Predicting the in vivo signature of human gene regulatory sequences -- Noble et al. 21 (Supplement 1): i338 -- Bioinformatics
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26 April 2006
Whole-genome disassembly -- Green 99 (7): 4143 -- Proceedings of the National Academy of Sciences
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21 April 2006
18 April 2006
http://dimacs.rutgers.edu/Workshops/ProteinFunction/program.html
Might be interesting to go to....
DIMACS Workshop on Sequence, Structure and Systems Approaches to Predict Protein Function
May 3 - 5, 2006
http://dimacs.rutgers.edu/Workshops/ProteinFunction/program.html
DIMACS Center, CoRE Building, Rutgers University
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17 April 2006
10 April 2006
The scaling laws of human travel -- Nature -- wheresgeorge.com
Interesting in relation to the diffusion of new ideas. I tried two bills, listed below.
Nature 439, 462-465 (26 January 2006) | doi:10.1038/nature04292;
The scaling laws of human travel
D. Brockmann1,2, L. Hufnagel3 and T. Geisel1,2,4
http://www.nature.com/nature/journal/v439/n7075/full/nature04292.html
http://www.wheresgeorge.com/
http://www.wheresgeorge.com/report.php?key=f792b12d7658a7c2a58d52248125692921a9a24b4d4ced2c
http://www.wheresgeorge.com/report.php?key=deea10fdfb0a897405541dd69f73b948525e395738c564a5
The website wheresgeorge.com invites its users to enter the serial numbers of their US dollar bills and track them across America and beyond. Why? "For fun and because it had not been done yet", they say. But the dataset accumulated since December 1998 has provided the ideal raw material to test the mathematical laws underlying human travel, and that has important implications for the epidemiology of infectious diseases.
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08 April 2006
When fins became limbs -- Nature
Wonder if it's possible to find a "transitional" form molecule.
6 April 2006
When fins became limbs
The transition between fishes and limbed vertebrates, or tetrapods, occurred over 370 million years ago and required changes to virtually the entire body. Sensational fossil finds, and reinterpretations of old ones, have radically altered thinking on this topic in the past 20 years...
http://www.nature.com/nature/journal/v440/n7085/edsumm/e060406-01.html
Similar also to the famous Archaeoptryx:
http://en.wikipedia.org/wiki/Archaeoptryx
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http://www.sanger.ac.uk/Software/Pfam/iPfam
http://www.sanger.ac.uk/Software/Pfam/iPfam
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Structural basis for the spectral difference in luciferase bioluminescence -- Nature
Check out the movies of the transition (in supplement). Might be interesting for morph server.
Nature 440, 372-376 (16 March 2006)
Structural basis for the spectral difference in luciferase bioluminescence
Toru Nakatsu, Susumu Ichiyama, Jun Hiratake, Adrian Saldanha, Nobuyuki Kobashi, Kanzo Sakata and Hiroaki Kato
http://www.nature.com/nature/journal/v440/n7082/full/nature04542.html
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Biologist aims to ease the pain for entrepreneurs -- Nature
Thought this interesting in relation to Y50K thing.
http://www.nature.com/nature/journal/v440/n7085/full/440738a.html
Nature 440, 738-739 (6 April 2006)
Biologist aims to ease the pain for entrepreneurs
Biotech start-ups face a struggle to survive. Virginia Gewin reports on an initiative that brings cash and experience together to improve their chances.
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Internet Calls Untethered From Your PC -- NY Times
Looks useful for office conference phone. Let's get it and SkypeOut!
http://www.nytimes.com/2006/04/06/technology/06pogue.html
David Pogue
Internet Calls Untethered From Your PC
Published: April 6, 2006
WHY does Skype get so much hype? Sure, this software lets you make free "phone calls," computer to computer, anywhere in the world. But it wasn't the first such program, it's not the most feature-laden, and it's still a mystery to most people over 25.....Enter the VoSky Call Center ($60 at actiontec.com), nicknamed the Liberator. (All right, I gave it that nickname, but still.) It's a tiny black box, about the size of a sandwich, that connects to a Windows PC (with a U.S.B. cable), to your phone line and to your telephone. ...If you've signed up for SkypeOut, that 2.1-cents-a-minute plan that lets you call phone numbers rather than computers, you make calls in exactly the same way. Pick up your phone and touch ##2 (or whatever the speed-dial number is), or even ## plus a standard phone number in international format....
