Augmented kurtosis-based projection pursuit: a novel, advanced machine learning approach for multi-omics data analysis and integration. Bong, F., Ahmed, I., Ramakrishna, N., Valenzuela-Valderas, K.N., Wentzell, P.D., Barra, J.*, Karakach, T.K.* (2025), Nucleic Acids Research 53 (17), DOI: 10.1093/nar/gkaf844 

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Uncovering the multivariate genetic architecture of frailty with genomic structural equation modeling

Isabelle F Foote, Jonny P Flint, Anna E Fürtjes, Jeremy M Lawrence, Donncha S Mullin, John D Fisk, Tobias K Karakach, Andrew Rutenberg, Nicholas G Martin, Michelle K Lupton, David J Llewellyn, Janice M Ranson, Simon R Cox, Michelle Luciano, Kenneth Rockwood, Andrew D Grotzinger. (2025), Nature Genetics 57 (8), 1848-1859 https://www.nature.com/articles/s41588-025-02269-0

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The Terry Fox Research Institute Marathon of Hope Cancer Centres Network: A pan-Canadian precision oncology initiative (2025). T Aalto, M Abacan, S Abadi, FA Aghababazadeh, Z Abbaszadeh, ...

Cancer Cell 43 (4), 587-592

 

IL-5 enhances human mast cell survival and interferon responses to viral infection. (2025) J Barra, CR Liwski, P Phonchareon, L Portales-Cervantes, D Gaston,  Tobias K. Karakach, Ian D. Haidl*,  Jean S. Marshall*. Journal of Allergy and Clinical Immunology, Volume 155, Issue 6, 1968 - 1980. DOI: 10.1016/j.jaci.2025.02.025

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Daily Consumption of Apigenin Prevents Acute Lymphoma/Lymphoblastic Leukemia in Male C57BL/6J Mice Exposed to Space-like Radiation (2025). T Peanlikhit, J Liu, T Ahmed, JS Welsh, T Karakach, KR Shroyer, ...

Cancers 17 (21), 3513

 

2024. Cardiac oxylipin perturbances in response to 2-monochloropropane-1, 3-diol exposure are ameliorated by dietary adequacy of the essential n-3 fatty acid, α-linolenic acid

LGJ Cayer, T Karakach, J Roberts, SPJ Brooks, J Raju, HM Aukema

Food and Chemical Toxicology 194, 115080. DOI: 10.1016/j.fct.2024.115080

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2024. An integrated multi-omics analysis of the effects of the food processing-induced contaminant 2-monochloropropane-1, 3-diol (2-MCPD) in rat heart

LGJ Cayer, T Buhrke, J Roberts, A Nunnikhoven, K Sommerkorn, ...

Archives of Toxicology 98 (12), 4033-4045

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2024. Multivariate genomic analyses of frailty reveal the unique importance of cognitive and multimorbidity pathways for aging‐related health outcomes

IF Foote, JP Flint, JD Fisk, TK Karakach, A Rutenberg, NG Martin, ...

Alzheimer's & Dementia 20, e087481

 

2024. Moving Beyond the Frailty Index as a Single Aggregate Measure: Genomic Analyses Reveal Clinically Relevant Subclusters Across Frailty Indicators

IF Foote, JP Flint, JD Fisk, TK Karakach, A Rutenberg, NG Martin, ...

BEHAVIOR GENETICS 54 (6), 559-559

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2024. Immuno-informatics study identifies conserved T cell epitopes in non-structural proteins of bluetongue virus serotypes: formulation of a computationally optimized next …

HB Kolla, M Dutt, A Kumar, R Hebbandi Nanjunadappa, T Karakach, ...

Frontiers in Immunology 15, 1424307

 

2024. Immuno-informatics Study Reveals Conserved T Cell Epitopes in Non-structural Proteins of Bluetongue Virus Serotypes: Formulation of Computationally Optimized Broad-spectrum …

C Sokke Umeshappa, H Babu Kolla, M Dutt, A Kumar, ...

The Journal of Immunology 212 (1_Supplement), 0634_6053-0634_6053

 

2024. Consumption of apigenin prevents radiation-induced gut dysbiosis in male C57BL/6J mice exposed to silicon ions

KN Rithidech, T Peanlikhit, L Honikel, J Li, J Liu, T Karakach, ...

Radiation Research 201 (4), 317-329

 

2024. Valvular prostaglandins are elevated in severe human aortic valve stenosis

LGJ Cayer, A Surendran, T Karakach, HM Aukema, A Ravandi

Arteriosclerosis, Thrombosis, and Vascular Biology 44 (4), e131-e144

 

2024. Error modelled gene expression analysis (EMOGEA) provides a superior overview of time course RNA-seq measurements and low count gene expression

J Barra, F Taverna, F Bong, I Ahmed, TK Karakach

Briefings in Bioinformatics 25 (3)

 

2024. Intron retention is a mechanism of erythropoietin regulation in brain cell models

V Northrup, LJ Perez, BA Edgett, T Karakach, JA Simpson, KR Brunt

Gene 898, 148099

 

2024. Peroxisome deficiency underlies failures in hepatic immune cell development and antigen presentation in a severe Zellweger disease model

BD Parsons, D Medina-Luna, M Scur, M Pinelli, GS Gamage, RA Chilvers, ...

Cell Reports 43 (2)

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2024. Computational prediction of highly conserved CD8+ and CD4+ T cell epitopes in bluetongue virus: A promising data for developing broad-spectrum bluetongue vaccine

CS Umeshappa, HB Kolla, KP Singh, T Karakach, RH Nanjundappa, ...

The Journal of Immunology 210 (Supplement_1), 224.11-224.11

 

2023. CD8+ T cell metabolic rewiring defined by scRNA-seq identifies a critical role of ASNS expression dynamics in T cell differentiation

J Fernandez-Garcia, F Franco, S Parik, P Altea-Manzano, AA Pane, ...

Cell reports 41 (7)

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2021. Examination of local and systemic inflammatory changes during lung surgery

A Bruinooge, E Poole, C Pascoe, T Karakach, G Buduhan, L Tan, ...

Canadian Journal of Surgery 64, S122-S122

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2021. BIOMEX: a software to alleviate the bottlenecks in the analysis-to-interpretation pipeline of omics datasets

F Taverna, P Carmeliet, T Karakach, A Subramanian

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2021. Integrating proteomes for lung tissues and lavage reveals pathways that link responses in allergen-challenged mice

TH Mahood, CD Pascoe, TK Karakach, A Jha, S Basu, P Ezzati, V Spicer, ...

Acs Omega 6 (2), 1171-1189

 

2021. Heterogeneous effects of calorie content and nutritional components underlie dietary influence on pancreatic cancer susceptibility

J Dooley, V Lagou, J Goveia, A Ulrich, K Rohlenova, N Heirman, ...

Cell Reports 32 (2)

 

2020. Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1

J Barra, GS Gaidosh, E Blumenthal, F Beckedorff, MM Tayari, N Kirstein, ...

Science advances 6 (27), eaaz9072

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2020. BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization

F Taverna, J Goveia, TK Karakach, S Khan, K Rohlenova, L Treps, ...

Nucleic acids research 48 (W1), W385-W394