Published articles from the last five years

18 Aug 2026
CycleMix: Gaussian mixture modeling of the cell cycle.
Jack Edward Peplinski, Tallulah S Andrews
Bioinformatics advances 6, vbag179 (2026)
07 Aug 2026
Human mesenchymal stromal cell extracellular vesicles maintain therapeutic miRNA cargo despite exposure to cystic fibrosis bronchoalveolar lavage fluid.
Sara Rolandsson Enes, Thomas H Hampton, Jayita Barua, Zeta Mui, Tobias Tertel, Bernd Giebel, David H McKenna, Pingzhao Hu, Alix Ashare, Bruce A Stanton, Claudia C Dos Santos, Daniel J Weiss
Cytotherapy 28, 102937 (2026)
28 Jul 2026
Spatial transcriptomics supports a role for SOX4-driven signaling throughout the disease course of biliary atresia.
Ioannis A Ziogas, Katie R Conover, Evgenia Dobrinskikh, Saif I Al-Juboori, Kyle D Gromer, Padmini Malladi, Clyde J Wright, Ronald J Sokol, Tallulah Andrews, Sarah A Taylor
Hepatology communications 10, (2026)
24 Jul 2026
Selection profiles in RNA viruses reflect the characteristics of viruses more than individual proteins.
Laura Muñoz-Baena, Hugo G Castelán-Sánchez, Sareh Bagherichimeh, Paula Magbor, Jorge Rojas-Vargas, Amjad Khan, Abayomi S Olabode, Art F Y Poon
PLoS pathogens 22, e1014457 (2026)
13 Jul 2026
Pervasive HIV recombination limits the utility of circulating recombinant form nomenclature.
Heather E Grant, Abayomi S Olabode, Dorothea Seiler Vellame, Art F Y Poon, Andrew J Leigh Brown, David L Robertson
PLoS pathogens 22, e1014286 (2026)
24 Jun 2026
Deep Unsupervised Domain Adaptation for Translating Cancer Dependency Maps From Cell Lines to Breast Cancer Tumor Genomics.
Yu Shi, Wei Xu, Pingzhao Hu
Genetic epidemiology 50, e70044 (2026)
20 Jun 2026
Chromosomal and immune dysregulation underlying granular mitosis in glioblastoma.
Rachel Barboza, Xuan Wang, August Lin, Eric Liu, Pramath Kakodkar, Yayuan Zhao, Quinn Le, Christina A Castellani, Qi Zhang
Brain pathology (Zurich, Switzerland) e70115 (2026)
17 Jun 2026
Hac1-independent functions of Ire1 drive morphogenesis in Candida albicans through distinct transcriptional programs.
Samuel Stack-Couture, Gabriela Nunes Marsiglio Librais, Bryan Lung, Julie Genereaux, Viola Halder, Vanessa Dumeaux, Rebecca S Shapiro, Patrick Lajoie
Journal of cell science 139, (2026)
12 Jun 2026
Heterozygous Nonsense Mutation in the Nuclear Transport Factor KPNA7, a Maternal Factor Active in Embryonic Tissues, Causes Autosomal Dominant Otosclerosis.
Tammy Benteau, Nelly Abdelfatah, Anne Griffin, Cindy Penney, Pingzhao Hu, Susan G Stanton, Guangju Zhai, Maxime Maheu, Curtis R French, Terry-Lynn Young
International journal of molecular sciences 27, (2026)
04 Jun 2026
NOD2 activation reprograms infiltrating inflammatory monocytes in the Zika virus infected CNS to maintain neural correlates of learning and memory.
Jeremy D Hill, Alice H W Dong, Joshua Liu, Marina Diniz Barbezani, Tallulah S Andrews, Robyn S Klein
bioRxiv : the preprint server for biology (2026)
27 Apr 2026
Mycobacteria Amplicon Sequencing Tool: automated resistance prediction and lineage classification for Mycobacterium tuberculosis.
Idowu B Olawoye, Maxim Fedorov, Robert A Petit, Jennifer L Guthrie
Microbiology resource announcements 15, e0003226 (2026)
20 Apr 2026
Systemic and Local Adiposity in the Bone Marrow Microenvironment Associated With Improved Prognosis in Hodgkin Lymphoma: Imaging and Molecular Analysis.
Andreia Matos, William P Cawthorn, Joana Marinho-Dias, Sofia Ramalheira, Susana Roncon, Dulcineia Pereira, Teresa Ribeiro, Carla Rodrigues, Mário Mariz, Ana Miranda, Helena Brízido, Manuel Bicho, Pedro Medeiros, Ana Carneiro, Fernanda Trigo, Pingzhao Hu, Flávia Pereira, Hugo Duarte, Calum D Gray, Tom Macgillivray, Alan G Ramsay, Maria J Oliveira, Ricardo Ribeiro
International journal of cancer 159, 782-796 (2026)
14 Apr 2026
PHYCUT: Scalable Multiplex CRISPR/Cas9 Editing for Genome Engineering in the Diatom Phaeodactylum tricornutum.
Emily E Stuckless, Lian S Gai, Samuel S Slattery, Kira H Dempsey, Tyler S Browne, Gregory B Gloor, David R Edgell
ACS synthetic biology 15, 1850-1865 (2026)
06 Apr 2026
A copula-infused graph neural network for cell type classification in single-cell RNA sequencing data.
Shijie Min, Leann Lac, Pingzhao Hu
Computational and structural biotechnology journal 31, 485-499 (2026)
02 Apr 2026
EpigeneticAgePipeline: An R Package for Comprehensive Assessment of Epigenetic Age Metrics From Methylation Microarrays.
Stanislav Rayevskiy, Quinn Le, Julia Nguyen, Steven Q Chen, Christina A Castellani
Bioinformatics and biology insights 20, 11779322261433665 (2026)
31 Mar 2026
Plant-based dietary patterns are associated with slower epigenetic aging.
Hyunju Kim, Christina A Castellani, Jiantao Ma, Alexis C Wood, Audrey Ting, Morgan E Grams, Bing Yu, Kelly Ruggles, James S Floyd, Dan E Arking, Casey M Rebholz
Aging 18, 138-158 (2026)
28 Feb 2026
Transcriptomic analysis of cells following decreased mitochondrial DNA-copy number reveals compensatory mechanisms in mitochondrial DNA replication and cellular energetics.
Jiaqi Xie, Phyo W Win, Charles Newcomb, Shaopeng Zeng, Christina A Castellani, Dan E Arking
Experimental cell research 458, 114951 (2026)
16 Feb 2026
Better data for better predictions: data curation improves deep learning for sgRNA/Cas9 prediction.
Tyler S Browne, David R Edgell, Gregory B Gloor
PeerJ 14, e20706 (2026)
12 Feb 2026
Applications of AI to single-cell and spatial transcriptomics: current state-of-the-art and challenges.
Boris Tchatchoua Ngassam, Huilin Niu, Sunny Pang, Valeryia Shydlouskaya, Tallulah S Andrews
Frontiers in bioinformatics 5, 1715821 (2025)
05 Feb 2026
Viral mimicry acts as a tumor suppressor in colitis.
Frederikke Larsen, Will Jeong, Daniel Schep, Hayley J Good, Alice E Shin, Liyue Zhang, Mathieu F Derouet, Timothy C Wang, Christina A Castellani, Parisa Shooshtari, Samuel Asfaha
Nature communications 17, 1313 (2026)
04 Feb 2026
Incorporating Scale Uncertainty into Differential Expression Analyses Using ALDEx2.
Scott J Dos Santos, Gregory B Gloor
Current protocols 6, e70307 (2026)
17 Jan 2026
Developing a comprehensive database and search tool for single-cell ATAC-seq data.