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07 April 2006
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes -- PLoS Comput Biol
Might be relevant to conservation patterns of pseudogenes
Citation: Yandell M, Mungall CJ, Smith C, Prochnik S, Kaminker J, et al. (2006) Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes. PLoS Comput Biol 2(3): e15
http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0020015
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A Third Approach to Gene Prediction Suggests Thousands of Additional Human Transcribed Regions -- PLoS Comput Biol
Might be relevant in relation to novel TARs
Citation: Glusman G, Qin S, El-Gewely MR, Siegel AF, Roach JC, et al. (2006) A Third Approach to Gene Prediction Suggests Thousands of Additional Human Transcribed Regions. PLoS Comput Biol 2(3): e18
http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0020018
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02 April 2006
Politics of Fat -=- Time
Makes me want to complain at about the vending machines prominent in my office lobby.
http://www.time.com/time/archive/preview/0,10987,1174679,00.html
The Politics of Fat
Experts say our expanding girth is killing us and costing the health-care system billions. But is this a problem government can solve? Or should? The debate grows as we do
By KAREN TUMULTY
Mar. 27, 2006
These are fat times in politics. Literally. Nearly 400 obesity-related bills were introduced in state legislatures across the country last year--more than double the number in 2003. A quarter of them were passed into law, up from only 12% two years before. In Washington the word obesity appears in 56 bills introduced during the current Congress; this, the Wall Street Journal points out, is fast catching up with the number containing the word gun. Surgeon General Richard Carmona says obesity is a greater threat than terrorism. Some public-health advocates have begun urging the government to put a warning label on soft drinks; others are calling for a "fat tax" on fast food.....
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The Multitasking Generation -- Time
Describes the gadget lifestyle. Here's a letter I wrote on this:
I read with great interest the recent article about the degree to which kids and young adults are multitasking using various electronic gadgets. I'm a University professor and often have the experience in giving seminars to people using Internet-enabled computers, cell phones, and other devices. I've definitely observed the distractive behavior described to in the article. In particular, I once had the fascinating experience demonstrating an online computer resource during a seminar. No one raised any questions during the seminar or said anything about the demo. Afterwards, when I returned to my computer, I went through a flurry of e-mails, most of them CC'd to me. It appears that during the seminar, one of the students was trying out the resource that I was discussing and e-mailed lots of his friends rather critical comments about it. They, of course, e-mailed him back and some of these responses were CC'd to me, so I could trace the dialogue. I later confronted the instigating student and asked him why he didn't simply just raise his hand and ask a question in the traditional style. He was rather dumbfounded and didn't seem to understand the point. I guess this is the new world we're in.
The Multitasking Generation
They're e-mailing, IMing and downloading while writing the history essay. What is all that digital juggling doing to kids' brains and their family life?
By CLAUDIA WALLIS
It's 9:30 p.m., and Stephen and Georgina Cox know exactly where their children are. Well, their bodies, at least. Piers, 14, is holed up in his bedroom--eyes fixed on his computer screen--where he has been logged onto a MySpace chat room and AOL Instant Messenger (IM) for the past three hours. His twin sister Bronte is planted in the living room, having commandeered her dad's iMac--as usual. She, too, is busily IMing, while chatting on her cell phone and chipping away at homework.....
http://www.time.com/time/archive/preview/0,10987,1174696,00.html
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Labels:
L2E,
UnpublishedLetter
30 March 2006
27 March 2006
David MacKay: Information Theory, Inference, and Learning Algorithms: Home
Fantastic book! ooo[link]ooo ooo[bioinfo]ooo ooo[teaching]ooo
22 March 2006
Virtual globes: The web-wide world (google earth) -- Nature [clip]
Describes the huge impact that Google Earth is having on the science. Here's a letter I wrote on this:
I was very impressed with Declan Butler's recent article on the impact that Google Earth is having on the scientific community. I have found this program extremely exciting to use and exhilarating as far as viewing common locations. I would like to point out that the success of this program underscores the importance of open standards for data and having easy interoperation between information resources.
To some degree, this same success has been achieved in the macromolecular structural world, where there are many programs giving people the ability to easily look at macromolecules in 3D and layer information on them.
Clearly, a good visualization program and open "browsing" system can catalyze a lot of interesting science. I would like to urge the development of comparable
browsing applications for other newly emerging areas in the biological sciences -- in particular, for visualizing the vast landscape of the genome and for navigating through complex biological networks.
Nature articles by Declan Butler
Published online: 15 February 2006; | doi:10.1038/news060213-7
How does Google Earth work?
Short cuts bring the globe to your screen without crashing your computer.
http://www.nature.com/news/2006/060213/full/060213-7.html
Published online: 15 February 2006; | doi:10.1038/439776a
Virtual globes: The web-wide world
Life happens in three dimensions, so why doesn't science? Declan Butler discovers that online tools, led by the Google Earth virtual globe, are changing the way we interact with spatial data.
http://www.nature.com/news/2006/060213/full/439776a.html
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20 March 2006
http://ongenetics.blogspot.com/2006/03/from-hapmap-to-selection-map.html [url]
Interesting reference to selection maps and PLOS bio. article
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How Do I Love Thee? -- The Atlantic Monthly [clip]
Interesting article talks about the pseudoscience of rigorously determining "Briggs-Myers" personality types and compatibility metrics between people. Personally I think this is more of an art than a science. In anycase, it appears that there will be a vast amount of "social" data mining on the internet in years to come!
The Atlantic Monthly | March 2006
How Do I Love Thee?
by Lori Gottlieb
http://www.theatlantic.com/doc/prem/200603/online-love
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