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Enabling Precision Surgery: Ricoh 3D for Healthcare and SimBioSys® to Explore Collaboration for Development of AI-Powered Personalized 3D-Printed Models

Our presence at ASBrS will be an excellent opportunity to demonstrate how this synergy has the potential to benefit surgeons and patients by providing a clearer understanding of complex cancer surgeries before the first incision is made. EXTON, Pa. & CHICAGO —11th April 2024 –(BUSINESS…

SimBioSys® Launches TumorSight Plan, A Pioneering Clinical Decision Support for…

TumorSight Plan is the first clinical decision support tool to support more effective…

Personalized 3D Tumor Models Drive Shared Decision-Making in Early Breast…

Decision-making for early (Stages 1-3) breast cancer (eBC)…

Enabling Precision Surgery: Ricoh 3D for Healthcare and SimBioSys® to Explore Collaboration for Development of AI-Powered Personalized 3D-Printed Models

Our presence at ASBrS will be an excellent opportunity to demonstrate how this synergy has the potential to benefit surgeons and patients by providing a clearer understanding of complex cancer…

SimBioSys® Launches TumorSight Plan, A Pioneering Clinical Decision Support for Early-Stage Breast Cancer

TumorSight Plan is the first clinical decision support tool to support more effective provider-patient decision making and individualize surgical planning to right-size care. Powered by FDA-cleared TumorSight Viz, it provides…

Precision Oncology Innovator SimBioSys® and General Inception Announce Strategic Partnership to Accelerate Cancer Drug Development

PhenoScope™, SimBioSys’ powerful proprietary technology and service, can analyze vast fields of multi-modal data seamlessly, generating novel insights, including unique spatial biophysical insights in a 4-dimension space, for cancer drug…

SimBioSys® Elevates Leadership Team as It Receives First FDA Clearance for Digital Precision Medicine Platform, TumorSight™

CHICAGO–(BUSINESS WIRE)–SimBioSys®, a trailblazing TechBio company unlocking the power of spatial biophysics with artificial intelligence (AI) and biophysical modeling to redefine cancer precision medicine, transform patient care and defeat cancer…

SimBioSys receives milestone FDA clearance for its foundational digital precision medicine technology, TumorSight™, enabling expansion to future cutting-edge applications

-TumorSight™ is a cloud-based digital precision medicine platform intended to support the end-to-end patient journey -TumorSight™ Viz, the first FDA cleared TumorSight™ application, provides clinicians with key 3D spatial visualizations…

SimBioSys and Mayo Clinic Enter Strategic Collaboration to Advance AI-powered Digital Precision Medicine Platform for Cancer Patients

January 02, 2024 07:00 AM Eastern Standard Time CHICAGO–(BUSINESS WIRE)–SimBioSys, a TechBio company unlocking the power of spatial biophysics with artificial intelligence (AI) and biophysical modeling to redefine precision medicine…

SimBioSys and UT Southwestern Enter Strategic Collaboration to Advance Multi-Modal Data Analysis and the Next Generation of Cancer Biomarkers for Immunotherapy

December 18, 2023 07:00 AM Eastern Standard Time CHICAGO–(BUSINESS WIRE)–SimBioSys, a TechBio company unlocking the power of spatial biophysics with artificial intelligence (AI) and biophysical modeling to redefine precision medicine…

Personalized 3D Tumor Models Drive Shared Decision-Making in Early Breast Cancer​

Decision-making for early (Stages 1-3) breast cancer (eBC) surgery is complex and highly personal, requiring discussions between patients and multiple physicians. Shared decision-making (SDM) is an accepted process but its use by physicians is low due…

A Combined Radiomics and Tumor Erosion Model to Predict Post-Neoadjuvant ​Therapy Tumor Characteristics for Personalized Breast Cancer Treatment

Neoadjuvant therapy (NAT) has become a standard-of-care (SOC) for patients diagnosed with locally advanced or early-stage breast cancer. While pathological complete response (pCR) is commonly used to measure NAT effectiveness, patients who do not achieve pCR may…

Predicting the feasibility of breast conserving surgery using pre-treatment standard of care ​DCE MRI: a novel clinical decision support tool for breast cancer surgical planning

The decision-making process regarding breast cancer treatment options, specifically breast conserving surgery (BCS) versus mastectomy, is a complex and sensitive matter that takes into account the patient’s preferences and the surgeon’s clinical…

Applying the Alliance Trial Guidelines in Multi-focal Breast Disease Using an​ Artificial Intelligence Computational Platform: Economic Analysis and Cosmetic Sensitivity​

Traditionally, multi-focal breast cancer results in mastectomy. The Alliance Trial offers a paradigm shift in surgical options available for multi-focal breast cancer patients in the context of adjuvant chemotherapy. In the trial, patients…

Biophysical simulation using SoC DCE-MRI to forecast response to NAT in HER2+ patients, with glucose characterization and orthogonal validation using 18FDG and 64Cu-DOTA-Trast PET

