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Algorithmic bioinformatics
The goal of my work is to develop state-of-the-art algorithms in computational biology to analyze DNA, RNA and protein molecules, and help solving problems in biology and medicine. This covers the following topics: high throughput sequencing, metagenomics, noncoding RNA, proteomics.
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 and resources
Our work on proteomics for paleontology and archeology is presented at JOBIM
[June 2024]
MSA for long reads: our paper Automated
evaluation of multiple sequence alignment methods to handle third
generation sequencing errors has been accepted for publication in
PeerJ. See the preprint
[June 2024]
PAMPA webserver is online (beta version)
[May 2024]
PAMPA (Protein Analysis by Mass Spectrometry for Ancient Species): v1 is available on GitHub. Feedbacks
are welcome !
[January 2024]
GDR Bioinformatique: The next national
meeting will take place in Lille, November 20-23 2023
[September 2023]
The software SortMeRNA reached the 2000+
citations! See the paper [September 2023]
PALEOMICS: We organize a
one-day workshop on paleogenomics and paleoproteomics, featuring
Céline Bon (MNHN), Andaine Seguin-Orlando (CAGT),
Patrick Auguste (EEP), Eva-Maria Geigl (Institut Jacques Monod)
Nicolas Rascovan (Institut Pasteur) and Fabrice Bray (MSAP) [July 2023]
Tnseek, our pipeline for Tn-seq analysis, was presented at
JOBIM
and at the International Ewinia
workshop [July 2023]
ISMB-ECCB, July 23-27, 2023: The conference is being
held in Lyon.
I am co-chair of the Bioinformatics of Microbes and Microbiomes
area, together with Robert Beiko [June 2023]
Bioinformatics and SARS-CoV-2: discover the popular
science dossier published in Interstices (in French)
[May 2023]
Paleo-info-evo: Our three-year project Algorithms and evolutionary models
for paleoproteomics is accepted by MITI CNRS [March 2023]
Adapter trimming in Nanopore reads: Porechop_ABI:
discovering unknown adapters in Oxford Nanopore Technology
sequencing reads for downstream trimming is published in
Bioinformatics Advances. Porechop_ABI 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 [November 2022]
reads2genpop : From sequence reads to genomes and populations,
Paris, MNHN (France). Program [September 2022]
Plant microRNAs:
The book chapter
Detecting MicroRNAs in Plant Genomes with miRkwood is available.
You can also read the full article in
BMC Genomics and discover the software
on our server
(also on GitHub) [July 2022]
Teaching
Other duties
- Member of the scientific board of the French bioinformatics network GDR Bioinformatique Moleculaire: Modelisation et Methodologie
- Member of the COMESP committee of Institut Pasteur
- Gender equality representative for CRIStAL. See our website (restricted access)
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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.