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List of works by Marie-France Sagot

A Combinatorial Algorithm for Microbial Consortia Synthetic Design

scientific article published on 4 July 2016

A new distance for high level RNA secondary structure comparison

scientific article published in January 2005

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs

scientific article published on 27 June 2015

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks

scientific article published on 10 July 2012

All maximal-pairs in step–leap representation of melodic sequence

article

An asymmetric approach to preserve common intervals while sorting by reversals

scientific article published on 30 December 2009

An efficient algorithm for the identification of structured motifs in DNA promoter sequences

scientific article published in April 2006

An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets.

scientific article published on 17 July 2018

An introduction to metabolic networks and their structural analysis

scientific article published on October 2008

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

scientific article published on 24 July 2009

Assessing the exceptionality of coloured motifs in networks

scientific article

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

scientific article (publication date: 2012)

BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

article

Bacterial syntenies: an exact approach with gene quorum ⬇️

scientific article published on May 24, 2011

Cassis: detection of genomic rearrangement breakpoints

scientific article published on 23 June 2010

Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny ⬇️

scientific article published on June 10, 2011

Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi

scientific article

Current methods of gene prediction, their strengths and weaknesses

scientific article

CycADS: an annotation database system to ease the development and update of BioCyc databases

scientific article

DegreeCox - a network-based regularization method for survival analysis

scientific article

EUCALYPT: efficient tree reconciliation enumerator

scientific article

Efficient Extraction of Structured Motifs Using Box-Links

article

Efficient representation and P-value computation for high-order Markov motifs

scientific article

Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers.

scientific article

Enumeration of minimal stoichiometric precursor sets in metabolic networks

scientific article

Evolution under reversals: parsimony and conservation of common intervals

scientific article published on April 2007

Exploration of the core metabolism of symbiotic bacteria

scientific article

Exploring the solution space of sorting by reversals, with experiments and an application to evolution

scientific article published in July 2008

Fast-SG: an alignment-free algorithm for hybrid assembly.

scientific article

Footprints of inversions at present and past pseudoautosomal boundaries in human sex chromosomes

scientific article

Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci

scientific article published on 21 March 2015

Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata

scientific article

How Long Does Wolbachia Remain on Board?

scientific article

ISMB/ECCB 2009 Stockholm

scientific article published on 14 May 2009

Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster

scientific article

Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling

scientific article (publication date: 13 May 2016)

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data

scientific article

Longest Repeats with a Block of Don’t Cares

article

Longest repeats with a block of k don’t cares

article

Lossless filter for multiple repeats with bounded edit distance

scientific article published on 30 January 2009

MassBlast: A workflow to accelerate RNA-seq and DNA database analysis

article

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

scientific article published on 5 May 2010

Metabolic network visualization eliminating node redundance and preserving metabolic pathways

scientific article

Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data

scientific article

Modes and cuts in metabolic networks: complexity and algorithms

scientific article

Motif search in graphs: application to metabolic networks

scientific article published in October 2006

Mycoplasma non-coding RNA: identification of small RNAs and targets

scientific article

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches

scientific article published on 10 October 2012

On the genetic architecture of cytoplasmic incompatibility: inference from phenotypic data

scientific article

OptPipe - a pipeline for optimizing metabolic engineering targets

scientific article published on 21 December 2017

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

scientific article published on 22 February 2017

Precise detection of rearrangement breakpoints in mammalian chromosomes

scientific article published on 18 June 2008

Predicting the proteins of Angomonas deanei, Strigomonas culicis and their respective endosymbionts reveals new aspects of the trypanosomatidae family

scientific article published in 2013

Sampling solution traces for the problem of sorting permutations by signed reversals

scientific article

Short and long-term genome stability analysis of prokaryotic genomes

scientific article

Sparse network-based regularization for the analysis of patientomics high-dimensional survival data

article

Structural and dynamical analysis of biological networks

scientific article published on 20 August 2012

Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum

scientific article published on 14 October 2009

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure

scientific article

Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets

article

Two host clades, two bacterial arsenals: evolution through gene losses in facultative endosymbionts

scientific article

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