News

2024

[Jun 11, 2024] The paper titled “Harnessing the deep learning power of foundation models in single-cell omics” has been accepted for publication in Nature Reviews Molecular Cell Biology.

[Jun 7, 2024] We are excited to share this news about our recent published paper “A Single-cell and Spatial RNA-seq Database for Alzheimer’s Disease (ssREAD)”!

[May 31, 2024] We are thrilled to share this news about our co-I research R21 grant (PI: Giovanni Nigita)!

[May 21, 2024] Led by Cankun Wang, the paper titled “A Single-cell and Spatial RNA-seq Database for Alzheimer’s Disease (ssREAD)” has been officially accepted for publication in Nature Communications!

[May 17, 2024] Our collaborative paper titled “Spatial and functional targeting of intratumoral Tregs reverses CD8+ T cell exhaustion and promotes cancer immunotherapy” has been officially accepted for publication in the Journal of Clinical Investigation!

[May 14, 2024] We are happy to announce that our current OSU undergraduate volunteer, Pavan Thota has been accepted to Georgia Institute of Technology, starting Fall 2024, M.S. in Computer Science and Bioinformatics.

[May 13, 2024] Yi Jiang is set to present an intriguing poster titled “HyperGRN: Elucidate High-order-relation Gene Regulatory Networks in the Spatial Context ” at the 2024 International Conference on Intelligent Systems for Molecular Biology (ISMB).

[May 7, 2024] We are overjoyed to share some delightful personal news from our graduate student, Michael Hsu. He and his wife, Vicky, have welcomed a beautiful baby girl into their family. Both mother and baby are doing well, and the family is taking some time to enjoy these precious early days together.

[May 3, 2024] We are happy to announce that Hangxiao Zhu, one of our OSU undergraduate volunteer, has been accepted into the Computer Science PhD program at Texas A&M University.

[May 3, 2024] Our graduate research assistant, Qi Guo, successfully presented his poster titled “An Integrated Mouse Spinal Cord Atlas Revealing Microglia Phenotypes in Health and Injury Conditions” for the 4th Annual Department of Neuroscience Research Day. Check out a live photo from the event.

[May 2, 2024] We are thrilled to share the wonderful news that Jack Wu, an alumnus of our high school trainee, has been accepted into the Computer Science major at the University of Minnesota this fall.

[May 1, 2024] We are delighted to announce that Dr. Anjun Ma has joined the editorial team of Heliyon Genetics (Impact Factor: 4). Dr. Ma brings with him a wealth of expertise in Single-cell and spatial omics, Deep Learning, and Bioinformatics.

[April 25, 2024] We are thrilled to share the exciting news about Dr. Ren Qi, an alumnus of our visiting scholar. Dr. Qi has been offered a position as an Assistant Professor in the Department of Computer Science at the Beijing Institute of Technology in China.

[April 23, 2024] Ana Xiong, an alumnus of our OSU undergraduate volunteer, has been admitted into the PhD program at the University of North Carolina at Chapel Hill. She will begin her studies this fall, focusing on machine learning and medical imaging under the guidance of Dr. Martin Styner. We look forward to witnessing her future academic achievements (Group Photo).

[April 19, 2024] We are excited to highlight the presentation by Dr. Jordan Krull at 2024 Pelotonia Scholars Symposium on how Deep Learning is revolutionizing digital pathology. His insights on extracting crucial numerical features from pathology slides are reshaping medical diagnostics.

[March 28, 2024] We are thrilled to extend our congratulations to our lab research technician Ms. Megan McNutt, who has been admitted to The Ohio State University Medical School!

[March 24, 2024] Dr. Qin Ma presented “Graph Representation Learning of Single-Cell and Spatial Transcriptomics Data,” at the 20th Annual Meeting of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS) held at the Rollins School of Public Health, Emory University.

[March 12, 2024] The paper titled “Abnormal progenitor cell differentiation and cardiomyocyte proliferation in hypoplastic right heart syndrome” has been officially published in Circulation (IF=39.9).

[March 6, 2024] We are thrilled to welcome a new cohort of students to our lab. Joining us as Graduate Research Assistants are Xiaojie Jin and Weidong Wu (co-mentored by Dr. Anjun Ma). Additionally, Zhantao Du will be joining as a rotation PhD student.

