Takis Benos

Congratulations to Khaled Sayed and former Benos’ Lab member, Haopu Yang, for the acceptance of their iScience paper, whichis entitled “The upper and lower respiratory tract microbiome in severe aspiration pneumonia”.   In this paper, Khaled and Haopu helped analyze microbiome and clinical data of ICU patients to identify clusters with different…

Khaled Sayed accepted a full-time tenure-track appointment as Assistant Professor in the Department of Electrical and Computer Engineering & Computer Science, University of New Haven.  His position is starting on September 1, 2023.  Khaled has been a valuable member of our group since 2019.  He has worked…

Wenjie Zeng successfully passed her oral examination today at the Department of Epidemiology.  She did an excellent job answering all questions. She will now focus on completing her thesis work.  Congratulations Wenjie!   Untitled-768×363…

Daniel Yuan presented his work on single cell RNA-seq (scRNA-seq) analysis in cancer immunoprevention.  So far, MUC1 vaccine for colorectal cancer has induced strong immunogenicity in 25-43% of the participants. Analysis of blood scRNA-seq can help understand the mechanisms behind the responsiveness (or lack thereof) and build predictive models of response. Daniel…

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: all…

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…