Takis Benos

Takis Benos,

William Bushnell Presidential Chaired Professor

Department: Department of Epidemiology
Business Email: pbenos@ufl.edu

About Takis Benos

Teaching Profile

Courses Taught
2022-2023
PHC7918 Independent Study
2022
GMS7858 Causal Artificial Intelligence for Health Research
2023
PHC7979 Advanced Research
2023
PHC7980 Research for Doctoral Dissertation

Research Profile

I am leading a diverse, interdisciplinary team who likes to tackle important questions in systems medicine by developing and using novel machine learning algorithms. Our ultimate goal is to identify risk factors and mechanisms affecting aging and contributing to the onset and progression of chronic diseases and cancer. We also develop predictive methods and tools that can directly improve health. We use probabilistic graphical models and other machine learning methods to integrate and mine high-dimensional, multi-modal biomedical data and to investigate biological processes pertinent to health and disease.

Open Researcher and Contributor ID (ORCID)

0000-0003-3172-3132

Areas of Interest
  • Aging
  • Causal inference
  • Chronic obstructive pulmonary disease (COPD)
  • Computational biology
  • Liver Disease
  • Lung cancer
  • Machine learning and applications

Publications

2023
An intrinsically interpretable neural network architecture for sequence-to-function learning.
Bioinformatics (Oxford, England). 39(39 Suppl 1):i413-i422 [DOI] 10.1093/bioinformatics/btad271. [PMID] 37387140.
2023
Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis.
Respiratory research. 24(1) [DOI] 10.1186/s12931-023-02316-6. [PMID] 36698131.
2023
Early events marking lung fibroblast transition to profibrotic state in idiopathic pulmonary fibrosis.
Respiratory research. 24(1) [DOI] 10.1186/s12931-023-02419-0. [PMID] 37085855.
2023
Early Evidence of COPD Obscured by Race-Specific Prediction Equations
American Journal of Respiratory and Critical Care Medicine. [DOI] 10.1164/rccm.202303-0444oc.
2023
Foxm1 regulates cardiomyocyte proliferation in adult zebrafish after cardiac injury
Development. 150(6) [DOI] 10.1242/dev.201163. [PMID] 36846912.
2023
Integrated BATF transcriptional network regulates suppressive intratumoral regulatory T cells
Science Immunology. 8(87) [DOI] 10.1126/sciimmunol.adf6717.
2023
Integrated unbiased multiomics defines disease-independent placental clusters in common obstetrical syndromes.
BMC medicine. 21(1) [DOI] 10.1186/s12916-023-03054-8. [PMID] 37679695.
2023
The plasma degradome reflects later development of NASH fibrosis after liver transplant.
Scientific reports. 13(1) [DOI] 10.1038/s41598-023-36867-x. [PMID] 37340062.
2023
The upper and lower respiratory tract microbiome in severe aspiration pneumonia.
iScience. 26(6) [DOI] 10.1016/j.isci.2023.106832. [PMID] 37250794.
2023
Transcriptional changes of the aging lung
Aging Cell. [DOI] 10.1111/acel.13969.
2022
Causal discovery in high-dimensional, multicollinear datasets
Frontiers in Epidemiology. 2 [DOI] 10.3389/fepid.2022.899655. [PMID] 36778756.
2022
Deep neural networks with knockoff features identify nonlinear causal relations and estimate effect sizes in complex biological systems
GigaScience. 12 [DOI] 10.1093/gigascience/giad044. [PMID] 37395630.
2022
Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets.
Patterns (New York, N.Y.). 3(5) [DOI] 10.1016/j.patter.2022.100473. [PMID] 35607614.
2022
Lipidomic signatures align with inflammatory patterns and outcomes in critical illness
Nature Communications. 13(1) [DOI] 10.1038/s41467-022-34420-4. [PMID] 36357394.
2021
A Pipeline for Integrated Theory and Data-Driven Modeling of Biomedical Data.
IEEE/ACM transactions on computational biology and bioinformatics. 18(3):811-822 [DOI] 10.1109/TCBB.2020.3019237. [PMID] 32841121.
2021
Bifurcated monocyte states are predictive of mortality in severe COVID-19.
bioRxiv : the preprint server for biology. [DOI] 10.1101/2021.02.10.430499. [PMID] 33594364.
2021
Compensatory hepatic adaptation accompanies permanent absence of intrahepatic biliary network due to YAP1 loss in liver progenitors.
Cell reports. 36(1) [DOI] 10.1016/j.celrep.2021.109310. [PMID] 34233187.
2021
Human ex vivo lung perfusion: a novel model to study human lung diseases.
Scientific reports. 11(1) [DOI] 10.1038/s41598-020-79434-4. [PMID] 33436736.
