Congratulations to our group members, Haiyi Mao and Minxue Jia, 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…
Congratulations to Shaira Kee for the acceptance of his AJRCMB paper (“Red journal”), which is entitled “eNAMPT Is a Novel DAMP and Therapeutic Target in Human and Murine Pulmonary Fibrosis”. This paper examines role of extracellular nicotinamide phosphoribosyltransferase (eNAMPT) in lung fibrosis. Shaira’s analysis of scRNA-seq data revealed that the expansion of…
Congratulations to both Haiyi and Tyler for defending their PhD thesis yesterday and today, respectively. Haiyi‘s dissertation is entitled “Causal Representation Learning for Omics Data and Its Applications in Biological Discovery” and represents the work he did with us since 2019. His work has been published in 4 first author…
Congratulations to our group member, Tyler Lovelace, for the acceptance of his first author paper in JAIDS. His paper is entitled “Identifying Metabolomic Biomarkers of Lung Function Decline in People with HIV”. In this study, Tyler analyzed metabolite data collected from baseline bronchoalveolar lavage fluid and serum samples and identified…
Congratulations to Tyler Lovelace for the acceptance of the Placenta paper he co-authored, which is entitled “Characterization of senescence-associated transcripts in the human placenta“. This is a continuation of the two previous papers we had with Drs. Oren Barak and Yoel Sadovsky at the Magee Women Research Institute in Pittsburgh. It…
Congratulations to our group member, Haiyi Mao, for the acceptance and presentation of a first author paper at the NeurIPS 2024 international conference. His paper is entitled “Learning Identifiable Factorized Causal Representations of Cellular Responses”, a study he started during his internship with Genentech. In this study, Haiyi developed…
