Computational Modeling/​Machine Learning/​Artificial Intelligence

Select Publications

• Aguilar CA et al. Transcriptional and Chromatin Dynamics of Muscle Regeneration After Severe Trauma. Stem Cell Reports. 2016.

• Aguilar CA et al. Multiscale analysis of a regenerative therapy for treatment of volumetric muscle loss injury. Cell Death Discov. 2018.

• Aguilar CA et al. Tuning Macrophage Phenotype to Mitigate Skeletal Muscle Fibrosis. J Immunology. 2020.

• Aguilar CA et al. Dissecting murine muscle stem cell aging through integrative genomic analysis. Cell Rep. 2020.

• Aguilar CA et al. Resolvin D1 supports skeletal myofiber regeneration via actions on myeloid and muscle stem cells. JCI Insight. 2020.

• Aguilar CA et al. Engineered Tools to Study Intercellular Communication. Adv Sci (Weinh). 2021.

• Aguilar CA et al. Metabolipidomic profiling reveals an age-related deficiency of skeletal muscle pro-resolving mediators that contributes to maladaptive tissue remodeling. Aging Cell. 2021.

• Aguilar CA et al. Sestrins regulate muscle stem cell metabolic homeostasis. Stem Cell Reports. 2021.

• Aguilar et al. Pre-innervated tissue-engineered muscle promotes a pro-regenerative microenvironment following volumetric muscle loss. Commun Biol. 2020.

• Aguilar et al. Neutrophil and natural killer cell imbalances prevent muscle stem cell-mediated regeneration following murine volumetric muscle loss. Proc Natl Acad Sci U S A. 2022.

• Cederna PS et al. Reinventing Extremity Amputation in the Era of Functional Limb Restoration. Ann Surg. 2021.

• Chandrasekaran et al. Purine metabolism regulates DNA repair and therapy resistance in glioblastoma. Nat Commun. 2020.

• Chandrasekaran et al. The deacylase SIRT5 supports melanoma viability by influencing chromatin dynamics. J Clin Invest. 2021.

• Chandrasekaran et al. Metabolic remodelling during early mouse embryo development. Nat Metab. 2021.

• Chandrasekaran et al. Metabolic signatures of regulation by phosphorylation and acetylation. iScience. 2022.

• Chandrasekaran et al. Machine learning to design antimicrobial combination therapies: Promises and pitfalls. Drug Discov Today. 2022.

• Chandrasekaran et al. TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes. mSystems. 2022.

• Chandrasekaran S et al. LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency. Cell Stem Cell. 2016.

• Chandrasekaran S et al. Comprehensive mapping of pluripotent stem cell metabolism using dynamic genome-scale network modeling. Cell Rep. 2017.

• Chandrasekaran S et al. Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors. Genome Biol. 2019.

• Chandrasekaran S et al. Dynamic Network Modeling of Stem Cell Metabolism, Methods in Molecular Biology: Computational Stem Cell Biology. Methods Mol Biol. 2019.

• Chandrasekaran S et al. Nutrient Sensing by Histone Marks: Reading the Metabolic Histone Code Using Tracing, Omics, and Modeling. Bioessays. 2020.

• Chandrasekaran S et al. Next-generation genome-scale metabolic modeling through integration of regulatory mechanisms. Metabolites. 2021.

• Chandrasekran et al. Single-cell RNA-sequencing identifies anti-cancer immune phenotypes in the early lung metastatic niche during breast cancer. Clin Exp Metastasis. 2022.

• Coleman et al. Engineering Closed-Loop, Autoregulatory Gene Circuits for Osteoarthritis Cell-Based Therapies. Curr Rheumatol Rep. 2022.

• Feldman EL et al. Human neural stem cell transplantation into the corpus callosum of Alzheimer’s mice. Ann Clin Transl Neurol. 2017.

• Feldman EL et al. Long-term Phase 1/2 intraspinal stem cell transplantation outcomes in ALS. Ann Clin Transl Neurol. 2018.

• Feldman EL et al. Human neural stem cell transplantation improves cognition in a murine model of Alzheimer’s disease. Sci Rep. 2018.

