Deep learning approach for predicting functional Z-DNA regions using omics data
Computational methods to predict Z-DNA regions are in high demand to understand the functional role of Z-DNA. The previous state-of-the-art method Z-Hunt is based on statistical mechanical and energy considerations about B- to Z-DNA transition using sequence information. Z-DNA CHiP-seq experiment results showed little overlap with Z-Hunt predictions implying that sequence information only is not sufficient to explain emergence of Z-DNA at different genomic locations. Adding epigenetic and other functional genomic mark-ups to DNA sequence level can help revealing the functional Z-DNA sites. Here we take advantage of the deep learning approach that can analyze and extract information from large volumes of molecular biology data. We developed a machine learning approach DeepZ that aggregates information from genome-wide maps of epigenetic markers, transcription factor and RNA polymerase binding sites, and chromosome accessibility maps. With the developed model we not only verify the experimental Z-DNA predictions, but also generate the whole-genome annotation, introducing new possible Z-DNA regions, which have not yet been found in experiments and can be of interest to the researchers from various fields.
The paper formulates the problem of constructing a broadly applicable and flexible Conceptual Metagrammar (CM). It is to be a collection of the rules enabling us to construct step by step a semantic representation (or text meaning representation) of practically arbitrary sentence or discourse pertaining to mass spheres of human’s professional activity. The opinion is grounded that the first version of broadly applicable and flexible CM is already available in the scientific literature. It is conjectured that the definition of the class of SK-languages (standard knowledge languages) provided by the theory of K-representations (knowledge representations) can be interpreted as the first version of broadly applicable and flexible CM. The current version of the latter theory is stated in the author’s monograph published by Springer in 2010. The final part of the paper describes the connections with the related approaches, in particular, with the studies on developing a Multilingual Semantic Web.
The paper describes the structure and possible applications of the theory of K-representations (knowledge representations) in bioinformatics and in the development of a Semantic Web of a new generation. It is an original theory of designing semantic-syntactic analyzers of natural language (NL) texts with the broad use of formal means for representing input, intermediary, and output data. The current version of the theory is set forth in a monograph by V. Fomichov (Springer, 2010). The first part of the theory is a formal model describing a system consisting of ten operations on conceptual structures. This model defines a new class of formal languages – the class of SK-languages. The broad possibilities of constructing semantic representations of complex discourses pertaining to biology are shown. A new formal approach to developing multilingual algorithms of semantic-syntactic analysis of NL-texts is outlined. This approach is realized by means of a program in the language PYTHON.
This volume covers some of the topics that are related to the rapidly growing field of biomedical informatics. In June 11–12, 2010 a workshop entitled ‘Optimization and Data Analysis in Biomedical Informatics’ was organized at The Fields Institute. Following this event, invited contributions were gathered based on the talks presented at the workshop, and additional invited chapters were solicited from leading experts. In this publication, the authors share their expertise in the form of state-of-the-art research and review chapters, bringing together researchers from different disciplines and emphasizing the value of mathematical methods in the areas of clinical sciences.
A comprehensive theoretical framework for the development of a Semantic Web of a new generation, or of a Multilingual Semantic Web, is outlined. Firstly, the paper grounds the possibility of using a mathematical model being the kernel of the theory of K-representations and describing a system of 10 partial operations on conceptual structures for building semantic representations (or text meaning representations) of, likely, arbitrary sentences and discourses in English, Russian, French, German, and other languages. The possibilities of using SK-languages defined by the theory of K-representations for building semantic annotations of informational sources and for constructing semantic representations of discourses pertaining to biology and medicine are illustrated. Secondly, an original strategy of transforming the existing Web into a Semantic Web of a new generation with the well-developed mechanisms of understanding natural language texts is described. The third subject of this paper is a description of the correspondence between the inputs and outputs of the elaborated algorithm of semantic-syntactic analysis and of its advantages; the semantic representations of the input texts are the expressions of SK-languages (standard knowledge languages). The input texts can be the statements, questions, and commands from the sublanguages of English, Russian, and German. The algorithm has been implemented by means of the programming language PYTHON.
The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.
Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data usually come up short in single-cell sequencing projects, algorithms actually used for single-cell error correction have been so far very simplistic.
We introduce several novel algorithms based on Hamming graphs and Bayesian subclustering in our new error correction tool BAYESHAMMER. While BAYESHAMMER was designed for single-cell sequencing, we demonstrate that it also improves on existing error correction tools for multi-cell sequencing data while working much faster on real-life datasets. We benchmark BAYESHAMMER on both k-mer counts and actual assembly results with the SPADES genome assembler.
Abstracts of the Ninth International Conference on Bioinformatics of Genome Regulation and Structure\Systems Biology. Printed without editing
A model for organizing cargo transportation between two node stations connected by a railway line which contains a certain number of intermediate stations is considered. The movement of cargo is in one direction. Such a situation may occur, for example, if one of the node stations is located in a region which produce raw material for manufacturing industry located in another region, and there is another node station. The organization of freight traﬃc is performed by means of a number of technologies. These technologies determine the rules for taking on cargo at the initial node station, the rules of interaction between neighboring stations, as well as the rule of distribution of cargo to the ﬁnal node stations. The process of cargo transportation is followed by the set rule of control. For such a model, one must determine possible modes of cargo transportation and describe their properties. This model is described by a ﬁnite-dimensional system of diﬀerential equations with nonlocal linear restrictions. The class of the solution satisfying nonlocal linear restrictions is extremely narrow. It results in the need for the “correct” extension of solutions of a system of diﬀerential equations to a class of quasi-solutions having the distinctive feature of gaps in a countable number of points. It was possible numerically using the Runge–Kutta method of the fourth order to build these quasi-solutions and determine their rate of growth. Let us note that in the technical plan the main complexity consisted in obtaining quasi-solutions satisfying the nonlocal linear restrictions. Furthermore, we investigated the dependence of quasi-solutions and, in particular, sizes of gaps (jumps) of solutions on a number of parameters of the model characterizing a rule of control, technologies for transportation of cargo and intensity of giving of cargo on a node station.
Event logs collected by modern information and technical systems usually contain enough data for automated process models discovery. A variety of algorithms was developed for process models discovery, conformance checking, log to model alignment, comparison of process models, etc., nevertheless a quick analysis of ad-hoc selected parts of a journal still have not get a full-fledged implementation. This paper describes an ROLAP-based method of multidimensional event logs storage for process mining. The result of the analysis of the journal is visualized as directed graph representing the union of all possible event sequences, ranked by their occurrence probability. Our implementation allows the analyst to discover process models for sublogs defined by ad-hoc selection of criteria and value of occurrence probability
Existing approaches suggest that IT strategy should be a reflection of business strategy. However, actually organisations do not often follow business strategy even if it is formally declared. In these conditions, IT strategy can be viewed not as a plan, but as an organisational shared view on the role of information systems. This approach generally reflects only a top-down perspective of IT strategy. So, it can be supplemented by a strategic behaviour pattern (i.e., more or less standard response to a changes that is formed as result of previous experience) to implement bottom-up approach. Two components that can help to establish effective reaction regarding new initiatives in IT are proposed here: model of IT-related decision making, and efficiency measurement metric to estimate maturity of business processes and appropriate IT. Usage of proposed tools is demonstrated in practical cases.