Arrian Gibson-Khademi, Jonathan Wang, Erik Christensen, Parisa Shooshtari
Scientific reports 16, 2201 (2026)
15 Jan 2026
Machine learning reveals sequence and methylation determinants of SaCas9-PAM interactions in bacteria.
Dalton T Ham, Tyler S Browne, Claire Q Zhang, Gary W Foo, Aathavan S Uruthirapathy, Gregory B Gloor, David R Edgell
Nucleic acids research 54, (2026)
07 Jan 2026
Estimating HIV-1 Viremic Time From Reservoir Sequence Diversity With Uncertainty Quantification.
Edward N Kankaka, Stephen Tomusange, Taddeo Kityamuweesi, Gabriel Quiros, Nicholas DiRico, Adam A Capoferri, Owen Baker, Erin E Brown, Jernelle Miller, Sharada Saraf, Charles Kirby, Briana Lynch, Jada Hackman, Craig Martens, Thomas C Quinn, Eileen P Scully, Amjad Khan, Art F Y Poon, Jessica L Prodger, Ronald M Galiwango, Steven J Reynolds, Andrew D Redd
The Journal of infectious diseases 233, e1165-e1172 (2026)
01 Jan 2026
4R-tau seeding activity reveals molecular subtypes in progressive supranuclear palsy.
Ivan Martinez-Valbuena, Seojin Lee, Enrique Santamaria, Joaquín Fernández-Irigoyen, Shelley L Forrest, Silvia Zampar, Jun Li, Hidetomo Tanaka, Blas Couto, Nikolai Gil D Reyes, Syeda Hania Qamar, Ali M Karakani, Ain Kim, Konstantin Senkevich, Ekaterina Rogaeva, Susan H Fox, M Carmela Tartaglia, Naomi P Visanji, Martin Ingelsson, Tallulah Andrews, Anthony E Lang, Gabor G Kovacs
Nature communications 17, 1006 (2025)
23 Dec 2025
Mitochondrial DNA copy number reduction via in vitro TFAM knockout remodels the nuclear epigenome and transcriptome.
Phyo W Win, Julia Nguyen, Elly H Shin, Tyler S Nagano, Brent Selimi, Katie Hong, Anahita M Meybodi, Bradley P Yates, Emma V Burke, David E Carter, Gregory A Newby, Charles Newcomb, Dan E Arking, Christina A Castellani
Epigenomics 18, 27-44 (2026)
03 Dec 2025
Epigenome-wide association study of nuclear DNA methylation in relation to mitochondrial heteroplasmy.
Meng Lai, Kyeezu Kim, Yinan Zheng, Christina A Castellani, Scott M Ratliff, Mengyao Wang, Xue Liu, Jeffrey Haessler, Tianxiao Huan, Kwadwo Bonsu, Charles Newcomb, Kyler McKessy, Lawrence F Bielak, Wei Zhao, Roby Joehanes, Jiantao Ma, Xiuqing Guo, JoAnn E Manson, Megan L Grove, Jan Bressler, Kent D Taylor, Tuuli Lappalainen, Silva Kasela, Thomas W Blackwell, Nicole J Lake, Jessica D Faul, Kendra R Ferrier, Stephen C Ekker, Lifang Hou, Charles Kooperberg, Alexander P Reiner, Kai Zhang, Patricia A Peyser, Myriam Fornage, Eric Boerwinkle, Laura M Raffield, April P Carson, Stephen S Rich, Yongmei Liu, Daniel Levy, Jerome I Rotter, Jennifer A Smith, Dan E Arking, Chunyu Liu,
Nature communications 16, 10962 (2025)
02 Dec 2025
Ancestral reconstruction supports that loss of Nef-mediated T cell modulation coincided with the emergence of pathogenic lentiviruses.
Angelina M Baldino, Mitchell J Mumby, Cassandra R Edgar, Abayomi S Olabode, Art F Y Poon, Jimmy D Dikeakos
Journal of virology 99, e0154825 (2025)
27 Nov 2025
Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures.
Mohamed Meawad, Dalwinder Singh, Alice Deng, Rohan Sonthalia, Evelyn Cai, Vanessa Dumeaux
Microbiome 13, 241 (2025)
26 Nov 2025
Transcriptomic analysis of cells following decreased mitochondrial DNA-copy number reveals compensatory mechanisms in mitochondrial DNA replication and cellular energetics.
Jiaqi Xie, Phyo W Win, Charles Newcomb, Shaopeng Zeng, Christina A Castellani, Dan E Arking
bioRxiv : the preprint server for biology (2025)
24 Nov 2025
Cholinergic synaptic plasticity shapes resilience and vulnerability to tau.
Kate M Onuska, Lauren A Devito, Hayley Rc Shanks, Qi Qi, Alycia M Crooks, Roy Am Haast, Tallulah S Andrews, Kayla M Williams, Flavio H Beraldo, Ting Qiu, Alfonso Fajardo-Valdez, Alfie Wearn, Gary R Turner, Etienne Aumont, Jonathan D Thiessen, Matthew S Fox, Justin W Hicks, Timothy J Bussey, Lisa M Saksida, Jennifer Tremblay-Mercier, John Cs Breitner, Jean-Paul Soucy, Judes Poirier, Marc-Andre Bedard, Sylvia Villeneuve, Vania F Prado, Marco Am Prado, R Nathan Spreng, Taylor W Schmitz,
bioRxiv : the preprint server for biology (2025)
19 Nov 2025
Generative AI for the Design of Molecules: Advances and Challenges.
Yan Sun, Lianghong Chen, Zihao Jing, Yan Yi Li, Dongkyu Kim, Jing-Yan Gao, Reza Noroozi, Grace Y Yi, Conrard Giresse Tetsassi Feugmo, Anna Klinkova, Kyla Sask, Agustinus Kristiadi, Boyu Wang, Elizabeth R Gillies, Kun Ping Lu, HaoTian Harvey Shi, Pingzhao Hu
Journal of chemical information and modeling 65, 12668-12690 (2025)
15 Nov 2025
Astrocytic Chromatin Remodeler ATRX Gates Hippocampal Memory Consolidation Through Metabolic and Synaptic Regulation.
Miguel A Pena-Ortiz, Julia K Sunstrum, Alireza Ghahramani, Haley McConkey, Vanessa Dumeaux, Wataru Inoue, Nathalie G Bérubé
Glia 74, e70098 (2026)
07 Nov 2025
Acinar-specific loss of activating transcription factor 3 restricts KRASG12D mediated transcriptional changes and PanIN progression.
Mickenzie B Martin, Fatemeh Mousavi, Gavin Goebel, Domenic Di Stasi, Alesia Mano, Andrei Glogov, Liena Zhao, Gianni Di Guglielmo, Parisa Shooshtari, Christopher L Pin
Cell death discovery 11, 503 (2025)
04 Nov 2025
Population structure of Mycobacterium avium subsp. hominissuis provides new insights into genomic evolution.
Idowu B Olawoye, David Alexander, Jennifer L Guthrie
Microbial genomics 11, (2025)
31 Oct 2025
Widespread emergence of Staphylococcus aureus with variant FarR regulators and enhanced resistance to antimicrobial fatty acids within clonal complex CC5, CC8, and CC97 strains from human and bovine hosts.
Camryn M Bonn-Dunbar, Idowu B Olawoye, Akanksha Thukral, Jennifer L Guthrie, Martin J McGavin
Microbiology spectrum 13, e0227825 (2025)
24 Oct 2025
Association of Epigenetic Age Acceleration and Mitochondrial DNA-Based Aging Metrics Provides Insights Into Mechanisms of Aging-Related Diseases.
