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5,500 | Probabilistic estimation of microarray data reliability and underlying gene expression | q-bio.QM | Background: The availability of high throughput methods for measurement of
mRNA concentrations makes the reliability of conclusions drawn from the data
and global quality control of samples and hybridization important issues. We
address these issues by an information theoretic approach, applied to
discretized expressio... | biology |
5,501 | Development of a Multiphoton Fluorescence Lifetime Imaging Microscopy (FLIM) system using a Streak Camera | q-bio.QM | We report the development and detailed calibration of a multiphoton
fluorescence lifetime imaging system (FLIM) using a streak camera. The present
system is versatile with high spatial (0.2 micron) and temporal (50 psec)
resolution and allows rapid data acquisition and reliable and reproducible
lifetime determinations.... | biology |
5,502 | Idl Signal Processing Library 1.0 | q-bio.QM | We make available a library of documented IDL .pro files as well as a
shareable object library that allows IDL to call routines from LAPACK. The
routines are for use in the spectral analysis of time series data. The primary
focus of these routines are David Thomson's multitaper methods but a whole
range of functions wi... | biology |
5,503 | Response kinetics of tethered bacteria to stepwise changes in nutrient concentration | q-bio.QM | We examined the changes in swimming behaviour of the bacterium Rhodobacter
sphaeroides in response to stepwise changes in a nutrient (propionate),
following the prestimulus motion, the initial response and the adaptation to
the sustained concentration of the chemical. This was carried out by tethering
motile cells by t... | biology |
5,504 | Solvent content of protein crystals from diffraction intensities by Independent Component Analysis | q-bio.QM | An analysis of the protein content of several crystal forms of proteins has
been performed. We apply a new numerical technique, the Independent Component
Analysis (ICA), to determine the volume fraction of the asymmetric unit
occupied by the protein. This technique requires only the crystallographic data
of structure f... | biology |
5,505 | Identification in models of biochemical reactions | q-bio.QM | We introduce, analyze, and implement a new method for parameter
identification for system of ordinary differential equations that are used to
model sets of biochemical reactions. Our method relies on the integral
formulation of the ODE system and a method of linear least squares applied to
the integral equations. Certa... | biology |
5,506 | Microelectromagnets for the manipulation of biological systems | q-bio.QM | Microelectromagnet devices, a ring trap and a matrix, were developed for the
microscopic control of biological systems. The ring trap is a circular Au wire
with an insulator on top. The matrix has two arrays of straight Au wires, one
array perpendicular to the other, that are separated and topped by insulating
layers. ... | biology |
5,507 | A Barrier Penetration Model for DNA Double Strand Separation | q-bio.QM | A barrier penetration model has been proposed to explain the spontaneous
melting of the DNA oligomers into two separate single strands whereas the
partially melted intermediate states are shown to be the bound state solution
of the same effective potential that generates the barrier. | biology |
5,508 | Open Mass Spectrometry Search Algorithm | q-bio.QM | Large numbers of MS/MS peptide spectra generated in proteomics experiments
require efficient, sensitive and specific algorithms for peptide
identification. In the Open Mass Spectrometry Search Algorithm [OMSSA],
specificity is calculated by a classic probability score using an explicit
model for matching experimental s... | biology |
5,509 | Finite Width Model Sequence Comparison | q-bio.QM | Sequence comparison is a widely used computational technique in modern
molecular biology. In spite of the frequent use of sequence comparisons the
important problem of assigning statistical significance to a given degree of
similarity is still outstanding. Analytical approaches to filling this gap
usually make use of a... | biology |
5,510 | Predicting Genetic Regulatory Response using Classification: Yeast Stress Response | q-bio.QM | We present a novel classification-based algorithm called GeneClass for
learning to predict gene regulatory response. Our approach is motivated by the
hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can
learn a decision rule for predicting whether a gene is up- or down-regulated in
a particular ... | biology |
5,511 | Rate-dependent propagation of cardiac action potentials in a one-dimensional fiber | q-bio.QM | Action potential duration (APD) restitution, which relates APD to the
preceding diastolic interval (DI), is a useful tool for predicting the onset of
abnormal cardiac rhythms. However, it is known that different pacing protocols
lead to different APD restitution curves (RCs). This phenomenon, known as APD
rate-dependen... | biology |
5,512 | Computation of amplification for systems arising from cellular signaling pathways | q-bio.QM | A commonly employed measure of the signal amplification properties of an
input/output system is its induced L2 norm, sometimes also known as "H
infinity" gain. In general, however, it is extremely difficult to compute the
