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
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 et al. Pre-innervated tissue-engineered muscle promotes a pro-regenerative microenvironment following volumetric muscle loss. Commun Biol. 2020.
Chandrasekaran et al. Purine metabolism regulates DNA repair and therapy resistance in glioblastoma. Nat Commun. 2020.
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.
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 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.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.
Kretzler et al. The genetic architecture of membranous nephropathy and its potential to improve non-invasive diagnosis. Nat Commun. 2020.
Kretzler et al.Transcriptome analysis of primary podocytes reveals novel calcium regulated regulatory networks. FASEB J. 2020
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.
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 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.
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.
Shea et al. Engineered immunological niches to monitor disease activity and treatment efficacy in relapsing multiple sclerosis. Nat Commun. 2020.
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.

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