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The associate editor of Genomics resigns because of the difficulties in accessing the articles by scientists from developing countries

Thursday, May 17, 2012

Dr. Winston Hide decides to resigns from his associate editor position of Genomics because of the expensive subscription rate of the journal precludes many in accessing important articles that are important for public health.

From The Guardian:

Today I resigned from the editorial board of a well respected journal in my field – Genomics. No longer can I work for a system that provides solid profits for the publisher while effectively denying colleagues in developing countries access to research findings.

A respectable decision! I must say that the situation in the developed countries is getting worse too. And I often have to ask my friends to download papers for me. Thus, publishing in open-access journals is a good alternative*. However, when the research budget is tight, who is going to pay for the publication fee?

*Disclaimer: I am an academic editor of PLoS ONE because I support their publication philosophy. This article reflects my personal view and does not reflect the Journal’s position.

 

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2012-05-16 New articles we read this week

Wednesday, May 16, 2012

Neuroimaging/ Connectomics

  1. Wedeen VJ, Rosene DL, Wang R, Dai G, Mortazavi F, Hagmann P, Kaas JH, Tseng WY. The geometric structure of the brain fiber pathways. Science. 2012 Mar 30;335(6076):1628-34. PubMed PMID: 22461612.

Neuroscience

  1. Rogulja D, Young MW. Control of sleep by cyclin A and its regulator. Science. 2012 Mar 30;335(6076):1617-21. PubMed PMID: 22461610.
  2. Koch C. Newsmaker interview: Christof Koch. A vision of how mouse vision can reveal consciousness’ secrets. Interview by Yudhijit Bhattacharjee. Science. 2012 Mar 23;335(6075):1426-7. PubMed PMID: 22442452.
  3. Morris RG, Takeuchi T. Neuroscience. The imaginary mind of a mouse. Science. 2012 Mar 23;335(6075):1455-6. PubMed PMID: 22442473.
  4. Bardin J. Neuroscience: Making connections. Nature. 2012 Mar 21;483(7390):394-6. doi: 10.1038/483394a. PubMed PMID: 22437591.

Behaviour

  1. Shohat-Ophir G, Kaun KR, Azanchi R, Heberlein U. Sexual deprivation increases ethanol intake in Drosophila. Science. 2012 Mar 16;335(6074):1351-5. PubMed PMID:22422983.
    • Commentary: Zars T. Physiology. She said no, pass me a beer. Science. 2012 Mar 16;335(6074):1309-10. PubMed PMID: 22422968.

Philosophy of Science

  1. Bodemer N, Ruggeri A. Finding a good research question, in theory. Science. 2012 Mar 23;335(6075):1439. PubMed PMID: 22442459.

Ethics, Social and Legel Issues

  1. Must try harder. Nature. 2012 Mar 28;483(7391):509. doi: 10.1038/483509a.PubMed PMID: 22460859.
  2. Begley CG, Ellis LM. Drug development: Raise standards for preclinical cancer research. Nature. 2012 Mar 28;483(7391):531-3. doi: 10.1038/483531a. PubMed PMID: 22460880.
  3. Incidental benefits. Nature. 2012 Mar 21;483(7390):373. doi: 10.1038/483373a. PubMed PMID: 22437569.
  4. Hayden EC. DNA donor rights affirmed. Nature. 2012 Mar 21;483(7390):387. doi: 10.1038/483387a. PubMed PMID: 22437587.