• Feldman EL et al. Stem cell treatments for amyotrophic lateral sclerosis: a critical overview of early phase trials. Expert Opin Investig Drugs. 2019.

• Feldman EL et al. Magnetic resonance imaging of human neural stem cells in rodent and primate brain. Stem Cells Transl Med. 2020.

• Feldman EL et al. Magnetic resonance imaging of human neural stem cells in rodent and primate brain. Stem Cells Transl Med. 2021.

• Feldman EL et al. Diabetic neuropathy in children and youth: New and emerging risk factors. Pediatr Diabetes. 2021.

• Feldman EL et al. Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis. Neuron. 2021.

• Feldman EL et al. Altered plasma serine and 1-deoxydihydroceramide profiles are associated with diabetic neuropathy in type 2 diabetes and obesity. J Diabetes Complications. 2021.

• Feldman EL et al. Amyotrophic Lateral Sclerosis Survival Associates With Neutrophils in a Sex-specific Manner. Neurol Neuroimmunol Neuroinflamm. 2021.

• Feldman EL et al. Immune-mediated vincristine-induced neuropathy: Unlocking therapies. J Exp Med. 2021.

• Feldman EL et al. Lessons for clinical trial design in Friedreich’s ataxia. Lancet Neurol. 2021.

• Feldman EL et al. High dietary fat consumption impairs axonal mitochondrial function in Vivo. J Neurosci. 2021.

• Feldman EL et al. Gene expression profiles of diabetic kidney disease and neuropathy in eNOS knockout mice: Predictors of pathology and RAS blockade effects. Faseb J. 2021.

• Feldman EL et al. Plasma lipid metabolites associate with diabetic polyneuropathy in a cohort with type 2 diabetes. Ann Clin Transl Neurol. 2021.

• Feldman EL et al. NK cells associate with ALS in a sex- and age-dependent manner. JCI Insight 2021.

• Feldman EL et al. The determinants of complication trajectories in American Indians with type 2 diabetes. JCI Insight. 2021.

• Feldman EL et al. Inclusion body myositis: small steps towards future advances. Lanc Rheum. 2021.

• Feldman et al. Untargeted metabolomics yields insight into ALS disease mechanisms. J Neurol Neurosurg Psychiatry. 2020.

• Feldman et al. Covid-19 and diabetes: A collision and collusion of two diseases. Diabetes. 2020.

• Feldman et al. Altered plasma serine and 1-deoxydihydroceramide profiles are associated with diabetic neuropathy in type 2 diabetes and obesity. J Diabetes Complications. 2021.

• Feldman et al. Interplay between immunity and amyotrophic lateral sclerosis: Clinical impact. Neurosci Biobehav Rev. 2021.

• Feldman et al. Association of Variants in the SPTLC1 Gene with Juvenile Amyotrophic Lateral Sclerosis. JAMA Neurol. 2021.

• Feldman et al. Dietary weight loss in people with severe obesity stabilizes neuropathy and improves symptomatology. Obesity (Silver Spring). 2021.

• Feldman et al. Advances in diet-induced rodent models of metabolically acquired peripheral neuropathy. Dis Model Mech. 2021.

• Feldman et al. Nox, Nox, Are You There? the Role of NADPH Oxidases in the Peripheral Nervous System. Antioxid Redox Signal. 2022.

• Feldman et al. Metabolomics identifies shared lipid pathways in independent amyotrophic lateral sclerosis cohorts. Brain. 2022.

• Feldman et al. A Role for Fatty Acids in Peripheral Neuropathy Associated with Type 2 Diabetes and Prediabetes. Antioxid Redox Signal. 2022.

• Feldman et al. Tofacitinib Suppresses Natural Killer Cells In Vitro and In Vivo: Implications for Amyotrophic Lateral Sclerosis. Front Immunol. 2022.

• Feldman et al. Recent advances in the diagnosis and prognosis of amyotrophic lateral sclerosis. Lancet Neurol. 2022.

• Feldman et al. Emerging insights into the complex genetics and pathophysiology of amyotrophic lateral sclerosis. Lancet Neurol. 2022.

