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.
2024#
Bhlhe40 Promotes CD4+ T Helper 1 Cell and Suppresses T Follicular Helper Cell Differentiation during Viral Infection
Nguyen C, Kudek M, Zander R, Niu H, Shen J, Bauer A, Alson D, Khatun A, Chen Y, Sun J, Drobyski W, Edelson BT, Cui W
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, Davies OMT, Tollefson MM, Frieden IJ, Basel D, Urrutia R, Drolet BA, Zimmermann MT
2023#
Bi-allelic variants in HMGCR cause an autosomal-recessive progressive limb-girdle muscular dystrophy
Morales-Rosado JA, Schwab TL, Macklin-Mantia SK, Zimmermann MT, Wierenga KJ, Bönnemann CG, Klee EW
Tensor-valued diffusion MRI of human acute stroke
Zhou M, Stobbe R, Szczepankiewicz F, Budde M, Buck B, Kate M, Lloret M, Fairall P, Butcher K, Shuaib A, Emery D, Nilsson M, Westin C, Beaulieu C
Associations of prior concussion severity with brain microstructure using mean apparent propagator magnetic resonance imaging
Goeckner BD, Brett BL, Mayer AR, España LY, Banerjee A, Muftuler LT, Meier TB
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, Pandey R, Liu P, Therani B, Qiu Q, Rao S, Geurts AM, Cowley AW, Greene AS, Liang M
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, Brown R, Chen Y, Nguyen C, Alson D, Bluemn T, Fan J, Gai K, Zhang B, Kudek M, Zhu N, Cui W
The effects of cytomegalovirus on brain structure following sport-related concussion
Savitz J, Goeckner BD, Ford BN, Teague TK, Zheng H, Harezlak J, Mannix R, Muftuler LT, Brett BL, McCrea MA, Meier TB
Lymphocytic Choriomeningitis Virus Clone 13 Infection Results in CD8 T Cell–Mediated Host Mortality in Diacylglycerol Kinase α–Deficient Mice
Kudek MR, Xin G, Alson D, Holzhauer S, Shen J, Kasmani MY, Riese M, Cui W
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, Peterson FC, Thomas MA, Schlimgen RR, Dwinell MB, Smith BC, Volkman BF
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, Cleland Harwig M, Bonate RP, De Anda J, Tessmer MH, Noey EL, Ihenacho UK, Liu Z, Peterson FC, Wong GCL, Widlansky ME, Hill RB
Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection
Topchyan P, Zander R, Kasmani MY, Nguyen C, Brown A, Lin S, Burns R, Cui W
Clonal lineage tracing reveals mechanisms skewing CD8+ T cell fate decisions in chronic infection
Kasmani MY,Zander R, Chung HK, Chen Y, Khatun A, Damo M, Topchyan P, Johnson KE, Levashova D, Burns R, Lorenz UM, Tarakanova VL, Joshi NS, Kaech SM, Cui W
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, Kasmani MY, Chen Y, Zheng S, Atkinson S, Nguyen C, Burns R, Taparowsky EJ, Salzman NH, Hand TW, Cui W
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, Sente A, Laskowski LJ, Szpakowska M, Calkins MM, Anderson EI, McNally LM, Heukers R, Bobkov V, Peterson FC, Thomas MA, Chevigne A, Smit MJ, McCorvy JD, Babu MM, Volkman BF
Autoreactive CD8 T cells in NOD mice exhibit phenotypic heterogeneity but restricted TCR gene usage
Kasmani MY, Ciecko AE, Brown AK, Petrova G, Gorski J, Chen Y, Cui W
Single-cell immune profiling reveals a developmentally distinct CD4+ GM-CSF+ T-cell lineage that induces GI tract GVHD
Piper C, Hainstock E, Yin-Yuan C, Chen Y, Khatun A, Kasmani MY, Evans J, Miller JA, Gorski J, Cui W, Drobyski, WR
Tfh-cell-derived interleukin 21 sustains effector CD8+ T cell responses during chronic viral infection
Zander R, Kasmani MY, Chen Y, Topchyan P, Shen J, Zheng S, Burns R, Ingram J, Cui C, Joshi N, Craft J, Zajac A, Cui W
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, Melynis M, Schlimgen RR, Hansen LH, Våbenø J, Peterson FC, Volkman BF, Rosenkilde MM, Lüttichau HR
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, Zheng S, Khatun A, Chen Y, Winkler W, Zander R, Burns R, Taparowsky EJ, Sun J, Cui W
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, Stodola T, Evans DB, Abrudan JL, Demos W, Tschannen M, Aldakkak M, Geurts J, Lomberk G, Tsai S, Urrutia RA
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, Kirk AJ, Nader AM, Powell JE, Nelson LD, Mayer AR, Brett BL
