Publications

2024

Karbelkar AA, Font M, Smith TJ, Sondermann H, O’Toole GA. Reconstitution of a biofilm adhesin system from a sulfate-reducing bacterium in Pseudomonas fluorescens. Proc Natl Acad Sci U S A. 2024 Mar 26;121(13):e2320410121. doi: 10.1073/pnas.2320410121. Epub 2024 Mar 18. PMID: 38498718.
O’Malley AJ, Ran X, An C, Rockmore D. Optimal Physician Shared-Patient Networks and the Diffusion of Medical Technologies. J Data Sci. 2023 Jul;21(3):578-598. doi: 10.6339/22-jds1064. Epub 2022 Aug 30. PMID: 38515560; PMCID: PMC10956597.
O’Toole GA. We have a community problem. J Bacteriol. 2024 Mar 26:e0007324. doi: 10.1128/jb.00073-24. Epub ahead of print. PMID: 38529952.
Tariq D, Maurici N, Bartholomai BM, Chandrasekaran S, Dunlap JC, Bah A, Crane BR. Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock. Elife. 2024 Mar 25;12:RP90259. doi: 10.7554/eLife.90259. PMID: 38526948; PMCID: PMC10963029.
Scodari BT, Schaefer AP, Kapadia NS, Brooks GA, O’Malley AJ, Moen EL. The Association Between Oncology Outreach and Timely Treatment for Rural Patients with Breast Cancer: A Claims-Based Approach. Ann Surg Oncol. 2024 Mar 27. doi: 10.1245/s10434-024-15195-y. Epub ahead of print. PMID: 38538822.
Dai T, Sloop AM, Rahman MR, Sunnerberg JP, Clark MA, Young R, Adamczyk S, Von Voigts-Rhetz P, Patane C, Turk M, Jarvis L, Pogue BW, Gladstone DJ, Bruza P, Zhang R. First Monte Carlo beam model for ultra-high dose rate radiotherapy with a compact electron LINAC. Med Phys. 2024 Mar 17. doi: 10.1002/mp.17031. Epub ahead of print. PMID: 38493501.
Mell LK, Pugh SL, Jones CU, Nelson TJ, Zakeri K, Rose BS, Zeitzer KL, Gore EM, Bahary JP, Souhami L, Michalski JM, Hartford AC, Mishra MV, Roach M 3rd, Parliament MB, Choi KN, Pisansky TM, Husain SM, Malone SC, Horwitz EM, Feng F. Effects of Androgen Deprivation Therapy on Prostate Cancer Outcomes According to Competing Event Risk: Secondary Analysis of a Phase 3 Randomised Trial. Eur Urol. 2024 Apr;85(4):373-381. doi: 10.1016/j.eururo.2023.01.020. Epub 2023 Jan 28. PMID: 36710205; PMCID: PMC10372191.
Davis BA, Chen HY, Ye Z, Ostlund I, Tippani M, Das D, Sripathy SR, Wang Y, Martin JM, Shim G, Panchwagh NM, Moses RL, Farinelli F, Bohlen JF, Li M, Luikart BW, Jaffe AE, Maher BJ. TCF4 Mutations Disrupt Synaptic Function Through Dysregulation of RIMBP2 in Patient-Derived Cortical Neurons. Biol Psychiatry. 2024 Apr 1;95(7):662-675. doi: 10.1016/j.biopsych.2023.07.021. Epub 2023 Aug 10. PMID: 37573005; PMCID: PMC10858293.
Davis BA, Chen HY, Ye Z, Ostlund I, Tippani M, Das D, Sripathy SR, Wang Y, Martin JM, Shim G, Panchwagh NM, Moses RL, Farinelli F, Bohlen JF, Li M, Luikart BW, Jaffe AE, Maher BJ. TCF4 Mutations Disrupt Synaptic Function Through Dysregulation of RIMBP2 in Patient-Derived Cortical Neurons. Biol Psychiatry. 2024 Apr 1;95(7):662-675. doi: 10.1016/j.biopsych.2023.07.021. Epub 2023 Aug 10. PMID: 37573005; PMCID: PMC10858293.
Weiner JA, Natarajan H, McIntosh CJ, Yang ES, Choe M, Papia CL, Axelrod KS, Kovacikova G, Pegu A, Ackerman ME. Selection of positive controls and their impact on anti-drug antibody assay performance. J Immunol Methods. 2024 Mar 11;528:113657. doi: 10.1016/j.jim.2024.113657. Epub ahead of print. PMID: 38479453.
Gemander N, Kemlin D, Depickère S, Kelkar NS, Pannus P, Sharma S, Waegemans A, Olislagers V, Georges D, Dhondt E, Braga M, Heyndrickx L, Michiels J, Thiriard A, Lemy A, Vandevenne M, Goossens ME, Matagne A, Desombere I, Ariën KK, Ackerman ME, Le Moine A, Marchant A. Hybrid Immunity Overcomes Defective Immune Response to COVID-19 Vaccination in Kidney Transplant Recipients. Kidney Int Rep. 2023 Dec 20;9(3):635-648. doi: 10.1016/j.ekir.2023.12.008. PMID: 38481503; PMCID: PMC10928013.
Kelkar NS, Goldberg BS, Dufloo J, Bruel T, Schwartz O, Hessell AJ, Ackerman ME. Sex- and species-associated differences in complement-mediated immunity in humans and rhesus macaques. mBio. 2024 Mar 13;15(3):e0028224. doi: 10.1128/mbio.00282-24. Epub 2024 Feb 22. PMID: 38385704; PMCID: PMC10936177.
Scodari BT, Schaefer AP, Kapadia NS, O’Malley AJ, Brooks GA, Tosteson ANA, Onega T, Wang C, Wang F, Moen EL. Characterizing the Traveling Oncology Workforce and Its Influence on Patient Travel Burden: A Claims-Based Approach. JCO Oncol Pract. 2024 Feb 22:OP2300690. doi: 10.1200/OP.23.00690. Epub ahead of print. PMID: 38386962.
Yen RW, Hagedorn R, Durand MA, Leyenaar JK, O’Malley AJ, Saunders CH, Isaacs T, Elwyn G. Clinician-Spoken Plain Language in Health Care Encounters: A Qualitative Analysis to Assess Measurable Elements. Acad Med. 2024 Feb 27. doi: 10.1097/ACM.0000000000005666. Epub ahead of print. PMID: 38412476.
Stevanovic M, Teuber Carvalho JP, Bittihn P, Schultz D. Dynamical model of antibiotic responses linking expression of resistance genes to metabolism explains emergence of heterogeneity during drug exposures. Phys Biol. 2024 Feb 27. doi: 10.1088/1478-3975/ad2d64. Epub ahead of print. PMID: 38412523.
de Anda J, Kuchma SL, Webster SS, Boromand A, Lewis KA, Lee CK, Contreras M, Medeiros Pereira VF, Schmidt W, Hogan DA, O’Hern CS, O’Toole GA, Wong GCL. How P. aeruginosa cells with diverse stator composition collectively swarm. mBio. 2024 Mar 1:e0332223. doi: 10.1128/mbio.03322-23. Epub ahead of print. PMID: 38426789.
Li Z, Barnaby R, Nymon AB, Roche C, Koeppen K, Ashare A, Hogan DA, Gerber SA, Taatjes DJ, Hampton TH, Stanton BA. P. aeruginosa tRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in Cystic Fibrosis. Am J Physiol Lung Cell Mol Physiol. 2024 Mar 5. doi: 10.1152/ajplung.00018.2024. Epub ahead of print. PMID: 38440830.
Bagheri M, Lee MK, Muller KE, Miller TW, Pattabiraman DR, Christensen BC. Alteration of DNA methyltransferases by eribulin elicits broad DNA methylation changes with potential therapeutic implications for triple-negative breast cancer. Epigenomics. 2024 Mar;16(5):293-308. doi: 10.2217/epi-2023-0339. Epub 2024 Feb 15. PMID: 38356412; PMCID: PMC10910603.
Arakelyan M, Freyleue SD, Schaefer AP, Austin AM, Moen EL, O’Malley AJ, Goodman DC, Leyenaar JK. Rural-urban disparities in health care delivery for children with medical complexity and moderating effects of payer, disability, and community poverty. J Rural Health. 2024 Mar;40(2):326-337. doi: 10.1111/jrh.12827. Epub 2024 Feb 20. PMID: 38379187; PMCID: PMC10954394.
