Published articles from the last five years

01 Sep 2023
Mitochondrial DNA Copy Number and Heteroplasmy in Monozygotic Twins Discordant for Schizophrenia.
Phyo W Win, Shiva M Singh, Christina A Castellani
Twin research and human genetics : the official journal of the International Society for Twin Studies 1-10 (2023)
19 May 2023
Developing OCHROdb, a comprehensive quality checked database of open chromatin regions from sequencing data.
Parisa Shooshtari, Samantha Feng, Viswateja Nelakuditi, Reza Asakereh, Nader Hosseini Naghavi, Justin Foong, Michael Brudno, Chris Cotsapas
Scientific reports 13, 8106 (2023)
28 Apr 2023
The EBV Gastric Cancer Resource (EBV-GCR): A Suite of Tools for Investigating EBV-Associated Human Gastric Carcinogenesis.
Mikhail Y Salnikov, Eric Wang, Erik Christensen, Martin A Prusinkiewicz, Parisa Shooshtari, Joe S Mymryk
Viruses 15, (2023)
28 Feb 2023
HexSE: Simulating evolution in overlapping reading frames.
Laura Muñoz-Baena, Kaitlyn E Wade, Art F Y Poon
Virus evolution 9, vead009 (2023)
23 Feb 2023
Clustering Highly Divergent Homologous Proteins: An Alignment-Free Method.
Laura Muñoz-Baena, Art F Y Poon
Current protocols 3, e666 (2023)
13 Jan 2023
bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression.
Roux-Cil Ferreira, Emmanuel Wong, Art F Y Poon
Virus evolution 9, veac120 (2023)
01 Jan 2023
Evaluation of single-cell RNAseq labelling algorithms using cancer datasets.
Erik Christensen, Ping Luo, Andrei Turinsky, Mia Husić, Alaina Mahalanabis, Alaine Naidas, Juan Javier Diaz-Mejia, Michael Brudno, Trevor Pugh, Arun Ramani, Parisa Shooshtari
Briefings in bioinformatics 24, (2023)
01 Dec 2022
Optimized phylogenetic clustering of HIV-1 sequence data for public health applications.
Connor Chato, Yi Feng, Yuhua Ruan, Hui Xing, Joshua Herbeck, Marcia Kalish, Art F Y Poon
PLoS computational biology 18, e1010745 (2022)
25 Nov 2022
Evaluation of single-cell RNA-seq clustering algorithms on cancer tumor datasets.
Alaina Mahalanabis, Andrei L Turinsky, Mia Husić, Erik Christensen, Ping Luo, Alaine Naidas, Michael Brudno, Trevor Pugh, Arun K Ramani, Parisa Shooshtari
Computational and structural biotechnology journal 20, 6375-6387 (2022)
25 Nov 2022
Mitochondrial genomic integrity and the nuclear epigenome in health and disease.
Amanda L Morin, Phyo W Win, Angela Z Lin, Christina A Castellani
Frontiers in endocrinology 13, 1059085 (2022)
18 Nov 2022
Molecular source attribution.
Elisa Chao, Connor Chato, Reid Vender, Abayomi S Olabode, Roux-Cil Ferreira, Art F Y Poon
PLoS computational biology 18, e1010649 (2022)
15 Oct 2022
Single-Cell Chromatin Accessibility Data Combined with GWAS Improves Detection of Relevant Cell Types in 59 Complex Phenotypes.
Akash Chandra Das, Aidin Foroutan, Brian Qian, Nader Hosseini Naghavi, Kayvan Shabani, Parisa Shooshtari
International journal of molecular sciences 23, (2022)
16 Sep 2022
Complementary approaches involving monozygotic twins and single neuron genomics support postzygotic somatic mutations in schizophrenia.
S M Singh, P W Win, C A Castellani
Schizophrenia research 248, 228-230 (2022)
10 Sep 2022
TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool.
Erik Christensen, Alaine Naidas, David Chen, Mia Husic, Parisa Shooshtari
PloS one 17, e0272302 (2022)
24 Aug 2022
A Deep Learning Approach to Capture the Essence of Candida albicans Morphologies
Van Bettauer, Anna Carolina Borges Pereira Costa, Raha P Omran, Samira Massahi, Eftyhios Kirbizakis, Shawn Simpson, Vanessa Dumeaux, Chris Law, Malcolm Whiteway, Michael T Hallett.
Microbiology Spectrum (2022)
22 Aug 2022
Candida albicans exhibits heterogeneous and adaptive cytoprotective responses to anti-fungal compounds
Vanessa Dumeaux^, Samira Massahi^, Van Bettauer, Sanny Khurdia, Anna Carolina Borges Pereira Costa, Raha Parvizi Omran, Shawn Simpson, Jinglin Lucy Xie, Malcolm Whiteway, Judith Berman, Michael T Hallett.
Biorxiv (2022)
20 Aug 2022
Exposure of Greenlandic Inuit and South African VhaVenda men to the persistent DDT metabolite is associated with an altered sperm epigenome at regions implicated in paternal epigenetic transmission and developmental disease – a cross-sectional study
Ariane Lismer, Xiaojian Shao^, Marie-Charlotte Dumargne^, Christine Lafleur, Romain Lambrot, Donovan Chan, Gunnar Toft, Jens Peter Bonde, Amanda J. MacFarlane, Riana Bornman, Natalie Aneck-Hahn, Sean Patrick, Janice M. Bailey, Christiaan de Jager, Vanessa Dumeaux†, Jacquetta M. Trasler†, and Sarah Kimmins†
Biorxiv (2022)
03 Aug 2022
Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada.
Angela McLaughlin, Vincent Montoya, Rachel L Miller, Gideon J Mordecai, , Michael Worobey, Art F Y Poon, Jeffrey B Joy
eLife 11, (2022)
21 Jun 2022
Local and systemic transcriptomic responses from acute exercise induced muscle damage of the human knee extensors.
Eric A Kirk, Christina A Castellani, Timothy J Doherty, Charles L Rice, Shiva M Singh
Physiological genomics 54, 305-315 (2022)
03 May 2022
Revisiting the recombinant history of HIV-1 group M with dynamic network community detection.
Abayomi S Olabode, Garway T Ng, Kaitlyn E Wade, Mikhail Salnikov, Heather E Grant, David W Dick, Art F Y Poon
Proceedings of the National Academy of Sciences of the United States of America 119, e2108815119 (2022)
24 Mar 2022
Sperm histone H3 lysine 4 tri-methylation serves as a metabolic sensor of paternal obesity and is associated with the inheritance of metabolic dysfunction
Anne-Sophie Pepin, Christine Lafleur, Romain Lambrot, Vanessa Dumeaux, Sarah Kimmins.
Molecular Metabolism (2022)
25 Feb 2022
Using networks to analyze and visualize the distribution of overlapping genes in virus genomes.
Laura Muñoz-Baena, Art F Y Poon
PLoS pathogens 18, e1010331 (2022)