Faculty profile
Carl de Boer
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Research
Latest papers
Evaluation and optimization of sequence-based gene regulatory deep learning models.
bioRxiv : the preprint server for biology · 2024
LegNet: a best-in-class deep learning model for short DNA regulatory regions.
Bioinformatics (Oxford, England) · 2023
GIL: a python package for designing custom indexing primers.
Bioinformatics (Oxford, England) · 2023 · senior author
Latest funding
- $1,105,426
Pooled multiplexed synthesis and screening of hundreds of thousands of genes
CIHR · 2026 · Nominated PI
- $30,000
Identifying altered gene regulatory network states and underlying mechanisms in atrial fibrillation, a model polygenic disease
CIHR · 2024 · Nominated PI
- $1,239,300
Identifying altered gene regulatory network states and underlying mechanisms in atrial fibrillation, a model polygenic disease
CIHR · 2024 · Nominated PI
3 publications.
Evaluation and optimization of sequence-based gene regulatory deep learning models.
Rafi AM, Nogina D, Penzar D, Lee D, Lee D, Kim N, Kim S, Kim D, Shin Y, Kwak IY, Meshcheryakov G, Lando A, Zinkevich A, Kim BC, Lee J, Kang T, Vaishnav ED, Yadollahpour P, Random Promoter DREAM Challenge Consortium, Kim S, Albrecht J, Regev A, Gong W, Kulakovskiy IV, Meyer P, de Boer C
LegNet: a best-in-class deep learning model for short DNA regulatory regions.
Penzar D, Nogina D, Noskova E, Zinkevich A, Meshcheryakov G, Lando A, Rafi AM, de Boer C, Kulakovskiy IV
GIL: a python package for designing custom indexing primers.
Mateyko N, Tariq O, Chen XE, Cheney W, Salaudeen AL, Luthra I, Nikpour N, Rafi AM, Kamali Deghan H, Jensen C, de Boer C
Pooled multiplexed synthesis and screening of hundreds of thousands of genes
Principal investigators: De Boer, Carl G
Keywords: Biotechnology; Functional Characterization; Gene Synthesis; Genetic Screens; Nucleases; Protein Engineering
Identifying altered gene regulatory network states and underlying mechanisms in atrial fibrillation, a model polygenic disease
Principal investigators: De Boer, Carl G
Keywords: Atac-Seq; Atrial Fibrillation; Cardiomyocytes; Gene Expression; Gwas; Ipscs; Polygenic Traits; Reporter Assays; Rna-Seq
Identifying altered gene regulatory network states and underlying mechanisms in atrial fibrillation, a model polygenic disease
Principal investigators: De Boer, Carl G
Keywords: Atac-Seq; Atrial Fibrillation; Cardiomyocytes; Gene Expression; Gwas; Ipscs; Polygenic Traits; Reporter Assays; Rna-Seq
Development and Validation of PPD-Predict: A Novel Machine Learning Platform for Predicting Cognitive Behavioral Therapy Responsiveness in Postpartum Depression
Principal investigators: Faltyn, Mateusz
Keywords: Bioinformatics; Biopsychosocial; Cognitive Behavioral Therapy; Deep Learning; Machine Learning; Omics; Postpartum Anxiety; Postpartum Depression
Générer des contrefactuels pour la biologie moléculaire: une nouvelle approche basée sur des modèles d'apprentissage profond génératifs
Principal investigators: Emad, Amin A
Keywords: counterfactual synthesis; deep learning; generative neural networks; mrna stability; perturbation prediction; single cell transcriptomics
Identifying altered gene regulatory network states and underlying mechanisms in atrial fibrillation, a model polygenic disease
Principal investigators: De Boer, Carl G
Keywords: Atac-Seq; Atrial Fibrillation; Cardiomyocytes; Gene Expression; Gene Regulatory Networks; Gwas; Ipscs; Polygenic Traits; Reporter Assays; Rna-Seq
High-throughput characterization of transcription factor variants in yeast
Principal investigators: De Boer, Carl G
Keywords: Chip-Seq; Deep Mutational Scanning; Gene Regulation; Reporter Assays; Tp53; Transcription Factors; Transcriptional Regulation; Yeast
Ultracentrifugation system for purification of synthetic biology constructs
Principal investigators: de Boer, Carl
Decoding human cis-regulatory logic in development and disease
Principal investigators: De Boer, Carl G
Keywords: Cis-Regulatory Logic; Complex Common Disease; Enhancers; Gene Regulation; Gwas; Pluripotent Stem Cells; Polygenic Disease; Promoters; Transcription Factors; Transcriptional Regulation
Molecular and computational tools for regulatory genomics
Principal investigators: de Boer, Carl
From CIHR, NSERC and SSHRC funding decisions: CIHR since 2008, NSERC since 1991 and SSHRC since 1998, including their latest published competition results.
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