Publications supported by Research Computing#

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Acknowledgement

This research was completed in part with computational resources and technical support provided by the Research Computing Center at the Medical College of Wisconsin.

List by year#

2026#

Multi-State Structural Genomics Enables Large-Scale, Mechanistic, and Context-Specific Classification of ABCC6 Genetic Variants Implicated in Calcification Diseases

Wagenknecht JB, Haque N, ... Zimmermann MT, *et al.*

Atypical GPCR Activation Resolved by Nanobody Engineering

Schlimgen RR, Jenjak SE, ... Volkman BF, *et al.*

2025#

Combination Hormonal Drug Therapy Inhibits In Vitro Growth of Adult Ovarian Granulosa Tumor Cells

Summey RM, Iden M, ... Hopp E, *et al.*

Biosafety assessment of engineered CCL20 locked dimers in vivo

Drouillard D, Poimenidou M, ... Dwinell MB, *et al.*

Workflow to detect exceeded dose constraints in pancreatic stereotactic body irradiation after intrafraction motion during magnetic resonance-guided adaptive radiotherapy using a deep learning-refined contour propagation tool

Sarosiek C, Amjad A, ... Paulson ES, *et al.*

The Relationship of Prior Concussion and Contact Sport Exposure With Cortical Macro and Microstructure

Meier TB, Muftuler LT, ... Brett BL, *et al.*

Multiomic Selection of Cancer-Testis Antigens as Precision Immuno-oncologic Targets in Head and Neck Cancer

Memon AA, Awan MJ, ... Zenga J, *et al.*

Target-Based Design of Praziquantel Analogs at Cestode TRPM_PZQ_

Sprague DJ, Park S, ... Marchant JS, *et al.*

Oscillating gradient spin echo diffusion time effects implicate variations in neurite beading for the heterogeneous reduced diffusion in human acute ischemic stroke lesions

Zhou M, Budde M, ... Beaulieu C, *et al.*

Impact of breathing technique and particle size on laryngopharyngeal dose delivered by dry powder inhalers

Dey S, Jadcherla A, Johnston N, Bock JM, Garcia GJM

Validation and application of a finite element model simulating failure thresholds of skin during blunt puncture with varying impactor geometries

LeSueur J, Hampton CE, Pintar FA

Molecular basis of pyruvate transport and inhibition of the human mitochondrial pyruvate carrier

Sichrovsky M, Leone V, ... Kunji ERS, *et al.*

Investigating the Association of Concussion and Contact Sport Exposure History With Brain Microstructure Using Quantitative Susceptibility Mapping

España LY, Brett BL, ... Meier TB, *et al.*

The Prevalence of Undiagnosed Concussions and Their Associations With Current Symptom Reporting in Collegiate-Aged Athletes

Bartels HM. Van Bortel KM, Mayer AR, Brett BL, Meier TB

Reutericyclin, a specialized metabolite of Limosilactobacillus reuteri, mitigates risperidone-induced weight gain in mice

Aboulalazm FA, Kazen AB, ... Kirby JR, *et al.*

A realistic FastQ-based framework FastQDesign for ScRNA-seq study design issues

Wang Y, Chen Y, Ahn KW, Lin C

Deep learning-based quick MLC sequencing for MRI-guided online adaptive radiotherapy: a feasibility study for pancreatic cancer patients

Ahunbay A, Paulson E, Ahunbay E, Zhang Y

Discovery of a MET-driven monogenic cause of steatotic liver disease

Pinto e Vairo F, Zimmermann MT, ... Lazaridis KN, *et al.*

An Analytical Approach that Combines Knowledge from Germline and Somatic Mutations Enhances Tumor Genomic Reanalyses in Precision Oncology

DeVoe E, Reddi HV, ... Zimmermann MT, *et al*

Dry powder inhaler deposition in the larynx and the risk of steroid inhaler laryngitis: A computational fluid dynamics study

Dey S, Bock JM, Garcia GJM

2024#

Systematic analysis of the relationship between fold-dependent flexibility and artificial intelligence protein structure prediction

Haque N, Wagenknecht JB, Ratnasinghe BD, Zimmermann MT

Expanded Functionality and Portability for the Colvars Library

Fiorina G, Marinelli F, ... Hénin J, *et al.*

Deep learning-based automatic contour quality assurance for auto-segmented abdominal MR-Linac contours

Zarenia M, Zhang Y, Sarosiek C, Conlin R, Amjad A, Paulson ES

Structural basis for selectivity and antagonism in extracellular GPCR-nanobodies

Schlimgen RR, Peterson FC, Heukers R, Smit MJ, McCorvy JD, Volkman BF

Bhlhe40 Promotes CD4+ T Helper 1 Cell and Suppresses T Follicular Helper Cell Differentiation during Viral Infection