• Feldman et al. Neurological sequela and disruption of neuron-glia homeostasis in SARS-CoV-2 infection. Neurobiol Dis. 2022.

• Feldman et al. Glial-neuron crosstalk in health and disease: A focus on metabolism, obesity, and cognitive impairment. Neurobiok Dis. 2022.

• Feldman et al. Serum lipidomic determinants of human diabetic neuropathy in type 2 diabetes. Ann Clin Transl Neurol. 2022.

• Feldman et al. Amyotrophic lateral sclerosis from genotoxins alone? – Authors’ reply. Lancet Neurol. 2022.

• Feldman et al. Towards prevention of diabetic peripheral neuropathy: clinical presentation, pathogenesis, and new treatments. Lancet Neurol. 2022.

• Feldman et al. Diabetes and dementia: Clinical perspective, innovation, knowledge gaps. J Diabetes Complications. 2022.

• Feldman et al. The conundrum of diabetic neuropathies—Past, present, and future. J Diabetes Complications. 2022.

• Feldman et al. ISPAD Clinical Practice Consensus Guidelines 2022: Microvascular and macrovascular complications in children and adolescents with diabetes. Pediatr Diabetes. 2022.

• Feldman et al. Obesity-induced neuroinflammation and cognitive impairment in young adult versus middle-aged mice. Immun Ageing. 2022.

• Feldman et al.Differential effects of empagliflozin on microvascular complications in murine models of type 1 and type 2 diabetes. Biology (Basel). 2020

• Heemskerk et al. Stable iPSC-derived NKX2-1+ lung bud tip progenitor organoids give rise to airway and alveolar cell types. Development. 2022.

• Heemskerk I Full of potential: Pluripotent stem cells for the systems biology of embryonic patterning. Dev Biol. 2020.

• Heemskerk I et al. Tissue cartography: compressing bio-image data by dimensional reduction. Nat Methods. 2015.

• Heemskerk I et al. Differential growth triggers mechanical feedback that elevates Hippo signaling. Proc Natl Acad Sci U S A. 2016.

• Heemskerk I et al. Rapid changes in morphogen concentration control self-organized patterning in human embryonic stem cells. Elife. 2019.

• Heemskerk I et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Phys Biol. 2021.

• Kretzler et al Genome-wide meta-analysis and omics integration identifies novel genes associated with diabetic kidney disease. Diabetologia. 2022.

• Kretzler et al. The clinical application of urine soluble CD163 in ANCA-associated vasculitis. J Am Soc Nephrol. 2021.

• Kretzler et al. The genetic architecture of membranous nephropathy and its potential to improve non-invasive diagnosis. Nat Commun. 2020.

• Kretzler et al. A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project. Physiol Genomics. 2021.

• Kretzler et al. Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline. Lab Invest. 2021.

• Kretzler et al. Nephrotic syndrome disease activity is proportional to its associated hypercoagulopathy. Thromb Res. 2021.

• Kretzler et al. Rationale and design of the Kidney Precision Medicine Project. Kidney Int. 2021.

• Kretzler et al. Patient perspectives and involvement in precision medicine research. Kidney Int. 2021.

• Kretzler et al. Innovating and invigorating the clinical trial infrastructure for glomerular diseases. Kidney Int. 2021.

• Kretzler et al. APOL1 genotype-associated morphologic changes among patients with focal segmental glomerulosclerosis. Pediatr Nephrol. 2021.

• Kretzler et al. Annexin A1 alleviates kidney injury by promoting the resolution of inflammation in diabetic nephropathy. Kidney Int. 2021.

• Kretzler et al. IGFBP-1 expression is reduced in human type 2 diabetic glomeruli and modulates β1-integrin/FAK signalling in human podocytes. Diabetologia. 2021.

• Kretzler et al. Angiotensin II up-regulates sodium-glucose co-transporter 2 expression and SGLT2 inhibitor attenuates Ang II-induced hypertensive renal injury in mice. Clin Sci (Lond). 2021.