Metabolic reprogramming and tumor angiogenesis are two tightly linked hallmarks of cancer. Regions of high metabolic activity within a tumor can become hypoxic or nutrient starved, eliciting a cascade of pro-angiogenic signals that…

Spatial PK/PD Model with HER2 Expression for Predicting ​Individual Tumor Response to T-DM1

As new antibody drug conjugates are developed, the question of which specific patients will respond to these therapies remains. This work develops a spatial PK/PD model for the antibody drug conjugate trastuzumab emtansine, T-DM1, and explores…

Highlights from ESMO 2022

The ESMO Breast Cancer 2022 took place in Berlin on May 3 – 5. A well-attended conference covering a broad range of breast cancer topics. Our team was there to…

Radiologist validation of a multi-tissue breast segmentation convolutional neural net ensemble

We developed an ensembled suite of convolutional neural networks (core components of SimBioSys TumorSight) that segmented tumor and other tissues, in and around the breast (chest, adipose, gland, vasculature, skin).…

Next generation immuno-oncology tumor profiling using a biophysics-based biomarker to predict immunotherapy response in early-stage breast cancer

Here, we applied an integrative computational approach to develop the IOScope biomarker, which predicts IO response in ESBC.

A rapid, non-invasive test to determine HER2-low status in triple negative breast cancer (TNBC) patients

The potential to expand the current treatment for HER2-low and -zero patients, highlights the limitations of traditional HER2 assessment, including HER2 intra-tumoral heterogeneity, differential IHC pathology staining, and inter-reader variability.…

Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format

Here, we developed two solutions to communication bottlenecks that speed-up simulation by ∼4-fold for hybrid stochastic-deterministic simulations and by over 100-fold for fully deterministic simulations.

Novel computational biology modeling system can accurately forecast response to neoadjuvant therapy in early breast cancer

Here, we perform a study in an independent cohort of early-stage and locally advanced breast cancer patients to forecast tumor response to NAT and assess the stability of a previously…

Next generation immuno-oncology tumor profiling using a rapid, non-invasive, computational biophysics biomarker in early-stage breast cancer

Here, we perform a study in an independent cohort of early-stage and locally advanced breast cancer patients to forecast tumor response to NAT and assess the stability of a previously…

Biophysical simulation approach for dose escalation in Phase I clinical trials

Here we performed a proof-of-concept study using trastuzumab emtansine (TDM1), a targeted drug for HER2-enriched breast cancer, to demonstrate how biophysical modeling can support dose selection in phase I clinical…

Harnessing the immune system to develop breakthrough cancer therapies

The last decade in cancer care has been defined by the rapid emergence (and in some cases, dominance), of monoclonal antibody therapies, where they serve as a critical foundation of…

Highly accurate response prediction in high-risk early breast cancer patients using a biophysical simulation platform

Pathologic complete response (pCR) to neoadjuvant chemotherapy (NAC) in early breast cancer (EBC) is largely dependent on breast cancer subtype, but no clinical-grade model exists to predict response and guide…

Takeaways from ESMO 2022

Our chief medical officer, Dr. Anuja Antony, represented SimBioSys at the ESMO 2022 conference last month. Among the many exciting advances and developments in the breast cancer field, two topics…

Enabling personalized cancer care through AI and computer simulations with NVIDIA

SimBioSys® is developing the TumorScope® platform to capture what is truly unique about each patient. The NVIDIA GPU-powered platform takes a holistic and multiscale approach to assess tumor response to…

2022 Best Tech Startups in Champaign

SimBioSys is one of the 2022 best tech startups in Champaign! “The Tech Tribune staff has compiled the very best tech startups in Champaign, Illinois. In doing our research, we considered…

Huge ASCO Breakthroughs: But will these Innovations Advance Equitable Cancer Care?

Our team was present at the American Society of Clinical Oncology (ASCO) annual meeting that took place from June 3 – 7, 2022. Perhaps the most impactful moment for breast…

SimBioSys to Showcase Latest Research on TumorScope at ASCO 2022

CHICAGO – JUNE 3, 2022 — SimBioSys, the technology company that predicts tumor responses to therapy, announced today it will showcase research at the American Society of Clinical Oncology (ASCO)…

Using a multimodal approach to elucidate racial disparities in breast cancer biology by integrating tumor imaging and -omics data

Abstract Background: Race-related differences in breast cancer incidence and clinical outcome have been well documented, with many studies focusing on socioeconomic determinants contributing to African American (AA) breast cancer patients…

Multimodal approach to capture spatially resolved single-cell tumor heterogeneity in breast cancer

Abstract Tumor heterogeneity is known to play a key role in drug response and resistance. However, knowledge of tumor heterogeneity is largely limited to genetics and biopsy samples representing one…

Novel imaging marker for low- and mid-recurrence score patients at risk for recurrence

Abstract Background: The 21-gene (Oncotype DX) recurrence score (RS) has been utilized as a prognostic assay in patients with hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2–) breast…

