Peer-Reviewed Publications
A collection of 15+ peer-reviewed papers spanning clinical AI, diagnostic RNA-Seq, multi-omics, pediatric immunology, and fundamental mRNA regulatory mechanisms.
AI-Driven Injury Reporting in Pediatric Emergency Departments
JAMA Network Open
2025-07-01
Authors:
Devin Singh, Alper Celik, Evangeline W J Zhang, Eric Liu, Daniel Rosenfield
Impact Summary: NLP transformer models accurately identified 90% of pediatric injury cases from emergency department records, reducing manual chart review by over 80% and enabling real-time surveillance for CHIRPP.
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Importance: Injury is a leading cause of morbidity and mortality among children worldwide. Prevention strategies rely on timely and accurate injury surveillance. Many national programs, including the Canadian Hospitals Injury Reporting and Prevention Program (CHIRPP), depend on manual review of emergency department (ED) medical records to track injury trends. Rising ED volumes have strained manual processes, delaying data analysis and compromising early detection of public health risks.
Safety and Efficacy of Very Low-Dose Multi-Nut Oral Immunotherapy in Children
Clinical and Translational Allergy
2025-06-11
Authors:
Julia EM Upton, Carmen H Li, Alireza Berenjy, Alana Galper, Xiaojun Yin, Alper Celik, Lucy Duan, Samantha Wong, Christina M Ditlof, Jennifer A Hoang, Moshe Ben-Shoshan, Akash Kothari, Lisa Hung, Mikhail Monteiro, Wut Hmone Phue, Theo J Moraes, Thomas Kaufmann, Thomas Eiwegger
Impact Summary: Evaluates the safety and efficacy of very low-dose multi-nut oral immunotherapy for children with multiple nut allergies, demonstrating significant desensitization.
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Background: Multi-nut allergies are common and increase the risk of severe accidental reactions. Very low-dose multi-nut oral immunotherapy (OIT) aims to safely induce desensitization while minimizing adverse effects during build-up.
Publication In Press
Assessing the Diagnostic Impact of Blood Transcriptome Profiling in a Pediatric Cohort Previously Assessed by Genome Sequencing
NPJ Genomic Medicine
2025-06-11
Authors:
Huayun Hou, Kyoko E. Yuki, Gregory Costain, Anna Szuto, Sierra Barnes, Arun K. Ramani, Alper Celik, Michael Braga, Meagan Gloven-Brown, Dimitri J. Stavropoulos, Sarah Bowdin, Ronald D. Cohn, Roberto Mendoza-Londono, Stephen W. Scherer, Michael Brudno, Christian R. Marshall, M. Stephen Meyn, Adam Shlien, James J. Dowling, Michael D. Wilson, Lianna Kyriakopoulou
Impact Summary: Evaluated blood-derived RNA-seq in 134 pediatric patients with rare genetic disorders. RNA-seq reinforced or revised diagnoses in 36% of diagnosed cases and identified novel candidate genes in ~7% of previously undiagnosed cases.
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Despite advances in genome sequencing, many individuals with rare genetic disorders remain undiagnosed. Transcriptional profiling via RNA-seq can reveal functional impacts of DNA variants and improve diagnosis. We assessed blood-derived RNA-seq in the largely undiagnosed SickKids Genome Clinic cohort (n = 134). Our RNA-centric analysis identifies gene expression outliers, aberrant splicing, and allele-specific expression. In one-third of diagnosed individuals (20/61), RNA-seq reinforced DNA-based findings. In 2/61 cases, RNA-seq revised diagnoses and discovered additional relevant genes.
Clinical Utility Analysis of the Hoxb8 Mast Cell Activation Test for the Diagnosis of Peanut Allergy
Allergy
2024-09-28
Authors:
Noemi Bachmeier-Zbären, Alper Celik, Robin van Brummelen, Nadine Roos, Melanie Steinmann, Jennifer A. Hoang, Xiaojun Yin, Christina M. Ditlof, Lucy Duan, Julia E. M. Upton, Thomas Kaufmann, Alexander Eggel, Thomas Eiwegger
Impact Summary: Evaluated the diagnostic accuracy of the Hoxb8 mast cell activation test (Hoxb8 MAT) in children and adolescents, proving superior accuracy compared to standard skin prick and specific IgE testing.
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Background: Accurate diagnosis of peanut allergy is vital to prevent severe reactions and unnecessary dietary restrictions. The Hoxb8 MAT utilizes cell-line-derived mast cells to measure allergen reactivity ex vivo.
