Taking the Least of You -- NY Times

Here's the letter I eventually wrote on this (incorporating suggestions):
I enjoyed the recent article describing the hidden value in biological specimens given to medical research. The article highlighted a conundrum, balancing the right of people to anything of value derived from their own tissue versus the importance of promoting research. One thing the article only alluded to was the additional complexities stemming from DNA sequencing. Sequencing the DNA of a specimen provides much information not only about the person from whom the specimen was taken but also about the parents and children of that individual. Thus, if people consent for their tissue specimens to be freely used for medical research, they are also implicitly consenting for genetic information to be revealed about their relatives. This is being given without the relatives having any direct role in the discussion. Moreover, what is possible in 2006 might be very different from what will be possible in 50 years when we might be able to glean a tremendous amount from a bit of genetic sequence -- e.g. precisely what diseases or behavior anomalies might befall someone.
--
The author appears to have her own wikipedia entry!

---

http://www.nytimes.com/2006/04/16/magazine/16tissue.html
http://www.nasw.org/users/skloot/TakingTheLeast.pdf
"Taking the Least of You"
By REBECCA SKLOOT, NY Times, April 16, 2006
http://www.rebeccaskloot.com/
http://en.wikipedia.org/wiki/Rebecca_Skloot
The Tissue-Industrial Complex
Anna O'Connell couldn't find Ted. She stood bent at the waist on a frigid afternoon last December, her head and all its fuzzy red hair crammed into an old stand-up freezer that looked like something you get milk from at the corner store: tall, white with a bit of rust and a pull handle. That freezer is the first thing you see when you walk into the Fox Chase Cancer Center laboratory in Philadelphia, where O'Connell has spent decades as a staff scientist. She pushed aside vial after vial. "I know we still have him somewhere," she yelled, her head still inside the freezer. "We've got serum from, like, 450,000 people."....

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[L2E]ooo

William Bialek

Very clean design

ooo[link]ooo

ooo[nice-web-design]ooo

Home Page of Steffen Möller

Like flipping picture

ooo[link]ooo

ooo[nice-web-design]ooo

Structural Bioinformatics EMBL Heidelberg

Like the rotating image

ooo[link]ooo

ooo[nice-web-design]ooo

The Scourge of Arial

ooo[clip]ooo

ooo[fun]ooo

Google Maps - 41st street and 5th avenue, ny, ny 10021

convenient meeting point near Grand Central

ooo[link]ooo

ooo[location]ooo

Predicting the in vivo signature of human gene regulatory sequences -- Noble et al. 21 (Supplement 1): i338 -- Bioinformatics

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[genomics]ooo

Whole-genome disassembly -- Green 99 (7): 4143 -- Proceedings of the National Academy of Sciences

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[genomics]ooo

TakingITGlobal - Global Gallery

ooo[link]ooo

ooo[fun]ooo

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

ooo[url]ooo

ooo[bioinfo]ooo

ooo[symposia]ooo

Word Spy - wallet biopsy

ooo[link]ooo

ooo[bioinfo]ooo

ooo[word]ooo

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.

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[networks]ooo

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

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[pseudogenes]ooo

http://www.sanger.ac.uk/Software/Pfam/iPfam

http://www.sanger.ac.uk/Software/Pfam/iPfam

ooo[url]ooo

ooo[bioinfo]ooo

ooo[networks]ooo

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

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[motions]ooo

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.

ooo[clip]ooo

ooo[general]ooo

ooo[business]ooo

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....

ooo[clip]ooo

ooo[general]ooo

ooo[computers]ooo

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

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[pseudogenes]ooo

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

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[tiling]ooo

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.....

ooo[clip]ooo

ooo[fun]ooo

ooo[food]ooo

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

ooo[clip]ooo

ooo[fun]ooo

ooo[L2E]ooo

Bra-ket notation - Wikipedia

ooo[link]ooo

ooo[bioinfo]ooo

ooo[teaching]ooo

David MacKay: Information Theory, Inference, and Learning Algorithms: Home

Fantastic book!

ooo[link]ooo

ooo[bioinfo]ooo

ooo[teaching]ooo

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

ooo[clip]ooo

ooo[general]ooo

ooo[mapping]ooo

http://ongenetics.blogspot.com/2006/03/from-hapmap-to-selection-map.html [url]

Interesting reference to selection maps and PLOS bio. article

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[variation]ooo

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

ooo[clip]ooo

ooo[fun]ooo

http://proteinatlas.org/ [url]

Antibody database indicating proteins present in different cancers and tissues -- and also in different sexes!