2021
Myofibroblast transcriptome indicates SFRP2hi fibroblast progenitors in systemic sclerosis skin.
Nature communications. 12(1) [DOI] 10.1038/s41467-021-24607-6. [PMID] 34282151.
2021
Neurological Complications Acquired During Pediatric Critical Illness: Exploratory “Mixed Graphical Modeling” Analysis Using Serum Biomarker Levels.
Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies. 22(10):906-914 [DOI] 10.1097/PCC.0000000000002776. [PMID] 34054117.
2021
People critically ill with COVID-19 exhibit peripheral immune profiles predictive of mortality and reflective of SARS-CoV-2 lung viral burden.
Cell reports. Medicine. 2(12) [DOI] 10.1016/j.xcrm.2021.100476. [PMID] 34873589.
2021
Plasma 1,3-╬▓-d-glucan levels predict adverse clinical outcomes in critical illness.
JCI insight. 6(14) [DOI] 10.1172/jci.insight.141277. [PMID] 34128840.
2021
Topographic heterogeneity of lung microbiota in end-stage idiopathic pulmonary fibrosis: the Microbiome in Lung Explants-2 (MiLEs-2) study.
Thorax. 76(3):239-247 [DOI] 10.1136/thoraxjnl-2020-214770. [PMID] 33268457.
2021
Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis.
The European respiratory journal. 58(6) [DOI] 10.1183/13993003.02950-2020. [PMID] 34083402.
2020
An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs.
BMC bioinformatics. 21(Suppl 8) [DOI] 10.1186/s12859-020-3519-5. [PMID] 32938407.
2020
Causal network perturbations for instance-specific analysis of single cell and disease samples.
Bioinformatics (Oxford, England). 36(8):2515-2521 [DOI] 10.1093/bioinformatics/btz949. [PMID] 31873725.
2020
CausalMGM: an interactive web-based causal discovery tool.
Nucleic acids research. 48(W1):W597-W602 [DOI] 10.1093/nar/gkaa350. [PMID] 32392295.
2020
miR-1207-5p Can Contribute to Dysregulation of Inflammatory Response in COVID-19 via Targeting SARS-CoV-2 RNA.
Frontiers in cellular and infection microbiology. 10 [DOI] 10.3389/fcimb.2020.586592. [PMID] 33194826.
2020
Protecting the lungs but hurting the kidneys: causal inference study for the risk of ventilation-induced kidney injury in ARDS.
Annals of translational medicine. 8(16) [DOI] 10.21037/atm-20-2050. [PMID] 32953785.
2020
Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients.
American journal of respiratory and critical care medicine. 202(12):1666-1677 [DOI] 10.1164/rccm.201912-2441OC. [PMID] 32717152.
2020
The evolution of radiographic edema in ARDS and its association with clinical outcomes: A prospective cohort study in adult patients.
Journal of critical care. 56:222-228 [DOI] 10.1016/j.jcrc.2020.01.012. [PMID] 32028223.
2019
COPDGene® 2019: Redefining the Diagnosis of Chronic Obstructive Pulmonary Disease.
Chronic obstructive pulmonary diseases (Miami, Fla.). 6(5):384-399 [DOI] 10.15326/jcopdf.6.5.2019.0149. [PMID] 31710793.
2019
Expression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers.
BMC cancer. 19(1) [DOI] 10.1186/s12885-019-5851-6. [PMID] 31299925.
2019
Feasibility of lung cancer prediction from low-dose CT scan and smoking factors using causal models.
Thorax. 74(7):643-649 [DOI] 10.1136/thoraxjnl-2018-212638. [PMID] 30862725.
2019
Host-Response Subphenotypes Offer Prognostic Enrichment in Patients With or at Risk for Acute Respiratory Distress Syndrome.
Critical care medicine. 47(12):1724-1734 [DOI] 10.1097/CCM.0000000000004018. [PMID] 31634231.
2019
PARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy.
Scientific reports. 9(1) [DOI] 10.1038/s41598-019-39542-2. [PMID] 30824778.
2019
Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis.
The European respiratory journal. 54(2) [DOI] 10.1183/13993003.02441-2018. [PMID] 31221805.
2019
Transcriptional regulatory model of fibrosis progression in the human lung.
JCI insight. 4(22) [DOI] 10.1172/jci.insight.131597. [PMID] 31600171.
2018
Evaluation of Causal Structure Learning Methods on Mixed Data Types.
Proceedings of machine learning research. 92:48-65 [PMID] 31080946.
2018
Evaluation of Causal Structure Learning Methods on Mixed Data Types.
Proceedings of machine learning research. 92:48-65 [PMID] 31080946.
2017
Genome-wide interaction study of dust mite allergen on lung function in children with asthma.
The Journal of allergy and clinical immunology. 140(4):996-1003.e7 [DOI] 10.1016/j.jaci.2016.12.967. [PMID] 28167095.

