NYTimes - Rewriting History: Snared in the Web of a Wikipedia Liar [clip-h]

thought this was interesting in relation to traceability of internet info. and also defamatory websites...

==

[clip-h]ooo

NYTimes - Rewriting History: Snared in the Web of a Wikipedia Liar

http://www.nytimes.com/2005/12/04/weekinreview/04seelye.html

 

FALSE WITNESS How true are "facts" online?

 

By KATHARINE Q. SEELYE

Published: December 4, 2005

 

ACCORDING to Wikipedia, the online encyclopedia, John Seigenthaler Sr. is 78 years old and the former editor of The Tennessean in Nashville. But is that information, or anything else in Mr. Seigenthaler's biography, true?

 

The question arises because Mr. Seigenthaler recently read about himself on Wikipedia and was shocked to learn that he "was thought to have been directly involved in the Kennedy assassinations of both John and his brother Bobby."....

The Gamer as Artiste - New York Times

Pixel Canvas
The Gamer as Artiste
By JOHN LELAND
Published: December 4, 2005

LAST week, I spent several days living - and dying - inside the new Xbox 360 console, with four popular games pegged as particularly cinematic. I entered as a curious novice, less concerned with breaking the games than with exploring the worlds they opened, and the worlds you die in.....
I died as a princess in a green miniskirt, as a space warrior, a World War II soldier named Vasili and a humorless F.B.I. agent tracking a sadistic killer. My deaths, rendered in state-of-the-art detail, were not illustrious or mourned.

Gimme an Rx! Cheerleaders Pep Up Drug Sales - New York Times

[fun]ooo

http://www.cfar.umd.edu/~fer/optical [url]ooo

Liked the optical illusions on :
http://www.cfar.umd.edu/~fer/optical ,
particularly,
http://www.cfar.umd.edu/~fer/optical/smoothing3.html
http://www.cfar.umd.edu/~fer/optical/line3.html
http://www.cfar.umd.edu/~fer/optical/movement2.html
http://www.cfar.umd.edu/~fer/optical/movement3.html

Do people study how they can trick mice with illusions?
--
[fun]ooo

http://monod.molsci.org [url]ooo

Thought this might be interesting in relation to future SPINE stuff.
==
http://monod.molsci.org/
http://monod.molsci.org/docs/Monod-June-2003.pdf
Monod is a web-based environment supporting collaborative work by scientists
studying complex biological systems.

NY Times: Sex and Chess. Is She a Queen or a Pawn? [clip-h]

the way to win in chess ---- distract your opponent!
==
http://www.nytimes.com/2005/11/27/fashion/sundaystyles/27CHESS.html
Sex and Chess. Is She a Queen or a Pawn?
Thomas Lohnes/Agence France-Presse--Getty Images
By DYLAN LOEB McCLAIN
Published: November 27, 2005

VANESS REID, a 16-year-old student from Sydney, Australia, runs cross-country,
plays touch football, enjoys in-line skating, swims and goes bodyboarding. She
also has a cerebral side: she plays competitive chess. ... But Ms. Reid, who has
auburn hair, light-blue eyes and a winning smile, is arguably the top player in
the world based on a more subjective criterion: her looks. A Web site called
World Chess Beauty Contest (www.1wcbc.com) ranks her as the world's most
beautiful woman in the game....

Google Local - from: New Rochelle Rd and Labelle Rd., New Rochelle, NY 10804 to: I-95., New Rochelle, NY

A potential interconnect between the beginning of the Hutch and I-95.

[FUN]

==

Distance: 2.2 mi (about 5 mins)

Start address: New Rochelle Rd & Labelle Rd, Bronxville, NY 10708
End address: New England Thwy, New Rochelle, NY
1. Head east from New Rochelle Rd - go 0.3 mi
2. Bear right at Pelhamdale Ave - go 0.1 mi
3. Turn left at Eastchester Rd - go 0.8 mi
4. Bear right and head toward North Ave - go 0.0 mi
5. Bear right at North Ave - go 1.0 mi

New York Area Roads, Crossings and Exits

Interesting histories of Bronx River and Hutchison River Parkways.

