Congratulations to Ha Vu, who successfully defended her thesis on August 22, 2023! She already has a position lined up as an Associate Lead Bioinformatician at the University of Michigan! Ha was an amazing student and will be missed greatly!!
Core conserved transcriptional regulatory networks define the invasive trophoblast cell lineage7/31/2023 Our collaborative manuscript was published in Development today! We worked with the Michael Soares group to integrate our previously published single-cell RNA-seq data generated in the rat uterine-placental interface with single-nucleus ATAC-seq data generated at the same stage and in the same tissue type. We identified chromatin accessibility profiles in different cell types and identified a conserved gene regulatory network in invasive trophoblast cells. This work will will facilitate future studies investigating regulatory mechanisms in the invasive trophoblast cell lineage. Our collaborative manuscript was published in Genome Research today! We worked with Yudi Zhang and Karin Dorman in the Statistics department on a novel peak caller that uses unsupervised contrastive learning to extract shared signals from multiple replicates. We focused on ATAC-seq data and demonstrated that our tool, replicative contrastive learner (RCL), outperformed other methods. Congrats all! Ha Vu, a PhD student in Bioinformatics and Computational Biology, has received a Research Excellence Award! This award recognizes graduate students for outstanding research accomplishments. Students receiving this award are thought to be academically superior, and the program recognizes only the best students that are nearing graduation. Congratulations, Ha! Congratulations to both of our undergraduate students on receiving fellowships to do research in the lab this summer! Jordan Hansen received the Dean's High Impact Award for Undergraduate Research and the GDCB summer internship. Alexis Ball received the Sui Tong Chan Fung Fund Internship. Congratulations Alexis and Jordan - we are excited to have you in the lab for the summer!
We are excited to have Alexis Ball, a first year student majoring in Genetics at Iowa State University join our lab. Welcome Alexis!
We contributed to a manuscript that was published in Frontiers in Cell and Developmental Biology today! This manuscript focuses on how an enhancer element contributes to the regulation of Satb1 in trophoblast cells. Congratulations, all! Identifying novel regulators of placental development using time-series transcriptome data12/13/2022 An article from the Tuteja lab, "Identifying novel regulators of placental development using time-series transcriptome data" was published in Life Science Alliance today! Ha Vu, a Bioinformatics and Computational Biology graduate student, is lead author on the manuscript. She analyzed RNA-seq data we generated from mouse fetal placenta tissues at embryonic day (e) 7.5, e8.5 and e9.5 to identify genes with timepoint-specific expression, then inferred gene interaction networks to analyze highly connected network modules. We determined that timepoint-specific gene network modules associated with distinct developmental processes, and with similar expression profiles to specific human placental cell populations. From each module, we obtained hub genes and their direct neighboring genes, which were predicted to govern placental functions. Haninder Kaur in our lab confirmed that four novel candidate regulators identified through our analyses regulate cell migration in vitro. In summary, we were able to predict several novel regulators of placental development using network analysis of bulk RNA-seq data. Our findings and analysis approaches could be used to study other tissues, or for future studies investigating the transcriptional landscape of early placental development.
Our collaborative manuscript was published in PNAS today! We worked with the Michael Soares group to describe the first single-cell RNA-seq atlas of the rat uterine-placental interface. Our team identified cell-specific transcripts for invasive trophoblast, endothelial, smooth muscle, natural killer, and macrophage cells. We also identied similarities in the transcriptomes of rat and human invasive trophoblast cells, leading to the discovery of conserved candidate regulators of the invasive trophoblast cell lineage. This creates opportunities to test hypotheses underlying the pathophysiologic basis of trophoblast cell-guided uterine transformation and new insights into the etiology of diseases of placentation. Congratulations, team! We are excited to have Jordan Hansen, a junior majoring in Biology at Iowa State University join our lab. Welcome Jordan!
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