Grants

Sep 2022 ACTIVE
Interpretable graphical models for large multi-modal COPD data (R01HL159805)
Role: Principal Investigator
Funding: NATL INST OF HLTH NHLBI
Sep 2022 ACTIVE
COPD SUBTYPES AND EARLY PREDICTION USING INTEGRATIVE PROBABILISTIC GRAPHICAL MODELS R01HL157879
Role: Principal Investigator
Funding: NATL INST OF HLTH NHLBI
Sep 2022 ACTIVE
(00014385) Clinical Validation Center for Lung Cancer Early Detection
Role: Principal Investigator
Funding: UNIV OF TEXAS MD ANDERSON CANCER CENTER via NATL INST OF HLTH NCI
Sep 2022 ACTIVE
Genomic Analysis of Tissue and Cellular Heterogeneity in IPF
Role: Principal Investigator
Funding: YALE UNIV via NATL INST OF HLTH NHLBI
Jul 2022 ACTIVE
Novel Biomarkers for Post-liver transplant NASH Fibrosis
Role: Principal Investigator
Funding: UNIV OF PITTSBURGH via NATL INST OF HLTH NIDDK
Jul 2022 – Jun 2023
Mapping Age-Related Changes in the Lung
Role: Principal Investigator
Funding: OHIO STATE UNIV via NATL INST OF HLTH NHLBI
Jun 2022 ACTIVE
The Physiology of the Weight Reduced State Data Coordinating Center
Role: Principal Investigator
Funding: UNIV OF PITTSBURGH via NATL INST OF HLTH NIDDK
Jun 2022 ACTIVE
Biomarkers of Alcoholic Hepatitis
Role: Principal Investigator
Funding: UNIV OF PITTSBURGH via NATL INST OF HLTH NIAAA

Contact Details

Emails:
Business:
pbenos@ufl.edu
Addresses:
Business Mailing:
BOX 100231
GAINESVILLE FL 32610
Business Street:
2004 MOWRY RD
GAINESVILLE FL 32611