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- Genetdes:
automatic
design of
transcriptiona
l networks: Bioinformatics
, Vol. 23, No.
14. (15 July
2007), pp.
1857-1858.Moti
vation: The
rational
design of
biological
networks with
prescribed
functions is
limited to
gene circuits
of a few
genes. Larger
networks
involve
complex
interactions
with many
parameters and
the use of
automated
computational
tools can be
very valuable.
We propose a
new tool to
design
transcriptiona
l networks
with targeted
behavior that
could be used
to better
understand the
design
principles of
genetic
circuits.
Results: We
have
implemented a
Simulated
Annealing
optimization
algorithm that
explores
throughout the
space of
transcription
networks to
obtain a
specific
behavior. The
software
outputs a
transcriptiona
l network with
all the
corresponding
kinetic
parameters in
SBML format.
We provide
examples of
transcriptiona
l circuits
with logical
and
oscillatory
behaviors. Our
tool can also
be applied to
design
networks with
multiple
external input
and output
genes.
Availability:
The software,
a tutorial
manual,
parameter sets
and examples
are freely
available at
http://synth-b
io.yi.org/gene
tdes.html
Contact:
Alfonso.Jarami
llo@polytechni
que.edu
10.1093/bioinf
ormatics/btm23
7Guillermo
Rodrigo,
Javier
Carrera,
Alfonso
Jaramillo
Source: Bioinformatics, Vol. 23, No. 14. (15 July 2007), pp. 1857-1858. - Evolving
complex
dynamics in
electronic
models of
genetic
networks.: Chaos
(Woodbury,
N.Y.), Vol.
14, No. 3.
(September
2004), pp.
707-715.Ordina
ry
differential
equations are
often used to
model the
dynamics and
interactions
in genetic
networks. In
one
particularly
simple class
of models, the
model genes
control the
production
rates of
products of
other genes by
a logical
function,
resulting in
piecewise
linear
differential
equations. In
this article,
we construct
and analyze an
electronic
circuit that
models this
class of
piecewise
linear
equations.
This circuit
combines CMOS
logic and RC
circuits to
model the
logical
control of the
increase and
decay of
protein
concentrations
in genetic
networks. We
use these
electronic
networks to
study the
evolution of
limit cycle
dynamics. By
mutating the
truth tables
giving the
logical
functions for
these
networks, we
evolve the
networks to
obtain limit
cycle
oscillations
of desired
period. We
also
investigate
the fitness
landscapes of
our networks
to determine
the optimal
mutation rate
for
evolution.Jona
than Mason,
Paul Linsay,
JJ Collins,
Leon Glass
Source: Chaos (Woodbury, N.Y.), Vol. 14, No. 3. (September 2004), pp. 707-715. - In silico
evolution of
functional
modules in
biochemical
networks.: Systems
biology, Vol.
153, No. 4.
(July 2006),
pp.
223-235.Unders
tanding the
large reaction
networks found
in biological
systems is a
daunting task.
One approach
is to divide a
network into
more
manageable
smaller
modules, thus
simplifying
the problem.
This is a
common
strategy used
in
engineering.
However, the
process of
identifying
biological
modules is
still in its
infancy and
very little is
understood
about the
range and
capabilities
of motif
structures
found in
biological
modules. In
order to
delineate
these modules,
a library of
functional
motifs has
been generated
via in silico
evolution
techniques. On
the basis of
their
functional
forms,
networks were
evolved from
four broad
areas:
oscillators,
bistable
switches,
homeostatic
systems and
frequency
filters. Some
of these
motifs were
constructed
from simple
mass action
kinetics,
others were
based on
Michaelis-Ment
en kinetics as
found in
protein/protei
n networks and
the remainder
were based on
Hill equations
as found in
gene/protein
interaction
networks. The
purpose of the
study is to
explore the
capabilities
of different
network
architectures
and the rich
variety of
functional
forms that can
be generated.
Ultimately,
the library
may be used to
delineate
functional
motifs in real
biological
networks.SR
Paladugu, V
Chickarmane, A
Deckard, JP
Frumkin, M
McCormack, HM
Sauro
Source: Systems biology, Vol. 153, No. 4. (July 2006), pp. 223-235. - Electricity
Market Design:
The Good, the
Bad, and the
Ugly: Hawaii
International
Conference on
System
Sciences, Vol.
2 (2003),
54b.This paper
examines
principles of
market design
as applied to
electricity
markets. I
illustrate the
principles
with examples
of both good
and bad
designs. I
discuss one of
the main
design
challenges-dea
ling with
market power.
I then discuss
FERC's choice
of a standard
market
design.Peter
Cramton
Source: Hawaii International Conference on System Sciences, Vol. 2 (2003), 54b. - The Landscape
of Electronic
Market Design: Management
Science, Vol.
51, No. 3.
(2005), pp.
316-327.This
paper presents
an
introductory
survey for
this special
issue of
"Managemen
t Science"
on electronic
markets. We
acquaint the
reader with
some
fundamental
concepts in
the study of
electronic
market
mechanisms,
while
simultaneously
presenting a
survey and
summary of the
essential
literature in
this area.
Along the way,
we position
each of the
papers
presented in
this special
issue within
the existing
literature,
demonstrating
the deep
impact of
these 14
articles on an
already broad
body of
knowledge.G
Anandalingam,
Robert Day, S
Raghavan
Source: Management Science, Vol. 51, No. 3. (2005), pp. 316-327.
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