2024
Zhang Z, Sehgal K, Shirai K, Butler RA, Wiencke JK, Koestler DC, Ramush G, Lee MK, Molinaro AM, Stolrow HG, Birnbaum A, Salas LA, Haddad RI, Kelsey KT, Christensen BC. Methylation cytometric pretreatment blood immune profiles with tumor mutation burden as prognostic indicators for survival outcomes in head and neck cancer patients on anti-PD-1 therapy. NPJ Precis Oncol. 2024 Nov 18;8(1):267. doi: 10.1038/s41698-024-00759-8. PMID: 39558036; PMCID: PMC11573993.
Wang Z, Lindgren KM, Loros JJ, Dunlap JC. The auxotrophic formate (for) mutant of Neurospora crassa has significantly delayed growth but a normal circadian clock. Fungal Genet Rep. 2024;68:1. doi: 10.4148/1941-4765.2185. PMID: 39555235; PMCID: PMC11565437.
Zhou Y, Song L, Li H. Full-resolution HLA and KIR gene annotations for human genome assemblies. Genome Res. 2024 Nov 20;34(11):1931-1941. doi: 10.1101/gr.278985.124. PMID: 38839374; PMCID: PMC11610593.
Wang S, Feng D, Zheng Y, Lu Y, Shi K, Yang R, Ma W, Li N, Liu M, Wang Y, Hong Y, McClung CR, Zhao J. EARLY FLOWERING 3 alleles affect the temperature responsiveness of the circadian clock in Chinese cabbage. Plant Physiol. 2024 Nov 15:kiae505. doi: 10.1093/plphys/kiae505. Epub ahead of print. PMID: 39545809.
Patel KR, Nguyen PL, Proudfoot JA, Liu Y, Pra AD, Spratt DE, Pollack A, Sandler HM, Efstathiou JA, Lawton C, Simko JP, Rosenthal SA, Zeitzer KL, Mendez LC, Hartford AC, Hall WA, Desai AB, Pugh SL, Davicioni E, Tran PT, Feng FY. Biopsy-based Basal-luminal Subtyping Classifier in High-risk Prostate Cancer: A Combined Analysis of the NRG Oncology/RTOG 9202, 9413, and 9902 Phase 3 Trials. Eur Urol Oncol. 2024 Nov 13:S2588-9311(24)00246-3. doi: 10.1016/j.euo.2024.10.017. Epub ahead of print. PMID: 39542826.
Rivera LM, Uwizeye G, Stolrow H, Christensen B, Rutherford J, Thayer Z. Prenatal exposure to genocide and subsequent adverse childhood events are associated with DNA methylation of SLC6A4, BDNF, and PRDM8 in early adulthood in Rwanda. Sci Rep. 2024 Nov 13;14(1):27879. doi: 10.1038/s41598-024-78035-9. PMID: 39537739; PMCID: PMC11560948.
Ramirez DE, Dragnev CPC, Searles TG, Spicer N, Chen T, Lines JL, Hawkes AR, Davis WL, Mohamed A, Shirai K, Phillips JD, Rosato PC, Huang YH, Turk MJ. Depletion of conventional CD4+ T cells is required for robust priming and dissemination of tumor antigen-specific CD8+ T cells in the setting of anti-CD4 therapy. J Immunother Cancer. 2024 Nov 9;12(11):e010170. doi: 10.1136/jitc-2024-010170. PMID: 39521617; PMCID: PMC11552015.
Song C, Zhang M, Kruse T, Møller MH, López-Méndez B, Zhang Y, Zhai Y, Wang Y, Lei T, Kettenbach AN, Nilsson J, Zhang G. Self-priming of Plk1 binding to BubR1 ensures accurate mitotic progression. Commun Biol. 2024 Nov 9;7(1):1473. doi: 10.1038/s42003-024-07205-2. PMID: 39516273; PMCID: PMC11549336.
El Hafi B, Jean-Pierre F, O’Toole GA. Pseudomonas aeruginosa supports the survival of Prevotella melaninogenica in a cystic fibrosis lung polymicrobial community through metabolic cross-feeding. bioRxiv [Preprint]. 2024 Oct 21:2024.10.21.619475. doi: 10.1101/2024.10.21.619475. PMID: 39484496; PMCID: PMC11527032.
Godin A, Connor RI, Degefu HN, Rosato PC, Wieland-Alter WF, Axelrod KS, Kovacikova G, Weiner JA, Ackerman ME, Chen EY, Arita M, Bandyopadhyay AS, Raja AI, Modlin JF, Brickley EB, Wright PF. Nasal and Pharyngeal Mucosal Immunity to Poliovirus in Children Following Routine Immunization With Inactivated Polio Vaccine in the United States. J Infect Dis. 2024 Nov 15;230(5):e1023-e1030. doi: 10.1093/infdis/jiae264. PMID: 38809190; PMCID: PMC11566227.
