27,322 research outputs found
Normalized Information Distance
The normalized information distance is a universal distance measure for
objects of all kinds. It is based on Kolmogorov complexity and thus
uncomputable, but there are ways to utilize it. First, compression algorithms
can be used to approximate the Kolmogorov complexity if the objects have a
string representation. Second, for names and abstract concepts, page count
statistics from the World Wide Web can be used. These practical realizations of
the normalized information distance can then be applied to machine learning
tasks, expecially clustering, to perform feature-free and parameter-free data
mining. This chapter discusses the theoretical foundations of the normalized
information distance and both practical realizations. It presents numerous
examples of successful real-world applications based on these distance
measures, ranging from bioinformatics to music clustering to machine
translation.Comment: 33 pages, 12 figures, pdf, in: Normalized information distance, in:
Information Theory and Statistical Learning, Eds. M. Dehmer, F.
Emmert-Streib, Springer-Verlag, New-York, To appea
Evaluation of points of improvement in NGS data analysis
[EN]DNA sequencing is a fundamental technique in molecular biology that allows the exact sequence of nucleotides in a DNA sample to be read. Over the past decades, DNA sequencing has seen significant advances, evolving from manual and laborious techniques to modern high-throughput techniques. Despite these advances, interpretation and analysis of sequencing data continue to present challenges. Artificial Intelligence (AI), and in particular machine learning, has emerged as an essential tool to address these challenges. The application of AI in the sequencing pipeline refers to the use of algorithms and models to automate, optimize and improve the precision of the sequencing process and its subsequent analysis. The Sanger sequencing method, introduced in the 1970s, was one of the first to be widely used. Although effective, this method is slow and is not suitable for sequencing large amounts of DNA, such as entire genomes. With the arrival of next generation sequencing (NGS) in the 21st century, greater speed and efficiency in obtaining genomic data has been achieved. However, the exponential increase in the amount of data produced has created a bottleneck in its analysis and interpretation
An Introduction to Programming for Bioscientists: A Python-based Primer
Computing has revolutionized the biological sciences over the past several
decades, such that virtually all contemporary research in the biosciences
utilizes computer programs. The computational advances have come on many
fronts, spurred by fundamental developments in hardware, software, and
algorithms. These advances have influenced, and even engendered, a phenomenal
array of bioscience fields, including molecular evolution and bioinformatics;
genome-, proteome-, transcriptome- and metabolome-wide experimental studies;
structural genomics; and atomistic simulations of cellular-scale molecular
assemblies as large as ribosomes and intact viruses. In short, much of
post-genomic biology is increasingly becoming a form of computational biology.
The ability to design and write computer programs is among the most
indispensable skills that a modern researcher can cultivate. Python has become
a popular programming language in the biosciences, largely because (i) its
straightforward semantics and clean syntax make it a readily accessible first
language; (ii) it is expressive and well-suited to object-oriented programming,
as well as other modern paradigms; and (iii) the many available libraries and
third-party toolkits extend the functionality of the core language into
virtually every biological domain (sequence and structure analyses,
phylogenomics, workflow management systems, etc.). This primer offers a basic
introduction to coding, via Python, and it includes concrete examples and
exercises to illustrate the language's usage and capabilities; the main text
culminates with a final project in structural bioinformatics. A suite of
Supplemental Chapters is also provided. Starting with basic concepts, such as
that of a 'variable', the Chapters methodically advance the reader to the point
of writing a graphical user interface to compute the Hamming distance between
two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables,
numerous exercises, and 19 pages of Supporting Information; currently in
press at PLOS Computational Biolog
In-silico-Systemanalyse von Biopathways
Chen M. In silico systems analysis of biopathways. Bielefeld (Germany): Bielefeld University; 2004.In the past decade with the advent of high-throughput technologies, biology has migrated from a descriptive science to a predictive one. A vast amount of information on the metabolism have been produced; a number of specific genetic/metabolic databases and computational systems have been developed, which makes it possible for biologists to perform in silico analysis of metabolism. With experimental data from laboratory, biologists wish to systematically conduct their analysis with an easy-to-use computational system. One major task is to implement molecular information systems that will allow to integrate different molecular database systems, and to design analysis tools (e.g. simulators of complex metabolic reactions). Three key problems are involved: 1) Modeling and simulation of biological processes; 2) Reconstruction of metabolic pathways, leading to predictions about the integrated function of the network; and 3) Comparison of metabolism, providing an important way to reveal the functional relationship between a set of metabolic pathways.
This dissertation addresses these problems of in silico systems analysis of biopathways. We developed a software system to integrate the access to different databases, and exploited the Petri net methodology to model and simulate metabolic networks in cells. It develops a computer modeling and simulation technique based on Petri net methodology; investigates metabolic networks at a system level; proposes a markup language for biological data interchange among diverse biological simulators and Petri net tools; establishes a web-based information retrieval system for metabolic pathway prediction; presents an algorithm for metabolic pathway alignment; recommends a nomenclature of cellular signal transduction; and attempts to standardize the representation of biological pathways.