Precision Cut Intestinal Slices, a Novel Model of Acute Food Allergic Reactions
Allergy
2023-05-04
Authors:
Lisa Hung, Alper Celik, Xiaojun Yin, Kai Yu, Alireza Berenjy, Akash Kothari, Helena Obernolte, Julia EM Upton, Katrine Lindholm Bøgh, Gino R Somers, Iram Siddiqui, Martin Grealish, Fayez A Quereshy, Katherina Sewald, Priscilla PL Chiu, Thomas Eiwegger
Impact Summary: Developed a novel ex vivo model using precision cut intestinal slices (PCIS) that reproduces allergen-specific IgE-mediated gut contractions for evaluating food allergy mechanisms and therapeutics.
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Background: Food allergic gut contractions have lacked relevant human/animal ex vivo tissue models. We established precision cut intestinal slices (PCIS) to evaluate allergen-induced contractions and drug interventions.
Trio RNA Sequencing in a Cohort of Medically Complex Children
The American Journal of Human Genetics
2023-05-04
Authors:
Ashish R Deshwar, Kyoko E Yuki, Huayun Hou, Yijing Liang, Tayyaba Khan, Alper Celik, Arun Ramani, Roberto Mendoza-Londono, Christian R Marshall, Michael Brudno, Adam Shlien, M Stephen Meyn, Robin Z Hayeems, Brandon J McKinlay, Panagiota Klentrou, Michael D Wilson, Lianna Kyriakopoulou, Gregory Costain, James J Dowling
Impact Summary: Combined genome sequencing with trio RNA sequencing in 39 families with complex pediatric cases. Trio RNA-seq significantly reduced manual variant filtering effort.
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Genome sequencing (GS) is a powerful test for the diagnosis of rare genetic disorders. Although GS can enumerate most non-coding variation, determining which non-coding variants are disease-causing is challenging. RNA sequencing (RNA-seq) has emerged as an important tool to help address this issue. We performed GS plus RNA-seq from blood using an automated high-throughput platform on 97 individuals from 39 families.
The Genomic Architecture of Pregnancy-Associated Plasticity in the Maternal Mouse Hippocampus
eNeuro
2022-07-17
Authors:
Alper Celik, Max Somer, Bharti Kukreja, Taiyi Wu, Brian T Kalish
Impact Summary: Used single-nucleus RNA-seq and snATAC-seq to uncover cell-type-specific transcriptional and epigenetic adaptations in the mouse hippocampus during and after pregnancy.
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Pregnancy is associated with extraordinary plasticity in the maternal brain. To gain insight into pregnancy-associated hippocampal plasticity, we performed single nucleus RNA sequencing (snRNA-seq) and snATAC-seq from the mouse hippocampus before, during, and after pregnancy, identifying cell-type-specific transcriptional and epigenetic signatures.
X-Linked Myotubular Myopathy is Associated with Epigenetic Alterations and is Ameliorated by HDAC Inhibition
Acta Neuropathologica
2022-07-17
Authors:
Jonathan R Volpatti, Mehdi M Ghahramani-Seno, Mélanie Mansat, Nesrin Sabha, Ege Sarikaya, Sarah J Goodman, Eric Chater-Diehl, Alper Celik, Emanuela Pannia, Carine Froment, Lucie Combes-Soia, Nika Maani, Kyoko E Yuki, Gaëtan Chicanne, Liis Uusküla-Reimand, Simon Monis, Sana Akhtar Alvi, Casie A Genetti, Bernard Payrastre, Alan H Beggs, Carsten G Bonnemann, Francesco Muntoni, Michael D Wilson, Rosanna Weksberg, Julien Viaud, James J Dowling
Impact Summary: High-throughput drug screening identified valproic acid as a potent suppressor of XLMTM via HDAC inhibition, discovering conserved DNA hypermethylation patterns in mouse and human patient samples.
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X-linked myotubular myopathy (XLMTM) is a fatal neuromuscular disorder caused by loss of function mutations in MTM1. We performed a drug screen in mtm1 mutant zebrafish and identified valproic acid as a potent suppressor, translating these findings to mouse models and patient epigenomes.
Variants in ASPH Cause Exertional Heat Illness and are Associated with Malignant Hyperthermia Susceptibility
Nature Communications
2022-06-13
Authors:
Yukari Endo, Linda Groom, Alper Celik, Natalia Kraeva, Chang Seok Lee, Sung Yun Jung, Lois Gardner, Marie-Anne Shaw, Susan L Hamilton, Philip M Hopkins, Robert T Dirksen, Sheila Riazi, James J Dowling
Impact Summary: Identified rare pathogenic variants in the ASPH gene as a novel genetic cause of exertional heat illness and malignant hyperthermia, validated in CRISPR-edited cellular and zebrafish models.
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Exertional heat illness (EHI) and malignant hyperthermia (MH) are life-threatening conditions associated with muscle breakdown. We performed genomic sequencing on a cohort with EHI/MH and identified pathogenic heterozygous variants in ASPH.
