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Information retrieval has transitioned from standalone systems into essential components across broader applications, with indexing efficiency, cost-effectiveness, and freshness becoming increasingly critical yet often overlooked. In this…
Research in the Life Sciences depends on the integration of large, distributed and heterogeneous data sources and web services. The discovery of which of these resources are the most appropriate to solve a given task is a complex research…
This article presents our steps to integrate complex and partly unstructured medical data into a clinical research database with subsequent decision support. Our main application is an integrated faceted search tool, accompanied by the…
Increasingly, keyword, natural language and NoSQL queries are being used for information retrieval from traditional as well as non-traditional databases such as web, document, image, GIS, legal, and health databases. While their popularity…
In the past few decades, the life sciences have experienced an unprecedented accumulation of data, ranging from genomic sequences and proteomic profiles to heavy-content imaging, clinical assays, and commercial biological products for…
Tackling the information retrieval gap between non-technical database end-users and those with the knowledge of formal query languages has been an interesting area of data management and analytics research. The use of natural language…
Structured merge tools exploit programming language syntactic structure to enhance merge accuracy by reducing spurious conflicts reported by unstructured tools. By creating and handling full ASTs, structured tools are language-specific and…
The need for discovering knowledge from XML documents according to both structure and content features has become challenging, due to the increase in application contexts for which handling both structure and content information in XML data…
We create synthetic biometric databases to study general, fundamental, biometric principles. First, we check the validity of the synthetic database design by comparing it to real data in terms of biometric performance. The real data used…
In the real world, most objects and data have multiple types of attributes and inter-connections. Such data structures are named "Heterogeneous Information Networks" (HIN) and have been widely researched. Biological systems are also…
Research papers in the biomedical field come with large and complex data sets that are shared with the scientific community as unstructured data files via public data repositories. Examples are sequencing, microarray, and mass spectroscopy…
Semi-supervised clustering techniques have emerged as valuable tools for leveraging prior information in the form of constraints to improve the quality of clustering outcomes. Despite the proliferation of such methods, the ability to…
Bioinformatics workflows are essential for complex biological data analyses and are often described in scientific articles with source code in public repositories. Extracting detailed workflow information from articles can improve…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Recent technological advancements in data acquisition tools allowed life scientists to acquire multimodal data from different biological application domains. Broadly categorized in three types (i.e., sequences, images, and signals), these…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
Finding patterns in data and being able to retrieve information from those patterns is an important task in Information retrieval. Complex search requirements which are not fulfilled by simple string matching and require exploring certain…
Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, such as metabolomics, systems biology, and drug discovery. However, no such database can be complete, and the…
RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…