[FUN]

A Big Debate on Little People: Ancient Species or Modern Dwarfs? - Free Preview - The New York Times

[GENERAL]

A Big Debate on Little People: Ancient Species or Modern Dwarfs?
October 12, 2005, Wednesday
By JOHN NOBLE WILFORD (NYT); Foreign Desk
Late Edition - Final, Section A, Page 11, Column 1, 983 words
DISPLAYING FIRST 50 OF 983 WORDS -New discoveries in a cave on the Indonesian island of Flores, notably another jawbone, appear to give additional support to the idea that a separate species of little people new to science and now extinct lived there as recently as 12,000 years ago. But a vigorous minority of skeptical..."

Web Based DNS Lookup (NSLookup) (ZoneEdit.com)

Nice web based NS lookup

[LINK]

Google Local - Bergen St & Nostrand Ave, Brooklyn, NY 11216

A pretty bad neighborhood as evident in the "the Interpreter". Location of the B133 busline in Crown Heights.

[GENERAL]

http://www.flagshipventures.com/news/06152005p.html [url]

http://www.compoundtherapeutics.com
http://www.flagshipventures.com/news/06152005p.html

John Mendlein's location after AFNM

[GENERAL]

NYTimes: $100 Billion in the Hands of a Computer [clip-h]

Thought this was interesting article about quantitative analysis. I think this
guy uses Data mining!
==
November 19, 2005
$100 Billion in the Hands of a Computer
By JOSEPH NOCERA

PEOPLE ask me all the time: What's your secret?" James Simons said.

We were sitting in an office in Manhattan that Mr. Simons uses when he's not at
the Long Island offices of Renaissance Technologies, the money management firm
he founded in 1982. He was wearing an elegant shirt and tie, and loafers with no
socks. He took a drag from a cigarette, the second of three he would smoke in
the course of a long interview....

ooo[clip]ooo[general]ooo

Yale Alumni Strike Back at Tailgating Limits - New York Times

Yale Alumni Strike Back at Tailgating Limits
By STACEY STOWE
Published: November 19, 2005

When Yale University distributed new rules last month to curb binge drinking and public drunkenness at football games, the reaction was swift. But the loudest outcry came not from students but from alumni who have returned here for decades to watch the Yale Bulldogs and to fraternize at often-elegant tailgate parties.....

NYTimes: 1955 Vision of an 2005 City: Times Square Dies but 2nd Ave. Has a Subway [clip-h]

Thought this was a fascinating glimpse of the past and where we thought we would
be. This is quite interesting from both a real-estate and demographic perspective.

[GENERAL-CLIP]
==

http://www.nytimes.com/2005/11/21/nyregion/21predict.html
+ attached gif

1955 Vision of an 2005 City: Times Square Dies but 2nd Ave. Has a Subway
By SAM ROBERTS
Published: November 21, 2005

TV antennas were beginning to sprout on rooftops like spindly metallic weeds,
the alternate-side parking minuet was just being choreographed and air raid
sirens still rumbled daily at noon in 1955 when New Yorkers paused briefly to
contemplate a city "strained almost to bursting" after the "tensest quarter
century" in its history.
Titled "Our Changing City," a 20-part series of articles in The New York Times
painted a largely optimistic panorama of the century's second half.....

==

See OLD 1955 PDFs at:
http://www.nytimes.com/ref/nyregion/changing_series.html

Our Changing City
In 1955, The New York Times ran a series that ran predictions about the future
of New York....

2can Genomes - Bacteria Genomes

useful listing of pathogen genomes

[SCI-LINK]

The Prodigy Puzzle - New York Times

The Prodigy Puzzle
By ANN HULBERT
Published: November 20, 2005
'So you're the geniuses," Senator Carl Levin said, looking pleased as he peered over his glasses. He was addressing the flaxen-haired Heidi Kaloustian, a 17-year-old freshman at the University of Michigan, and John Zhou, a superfriendly 17-year-old senior at Detroit Country Day School, unusual visitors to Room 269 of the Russell Office Building on Capitol Hill....

Science: Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer [clip]

Article includes Mark Rubin....

