Michael Brudno

83 papers A* 3A 5B 4C 4Misc 6Journal 49Unranked 11

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Approaches to identify scenarios for data science implementations within healthcare settings: recommendations based on experiences at multiple academic institutions. Frontiers Digit. Health 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
2025	J	`jnl`	LIFT: Latent Implicit Functions for Task- and Data-Agnostic Encoding. CoRR Amirhossein Kazerouni, Soroush Mehraban, Michael Brudno, Babak Taati
2025	—	`conf`	Optimizing Segmentation of Neonatal Brain MRIs with Partially Annotated Multi-Label Data. MLHC Dariia Kucheruk, Sam Osia, Pouria Mashouri, Elizaveta Rybnikova, Sergey Protserov, Jaryd Hunter, Maksym Muzychenko, Jessie Ting Guo, Michael Brudno
2025	A	`conf`	SUM: Saliency Unification Through Mamba for Visual Attention Modeling. WACV Alireza Hosseini, Amirhossein Kazerouni, Saeed Akhavan, Michael Brudno, Babak Taati
2024	J	`jnl`	Development, deployment and scaling of operating room-ready artificial intelligence for real-time surgical decision support. npj Digit. Medicine Sergey Protserov, Jaryd Hunter, Haochi Zhang, Pouria Mashouri, Caterina Masino, Michael Brudno, Amin Madani
2024	J	`jnl`	SUM: Saliency Unification through Mamba for Visual Attention Modeling. CoRR Alireza Hosseini, Amirhossein Kazerouni, Saeed Akhavan, Michael Brudno, Babak Taati
2024	J	`jnl`	Shortcut learning in medical AI hinders generalization: method for estimating AI model generalization without external data. npj Digit. Medicine Cathy Ong Ly, Balagopal Unnikrishnan, Tony Tadic, Tirth Patel, Joe Duhamel, Sonja Kandel, Yasbanoo Moayedi, Michael Brudno, Andrew Hope, Heather J. Ross, Chris McIntosh
2023	J	`jnl`	: Navigating large collections of text notes in electronic health records for clinical chart review. IEEE Trans. Vis. Comput. Graph. Nicole Sultanum, Farooq Naeem, Michael Brudno, Fanny Chevalier
2023	J	`jnl`	Evaluation of single-cell RNAseq labelling algorithms using cancer datasets. Briefings Bioinform. 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
2022	J	`jnl`	Grad2Task: Improved Few-shot Text Classification Using Gradients for Task Representation. CoRR Jixuan Wang, Kuan-Chieh Wang, Frank Rudzicz, Michael Brudno
2022	J	`jnl`	PhenoPad: Building AI enabled note-taking interfaces for patient encounters. npj Digit. Medicine Jixuan Wang, Jingbo Yang, Haochi Zhang, Helen Lu, Marta Skreta, Mia Husic, Aryan Arbabi, Nicole Sultanum, Michael Brudno
2021	A*	`conf`	Grad2Task: Improved Few-shot Text Classification Using Gradients for Task Representation. NeurIPS Jixuan Wang, Kuan-Chieh Wang, Frank Rudzicz, Michael Brudno
2021	J	`jnl`	MetaFusion: a high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates. Bioinform. Michael Apostolides, Yue Jiang, Mia Husic, Robert Siddaway, Cynthia Hawkins, Andrei L. Turinsky, Michael Brudno, Arun K. Ramani
2021	J	`jnl`	Speaker attribution with voice profiles by graph-based semi-supervised learning. CoRR Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno
2020	—	`conf`	3D Photography Based Neural Network Craniosynostosis Triaging System. ML4H@NeurIPS Pouria Mashouri, Marta Skreta, John Phillips, Dianna McAllister, Melissa Roy, Senthujan Senkaiahliyan, Michael Brudno, Devin Singh
2020	J	`jnl`	CReSCENT: CanceR Single Cell ExpressioN Toolkit. Nucleic Acids Res. 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
