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5,000 | Human housekeeping genes are compact | q-bio.GN | We identify a set of 575 human genes that are expressed in all conditions
tested in a publicly available database of microarray results. Based on this
common occurrence, the set is expected to be rich in "housekeeping" genes,
showing constitutive expression in all tissues. We compare selected aspects of
their genomic s... | biology |
5,001 | A covariance kernel for proteins | q-bio.GN | We propose a new kernel for biological sequences which borrows ideas and
techniques from information theory and data compression. This kernel can be
used in combination with any kernel method, in particular Support Vector
Machines for protein classification. By incorporating prior biological
assumptions on the properti... | biology |
5,002 | Random model for RNA interference yields scale free network | q-bio.GN | We introduce a random bit-string model of post-transcriptional genetic
regulation based on sequence matching. The model spontaneously yields a scale
free network with power law scaling with $ \gamma=-1$ and also exhibits
log-periodic behaviour. The in-degree distribution is much narrower, and
exhibits a pronounced peak... | biology |
5,003 | Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs | q-bio.GN | BACKGROUND: Transcriptional regulation is a key mechanism in the functioning
of the cell, and is mostly effected through transcription factors binding to
specific recognition motifs located upstream of the coding region of the
regulated gene. The computational identification of such motifs is made easier
by the fact th... | biology |
5,004 | MAVID: Constrained ancestral alignment of multiple sequences | q-bio.GN | We describe a new global multiple alignment program capable of aligning a
large number of genomic regions. Our progressive alignment approach
incorporates the following ideas: maximum-likelihood inference of ancestral
sequences, automatic guide-tree construction, protein based anchoring of
ab-initio gene predictions, a... | biology |
5,005 | Relevance Vector Machines for classifying points and regions in biological sequences | q-bio.GN | The Relevance Vector Machine (RVM) is a recently developed machine learning
framework capable of building simple models from large sets of candidate
features. Here, we describe a protocol for using the RVM to explore very large
numbers of candidate features, and a family of models which apply the power of
the RVM to cl... | biology |
5,006 | What can we learn from noncoding regions of similarity between genomes? | q-bio.GN | Background: In addition to known protein-coding genes, large amount of
apparently non-coding sequence are conserved between the human and mouse
genomes. It seems reasonable to assume that these conserved regions are more
likely to contain functional elements than less-conserved portions of the
genome. Here we used a mo... | biology |
5,007 | Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments | q-bio.GN | This paper studies sequencing and mapping methods that rely solely on pooling
and shotgun sequencing of clones. First, we scrutinize and improve the recently
proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a
BAC-linked assembly of a whole genome sequence. Secondly, we introduce a novel
phy... | biology |
5,008 | Genetic Paralog Analysis and Simulations | q-bio.GN | Using Monte Carlo methods, we simulated the effects of bias in generation and
elimination of paralogs on the size distribution of paralog groups. It was
found that the function describing the decay of the number of paralog groups
with their size depends on the ratio between the probability of duplications of
genes and ... | biology |
5,009 | RNA Binding Density on X-chromosome Differing from that on 22 Autosomes in Human | q-bio.GN | To test whether X-chromosome has unique genomic characteristics, X-chromosome
and 22 autosomes were compared for RNA binding density. Nucleotide sequences on
the chromosomes were divided into 50kb per segment that was recoded as a set of
frequency values of 7-nucleotide (7nt) strings using all possible 7nt strings
(47=... | biology |
5,010 | Solution of the Quasispecies Model for an Arbitrary Gene Network | q-bio.GN | In this paper, we study the equilibrium behavior of Eigen's quasispecies
equations for an arbitrary gene network. We consider a genome consisting of $ N
$ genes, so that each gene sequence $ \sigma $ may be written as $ \sigma =
\sigma_1 \sigma_2 ... \sigma_N $. We assume a single fitness peak (SFP) model
for each gene... | biology |
5,011 | A Machine Learning Strategy to Identity Exonic Splice Enhancers in Human Protein-coding Sequence | q-bio.GN | Background: Exonic splice enhancers are sequences embedded within exons which
promote and regulate the splicing of the transcript in which they are located.