One Size Does Not Fit All — Lessons Learned from a Multiple-Methods Study of a Resident Wellness Curriculum Across Sites and Specialties
BMC Medical Education
2021-11-13
Authors:
Deanna Chaukos, Jonathan P Zebrowski, Nicole M Benson, Alper Celik, Emma Chad-Friedman, Aviva Teitelbaum, Carol Bernstein, Rebecca Cook, Afia Genfi, John W Denninger
Impact Summary: Evaluated stress-reduction curricula across multi-center medical resident cohorts using longitudinal statistical modeling to identify demographic and self-efficacy subgroups needing tailored wellness support.
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Background: The authors conducted a multiple-methods study exploring contributors to wellbeing for junior medical residents across diverse specialties participating in the SMART-R stress management program.
Basophil Activation Test Shows High Accuracy in the Diagnosis of Peanut and Tree Nut Allergy: The Markers of Nut Allergy Study
Allergy
2021-06-01
Authors:
Lucy Duan, Alper Celik, Jennifer A Hoang, Klara Schmidthaler, Delvin So, Xiaojun Yin, Christina M Ditlof, Marta Ponce, Julia E M Upton, Jean-Soo Lee, Lisa Hung, Heimo Breiteneder, Chiara Palladino, Adelle R Atkinson, Vy H D Kim, Alireza Berenjy, Maria Asper, David Hummel, Samantha Wong, Mara Alexanian-Farr, Ahuva Magder, Sharon R Chinthrajah, Kaori Mukai, Mindy Tsai, Kari Nadeau, Stephen J Galli, Arun K Ramani, Zsolt Szépfalusi, Thomas Eiwegger
Impact Summary: Demonstrated that the basophil activation test (BAT) accurately diagnoses peanut and tree nut allergies in children, significantly outperforming standard IgE tests and reducing the need for oral food challenges.
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Background: Peanut and tree nut allergies are major causes of anaphylaxis. Confirmatory oral food challenges (OFCs) carry risks. We prospectively evaluated the accuracy of BAT in pediatric cohorts.
Modeling the Conversion Between Specific IgE Test Platforms for Nut Allergens in Children and Adolescents
Journal of Allergy and Clinical Immunology
2021-05-01
Authors:
Jennifer A Hoang, Alper Celik, Christian Lupinek, Rudolf Valenta, Lucy Duan, Ruixue Dai, May G Brydges, Aimée Dubeau, Claire Lépine, Samantha Wong, Mara Alexanian-Farr, Ahuva Magder, Padmaja Subbarao, Julia E M Upton, Klara Schmidthaler, Zsolt Szépfalusi, Arun Ramani, Thomas Eiwegger
Impact Summary: Developed statistical mathematical transformation models to harmonize specific IgE values across three multiplex diagnostic test platforms for pediatric nut allergies.
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Background: Multiplex diagnostic platforms allow measurement of allergen-specific IgE to multiple extracts. We created statistical models to integrate allergen-specific IgE metrics across three testing platforms.
General Decapping Activators Target Different Subsets of Inefficiently Translated mRNAs
eLife
2018-12-06
Authors:
Feng He, Alper Celik, Chan Wu, Allan Jacobson
Impact Summary: Genome-wide RNA-seq revealed that decapping factors Pat1, Lsm1, and Dhh1 directly target specific subsets of inefficiently translated mRNAs rather than acting as global activators.
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The Dcp1-Dcp2 decapping enzyme and decapping activators Pat1, Dhh1, and Lsm1 regulate mRNA decapping. We analyzed the gene expression consequences of deleting PAT1, LSM1, or DHH1, defining target specificity and translational coupling.
High-Resolution Profiling of NMD Targets in Yeast
Methods in Enzymology
2018-08-09
Authors:
Feng He, Alper Celik, Richard Baker, Allan Jacobson
Impact Summary: Detailed high-throughput RNA-Seq methodologies, rRNA depletion protocols, and computational pipelines to identify ~900 nonsense-mediated mRNA decay (NMD) targets.
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Contemporary high-throughput sequencing methods permit systematic identification of transcripts whose levels change significantly in response to altered biological states. We outline computational and experimental protocols to profile NMD targets.
High-Resolution Profiling of NMD Targets in Yeast Reveals Translational Fidelity as a Basis for Substrate Selection
RNA
2017-05-23
Authors:
Alper Celik, Feng He, Richard Baker, Allan Jacobson
Impact Summary: Uncovered hundreds of novel NMD-regulated transcripts and demonstrated that low codon optimality and reduced translation efficiency are primary determinants for NMD substrate selection.
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Nonsense-mediated mRNA decay (NMD) plays a critical role in eukaryotic gene expression. Our bioinformatics analyses revealed that NMD-regulated transcripts generally have lower translational efficiency and higher out-of-frame translation rates.