Systems Biology

  1. Weinstein JN. Drug discovery: Cell lines battle cancer. Nature. 2012 Mar 28;483(7391):544-5. doi: 10.1038/483544a. PubMed PMID: 22460893.
  2. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P Jr, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012 Mar 28;483(7391):603-7. doi: 10.1038/nature11003. PubMed PMID: 22460905.
  3. Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D, Chen L, Milano RJ, Bignell GR, Tam AT, Davies H, Stevenson JA, Barthorpe S, Lutz SR, Kogera F, Lawrence K, McLaren-Douglas A, Mitropoulos X, Mironenko T, Thi H, Richardson L, Zhou W, Jewitt F, Zhang T, O’Brien P, Boisvert JL, Price S, Hur W, Yang W, Deng X, Butler A, Choi HG, Chang JW, Baselga J, Stamenkovic I, Engelman JA, Sharma SV, Delattre O, Saez-Rodriguez J, Gray NS, Settleman J, Futreal PA, Haber DA, Stratton MR, Ramaswamy S, McDermott U, Benes CH. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature. 2012 Mar 28;483(7391):570-5. doi: 10.1038/nature11005. PubMed PMID: 22460902.
  4. Pujadas E, Feinberg AP. Regulated noise in the epigenetic landscape of development and disease. Cell. 2012 Mar 16;148(6):1123-31. PubMed PMID: 22424224.

Eye disease

  1. Zhang J, Benavente CA, McEvoy J, Flores-Otero J, Ding L, Chen X, Ulyanov A, Wu G, Wilson M, Wang J, Brennan R, Rusch M, Manning AL, Ma J, Easton J, Shurtleff S, Mullighan C, Pounds S, Mukatira S, Gupta P, Neale G, Zhao D, Lu C, Fulton RS, Fulton LL, Hong X, Dooling DJ, Ochoa K, Naeve C, Dyson NJ, Mardis ER, Bahrami A, Ellison D, Wilson RK, Downing JR, Dyer MA. A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature. 2012 Jan 11;481(7381):329-34. doi: 10.1038/nature10733. PubMed PMID: 22237022; PubMed Central PMCID: PMC3289956.

Medicine

  1. Vaidyanathan G. Redefining clinical trials: the age of personalized medicine.  Cell. 2012 Mar 16;148(6):1079-80. PubMed PMID: 22424218.

Stem cells

  1. Cherry AB, Daley GQ. Reprogramming Cellular Identity for Regenerative Medicine. Cell. 2012 Mar 16;148(6):1110-1122. Epub 2012 Mar 15. PubMed PMID: 22424223.

Career

  1. Perkel JM Ph D. Run your lab on dollars a day! Biotechniques. 2012 Mar;52(3):141-143. PubMed PMID: 22401545.
  2. Blow N Ph D. Reflections on the modern lab. Biotechniques. 2012 Mar;52(3):145-147. PubMed PMID: 22401546.
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University of Florida eliminates Computer Science Department

Monday, April 23, 2012

There are  budget cuts and layoff everywhere. We have already heard before that Florida State dissolved academic departments to fight the financial crisis. And now the University of Florida is going to eliminate Computer Science Department, a really disturbing move. From Steven Salzberg’s blog:

The University of Florida announced this past week that it was dropping its computer science department, which will allow it to save about $1.7 million.  The school is eliminating all funding for teaching assistants in computer science, cutting the graduate and research programs entirely, and moving the tattered remnants into other departments.

 

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A collection of videos for discussion of ethical and social issues in developmental biology – Stem cells: II. Desperate patients and people who want to take advantage of their situation

Monday, March 26, 2012

In my last post, I provided several links to general introductions of stem cells. In this post, I will share several documentaries that show how bad people are taking advantage of desperate patients who have heard stem cells therapy may give them a last hope.

II. Desperate patients and people who take advantage of their situation

1. BBC Panorama – Stem Cells & Miracles (2009)

(2015-02-22) Youtube.com has taken this BBC video off from their site.

2. CBS 60 Minutes – Stem Cell Snake Oil (2010)

 

This is part 1 of the show; here are the links to part 2, part 3 and part 4.

3. CBS 60 Minutes – Stem cell fraud (2012)

Youtube link

CBS link

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2012-03-24 new articles we read this week

Saturday, March 24, 2012

Development

  1. Vogel G. Reproductive biology. Potential egg stem cells reignite debate. Science. 2012 Mar 2;335(6072):1029-30. PubMed PMID: 22383817.

Scientific career

  1. Mervis J. Scientific careers. Is motherhood the biggest reason for academia’s gender imbalance? Science. 2012 Mar 2;335(6072):1030-1. PubMed PMID: 22383818.