A class of exonic splice enhancers are the SR proteins, which are thought to
mediate interactions between splicing factors bound to the 5' and 3' splice
sites. Met... | biology |
5,012 | Statistical analysis of the distribution of amino acids in Borrelia burgdorferi genome under different genetic codes | q-bio.GN | The genetic code is considered to be universal. In order to test if some
statistical properties of the coding bacterial genome were due to inherent
properties of the genetic code, we compared the autocorrelation function, the
scaling properties and the maximum entropy of the distribution of distances of
amino acids in ... | biology |
5,013 | Statistical analysis of Gene and Intergenic DNA Sequences | q-bio.GN | Much of the on-going statistical analysis of DNA sequences is focused on the
estimation of characteristics of coding and non-coding regions that would
possibly allow discrimination of these regions. In the current approach, we
concentrate specifically on genes and intergenic regions. To estimate the level
and type of c... | biology |
5,014 | Statistical properties of DNA sequences revisited: the role of inverse bilateral symmetry in bacterial chromosomes | q-bio.GN | Herein it is shown that in order to study the statistical properties of DNA
sequences in bacterial chromosomes it suffices to consider only one half of the
chromosome because they are similar to its corresponding complementary sequence
in the other half. This is due to the inverse bilateral symmetry of bacterial
chromo... | biology |
5,015 | Monte Carlo Simulation and Statistical Analysis of Genetic Information Coding | q-bio.GN | The rules that specify how the information contained in DNA codes amino
acids, is called "the genetic code". Using a simplified version of the Penna
nodel, we are using computer simulations to investigate the importance of the
genetic code and the number of amino acids in Nature on population dynamics. We
find that the... | biology |
5,016 | SUMO Substrates and Sites Prediction Combining Pattern Recognition and Phylogenetic Conservation | q-bio.GN | Small Ubiquitin-related modifier (SUMO) proteins are widely expressed in
eukaryotic cells, which are reversibly coupled to their substrates by motif
recognition, called sumoylation. Two interesting questions are 1) how many
potential SUMO substrates may be included in mammalian proteomes, such as human
and mouse, 2) an... | biology |
5,017 | Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models | q-bio.GN | With the sponsorship of ``Fundacio La Caixa'' we met in Barcelona, November
21st and 22nd, to analyze the reasons why, after the completion of the human
genome sequence, the identification all protein coding genes and their variants
remains a distant goal. Here we report on our discussions and summarize some of
the maj... | biology |
5,018 | Gene splice sites correlate with nucleosome positions | q-bio.GN | Gene sequences in the vicinity of splice sites are found to possess
dinucleotide periodicities, especially RR and YY, with the period close to the
pitch of nucleosome DNA. This confirms previously reported finding about
preferential positioning of splice junctions within the nucleosomes. The RR and
YY dinucleotides osc... | biology |
5,019 | Systematic identification of abundant A-to-I editing sites in the human transcriptome | q-bio.GN | RNA editing by members of the double-stranded RNA-specific ADAR family leads
to site-specific conversion of adenosine to inosine (A-to-I) in precursor
messenger RNAs. Editing by ADARs is believed to occur in all metazoa, and is
essential for mammalian development. Currently, only a limited number of human
ADAR substrat... | biology |
5,020 | Divergence and Shannon information in genomes | q-bio.GN | Shannon information (SI) and its special case, divergence, are defined for a
DNA sequence in terms of probabilities of chemical words in the sequence and
are computed for a set of complete genomes highly diverse in length and
composition. We find the following: SI (but not divergence) is inversely
proportional to seque... | biology |
5,021 | Is abundant A-to-I RNA editing primate-specific? | q-bio.GN | A-To-I RNA editing is common to all eukaryotes, associated with various
neurological functions. Recently, A-to-I editing was found to occur abundantly
in the human transcriptome. Here we show that the frequency of A-to-I editing
in humans is at least an order of magnitude higher as that of mouse, rat,
chicken or fly. T... | biology |
5,022 | A New Simulated Annealing Algorithm for the Multiple Sequence Alignment Problem: The approach of Polymers in a Random Media | q-bio.GN | We proposed a probabilistic algorithm to solve the Multiple Sequence
Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits
the representation of the Multiple Alignment between $D$ sequences as a
directed polymer in $D$ dimensions. Within this representation we can easily
track the evolution in th... | biology |
5,023 | Identification and Measurement of Neighbor Dependent Nucleotide Substitution Processes | q-bio.GN | The presence of neighbor dependencies generated a specific pattern of
dinucleotide frequencies in all organisms. Especially, the
CpG-methylation-deamination process is the predominant substitution process in
vertebrates and needs to be incorporated into a more realistic model for
nucleotide substitutions. Based on a ge... | biology |
5,024 | Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density and telomere-specific effects | q-bio.GN | This study presents the first global, 1 Mbp level analysis of patterns of
nucleotide substitutions along the human lineage. The study is based on the
analysis of a large amount of repetitive elements deposited into the human
genome since the mammalian radiation, yielding a number of results that would
have been difficu... | biology |
5,025 | Molecular Phylogenetic Analyses and Real Life Data | q-bio.GN | In molecular phylogeny, relationships among organisms are reconstructed using
DNA or protein sequences and are displayed as trees. A linear increase in the
number of sequences results in an exponential increase of possible trees. Thus,
inferring trees from molecular data was shown to be NP-hard. This causes
problems, i... | biology |
5,026 | Global divergence of microbial genome sequences mediated by propagating fronts | q-bio.GN | We model the competition between recombination and point mutation in
microbial genomes, and present evidence for two distinct phases, one uniform,
the other genetically diverse. Depending on the specifics of homologous
recombination, we find that global sequence divergence can be mediated by
fronts propagating along th... | biology |
5,027 | Statistical analysis of simple repeats in the human genome | q-bio.GN | The human genome contains repetitive DNA at different level of sequence
length, number and dispersion. Highly repetitive DNA is particularly rich in
homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of
families of interspersed, mobile elements hundreds of base pairs (bp) long,
among which the Alu f... | biology |
5,028 | Evolutionarily conserved human targets of adenosine to inosine RNA editing | q-bio.GN | A-to-I RNA editing by ADARs is a post-transcriptional mechanism for expanding
the proteomic repertoire. Genetic recoding by editing was so far observed for
only a few mammalian RNAs that are predominantly expressed in nervous tissues.