Mengyao Wang, Yinan Zheng, Meng Lai, Emmanuel Saake, Xue Liu, Xiuqing Guo, Kent D Taylor, Tianxiao Huan, Roby Joehanes, Drew R Nannini, Kai Zhang, Nicole J Lake, Christina A Castellani, Stephen S Rich, Jerome I Rotter, Yongmei Liu, Laura M Raffield, April P Carson, Myriam Fornage, Jiantao Ma, Dan E Arking, Lifang Hou, Daniel Levy, Chunyu Liu
Aging cell 24, e70279 (2025)
24 Oct 2025
Author Correction: Towards a reference cell atlas of liver diversity over the human lifespan.
Sarah A Taylor, Gary D Bader, Sonya MacParland, Alan C Mullen, Tallulah Andrews, Alex G Cuenca, Ramanuj DasGupta, Adam J Gehring, Dominic Grün, Martin Guilliams, Aliya Gulamhusein, Neil C Henderson, Gideon Hirschfield, Stacey S Huppert, Shalev Itzkovitz, Z Gordon Jiang, Georg M Lauer, Ian McGilvray, Krupa R Mysore, Carlos J Pirola, Gerald Quon, Mohammad Rahbari, Aviv Regev, Amanda Ricciuto, Charlotte L Scott, Ankur Sharma, Silvia Sookoian, Michele M Tana, Sarah A Teichmann, Ludovic Vallier, Ioannis S Vlachos, Bruce Wang, Mei Zhen
Nature reviews. Gastroenterology & hepatology 23, 110 (2026)
16 Oct 2025
Spatiotemporal structure of SARS-CoV-2 mutational frequencies in wastewater samples from Ontario.
Paula Magbor, William Z Wang, Gopi Gugan, Abayomi S Olabode, Devan G Becker, Valeria R Parreira, Opeyemi U Lawal, Amber Fedynak, Linkang Zhang, Fozia Rizvi, Melinda Precious, Christopher T DeGroot, Lawrence Goodridge, Art F Y Poon
PloS one 20, e0333945 (2025)
14 Oct 2025
Towards a reference cell atlas of liver diversity over the human lifespan.
Sarah A Taylor, Gary D Bader, Sonya MacParland, Alan C Mullen, Tallulah Andrews, Alex G Cuenca, Ramanuj DasGupta, Adam J Gehring, Dominic Grün, Martin Guilliams, Aliya Gulamhusein, Neil C Henderson, Gideon Hirschfield, Stacey S Huppert, Shalev Itzkovitz, Z Gordon Jiang, Georg M Lauer, Ian McGilvray, Krupa R Mysore, Carlos J Pirola, Gerald Quon, Mohammad Rahbari, Aviv Regev, Amanda Ricciuto, Charlotte L Scott, Ankur Sharma, Silvia Sookoian, Michele M Tana, Sarah A Teichmann, Ludovic Vallier, Ioannis S Vlachos, Bruce Wang, Mei Zhen
Nature reviews. Gastroenterology & hepatology 23, 97-109 (2026)
13 Oct 2025
B-cell subsets have different capacities for phagocytosis and subsequent presentation of antigen to cognate T cells.
Daniel M Morelli, Morgan Langille, Richard Zhang, Heather C Craig, Ahmed Eltom Mohamed, Parisa Shooshtari, Bryan Heit, Steven M Kerfoot
Journal of immunology (Baltimore, Md. : 1950) 215, (2026)
10 Oct 2025
Social determinants and community-level risk factors in CA-MRSA transmission among disadvantaged populations in North America: A scoping review.
Sophie C Dembski, Celeste Giedroyc, Niharika Karol, Tanya Misra, Jennifer L Guthrie
Epidemiology and infection 153, e126 (2025)
01 Oct 2025
Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.
Eliseos J Mucaki, Wenhan Zhang, Aryamaan Saha, Sabina Trebinjac, Sharon Nofech-Mozes, Eileen Rakovitch, Vanessa Dumeaux, Michael T Hallett
Journal of translational medicine 23, 1023 (2025)
30 Sep 2025
MolGraph-xLSTM as a graph-based dual-level xLSTM framework for enhanced molecular representation and interpretability.
Yan Sun, Yutong Lu, Yan Yi Li, Zihao Jing, Carson K Leung, Pingzhao Hu
Communications chemistry 8, 286 (2025)
11 Sep 2025
Integrative analysis of taste genetics and the dental plaque microbiome in early childhood caries.
Mohd Wasif Khan, Vivianne Cruz de Jesus, Betty-Anne Mittermuller, Robert J Schroth, Pingzhao Hu, Prashen Chelikani
Cell reports 44, 116245 (2025)
01 Sep 2025
FusionCLM: enhanced molecular property prediction via knowledge fusion of chemical language models.
Yutong Lu, Yan Yi Li, Yan Sun, Pingzhao Hu
Journal of cheminformatics 17, 133 (2025)
23 Aug 2025
Claudin-1 is a mediator and therapeutic target in primary sclerosing cholangitis.
Fabio Del Zompo, Emilie Crouchet, Tessa Ostyn, Zeina Nehme, Mélissa Messé, Frank Jühling, Romain Désert, Angelica T Vieira, Julien Moehlin, Diana Nakib, Tallulah Andrews, Catia Perciani, Sai Chung, Gary D Bader, Ian McGilvray, Chiara Caime, Miki Scaravaglio, Marco Carbone, Pietro Invernizzi, Sheraz Yaqub, Trine Folseraas, Tom H Karlsen, Gautam Shankar, Mark Primeaux, Punita Dhawan, Jesus M Banales, Natascha Roehlen, Roberto Iacone, Geoffrey Teixeira, Mathias Heikenwälder, Laurent Mailly, Sonya MacParland, Tania Roskams, Olivier Govaere, Catherine Schuster, Thomas F Baumert
Journal of hepatology 83, 1305-1319 (2025)
21 Aug 2025
Explicit Scale Simulation for analysis of RNA-sequencing count data with ALDEx2.
Gregory B Gloor, Michelle Pistner Nixon, Justin D Silverman
NAR genomics and bioinformatics 7, lqaf108 (2025)
09 Aug 2025
Enhanced Interpretable Neural Network Approach for Unified Batch Effect Mitigation and Disease Classification Using Cross-Cohort Microbiome Profiles.
Daryl L X Fung, Mohd Wasif Khan, Carson Kai-Sang Leung, Pingzhao Hu
Journal of computational biology : a journal of computational molecular cell biology 32, 951-964 (2025)
09 Jul 2025
Mutational landscape of pure ductal carcinoma in situ and associations with disease prognosis and response to radiotherapy.
Noor Rizvi, Eliseos J Mucaki, Emily L Salmini, Monica Zhang, Sabina Trebinjac, Ezra Hahn, Lawrence Paszat, Sharon Nofech-Mozes, Michael T Hallett, Eileen Rakovitch, Vanessa Dumeaux
Breast cancer research : BCR 27, 127 (2025)
02 Jul 2025
Mining, validating, and quantifying circular RNA transcriptome from total RNA as a biomarker or target.
Tan Ze Wang, Raj Kumar Thapa, Frank Yu, Ayesha Warsi, Kassie Rong, Pious Jose, Tahereh Kashkoulinejad-Kouhi, Phyo Wei Win, Christina A Castellani, Tina Mele, Xiufen Zheng
Scientific reports 15, 20418 (2025)
27 Jun 2025
Out of distribution learning in bioinformatics: advancements and challenges.
