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)
24 Dec 2021
Network science inspires novel tree shape statistics.
Leonid Chindelevitch, Maryam Hayati, Art F Y Poon, Caroline Colijn
PloS one 16, e0259877 (2021)
11 Dec 2021
Circular RNA mediated gene regulation in chronic diabetic complications.
Nikhil S Patil, Biao Feng, Zhaoliang Su, Christina A Castellani, Subrata Chakrabarti
Scientific reports 11, 23766 (2021)
04 Dec 2021
Genome-wide analysis of mitochondrial DNA copy number reveals loci implicated in nucleotide metabolism, platelet activation, and megakaryocyte proliferation.
R J Longchamps, S Y Yang, C A Castellani, W Shi, J Lane, M L Grove, T M Bartz, C Sarnowski, C Liu, K Burrows, A L Guyatt, T R Gaunt, T Kacprowski, J Yang, P L De Jager, L Yu, A Bergman, R Xia, M Fornage, M F Feitosa, M K Wojczynski, A T Kraja, M A Province, N Amin, F Rivadeneira, H Tiemeier, A G Uitterlinden, L Broer, J B J Van Meurs, C M Van Duijn, L M Raffield, L Lange, S S Rich, R N Lemaitre, M O Goodarzi, C M Sitlani, A C Y Mak, D A Bennett, S Rodriguez, J M Murabito, K L Lunetta, N Sotoodehnia, G Atzmon, K Ye, N Barzilai, J A Brody, B M Psaty, K D Taylor, J I Rotter, E Boerwinkle, N Pankratz, D E Arking
Human genetics 141, 127-146 (2022)
29 Sep 2021
Validation of a Genotype-Independent Hepatitis C Virus Near-Whole Genome Sequencing Assay.
Hope R Lapointe, Weiyan Dong, Winnie W Y Dong, Don Kirkby, Conan Woods, Art F Y Poon, Anita Y M Howe, P Richard Harrigan, Chanson J Brumme
Viruses 13, (2021)
13 Sep 2021
Genetic-epigenetic interactions in paternal transgenerational inheritance of metabolic disorders
Anne-Sophie Pepin, Christine Lafleur, Romain Lambrot, Vanessa Dumeaux, Sarah Kimmins.
Biorxiv (2021)
21 Aug 2021
Epigenome-wide association study of mitochondrial genome copy number.
Penglong Wang, Christina A Castellani, Jie Yao, Tianxiao Huan, Lawrence F Bielak, Wei Zhao, Jeffrey Haessler, Roby Joehanes, Xianbang Sun, Xiuqing Guo, Ryan J Longchamps, JoAnn E Manson, Megan L Grove, Jan Bressler, Kent D Taylor, Tuuli Lappalainen, Silva Kasela, David J Van Den Berg, Lifang Hou, Alexander Reiner, Yongmei Liu, Eric Boerwinkle, Jennifer A Smith, Patricia A Peyser, Myriam Fornage, Stephen S Rich, Jerome I Rotter, Charles Kooperberg, Dan E Arking, Daniel Levy, Chunyu Liu,
Human molecular genetics 31, 309-319 (2021)
21 Jul 2021
Whole-genome sequencing of H3K4me3 and DNA methylation in human sperm reveals regions of overlap linked to fertility and development
Romain Lambrot, Donovan Chan, Xiaojian Shao, Mahmoud Aarabbi, Toni Kwan, Guillaume Bourque, Sergey Moskovtsev, Clifford Librach, Jacquetta Trasler, Vanessa Dumeaux", Sarah Kimmins". ("co-corresponding authors)
Cell Reports (2021)
11 Jun 2021
ChIP-seq protocol for sperm cells and embryos to assess environmental impacts and epigenetic inheritance
Ariane Lismer, Romain Lambrot, Christine Lafleur, Vanessa Dumeaux, Sarah Kimmins
STAR Protocols (2021)
11 Jun 2021
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.
Biorxiv (2021)
01 May 2021
Analysis of TERT Isoforms across TCGA, GTEx and CCLE Datasets.
Mathushan Subasri, Parisa Shooshtari, Andrew J Watson, Dean H Betts
Cancers 13, (2021)
23 Feb 2021
Tuning intrinsic disorder predictors for virus proteins.
Gal Almog, Abayomi S Olabode, Art F Y Poon
Virus evolution 7, veaa106 (2021)
16 Feb 2021
Histone H3 lysine 4 trimethylation in sperm is transmitted to the embryo and associated with diet-induced phenotypes in the offspring
Ariane Lismer, Vanessa Dumeaux, Christine Lafleur, Romain Lambrot, Julie Brind'Amour, Matthew C. Lorincz, Sarah Kimmins
Developmental Cell (2021)
29 Jan 2021
Quantifying the clonality and dynamics of the within-host HIV-1 latent reservoir.
Roux-Cil Ferreira, Jessica L Prodger, Andrew D Redd, Art F Y Poon
Virus evolution 7, veaa104 (2021)
15 Jan 2021
Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease.
Stephanie Y Yang, Christina A Castellani, Ryan J Longchamps, Vamsee K Pillalamarri, Brian O'Rourke, Eliseo Guallar, Dan E Arking
Genome research 31, 349-358 (2021)
06 Jan 2021
A metagenomic-based study of two sites from the Barbadian reef system
Shawn Simpson, Van Bettauer, Arthi Ramachandran, Susanne Kramer, Susan Mahon, Monica Medina, Yvonne Valles, Vanessa Dumeaux, Henri Valles, David Walsh, Michael T Hallett
Biorxiv (2021)