[February 22, 2024] We are delighted to announce Mr. Hu Chen will be joining our lab as a Graduate Research Assistant in the summer of 2024. Welcome aboard!

[February 21, 2024] Congratulations on Dr. Anjun Ma, who has been awarded the PKD RRC Pilot and Feasibility Award, securing a grant of $63,500 for his project titled “Constructing a Cross-Species Single-cell Database in Polycystic Kidney Disease”.

[February 20, 2024] We are delighted to announce that Dr. Ahmed Hamdy Ghobashi will be joining our lab as a postdoc fellow. His start date will be on June 17, 2024. Welcome aboard!

[Feb-14-2024] Led by Jianying Li, the manuscript “Targeting metabolic sensing switch GPR84 on macrophages for cancer immunotherapy” has been officially published in Cancer Immunology, Immunotherapy.

[Feb-7-2024] Dr. Qin Ma has been featured in interview by the “The Multi-Omics Playbook”. This playbook is a comprehensive guide that delves into the integrated application of multi-omics approaches in our research. It covers essential methodologies, best practices, and insightful case studies that can enhance our understanding and application of multi-omics data.

[Jan-24-2024] The manuscript “MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer” was recently recognized among the top 50 Biotechnology and methods papers by Nature Communications.

[Jan-23-2024] Led by Cankun Wang, the paper titled “A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset” has been officially published in Cancer Research Communications.

[Jan-20-2024] Congratulations on Yingjie Li’s abstract “Identification of HPV oncogene and host cell differentiation associated heterogeneity in cervical cancer via single‐cell transcriptomics” has been selected for an oral presentation at Translational Research Cancer Centers Consortium (TRCCC) 2024!

[Jan-19-2024] We warmly welcome Michael Parthun, a graduate student from OSU, has joined the lab as a rotating student.

[Jan-6-2024] The paper titled “CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq” has been officially published in Briefings in Bioinformatics.

[Jan-6-2024] Our collaborative paper titled “Human iPSC-based model of COPD to investigate disease mechanisms, predict SARS-COV-2 outcome, and test preventive immunotherapy,” has been officially published in Stem Cells!

[Jan-6-2024] Led by Dr. Xiaoying Wang, the paper titled “MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer” has been officially published in Nature Communications.

[Jan-4-2024] Our collaborative paper titled “mRNA vaccines against SARS-CoV-2 induce divergent antigen-specific T-cell responses in patients with lung cancer,” has been officially published in Journal for Immunotherapy of Cancer!


2023

[Dec-14-2023] Congratulations to Dr. Jordan Krull for securing 2nd place in the Postdoc/Resident/Fellows category at the PIIO Symposium Poster Session!

[Dec-12-2023] Our collaborative paper titled “Targeting Metabolic Sensing Switch GPR84 on Macrophages for Cancer Immunotherapy,” is accepted to be published in Cancer Immunology, Immunotherapy!

[Dec-12-2023] Congratulations to Yuzhou Chang on a successful defense and a smooth Ph.D. graduation journey!

[Dec-12-2023] Dr. Qin Ma was awarded Excellence in Faculty Teaching in the Department of Biomedical Informatics for the year 2023. Congratulations!

[Dec-12-2023] Dr. Qin Ma was awarded Excellence in Faculty Teaching in the Department of Biomedical Informatics for the year 2023. Congratulations!

[Dec-12-2023] Dr. Jordan Krull was awarded Excellence in Postdoc Research in the Department of Biomedical Informatics for the year 2023. Congratulations!

[Dec-3-2023] The paper titled “CEMIG: Prediction of the cis-regulatory motif using the De Bruijn graph from ATAC-seq,” is accepted to be published in Briefings in Bioinformatics.

[Nov-29-2023] Lead by Xiaoying Wang, the paper titled “MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer” has been officially accepted for publication in Nature Communications.

[Nov-29-2023] Our manuscript “Dimension-agnostic and granularity-based spatially variable gene identification using BSP”, has been featured in Nature Communications Editors’ Highlights page among the top 50 papers in Biotechnology and methods.

[Nov-23-2023] The paper titled “mRNA vaccines against SARS-CoV-2 induce divergent antigen-specific T cell responses in lung cancer patients,” is accepted to be published in Journal for ImmunoTherapy of Cancer.