Yu Shi, Wei Xu, Pingzhao Hu
Briefings in bioinformatics 26, (2025)
28 May 2025
High Genetic Diversity Among Bacillus cereus Isolates Contaminating Donated Milk at a Canadian Human Milk Bank.
Mathew Gene, Jennifer L Guthrie, Kevin Li, Sarah Teatero, Aimee Paterson, Angel Li, Alain Doyen, Deborah Yamamura, Sarah Khan, Jocelyn A Srigley, Debbie Stone, Deborah L O'Connor, Susan Poutanen, Sharon Unger, Allison McGeer, Nahuel Fittipaldi
Microorganisms 13, (2025)
23 May 2025
Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization.
Michelle Pistner Nixon, Gregory B Gloor, Justin D Silverman
Genome biology 26, 139 (2025)
18 May 2025
The impact of progressive chronic kidney disease on hepatic drug metabolism.
Emily D Hartjes, Yong Jin Lim, Thomas J Velenosi, Kait F Al, Jean M Macklaim, Andrew S Kucey, Gregor Reid, Jeremy P Burton, Gregory B Gloor, Bradley L Urquhart
Drug metabolism and disposition: the biological fate of chemicals 53, 100085 (2025)
06 May 2025
Transcriptomic Features of Recurrence Rates in Idiopathic Subglottic Stenosis.
Shengjie Ying, Peter Y F Zeng, Kevin Fung, Halema Khan, Matthew J Cecchini, Elissa Woo, Jennifer Anderson, Patrick MacInnis, Amir H Karimi, MohdWessam Al Jawhri, Harrison Pan, Nhi Le, Krista Joris, Rui Wen, Joe S Mymryk, Richard Inculet, Vanessa Dumeaux, John W Barrett, Anthony C Nichols, R Jun Lin,
The Laryngoscope 135, 3273-3279 (2025)
28 Apr 2025
Correction: Simultaneous assessment of mitochondrial DNA copy number and nuclear epigenetic age towards predictive models of development and aging.
Phyo W Win, Julia Nguyen, Amanda L Morin, Charles E Newcomb, Shiva M Singh, Noha Gomaa, Christina A Castellani
BMC research notes 18, 197 (2025)
21 Apr 2025
Mitochondrial transplantation: Triumphs, challenges, and impacts on nuclear genome remodelling.
Elly H Shin, Quinn Le, Rachel Barboza, Amanda Morin, Shiva M Singh, Christina A Castellani
Mitochondrion 84, 102042 (2025)
17 Apr 2025
Variability of Clinical Metrics in Small Population Communities Drive Perceived Wastewater and Environmental Surveillance Data Quality: Ontario, Canada-Wide Study.
Nada Hegazy, K Ken Peng, Patrick M D'Aoust, Lakshmi Pisharody, Elisabeth Mercier, Nathan Thomas Ramsay, Md Pervez Kabir, Tram Bich Nguyen, Emma Tomalty, Felix Addo, Chandler Hayying Wong, Shen Wan, Joan Hu, Charmaine Dean, Minqing Ivy Yang, Hadi Dhiyebi, Elizabeth A Edwards, Mark R Servos, Gustavo Ybazeta, Marc Habash, Lawrence Goodridge, Art F Y Poon, Eric J Arts, Stephen Brown, Sarah Jane Payne, Andrea Kirkwood, Denina Bobbie Dawn Simmons, Jean-Paul Desaulniers, Banu Ormeci, Christopher Kyle, David Bulir, Trevor Charles, R Michael McKay, K A Gilbride, Claire Jocelyn Oswald, Hui Peng, Christopher DeGroot, , Elizabeth Renouf, Robert Delatolla
ACS ES&T water 5, 1605-1619 (2025)
16 Apr 2025
Effect of Serial Intralesional Steroid Injections on Risk of Recurrence in Idiopathic Subglottic Stenosis.
Shengjie Ying, Peter Y F Zeng, Kevin Fung, Halema Khan, Matthew J Cecchini, Patrick MacInnis, Jennifer Anderson, Amir H Karimi, MohdWessam Al Jawhri, Harrison Pan, Nhi Le, Krista Joris, Joe S Mymryk, Vanessa Dumeaux, John W Barrett, Anthony C Nichols, R Jun Lin,
The Laryngoscope 135, 3265-3272 (2025)
22 Mar 2025
An interpretable deep geometric learning model to predict the effects of mutations on protein-protein interactions using large-scale protein language model.
Caiya Zhang, Yan Sun, Pingzhao Hu
Journal of cheminformatics 17, 35 (2025)
19 Mar 2025
GraphBAN: An inductive graph-based approach for enhanced prediction of compound-protein interactions.
Hamid Hadipour, Yan Yi Li, Yan Sun, Chutong Deng, Leann Lac, Rebecca Davis, Silvia T Cardona, Pingzhao Hu
Nature communications 16, 2541 (2025)
16 Mar 2025
Association between HIV-1 Nef-mediated MHC-I downregulation and the maintenance of the replication-competent latent viral reservoir in individuals with virally suppressed HIV-1 in Uganda: an exploratory cohort study.
Mitchell J Mumby, Jessica L Prodger, Jada Hackman, Sharada Saraf, Xianming Zhu, Roux-Cil Ferreira, Stephen Tomusange, Samiri Jamiru, Aggrey Anok, Taddeo Kityamuweesi, Paul Buule, Corby Fink, Cassandra R Edgar, Steven M Trothen, Gregory A Dekaban, Erin E Brown, Adam A Capoferri, Owen R Baker, Ethan Klock, Jernelle C Miller, Charles Kirby, Briana Lynch, Aaron A R Tobian, Art F Y Poon, Thomas C Quinn, Ronald M Galiwango, Steven J Reynolds, Andrew D Redd, Jimmy D Dikeakos
The Lancet. Microbe 6, 101018 (2025)
16 Mar 2025
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients.
Yered Pita-Juarez, Dimitra Karagkouni, Nikolaos Kalavros, Johannes C Melms, Sebastian Niezen, Toni M Delorey, Adam L Essene, Olga R Brook, Deepti Pant, Disha Skelton-Badlani, Pourya Naderi, Pinzhu Huang, Liuliu Pan, Tyler Hether, Tallulah S Andrews, Carly G K Ziegler, Jason Reeves, Andriy Myloserdnyy, Rachel Chen, Andy Nam, Stefan Phelan, Yan Liang, Mark Gregory, Shanshan He, Michael Patrick, Tushar Rane, Aster Wardhani, Amit Dipak Amin, Jana Biermann, Hanina Hibshoosh, Molly Veregge, Zachary Kramer, Christopher Jacobs, Yusuf Yalcin, Devan Phillips, Michal Slyper, Ayshwarya Subramanian, Orr Ashenberg, Zohar Bloom-Ackermann, Victoria M Tran, James Gomez, Alexander Sturm, Shuting Zhang, Stephen J Fleming, Sarah Warren, Joseph Beechem, Deborah Hung, Mehrtash Babadi, Robert F Padera, Sonya A MacParland, Gary D Bader, Nasser Imad, Isaac H Solomon, Eric Miller, Stefan Riedel, Caroline B M Porter, Alexandra-Chloé Villani, Linus T-Y Tsai, Winston Hide, Gyongyi Szabo, Jonathan Hecht, Orit Rozenblatt-Rosen, Alex K Shalek, Benjamin Izar, Aviv Regev, Yury V Popov, Z Gordon Jiang, Ioannis S Vlachos
Genome biology 26, 56 (2025)
23 Feb 2025
Interpretable single-cell factor decomposition using sciRED.