numerical value for this norm, or even to check that it is finite, unless the
system being studied... | biology |
5,513 | Dependence of RNA secondary structure on the energy model | q-bio.QM | We analyze a microscopic RNA model, which includes two widely used models as
limiting cases, namely it contains terms for bond as well as for stacking
energies. We numerically investigate possible changes in the qualitative and
quantitative behaviour while going from one model to the other; in particular
we test, wheth... | biology |
5,514 | Nonstationary time series analysis of heart rate variability | q-bio.QM | An analysis of the RR-interval time series, $t_i$, is presented for the case
in which the average time, $\bar{t}$, changes slowly. In particular, $\bar{t}$
and a short-time scale variability parameter, $V$, are simultaneously measured
while $\bar{t}$ decreases for subjects in the reclined position. The initial
decrease... | biology |
5,515 | Predicting Genetic Regulatory Response Using Classification | q-bio.QM | We present a novel classification-based method for learning to predict gene
regulatory response. Our approach is motivated by the hypothesis that in simple
organisms such as Saccharomyces cerevisiae, we can learn a decision rule for
predicting whether a gene is up- or down-regulated in a particular experiment
based on ... | biology |
5,516 | Multiple sequence alignment based on set covers | q-bio.QM | We introduce a new heuristic for the multiple alignment of a set of
sequences. The heuristic is based on a set cover of the residue alphabet of the
sequences, and also on the determination of a significant set of blocks
comprising subsequences of the sequences to be aligned. These blocks are
obtained with the aid of a ... | biology |
5,517 | Computational Methods and Results for Structured Multiscale Models of Tumor Invasion | q-bio.QM | We present multiscale models of cancer tumor invasion with components at the
molecular, cellular, and tissue levels. We provide biological justifications
for the model components, present computational results from the model, and
discuss the scientific-computing methodology used to solve the model equations.
The models... | biology |
5,518 | Variable selection from random forests: application to gene expression data | q-bio.QM | Random forest is a classification algorithm well suited for microarray data:
it shows excellent performance even when most predictive variables are noise,
can be used when the number of variables is much larger than the number of
observations, and returns measures of variable importance. Thus, it is
important to unders... | biology |
5,519 | A methodology for determining amino-acid substitution matrices from set covers | q-bio.QM | We introduce a new methodology for the determination of amino-acid
substitution matrices for use in the alignment of proteins. The new methodology
is based on a pre-existing set cover on the set of residues and on the
undirected graph that describes residue exchangeability given the set cover.
For fixed functional form... | biology |
5,520 | Modeling multi-cellular systems using sub-cellular elements | q-bio.QM | We introduce a model for describing the dynamics of large numbers of
interacting cells. The fundamental dynamical variables in the model are
sub-cellular elements, which interact with each other through phenomenological
intra- and inter-cellular potentials. Advantages of the model include i)
adaptive cell-shape dynamic... | biology |
5,521 | Combinatorial rules of icosahedral capsid growth | q-bio.QM | A model of growth of icosahedral viral capsids is proposed. It takes into
account the diversity of hexamers' compositions, leading to definite capsid
size. We show that the observed yield of capsid production implies a very high
level of self-organization of elementary building blocks. The exact number of
different pro... | biology |
5,522 | Quantitative Measure of Stability in Gene Regulatory Networks | q-bio.QM | A quantitative measure of stability in stochastic dynamics starts to emerge
in recent experiments on bioswitches. This quantity, similar to the potential
function in mathematics, is deeply rooted in biology, dated back at the
beginning of quantitative description of biological processes: the adaptive
landscape of Wrigh... | biology |
5,523 | A Modified Iterative IOM Approach for Optimization of Biochemical Systems | q-bio.QM | The presented previously indirect optimization method (IOM) developed within
biochemical systems theory (BST) provides a versatile and mathematically
tractable optimization strategy for biochemical systems. However, due to the
local approximations nature of the BST formalism, the iterative version of this
technique pos... | biology |
5,524 | Statistical Predictive Models in Ecology: Comparison of Performances and Assessment of Applicability | q-bio.QM | Ecological systems are governed by complex interactions which are mainly
nonlinear. In order to capture this complexity and nonlinearity, statistical
models recently gained popularity. However, although these models are commonly
applied in ecology, there are no studies to date aiming to assess the
applicability and per... | biology |
5,525 | Kernel methods in genomics and computational biology | q-bio.QM | Support vector machines and kernel methods are increasingly popular in
genomics and computational biology, due to their good performance in real-world
applications and strong modularity that makes them suitable to a wide range of