---

Science. 2005 Aug 26;309(5739):1310. 
Proteomics. New database to track protein locations.
Service RF.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16123272&query_hl=1&itool=pubmed_docsum
http://proteinatlas.org

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[arrays]ooo

http://www.gnetbrowse.org [url]

perhaps useful to investigate again... contains many nets

ooo[link]ooo

ooo[bioinfo]ooo

ooo[nets]ooo

http://rnai.org [url]

perhaps useful to investigate for connecting phenotypes to genotypes

ooo[link]ooo

ooo[bioinfo]ooo

ooo[phenotypes]ooo

emPAI -- MCP [clip]

Useful to refer to in relation to quantifying protein abundance. (Note earlier paper too.)

---

Mol Cell Proteomics. 2005 Sep;4(9):1265-72.
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein.
Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15958392&query_hl=2&itool=pubmed_docsum
To estimate absolute protein contents in complex mixtures, we previously defined a protein abundance index (PAI) as the number of observed peptides divided by the number of observable peptides per protein (Rappsilber, J., Ryder, U., Lamond, A. I., and Mann, M. (2002) Large-scale proteomic analysis of the human spliceosome. Genome. Res. 12, 1231-1245). Here we report that PAI values obtained at different concentrations of serum albumin show a linear relationship with the logarithm of protein concentration in LC-MS/MS experiments. This was also the case for 46 proteins in a mouse whole cell lysate. For absolute quantitation, PAI was converted to exponentially modified PAI (emPAI), equal to 10PAI minus one, which is proportional to protein content in a protein mixture.....

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[proteomics]ooo

McPherson Clathrin Vesicle Protein Abundance Set [clip]

Papers and person below associated with ~200 protein abundance values with can
be compared with brain mRNA expression levels.
______________
http://www.mni.mcgill.ca/cbet/mcpherson/

Girard, M., Allaire, P.D., McPherson, P.S., and Blondeau, F. (2005).
Non-stoichiometric relationship between clathrin heavy and light chains revealed
by subcellular proteomics of clathrin-coated vesicles from brain and liver. Mol.
Cell Prot. 4:1145-1154.

Blondeau, F., Ritter, B., Allaire, P.D., Wasiak, S., Girard, M., Hussain, N.K.,
Angers, A., Legendre-Guillemin, V., Roy, L., Boismenu, D., Kearney, R.E., Bell,
A.W., Bergeron, J.J.M., and McPherson, P.S. (2004) Tandem mass spectrometry
analysis of brain clathrin-coated vesicles reveals their critical involvement in
synaptic vesicle recycling. Proc. Natl. Acad. Sci., USA 101:3833-3838.

[bioinfo]ooo[clip]ooo[proteomics]

http://channingdaughters.com/ [url]

Thought this might be a nice drink to keep an eye out for....

---

The Tasting Room is open 7 days a week for visitors from 11am-5pm. We taste 6 different wines each day, and provide very informative tastings.
Starting July 4th, we will be open every day from 11-6pm. However, please note that on Sunday, July 6th we will close for tastings at 4:30 in preparation for our fabulous Salsa Party, which begins at 5pm.
CHANNING DAUGHTERS WINERY
1927 Scuttlehole Rd    PO BOX 2202    Bridgehampton, NY 11932
phone: 631-537-7224    fax: 631-537-7243
http://channingdaughters.com

ooo[link]ooo

ooo[general]ooo

ooo[fun]ooo

HealthText Audio, Audio Books for Your Health

ooo[link]ooo

ooo[general]ooo

ooo[useful]ooo

potassium iodide + Prussian Blue [url]

Thoughts for those in stress... perhaps useful for the paranoid (potassium iodide + Prussian Blue)! Wonder if a doctor would perscribe these....

