Search Results - "Luca Freschi"

GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions by Farhat, Maha R., Freschi, Luca, Calderon, Roger, Ioerger, Thomas, Snyder, Matthew, Meehan, Conor J., de Jong, Bouke, Rigouts, Leen, Sloutsky, Alex, Kaur, Devinder, Sunyaev, Shamil, van Soolingen, Dick, Shendure, Jay, Sacchettini, Jim, Murray, Megan

“…Drug resistance diagnostics that rely on the detection of resistance-related mutations could expedite patient care and TB eradication. We perform minimum…”
Get full text

Population structure, biogeography and transmissibility of Mycobacterium tuberculosis by Freschi, Luca, Vargas, Roger, Husain, Ashaque, Kamal, S. M. Mostofa, Skrahina, Alena, Tahseen, Sabira, Ismail, Nazir, Barbova, Anna, Niemann, Stefan, Cirillo, Daniela Maria, Dean, Anna S., Zignol, Matteo, Farhat, Maha Reda

“…Mycobacterium tuberculosis is a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity…”
Get full text

In-host population dynamics of Mycobacterium tuberculosis complex during active disease by Vargas, Roger, Freschi, Luca, Marin, Maximillian, Epperson, L Elaine, Smith, Melissa, Oussenko, Irina, Durbin, David, Strong, Michael, Salfinger, Max, Farhat, Maha Reda

“…Tuberculosis (TB) is a leading cause of death globally. Understanding the population dynamics of TB's causative agent complex (Mtbc) in-host is vital for…”
Get full text

A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis by Green, Anna G., Yoon, Chang Ho, Chen, Michael L., Ektefaie, Yasha, Fina, Mack, Freschi, Luca, Gröschel, Matthias I., Kohane, Isaac, Beam, Andrew, Farhat, Maha

“…Long diagnostic wait times hinder international efforts to address antibiotic resistance in M. tuberculosis . Pathogen whole genome sequencing, coupled with…”
Get full text

Genomics of antibiotic‐resistance prediction in Pseudomonas aeruginosa by Jeukens, Julie, Freschi, Luca, Kukavica‐Ibrulj, Irena, Emond‐Rheault, Jean‐Guillaume, Tucker, Nicholas P., Levesque, Roger C.

“…Antibiotic resistance is a worldwide health issue spreading quickly among human and animal pathogens, as well as environmental bacteria. Misuse of antibiotics…”
Get full text

GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning by Gröschel, Matthias I, Owens, Martin, Freschi, Luca, Vargas, Jr, Roger, Marin, Maximilian G, Phelan, Jody, Iqbal, Zamin, Dixit, Avika, Farhat, Maha R

“…Multidrug-resistant Mycobacterium tuberculosis (Mtb) is a significant global public health threat. Genotypic resistance prediction from Mtb DNA sequences…”
Get full text

Functional divergence and evolutionary turnover in mammalian phosphoproteomes by Freschi, Luca, Osseni, Mazid, Landry, Christian R

“…Protein phosphorylation is a key mechanism to regulate protein functions. However, the contribution of this protein modification to species divergence is still…”
Get full text

Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium by Freschi, Luca, Jeukens, Julie, Kukavica-Ibrulj, Irena, Boyle, Brian, Dupont, Marie-Josée, Laroche, Jérôme, Larose, Stéphane, Maaroufi, Halim, Fothergill, Joanne L, Moore, Matthew, Winsor, Geoffrey L, Aaron, Shawn D, Barbeau, Jean, Bell, Scott C, Burns, Jane L, Camara, Miguel, Cantin, André, Charette, Steve J, Dewar, Ken, Déziel, Éric, Grimwood, Keith, Hancock, Robert E W, Harrison, Joe J, Heeb, Stephan, Jelsbak, Lars, Jia, Baofeng, Kenna, Dervla T, Kidd, Timothy J, Klockgether, Jens, Lam, Joseph S, Lamont, Iain L, Lewenza, Shawn, Loman, Nick, Malouin, François, Manos, Jim, McArthur, Andrew G, McKeown, Josie, Milot, Julie, Naghra, Hardeep, Nguyen, Dao, Pereira, Sheldon K, Perron, Gabriel G, Pirnay, Jean-Paul, Rainey, Paul B, Rousseau, Simon, Santos, Pedro M, Stephenson, Anne, Taylor, Véronique, Turton, Jane F, Waglechner, Nicholas, Williams, Paul, Thrane, Sandra W, Wright, Gerard D, Brinkman, Fiona S L, Tucker, Nicholas P, Tümmler, Burkhard, Winstanley, Craig, Levesque, Roger C

