The New York Times > Real Estate > Interactive Feature > Dodging a Downturn
11 September 2005
07 September 2005
06 September 2005
Quote on introverts [quote]
Introverts recharge by being by themselves, whereas extroverts energize through being with others.
05 September 2005
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.
04 September 2005
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
~ { : DNAstuff : } ~ what stuff life is made of...+ [fun]
Some interesting things to buy, shaped like DNA.
dnastuff.com
03 September 2005
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.
...
30 August 2005
'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?
29 August 2005
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
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