---

http://www.nitro-pak.com/index.php?cPath=37
http://www.nukepills.com/pages/656402

ooo[link]ooo

ooo[general]ooo

ooo[useful]ooo

http://bio.chip.org/mapper [url]

Interesting DB of TFBS, with new extensions to ENCODE regions and SNPs. Based on building HMMs from TRANSFAC and then running these against genomes.

---

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15608292&dopt=Abstract
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D91-7.   
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.
Marinescu VD, Kohane IS, Riva A.
http://bio.chip.org/mapper

ooo[clip]ooo

ooo[bioinfo]ooo

ooo[arrays]ooo

Two recent microarray platform evaluation manuscripts from Kohane

Thought these might be good to refer to in relation to the platform
comparison work we are doing. The 2nd one is a glass slide vs. Affy study.
_____________________________________________________________

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12823866&query_hl=8&itool=pubmed_DocSum
BMC Bioinformatics. 2003 Jun 25;4:27. Epub 2003 Jun 25
Reproducibility of gene expression across generations of Affymetrix
microarrays.
Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH,
Kohane IS.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11934739&query_hl=8&itool=pubmed_DocSum
Bioinformatics. 2002 Mar;18(3):405-12.
Analysis of matched mRNA measurements from two different microarray
technologies.
Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS.

ooo[clip]ooo ooo[bioinfo]ooo ooo[arrays]ooo

http://www.returnpath.net/ [url]

perhaps useful to investigate for re-routing hotmail to gmail (and other similar combinations).....

ooo[link]ooo

ooo[general]ooo

ooo[computer]ooo

jccmanhattan.org [url]

Might have interesting activities

---

http://www.jccmanhattan.org

ooo[link]ooo

ooo[fun]ooo

Infamous email writers aren't always killing their careers after all -- WSJ [clip]

A true email exchange and was the subject a WSJ article.
(http://online.wsj.com/public/article/SB114047541194578433-fhRaaapScYVZcvUjXB7wdHSN6Xc_20070221.html?mod=rss_free)

Read from the bottom up.
_________________________________________________________________________________________
ooo[clip]ooo[general]ooo[computer]ooo

-----Original Message-----
From: David Breen
Sent: Friday, February 10, 2006 9:54 AM
To: Stacey G. Bloom
Subject: FW: Thank you

Read from the bottom to the top.there was an intervening exchange of
voice mails as well.as <http://well.as/> you can imagine, they were
as unprofessional as
her e-mails.

-----Original Message-----
From: William A. Korman
Sent: Friday, February 10, 2006 9:55 AM
To: 'David Breen'
Subject: RE: Thank you

You can e-mail this to whomever you want.

-----Original Message-----
From: David Breen
Sent: Friday, February 10, 2006 9:47 AM
To: 'William A. Korman'
Subject: RE: Thank you

OH MY GOD!

Where to begin?

First of all, how unprofessional, and secondly, it is "reap what you
'sow,'" now "sew". If she is going to use a cliche, couldn't she at
least spell it right? And WTF is with her "blab la bla"? Does she not
read your e-mail about it being a small community?! So, finally, can I
forward this along to some folks? I am sure they would love to see how
the up-and-coming lawyers are comporting themselves! (Clearly she did
not go to BU!!!) J

-----Original Message-----
From: William A. Korman
Sent: Friday, February 10, 2006 7:59 AM
To: 'David Breen'
Subject: FW: Thank you

Did I already forward this to you?

-----Original Message-----
From: Dianna Abdala
Sent: Monday, February 06, 2006 4:29 PM
To: William A. Korman
Subject: Re: Thank you

bla bla bla

----- Original Message -----

From: William A. Korman
To: 'Dianna Abdala'
Sent: Monday, February 06, 2006 4:18 PM
Subject: RE: Thank you

Thank you for the refresher course on contracts. This is not a bar exam
question. You need to realize that this is a very small legal
community,
especially the criminal defense bar. Do you really want to start
pissing off more experienced lawyers at this early stage of your
career?