[Nov-15-2023] Our collaborative paper titled “Abnormal progenitor cell differentiation and cardiomyocyte proliferation in hypoplastic right heart syndrome,” is accepted to be published in Circulation (IF=40)!.

[Nov-13-2023] A new paper titled “DeepProSite: Structure-aware Protein Binding Sites Prediction Using ESMFold and Pre-trained Language Model,” is accepted to be published in Bioinformatics.

[Nov-3-2023] The paper titled “Dimension-agnostic and granularity-based spatially variable gene identification using BSP” has been officially accepted for publication in Nature Communications.

[Oct-20-2023] The paper titled “A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset” lead by Cankun Wang has been accepted for publication in Cancer Research Communications.

[Oct-13-2023] Dr. Qin Ma has offered his expert opinion for the Research Briefing accompanying the paper titled “STAligner: Enabling the Integration and Alignment of Multiple Spatial Transcriptomics Datasets” on Nature Computational Science.

[Sep-17-2023] We are delighted to welcome Pavan Thotas, currently pursuing a Bachelor of Science with a major in Health Sciences and a minor in Biology at OSU, to the BMBL team as an undergraduate intern volunteer.

[Sep-6-2023] Dr. Qin Ma has been invited to deliver a talk at the NIH/NIEHS Biostatistics and Computational Biology Branch DIR Seminar. The seminar, titled “Graph Representation Learning of Single-cell Omics Data,” will take place on Wednesday, September 20, 2023, at 11 AM (EST). To join the seminar remotely, use this Zoom link.

[Sep-4-2023] The paper titled “Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data” lead by Dr. Zhaoqian Liu has been accepted for publication in Computers in Biology and Medicine.

[Aug-25-2023] The New York Times featured the news titled “Researchers Dispute High-Profile Discoveries of Cancer Microbes,” reported on the recent scientific discourse surrounding the presence of microorganisms within tumors. Dr. Ma has been interviewed to provide his insights on this matter.

[Aug-16-2023] We are thrilled to share that Yingjie Li, in her first year of PhD studies, has achieved a remarkable milestone with her first author paper. The manuscript, titled “Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single-cell transcriptomic analysis,” has been accepted for publication in the Journal of Medical Virology.

[Aug-14-2023] We’re pleased to welcome Dr. Qianjiang Hu to our lab as a PostDoc Fellow. Collaboratively mentored by Dr. Melanie Königshoff from the University of Pittsburgh.

[Aug-14-2023] We’re delighted to have Qufei Wu join us as a High School Intern from the Class of 2024 at Culver Military Academy.

[Aug-10-2023] Dr. Qin Ma recently delivered a presentation at the 2023 Joint Statistical Meetings (JSM).

[Aug-4-2023] Kevin Liu, a BMI summer intern under the primary mentorship of Dr. Lang Li and secondary mentorship of Dr. Qin Ma, has been awarded Graduate Honorable Mention for his poster on “Data Curation of Hydroxyurea for Pediatric and Maternal Populations.”

[Jul-24-2023] We are delighted to share that Mirage Modi, previously a rotating student from the Medical Scientist Training Program (MSTP) MD-PhD program, has made the decision to join our BMBL team!

[Jul-20-2023] Cindy Tong, an alumnus of our high school trainee, has been admitted into Princeton University with a Computer Science major. We look forward to witnessing her future academic achievements.

[Jul-18-2023] Exciting development as our P01 program “Sex, Chromosomes, and Immunity in Bladder Cancer” (1P01CA278732) is officially launched! Visit our website at https://www.bcgsp.org/ to learn more about our latest research endeavors.

[Jul-6-2023] Yuzhou Chang has been honored with the Student & Trainee Travel Award at the International Conference on Intelligent Biology and Medicine (ICIBM 2023).

[Jul-6-2023] Our collaborative work with Dr. Dongjun Chung, titled “LRT: Integrative Analysis of scRNA-seq and scTCR-seq Data to Investigate Clonal Differentiation Heterogeneity,” has been formally accepted for publication in PLOS Computational Biology.

[Jun-20-2023] Dr. Anjun Ma’s abstract, “Deep Transfer Learning of Cancer Drug Responses by Integrating Bulk and Single-cell RNA-seq data”, has been selected for a 10-minute flash talk at the International Conference on Intelligent Biology and Medicine (ICIBM 2023) on July 18th, 2023.

