Gary Bader
Professor
Develops data integration, machine learning and biomedical text mining methods for precision medicine.
Gary Bader's lab at Toronto works on medical imaging & healthcare AI, proteins, drugs & materials and medical image analysis. 46 papers since 2023, 1 at top venues, mostly Findings of EMNLP and NeurIPS. 82 alumni. Applications close .
At a glance
- papers, 2023–2026
- 12/ year
- at T1 venues
- 2%
- PhD students
- 0
- MS students
- 0
- alumni listed
- 82
Papers by yearfrom the lab homepage, 2023–2026
- 8 papers2026 · T1 0 · collecting
- 16 papers2025 · T1 0
- 10 papers2024 · T1 0
- 12 papers2023 · T1 1
T1 venuesOtherVenues: Findings of EMNLP, NeurIPS, NPJ Syst Biol Appl. Mar 27;12(1):77
Research focuspaper titles that use each topic's words
- Medical image analysis8 papers
- Medical imaging & healthcare AI2 papers
- Proteins, drugs & materials1 paper
- donnelly0 papers
- donnelly centre0 papers
Paper list
From the lab homepage.
20268 papers
- J Hepatol. May;84(5):962-975A single-cell atlas of the woodchuck liver reveals cellular programs conserved in human HBV infection (opens in a new tab)
- Nat Commun. Feb 5;17(1):2384FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models (opens in a new tab)
- NPJ Syst Biol Appl. Mar 27;12(1):77From FAIR to CURE: guidelines for computational models of biological systems (opens in a new tab)
- Commun Biol. Jan 23;9Glioblastoma stem cells show transcriptionally correlated spatial organization (opens in a new tab)
- Cell. Jun 11;189(12):3736-3759Global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles. (opens in a new tab)
- Sci Data. Jun 24;13(1):1411High-resolution spatial transcriptomics of adult and pediatric human liver with Visium HD (opens in a new tab)
- Hematol Rep. Apr 7;18(2):27.Metabolomic Signatures of Relapse and Survival in AML Patients Receiving Allogeneic Hematopoietic Stem Cell Transplantation (opens in a new tab)
- Nat Protoc. Jul;21(7):2883-2893Tutorial: annotation of animal genomes (opens in a new tab)
202516 papers
- Genome Biol. Mar 14;26(1):56A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients (opens in a new tab)
- McGuiganAnalysis of an engineered organoid model of pancreatic cancer identifies hypoxia as a contributing factor in determining transcriptional subtypes. (opens in a new tab)
- Front Digit Health. Mar 14;7:1511943Approaches to identify scenarios for data science implementations within healthcare settings: recommendations based on experiences at multiple academic institutions (opens in a new tab)
- Stem Cell Reports. Nov 11;20Cell networks in the mouse liver during partial hepatectomy (opens in a new tab)
- J Hepatol. Dec;83(6):1305-1319Claudin-1 is a mediator and therapeutic target in primary sclerosing cholangitis (opens in a new tab)
- Nucleic Acids Res. Jul 7;53(W1):W203-W212Cytoscape Web: bringing network biology to the browser (opens in a new tab)
- Nat Commun. Apr 16;16(1):3306Elevated mitochondrial membrane potential is a therapeutic vulnerability in Dnmt3a-mutant clonal hematopoiesis (opens in a new tab)
- Bioinform Adv. Jul 24;5Gene-set enrichment analysis and visualization on the web using EnrichmentMap:RNASeq (opens in a new tab)
- Nat Commun. Feb 22;16(1):1878Interpretable single-cell factor decomposition using sciRED (opens in a new tab)
- Nature. Apr 16;642(8067):421-430Metformin reduces the competitive advantage of Dnmt3aR878H HSPCs (opens in a new tab)
- Nucleic Acids Res. Apr 22;53PRMT5 promotes full-length HTT expression by repressing multiple proximal intronic polyadenylation sites (opens in a new tab)
- PLoS Comput Biol. May 28;21RETINA: Reconstruction-based pre-trained enhanced TransUNet for electron microscopy segmentation on the CEM500K dataset (opens in a new tab)
202410 papers
- Nucleic Acids Res. Jul 5;52(W1):W481-W488Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing (opens in a new tab)
- Cell Rep Methods. Jul 15;4(7):100819Fatecode enables cell fate regulator prediction using classification-supervised autoencoder perturbation. (opens in a new tab)
- BMC Cancer. Feb 13;24(1):199Integrated transcriptomics uncovers an enhanced association between the prion protein gene expression and vesicle dynamics signatures in glioblastomas (opens in a new tab)
- . WangLab at MEDIQA-M3G : In Proceedings of the Clinical Natural Language Processing WorkshopMultimodal Medical Answer Generation using Large Language Models (opens in a new tab)
- Nature. Aug;632(8025):603-613Single-cell atlas of the human brain vasculature across development, adulthood and disease (opens in a new tab)
- Nat Commun. Nov 27;15(1):10206Single-cell transcriptome analysis reveals CD34 as a marker of human sinoatrial node pacemaker cardiomyocytes (opens in a new tab)
- J Hepatol. May;80(5):730-743Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver (opens in a new tab)
- J Integr Bioinform. Jul 22;21Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024 (opens in a new tab)
- Nat Commun. Nov 20;15The commitment of the human cell atlas to humanity (opens in a new tab)
- Nat Methods. Jun;21(6):1103-1113The multimodality cell segmentation challenge: toward universal solutions (opens in a new tab)
202312 papers
- iScience. Oct 14;26(11):108213A rat liver cell atlas reveals intrahepatic myeloid heterogeneity (opens in a new tab)
- Bioinform Adv. Nov 23;3Adversarial training improves model interpretability in single-cell RNA-seq analysis (opens in a new tab)
- Bioinformatics Jan 1;39Cytoscape.js 2023 update: a graph theory library for visualisation and analysis. Bioinformatics (opens in a new tab)
- Nat Commun. Jul 18;14(1):4313Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer (opens in a new tab)
- Stem Cells Dev. Oct;32(19-20):606-621Fate specification of GFAP-negative primitive neural stem cells and their progeny at clonal resolution (opens in a new tab)
- Anal Chem. Apr 11;95(14):5877-5885Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels (opens in a new tab)
- Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)MAESTER: Masked Autoencoder Guided Segmentation at Pixel Resolution for Accurate, Self-Supervised Subcellular Structure Recognition (opens in a new tab)
- Cereb Cortex. AprMulti-scale systems genomics analysis predicts pathways, cell types, and drug targets involved in normative variation in peri-adolescent human cognition (opens in a new tab)
- Nat Commun. May 10;14(1):2696Multiplatform molecular profiling uncovers two subgroups of malignant peripheral nerve sheath tumors with distinct therapeutic vulnerabilities (opens in a new tab)
- Findings of EMNLPOpen Domain Multi-document Summarization: A Comprehensive Study of Model Brittleness under Retrieval (opens in a new tab)
- Front. Transplant., 12 JuneRobust segregation of donor and recipient cells from single-cell RNA-sequencing of transplant samples (opens in a new tab)
- NeurIPS (T1)Spatially Resolved Gene Expression Prediction from Histology Images via Bi-modal Contrastive Learning (opens in a new tab)
Where alumni went82 listed
Apply to TorontoFall 2027
Computer Science MSc/PhD
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- Single round (Dec 1)
- Opens
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- GRE
- optional
- English
- TOEFL/IELTS if applicable
- Fee
- CAD 135
Confirmed on the program page.
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