[SCI]
==
1: Science. 2005 Oct 28;310(5748):644-8.

Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate
cancer.

Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S,
Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA,
Chinnaiyan AM.

Recurrent chromosomal rearrangements have not been well characterized in common
carcinomas. We used a bioinformatics approach to discover candidate oncogenic
chromosomal aberrations on the basis of outlier gene expression. Two ETS
transcription factors, ERG and ETV1, were identified as outliers in prostate
cancer. We identified recurrent gene fusions of the 5' untranslated region of
TMPRSS2 to ERG or ETV1 in prostate cancer tissues with outlier expression....

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16254181&query_hl=1

USATODAY.com - Findings identify likely origins of prostate cancer

USA Today article on Mark Rubin's finding gene alterations linked to prostate cancer

==
Posted 10/27/2005 10:06 PM

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Findings identify likely origins of prostate cancer
By Liz Szabo, USA TODAY
Researchers have found a set of genes that may play a key role in prostate cancer — a discovery that doctors are hailing as a major breakthrough that changes the way they think about the genetic roots of the disease.

If further research confirms these findings, published Friday in the journal Science, the discovery eventually might lead to better tests for prostate cancer as well as targeted therapies, says one of the study's authors, Mark Rubin, chief of urologic pathology at Brigham and Women's Hospital in Boston.....

USATODAY.com - Findings identify likely origins of prostate cancer

Phys-Rev-E: Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays. [clip]

Fig. 3 of this paper looks a lot like the "C-runs" artifact on Affy chips.
Other Naef & Magnasco and Magnasco lab papers are also quite interesting in
relation to Affy analysis -- see http://asterion.rockefeller.edu/felix/CV .

[SCIENCE]

==

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Jul;68(1 Pt 1):011906. Epub 2003
Jul 16.
Solving the riddle of the bright mismatches: labeling and effective binding
in oligonucleotide arrays.

Naef F, Magnasco MO.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12935175&query_hl=7

http://asterion.rockefeller.edu/felix/CV/PDFs/riddle.pdf

RNA binding to high-density oligonucleotide arrays has shown tantalizing
differences with solution experiments. We analyze here its sequence specificity,
fitting binding affinities to sequence composition in large datasets. Our
results suggest that the fluorescent labels interfere with binding.....
==

Home Page for Gonçalo Abecasis

An interesting overview of the Hapmap project at Renal Week.

Rafael Irizarry's Web Page

Interesting work on Affy analysis described at a recent talk in NY.

O'Reilly Network: What Is Web 2.0

8th Annual Conference on Computational Genomics - The Jackson Laboratory

Computational Genomics

[Science]

Routine Changes, or 'Bait and Switch'? - New York Times

Routine Changes, or 'Bait and Switch'?

By NICHOLAS CONFESSORE
Published: November 6, 2005

When the Atlantic Yards project in Brooklyn was unveiled in 2003, pamphlets given out at a news conference said it would feature "iconic" new buildings while balancing "the needs of the existing communities and those of the people who would live, work in or visit the new complex."
...

Web of the Free - New York Times

[General]

==
Op-Ed Contributors
Web of the Free

By MARK A. SHIFFRIN and AVI SILBERSCHATZ
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.
...

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

By HOWARD W. FRENCH
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....

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

Starts with a great quote (below).
[article-general]
--
By ANTHONY GOTTLIEB
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

[bookmark-general]

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....
--
[general-article]
==
Style: The Way We Drive Now : Motoring Toward A Post-Gasoline Age; The
High-Performance Hybrids
September 25, 2005, Sunday
By CLIVE THOMPSON (NYT); Magazine
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
By ANDREW TILIN (NYT); Magazine
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]

[general-article]

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

[bookmark-general]

Wired 13.10: The Elements Get Some Style

[general-article]
interesting graphic

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

[general-article]

==
Exxon Mobil Back at No. 1 in Market Value, Even as It Shrinks Shares
By FLOYD NORRIS
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

[general-article]

Meet the Life Hackers - New York Times

[general-article]

Chasing Ground - New York Times

[general-article]

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

By NICHOLAS CONFESSORE
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.
...
http://www.nytimes.com/2005/10/14/nyregion/14yards.html

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

Forms from Yale University | Postdoctoral Office

includes a sample appointment letter...