problems, from the classification of tumors to the automatic annotation of
proteins. Their... | biology |
5,526 | Maximum likelihood estimation of phylogenetic tree and substitution rates via generalized neighbor-joining and the EM algorithm | q-bio.QM | A central task in the study of molecular sequence data from present-day
species is the reconstruction of the ancestral relationships. The most
established approach to tree reconstruction is the maximum likelihood (ML)
method. In this method, evolution is described in terms of a discrete-state
continuous-time Markov pro... | biology |
5,527 | Information based clustering: Supplementary material | q-bio.QM | This technical report provides the supplementary material for a paper
entitled "Information based clustering", to appear shortly in Proceedings of
the National Academy of Sciences (USA). In Section I we present in detail the
iterative clustering algorithm used in our experiments and in Section II we
describe the valida... | biology |
5,528 | Information based clustering | q-bio.QM | In an age of increasingly large data sets, investigators in many different
disciplines have turned to clustering as a tool for data analysis and
exploration. Existing clustering methods, however, typically depend on several
nontrivial assumptions about the structure of data. Here we reformulate the
clustering problem f... | biology |
5,529 | Co-transport-induced instability of membrane voltage in tip-growing cells | q-bio.QM | A salient feature of stationary patterns in tip-growing cells is the key role
played by the symports and antiports, membrane proteins that translocate two
ionic species at the same time. It is shown that these co-transporters
destabilize generically the membrane voltage if the two translocated ions
diffuse differently ... | biology |
5,530 | Surprises in approximating Levenshtein distances | q-bio.QM | The Levenshtein distance is an important tool for the comparison of symbolic
sequences, with many appearances in genome research, linguistics and other
areas. For efficient applications, an approximation by a distance of smaller
computational complexity is highly desirable. However, our comparison of the
Levenshtein wi... | biology |
5,531 | Statistical Properties of the Interbeat Interval Cascade in Human Subjects | q-bio.QM | Statistical properties of interbeat intervals cascade are evaluated by
considering the joint probability distribution $P(\Delta x_2,\tau_2;\Delta
x_1,\tau_1)$ for two interbeat increments $\Delta x_1$ and $\Delta x_2$ of
different time scales $\tau_1$ and $\tau_2$. We present evidence that the
conditional probability d... | biology |
5,532 | New Computational Approaches to Analysis of Interbeat Intervals in Human Subjects | q-bio.QM | We investigate the Markov nature, Cascade of information from large time
scale to small scale and extended self similarity properties of the beat to
beat fluctuations of healthy subjects as well as those with congestive heart
failure. To check the Markov nature, we use a novel inverse method that
utilizes a set of data... | biology |
5,533 | A quantitative model for refilling of the sarcoplasmic reticulum during vascular smooth muscle asynchronous [Ca2+] oscillations | q-bio.QM | We have developed a quantitative model for the creation of cytoplasmic Ca2+
gradients near the inner surface of the plasma membrane (PM). In particular we
simulated the refilling of the sarcoplasmic reticulum (SR) via PM-SR junctions
during asynchronous [Ca2+] oscillations in smooth muscle cells of the rabbit
inferior ... | biology |
5,534 | The pharmacophore kernel for virtual screening with support vector machines | q-bio.QM | We introduce a family of positive definite kernels specifically optimized for
the manipulation of 3D structures of molecules with kernel methods. The kernels
are based on the comparison of the three-points pharmacophores present in the
3D structures of molecul es, a set of molecular features known to be
particularly re... | biology |
5,535 | Spectral analysis of gene expression profiles using gene networks | q-bio.QM | Microarrays have become extremely useful for analysing genetic phenomena, but
establishing a relation between microarray analysis results (typically a list
of genes) and their biological significance is often difficult. Currently, the
standard approach is to map a posteriori the results onto gene networks to
elucidate ... | biology |
5,536 | Form follows function -- how PufX increases the efficiency of the light-harvesting complexes of Rhodobacter sphaeroides | q-bio.QM | Some species of purple bacteria as, e.g., Rhodobacter sphaeroides contain the
protein PufX. Concurrently, the light harvesting complexes 1 (LH1) form dimers
of open rings. In mutants without PufX, the LH1s are closed rings and
photosynthesis breaks down, because the ubiquinone exchange at the reaction
center is blocked... | biology |
5,537 | Targeted Projection Pursuit for Gene Expression Data Classification and Visualisation | q-bio.QM | We present a novel method for finding low dimensional views of high
dimensional data: Targeted Projection Pursuit. The method proceeds by finding
projections of the data that best approximate a target view. Two versions of
the method are introduced; one version based on Procrustes analysis and one
based on a single lay... | biology |