Prediction of Response to Neoadjuvant Therapy (NAT) in Early Breast Cancer (EBC) at Community Hospitals – SimBioSys® TumorScope(TM) Validation Study

Abstract While most cancer patients are treated at community hospitals, specialized equipment, diagnostic tests, and therapeutic regimens are generally validated at academic settings. Here we present a novel approach to…

The case for simul-omics: identifying IO biomarkers of Ganitumab-Metformin pathological complete response (pCR)

Abstract Background: During the I-SPY2 clinical trial, ganitumab (G) immunotherapy (IO) was co-administered with metformin (GM) to counteract G-induced hyperglycemia. The GM + standard of care (SOC) combination showed promising…

Highlights from ESMO Breast Cancer 2022

The ESMO Breast Cancer 2022 took place in Berlin on May 3 – 5. A well-attended conference covering a broad range of breast cancer topics. Our team was there to…

Spatially-resolved single-cell HER2 tumor heterogeneity captured by biophysical modeling

Abstract: Breast cancer is a highly heterogeneous disease. Prognosis and treatment are usually decided based on the expression of 3 molecular markers; one being the human epidermal growth factor receptor…

Novel platform combines pathology and transcriptomics for a multi-scale analysis and visualization of the breast tumor heterogeneity

Abstract: Cancer heterogeneity is associated with drug resistance, risk of disease recurrence and metastasis. Pathology allows for the assessment of heterogeneity in the tumor. However, this assessment is limited to…

Prediction of Response to Neoadjuvant Therapy in Early-Stage Breast Cancer using a Biophysical Simulation Platform

Abstract: With the rapidly changing landscape of early-stage breast cancer, there is a significant need for upfront biomarkers to enable physicians to “right-size” therapy for patients. It is well known…

Highlights from AACR2022

After two consecutive years of virtually holding the annual meeting of the American Association for Cancer Research (AACR), the conference returned to an in-person format, while retaining a hybrid option…

SimBioSys Presents 9 Applications of TumorScope Platform at AACR 2022

The company’s first appearance at this prestigious cancer research conference profiles use cases of platform for cancer treatment planning and as a cancer research tool.

A multi-scale analysis and visualization platform for cancer data – deriving tumor microenvironment behavior from pathology and transcriptomics

Abstract: Heterogeneity is a hallmark of cancer and perhaps one of the most important features associated with resistance to therapies and likelihood of recurrence and/or metastasis. Genomic instability contributes to…

Accurate modeling of HER2 positive breast cancer disease progression with a biophysical modeling software

Abstract: Breast cancer (BC) progression during NAT is associated with development of distant metastases, positive LN status, and decreased OS/RFS. These can occur in the context of clinical trials and…

Accurate prediction of tumor growth and doubling times for triple negative breast cancer (TNBC) allows for patient-specific assessment of tumor aggressiveness

Abstract: TNBC is the most aggressive of breast cancer subtypes and lacks targeted therapies. Thus, tumor aggressiveness is an important factor to determine escalation of care for TNBC patients. Currently,…

Using systems medicine for comprehensive metabolic profiling of tumors: how tumor metabolism shapes prognosis and response to chemotherapy

Abstract: Background: Metabolic disfunction is one of the hallmarks of cancer, and metabolism-based therapies are a key class of chemotherapeutics. Despite this, there has previously been no systematic way to…

Profiling the metabolism of pancreatic adenocarcinoma using a systems medicine-based approach reveals insights into tumor biology, prognosis, and new therapeutic strategies

Abstract: Background: One of the hallmarks of cancer is metabolic dysregulation that has been therapeutically targeted with metabolism-based therapies, an important class of chemotherapeutics. However, there has previously been no…

Systems medicine based metabolic profiling of metastatic melanoma reveals insights into tumor biology, prognosis, and new therapeutic strategies

Abstract: Background: Tumor cells are able to reprogram their metabolism in order to sustain continuous growth and proliferation. Although, this has led to the development of metabolism-based therapies, until now…

SimBioSys® TumorScope(TM) accurately models and predicts response to neoadjuvant therapy in Breast Cancer – Validation study

Abstract: Neoadjuvant Therapy (NAT) for breast cancer results in higher rates of breast conservation surgery. Importantly, there is data supporting the use of multiple NAT regimens, with little guidance as…

Spatio-temporal modeling of the tumor microenvironment for prediction of patient-specific response to chemotherapy

Abstract: Tumor heterogeneity, understood as the intrinsic (e.g., mutations, dysregulation, metabolic reprogramming) and extrinsic (e.g., nutrient/drug perfusion, interactions with surrounding tissues and the tumor microenvironment (TME)) to the cells that…

Integrating imaging and multi-omics data to elucidate racial differences in breast tumor biology to optimize precision oncology approaches and patient outcome

Abstract: Background: Racial disparities in breast cancer incidence and clinical outcome have been well characterized. In particular, African American (AA) patients have higher mortality rates than other racial groups. Research…

Biopharma Dealmakers: Virtualizing cancer to eliminate uncertainty and individualize care

No two tumors are alike. What if we could model treatment planning for each individual patient? Meet TumorScope – the first of its kind 4D Tumor Modeling platform that combines…

Key take home messages from the San Antonio Breast Cancer Symposium 2021

From December 7th -10th the San Antonio Breast Cancer Symposium gathered breast cancer experts from all over the world to share the latest medical and scientific advances in the breast…

Why is it important to raise breast cancer awareness?

