Qianqian Song,
Assistant Professor & Director of Translational Bioinformatics
Department:
MD-HOBI-GENERAL
Business Email:
qsong1@ufl.edu
About Qianqian Song
Dr. Qianqian Song is a tenure-track Assistant Professor in the Department of Health Outcomes & Biomedical Informatics at the University of Florida College of Medicine. She serves as Director of the Cancer Data Commons & Director of Translational Bioinformatics at the UF Health Cancer Center (UFHCC). Dr. Song also co-leads the UFHCC Cancer AI Working Group and the UFHCC Computational Biology Unit.
Related Links:
Accomplishments
American Cancer Society Institutional Research Grant Pilot
2023
·
American Cancer Society
Maximizing Investigators’ Research Award
2023
·
National Institute of General Medical Sciences
Cancer Genetics and Metabolism Program Inter-programmatic Collaborative Research Pilot Award
2022
·
AHWFCCC
Deal Fund Travel Award
2020
·
WFBCCC
Teaching Profile
Courses Taught
2024-2025
GMS6804 Translational Bioinformatics
Research Profile
Dr. Qianqian Song specializes in artificial intelligence (AI)-driven biomedical research to advance precision medicine. Her work focuses on developing advanced computational and AI models to decipher disease mechanisms and identify novel therapeutic targets. With deep expertise in large-scale biomedical data, ranging from molecular-level genomics, transcriptomics, and proteomics, to single-cell and high-plex spatial imaging, and population-level electronic health records, Dr. Song has designed a suite of tailored deep learning, machine learning, and statistical tools for multi-modal data integration and interpretation. Her research has led to high-impact publications in Nature Communications, Advanced Science, Nucleic Acids Research, and the Journal of Clinical Oncology, highlighting the transformative power of AI in decoding complex diseases and accelerating therapeutic discovery.
Areas of Interest
- Bioinformatics
- Biomedical informatics
- Computational Oncology
Publications
Academic Articles
2025
CRISPRoffT: comprehensive database of CRISPR/Cas off-targets
Nucleic Acids Research.
53(D1):D914-D924
[DOI] 10.1093/nar/gkae1025.
[PMID] 39526384.
2025
Demystifying the black box: A survey on explainable artificial intelligence (XAI) in bioinformatics
Computational and Structural Biotechnology Journal.
27:346-359
[DOI] 10.1016/j.csbj.2024.12.027.
2024
Health disparities in the risk of severe acidosis: real-world evidence from the All of Us cohort
Journal of the American Medical Informatics Association.
31(12):2932-2939
[DOI] 10.1093/jamia/ocae256.
[PMID] 39401251.
2024
SCRN: Single-cell Gene Regulatory Network Identification in Alzheimer’s Disease.
IEEE/ACM transactions on computational biology and bioinformatics.
PP(6):1886-1896
[DOI] 10.1109/TCBB.2024.3424400.
2024
The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe
PLOS Genetics.
20(1)
[DOI] 10.1371/journal.pgen.1011107.
[PMID] 38181050.
2024
TrajVis: a visual clinical decision support system to translate artificial intelligence trajectory models in the precision management of chronic kidney disease.
Journal of the American Medical Informatics Association : JAMIA.
31(11):2474-2485
[DOI] 10.1093/jamia/ocae158.
[PMID] 38916922.
2023
An immune-related signature for optimizing prognosis prediction and treatment decision of hepatocellular carcinoma.
European journal of medical research.
28(1)
[DOI] 10.1186/s40001-023-01091-w.
[PMID] 36918943.
2023
c-Met Mediated Cytokine Network Promotes Brain Metastasis of Breast Cancer by Remodeling Neutrophil Activities.
Cancers.
15(9)
[DOI] 10.3390/cancers15092626.
[PMID] 37174093.
2023
Detection of lineage-reprogramming efficiency of tumor cells in a 3D-printed liver-on-a-chip model.
Theranostics.
13(14):4905-4918
[DOI] 10.7150/thno.86921.
