Sébastien Boisvert

Sébastien Boisvert
Gydle Inc. · Optical Mapping Team

PhD

About

61
Publications
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3,369
Citations

Publications

Publications (61)
Article
Full-text available
Identification of proteins is one of the most computationally intensive steps in genomics studies. It usually relies on aligners that do not accommodate rich information on proteins and require additional pipelining steps for protein identification. We introduce kAAmer, a protein database engine based on amino-acid k-mers that provides efficient id...
Preprint
Full-text available
Identification of proteins is one of the most computationally intensive steps in genomics studies. It usually relies on aligners that don't accommodate rich information on proteins and require additional pipelining steps for protein identification. We introduce kAAmer, a protein database engine based on amino-acid k-mers, that supports fast identif...
Preprint
Full-text available
Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase scale sections of this chromosome were established by combining...
Article
Full-text available
GK-G, PR, JT contributed equally to experimental design, data analysis andinterpretation/writing of manuscript;, RP, MH, KF, RA genome analyses andinterpretation; ZF, AK data analysis and physical map construction; EH, CC, JTMAGIC map construction; MA rice-wheat phylogenomic; AS, DK, mate-pairlibraries; PS. BD, FC, PL, Chinese Spring x Renan molecu...
Article
Full-text available
Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated...
Article
Full-text available
Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological,...
Article
Full-text available
Brucella suis is a Gram-negative, facultative intracellular pathogen that has pigs as its preferred host, but it can also infect humans. Here, we report the draft genome sequences of two B. suis strains that were isolated from the same patient, 8 years apart.
Article
Full-text available
Brucella canis is a facultative intracellular pathogen that preferentially infects members of the Canidae family. Here, we report the genome sequencing of two Brucella canis strains isolated from humans and one isolated from a dog host.
Article
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface all...
Article
Full-text available
The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to identify the genetic mechanisms of AMR and predict the resistance phenotypes of bacterial pathogens prior to culturing could inform clinical decis...
Conference Paper
Full-text available
American eel (Anguilla rostrata) reproduce in a single panmictic population in the Sargasso Sea in the Atlantic Ocean. After hatching, they migrate as leptocephali to a large diversity of salt, brackish, and freshwater habitats in Eastern North America. Despite panmixia, there are extreme differences in morphology, growth rate, and sex ratio by rea...
Article
Full-text available
As analysts are expected to process a greater amount of information in a shorter amount of time, creators of big data software are challenged with the need for improved efficiency. Ray, our group's usable, scalable genome assembler, addresses big data problems by using optimal resources and producing one, correct and conservative, timely solution....
Article
Full-text available
The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, accept...
Conference Paper
Full-text available
ecent progress in DNA sequencing technology has yielded a new class of devices that allow for the analysis of genetic material with unprecedented speed and efficiency. These advances, styled under the name Next-Generation Sequencing (NGS), increasingly shift the burden from chemistry done in a laboratory to a string manipulation problem, well suite...
Article
Antimonials are still the mainstay of treatment against leishmaniasis but drug resistance is increasing. We carried out short read next generation sequencing (NGS) and comparative genomic hybridization (CGH) of three independent Leishmania major antimony resistant mutants. Copy number variations were consistently detected with both NGS and CGH. A m...
Article
Full-text available
Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a...
Data
Protein sequence alignment of L. major PK (LmjF31.1250) with its respective orthologs of L. infantum (LinJ13_V3.1590), L. braziliensis (LbrM13_V2.1380), T. brucei (Tb06.5F5.240), E. coli (NP_416153) and Homo sapiens (NP_003672). Alignment was performed using the ClustalW algorithm implemented in the Lasergene software (DNASTAR, Inc.). Identical res...
Data
Homozygous SNPs found after resequencing the genome of L. major Friedlin. All the SNPs were identified in L. major Friedlin wild-type and in the mutants MF80.3 and MF80.5. The symbol * corresponds to a potential stop codon. (DOC)
Data
MSH2 knockout cells grow similarly to wild-type cells but have increased alkylation tolerance. (A) Growth of promastigotes in vitro. Parasites were inoculated at 2×105 cells/ml and then they were counted every 24 hours. The mean of three independent experiments are indicated. L. infantum 263 wild-type parasite (Δ), double replacement clone (Li263ΔM...
Data
Protein sequence alignment of L. majorα-adaptin like protein (LmjF07.0050) with its respective orthologs of L. infantum (LinJ07_V3.0060) and L. braziliensis (LbrM7_V2.0050). Alignment was performed using the ClustalW algorithm implemented in the Lasergene software (DNASTAR, Inc.). Identical residues are shaded in black. The amino acids mutated in t...
Data
Primers used in this study for amplifying the genes MT (LmjF13.1530), PK (LmjF30.1250) and the α-adaptin like protein (LmjF07.0050) of L. major. Restriction sites are underlined. Primers are also listed to sequence the genes MT, the α-adaptin like protein and Ros3 (LmjF32.0510) of L. major and to generate PK-KO constructs. (DOC)