Hybrid Petri net methodology is exploited to model metabolic networks. Kinetic modeling strategy and Petri net modeling algorithm are applied to perform the processes of elements functioning and model analysis. The proposed methodology can be used for all other metabolic networks or the virtual cell metabolism. Moreover, perspectives of Petri net modeling and simulation of metabolic networks are outlined.
A proposal for the Biology Petri Net Markup Language (BioPNML) is presented. The concepts and terminology of the interchange format, as well as its syntax (which is based on XML) are introduced. BioPNML is designed to provide a starting point for the development of a standard interchange format for Bioinformatics and Petri nets. The language makes it possible to exchange biology Petri net diagrams between all supported hardware platforms and versions. It is also designed to associate Petri net models and other known metabolic simulators.
A web-based metabolic information retrieval system, PathAligner, is developed in order to predict metabolic pathways from rudimentary elements of pathways. It extracts metabolic information from biological databases via the Internet, and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites, etc. The system also provides a navigation platform to investigate metabolic related information, and transforms the output data into XML files for further modeling and simulation of the reconstructed pathway.
An alignment algorithm to compare the similarity between metabolic pathways is presented. A new definition of the metabolic pathway is proposed. The pathway defined as a linear event sequence is practical for our alignment algorithm. The algorithm is based on strip scoring the similarity of 4-hierarchical EC numbers involved in the pathways. The algorithm described has been implemented and is in current use in the context of the PathAligner system.
Furthermore, new methods for the classification and nomenclature of cellular signal transductions are recommended. For each type of characterized signal transduction, a unique ST number is provided. The Signal Transduction Classification Database (STCDB), based on the proposed classification and nomenclature, has been established. By merging the ST numbers with EC numbers, alignments of biopathways are possible.
Finally, a detailed model of urea cycle that includes gene regulatory networks, metabolic pathways and signal transduction is demonstrated by using our approaches. A system biological interpretation of the observed behavior of the urea cycle and its related transcriptomics information is proposed to provide new insights for metabolic engineering and medical care
Hidden Markov Models for Gene Sequence Classification: Classifying the VSG genes in the Trypanosoma brucei Genome
The article presents an application of Hidden Markov Models (HMMs) for
pattern recognition on genome sequences. We apply HMM for identifying genes
encoding the Variant Surface Glycoprotein (VSG) in the genomes of Trypanosoma
brucei (T. brucei) and other African trypanosomes. These are parasitic protozoa
causative agents of sleeping sickness and several diseases in domestic and wild
animals. These parasites have a peculiar strategy to evade the host's immune
system that consists in periodically changing their predominant cellular
surface protein (VSG). The motivation for using patterns recognition methods to
identify these genes, instead of traditional homology based ones, is that the
levels of sequence identity (amino acid and DNA sequence) amongst these genes
is often below of what is considered reliable in these methods. Among pattern
recognition approaches, HMM are particularly suitable to tackle this problem
because they can handle more naturally the determination of gene edges. We
evaluate the performance of the model using different number of states in the
Markov model, as well as several performance metrics. The model is applied
using public genomic data. Our empirical results show that the VSG genes on T.
brucei can be safely identified (high sensitivity and low rate of false
positives) using HMM.Comment: Accepted article in July, 2015 in Pattern Analysis and Applications,
Springer. The article contains 23 pages, 4 figures, 8 tables and 51
reference
Robust Algorithms for Detecting Hidden Structure in Biological Data
Biological data, such as molecular abundance measurements and protein
sequences, harbor complex hidden structure that reflects its underlying
biological mechanisms. For example, high-throughput abundance measurements
provide a snapshot the global state of a living cell, while homologous
protein sequences encode the residue-level logic of the proteins\u27 function
and provide a snapshot of the evolutionary trajectory of the protein family.
In this work I describe algorithmic approaches and analysis software I
developed for uncovering hidden structure in both kinds of data.
Clustering is an unsurpervised machine learning technique commonly used
to map the structure of data collected in high-throughput experiments,
such as quantification of gene expression by DNA microarrays or
short-read sequencing. Clustering algorithms always yield a partitioning
of the data, but relying on a single partitioning solution can lead to
spurious conclusions. In particular, noise in the data can cause objects
to fall into the same cluster by chance rather than due to meaningful
association. In the first part of this thesis I demonstrate approaches to
clustering data robustly in the presence of noise and apply robust clustering
to analyze the transcriptional response to injury in a neuron cell.
In the second part of this thesis I describe identifying hidden specificity
determining residues (SDPs) from alignments of protein sequences descended
through gene duplication from a common ancestor (paralogs) and apply the
approach to identify numerous putative SDPs in bacterial transcription
factors in the LacI family. Finally, I describe and demonstrate a new
algorithm for reconstructing the history of duplications by which paralogs
descended from their common ancestor. This algorithm addresses the
complexity of such reconstruction due to indeterminate or erroneous
homology assignments made by sequence alignment algorithms and to the
vast prevalence of divergence through speciation over divergence through
gene duplication in protein evolution
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