Crypt4GH: a file format standard enabling native access to encrypted data

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KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation

Jonas Caspar De Tribolet-Hardy

There are 377 Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) in the human genome, making them the largest family of transcription factors. KZFPs are defined by a N-terminal KRAB domain and several zinc-finger domains arranged ...

EPFL2022

Towards mouse genetic-specific RNA-sequencing read mapping

Maxime Jan, Ioannis Xenarios

Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using ...

2022

Lightweight HI source finding for next generation radio surveys

Jean-Paul Richard Kneib, Frédéric Courbin, Emma Elizabeth Tolley, Aymeric Alexandre Galan, Austin Chandler Peel, Mark Thomas Sargent

Future deep HI surveys will be essential for understanding the nature of galaxies and the content of the Universe. However, the large volume of these data will require distributed and automated processing techniques. We introduce LiSA, a set of python modu ...

ELSEVIER2022

Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter

Christof Holliger, Julien Maillard, Aline Sondra Adler, Marco Pagni, Simon Marius Jean Poirier

Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...

WILEY2022

Clouseau: Blockchain-based Data Integrity for HDFS Clusters

Ioannis Mytilinis

As the volume of produced data is exponentially increasing, companies tend to rely on distributed systems to meet the surging demand for storage capacity. With the business workflows becoming more and more complex, such systems often consist of or are acce ...

IEEE COMPUTER SOC2021

Analyzing and Protecting Communication Metadata

Ludovic Barman

Most communication systems (e.g., e-mails, instant messengers, VPNs) use encryption to prevent third parties from learning sensitive information. However, encrypted communications protect the contents but often leak metadata: the amount of data sent and th ...

EPFL2021

An Introduction to MPEG-G: The First Open ISO/IEC Standard for the Compression and Exchange of Genomic Sequencing Data

Marco Mattavelli

The development and progress of high-throughput sequencing technologies have transformed the sequencing of DNA from a scientific research challenge to practice. With the release of the latest generation of sequencing machines, the cost of sequencing a whol ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2021

Software Support for Non-Volatile Memory (NVM) Programming

David Teksen Aksun

Non-Volatile Memory (NVM) is an emerging type of memory device that provides fast, byte-addressable, and high-capacity durable storage. NVM sits on the memory bus and allows durable data structures designs similar to the in-memory equivalent ones. Expensiv ...

EPFL2021

An Architecture for Load Balance in Computer Cluster Applications

Laurent Bindschaedler

Amid a data revolution that is transforming industries around the globe, computing systems have undergone a paradigm shift where many applications are scaled out to run on multiple computers in a computing cluster. As the storage and processing capabilitie ...

EPFL2020

Adaptive partitioning and indexing for in situ query processing

Anastasia Ailamaki, Manolis Karpathiotakis, Ioannis Alagiannis, Manoussos Gavriil Athanassoulis, Matthaios Alexandros Olma

The constant flux of data and queries alike has been pushing the boundaries of data analysis systems. The increasing size of raw data files has made data loading an expensive operation that delays the data-to-insight time. To alleviate the loading cost, in ...

SPRINGER2020

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Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter

Christof Holliger, Julien Maillard, Aline Sondra Adler, Marco Pagni, Simon Marius Jean Poirier

WILEY2022