[Jun-15-2023] We warmly welcome Anjali Byappanahalli, a dedicated PhD student from the Biomedical Sciences Graduate Program at OSU, who has joined our lab as a rotating student!

[Jun-15-2023] A hearty welcome to Mirage Modi, an ambitious MD & PhD student from the Biomedical Sciences Graduate Program at OSU, who has now joined our lab as a rotating student!

[Jun-10-2023] Congratulations to Megan McNutt and her team from The Ohio State University, who were among the top three finalists in the American Society for Artificial Internal Organs: For Young Innovators (ASAIOfyi) Student Design Competition. They presented their groundbreaking project, “A Removal Device for Tunneled Intravascular Catheters,” at the American Society for Artificial Internal Organs Conference in San Francisco.

[Jun-6-2023] The International Conference on Intelligent Biology and Medicine (ICIBM 2023) accepts four of BMBL’s work for presentations:

Dr. Qin Ma will present a poster on “Single-cell biological network inference using a heterogeneous graph transformer“, which was recently recognized among the top 50 cancer papers by Nature Communications.

Dr. Anjun Ma will present a poster on “Deep Transfer Learning of Cancer Drug Responses by Integrating Bulk and Single-cell RNA-seq data“, published in Nature Communications.

Yuzhou Chang will present a poster on “Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning“, published in the Computational and Structural Biotechnology Journal.

Cankun Wang will give an oral presentation on “A Weighted Two-stage Sequence Alignment Framework to Identify DNA Motifs from ChIP-exo Data“, accepted as a regular paper in ICIBM 2023.

[Jun-1-2023] Yuzhou Chang is set to present an intriguing poster titled “Spatial omics feature representation using graph Fourier transform” at the Spatial Biology 2023 US Conference.

[May-29-2023] We are thrilled to announce Dr. Anjun Ma’s commencement in his new role as Clinical Assistant Professor at The Ohio State University, marking an exciting milestone in his professional journey!

[May-25-2023] The paper “scREAD: A Single-Cell RNA-Seq Database for Alzheimer’s Disease” earns a spot on SSRN’s Top Ten download list in the NeurosciRN: Neurodegenerative Disorders & Injuries (Topic).

[May-22-2023] Congratulations Yi Jiang’s triumphant graduation from Shandong University, where he majored in Software Engineering!

[May-21-2023] Congratulations to Xiaoying Wang for successfully completing her PhD dissertation! We commend her exceptional scholarly achievement and profound dedication to her academic journey.

[May-19-2023] Congratulations to Dr. Qin Ma on his promotion to Full Professor by The Ohio State University! We celebrate his outstanding accomplishments and unwavering dedication to his field.

[May-17-2023] Exciting development at BMBL as Megan McNutt accepts the position of Senior Research Technician, commencing her role from June 5, 2023.

[May-13-2023] Dr. Yang Li’s paper entitled “A Weighted Two-stage Sequence Alignment Framework to Identify DNA Motifs from ChIP-exo Data” has been accepted as a regular paper for oral presentation at the International Conference on Intelligent Biology and Medicine (ICIBM 2023).

[May-4-2023] Dr. Jordan Krull had been selected as a Pelotonia Post-Doctoral Scholar through the Pelotonia Scholars Program. Congratulations to Dr. Krull on this achievement!

[Apr-19-2023] The poster “The tumor microbiome associates with features of the tumor microenvironment, treatment outcomes, and histologies; a national collaboration of the exORIEN Consortium” was presented at the 2023 American Association for Cancer Research Annual Meeting.

[Apr-13-2023] Dr. Qin Ma will give an invited keynote presentation “Graph Representation Learning of Single-Cell Omics Data” at the 21st Asia Pacific Bioinformatics Conference (APBC 2023) .

[Apr-10-2023] Hao Cheng presented his project Identifying cell-type-specific senescent cells and signature genes using heterogeneous graph contrastive learning and received the second place poster award in the poster session at the TriState SenNet Annual Conference.

[Mar-22-2023] Our DeepMAPS paper is highlighted by Nature Communications editor, as one of the 50 best papers in the field of Cancer research published at Nature Communications.

[Mar-20-2023] Dr. Qin Ma will give an invited presentation “Graph Representation Learning of Single-cell Omics Data” at the School of Artificial Intelligence at Jilin University.

[Mar-16-2023] The published article “IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis” has been selected to appear in the PLOS Showcase on Kudos.