Kolmogorov-Smirnov Test

Useful page with web form

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

A bit of discussion of the way to interface programming languange objects with
standard relational tables.
--
http://www.linuxjournal.com/article/8490
http://www.linuxjournal.com/article/8217
http://wiki.rubyonrails.com/rails/pages/StartAtTheBeginning

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

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

Thinkmap Visual Thesaurus

Ferrell Lab at Stanford

http://www.stanford.edu/group/ferrelllab

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"

http://www.chem.ufl.edu/~richards/loew2005/ [url]

NY area meeting, very easy to go to for some....

If You Can Make It in Silicon Valley, You Can Make It . . . in Silicon Valley Again - New York Times [clip-h]

Amazing examples of wealth creation !

--
http://www.nytimes.com/2005/06/05/magazine/05RATPACK.html?ei=5070&en=d67f7b5
6e7503c13&ex=1127707200&pagewanted=print

June 5, 2005
If You Can Make It in Silicon Valley, You Can Make It . . . in Silicon
Valley Again
By GARY RIVLIN

One evening this spring, Marc Andreessen, the first outsize icon of the
Internet era, caught a glimpse of his former life while mingling at the San
Francisco launch party for Current, Al Gore's new 24-hour cable station. In
1994, when Andreessen was only 22, he and a high-tech veteran named Jim
Clark created the Internet-browser company Netscape Communications. Two
years later, there he was on the cover of Time, sitting barefoot on a golden
throne, dressed in jeans and a rumpled black polo. The magazine cast him as
the king of the ''golden geeks,'' a group that popularized the formerly
novel notion of surfing the Web and, not incidentally, helped create a
vision of Silicon Valley as a glittering gold field where the young, bright
and vigorous could stake a claim and make themselves unimaginably wealthy
before they even had the time to put up posters in their barely furnished
apartments......

The Quantitative, Data-Based, Risk-Massaging Road to Riches - New York Times [clip-h]

Thought this was an interesting in relation to Yale, Goldman Sachs, and
Quantitative modeling. Looks like the Yale finance people -- in particular,
David Swensen -- are pretty good at this!

==

http://www.nytimes.com/2005/06/05/magazine/05HEDGE.html?ei=5070&en=ca0716102
0116727&ex=1127707200&pagewanted=print

June 5, 2005
The Quantitative, Data-Based, Risk-Massaging Road to Riches
By JOSEPH NOCERA

Clifford Asness is probably going to be annoyed when he sees that this
article begins with a discussion about how much money he makes, but there's
no way around it. Asness is a very successful hedge-fund manager, and very
successful hedge-fund managers make stupendous amounts of money, even by
Wall Street's extravagant standards. And in the public mind, their
staggering compensation tends to overshadow pretty much everything else.
''Filthy Stinking Rich'' was New York magazine's unambiguous take on the
hedge-fund phenomenon some months ago. Last month, in its survey of the
best-paid hedge-fund managers, Institutional Investor's Alpha magazine
reported that the average pay for the top 25 hedge-fund managers was an
astounding $251 million in 2004. Asness himself has written, in one of his
better lines, that hedge funds ''are generally run for rich people in
Geneva, Switzerland, by rich people in Greenwich, Conn.'' .....

Web Sudoku - Billions of Free Sudoku Puzzles to Play Online [fun]

Emacs - Using Emacs with Ange-FTP

a useful page

MTV.com - Lifehouse

You and Me (2005) -- nice song.

FEBS-let: Functional essentiality from topology features in metabolic

Interesting in relation to ongoing work on essentiality and lethality.
--
FEBS Lett. 2005 Aug 29;579(21):4642-4646.

Functional essentiality from topology features in metabolic networks: A
case study in yeast.

Palumbo MC, Colosimo A, Giuliani A, Farina L.

