Michael Brudno

Orcid: 0000-0001-7947-2243

Affiliations:
  • University of Toronto, Canada


According to our database1, Michael Brudno authored at least 73 papers between 2000 and 2024.

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Bibliography

2024
Development, deployment and scaling of operating room-ready artificial intelligence for real-time surgical decision support.
npj Digit. Medicine, 2024

Shortcut learning in medical AI hinders generalization: method for estimating AI model generalization without external data.
npj Digit. Medicine, 2024

SUM: Saliency Unification through Mamba for Visual Attention Modeling.
CoRR, 2024

2023
Evaluation of single-cell RNAseq labelling algorithms using cancer datasets.
Briefings Bioinform., January, 2023

: Navigating large collections of text notes in electronic health records for clinical chart review.
IEEE Trans. Vis. Comput. Graph., 2023

2022
PhenoPad: Building AI enabled note-taking interfaces for patient encounters.
npj Digit. Medicine, 2022

2021
MetaFusion: a high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates.
Bioinform., 2021

Grad2Task: Improved Few-shot Text Classification Using Gradients for Task Representation.
Proceedings of the Advances in Neural Information Processing Systems 34: Annual Conference on Neural Information Processing Systems 2021, 2021

2020
CReSCENT: CanceR Single Cell ExpressioN Toolkit.
Nucleic Acids Res., 2020

Essential requirements for establishing and operating data trusts: practical guidance based on a working meeting of fifteen Canadian organizations and initiatives.
CoRR, 2020

3D Photography Based Neural Network Craniosynostosis Triaging System.
Proceedings of the Machine Learning for Health Workshop, 2020

Predicting Obstructive Hydronephrosis Based on Ultrasound Alone.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2020, 2020

Speaker Attribution with Voice Profiles by Graph-Based Semi-Supervised Learning.
Proceedings of the 21st Annual Conference of the International Speech Communication Association, 2020

Speaker Diarization with Session-Level Speaker Embedding Refinement Using Graph Neural Networks.
Proceedings of the 2020 IEEE International Conference on Acoustics, 2020

2019
Doccurate: A Curation-Based Approach for Clinical Text Visualization.
IEEE Trans. Vis. Comput. Graph., 2019

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
Nucleic Acids Res., 2019

Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning.
Proceedings of the Research in Computational Molecular Biology, 2019

Training without training data: Improving the generalizability of automated medical abbreviation disambiguation.
Proceedings of the Machine Learning for Health Workshop, 2019

Centroid-based Deep Metric Learning for Speaker Recognition.
Proceedings of the IEEE International Conference on Acoustics, 2019

2018
PhenoLines: Phenotype Comparison Visualizations for Disease Subtyping via Topic Models.
IEEE Trans. Vis. Comput. Graph., 2018

Prediction of Cardiac Arrest from Physiological Signals in the Pediatric ICU.
Proceedings of the Machine Learning for Healthcare Conference, 2018

More Text Please! Understanding and Supporting the Use of Visualization for Clinical Text Overview.
Proceedings of the 2018 CHI Conference on Human Factors in Computing Systems, 2018

2017
PhenoStacks: Cross-Sectional Cohort Phenotype Comparison Visualizations.
IEEE Trans. Vis. Comput. Graph., 2017

The Human Phenotype Ontology in 2017.
Nucleic Acids Res., 2017

Size and Texture-Based Classification of Lung Tumors with 3D CNNs.
Proceedings of the 2017 IEEE Winter Conference on Applications of Computer Vision, 2017

Towards a Directory of Rare Disease Specialists: Identifying Experts from Publication History.
Proceedings of the Machine Learning for Health Care Conference, 2017

2016
PhenoBlocks: Phenotype Comparison Visualizations.
IEEE Trans. Vis. Comput. Graph., 2016

deBGA: read alignment with de Bruijn graph-based seed and extension.
Bioinform., 2016

Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction.
Bioinform., 2016

Integrating Rare Disease Research Patient Workflows and Deep Phenotyping into the Epic© EMR.
Proceedings of the Summit on Clinical Research Informatics, 2016

2015
Identification of deleterious synonymous variants in human genomes.
Bioinform., 2015

2014
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.
Nucleic Acids Res., 2014

Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing.
Bioinform., 2014

GenomeVISTA - an integrated software package for whole-genome alignment and visualization.
Bioinform., 2014

2013
SCARPA: scaffolding reads with practical algorithms.
Bioinform., 2013

2012
Savant Genome Browser 2: visualization and analysis for population-scale genomics.
Nucleic Acids Res., 2012

PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants.
Bioinform., 2012

Mixture Model for Sub-Phenotyping in GWAS.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

2011
SnowFlock: Virtual Machine Cloning as a First-Class Cloud Primitive.
ACM Trans. Comput. Syst., 2011

Variant detection and the Autism sequencing project.
BMC Bioinform., 2011

SHRiMP2: Sensitive yet Practical Short Read Mapping.
Bioinform., 2011

Clustering with Overlap for Genetic Interaction Networks via Local Search Optimization.
Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

Hapsembler: An Assembler for Highly Polymorphic Genomes.
Proceedings of the Research in Computational Molecular Biology, 2011

2010
Savant: genome browser for high-throughput sequencing data.
Bioinform., 2010

VARiD: A variation detection framework for color-space and letter-space platforms.
Bioinform., 2010

Genome variation discovery with high-throughput sequencing data.
Briefings Bioinform., 2010

MoGUL: Detecting Common Insertions and Deletions in a Population.
Proceedings of the Research in Computational Molecular Biology, 2010

Session Introduction.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009
SHRiMP: Accurate Mapping of Short Color-space Reads.
PLoS Comput. Biol., 2009

Maximum Likelihood Genome Assembly.
J. Comput. Biol., 2009

A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG).
Bioinform., 2009

Adding the easy button to the cloud with SnowFlock and MPI.
Proceedings of the 3rd ACM Workshop on System-level Virtualization for High Performance Computing, 2009

SnowFlock: rapid virtual machine cloning for cloud computing.
Proceedings of the 2009 EuroSys Conference, Nuremberg, Germany, April 1-3, 2009, 2009

2008
Read Mapping Algorithms for Single Molecule Sequencing Data.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads.
Proceedings of the Research in Computational Molecular Biology, 2008

FRESCO: Flexible Alignment with Rectangle Scoring Schemes.
Proceedings of the Biocomputing 2008, 2008

Session Introduction.
Proceedings of the Biocomputing 2008, 2008

A mixture model for the evolution of gene expression in non-homogeneous datasets.
Proceedings of the Advances in Neural Information Processing Systems 21, 2008

A robust framework for detecting structural variations in a genome.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

2007
Multiple whole genome alignments and novel biomedical applications at the VISTA portal.
Nucleic Acids Res., 2007

Computability of Models for Sequence Assembly.
Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

2006
Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter.
J. Bioinform. Comput. Biol., 2006

2004
Algorithms for comparison of DNA sequences.
PhD thesis, 2004

The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences.
Nucleic Acids Res., 2004

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.
Bioinform., 2004

Chaining Algorithms for Alignment of Draft Sequence.
Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences.
Proceedings of the Nineteenth National Conference on Artificial Intelligence, 2004

2003
Fast and sensitive multiple alignment of large genomic sequences.
BMC Bioinform., 2003

AGenDA: homology-based gene prediction.
Bioinform., 2003

Glocal alignment: finding rearrangements during alignment.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002
Fast and Sensitive Alignment of Large Genomic Sequences.
Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002

2000
ASDB: database of alternatively spliced genes.
Nucleic Acids Res., 2000

VISTA : visualizing global DNA sequence alignments of arbitrary length.
Bioinform., 2000


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