About

John M. Collins is an Associate Professor at the University of Chicago in the Department of Radiology-Neuroradiology. His research encompasses a broad range of topics within biomedical imaging, neuro-oncology, and neural disorders. His work includes studies on the surgical outcomes and prognostic factors in epilepsy treatment, biomechanical and morphological analysis of craniofacial structures, and the application of advanced imaging techniques to understand neural and vascular diseases. Collins has contributed to research on the structural and functional recovery of skeletal muscle, the migration and proliferation of human mesenchymal stem cells, and the development of microstructures in 3D biological gels affecting cell proliferation. His publications also include investigations into the molecular and cellular mechanisms underlying various neurological and vascular conditions, such as hemangioblastomatosis and cranial neuropathies, as well as the application of imaging technology in diagnosing and understanding these diseases. His work is characterized by a focus on translating biomedical research into clinical insights, with an emphasis on imaging, neural pathology, and regenerative medicine.

Research topics

• Surgery
• Computer Science
• Medicine
• Psychology
• Manufacturing engineering
• Internal medicine
• Pathology
• Engineering
• Orthodontics
• Process management
• Operating system
• Anesthesia
• Mechanical engineering
• Psychiatry

Selected publications

• Metal oxide dry resist precursor requirement and advantage towards high-NA EUV lithography

  2026-04-09

  article

  Metal Oxide Resists (MOR) are critical for achieving high-resolution patterning in extreme ultraviolet (EUV) lithography. Lam’s Aether program has demonstrated that dry development of MORs can address pattern collapse, enhanced resolution, and reduce line edge roughness. Here we discuss the chemistry of dry resist precursors, their advantages compared to spin-on MOR materials, and how Gelest is ready to move toward HVM manufacturing to support Lam Aether program into the industry.

  PublisherDOI

• An Investigation of Thermal Ionization of a Trap within the Framework of Proper Adiabatic Approximation

  ECS Meeting Abstracts · 2025-11-24

  article1st authorCorresponding

  We have investigated the rate of ionization of traps using the proper adiabatic approximation. This rate is usually described by an Arrhenius-type equation in the experimental determination of trap depths from thermoluminescence measurements, R = νe -E/kT where R is the rate of ionization, E is the trap depth, and ν is the frequency factor. Although Eq. 1 has the form of an Arrhenius equation, in the exponent is the trap depth, not the activation barrier, E b , as in a typical Arrhenius equation. (See Figure 1.) In a typical analysis of glow curves, ν is assumed to be a constant, although a weak temperature dependence is generally indicated by various authors. We have formulated this trap ionization problem using the proper adiabatic approximation for a single configurational coordinate system. In our formulation the nonadiabaticity operator drives the system from the ground state to the excited state nonradiatively. Using a first-order perturbation theory we have obtained the transition rate using the Fermi golden rule. We show that E in the exponent is indeed the trap depth, and that has a weak temperature dependence. We investigated the effect of this temperature dependence on calculating the trap depth from the glow curves. This will be discussed in detail in the presentation. Fig. 1: Adiabatic potentials for the electron in the ground state of the trap and in the excited state following ionization for a single configurational coordinate system . Figure 1

  PublisherDOI

• Clinical and analytical validation of MI Cancer Seek®, a companion diagnostic whole exome and whole transcriptome sequencing-based comprehensive molecular profiling assay

  Oncotarget · 2025-08-13 · 9 citations

  articleOpen access

  , an FDA-approved whole exome and whole transcriptome sequencing-based molecular test encompassing adult and pediatric tumor profiling, eight companion diagnostics (CDx), and additional laboratory developed test (LDT) capabilities. Patient tissue is maximized through simultaneous analysis of DNA and RNA with minimum input of 50 ng. The clinical and analytical validation presented herein demonstrates non-inferiority of MI Cancer Seek relative to other FDA-approved CDx tests (>97% negative and positive percent agreement), as well as its precision, sensitivity, and specificity. Accordingly, MI Cancer Seek represents a safe and effective comprehensive molecular test option supporting biomarker-directed care for oncology patients.

