. Viewing research participation as a moral obligation: in whose interests? Hastings Cent Rep. 2011 Mar-Apr;41(2):40-7. PubMed PMID: 21495516.
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2011-04-23 new articles we read this week

Saturday, April 23, 2011

Education

Nature Magazine has published a series of papers that discuss “The Future of The PhD“. Another discussion of the challenges that PhD students encounter and a debate on whether a doctoral degree should be a training for job or a training for scientific thinking. The discussions from the readers under each article on the website are also interesting.

  1. Fix the PhD. Nature. 2011 Apr 21;472(7343):259-260. PubMed PMID: 21512527.
  2. Cyranoski D, Gilbert N, Ledford H, Nayar A, Yahia M. Education: The PhD factory. Nature. 2011 Apr 21;472(7343):276-279. PubMed PMID: 21512548.
  3. McCook A. Education: Rethinking PhDs. Nature. 2011 Apr 21;472(7343):280-282.PubMed PMID: 21512549.
  4. Gosling R, Tickle C, Running SW, Tandong Y, Dinnyes A, Osowole AA, Cule E. Seven ages of the PhD. Nature. 2011 Apr 21;472(7343):283-286. PubMed PMID: 21512550.
  5. Taylor M. Reform the PhD system or close it down. Nature. 2011 Apr 21;472(7343):261. PubMed PMID: 21512530.
  6. Fiske P. What is a PhD really worth?. Nature 2011 Apr 22;472(7343):381
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2011-04-16 New articles we read this week

Saturday, April 16, 2011

Development

  1. Eiraku M, Takata N, Ishibashi H, Kawada M, Sakakura E, Okuda S, Sekiguchi K, Adachi T, Sasai Y. Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature. 2011 Apr 7;472(7341):51-6. PubMed PMID: 21475194.
    1. Commentary: Ali RR, Sowden JC. Regenerative medicine: DIY eye. Nature. 2011 Apr 7;472(7341):42-3. PubMed PMID: 21475187.
    2. News report from the Telegraph. “Scientists grow ’embryonic eye’ in test tube“.
    • A whole eye cup with properly laminated retina and RPE can spontaneously generate from mouse embryonic stem cell culture!

Eye disease

  1. Morris AC, Forbes-Osborne MA, Pillai LS, Fadool JM. Microarray Analysis of XOPS-mCFP Zebrafish Retina Identifies Genes Associated with Rod Photoreceptor Degeneration and Regeneration. Invest Ophthalmol Vis Sci. 2011 Apr6;52(5):2255-66. Print 2011 Apr. PubMed PMID: 21217106.
  2. Stujenske JM, Dowling JE, Emran F. The Bugeye Mutant Zebrafish Exhibits Visual Deficits that Arise with the Onset of an Enlarged Eye Phenotype. Invest Ophthalmol Vis Sci. 2011 Apr 1. [Epub ahead of print] PubMed PMID: 21460263.

Retinal development

  1. Glaschke A, Weiland J, Del Turco D, Steiner M, Peichl L, Glösmann M. Thyroid hormone controls cone opsin expression in the retina of adult rodents. JNeurosci. 2011 Mar 30;31(13):4844-51. PubMed PMID: 21451022.

Ethical, Social and Legal Issues

  1. Hayden EC. Patent dispute threatens US Alzheimer’s research. Nature. 2011 Apr 7;472(7341):20. PubMed PMID: 21475170.

Education

  1. Nayar A. Developing world: educating India. Nature. 2011 Apr 7;472(7341):24-6. PubMed PMID: 21475172.

Cancer

  1. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie WR, Hicks J, Wigler M. Tumour evolution inferred by single-cell sequencing. Nature. 2011 Apr7;472(7341):90-4. Epub 2011 Mar 13. PubMed PMID: 21399628.

Neurobehavior

  1. Liu Y, Jiang Y, Si Y, Kim JY, Chen ZF, Rao Y. Molecular regulation of sexual preference revealed by genetic studies of 5-HT in the brains of male mice. Nature. 2011 Apr 7;472(7341):95-9. Epub 2011 Mar 23. PubMed PMID: 21441904.
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2011-04-10 new articles we read this week

Sunday, April 10, 2011

Vision

  1. Standfuss J, Edwards PC, D’Antona A, Fransen M, Xie G, Oprian DD, Schertler GF. The structural basis of agonist-induced activation in constitutively active rhodopsin. Nature. 2011 Mar 31;471(7340):656-60. Epub 2011 Mar 9. PubMed PMID: 21389983.