-----Original Message-----
From: Dianna Abdala
Sent: Monday, February 06, 2006 4:01 PM
To: William A. Korman
Subject: Re: Thank you

A real lawyer would have put the contract into writing and not exercised
any such reliance until he did so.

Again, thank you.

----- Original Message -----
From: William A. Korman
To: 'Dianna Abdala'
Sent: Monday, February 06, 2006 12:15 PM
Subject: RE: Thank you

Dianna -

Given that you had two interviews, were offered and accepted the job
(indeed, you had a definite start date), I am surprised that you chose
an e-mail and a 9:30 PM voicemail message to convey this information to
me. It smacks of immaturity and is quite unprofessional. Indeed, I
did
rely upon your acceptance by ordering stationery and business cards with
your name, reformatting a computer and setting up both internal and
external e-mails for you here at the office. While I do not quarrel
with your reasoning, I am extremely disappointed in the way this played
out. I sincerely wish you the best of luck in your future endeavors.

- Will Korman

-----Original Message-----
From: Dianna Abdala
Sent: Friday, February 03, 2006 9:23 PM
To: William A. Korman
Subject: Thank you

Dear Attorney Korman,

At this time, I am writing to inform you that I will not be accepting
your offer.

After careful consideration, I have come to the conclusion that the pay
you are offering would neither fulfill me nor support the lifestyle I am
living in light of the work I would be doing for you. I have decided
instead to work for myself, and reap 100% of the benefits that I sew.

Thank you for the interviews.

Dianna L. Abdala, Esq.

A Ray of Hope for Diabetics -- Times [clip]

Interesting article about a drug that slows digestion of food (making you feel fuller). It pointed out how doctors might be under pressure to prescribe off-label.

---

http://www.nytimes.com/2006/03/02/business/02drug.html
A Ray of Hope for Diabetics
Peter DaSilva for The New York Times
Byetta, a diabetes drug that was approved for marketing last April, has shown strong growth in the number of prescriptions written.
By ALEX BERENSON
Published: March 2, 2006
The users call the drug Lizzie, the Big Brother or sometimes Gilly. On blogs they rave over its uncanny ability to melt away pounds, although some are wary of its side effects, which can include nausea and strange welts. The users are not fad dieters or methamphetamine addicts, but people with diabetes. And the subject of their rhapsodies is not a gray-market diet pill sold on late-night television but Byetta, a federally approved diabetes medicine, available only by prescription, whose popularity and sales have soared since its introduction last June....

ooo[clip]ooo

ooo[general]ooo

ooo[drugs]ooo

Negative selection - Wikipedia, the free encyclopedia

In contrast: Positive Selection - Wikipedia, the free encyclopedia

ooo[link]ooo

ooo[bioinfo]ooo

Chemical Biophysics Mini-Symposia Series - Upcoming Symposia

ooo[link]ooo

ooo[bioinfo]ooo

ooo[conference]ooo

Yale Information Society Project Lunches

ooo[link]ooo

ooo[general]ooo

ooo[useful]ooo

Taking Snooping Further; Government Looks at Ways To Mine Databases -- Times [clip]

Thought this was an interesting article about the practical value of data mining. It seems that of the big applications of mining -- e.g. genomics, credit-card fraud, marketing, anti-terrorism -- mine is the only one that's open and not shrouded in secrecy...

---

Taking Snooping Further; Government Looks at Ways To Mine Databases
By JOHN MARKOFF; SCOTT SHANE CONTRIBUTED REPORTING FROM WASHINGTON FOR THIS ARTICLE. (NYT) 2023 words
Published: February 25, 2006
PALO ALTO, Calif., Feb. 23 - A small group of National Security Agency officials slipped into Silicon Valley on one of the agency's periodic technology shopping expeditions this month.On the wish list, according to several venture capitalists who met with the officials, were an array of technologies that underlie the fierce debate over the Bush administration's anti-terrorist eavesdropping program: computerized systems that reveal connections between seemingly innocuous and unrelated pieces of information.The tools they were looking for are new, but their application would fall under the well-established practice of data mining: using mathematical and statistical techniques to scan for hidden relationships in streams of digital data or large databases.Supercomputer companies looking for commercial markets have used the practice for decades. Now intelligence agencies, hardly newcomers to data mining, are using new technologies to take the practice to another level...
http://select.nytimes.com/search/restricted/article?res=F70C16F8345A0C768EDDAB0894DE404482

ooo[clip]ooo

ooo[general]ooo

ooo[mining]ooo

The Freshman -- nytimes [clip]

Perhaps I'll run into him at the dining hall at some point. Don't know what I'd say though!

---

The Freshman
By CHIP BROWN
Published: February 26, 2006
Sometimes walking up College Street, when the bells were ringing in Harkness Tower and the light on the gabled dorms and leafy quads made the whole campus seem part of some Platonic dream, he could almost forget that there were people back home who would be happy to kill him.His formal introduction to the terrain of the Western mind came in July at the start of the summer term; most of the class of '09 would not arrive until the fall term. He was glad for the chance to get his bearings. The direction of Mecca he knew from the compass on his watch. For local attractions he had a map of the campus; he got a cellphone, a Yale e-mail account. His student ID card admitted him to lots of campus dining halls...
http://www.nytimes.com/2006/02/26/magazine/26taliban.html

ooo[clip]ooo

ooo[fun]ooo

ooo[Yale]ooo

The O'Hern Group | The O'Hern Group

Clustering - K-means demo

Used in Data Mining (CS445)

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The New York City Parades - June - JimsDeli NYC Guide

Parades in NY

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FlatPrice Moving

Avi Mover

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Barriers to progress in systems biology -- Nature [clip]

Emphasizes the importance of standards!

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Nature 438, 1079 (22 December 2005) | doi:10.1038/4381079a
Barriers to progress in systems biology
Marvin Cassman 1,a
1. Marvin Cassman lives in San Francisco, California, USA.
a Co-authors are Adam Arkin of the Bioengineering Department, University of California, Berkeley; Fumiaki Katagiri of the Department of Plant Biology, University of Minnesota, St Paul; Douglas Lauffenburger of the Biological Engineering Division, Massachusetts Institute of Technology, Cambridge; Frank J. Doyle III of the Department of Chemical Engineering, University of California, Santa Barbara; and Cynthia L. Stokes who is at Entelos, Foster City, California.
For the past half-century, biologists have been uncovering details of countless molecular events. Linking these data to dynamic models requires new software and data standards, argue Marvin Cassman and his colleagues.
The field of systems biology is lurching forwards, propelled by a mixture of faith, hope and even charity. But if it is to become a true discipline, several problems with core infrastructure (data and software) need to be addressed. In our view, they are too critical to be left to ad hoc developments by individual laboratories......
http://www.nature.com/nature/journal/v438/n7071/full/4381079a.html

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Here I Am Taking My Own Picture -- Times.com [clip]

Looks like this digital camera phenomena is quite widespread

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Here I Am Taking My Own Picture
By ALEX WILLIAMS
Published: February 19, 2006
MORGAN ADAMS, a recent college graduate, decided that her picture on her home page at MySpace.com had lingered a little too long, a full month. To snap a new one she called on the only photographer she thought she could trust: herself.
In her bedroom in Lubbock, Tex., Ms. Adams, 21, tried out a variety of poses — coy, friendly, sultry, goofy — in the kind of performance young people have engaged in privately for generations before a mirror. But Ms. Adams's mirror was a Web cam, and her journey of self-expression, documented in five digital self-portraits, was soon visible to the 56 million registered users of MySpace.
http://www.nytimes.com/2006/02/19/fashion/sundaystyles/19SELF.html

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Machine Learning textbook slides

Chap. 4 from Machine Learning Book was lecture in class

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Useful lecture on Perceptron

For data mining course (CS445)

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YaleInfo 2.5.1 - New Portal with UPI number

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MinGW - Home

useful for compiling linux programs under XP

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Calories in a plain bagel [fact]

More food thoughts... found this stat, which thought was quite interesting:
290 calories with 20 from fat for a plain bagel (2g fat, 56g carbo). With 1 oz of cream cheese this goes to
390 and 120, respectively. Rather amazing how much there is in a bagel.

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A short course in human relations [fact]

Found this quite interesting and succinct

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A short course in human relations

the 6 most important words:
"I admit I made a mistake."

the 5 most important words:
"you did a good job."

the 4 most important words:
"what is your opinion?"

the 3 most important words:
"if you please."

the 2 most important words:
"thank you."

the 1 most important word:
"we".

the least important word:
"I".

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Map of Latitude: 41.3185 Longitude: -72.92300, by MapQuest and Google

Found out how to query mapquest and Google with lat. and longitude. Quite useful for walking the center of a map and precisely marking objects.

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http://www.mapquest.com/maps/map.adp?searchtype=address&amp;formtype=latlong&latlongtype=decimal&latitude=41.3125&longitude=-72.9375
http://maps.google.com/maps?f=q&amp;hl=en&q=41.3185,+-72.92300+(Approx.+Location+of+Science+Hill)&amp;ll=41.318504,-72.922997&spn=0.006269,0.012199

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http://www.moobella.com/moobellastory.php [url]

Food dreaming...

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Zitomer Store

Has lots of small pens

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Chemical Biophysics Mini-Symposia Series - Upcoming Symposia

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Reading For CPSC 445b/545b

Reading For CPSC 445b/545b

Covered by Thursday, Feb 2, 2006

Witten and Frank (or the equivalent):

Chap 1,2 3 (introduction, data precessing): pp 1-82
Chap 4, Sections 4.1 and 4.3 (classification): pp 83-88, 97-105
Chap 5, Sections 5.1, 5.2, 5.3, and 5.4 (evaluation): pp 143-152
Chap 6, Sections 6.1 and 6.2 (implementations): pp 189-213
Chap 9 (introduction to Weka): pp 345-361
Chap 10 (introduction to Weka Explorer): pp 369-414

URLs for some Two Crows Datamining Materials:

http://www.twocrows.com/about-dm.htm
http://www.twocrows.com/intro-dm.pdf
http://www.twocrows.com/applics.htm

URL for Thearling overview of datamining and glossary:
http://www.thearling.com/text/dmwhite/dmwhite.htm
http://www.thearling.com/glossary.htm

URL for Article on Gene Mining:
http://www.eweek.com/article2/0,1895,1911284,00.asp

An URL for Friedman’s Paper on “The Connection Between Statistics and Datamining”
http://www.cba.ua.edu/~mhardin/dm-stat.pdf

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Data mining lecture slides

Data mining lecture slides for courses based on reference text books:

Ian Witten and Eibe Frank:

http://books.elsevier.com/us//mk/us/subindex.asp?maintarget=companions/defaultindividual.asp&isbn=0120884070&country=United+States&srccode=&ref=&subcode=&head=&pdf=&basiccode=&txtSearch=&SearchField=&operator=&order=&community=mk

Margaret Dunham:

http://engr.smu.edu/~mhd/

Pang-Ning Tan, Michael Steinbach, and Vipin Kumar:

http://www-users.cs.umn.edu/%7Ekumar/dmbook/index.php#item4

Jiawei Han and Micheline Kamber:

http://www.cs.uiuc.edu/class/fa05/cs412/schedule.htm link + bioinfo + teaching

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Disprot - Database of Protein Disorder

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A Comparison of Search Technology Part 1 - Beginner SEO

Overview of the technology behind the "big four" search engines (Google, Yahoo, MSN, Ask Jeeves) (From AS)

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yahoo! vs. google: Bioinformatics

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MIT Sloan Lecture on Logistic Regression

Used in Data Mining Course -- Data Mining Course

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CSE5230: Data Mining Lectures

Used in Data Mining Course

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Karl Pearson - Wikipedia, the free encyclopedia

Correlation coefficient + eugenics

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Some bioinformatics people potentially interested in phenotypes [url]

http://www.nyu.edu/fas/dept/biology/faculty/gunsalus/
http://mips.gsf.de/cgi-bin/webapp/ibi/person/getPerson.pl?Person=meweshans-werner
http://binfo.bio.wzw.tum.de/groups/frishman/people/frishman
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Some bioinformatics people [url]

Some bioinformatics people

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Mike Daly - http://www.broad.mit.edu/personal/mjdaly
Michael Cherry - http://genetics.stanford.edu/~cherry
Rainer Fuchs - http://bioitworldexpo.com/live/26/events/26BOS05A/conference/bio//CMONYA00B50F
Isaac Kohane - http://www.childrenshospital.org/cfapps/research/data_admin/Site113/mainpageS113P0.html

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Boys from Brazil [clip]

Just saw this. Amazing how it anticipates the current cloning situation.

