Research Interests

 

Our lab focuses on developing computational methods to discover heterogeneous transcriptional regulatory mechanisms from single-cell sequencing data. Our efforts are split between inferring cell-type-specific regulatory signals and constructing reliable gene regulatory networks via the integration of single-cell multi-omics. We are also going into the development of novel computational algorithms for spatial transcriptomic data analysis in immuno-oncology and neuroscience. https://bmbl.bmi.osumc.edu


We are developing enabling tools and databases, using metagenomic and metatranscriptomic data, to elucidate microbial systems and their interactions with human diseases. Our goal is to deliver reproducible and integrated analyses of complex gut microbiome data, detect functional and taxonomic abundances (biomarkers) in a microbial community, and infer significant associations between clinical measurements of human diseases and transformed microbial biomarkers. https://bmbl.bmi.osumc.edu/magical

Recent news

 

[Oct-6-2021] Dr. Qin Ma takes an interview about Decoding cell behavior and disease with AI and single-cell transcriptomic at Drug Discovery News.

[Sep-10-2021] Dr. Jing Zhao has been promoted to Assistant Professor (Clinical) in the Department of Biomedical Informatics, effective on October 01, 2021. Big congratulations!

[August-24-2021] Dr. Qin Ma will give an invited presentation on September 22nd at Nature portfolio webcast, with the topic of “single-cell multi-omics methods in cancer research”. Register now for free!

[August-23-2021] Dr. Qin Ma was appointed editorial board member with Computational and Structural Biotechnology Journal.

[August-2-2021] The manuscript “Deep Transfer Learning of Drug Sensitivity by Integrating Bulk and Single-cell RNA-seq data” is online on bioRxiv.

[July-28-2021] The manuscript “scGNN is a novel graph neural network model for single-cell RNA-Seq analysis” is reported in the 97th percentile of the 320,570 tracked articles of a similar age in all journals and ranked 1st of the tracked articles of a similar age in Nature Communications.

[July-28-2021] The manuscript “scREAD: A Single-Cell RNA-Seq Database for Alzheimer’s Disease” was recently listed on SSRN’s Top Ten download list for: NeurosciRN: Neuroinformatics & Information Systems (Topic).

[July-9-2021] The manuscript “RESEPT: tissue architecture inference and visualization from spatially resolved transcriptomics” is online on bioRxiv.

[July-8-2021] The manuscript “Spatially resolved transcriptomics reveals unique gene signatures associated with human temporal cortical architecture and Alzheimer’s pathology” is online on bioRxiv.

[June-10-2021] Yuzhou Chang with his project “RESEPT: a computational framework for REconstructing and Segmenting Expression mapped pseudo-image based on sPatially resolved Transcriptomics” has been invited for a poster presentation at ISMB/ECCB 2021 as part of the Special Session Single Cell and Spatial Data Analysis.

[June-9-2021] Dr. Qin Ma have presented “Deep learning methods for cis-regulatory motif identification and gene regulatory mechanism elucidation” at the AI in Digital Health Conference 2021.

[May-28-2021] Dr. Qin Ma and Dr. Anjun Ma have presented “DeepMAPS: Deep learning based Multi-omics Analysis Portal for Single cells” at the PIIO Research in Progress series.

[May-14-2021] Haocheng (Edison) Gu, an undergraduate student from the Department of Data Analytics, OSU, has joined the lab as an undergraduate volunteer. Welcome!

[May-14-2021] Xinqi (Ana) Xiong, an undergraduate student from the Department of Mathematics, OSU, has joined the lab as an undergraduate assistant. Welcome!

[May-8-2021] The manuscript “Use of scREAD to Explore and Analyze Single-cell and Single-nucleus RNA-Seq data for Alzheimer’s Disease” has been published on STAR protocols.

[Apr-21-2021] The BMI pilot grant “Identifying master transcription factors in adaptive immune systems using single-cell RNA/ATAC-seq data” has been funded (PI) (2021-2022).

[Apr-21-2021] The BMI pilot grant “Title: A Computational Framework for Integrative Analysis of Single Cell TCR-seq and RNA-seq Data for the Immuno-Oncology Investigation of Sex Differences” has been funded (MPI) (2021-2022).

[Apr-6-2021] Jiaxin Yang, an undergraduate student from the Department of Statistics, OSU, has joined the lab as an undergraduate assistant. Welcome!

[Mar-25-2021] The manuscript “scGNN is a novel graph neural network model for single-cell RNA-Seq analysis” has been officially published on Nature Communications.

[Mar-18-2021] The scGNN online website has launched.

[Mar-18-2021] Yingyi Zhu, an undergraduate student from the Department of Biological Engineering, OSU, has joined the lab as an undergraduate assistant. Welcome!

[Mar-15-2021] Mr. Paul Toth, a PhD student from the Molecular, Cellular & Developmental Biology Graduate Program, OSU, has joined the lab as a rotating student. Welcome.

[Mar-1-2021] The “IRIS-FGM” R package has been released on Bioconductor.

[Feb-16-2021] The grant “A reinforced imputation framework for accurate gene expression recovery from single-cell RNA-seq data” is funded by NSF IIBR (2021-2023).

[Feb-10-2021] The manuscript “IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis” has been accepted by Bioinformatics. Congratulations, Yuzhou Chang!

[Feb-8-2021] Cindy Tong, a student from Watkins Memorial High School, OH, has joined the lab. Welcome!

[Feb-5-2021] Shicong Wang, an undergraduate student from the Department of Computer Science and Engineering, OSU, has joined the lab as an undergraduate assistant. Welcome!

[Jan-15-2021] LncFinder has been evaluated as one of the state-of-the-art approaches (outperform others on the mouse dataset) in lncRNA identification (Amin, McGrath & Chen, 2019).

[Jan-15-2021] The manuscript “Single-cell Techniques and Deep Learning in Predicting Drug Response” has been selected as the featured publication by Ohio State Postdocs Quarterly Newsletter January 2021. Congratulations, Yang Li!

[Jan-8-2021] Yi Wang, a PhD student from the Molecular, Cellular & Developmental Biology Graduate Program, OSU, has joined the lab as a rotating student. Welcome!

 

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