Group news
- 2024.07 Congratulations to Yuxing Sun for winning the President’s Undergraduate Research Award (PURA)!
- 2024.07 Xinhai Pan, Macrina Lobo and Dr. Zhang presented and participated at ISMB2024 in Montreal, Canada.
- 2024.04 Our group presented at AWSOM2024. Dr. Zhang gave a keynote talk.
- 2024.04 Huge congratulations to current undergraduate student Mihir Bafna, for winning the prestigious NSF Graduate Research Fellowship Program (GRFP) Award!
- 2024.03 Our group participated and presented at MCBIOS2024. Congratulations to Ziqi Zhang for winning a Best Poster Award!
- 2024.01 Our paper scDisInFact: Disentangled Learning for Integration and Prediction of Multi-Batch Multi-Condition Single-Cell RNA-Sequencing Data has been accepted by Nature Communication! Congratulations to Ziqi and co-authors!
- 2023.12 Our paper LinRace: cell division history reconstruction of single cells using paired lineage barcode and gene expression data has been accepted by Nature Communications! Congratulations to Xinhai and co-authros!
- 2023.11 Yuqi attended RSGDREAM2023 to present his work on EpiPack, a tool for batch mapping and integration of scATAC-seq data.
- 2023.08 Our group presented at the InQuBATE Workshop: Computational Problems in Single Cell Transcriptomics and Multi-omics.
- 2023.07 Mihir and Hechen traveled to Lyon, France to attend ISMB/ECCB2023, where Mihir gave a talk on CLARIFY (accepted proceeding paper) and Hechen presented a poster on scMultiSim.
- 2023.06 Read our research story highlighted on the CoC website Award-winning Computer Models Propel Research in Cellular Differentiation!
- 2023.04 Our group attended the awesome 2-day Atlanta Workshop on Single-cell Omics (AWSOM2023). Ziqi won a Best Talk Award and Mihir won a Best Poster Award! Congratulations to all!
- 2023.04 Our paper CLARIFY: Cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics has been accepted by ISMB 2023! Congratulations to Mihir and co-authors!
- 2023.01 Our paper scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection has been accepted by Nature Communications. Congratulations to Ziqi and co-authors!
- 2022.11 Xinhai Pan, Hechen Li and Ziqi Zhang traveled to Las Vegas to present our work at the 14th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges.
- 2022.09 Congratulations to Mihir Bafna for being selected to participate in the 2022 National Symposium for Undergraduate Research (NSUR) hosted by the St. Jude Children’s Research Hospital Graduate School of Biomedical Sciences!
- 2022.07 Congratulations to Mihir Bafna for winning the President’s Undergraduate Research Award (PURA)!
- 2022.06 Our paper scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously has been accepted by Genome Biology. Congratulations to Ziqi and Chengkai!
- 2022.04 Our group attended the awesome 2-day Atlanta Workshop on Single-cell Omics (AWSOM2022). Ziqi and Hechen’s respective abstracts were selected to give oral presentations and Xinhai’s poster won the Best Poster Award! Congratulations to all!
- 2022.03 Our paper TedSim: temporal dynamics simulation of single cell RNA sequencing data and cell division history has been accepted by Nucleic Acids Research. Congratulations to Xinhai and Hechen!
- 2022.01 We received an NSF CAREER award to support our research on learning mechanisms from single cell multi-omics data!
- 2020.12 Thanks to Google Cloud Platform for granting us $5000 of Google Cloud Research Credits to support our research in single cell genomics.
- 2020.12 Our paper “An Unrolled Deep Learning Framework for Single Cell Gene Regulatory Networks” by Harsh Shrivastava, Xiuwei Zhang, Le Song and Srinivas Aluru was accepted by RECOMB 2021.
- 2020.10 Our paper “Maximum Likelihood Reconstruction of Ancestral Networks by Integer Linear Programming” by Vaibhav Rajan, Ziqi Zhang, Carl Kingsford and Xiuwei Zhang was accepted by Bioinformatics.
Group members
Dongjae Lee
MSCS student
Mehak Bindra
BINF MS student
Yuxing Sun
Undergraduate student (PURA award)
Chandra Sekhar Reddy E
MS CSE student
Baran Abbasi
Undergraduate student
Shivali Singh
High school student
Alumni
Huaijin (Tony) Tu, undergraduate student, 2024 Fall
Alejandro Danies-Lopez, MS CSE student (2024 Summer-Fall)
Mihir Bafna, undergraduate student (2022 Spring – 2024 Spring), now PhD student at MIT
Anwesha Gorantla, undergraduate student (2022 Fall, 2024 Fall)
Han Bao, undergraduate student (2022 Spring-Summer)
Xinye Zhao, MS student (2022 Spring-Summer)
Chukang Zhong, MS student (2022 Spring)
Pranav Putta, undergraduate student (2022 Spring)
Sooyoun Oh, PhD student (2020 Spring – 2021 Fall)
Jongseok Han, MS student (2021 Summer to Fall)
Paarth Parekh, MS student for Special Problems (2021 Spring), now Bioinformatics Scientist-II at Javelin Biotech
Chengkai Yang, undergraduate student (2020 Summer to Fall)
Rohan Goel, MS student and GRA (2020 Spring to Fall), now at Amazon
Pranit Kaul, MS student for Special Problems (2020 Spring)
Amir Girgis, undergraduate student, PURA Award, 2020 Summer
Xiuwei Zhang 