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Current challenge in landscape genomics: what about the environmental counterpart of high-throughput genomic data?
Related publications (39)
Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics
Tamar Kohn, Xavier Fernandez Cassi
Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...
2024Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing
Bart Deplancke, Daniel Migliozzi, Gilles Weder, Riccardo Dainese, Daniel Alpern, Hüseyin Baris Atakan, Mustafa Demir, Dariia Gudkova
High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...
Dordrecht2024Bubble-enhanced ultrasonic microfluidic chip for rapid DNA fragmentation
Martinus Gijs, Thomas Lehnert, Lin Sun
DNA fragmentation is an essential process in developing genetic sequencing strategies, genetic research, as well as for the diagnosis of diseases with a genetic signature like cancer. Efficient on-chip DNA fragmentation protocols would be beneficial to pro ...
ROYAL SOC CHEMISTRY2022Inferring Transmission Fitness Advantage of SARS-CoV-2 Variants of Concern in Wastewater Using Digital PCR
Tamar Kohn, Xavier Fernandez Cassi, Timothy R. Julian
Throughout the global COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterized by increased transmissibility, increased virulence, or reduced neutralization by antibodies obtained fro ...
2022The enhancement of DNA fragmentation in a bench top ultrasonic water bath with needle-induced air bubbles: Simulation and experimental investigation
Martinus Gijs, Thomas Lehnert, Yang Liu, Lin Sun
Shearing DNA to a certain size is the first step in many medical and biological applications, especially in next-generation gene sequencing technology. In this article, we introduced a highly efficient ultrasonic DNA fragmentation method enhanced by needle ...
AIP Publishing2022One Fuzz Doesn’t Fit All: Optimizing Directed Fuzzing via Target-tailored Program State Restriction
Fuzzing is the de-facto default technique to discover software flaws, randomly testing programs to discover crashing test cases. Yet, a particular scenario may only care about specific code regions (for, e.g., bug reproduction, patch or regression testing) ...
ASSOC COMPUTING MACHINERY2022An Introduction to MPEG-G: The First Open ISO/IEC Standard for the Compression and Exchange of Genomic Sequencing Data
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 INC2021Detection and surveillance of SARS-CoV-2 genomic variants in wastewater
Tamar Kohn, Xavier Fernandez Cassi, Federica Cariti, Alex Tunas Corzon, Timothy R. Julian, Carola Bänziger
The emergence of SARS-CoV-2 mutants with altered transmissibility, virulence, or immunogenicity emphasizes the need for early detection and epidemiological surveillance of genomic variants. Wastewater samples provide an opportunity to assess circulating vi ...
2021A Crowdsourced Gameplay for Whole-Genome Assembly via Short Reads
Next-generation sequencing has revolutionized the field of genomics by producing accurate, rapid and cost-effective genome analysis with the use of high throughput sequencing technologies. This has intensified the need for accurate and performance efficien ...
INT ASSOC ONLINE ENGINEERING2020Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures
David Atienza Alonso, Marina Zapater Sancho, Yasir Mahmood Qureshi, José Manuel Herruzo Ruiz
Next generation workloads, such as genome sequencing, have an astounding impact in the healthcare sector. Sequence alignment, the first step in genome sequencing, has experienced recent breakthroughs, which resulted in next generation sequencing (NGS). As ...
2020