However, as these editing targets fail to explain the broad and severe
phenotypes of ... | biology |
5,029 | Mimivirus Gene Promoters Exhibit an Unprecedented Conservation among all Eukaryotes | q-bio.GN | The initial analysis of the recently sequenced genome of Acanthamoeba
polyphaga Mimivirus, the largest known double-stranded DNA virus, predicted a
proteome of size and complexity more akin to small parasitic bacteria than to
other nucleo-cytoplasmic large DNA viruses, and identified numerous functions
never before des... | biology |
5,030 | Ab initio identification of putative human transcription factor binding sites by comparative genomics | q-bio.GN | We discuss a simple and powerful approach for the ab initio identification of
cis-regulatory motifs involved in transcriptional regulation. The method we
present integrates several elements: human-mouse comparison, statistical
analysis of genomic sequences and the concept of coregulation. We apply it to a
complete scan... | biology |
5,031 | On the Complexity of Several Haplotyping Problems | q-bio.GN | In this paper we present a collection of results pertaining to haplotyping.
The first set of results concerns the combinatorial problem of reconstructing
haplotypes from incomplete and/or imperfectly sequenced haplotype data. More
specifically, we show that an interesting, restricted case of Minimum Error
Correction (M... | biology |
5,032 | Gene & Genome Duplication in Acanthamoeba Polyphaga Mimivirus | q-bio.GN | Gene duplication is key to molecular evolution in all three domains of life
and may be the first step in the emergence of new gene function. It is a well
recognized feature in large DNA viruses, but has not been studied extensively
in the largest known virus to date, the recently discovered Acanthamoeba
Polyphaga Mimiv... | biology |
5,033 | Identity Elements of Archaeal tRNA | q-bio.GN | Features unique to a transfer-RNA are recognized by the corresponding
tRNA-synthetase. Keeping this in view we isolate the discriminating features of
all archaeal tRNA. These are our identity elements. Further, we investigate
tRNA-characteristics that delineate the different orders of archaea. | biology |
5,034 | Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome | q-bio.GN | Background: Recent studies in a growing number of organisms have yielded
accumulating evidence that a significant portion of the non-coding region in
the genome is transcribed. We address this issue in the yeast Saccharomyces
cerevisiae.
