Takis Benos

Congratulations to Minxue Jia for the acceptance of his first author Respiratory Research paper, which is entitled “Early events marking lung fibroblast transition to profibrotic state in idiopathic pulmonary fibrosis”. In this paper, Minxue analyzed two publicly available scRNA-seq data from IPF patients and controls focusing on the transition of fibroblasts from normal to…

Congratulations to Mark Ebeid for the acceptance of his paper to ISMB 2023 conference. The paper is entitled “An intrinsically interpretable neural network architecture for sequence to function learning“. This paper presents a new computational method to infer DNA sequence functionality in an interpretable way. Paper availability: […

Congratulations to Wenjie for winning the first place in the Research Day of the College of Public Health and Health Professional (PHHP) at UF. There were a total of 6 awards for two categories selected from 100+ abstracts / presentations. Her presentation competed in the…

One Abstract that Minxue had submitted to the 2023 American Thoracic Society conference (ATS 2023) was selected for a poster discussion session and another for a thematic poster presentation at the following sessions: Poster Discussion Session: A107 – AGING AND LUNG DISEASES COMING TO AGE. Poster title:…

Congratulations to McKayla Ro for her acceptance to MIT at the Computer Science, Economics, and Data Science program. McKayla is a senior student at Buchholz high-school at Gainesville. She started working with our group during the summer under the direct supervision of Robert (Gregg). They investigated healthcare disparities in COPD. …

Congratulations to Dr. Kristina Buschur for the acceptance of her first author Respiratory Research paper, which is entitled “Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis”. In this paper, Kristina used her ssNPA algorithm (Bushur, Chikina, Benos, 2020, Bioinformatics) to identify COPD subtypes from blood gene expression…

Congratulations to Tyler Lovelace for the acceptance of his Nature Communications paper, which is entitled “Lipidomic signatures align with inflammatory patterns and outcomes in critical illness”. This paper addresses the question: why administration of thawed plasma during transport of critically ill patients improves survival? Multiple analytic methods were used, including causal models,…

Congratulations to Haiyi Mao for the acceptance of his first author paper to the proceedings track of the Machine Learning for Health (ML4H) 2022 Symposium.  The paper is entitled “Towards Cross-Modal Causal Structure and Representation Learning”. This paper introduces a new method to perform causal discovery between structured data (e.g., clinical…

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…