Nguyen C, Kudek M, ... Cui W, *et al.*

Single Cell RNAseq analysis of cytokine-treated human islets: Association of cellular stress with impaired cytokine responsiveness

Stancill JS, Kasmani MY, Cui W, Corbett JA

Structural and Dynamic Analyses of Pathogenic Variants in PIK3R1 Reveal a Shared Mechanism Associated among Cancer, Undergrowth, and Overgrowth Syndromes

Dsouza NR, Cottrell CE, ... Zimmermann MT, *et al.*

2023#

Bi-allelic variants in HMGCR cause an autosomal-recessive progressive limb-girdle muscular dystrophy

Morales-Rosado JA, Schwab TL, ... Klee EW, *et al.*

Tensor-valued diffusion MRI of human acute stroke

Zhou M, Stobbe R, ... Beaulieu C, *et al.*

Associations of prior concussion severity with brain microstructure using mean apparent propagator magnetic resonance imaging

Goeckner BD, Brett BL, ... Meier TB, *et al.*

Molecular and cellular basis of praziquantel action in the cardiovascular system

Yahya NA, Lanham JK, Sprague DJ, Palygin O, McCorvy JD, Marchant JS

Robustness of single-cell RNA-seq for identifying differentially expressed genes

Liu Y, Huang J, ... Liang M, *et al.*

Effect of muscle activation scheme in human head-neck model on estimating cervical spine ligament strain from military volunteer frontal impact data

Gerringer JW, Somasundaram K, Pintar FA

Conformational changes in the activation loop of a bacterial PASTA kinase

Bluma MS, Schultz KM, Kristich CJ, Klug CS

Loss of PBAF promotes expansion and effector differentiation of CD8+ T cells during chronic viral infection and cancer

Kharel A, Shen J, ... Cui W, *et al.*

The effects of cytomegalovirus on brain structure following sport-related concussion

Savitz J, Goeckner BD, ... Meier TB, *et al.*

Lymphocytic Choriomeningitis Virus Clone 13 Infection Results in CD8 T Cell-Mediated Host Mortality in Diacylglycerol Kinase α–Deficient Mice

Kudek MR, Xin G, ... Cui W, *et al.*

Nonparametric failure time: Time-to-event machine learning with heteroskedastic bayesian additive regression trees and low information omnibus dirichlet process mixtures

Sparapani RA, Logan BR, Maiers MJ, Laud PW, McCulloch RE

Fragment-based drug discovery of small molecule ligands for the human chemokine CCL28

Zhou AL, Jensen DR, ... Volkman BF, *et al.*

Comparison of Various Metrics of Repetitive Head Impact Exposure And Their Associations With Neurocognition in Collegiate-Aged Athletes

Amadon GK, Goeckner BD, Brett BL, Meier TB

2022#

Natural variation in the binding pocket of a parasitic flatworm TRPM channel resolves the basis for praziquantel sensitivity

Rohr CM, Sprague DJ, Park S, Marchant JS

Structural studies of human fission protein FIS1 reveal a dynamic region important for GTPase DRP1 recruitment and mitochondrial fission

Egner JM, Nolden KA, ... Hill RB, *et al.*

Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection

Topchyan P, Zander R, ... Cui W, *et al.*

Clonal lineage tracing reveals mechanisms skewing CD8+ T cell fate decisions in chronic infection

Kasmani MY,Zander R, ... Cui W, *et al.*

Tension-bending risk curves for the ATD lower lumbar spine subjected to oblique impact under FAA emergency landing conditions

Somasundaram K, Humm JR, Yoganandan N, Moorcroft DM, Pintar FA

Occupant Injury and Response on Oblique-Facing Aircraft Seats: A Computational Study

Somasundaram K, Humm JR, Khandelwal P, Umale S, Moorcroft DM, Pintar FA

Multi-Omic Integration by Machine Learning (MIMaL)

Dickinson Q, Aufschnaiter A, Ott M, Meyer JG

Group 3 innate lymphoid cells require BATF to regulate gut homeostasis in mice

Wu X, Khatun A, ... Cui W, *et al.*

A single, peri-operative antibiotic can persistently alter the post-operative gut microbiome after Roux-en-Y gastric bypass

Fernando DG, Saravia FL, Atkinson SN, Barron M, Kirby JR, Kindel TL

Bias or biology? Importance of model interpretation in machine learning studies from electronic health records

Momenzadeh A, Shamsa A, Meyer JG

Conformational selection guides b-arrestin recruitment at a biased G protein-coupled receptor