Precision medicine has come a long way in terms of breast cancer treatment but more needs to be done for the non-responder patients, for those who need financial support, for…

Novel Device May Predict Response to Therapy in Patients With Early Breast Cancer

Frederick Howard, MD, a medical oncology fellow in the Department of Medicine at the University of Chicago, discussed the clinical benefits of the SimBioSys TumorScope model for the treatment of…

SimBioSys Raises $15 Million Series A to Develop the Future of Precision Cancer Care

Genoa Ventures and Northpond Ventures co-lead investment in precision medicine platform that develops virtual tumors in 3D to predict response to therapy using standard-of-care data

Why Cancer? Why Us? Why Now?

Most of us have experienced the pain of a friend or family member’s cancer diagnosis and treatment in our lives. The process of diagnosis, treatment and monitoring — and the…

Wired in: Interview with Tushar Pandey

Each week, staff writer Paul Wood interviews a high-tech difference-maker. This week, meet TUSHAR PANDEY, chief executive officer at SimBioSys Inc. in the University of Illinois Research Park. The company is…

An in-silico human cell model reveals the influence of spatial organization on RNA splicing

Abstract: Spatial organization is a characteristic of all cells, achieved in eukaryotic cells by utilizing both membrane-bound and membrane-less organelles. One of the key processes in eukaryotes is RNA splicing,…

Essential metabolism for a minimal cell

Abstract: JCVI-syn3A, a robust minimal cell with a 543 kbp genome and 493 genes, provides a versatile platform to study the basics of life. Using the vast amount of experimental…

Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane

Abstract: The plasma membrane of the cell is a complex, tightly regulated, heterogeneous environment shaped by proteins, lipids, and small molecules. Ca2+ ions are important cellular messengers, spatially separated from…

Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics

Abstract: Background Recent results from single cell gene and protein regulation studies are starting to uncover the previously underappreciated fact that individual cells within a population exhibit high variability in…

Population FBA predicts metabolic phenotypes in yeast

Abstract: Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism, Population flux balance analysis (Population FBA) successfully described metabolic heterogeneity in…

Multimodal Assessment of Mesenchymal Stem Cell Therapy for Diabetic Vascular Complications

Abstract: Peripheral arterial disease (PAD) is a debilitating complication of diabetes mellitus (DM) that leads to thousands of injuries, amputations, and deaths each year. The use of mesenchymal stem cells…

Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects

Abstract: Characterizing the complex spatial and temporal interactions among cells in a biological system (i.e. bacterial colony, microbiome, tissue, etc.) remains a challenge. Metabolic cooperativity in these systems can arise…

A Careful Accounting of Extrinsic Noise in Protein Expression Reveals Correlations Among its Sources

Abstract: In order to grow and replicate, living cells must express a diverse array of proteins, but the process by which proteins are made includes a great deal of inherent…

Challenges of integrating stochastic dynamics and cryo-electron tomograms in whole-cell simulations

Abstract: Cryo-electron tomography (cryo-ET) has rapidly emerged as a powerful tool to investigate the internal, three-dimensional spatial organization of the cell. In parallel, the GPU-based technology to perform spatially resolved…

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

Background While a few studies on the variations in mRNA expression and half-lives measured under different growth conditions have been used to predict patterns of regulation in bacterial organisms, the…

Ribosome biogenesis in replicating cells: integration of experiment and theory

Abstract: Ribosomes-the primary macromolecular machines responsible for translating the genetic code into proteins-are complexes of precisely folded RNA and proteins. The ways in which their production and assembly are managed…

Effects of DNA replication on mRNA noise

Abstract: There are several sources of fluctuations in gene expression. Here we study the effects of time-dependent DNA replication, itself a tightly controlled process, on noise in mRNA levels. Stochastic…

Systems analysis of non-parenchymal cell modulation of liver repair across multiple regeneration modes

Abstract: Background A hallmark of chronic liver disease is the impairment of the liver’s innate regenerative ability. In this work we use a computational approach to unravel the principles underlying…

A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes

Abstract: Following partial hepatectomy, a coordinated series of molecular events occurs to regulate hepatocyte entry into the cell cycle to recover lost mass. In rats during the first 6 h…

Spatially-resolved metabolic cooperativity within dense bacterial colonies

Background The exchange of metabolites and the reprogramming of metabolism in response to shifting microenvironmental conditions can drive subpopulations of cells within colonies toward divergent behaviors. Understanding the interactions of…

