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2026

2 papers
Seed size influences the germination outcome of manure phytotoxicity bioassays

Kebrom et al., Waste Management Bulletin, Sept. 2026, vol. 4 - 2026| | https://10.1016/j.wmb.2026.100363

Seed size influences the germination outcome of manure phytotoxicity bioassays
Training Perspectives from the NIH T32 Artificial Intelligence for Precision Nutrition Programs

Mehta et al., The Journal of Nutrition, August 22. 2026, 101796

Training Perspectives from the NIH T32 Artificial Intelligence for Precision Nutrition Programs

2025

1 paper
Data augmentation via diffusion model to enhance AI fairness

Blow et al., Front. Artif. Intell. 18 March 2025, vol. 8 - 2025| | https://doi.org/10.3389/frai.2025.1530397.

Data augmentation via diffusion model to enhance AI fairness

2024

4 papers
EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks

Shuvo, Compu. and Struct. Biotech, Dec 2024, vol. 27, 160-170

EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks
Reversal of inflammatory reprogramming by vasodilator agents in pulmonary hypertension

Kirillova, ERJ Open Research Jan 2024, 00486-2024

Reversal of inflammatory reprogramming by vasodilator agents in pulmonary hypertension
Shade signals activate distinct molecular mechanisms that induce dormancy and inhibit flowering in vegetative axillary buds of sorghum

Kebrom, Plant Direct. 2024:8:e626

Shade signals activate distinct molecular mechanisms that induce dormancy and inhibit flowering in vegetative axillary buds of sorghum
Allele-specific control of rodent and human lncRNA KMT2E-AS1 promotes hypoxic endothelial pathology in pulmonary hypertension

Tai et. al., Science Translational Medicine 16:729, Article 2029 (2024)

Allele-specific control of rodent and human lncRNA KMT2E-AS1 promotes hypoxic endothelial pathology in pulmonary hypertension

2023

4 papers
Semi-supervised Single-Shot Object Detection for Table Detection in Scanned Documents

Bello et. al., FTC 2023, pp. 430-441

Semi-supervised Single-Shot Object Detection for Table Detection in Scanned Documents
Medical Data Augmentation via ChatGPT: A Case Study on Medication Identification and Medication Event Classification

Sarker et. al., IEEE-EMBS BHI 2023

Medical Data Augmentation via ChatGPT: A Case Study on Medication Identification and Medication Event Classification
Systematic Comparative Analysis of Pre-trained Large Language Models on Contextualized Medication Event Extraction

Abdul-Quddoos et. al., IEEE-EMBS BHI 2023

Identification of Lineage-specific Transcriptional Factor-defined Molecular Subtypes in Small Cell Bladder Cancer

Feng and Matoso, European Urology (2023) (in press)

Identification of Lineage-specific Transcriptional Factor-defined Molecular Subtypes in Small Cell Bladder Cancer

2022

8 papers
Semi-supervised bidirectional RNN for misinformation detection

Dong and Qian, Machine Learning with Applications (2022) 100428

Semi-supervised bidirectional RNN for misinformation detection
Calibrated bagging deep learning for image semantic segmentation: A case study on COVID-19 chest X-ray image

Nwosu et al., PLoS One. 2022; 17(11):e0276250

Calibrated bagging deep learning for image semantic segmentation: A case study on COVID-19 chest X-ray image
Activation of apoplastic sugar at the transition stage may be essential for axillary bud outgrowth in the grasses

Kebrom and Doust., Front. Plant Sci., 26 October 2022, https://doi.org/10.3389/fpls.2022.1023581

Activation of apoplastic sugar at the transition stage may be essential for axillary bud outgrowth in the grasses
Performance Evaluation of Data Augmentation for Object Detection in XView Dataset

Olamofe, 2022 IDSTA 26-33, DOI:10.1109/IDSTA55301.2022.9923040

Performance Evaluation of Data Augmentation for Object Detection in XView Dataset
Integrating Human-in-the-loop into Swarm Learning for Decentralized Fake News Detection

