Positions

We are excited about the opportunity to reshape our team due to relocation. Currently, we are recruiting postdocs and graduate students in the following areas.

1. Spatial Transcriptomics. During the past few years, numerous technologies have been developed to profile spatial transcriptomics and/or multiplexed proteins. We aim to develop generally applicable and user-friendly computational tools that will enable comprehensive, robust, efficient computational analyses of such data. We have developed Giotto, the first comprehensive toolbox specifically designed for spatial transcriptomic data analysis and visualization. We have also developed a number of novel methods for characterizing the spatial patterns (Zhu et al. 2018, Nature Biotech) and cell-cell interaction pathways (Dries et al. 2021, Genome Biology). Our bioinformatic expertise has also contributed to the development of several pioneering technologies (Eng et al. 2019, Nature; Takei et al. 2021, Nature). We welcome new members to develop new creative and powerful computational methods and to improve the scalability, functionality, and inter-operability of Giotto.

2. Single-cell Analysis.  Our lab has a long interest in single-cell analysis and developed a number of innovative computational methods including SCUBA, ECLAIR, GiniClust, MCA Network, RESCUE, STREAM, and DWLS. We have also applied single-cell analysis to gain mechanistic insights into cancer and various diseases (e.g. Luoma et al. 2020, Cell). Our current focus is the integration with additional single-cell modalities such as epigenomics, proteomics, and cell morphologies. We welcome new members who are interested to develop innovative computational methods and/or to apply these approaches to study cancer and neurological diseases.

3. Epigenetics. Epigenetic regulation plays an essential role in maintaining cell-type specific transcriptional programs. Abnormal activities of epigenetic regulators have been linked to various human diseases. Our lab has a long-term interest in developing computational methods for characterizing chromatin state organization (Pinello et al. 2014, PNAS; Pinello et al. 2016, Nature Biotech; Marco et al. 2017, Nature Comm; Huang et al. 2018, Nature Comm; Zhu et al. 2019, Genome Biology) and studying the role of epigenetic mechanisms in developmental-stage and cell-type specific gene regulation (Xu et al. 2012, Dev Cell; Huang et al. 2016, Dev Cell; Cai et al. 2020, PNAS). Our collaborative work with Dr. Stuart Orkin’s group has led to development of new therapeutic methods for sickle cell disease (Canver et al. 2015, Nature).  Our current focus is on studying the interaction between 3D chromatin and transcriptional regulation.

Please send a cover letter, updated CV, and contact information for at least two references via email to Dr. Guo-Cheng Yuan.