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations

Abstract: Simulation of in vivo cellular processes with the reaction–diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria…

DNA looping increases the range of bistability in a stochastic model of the lac genetic switch

Abstract: Conditions and parameters affecting the range of bistability of the lac genetic switch in Escherichia coli are examined for a model which includes DNA looping interactions with the lac…

Personalized 3D Tumor Models Drive Shared Decision-Making in Early Breast Cancer​

Decision-making for early (Stages 1-3) breast cancer (eBC) surgery is complex and highly personal, requiring discussions between patients and multiple physicians. Shared decision-making (SDM) is an accepted process but its use by physicians is low due…

A Combined Radiomics and Tumor Erosion Model to Predict Post-Neoadjuvant ​Therapy Tumor Characteristics for Personalized Breast Cancer Treatment

Neoadjuvant therapy (NAT) has become a standard-of-care (SOC) for patients diagnosed with locally advanced or early-stage breast cancer. While pathological complete response (pCR) is commonly used to measure NAT effectiveness, patients who do not achieve pCR may…

Predicting the feasibility of breast conserving surgery using pre-treatment standard of care ​DCE MRI: a novel clinical decision support tool for breast cancer surgical planning

The decision-making process regarding breast cancer treatment options, specifically breast conserving surgery (BCS) versus mastectomy, is a complex and sensitive matter that takes into account the patient’s preferences and the surgeon’s clinical…

Applying the Alliance Trial Guidelines in Multi-focal Breast Disease Using an​ Artificial Intelligence Computational Platform: Economic Analysis and Cosmetic Sensitivity​

Traditionally, multi-focal breast cancer results in mastectomy. The Alliance Trial offers a paradigm shift in surgical options available for multi-focal breast cancer patients in the context of adjuvant chemotherapy. In the trial, patients…

Biophysical simulation using SoC DCE-MRI to forecast response to NAT in HER2+ patients, with glucose characterization and orthogonal validation using 18FDG and 64Cu-DOTA-Trast PET

Metabolic reprogramming and tumor angiogenesis are two tightly linked hallmarks of cancer. Regions of high metabolic activity within a tumor can become hypoxic or nutrient starved, eliciting a cascade of pro-angiogenic signals that…

Spatial PK/PD Model with HER2 Expression for Predicting ​Individual Tumor Response to T-DM1

As new antibody drug conjugates are developed, the question of which specific patients will respond to these therapies remains. This work develops a spatial PK/PD model for the antibody drug conjugate trastuzumab emtansine, T-DM1, and explores…

Radiologist validation of a multi-tissue breast segmentation convolutional neural net ensemble

We developed an ensembled suite of convolutional neural networks (core components of SimBioSys TumorSight) that segmented tumor and other tissues, in and around the breast (chest, adipose, gland, vasculature, skin).…

Next generation immuno-oncology tumor profiling using a biophysics-based biomarker to predict immunotherapy response in early-stage breast cancer

Here, we applied an integrative computational approach to develop the IOScope biomarker, which predicts IO response in ESBC.

A rapid, non-invasive test to determine HER2-low status in triple negative breast cancer (TNBC) patients

The potential to expand the current treatment for HER2-low and -zero patients, highlights the limitations of traditional HER2 assessment, including HER2 intra-tumoral heterogeneity, differential IHC pathology staining, and inter-reader variability.…

Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format

Here, we developed two solutions to communication bottlenecks that speed-up simulation by ∼4-fold for hybrid stochastic-deterministic simulations and by over 100-fold for fully deterministic simulations.

Novel computational biology modeling system can accurately forecast response to neoadjuvant therapy in early breast cancer

Here, we perform a study in an independent cohort of early-stage and locally advanced breast cancer patients to forecast tumor response to NAT and assess the stability of a previously…

Next generation immuno-oncology tumor profiling using a rapid, non-invasive, computational biophysics biomarker in early-stage breast cancer

Here, we perform a study in an independent cohort of early-stage and locally advanced breast cancer patients to forecast tumor response to NAT and assess the stability of a previously…

Biophysical simulation approach for dose escalation in Phase I clinical trials

Here we performed a proof-of-concept study using trastuzumab emtansine (TDM1), a targeted drug for HER2-enriched breast cancer, to demonstrate how biophysical modeling can support dose selection in phase I clinical…

Highly accurate response prediction in high-risk early breast cancer patients using a biophysical simulation platform

Pathologic complete response (pCR) to neoadjuvant chemotherapy (NAC) in early breast cancer (EBC) is largely dependent on breast cancer subtype, but no clinical-grade model exists to predict response and guide…

Using a multimodal approach to elucidate racial disparities in breast cancer biology by integrating tumor imaging and -omics data

Abstract Background: Race-related differences in breast cancer incidence and clinical outcome have been well documented, with many studies focusing on socioeconomic determinants contributing to African American (AA) breast cancer patients…