[PMID] 37771785.
2023
Distinct inflammatory Th17 subsets emerge in autoimmunity and infection.
The Journal of experimental medicine.
220(10)
[DOI] 10.1084/jem.20221911.
[PMID] 37367944.
2023
DRMref: comprehensive reference map of drug resistance mechanisms in human cancer.
Nucleic acids research.
52(D1):D1253-D1264
[DOI] 10.1093/nar/gkad1087.
[PMID] 37986230.
2023
Editorial: Advanced computational systems biology approaches for accelerating comprehensive research of the human brain.
Frontiers in genetics.
14
[DOI] 10.3389/fgene.2023.1143789.
[PMID] 36845385.
2023
Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup.
Journal of the American Medical Informatics Association : JAMIA.
31(2):536-541
[DOI] 10.1093/jamia/ocad211.
[PMID] 38037121.
2023
Enhancing prognostic accuracy in head and neck squamous cell carcinoma chemotherapy via a lipid metabolism-related clustered polygenic model.
Cancer cell international.
23(1)
[DOI] 10.1186/s12935-023-03014-5.
[PMID] 37568192.
2023
Pathology steered stratification network for subtype identification in Alzheimer’s disease.
Medical physics.
[DOI] 10.1002/mp.16655.
[PMID] 37522278.
2023
PINet: Privileged Information Improve the Interpretablity and generalization of structural MRI in Alzheimer’s Disease
ACM-BCB.
2023
Pyruvate dehydrogenase kinase supports macrophage NLRP3 inflammasome activation during acute inflammation.
Cell reports.
42(1)
[DOI] 10.1016/j.celrep.2022.111941.
[PMID] 36640341.
2023
ROS-mediated SRMS activation confers platinum resistance in ovarian cancer.
Oncogene.
42(20):1672-1684
[DOI] 10.1038/s41388-023-02679-6.
[PMID] 37020040.
2023
Sample average treatment effect on the treated (SATT) analysis using counterfactual explanation identifies BMT and SARS-CoV-2 vaccination as protective risk factors associated with COVID-19 severity and survival in patients with multiple myeloma
Blood Cancer Journal.
2023
scENT for Revealing Gene Clusters From Single-Cell RNA-Seq Data.
IEEE/ACM transactions on computational biology and bioinformatics.
20(3):2266-2277
[DOI] 10.1109/TCBB.2023.3242260.
[PMID] 37022879.
2023
SiGra: single-cell spatial elucidation through an image-augmented graph transformer.
Nature communications.
14(1)
[DOI] 10.1038/s41467-023-41437-w.
[PMID] 37699885.
2023
Single-cell sequencing reveals the landscape of the human brain metastatic microenvironment.
Communications biology.
6(1)
[DOI] 10.1038/s42003-023-05124-2.
[PMID] 37479733.
2023
spaCI: deciphering spatial cellular communications through adaptive graph model.
Briefings in bioinformatics.
24(1)
[DOI] 10.1093/bib/bbac563.
[PMID] 36545790.
2023
SpaRx: elucidate single-cell spatial heterogeneity of drug responses for personalized treatment.
Briefings in bioinformatics.
24(6)
[DOI] 10.1093/bib/bbad338.
[PMID] 37798249.
2023
Uncovering the System Vulnerability and Criticality of Human Brain Under Dynamical Neuropathological Events in Alzheimer’s Disease.
Journal of Alzheimer's disease : JAD.
95(3):1201-1219
[DOI] 10.3233/JAD-230027.
[PMID] 37661878.
2022
Circulating Immune Bioenergetic, Metabolic, and Genetic Signatures Predict Melanoma Patients’ Response to Anti-PD-1 Immune Checkpoint Blockade.
Clinical cancer research : an official journal of the American Association for Cancer Research.
28(6):1192-1202
[DOI] 10.1158/1078-0432.CCR-21-3114.
[PMID] 35284940.
2022
Dual-Stream Subspace Clustering Network for revealing gene targets in Alzheimer’s disease.