[Mar-16-2023] Dr. Qin Ma will give an invited presentation “Single-cell biological network inference using deep learning” at the 2023 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference in Dallas, TX.

[Feb-6-2023] The manuscript “Single-cell biological network inference using a heterogeneous graph transformer” is officially accepted for publication in Nature Communications!

[Jan-28-2023] The manuscript “Explainable deep hypergraph learning modeling the peptide secondary structure prediction” has been accepted for publication in Advanced Science!

[Jan-25-2023] Mrs. Jia Qu has joined BMBL as a Student Research Assistant. Welcome!

[Jan-25-2023] The manuscript “Computational methods and challenges in analyzing intratumoral microbiome data” has been accepted for publication in Trends in Microbiology!

[Jan-6-2023] The manuscript “Promoting patient engagement in cancer genomics research programs: An environmental scan” has now been accepted for publication in Frontiers in Genetics!

[Jan-5-2023] Dr. Qin Ma gave an invited presentation “Graph Fourier Transform for tissue module identification from spatial multi-omics” at the Pelotonia Institute for Immuno-Oncology (PIIO) experimental IO group meeting.

2022


[Dec-16-2022] Dr. Anjun Ma gave an invited presentation “Predicting Drug Response at the Single-Cell Level in Cancer Drug Therapy Using Deep Transfer Learning” at the School of Artificial Intelligence in Jilin University.

[Dec-13-2022] The manuscript “Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer’s disease” has now been accepted for publication in Acta Neuropathologica Communications!

[Dec-9-2022] Dr. Qin Ma was awarded Excellence in Faculty Research in the Department of Biomedical Informatics for the year 2022. Congratulations!

[Dec-9-2022] Cankun Wang was awarded Excellence in Team Science (staff) in the Department of Biomedical Informatics for the year 2022. Congratulations!

[Dec-8-2022] Our collaborative study “Single-cell transcriptomics reveals impaired human cardiac cell lineage determination and cardiomyocyte proliferation due to NOTCH1 deficiency” has been officially accepted by Circulation Research, featuring Cankun Wang as the co-first author. Congratulations!

[Dec-6-2022] Dr. Qin Ma will give an invited presentation “Graph Representation Learning of Gene Expression Data” at the Nankai University International E-Forum on Artificial Intelligence and Robotics on Dec 9, 2022. Register now!

[Nov-16-2022] Jianying Li presented “Harnessing Anti-Tumor Metabolic Sensing Switch GPR84 on Macrophages for Cancer Immunotherapy” and received the second place poster award at the Pelotonia Institute for Immuno-Oncology (PIIO) Fourth Annual Immuno-Oncology Symposium. Congratulations!

[Nov-16-2022] Dr. Qin Ma gave an invited presentation “The use of single-cell multi-omics in immuno-oncology” at the Pelotonia Institute for Immuno-Oncology (PIIO) Fourth Annual Immuno-Oncology Symposium.

[Nov-4-2022] Dr. Qin Ma presented “The Immuno-Oncology Informatics Group” at OSU Comprehensive Cancer Center IMDP/SR directors meeting.

[Nov-1-2022] Dr. Qin Ma gave an invited presentation “AI methods development in multi-omics” for OSU AI retreat.

[Oct-28-2022] Dr. Qin Ma will give an invited presentation “Deep learning shapes single-cell and spatial transcriptomics data analysis” at the 10x Genomics Workshop on November 1, 2022. Register now!

[Oct-28-2022] The manuscript “NIH SenNet Consortium: Mapping the landscape of senescent cells throughout the human lifespan to understand physiological health” has now been accepted for publication in Nature Aging!

[Oct-20-2022] Dr. Qin Ma gave an invited presentation “Bioinformatics Research Development and Updates” at the OSU College of Medicine Grants Management Office.

[Oct-19-2022] The manuscript “Deep Transfer Learning of Cancer Drug Responses by Integrating Bulk and Single-cell RNA-seq data” has been accepted for publication in Nature Communications and will be available online soon!

[Oct-18-2022] Yuzhou Chang gave an invited talk “Spatial transcriptomics algorithms and the trend of spatial omics” at MWACD 2022 annual meeting.

[Oct-10-2022] The manuscript “scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data” has been accepted for publication in Bioinformatics and will be available online soon!