5,538 | Overlapping Probabilities of Top Ranking Gene Lists, Hypergeometric Distribution, and Stringency of Gene Selection Criterion | q-bio.QM | When the same set of genes appear in two top ranking gene lists in two
different studies, it is often of interest to estimate the probability for this
being a chance event. This overlapping probability is well known to follow the
hypergeometric distribution. Usually, the lengths of top-ranking gene lists are
assumed to... | biology |
5,539 | Does Logarithm Transformation of Microarray Data Affect Ranking Order of Differentially Expressed Genes? | q-bio.QM | A common practice in microarray analysis is to transform the microarray raw
data (light intensity) by a logarithmic transformation, and the justification
for this transformation is to make the distribution more symmetric and
Gaussian-like. Since this transformation is not universally practiced in all
microarray analysi... | biology |
5,540 | Towards a model for protein production rates | q-bio.QM | This submission is a duplicate of arXiv:q-bio/0602024 and has been removed. | biology |
5,541 | Scaling graphs of heart rate time series in athletes demonstrate the VLF, LF and HF regions | q-bio.QM | Scaling analysis of heart rate time series has emerged as an useful tool for
assessment of autonomic cardiac control. We investigate the heart rate time
series of ten athletes (five males and five females), by applying detrended
fluctuation analysis (DFA). High resolution ECGs are recorded under
standardized resting co... | biology |
5,542 | A Simple Solution of the Lotka-Volterra Equations | q-bio.QM | In this work we consider a simple, approximate, tending toward exact,
solution of the system of two usual Lotka-Volterra differential equations.
Given solution is obtained by an iterative method. In any finite approximation
order of this solution, exponents of the corresponding Lotka-Volterra variables
have simple, tim... | biology |
5,543 | Granger Causality: Basic Theory and Application to Neuroscience | q-bio.QM | Multi-electrode neurophysiological recordings produce massive quantities of
data. Multivariate time series analysis provides the basic framework for
analyzing the patterns of neural interactions in these data. It has long been
recognized that neural interactions are directional. Being able to assess the
directionality ... | biology |
5,544 | Lagrangian Approaches for a class of Matching Problems in Computational Biology | q-bio.QM | This paper presents efficient algorithms for solving the problem of aligning
a protein structure template to a query amino-acid sequence, known as protein
threading problem. We consider the problem as a special case of graph matching
problem. We give formal graph and integer programming models of the problem.
After stu... | biology |
5,545 | A simple model of energy expenditure in human locomotion | q-bio.QM | A simple harmonic oscillator model is proposed to describe the mechanical
power involved in human locomotion. In this framework, by taking into account
the anthropometric parameters of a standard individual, we are able to
calculate the speed-power curves in human walking. The proposed model accounts
for the well known... | biology |
5,546 | Dynamic behaviors in directed networks | q-bio.QM | Motivated by the abundance of directed synaptic couplings in a real
biological neuronal network, we investigate the synchronization behavior of the
Hodgkin-Huxley model in a directed network. We start from the standard model of
the Watts-Strogatz undirected network and then change undirected edges to
directed arcs with... | biology |
5,547 | Graph kernels based on tree patterns for molecules | q-bio.QM | Motivated by chemical applications, we revisit and extend a family of
positive definite kernels for graphs based on the detection of common subtrees,
initially proposed by Ramon et al. (2003). We propose new kernels with a
parameter to control the complexity of the subtrees used as features to
represent the graphs. Thi... | biology |
5,548 | An algorithm for real-time estimation of Mezcal fermentation parameters based on redox potential measurements | q-bio.QM | We present an algorithm for the continuous monitoring of the biomass and
ethanol concentrations and moreover the kinetic rate in the Mezcal fermentation
process. This algorithm performs its task having only available the on-line
measurements of the redox potential. The procedure includes an artificial
neural network (A... | biology |
5,549 | A family tree of Markov models in systems biology | q-bio.QM | Motivated by applications in systems biology, we seek a probabilistic
framework based on Markov processes to represent intracellular processes. We
review the formal relationships between different stochastic models referred to
in the systems biology literature. As part of this review, we present a novel
derivation of t... | biology |
5,550 | Determination and Spectroscopy of Quantum Yields in Bio/Chemiluminescence via Novel Light-Collection-Efficiency Calibration: Reexamination of The Aqueous Luminol Chemiluminescence Standard | q-bio.QM | We have developed a luminescence-measurement system for liquid
bio/chemiluminescence that can obtain quantitative luminescence spectra as the
absolute total number of luminescence photons at each wavelength or photon
energy and quantum yields. Calibration of light-collection efficiency in the
system is performed with a... | biology |
5,551 | Integrated Cell Manipulation Systems | q-bio.QM | A new type of microfluidic system for biological cell manipulation, a