Delaram Pouyabahar, Tallulah Andrews, Gary D Bader
Nature communications 16, 1878 (2025)
13 Feb 2025
Acute respiratory distress vs healthy lung environments differently affect mesenchymal stromal cell extracellular vesicle miRNAs.
Sara Rolandsson Enes, Irakli Dzneladze, Thomas H Hampton, Samuel L Neff, Lori Asarian, Jayita Barua, Tobias Tertel, Bernd Giebel, Nicolas Pereyra, David H McKenna, Pingzhao Hu, Erica Acton, Alix Ashare, Kathleen D Liu, Anna D Krasnodembskaya, Karen English, Bruce A Stanton, Patricia R M Rocco, Michael A Matthay, Claudia C Dos Santos, Daniel J Weiss
Cytotherapy 27, 581-596 (2025)
31 Jan 2025
Uropygial gland microbiota of nearctic-neotropical migrants vary with season and migration distance.
Leanne A Grieves, Gregory B Gloor
Animal microbiome 7, 11 (2025)
01 Jan 2025
EZH2 deletion does not affect acinar regeneration but restricts progression to pancreatic cancer in mice.
Emilie Jaune-Pons, Xiaoyi Wang, Fatemeh Mousavi, Zachary Klassen, Abdessamad El Kaoutari, Kurt Berger, Charis Johnson, Mickenzie B Martin, Saloni Aggarwal, Sukhman Brar, Muhammad Khalid, Joanna F Ryan, Parisa Shooshtari, Angela J Mathison, Nelson Dusetti, Raul Urrutia, Gwen Lomberk, Christopher L Pin
JCI insight 10, (2024)
31 Dec 2024
Proportional Assist Ventilation for Minimizing the Duration of Mechanical Ventilation (the PROMIZING study): update to the statistical analysis plan for a randomized controlled trial.
Karen J Bosma, Myriam Lafreniere-Roula, Arlene Jiang, Anna Heath, Yongdong Ouyang, Kaitlyn Wade, Pingzhao Hu, Karen E A Burns, Claudio M Martin, Yoanna Skrobik, Sorcha Mulligan, Kevin E Thorpe, Laurent Brochard,
Trials 25, 855 (2024)
22 Dec 2024
Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies.
Scott J Dos Santos, Clara Copeland, Jean M Macklaim, Gregor Reid, Gregory B Gloor
Microbiome 12, 271 (2024)
16 Dec 2024
Epigenome-wide Association Analysis of Mitochondrial Heteroplasmy Provides Insight into Molecular Mechanisms of Disease.
Meng Lai, Kyeezu Kim, Yinan Zheng, Christina A Castellani, Scott M Ratliff, Mengyao Wang, Xue Liu, Jeffrey Haessler, Tianxiao Huan, Lawrence F Bielak, Wei Zhao, Roby Joehanes, Jiantao Ma, Xiuqing Guo, JoAnn E Manson, Megan L Grove, Jan Bressler, Kent D Taylor, Tuuli Lappalainen, Silva Kasela, Thomas W Blackwell, Nicole J Lake, Jessica D Faul, Kendra R Ferrier, Lifang Hou, Charles Kooperberg, Alexander P Reiner, Kai Zhang, Patricia A Peyser, Myriam Fornage, Eric Boerwinkle, Laura M Raffield, April P Carson, Stephen S Rich, Yongmei Liu, Daniel Levy, Jerome I Rotter, Jennifer A Smith, Dan E Arking, Chunyu Liu,
medRxiv : the preprint server for health sciences (2024)
02 Dec 2024
Correction: Large-scale population disappearances and cycling in the white-lipped peccary, a tropical forest mammal.
José M V Fragoso, André P Antunes, Kirsten M Silvius, Pedro A L Constantino, Galo Zapata-Ríos, Hani R El Bizri, Richard E Bodmer, Micaela Camino, Benoit de Thoisy, Robert B Wallace, Thais Q Morcatty, Pedro Mayor, Cecile Richard-Hansen, Mathew T Hallett, Rafael A Reyna-Hurtado, H Harald Beck, Soledad de Bustos, Alexine Keuroghlian, Alessandra Nava, Olga L Montenegro, Ennio Painkow Neto, Mariana Altrichter
PloS one 19, e0314917 (2024)
29 Nov 2024
Determining the effects of paternal obesity on sperm chromatin at histone H3 lysine 4 tri-methylation in relation to the placental transcriptome and cellular composition.
Anne-Sophie Pepin, Patrycja A Jazwiec, Vanessa Dumeaux, Deborah M Sloboda, Sarah Kimmins
eLife 13, (2024)
16 Nov 2024
Mouse Models for Pancreatic Ductal Adenocarcinoma are Affected by the cre-driver Used to Promote KRASG12D Activation.
Fatemeh Mousavi, Joyce Thompson, Justine Lau, Nur Renollet, Mickenzie B Martin, Jake McGue, Oneeb Hassan, Timothy Frankel, Parisa Shooshtari, Christopher L Pin, Filip Bednar
Cellular and molecular gastroenterology and hepatology 19, 101428 (2025)
14 Oct 2024
The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.
Erin E Gill, Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, Nithu Sara John, Justin Richardsson, Ashley Hobb, Abayomi S Olabode, Alexandru Lepsa, Ana T Duggan, Andrea D Tyler, Arnaud N'Guessan, Atul Kachru, Brandon Chan, Catherine Yoshida, Christina K Yung, David Bujold, Dusan Andric, Edmund Su, Emma J Griffiths, Gary Van Domselaar, Gordon W Jolly, Heather K E Ward, Henrich Feher, Jared Baker, Jared T Simpson, Jaser Uddin, Jiannis Ragoussis, Jon Eubank, Jörg H Fritz, José Héctor Gálvez, Karen Fang, Kim Cullion, Leonardo Rivera, Linda Xiang, Matthew A Croxen, Mitchell Shiell, Natalie Prystajecky, Pierre-Olivier Quirion, Rosita Bajari, Samantha Rich, Samira Mubareka, Sandrine Moreira, Scott Cain, Steven G Sutcliffe, Susanne A Kraemer, Yelizar Alturmessov, Yann Joly, Cphln Consortium, CanCOGeN Consortium, VirusSeq Data Portal Academic And Health Network, Marc Fiume, Terrance P Snutch, Cindy Bell, Catalina Lopez-Correa, Julie G Hussin, Jeffrey B Joy, Caroline Colijn, Paul M K Gordon, William W L Hsiao, Art F Y Poon, Natalie C Knox, Mélanie Courtot, Lincoln Stein, Sarah P Otto, Guillaume Bourque, B Jesse Shapiro, Fiona S L Brinkman
Microbial genomics 10, (2024)
07 Oct 2024
Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer.
Lianghong Chen, Zi Huai Huang, Yan Sun, Mike Domaratzki, Qian Liu, Pingzhao Hu
PLoS computational biology 20, e1012490 (2024)
09 Sep 2024
Prospects for a sequence-based taxonomy of influenza A virus subtypes.
Art F Y Poon
Virus evolution 10, veae064 (2024)
04 Sep 2024
Investigating alignment-free machine learning methods for HIV-1 subtype classification.
Kaitlyn E Wade, Lianghong Chen, Chutong Deng, Gen Zhou, Pingzhao Hu
Bioinformatics advances 4, vbae108 (2024)
27 Aug 2024
Genomic Epidemiology of Mycobacterium abscessus on the Island of Montréal Is Not Suggestive of Health Care-Associated Person-to-Person Transmission.
