Congratulations to our group member (now alumnus), Tyler Lovelace, for the acceptance of his paper in the journal GigaScience. His paper is entitled “New causal discovery algorithm over censored variables identifies subtype-specific drivers of breast cancer progression” and constitutes one major part of his thesis. In this important paper, Tyler…
Congratulations to Marissa for defending her PhD thesis, entitled “Identifying regulatory mechanisms in biological systems using nonlinear causal discovery”. Marissa worked on algorithm development for causal graph learning on non-linear data and participated in the development of HALO (Mao*, Jia*, Di*, et al, 2025, Nature Commun). Her work could not have…
Congratulations to our group member (now alumnus), Mark Ebeid, for the acceptance of his paper in the RECOMB-CG conference. His paper is entitled ““Frustratingly Easy” Domain Adaptation for Cross-Species Transcription Factor Binding Prediction” and constitutes a major part of his thesis. In this paper, Mark presents a new method for…
Robert will have an oral presentation at the upcoming 2026 American Thoracic Society conference (ATS2026): Oral presentation Session: B101 – DECODING DISEASE: BIOMARKERS, PHENOTYPES, AND PRECISION MEDICINE. Poster title: “COPD Spirometric Trajectory Clusters Reveal Differences in the Complement Pathway“. Monday May 18, 2026 2:15-4:15 pm. Shaira will participate…
Congratulations to our group member, Marissa Di, for the acceptance of her collaborative paper in JCI Insight. The paper is entitled “Alpha diversity analysis of hepatic transcriptome reveals distinct pathways in alcohol-associated hepatitis”. This work investigates the utility of alpha-diversity, which is typically used in the analysis of microbiome communities,…
Congratulations to our group member, Minxue Jia, for the acceptance of his first co-author paper in European Respiratory Journal. His paper is entitled “The transcriptome of CD14+CD163-HLA-DRlow monocytes predicts mortality in Idiopathic Pulmonary Fibrosis”. In this study, Minxue analyzed scRNA-seq data from peripheral blood and found that transcriptome and proportions…
Congratulations to Mark for defending his PhD thesis, entitled “Advancing Causal Machine Learning for Metabolomic Biomarker Discovery and Cross-Species Gene Regulation”. Mark has done a great job in two fronts. First, he developed a new algorithm (MORALE) that uses cross-species comparisons to predict the transcription factor binding potential of a…
Congratulations to Shaira Kee for the acceptance of her co-first author paper in the Cell Communication and Signaling. Her paper is entitled “eNAMPT/TLR4 signaling drives PAH cellular phenotypic switching and lung vascular remodeling” and is a collaboration with Dr. Skip Garcia‘s lab. This paper shows that an eNAMPT monoclonal…
Our group member, Mark Ebeid, presented his recent results on cross-species transcription factor binding prediction. His oral presentation was entitled ““Frustratingly Easy” Domain Adaptation for Cross-Species Transcription Factor Binding Prediction”. The work is a collaboration with Drs Dennis kostka and Maria Chikina. Abstract availability: [conference web site]…
Congratulations to our group member (now alumnus), Daniel Yuan for the acceptance of his first author paper in the European Journal of Cancer. His paper is entitled “Immune cell transcriptional profiles from pre-vaccination peripheral blood predict immune response to preventative MUC1 cancer vaccine” and is a collaboration with Dr. Olja Finn, University of Pittsburgh. …