Genomics

  1. Xu X, Hou Y, Yin X, Bao L, Tang A, Song L, Li F, Tsang S, Wu K, Wu H, He W, Zeng L, Xing M, Wu R, Jiang H, Liu X, Cao D, Guo G, Hu X, Gui Y, Li Z, Xie W, Sun X, Shi M, Cai Z, Wang B, Zhong M, Li J, Lu Z, Gu N, Zhang X, Goodman L, Bolund L, Wang J, Yang H, Kristiansen K, Dean M, Li Y, Wang J. Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell. 2012 Mar 2;148(5):886-95. PubMed PMID: 22385958.
  2. Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, Li F, Wu K, Liang J, Shao D, Wu H, Ye X, Ye C, Wu R, Jian M, Chen Y, Xie W, Zhang R, Chen L, Liu X, Yao X, Zheng H, Yu C, Li Q, Gong Z, Mao M, Yang X, Yang L, Li J, Wang W, Lu Z, Gu N, Laurie G, Bolund L, Kristiansen K, Wang J, Yang H, Li Y, Zhang X, Wang J. Single-Cell ExomeSequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm. Cell. 2012 Mar 2;148(5):873-85. PubMed PMID: 22385957.

Systems biology

  1. Angermann BR, Klauschen F, Garcia AD, Prustel T, Zhang F, Germain RN, Meier-Schellersheim M. Computational modeling of cellular signaling processes embedded into dynamic spatial contexts. Nat Methods. 2012 Jan 29;9(3):283-9. doi: 10.1038/nmeth.1861. PubMed PMID: 22286385.
    • Commentary: Sneddon MW, Emonet T. Modeling cellular signaling: taking space into the computation. Nat Methods. 2012 Feb 28;9(3):239-42. doi: 10.1038/nmeth.1900. PubMed PMID: 22373909.

Imaging

  1. Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR. OMERO: flexible, model-driven data management for experimental biology. Nat Methods. 2012 Feb 28;9(3):245-53. doi: 10.1038/nmeth.1896. PubMed PMID: 22373911.
  2. Ragan T, Kadiri LR, Venkataraju KU, Bahlmann K, Sutin J, Taranda J, Arganda-Carreras I, Kim Y, Seung HS, Osten P. Serial two-photon tomography for automated ex vivo mouse brain imaging. Nat Methods. 2012 Jan 15;9(3):255-8. doi:  10.1038/nmeth.1854. PubMed PMID: 22245809; PubMed Central PMCID: PMC3297424

Genetics

  1. Wang X, Chen X, Yang Y. Spatiotemporal control of gene expression by a light-switchable transgene system. Nat Methods. 2012 Feb 12;9(3):266-9. doi: 10.1038/nmeth.1892. PubMed PMID: 22327833.

 

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Building cheap machines with LEGO for research

Wednesday, March 21, 2012

I am so envious of these people who can build a useful machine by LEGO which can save money. The building part itself must be a lot of fun!


From boingboing.net:  LEGO robots in the laboratory

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2012-03-11 new articles we read this week

Monday, March 12, 2012

Evolution

  1. Ramani AK, Chuluunbaatar T, Verster AJ, Na H, Vu V, Pelte N, Wannissorn N, Jiao A, Fraser AG. The majority of animal genes are required for wild-type fitness. Cell. 2012 Feb 17;148(4):792-802. PubMed PMID: 22341449.
  2. Loehlin DW, Werren JH. Evolution of shape by multiple regulatory changes to a growth gene. Science. 2012 Feb 24;335(6071):943-7. PubMed PMID: 22363002.

Psychology and human behaviour

  1. Pazda AD, Elliot AJ, Greitemeyer T. Sexy red: Perceived sexual receptivity mediates the red-attraction relation in men viewing woman. J Exp Soc Psychol. 2012; 48: 787-790
  2. Cohen S, Schulz MS, Weiss E, Waldinger RJ. Eye of the Beholder: The Individual and Dyadic Contributions of Empathic Accuracy and Perceived Empathic Effort to Relationship Satisfaction. J Fam Psychol. 2012 Feb 27. [Epub ahead of print] PubMed PMID: 22369462.