2020	J	`jnl`	Essential requirements for establishing and operating data trusts: practical guidance based on a working meeting of fifteen Canadian organizations and initiatives. CoRR 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
2020	—	`conf`	Predicting Obstructive Hydronephrosis Based on Ultrasound Alone. MICCAI (3) Lauren Erdman, Marta Skreta, Mandy Rickard, Carson McLean, Aziz Mezlini, Daniel T. Keefe, Anne-Sophie Blais, Michael Brudno, Armando J. Lorenzo, Anna Goldenberg
2020	A	`conf`	Speaker Attribution with Voice Profiles by Graph-Based Semi-Supervised Learning. INTERSPEECH Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno
2020	Misc	`conf`	Speaker Diarization with Session-Level Speaker Embedding Refinement Using Graph Neural Networks. ICASSP Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno
2020	J	`jnl`	Speaker diarization with session-level speaker embedding refinement using graph neural networks. CoRR Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno
2019	Misc	`conf`	Centroid-based Deep Metric Learning for Speaker Recognition. ICASSP Jixuan Wang, Kuan-Chieh Wang, Marc T. Law, Frank Rudzicz, Michael Brudno
2019	J	`jnl`	Centroid-based deep metric learning for speaker recognition. CoRR Jixuan Wang, Kuan-Chieh Wang, Marc T. Law, Frank Rudzicz, Michael Brudno
2019	J	`jnl`	Doccurate: A Curation-Based Approach for Clinical Text Visualization. IEEE Trans. Vis. Comput. Graph. Nicole Sultanum, Devin Singh, Michael Brudno, Fanny Chevalier
2019	J	`jnl`	Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 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
2019	B	`conf`	Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning. RECOMB Aryan Arbabi, David R. Adams, Sanja Fidler, Michael Brudno
2019	—	`conf`	Training without training data: Improving the generalizability of automated medical abbreviation disambiguation. ML4H@NeurIPS Marta Skreta, Aryan Arbabi, Jixuan Wang, Michael Brudno
2019	J	`jnl`	Training without training data: Improving the generalizability of automated medical abbreviation disambiguation. CoRR Marta Skreta, Aryan Arbabi, Jixuan Wang, Michael Brudno
2018	A*	`conf`	More Text Please! Understanding and Supporting the Use of Visualization for Clinical Text Overview. CHI Nicole Sultanum, Michael Brudno, Daniel Wigdor, Fanny Chevalier
2018	J	`jnl`	PhenoLines: Phenotype Comparison Visualizations for Disease Subtyping via Topic Models. IEEE Trans. Vis. Comput. Graph. Michael Glueck, Mahdi Pakdaman Naeini, Finale Doshi-Velez, Fanny Chevalier, Azam Khan, Daniel Wigdor, Michael Brudno
2018	—	`conf`	Prediction of Cardiac Arrest from Physiological Signals in the Pediatric ICU. MLHC Sana Tonekaboni, Mjaye Mazwi, Peter Laussen, Danny Eytan, Robert Greer, Sebastian D. Goodfellow, Andrew J. Goodwin, Michael Brudno, Anna Goldenberg
2017	J	`jnl`	PhenoStacks: Cross-Sectional Cohort Phenotype Comparison Visualizations. IEEE Trans. Vis. Comput. Graph. Michael Glueck, Alina Gvozdik, Fanny Chevalier, Azam Khan, Michael Brudno, Daniel Wigdor
2017	A	`conf`	Size and Texture-Based Classification of Lung Tumors with 3D CNNs. WACV Zhihao Luo, Marcus A. Brubaker, Michael Brudno
2017	J	`jnl`	The Human Phenotype Ontology in 2017. Nucleic Acids Res. 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
2017	—	`conf`	Towards a Directory of Rare Disease Specialists: Identifying Experts from Publication History. MLHC Zihan Wang, Michael Brudno, Orion J. Buske
2016	J	`jnl`	Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction. Bioinform. Aryan Arbabi, Ladislav Rampásek, Michael Brudno
