Computational Modeling/Machine Learning/Artificial Intelligence

Research in computational modeling/ machine learning/ artificial intelligence has the ability to accelerate and empower the investigation of complex biological systems through the development of visualization tools and exploitation of data to develop algorithms and models.

Join Our Research

Researchers

Carlos Aguilar

Engineering
Sriram Chandrasekaran

Medicine
Rhima Coleman

Engineering
Joshua Emrick

Dentistry
Eva Feldman

Medicine
Idse Heemskerk

Medicine
Matthias Kretzler

Medicine
Grant Kruger

Engineering
Mark Kushner

Engineering
Paul Lee

Medicine
Geeta Mehta

Engineering
Mary-Ann Mycek

Engineering
Deepak Nagrath

Engineering
Kazuhiro Saitou

Engineering
Peter Scott

Medicine
Lonnie Shea

Engineering
James Weiland

Medicine

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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 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.
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. Tofacitinib Suppresses Natural Killer Cells In Vitro and In Vivo: Implications for Amyotrophic Lateral Sclerosis. Front Immunol. 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 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. 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. 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. 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. 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. Positive charging of grains in an afterglow plasma is enhanced by ions drifting in an electric field. Phys Plasmas. 2021.
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. 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. 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.
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.
Mehta et al. The MEK1/2 pathway as a therapeutic target in high-grade serous ovarian carcinoma. Cancers (Basel). 2021.
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
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. 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.
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. 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.
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 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.

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