  PublisherDOI

• A Statistical Interpretation of Thermoluminescence

  ECS Meeting Abstracts · 2024-11-22

  article1st authorCorresponding

  In this talk we will discuss thermoluminescence-related processes using methods of statistical mechanics. With the assumption of thermal and diffusive equilibrium between the traps and the conduction electrons, we calculate the trap ionization probabilities over a wide temperature range and for traps at a variety of trap depths. These ionization probability vs. temperature curves show the expected behavior, with trap ionization increasing with increasing temperature. Using the ionization curves, it will be shown that one can reproduce, with good accuracy, the peak positions fitting of the glow curves of five traps observed in YAG:Ce. 1 We find the position and shape of the glow curves depends on two factors, the trap depth and the conduction electron density. Also, the widths and shapes of the calculated glow curves have been examined in detail, and have been compared with band width expressions found in the literature 2 . The shapes of the calculated glow curves have been determined to be consistent with second order kinetics processes. J. Ueda, P. Dorenbos, A. J. J. Bos, A. Meijerink, and S. Tanabe, J. Phys. Chem. C 2015, 119, 25003−25008, doi:10.1021/acs.jpcc.5b08828 R. Chen, J. Appl. Phys. 40, 570–585 (1969) doi.org/10.1063/1.1657437

  PublisherDOI

• Contribution of RADx® Tech to the Rapid Development of COVID-19 Diagnostic Tests

  Cambridge University Press eBooks · 2024-01-06

  book-chapter

  Rapid Acceleration of Diagnostics (RADx®) Tech was the key diagnostics component of a three-pronged national strategy, including vaccines and therapeutics, to respond to the COVID-19 pandemic. Unprecedented in the scale of its mission, its budget, its accelerated time frame, the extent of cross-government agency collaboration and information exchange, and the blending of business, academic, and investment best practices, RAD Tech successfully launched dozens of US Food and Drug Administration Emergency Use Authorization diagnostic tests, established a new model for rapidly translating diagnostic tests from the laboratory to the marketplace, and accelerated public acceptance of home-based diagnostic tests. This chapter provides an overview of the processes utilized by RADx Tech during the COVID-19 pandemic to improve clinical laboratory tests and identify, evaluate, support, validate, and commercialize innovative point-of-care and home-based tests that directly detected the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus.

  PublisherDOI

• A multi-institutional phase I study of acetazolamide with temozolomide in adults with newly diagnosed <i>MGMT</i>-methylated malignant glioma

  Neuro-Oncology Advances · 2024-01-01 · 6 citations

  articleOpen access

  Abstract Background A significant unmet need exists for the treatment of glioblastoma, IDH-wildtype (GBM). Preclinical work shows that acetazolamide sensitizes GBM to temozolomide (TMZ) by overcoming TMZ resistance due to BCL-3-dependent upregulation of carbonic anhydrase. Acetazolamide is Food and Drug Administration-approved for the treatment of altitude sickness. Drug repurposing enables the application of drugs to diseases beyond initial indications. This multi-institutional, open-label, phase I trial examined a combination of acetazolamide and TMZ in patients with MGMT promoter-methylated high-grade glioma. Methods A total of 24 patients (GBM, IDH-wildtype = 22; Grade 4 astrocytoma, IDH-mutant = 1; Grade 3 astrocytoma, IDH-mutant = 1) were accrued over 17 months. All patients received oral acetazolamide (250 mg BID for 7 days increased to 500 mg BID for Days 8–21 of each 28-day cycle) during the adjuvant phase of TMZ for up to 6 cycles. Results No patient had a dose-limiting toxicity. Adverse events were consistent with known sequelae of acetazolamide and TMZ. In the 23 WHO Grade 4 patients, the median overall survival (OS) was 30.1 months and the median progression-free survival was 16.0 months. The 2-year OS was 60.9%. In total 37% of the study population had high BCL-3 staining and trended toward shorter OS (17.2 months vs N.R., P = .06). Conclusions The addition of acetazolamide is safe and tolerable in GBM patients receiving standard TMZ. Survival results compare favorably to historical data from randomized trials in patients with MGMT promoter-methylated GBM and support examination of acetazolamide in a randomized trial. BCL-3 expression is a potential biomarker for prognosis in GBM or for patients more likely to benefit from TMZ.

  PublisherOA PDFDOI

• (Invited) A Statistical Model of Thermal Ionization of Excited Ce Ions in YAG

  ECS Meeting Abstracts · 2024-11-22

  article1st authorCorresponding

  In this talk we present a statistical model for quantifying the thermal ionization process of an excited impurity ion in a level just below the conduction band of the host while the impurity ion is under constant excitation. YAG:Ce is used as an example. We assume that under constant pumping of the Ce 3+ ion into the 5d 1 with a blue LED, a condition of thermal and diffusive equilibrium will exist between the conduction electrons and the electrons in the excited 5d 1 level of Ce 3+ ion. Using the Gibbs sum, we calculate the probability for an excited Ce 3+ ion to be thermally ionized, leading to an electron in the conduction band. The density of conduction electrons is then calculated over a wide range of temperatures and excitation densities. The observed quenching of emission at high temperature in Ce-doped YAG with low Ce concentrations is also investigated within this model. It is shown that the experimentally-observed nonradiative losses in this phosphor can be reasonably simulated assuming losses occur via nonradiative decay from the conduction band to the Ce 4+ ground state.

