28 November 2005

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

Thought this might be interesting in relation to future SPINE stuff.
Monod is a web-based environment supporting collaborative work by scientists
studying complex biological systems.

27 November 2005

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

the way to win in chess ---- distract your opponent!
Sex and Chess. Is She a Queen or a Pawn?
Thomas Lohnes/Agence France-Presse--Getty Images
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.



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.


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


A Big Debate on Little People: Ancient Species or Modern Dwarfs?
October 12, 2005, Wednesday
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..."

25 November 2005

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

Nice web based NS lookup


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.


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


John Mendlein's location after AFNM


21 November 2005

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

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....


Yale Alumni Strike Back at Tailgating Limits - New York Times

Yale Alumni Strike Back at Tailgating Limits
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.


+ attached gif

1955 Vision of an 2005 City: Times Square Dies but 2nd Ave. Has a Subway
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:

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

20 November 2005

2can Genomes - Bacteria Genomes

useful listing of pathogen genomes


The Prodigy Puzzle - New York Times

The Prodigy Puzzle
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....

18 November 2005

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

Article includes Mark Rubin....

1: Science. 2005 Oct 28;310(5748):644-8.

Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate

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....


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

14 November 2005

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 .



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.



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.....

13 November 2005

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

07 November 2005

8th Annual Conference on Computational Genomics - The Jackson Laboratory

Computational Genomics


06 November 2005

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

Routine Changes, or 'Bait and Switch'?

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."

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