Computers in biology and medicine.
151(Pt A)
[DOI] 10.1016/j.compbiomed.2022.106305.
[PMID] 36401971.
2022
Flap endonuclease 1 Facilitated Hepatocellular Carcinoma Progression by Enhancing USP7/MDM2-mediated P53 Inactivation.
International journal of biological sciences.
18(3):1022-1038
[DOI] 10.7150/ijbs.68179.
[PMID] 35173534.
2022
HSP90-CDC37 functions as a chaperone for the oncogenic FGFR3-TACC3 fusion.
Molecular therapy : the journal of the American Society of Gene Therapy.
30(4):1610-1627
[DOI] 10.1016/j.ymthe.2022.02.009.
[PMID] 35151844.
2022
Intrapleural nano-immunotherapy promotes innate and adaptive immune responses to enhance anti-PD-L1 therapy for malignant pleural effusion.
Nature nanotechnology.
17(2):206-216
[DOI] 10.1038/s41565-021-01032-w.
[PMID] 34916656.
2022
Organoids in recapitulating tumorigenesis driven by risk factors: Current trends and future perspectives.
International journal of biological sciences.
18(7):2729-2743
[DOI] 10.7150/ijbs.70406.
[PMID] 35541903.
2022
Risk and Outcome of Breakthrough COVID-19 Infections in Vaccinated Patients With Cancer: Real-World Evidence From the National COVID Cohort Collaborative.
Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
40(13):1414-1427
[DOI] 10.1200/JCO.21.02419.
[PMID] 35286152.
2022
Single-Cell RNA-Seq Technologies and Computational Analysis Tools: Application in Cancer Research.
Methods in molecular biology (Clifton, N.J.).
2413:245-255
[DOI] 10.1007/978-1-0716-1896-7_23.
[PMID] 35044670.
2022
SMGR: a joint statistical method for integrative analysis of single-cell multi-omics data.
NAR genomics and bioinformatics.
4(3)
[DOI] 10.1093/nargab/lqac056.
[PMID] 35910046.
2022
Targeting DNA polymerase to DNA double-strand breaks reduces DNA deletion size and increases templated insertions generated by CRISPR/Cas9.
Nucleic acids research.
50(7):3944-3957
[DOI] 10.1093/nar/gkac186.
[PMID] 35323942.
2022
Uncovering the dynamic effects of DEX treatment on lung cancer by integrating bioinformatic inference and multiscale modeling of scRNA-seq and proteomics data.
Computers in biology and medicine.
149
[DOI] 10.1016/j.compbiomed.2022.105999.
[PMID] 35998480.
2021
3D scaffold-free microlivers with drug metabolic function generated by lineage-reprogrammed hepatocytes from human fibroblasts
Biomaterials.
269
[DOI] 10.1016/j.biomaterials.2021.120668.
2021
DNA primase subunit 1 deteriorated progression of hepatocellular carcinoma by activating AKT/mTOR signaling and UBE2C-mediated P53 ubiquitination.
Cell & bioscience.
11(1)
[DOI] 10.1186/s13578-021-00555-y.
[PMID] 33622397.
2021
DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence.
Briefings in bioinformatics.
22(5)
[DOI] 10.1093/bib/bbaa414.
[PMID] 33480403.
2021
Identification and Validation of Ubiquitin-Specific Proteases as a Novel Prognostic Signature for Hepatocellular Carcinoma.
Frontiers in oncology.
11
[DOI] 10.3389/fonc.2021.629327.
[PMID] 33718205.
2021
IGFBP2 promotes tumor progression by inducing alternative polarization of macrophages in pancreatic ductal adenocarcinoma through the STAT3 pathway.
Cancer letters.
500:132-146
[DOI] 10.1016/j.canlet.2020.12.008.
[PMID] 33309859.
2021
Organoids: Current Implications and Pharmaceutical Applications in Liver Diseases.
Current molecular pharmacology.
