Amin Emad

shayan.hajhashemi@mila.quebec

Google Scholar

Shayan Hajhashemi

PhD - McGill University

William Ma

Master's Research - McGill University

william.ma@mila.quebec

cedrique.shum-tim@mila.quebec

Ali Saberi

PhD - McGill University

ali.saberi@mila.quebec

Cedrique Shum-Tim

PhD - McGill University

Kiri Stern

PhD - McGill University

kiri.stern@mila.quebec

Chen Su

PhD - McGill University

chen.su@mila.quebec

Justin Szeto

PhD - McGill University

szetojus@mila.quebec

joseph.szymborski@mila.quebec

Joseph Szymborski

Postdoctorate - McGill University

Website

Publications

RAPPPID: towards generalizable protein interaction prediction with AWD-LSTM twin networks

Joseph Szymborski

Online-only supplementary data is available at the journal’s website.

2021-12-31

Bioinformatics (published)

Identification of transcriptional regulatory network associated with response of host epithelial cells to SARS-CoV-2

Su Chen

Simon Rousseau

Identification of transcriptional regulatory mechanisms and signaling networks involved in the response of host cells to infection by SARS-C… (see more)oV-2 is a powerful approach that provides a systems biology view of gene expression programs involved in COVID-19 and may enable the identification of novel therapeutic targets and strategies to mitigate the impact of this disease. In this study, our goal was to identify a transcriptional regulatory network that is associated with gene expression changes between samples infected by SARS-CoV-2 and those that are infected by other respiratory viruses to narrow the results on those enriched or specific to SARS-CoV-2. We combined a series of recently developed computational tools to identify transcriptional regulatory mechanisms involved in the response of epithelial cells to infection by SARS-CoV-2, and particularly regulatory mechanisms that are specific to this virus when compared to other viruses. In addition, using network-guided analyses, we identified kinases associated with this network. The results identified pathways associated with regulation of inflammation (MAPK14) and immunity (BTK, MBX) that may contribute to exacerbate organ damage linked with complications of COVID-19. The regulatory network identified herein reflects a combination of known hits and novel candidate pathways supporting the novel computational pipeline presented herein to quickly narrow down promising avenues of investigation when facing an emerging and novel disease such as COVID-19.

2021-12-13

Scientific Reports (published)

Distinct miRNA Profile of Cellular and Extracellular Vesicles Released from Chicken Tracheal Cells Following Avian Influenza Virus Infection

Kelsey O’Dowd

Mehdi Emam

Mohamed Reda El Khili

Eveline M. Ibeagha-Awemu

Carl A. Gagnon

Neda Barjesteh

Innate responses provide the first line of defense against viral infections, including the influenza virus at mucosal surfaces. Communicatio… (see more)n and interaction between different host cells at the early stage of viral infections determine the quality and magnitude of immune responses against the invading virus. The release of membrane-encapsulated extracellular vesicles (EVs), from host cells, is defined as a refined system of cell-to-cell communication. EVs contain a diverse array of biomolecules, including microRNAs (miRNAs). We hypothesized that the activation of the tracheal cells with different stimuli impacts the cellular and EV miRNA profiles. Chicken tracheal rings were stimulated with polyI:C and LPS from Escherichia coli 026:B6 or infected with low pathogenic avian influenza virus H4N6. Subsequently, miRNAs were isolated from chicken tracheal cells or from EVs released from chicken tracheal cells. Differentially expressed (DE) miRNAs were identified in treated groups when compared to the control group. Our results demonstrated that there were 67 up-regulated miRNAs, 157 down-regulated miRNAs across all cellular and EV samples. In the next step, several genes or pathways targeted by DE miRNAs were predicted. Overall, this study presented a global miRNA expression profile in chicken tracheas in response to avian influenza viruses (AIV) and toll-like receptor (TLR) ligands. The results presented predicted the possible roles of some DE miRNAs in the induction of antiviral responses. The DE candidate miRNAs, including miR-146a, miR-146b, miR-205a, miR-205b and miR-449, can be investigated further for functional validation studies and to be used as novel prophylactic and therapeutic targets in tailoring or enhancing antiviral responses against AIV.

2020-08-04

Vaccines (published)

Poisson Group Testing: A Probabilistic Model for Boolean Compressed Sensing

Olgica Milenkovic

We introduce a novel probabilistic group testing framework, termed Poisson group testing, in which the number of defectives follows a right-… (see more)truncated Poisson distribution. The Poisson model has a number of new applications, including dynamic testing with diminishing relative rates of defectives. We consider both nonadaptive and semi-adaptive identification methods. For nonadaptive methods, we derive a lower bound on the number of tests required to identify the defectives with a probability of error that asymptotically converges to zero; in addition, we propose test matrix constructions for which the number of tests closely matches the lower bound. For semiadaptive methods, we describe a lower bound on the expected number of tests required to identify the defectives with zero error probability. In addition, we propose a stage-wise reconstruction algorithm for which the expected number of tests is only a constant factor away from the lower bound. The methods rely only on an estimate of the average number of defectives, rather than on the individual probabilities of subjects being defective.

2015-08-14

IEEE Transactions on Signal Processing (published)