Idowu B Olawoye, Nicholas Waglechner, Fiona McIntosh, Pierre-Marie Akochy, Nancy Cloutier, Simon Grandjean Lapierre, Bouchra Tannir, Christina Greenaway, Elias Matouk, Louise Poirier, Roger C Levesque, Brian Boyle, Caroline Quach, Hafid Soualhine, Jane Batt, Marcel A Behr, Robyn S Lee, Jennifer L Guthrie
The Journal of infectious diseases 231, e396-e406 (2025)
18 Aug 2024
Role of socioeconomic factors and interkingdom crosstalk in the dental plaque microbiome in early childhood caries.
Mohd Wasif Khan, Vivianne Cruz de Jesus, Betty-Anne Mittermuller, Shaan Sareen, Victor Lee, Robert J Schroth, Pingzhao Hu, Prashen Chelikani
Cell reports 43, 114635 (2024)
16 Aug 2024
Interpretable single-cell factor decomposition using sciRED.
Delaram Pouyabahar, Tallulah Andrews, Gary D Bader
Research square (2024)
16 Aug 2024
Interpretable single-cell factor decomposition using sciRED.
Delaram Pouyabahar, Tallulah Andrews, Gary D Bader
bioRxiv : the preprint server for biology (2024)
15 Aug 2024
Human liver sinusoidal endothelial cells support the development of functional human pluripotent stem cell-derived Kupffer cells.
Gregory M Kent, Michael H Atkins, Bryan Lung, Adele Nikitina, Ian M Fernandes, Jamie J Kwan, Tallulah S Andrews, Sonya A MacParland, Gordon M Keller, Blair K Gage
Cell reports 43, 114629 (2024)
13 Aug 2024
Elongation factor 1A1 inhibition elicits changes in lipid droplet size, the bulk transcriptome, and cell type-associated gene expression in MASLD mouse liver.
Rachel B Wilson, Yun Jin Chen, Richard Zhang, Siddhant Maini, Tallulah S Andrews, Rennian Wang, Nica M Borradaile
American journal of physiology. Gastrointestinal and liver physiology 327, G608-G622 (2024)
06 Aug 2024
A cross-cohort analysis of dental plaque microbiome in early childhood caries.
Mohd Wasif Khan, Daryl Lerh Xing Fung, Robert J Schroth, Prashen Chelikani, Pingzhao Hu
iScience 27, 110447 (2024)
27 Jun 2024
ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multi-scale manifold learning.
Youcheng Li, Leann Lac, Qian Liu, Pingzhao Hu
PLoS computational biology 20, e1012254 (2024)
22 Jun 2024
SARS-CoV-2 viral titer measurements in Ontario, Canada wastewaters throughout the COVID-19 pandemic.
Patrick M D'Aoust, Nada Hegazy, Nathan T Ramsay, Minqing Ivy Yang, Hadi A Dhiyebi, Elizabeth Edwards, Mark R Servos, Gustavo Ybazeta, Marc Habash, Lawrence Goodridge, Art Poon, Eric Arts, R Stephen Brown, Sarah Jane Payne, Andrea Kirkwood, Denina Simmons, Jean-Paul Desaulniers, Banu Ormeci, Christopher Kyle, David Bulir, Trevor Charles, R Michael McKay, Kimberley Gilbride, Claire Oswald, Hui Peng, Vince Pileggi, Menglu L Wang, Arthur Tong, Diego Orellano, , Christopher T DeGroot, Robert Delatolla
Scientific data 11, 656 (2024)
11 Jun 2024
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.
Emma J Griffiths, Inês Mendes, Finlay Maguire, Jennifer L Guthrie, Bryan A Wee, Sarah Schmedes, Kathryn Holt, Chanchal Yadav, Rhiannon Cameron, Charlotte Barclay, Damion Dooley, Duncan MacCannell, Leonid Chindelevitch, Ilene Karsch-Mizrachi, Zahra Waheed, Lee Katz, Robert Petit Iii, Mugdha Dave, Paul Oluniyi, Muhammad Ibtisam Nasar, Amogelang Raphenya, William W L Hsiao, Ruth E Timme
Microbial genomics 10, (2024)
31 May 2024
Impact of Variable Sampling on Estimates of HIV-1 Reservoir Formation Dates.
Edward N Kankaka, Art F Y Poon, Thomas C Quinn, Larry W Chang, Jessica L Prodger, Andrew D Redd
The Journal of infectious diseases 230, 928-932 (2024)
24 May 2024
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.
Steven G Sutcliffe, Susanne A Kraemer, Isaac Ellmen, Jennifer J Knapp, Alyssa K Overton, Delaney Nash, Jozef I Nissimov, Trevor C Charles, David Dreifuss, Ivan Topolsky, Pelin I Baykal, Lara Fuhrmann, Kim P Jablonski, Niko Beerenwinkel, Joshua I Levy, Abayomi S Olabode, Devan G Becker, Gopi Gugan, Erin Brintnell, Art F Y Poon, Renan Valieris, Rodrigo D Drummond, Alexandre Defelicibus, Emmanuel Dias-Neto, Rafael A Rosales, Israel Tojal da Silva, Aspasia Orfanou, Fotis Psomopoulos, Nikolaos Pechlivanis, Lenore Pipes, Zihao Chen, Jasmijn A Baaijens, Michael Baym, B Jesse Shapiro
Microbial genomics 10, (2024)
20 May 2024
The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.
Erin E Gill, Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, Nithu Sara John, Justin Richardsson, Ashley Hobb, Abayomi S Olabode, Alexandru Lepsa, Ana T Duggan, Andrea D Tyler, Arnaud N'Guessan, Atul Kachru, Brandon Chan, Catherine Yoshida, Christina K Yung, David Bujold, Dusan Andric, Edmund Su, Emma J Griffiths, Gary Van Domselaar, Gordon W Jolly, Heather K E Ward, Henrich Feher, Jared Baker, Jared T Simpson, Jaser Uddin, Jiannis Ragoussis, Jon Eubank, Jörg H Fritz, José Héctor Gálvez, Karen Fang, Kim Cullion, Leonardo Rivera, Linda Xiang, Matthew A Croxen, Mitchell Shiell, Natalie Prystajecky, Pierre-Olivier Quirion, Rosita Bajari, Samantha Rich, Samira Mubareka, Sandrine Moreira, Scott Cain, Steven G Sutcliffe, Susanne A Kraemer, Yann Joly, Yelizar Alturmessov, Cphln Consortium, CanCOGeN Consortium, , Marc Fiume, Terrance P Snutch, Cindy Bell, Catalina Lopez-Correa, Julie G Hussin, Jeffrey B Joy, Caroline Colijn, Paul M K Gordon, William W L Hsiao, Art F Y Poon, Natalie C Knox, Mélanie Courtot, Lincoln Stein, Sarah P Otto, Guillaume Bourque, B Jesse Shapiro, Fiona S L Brinkman
ArXiv (2024)
15 Apr 2024
Beyond Normalization: Incorporating Scale Uncertainty in Microbiome and Gene Expression Analysis.
Michelle Pistner Nixon, Gregory B Gloor, Justin D Silverman
bioRxiv : the preprint server for biology (2024)
15 Mar 2024
Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen.
Roux-Cil Ferreira, Steven J Reynolds, Adam A Capoferri, Owen R Baker, Erin E Brown, Ethan Klock, Jernelle Miller, Jun Lai, Sharada Saraf, Charles Kirby, Briana Lynch, Jada Hackman, Sarah N Gowanlock, Stephen Tomusange, Samiri Jamiru, Aggrey Anok, Taddeo Kityamuweesi, Paul Buule, Daniel Bruno, Craig Martens, Rebecca Rose, Susanna L Lamers, Ronald M Galiwango, Art F Y Poon, Thomas C Quinn, Jessica L Prodger, Andrew D Redd
EBioMedicine 102, 105040 (2024)
04 Mar 2024
COVID-19 outbreak at a residential apartment building in Northern Ontario, Canada.
