Related papers: Data Management for High-Throughput Genomics
Traditional DBMSs execute user- or application-provided SQL queries over relational data with strong semantic guarantees and advanced query optimization, but writing complex SQL is hard and focuses only on structured tables. Contemporary…
The ability to estimate resource consumption of SQL queries is crucial for a number of tasks in a database system such as admission control, query scheduling and costing during query optimization. Recent work has explored the use of…
The term Big Data is usually used to describe huge amount of data that is generated by humans from digital media such as cameras, internet, phones, sensors etc. By building advanced analytics on the top of big data, one can predict many…
Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…
In order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which…
Deep learning has recently become very popular on account of its incredible success in many complex data-driven applications, such as image classification and speech recognition. The database community has worked on data-driven applications…
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and tradeoffs of DNA-based storage systems under a simple model, motivated by current…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
High-throughput technologies such as next generation sequencing allow biologists to observe cell function with unprecedented resolution, but the resulting datasets are too large and complicated for humans to understand without the aid of…
Generating accurate SQL from users' natural language questions (text-to-SQL) remains a long-standing challenge due to the complexities involved in user question understanding, database schema comprehension, and SQL generation. Traditional…
Heterogeneous, interconnected, systems-level, molecular data have become increasingly available and key in precision medicine. We need to utilize them to better stratify patients into risk groups, discover new biomarkers and targets,…
DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between…
A new family of Intensional RDBs (IRDBs), introduced in [1], extends the traditional RDBs with the Big Data and flexible and 'Open schema' features, able to preserve the user-defined relational database schemas and all preexisting user's…
Querying databases for the right information is a time consuming and error-prone task and often requires experienced professionals for the job. Furthermore, the user needs to have some prior knowledge about the database. There have been…
This tutorial overviews the state of the art in learning models over relational databases and makes the case for a first-principles approach that exploits recent developments in database research. The input to learning classification and…
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of…
Large scale initiatives such as the Human Genome Project, Structural Genomics, and individual research teams have provided large deposits of genomic and proteomic data. The transfer of data to knowledge has become one of the existing…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. However, sequencing…