Papers by Jocelyne Bruand
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Structure-based RNA multiple alignment is particularly challenging because covarying mutations ma... more Structure-based RNA multiple alignment is particularly challenging because covarying mutations make sequence information alone insufficient. Existing tools for RNA multiple alignment first generate pairwise RNA structure alignments and then build the multiple alignment using only sequence information. Here we present PMFastR, an algorithm which iteratively uses a sequence-structure alignment procedure to build a structure-based RNA multiple alignment from one sequence with known structure and a database of sequences from the same family. PMFastR also has low memory consumption allowing for the alignment of large sequences such as 16S and 23S rRNA. The algorithm also provides a method to utilize a multi-core environment. We present results on benchmark data sets from BRAliBase, which shows PMFastR performs comparably to other state-of-the-art programs. Finally, we regenerate 607 Rfam seed alignments and show that our automated process creates multiple alignments similar to the manual...
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Imaging to assess the presence and localization of specific molecules in tissues and cells is cen... more Imaging to assess the presence and localization of specific molecules in tissues and cells is central to the study of biological systems. However, most imaging technologies focus on specific molecules of interest. An exciting recent advance is the development of Mass Spectrometry Imaging (MSI), which allows for the generation of topographic 2D maps for various endogenous and some exogenous molecules (e.g., drugs and their metabolites) without prior specification. Advances in MSI have transformative potential, allowing us to answer questions about the localization of proteins, peptides, lipids, metabolites and other molecules. To help MSI realize its potential, we describe several algorithms for the analysis of MSI data from different angles. In a first problem, we start with the premise that we are given a pre -defined region of interest (ROI) based on the morphology of the tissue or organism. We aim to find and identify molecules that are specifically expressed in the ROI. We solve...
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L'invention concerne des procedes et des systemes pour aligner des elements d'ADN repetit... more L'invention concerne des procedes et des systemes pour aligner des elements d'ADN repetitifs. Les procedes et les systemes consistent a utiliser les flancs conserves des loci polymorphiques repetitifs pour determiner efficacement la longueur et la sequence de l'element d'ADN repetitif.
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Genome engineering methodologies are transforming biological research and discovery. Approaches b... more Genome engineering methodologies are transforming biological research and discovery. Approaches based on CRISPR technology have been broadly adopted and there is growing interest in the generation of massively parallel edited cell libraries. Comparing the libraries generated by these varying approaches is challenging and researchers lack a common framework for defining and assessing the characteristics of these libraries. Here we describe a framework for evaluating massively parallel libraries of edited genomes based on established methods for sampling complex populations. We define specific attributes and metrics that are informative for describing a complex cell library and provide examples for estimating these values. We also connect this analysis to generic phenotyping approaches, using either pooled (typically via a selection assay) or isolate (often referred to as screening) phenotyping approaches. We approach this from the context of creating massively parallel, precisely edi...
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Forensic science international. Genetics, May 27, 2017
Human DNA profiling using PCR at polymorphic short tandem repeat (STR) loci followed by capillary... more Human DNA profiling using PCR at polymorphic short tandem repeat (STR) loci followed by capillary electrophoresis (CE) size separation and length-based allele typing has been the standard in the forensic community for over 20 years. Over the last decade, Next-Generation Sequencing (NGS) matured rapidly, bringing modern advantages to forensic DNA analysis. The MiSeq FGx™ Forensic Genomics System, comprised of the ForenSeq™ DNA Signature Prep Kit, MiSeq FGx™ Reagent Kit, MiSeq FGx™ instrument and ForenSeq™ Universal Analysis Software, uses PCR to simultaneously amplify up to 231 forensic loci in a single multiplex reaction. Targeted loci include Amelogenin, 27 common, forensic autosomal STRs, 24 Y-STRs, 7 X-STRs and three classes of single nucleotide polymorphisms (SNPs). The ForenSeq™ kit includes two primer sets: Amelogenin, 58 STRs and 94 identity informative SNPs (iiSNPs) are amplified using DNA Primer Set A (DPMA; 153 loci); if a laboratory chooses to generate investigative leads...
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The Faseb Journal, Apr 1, 2010
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Lecture Notes in Computer Science, 2009
Abstract. Multiple RNA structure alignment is particularly challenging because covarying mutation... more Abstract. Multiple RNA structure alignment is particularly challenging because covarying mutations make sequence information alone insufficient. Many existing tools for multiple RNA alignments first generate pairwise RNA structure alignments and then build the multiple alignment using only the sequence information. Here we present PMFastR, an algorithm which iteratively uses a sequence-structure alignment procedure to build a multiple RNA structure alignment. PMFastR has low memory consumption allowing for the ...
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Journal of Proteome Research, 2011
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Journal of Proteome Research, 2011
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IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2000
Structure-based RNA multiple alignment is particularly challenging because covarying mutations ma... more Structure-based RNA multiple alignment is particularly challenging because covarying mutations make sequence information alone insufficient. Existing tools for RNA multiple alignment first generate pairwise RNA structure alignments and then build the multiple alignment using only sequence information. Here we present PMFastR, an algorithm which iteratively uses a sequence-structure alignment procedure to build a structure-based RNA multiple alignment from one sequence with known structure and a database of sequences from the same family. PMFastR also has low memory consumption allowing for the alignment of large sequences such as 16S and 23S rRNA. The algorithm also provides a method to utilize a multicore environment. We present results on benchmark data sets from BRAliBase, which shows PMFastR performs comparably to other state-of-the-art programs. Finally, we regenerate 607 Rfam seed alignments and show that our automated process creates multiple alignments similar to the manually curated Rfam seed alignments. Thus, the techniques presented in this paper allow for the generation of multiple alignments using sequence-structure guidance, while limiting memory consumption. As a result, multiple alignments of long RNA sequences, such as 16S and 23S rRNAs, can easily be generated locally on a personal computer. The software and supplementary data are available at http://genome.ucf.edu/PMFastR.
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Bioinformatics, 2005
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Bioinformatics, 2005
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Plos One, 2011
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Papers by Jocelyne Bruand