Dinna Lozano, Carolyn Dohoo, David Elfstrom, Kendra Carswell, Jennifer L Guthrie
Epidemiology and infection 152, e53 (2024)
15 Feb 2024
Real-time evaluation of signal accuracy in wastewater surveillance of pathogens with high rates of mutation.
Ocean Thakali, Élisabeth Mercier, Walaa Eid, Martin Wellman, Julia Brasset-Gorny, Alyssa K Overton, Jennifer J Knapp, Douglas Manuel, Trevor C Charles, Lawrence Goodridge, Eric J Arts, Art F Y Poon, R Stephen Brown, Tyson E Graber, Robert Delatolla, Christopher T DeGroot,
Scientific reports 14, 3728 (2024)
14 Feb 2024
Mitochondrial DNA copy number reduction via in vitro TFAM knockout remodels the nuclear epigenome and transcriptome.
Julia Nguyen, Phyo W Win, Tyler Shin Nagano, Elly H Shin, Charles Newcomb, Dan E Arking, Christina A Castellani
bioRxiv : the preprint server for biology (2024)
31 Jan 2024
The Association between Long-Term DDT or DDE Exposures and an Altered Sperm Epigenome-a Cross-Sectional Study of Greenlandic Inuit and South African VhaVenda Men.
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, Sarah Kimmins
Environmental health perspectives 132, 17008 (2024)
12 Jan 2024
Simultaneous assessment of mitochondrial DNA copy number and nuclear epigenetic age towards predictive models of development and aging.
Phyo W Win, Julia Nguyen, Amanda L Morin, Charles E Newcomb, Shiva M Singh, Noha Gomaa, Christina A Castellani
BMC research notes 17, 21 (2024)
11 Jan 2024
Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver.
Tallulah S Andrews, Diana Nakib, Catia T Perciani, Xue Zhong Ma, Lewis Liu, Erin Winter, Damra Camat, Sai W Chung, Patricia Lumanto, Justin Manuel, Shantel Mangroo, Bettina Hansen, Bal Arpinder, Cornelia Thoeni, Blayne Sayed, Jordan Feld, Adam Gehring, Aliya Gulamhusein, Gideon M Hirschfield, Amanda Ricciuto, Gary D Bader, Ian D McGilvray, Sonya MacParland
Journal of hepatology 80, 730-743 (2024)
12 Dec 2023
Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications.
Ruth E Timme, Ilene Karsch-Mizrachi, Zahra Waheed, Masanori Arita, Duncan MacCannell, Finlay Maguire, Robert Petit Iii, Andrew J Page, Catarina Inês Mendes, Muhammad Ibtisam Nasar, Paul Oluniyi, Andrea D Tyler, Amogelang R Raphenya, Jennifer L Guthrie, Idowu Olawoye, Gabriele Rinck, Colman O'Cathail, John Lees, Guy Cochrane, Carla Cummins, J Rodney Brister, William Klimke, Michael Feldgarden, Emma Griffiths
Microbial genomics 9, (2023)
05 Dec 2023
De Novo Synthesis of a Conjugative System from Human Gut Metagenomic Data for Targeted Delivery of Cas9 Antimicrobials.
Thomas A Hamilton, Benjamin R Joris, Arina Shrestha, Tyler S Browne, Sébastien Rodrigue, Bogumil J Karas, Gregory B Gloor, David R Edgell
ACS synthetic biology 12, 3578-3590 (2023)
01 Dec 2023
Respiration supports intraphagosomal filamentation and escape of Candida albicans from macrophages.
Nicola T Case, Johannes Westman, Michael T Hallett, Jonathan Plumb, Aiman Farheen, Michelle E Maxson, Jessie MacAlpine, Sean D Liston, Bernhard Hube, Nicole Robbins, Luke Whitesell, Sergio Grinstein, Leah E Cowen
mBio 14, e0274523 (2023)
30 Nov 2023
Decoding mitochondrial-nuclear (epi)genome interactions: the emerging role of ncRNAs.
Julia Nguyen, Quinn Le, Phyo W Win, Kathleen A Hill, Shiva M Singh, Christina A Castellani
Epigenomics 15, 1121-1136 (2023)
26 Nov 2023
Multi-site microbiota alteration is a hallmark of kidney stone formation.
Kait F Al, Benjamin R Joris, Brendan A Daisley, John A Chmiel, Jennifer Bjazevic, Gregor Reid, Gregory B Gloor, John D Denstedt, Hassan Razvi, Jeremy P Burton
Microbiome 11, 263 (2023)
05 Nov 2023
Systemic and intrinsic functions of ATRX in glial cell fate and CNS myelination in male mice.
Megan E Rowland, Yan Jiang, Sarfraz Shafiq, Alireza Ghahramani, Miguel A Pena-Ortiz, Vanessa Dumeaux, Nathalie G Bérubé
Nature communications 14, 7090 (2023)
27 Oct 2023
Candida albicans exhibits heterogeneous and adaptive cytoprotective responses to antifungal compounds.
Vanessa Dumeaux, Samira Massahi, Van Bettauer, Austin Mottola, Anna Dukovny, Sanny Singh Khurdia, Anna Carolina Borges Pereira Costa, Raha Parvizi Omran, Shawn Simpson, Jinglin Lucy Xie, Malcolm Whiteway, Judith Berman, Michael T Hallett
eLife 12, (2023)
09 Oct 2023
4R-Tau seeding activity unravels molecular subtypes in patients with Progressive Supranuclear Palsy.
Ivan Martinez-Valbuena, Seojin Lee, Enrique Santamaria, Joaquin Fernandez Irigoyen, Shelley Forrest, Jun Li, Hidetomo Tanaka, Blas Couto, Nikolai Gil Reyes, Hania Qamar, Ali M Karakani, Ain Kim, Konstantin Senkevich, Ekaterina Rogaeva, Susan H Fox, Carmela Tartaglia, Naomi P Visanji, Tallulah Andrews, Anthony E Lang, Gabor Geza Kovacs
bioRxiv : the preprint server for biology (2023)
08 Sep 2023
A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets.
Dalton T Ham, Tyler S Browne, Pooja N Banglorewala, Tyler L Wilson, Richard K Michael, Gregory B Gloor, David R Edgell
Nature communications 14, 5514 (2023)
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 26, 280-289 (2023)
07 Aug 2023
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda.
Edward Nelson Kankaka, Andrew D Redd, Amjad Khan, Steven J Reynolds, Sharada Saraf, Charles Kirby, Briana Lynch, Jada Hackman, Stephen Tomusange, Taddeo Kityamuweesi, Samiri Jamiru, Aggrey Anok, Paul Buule, Daniel Bruno, Craig Martens, Larry W Chang, Thomas C Quinn, Jessica L Prodger, Art Poon
Virus evolution 9, vead046 (2023)
18 Jul 2023
Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses.
Abayomi S Olabode, Mitchell J Mumby, Tristan A Wild, Laura Muñoz-Baena, Jimmy D Dikeakos, Art F Y Poon
Molecular biology and evolution 40, (2023)
09 Jun 2023
Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen.
