VISTA : visualizing global DNA sequence alignments of arbitrary length. - Chris Mayor; Michael Brudno; Jody R. Schwartz; Alexander Poliakov; Edward M. Rubin; Kelly A. Frazer; Lior Pachter; Inna Dubchak (Bioinform., 2000)

ASDB: database of alternatively spliced genes. - I. Dralyuk; Michael Brudno; Mikhail S. Gelfand; Manfred Zorn; Inna Dubchak (Nucleic Acids Res., 2000)

Fast and Sensitive Alignment of Large Genomic Sequences. - Michael Brudno; Burkhard Morgenstern (CSB, 2002)

Glocal alignment: finding rearrangements during alignment. - Michael Brudno; Sanket Malde; Alexander Poliakov; Chuong B. Do; Olivier Couronne; Inna Dubchak; Serafim Batzoglou (ISMB (Supplement of Bioinformatics), 2003)

AGenDA: homology-based gene prediction. - Leila Taher; Oliver Rinner; Saurabh Garg; Alexander Sczyrba; Michael Brudno; Serafim Batzoglou; Burkhard Morgenstern (Bioinform., 2003)

Fast and sensitive multiple alignment of large genomic sequences. - Michael Brudno; Michael Chapman; Berthold Göttgens; Serafim Batzoglou; Burkhard Morgenstern (BMC Bioinform., 2003)

PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences. - Chuong B. Do; Michael Brudno; Serafim Batzoglou (AAAI, 2004)

Chaining Algorithms for Alignment of Draft Sequence. - Mukund Sundararajan; Michael Brudno; Kerrin S. Small; Arend Sidow; Serafim Batzoglou (WABI, 2004)

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. - Nameeta Y. Shah; Olivier Couronne; Len A. Pennacchio; Michael Brudno; Serafim Batzoglou; E. Wes Bethel; Edward M. Rubin; Bernd Hamann; Inna Dubchak (Bioinform., 2004)

The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. - Michael Brudno; Rasmus Steinkamp; Burkhard Morgenstern (Nucleic Acids Res., 2004)

Algorithms for comparison of DNA sequences. - Michael Brudno (2004)

Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter. - Galina Yu. Kovaleva; Georgii A. Bazykin; Michael Brudno; Mikhail S. Gelfand (J. Bioinform. Comput. Biol., 2006)

Computability of Models for Sequence Assembly. - Paul Medvedev; Konstantinos Georgiou; Gene Myers; Michael Brudno (WABI, 2007)

Multiple whole genome alignments and novel biomedical applications at the VISTA portal. - Michael Brudno; Alexander Poliakov; Simon Minovitsky; Igor Ratnere; Inna Dubchak (Nucleic Acids Res., 2007)

A robust framework for detecting structural variations in a genome. - Seunghak Lee; Elango Cheran; Michael Brudno (ISMB, 2008)

A mixture model for the evolution of gene expression in non-homogeneous datasets. - Gerald T. Quon; Yee Whye Teh; Esther T. Chan; Timothy R. Hughes; Michael Brudno; Quaid Morris (NIPS, 2008)

Session Introduction. - Michael Brudno; Bernard M. E. Moret; C. Randal Linder; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2008)

FRESCO: Flexible Alignment with Rectangle Scoring Schemes. - Adrian V. Dalca; Michael Brudno (Pacific Symposium on Biocomputing, 2008)

Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. - Paul Medvedev; Michael Brudno (RECOMB, 2008)

Read Mapping Algorithms for Single Molecule Sequencing Data. - Vladimir Yanovski; Stephen M. Rumble; Michael Brudno (WABI, 2008)

SnowFlock: rapid virtual machine cloning for cloud computing. - Horacio Andrés Lagar-Cavilla; Joseph Andrew Whitney; Adin Matthew Scannell; Philip Patchin; Stephen M. Rumble; Eyal de Lara; Michael Brudno; Mahadev Satyanarayanan (EuroSys, 2009)

Adding the easy button to the cloud with SnowFlock and MPI. - Philip Patchin; H. Andrés Lagar-Cavilla; Eyal de Lara; Michael Brudno (HPCVirt@EuroSys, 2009)

A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). - Michael Brudno; Paul Medvedev; Jens Stoye; Francisco M. de la Vega (Bioinform., 2009)