The relation between the position of mutations in Saccharomyces cerevisiae
metabolic network and their lethality is the subject of this work. We represent
the topology of the network by a directed graph: nodes are metabolites and arcs
represent the reactions; a mutation corresponds to the removal of all the arcs
referring to the deleted enzyme. Using publicly available knock-out data, we
show that lethality corresponds to the lack of alternative paths in the
perturbed network linking the nodes affected by the enzyme deletion. Such
feature is at the basis of the recently recognized importance of 'marginal' arcs
of metabolic networks.

==

http://www.dis.uniroma1.it/~farina/

postdoctoral fellowship deadlines (uk applicant) [url]

Hi, I've added to the list and posted to my bookmarks. -cheers, marK

==

- Helen Hay Whitney Foundation (http://www.hhwf.org): July 15

- Life Sciences Research Foundation (www.lsrf.org): October 1st

- GWIS Grants and Fellowships (http://www.gwis.org/grants/Gerry.htm)
Is this only for graduates?: December 1st

- Jane Coffin Childs Memorial Fund (www.jccfund.org): February 1st

- Damon Runyon Cancer Research Foundation (www.drcrf.org): March 15th

- 1851 Royal Commission (www.royalcommission1851.org.uk): Feb 1st

The New York Times > Real Estate > Interactive Feature > Dodging a Downturn

Life Sciences Research Foundation | Welcome

Quote on introverts [quote]

Introverts recharge by being by themselves, whereas extroverts energize through being with others.

Bioinformatics: A statistical framework for genomic data fusion + Other papers by Noble et al. on Kernel methods [clip]

Papers of interest:

In some recent work, Noble and colleagues describe the way they
develop kernel methods that generalize their (and other's) earlier
work on SVMs. Kernel methods allow one to express the similarity
between a pair of objects with respect to various different types of
data (e.g. expression correlations or similarity in hydrophobicity) in
a uniform framework, and then to combine all these methods of
similarity in an optimized fashion. Lanckreit et al describe an
overall formalism for using these kernel methods in the framework of
bioinformatics. Ben-Hur & Noble describe how these kernel methods can
be specifically adapted to protein-protein interactions where one is
computing the similarity between pairs of proteins rather than
individuals. Tsuda & Noble describe a particular method of kernel
construction.

--

Tsuda K, Noble WS. Learning kernels from biological networks by
maximizing entropy. Bioinformatics. 2004 Aug 4;20 Suppl 1:I326-I333.

Ben-Hur A, Noble WS. Kernel methods for predicting protein-protein
interactions. Bioinformatics. 2005 Jun 1;21 Suppl 1:i38-i46.

Lanckriet GR, De Bie T, Cristianini N, Jordan MI, Noble WS. A
statistical framework for genomic data fusion. Bioinformatics. 2004
Nov 1;20(16):2626-35. Epub 2004 May 6.

PNAS: Protein ranking: from local to global structure in the protein similarity network [clip]

A paper of interest:

In Weston et al., Noble and colleagues develop an algorithm for
comparing protein sequences that has inspired from this similarity
measures used by the Google search engine. They use a diffusion
distance type of approach that takes into account the overall
connectivity of similarity relationships. This paper represents a
great synthesis of the way a computer scientist can apply general
methods developed outside of biology into the biological context.

--
Weston J, Elisseeff A, Zhou D, Leslie CS, Noble WS. Protein ranking:
from local to global structure in the protein similarity network.
Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6559-63. Epub 2004 Apr
15.

Yale University's Interdisciplinary Bioethics Project -- yale.edu/bioethics [url]

Phys Rev E: Information-theoretic approach to network modularity [clip]

Uses diffusion distance in relationship to modularity
--
http://arxiv.org/PS_cache/q-bio/pdf/0411/0411033.pdf
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15903736&dopt=Citation

Ann Rev Soc: The New Science of Networks by Duncan Watts [clip]

Looks interesting and simultaneous in relation to our review
--
http://cdg.columbia.edu/docs/papers/watts7.pdf
http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.soc.30.020404.104342

kleinbottle.com [fun]

Got something from them!

~ { : DNAstuff : } ~ what stuff life is made of...+ [fun]

Some interesting things to buy, shaped like DNA.
dnastuff.com

Listen & Live Audio: Ear-Catching Audiobooks [fun]

A slightly useful audiobooks list

HarperCollins Publishers -- Audiobooks [url]

A listing of audiobooks, not that useful.