Dong et. al., 2022 IDSTA 46-53, DOI:10.1109/IDSTA55301.2022.9923043

Integrating Human-in-the-loop into Swarm Learning for Decentralized Fake News Detection
An Exosome-based Transcriptomic Signature for Noninvasive, Early Detection of Patients With Pancreatic Ductal Adenocarcinoma: A Multicenter Cohort Study

Nakamura et al., Gastroenterology. 2022, (in-press) https://doi.org/10.1053/j.gastro.2022.06.090

An Exosome-based Transcriptomic Signature for Noninvasive, Early Detection of Patients With Pancreatic Ductal Adenocarcinoma: A Multicenter Cohort Study
Semi-supervised Deep Learning for Cell Type Identification from Single-Cell Transcriptomic Data

Dong et al., IEEE/ACM Trans Comput Biol Bioinform. 2022 May 10

Semi-supervised Deep Learning for Cell Type Identification from Single-Cell Transcriptomic Data
Personalized 3-Gene Panel for Prostate Cancer Target Therapy

Iacobas and Iacobas, Curr. Issues Mol. Biol. 2022, 44(1), 360-382; https://doi.org/10.3390/cimb44010027

Personalized 3-Gene Panel for Prostate Cancer Target Therapy

2021

13 papers
Efficient Privacy Preserving Edge Computing Framework for Image Classification

Fagbohungbe et al., arXiv:2005.04563v2

Efficient Privacy Preserving Edge Computing Framework for Image Classification
Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension

Negi et al., Sci. Adv. 2021; 7:eabh3794

Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension
PPAR-γ activation enhances myelination and neurological recovery in premature rabbits with intraventricular hemorrhage

Krishna et al., PNAS Sept 7, 2021;118(36) e2103084118; https://doi.org/10.1073/pnas.2103084118

PPAR-γ activation enhances myelination and neurological recovery in premature rabbits with intraventricular hemorrhage
Semi-supervised Learning for COVID-19 Image Classification via ResNet

Nwosu et al., EAI Endorsed Trans. Bioeng. and Bioinfo. (accepted)

Semi-supervised Learning for COVID-19 Image Classification via ResNet
RNA sequencing of whole blood reveals early alterations in immune cells and gene expression in Parkinson’s disease

Craig et al., Nat Aging 1, 734-747 (2021)

RNA sequencing of whole blood reveals early alterations in immune cells and gene expression in Parkinson’s disease
TWEAKing the Hippocampus: The Effects of TWEAK on the Genomic Fabric of the Hippocampus in a Neuropsychiatric Lupus Mouse Model

Iacobas et al., Genes 2021 July 29;12(8):1172

TWEAKing the Hippocampus: The Effects of TWEAK on the Genomic Fabric of the Hippocampus in a Neuropsychiatric Lupus Mouse Model
Robust Face Mask Detection using Deep Learning on IoT Devices

Reza et al., IEEE ICC Workshops 2021, pp. 1-6

Robust Face Mask Detection using Deep Learning on IoT Devices
A Personalized Genomics Approach of the Prostate Cancer

Iacobas et al., Cells 2021 Jun 30;10(7):1644

A Personalized Genomics Approach of the Prostate Cancer
Frataxin deficiency promotes endothelial senescence in pulmonary hypertension

Culley et al., J Clin Invest. 2021 Apr 27;136459

Frataxin deficiency promotes endothelial senescence in pulmonary hypertension
Retinal Genomic Fabric Remodeling after Optic Nerve Injury

Victorino et al., Genes 2021, 12(3), 403

Retinal Genomic Fabric Remodeling after Optic Nerve Injury
Matrix Stiffening Induces a Pathogenic QKI-miR-7-SRSF1 Signaling Axis in Pulmonary Arterial Endothelial Cells

Woodcock et al., Am J Physiol Lung Cell Mol Physiol. 2021 Feb 10

Matrix Stiffening Induces a Pathogenic QKI-miR-7-SRSF1 Signaling Axis in Pulmonary Arterial Endothelial Cells
Remodeling of Neurotransmission, Chemokine, and PI3K-AKT Signaling Genomic Fabrics in Neuropsychiatric Systemic Lupus Erythematosus

