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With the wide usage of data visualizations, a huge number of Scalable Vector Graphic (SVG)-based visualizations have been created and shared online. Accordingly, there has been an increasing interest in exploring how to retrieve…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
We propose a new technique to infer the structure and extract the tokens of data from the semi-structured web sources which are generated using a consistent template or layout with some implicit regularities. The attributes are extracted…
Substructure search in chemical compound databases is a fundamental task in cheminformatics with critical implications for fields such as drug discovery, materials science, and toxicology. However, the increasing size and complexity of…
During the past decades significant efforts have been made to propose data structures for answering connectivity queries on fully dynamic graphs, i.e., graphs with frequent insertions and deletions of edges. However, a comprehensive…
Large systems biology projects can encompass several workgroups often located in different countries. An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
In this paper we represent a new framework for integrated distributed and reliable systems. In the proposed framework we have used three parts to increase Satisfaction and Performance of this framework. At first we analyze previous…
Due to the advancements in technology number of entries in the structural database of proteins are increasing day by day. Methods for retrieving protein tertiary structures from this large database is the key to comparative analysis of…
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving…
The transfer of the medical care services to the patient, rather than the transport of the patient to the medical services providers is aim of the project. This is achieved by using web-based applications including Modern Medical…
Biclustering is an unsupervised data mining technique that aims to unveil patterns (biclusters) from gene expression data matrices. In the framework of this thesis, we propose new biclustering algorithms for microarray data. The latter is…
Linked lists have long served as a valuable teaching tool in programming. However, the question arises: Are they truly practical for everyday program use? In most cases, it appears that array-based data structures offer distinct advantages,…
Discovering valuable insights from data through meaningful associations is a crucial task. However, it becomes challenging when trying to identify representative patterns in quantitative databases, especially with large datasets, as…
Nowadays, the explosion of unstructured data presents immense analytical value. Leveraging the remarkable capability of large language models (LLMs) in extracting attributes of structured tables from unstructured data, researchers are…
Recent advances in single cell sequencing and multi-omics techniques have significantly improved our understanding of biological phenomena and our capacity to model them. Despite combined capture of data modalities showing similar progress,…
The amount of scientific papers published every day is daunting and constantly increasing. Keeping up with literature represents a challenge. If one wants to start exploring new topics it is hard to have a big picture without reading lots…
Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is…
Curating, processing, and combining large-scale medical imaging datasets from national studies is a non-trivial task due to the intense computation and data throughput required, variability of acquired data, and associated financial…
High dimensional and heterogeneous count data are collected in various applied fields. In this paper, we look closely at high-resolution sequencing data on the microbiome, which have enabled researchers to study the genomes of entire…