Men like it when women let them know when they’re happy. Women like it when men share their anger and frustration.

Evidently we women see a man’s willingness to share negative feelings as a sign that he’s invested in the relationship. Cohen says: “That’s telling her something about his availability to engage in the conflict.”

Men feel exactly the opposite about those moments of conflict: They see it as a threat to the relationship. Instead, Cohen says, “They do derive satisfaction when their girlfriends or wives are happy.”

Stem cells/ development

  1. White YA, Woods DC, Takai Y, Ishihara O, Seki H, Tilly JL. Oocyte formation by mitotically active germ cells purified from ovaries of reproductive-age women. Nat Med. 2012 Feb 26;18(3):413-21. doi: 10.1038/nm.2669. PubMed PMID: 22366948; PubMed Central PMCID: PMC3296965.
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2012-02-16 New articles we read this week

Sunday, February 26, 2012

Stem cells/ regeneration

  1. Makkar RR, Smith RR, Cheng K, Malliaras K, Thomson LE, Berman D, Czer LS, Marbán L, Mendizabal A, Johnston PV, Russell SD, Schuleri KH, Lardo AC, Gerstenblith G, Marbán E. Intracoronary cardiosphere-derived cells for heart regeneration after myocardial infarction (CADUCEUS): a prospective, randomised phase 1 trial. Lancet. 2012 Feb 13. [Epub ahead of print] PubMed PMID: 22336189.
    • News coverage by the BBC

Genetics/Genomics

  1. MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG; 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012 Feb 17;335(6070):823-8. PubMed PMID: 22344438.
    • Commentary: Quintana-Murci L. Genetics. Gene losses in the human genome. Science. 2012 Feb 17;335(6070):806-7. PubMed PMID: 22344433.

Development

  1. Inaba M, Yamanaka H, Kondo S. Pigment pattern formation by contact-dependent depolarization. Science. 2012 Feb 10;335(6069):677. PubMed PMID: 22323812.

Funding

  1. Mervis J. U.S. budget. Science spared brunt of ax in budget request. Science.  2012 Feb 17;335(6070):783-4. PubMed PMID: 22344417.

Academic career

  1. Kaminski D, Geisler C. Survival analysis of faculty retention in science and engineering by gender. Science. 2012 Feb 17;335(6070):864-6. PubMed PMID: 22344445.
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3-D printing for regenerative medicine

Thursday, February 23, 2012

There is an interesting news article “Printing Muscle” from Technology Review about using 3-D printers to print muscle cells so that they may assume a 3-D shape that resembles muscle fiber. The idea sounds interesting, because one can potentially print tissues or even organs that have complicated cellular composition in 3-D for regenerative medicine.

 

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A collection of videos for discussion of ethical and social issues in developmental biology – Stem cells: I. Introduction to the topic

Monday, February 13, 2012

Over the years, I have been leading a discussion about the ethical and social issues of stem cells research in my class and have used a few useful videos on various aspects. You may find them useful too.

I. Introduction to the topic

References

Here are two recent scientific references that give the current status of iPSCs research and compared that with hESCs, as well as the challenges ahead in research and ethical issues.

  1. Robinton DA, Daley GQ. The promise of induced pluripotent stem cells in research and therapy. Nature. 2012 Jan 18;481(7381):295-305. PubMed PMID: 22258608.
  2. Hug K, Hermerén G. Do we still need human embryonic stem cells for stem cell-based therapies? Epistemic and ethical aspects. Stem Cell Rev. 2011 Nov;7(4):761-74. PubMed PMID: 21461713.

This reference is a general scientific review on various ways that one can reprogramming cells that may potentially be used for therapeutic purposes.

  1.  Gurdon JB, Melton DA. Nuclear reprogramming in cells. Science. 2008 Dec 19;322(5909):1811-5. Review. PubMed PMID: 19095934.
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