Results: Taking into account the absence of a significantly large yeast EST
data... | biology |
5,035 | Is there any sense in antisense editing? | q-bio.GN | A number of recent studies have hypothesized that sense-antisense RNA
transcript pairs create dsRNA duplexes that undergo extensive A-to-I RNA
editing. Here we studied human and mouse genomic antisense regions, and found
that the editing level in these areas is negligible. This observation puts in
question the scope of... | biology |
5,036 | Introns Restructure tRNA Genes of Archaea | q-bio.GN | This paper has been withdrawn by the author. | biology |
5,037 | Conspiracy in bacterial genomes | q-bio.GN | The rank ordered distribution of the codon usage frequencies for 123
bacteriae is best fitted by a three parameters function that is the sum of a
constant, an exponential and a linear term in the rank n. The parameters depend
(two parabolically) from the total GC content. The rank ordered distribution of
the amino acid... | biology |
5,038 | Positioning Crenarchaeal tRNA-Introns | q-bio.GN | We precisely position a noncanonical intron in the odd second copy of
tRNAAsp(GTC) gene in the newly sequenced crenarchaea S.acidocaldarius. The
uniform assortment of some features from normal aspartate tDNA and some from
those corresponding to non-standard amino acids conduce us to conjecture it to
be a novel tRNA gen... | biology |
5,039 | Universality of Long-Range Correlations in Expansion-Randomization Systems | q-bio.GN | We study the stochastic dynamics of sequences evolving by single site
mutations, segmental duplications, deletions, and random insertions. These
processes are relevant for the evolution of genomic DNA. They define a
universality class of non-equilibrium 1D expansion-randomization systems with
generic stationary long-ra... | biology |
5,040 | Domesticated P elements in the Drosophila montium species subgroup have a new function related to a DNA binding property | q-bio.GN | Molecular domestication of a transposable element is defined as its
functional recruitment by the host genome. To date, two independent events of
molecular domestication of the P transposable element have been described: in
the Drosophila obscura species group and in the Drosophila montium species
subgroup. These P neo... | biology |
5,041 | Statistical Indicators of Collective Behavior and Functional Clusters in Gene Networks of Yeast | q-bio.GN | We analyze gene expression time-series data of yeast S. cerevisiae measured
along two full cell-cycles. We quantify these data by using q-exponentials,
gene expression ranking and a temporal mean-variance analysis. We construct
gene interaction networks based on correlation coefficients and study the
formation of the c... | biology |
5,042 | The protein map of Synechococcus sp. PCC 7942 - the first overlook | q-bio.GN | The unicellular cyanobacterium Synechococcus PCC 7942 has been used as a
model organism for studies of prokaryotic circadian rhythms,
carbon-concentrating mechanisms, response to a variety of nutrient and
environmental stresses, and cell division. This paper presents the results of
the first proteomic exploratory study... | biology |
5,043 | Non-extensive Trends in the Size Distribution of Coding and Non-coding DNA Sequences in the Human Genome | q-bio.GN | We study the primary DNA structure of four of the most completely sequenced
human chromosomes (including chromosome 19 which is the most dense in coding),
using Non-extensive Statistics. We show that the exponents governing the decay
of the coding size distributions vary between $5.2 \le r \le 5.7$ for the short
scales... | biology |
5,044 | tRNA-isoleucine-tryptophan Composite Gene | q-bio.GN | Transfer-RNA genes in archaea often have introns intervening between exon
sequences. The structural motif at the boundary between exon and intron is the
bulge-helix-bulge. Computational investigations of these boundary structures in
H. marismortui lead us to propose that tRNA-isoleucine and tRNA-tryptophan
genes are co... | biology |
5,045 | Quantitative modeling and data analysis of SELEX experiments | q-bio.GN | SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is an
experimental procedure that allows extracting, from an initially random pool of
DNA, those oligomers with high affinity for a given DNA-binding protein. We
address what is a suitable experimental and computational procedure to infer
parameters of t... | biology |
5,046 | Cloning, expression and purification of the general stress protein Yhbo from Escherichia coli | q-bio.GN | We cloned, expressed and purified the Escherichia coli yhbO gene product,
which is homolog to the Bacillus subtilis general stress protein 18 (the yfkM
gene product), the Pyrococcus furiosus intracellular protease PfpI, and the
human Parkinson disease protein DJ-1. The gene coding for YhbO was generated by
amplifying t... | biology |
5,047 | Regularization Strategies for Hyperplane Classifiers: Application to Cancer Classification with Gene Expression Data | q-bio.GN | Linear discrimination, from the point of view of numerical linear algebra,
can be treated as solving an ill-posed system of linear equations. In order to
generate a solution that is robust in the presence of noise, these problems
require regularization. Here, we examine the ill-posedness involved in the
linear discrimi... | biology |
5,048 | Qualitative Assessment of Gene Expression in Affymetrix Genechip Arrays | q-bio.GN | Affymetrix Genechip microarrays are used widely to determine the simultaneous
expression of genes in a given biological paradigm. Probes on the Genechip
