Past CCB Seminars
December 2022 Seminars
November 2022 Seminars
Speaker: Dr. Matthew Crowson, MD MPA MASc FRCSCAssistant Professor, Investigator, Department of Otolaryngology-Head & Neck Surgery, Massachusetts Eye & Ear
Topic: Computer Vision for Irritable Toddlers: Improving Diagnostic Accuracy for Ear Infections
Recording: Click here
Speaker: Faisal Mahmood, PhD, Assistant Professor, Pathology, Harvard Medical School
Affiliation: Division of Computational Pathology, Brigham and Women’s Hospital; Data Science Program, Dana-Farber/Harvard Cancer Center; Cancer Program, Broad Institute of Harvard and MIT
Topic: Data-efficient and multimodal computational pathology
Abstract Advances in digital pathology and artificial intelligence have presented the potential to build assistive tools for objective diagnosis, prognosis and therapeutic-response and resistance prediction. In this talk we will discuss our work on: 1) Data-efficient methods for weakly-supervised whole slide classification with examples in cancer diagnosis and subtyping (Nature BME, 2021), and allograft rejection (Nature Medicine, 2022) 2) Harnessing weakly-supervised, fast and data-efficient WSI classification for identifying origins for cancers of unknown primary (Nature, 2021). 3) Discovering integrative histology-genomic prognostic markers via interpretable multimodal deep learning (IEEE TMI, 2020; ICCV, 2021; Cancer Cell, 2022). 4) Self-supervised deep learning for pathology and image retrieval (CVPR, 2022; Nature BME, 2022). 5) Deploying weakly supervised models in low resource settings without slide scanners, network connections, computational resources, and expensive microscopes. 6) Bias and fairness in computational pathology algorithms.
Relevant links:
Lu et al. Nat BME, 2021 Data-efficient and weakly supervised computational pathology on whole-slide images
Ming et al. Nature, 2021 AI-based pathology predicts origins for cancers of unknown primary
Lipkova et al. Nature Medicine, 2022 Deep learning-enabled assessment of cardiac allograft rejection from endomyocardial biopsies
Chen et al. Cancer Cell, 2022 Pan-cancer integrative histology-genomic analysis via multimodal deep learning
Recording: Click here
Speaker: Jeffrey Moffitt, PhD, Assistant Professor, Department of Microbiology, HMS
Topic: Building tissues atlases with MERFISH: The new opportunities and challenges of image-based single-cell transcriptomics
Recording: Click here
October 2022 Seminars
Speaker: Shila Ghazanfar, PhD, ARC Discovery Early Career Researcher, The University of Sydney, Faculty of Science, School of Mathematics and Statistics
Topic: StabMap: Mosaic single cell data integration using non-overlapping features
Recording: Click here
Speaker: Simon Norrelykke, Ph.D., Director of Image Analysis, Department of Systems Biology, HMS
Topic: Emerging Tools and Technologies in Bioimage Analysis and Processing
Recording: Click here
Speaker: Benjamin M. Gyori, Ph.D., Research Fellow, Director of Machine-assisted Modeling & Analysis, Laboratory of Systems Pharmacology, HMS
Topic: Large-scale biomedical knowledge assembly for hypothesis generation and human-machine interaction
Recording: Click here
Speaker: Jeremy Manning, PhD, Assistant Professor of Psychological & Brain Sciences, Dartmouth College
Topic: Geometric approaches to understanding the neural basis of human thought
Recording: Click here
September 2022 Seminars
Speaker: Antonios Lioutas, Ph.D., Research Associate in Genetics, Harvard Medical School
Topic: Super-resolution imaging of the human genome
Recording: Not available
Speaker(s): Laurent Gatto, PhD, Associate Professor of Bioinformatics, UCLouvain, Belgium and Charlotte Soneson, PhD, Research Associate, FMI, Switzerland
Topic: The Bioconductor Education Committee and Its Initiatives
Related link: Bioconductor Education and Training
Recording: Click here
June 2022 Seminars
Speaker: Dan Triviglia, Director, DBMI IT Core, HMS