Multimodal approach to capture spatially resolved single-cell tumor heterogeneity in breast cancer

Abstract Tumor heterogeneity is known to play a key role in drug response and resistance. However, knowledge of tumor heterogeneity is largely limited to genetics and biopsy samples representing one…

Novel imaging marker for low- and mid-recurrence score patients at risk for recurrence

Abstract Background: The 21-gene (Oncotype DX) recurrence score (RS) has been utilized as a prognostic assay in patients with hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2–) breast…

Prediction of Response to Neoadjuvant Therapy (NAT) in Early Breast Cancer (EBC) at Community Hospitals – SimBioSys® TumorScope(TM) Validation Study

Abstract While most cancer patients are treated at community hospitals, specialized equipment, diagnostic tests, and therapeutic regimens are generally validated at academic settings. Here we present a novel approach to…

The case for simul-omics: identifying IO biomarkers of Ganitumab-Metformin pathological complete response (pCR)

Abstract Background: During the I-SPY2 clinical trial, ganitumab (G) immunotherapy (IO) was co-administered with metformin (GM) to counteract G-induced hyperglycemia. The GM + standard of care (SOC) combination showed promising…

Spatially-resolved single-cell HER2 tumor heterogeneity captured by biophysical modeling

Abstract: Breast cancer is a highly heterogeneous disease. Prognosis and treatment are usually decided based on the expression of 3 molecular markers; one being the human epidermal growth factor receptor…

Novel platform combines pathology and transcriptomics for a multi-scale analysis and visualization of the breast tumor heterogeneity

Abstract: Cancer heterogeneity is associated with drug resistance, risk of disease recurrence and metastasis. Pathology allows for the assessment of heterogeneity in the tumor. However, this assessment is limited to…

Prediction of Response to Neoadjuvant Therapy in Early-Stage Breast Cancer using a Biophysical Simulation Platform

Abstract: With the rapidly changing landscape of early-stage breast cancer, there is a significant need for upfront biomarkers to enable physicians to “right-size” therapy for patients. It is well known…

A multi-scale analysis and visualization platform for cancer data – deriving tumor microenvironment behavior from pathology and transcriptomics

Abstract: Heterogeneity is a hallmark of cancer and perhaps one of the most important features associated with resistance to therapies and likelihood of recurrence and/or metastasis. Genomic instability contributes to…

Accurate modeling of HER2 positive breast cancer disease progression with a biophysical modeling software

Abstract: Breast cancer (BC) progression during NAT is associated with development of distant metastases, positive LN status, and decreased OS/RFS. These can occur in the context of clinical trials and…

Accurate prediction of tumor growth and doubling times for triple negative breast cancer (TNBC) allows for patient-specific assessment of tumor aggressiveness

Abstract: TNBC is the most aggressive of breast cancer subtypes and lacks targeted therapies. Thus, tumor aggressiveness is an important factor to determine escalation of care for TNBC patients. Currently,…

Using systems medicine for comprehensive metabolic profiling of tumors: how tumor metabolism shapes prognosis and response to chemotherapy

Abstract: Background: Metabolic disfunction is one of the hallmarks of cancer, and metabolism-based therapies are a key class of chemotherapeutics. Despite this, there has previously been no systematic way to…

Profiling the metabolism of pancreatic adenocarcinoma using a systems medicine-based approach reveals insights into tumor biology, prognosis, and new therapeutic strategies

Abstract: Background: One of the hallmarks of cancer is metabolic dysregulation that has been therapeutically targeted with metabolism-based therapies, an important class of chemotherapeutics. However, there has previously been no…

Systems medicine based metabolic profiling of metastatic melanoma reveals insights into tumor biology, prognosis, and new therapeutic strategies

Abstract: Background: Tumor cells are able to reprogram their metabolism in order to sustain continuous growth and proliferation. Although, this has led to the development of metabolism-based therapies, until now…

SimBioSys® TumorScope(TM) accurately models and predicts response to neoadjuvant therapy in Breast Cancer – Validation study

Abstract: Neoadjuvant Therapy (NAT) for breast cancer results in higher rates of breast conservation surgery. Importantly, there is data supporting the use of multiple NAT regimens, with little guidance as…

Spatio-temporal modeling of the tumor microenvironment for prediction of patient-specific response to chemotherapy

Abstract: Tumor heterogeneity, understood as the intrinsic (e.g., mutations, dysregulation, metabolic reprogramming) and extrinsic (e.g., nutrient/drug perfusion, interactions with surrounding tissues and the tumor microenvironment (TME)) to the cells that…

Integrating imaging and multi-omics data to elucidate racial differences in breast tumor biology to optimize precision oncology approaches and patient outcome

Abstract: Background: Racial disparities in breast cancer incidence and clinical outcome have been well characterized. In particular, African American (AA) patients have higher mortality rates than other racial groups. Research…

An in-silico human cell model reveals the influence of spatial organization on RNA splicing