• Kretzler et al. Urinary EGF and MCP-1 and risk of CKD after cardiac surgery. JCI Insight 2021.

• Kretzler et al. Perspectives on a Way Forward to Implementation of Precision Medicine in Patients With Diabetic Kidney Disease; Results of a Stakeholder Consensus-Building Meeting. Front Pharmacol. 2021.

• Kretzler et al. Cadherin-11, Sparc-related modular calcium binding protein-2, and Pigment epithelium-derived factor are promising non-invasive biomarkers of kidney fibrosis. Kidney Int. 2021.

• Kretzler et al. Pro-cachectic factors link experimental and human chronic kidney disease to skeletal muscle wasting programs. J Clin Invest. 2021.

• Kretzler et al. Comprehensive search for novel circulating mirnas and axon guidance pathway proteins associated with risk of eskd in diabetes. J Am Soc Nephrol. 2021.

• Kretzler et al. Renin-angiotensin system inhibition reverses the altered triacylglycerol metabolic network in diabetic kidney disease. Metabolomics. 2021.

• Kretzler et al. Diminished retinal complex lipid synthesis and impaired fatty acid β-oxidation associated with human diabetic retinopathy. JCI Insight. 2021.

• Kretzler et al. Serum Level of Polyubiquitinated PTEN and Loss of Kidney Function in American Indians With Type 2 Diabetes. Am J Kidney Dis. 2022.

• Kretzler et al. Multiplexed droplet single-cell sequencing (Mux-Seq) of normal and transplant kidney. Am J Transplant. 2022.

• Kretzler et al. Quantification of Glomerular Structural Lesions: Associations With Clinical Outcomes and Transcriptomic Profiles in Nephrotic Syndrome. Am J Kidney Dis. 2022.

• Kretzler et al. A Participant-Centered Approach to Understanding Risks and Benefits of Participation in Research Informed by the Kidney Precision Medicine Project. Am J Kidney Dis. 2022.

• Kretzler et al. A glomerular transcriptomic landscape of apolipoprotein L1 in Black patients with focal segmental glomerulosclerosis. Kidney Int. 2022.

• Kretzler et al. Glomerular endothelial cell-podocyte stresses and crosstalk in structurally normal kidney transplants. Kidney Int. 2022.

• Kretzler et al. Unsupervised machine learning for identifying important visual features through bag-of-words using histopathology data from chronic kidney disease. Sci Rep. 2022.

• Kretzler et al. Integrated single-cell sequencing and histopathological analyses reveal diverse injury and repair responses in a participant with acute kidney injury: a clinical-molecular-pathologic correlation. Kidney Int. 2022.

• Kretzler et al. Urinary Proteomics Identifies Cathepsin D as a Biomarker of Rapid eGFR Decline in Type 1 Diabetes. Diabetes Care. 2022.

• Kretzler et al. Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms. PLoS Comput Biol. 2022.

• Kretzler et al. Molecular Characterization of Membranous Nephropathy. J Am Soc Nephrol. 2022.

• Kretzler et al. Kidney Biopsy Features Most Predictive of Clinical Outcomes in the Spectrum of Minimal Change Disease and Focal Segmental Glomerulosclerosis. J Am Soc Nephrol. 2022.

• Kretzler et al. A reference tissue atlas for the human kidney. Sci Adv. 2022.

• Kretzler et al. The Michigan O’Brien Kidney Research Center: transforming translational kidney research through systems biology. Am J Physiol Renal Physiol. 2022.

• Kretzler et al. Molecular programs associated with glomerular hyperfiltration in early diabetic kidney disease. Kidney Int. 2022.

• Kretzler et al. Authors’ Reply: In Silico–Based Approach to the Discovery of New Antigens in Membranous Nephropathy. J Am Soc Nephrol. 2022.

• Kretzler et al. Activation of Stimulator of IFN Genes (STING) Causes Proteinuria and Contributes to Glomerular Diseases. J Am Soc Nephrol. 2022.

• Kretzler et al. Multi-Scalar Data Integration Links Glomerular Angiopoietin-Tie Signaling Pathway Activation With Progression of Diabetic Kidney Disease. Diabetes. 2022.