Title: Cloud Computing at HMS-DBMI
Recording: Click here
Speaker: Catia Pesquita, PhD, Assistant Professor at LASIGE, Faculty of Sciences University of Lisbon and Vice President of BioData.pt
Title: Biomedical Semantic Similarity for Humans and Machines
Recording: Click here
Speaker: William “Gaby” Rodriguez, PhD, Computational Research Consultant & Amir Karger, PhD, Associate Director of Research Computing
Title: The New Web Portal for HMS’ O2 Cluster: Simplifying the Experience of High Performance Computing with Open OnDemand
Recording: Click here
May 2022 Seminars
Speaker: Katy Börner, PhD, Victor H. Yngve Distinguished Professor of Intelligent Systems Engineering, Indiana University
Title: Human Reference Atlas Construction and Usage
Recording: Click here
Speaker: Robert Hoehndorf, PhD, King Abdullah University of Science and Technology
Title: Semantic Similarity and Machine Learning with Ontologies
Recording: Click here
Speaker: Jaclyn Mallard, PhD, CCB Center Administrator
Title: Filling in the Gaps: CCB’s Role in Quantitative Education at HMS
Recording: Click here
April 2022 Seminars
Speaker: Fabian Theis, PhD, Institute Director andResearch Group Leaderand Giovanni Palla, PhD Candidate at Helmholtz Munich
Title: Squidpy: A Scalable Framework for Spatial Omics Analysis
Recording: Click here
Speaker: Vincent Carey, PhD, Professor of Medicine at HMS and Associate Biostatistician at Channing Laboratory, Brigham And Women’s Hospital
Title: Open Computational eCosystems for Modern Genomics
Recording: Click here
Speaker: Artem Sokolov, PhD, HMS DBMI
Title: A Scalable, Modular Image-processing Pipeline for Multiplexed Tissue Imaging
Recording: Click here
Speaker: Constantin Ahlmann-Eltze, PhD student at the EMBL Heidelberg in the Huber group, European Molecular Biology Laboratory, Heidelberg, Germany
Title: Transformation and Preprocessing of Single-Cell RNA-Seq Data
Recording: Click here
March 2022 Seminars
Speaker: Nitesh Turaga, PhD, Scientist in the Department of Data Science, at the Dana Farber Cancer Institute of Harvard Medical School and a Core Team member at the Bioconductor Project, working at the intersection of Data Science, Computational biology, and Software Engineering
Title: Containerized and Parallel Computation in R/Bioconductor
Recording: N/A
Speaker: Paul Macklin, PhD, Associate Professor and Director of Undergraduate Studies in the Department of Intelligent Systems Engineering at Indiana University
Title: The Human Body at Cellular Resolution: the NIH Human Biomolecular Atlas Program
Recording: Click here
Speaker: Nils Eling, PhD, Postdoctoral Researcher at the Bodenmiller Laboratory at the University of Zurich
Title: Visualization and Analysis of Highly Multiplexed Imaging Data
Recording: Click here
February 2022 Seminars
Speaker: Sean Maden, Ph.D candidate in Computational Biology. Biomedical Engineering Dept (OHSU)
Title: Human Methylome Variation Across Infinium 450K Data on the Gene Expression Omnibus
Recording: N/A
Speaker: Marinka Zitnik, PhD, Assistant Professor of Biomedical Informatics, Harvard Medical School
Title: Leveraging the Cell Ontology to Classify Unseen Cell Types
Recording: Click here
Speaker: Levi Waldron, PhD, Associate Professor of Biostatistics at CUNY Graduate School of Public Health and Health Policy
Title: Curated Single Cell Multimodal Landmark Datasets for R/Bioconductor
Recording: Click Here
January 2022 Seminars
Speaker(s): Allon Klein, PhD, Assistant Professor of Systems Biology at HMS and Sahand Hormoz, PhD, Assistant Professor of Systems Biology at HMS
Title: Atlas of Human Population Variation in Bone Marrow Hematopoiesis
Recording: N/A
Date: January 31st, 2022
Speaker(s): Helena Crowell, PhD Candidate at University of Zurich and Dario Righelli, Assistant Researcher at Department of Statistics,University of Padua
Title: Orchestrating Spatially Resolved Transcriptomics Analysis with Bioconductor
Recording: Click here