Abstract: Spatial organization is a characteristic of all cells, achieved in eukaryotic cells by utilizing both membrane-bound and membrane-less organelles. One of the key processes in eukaryotes is RNA splicing,…

Essential metabolism for a minimal cell

Abstract: JCVI-syn3A, a robust minimal cell with a 543 kbp genome and 493 genes, provides a versatile platform to study the basics of life. Using the vast amount of experimental…

Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane

Abstract: The plasma membrane of the cell is a complex, tightly regulated, heterogeneous environment shaped by proteins, lipids, and small molecules. Ca2+ ions are important cellular messengers, spatially separated from…

Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics

Abstract: Background Recent results from single cell gene and protein regulation studies are starting to uncover the previously underappreciated fact that individual cells within a population exhibit high variability in…

Population FBA predicts metabolic phenotypes in yeast

Abstract: Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism, Population flux balance analysis (Population FBA) successfully described metabolic heterogeneity in…

Multimodal Assessment of Mesenchymal Stem Cell Therapy for Diabetic Vascular Complications

Abstract: Peripheral arterial disease (PAD) is a debilitating complication of diabetes mellitus (DM) that leads to thousands of injuries, amputations, and deaths each year. The use of mesenchymal stem cells…

Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects

Abstract: Characterizing the complex spatial and temporal interactions among cells in a biological system (i.e. bacterial colony, microbiome, tissue, etc.) remains a challenge. Metabolic cooperativity in these systems can arise…

A Careful Accounting of Extrinsic Noise in Protein Expression Reveals Correlations Among its Sources

Abstract: In order to grow and replicate, living cells must express a diverse array of proteins, but the process by which proteins are made includes a great deal of inherent…

Challenges of integrating stochastic dynamics and cryo-electron tomograms in whole-cell simulations

Abstract: Cryo-electron tomography (cryo-ET) has rapidly emerged as a powerful tool to investigate the internal, three-dimensional spatial organization of the cell. In parallel, the GPU-based technology to perform spatially resolved…

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

Background While a few studies on the variations in mRNA expression and half-lives measured under different growth conditions have been used to predict patterns of regulation in bacterial organisms, the…

Ribosome biogenesis in replicating cells: integration of experiment and theory

Abstract: Ribosomes-the primary macromolecular machines responsible for translating the genetic code into proteins-are complexes of precisely folded RNA and proteins. The ways in which their production and assembly are managed…

Effects of DNA replication on mRNA noise

Abstract: There are several sources of fluctuations in gene expression. Here we study the effects of time-dependent DNA replication, itself a tightly controlled process, on noise in mRNA levels. Stochastic…

Systems analysis of non-parenchymal cell modulation of liver repair across multiple regeneration modes

Abstract: Background A hallmark of chronic liver disease is the impairment of the liver’s innate regenerative ability. In this work we use a computational approach to unravel the principles underlying…

A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes

Abstract: Following partial hepatectomy, a coordinated series of molecular events occurs to regulate hepatocyte entry into the cell cycle to recover lost mass. In rats during the first 6 h…

Spatially-resolved metabolic cooperativity within dense bacterial colonies

Background The exchange of metabolites and the reprogramming of metabolism in response to shifting microenvironmental conditions can drive subpopulations of cells within colonies toward divergent behaviors. Understanding the interactions of…

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations

Abstract: Simulation of in vivo cellular processes with the reaction–diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria…

DNA looping increases the range of bistability in a stochastic model of the lac genetic switch

Abstract: Conditions and parameters affecting the range of bistability of the lac genetic switch in Escherichia coli are examined for a model which includes DNA looping interactions with the lac…

Enabling Precision Surgery: Ricoh 3D for Healthcare and SimBioSys® to Explore Collaboration for Development of AI-Powered Personalized 3D-Printed Models

Our presence at ASBrS will be an excellent opportunity to demonstrate how this synergy has the potential to benefit surgeons and patients by providing a clearer understanding of complex cancer…

SimBioSys® Launches TumorSight Plan, A Pioneering Clinical Decision Support for Early-Stage Breast Cancer

TumorSight Plan is the first clinical decision support tool to support more effective provider-patient decision making and individualize surgical planning to right-size care. Powered by FDA-cleared TumorSight Viz, it provides…

Precision Oncology Innovator SimBioSys® and General Inception Announce Strategic Partnership to Accelerate Cancer Drug Development

PhenoScope™, SimBioSys’ powerful proprietary technology and service, can analyze vast fields of multi-modal data seamlessly, generating novel insights, including unique spatial biophysical insights in a 4-dimension space, for cancer drug…

SimBioSys® Elevates Leadership Team as It Receives First FDA Clearance for Digital Precision Medicine Platform, TumorSight™

CHICAGO–(BUSINESS WIRE)–SimBioSys®, a trailblazing TechBio company unlocking the power of spatial biophysics with artificial intelligence (AI) and biophysical modeling to redefine cancer precision medicine, transform patient care and defeat cancer…

