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ORCIDMichael Brudno
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- affiliation: University of Toronto, Canada
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2020 – today
- 2024
[j40]Cathy Ong Ly, Balagopal Unnikrishnan, Tony Tadic, Tirth Patel
, Joe Duhamel, Sonja Kandel, Yasbanoo Moayedi, Michael Brudno, Andrew Hope, Heather Ross, Chris McIntosh:
Shortcut learning in medical AI hinders generalization: method for estimating AI model generalization without external data. npj Digit. Medicine 7(1) (2024)- [j39]Sergey Protserov, Jaryd Hunter, Haochi Zhang, Pouria Mashouri, Caterina Masino, Michael Brudno, Amin Madani:
Development, deployment and scaling of operating room-ready artificial intelligence for real-time surgical decision support. npj Digit. Medicine 7(1) (2024) - [i7]Alireza Hosseini, Amirhossein Kazerouni, Saeed Akhavan, Michael Brudno, Babak Taati:
SUM: Saliency Unification through Mamba for Visual Attention Modeling. CoRR abs/2406.17815 (2024) - 2023
- [j38]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:
Evaluation of single-cell RNAseq labelling algorithms using cancer datasets. Briefings Bioinform. 24(1) (2023) - [j37]Nicole Sultanum, Farooq Naeem, Michael Brudno, Fanny Chevalier:
: Navigating large collections of text notes in electronic health records for clinical chart review. IEEE Trans. Vis. Comput. Graph. 29(1): 1244-1254 (2023) - 2022
- [j36]Jixuan Wang, Jingbo Yang, Haochi Zhang, Helen Lu, Marta Skreta, Mia Husic, Aryan Arbabi, Nicole Sultanum, Michael Brudno:
PhenoPad: Building AI enabled note-taking interfaces for patient encounters. npj Digit. Medicine 5 (2022) - [i6]Jixuan Wang, Kuan-Chieh Wang, Frank Rudzicz, Michael Brudno:
Grad2Task: Improved Few-shot Text Classification Using Gradients for Task Representation. CoRR abs/2201.11576 (2022) - 2021
- [j35]Michael Apostolides, Yue Jiang, Mia Husic, Robert Siddaway, Cynthia Hawkins, Andrei L. Turinsky, Michael Brudno, Arun K. Ramani:
MetaFusion: a high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates. Bioinform. 37(19): 3144-3151 (2021) - [c31]Jixuan Wang, Kuan-Chieh Wang, Frank Rudzicz, Michael Brudno:
Grad2Task: Improved Few-shot Text Classification Using Gradients for Task Representation. NeurIPS 2021: 6542-6554 - [i5]Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno:
Speaker attribution with voice profiles by graph-based semi-supervised learning. CoRR abs/2102.03634 (2021) - 2020
- [j34]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, Erik Christensen, Danielle Croucher, Laura M. Richards, Parisa Shooshtari, Michael Brudno, Arun K. Ramani, Trevor J. Pugh:
CReSCENT: CanceR Single Cell ExpressioN Toolkit. Nucleic Acids Res. 48(Webserver-Issue): W372-W379 (2020) - [c30]Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno:
Speaker Diarization with Session-Level Speaker Embedding Refinement Using Graph Neural Networks. ICASSP 2020: 7109-7113 - [c29]Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno:
Speaker Attribution with Voice Profiles by Graph-Based Semi-Supervised Learning. INTERSPEECH 2020: 289-293 - [c28]Lauren Erdman, Marta Skreta, Mandy Rickard, Carson McLean, Aziz Mezlini, Daniel T. Keefe, Anne-Sophie Blais, Michael Brudno, Armando J. Lorenzo, Anna Goldenberg:
Predicting Obstructive Hydronephrosis Based on Ultrasound Alone. MICCAI (3) 2020: 493-503 - [c27]Pouria Mashouri, Marta Skreta, John Phillips, Dianna McAllister, Melissa Roy, Senthujan Senkaiahliyan, Michael Brudno, Devin Singh:
3D Photography Based Neural Network Craniosynostosis Triaging System. ML4H@NeurIPS 2020: 226-237 - [i4]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, Carl Virtanen, Kathleen Yang:
Essential requirements for establishing and operating data trusts: practical guidance based on a working meeting of fifteen Canadian organizations and initiatives. CoRR abs/2005.06604 (2020) - [i3]Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno:
Speaker diarization with session-level speaker embedding refinement using graph neural networks. CoRR abs/2005.11371 (2020)
2010 – 2019
- 2019
- [j33]Sebastian Köhler, 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, James P. Balhoff, Tom Conlin, Hannah Blau, Gareth Baynam, Richard Palmer, Dylan Gratian, Hugh J. S. Dawkins, Michael Segal, Anna C. Jansen, Ahmed Muaz, Willie H. Chang, Jenna Bergerson, Stanley J. F. Laulederkind, Zafer Yüksel, Sergi Beltran, Alexandra F. Freeman, Panagiotis I. Sergouniotis, Daniel Durkin, Andrea L. Storm, Marc Hanauer, Michael Brudno, Susan M. Bello, Murat Sincan, Kayli Rageth, Matthew T. Wheeler, Renske Oegema, Halima Lourghi, Maria G. Della Rocca, Rachel Thompson, Francisco Castellanos, James Priest, Charlotte Cunningham-Rundles, Ayushi Hegde, Ruth C. Lovering, Catherine Hajek, Annie Olry, Luigi Notarangelo, Morgan Similuk, Xingmin Aaron Zhang, David Gómez-Andrés, Hanns Lochmüller, Hélène Dollfus, Sergio Rosenzweig, Shruti Marwaha, Ana Rath, Kathleen Sullivan, Cynthia L. Smith, Joshua D. Milner, Dorothée Leroux, Cornelius F. Boerkoel, Amy Klion, Melody C. Carter, Tudor Groza, Damian Smedley, Melissa A. Haendel, Chris Mungall, Peter N. Robinson:
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 47(Database-Issue): D1018-D1027 (2019) - [j32]Nicole Sultanum, Devin Singh, Michael Brudno, Fanny Chevalier:
Doccurate: A Curation-Based Approach for Clinical Text Visualization. IEEE Trans. Vis. Comput. Graph. 25(1): 142-151 (2019) - [c26]Jixuan Wang, Kuan-Chieh Wang, Marc T. Law, Frank Rudzicz, Michael Brudno:
Centroid-based Deep Metric Learning for Speaker Recognition. ICASSP 2019: 3652-3656 - [c25]Marta Skreta, Aryan Arbabi, Jixuan Wang, Michael Brudno:
Training without training data: Improving the generalizability of automated medical abbreviation disambiguation. ML4H@NeurIPS 2019: 233-245 - [c24]Aryan Arbabi, David R. Adams, Sanja Fidler, Michael Brudno:
Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning. RECOMB 2019: 19-34 - [i2]Jixuan Wang, Kuan-Chieh Wang, Marc T. Law, Frank Rudzicz, Michael Brudno:
Centroid-based deep metric learning for speaker recognition. CoRR abs/1902.02375 (2019) - [i1]Marta Skreta, Aryan Arbabi, Jixuan Wang, Michael Brudno:
Training without training data: Improving the generalizability of automated medical abbreviation disambiguation. CoRR abs/1912.06174 (2019) - 2018
- [j31]Michael Glueck, Mahdi Pakdaman Naeini, Finale Doshi-Velez, Fanny Chevalier, Azam Khan, Daniel Wigdor, Michael Brudno:
PhenoLines: Phenotype Comparison Visualizations for Disease Subtyping via Topic Models. IEEE Trans. Vis. Comput. Graph. 24(1): 371-381 (2018) - [c23]Nicole Sultanum, Michael Brudno, Daniel Wigdor, Fanny Chevalier:
More Text Please! Understanding and Supporting the Use of Visualization for Clinical Text Overview. CHI 2018: 422 - [c22]Sana Tonekaboni, Mjaye Mazwi, Peter Laussen, Danny Eytan, Robert Greer, Sebastian D. Goodfellow, Andrew J. Goodwin, Michael Brudno, Anna Goldenberg:
Prediction of Cardiac Arrest from Physiological Signals in the Pediatric ICU. MLHC 2018: 534-550 - 2017
- [j30]Sebastian Köhler, 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, Patrick F. Chinnery, Valentina Cipriani, Laureen E. Connell, Hugh J. S. Dawkins, Laura E. DeMare, Andrew Devereau, Bert B. A. de Vries, Helen V. Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna Jähn, Roger James, Roland Krause, Stanley J. F. Laulederkind, Hanns Lochmüller, Gholson J. Lyon, Soichi Ogishima, Annie Olry, Willem H. Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H. Scott, Michael Segal, Panagiotis I. Sergouniotis, Richard Sever, Cynthia L. Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W. M. Veltman, Tom Vulliamy, Jing Yu, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O. B. Jacobsen, Tudor Groza, Damian Smedley, Christopher J. Mungall, Melissa A. Haendel, Peter N. Robinson:
The Human Phenotype Ontology in 2017. Nucleic Acids Res. 45(Database-Issue): D865-D876 (2017) - [j29]Michael Glueck, Alina Gvozdik, Fanny Chevalier, Azam Khan, Michael Brudno, Daniel Wigdor:
PhenoStacks: Cross-Sectional Cohort Phenotype Comparison Visualizations. IEEE Trans. Vis. Comput. Graph. 23(1): 191-200 (2017) - [c21]Zihan Wang, Michael Brudno, Orion J. Buske:
Towards a Directory of Rare Disease Specialists: Identifying Experts from Publication History. MLHC 2017: 352-360 - [c20]Zhihao Luo, Marcus A. Brubaker, Michael Brudno:
Size and Texture-Based Classification of Lung Tumors with 3D CNNs. WACV 2017: 806-814 - 2016
- [j28]Aryan Arbabi, Ladislav Rampásek, Michael Brudno:
Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction. Bioinform. 32(11): 1662-1669 (2016) - [j27]Bo Liu, Hongzhe Guo, Michael Brudno, Yadong Wang:
deBGA: read alignment with de Bruijn graph-based seed and extension. Bioinform. 32(21): 3224-3232 (2016) - [j26]Michael Glueck, Peter Hamilton, Fanny Chevalier, Simon Breslav, Azam Khan, Daniel J. Wigdor, Michael Brudno:
PhenoBlocks: Phenotype Comparison Visualizations. IEEE Trans. Vis. Comput. Graph. 22(1): 101-110 (2016) - [c19]Yael Kamil, Kym M. Boycott, Daniel Gross, Marta Gîrdea, Sergiu Dumitriu, Michael Brudno:
Integrating Rare Disease Research Patient Workflows and Deep Phenotyping into the Epic© EMR. CRI 2016 - 2015
- [j25]Orion J. Buske, AshokKumar Manickaraj, Seema Mital, Peter N. Ray, Michael Brudno:
Identification of deleterious synonymous variants in human genomes. Bioinform. 31(5): 799 (2015) - 2014
- [j24]Ladislav Rampásek, Aryan Arbabi, Michael Brudno:
Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing. Bioinform. 30(12): 212-218 (2014) - [j23]Alexander Poliakov, Justin Foong, Michael Brudno, Inna Dubchak:
GenomeVISTA - an integrated software package for whole-genome alignment and visualization. Bioinform. 30(18): 2654-2655 (2014) - [j22]Sebastian Köhler, Sandra C. Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, Isabelle Bailleul-Forestier, Graeme C. M. Black, Danielle L. Brown, Michael Brudno, Jennifer Campbell, David R. FitzPatrick, Janan T. Eppig, Andrew P. Jackson, Kathleen Freson, Marta Gîrdea, Ingo Helbig, Jane A. Hurst, Johanna Jähn, Laird G. Jackson, Anne M. Kelly, David H. Ledbetter, Sahar Mansour, Christa L. Martin, Celia Moss, Andrew D. Mumford, Willem H. Ouwehand, Soo-Mi Park, Erin Rooney Riggs, Richard H. Scott, Sanjay Sisodiya, Steven Van Vooren, Ronald J. Wapner, Andrew O. M. Wilkie, Caroline F. Wright, Anneke T. Vulto-van Silfhout, Nicole de Leeuw, Bert B. A. de Vries, Nicole L. Washington, Cynthia L. Smith, Monte Westerfield, Paul N. Schofield, Barbara J. Ruef, Georgios V. Gkoutos, Melissa A. Haendel, Damian Smedley, Suzanna E. Lewis, Peter N. Robinson:
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 42(Database-Issue): 966-974 (2014) - 2013
- [j21]Nilgun Donmez, Michael Brudno:
SCARPA: scaffolding reads with practical algorithms. Bioinform. 29(4): 428-434 (2013) - [j20]Orion J. Buske, AshokKumar Manickaraj, Seema Mital, Peter N. Ray, Michael Brudno:
Identification of deleterious synonymous variants in human genomes. Bioinform. 29(15): 1843-1850 (2013) - 2012
- [j19]Yue Jiang, Yadong Wang, Michael Brudno:
PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinform. 28(20): 2576-2583 (2012) - [j18]Marc Fiume, Eric J. M. Smith, Andrew Brook, Dario Strbenac, Brian Turner, Aziz M. Mezlini, Mark D. Robinson, Shoshana J. Wodak, Michael Brudno:
Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Res. 40(Web-Server-Issue): 615-621 (2012) - [c18]David Warde-Farley, Michael Brudno, Quaid Morris, Anna Goldenberg:
Mixture Model for Sub-Phenotyping in GWAS. Pacific Symposium on Biocomputing 2012: 363-374 - 2011
- [j17]Matei David, Misko Dzamba, Dan Lister, Lucian Ilie, Michael Brudno:
SHRiMP2: Sensitive yet Practical Short Read Mapping. Bioinform. 27(7): 1011-1012 (2011) - [j16]Orion J. Buske, Misko Dzamba, Justin Foong, Lynette Lau, Marc Fiume, Christian Marshall, Susan Walker, Aparna Prasad, Michael Brudno:
Variant detection and the Autism sequencing project. BMC Bioinform. 12(S-11): A4 (2011) - [j15]H. Andrés Lagar-Cavilla, Joseph Andrew Whitney, Roy Bryant, Philip Patchin, Michael Brudno, Eyal de Lara, Stephen M. Rumble, Mahadev Satyanarayanan, Adin Scannell:
SnowFlock: Virtual Machine Cloning as a First-Class Cloud Primitive. ACM Trans. Comput. Syst. 29(1): 2:1-2:45 (2011) - [c17]Nilgun Donmez, Michael Brudno:
Hapsembler: An Assembler for Highly Polymorphic Genomes. RECOMB 2011: 38-52 - [c16]Joseph Andrew Whitney, Judice L. Y. Koh, Michael Costanzo, Grant Brown, Charles Boone, Michael Brudno:
Clustering with Overlap for Genetic Interaction Networks via Local Search Optimization. WABI 2011: 326-338 - 2010
- [j14]Adrian V. Dalca, Michael Brudno:
Genome variation discovery with high-throughput sequencing data. Briefings Bioinform. 11(1): 3-14 (2010) - [j13]Adrian V. Dalca, Stephen M. Rumble, Samuel Levy, Michael Brudno:
VARiD: A variation detection framework for color-space and letter-space platforms. Bioinform. 26(12): 343-349 (2010) - [j12]Marc Fiume, Vanessa Williams, Andrew Brook, Michael Brudno:
Savant: genome browser for high-throughput sequencing data. Bioinform. 26(16): 1938-1944 (2010) - [c15]Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp:
Session Introduction. Pacific Symposium on Biocomputing 2010: 302-304 - [c14]Seunghak Lee, Eric P. Xing, Michael Brudno:
MoGUL: Detecting Common Insertions and Deletions in a Population. RECOMB 2010: 357-368
2000 – 2009
- 2009
- [j11]Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. de la Vega:
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinform. 25(21): 2863-2864 (2009) - [j10]Paul Medvedev, Michael Brudno:
Maximum Likelihood Genome Assembly. J. Comput. Biol. 16(8): 1101-1116 (2009) - [j9]Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno:
SHRiMP: Accurate Mapping of Short Color-space Reads. PLoS Comput. Biol. 5(5) (2009) - [c13]Horacio Andrés Lagar-Cavilla, Joseph Andrew Whitney, Adin Matthew Scannell, Philip Patchin, Stephen M. Rumble, Eyal de Lara, Michael Brudno, Mahadev Satyanarayanan:
SnowFlock: rapid virtual machine cloning for cloud computing. EuroSys 2009: 1-12 - [c12]Philip Patchin, H. Andrés Lagar-Cavilla, Eyal de Lara, Michael Brudno:
Adding the easy button to the cloud with SnowFlock and MPI. HPCVirt@EuroSys 2009: 1-8 - 2008
- [c11]Seunghak Lee, Elango Cheran, Michael Brudno:
A robust framework for detecting structural variations in a genome. ISMB 2008: 59-67 - [c10]Gerald T. Quon, Yee Whye Teh, Esther T. Chan, Timothy R. Hughes, Michael Brudno, Quaid Morris:
A mixture model for the evolution of gene expression in non-homogeneous datasets. NIPS 2008: 1297-1304 - [c9]Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy J. Warnow:
Session Introduction. Pacific Symposium on Biocomputing 2008: 1-2 - [c8]Adrian V. Dalca, Michael Brudno:
FRESCO: Flexible Alignment with Rectangle Scoring Schemes. Pacific Symposium on Biocomputing 2008: 3-14 - [c7]Paul Medvedev, Michael Brudno:
Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. RECOMB 2008: 50-64 - [c6]Vladimir Yanovski, Stephen M. Rumble, Michael Brudno:
Read Mapping Algorithms for Single Molecule Sequencing Data. WABI 2008: 38-49 - 2007
- [j8]Michael Brudno, Alexander Poliakov, Simon Minovitsky, Igor Ratnere, Inna Dubchak:
Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Res. 35(Web-Server-Issue): 669-674 (2007) - [c5]Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno:
Computability of Models for Sequence Assembly. WABI 2007: 289-301 - 2006
- [j7]Galina Yu. Kovaleva, Georgii A. Bazykin, Michael Brudno, Mikhail S. Gelfand:
Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter. J. Bioinform. Comput. Biol. 4(5): 981-998 (2006) - 2004
- [b1]Michael Brudno:
Algorithms for comparison of DNA sequences. Stanford University, USA, 2004 - [j6]Nameeta Y. Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak:
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinform. 20(5): 636-643 (2004) - [j5]Michael Brudno, Rasmus Steinkamp, Burkhard Morgenstern:
The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. Nucleic Acids Res. 32(Web-Server-Issue): 41-44 (2004) - [c4]Chuong B. Do, Michael Brudno, Serafim Batzoglou:
PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences. AAAI 2004: 703-708 - [c3]Mukund Sundararajan, Michael Brudno, Kerrin S. Small, Arend Sidow, Serafim Batzoglou:
Chaining Algorithms for Alignment of Draft Sequence. WABI 2004: 326-337 - 2003
- [j4]Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern:
AGenDA: homology-based gene prediction. Bioinform. 19(12): 1575-1577 (2003) - [j3]Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou, Burkhard Morgenstern:
Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinform. 4: 66 (2003) - [c2]Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou:
Glocal alignment: finding rearrangements during alignment. ISMB (Supplement of Bioinformatics) 2003: 54-62 - 2002
- [c1]Michael Brudno, Burkhard Morgenstern:
Fast and Sensitive Alignment of Large Genomic Sequences. CSB 2002: 138- - 2000
- [j2]Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak:
VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinform. 16(11): 1046-1047 (2000) - [j1]I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak:
ASDB: database of alternatively spliced genes. Nucleic Acids Res. 28(1): 296-297 (2000)
Coauthor Index
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