Genetics

  1. Hurst LD. Molecular genetics: The sound of silence. Nature. 2011 Mar 31;471(7340):582-3. PubMed PMID: 21455166.
    • How silence mutations can cause disease? One more example from the study of Crohn’s disease.
  2. Lachke SA, Alkuraya FS, Kneeland SC, Ohn T, Aboukhalil A, Howell GR, Saadi I, Cavallesco R, Yue Y, Tsai AC, Nair KS, Cosma MI, Smith RS, Hodges E, Alfadhli SM, Al-Hajeri A, Shamseldin HE, Behbehani A, Hannon GJ, Bulyk ML, Drack AV, Anderson PJ, John SW, Maas RL. Mutations in the RNA granule component TDRD7 cause cataract and glaucoma. Science. 2011 Mar 25;331(6024):1571-6. PubMed PMID: 21436445.
    • Commentary: Duncan MK. Development. A new focus on RNA in the lens. Science. 2011 Mar 25;331(6024):1523-4. PubMed PMID: 21436425.
  3. Horn T, Sandmann T, Fischer B, Axelsson E, Huber W, Boutros M. Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nat Methods. 2011 Apr;8(4):341-6. Epub 2011 Mar 6. PubMed PMID: 21378980.

 

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2011-04-02 New articles we read this week

Saturday, April 2, 2011

Neuroscience

  1. Rothenaigner I, Krecsmarik M, Hayes JA, Bahn B, Lepier A, Fortin G, Götz M, Jagasia R, Bally-Cuif L. Clonal analysis by distinct viral vectors identifies bona fide neural stem cells in the adult zebrafish telencephalon and characterizes their division properties and fate. Development. 2011Apr;138(8):1459-69. Epub 2011 Mar 2. PubMed PMID: 21367818.

Eye disease

  1. Leung CK, Weinreb RN, Li ZW, Liu S, Lindsey JD, Choi N, Liu L, Cheung CY, Ye C, Qiu K, Chen LJ, Yung WH, Crowston JG, Pu M, So KF, Pang CP, Lam DS. Long-term in vivo imaging and measurement of dendritic shrinkage of retinal ganglion cells.Invest Ophthalmol Vis Sci. 2011 Mar 1;52(3):1539-47. Print 2011. PubMed PMID:21245394.

Retina

  1. Cederlund ML, Morrissey ME, Baden T, Scholz D, Vendrell V, Lagnado L, Connaughton VP, Kennedy BN. Zebrafish Tg(7.2mab21l2:EGFP)ucd2 Transgenics Reveal a Unique Population of Retinal Amacrine Cells. Invest Ophthalmol Vis Sci. 2011Mar 1;52(3):1613-21. Print 2011. PubMed PMID: 21051702.

Genomics

  1. Thompson JF, Milos PM. The properties and applications of single-molecule DNA sequencing. Genome Biol. 2011 Feb 24;12(2):217. [Epub ahead of print] PubMedPMID: 21349208.
  2. Commentary: Furlong EE. Molecular biology: A fly in the face of genomics. Nature. 2011 Mar 24;471(7339):458-9. PubMed PMID: 21430772.
    1. Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011 Mar 24;471(7339):480-5. Epub 2010 Dec 22. PubMed PMID: 21179089.
    2. Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. The developmental transcriptome of Drosophila melanogaster. Nature. 2011 Mar 24;471(7339):473-9. Epub 2010 Dec 22. PubMed PMID: 21179090.
    3. Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, Cheng C, Auburn RP, Davis MB, Domanus M, Shah PK, Morrison CA, Zieba J, Suchy S, Senderowicz L, Victorsen A, Bild NA, Grundstad AJ, Hanley D, MacAlpine DM, Mannervik M, Venken K, Bellen H, White R, Gerstein M, Russell S, Grossman RL, Ren B, Posakony JW, Kellis M, White KP. A cis-regulatory map of the Drosophila genome. Nature. 2011 Mar 24;471(7339):527-31. PubMed PMID: 21430782.