SimBioSys receives milestone FDA clearance for its foundational digital precision medicine technology, TumorSight™, enabling expansion to future cutting-edge applications

-TumorSight™ is a cloud-based digital precision medicine platform intended to support the end-to-end patient journey -TumorSight™ Viz, the first FDA cleared TumorSight™ application, provides clinicians with key 3D spatial visualizations…

SimBioSys and Mayo Clinic Enter Strategic Collaboration to Advance AI-powered Digital Precision Medicine Platform for Cancer Patients

January 02, 2024 07:00 AM Eastern Standard Time CHICAGO–(BUSINESS WIRE)–SimBioSys, a TechBio company unlocking the power of spatial biophysics with artificial intelligence (AI) and biophysical modeling to redefine precision medicine…

SimBioSys and UT Southwestern Enter Strategic Collaboration to Advance Multi-Modal Data Analysis and the Next Generation of Cancer Biomarkers for Immunotherapy

December 18, 2023 07:00 AM Eastern Standard Time CHICAGO–(BUSINESS WIRE)–SimBioSys, a TechBio company unlocking the power of spatial biophysics with artificial intelligence (AI) and biophysical modeling to redefine precision medicine…

SimBioSys to Showcase Latest Research on TumorScope at ASCO 2022

CHICAGO – JUNE 3, 2022 — SimBioSys, the technology company that predicts tumor responses to therapy, announced today it will showcase research at the American Society of Clinical Oncology (ASCO)…

SimBioSys Presents 9 Applications of TumorScope Platform at AACR 2022

The company’s first appearance at this prestigious cancer research conference profiles use cases of platform for cancer treatment planning and as a cancer research tool.

SimBioSys Raises $15 Million Series A to Develop the Future of Precision Cancer Care

Genoa Ventures and Northpond Ventures co-lead investment in precision medicine platform that develops virtual tumors in 3D to predict response to therapy using standard-of-care data

2022 Best Tech Startups in Champaign

SimBioSys is one of the 2022 best tech startups in Champaign! “The Tech Tribune staff has compiled the very best tech startups in Champaign, Illinois. In doing our research, we considered…

Biopharma Dealmakers: Virtualizing cancer to eliminate uncertainty and individualize care

No two tumors are alike. What if we could model treatment planning for each individual patient? Meet TumorScope – the first of its kind 4D Tumor Modeling platform that combines…

Novel Device May Predict Response to Therapy in Patients With Early Breast Cancer

Frederick Howard, MD, a medical oncology fellow in the Department of Medicine at the University of Chicago, discussed the clinical benefits of the SimBioSys TumorScope model for the treatment of…

Wired in: Interview with Tushar Pandey

Each week, staff writer Paul Wood interviews a high-tech difference-maker. This week, meet TUSHAR PANDEY, chief executive officer at SimBioSys Inc. in the University of Illinois Research Park. The company is…

Highlights from ESMO 2022

The ESMO Breast Cancer 2022 took place in Berlin on May 3 – 5. A well-attended conference covering a broad range of breast cancer topics. Our team was there to…

Harnessing the immune system to develop breakthrough cancer therapies

The last decade in cancer care has been defined by the rapid emergence (and in some cases, dominance), of monoclonal antibody therapies, where they serve as a critical foundation of…

Takeaways from ESMO 2022

Our chief medical officer, Dr. Anuja Antony, represented SimBioSys at the ESMO 2022 conference last month. Among the many exciting advances and developments in the breast cancer field, two topics…

Enabling personalized cancer care through AI and computer simulations with NVIDIA

SimBioSys® is developing the TumorScope® platform to capture what is truly unique about each patient. The NVIDIA GPU-powered platform takes a holistic and multiscale approach to assess tumor response to…

Huge ASCO Breakthroughs: But will these Innovations Advance Equitable Cancer Care?

Our team was present at the American Society of Clinical Oncology (ASCO) annual meeting that took place from June 3 – 7, 2022. Perhaps the most impactful moment for breast…

Highlights from ESMO Breast Cancer 2022

The ESMO Breast Cancer 2022 took place in Berlin on May 3 – 5. A well-attended conference covering a broad range of breast cancer topics. Our team was there to…

Highlights from AACR2022

After two consecutive years of virtually holding the annual meeting of the American Association for Cancer Research (AACR), the conference returned to an in-person format, while retaining a hybrid option…

Key take home messages from the San Antonio Breast Cancer Symposium 2021

From December 7th -10th the San Antonio Breast Cancer Symposium gathered breast cancer experts from all over the world to share the latest medical and scientific advances in the breast…

Why is it important to raise breast cancer awareness?

Precision medicine has come a long way in terms of breast cancer treatment but more needs to be done for the non-responder patients, for those who need financial support, for…

Why Cancer? Why Us? Why Now?

Most of us have experienced the pain of a friend or family member’s cancer diagnosis and treatment in our lives. The process of diagnosis, treatment and monitoring — and the…