Hélène Touzet
CNRS research director
CRIStAL - ESPRIT
Cité scientifique
59655 Villeneuve d'Ascq Cedex
France
+33 (0)3 28 77 85 59
helene.touzet(AT)univ-lille.fr


Algorithmic bioinformatics

The goal of my work is to develop state-of-the-art algorithms in computational biology to analyze DNA and RNA molecules, and help solving problems in biology and medicine. This covers the following topics: high throughput sequencing, metagenomics, noncoding RNA.

ORCID iD: 0000-0001-5305-9987

idHal: helene-touzet

Google scholar profile: google scholar

Software: For the full list, see the Bonsai GitHub repository, and our website

News

October 30: Lockdown, season 2

Special Issue of Algorithms: Algorithms in Computational Biology. Deadline for submission is 31 March 2021 [September 2020]

August 29: SortMeRNA reached the 1000+ citations! See the paper [September 2020]

July 2: virtual mini-symposium on Long reads at JOBIM 2020 [June 2020]

Since March 16: working from home [March 2020]

June 8-12, Nouan-le-Fuzelier, summer school in bioinformatics: statistics, algorithms and combinatorics for high-throughput sequencing data analysis in beautiful Sologne. All information. Postponed to 2021 (March 29-April 2) [June 2020]

Our study on the Human coronavirus OC43 (not the novel coronavirus) is now available in Journal of Clinical Virology. This work is a follow-up of A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43, appeared in 2019 in Virology [January 2020]

February 5, Institut Curie, Omics and Systems Biology for Health: program and registration [January 2020]

The TNPhyto project (Genetic traits required by bacterial phytopathogens for plant infection and fitness in non-agricultural habitats using high-throughput transposon sequencing) is funded by the French National Research Agency [July 2019]

Which genome browser to use to visualize my sequences ? We have conducted a comprehensive comparative analysis of seven genome browsers: Artemis, Give, IGB, IGV, Jbrowse, Tablet and UCSC genome browser. Read our report. If you think you already know everything, you can try our quiz [July 2019]

Plant microRNAs: Our work miRkwood: a tool for the reliable identification of microRNAs in plant genomes has been accepted to BMC Genomics. Discover the software (also on GitHub) [June 2019]

Want to know more about long read correction ? The paper of the ASTER consortium Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data is now available in Briefings in Bioinformatics [June 2019]

Adapter trimming in Nanopore reads : The first release of Porechop_ABI (Porechop ab initio) is available on GitHub. This new program is an extension of the original well-known Porechop (R. Wick). The novelty is that it is able to infer the adapter sequences from the raw reads, without any external information. The algorithm uses approximate k-mers and assembly. We also maintain all other great functionalities of Porechop [June 2019]

Teaching

See the webpage.


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I subscribe to an open-access scientific model, and try to make all source code, publication, material and protocols available.
Do not hesitate to contact me by email for any request.