14(4):498-508
[DOI] 10.2174/1874467213666201217115854.
[PMID] 33334301.
2021
Outcomes of COVID-19 in Patients With Cancer: Report From the National COVID Cohort Collaborative (N3C).
Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
39(20):2232-2246
[DOI] 10.1200/JCO.21.01074.
[PMID] 34085538.
2021
Rac Family Small GTPase 3 Correlates with Progression and Poor Prognosis in Bladder Cancer.
DNA and cell biology.
40(3):469-481
[DOI] 10.1089/dna.2020.5613.
[PMID] 33600260.
2021
Reply to K. Takada et al.
Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
39(35):3997-3998
[DOI] 10.1200/JCO.21.02150.
[PMID] 34623872.
2021
scGCN is a graph convolutional networks algorithm for knowledge transfer in single cell omics.
Nature communications.
12(1)
[DOI] 10.1038/s41467-021-24172-y.
[PMID] 34158507.
2021
scLM: Automatic Detection of Consensus Gene Clusters Across Multiple Single-cell Datasets.
Genomics, proteomics & bioinformatics.
19(2):330-341
[DOI] 10.1016/j.gpb.2020.09.002.
[PMID] 33359676.
2021
The Emerging Roles of Exosomes in the Chemoresistance of Hepatocellular Carcinoma
Current Medicinal Chemistry.
28(1):93-109
[DOI] 10.2174/1875533xmta0imdkhx.
2020
Identification and Validation of the N6-Methyladenosine RNA Methylation Regulator YTHDF1 as a Novel Prognostic Marker and Potential Target for Hepatocellular Carcinoma.
Frontiers in molecular biosciences.
7
[DOI] 10.3389/fmolb.2020.604766.
[PMID] 33363211.
2020
Identifying cancer-associated fibroblasts as emerging targets for hepatocellular carcinoma.
Cell & bioscience.
10(1)
[DOI] 10.1186/s13578-020-00488-y.
[PMID] 33292459.
2020
Multi-Omics Analysis of Brain Metastasis Outcomes Following Craniotomy.
Frontiers in oncology.
10
[DOI] 10.3389/fonc.2020.615472.
[PMID] 33889540.
2020
Secretory Clusterin: A Promising Target for Chemoresistance of Hepatocellular Carcinoma.
Mini reviews in medicinal chemistry.
20(12):1153-1165
[DOI] 10.2174/1389557520666200331072122.
[PMID] 32228422.
2019
Cyclin-Dependent Kinase Regulatory Subunit 2 Indicated Poor Prognosis and Facilitated Aggressive Phenotype of Hepatocellular Carcinoma.
Disease markers.
2019
[DOI] 10.1155/2019/8964015.
[PMID] 31781310.
2019
Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq.
Cancer medicine.
8(6):3072-3085
[DOI] 10.1002/cam4.2113.
[PMID] 31033233.
2018
A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.
Cancer cell.
33(4):690-705.e9
[DOI] 10.1016/j.ccell.2018.03.014.
[PMID] 29622464.
2017
Haploinsufficiency and mutation are two sides of the cancer coin as cause and therapeutics target
Translational Cancer Research.
2017
RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites.
Scientific reports.
7(1)
[DOI] 10.1038/s41598-017-00795-4.
[PMID] 28377624.
2015
Systems biology approach to studying proliferation-dependent prognostic subnetworks in breast cancer.
Scientific reports.
5
[DOI] 10.1038/srep12981.
[PMID] 26257336.
Grants
Oct 2023
ACTIVE
Multi-modal insights of spatially distributed cells with associations of diseases and drug response
Role: Principal Investigator
Funding: NATL INST OF HLTH NIGMS
Contact Details
Emails:
- Business:
- qsong1@ufl.edu
Addresses:
- Business Mailing:
-
PO Box 100147
Gainesville FL 32610 - Business Street:
-
1889 Museum Rd, Suite 7116
Department of Health Outcomes & Biomedical Informatics
GAINESVILLE FL 32611