Maximum Likelihood Genome Assembly. - Paul Medvedev; Michael Brudno (J. Comput. Biol., 2009)

SHRiMP: Accurate Mapping of Short Color-space Reads. - Stephen M. Rumble; Phil Lacroute; Adrian V. Dalca; Marc Fiume; Arend Sidow; Michael Brudno (PLoS Comput. Biol., 2009)

Session Introduction. - Can Alkan; Michael Brudno; Evan E. Eichler; Maricel G. Kann; Süleyman Cenk Sahinalp (Pacific Symposium on Biocomputing, 2010)

MoGUL: Detecting Common Insertions and Deletions in a Population. - Seunghak Lee; Eric P. Xing; Michael Brudno (RECOMB, 2010)

Genome variation discovery with high-throughput sequencing data. - Adrian V. Dalca; Michael Brudno (Briefings Bioinform., 2010)

VARiD: A variation detection framework for color-space and letter-space platforms. - Adrian V. Dalca; Stephen M. Rumble; Samuel Levy; Michael Brudno (Bioinform., 2010)

Savant: genome browser for high-throughput sequencing data. - Marc Fiume; Vanessa Williams; Andrew Brook; Michael Brudno (Bioinform., 2010)

Hapsembler: An Assembler for Highly Polymorphic Genomes. - Nilgun Donmez; Michael Brudno (RECOMB, 2011)

Clustering with Overlap for Genetic Interaction Networks via Local Search Optimization. - Joseph Andrew Whitney; Judice L. Y. Koh; Michael Costanzo; Grant Brown; Charles Boone; Michael Brudno (WABI, 2011)

SHRiMP2: Sensitive yet Practical Short Read Mapping. - Matei David; Misko Dzamba; Dan Lister; Lucian Ilie; Michael Brudno (Bioinform., 2011)

Variant detection and the Autism sequencing project. - Orion J. Buske; Misko Dzamba; Justin Foong; Lynette Lau; Marc Fiume; Christian Marshall; Susan Walker; Aparna Prasad; Michael Brudno (BMC Bioinform., 2011)

SnowFlock: Virtual Machine Cloning as a First-Class Cloud Primitive. - H. Andrés Lagar-Cavilla; Joseph Andrew Whitney; Roy Bryant; Philip Patchin; Michael Brudno; Eyal de Lara; Stephen M. Rumble; Mahadev Satyanarayanan; Adin Scannell (ACM Trans. Comput. Syst., 2011)

Mixture Model for Sub-Phenotyping in GWAS. - David Warde-Farley; Michael Brudno; Quaid Morris; Anna Goldenberg (Pacific Symposium on Biocomputing, 2012)

PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. - Yue Jiang; Yadong Wang 001; Michael Brudno (Bioinform., 2012)

Savant Genome Browser 2: visualization and analysis for population-scale genomics. - Marc Fiume; Eric J. M. Smith; Andrew Brook; Dario Strbenac; Brian Turner; Aziz M. Mezlini; Mark D. Robinson; Shoshana J. Wodak; Michael Brudno (Nucleic Acids Res., 2012)

SCARPA: scaffolding reads with practical algorithms. - Nilgun Donmez; Michael Brudno (Bioinform., 2013)

GenomeVISTA - an integrated software package for whole-genome alignment and visualization. - Alexander Poliakov; Justin Foong; Michael Brudno; Inna Dubchak (Bioinform., 2014)

Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing. - Ladislav Rampásek; Aryan Arbabi; Michael Brudno (Bioinform., 2014)

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. - Sebastian Köhler 001; Sandra C. Doelken; Christopher J. Mungall; Sebastian Bauer 002; Helen V. Firth; Isabelle Bailleul-Forestier; Graeme C. M. Black; Danielle L. Brown; Michael Brudno; Jennifer Campbell; David R. FitzPatrick; Janan T. Eppig; et al. (Nucleic Acids Res., 2014)

Identification of deleterious synonymous variants in human genomes. - Orion J. Buske; AshokKumar Manickaraj; Seema Mital; Peter N. Ray; Michael Brudno (Bioinform., 2015)

Integrating Rare Disease Research Patient Workflows and Deep Phenotyping into the Epic© EMR. - Yael Kamil; Kym M. Boycott; Daniel Gross; Marta Gîrdea; Sergiu Dumitriu; Michael Brudno (CRI, 2016)

Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction. - Aryan Arbabi; Ladislav Rampásek; Michael Brudno (Bioinform., 2016)

deBGA: read alignment with de Bruijn graph-based seed and extension. - Bo Liu 023; Hongzhe Guo; Michael Brudno; Yadong Wang 001 (Bioinform., 2016)

PhenoBlocks: Phenotype Comparison Visualizations. - Michael Glueck; Peter Hamilton; Fanny Chevalier; Simon Breslav; Azam Khan; Daniel J. Wigdor; Michael Brudno (IEEE Trans. Vis. Comput. Graph., 2016)

Towards a Directory of Rare Disease Specialists: Identifying Experts from Publication History. - Zihan Wang; Michael Brudno; Orion J. Buske (MLHC, 2017)

Size and Texture-Based Classification of Lung Tumors with 3D CNNs. - Zhihao Luo; Marcus A. Brubaker; Michael Brudno (WACV, 2017)

The Human Phenotype Ontology in 2017. - Sebastian Köhler 001; Nicole A. Vasilevsky; Mark Engelstad; Erin Foster; Julie A. McMurry; Ségolène Aymé; Gareth Baynam; Susan M. Bello; Cornelius F. Boerkoel; Kym M. Boycott; Michael Brudno; Orion J. Buske; et al. (Nucleic Acids Res., 2017)

PhenoStacks: Cross-Sectional Cohort Phenotype Comparison Visualizations. - Michael Glueck; Alina Gvozdik; Fanny Chevalier; Azam Khan; Michael Brudno; Daniel Wigdor (IEEE Trans. Vis. Comput. Graph., 2017)

More Text Please! Understanding and Supporting the Use of Visualization for Clinical Text Overview. - Nicole Sultanum; Michael Brudno; Daniel Wigdor; Fanny Chevalier (CHI, 2018)

Prediction of Cardiac Arrest from Physiological Signals in the Pediatric ICU. - Sana Tonekaboni; Mjaye Mazwi; Peter Laussen; Danny Eytan; Robert Greer; Sebastian D. Goodfellow; Andrew J. Goodwin; Michael Brudno; Anna Goldenberg (MLHC, 2018)

PhenoLines: Phenotype Comparison Visualizations for Disease Subtyping via Topic Models. - Michael Glueck; Mahdi Pakdaman Naeini; Finale Doshi-Velez; Fanny Chevalier; Azam Khan; Daniel Wigdor; Michael Brudno (IEEE Trans. Vis. Comput. Graph., 2018)

Centroid-based Deep Metric Learning for Speaker Recognition. - Jixuan Wang; Kuan-Chieh Wang; Marc T. Law; Frank Rudzicz; Michael Brudno (ICASSP, 2019)

Training without training data: Improving the generalizability of automated medical abbreviation disambiguation. - Marta Skreta; Aryan Arbabi; Jixuan Wang; Michael Brudno (ML4H@NeurIPS, 2019)

Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning. - Aryan Arbabi; David R. Adams; Sanja Fidler; Michael Brudno (RECOMB, 2019)

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. - Sebastian Köhler 001; Leigh Carmody; Nicole A. Vasilevsky; Julius O. B. Jacobsen; Daniel Danis; Jean-Philippe F. Gourdine; Michael A. Gargano; Nomi L. Harris; Nicolas Matentzoglu; Julie A. McMurry; David Osumi-Sutherland; Valentina Cipriani; et al. (Nucleic Acids Res., 2019)

Doccurate: A Curation-Based Approach for Clinical Text Visualization. - Nicole Sultanum; Devin Singh; Michael Brudno; Fanny Chevalier (IEEE Trans. Vis. Comput. Graph., 2019)

Speaker Diarization with Session-Level Speaker Embedding Refinement Using Graph Neural Networks. - Jixuan Wang; Xiong Xiao; Jian Wu 027; Ranjani Ramamurthy; Frank Rudzicz; Michael Brudno (ICASSP, 2020)

Speaker Attribution with Voice Profiles by Graph-Based Semi-Supervised Learning. - Jixuan Wang; Xiong Xiao; Jian Wu 027; Ranjani Ramamurthy; Frank Rudzicz; Michael Brudno (INTERSPEECH, 2020)

