News

2021


[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!

[Aug-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!

[Aug-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.

[Jul-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.

[Jul-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).

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

[Jul-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.

[Jun-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.

[Jun-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!

2020


[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!

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

[Jun-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-7-2020] The manuscript ‘Network analyses in microbiome based on high-throughput multi-omics data ‘ has been officially published in Briefings in Bioinformatics!

2019


[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-1-2019] 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-1-2019] Zichun Zhang, an undergraduate student from the Department of Mathematics, OSU, has officially joined the lab as an intern.

[Apr-1-2019] Weiliang Liu, an undergraduate student from the Department of Mathematics, OSU, has officially joined the lab as an intern.

[Apr-1-2019] 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-1-2019] The BMBL official website is online!

[Jan-7-2019] 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-1-2019] BMBL is officially set up in the Department of Biomedical Informatics, Ohio State University.

2018


[Aug-20-2018] An excellent new undergraduate student, Paige Hinton, from the Mathematics and Statistics Department has officially joined the BMBL. Congratulations!

[Aug-14-2018] The GeneQC paper: A new machine learning-based framework for mapping uncertainty analysis in RNA-Seq read alignment and gene expression estimation, has officially published on Frontiers in Genetics. Cheers!

[Jul-3-2018] A new graduate course, PS 735 Next Generation Sequencing Data Analysis, will be open to students who are interesting in studying computational techniques for NGS data analysis and bioinformatic algorithms.

[Jul-1-2018] Dr. Adam McDermaid has officially started Post Doc career in our lab. Congratulations!

[Jun-18-2018] Mr. Adam McDermaid successfully passes his thesis defense and become Dr. McDermaid! Congratulations!

[Jun-14-2018] The proposal of “A Computational Pipeline for Cell Type Classification and Cell-type-specific Gene Markers Identification based on Single-cell RNA-Sequencing Data” has been approved by XSEDE, and a new research allocation with 50,000 SUs has been successfully assigned which will be activated on July 1. Cheers!

[May-23-2018] The undergraduate students, Minxuan Sun successfully received Agriculture and Biological Sciences (ABS) Undergraduate Engagement Award with the research topic: An R package of metagenome and metatranscriptome data analysis for biofuel. Congratulations!

[May-22-2018] A newly published paper, “Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1”, on JCB (IF=9.834) highlighted DMINDA2.0 as a great tool to support the biological insights discovery and be competitive with MEME suite.

[Jan-16-2018] Ms. Juan Xie gave a presentation of Hypothesis-driven and discovery-driven analysis of Grapevine expression data, at the Plant and Animal Genome Conference, Jan. 14-18, San Diego, CA, USA.

[Jan-8-2018] Mr. Minxuan Sun, an undergraduate student from Department of Computer Science, was hired in BMBL.

2017


[Dec-22-2017] Mr. Cankun Wang, a master student from Department of Plant Science, was hired in BMBL.

[Nov-17-2017] Mr. Adam McDermaid has successfully completed his comprehensive written and oral examinations and has been admitted to Ph.D. candidate by the Graduate School. Congratulations!

[Nov-7-2017] Mr. Jinyu Yang successfully passed his Master’s defense on the topic: “Regulatory DNA Motif Identification Based on Big Biological Data and Deep Learning”. Congratulations!

[Nov-1-2017] Our proposal “A Deep Learning Model for Regulatory DNA Motif Prediction Based on Next Generation Sequencing Data” is funded by Scholarly Excellence Funds of SDSU.

[Aug-28-2017] Mr. Minxuan Sun, an undergraduate student from Department of Computer Science, joined the lab as volunteer students.

[Aug-28-2017] The paper ‘A probabilistic model-based bi-clustering method for single-cell transcriptomic data analysis.’ was preprinted in bioRxiv.

[Aug-25-2017] Mr. Adam McDermaid gave a presentation of RNA Sequencing Analyses & Mapping Uncertainty at the Plant Genome Research Program (PGRP) meeting at the University of California, Davis campus, CA.

[Aug-22-2017] Mr. Anjun Ma, a master student from Department of Mathematics and Statistics, was hired in BMBL.

[Aug-22-2017] Ms. Shihan Wu, a master student from Department of Computer Science, was hired in BMBL.

[Aug-19-2017] Juan Xie and Jingyu Yang received academic award and research award from BCC for their excellent performance.

[Jul-18-2017] A new grant was received from the Sanford Health – SDSU Collaborative Research Seed Grant Program.

[Apr-21-2017] Mr. Shuai Li, an undergraduate student from Department of Computer Science, was hired in BMBL. He also received the BioSNTR Summer Undergraduate Research Grant.

[Apr-12-2017] The paper ‘Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes’ was officially accepted by Briefings in Bioinformatics. (IF=5.134)

[Apr-10-2017] The paper ‘DMINDA-2.0: integrated and systematic views of regulatory DNA motif identification and analyses’ was officially accepted by Bioinformatics. (IF=7.307)

[Mar-27-2017] Yiran Zhang received the “Meeting the Grand Challenges” Award for-2017 from SDSU!

[Mar-8-2017] The paper An algorithmic perspective of de-novo cis-regulatory motif finding based on ChIP-seq datawas published in Briefings in Bioinformatics. (IF=5.134)

2016


[Oct-2016] The paper QUBIC: a Bioconductor package for qualitative biclustering analysis of gene co-expression data was published in Bioinformatics. (IF=7.307)

[Oct-2016] A new grant was received from NSF.

[Oct-2016] A new biclustering R package was published in Bioinformatics.

[Aug-2016] Ms. Juan Xie, a master student from Department of Mathematics and Statistics, was hired in BMBL.

[Jun-2016] ‘DMINDA2 web server: regulatory DNA motif identification and analyses’, has been accepted to the ISMB-2016 – Technology Track.

[May-2016] Mr. Xiaozhu Jin received the BioSNTR Summer Undergraduate Research Grant.

[May-2016] The Research/Scholarship Support Fund received from SDSU.

[Apr-2016] Mr. Xiaozhu Jin, an undergraduate student from Department of Computer Science, was hired in BMBL.

[Apr-2016] Mr. Adam McDermaid, a Ph.D. student from Department of Mathematics and Statistics, was hired in BMBL.

[Mar-2016] Dr. Dong Xu is invited to visit our lab.

[Mar-2016] A paper regarding regulon identification was published in Scientific Reports.

[Feb-2016] Mr. Yiran Zhang, an undergraduate student from Department of Computer Science, was hired in BMBL.

[Jan-2016] A new grant was received from BioSNTR Seed Opportunity Program.

[Jan-2016] Mr. Jinyu Yang, a master student from Department of Mathematics and Statistics, was hired in BMBL.

2015


[Oct-2015] Scholarly Excellence Funds was received from SDSU.

[May-2015] The paper Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum was published in Nucleic Acids Research. (IF=9.202)