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Advanced Biomedical Computation (ABC) Seminar Series

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Ales Varabyou, Johns Hopkins – “Novel Approaches for Segregating Noise and True Signals in RNA-seq Data for Comprehensive Genome Annotation”

This talk presents new methods to analyze and annotate the complex and noisy transcriptional landscapes revealed by large-scale RNA-seq studies. It introduces CHESS, a comprehensive catalog of human genes and transcripts derived from deep RNA sequencing, which covers both protein-coding and noncoding genes and captures a high level of transcriptional noise. It shows how transcriptional […]

Yongju Lee, PhD, Genentech – “Contextual representation of pathology, immune repertoire by transformer and graph neural network, and transcriptomic contextual embedding via single-cell foundation model”

Zoom

The graph neural network (GNN) and transformer model are two renowned neural network architectures for obtaining contextual embeddings from biomedical data. However, each model has a trade-off in terms of the required dataset for training and representation power of the model. As examples, I will discuss the TEA-graph which employs GNN to define the contextual […]

Weiruo Zhang, PhD, Stanford University-“Integrative spatial-omics analysis of cellular architecture mediating lymph node metastasis in head and neck cancer”

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Spatial biology is a new frontier that has become accessible through advances in spatial profiling technologies, such as multiplexed in situ imaging spatial proteomics, which can provide single-cell resolution up to 60 markers. In this talk, I will introduce a computational analysis pipeline that performs integrative analysis of spatial proteomics and single-cell RNA sequencing to […]

Gennady Gorin, PhD – California Institute of Technology – “Stochastic foundations for single-cell RNA sequencing”

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  Single-cell RNA sequencing, which quantifies cell transcriptomes, has seen widespread adoption, accompanied by a proliferation of analytic methods. However, there has been relatively little systematic investigation of its best practices and their underlying assumptions, leading to challenges and discrepancies in analysis. I motivate a set of generic, principled strategies for modeling the biological and […]

Miriam Adler, PhD – Hebrew University – “Principles of wound healing and fibrosis: A circuit-to-target approach to reduce fibrosis”

Zoom

ABC Seminar Series Speaker: Miriam Adler, PhD Speaker Affiliation: Alexander Silberman Institute of Life Sciences and the Faculty of Medicine, Hebrew University of Jerusalem Speaker Position: Senior Lecturer Hosted by:  Utkarsh Sharma, Gibson Lab Fibrosis is a pathology of excessive scarring which causes morbidity and mortality worldwide. Fibrosis is a complex process involving thousands of […]

Efrat Muller, Tel Aviv University – “Methods for integrating metagenomics and metabolomics data”

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Speaker Name: Efrat Muller Affiliation: Prof. Elhanan Borenstein Lab, Tel Aviv University Position: Doctoral Candidate Hosted by: Jennifer Dawkins, Gerber Lab The human gut microbiome, and its metabolic activity in particular, have been implicated in a wide range of disease states, including metabolic disorders, inflammatory bowel diseases, and colorectal cancer. This growing appreciation for the […]

Vitalii Kleshchevnikov, PhD – Wellcome Sanger Institute – “Probabilistic models to resolve cell identity and tissue architecture”

Zoom

Speaker:  Vitalii Kleshchevnikov, PhD Affiliation:  Wellcome Sanger Institute Position:  Bioinformatician @ Bayraktar, Stegle, Teichmann group Host: Daniel MacDonald, Gibson Lab Abstract:  Cell identity drives cell-cell communication and tissue architecture and is in return regulated by cell-extrinsic cues. Cell identity is determined by the combination of intrinsic developmentally established transcription factor use (TF) and constitutive as […]

Andrew H. Song, PhD – Brigham and Women’s Hospital, Harvard Medical School – “Towards 3D pathology – The opportunities and challenges”

Hybrid-Zoom and Hale BTM VTC-2006b

Speaker:  Andrew H. Song, PhD Affiliation:  Brigham and Women’s Hospital, Harvard Medical School Position:  Research Fellow Date: Monday March 25, 2024 Time: 4:00PM-5:00PM ET Zoom: https://partners.zoom.us/j/82163676866 Meeting ID: 821 6367 6866 In person:  VTC-2006b, Hale BTM 2nd Floor Abstract: Human tissue, which is inherently three-dimensional (3D), is traditionally examined through standard-of-care histopathology as limited two-dimensional […]

Jean Du Terrail, PhD, Owkin – “Federated Learning in Healthcare in the Real-World: Examples and Practical Challenges”

Zoom

ABC Seminar Series Speaker: Jean du Terrail, PhD Speaker Affiliation: Fundamental Machine Learning Team, R&D, Owkin Speaker Position: Lead Research Scientist Hosted by: Guillaume Jaume, Mahmood Lab With the never-ending revolutions of data-driven approaches that started already more than a decade ago, it is surprising at first that the pace of ML discoveries in medicine […]

Jean-Baptiste Lugagne, PhD – Boston University – “Real-time control of antibiotic resistance genes with interactive AI”

Hybrid-Zoom and Ramzi Cotran Conference Center 75 Francis St

Speaker: Jean-Baptist Lugagne, PhD Affiliation: Boston University Position: Postdoctoral Researcher, Dunlop Lab Hosted by: Gibson Lab Date: Wednesday August 28th 2024 Time: 10:00-11:00AM ET In Person: Ramzi Cotran Conference Center, 75 Francis St, Brigham and Women’s Hospital (directions below) Zoom: https://partners.zoom.us/j/82163676866 Meeting ID: 821 6367 6866 Biological systems are inherently dynamic, stochastic, and multi-dimensional. Traditionally, manipulating […]