“…The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome…”
Get full text

Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting by Dixit, Avika, Freschi, Luca, Vargas, Roger, Calderon, Roger, Sacchettini, James, Drobniewski, Francis, Galea, Jerome T., Contreras, Carmen, Yataco, Rosa, Zhang, Zibiao, Lecca, Leonid, Kolokotronis, Sergios-Orestis, Mathema, Barun, Farhat, Maha R.

“…Whole genome sequencing (WGS) can elucidate Mycobacterium tuberculosis (Mtb) transmission patterns but more data is needed to guide its use in high-burden…”
Get full text

Comparative analysis of mitochondrial genomes of geographic variants of the gypsy moth, Lymantria dispar, reveals a previously undescribed genotypic entity by Djoumad, Abdelmadjid, Nisole, Audrey, Zahiri, Reza, Freschi, Luca, Picq, Sandrine, Gundersen-Rindal, Dawn E., Sparks, Michael E., Dewar, Ken, Stewart, Don, Maaroufi, Halim, Levesque, Roger C., Hamelin, Richard C., Cusson, Michel

“…The gypsy moth, Lymantria dispar L., is one of the most destructive forest pests in the world. While the subspecies established in North America is the…”
Get full text

Prophage Integrase Typing Is a Useful Indicator of Genomic Diversity in Salmonella enterica by Colavecchio, Anna, D'Souza, Yasmin, Tompkins, Elizabeth, Jeukens, Julie, Freschi, Luca, Emond-Rheault, Jean-Guillaume, Kukavica-Ibrulj, Irena, Boyle, Brian, Bekal, Sadjia, Tamber, Sandeep, Levesque, Roger C, Goodridge, Lawrence D

“…is a bacterial species that is a major cause of illness in humans and food-producing animals. exhibits considerable inter-serovar diversity, as evidenced by…”
Get full text

A Multi-Species TaqMan PCR Assay for the Identification of Asian Gypsy Moths (Lymantria spp.) and Other Invasive Lymantriines of Biosecurity Concern to North America by Stewart, Donald, Zahiri, Reza, Djoumad, Abdelmadjid, Freschi, Luca, Lamarche, Josyanne, Holden, Dave, Cervantes, Sandra, Ojeda, Dario I, Potvin, Amélie, Nisole, Audrey, Béliveau, Catherine, Capron, Arnaud, Kimoto, Troy, Day, Brittany, Yueh, Hesther, Duff, Cameron, Levesque, Roger C, Hamelin, Richard C, Cusson, Michel

“…Preventing the introduction and establishment of forest invasive alien species (FIAS) such as the Asian gypsy moth (AGM) is a high-priority goal for countries…”
Get full text

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping by Mottawea, Walid, Duceppe, Marc-Olivier, Dupras, Andrée A, Usongo, Valentine, Jeukens, Julie, Freschi, Luca, Emond-Rheault, Jean-Guillaume, Hamel, Jeremie, Kukavica-Ibrulj, Irena, Boyle, Brian, Gill, Alexander, Burnett, Elton, Franz, Eelco, Arya, Gitanjali, Weadge, Joel T, Gruenheid, Samantha, Wiedmann, Martin, Huang, Hongsheng, Daigle, France, Moineau, Sylvain, Bekal, Sadjia, Levesque, Roger C, Goodridge, Lawrence D, Ogunremi, Dele