Ross AE, Zhang J, Huang HC, Yamashita R, Keim-Malpass J, Simko JP, DeVries S, Morgan TM, Souhami L, Dobelbower MC, McGinnis LS, Jones CU, Dess RT, Zeitzer KL, Choi K, Hartford AC, Michalski JM, Raben A, Gomella LG, Sartor AO, Rosenthal SA, Sandler HM, Spratt DE, Pugh SL, Mohamad O, Esteva A, Chen E, Schaeffer EM, Tran PT, Feng FY. External Validation of a Digital Pathology-based Multimodal Artificial Intelligence Architecture in the NRG/RTOG 9902 Phase 3 Trial. Eur Urol Oncol. 2024 Jan 31:S2588-9311(24)00029-4. doi: 10.1016/j.euo.2024.01.004. Epub ahead of print. PMID: 38302323.
Mak KS, Scannell Bryan M, Dignam JJ, Shipley WU, Lin Y, Peters CA, Gore EM, Rosenthal SA, Zeitzer KL, D’Souza DP, Horwitz EM, Pisansky TM, Maier JM, Chafe SM, Robin TP, Roach M 3rd, Tran PT, Souhami L, Michalski JM, Hartford AC, Feng FY, Sandler HM, Efstathiou JA. Cardiovascular Mortality and Duration of Androgen Deprivation in Locally Advanced Prostate Cancer: Long-term Update of NRG/RTOG 9202. Eur Urol Focus. 2024 Feb 1:S2405-4569(24)00011-7. doi: 10.1016/j.euf.2024.01.008. Epub ahead of print. PMID: 38307806.
Zhao S, Crouse W, Qian S, Luo K, Stephens M, He X. Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits. Nat Genet. 2024 Feb;56(2):336-347. doi: 10.1038/s41588-023-01648-9. Epub 2024 Jan 26. PMID: 38279041; PMCID: PMC10864181.
Zhou Y, Song L, Li H. Full resolution HLA and KIR genes annotation for human genome assemblies. bioRxiv [Preprint]. 2024 Jan 23:2024.01.20.576452. doi: 10.1101/2024.01.20.576452. PMID: 38328160; PMCID: PMC10849470.
Muse ME, Armstrong DA, Hoen AG, Gilbert-Diamond D, Gui J, Palys TJ, Kolling FW, Christensen BC, Karagas MR, Howe CG. Maternal-Infant Factors in Relation to Extracellular Vesicle and Particle miRNA in Prenatal Plasma and in Postpartum Human Milk. Int J Mol Sci. 2024 Jan 26;25(3):1538. doi: 10.3390/ijms25031538. PMID: 38338815; PMCID: PMC10855220.
Barrack KE, Hampton TH, Valls RA, Surve SV, Gardner TB, Sanville JL, Madan JL, O’Toole GA. An in vitro medium for modeling gut dysbiosis associated with cystic fibrosis. J Bacteriol. 2024 Jan 25;206(1):e0028623. doi: 10.1128/jb.00286-23. Epub 2024 Jan 3. PMID: 38169295; PMCID: PMC10810206.
Davis MJ, Srinivasan G, Chacko R, Chen S, Suvarna A, Vaickus LJ, Torres VC, Hodge S, Chen EY, Preum S, Samkoe KS, Christensen BC, LeBoeuf MR, Levy JJ. A deep learning algorithm to detect cutaneous squamous cell carcinoma on frozen sections in Mohs micrographic surgery: A retrospective assessment. Exp Dermatol. 2024 Jan;33(1):e14949. doi: 10.1111/exd.14949. Epub 2023 Oct 21. PMID: 37864429.
Lo Y, Lester SC, Ellis IO, Lanjewar S, Laurini J, Patel A, Bhattarai A, Ustun B, Harmon B, Kleer CG, Ross D, Amin A, Wang Y, Bradley R, Turashvili G, Zeng J, Baum J, Singh K, Hakima L, Harigopal M, Komforti M, Shin SJ, Abbott SE, Jaffer S, Badve SS, Khoury T, D’Alfonso TM, Ginter PS, Collins V, Towne W, Gan Y, Nassar A, Sahin AA, Flieder A, Aldrees R, Ngo MH, Edema U, Sapna F, Schnitt SJ, Fineberg SA. Identification of Glandular (Acinar)/Tubule Formation in Invasive Carcinoma of the Breast: A Study to Determine Concordance Using the World Health Organization Definition. Arch Pathol Lab Med. 2024 Jan 20. doi: 10.5858/arpa.2023-0163-OA. Epub ahead of print. PMID: 38244086.
Chen JQ, Salas LA, Wiencke JK, Koestler DC, Molinaro AM, Andrew AS, Seigne JD, Karagas MR, Kelsey KT, Christensen BC. Matched analysis of detailed peripheral blood and tumor immune microenvironment profiles in bladder cancer. Epigenomics. 2024 Jan;16(1):41-56. doi: 10.2217/epi-2023-0358. Epub 2024 Jan 15. PMID: 38221889; PMCID: PMC10804212.
Frost HR. Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue. PLoS Comput Biol. 2024 Jan 11;20(1):e1011717. doi: 10.1371/journal.pcbi.1011717. PMID: 38206988; PMCID: PMC10807770.
Srinivasan G, Davis MJ, LeBoeuf MR, Fatemi M, Azher ZL, Lu Y, Diallo AB, Saldias Montivero MK, Kolling FW, Perrard L, Salas LA, Christensen BC, Palys TJ, Karagas MR, Palisoul SM, Tsongalis GJ, Vaickus LJ, Preum SM, Levy JJ. Potential to Enhance Large Scale Molecular Assessments of Skin Photoaging through Virtual Inference of Spatial Transcriptomics from Routine Staining. Pac Symp Biocomput. 2024;29:477-491. PMID: 38160301.
Azher ZL, Fatemi M, Lu Y, Srinivasan G, Diallo AB, Christensen BC, Salas LA, Kolling FW, Perreard L, Palisoul SM, Vaickus LJ, Levy JJ. Spatial Omics Driven Crossmodal Pretraining Applied to Graph-based Deep Learning for Cancer Pathology Analysis. Pac Symp Biocomput. 2024;29:464-476. PMID: 38160300; PMCID: PMC10783797.
Price CE, Valls RA, Ramsey AR, Loeven NA, Jones JT, Barrack KE, Schwartzman JD, Royce DB, Cramer RA, Madan JC, Ross BD, Bliska J, O’Toole GA. Intestinal Bacteroides modulates inflammation, systemic cytokines, and microbial ecology via propionate in a mouse model of cystic fibrosis. mBio. 2024 Jan 5:e0314423. doi: 10.1128/mbio.03144-23. Epub ahead of print. PMID: 38179971.
Van Loon JC, Whitfield GB, Wong N, O’Neal L, Henrickson A, Demeler B, O’Toole GA, Parsek MR, Howell PL. Binding of GTP to BifA is required for the production of Pel-dependent biofilms inPseudomonas aeruginosa. J Bacteriol. 2024 Jan 10:e0033123. doi: 10.1128/jb.00331-23. Epub ahead of print. PMID: 38197635.
O’Toole GA. 2023 Jack Kenney Award for Outstanding Service. J Bacteriol. 2024 Jan 25;206(1):e0038523. doi: 10.1128/jb.00385-23. Epub 2024 Jan 3. PMID: 38168601; PMCID: PMC10809996.
Levy JJ, Davis MJ, Chacko RS, Davis MJ, Fu LJ, Goel T, Pamal A, Nafi I, Angirekula A, Suvarna A, Vempati R, Christensen BC, Hayden MS, Vaickus LJ, LeBoeuf MR. Intraoperative margin assessment for basal cell carcinoma with deep learning and histologic tumor mapping to surgical site. NPJ Precis Oncol. 2024 Jan 3;8(1):2. doi: 10.1038/s41698-023-00477-7. PMID: 38172524; PMCID: PMC10764333.
Reynolds SR, Zhang Z, Salas LA, Christensen BC. Tumor microenvironment deconvolution identifies cell-type-independent aberrant DNA methylation and gene expression in prostate cancer. Clin Epigenetics. 2024 Jan 3;16(1):5. doi: 10.1186/s13148-023-01609-3. PMID: 38173042; PMCID: PMC10765773.