• Kretzler et al. Present and future directions in diabetic kidney disease. J Diabetes Complications. 2022.

• Kretzler et al. Epigenome-wide meta-analysis identifies DNA methylation biomarkers associated with diabetic kidney disease. Nat Commun. 2022.

• Kretzler et al. Development and evaluation of deep learning–based segmentation of histologic structures in the kidney cortex with multiple histologic stains. Kidney Int. 2021.

• Kretzler et al. Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney. Nat Genet. 2021.

• Kretzler et al.Transcriptome analysis of primary podocytes reveals novel calcium regulated regulatory networks. FASEB J. 2020

• Kruger et al. Acupressure for cancer-fatigue in ovarian cancer survivor (The AcuOva Study): A community-based clinical trial study protocol examining the impact of self-acupressure on persistent cancer related fatigue in ovarian cancer survivors. Contemp Clin Trials. 2021.

• Kruger et al. Experimental Pain and Auditory Sensitivity in Overactive Bladder Syndrome: A Symptoms of the Lower Urinary Tract Dysfunction Research Network (LURN) Study. J Urol. 2022.

• Kruger et al. Reply by Authors. J Urol. 2022.

• Kushner et al. Pulsed power to control growth of silicon nanoparticles in low temperature flowing plasmas. J Appl Phys. 2022.

• Kushner et al. Positive charging of grains in an afterglow plasma is enhanced by ions drifting in an electric field. Phys Plasmas. 2021.

• Kushner et al. Comparison of glancing-angle scatterings on different materials in a high aspect ratio plasma etching process using molecular dynamics simulation. J Vac Sci Technol. 2022.

• Kushner et al. Scaling of atomic layer etching of SiO2in fluorocarbon plasmas: Transient etching and surface roughness. J. Vac. Sci. Technol. 2021.

• Kushner et al. Interactions between atmospheric pressure plasmas and metallic catalyst particles in packed bed reactors. J. Phys. D: Appl. Phys. 2021.

• Kushner et al. Plasma breakdown in bubbles passing between two pin electrodes. J Phys D. 2022.

• Kushner et al. Size-tunable silver nanoparticle synthesis in glycerol driven by a low-pressure nonthermal plasma. J Phys D: Appl Phys. 2022.

• Kushner et al. Propagation of positive discharges in an air bubble having an embedded water droplet. Plasma Sources Sci. 2021.

• Kushner et al. Electric field reversals resulting from voltage waveform tailoring in Ar/O2capacitively coupled plasmas sustained in asymmetric systems. Plasma Sources Sci. Technol. 2021.

• Kushner et al. Surface ionization waves propagating over non-planar substrates: wavy surfaces, cut-pores and droplets. Plasma Sources Sci Technol. 2022.

• Kushner et al. Propagation of atmospheric pressure plasmas through interconnected pores in dielectric materials. J Appl Phys. 2021.

• Lee et al. Reduced Mammography Screening for Breast Cancer among Women with Visual Impairment. Opthalmology. 2021.

• Lee et al. Change in Ophthalmic Clinicians’ Attitudes Toward Telemedicine during the Coronavirus 2019 Pandemic. Telemed J E Health. 2021.

• Lee et al. Feasibility of a Risk-Based Approach to Cataract Surgery Preoperative Medical Evaluation. JAMA Ophthalmol. 2021.

• Lee et al. Small Payments, Large Consequences. JAMA Ophthalmol. 2022.

• Lee et al. Disparities in Vision Health and Eye Care. Ophthalmology. 2022.

• Lempka et al. The Effect of Clinically Controllable Factors on Neural Activation During Dorsal Root Ganglion Stimulation. Neuromodulation. 2021.

• Lempka et al. Quantitative Sensory Testing of Spinal Cord and Dorsal Root Ganglion Stimulation in Chronic Pain Patients. Neuromodulation. 2021.

• Lempka et al. Dorsal Root Ganglion Stimulation for Chronic Pain: Hypothesized Mechanisms of Action. J Pain. 2022.