[Sep-23-2022] Dr. Jordan Krull will join BMBL and PIIO immuno-oncology informatics group as a post-doc researcher. Welcome!

[Sep-7-2022] Our collaborative study “ Durability of Booster mRNA Vaccine against SARS-CoV-2 BA.2.12.1, BA.4, and BA.5 Subvariants” has been officially published on New England Journal of Medicine!

[Aug-12-2022] The manuscript “Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning” has been accepted for publication in Computational and Structural Biotechnology Journal and will be available online soon!

[Jul-29-2022] We are pleased to announce the appointment of Qin Ma, PhD, as the Section Chief of Computational Biology and Bioinformatics in the Department of Biomedical Informatics, OSU.

[Jul-25-2022] Dr. Qin Ma and Dr. Anjun Ma have been invited as guest editors for the special issue “Single-Cell and Spatial Multi-Omics Technologies in Human Health” of Biomolecules. Submissions are welcome!

[Jul-20-2022] The manuscript “Deep Learning Analysis of Single-Cell Data in Empowering Clinical Implementation” has been published on Clinical and Translational Medicine!

[Jul-18-2022] The manuscript “A Bayesian Multivariate Mixture Model for High Throughput Spatial Transcriptomics” has been accepted for publication in Biometrics and will be available online soon!

[Jul-12-2022] Our collaborative study “Sampling and ranking spatial transcriptomics data embeddings to identify tissue architecture” with Dr. Dong Xu has been accepted by Frontiers in Genetics!

[Jul-10-2022] Our collaborative study “FACT subunit SUPT16H associates with BRD4 and contributes to silencing of interferon signaling” has been officially accepted by Nucleic Acids Research and will be available online soon!

[Jul-06-2022] The Computational Biology and Chemistry (CBAC) journal, in which Dr. Qin Ma serves as an Editor, has achieved a new high impact factor of 3.737 in 2022! The impact factor of CBAC has continuously increased with a huge bump from 1.8 (2019) and 2.877 (2020) to 3.737 (2021).

[Jul-06-2022] Our collaborative study “A Concurrent Canonical and Modified miRNAome Pan-Cancer Study on TCGA and TARGET Cohorts Leads to an Enhanced Resolution in Cancer” has been provisionally accepted by Cancer Research.

[Jul-01-2022] Our collaborative study “Microglia coordinate cellular interactions during spinal cord repair in mice” has been officially accepted by Nature Communications and will be available online soon!

[Jun-29-2022] The manuscript “Sex-Biased Adaptive Immune Regulation in Cancer Development and Therapy” has been accepted by iScience and will be available online soon!

[Jun-23-2022] Mrs. Jia Qu has been enrolled in the BMI graduate program and will join BMBL next semester. Welcome!

[Jun-21-2022] Our XSEDE Research Grant ‘A Computational Pipeline for Cell Type Classification and Cell-type-specific Gene Markers Identification based on Single-cell RNA-Sequencing Data’ has been awarded for three months extension.

[Jun-17-2022] We are pleased to announce the appointment of Qin Ma, PhD, as leader of the Immuno-Oncology Informatics Group (IOIG) within the Pelotonia Institute for Immuno-Oncology (PIIO) at the OSUCCC – James. He will be responsible for bolstering the data-science needs of the PIIO and will help us eliminate the bottleneck of data analysis. Please check the details here. Cheers!

[Jun-16-2022] Our manuscript “DESSO-DB: A web database for sequence and shape motif analyses and identification” has been officially published in the Computational and Structural Biotechnology Journal (IF=7.2). Xiaoying Wang and Cankun Wang are the co-first authors. Congratulations!

[Jun-13-2022] Our review manuscript “Deep Learning Analysis of Single-Cell Data in Empowering Clinical Implementation” has been officially accepted by Clinical and Translational Medicine (IF=11.5).

[May-19-2022] Our collaborative study “A shared disease-associated oligodendrocyte signature among multiple CNS pathologies” has been officially accepted by Nature Neuroscience and will be available online soon!

[May-18-2022] The review article “The use of single-cell multi-omics in immuno-oncology” has been officially published online in Nature Communications!

[May-06-2022] Mr. Mohnish Karthikeyan joins BMBL as a new high school student volunteer. Welcome!