Cancer

  1. Buchen L. Cancer: Missing the mark. Nature. 2011 Mar 24;471(7339):428-32.PubMed PMID: 21430749.
  2. Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M, Anderson KC, Ardlie KG, Auclair D, Baker A, Bergsagel PL, Bernstein BE, Drier Y, Fonseca R, Gabriel SB, Hofmeister CC, Jagannath S, Jakubowiak AJ, Krishnan A, Levy J, Liefeld T, Lonial S, Mahan S, Mfuko B, Monti S, Perkins LM, Onofrio R, Pugh TJ, Rajkumar SV, Ramos AH, Siegel DS, Sivachenko A, Stewart AK, Trudel S, Vij R, Voet D, Winckler W, Zimmerman T, Carpten J, Trent J, Hahn WC, Garraway LA, Meyerson M, Lander ES, Getz G, Golub
    TR. Initial genome sequencing and analysis of multiple myeloma. Nature. 2011 Mar 24;471(7339):467-72. PubMed PMID: 21430775.
  3. White RM, Cech J, Ratanasirintrawoot S, Lin CY, Rahl PB, Burke CJ, Langdon E,  Tomlinson ML, Mosher J, Kaufman C, Chen F, Long HK, Kramer M, Datta S, Neuberg D, Granter S, Young RA, Morrison S, Wheeler GN, Zon LI. DHODH modulates transcriptional elongation in the neural crest and melanoma. Nature. 2011 Mar 24;471(7339):518-22. PubMed PMID: 21430780.
  4. Ceol CJ, Houvras Y, Jane-Valbuena J, Bilodeau S, Orlando DA, Battisti V, Fritsch L, Lin WM, Hollmann TJ, Ferré F, Bourque C, Burke CJ, Turner L, Uong A, Johnson LA, Beroukhim R, Mermel CH, Loda M, Ait-Si-Ali S, Garraway LA, Young RA, Zon LI. The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset. Nature. 2011 Mar 24;471(7339):513-7. PubMed PMID: 21430779.

Reproduction

  1. Seandel M, Rafii S. Reproductive biology: In vitro sperm maturation. Nature.2011 Mar 24;471(7339):453-5. PubMed PMID: 21430767.

Disease gene mapping

  1. Piggins HD. Schizophrenia: Zooming in on a gene. Nature. 2011 Mar 24;471(7339):455-6. PubMed PMID: 21430769.

Development

  1. Rossant J. Developmental biology: A mouse is not a cow. Nature. 2011 Mar 24;471(7339):457-8. PubMed PMID: 21430771.
  2. Mou C, Pitel F, Gourichon D, Vignoles F, Tzika A, Tato P, Yu L, Burt DW, Bed’hom B, Tixier-Boichard M, Painter KJ, Headon DJ. Cryptic patterning of avian skin confers a developmental facility for loss of neck feathering. PLoS Biol. 2011 Mar;9(3):e1001028. Epub 2011 Mar 15. PubMed PMID: 21423653; PubMed Central PMCID: PMC3057954.

Evolution

  1. Woods RJ, Barrick JE, Cooper TF, Shrestha U, Kauth MR, Lenski RE. Second-order selection for evolvability in a large Escherichia coli population. Science. 2011 Mar 18;331(6023):1433-6. PubMed PMID: 21415350.
  2. Philippe H, Brinkmann H, Lavrov DV, Littlewood DT, Manuel M, Wörheide G, Baurain D. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 2011 Mar;9(3):e1000602. Epub 2011 Mar 15. PubMed PMID: 21423652; PubMed Central PMCID: PMC3057953.

Medicine

  1. Physicians as guardians of genetic knowledge. Lancet. 2011 Mar 19;377(9770):967. PubMed PMID: 21420539.
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2011-03-27 new articles we read this week

