Takis Benos

Marissa, Haiyi, and Mark successfully defended their thesis proposals this month.  The theses are about developing methods for identifying clinical and genetic factors in disease (Marissa), developing methods for multi-modal causal representation learning (Haiyi), and using ML methods in regulatory genomics (Mark).  Congratulations Marissa, Haiyi, and Mark!…

A collaborative paper of three members of the Benos Lab was accepted for publication by the journal Frontiers in Epidemiology. The paper is entitled “Causal Discovery in High-dimensional, Multicollinear Datasets”.  As the title says, this paper addresses two important problems of causal discovery. Different methods for dimensionality reduction are compared on simulated…

The Benos Lab received an R01 grant from NIDDK-NIH to study the molecular mechanisms that lead some people to develop liver fibrosis after transplant. Part of the grant is to build efficient predictors of fibrosis from blood samples. This new R01 is a collaboration with Gavin Arteel (leading PI;…

The Abstract that Wenjie had submitted to the 15th International Symposium on Sjögren’s Syndrome (2022 ISS) has been selected for an oral presentation.  The title of the abstract is “The University of Florida Cohort with Childhood Sjögren’s Disease Classified by the Latent Class Analysis“. Congratulations Wenjie!…

The paper of Haiyi and Minxue entitled “COEM: Cross-Modal Embedding for MetaCell Identification” was selected for a spotlight talk at the Computational Biology Workshop in the 39th International Conference on Machine Learning (ICML 2022) to be held in Baltimore, MD in July 22, 2022. Congratulations…

Robert presented his work on COPD subtyping at the American Thoracic Society (ATS) 2022 meeting. Congratulations Robert!   …

Takis gave an invited talk and met with colleagues at the Department of Biomedical Engineering at the University of Virginia, Charlottesville. The title of the talk was “Multi-scale Data Integration and Causal Inference for Medical Research”.   …

Congratulations to Tyler for the acceptance by Patterns of the paper “Essential Regression – a generalizable framework for inferring causal latent factors from multi-omic datasets“, which he is first co-author. The paper describes a new method to develop predictive causal models in high-dimensional, highly collinear data. A pre-print of this paper…

Tyler Lovelace, a CPCB PhD student in our group, was awarded an NIH F31 Predoctoral Fellowship from the National Library of Medicine (NLM). The F31 award is entitled “Causal graphical methods for high-dimensional heterogeneous biomedical data“.  We are very proud of Tyler who got this highly…

In the first in-person computational biology conference, ROCKY 2021, Takis made an oral and poster presentation regarding the work of former PhD student, Kristina Buschur, on COPD subtyping.  ROCKY conference was held in Snowmass, CO and followed all COVID guidances, requiring attendees to either show proof of vaccination or subjected…