Microbiome studies hold tremendous potential along with substantial computational challenges. I will present two computational approaches for microbiome data analysis. First, I will present SCRuB, a new method for in silico removal of contamination from microbiome data. We show that modeling the taxonomic composition of contamination sources, rather than trying to infer whether specific taxa […]
Spatial transcriptomics technologies are an emerging class of high-throughput sequencing methodologies for measuring gene expression at near single-cell resolution at spatially-defined measurement spots across a biological tissue. We show how measuring cells in their native environment has the potential to identify spatial patterns of cell types, cell-to-cell interactions, and spatial variation in cellular behavior. However, […]
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 […]
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 […]
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 […]
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 […]
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 […]
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 […]
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 […]
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 […]