array are atomic entities which by definition are randomly distributed across
the array and in turn govern the gene expression. In the present study, we make
several i... | biology |
5,049 | Effects of Growth on Dinitrogen on the Transcriptome and Predicted Proteome of Nostoc PCC 7120 | q-bio.GN | Upon growth on dinitrogen, the filamentous cyanobacterium Nostoc PCC 7120
initiates metabolic and morphological changes. We analyzed the expression of
1249 genes from major metabolic categories under nitrogen fixing and
non-nitrogen fixing growth. The expression data were correlated with potential
target secondary stru... | biology |
5,050 | Microarray Data Management. An Enterprise Information Approach: Implementations and Challenges | q-bio.GN | The extraction of information form high-throughput experiments is a key
aspect of modern biology. Early in the development of microarray technology,
researchers recognized that the size of the datasets and the limitations of
both computational and visualization techniques restricted their ability to
find the biological... | biology |
5,051 | Gene Function Classification Using Bayesian Models with Hierarchy-Based Priors | q-bio.GN | We investigate the application of hierarchical classification schemes to the
annotation of gene function based on several characteristics of protein
sequences including phylogenic descriptors, sequence based attributes, and
predicted secondary structure. We discuss three Bayesian models and compare
their performance in... | biology |
5,052 | Large-scale Oscillation of Structure-Related DNA Sequence Features in Human Chromosome 21 | q-bio.GN | Human chromosome 21 is the only chromosome in human genome that exhibits
oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near
the right telomere). We aim at establishing the existence of similar
periodicity in structure-related sequence features in order to relate this
(G+C)% oscillation to o... | biology |
5,053 | Modeling gene's length distribution in genomes | q-bio.GN | We show, that the specific distribution of gene's length, which is observed
in natural genomes, might be a result of a growth process, in which a single
length scale $L(t)$ develops that grows with time as $t^{1/3}$. This length
scale could be associated with the length of the longest gene in an evolving
genome. The gr... | biology |
5,054 | Mathematic principles underlying genetic structures | q-bio.GN | Many people are familiar with the physico-chemical properties of gene
sequences. In this paper I present a mathematical perspective: how do
mathematical principles such as information theory, coding theory, and
combinatorics influence the beginnings of life and the formation of the genetic
codes we observe today? What ... | biology |
5,055 | Invertibility of the TKF model of sequence evolution | q-bio.GN | We consider character sequences evolving on a phylogenetic tree under the
TKF91 model. We show that as the sequence lengths tend to infinity the the
topology of the phylogenetic tree and the edge lengths are determined by any
one of (a) the alignment of sequences (b) the collection of sequence lengths.
We also show tha... | biology |
5,056 | Maximum-frequency gene tree: a simplified genome-scale approach to overcoming incongruence in molecular phylogenies | q-bio.GN | Genomes and genes diversify during evolution; however, it is unclear to what
extent genes still retain the relationship among species. Model species for
molecular phylogenetic studies include yeasts and viruses whose genomes were
sequenced as well as plants that have the fossil-supported true phylogenetic
trees availab... | biology |
5,057 | Genome-wide EST data mining approaches to resolving incongruence of molecular phylogenies | q-bio.GN | 36 single genes of six plants inferred 18 unique trees using maximum
parsimony. Such incongruence is an important issue and how to reconstruct the
congruent tree still is one of the most challenges in molecular phylogenetics.
For resolving this problem, a genome-wide EST data mining approach was
systematically investig... | biology |
5,058 | Expression of MHC II genes | q-bio.GN | Innate and adaptive immunity are connected via antigen processing and
presentation (APP), which results in the presentation of antigenic peptides to
T cells in the complex with the major histocompatibility (MHC) determinants.
MHC class II (MHC II) determinants present antigens to CD4+ T cells, which are
the main regula... | biology |
5,059 | Reconsidering the significance of genomic word frequency | q-bio.GN | We propose that the distribution of DNA words in genomic sequences can be
primarily characterized by a double Pareto-lognormal distribution, which
explains lognormal and power-law features found across all known genomes. Such
a distribution may be the result of completely random sequence evolution by
duplication proces... | biology |
5,060 | Cell wall proteins: a new insight through proteomics | q-bio.GN | Cell wall proteins are essential constituents of plant cell walls; they are
involved in modifications of cell wall components, wall structure, signaling
and interactions with plasma membrane proteins at the cell surface. The
application of proteomic approaches to the cell wall compartment raises
important questions: ar... | biology |
5,061 | Evaluation of cell wall preparations for proteomics: a new procedure for purifying cell walls from Arabidopsis hypocotyls | q-bio.GN | The ultimate goal of proteomic analysis of a cell compartment should be the
exhaustive identification of resident proteins; excluding proteins from other
cell compartments. Plant cell walls possess specific difficulties. Several
reported procedures to isolate cell walls for proteomic analyses led to the
isolation of a ... | biology |
5,062 | The riddle of the plant vacuolar sorting receptors | q-bio.GN | Proteins synthesized on membrane-bound ribosomes are sorted at the Golgi
apparatus level for delivery to various cellular destinations: the plasma
membrane or the extracellular space, and the lytic vacuole or lysosome. Sorting
involves the assembly of vesicles, which preferentially package soluble
proteins with a commo... | biology |
5,063 | Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis | q-bio.GN | Common fragile sites (cfs) are specific regions in the human genome that are
particularly prone to genomic instability under conditions of replicative
stress. Several investigations support the view that common fragile sites play
a role in carcinogenesis. We discuss a genome-wide approach based on graph
theory and Gene... | biology |
5,064 | Proteomic nonlinear waves in networks of transcriptional regulators | q-bio.GN | A chain of connected genes with activation-repression links is analysed. It
is shown that for various promoter activity functions (parametrised by Hill
coefficient) the equations describing the concentrations of transcription
factors, are differential-difference KdV-type with perturbations. In the case
of large Hill co... | biology |
5,065 | Networks from gene expression time series: characterization of correlation patterns | q-bio.GN | This paper describes characteristic features of networks reconstructed from
gene expression time series data. Several null models are considered in order
to discriminate between informations embedded in the network that are related
to real data, and features that are due to the method used for network
reconstruction (t... | biology |
5,066 | How much non-coding DNA do eukaryotes require? | q-bio.GN | Despite tremendous advances in the field of genomics, the amount and function
of the large non-coding part of the genome in higher organisms remains poorly
understood. Here we report an observation, made for 37 fully sequenced
eukaryotic genomes, which indicates that eukaryotes require a certain minimum
amount of non-c... | biology |
5,067 | Di-nucleotide Entropy as a Measure of Genomic Sequence Functionality | q-bio.GN | Considering vast amounts of genomic sequences of mostly unknown
functionality, in-silico prediction of functional regions is an important
enterprise. Many genomic browsers employ GC content, which was observed to be
elevated in gene-rich functional regions. This report shows that the entropy of
di- and tri-nucleotides ... | biology |
5,068 | Genetic Variability of Splicing Sites | q-bio.GN | Splicing sites provide unique statistics in human genome due to their large
number and reasonably complete annotation. Analyses of the cumulative SNPs
distribution in splicing sites reveal a few interesting observations. While a
degree of the nucleotide conservation reflects on the SNPs density
monotonically, no detect... | biology |
5,069 | Progress in the definition of a reference human mitochondrial proteome | q-bio.GN | Owing to the complexity of higher eukaryotic cells, a complete proteome is
likely to be very difficult to achieve. However, advantage can be taken of the
cell compartmentalization to build organelle proteomes, which can moreover be
viewed as specialized tools to study specifically the biology and "physiology"
of the ta... | biology |
5,070 | Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis | q-bio.GN | The solubilizing power of various nonionic and zwitterionic detergents as
membrane protein solubilizers for two-dimensional electrophoresis was
investigated. Human red blood cell ghosts and Arabidopsis thaliana leaf
membrane proteins were used as model systems. Efficient detergents could be
found in each class, i.e. wi... | biology |
5,071 | Detergents and Chaotropes for Protein Solubilization before Two-Dimensional Electrophoresis | q-bio.GN | Because of the outstanding separating capabilities of two-dimensional
electrophoresis for complete proteins, it would be advantageous to be able to
apply it to all types of proteins. Unfortunately, severe solubility problems
hamper the analysis of many classes of proteins, but especially membrane
proteins. These proble... | biology |
5,072 | About thiol derivatization and resolution of basic proteins in two-dimensional electrophoresis | q-bio.GN | The influence of thiol blocking on the resolution of basic proteins by
two-dimensional electrophoresis was investigated. Cysteine blocking greatly
increased resolution and decreased streaking, especially in the basic region of
the gels. Two strategies for cysteine blocking were found to be efficient:
classical alkylati... | biology |
5,073 | Alterations of the mitochondrial proteome caused by the absence of mitochondrial DNA: A proteomic view | q-bio.GN | The proper functioning of mitochondria requires that both the mitochondrial
and the nuclear genome are functional. To investigate the importance of the
mitochondrial genome, which encodes only 13 subunits of the respiratory
complexes, the mitochondrial rRNAs and a few tRNAs, we performed a comparative
study on the 143B... | biology |
5,074 | High expression of antioxidant proteins in dendritic cells: possible implications in atherosclerosis | q-bio.GN | Dendritic cells (DCs) display the unique ability to activate naive T cells
and to initiate primary T cell responses revealed in DC-T cell alloreactions.