Saturday, March 26, 2011

Systems Biology

  1. CELL Review issue: Systems Biology
    1. Systems Biology: What’s the Next Challenge?
    2. Macilwain C. Systems biology: evolving into the mainstream. Cell. 2011 Mar 18;144(6):839-41. PubMed PMID: 21414474.
    3. Arkin AP, Schaffer DV. Network news: innovations in 21st century systems biology. Cell. 2011 Mar 18;144(6):844-9. PubMed PMID: 21414475.
    4. Nurse P, Hayles J. The cell in an era of systems biology. Cell. 2011 Mar 18;144(6):850-4. PubMed PMID: 21414476.
    5. Smolke CD, Silver PA. Informing biological design by integration of systems and synthetic biology. Cell. 2011 Mar 18;144(6):855-9. PubMed PMID: 21414477.
    6. Ideker T, Dutkowski J, Hood L. Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power. Cell. 2011 Mar 18;144(6):860-3. PubMed PMID: 21414478.
    7. Pe’er D, Hacohen N. Principles and strategies for developing network models in cancer. Cell. 2011 Mar 18;144(6):864-73. PubMed PMID: 21414479.
    8. Ferrell JE Jr, Tsai TY, Yang Q. Modeling the cell cycle: why do certain circuits oscillate? Cell. 2011 Mar 18;144(6):874-85. PubMed PMID: 21414480.
    9. Yosef N, Regev A. Impulse control: temporal dynamics in gene transcription. Cell. 2011 Mar 18;144(6):886-96. PubMed PMID: 21414481.
    10. Grecco HE, Schmick M, Bastiaens PI. Signaling from the living plasma membrane. Cell. 2011 Mar 18;144(6):897-909. PubMed PMID: 21414482.
    11. Balázsi G, van Oudenaarden A, Collins JJ. Cellular decision making and biological noise: from microbes to mammals. Cell. 2011 Mar 18;144(6):910-25. PubMed PMID: 21414483.
    12. Spencer SL, Sorger PK. Measuring and modeling apoptosis in single cells. Cell. 2011 Mar 18;144(6):926-39. PubMed PMID: 21414484.
    13. Young RA. Control of the embryonic stem cell state. Cell. 2011 Mar 18;144(6):940-54. PubMed PMID: 21414485.
    14. Lander AD. Pattern, growth, and control. Cell. 2011 Mar 18;144(6):955-69. PubMed PMID: 21414486.
    15. Peter IS, Davidson EH. Evolution of gene regulatory networks controlling body plan development. Cell. 2011 Mar 18;144(6):970-85. PubMed PMID: 21414487.
    16. Vidal M, Cusick ME, Barabási AL. Interactome networks and human disease. Cell. 2011 Mar 18;144(6):986-98. PubMed PMID: 21414488.
    17. Seebacher J, Gavin AC. SnapShot: Protein-Protein Interaction Networks. Cell. 2011 Mar 18;144(6):1000-1000.e1. PubMed PMID: 21414489.

Stem cells

  1. NATURE REVIEW GENETICS: Focus on: Stem cells
    1. González F, Boué S, Belmonte JC. Methods for making induced pluripotent stem cells: reprogramming à la carte. Nat Rev Genet. 2011 Apr;12(4):231-42. Epub 2011 Feb 22. PubMed PMID: 21339765.
    2. Cohen DE, Melton D. Turning straw into gold: directing cell fate for regenerative medicine. Nat Rev Genet. 2011 Apr;12(4):243-52. Epub 2011 Mar 9. PubMed PMID: 21386864.
    3. Plath K, Lowry WE. Progress in understanding reprogramming to the induced pluripotent state. Nat Rev Genet. 2011 Apr;12(4):253-65. PubMed PMID: 21415849.
    4. Zhu H, Lensch MW, Cahan P, Daley GQ. Investigating monogenic and complex diseases with pluripotent stem cells. Nat Rev Genet. 2011 Apr;12(4):266-75. Epub 2011 Mar 9. PubMed PMID: 21386866.
    5. Montgomery SB, Dermitzakis ET. From expression QTLs to personalized transcriptomics. Nat Rev Genet. 2011 Apr;12(4):277-82. Epub 2011 Mar 9. PubMed PMID: 21386863.
    6. Ong CT, Corces VG. Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat Rev Genet. 2011 Apr;12(4):283-93. Epub 2011 Mar 1. PubMed PMID: 21358745.
  2. Ledford H. Hidden toll of embryo ethics war. Nature. 2011 Mar 17;471(7338):279. PubMed PMID: 21412306.
  3. Abbott A. Europe rules against stem-cell patents. Nature. 2011 Mar 17;471(7338):280. PubMed PMID: 21412307.

Neuroscience

  1. Bock DD, Lee WC, Kerlin AM, Andermann ML, Hood G, Wetzel AW, Yurgenson S, Soucy ER, Kim HS, Reid RC. Network anatomy and in vivo physiology of visual cortical neurons. Nature. 2011 Mar 10;471(7337):177-82. PubMed PMID: 21390124.
  2. Briggman KL, Helmstaedter M, Denk W. Wiring specificity in the direction-selectivity circuit of the retina. Nature. 2011 Mar 10;471(7337):183-8. PubMed PMID: 21390125.
    • Commentary: Seung HS. Neuroscience: Towards functional connectomics. Nature. 2011 Mar 10;471(7337):170-2. PubMed PMID: 2139011

Retinal pigment epithelium

  1. Iacovelli J, Zhao C, Wolkow N, Veldman P, Gollomp K, Ojha P, Lukinova N, King A, Feiner L, Esumi N, Zack DJ, Pierce EA, Vollrath D, Dunaief JL. Generation of Cre Transgenic Mice with Postnatal RPE-Specific Ocular Expression. Invest Ophthalmol Vis Sci. 2011 Mar 14;52(3):1378-83. Print 2011 Mar. PubMed PMID: 21212186.

Regeneration

  1. Kikuchi K, Holdway JE, Major RJ, Blum N, Dahn RD, Begemann G, Poss KD. Retinoic Acid production by endocardium and epicardium is an injury response essential for zebrafish heart regeneration. Dev Cell. 2011 Mar 15;20(3):397-404. PubMed PMID: 21397850.

Retina

  1. Mollema NJ, Yuan Y, Jelcick AS, Sachs AJ, von Alpen D, Schorderet D, Escher P, Haider NB. Nuclear Receptor Rev-erb Alpha (Nr1d1) Functions in Concert with Nr2e3 to Regulate Transcriptional Networks in the Retina. PLoS One. 2011 Mar 8;6(3):e17494. PubMed PMID: 21408158.
  2. Minke B, Peters M. Cell biology. Rhodopsin as thermosensor? Science. 2011 Mar 11;331(6022):1272-3. PubMed PMID: 21393531.

Eye disease

  1. Volkmann BA, Zinkevich NS, Mustonen A, Schilter KF, Bosenko DV, Reis LM, Broeckel U, Link BA, Semina E. Potential novel mechanism for Axenfeld-Rieger syndrome: deletion of a distant region containing regulatory elements of PITX2. Invest Ophthalmol Vis Sci. 2010 Sep 29. [Epub ahead of print] PubMed PMID: 20881290.
  2. Kaneko H, Dridi S, Tarallo V, Gelfand BD, Fowler BJ, Cho WG, Kleinman ME, Ponicsan SL, Hauswirth WW, Chiodo VA, Karikó K, Yoo JW, Lee DK, Hadziahmetovic M, Song Y, Misra S, Chaudhuri G, Buaas FW, Braun RE, Hinton DR, Zhang Q, Grossniklaus HE, Provis JM, Madigan MC, Milam AH, Justice NL, Albuquerque RJ, Blandford AD, Bogdanovich S, Hirano Y, Witta J, Fuchs E, Littman DR, Ambati BK, Rudin CM, Chong MM, Provost P, Kugel JF, Goodrich JA, Dunaief JL, Baffi JZ, Ambati J. DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature. 2011 Mar 17;471(7338):325-30. Epub 2011 Feb 6. PubMed PMID: 21297615.
    1. Commentary: Meister G. Vision: Dicer leaps into view. Nature. 2011 Mar 17;471(7338):308-9. PubMed PMID: 21412326.
    • A new way of causing geographical atrophy by an unknown role of DICER.

Disease

  1. Kawahara G, Karpf JA, Myers JA, Alexander MS, Guyon JR, Kunkel LM. Drug screening in a zebrafish model of Duchenne muscular dystrophy. Proc Natl Acad Sci U S A. 2011 Mar 14. [Epub ahead of print] PubMed PMID: 21402949.

Behavior

  1. Cachat J, Stewart A, Utterback E, Hart P, Gaikwad S, Wong K, Kyzar E, Wu N, Kalueff AV. Three-dimensional neurophenotyping of adult zebrafish behavior. PLoS One. 2011 Mar 7;6(3):e17597. PubMed PMID: 21408171.