Iacobas et al., Genes 2021, 12(2):251

Remodeling of Neurotransmission, Chemokine, and PI3K-AKT Signaling Genomic Fabrics in Neuropsychiatric Systemic Lupus Erythematosus
Transcriptomic uniqueness and commonality of the ion channels and transporters in the four heart chambers

Iacobas et al., Sci Rep. 2021, 11(1):2743

Transcriptomic uniqueness and commonality of the ion channels and transporters in the four heart chambers

2020

16 papers
Data Driven Network Monitoring and Intrusion Detection using Machine Learning

Williams et al., SNAMS 2020, pp. 1-7.

Genomic Fabric Remodeling in Metastatic Clear Cell Renal Cell Carcinoma (ccRCC): A New Paradigm and Proposal for a Personalized Gene Therapy Approach

Iacobas et al., Cancers 2020, 12, 3678

Genomic Fabric Remodeling in Metastatic Clear Cell Renal Cell Carcinoma (ccRCC): A New Paradigm and Proposal for a Personalized Gene Therapy Approach
Inference Performance Comparison of Convolutional Neural Networks on Edge Devices

Rezq et al., Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, vol 372, pp 323-335 (2020).

Inference Performance Comparison of Convolutional Neural Networks on Edge Devices
Two-Path Deep Semisupervised Learning for Timely Fake News Detection

Dong et al., IEEE Trans. Compu. Soc. Systems 7(6), pp.1386-1398

Two-Path Deep Semisupervised Learning for Timely Fake News Detection
SCUBE1 Controls BMPR2-Relevant Pulmonary Endothelial Function: Implications for Diagnostic Marker Development in Pulmonary Arterial Hypertension

Sun et al., JACC Basic Transl Sci. 2020

SCUBE1 Controls BMPR2-Relevant Pulmonary Endothelial Function: Implications for Diagnostic Marker Development in Pulmonary Arterial Hypertension
Identification of Phytotoxic Levels of Copper and Nickel in Commercial Organic Soil Amendments Recycled from Poultry Farms and Municipal Wastes

Kebrom et al., Bull Environ Contam Toxicol 2020

Identification of Phytotoxic Levels of Copper and Nickel in Commercial Organic Soil Amendments Recycled from Poultry Farms and Municipal Wastes
Ensemble Deep Learning on Time-Series Representation of Tweets for Rumor Detection in Social Media

Kotteti et al., Appl, Sci. 2020, 10(21), 7541

Ensemble Deep Learning on Time-Series Representation of Tweets for Rumor Detection in Social Media
A team science approach to discover novel targets for infantile spasms (IS)

The CURE Infantile Spasms Consortium, CURE Staff et al., Epilepsia Open 2020

A team science approach to discover novel targets for infantile spasms (IS)
Effective covid-19 screening using chest radiography images via deep learning

Victor et al., MCNA 2020, 126-130 (2020)

Effective covid-19 screening using chest radiography images via deep learning
Biomarkers, Master Regulators and Genomic Fabric Remodeling in a Case of Papillary Thyroid Carcinoma

Iacobas, Genes 2020, 11, 1030

Biomarkers, Master Regulators and Genomic Fabric Remodeling in a Case of Papillary Thyroid Carcinoma
Powerful quantifiers for cancer transcriptomics

Iacobas, World Journal of Clinical Oncology 2020; 11(8):0-0

Powerful quantifiers for cancer transcriptomics
Shade signals alter the expression of circadian clock genes in newly‐formed bioenergy sorghum internodes

Kebrom et al. Plant Direct 2020; 4:e00235

Shade signals alter the expression of circadian clock genes in newly‐formed bioenergy sorghum internodes
Trypanosoma cruzi Promotes Transcriptomic Remodeling of the JAK/STAT Signaling and Cell Cycle Pathways in Myoblasts