Kleist AB, Jenjak S, ... Volkman BF, *et al.*

Autoreactive CD8 T cells in NOD mice exhibit phenotypic heterogeneity but restricted TCR gene usage

Kasmani MY, Ciecko AE, ... Cui W, *et al.*

Single-cell immune profiling reveals a developmentally distinct CD4+ GM-CSF+ T-cell lineage that induces GI tract GVHD

Piper C, Hainstock E, ... Drobyski WR, *et al.*

Tfh-cell-derived interleukin 21 sustains effector CD8+ T cell responses during chronic viral infection

Zander R, Kasmani MY, ... Cui W, *et al.*

Cytokine and Nitric Oxide-Dependent Gene Regulation in Islet Endocrine and Nonendocrine Cells

Stancill JS, Kasmani MY, Khatun A, Cui W, Corbett JA

The non-ELR CXC chemokine encoded by human cytomegalovirus UL146 genotype 5 contains a C-terminal β-hairpin and induces neutrophil migration as a selective CXCR2 agonist

Berg C, Wedemeyer MJ, ... Lüttichau HR, *et al.*

Investigating the overlapping associations of prior concussion, default mode connectivity, and executive function-based symptoms

Brett BL, Bryant AM, España LY, Mayer AR, Meier TB

BATF promotes group 2 innate lymphoid cell-mediated lung tissue protection during acute respiratory virus infection

Wu X, Kasmani MY, ... Cui W, *et al.*

Enhanced interpretation of 935 hotspot and non-hotspot RAS variants using evidence-based structural bioinformatics

Tripathi S, Dsouza NR, Mathison AJ, Leverence E, Urrutia R, Zimmermann MT

Improved prediction of older adult discharge after trauma using a novel machine learning paradigm

Morris RS, Tignanelli CJ, deRoon-Cassini T, Laud P, Sparapani R

The association between concussion history and increased symptom severity reporting is independent of common medical comorbidities, personality factors, and sleep quality in collegiate athletes

Brett BL, Nelson LD, Meier TB

Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences

Dickinson Q, Meyer JG

2021#

Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level

Zimmermann MT, Mathison AJ, ... Urrutia RA, *et al.*

Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations

Tripathi S, Dsouza NR, Urrutia R, Zimmermann MT

Association of Previous Concussion with Hippocampal Volume and Symptoms in Collegiate-Aged Athletes

Meier TB, España LY, ... Brett BL, *et al.*

Association of Head Impact Exposure with White Matter Macrostructure and Microstructure Metrics

Brett BL, Koch KM, Muftuler LT, Budde M, McCrea MA, Meier TB

Acute post-concussive assessments of brain tissue magnetism using magnetic resonance imaging

Koch KM, Nencka AS, Swearingen B, Bauer A, Meier TB, McCrea MA

P2T2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants

DeVoe E, Oliver GR, ... Zimmermann MT, *et al.*

Influence of cervical spine sagittal alignment on range of motion after corpectomy: a finite element study

John JD, Kumar GS, Yoganandan N, Rajshekhar V

BATF regulates progenitor to cytolytic effector CD8+ T cell transition during chronic viral infection

Chen Y, Zander RA, ... Cui W, *et al.*

E2A-regulated epigenetic landscape promotes memory CD8 T cell differentiation

Schauder DM, Shen J, ... Cui W, *et al.*

Single-cell RNA sequencing of mouse islets exposed to proinflammatory cytokines

Stancill JS, Kasmani MY, Khatun A, Cui W, Corbett JA

Suppressive neutrophils require PIM1 for metabolic fitness and survival during chronic viral infection

Volberding PJ, Xin G, ... Cui W, *et al.*

2020#

Conditional Deletion of PGC-1α Results in Energetic and Functional Defects in NK Cells

Gerbec ZJ, Hashemi E, ... Malarkannan S, *et al.*

The chemokine X-factor: Structure-function analysis of the CXC motif at CXCR4 and ACKR3

Wedemeyer MJ, Mahn SA, ... Volkman BF, *et al.*

Single-cell lineage mapping of a diverse virus-specific naive CD4 T cell repertoire

Khatun A, Kasmani MY, ... Williams MA, *et al.*

Comparative modeling and docking of chemokine-receptor interactions with Rosetta

Wedemeyer MJ, Mueller BK, Bender BJ, Meiler J, Volkman BF

Amygdala response to emotional faces in adolescents with persistent post-concussion symptoms

Bohorquez-Montoya L, España LY, Nader AM, Furger RE, Mayer AR, Meier TB

Accurate segmentation of prostate cancer histomorphometric features using a weakly supervised convolutional neural network