[May-06-2022] Our review article “Single-cell multi-omics in immuno-oncology” has been officially accepted by Nature Communication and will be available online soon!

[Apr-21-2022] The article “A New Machine Learning-Based Framework for Mapping Uncertainty Analysis in RNA-Seq Read Alignment and Gene Expression Estimation” is among the topmost viewed articles in Frontiers in Genetics with 6778 views.

[Apr-14-2022] Our collaborative work with Dr. Zihai Li and PIIO, entitled “Androgen conspires with the CD8+ T cell exhaustion program and contributes to sex bias in cancer“, has been officially published in Science Immunology (IF= 17.73)!

[Apr-05-2022] Mr. Qin Ma has been invited to present at the CTSI Analytics Colloquium, University of Rochester Medical Center, on April 25th.  Online registration is now available. check details here.

[Mar-31-2022] Our collaborative work (Wolframin is a novel regulator of tau pathology and neurodegeneration) with Dr. Hongjun Fu has been accepted by Acta neuropathological (IF= 18.17)!

[Feb-25-2022] Dr. Jing Zhao has received a new NSF-SCH grant (title: A deep learning framework to identify cancer associated microbial signatures). Congratulations!

[Feb-23-2022] Our Comment paper “Deep learning shapes single-cell data analysis” has been officially published online in Nature Review Molecular Cell Biology (IF=94.44)!

[Feb-21-2022] Dr. Qin Ma has been awarded two new Pelotonia Idea Grants as an MPI, together with Drs. Chung, Hanel, Vilgelm (Title: Integrating Biomimetic Tissue Engineering and Multi-Omics Systems Analysis to Overcome CTCL Drug Resistance), and Drs. Carson and Xin (Title: Targeting GPR84 to Overcome Macrophage Mediated Resistance to Immunotherapy for Breast Cancer). A new milestone of the collaboration between BMBL and PIIO. Congratulations!

[Feb-18-2022] Dr. Jing Zhao starts a new career chapter in Bristol Myers Squibb (New York) as a Senior Manager Biostatistics. Congratulations and set sail!

[Feb-17-2022] Mr. Sheen Bower, who majored in Mathematics, joins BMBL as a new undergraduate volunteer. Welcome!

[Feb-16-2022] Our collaborative paper entitled “Provable Second-order Riemannian Gauss-Newton Method for Low-rank Tensor Estimation” has been accepted at ICASSP 2022.

[Feb-14-2022] Our Comment paper “Deep learning shapes single-cell data analysis” has been officially accepted and will soon be published in Nature Review Molecular Cell Biology (IF=94.44)!

[Jan-26-2022] The web services at bmbl.bmi.osumc.edu are unavailable due to server attacks. We are actively working on restoring the web services at our backup server. We apologize for the inconvenience and thank you for your understanding.

[Jan-05-2022] Yuzhou Chang has successfully completed his Ph.D. candidacy defense. Congratulations!

2021


[Dec-10-2021] Yuzhou Chang was awarded for Excellence in Research (Grad Student) in the Department of Biomedical Informatics of the year 2021. Congratulations!

[Dec-10-2021] Dr. Jing Zhao was awarded for Excellence in Collaborative Research (Staff-Grant) in the Department of Biomedical Informatics of the year 2021. Congratulations!

[Nov-16-2021] Dr. Anjun Ma has been invited for a presentation titled “Graph neural network applications in single-cell Multi-omics analysis” at Front Line Genomics as part of the Integrated Single-cell multi-omics session on December 9th.

[Nov-13-2021] The manuscript “Artificial Intelligence in Clinical Research of Cancers” has been accepted for publication in Briefings in Bioinformatics. Congratulations, Dr. Jing Zhao!

[Nov-9-2021] Dr. Qin Ma is reported as an innovator in medicine by the OSU College of Medicine news channel for co-leading the Ohio State coordinating center for the NCI’s new $85 million PE-CGS network that will combat disparities in cancer genome sequencing.

[Oct-21-2021] Yuzhou Chang has been selected for presentation for the upcoming Rocky 2021 conference at Snowmass, Colorado (December 2-4).

[Oct-20-2021] The TriState SenNet Tissue Mapping Center (U54) was officially funded by NIH. Congratulations!

[Oct-20-2021] Dr. Anjun Ma has been promoted to Research Scientist in the Department of Biomedical Informatics. Big congratulations!

[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)