2023

Zhang Z, Reynolds SR, Stolrow HG, Chen JQ, Christensen BC, Salas LA. Deciphering the role of immune cell composition in epigenetic age acceleration: Insights from cell-type deconvolution applied to human blood epigenetic clocks. Aging Cell. 2023 Dec 25:e14071. doi: 10.1111/acel.14071. Epub ahead of print. PMID: 38146185.
Renier TJ, Yeum D, Emond JA, Lansigan RK, Ballarino GA, Carlson DD, Loos RJF, Gilbert-Diamond D. Elucidating pathways to pediatric obesity: a study evaluating obesity polygenic risk scores related to appetitive traits in children. Int J Obes (Lond). 2024 Jan;48(1):71-77. doi: 10.1038/s41366-023-01385-3. Epub 2023 Sep 22. PMID: 37736781.
Reynolds SR, Salas LA, Chen JQ, Christensen BC. Detailed immune profiling in pediatric Crohn’s disease using methylation cytometry. Epigenetics. 2024 Dec;19(1):2289786. doi: 10.1080/15592294.2023.2289786. Epub 2023 Dec 13. PMID: 38090774; PMCID: PMC10761011.
Mindiola Romero AE, Tafe LJ, Green DC, Deharvengt SJ, Winnick KN, Tsongalis GJ, Baker ML, Linos K, Levy JJ, Kerr DA. Utility of Retrospective Molecular Analysis in Diagnostically Challenging Mesenchymal Neoplasms. Int J Surg Pathol. 2023 Dec;31(8):1473-1484. doi: 10.1177/10668969231157783. Epub 2023 Mar 13. PMID: 36911994.
Wang Y, Guo S, Opfermann JD, Kaluna J, Gensheimer BG, Krieger A, Kang JU. Common-path optical coherence tomography guided vertical pneumodissection for DALK. Proc SPIE Int Soc Opt Eng. 2023 Feb;12372:1237204. doi: 10.1117/12.2650533. Epub 2023 Mar 6. PMID: 38090625; PMCID: PMC10714572.
Howe CG, Armstrong DA, Muse ME, Gilbert-Diamond D, Gui J, Hoen AG, Palys TJ, Barnaby RL, Stanton BA, Jackson BP, Christensen BC, Karagas MR. Periconceptional and Prenatal Exposure to Metals and Extracellular Vesicle and Particle miRNAs in Human Milk: A Pilot Study. Expo Health. 2023 Dec;15(4):731-743. doi: 10.1007/s12403-022-00520-1. Epub 2022 Nov 3. PMID: 38074282; PMCID: PMC10707483.
Mohan D, O’Malley AJ, Chelen J, MacMartin M, Murphy M, Rudolph M, Engel JA, Barnato AE. Using a Video Game Intervention to Increase Hospitalists’ Advance Care Planning Conversations with Older Adults: a Stepped Wedge Randomized Clinical Trial. J Gen Intern Med. 2023 Nov;38(14):3224-3234. doi: 10.1007/s11606-023-08297-y. Epub 2023 Jul 10. PMID: 37429972; PMCID: PMC10651818.
Mitchell K, Panicker SS, Adler CL, O’Toole GA, Hixon KR. Antibacterial Efficacy of Manuka Honey-Doped Chitosan-Gelatin Cryogel and Hydrogel Scaffolds in Reducing Infection. Gels. 2023 Nov 6;9(11):877. doi: 10.3390/gels9110877. PMID: 37998967; PMCID: PMC10670823.
Song L, Langmead B. Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification. bioRxiv [Preprint]. 2023 Nov 17:2023.11.15.567129. doi: 10.1101/2023.11.15.567129. PMID: 38014029; PMCID: PMC10680779.
Neff SL, Hampton TH, Koeppen K, Sarkar S, Latario CJ, Ross BD, Stanton BA. Rocket-miR, a translational launchpad for miRNA-based antimicrobial drug development. mSystems. 2023 Dec 21;8(6):e0065323. doi: 10.1128/msystems.00653-23. Epub 2023 Nov 17. PMID: 37975659; PMCID: PMC10734502.
Mitchell K, Panicker SS, Adler CL, O’Toole GA, Hixon KR. Antibacterial Efficacy of Manuka Honey-Doped Chitosan-Gelatin Cryogel and Hydrogel Scaffolds in Reducing Infection. Gels. 2023 Nov 6;9(11):877. doi: 10.3390/gels9110877. PMID: 37998967; PMCID: PMC10670823.
Li C, Fan X, Aronson JP, Hong J, Khan T, Paulsen KD. Model-based image updating in deep brain stimulation with assimilation of deep brain sparse data. Med Phys. 2023 Dec;50(12):7904-7920. doi: 10.1002/mp.16578. Epub 2023 Jul 7. PMID: 37418478.
Bobak CA, Mohan D, Murphy MA, Barnato AE, O’Malley AJ. Constructing within and between hospital physician social networks for modeling physician research participation. BMC Med Res Methodol. 2023 Oct 28;23(1):253. doi: 10.1186/s12874-023-02069-2. PMID: 37898745; PMCID: PMC10613378.
Robitaille S, Simmons EL, Verster AJ, McClure EA, Royce DB, Trus E, Swartz K, Schultz D, Nadell CD, Ross BD. Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria. Nat Ecol Evol. 2023 Dec;7(12):2092-2107. doi: 10.1038/s41559-023-02230-6. Epub 2023 Oct 26. PMID: 37884689.
Zeitler EP, Joly J, Leggett CG, Wong SL, O’Malley AJ, Kraft SA, Mackwood MB, Jones ST, Skinner JS. The role of comorbidities, medications, and social determinants of health in understanding urban-rural outcome differences among patients with heart failure. J Rural Health. 2023 Oct 22. doi: 10.1111/jrh.12803. Epub ahead of print. PMID: 37867249.
Zhao X, Yang M, Fan J, Wang M, Wang Y, Qin N, Zhu M, Jiang Y, Gorlova OY, Gorlov IP, Albanes D, Lam S, Tardón A, Chen C, Goodman GE, Bojesen SE, Landi MT, Johansson M, Risch A, Wichmann HE, Bickeböller H, Christiani DC, Rennert G, Arnold SM, Brennan P, Field JK, Shete S, Le Marchand L, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Zienolddiny S, Grankvist K, Johansson M, Caporaso NE, Woll PJ, Lazarus P, Schabath MB, Aldrich MC, Patel AV, Davies MPA, Ma H, Jin G, Hu Z, Amos CI, Shen H, Dai J. Identification of genetically predicted DNA methylation markers associated with non-small cell lung cancer risk among 34,964 cases and 448,579 controls. Cancer. 2023 Dec 6. doi: 10.1002/cncr.35130. Epub ahead of print. PMID: 38055287.

Torres GM, Jarnagin HC, Park C, Yang H, Kosarek NN, Bhandari R, Wang CY, Kolling FW, Whitfield ML, Turk MJ, Liby KT, Pioli PA. (2023). CDDO-Methyl Ester Inhibits BRAF Inhibitor Resistance and Remodels the Myeloid Compartment in BRAF-mutant Melanoma. bioRxiv. PMID: 37577680 PMCID: PMC10418171

Traphagen NA, Schwartz GN, Tau S, Roberts AM, Jiang A, Hosford SR, Marotti JD, Goen AE, Romo BA, Johnson AL, Duffy EK, Demidenko E, Heverly P, Mosesson Y, Soucy SM, Kolling F, Miller TW. (2023) Estrogen Therapy Induces Receptor-Dependent DNA Damage Enhanced by PARP Inhibition in ER+ Breast Cancer. Clin Cancer Res. 15;29(18):3717-3728. PMID: 37439680 PMCID: PMC10528687

Schwartz GN, Kaufman PA, Giridhar KV, Marotti JD, Chamberlin MD, Arrick BA, Makari-Judson G, Goetz MP, Soucy SM, Kolling F, Demidenko E, Miller TW. (2023). Alternating 17β-Estradiol and Aromatase Inhibitor Therapies Is Efficacious in Postmenopausal Women with Advanced Endocrine-Resistant ER+ Breast Cancer. Clin Cancer Res. 1;29(15):2767-2773. PMID: 37260292 CITED no PMCID

Preiss NK, Kamal Y, Wilkins OM, Li C, Kolling FW 4th, Trask HW, Usherwood YK, Cheng C, Frost HR, Usherwood EJ. (2023) Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20. Life Sci Alliance. 6;6(9):e202201683. PMID: 37414528 PMCID: PMC10326419

