30 September 2005

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

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

25 September 2005

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 !


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

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

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!



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

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.'' .....

12 September 2005

11 September 2005

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.



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

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


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

04 September 2005

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

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

Looks interesting and simultaneous in relation to our review

kleinbottle.com [fun]

Got something from them!

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

Some interesting things to buy, shaped like DNA.

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

A slightly useful audiobooks list

HarperCollins Publishers -- Audiobooks [url]

A listing of audiobooks, not that useful.

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?


In Chimpanzee DNA, Signs of Y Chromosome's Evolution

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

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

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



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.