CMOS/microfluidic hybrid, is demonstrated. The hybrid system starts with a
custom-designed CMOS (complementary metal-oxide semiconductor) chip fabricated
in a semiconductor foundry using standard integration circuit technology. A
microfluidic channel... | biology |
5,552 | Heterogeneous Cell Population Dynamics: Equation-Free Uncertainty Quantification Computations | q-bio.QM | We propose a computational approach to modeling the collective dynamics of
populations of coupled heterogeneous biological oscillators. In contrast to
Monte Carlo simulation, this approach utilizes generalized Polynomial Chaos
(gPC) to represent random properties of the population, thus reducing the
dynamics of ensembl... | biology |
5,553 | Effective Sample Size: Quick Estimation of the Effect of Related Samples in Genetic Case-Control Association Analyses | q-bio.QM | Affected relatives are essential for pedigree linkage analysis, however, they
cause a violation of the independent sample assumption in case-control
association studies. To avoid the correlation between samples, a common
practice is to take only one affected sample per pedigree in association
analysis. Although several... | biology |
5,554 | Effects of Selection Logging on Rainforest Productivity | q-bio.QM | An analysis of data from 212 permanent sample plots provided no evidence of
any decline in rainforest productivity after three cycles of selection logging
in the tropical rainforests of north Queensland. Relative productivity was
determined as the difference between observed diameter increments and
increments predicted... | biology |
5,555 | A complete classification of epistatic two-locus models | q-bio.QM | The study of epistasis is of great importance in statistical genetics in
fields such as linkage and association analysis and QTL mapping. In an effort
to classify the types of epistasis in the case of two biallelic loci Li and
Reich listed and described all models in the simplest case of 0/1 penetrance
values. However,... | biology |
5,556 | Genetic code on the dyadic plane | q-bio.QM | We introduce the simple parametrization for the space of codons (triples of
nucleotides) by 8\times 8 table. This table (which we call the dyadic plane)
possesses the natural 2-adic ultrametric. We show that after this
parametrization the genetic code will be a locally constant map of the simple
form. The local constan... | biology |
5,557 | Epitope prediction improved by multitask support vector machines | q-bio.QM | Motivation: In silico methods for the prediction of antigenic peptides
binding to MHC class I molecules play an increasingly important role in the
identification of T-cell epitopes. Statistical and machine learning methods, in
particular, are widely used to score candidate epitopes based on their
similarity with known ... | biology |
5,558 | Coincident Frequencies and Relative Phases Among Female-Brain Signals and Progesterone-Estrogen levels | q-bio.QM | Fourier transform has become a basic tool for analyzing biological signals
1,2,3. Mostly a fast Fourier transform is computed for a finite sequence of
data sample 4. This is the standard way apparatuses and modern computerized
technology provide information, according with their frequency range, of the
well known brain... | biology |
5,559 | On the relationships between kinetic schemes and two-state single molecule trajectories | q-bio.QM | Trajectories of a signal that fluctuates between two states which originate
from single molecule activities have become ubiquitous. Common examples are
trajectories of ionic flux through individual membrane-channels, and of photon
counts collected from diffusion, activity, and conformational changes of
biopolymers. By ... | biology |
5,560 | Multifractal analysis of normal RR heart-interbeat signals in power spectra ranges | q-bio.QM | Power spectral density is an accepted measure of heart rate variability. Two
estimators of multifractal properties: Wavelet Transform Modulus Maxima and
Multifractal Detrended Fluctuation Analysis are used to investigate
multifractal properties for the three strongly physiologically grounded
components of power spectra... | biology |
5,561 | Symbolic Reachability Analysis of Genetic Regulatory Networks using Qualitative Abstractions | q-bio.QM | The switch-like character of gene regulation has motivated the use of hybrid,
discrete-continuous models of genetic regulatory networks. While powerful
techniques for the analysis, verification, and control of hybrid systems have
been developed, the specificities of the biological application domain pose a
number of ch... | biology |
5,562 | Utilizing the information content in two-state trajectories | q-bio.QM | The signal from many single molecule experiments monitoring molecular
processes, such as enzyme turnover via fluorescence and opening and closing of
ion channel via the flux of ions, consists of a time series of stochastic on
and off (or open and closed) periods, termed a two-state trajectory. This
signal reflects the ... | biology |
5,563 | Extracting falsifiable predictions from sloppy models | q-bio.QM | Successful predictions are among the most compelling validations of any
model. Extracting falsifiable predictions from nonlinear multiparameter models
is complicated by the fact that such models are commonly sloppy, possessing
sensitivities to different parameter combinations that range over many decades.
