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. …
Congratulations to our group members, Haiyi Mao, Minxue Jia, and Marissa Di for their paper accepted in Nature Communications. Their paper is entitled “HALO: Hierarchical Causal Modeling for Single Cell Multi-Omics Data”. This paper presents a novel method, HALO, to model multi-omits single cell data (scRNAseq and scATACseq measured concurrently). HALO adopts a causal…
Our group member, Dr. Robert Gregg, presented his recent results on COPD trajectory modeling in a Poster Discussion session at ATS 2025 international conference. His poster is entitled “Clustering Spirometric Trajectory Patterns in COPD to Reveals a Branching Tree Structure“. Abstract availability: [conference…
Today was a specifically great day, since three of our student members were hooded and officially became “Drs”! Congratulations to Drs Minxue Jia, Haiyi Mao, and Tyler Lovelace for all their hard work and dedication. All three continue their research careers in academia and industry. Good luck everyone!…
Congratulations to our group member, Minxue Jia, for the acceptance of his first author paper in Molecular Systems Biology. His paper is entitled “LaGrACE: Estimating gene program dysregulation with latent regulatory network”. In this study, Minxue presents a novel method for estimating disease-specific dysregulation of gene programs by combining omics data…
Congratulations to Tyler Lovelace for the acceptance of his Crit Care Med paper , which is entitled “Plasma Levels of Soluble Suppression of Tumorigenicity-2 (sST2) Reflect Extra-Pulmonary Organ Dysfunction and Predict Outcome in Acute Respiratory Failure”. This paper investigates the prognostic value of soluble suppression of tumorigenicity (sST2) protein in blood and…