In Chimpanzee DNA, Signs of Y Chromosome's Evolution - New York Times [clip]

Does the Nature paper discuss the inactivation in terms of pseudogenes?
==

http://www.nytimes.com/2005/09/01/science/01chimp.html

In Chimpanzee DNA, Signs of Y Chromosome's Evolution
By NICHOLAS WADE

Scientists have decoded the chimp genome and compared it with that of
humans, a major step toward defining what makes people human and developing
a deep insight into the evolution of human sexual behavior.

The comparison pinpoints the genetic differences that have arisen in the two
species since they split from a common ancestor some six million years
ago....

A Baby Step Toward Wi-Fi Photos - New York Times [clip-h]

Useful to think about in relation to taking photos of the board.

==

http://www.nytimes.com/2005/09/01/technology/circuits/01pogue.html

David Pogue
A Baby Step Toward Wi-Fi Photos

Published: September 1, 2005

EVERY now and then, someone combines two technologies into a single new
product, and the result is a triumphant new category that changes the
industry. Clock + radio. Cellphone + camera. Music player + hard drive.
...

the new Nikon P1, due in stores on Sept. 15. It's an iPod-size,
eight-megapixel camera dressed in brushed-metal black, with a list price of
$550. (A sister model, the P2, is a silver, 5.1-megapixel version that lists
for $400. Online prices will be much lower once the cameras actually arrive
in stores.)

...

But the best Shoot & Transfer feature of all is a true parlor trick. At a
party, conference or any other social gathering, you can start up a slide
show on your Mac or PC, complete with music. You can then walk around the
room, snapping pictures of the guests or attendees. These photos join the
slide show already in progress, automatically, in real time.
...

'The Man Behind the Microchip': The Next Small Thing - New York Times [clip]

http://www.nytimes.com/2005/08/28/books/review/28THOMPSO.html

'The Man Behind the Microchip': The Next Small Thing - New York Times: "THE MAN BEHIND THE MICROCHIP
Robert Noyce and the Invention of Silicon Valley.
By Leslie Berlin.
402 pp. Oxford University Press. $30."

Noyce & Fairchild vs. TI, who's the inventor?

Columbus Avenue Business Improvement District - columbusavenuebid.org [ref]

Contains a useful map.

Manhattan Kayak Company - Home Page [fun]

Potentially interesting but maybe a little dirty!

http://cyclelogicaltours.com [fun]

A cycle touring organization

Genome Biology | Full text | Statistical tests for differential expression in cDNA microarray experiments

Nice discussion of instability of the denominator of the t-test.

Phys Rev E : Software systems as complex networks: structure, function, and evolvability of software collaboration graphs. [clip]

http://arxiv.org/PS_cache/cond-mat/pdf/0305/0305575.pdf
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=14683011&dopt=Citation

Take a Chance: Science News Online, Dec. 4, 2004

Points out the problem of the seed and the difficulty in generating random numbers.
--
Science News Online

Week of Dec. 4, 2004; Vol. 166, No. 23
Take a Chance
Scientists put randomness to work

Erica Klarreich

Since the dawn of written history, people have exploited the randomness of a roll of a die to inject their games with the thrill of the unpredictable. Today, randomness is finding myriad other uses, such as encrypting credit card numbers in Internet transactions, deciding how to allocate treatments in drug trials, choosing precincts to call in national polls, running online gambling sites, and helping physicists simulate phenomena ranging from the weather to traffic patterns.........

A Few Words About Sudoku, Which Has None - New York Times

http://graphics8.nytimes.com/images/2005/08/28/weekinreview/sudoku_solution.gif
http://graphics8.nytimes.com/images/2005/08/28/weekinreview/nwr_SUDOKU_GRAPHIC.gif

Notes of a Wayfarer: Preface

Notes of a Wayfarer: Preface

Interesting recollections....