Here we discu... | biology |
5,564 | Converting genetic network oscillations into somite spatial pattern | q-bio.QM | In most vertebrate species, the body axis is generated by the formation of
repeated transient structures called somites. This spatial periodicity in
somitogenesis has been related to the temporally sustained oscillations in
certain mRNAs and their associated gene products in the cells forming the
presomatic mesoderm. T... | biology |
5,565 | Theoretical Analysis of Subthreshold Oscillatory Behaviors in Nonlinear Autonomous Systems | q-bio.QM | We have developed a linearization method to investigate the subthreshold
oscillatory behaviors in nonlinear autonomous systems. By considering firstly
the neuronal system as an example, we show that this theoretical approach can
predict quantitatively the subthreshold oscillatory activities, including the
damping coeff... | biology |
5,566 | Detection of Aneuploidy with Digital PCR | q-bio.QM | The widespread use of genetic testing in high risk pregnancies has created
strong interest in rapid and accurate molecular diagnostics for common
chromosomal aneuploidies. We show here that digital polymerase chain reaction
(dPCR) can be used for accurate measurement of trisomy 21 (Down's Syndrome),
the most common hum... | biology |
5,567 | Visual Data Mining of Genomic Databases by Immersive Graph-Based Exploration | q-bio.QM | Biologists are leading current research on genome characterization
(sequencing, alignment, transcription), providing a huge quantity of raw data
about many genome organisms. Extracting knowledge from this raw data is an
important process for biologists, using usually data mining approaches.
However, it is difficult to ... | biology |
5,568 | A passivity-based stability criterion for a class of interconnected systems and applications to biochemical reaction networks | q-bio.QM | This paper presents a stability test for a class of interconnected nonlinear
systems motivated by biochemical reaction networks. One of the main results
determines global asymptotic stability of the network from the diagonal
stability of a "dissipativity matrix" which incorporates information about the
passivity proper... | biology |
5,569 | Analytic steady-state space use patterns and rapid computations in mechanistic home range analysis | q-bio.QM | Mechanistic home range models are important tools in modeling animal dynamics
in spatially-complex environments. We introduce a class of stochastic models
for animal movement in a habitat of varying preference. Such models interpolate
between spatially-implicit resource selection analysis (RSA) and
advection-diffusion ... | biology |
5,570 | DIA-MCIS. An Importance Sampling Network Randomizer for Network Motif Discovery and Other Topological Observables in Transcription Networks | q-bio.QM | Transcription networks, and other directed networks can be characterized by
some topological observables such as for example subgraph occurrence (network
motifs). In order to perform such kind of analysis, it is necessary to be able
to generate suitable randomized network ensembles. Typically, one considers
null networ... | biology |
5,571 | Spectral plots and the representation and interpretation of biological data | q-bio.QM | It is basic question in biology and other fields to identify the char-
acteristic properties that on one hand are shared by structures from a
particular realm, like gene regulation, protein-protein interaction or neu- ral
networks or foodwebs, and that on the other hand distinguish them from other
structures. We introd... | biology |
5,572 | Attenuation Regulation as a Term Rewriting System | q-bio.QM | The classical attenuation regulation of gene expression in bacteria is
considered. We propose to represent the secondary RNA structure in the leader
region of a gene or an operon by a term, and we give a probabilistic term
rewriting system modeling the whole process of such a regulation. | biology |
5,573 | Persistence of direction increases the drift velocity of run and tumble chemotaxis | q-bio.QM | Escherichia coli is a motile bacterium that moves up a chemoattractant
gradient by performing a biased random walk composed of alternating runs and
tumbles. Previous models of run and tumble chemotaxis neglect one or more
features of the motion, namely (i) a cell cannot directly detect a
chemoattractant gradient but ra... | biology |
5,574 | Eutacticity in sea urchin evolution | q-bio.QM | An eutactic star, in a n-dimensional space, is a set of N vectors which can
be viewed as the projection of N orthogonal vectors in a N-dimensional space.