2016	—	`conf`	Integrating Rare Disease Research Patient Workflows and Deep Phenotyping into the Epic© EMR. CRI Yael Kamil, Kym M. Boycott, Daniel Gross, Marta Gîrdea, Sergiu Dumitriu, Michael Brudno
2016	J	`jnl`	PhenoBlocks: Phenotype Comparison Visualizations. IEEE Trans. Vis. Comput. Graph. Michael Glueck, Peter Hamilton, Fanny Chevalier, Simon Breslav, Azam Khan, Daniel J. Wigdor, Michael Brudno
2016	J	`jnl`	deBGA: read alignment with de Bruijn graph-based seed and extension. Bioinform. Bo Liu, Hongzhe Guo, Michael Brudno, Yadong Wang
2015	J	`jnl`	Identification of deleterious synonymous variants in human genomes. Bioinform. Orion J. Buske, AshokKumar Manickaraj, Seema Mital, Peter N. Ray, Michael Brudno
2014	J	`jnl`	GenomeVISTA - an integrated software package for whole-genome alignment and visualization. Bioinform. Alexander Poliakov, Justin Foong, Michael Brudno, Inna Dubchak
2014	J	`jnl`	Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing. Bioinform. Ladislav Rampásek, Aryan Arbabi, Michael Brudno
2014	J	`jnl`	The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 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
2013	J	`jnl`	Identification of deleterious synonymous variants in human genomes. Bioinform. Orion J. Buske, AshokKumar Manickaraj, Seema Mital, Peter N. Ray, Michael Brudno
2013	J	`jnl`	SCARPA: scaffolding reads with practical algorithms. Bioinform. Nilgun Donmez, Michael Brudno
2012	Misc	`conf`	Mixture Model for Sub-Phenotyping in GWAS. Pacific Symposium on Biocomputing David Warde-Farley, Michael Brudno, Quaid Morris, Anna Goldenberg
2012	J	`jnl`	PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinform. Yue Jiang, Yadong Wang, Michael Brudno
2012	J	`jnl`	Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Res. Marc Fiume, Eric J. M. Smith, Andrew Brook, Dario Strbenac, Brian Turner, Aziz M. Mezlini, Mark D. Robinson, Shoshana J. Wodak, Michael Brudno
2011	C	`conf`	Clustering with Overlap for Genetic Interaction Networks via Local Search Optimization. WABI Joseph Andrew Whitney, Judice L. Y. Koh, Michael Costanzo, Grant Brown, Charles Boone, Michael Brudno
2011	B	`conf`	Hapsembler: An Assembler for Highly Polymorphic Genomes. RECOMB Nilgun Donmez, Michael Brudno
2011	J	`jnl`	SHRiMP2: Sensitive yet Practical Short Read Mapping. Bioinform. Matei David, Misko Dzamba, Dan Lister, Lucian Ilie, Michael Brudno
2011	J	`jnl`	SnowFlock: Virtual Machine Cloning as a First-Class Cloud Primitive. ACM Trans. Comput. Syst. H. Andrés Lagar-Cavilla, Joseph Andrew Whitney, Roy Bryant, Philip Patchin, Michael Brudno, Eyal de Lara, Stephen M. Rumble, Mahadev Satyanarayanan, Adin Scannell
2011	J	`jnl`	Variant detection and the Autism sequencing project. BMC Bioinform. Orion J. Buske, Misko Dzamba, Justin Foong, Lynette Lau, Marc Fiume, Christian Marshall, Susan Walker, Aparna Prasad, Michael Brudno
2010	J	`jnl`	Genome variation discovery with high-throughput sequencing data. Briefings Bioinform. Adrian V. Dalca, Michael Brudno
2010	B	`conf`	MoGUL: Detecting Common Insertions and Deletions in a Population. RECOMB Seunghak Lee, Eric P. Xing, Michael Brudno
2010	J	`jnl`	Savant: genome browser for high-throughput sequencing data. Bioinform. Marc Fiume, Vanessa Williams, Andrew Brook, Michael Brudno
2010	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp
2010	J	`jnl`	VARiD: A variation detection framework for color-space and letter-space platforms. Bioinform. Adrian V. Dalca, Stephen M. Rumble, Samuel Levy, Michael Brudno