• Lempka et al. Neural Recruitment During Conventional, Burst, and 10-kHz Spinal Cord Stimulation for Pain. J Pain. 2022.

• Lempka et al. Augmented Transcutaneous Stimulation Using an Injectable Electrode: A Computational Study. Front Bioeng Biotechnol. 2021.

• Lempka et al. Glossary of Neurostimulation Terminology: A Collaborative Neuromodulation Foundation, Institute of Neuromodulation, and International Neuromodulation Society Project. Neuromodulation. 2022.

• Mehta et al. Atovaquone: An Inhibitor of Oxidative Phosphorylation as Studied in Gynecologic Cancers. Cancers (Basel). 2022.

• Mehta et al. The MEK1/2 pathway as a therapeutic target in high-grade serous ovarian carcinoma. Cancers (Basel). 2021.

• Mehta et al. Injectable three-dimensional tumor microenvironments to study mechanobiology in ovarian cancer. Acta Biomater. 2022.

• Mehta G et al. Personalized Medicine–Based Approach to Model Patterns of Chemoresistance and Tumor Recurrence Using Ovarian Cancer Stem Cell Spheroids. Clin Cancer Res. 2017.

• Mehta G et al. Integrated cancer tissue engineering models for precision medicine. PLoS One. 2019.

• Mehta G et al. Engineered 3D Model of Cancer Stem Cell Enrichment and Chemoresistance. Neoplasia. 2019.

• Mehta G et al. Ovarian cancer stem cells and macrophages reciprocally interact through the WNT pathway to promote pro-tumoral and malignant phenotypes in 3D engineered microenvironments. J Immunother Cancer. 2019.

• Mehta G et al. Compressive Stimulation Enhances Ovarian Cancer Proliferation, Invasion, Chemoresistance, and Mechanotransduction via CDC42 in a 3D Bioreactor. Cancers (Basel). 2020.

• Mehta G et al. Personalized models of heterogeneous 3D epithelial tumor microenvironments: Ovarian cancer as a model. Acta Biomater. 2021.

• Mehta G et al. Design and applications of surfaces that control the accretion of matter. Sci. 2021.

• Mycek et al. Reconstruction of optical coefficients in turbid media using time-resolved reflectance and calibration-free instrument response functions. Biomed Opt Express. 2022.

• Mycek et al. Noninvasive Optical Assessment of Implanted Tissue-Engineered Construct Success in Situ. Tissue Eng Part C Methods. 2021.

• Mycek et al.Needle-compatible miniaturized optoelectronic sensor for pancreatic cancer detection. Sci Adv. 2020

• Nagarth et al. Therapeutic implications of mitochondrial stress-induced proteasome inhibitor resistance in multiple myeloma. Sci Adv. 2022.

• Nagrath D et al. Genomic deletion of malic enzyme 2 confers collateral lethality in pancreatic cancer. Nature. 2017.

• Nagrath D et al. Generation of Human Fatty Livers Using Custom-Engineered Induced Pluripotent Stem Cells with Modifiable SIRT1 Metabolism. Cell Metab. 2019.

• Nagrath D et al. Tumour-reprogrammed stromal BCAT1 fuels branched-chain ketoacid dependency in stromal-rich PDAC tumours. Nat Metab. 2020.

• Nagrath D et al. Corrigendum to ‘Synthetic lethality: a step forward for personalized medicine in cancer’ [Drug Discov. Today 25 (2020) 305–320] (Drug Discovery Today (2020) 25(2) (305–320), (S1359644619304568), (10.1016/j.drudis.2019.11.014)). Drug Discov Today. 2021.

• Nagrath et al. Circulating tumor cells in precision medicine: challenges and opportunities. Trends Pharmacol Sci. 2022.

• Nagrath et al. Electron transport chain activity is a predictor and target for venetoclax sensitivity in multiple myeloma. Nat Commun. 2020.

• Nagrath et al. ITLN1 modulates invasive potential and metabolic reprogramming of ovarian cancer cells in omental microenvironment. Nat Commun. 2020.

• Nagrath et al. Generation of systemic antitumour immunity via the in situ modulation of the gut microbiome by an orally administered inulin gel. Nat Biomed Eng. 2021.