By adequately associating a star of vectors to a particular sea urchin we
propose that a measure of the eutacticity of the star constitutes a measure of
the regularit... | biology |
5,575 | A First Exposure to Statistical Mechanics for Life Scientists | q-bio.QM | Statistical mechanics is one of the most powerful and elegant tools in the
quantitative sciences. One key virtue of statistical mechanics is that it is
designed to examine large systems with many interacting degrees of freedom,
providing a clue that it might have some bearing on the analysis of the
molecules of living ... | biology |
5,576 | THEA: ontology-driven analysis of microarray data | q-bio.QM | MOTIVATION: Microarray technology makes it possible to measure thousands of
variables and to compare their values under hundreds of conditions. Once
microarray data are quantified, normalized and classified, the analysis phase
is essentially a manual and subjective task based on visual inspection of
classes in the ligh... | biology |
5,577 | Parameter Estimation in Biokinetic Degradation Models in Wastewater Treatment - A Novel Approach Relevant for Micro-pollutant Removal | q-bio.QM | In this paper we address a general parameter estimation methodology for an
extended biokinetic degradation model [1] for poorly degradable
micropollutants. In particular we concentrate on parameter estimation of the
micropollutant degradation sub-model by specialised microorganisms. In this
case we focus on the case wh... | biology |
5,578 | Kernel methods for in silico chemogenomics | q-bio.QM | Predicting interactions between small molecules and proteins is a crucial
ingredient of the drug discovery process. In particular, accurate predictive
models are increasingly used to preselect potential lead compounds from large
molecule databases, or to screen for side-effects. While classical in silico
approaches foc... | biology |
5,579 | Probabilistic annotation of protein sequences based on functional classifications | q-bio.QM | BACKGROUND: One of the most evident achievements of bioinformatics is the
development of methods that transfer biological knowledge from characterised
proteins to uncharacterised sequences. This mode of protein function assignment
is mostly based on the detection of sequence similarity and the premise that
functional p... | biology |
5,580 | Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments | q-bio.QM | In many biochemical processes, proteins bound to DNA at distant sites are
brought into close proximity by loops in the underlying DNA. For example, the
function of some gene-regulatory proteins depends on such DNA looping
interactions. We present a new technique for characterizing the kinetics of
loop formation in vitr... | biology |
5,581 | Geometric Aspects of Biological Sequence Comparison | q-bio.QM | We propose a general framework for converting global and local similarities
between biological sequences to quasi-metrics. In contrast to previous works,
our formulation allows asymmetric distances, originating from uneven weighting
of strings, that may induce non-trivial partial orders on sets of biosequences.
Further... | biology |
5,582 | Identification of specificity determining residues in enzymes using environment specific substitution tables | q-bio.QM | Environment specific substitution tables have been used effectively for
distinguishing structural and functional constraints on proteins and thereby
identify their active sites (Chelliah et al. (2004)). This work explores
whether a similar approach can be used to identify specificity determining
residues (SDRs) respons... | biology |
5,583 | A mathematical model quantifies proliferation and motility effects of TGF--$β$ on cancer cells | q-bio.QM | Transforming growth factor (TGF) $\beta$ is known to have properties of both
a tumor suppressor and a tumor promoter. While it inhibits cell proliferation,
it also increases cell motility and decreases cell--cell adhesion. Coupling
mathematical modeling and experiments, we investigate the growth and motility
of oncogen... | biology |
5,584 | CLePAPS: Fast Pair Alignment of Protein Structures Based on Conformational Letters | q-bio.QM | Fast, efficient and reliable algorithms for pairwise alignment of protein
structures are in ever increasing demand for analyzing the rapidly growing data
of protein structures. CLePAPS is a tool developed for this purpose. It
distinguishes itself from other existing algorithms by the use of
conformational letters, whic... | biology |
5,585 | Inherent flexibility and protein function: the open/closed conformational transition of the N-terminal domain of calmodulin | q-bio.QM | The key to understanding a protein's function often lies in its
conformational dynamics. We develop a coarse-grained variational model to
investigate the interplay between structural transitions, conformational
flexibility and function of N-terminal calmodulin (nCaM) domain. In this model,
two energy basins correspondi... | biology |
5,586 | Dependence of nucleotide physical properties on their placement in codons and determinative degree | q-bio.QM | Various physical properties such as dipole moment, heat of formation and
energy of the most stable formation of nucleotides and bases were calculated by
PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1
(Austin model 1) methods. As distinct from previous calculations, for
nucleotides the in... | biology |