Data
Copy number sequencing analysis for all Leishmania chromosomes for L. major Friedlin wild-type parasites (A) and the mutants MF80.3 (B) and MF80.5 (C). The 36 chromosomes have been mapped as circles representing the normalized read counts for each chromosome (blue line). For the MF80.3 and MF80.5 mutants, the log2 ratios of normalized read counts c...
Data
Heterozygous allelic polymorphisms in L. major Friedlin. All the same SNPs were identified in L. major Friedlin wild-type and in the mutants MF80.3 and MF80.5. (DOC)
Article
Full-text available
Miltefosine (MF) is the first oral compound used in the chemotherapy against leishmaniasis. Since the mechanism of action of this drug and the targets of MF in Leishmania are unclear, we generated in a step-by-step manner Leishmania major promastigote mutants highly resistant to MF. Two of the mutants were submitted to a short-read whole genome seq...
Article
Full-text available
The Leishmania tarentolae Parrot-TarII strain genome sequence was resolved to an average 16-fold mean coverage by next-generation DNA sequencing technologies. This is the first non-pathogenic to humans kinetoplastid protozoan genome to be described thus providing an opportunity for comparison with the completed genomes of pathogenic Leishmania spec...
Article
Various endonucleases can be engineered to induce double-strand breaks (DSBs) in chosen DNA sequences. These DSBs are spontaneously repaired by nonhomologous-end-joining, resulting in micro-insertions or micro-deletions (INDELs). We detected, characterized and quantified the frequency of INDELs produced by one meganuclease (MGN) targeting the RAG1...
Article
Full-text available
An accurate genome sequence of a desired species is now a pre-requisite for genome research. An important step in obtaining a high-quality genome sequence is to correctly assemble short reads into longer sequences accurately representing contiguous genomic regions. Current sequencing technologies continue to offer increases in throughput, and corre...
Article
Full-text available
Respiratory virus infections are a major health concern and represent the primary cause of testing consultation and hospitalization for young children. We developed and compared two assays that allow the detection of up to 23 different respiratory viruses that frequently infect children. The first method consisted of single TaqMan quantitative real...
Article
Full-text available
Human immunodeficiency virus type 1 (HIV-1) infects cells by means of ligand-receptor interactions. This lentivirus uses the CD4 receptor in conjunction with a chemokine coreceptor, either CXCR4 or CCR5, to enter a target cell. HIV-1 is characterized by high sequence variability. Nonetheless, within this extensive variability, certain features must...
Data
Source code and data. Web server, classifiers, discriminant vectors and data sets.
Data
Figure S1 shows the direct repeats flanking the DHFR-TS locus of L. major and L. infantum chromosome 6, and also provides the circular junction sequence formed by homologous recombination. Figure S2 shows the inverted repeats present on chromosome 23 of L. infantum, and provides the sequence of the new junction formed through the inverted duplicati...
Data
Results of the comparative genomic hybridization analyses of L. major MTX60.4 versus the respective wild-type cells.
Data
Differential expression measured by the full-genome microarray analysis.
Article
Full-text available
Drug resistance can be complex, and several mutations responsible for it can co-exist in a resistant cell. Transcriptional profiling is ideally suited for studying complex resistance genotypes and has the potential to lead to novel discoveries. We generated full genome 70-mer oligonucleotide microarrays for all protein coding genes of the human pro...
Data
Genes differentially expressed in Leishmania infantum intracellular amastigotes. This Table lists all the Leishmania infantum genes that are differentially expressed in intracellular amastigotes as determined by DNA microarray studies.
Data
Genes differentially expressed in Leishmania major promastigotes. This Table lists all the Leishmania major genes that are differentially expressed in promastigotes as determined by DNA microarray studies.
Data
Genes differentially expressed in Leishmania infantum promastigotes. This Table lists all the Leishmania infantum genes that are differentially expressed in promastigotes as determined by DNA microarray studies.
Data
Genes differentially expressed in Leishmania major intracellular amastigotes. This Table lists all the Leishmania major genes that are differentially expressed in lesion-derived amastigotes as determined by DNA microarray studies.
Data
Comparison of expression levels obtained by quantitative real-time PCR between different Leishmania species or experimental models of infection. qRT-PCR analysis was performed on selected differentially expressed genes as determined by microarray experiments. The same RNA used for the microarray analysis was also used for qRT-PCR. (A) Expression va...
Data
Primers used for quantitative real-time PCR expression analysis. Table lists the sequences of the primers used for quantitative real-time PCR expression analysis to validate DNA microarray studies.
Article
Full-text available
Leishmania parasites cause a diverse spectrum of diseases in humans ranging from spontaneously healing skin lesions (e.g., L. major) to life-threatening visceral diseases (e.g., L. infantum). The high conservation in gene content and genome organization between Leishmania major and Leishmania infantum contrasts their distinct pathophysiologies, sug...