News


[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 graduate student from the Molecular, Cellular & Developmental Biology Graduate Program, OSU, has joined the lab as a rotating student. Welcome!

[Dec-12-2020] Visiting scholar, Jing Jiang, has successfully completed his Ph.D. thesis defense. She will soon get her Doctorate degree. Congratulations!

[Dec-10-2020] Three visiting scholars, Zhaoqian Liu, Ren Qi, and Jing Jiang are departing BMBL. We are very appreciative of all the hard work they have done with us over the last year, and they will be missed.

[Dec-4-2020] Wantong Li, a graduate student from the Molecular, Cellular & Developmental Biology Graduate Program, OSU, has joined the lab as a rotating student. Welcome!

[Nov-18-2020] Graduate student, Anjun Ma, has successfully completed his Ph.D. thesis defense. He will soon get his Doctorate degree. Congratulations!

[Oct-25-2020] The manuscript “scREAD: A single-cell RNA-Seq database for Alzheimer’s Disease.” has been officially published by iScience!

[Oct-21-2020] The manuscript “Inductive Inference of Gene Regulatory Network Using Supervised and Semi-supervised Graph Neural Networks” has been officially published by Computational and Structural Biotechnology Journal!

[Oct-12-2020] The manuscript “Single-cell Techniques and Deep Learning in Predicting Drug Response” has been officially published by Trends in Pharmacological Sciences!

[Aug-29-2020] The manuscript “Elucidation of Biological Networks across Complex Diseases Using Single-Cell Omics” has been officially published by Trends in Genetics!

[Aug-12-2020] A five-year U24 project, entitled “Participant engagement and cancer genome sequencing (PE-CGS): coordinating center”, has been officially awarded (U24CA252977). Dr. Ma will serve as an MPI in the project for data analysis and statistical evaluations. Congratulations!


[Jul-23-2020] The grant Administrative Supplements Equipment (R01GM131399-03S1) is funded for equipment purchases. Congratulations!

[June-22-2020] Jennifer Xu, a summer intern student in 2019, has started a career in the Duke Clinical Research Institute. Congratulations!

[June-19-2020] Patrick J. Lawrence, a graduate student from Biomedical Sciences Graduate Program, OSU, has joined the lab as a rotating student. Welcome!

[May-21-2020] The grant ‘Deep Transfer Learning of Drug Sensitivity by Integrating Bulk and Single-cell RNA-Seq data’ has been selected for funding the CCTS Pilot Translational & Clinical Studies Program of the CCTS!

[May-18-2020] The manuscript ‘IRIS3: Integrated Cell-type-specific Regulon Inference Server from Single-cell RNA-Seq‘ has been officially published in Nucleic Acids Research!

[Mar-26-2020] The manuscript ‘Integrative Methods and Practical Challenges for Singl-cell Multi-omics‘ has been officially published in Trends in Biotechnology!

[Feb-24-2020] Zhenyu Wu, a graduate student from the Molecular, Cellular & Developmental Biology Graduate Program, OSU, has joined the lab as a rotating student.

[Feb-13-2020] The manuscript ‘Gene regulatory networks associated with lateral root and nodule development in soybean‘ has been officially published in In Silico Plants! Explore the description video here.

[Jan-07-2020] The manuscript ‘Network analyses in microbiome based on high-throughput multi-omics data ‘ has been officially published in Briefings in Bioinformatics!

[Dec-23-2019] Ren Qi (PhD student from Tianjin University, China) has joined the lab.

[Dec-18-2019] Yang Li, PhD has joined the lab as a postdoctoral researcher.

[Nov-26-2019] Dr. Qin Ma has been promoted and appointed as Tenured Associate Professor. Many congratulations!

[Sep-19-2019] The manuscript ‘SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting‘ has been officially published in Bioinformatics!

[Sep-16-2019] The graduate student Cankun Wang has been offered a Biomedical Informatics Specialist position in the Ohio State University Wexner Medical Center, Columbus, OH. Congratulations!

[Aug-29-2019] The manuscript ‘QUBIC2: A novel and robust biclustering algorithm for functional gene modules detection from high-throughput RNA-Sequencing data‘ has been officially published in Bioinformatics! Cheers!

[Aug-14-2019] Dr. Qin Ma has joined the editorial board in Briefings in Bioinformatics. Welcome for submissions!

[Aug-12-2019] Marlena Merling, a graduate student from the Department of Biomedical Informatics, OSU, has joined the lab as a rotating student.

[Aug-12-2019] Dr. Qin Ma is co-editing in a special issue of IEEE access in Feature Representation and Learning Methods With Applications in Large-Scale Biological Sequence Analysis Welcome for submissions!

[Jul-20-2019] The graduate student Shaopeng Gu has been offered a Computational Bioinformatics Analyst position in Sanford Health, Sioux Falls, SD. Congratulations!

[Jul-20-2019] The manuscript ‘Prediction of Regulatory Motifs from Human ChIP-Sequencing Data using a Deep Learning Framework‘ has been officially published in Nucleic Acids Research! Cheers!

[Jul-18-2019] Graduate student, Cankun Wang, has successfully completed his Master’s thesis defense. He will soon get his Master’s degree in August. Congratulations!

[Jul-15-2019] The manuscript ‘LTMG: A novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data‘ has been officially published in Nucleic Acids Research.

[Jun-01-2019] Three visiting Ph.D. students, Jing Jiang (from Xiamen University, China), Junyi Chen (from City University of Hong Kong, China), and Zhaoqian Liu (from Shandong University, China), have been joined the lab.

[May-22-2019] The paper ‘MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome‘ has been officially published in Bioinformatics. Cheers!

[May-20-2019] A graduate student from the South Dakota State University, Cankun Wang, and an undergraduate student from the University of North Carolina Chapel Hill, Jeniffer Xu, are admitted as 2019 BMI Summer Interns in BMBL.  They will start the 10-week intern work from May 20th. Congratulations!

[May-01-2019] Zichun Zhang, an undergraduate student from the Department of Mathematics, OSU, has officially joined the lab as an intern.

[Apr-01-2019] Weiliang Liu, an undergraduate student from the Department of Mathematics, OSU, has officially joined the lab as an intern.

[Apr-01-2019] Yuzhou Chang, a graduate student from the Department of Biomedical Informatics, OSU, has officially joined the lab as a research assistant.

[Mar-31-2019] BMBL has been awarded the 2019-2020 OSU CCTS Pilot grant on behalf of the project: ‘A computational pipeline for functional profiling of human gut microbiome and their associations with human chronic diseases’. Cheers!

[Feb-01-2019] The BMBL official website is online!

[Jan-07-2019] Mr. Anjun Ma has been admitted as a doctoral student in the Biomedical Sciences Graduate Program and will be a Graduate Research Assistant in BMBL.

[Jan-01-2019] BMBL is officially set up in the Department of Biomedical Informatics, Ohio State University.