Tedbury PR, Manfredi C, Degenhardt F, Conway J, Horwath MC, McCracken C, Sorscher AJ, Moreau S, Wright C, Edwards C, Brewer J, Guarner J, de Wit E, Williamson BN, Suthar MS, Ong YT, Roback JD, Alter DN, Holter JC, Karlsen TH, Sacchi N, Romero-Gómez M, Invernizzi P, Fernández J, Buti M, Albillos A, Julià A, Valenti L, Asselta R, Banales JM, Bujanda L, de Cid R, Franke A; Severe COVID-19 GWAS group; Sarafianos SG, Hong JS, Sorscher EJ, Ehrhardt A. Mechanisms by which the cystic fibrosis transmembrane conductance regulator may influence SARS-CoV-2 infection and COVID-19 disease severity. FASEB J. 2023 Nov;37(11):e23220. doi: 10.1096/fj.202300077R. PMID: 37801035; PMCID: PMC10760435.
Politi MC, Forcino RC, Parrish K, Durand MA, O’Malley AJ, Moses R, Cooksey K, Elwyn G. The impact of adding cost information to a conversation aid to support shared decision making about low-risk prostate cancer treatment: Results of a stepped-wedge cluster randomised trial. Health Expect. 2023 Oct;26(5):2023-2039. doi: 10.1111/hex.13810. Epub 2023 Jul 2. PMID: 37394739; PMCID: PMC10485319.
Carpenter MC, Souter SC, Zipkin RJ, Ackerman ME. Current Insights Into K-associated Fetal Anemia and Potential Treatment Strategies for Sensitized Pregnancies. Transfus Med Rev. 2024 Jan;38(1):150779. doi: 10.1016/j.tmrv.2023.150779. Epub 2023 Oct 15. PMID: 37926651.
Jones JT, Morelli KA, Vesely EM, Puerner CTS, Pavuluri CK, Ross BS, van Rhijn N, Bromley MJ, Cramer RA. The cystic fibrosis treatment Trikafta affects the growth, viability, and cell wall of Aspergillus fumigatus biofilms. mBio. 2023 Oct 31;14(5):e0151623. doi: 10.1128/mbio.01516-23. Epub 2023 Oct 13. PMID: 37830825; PMCID: PMC10653927.
Ganguli I, Mackwood MB, Yang CW, Crawford M, Mulligan KL, O’Malley AJ, Fisher ES, Morden NE. Racial differences in low value care among older adult Medicare patients in US health systems: retrospective cohort study. BMJ. 2023 Oct 25;383:e074908. doi: 10.1136/bmj-2023-074908. PMID: 37879735; PMCID: PMC10599254.
Wang L, Wong YC, Correira JM, Wancura M, Geiger CJ, Webster SS, Touhami A, Butler BJ, O’Toole GA, Langford RM, Brown KA, Dortdivanlioglu B, Webb L, Cosgriff-Hernandez E, Gordon VD. The accumulation and growth of Pseudomonas aeruginosa on surfaces is modulated by surface mechanics via cyclic-di-GMP signaling. NPJ Biofilms Microbiomes. 2023 Oct 10;9(1):78. doi: 10.1038/s41522-023-00436-x. PMID: 37816780; PMCID: PMC10564899.
Chen HW, Zhu JL, Martyanov V, Tsoi LC, Johnson ME, Barber G, Popovich D, O’Brien JC, Coias J, Cyrus N, Malviya N, Florez-Pollack S, Kunzler E, Hosler GA, Gudjonsson JE, Khanna D, Whitfield M, Jacobe HT. Gene Expression Signatures in Inflammatory and Sclerotic Morphea Skin and Sera Distinguish Morphea from Systemic Sclerosis. J Invest Dermatol. 2023 Oct;143(10):1886-1895.e10. doi: 10.1016/j.jid.2023.02.036. Epub 2023 Apr 6. PMID: 37028702.
Nguyen ED, Fard VN, Kim BY, Collins S, Galey M, Nelson BR, Wakenight P, Gable SM, McKenna A, Bammler TK, MacDonald J, Okamura DM, Shendure J, Beier DR, Ramirez JM, Majesky MW, Millen KJ, Tollis M, Miller DE. Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus). G3 (Bethesda). 2023 Sep 30;13(10):jkad177. doi: 10.1093/g3journal/jkad177. PMID: 37552705; PMCID: PMC10542272.
Kesthely CA, Rogers RR, El Hafi B, Jean-Pierre F, O’Toole GA. Transcriptional profiling and genetic analysis of a cystic fibrosis airway-relevant model shows asymmetric responses to growth in a polymicrobial community. Microbiol Spectr. 2023 Sep 29;11(5):e0220123. doi: 10.1128/spectrum.02201-23. Epub ahead of print. PMID: 37772884; PMCID: PMC10580927.
Martinez Coconubo D, Levy JJ, Kerr DA, Vaickus LJ, Vidis L, Glass RE, Gutmann EJ, Marotti JD, Liu X. Use of molecular testing results to analyze the overuse of atypia of undetermined significance in thyroid cytology. J Am Soc Cytopathol. 2023 Nov-Dec;12(6):451-460. doi: 10.1016/j.jasc.2023.09.002. Epub 2023 Sep 7. PMID: 37775434.
O’Toole GA. Double-anonymous peer review comes to JB. J Bacteriol. 2023 Oct 26;205(10):e0008022. doi: 10.1128/jb.00080-22. Epub 2023 Sep 25. PMID: 37747191; PMCID: PMC10601697.
Leyenaar JK, Freyleue SD, Arakelyan M, Goodman DC, O’Malley AJ. Pediatric Hospitalizations at Rural and Urban Teaching and Nonteaching Hospitals in the US, 2009-2019. JAMA Netw Open. 2023 Sep 5;6(9):e2331807. doi: 10.1001/jamanetworkopen.2023.31807. PMID: 37656457; PMCID: PMC10474556.
Moen EL, Schmidt RO, Onega T, Brooks GA, O’Malley AJ. Association between a network-based physician linchpin score and cancer patient mortality: A SEER-Medicare analysis. J Natl Cancer Inst. 2023 Sep 7:djad180. doi: 10.1093/jnci/djad180. Epub ahead of print. PMID: 37676831.
Pastora AB, O’Toole GA. The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens. J Bacteriol. 2023 Sep 26;205(9):e0015223. doi: 10.1128/jb.00152-23. Epub 2023 Sep 1. PMID: 37655913; PMCID: PMC10521353.
Levy JJ, Chan N, Marotti JD, Rodrigues NJ, Ismail AAO, Kerr DA, Gutmann EJ, Glass RE, Dodge CP, Suriawinata AA, Christensen BC, Liu X, Vaickus LJ. Examining longitudinal markers of bladder cancer recurrence through a semiautonomous machine learning system for quantifying specimen atypia from urine cytology. Cancer Cytopathol. 2023 Sep;131(9):561-573. doi: 10.1002/cncy.22725. Epub 2023 Jun 26. PMID: 37358142; PMCID: PMC10527805.
Khayal IS, O’Malley AJ, Barnato AE. Clinically informed machine learning elucidates the shape of hospice racial disparities within hospitals. NPJ Digit Med. 2023 Oct 12;6(1):190. doi: 10.1038/s41746-023-00925-5. PMID: 37828119; PMCID: PMC10570342.
Sobieszczyk ME, Mannheimer S, Paez CA, Yu C, Gamble T, Theodore DA, Chege W, Yacovone M, Hanscom B, Heptinstall J, Seaton KE, Zhang L, Miner MD, Eaton A, Weiner JA, Mayer K, Kalams S, Stephenson K, Julg B, Caskey M, Nussenzweig M, Gama L, Barouch DH, Ackerman ME, Tomaras GD, Huang Y, Montefiori D; HVTN 130/HPTN 089 Study Team. Safety, tolerability, pharmacokinetics, and immunological activity of dual-combinations and triple-combinations of anti-HIV monoclonal antibodies PGT121, PGDM1400, 10-1074, and VRC07-523LS administered intravenously to HIV-uninfected adults: a phase 1 randomised trial. Lancet HIV. 2023 Oct;10(10):e653-e662. doi: 10.1016/S2352-3018(23)00140-6. PMID: 37802566; PMCID: PMC10629933.
Brooks GA, Tomaino MR, Ramkumar N, Wang Q, Kapadia NS, O’Malley AJ, Wong SL, Loehrer AP, Tosteson ANA. Association of rurality, socioeconomic status, and race with pancreatic cancer surgical treatment and survival. J Natl Cancer Inst. 2023 Oct 9;115(10):1171-1178. doi: 10.1093/jnci/djad102. PMID: 37233399; PMCID: PMC10560598.
Spencer ZT, Ng VH, Benchabane H, Siddiqui GS, Duwadi D, Maines B, Bryant JM, Schwarzkopf A, Yuan K, Kassel SN, Mishra A, Pimentel A, Lebensohn AM, Rohatgi R, Gerber SA, Robbins DJ, Lee E, Ahmed Y. The USP46 deubiquitylase complex increases Wingless/Wnt signaling strength by stabilizing Arrow/LRP6. Nat Commun. 2023 Oct 5;14(1):6174. doi: 10.1038/s41467-023-41843-0. PMID: 37798281; PMCID: PMC10556106.
Chen JQ, Salas LA, Wiencke JK, Koestler DC, Molinaro AM, Andrew AS, Seigne JD, Karagas MR, Kelsey KT, Christensen BC. Genome-Scale Methylation Analysis Identifies Immune Profiles and Age Acceleration Associations with Bladder Cancer Outcomes. Cancer Epidemiol Biomarkers Prev. 2023 Oct 2;32(10):1328-1337. doi: 10.1158/1055-9965.EPI-23-0331. PMID: 37527159; PMCID: PMC10543967.

Javaid A, Frost HR (2023). STREAK: A Supervised Cell Surface Receptor Abundance Estimation Strategy for Single Cell RNA-Sequencing Data using Feature Selection and Thresholded Gene Set Scoring. PLOS Computational Biology. PMID: 37603589 PMCID: PMC10470905

Frost HR (2023). Reconstruction Set Test (RESET): a computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error. bioRxiv https://doi.org/10.1101/2023.04.03.535366 PMID: 37066315 PMCID: PMC10104009

Schiebout CT, Lust HE, Huang YH, Frost HR (2023). Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA). Bioinformatics Advances. PMID: 37745004 PMCID: PMC10516525

Price CE, Hampton TH, Valls RA, Barrack KE, O’Toole GA, Madan JC, Coker MO. Development of the intestinal microbiome in cystic fibrosis in early life. mSphere. 2023 Aug 24;8(4):e0004623. doi: 10.1128/msphere.00046-23. Epub 2023 Jul 5. PMID: 37404016; PMCID: PMC10449510.
Glaubitz A, Fu F. Population heterogeneity in vaccine coverage impacts epidemic thresholds and bifurcation dynamics. Heliyon. 2023 Aug 21;9(9):e19094. doi: 10.1016/j.heliyon.2023.e19094. PMID: 37810104; PMCID: PMC10558294.

Gnecco JS, Brown A, Buttrey K, Ives C, Goods BA, Baugh L, Hernandez-Gordillo V, Loring M, Isaacson KB, Griffith LG. Organoid co-culture model of the human endometrium in a fully synthetic extracellular matrix enables the study of epithelial-stromal crosstalk. Med. 2023 Aug 11;4(8):554-579.e9. doi: 10.1016/j.medj.2023.07.004. PMID: 37572651

Zhang J, Russo DD, Wang Y, Zhang Q, Zelinski MB, Shalek AK, Goods BA, Xiao S. Vitrification preserves follicular transcriptomic dynamics during ex vivo ovulation†. Biol Reprod. 2023 Sep 12;109(3):240-243. doi: 10.1093/biolre/ioad083. PMID: 37498173; PMCID: PMC10502570.

Stevanovic M, Carvalho JPT, Bittihn P, Schultz D. (2023) Dynamical model of antibiotic responses linking expression of resistance to metabolism explains emergence of heterogeneity during drug exposures. bioRxiv: doi.org/10.1101/2023.09.22.558994 CITED –

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Columbo JA, Stone DH, Martinez-Camblor P, Goodney PP, O’Malley AJ. Adoption and Diffusion of Transcarotid Artery Revascularization in Contemporary Practice. Circ Cardiovasc Interv. 2023 Sep;16(9):e012805. doi: 10.1161/CIRCINTERVENTIONS.122.012805. Epub 2023 Sep 19. PMID: 37725675; PMCID: PMC10516509.
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Levy JJ, Chan N, Marotti JD, Kerr DA, Gutmann EJ, Glass RE, Dodge CP, Suriawinata AA, Christensen BC, Liu X, Vaickus LJ. Large-scale validation study of an improved semiautonomous urine cytology assessment tool: AutoParis-X. Cancer Cytopathol. 2023 Oct;131(10):637-654. doi: 10.1002/cncy.22732. Epub 2023 Jun 28. PMID: 37377320.

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Jeffrey L. Brabec, Montana Kay Lara, Anna L. Tyler, J. Matthew Mahoney. A multi-network approach to Alzheimer’s Disease gene prioritization complements cis-regulatory prioritization with molecular quantitative trait loci. bioRxiv [Preprint]. 2023 May 3. doi: 10.1101/2023.05.03.539189

Tyler AL, Spruce C, Kursawe R, Haber A, Ball RL, Pitman WA, Fine AD, Raghupathy N, Walker M, Philip VM, Baker CL, Mahoney JM, Churchill GA, Trowbridge JJ, Stitzel ML, Paigen K, Petkov PM, Carter GW. Variation in histone configurations correlates with gene expression across nine inbred strains of mice. Genome Res. 2023 Jun;33(6):857-871. doi: 10.1101/gr.277467.122. Epub 2023 May 22. PMID: 37217254; PMCID: PMC10519406.

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Rawat K, Tewari A, Li X, Mara AB, King WT, Gibbings SL, Nnam CF, Kolling FW, Lambrecht BN, Jakubzick CV. CCL5-producing migratory dendritic cells guide CCR5+ monocytes into the draining lymph nodes. J Exp Med. 2023 Jun 5;220(6):e20222129. doi: 10.1084/jem.20222129. Epub 2023 Mar 22. PMID: 36946983; PMCID: PMC10072223.

Bagheri M, Mohamed GA, Ashick M, Saleem M, Ognjenovic NB, Lu H, Kolling FW, Wilkins OM, Das S, Croix IS, Nagaraj SH, Muller KE, Gerber SA, Miller TW, Pattabiraman DR. Pharmacological Induction of mesenchymal-epithelial transition chemosensitizes breast cancer cells and prevents metastatic progression. bioRxiv. 2023 Apr 21;. doi: 10.1101/2023.04.19.537586. PubMed PMID: 37131809;
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Zhang Z, Lu Y, Vosoughi S, Levy JJ, Christensen BC, Salas LA. HiTAIC: hierarchical tumor artificial intelligence classifier traces tissue of origin and tumor type in primary and metastasized tumors using DNA methylation. NAR Cancer. 2023 Apr 19;5(2):zcad017. doi: 10.1093/narcan/zcad017. PMID: 37089814; PMCID: PMC10113876.

Zhang J, Goods BA, Pattarawat P, Wang Y, Haining T, Zhang Q, Shalek AK, Duncan FE, Woodruff TK, Xiao S. An ex vivo ovulation system enables the discovery of novel ovulatory pathways and nonhormonal contraceptive candidates†. Biol Reprod. 2023 Apr 11;108(4):629-644. doi: 10.1093/biolre/ioad009. PMID: 36708230; PMCID: PMC10106841.

Levy JJ, Zavras JP, Veziroglu EM, Nasir-Moin M, Kolling FW, Christensen BC, Salas LA, Barney RE, Palisoul SM, Ren B, Liu X, Kerr DA, Pointer KB, Tsongalis GJ, Vaickus LJ. Identification of Spatial Proteomic Signatures of Colon Tumor Metastasis: A Digital Spatial Profiling Approach. Am J Pathol. 2023 Apr 8:S0002-9440(23)00123-2. doi: 10.1016/j.ajpath.2023.02.020. Epub ahead of print. PMID: 37037284.

Fatemi M, Feng E, Sharma C, Azher Z, Goel T, Ramwala O, Palisoul SM, Barney RE, Perreard L, Kolling FW, Salas LA, Christensen BC, Tsongalis GJ, Vaickus LJ, Levy JJ. Inferring spatial transcriptomics markers from whole slide images to characterize metastasis-related spatial heterogeneity of colorectal tumors: A pilot study. J Pathol Inform. 2023 Mar 29;14:100308. doi: 10.1016/j.jpi.2023.100308. PMID: 37114077; PMCID: PMC10127126.

Whittaker CA, Kucukural A, Gates C, Wilkins OM, Bell GW, Hutchinson JN, Polson SW, Dragon J. Functional Annotation Routines Used by ABRF Bioinformatics Core Facilities – Observations, Comparisons, and Considerations. J Biomol Tech. 2023 Mar 27;34(1):3fc1f5fe.0b74b9db. doi: 10.7171/3fc1f5fe.0b74b9db. PMID: 37089874; PMCID: PMC10121236.

Traphagen NA, Schwartz GN, Tau S, Jiang A, Hosford SR, Goen AE, Roberts AM, Romo BA, Johnson AL, Duffy EK, Demidenko E, Heverly P, Mosesson Y, Soucy SM, Kolling F, Miller TW. Estrogen therapy induces receptor-dependent DNA damage enhanced by PARP inhibition in ER+ breast cancer. bioRxiv. 2023 Mar 17;. doi: 10.1101/2023.03.16.532956. PubMed PMID: 36993590; PubMed Central
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Raza A, Diehl SA, Krementsov DN, Case LK, Li D, Kost J, Ball RL, Chesler EJ, Philip VM, Huang R, Chen Y, Ma R, Tyler AL, Mahoney JM, Blankenhorn EP, Teuscher C. A genetic locus complements resistance to Bordetella pertussis-induced histamine sensitization. Commun Biol. 2023 Mar 6;6(1):244. doi: 10.1038/s42003-023-04603-w. PubMed PMID: 36879097; PubMed Central PMCID: PMC9988836.

Mohamed GA, Mahmood S, Ognjenovic NB, Lee MK, Wilkins OM, Christensen BC, Muller KE, Pattabiraman DR. Lineage plasticity enables low-ER luminal tumors to evolve and gain basal-like traits. Breast Cancer Res. 2023 Mar 1;25(1):23. doi: 10.1186/s13058-023-01621-8. PMID: 36859337; PMCID: PMC9979432.

Lee MK, Azizgolshani N, Zhang Z, Perreard L, Iv FK, Nguyen L, Zanazzi G, Salas L, Christensen B. Hydroxymethylation alterations in progenitor-like cell types of pediatric central nervous system tumors are associated with cell type-specific transcriptional changes. Res Sq. 2023 Feb 28;. doi: 10.21203/rs.3.rs2517758/v1. PubMed PMID: 36909536; PubMed Central PMCID: PMC10002842.

Lee MK, Azizgolshani N, Shapiro J, Nguyen L, Iv FK, Zanazzi G, Frost H, Christensen B. Tumor type and cell type-specific gene expression alterations in diverse pediatric central nervous system tumors identified using single nuclei RNA-seq. Res Sq. 2023 Feb 23;. doi: 10.21203/rs.3.rs-2517703/v1. PubMed PMID: 36865335; PubMed Central PMCID: PMC9980204.

Robitaille S, Simmons EL, Verster AJ, McClure EA, Royce DB, Trus E, Swartz K, Schultz D, Nadell CD, Ross BD. Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria. bioRxiv. 2023 Feb 21;. doi: 10.1101/2023.02.20.529031. PubMed PMID: 36865186; PubMed Central PMCID: PMC9980007.

Schultz D. mSphere of Influence: Learning Biology from the Radio. mSphere. 2023 Feb 21;8(1):e0002623. doi: 10.1128/msphere.00026-23. Epub 2023 Feb 2. PMID: 36728432; PMCID: PMC9942574.

Levis M, Levy J, Dufort V, Russ CJ, Shiner B. Dynamic suicide topic modelling: Deriving population-specific, psychosocial and time-sensitive suicide risk variables from Electronic Health Record psychotherapy notes. Clin Psychol Psychother. 2023 Feb 16. doi: 10.1002/cpp.2842. Epub ahead of print. PMID: 36797651.

Schiebout C, Lust HE, Huang YH, Frost HR. Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA). bioRxiv [Preprint]. 2023 Feb 15:2023.02.13.528326. doi: 10.1101/2023.02.13.528326. PMID: 36824707; PMCID: PMC9949061.

Bhandari R, Yang H, Kosarek NN, Smith AE, Garlick JA, Hinchcliff M, Whitfield ML, Pioli PA. Human dermal fibroblast-derived exosomes induce macrophage activation in systemic sclerosis. Rheumatology (Oxford). 2023 Feb 6;62(SI):SI114-SI124. doi: 10.1093/rheumatology/keac453. PMID: 35946522; PMCID: PMC9910573.

Richmond JM, Patel D, Watanabe T, Chen HW, Martyanov V, Werner G, Garg M, Haddadi NS, Refat MA, Mahmoud BH, Wong LD, Dresser K, Deng A, Zhu JL, McAlpine W, Hosler GA, Feghali-Bostwick CA, Whitfield ML, Harris JE, Torok KS, Jacobe HT. CXCL9 links skin inflammation and fibrosis via CXCR3-dependent upregulation of collagen 1a1 in fibroblasts. J Invest Dermatol. 2023 Jan 25:S0022-202X(23)00021-0. doi: 10.1016/j.jid.2022.11.025. Epub ahead of print. PMID: 36708947.

Jean-Pierre F, Hampton TH, Schultz D, Hogan DA, Groleau MC, Déziel E, O’Toole GA. Community composition shapes microbial-specific phenotypes in a cystic fibrosis polymicrobial model system. Elife. 2023 Jan 20;12:e81604. doi: 10.7554/eLife.81604. PMID: 36661299; PMCID: PMC9897730.

Greenburg J, Lu Y, Lu S, Kamau U, Hamilton R, Pettus J, Preum S, Vaickus L, Levy J. Development of an interactive web dashboard to facilitate the reexamination of pathology reportsfor instances of underbilling of CPT codes. J PatholInform. 2023;14:100187. doi: 10.1016/j.jpi.2023.100187. eCollection 2023. PubMed PMID: 36700236; PubMed Central PMCID: PMC9867971.

 

2022

Schiebout C, Frost HR. CAMML with the Integration of Marker Proteins (ChIMP). Bioinformatics. 2022 Nov 30;38(23):5206-5213. doi: 10.1093/bioinformatics/btac674. PubMed PMID: 36214642; PubMed Central PMCID: PMC9710548.

Tripp EA, Fu F, Pauls SD. Evolutionary Kuramoto dynamics. Proc Biol Sci. 2022 Nov 9;289(1986):20220999. doi: 10.1098/rspb.2022.0999. Epub 2022 Nov 9. PubMed PMID: 36350204; PubMed Central PMCID: PMC9653234.

Skopelja-Gardner S, An J, Elkon KB. (2022) Role of the cGAS-STING pathway in systemic and organ-specific diseases. Nat Rev Nephrol. PMID: 35732833

Schultz D, Stevanovic M, Tsimring LS. Optimal transcriptional regulation of dynamic bacterial responses to sudden drug exposures. Biophys J. 2022 Nov 1;121(21):4137-4152. doi: 10.1016/j.bpj.2022.09.028. Epub 2022 Sep 26. PubMed PMID: 36168291; PubMed Central PMCID: PMC9675034.

Brabec JL, Ouardouz M, Mahoney JM, Scott RC, Hernan AE. Differential regulation of gene expression pathways with dexamethasone and ACTH after early life seizures. Neurobiol Dis. 2022 Nov;174:105873. doi: 10.1016/j.nbd.2022.105873. Epub 2022 Sep 21. PubMed PMID: 36152945; PubMed Central PMCID: PMC10048589.

Li X, Kolling FW, Aridgides D, Mellinger D, Ashare A, Jakubzick CV. ScRNA-seq expression of IFI27 and APOC2 identifies four alveolar macrophage superclusters in healthy BALF. Life Sci Alliance. 2022 Nov;5(11). doi: 10.26508/lsa.202201458. Print 2022 Nov. PubMed PMID: 35820705; PubMed Central PMCID: PMC9275597.

Rawat K, Soucy SM, Kolling FW, Diaz KM, King WT, Tewari A, Jakubzick CV. Natural Antibodies Alert the Adaptive Immune System of the Presence of Transformed Cells in Early Tumorigenesis. J Immunol. 2022 Oct 1;209(7):1252-1259. doi: 10.4049/jimmunol.2200447. Epub 2022 Aug 26. PubMed PMID: 36028292; PubMed Central PMCID: PMC9515310.

Hinds JW, Feris EJ, Wilkins OM, Deary LT, Wang X, Cole MD. S146L in MYC is a context-dependent activating substitution in cancer development. PLoS One. 2022;17(8):e0272771. doi: 10.1371/journal.pone.0272771. eCollection 2022. PubMed PMID: 36018850; PubMed Central PMCID: PMC9417018.

Brown MS, Abdollahi B, Wilkins OM, Lu H, Chakraborty P, Ognjenovic NB, Muller KE, Jolly MK, Christensen BC, Hassanpour S, Pattabiraman DR. Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer. Sci Adv. 2022 Aug 5;8(31):eabj8002. doi: 10.1126/sciadv.abj8002. Epub 2022 Aug 3. PubMed PMID: 35921406; PubMed Central PMCID: PMC9348802.

Brog RA, Ferry SL, Schiebout CT, Messier CM, Cook WJ, Abdullah L, Zou J, Kumar P, Sentman CL, Frost HR, Huang YH. Superkine IL-2 and IL-33 Armored CAR T Cells Reshape the Tumor Microenvironment and Reduce Growth of Multiple Solid Tumors. Cancer Immunol Res. 2022 Aug 3;10(8):962-977. doi: 10.1158/2326-6066.CIR-21-0536. PubMed PMID: 35696724; PubMed Central PMCID: PMC9357153.