5,587 | Towards Structural Classification of Proteins based on Contact Map Overlap | q-bio.QM | A multitude of measures have been proposed to quantify the similarity between
protein 3-D structure. Among these measures, contact map overlap (CMO)
maximization deserved sustained attention during past decade because it offers
a fine estimation of the natural homology relation between proteins. Despite
this large invo... | biology |
5,588 | Network reconstruction based on quasi-steady state data | q-bio.QM | This note discusses a theoretical issue regarding the application of the
"Modular Response Analysis" method to quasi-steady state (rather than
steady-state) data. | biology |
5,589 | The effect of time distribution shape on simulated epidemic models | q-bio.QM | By convention, and even more often, as an unintentional consequence of
design, time distributions of latency and infectious durations in stochastic
epidemic simulations are often exponential. The skewed distribtion typically
leads to unrealistically short times. We examine the effects of altering the
distribution laten... | biology |
5,590 | Cross-Scale Sensitivity Analysis of a Non-Small Cell Lung Cancer Model: Linking Molecular Signaling Properties to Cellular Behavior | q-bio.QM | Sensitivity analysis is an effective tool for systematically identifying
specific perturbations in parameters that have significant effects on the
behavior of a given biosystem, at the scale investigated. In this work, using a
two-dimensional, multiscale non-small cell lung cancer (NSCLC) model, we
examine the effects ... | biology |
5,591 | On fitting power laws to ecological data | q-bio.QM | Heavy-tailed or power-law distributions are becoming increasingly common in
biological literature. A wide range of biological data has been fitted to
distributions with heavy tails. Many of these studies use simple fitting
methods to find the parameters in the distribution, which can give highly
misleading results. The... | biology |
5,592 | Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach | q-bio.QM | Despite recent molecular technique improvements, biological knowledge remains
incomplete. Reasoning on living systems hence implies to integrate
heterogeneous and partial informations. Although current investigations
successfully focus on qualitative behaviors of macromolecular networks, others
approaches show partial ... | biology |
5,593 | Offdiagonal complexity: A computationally quick network complexity measure. Application to protein networks and cell division | q-bio.QM | Many complex biological, social, and economical networks show topologies
drastically differing from random graphs. But, what is a complex network, i.e.\
how can one quantify the complexity of a graph? Here the Offdiagonal Complexity
(OdC), a new, and computationally cheap, measure of complexity is defined,
based on the... | biology |
5,594 | Rediscovering the power of pairwise interactions | q-bio.QM | Two recent streams of work suggest that pairwise interactions may be
sufficient to capture the complexity of biological systems ranging from protein
structure to networks of neurons. In one approach, possible amino acid
sequences in a family of proteins are generated by Monte Carlo annealing of a
"Hamiltonian" that for... | biology |
5,595 | Computing knock out strategies in metabolic networks | q-bio.QM | Given a metabolic network in terms of its metabolites and reactions, our goal
is to efficiently compute the minimal knock out sets of reactions required to
block a given behaviour. We describe an algorithm which improves the
computation of these knock out sets when the elementary modes (minimal
functional subsystems) o... | biology |
5,596 | Analysis of a Gibbs sampler method for model based clustering of gene expression data | q-bio.QM | Over the last decade, a large variety of clustering algorithms have been
developed to detect coregulatory relationships among genes from microarray gene
expression data. Model based clustering approaches have emerged as
statistically well grounded methods, but the properties of these algorithms
when applied to large-sc... | biology |
5,597 | Virtual screening of GPCRs: an in silico chemogenomics approach | q-bio.QM | The G-protein coupled receptor (GPCR) superfamily is currently the largest
class of therapeutic targets. \textit{In silico} prediction of interactions
between GPCRs and small molecules is therefore a crucial step in the drug
discovery process, which remains a daunting task due to the difficulty to
characterize the 3D s... | biology |
5,598 | Transition from 12 to near-24 hours glucose circadian rhythm on relaxation of a hyperglycemic condition | q-bio.QM | A composite, exponential relaxation function, modulated by a periodic
component, was used to fit to an experimental time series of blood glucose
levels. The 11 parameters function that allows for the detection of a possible
rhythm transition was fitted to the experimental time series using a genetic
algorithm. It has b... | biology |
5,599 | Toolbox for analyzing finite two-state trajectories | q-bio.QM | In many experiments, the aim is to deduce an underlying multi-substate on-off
kinetic scheme (KS) from the statistical properties of a two-state trajectory.
However, the mapping of a KS into a two-state trajectory leads to the loss of
information about the KS, and so, in many cases, more than one KS can be
associated w... | biology |
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