Roux-Cil Ferreira, Steven J Reynolds, Adam A Capoferri, Owen Baker, Erin E Brown, Ethan Klock, Jernelle Miller, Jun Lai, Sharada Saraf, Charles Kirby, Briana Lynch, Jada Hackman, Sarah N Gowanlock, Stephen Tomusange, Samiri Jamiru, Aggrey Anok, Taddeo Kityamuweesi, Paul Buule, Daniel Bruno, Craig Martens, Rebecca Rose, Susanna L Lamers, Ronald M Galiwango, Art F Y Poon, Thomas C Quinn, Jessica L Prodger, Andrew D Redd
medRxiv : the preprint server for health sciences (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)
16 May 2023
From components to communities: bringing network science to clustering for molecular epidemiology.
Molly Liu, Connor Chato, Art F Y Poon
Virus evolution 9, vead026 (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)
27 Apr 2023
SUP: a probabilistic framework to propagate genome sequence uncertainty, with applications.
Devan Becker, David Champredon, Connor Chato, Gopi Gugan, Art Poon
NAR genomics and bioinformatics 5, lqad038 (2023)
04 Apr 2023
A metagenomic-based study of two sites from the Barbadian reef system.
S Simpson, V Bettauer, A Ramachandran, S Kraemer, S Mahon, M Medina, Y Vallès, V Dumeaux, H Vallès, D Walsh, M T Hallett
Coral reefs (Online) 42, 359-366 (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)
08 Feb 2023
The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.
Ivan S Gill, Emma J Griffiths, Damion Dooley, Rhiannon Cameron, Sarah Savić Kallesøe, Nithu Sara John, Anoosha Sehar, Gurinder Gosal, David Alexander, Madison Chapel, Matthew A Croxen, Benjamin Delisle, Rachelle Di Tullio, Daniel Gaston, Ana Duggan, Jennifer L Guthrie, Mark Horsman, Esha Joshi, Levon Kearny, Natalie Knox, Lynette Lau, Jason J LeBlanc, Vincent Li, Pierre Lyons, Keith MacKenzie, Andrew G McArthur, Emily M Panousis, John Palmer, Natalie Prystajecky, Kerri N Smith, Jennifer Tanner, Christopher Townend, Andrea Tyler, Gary Van Domselaar, William W L Hsiao
Microbial genomics 9, (2023)
07 Feb 2023
Repeated Emergence of Variant TetR Family Regulator, FarR, and Increased Resistance to Antimicrobial Unsaturated Fatty Acid among Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus.
Camryn M Bonn, Iftekhar M Rafiqullah, John A Crawford, Yi Meng Qian, Jennifer L Guthrie, Marta Matuszewska, D Ashley Robinson, Martin J McGavin
Antimicrobial agents and chemotherapy 67, e0074922 (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)
12 Jan 2023
Metabolically-targeted dCas9 expression in bacteria.
Gregory M Pellegrino, Tyler S Browne, Keerthana Sharath, Khaleda A Bari, Sarah J Vancuren, Emma Allen-Vercoe, Gregory B Gloor, David R Edgell
Nucleic acids research 51, 982-996 (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)
13 Dec 2022
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission.
Bradley Pickering, Oliver Lung, Finlay Maguire, Peter Kruczkiewicz, Jonathon D Kotwa, Tore Buchanan, Marianne Gagnier, Jennifer L Guthrie, Claire M Jardine, Alex Marchand-Austin, Ariane Massé, Heather McClinchey, Kuganya Nirmalarajah, Patryk Aftanas, Juliette Blais-Savoie, Hsien-Yao Chee, Emily Chien, Winfield Yim, Andra Banete, Bryan D Griffin, Lily Yip, Melissa Goolia, Matthew Suderman, Mathieu Pinette, Greg Smith, Daniel Sullivan, Josip Rudar, Oksana Vernygora, Elizabeth Adey, Michelle Nebroski, Guillaume Goyette, Andrés Finzi, Geneviève Laroche, Ardeshir Ariana, Brett Vahkal, Marceline Côté, Allison J McGeer, Larissa Nituch, Samira Mubareka, Jeff Bowman
Nature microbiology 8, 188 (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)
29 Nov 2022
The multifaceted role of GCM1 during trophoblast differentiation in the human placenta.
Mariyan J Jeyarajah, Gargi Jaju Bhattad, Rachel D Kelly, Kelly J Baines, Adam Jaremek, Fei-Hung P Yang, Hiroaki Okae, Takahiro Arima, Vanessa Dumeaux, Stephen J Renaud
Proceedings of the National Academy of Sciences of the United States of America 119, e2203071119 (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)
11 Nov 2022
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission.
Bradley Pickering, Oliver Lung, Finlay Maguire, Peter Kruczkiewicz, Jonathon D Kotwa, Tore Buchanan, Marianne Gagnier, Jennifer L Guthrie, Claire M Jardine, Alex Marchand-Austin, Ariane Massé, Heather McClinchey, Kuganya Nirmalarajah, Patryk Aftanas, Juliette Blais-Savoie, Hsien-Yao Chee, Emily Chien, Winfield Yim, Andra Banete, Bryan D Griffin, Lily Yip, Melissa Goolia, Matthew Suderman, Mathieu Pinette, Greg Smith, Daniel Sullivan, Josip Rudar, Oksana Vernygora, Elizabeth Adey, Michelle Nebroski, Guillaume Goyette, Andrés Finzi, Geneviève Laroche, Ardeshir Ariana, Brett Vahkal, Marceline Côté, Allison J McGeer, Larissa Nituch, Samira Mubareka, Jeff Bowman
Nature microbiology 7, 2011-2024 (2022)
04 Nov 2022
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients.
Yered Pita-Juarez, Dimitra Karagkouni, Nikolaos Kalavros, Johannes C Melms, Sebastian Niezen, Toni M Delorey, Adam L Essene, Olga R Brook, Deepti Pant, Disha Skelton-Badlani, Pourya Naderi, Pinzhu Huang, Liuliu Pan, Tyler Hether, Tallulah S Andrews, Carly G K Ziegler, Jason Reeves, Andriy Myloserdnyy, Rachel Chen, Andy Nam, Stefan Phelan, Yan Liang, Amit Dipak Amin, Jana Biermann, Hanina Hibshoosh, Molly Veregge, Zachary Kramer, Christopher Jacobs, Yusuf Yalcin, Devan Phillips, Michal Slyper, Ayshwarya Subramanian, Orr Ashenberg, Zohar Bloom-Ackermann, Victoria M Tran, James Gomez, Alexander Sturm, Shuting Zhang, Stephen J Fleming, Sarah Warren, Joseph Beechem, Deborah Hung, Mehrtash Babadi, Robert F Padera, Sonya A MacParland, Gary D Bader, Nasser Imad, Isaac H Solomon, Eric Miller, Stefan Riedel, Caroline B M Porter, Alexandra-Chloé Villani, Linus T-Y Tsai, Winston Hide, Gyongyi Szabo, Jonathan Hecht, Orit Rozenblatt-Rosen, Alex K Shalek, Benjamin Izar, Aviv Regev, Yury Popov, Z Gordon Jiang, Ioannis S Vlachos
bioRxiv : the preprint server for biology (2022)
21 Oct 2022
Large-scale population disappearances and cycling in the white-lipped peccary, a tropical forest mammal.
José M V Fragoso, André P Antunes, Kirsten M Silvius, Pedro A L Constantino, Galo Zapata-Ríos, Hani R El Bizri, Richard E Bodmer, Micaela Camino, Benoit de Thoisy, Robert B Wallace, Thais Q Morcatty, Pedro Mayor, Cecile Richard-Hansen, Mathew T Hallett, Rafael A Reyna-Hurtado, H Harald Beck, Soledad de Bustos, Alexine Keuroghlian, Alessandra Nava, Olga L Montenegro, Ennio Painkow Neto, Mariana Altrichter
PloS one 17, e0276297 (2022)
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