Development

  1. England SJ, Blanchard GB, Mahadevan L, Adams RJ. A dynamic fate map of the forebrain shows how vertebrate eyes form and explains two causes of cyclopia. Development. 2006 Dec;133(23):4613-7. Epub 2006 Nov 1. PubMed PMID: 17079266.
  2. Publicover S, Barratt C. Reproductive biology: Progesterone’s gateway into sperm. Nature. 2011 Mar 17;471(7338):313-4. PubMed PMID: 21412330.
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2011-03-19 new articles we read this week

Monday, March 21, 2011

Evolution

  1. Mallarino R, Grant PR, Grant BR, Herrel A, Kuo WP, Abzhanov A. Two developmental modules establish 3D beak-shape variation in Darwin’s finches. Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4057-62. Epub 2011 Feb 22. PubMed PMID: 21368127.

Signal transduction

  1. Pierfelice T, Alberi L, Gaiano N. Notch in the vertebrate nervous system: an old dog with new tricks. Neuron. 2011 Mar 10;69(5):840-55. PubMed PMID: 21382546.

Systems biology

  1. Heo M, Maslov S, Shakhnovich E. Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions. Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4258-63. Epub 2011 Feb 22. PubMed PMID: 21368118.

Stem cells

  1. Boulting GL, Kiskinis E, Croft GF, Amoroso MW, Oakley DH, Wainger BJ, Williams DJ, Kahler DJ, Yamaki M, Davidow L, Rodolfa CT, Dimos JT, Mikkilineni S, Macdermott AB, Woolf CJ, Henderson CE, Wichterle H, Eggan K. A functionally characterized test set of human induced pluripotent stem cells. Nat Biotechnol. 2011 Mar;29(3):279-86. Epub 2011 Feb 3. PubMed PMID: 21293464.
    • Commentary: Kim H, Studer L. IPSCs put to the test. Nat Biotechnol. 2011 Mar;29(3):233-5. PubMed PMID: 21390027.
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2011-03-12 new articles we read this week

Saturday, March 12, 2011

Research life

  • Schwartz MA. The importance of stupidity in scientific research. J Cell Sci. 2008 Jun 1;121(Pt 11):1771. PubMed PMID: 18492790.
    • What is the difference between class room learning and research? Is being good in class room good enough to make one a research scientist?

Systems biology

  • Burrill DR, Silver PA. Synthetic circuit identifies subpopulations with sustained memory of DNA damage. Genes Dev. 2011 Mar 1;25(5):434-9. PubMed PMID: 21363961.

Genomics

  • Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 2011 Mar;21(3):447-55. Epub 2010 Nov 24. PubMed PMID: 21106904.
  • Xu W, Seok J, Mindrinos MN, Schweitzer AC, Jiang H, Wilhelmy J, Clark TA, Kapur K, Xing Y, Faham M, Storey JD, Moldawer LL, Maier RV, Tompkins RG, Wong WH, Davis RW, Xiao W; the Inflammation and Host Response to Injury Large-Scale Collaborative Research Program. Human transcriptome array for high-throughput clinical studies. Proc Natl Acad Sci U S A. 2011 Mar 1;108(9):3707-3712. Epub 2011 Feb 11. PubMed PMID: 21317363.
    • A comparative study of RNA-seq and microarrays for disease research. The authors showed that the performance of microarrays, can be more reliable than RNA-seq. That includes a higher sensitivity at the exon level for the low abundance transcripts
  • Maxmen A. Exome sequencing deciphers rare diseases. Cell. 2011 Mar 4;144(5):635-7. PubMed PMID: 21376225.
    • Whole genome sequencing helps to find the disease genes that haven’t been able to mapped.

Bioinformatics

  • Swedlow JR. Finding an image in a haystack: the case for public image repositories. Nat Cell Biol. 2011 Mar;13(3):183. PubMed PMID: 21364564.

Behaviour

  • Mathur P, Lau B, Guo S. Conditioned place preference behavior in zebrafish. Nat Protoc. 2011 Feb;6(3):338-45. Epub 2011 Feb 24. PubMed PMID: 21372814.

Retina

  • Lamba DA, Reh TA. Microarray Characterization of Human Embryonic Stem Cell-Derived Retinal Cultures. Invest Ophthalmol Vis Sci. 2011 Feb 23. [Epub ahead of print] PubMed PMID: 21345990.
  • Roberts MR, Srinivas M, Forrest D, Morreale de Escobar G, Reh TA. Making the gradient: thyroid hormone regulates cone opsin expression in the developing mouse retina. Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6218-23. Epub 2006 Apr 10. PubMed PMID: 16606843; PubMed Central PMCID: PMC1458858.