• Nagrath et al. Targeting integrated epigenetic and metabolic pathways in lethal childhood PFA ependymomas. Sci Transl Med. 2021.

• Nagrath et al. Radiotherapy-induced metabolic hallmarks in the tumor microenvironment. Trends Cancer. 2022.

• Nagrath et al. Driving with Both Feet: Supplementing AKG While Inhibiting BCAT1 Leads to Synthetic Lethality in GBM. Cancer Res. 2022.

• Nagrath et al. Metabolic collateral lethal target identification reveals MTHFD2 paralogue dependency in ovarian cancer. Nat Metab. 2022.

• Saitou et al. A novel predictive-reactive rescheduling method for products assembly lines with optimal dynamic pegging. Comput Ind Eng. 2022.

• Saitou K et al. Anisotropic multicomponent topology optimization for additive manufacturing with build orientation design and stress-constrained interfaces. ASME 2019. 2019.

• Saitou K et al. Distance-preserving rigidity penalty on deformable image registration of multiple skeletal components in the neck. Med Phys. 2013.

• Saitou K et al. ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures. BMC Bioinformatics. 2014.

• Scott et al. In vitro binding affinity vs. in vivo site occupancy: A PET study of four diastereomers of dihydrotetrabenazine (DTBZ) in monkey brain. Nucl Med Biol. 2021.

• Scott et al. Iridium-Catalysed C−H Borylation of Heteroarenes: Balancing Steric and Electronic Regiocontrol. Angew Chem Int Ed Engl. 2021.

• Scott et al. On the consensus nomenclature rules for radiopharmaceutical chemistry – Reconsideration of radiochemical conversion. Nucl Med Biol. 2021.

• Scott et al. An updated synthesis of N1′-([11C]methyl)naltrindole for positron emission tomography imaging of the delta opioid receptor. J Labelled Comp Radiopharm. 2021.

• Scott et al. Radiofluorination of oxazole-carboxamides for preclinical PET neuroimaging of GSK-3. J Fluor Chem. 2021.

• Scott et al. Tetramethylammonium Fluoride Alcohol Adducts for SNAr Fluorination. Org Lett. 2021.

• Scott et al. A Comprehensive Assessment of 68Ga-PSMA-11 PET in Biochemically Recurrent Prostate Cancer: Results from a Prospective Multicenter Study on 2,005 Patients. J Nucl Med. 2022.

• Scott et al. Preclinical evaluation of (S)-[18F]GE387, a novel 18-kDa translocator protein (TSPO) PET radioligand with low binding sensitivity to human polymorphism rs6971. Eur J Nucl Med Mol Imaging. 2021.

• Scott et al. Potential Applications of Artificial Intelligence and Machine Learning in Radiochemistry and Radiochemical Engineering. PET Clin. 2021.

• Scott et al. Preliminary Evaluations of [11C]Verubulin: Implications for Microtubule Imaging With PET. Front Neurosci. 2021.

• Scott et al. Nuclear Medicine and Artificial Intelligence: Best Practices for Algorithm Development. J Nucl Med. 2022.

• Scott et al. Synthesis and Evaluation of a Fluorine-18 Radioligand for Imaging Huntingtin Aggregates by Positron Emission Tomographic Imaging. Front Neurosci. 2021.

• Scott et al. Proceedings: PET Drugs-A Workshop on Inspections Management and Regulatory Considerations. J Nucl Med. 2022.

• Scott et al. Synthesis of 68Ga-radiopharmaceuticals using both generator-derived and cyclotron-produced 68Ga as exemplified by [68Ga]Ga-PSMA-11 for prostate cancer PET imaging. Nat Protoc. 2022.

• Scott et al. No Dopamine Agonist Modulation of Brain [18F]FEOBV Binding in Parkinson’s Disease. Mol Pharm. 2022.

• Scott et al. Radiosynthesis and In Vivo Evaluation of Four Positron Emission Tomography Tracer Candidates for Imaging of Melatonin Receptors. ACS Chem Neurosci. 2022.