Ninimura et al. Frontiers in Cellular and Infection Microbiology, 2020; 10:255

Trypanosoma cruzi Promotes Transcriptomic Remodeling of the JAK/STAT Signaling and Cell Cycle Pathways in Myoblasts
Cellular Environment Remodels the Genomic Fabrics of Functional Pathways in Astrocytes

Iacobas et al. Genes 2020; 11:520

Cellular Environment Remodels the Genomic Fabrics of Functional Pathways in Astrocytes
Extracellular microRNAs in blood differentiate between ischaemic and haemorrhagic stroke subtypes

Kalani et al. J. of Extracelluar Vescicles, 2020; 9:1, 1713540

Extracellular microRNAs in blood differentiate between ischaemic and haemorrhagic stroke subtypes
Pulmonary Hypertension Remodels the Genomic Fabrics of Major Functional Pathways

Matthew et al. Genes 2020; 11:126

Pulmonary Hypertension Remodels the Genomic Fabrics of Major Functional Pathways

2019

10 papers
Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas

Berens et al. PLoS ONE 2019; 14(12):e0219724.

Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas
Recurrent Neural Network Based Feature Selection for High Dimensional and Low Sample Size Micro-array Data

Chwodhury et al. Dec 2019. BigData'19 KDDBHI

Recurrent Neural Network Based Feature Selection for High Dimensional and Low Sample Size Micro-array Data
Probing glioblastoma and its microenvironment using single-nucleus and single-cell sequencing

Peng et al. Nov 2019. BIBM'19 Single Cell-omics - Challenges and Opportunities

Probing glioblastoma and its microenvironment using single-nucleus and single-cell sequencing
Commentary on The Gene Master Regulators GMR Approach Provides Legitimate Targets for Personalized, Time-Sensitive Cancer Gene Therapy

Iacobas, J. Cancer Immunology 2019; 1(1):31-33.

Commentary on The Gene Master Regulators GMR Approach Provides Legitimate Targets for Personalized, Time-Sensitive Cancer Gene Therapy
Coordinated Activity of Transcriptional Networks Responding to the Pattern of Action Potential Firing in Neurons

Iacobas et al. 26 September 2019. Genes 10(10):754.

Coordinated Activity of Transcriptional Networks Responding to the Pattern of Action Potential Firing in Neurons
The Gene Master Regulators (GMR) Approach Provides Legitimate Targets for Personalized, Time-Sensitive Cancer Gene Therapy

Iacobas et al. 25 July 2019. Genes 10(8):560.

The Gene Master Regulators (GMR) Approach Provides Legitimate Targets for Personalized, Time-Sensitive Cancer Gene Therapy
Deep learning for named entity recognition on Chinese electronic medical records: Combining deep transfer learning with multitask bi-directional LSTM RNN

Dong et al. 2 May 2019. PLoS One 2;14(5):e0216046.

Deep learning for named entity recognition on Chinese electronic medical records: Combining deep transfer learning with multitask bi-directional LSTM RNN
Leveraging Spatial Variation in Tumor Purity for Improved Somatic Variant Calling of Archival Tumor Only Samples

Halperin et al. 20 March 2019. Front. Oncol. 9:119.

Leveraging Spatial Variation in Tumor Purity for Improved Somatic Variant Calling of Archival Tumor Only Samples
Evaluation of phytotoxicity of three organic amendments to collard greens using the seed germination bioassay

Kebrom et al. February 2019. Environ Sci Pollut Res Int. 26(6):5454-5462.