2009	J	`jnl`	A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinform. Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. de la Vega
2009	—	`conf`	Adding the easy button to the cloud with SnowFlock and MPI. HPCVirt@EuroSys Philip Patchin, H. Andrés Lagar-Cavilla, Eyal de Lara, Michael Brudno
2009	J	`jnl`	Maximum Likelihood Genome Assembly. J. Comput. Biol. Paul Medvedev, Michael Brudno
2009	J	`jnl`	SHRiMP: Accurate Mapping of Short Color-space Reads. PLoS Comput. Biol. Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno
2009	A	`conf`	SnowFlock: rapid virtual machine cloning for cloud computing. EuroSys Horacio Andrés Lagar-Cavilla, Joseph Andrew Whitney, Adin Matthew Scannell, Philip Patchin, Stephen M. Rumble, Eyal de Lara, Michael Brudno, Mahadev Satyanarayanan
2008	—	`conf`	A mixture model for the evolution of gene expression in non-homogeneous datasets. NIPS Gerald T. Quon, Yee Whye Teh, Esther T. Chan, Timothy R. Hughes, Michael Brudno, Quaid Morris
2008	A	`conf`	A robust framework for detecting structural variations in a genome. ISMB Seunghak Lee, Elango Cheran, Michael Brudno
2008	B	`conf`	Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. RECOMB Paul Medvedev, Michael Brudno
2008	Misc	`conf`	FRESCO: Flexible Alignment with Rectangle Scoring Schemes. Pacific Symposium on Biocomputing Adrian V. Dalca, Michael Brudno
2008	C	`conf`	Read Mapping Algorithms for Single Molecule Sequencing Data. WABI Vladimir Yanovski, Stephen M. Rumble, Michael Brudno
2008	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy J. Warnow
2007	C	`conf`	Computability of Models for Sequence Assembly. WABI Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno
2007	J	`jnl`	Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Res. Michael Brudno, Alexander Poliakov, Simon Minovitsky, Igor Ratnere, Inna Dubchak
2006	J	`jnl`	Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter. J. Bioinform. Comput. Biol. Galina Yu. Kovaleva, Georgii A. Bazykin, Michael Brudno, Mikhail S. Gelfand
2004	—	`—`	Algorithms for comparison of DNA sequences. Michael Brudno
2004	C	`conf`	Chaining Algorithms for Alignment of Draft Sequence. WABI Mukund Sundararajan, Michael Brudno, Kerrin S. Small, Arend Sidow, Serafim Batzoglou
2004	A*	`conf`	PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences. AAAI Chuong B. Do, Michael Brudno, Serafim Batzoglou
2004	J	`jnl`	Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinform. Nameeta Y. Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak
2004	J	`jnl`	The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. Nucleic Acids Res. Michael Brudno, Rasmus Steinkamp, Burkhard Morgenstern
2003	J	`jnl`	AGenDA: homology-based gene prediction. Bioinform. Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern
2003	J	`jnl`	Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinform. Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou, Burkhard Morgenstern
2003	—	`conf`	Glocal alignment: finding rearrangements during alignment. ISMB (Supplement of Bioinformatics) Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou
2002	—	`conf`	Fast and Sensitive Alignment of Large Genomic Sequences. CSB Michael Brudno, Burkhard Morgenstern
2000	J	`jnl`	ASDB: database of alternatively spliced genes. Nucleic Acids Res. I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak
2000	J	`jnl`	VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinform. Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak