23 October 2005

Web of the Free - New York Times


Op-Ed Contributors
Web of the Free

Published: October 23, 2005

New Haven

THERE is a move afoot at the United Nations and in the European Union to get the United States to give up control of the Internet - a medium that America created and on which it now critically relies.

22 October 2005

A Lifetime in Recovery From the Cultural Revolution - New York Times

A profile of Xu Tian, Yale Genetics.
The Saturday Profile
A Lifetime in Recovery From the Cultural Revolution

Published: October 22, 2005

SOMETIMES a single life can tell more about a country's experience than a shelfful of history books. Many Chinese people of a certain age have such lives - rich in struggle, in suffering, in the consequences of man's folly, but often enough, too, in a measure of redemption....

17 October 2005

'Postwar': Picking Up the Pieces - New York Times

Starts with a great quote (below).
Published: October 16, 2005

An old Soviet-era joke, retold by Tony Judt on the next-to-last page of his enormous book 'Postwar,' is about a phone-in on 'Armenian Radio.' Is it possible, an eager caller asks, to foretell the future? 'Yes,' comes the weary answer. 'No problem. We know exactly what the future will be. Our problem is with the past: that keeps changing.'


Asthma Medication: Learn more about asthma & asthma treatment


nytimes.com: The Way We Drive Now : Motoring Toward A Post-Gasoline Age; The High-Performance Hybrids [clip-h]

These are the articles I alluded to about hybrids....
Style: The Way We Drive Now : Motoring Toward A Post-Gasoline Age; The
High-Performance Hybrids
September 25, 2005, Sunday
Late Edition - Final, Section 6, Page 77, Column 1, 3893 words

DISPLAYING FIRST 50 OF 3893 WORDS -''Hold on to your hat!'' Jim Burns shouted as
he slammed the accelerator to the floor. With a high-pitched whine, the electric
motor behind my seat burst into action, and ''the Enigma'' -- an experimental
red sports car in which I was riding shotgun -- bolted forward, pressing me...

Style: The Way We Drive Now: Motoring Toward A Post-Gasoline Age; Pimp My Prius
September 25, 2005, Sunday
Late Edition - Final, Section 6, Page 94, Column 1, 816 words

DISPLAYING FIRST 50 OF 816 WORDS -Driving a hybrid can satisfy more than your
conscience. With a little help from the flourishing car-customization business,
it's an easy matter to add a bit of style -- some blue racing stripes, beige
leather interior -- to an otherwise anonymous Prius. Or fully surrender to your
id, and...

WSJ: Wi-Fi Camera Offers Email, Quality Photos, But Still Needs Work [clip]


Might be the best solution to the office camera.

Wi-Fi Camera Offers Email, Quality Photos, But Still Needs Work
September 29, 2005; Page B1

If a wireless device like a cellphone can have a built-in camera, why can't
a camera have built-in wireless capability?

That's the question Kodak seeks to answer this week as it ships an unusual
digital camera that's able to wirelessly email the photos it takes, and
upload them to a Web site, all by itself -- without the need for a computer
or a cellphone.

Besttaxi in New Haven


Wired 13.10: The Elements Get Some Style

interesting graphic

The New York Times > Exxon Mobil is back on top, and for the first time is worth more than $400 billion.\


Exxon Mobil Back at No. 1 in Market Value, Even as It Shrinks Shares
Published: September 24, 2005

Exxon Mobil is back on top, and for the first time is worth more than $400 billion."

The Short of It - New York Times


Meet the Life Hackers - New York Times


Chasing Ground - New York Times


15 October 2005

To Build Arena in Brooklyn, Developer First Builds Bridges - New York Times [clip-h]

Ratner seems to be quite organized

To Build Arena in Brooklyn, Developer First Builds Bridges

Published: October 14, 2005

In the two years since he announced his ambitious Atlantic Yards development
in downtown Brooklyn, Bruce Ratner has lined up an impressive roster of
supporters, including Gov. George E. Pataki, Mayor Michael R. Bloomberg, the
Rev. Al Sharpton, and even the rap artist Jay-Z.

Lipitor or Generic? Billion-Dollar Battle Looms - New York Times [clip-gen]

Forms from Yale University | Postdoctoral Office

includes a sample appointment letter...

14 October 2005

Kolmogorov-Smirnov Test

Useful page with web form

10 October 2005

LJ: At the Forge - Rails and Databases [clip]

A bit of discussion of the way to interface programming languange objects with
standard relational tables.

09 October 2005

http://dynamite.biop.ox.ac.uk/dynamite [url]

04 October 2005

http://sleepycat.com/products/xml.shtml [url]

Might be of use:

Berkeley DB XML is the native XML database engine for your product. Berkeley DB
XML provides XQuery access into a database of document containers. XML documents
are stored and indexed in their native format using Berkeley DB as the
transactional database engine. Berkeley DB XML is not a client/server database
management system; it is a C++ library linked into your application.....

Nat Gen: Clustering of housekeeping genes provides a unified model [clip]

might be useful in relation to ongoing work....
Nat Genet. 2002 Jun;31(2):180-3. Epub 2002 May 6.
Clustering of housekeeping genes provides a unified model of gene order in the
human genome.
Lercher MJ, Urrutia AO, Hurst LD.


It is often supposed that, except for tandem duplicates, genes are randomly
distributed throughout the human genome. However, recent analyses suggest that
when all the genes expressed in a given tissue (notably placenta and skeletal
muscle) are examined, these genes do not map to random locations but instead
resolve to clusters. We have asked three questions: (i) is this clustering true
for most tissues, or are these the exceptions; (ii) is any clustering simply the
result of the expression of tandem duplicates and (iii) how, if at all, does
this relate to the observed clustering of genes with high expression rates? We
provide a unified model of gene clustering that explains the previous
observations. We examined Serial Analysis of Gene Expression (SAGE) data for 14
tissues and found significant clustering, in each tissue, that persists even
after the removal of tandem duplicates. We confirmed clustering by analysis of
independent expressed-sequence tag (EST) data. We then tested the possibility
that the human genome is organized into subregions, each specializing in genes
needed in a given tissue. By comparing genes expressed in different tissues, we
show that this is not the case: those genes that seem to be tissue-specific in
their expression do not, as a rule, cluster. We report that genes that are
expressed in most tissues (housekeeping genes) show strong clustering. In
addition, we show that the apparent clustering of genes with high expression
rates is a consequence of the clustering of housekeeping genes.

Rick Weissman's FunWithWine.com [fun]

3 Share Nobel for Work on Behavior and Use of Light - New York Times

2005 Physics Nobel !

Slashdot | Bioinformatics in the Post-Genomic Era

03 October 2005

Thinkmap Visual Thesaurus

Ferrell Lab at Stanford


02 October 2005

Bioinformatics: Mining ChIP-chip data for transcription factor and

Looks interesting...

Bioinformatics. 2005 Jun 1;21 Suppl 1:i403-i412.
Mining ChIP-chip data for transcription factor and cofactor binding sites.
Smith AD, Sumazin P, Das D, Zhang MQ.

MOTIVATION: Identification of single motifs and motif pairs that can be
used to predict transcription factor localization in ChIP-chip data, and gene
expression in tissue-specific microarray data. RESULTS: We describe methodology
to identify de novo individual and interacting pairs of binding site motifs from
ChIP-chip data, using an algorithm that integrates localization data directly
into the motif discovery process. We combine matrix-enumeration based motif
discovery with multivariate regression to evaluate candidate motifs and identify
motif interactions. When applied to the HNF localization data in liver and
pancreatic islets, our methods produce motifs that are either novel or improved
known motifs. All motif pairs identified to predict localization are further
evaluated according to how well they predict expression in liver and islets and
according to how conserved are the relative positions of their occurrences. We
find that interaction models of HNF1 and CDP motifs provide excellent prediction
of both HNF1 localization and gene expression in liver. Our results demonstrate
that ChIP-chip data can be used to identify interacting binding site motifs.
AVAILABILITY: Motif discovery programs and analysis tools are available on
request from the authors. CONTACT: asmith@cshl.edu.

Just a Really Bad Stretch? - New York Times

A really good "network graphic"

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