“…Non-typhoidal is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of responsible for disease outbreaks is…”
Get full text

The Widespread Multidrug-Resistant Serotype O12 Pseudomonas aeruginosa Clone Emerged through Concomitant Horizontal Transfer of Serotype Antigen and Antibiotic Resistance Gene Clusters by Thrane, Sandra Wingaard, Taylor, Véronique L, Freschi, Luca, Kukavica-Ibrulj, Irena, Boyle, Brian, Laroche, Jérôme, Pirnay, Jean-Paul, Lévesque, Roger C, Lam, Joseph S, Jelsbak, Lars

“…The O-specific antigen (OSA) in Pseudomonas aeruginosa lipopolysaccharide is highly varied by sugar identity, side chains, and bond between O-repeats. These…”
Get full text

Estimation of country-specific tuberculosis resistance antibiograms using pathogen genomics and machine learning by Dixit, Avika, Freschi, Luca, Vargas, Roger, Gröschel, Matthias I, Nakhoul, Maria, Tahseen, Sabira, Alam, S M Masud, Kamal, S M Mostofa, Skrahina, Alena, Basilio, Ramon P, Lim, Dodge R, Ismail, Nazir, Farhat, Maha R

“…BackgroundGlobal tuberculosis (TB) drug resistance (DR) surveillance focuses on rifampicin. We examined the potential of public and surveillance Mycobacterium…”
Get full text

Phosphorylation network rewiring by gene duplication by Freschi, Luca, Courcelles, Mathieu, Thibault, Pierre, Michnick, Stephen W, Landry, Christian R

“…Elucidating how complex regulatory networks have assembled during evolution requires a detailed understanding of the evolutionary dynamics that follow gene…”
Get full text

The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance by Emond-Rheault, Jean-Guillaume, Hamel, Jérémie, Jeukens, Julie, Freschi, Luca, Kukavica-Ibrulj, Irena, Boyle, Brian, Tamber, Sandeep, Malo, Danielle, Franz, Eelco, Burnett, Elton, Daigle, France, Arya, Gitanjali, Sanderson, Kenneth, Wiedmann, Martin, Slawson, Robin M., Weadge, Joel T., Stephan, Roger, Bekal, Sadjia, Gruenheid, Samantha, Goodridge, Lawrence D., Levesque, Roger C.

“…The emergence of multidrug-resistant bacterial strains worldwide has become a serious problem for public health over recent decades. The increase in…”
Get full text

Complete Genome Sequences of Two Phage-Like Plasmids Carrying the CTX-M-15 Extended-Spectrum β-Lactamase Gene by Colavecchio, Anna, Jeukens, Julie, Freschi, Luca, Edmond Rheault, Jean-Guillaume, Kukavica-Ibrulj, Irena, Levesque, Roger C, LeJeune, Jeffrey, Goodridge, Lawrence

“…Two similar phage-like plasmids carrying CTX-M-15 resistance cassettes were identified from two environmental isolates. They demonstrate strong nucleotide…”
Get full text

qPCA: a scalable assay to measure the perturbation of protein-protein interactions in living cells by Freschi, Luca, Torres-Quiroz, Francisco, Dubé, Alexandre K, Landry, Christian R

“…One of the most important challenges in systems biology is to understand how cells respond to genetic and environmental perturbations. Here we show that the…”
Get more information

AnCo3, a New Member of the Emerging Family of Phage-Like Plasmids by Colavecchio, Anna, Jeukens, Julie, Freschi, Luca, Edmond Rheault, Jean-Guillaume, Kukavica-Ibrulj, Irena, Levesque, Roger, Goodridge, Lawrence

“…A phage-like plasmid isolated from a clinical isolate of serovar Derby has strong nucleotide sequence identity to the phage-like plasmids pSTM_phi isolated…”
Get full text