Lee MK, Brown MS, Wilkins OM, Pattabiraman DR, Christensen BC. Distinct cytosine modification profiles define epithelial-to-mesenchymal cell-state transitions. Epigenomics. 2022 May;14(9):519-535. doi: 10.2217/epi-2022-0023. Epub 2022 Apr 6. PubMed PMID: 35382559; PubMed Central PMCID: PMC9118069.

Mould DL, Stevanovic M, Ashare A, Schultz D, Hogan DA. Metabolic basis for the evolution of a common pathogenic Pseudomonas aeruginosa variant. Elife. 2022 May 3;11. doi: 10.7554/eLife.76555. PubMed PMID: 35502894; PubMed Central PMCID: PMC9224983.

Salas LA, Zhang Z, Koestler DC, Butler RA, Hansen HM, Molinaro AM, Wiencke JK, Kelsey KT, Christensen BC. Enhanced cell deconvolution of peripheral blood using DNA methylation for highresolution immune profiling. Nat Commun. 2022 Feb 9;13(1):761. doi: 10.1038/s41467-021-27864-7. PubMed PMID: 35140201; PubMed Central PMCID: PMC8828780.

Webster SS, Mathelié-Guinlet M, Verissimo AF, Schultz D, Viljoen A, Lee CK, Schmidt WC, Wong GCL, Dufrêne YF, O’Toole GA. Force-Induced Changes of PilY1 Drive Surface Sensing by Pseudomonas aeruginosa. mBio. 2021 Feb 22;13(1):e0375421. doi: 10.1128/mbio.03754-21. Epub 2022 Feb 1. PubMed PMID: 35100866; PubMed Central PMCID: PMC8806160.

Frost HR. Eigenvectors from Eigenvalues Sparse Principal Component Analysis (EESPCA). J Comput Graph Stat. 2022;31(2):486-501. doi: 10.1080/10618600.2021.1987254. Epub 2021 Nov 12. PubMed PMID: 35693984; PubMed Central PMCID: PMC9187050.

Schiebout C, Frost HR. CAMML: Multi-Label Immune Cell-Typing and Stemness Analysis for SingleCell RNA-sequencing. Pac Symp Biocomput. 2022;27:199-210. PubMed PMID: 34890149; PubMed Central PMCID: PMC8669732.

Chen YY, Russo DD, Drake RS, Duncan FE, Shalek AK, Goods BA*, Woodruff TK*. Single-cell transcriptomics of staged oocytes and somatic cells reveal novel regulators of follicle activation. Reproduction. 2022 Jul 7;164(2):55-70. doi: 10.1530/REP-22-0053. PMID: 35899878; PMCID: PMC9354060. (NOTE: A correction request has been submitted to the publisher to ensure equal contribution between Goods BA and Woodruff TK is noted in the published manuscript. This was omitted accidentally during the editing process.)

Svoboda M, Frost HR, Bosco G. Internal oligo(dT) priming introduces systematic bias in bulk and single-cell RNA sequencing count data. NAR Genom Bioinform. 2022 May 25;4(2):lqac035. doi: 10.1093/nargab/lqac035. PMID: 35651651; PMCID: PMC9142200.

Nguyen QP, Hoen AG, Frost HR. CBEA: Competitive balances for taxonomic enrichment analysis. PLoS Comput Biol. 2022 May 18;18(5):e1010091. doi: 10.1371/journal.pcbi.1010091. PMID: 35584140; PMCID: PMC9154102.

Stevanovic M, Boukéké-Lesplulier T, Hupe L, Hasty J, Bittihn P, Schultz D. (2022) Nutrient Gradients Mediate Complex Colony-Level Antibiotic Responses in Structured Microbial Populations. Front Microbiol. 2022 Apr 27;13:740259. doi: 10.3389/fmicb.2022.740259. PMID: 35572643; PMCID: PMC9093743.

2021

Jones MI, Pauls SD, Fu F. The dual problems of coordination and anti-coordination on random bipartite graphs. New J Phys. 2021 Nov;23(11). doi: 10.1088/1367-2630/ac3319. Epub 2021 Nov 10. PubMed PMID: 35663516; PubMed Central PMCID: PMC9165663.

Spencer C, Tripp E, Fu F, Pauls S. Evolutionary Constraints on Connectivity Patternsin the Mammalian Suprachiasmatic Nucleus. Front Netw Physiol. 2021;1:716883. doi: 10.3389/fnetp.2021.716883. eCollection 2021. PubMed PMID: 36925572; PubMed Central PMCID: PMC10013059.

O’Toole GA, Crabbé A, Kümmerli R, LiPuma JJ, Bomberger JM, Davies JC, Limoli D, Phelan VV, Bliska JB, DePas WH, Dietrich LE, Hampton TH, Hunter R, Khursigara CM, Price-Whelan A, Ashare A, Cramer RA, Goldberg JB, Harrison F, Hogan DA, Henson MA, Madden DR, Mayers JR, Nadell C, Newman D, Prince A, Rivett DW, Schwartzman JD, Schultz D, Sheppard DC, Smyth AR, Spero MA, Stanton BA, Turner PE, van der Gast C, Whelan FJ, Whitaker R, Whiteson K. Model Systems to Study the Chronic, Polymicrobial Infections in Cystic Fibrosis: Current Approaches and Exploring Future Directions. mBio. 2021 Oct 26;12(5):e0176321. doi: 10.1128/mBio.01763-21. Epub 2021 Sep 21. PMID: 34544277; PMCID: PMC8546538.

Mehta BK, Espinoza ME, Hinchcliff M, Whitfield ML. Molecular “omic” signatures in systemic sclerosis. Eur J Rheumatol. 2020 Oct;7(Suppl 3):S173-S180. doi: 10.5152/eurjrheum.2020.19192. Epub 2020 Oct 1. PMID: 33164732; PMCID: PMC7647683.

Rangel LT, Soucy SM, Setubal JC, Gogarten JP, Fournier GP. An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets. Genome Biol Evol. 2021 Sep 1;13(9):evab187. doi: 10.1093/gbe/evab187. PMID: 34390574; PMCID: PMC8483891.

Kamran Kaveh, Feng Fu. Immune checkpoint therapy modeling of PD-1/PD-L1 blockades reveals subtle difference in their response dynamics and potential synergy in combination. ImmunoInformatics, Volumes 1–2, 2021,100004, ISSN 2667-1190, Oct 2021. doi: 10.1016/j.immuno.2021.100004.

Zheng X, Amos CI, Frost HR. Pan-cancer evaluation of gene expression and somatic alteration data for cancer prognosis prediction. BMC Cancer. 2021 Sep 25;21(1):1053. doi: 10.1186/s12885-021-08796-3. PMID: 34563154; PMCID: PMC8467202.

Nguyen, Q.P., Hoen, A.G., Frost, H.R. cILR: Competitive isometric log-ratio for taxonomic enrichment analysis. bioRxiv 2021.09.07.459294; doi: 10.1101/2021.09.07.459294.

Nguyen QP, Karagas MR, Madan JC, Dade E, Palys TJ, Morrison HG, Pathmasiri WW, McRitche S, Sumner SJ, Frost HR, Hoen AG. Associations between the gut microbiome and metabolome in early life. BMC Microbiol. 2021 Aug 28;21(1):238. doi: 10.1186/s12866-021-02282-3. PMID: 34454437; PMCID: PMC8400760.

Casey DT, Bou Jawde S, Herrmann J, Mori V, Mahoney JM, Suki B, Bates JHT. Percolation of collagen stress in a random network model of the alveolar wall. Sci Rep. 2021 Aug 17;11(1):16654. doi: 10.1038/s41598-021-95911-w. PMID: 34404841; PMCID: PMC8371101.

Connor Spencer, Elizabeth Tripp, Feng Fu, Scott Pauls. Evolutionary Constraints on Connectivity Patterns in the Mammalian Suprachiasmatic Nucleus. Frontiers in Network Physiology, Volume 1, August 2021, pg. 3, doi:10.3389/fnetp.2021.716883.

Hsu KS, Goodale BC, Ely KH, Hampton TH, Stanton BA, Enelow RI. Single-cell RNA-seq Analysis Reveals That Prenatal Arsenic Exposure Results in Long-term, Adverse Effects on Immune Gene Expression in Response to Influenza A Infection. Toxicol Sci. 2020 Aug 1;176(2):312-328. doi: 10.1093/toxsci/kfaa080. PMID: 32514536; PMCID: PMC7416320.

Frost HR. Analyzing cancer gene expression data through the lens of normal tissue-specificity. PLoS Comput Biol. 2021 Jun 18;17(6):e1009085. doi: 10.1371/journal.pcbi.1009085. PMID: 34143767; PMCID: PMC8244857.

