Nanopore-based scanning system and method

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Related publications (29)

Microbiota Analysis Using an Illumina MiSeq Platform to Sequence 16S rRNA Genes

Alexis Rapin, Céline Pattaroni, Nicola Harris, Benjamin John Marsland

The microbiota have been shown to play an important role in diverse biological processes including immunity, metabolism, and digestion. Assessing the exact composition of the microbiota has proven challenging due to the often unknown growth specificities o ...

2017

Persona: A High-Performance Bioinformatics Framework

Edouard Bugnion, Christos Kozyrakis, Sam David Whitlock, James Richard Larus, Stuart Anthony Byma

Next-generation genome sequencing technology has reached a point at which it is becoming cost-effective to sequence all patients. Biobanks and researchers are faced with an oncoming deluge of genomic data, whose processing requires new and scalable bioinfo ...

2017

Simple rules for an efficient use of Geographic Information Systems in molecular ecology

Stéphane Joost, Estelle Rochat, Solange Catherine Gaillard, Kevin Leempoel, Ivo Widmer

Geographic Information Systems (GIS) are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and liv ...

2017

Probing chemical structures and physical processes with nanopores

Jiandong Feng

This thesis develops and applies the nanopore tool to probe chemical structures and physical processes at the single-molecule level: from single ions to DNA molecules. Nanopore experiments electrically measure the ionic transport through the pore and its m ...

EPFL2016

Cycling temperature capillary electrophoresis: A quantitative, fast and inexpensive method to detect mutations in mixed populations of human mitochondrial DNA

Stephan Morgenthaler, Paul Refinetti, Per Olaf Ekstrom

Cycling temperature capillary electrophoresis has been optimised for mutation detection in 76% of the mitochondrial genome. The method was tested on a mixed sample and compared to mutation detection by next generation sequencing. Out of 152 fragments 90 we ...

Elsevier Sci Ltd2016

DNA barcoding of formalin‑fixed aquatic oligochaetes for biomonitoring

Régis Lionel Vivien

Background: Oligochaetes are valuable bioindicators of the quality of watercourse and lake sediments. The morphological identification of aquatic oligochaetes is difficult, prompting the development of new molecular oligochaete indices based on DNA barcodi ...

2016

Comparison of high-throughput sequencing data compression tools

Marco Mattavelli, Claudio Paolo Alberti

High-throughput sequencing (HTS) data are commonly stored as raw sequencing reads in FASTQ format or as reads mapped to a reference, in SAM format, both with large memory footprints. Worldwide growth of HTS data has prompted the development of compression ...

Nature Publishing Group2016

A privacy-preserving solution for compressed storage and selective retrieval of genomic data

Jean-Pierre Hubaux, Adam Molyneaux, Jacques Fellay, Erman Ayday, Zhicong Huang, Huang Lin, Zhi Ming Xu

In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients' complete aligned genomic data in addition to variant calls relative to a reference sequence. Due to the large size of ...

Cold Spring Harbor Laboratory2016

A Statistical Guide to the Design of Deep Mutational Scanning Experiments

Jeffrey David Jensen, Claudia Bank, Sebastian Matuszewski

The characterization of the distribution of mutational effects is a key goal in evolutionary biology. Recently developed deep-sequencing approaches allow for accurate and simultaneous estimation of the fitness effects of hundreds of engineered mutations by ...

Genetics Society America2016

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