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Genomic fossils as a snapshot of the human transcriptome -- PNAS [clip]

Heard of this earlier... based on screening pseudogene.org !

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Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1364-9. Epub 2006 Jan 23.  
Genomic fossils as a snapshot of the human transcriptome.
Shemesh R, Novik A, Edelheit S, Sorek R.
Processed pseudogenes (PPGs) are cDNA sequences that were generated
through reverse transcription of mature, spliced mRNAs and have
subsequently been reinserted at a new genomic location. These cDNA
sequences are usually no longer transcribed and are considered "dead on
arrival." Here we show that PPGs can be used to generate a map of the
transcriptome. By analyzing thousands of human PPGs, we were able to
discover hundreds of transcript variants so far unidentified. An
experimental verification of a subset of these variants by RT-PCR
indicates that most of them are still active in the human transcriptome.
Furthermore, we demonstrate that PPGs can enable the identification of
ancient splice variants that were expressed ancestrally but are now
extinct. Our results show that the genome itself carries a "virtual cDNA
library" that can readily be used to analyze both present and ancestral
transcripts. Our approach can be applied to sequenced metazoan genomes
to computationally annotate splicing variation even when expressed
sequences are unavailable.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16432206&query_hl=1&itool=pubmed_docsum

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Invitrogen - ProtoArray™ Home

Brad Love
PPT on this

data bleach

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Refining Protein Subcellular Localization -- PLoS Comput Biol [clip]

Update of Drawid & Gerstein (2000) adding in interactions as a feature and predicting subcellular localization in a finer-grain fashion.  Perhaps could have done a better comparison with past work.

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Citation: Scott MS, Calafell SJ, Thomas DY, Hallett MT (2005) Refining Protein Subcellular Localization. PLoS Comput Biol 1(6): e66
http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0010066
The study of protein subcellular localization is important to elucidate protein function. Even in well-studied organisms such as yeast, experimental methods have not been able to provide a full coverage of localization. The development of bioinformatic predictors of localization can bridge this gap. We have created a Bayesian network predictor called PSLT2 that considers diverse protein characteristics, including the combinatorial presence of InterPro motifs and protein interaction data. We compared the localization predictions of PSLT2 to high-throughput experimental localization datasets. Disagreements between these methods generally involve proteins that transit through or reside in the secretory pathway. We used our multi-compartmental predictions to refine the localization annotations of yeast proteins primarily by distinguishing between soluble lumenal proteins and soluble proteins peripherally associated with organelles. To our knowledge, this is the first tool to provide this functionality. We used these sub-compartmental predictions to characterize cellular processes on an organellar scale. The integration of diverse protein characteristics and protein interaction data in an appropriate setting can lead to high-quality detailed localization annotations for whole proteomes. This type of resource is instrumental in developing models of whole organelles that provide insight into the extent of interaction and communication between organelles and help define organellar functionality..

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http://arep.med.harvard.edu/PGP [url]

URL to George Church's "Personal Genome Project." Looks of DB, identification and privacy issues associated with this!

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Four recent reviews on protein networks [clip]

Four recent reviews on protein networks (based on some research help from PMK).

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1 - Nat Rev Genet. 2004 Feb;5(2):101-13. Network biology: understanding the cell's functional organization. Barabasi AL, Oltvai ZN.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14735121&query_hl=8&itool=pubmed_docsum

2 - A SIAM review, very in depth covering a variety of topics in networks
(more than just biological networks), community structure is covered quite well. (LONG)
http://homes.gersteinlab.org/people/pmkim/outbox/2004_Newman_review.pdf

3 - Curr Opin Struct Biol. 2004 Jun;14(3):292-9.    Protein interaction networks from yeast to human. Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15193308&query_hl=10&itool=pubmed_docsum
A recent review about different methods of protein interaction detection
and analysis.