Neuroscience

  • Suzuki A, Stern SA, Bozdagi O, Huntley GW, Walker RH, Magistretti PJ, Alberini CM. Astrocyte-neuron lactate transport is required for long-term memory formation. Cell. 2011 Mar 4;144(5):810-23. PubMed PMID: 21376239.
    • Commentary Bezzi P, Volterra A. Astrocytes: powering memory. Cell. 2011 Mar 4;144(5):644-5. PubMed PMID: 21376229.
  • Anderson JR, Gallup GG. Which primates recognize themselves in mirrors? PLoSBiol. 2011 Mar;9(3):e1001024. Epub 2011 Mar 1. PubMed PMID: 21390247.

Cancer

  • Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011 Mar 4;144(5):646-74. PubMed PMID: 21376230.

Epidemiology

  • The longest longitudinal study of the same group of people starting from birth to 65 years old! Many interesting observations.
    • The generation game. Nature. 2011 Mar 3;471(7336):5. PubMed PMID: 21368778.
    • Pearson H. Epidemiology: Study of a lifetime. Nature. 2011 Mar 3;471(7336):20-4. PubMed PMID: 21368799.

Development

  • Wartlick O, Mumcu P, Kicheva A, Bittig T, Seum C, Jülicher F, González-Gaitán M. Dynamics of Dpp signaling and proliferation control. Science. 2011 Mar 4;331(6021):1154-9. PubMed PMID: 21385708.
    • Commentary: Le Goff L, Lecuit T. Developmental biology. Gradient scaling and growth. Science. 2011 Mar 4;331(6021):1141-2. PubMed PMID: 21385701.

Stem cells

  • A series of papers reveal the differences of iPS cells, suggesting more research has to be done before using these cells to treat human disease.
    • Commentary: Pera MF. Stem cells: The dark side of induced pluripotency. Nature. 2011 Mar 3;471(7336):46-7. PubMed PMID: 21368819.
    • Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O’Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, Ecker JR. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 2011 Mar 3;471(7336):68-73. Epub 2011 Feb 2. PubMed PMID: 21289626.
    • Gore A, Li Z, Fung HL, Young JE, Agarwal S, Antosiewicz-Bourget J, Canto I, Giorgetti A, Israel MA, Kiskinis E, Lee JH, Loh YH, Manos PD, Montserrat N, Panopoulos AD, Ruiz S, Wilbert ML, Yu J, Kirkness EF, Izpisua Belmonte JC, Rossi DJ, Thomson JA, Eggan K, Daley GQ, Goldstein LS, Zhang K. Somatic coding mutations in human induced pluripotent stem cells. Nature. 2011 Mar
      3;471(7336):63-7. PubMed PMID: 21368825.
    • Hussein SM, Batada NN, Vuoristo S, Ching RW, Autio R, Närvä E, Ng S, Sourour M, Hämäläinen R, Olsson C, Lundin K, Mikkola M, Trokovic R, Peitz M, Brüstle O, Bazett-Jones DP, Alitalo K, Lahesmaa R, Nagy A, Otonkoski T. Copy number variation and selection during reprogramming to pluripotency. Nature. 2011 Mar 3;471(7336):58-62. PubMed PMID: 21368824.

Structural biology

  • Spudich JA. Biochemistry. Molecular motors, beauty in complexity. Science. 2011 Mar 4;331(6021):1143-4. PubMed PMID: 21385703.

Eye

  • Veth KN, Willer JR, Collery RF, Gray MP, Willer GB, Wagner DS, Mullins MC, Udvadia AJ, Smith RS, John SW, Gregg RG, Link BA. Mutations in Zebrafish lrp2 Result in Adult-Onset Ocular Pathogenesis That Models Myopia and Other Risk Factors for Glaucoma. PLoS Genet. 2011 Feb;7(2):e1001310. Epub 2011 Feb 17. PubMed PMID: 21379331; PubMed Central PMCID: PMC3040661.
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Sir Ken Robinson – The Element

Sunday, March 6, 2011

Another great talk by Sir Ken Robinson.

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