Bukowy JD, Foss H, ... LaViolette PS, *et al.*

Systemic inflammation moderates the association of prior concussion with hippocampal volume and episodic memory in high school and collegiate athletes

Brett BL, Savitz J, ... Meier TB, *et al.*

Genetic variants in DGAT1 cause diverse clinical presentations of malnutrition through a specific molecular mechanism

Gupta A, Dsouza NR, ... Zimmermann MT, *et al.*

Cumulative effects of prior concussion and primary sport participation on brain morphometry in collegiate athletes: a study from the NCAA-DoD CARE consortium

Brett BL, Bobholz SA, ... Meier TB, *et al.*

Resting-state fMRI metrics in acute sport-related concussion and their association with clinical recovery: a study from the NCAA-DOD CARE Consortium

Meier TB, Giraldo-Chica M, ... McCrea MA, *et al.*

Novel destabilizing Dynactin variant (DCTN1 p. Tyr78His) in patient with Perry syndrome

Čierny M, Zimmermann MT ... Brennan R, *et al.*

Optimization of hyperparameters for SMS reconstruction

Muftuler LT, Arpinar VE, ... Nencka AS, *et al.*

Amygdala functional connectivity features in grief: a pilot longitudinal study

Chen G, Ward BD, Claesges SA, Li SJ, Goveas JS

Serial diffusion kurtosis magnetic resonance imaging study during acute, subacute, and recovery periods after sport-related concussion

Muftuler LT, Meier TB, Keith M, Budde MD, Huber DL, McCrea MA

Covalent-fragment screening of BRD4 identifies a ligandable site orthogonal to the acetyl-lysine binding sites

Olp MD, Sprague DJ, ... Smith BC, *et al.*

2019#

Integration of Multi-level Molecular Scoring for the Interpretation of RAS-Family Genetic Variation

Tripathi S, Dsouza NR, Urrutia RA, Zimmermann MT

Modeling the complete chemokine-receptor interaction

Wedemeyer MJ, Mueller BK, Bender BJ, Meiler J, Volkman BF

Prevalence of potentially clinically significant MRI findings in athletes with and without sport-related concussion

Klein AP, Tetzlaff JE, ... Meier TB, *et al.*

Identification and verification of ubiquitin-activated bacterial phospholipases

Tessmer MH, Anderson DM, Pickrum AM, Riegert MO, Frank DW

CD4+ T cell help is required for the formation of a cytolytic CD8+ T cell subset that protects against chronic infection and cancer

Zander R, Schauder D, ... Cui W, *et al.*

2018#

The solution structure of CCL28 reveals structural lability that does not constrain antifungal activity

Thomas MA, He J, Peterson FC, Huppler AR, Volkman BF

mTORC1 and mTORC2 differentially promote natural killer cell development

Yang C, Tsaih SW, Lemke A, Flister MJ, Thakar MS, Malarkannan S

The importance of biologic knowledge and gene expression context for genomic data interpretation

Zimmermann MT

Region-based convolutional neural nets for localization of glomeruli in trichrome-stained whole kidney sections

Bukowy JD, Dayton A, ... Cowley AW, *et al.*

Resting-state functional connectivity after concussion is associated with clinical recovery

Kaushal M, Espana LY, ... Meier TB, *et al.*

Transient receptor potential vanilloid 4 (TRPV4) activation by arachidonic acid requires protein kinase A-mediated phosphorylation

Cao S, Anishkin A, ... Zhang DX, *et al.*

Simulating Airway Collapse in Obstructive Sleep Apnea using Fluid-Structure Interaction Methodologies

Le TB, Garcia GJM

2017#

Development and Validation of 2D Difference Intensity Analysis for Chemical Library Screening by Protein-Detected NMR Spectroscopy

Egner JM, Jensen DR, ... Hill RB, *et al.*

Metabolically Derived Lysine Acylations and Neighboring Modifications Tune the Binding of the BET Bromodomains to Histone H4

Olp MD, Zhu N, Smith BC

2016#

Mechanism of Sirt1 NAD+-dependent Protein Deacetylase Inhibition by Cysteine S-Nitrosation

Kalous KS, Wynia-Smith SL, Olp MD, Smith BC

Summary#

Research Computing has supported research resulting in 103 publications over 11 years.

xychart title "Publications per Year"
    x-axis ["2016", "2017", "2018", "2019", "2020", "2021", "2022", "2023", "2024", "2025", "2026"]
    y-axis "Count" 0 --> 27
    bar [1, 2, 7, 5, 15, 11, 22, 13, 7, 18, 2]