• Scott et al. Development of Fluorinated NP-59: A Revival of Cholesterol Use Imaging with PET. J Nucl Med. 2022.

• Scott et al. In Silico Approaches for Addressing Challenges in CNS Radiopharmaceutical Design. ACS Chem Neurosci. 2022.

• Scott et al. Unnatural amino acids offer new hope for accurate bacterial infection PET imaging in prosthetic joint infection. Eur J Nucl Med Mol Imaging. 2022.

• Scott et al. Cholinergic brain network deficits associated with vestibular sensory conflict deficits in Parkinson’s disease: correlation with postural and gait deficits. J Neural Transm (Vienna). 2022.

• Scott et al. Classics in Neuroimaging: Untangling the Role of Tau in Neurodegenerative Disorders Using Positron Emission Tomography. ACS Chem Neurosci. 2022.

• Scott et al. Differential cholinergic systems’ changes in progressive supranuclear palsy versus Parkinson’s disease: an exploratory analysis. J Neural Transm (Vienna). 2022.

• Shea et al. Restoring normal islet mass and function in type 1 diabetes through regenerative medicine and tissue engineering. Lancet Diabetes Endocrinol. 2021.

• Shea et al. Engineered immunological niches to monitor disease activity and treatment efficacy in relapsing multiple sclerosis. Nat Commun. 2020.

• Shea et al. Tolerance induced by antigen-loaded plg nanoparticles affects the phenotype and trafficking of transgenic cd4+ and cd8+ t cells. Cells. 2021.

• Shea et al. Mechanistic contributions of Kupffer cells and liver sinusoidal endothelial cells in nanoparticle-induced antigen-specific immune tolerance. Biomaterials. 2022.

• Shea et al. Neutrophil and natural killer cell imbalances prevent muscle stem cell-mediated regeneration following murine volumetric muscle loss. Proc Natl Acad Sci U S A. 2022.

• Shea et al. Single-cell RNA-sequencing identifies anti-cancer immune phenotypes in the early lung metastatic niche during breast cancer. Clin Exp Metastasis. 2022.

• Shea et al. Human Lung Organoid Culture in Alginate With and Without Matrigel to Model Development and Disease. Tissue Eng Part A. 2022.

• Shea LD et al. Microporous scaffolds support assembly and differentiation of pancreatic progenitors into ß-cell clusters. Acta Biomater. 2019.

• Shea LD et al. Intravascular innate immune cells reprogrammed via intravenous nanoparticles to promote functional recovery after spinal cord injury. Proc Natl Acad Sci U S A. 2019.

• Shea LD et al. Metastatic Conditioning of Myeloid Cells at a Subcutaneous Synthetic Niche Reflects Disease Progression and Predicts Therapeutic Outcomes. Cancer Res. 2020.

• Shea LD et al. Polycistronic Delivery of IL-10 and NT-3 Promotes Oligodendrocyte Myelination and Functional Recovery in a Mouse Spinal Cord Injury Model. Tissue Eng Part A. 2020.

• Shea LD et al. Engineered immunological niches to monitor disease activity and treatment efficacy in relapsing multiple sclerosis. Nat Commun. 2020.

• Shea LD et al. An injectable PEG hydrogel controlling neurotrophin-3 release by affinity peptides. J Control Release. 2021.

• Shea LD et al. Disease-induced immunomodulation at biomaterial scaffolds detects early pancreatic cancer in a spontaneous model. Biomaterials. 2021.

• Shea LD et al. Cargo-free immunomodulatory nanoparticles combined with anti-PD-1 antibody for treating metastatic breast cancer. Biomaterials. 2021.

• Shea LD et al. IL-10 lentivirus-laden hydrogel tubes increase spinal progenitor survival and neuronal differentiation after spinal cord injury. Biotechnol Bioeng. 2021.

• Weiland et al. Spatial Transcriptomics as a Novel Approach to Redefine Electrical Stimulation Safety. Front Neurosci. 2022.

• Weiland et al. Retinal ganglion cell desensitization is mitigated by varying parameter constant excitation pulse trains. Front Cell Neurosci. 2022.