DCs frequently operate under stress conditions. Oxidative stress enhances the
production of inflammatory cytokines by DCs. We performed a proteomic analysis
to see whi... | biology |
5,075 | Improved mass spectrometry compatibility is afforded by ammoniacal silver staining | q-bio.GN | Sequence coverage in MS analysis of protein digestion-derived peptides is a
key issue for detailed characterization of proteins or identification at low
quantities. In gel-based proteomics studies, the sequence coverage greatly
depends on the protein detection method. It is shown here that ammoniacal
silver detection m... | biology |
5,076 | A versatile electrophoresis system for the analysis of high- and low-molecular-weight proteins | q-bio.GN | A new, versatile, multiphasic buffer system for high-resolution sodium
dodecyl sulfate-polyacrylamide gel electrophoresis of proteins in the relative
molecular weight range of 300 000-3000 Da is described. The system, based on
the theory of multiphasic zone electrophoresis, allows complete stacking and
destacking of pr... | biology |
5,077 | Improvement of the solubilization of proteins in two-dimensional electrophoresis with immobilized pH gradients | q-bio.GN | Membrane and nuclear proteins of poor solubility have been separated by high
resolution two-dimensional (2-D) gel electrophoresis. Isoelectric focusing with
immobilized pH gradients leads to severe quantitative losses of proteins in the
resulting 2-D map, although the resolution is usually high. Protein solubility
coul... | biology |
5,078 | Gene induction during differentiation of human monocytes into dendritic cells: an integrated study at the RNA and protein levels | q-bio.GN | Changes in gene expression occurring during differentiation of human
monocytes into dendritic cells were studied at the RNA and protein levels.
These studies showed the induction of several gene classes corresponding to
various biological functions. These functions encompass antigen processing and
presentation, cytoske... | biology |
5,079 | Linguistic mechanism of the evolution of amino acid frequencies and genomic GC content | q-bio.GN | Much information is stored in amino acid composition of protein and base
composition of DNA. We simulated the evolution of amino acid frequencies and
genomic GC content by a linguistic model. It is showed that the evolution of
genetic code determines the evolution of amino acid frequencies and genomic GC
content. We ex... | biology |
5,080 | Motif Discovery through Predictive Modeling of Gene Regulation | q-bio.GN | We present MEDUSA, an integrative method for learning motif models of
transcription factor binding sites by incorporating promoter sequence and gene
expression data. We use a modern large-margin machine learning approach, based
on boosting, to enable feature selection from the high-dimensional search space
of candidate... | biology |
5,081 | Marker enzyme phenotype ratios in agamospermous sugarbeet progenies as a demonstration of multidimensional encoding of inherited information in plants | q-bio.GN | It has been demonstrated that the observed ratio of phenotypes of marker
enzymes in some sugarbeet plants produced by mitotic agamospermy can be
explained by different degrees of endoreduplication of chromosomes carrying
different alleles of the enzyme loci. In these plants, different patterns of
variability of the enz... | biology |
5,082 | Finding Sequence Features in Tissue-specific Sequences | q-bio.GN | The discovery of motifs underlying gene expression is a challenging one. Some
of these motifs are known transcription factors, but sequence inspection often
provides valuable clues, even discovery of novel motifs with uncharacterized
function in gene expression. Coupled with the complexity underlying
tissue-specific ge... | biology |
5,083 | Bacteria are not Lamarckian | q-bio.GN | Instructive influence of environment on heredity has been a debated topic for
centuries. Darwin's identification of natural selection coupled to chance
variation as the driving force for evolution, against a formal interpretation
proposed by Lamarck, convinced most scientists that environment does not
specifically inst... | biology |
5,084 | Nucleotide Distribution Patterns in Insect Genomes | q-bio.GN | This work analyzed genome-wide nucleotide distribution patterns in ten insect
genomes. Two internal measures were applied: (i) GC variation and (ii) third
codon nucleotide preference. Although the genome size and overall GC level did
not show any correlation with insect order, the internal measures usually
displayed hi... | biology |
5,085 | Ultraconserved Sequences in the Honeybee Genome - Are GC-rich Regions Preferred? | q-bio.GN | Among all insect genomes, honeybee displays one of the most unusual patterns
with interspersed long AT and GC-rich segments. Nearly 75% of the
protein-coding genes are located in the AT-rich segments of the genome, but the
biological significance of the GC-rich regions is not well understood. Based on
an observation th... | biology |
5,086 | Toward a better analysis of secreted proteins: the example of the myeloid cells secretome | q-bio.GN | The analysis of secreted proteins represents a challenge for current
proteomics techniques. Proteins are usually secreted at low concentrations in
the culture media, which makes their recovery difficult. In addition, culture
media are rich in salts and other compounds interfering with most proteomics
techniques, which ... | biology |