Predicting Obstructive Hydronephrosis Based on Ultrasound Alone. - Lauren Erdman; Marta Skreta; Mandy Rickard; Carson McLean; Aziz Mezlini; Daniel T. Keefe; Anne-Sophie Blais; Michael Brudno; Armando J. Lorenzo; Anna Goldenberg (MICCAI (3), 2020)

3D Photography Based Neural Network Craniosynostosis Triaging System. - Pouria Mashouri; Marta Skreta; John Phillips; Dianna McAllister; Melissa Roy; Senthujan Senkaiahliyan; Michael Brudno; Devin Singh (ML4H@NeurIPS, 2020)

Essential requirements for establishing and operating data trusts: practical guidance based on a working meeting of fifteen Canadian organizations and initiatives. - P. Alison Paprica; Eric Sutherland; Andrea Smith; Michael Brudno; Rosario G. Cartagena; Monique Crichlow; Brian K. Courtney; Chris Loken; Kimberlyn M. McGrail; Alex Ryan; Michael J. Schull; Adrian Thorogood; et al. (CoRR, 2020)

CReSCENT: CanceR Single Cell ExpressioN Toolkit. - Suluxan Mohanraj; Juan Javier Díaz-Mejía; Martin D. Pham; Hillary Elrick; Mia Husic; Shaikh Rashid; Ping Luo; Prabnur Bal; Kevin Lu; Samarth Patel; Alaina Mahalanabis; Alaine Naidas; et al. (Nucleic Acids Res., 2020)

Grad2Task: Improved Few-shot Text Classification Using Gradients for Task Representation. - Jixuan Wang; Kuan-Chieh Wang; Frank Rudzicz; Michael Brudno (NeurIPS, 2021)

MetaFusion: a high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates. - Michael Apostolides; Yue Jiang; Mia Husic; Robert Siddaway; Cynthia Hawkins; Andrei L. Turinsky; Michael Brudno; Arun K. Ramani (Bioinform., 2021)

PhenoPad: Building AI enabled note-taking interfaces for patient encounters. - Jixuan Wang; Jingbo Yang; Haochi Zhang; Helen Lu; Marta Skreta; Mia Husic; Aryan Arbabi; Nicole Sultanum; Michael Brudno (npj Digit. Medicine, 2022)

: Navigating large collections of text notes in electronic health records for clinical chart review. - Nicole Sultanum; Farooq Naeem; Michael Brudno; Fanny Chevalier (IEEE Trans. Vis. Comput. Graph., 2023)

Evaluation of single-cell RNAseq labelling algorithms using cancer datasets. - Erik Christensen; Ping Luo; Andrei L. Turinsky; Mia Husic; Alaina Mahalanabis; Alaine Naidas; Juan Javier Díaz-Mejía; Michael Brudno; Trevor J. Pugh; Arun K. Ramani; Parisa Shooshtari (Briefings Bioinform., 2023)

Shortcut learning in medical AI hinders generalization: method for estimating AI model generalization without external data. - Cathy Ong Ly; Balagopal Unnikrishnan; Tony Tadic; Tirth Patel; Joe Duhamel; Sonja Kandel; Yasbanoo Moayedi; Michael Brudno; Andrew Hope; Heather Ross; Chris McIntosh (npj Digit. Medicine, 2024)

Development, deployment and scaling of operating room-ready artificial intelligence for real-time surgical decision support. - Sergey Protserov; Jaryd Hunter; Haochi Zhang; Pouria Mashouri; Caterina Masino; Michael Brudno; Amin Madani (npj Digit. Medicine, 2024)

SUM: Saliency Unification Through Mamba for Visual Attention Modeling. - Alireza Hosseini; Amirhossein Kazerouni; Saeed Akhavan; Michael Brudno; Babak Taati (WACV, 2025)

Approaches to identify scenarios for data science implementations within healthcare settings: recommendations based on experiences at multiple academic institutions. - Lillian Sung; Michael Brudno; Michael C. W. Caesar; Amol A. Verma; Brad Buchsbaum; Ravi Retnakaran; Vasily Giannakeas; Azadeh Kushki; Gary D. Bader; Helen Lasthiotakis; Muhammad Mamdani; Lisa Strug (Frontiers Digit. Health, 2025)

LIFT: Latent Implicit Functions for Task- and Data-Agnostic Encoding. - Amirhossein Kazerouni; Soroush Mehraban; Michael Brudno; Babak Taati (CoRR, 2025)