  PublisherDOI

• Creating Normative Growth Curves for Pediatric Upper Airway Volume

  FACE · 2023-04-07

  articleSenior author

  Background: The objective of this study was to create normative growth curves for pediatric upper airway volume using 3D computed tomography with emphasis on the neonatal age group. Methods: We completed a single-institution, retrospective review of all patients with available CT scans between the ages of 0 and 60 months. Patients were excluded if they exhibited any maxillofacial dysmorphism or upper airway pathology or if scans showed the presence of airway appliances or tubes. 3D volumetric upper airway analysis was performed and 2D cephalometric measurements and growth parameters including height, weight and age were recorded for all patients. Linear regression analysis was used to develop a prediction model for airway volume in terms of age adjusting for cephalometric and growth parameters stratified by sex and the resulting model was used to create separate percentile curves for each sex group. Results: The growth curves were created based on CT scans from 217 healthy patients. Mean airway volume was significantly larger in males than females (3.23 ± 1.98 mm 3 vs 2.61 ± 1.64 mm 3 , p = 0.017). Conclusions: Normative growth curves for neonatal and pediatric upper airway volume are a useful tool for tracking changes in airway volume in the growing infant.

  PublisherDOI

• OA3‐AM23‐TU‐13 | Platelet Transfusion in Critical Care: A New Method to Analyze Transfusion Practice Based on Decision Time Intervals

  Transfusion · 2023-10-01

  article
  PublisherDOI

• CTNI-47. INTERIM RESULTS OF NCT03011671: A MULTI-INSTITUTIONAL PHASE I STUDY OF ACETAZOLAMIDE WITH TEMOZOLOMIDE IN ADULTS WITH NEWLY DIAGNOSED MGMT-METHYLATED MALIGNANT GLIOMA

  Neuro-Oncology · 2021-11-02 · 4 citations

  articleOpen access

  Abstract Preclinical studies indicate that up-regulation of carbonic anhydrase (CA) by temozolomide (TMZ), via a mechanism requiring the proto-oncogene BCL-3, promotes resistance to therapy in glioblastoma (GBM) cells. Moreover, the CA inhibitor, acetazolamide (ACZ), sensitizes patient-derived GBM cells and xenografts to TMZ. These findings led to the current Phase I study investigating the safety and efficacy of adding ACZ to adjuvant TMZ in patients with newly diagnosed, MGMT-methylated malignant glioma. 24 patients were enrolled (23 GBM and one Grade III IDH-mutant astrocytoma), median age was 53.5 and mean KPS 91. ACZ was given on days 1-21 of each adjuvant TMZ cycle (250 mg BID days 1-7, increased to 500 mg BID days 8-21). No patient experienced the primary outcome of regimen limiting toxicity (RLT) and there were only three grade III adverse events deemed likely unrelated to ACZ. For the secondary endpoints of overall and progression free survival (OS and PFS, respectively), only the 23 GBM patients were included (22 IDH-wildtype and 1 IDH-mutant). From diagnosis, median PFS was 18.8 months (95% CI: 10.4-23.0) and median OS was 25.0 months (95% CI: 19.9-28.4). Median time from diagnosis to consent was 2.9 months. As of April 2021, only 7 of 23 deaths had occurred. 2-year OS% was 68.2%. Further analysis of secondary endpoints including 6-month objective response rate (ORR) and biomarker analysis of BCL-3 by IHC will be available in the coming months. In sum, the data indicate that addition of ACZ to TMZ is safe and does not lead to reduced TMZ dosing. Also, compared to historical data, interim outcomes suggest that addition of ACZ may substantially improve PFS and 2-year overall survival. These findings support the hypothesis that ACZ acts as a chemosensitizer of alkylating chemotherapy in GBM and support examination of this regimen in a randomized, placebo-controlled study.

  PublisherOA PDFDOI

Frequent coauthors

• Elizabeth Ann Severns

  14 shared

• Michael K. Dempsey

  12 shared

• Thomas P. Glakas

  11 shared

• Baldassare Di Bartolo

  Boston College

  10 shared

• Brenda Russell

  7 shared

• Paul Tessier

  7 shared

• Roger Stupp

  4 shared

• Steve Schachter

  Harvard University

  4 shared

Labs

• Radiology-NeuroradiologyPI

Education

• M.D., Medicine

  University of Chicago

  1990

• B.S., Biology

  University of Chicago

  1986