Evaluation of phytotoxicity of three organic amendments to collard greens using the seed germination bioassay
Systems Analysis of the Human Pulmonary Arterial Hypertension Lung Transcriptome

Stearman et al. 2019. Am J Respir Cell Mol Biol. 2019 Jun;60(6):637-649

Systems Analysis of the Human Pulmonary Arterial Hypertension Lung Transcriptome

2018

11 papers
Expression of Genes Encoding for Xenobiotic Metabolism after Exposure to Dialkylnitrosamines in the Chicken Egg Genotoxicity Alternative Model

Kobets et al. 2018. Toxicol Sci. 2018 Nov 1;166(1):82-96

Expression of Genes Encoding for Xenobiotic Metabolism after Exposure to Dialkylnitrosamines in the Chicken Egg Genotoxicity Alternative Model
Regeneration of Neurotransmission Transcriptome in a Model of Epileptic Encephalopathy after Antiinflammatory Treatment

Iacobas and Velisek. 2018. Neural Regen Res. 2018 Oct;13(10):1715-1718

Regeneration of Neurotransmission Transcriptome in a Model of Epileptic Encephalopathy after Antiinflammatory Treatment
Estrogen Protects Neurotransmission Transcriptome During Status Epilepticus

Iacobas et al. 2018. Front Neurosci. 2018 Jun 20;12:332

Estrogen Protects Neurotransmission Transcriptome During Status Epilepticus
A multitask bi-directional RNN model for named entity recognition on electronic medical records

Chowdhury et al. 2018. International Conference on Intelligent Biology and Medicine (ICIBM 2018); June 10-12, 2018; Los Angeles, CA.

A multitask bi-directional RNN model for named entity recognition on electronic medical records
ACTH and PMX53 recover synaptic transcriptome alterations in a rat model of infantile spasms

Iacobas et al. 2018. Sci Rep. 2018 Apr 10;8(1):5722.

ACTH and PMX53 recover synaptic transcriptome alterations in a rat model of infantile spasms
Phenotype Classification Using Moment Features of Single-Cell Data

Sima et al. 2018. Cancer Inform.

Phenotype Classification Using Moment Features of Single-Cell Data
GPU-accelerated differential dependency network analysis

Speyer et al. 2018. Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP 2018), Mar 21-23, 2018.

GPU-accelerated differential dependency network analysis
Gene master regulators of papillary and anaplastic thyroid cancers

Iacobas et al. 2018. Oncotarget. 9(2):2410–2424.

Gene master regulators of papillary and anaplastic thyroid cancers
Differential Response of Glioma Stem Cells to Arsenic Trioxide Therapy Is Regulated by MNK1 and mRNA Translation

Bell et al. 2018. Mol Cancer Res. 2018 Jan;16(1):32-46.

Differential Response of Glioma Stem Cells to Arsenic Trioxide Therapy Is Regulated by MNK1 and mRNA Translation
Functional genomic fabrics are remodeled in a mouse model of Chagasic cardiomyopathy and restored following cell therapy

Iacobas et al. 2018. Microbes Infect. 2018 Mar;20(3):185-195

Functional genomic fabrics are remodeled in a mouse model of Chagasic cardiomyopathy and restored following cell therapy
Sequential Therapeutic Response Modeling for Tumor Treatment Using Computational Hybrid Control Systems Approach

Oduola et al. 2018. IEEE Trans Biomed Eng. 65(4):866-74.

Sequential Therapeutic Response Modeling for Tumor Treatment Using Computational Hybrid Control Systems Approach

2017

4 papers
Closed loop control of blood glucose level with neural network predictor for diabetic patients

Bamgbose et al. 2017. IEEE HealthCom; Oct. 12-15, 2017; Dalian, China.

Closed loop control of blood glucose level with neural network predictor for diabetic patients
Review of stochastic hybrid systems with applications in biological systems modeling and analysis

Li et al. 2017. EURASIP J Bioinform Syst Biol. 2017 Dec;2017(1):8

Review of stochastic hybrid systems with applications in biological systems modeling and analysis
Time-Based Switching Control of Genetic Regulatory Networks: Toward Sequential Drug Intake for Cancer Therapy

Oduola et al. 2017. Cancer Inform. 2017;16:1176935117706888.

Time-Based Switching Control of Genetic Regulatory Networks: Toward Sequential Drug Intake for Cancer Therapy
Contextualization of drug-mediator relations using evidence networks

Tran et al. 2017. BMC Bioinformatics. 2017; 18(Suppl 7):252.

Contextualization of drug-mediator relations using evidence networks