4 - The Yale perspective on networks.
http://papers.gersteinlab.org/papers/netrev/

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Google's Report Card - Forbes.com

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SBGrid: Structural Biology Grid

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HHMI: Lab Management

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Wicked Whoopies -- Whoopie Pies

Isabella + Max

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From Shakespeare to Star Trek and beyond: a Medline search for literary and,other allusions in biomedical titles -- BMJ [clip]

Thought this was a new perspective on the biomedical literature and a way of turning some light research and text searching into something interesting.

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http://bmj.bmjjournals.com/cgi/content/full/331/7531/1540
http://meta.wikimedia.org/wiki/Wikiauthors
BMJ. 2005 Dec 24;331(7531):1540-2.     
>From Shakespeare to Star Trek and beyond: a Medline search for literary and other allusions in biomedical titles.
Goodman NW.
OBJECTIVES: To document biomedical paper titles containing literary and
other allusions. DESIGN: Retrospective survey. SETTING: Medline (1951 to
mid-2005) through Dialog Datastar. MAIN OUTCOME MEASURE: Allusions to
Shakespeare, Hans Christian Andersen, proverbs, the Bible, Lewis Carroll, and
movie titles, corrected and scaled for five year periods 1950-4 to 2000-4.
RESULTS: More than 1400 Shakespearean allusions exist, a third of them to
"What's in a name" and another third to Hamlet-mostly to "To be or not to be."
The trend of increasing use of allusive titles, identified from Shakespeare and
Andersen, is paralleled by allusions to Carroll and proverbs; the trend of
biblical allusions is also upward but is more erratic. Trends for newer
allusions are also upwards, including the previously surveyed "paradigm shift."
Allusive titles are likely to be to editorial or comment rather than to original
research. CONCLUSIONS: The similar trends are presumably a mark of a particular
learnt author behaviour. Newer allusions may be becoming more popular than older
ones. Allusive titles can be unhelpful to reviewers and researchers, and many
are now cliches. Whether they attract readers or citations is unknown, but
better ways of gaining attention exist.

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http://function.princeton.edu/ChARM/ [url]

Another aCGH approach.
http://function.cs.princeton.edu/charm-press-release.htm

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http://www.yeastract.com [url]

Is this a bigger yeast regulatory network than what we've used previously?

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David MacKay: Information Theory, Inference, and Learning Algorithms: Home

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McSweeney's Internet Tendency: The iPod Zepto: Inconceivably Small.

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Useful Bioinformatics Related Courses at Yale

Probability and Statistics for Scientists (STAT 238a/STAT 538a)
http://www.stat.yale.edu/courses.html#238a/538a

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http://www.biology.yale.edu/courses
MCDB 200a. Genetics. Stephen Dellaporta and staff. TTh 11:30-12:45
An introduction to classical, molecular and population genetics, of both prokaryotes and eukaryotes and their central importance in biological sciences. Emphasis on analytical approaches and techniques of genetics used to investigate mechanisms of heredity and variation. Topics include transmission genetics, cytogenetics, DNA structure and function, recombination, gene mutation, selection, and recombinant DNA technology.

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Gene Mining Strikes Gold - eweek [clip]

Thought this was a very neat way of inter-relating genex data and context.

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http://www.eweek.com/article2/0,1895,1911280,00.asp
http://genotext.stanford.edu

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Plackett-Burman designs [clip]

Might be useful for laying out cross-hyb. experiments.

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http://www.itl.nist.gov/div898/handbook/pri/section3/pri335.htm

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http://www-ai.cs.uni-dortmund.de/SOFTWARE/YALE/index.html [url]

Perhaps this might be more appropriate for New Haven than Weka.

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YALE is an environment for machine learning experiments and data mining. Experiments can be made up of a large number of arbitrarily nestable operators and their setup is described by XML files which can easily be created with a graphical user interface. Applications of YALE cover both research and real-world data mining tasks.

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Google Gene Project Comes into Question

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