Notes of a Wayfarer: Page 17

Notes of a Wayfarer: Page 17

Do You MySpace? - New York Times

Do You MySpace? - New York Times

Google Anything, so Long as It's Not Google - New York Times

Google Anything, so Long as It's Not Google - New York Times

with associated stuff:

Google balances privacy, reach | CNET News.com

Eric Schmidt's Home Page

Does Lighter Equal Deadlier? - New York Times

Does Lighter Equal Deadlier? - New York Times

Times: If the Law Is an Ass, the Law Professor Is a Donkey [clip]

Thought this was an interesting article about the academic outlook.
http://www.nytimes.com/2005/08/28/weekinreview/28liptak.html

==
August 28, 2005
If the Law Is an Ass, the Law Professor Is a Donkey
By ADAM LIPTAK

PROFESSORS at the best law schools are generally assumed to be overwhelmingly
liberal, and now a new study lends proof. But whether the ideological imbalance
matters - to the academic environment students encounter, to the kinds of
lawyers the schools produce and to the stock of ideas the professors generate -
depends on whom you ask.

The study, to be published this fall in The Georgetown Law Journal, analyzes 11
years of records reflecting federal campaign contributions by professors at the
top 21 law schools as ranked by U.S. News & World Report. Almost a third of
these law professors contribute to campaigns, but of them, the study finds, 81
percent who contributed $200 or more gave wholly or mostly to Democrats; 15
percent gave wholly or mostly to Republicans.

...

Coach Carter Movie Info - Yahoo! Movies

A good movie!

The Breaking Point - New York Times

An interesting article potentially pointing out the importance of energy conservation.

Million Dollar Baby Movie Info - Yahoo! Movies

this-is-not-spam header

http://cm.bell-labs.com/who/ehg
thought this guy had a interesting way of avoiding losing mail due to spam filters

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

Thought this was fun!

A face from Morphases by

This e-mail was sent from www.morphases.com by your friend .

Message:
Hi! Check the picture of me :)

Generation ID (GID) of this face is 47877:CD84D57A
View this face at http://www.morphases.com/editor/viewer.php?GID=47877:CD84D57A

Some useful exercises

Legs
quadriceps-exercises-smith-machine-squats
 
Dumbbell-lunges
http://www.changingshape.com/exercise/strengthtraining/gym/dumbbelllunges.asp

Lever-Lying-Leg-Curl
http://www.exrx.net/WeightExercises/Hamstrings/LVLyingLegCurl.html

Abs
Sit up with arms in front (abdominal crunch)
http://www.changingshape.com/exercise/strengthtraining/abdominalcrunch.asp
reverse-machine-abdominal-crunch
Shoulders
Dumbell shoulder Shrug
http://www.changingshape.com/exercise/strengthtraining/gym/dumbbellshouldershrug.asp
Arms
Bicep curls
http://www.exrx.net/WeightExercises/Biceps/DBCurl.html
Tricep pressdowns
http://www.femalemuscle.com/fitness/workouts/triceps2.html
front-and-side-arm-raises
http://exercise.about.com/cs/exerciseworkouts/l/blarmsshoulders.htm

Stretches
hamstring stretch
thigh pull
http://www.webefit.com/Stretch/Str_07.html
Hip flexor stretch
http://www.exrx.net/Stretches/HipFlexors/KneelingHipFlexor.html
butterfly stretch for inner thighs
http://www.webefit.com/Stretch/Str_15.html
Back
free weight lat pull down machine
http://www.exrx.net/WeightExercises/LatissimusDorsi/CBFrontPulldown.html
Resistance-band-row
http://www.changingshape.com/exercise/strengthtraining/bandrow.asp
seated row
http://www.changingshape.com/exercise/strengthtraining/gym/seatedrow.asp
single-leg-calf-raise
http://www.exrx.net/WeightExercises/Gastrocnemius/DBSingleLegCalfRaise.html

Nice directory of exercises

best ab exercises - lower abdominal exercises, free ab workouts, thigh pictures hip stomach leg knee inner outer butt waist back

Nice directory of exercises

All Yankees, All the Time Works for YES - New York Times

List - Edmunds.com's Top 10

Useful lists for cars!

Popular baby names

Popular baby names

This is a great website for stats!