Jones MI, Pauls SD, Fu F. Random choices facilitate solutions to collective network coloring problems by artificial agents. iScience. 2021 Apr 23;24(4):102340. doi: 10.1016/j.isci.2021.102340. eCollection 2021 Apr 23. PubMed PMID: 33870136; PubMed Central PMCID: PMC8047171.

Guage C, Fu F. Asymmetric Partisan Voter Turnout Games. Dyn Games Appl. 2021;11(4):738-758. doi: 10.1007/s13235-021-00384-1. Epub 2021 Apr 16. PubMed PMID: 34760327; PubMed Central PMCID: PMC8542561.

Brabec JL, Lara MK, Tyler AL, Mahoney JM. System-Level Analysis of Alzheimer’s Disease Prioritizes Candidate Genes for Neurodegeneration. Front Genet. 2021 Apr 6;12:625246. doi: 10.3389/fgene.2021.625246. PMID: 33889174; PMCID: PMC8056044.

Han J, Zhao Y, Shirai K, Molodtsov A, Kolling FW, Fisher JL, Zhang P, Yan S, Searles TG, Bader JM, Gui J, Cheng C, Ernstoff MS, Turk MJ, Angeles CV. Resident and circulating memory T cells persist for years in melanoma patients with durable responses to immunotherapy. Nat Cancer. 2021 Mar;2(3):300-311. doi: 10.1038/s43018-021-00180-1. Epub 2021 Mar 24. PMID: 34179824; PMCID: PMC8223731.

Kamal Y, Dwan D, Hoehn HJ, Sanz-Pamplona R, Alonso MH, Moreno V, Cheng C, Schell MJ, Kim Y, Felder SI, Rennert HS, Melas M, Lazaris C, Bonner JD, Siegel EM, Shibata D, Rennert G, Gruber SB, Frost HR, Amos CI, Schmit SL. Tumor immune infiltration estimated from gene expression profiles predicts colorectal cancer relapse. Oncoimmunology. 2021 Mar 9;10(1):1862529. doi: 10.1080/2162402X.2020.1862529. PMID: 33763292; PMCID: PMC7951964.

Columbo JA, Martinez-Camblor P, O’Malley AJ, Stone DH, Kashyap VS, Powell RJ, Schermerhorn ML, Malas M, Nolan BW, Goodney PP. Association of Adoption of Transcarotid Artery Revascularization With Center-Level Perioperative Outcomes. JAMA Netw Open. 2021 Feb 1;4(2):e2037885. doi: 10.1001/jamanetworkopen.2020.37885. PMID: 33616666; PMCID: PMC7900862.

Wang T, Vasconcellos A, Marken J, Skopelja-Gardner S, Lood C, Giltiay N. (2022) Immune complex–driven neutrophil activation and BAFF release: a link to B cell responses in SLE. Lupus Science & Medicine 2022;9:e000709.

2020

Glaubitz A, Fu F. Oscillatory dynamics in the dilemma of social distancing. Proc Math Phys Eng Sci.2020 Nov;476(2243):20200686. doi: 10.1098/rspa.2020.0686. Epub 2020 Nov 25. PubMed PMID: 33363444; PubMed Central PMCID: PMC7735308.

Petersen CL, Chen JQ, Salas LA, Christensen BC. Altered immune phenotype and DNA methylation in panic disorder. Clin Epigenetics. 2020 Nov 18;12(1):177. doi: 10.1186/s13148-020-00972-9. PubMed PMID: 33208194; PubMed Central PMCID: PMC7672933.

Sun Y, Preiss NK, Valenteros KB, Kamal Y, Usherwood YK, Frost HR, Usherwood EJ. Zbtb20 Restrains CD8 T Cell Immunometabolism and Restricts Memory Differentiation and Antitumor Immunity. J Immunol. 2020 Nov 15;205(10):2649-2666. doi: 10.4049/jimmunol.2000459. Epub 2020 Sep 30. PubMed PMID: 32998985; PubMed Central PMCID: PMC7931848.

Zheng X, Amos CI, Frost HR. Cancer prognosis prediction using somatic point mutation and copy number variation data: a comparison of gene-level and pathway-based models. BMC Bioinformatics. 2020 Oct 20;21(1):467. doi: 10.1186/s12859-020-03791-0. PubMed PMID: 33081688; PubMed Central PMCID: PMC7574407.

Lahue KG, Lara MK, Linton AA, Lavoie B, Fang Q, McGill MM, Crothers JW, Teuscher C, Mawe GM, Tyler AL, Mahoney JM, Krementsov DN. Identification of novel loci controlling inflammatory bowel disease susceptibility utilizing the genetic diversity of wild-derived mice. Genes Immun. 2020 Nov;21(5):311-325. doi: 10.1038/s41435-020-00110-8. Epub 2020 Aug 26. PMID: 32848229; PMCID: PMC7657953

Kamal Y, Schmit SL, Frost HR, Amos CI. The tumor microenvironment of colorectal cancer metastases: opportunities in cancer immunotherapy. Immunotherapy. 2020 Oct;12(14):1083-1100. doi: 10.2217/imt2020-0026. Epub 2020 Aug 13. Review. PubMed PMID: 32787587; PubMed Central PMCID: PMC8411393.

Skopelja-Gardner S, An J, Elkon KB. Role of the cGAS-STING pathway in systemic and organ-specific diseases. Nat Rev Nephrol. 2022 Sep;18(9):558-572. doi: 10.1038/s41581-022-00589-6. Epub 2022 Jun 22. PMID: 35732833; PMCID: PMC9214686

O’Malley AJ, Park S. A Novel Cluster Sampling Design that Couples Multiple Surveys to Support Multiple Inferential Objectives. Health Serv Outcomes Res Methodol. 2020 Sep;20(2-3):85-110. doi: 10.1007/s10742-020-00210-y. Epub 2020 Jun 9. PMID: 33613088; PMCID: PMC7888270.

Frost HR. Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring. Nucleic Acids Res. 2020 Sep 18;48(16):e94. doi: 10.1093/nar/gkaa582. PubMed PMID: 32633778; PubMed Central PMCID: PMC7498348.

Garcia V, Bonhoeffer S, Fu F. Cancer-induced immunosuppression can enable effectiveness of immunotherapy through bistability generation: A mathematical and computational examination. J Theor Biol. 2020 May 7;492:110185. doi: 10.1016/j.jtbi.2020.110185. Epub 2020 Feb 6. PMID: 32035826; PMCID: PMC7079339.

Correia C, Mawe S, Lofgren S, Marangoni RG, Lee J, Saber R, Aren K, Cheng M, Teaw S, Hoffmann A, Goldberg I, Cowper SE, Khatri P, Hinchcliff M, Mahoney JM. High-throughput quantitative histology in systemic sclerosis skin disease using computer vision. Arthritis Res Ther. 2020 Mar 14;22(1):48. doi: 10.1186/s13075-020-2127-0. PMID: 32171325; PMCID: PMC7071594.

Zheng X, Amos CI, Frost HR. Comparison of pathway and gene-level models for cancer prognosis prediction. BMC Bioinformatics. 2020 Feb 28;21(1):76. doi: 10.1186/s12859-020-3423-z. PMID: 32111152; PMCID: PMC7048092.

Wang X, Zheng Z, Fu F. Steering eco-evolutionary game dynamics with manifold control. Proc Math Phys Eng Sci. 2020 Jan;476(2233):20190643. doi: 10.1098/rspa.2019.0643. Epub 2020 Jan 8. PMID: 32082066; PMCID: PMC7016546.

Tyler A, Mahoney JM, Carter GW. Genetic Interactions Affect Lung Function in Patients with Systemic Sclerosis. G3 (Bethesda). 2020 Jan 7;10(1):151-163. doi: 10.1534/g3.119.400775. PMID: 31694854; PMCID: PMC6945038.

2019

Chamberlin MD, Forbes V, Dushimimana G, Kettenbach A, Muller K, Musoni E, Rutaganda E, Wilkins OW, Kolling FW, Christensen BC. Capacity-building for molecular analyses of formalin-fixed paraffin- embedded breast cancer samples from Rwanda. Abstract 12/10/2019

Tyler AL, Raza A, Krementsov DN, Case LK, Huang R, Ma RZ, Blankenhorn EP, Teuscher C, Mahoney JM. Network-Based Functional Prediction Augments Genetic Association To Predict Candidate Genes for Histamine Hypersensitivity in Mice. G3 (Bethesda). 2019 Dec 3;9(12):4223-4233. doi: 10.1534/g3.119.400740. PMID: 31645420; PMCID: PMC6893195.