5,087 | Noise-filtering features of transcription regulation in the yeast S. cerevisiae | q-bio.GN | Transcription regulation is largely governed by the profile and the dynamics
of transcription factors' binding to DNA. Stochastic effects are intrinsic to
this dynamics and the binding to functional sites must be controled with a
certain specificity for living organisms to be able to elicit specific cellular
responses.... | biology |
5,088 | Mismatch Repair Error Implies Chargaff's Second Parity Rule | q-bio.GN | Chargaff's second parity rule holds empirically for most types of DNA that
along single strands of DNA the base contents are equal for complimentary
bases, A = T, G = C. A Markov chain model is constructed to track the evolution
of any single base position along single strands of genomes whose organisms are
equipped wi... | biology |
5,089 | Chromatin Folding in Relation to Human Genome Function | q-bio.GN | Three-dimensional (3D) chromatin structure is closely related to genome
function, in particular transcription. However, the folding path of the
chromatin fiber in the interphase nucleus is unknown. Here, we systematically
measured the 3D physical distance between pairwise labeled genomic positions in
gene-dense, highly... | biology |
5,090 | Reciprocal best hits are not a logically sufficient condition for orthology | q-bio.GN | It is common to use reciprocal best hits, also known as a boomerang
criterion, for determining orthology between sequences. The best hits may be
found by blast, or by other more recently developed algorithms. Previous work
seems to have assumed that reciprocal best hits is a sufficient but not
necessary condition for o... | biology |
5,091 | Codon Usage Bias Measured Through Entropy Approach | q-bio.GN | Codon usage bias measure is defined through the mutual entropy calculation of
real codon frequency distribution against the quasi-equilibrium one. This
latter is defined in three manners: (1) the frequency of synonymous codons is
supposed to be equal (i.e., the arithmetic mean of their frequencies); (2) it
coincides to... | biology |
5,092 | OrfMapper: A Web-Based Application for Visualizing Gene Clusters on Metabolic Pathway Maps | q-bio.GN | Computational analyses of, e.g., genomic, proteomic, or metabolomic data,
commonly result in one or more sets of candidate genes, proteins, or enzymes.
These sets are often the outcome of clustering algorithms. Subsequently, it has
to be tested if, e.g., the candidate gene-products are members of known
metabolic proces... | biology |
5,093 | Silver staining of proteins in polyacrylamide gels | q-bio.GN | Silver staining is used to detect proteins after electrophoretic separation
on polyacrylamide gels. It combines excellent sensitivity (in the low nanogram
range) with the use of very simple and cheap equipment and chemicals. It is
compatible with downstream processing, such as mass spectrometry analysis after
protein d... | biology |
5,094 | Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions | q-bio.GN | 3' untranslated regions (3' UTRs) contain binding sites for many regulatory
elements, and in particular for microRNAs (miRNAs). The importance of
miRNA-mediated post-transcriptional regulation has become increasingly clear in
the last few years.
We propose two complementary approaches to the statistical analysis of
o... | biology |
5,095 | Global regulation of genome duplication in eukaryotes: an overview from the epifluorescence microscope | q-bio.GN | In eukaryotes, DNA replication is initiated along each chromosome at multiple
sites called replication origins. Locally, each replication origin is
"licensed", or specified, at the end of the M and the beginning of G1 phases of
the cell cycle. During S phase when DNA synthesis takes place, origins are
activated in stag... | biology |
5,096 | Genomes: at the edge of chaos with maximum information capacity | q-bio.GN | We propose an order index, phi, which quantifies the notion of ``life at the
edge of chaos'' when applied to genome sequences. It maps genomes to a number
from 0 (random and of infinite length) to 1 (fully ordered) and applies
regardless of sequence length. The 786 complete genomic sequences in GenBank
were found to ha... | biology |
5,097 | Genome landscapes and bacteriophage codon usage | q-bio.GN | Across all kingdoms of biological life, protein-coding genes exhibit unequal
usage of synonmous codons. Although alternative theories abound, translational
selection has been accepted as an important mechanism that shapes the patterns
of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns
of codo... | biology |
5,098 | CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads | q-bio.GN | A major hindrance to studies of microbial diversity has been that the vast
majority of microbes cannot be cultured in the laboratory and thus are not
amenable to traditional methods of characterization. Environmental shotgun
sequencing (ESS) overcomes this hurdle by sequencing the DNA from the organisms
present in a mi... | biology |
5,099 | Ultrafast coelectrophoretic fluorescent staining of proteins with carbocyanines | q-bio.GN | Protein detection on SDS gels or on 2-D gels must combine several features,
such as sensitivity, homogeneity from one protein to another, speed, low cost,
and user-friendliness. For some applications, it is also interesting to have a
nonfixing stain, so that proteins can be mobilized from the gel for further use
(elect... | biology |
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