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, Zenka R, Blackburn PR, Cousin MA, Boczek NJ, Kocher JA, Urrutia R, Klee EW, Zimmermann MT
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, Wu X, Schauder DM, Kasmani MY, Shen J, Zheng S, Burns R, Taparowsky EJ, Cui W
E2A-regulated epigenetic landscape promotes memory CD8 T cell differentiation
Schauder DM, Shen J, Chen Y, Kasmani MY, Kudek MR, Burns R, Cui W
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, Kasmani MY, Khatun A, Brown AK, Nguyen C, Stancill JS, Martinez E, Corbett JA, Cui W
2020#
Conditional Deletion of PGC-1α Results in Energetic and Functional Defects in NK Cells
Gerbec ZJ, Hashemi E, Nanbakhsh A, Holzhauer S, Yang C, Mei A, Tsaih SW, Lemke A, Flister MJ, Riese MJ, Thakar MS, Malarkannan S
The chemokine X-factor: Structure-function analysis of the CXC motif at CXCR4 and ACKR3
Wedemeyer MJ, Mahn SA, Getschman AE, Crawford KS, Peterson FC, Marchese A, McCorvy JD, Volkman BF
Single-cell lineage mapping of a diverse virus-specific naive CD4 T cell repertoire
Khatun A, Kasmani MY, Zander R, Schauder DM, Snook JP, Shen J, Wu X, Burns R, Chen YG, Lin CW, Williams MA
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, McGarry SD, Lowman AK, Hurrell SL, Iczkowski KA, Banerjee A, Bobholz SA, Barrington A, Dayton A, Unteriner JG, Jacobsohn KM, See WA, Nevalainen MT, Nencka AS, Ethridge T, Jarrard DF, LaViolette PS
Systemic inflammation moderates the association of prior concussion with hippocampal volume and episodic memory in high school and collegiate athletes
Brett BL, Savitz J, Nitta M, Espana L, Teague TK, Nelson LD, McCrea MA, Meier TB
Genetic variants in DGAT1 cause diverse clinical presentations of malnutrition through a specific molecular mechanism
Gupta A, Dsouza NR, Zarate YA, Lombardo R, Hopkin R, Linehan AR, Simpson J, McCarrier J, Agre KE, Gavrilova RH, Stephens MC, Grothe RM, Monaghan KG, Xie Y, Basel D, Urrutia RA, Cole CR, Klee EW, Zimmermann MT
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, España LY, Huber DL, Mayer AR, Harezlak J, Broglio SP, McAllister TW, McCrea MA, Meier TB, CARE Consortium Investigators
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, España LY, Mayer AR, Harezlak J, Nencka AS, Wang Y, Koch KM, Wu YC, Saykin AJ, Giza CC, Goldman J, DiFiori JP, Guskiewicz KM, Mihalik JP, Brooks A, Broglio SP, McAllister T, McCrea MA
Novel destabilizing Dynactin variant (DCTN1 p. Tyr78His) in patient with Perry syndrome
Čierny M, Hooshmand SI, Fee D, Tripathi S, Dsouza NR, Kirschner AL, Zimmermann MT, Brennan R
Optimization of hyperparameters for SMS reconstruction
Muftuler LT, Arpinar VE, Koch K, Bhave S, Yang B, Kaushik S, Banerjee S, Nencka A
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, Goetz CJ, Kathman SG, Wynia-Smith SL, Shishodia S, Summers SB, Xu Z, Statsyuk AV, Smith BC
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, Bonis JM, Nelson LD, Mayer A, Huber DL, Harezlak J, Mathews VP, Ulmer JL, Sinson GP, Nencka AS, Koch KM, Wu YC, Saykin AJ, DiFiori JP, Giza CC, Goldman J, Guskiewicz KK, Mihalik J, Duma SM, Rowson S, Brooks A, Broglio SP, McAllister T, McCrea MA, Meier TB
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, Xin G, Nguyen C, Wu X, Zajac A, Cui W
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, Cloutier D, Manis AD, Staruschenko A, Lombard JH, Woods LC, Beard DA, Cowley AW
Resting-state functional connectivity after concussion is associated with clinical recovery
Kaushal M, Espana LY, Nencka AS, Wang Y, Nelson LD, McCrea MA, Meier TB
Transient receptor potential vanilloid 4 (TRPV4) activation by arachidonic acid requires protein kinase A-mediated phosphorylation
Cao S, Anishkin A, Zinkevich NS, Nishijima Y, Korishettar A, Wang Z, Fang J, Wilcox DA, Zhang DX
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, Olp MD, Kennedy NW, Volkman BF, Peterson FC, Smith BC, Hill RB
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