Criswell RL, Bauer JA, Christensen BC, Meijer J, Peterson LA, Huset CA, Walker DI, Karagas MR, Romano ME. Associations of per- and polyfluoroalkyl substances with human milk metabolomic profiles in a rural North American cohort. Environ Epidemiol. 2024 Oct 28;8(6):e352. doi: 10.1097/EE9.0000000000000352. PMID: 39474471; PMCID: PMC11521063.
Pike SC, Wiencke JK, Zhang Z, Molinaro AM, Hansen HM, Koestler DC, Christensen BC, Kelsey KT, Salas LA. Glioma immune microenvironment composition calculator (GIMiCC): a method of estimating the proportions of eighteen cell types from DNA methylation microarray data. Acta Neuropathol Commun. 2024 Oct 28;12(1):170. doi: 10.1186/s40478-024-01874-0. PMID: 39468647; PMCID: PMC11514818.
Fatemi MY, Lu Y, Diallo AB, Srinivasan G, Azher ZL, Christensen BC, Salas LA, Tsongalis GJ, Palisoul SM, Perreard L, Kolling FW 4th, Vaickus LJ, Levy JJ. An initial game-theoretic assessment of enhanced tissue preparation and imaging protocols for improved deep learning inference of spatial transcriptomics from tissue morphology. Brief Bioinform. 2024 Sep 23;25(6):bbae476. doi: 10.1093/bib/bbae476. PMID: 39367648; PMCID: PMC11452536.
Butler SE, Ackerman ME. Challenges and future perspectives for high-throughput chimeric antigen receptor T cell discovery. Curr Opin Biotechnol. 2024 Dec;90:103216. doi: 10.1016/j.copbio.2024.103216. Epub 2024 Oct 21. PMID: 39437676.
Zaniker EJ, Zhang J, Russo D, Huang R, Suritis K, Drake RS, Barlow-Smith E, Shalek AK, Woodruff TK, Xiao S, Goods BA, Duncan FE. Follicle-intrinsic and spatially distinct molecular programs drive follicle rupture and luteinization during ex vivo mammalian ovulation. Commun Biol. 2024 Oct 23;7(1):1374. doi: 10.1038/s42003-024-07074-9. PMID: 39443665; PMCID: PMC11500180.
Onega T, Ramkumar N, Brooks GA, Loehrer AP, Kapadia NS, O’Malley AJ, Fraze TK, Smith RE, Wang Q, Wong SL, Tosteson ANA. Travel burden and bypassing closest site for surgical cancer treatment for urban and rural oncology patients. J Rural Health. 2024 Oct 12. doi: 10.1111/jrh.12890. Epub ahead of print. PMID: 39394970.
Frost HR. Leveraging cell type-specificity for gene set analysis of single cell transcriptomics. bioRxiv [Preprint]. 2024 Sep 27:2024.09.25.615040. doi: 10.1101/2024.09.25.615040. PMID: 39386631; PMCID: PMC11463668.
Ran X, Meara E, Morden NE, Moen EL, Rockmore DN, O’Malley AJ. Estimating the impact of physician risky-prescribing on the network structure underlying physician shared-patient relationships. Appl Netw Sci. 2024;9(1):63. doi: 10.1007/s41109-024-00670-y. Epub 2024 Oct 3. PMID: 39372037; PMCID: PMC11450072.
GBD 2021 Tobacco Forecasting Collaborators. Forecasting the effects of smoking prevalence scenarios on years of life lost and life expectancy from 2022 to 2050: a systematic analysis for the Global Burden of Disease Study 2021. Lancet Public Health. 2024 Oct;9(10):e729-e744. doi: 10.1016/S2468-2667(24)00166-X. PMID: 39366729; PMCID: PMC11447278.
Sacks OA, Murphy M, O’Malley J, Birkmeyer N, Barnato AE. A Quality Improvement Initiative for Inpatient Advance Care Planning. JAMA Health Forum. 2024 Oct 4;5(10):e243172. doi: 10.1001/jamahealthforum.2024.3172. PMID: 39365606; PMCID: PMC11452818.
Schubbe D, Durand MA, Forcino RC, Engel J, Tomaino M, Adams-Foster M, Bacon C, Mulligan CC, Venable S, Foster T, Barr PJ, Anchan RM, Laughlin-Tommaso S, Lindholm A, Seshan M, Gargiulo RM, Stephenson P, George K, Ajao M, Madden T, Banks E, Gargiulo AR, O’Malley J, van den Muijsenbergh M, Aarts JWM, Elwyn G. Continuous adaptation of conversation aids for uterine fibroids treatment options in a four-year multi-center implementation project. BMC Med Inform Decis Mak. 2024 Sep 30;24(1):277. doi: 10.1186/s12911-024-02637-6. PMID: 39350254; PMCID: PMC11441251.
Ash R, Scodari BT, Schaefer AP, Cornelius SL, Brooks GA, O’Malley AJ, Onega T, Verhoeven DC, Moen EL. Surgeon and Care Team Network Measures and Timely Breast Cancer Treatment. JAMA Netw Open. 2024 Aug 1;7(8):e2427451. doi: 10.1001/jamanetworkopen.2024.27451. PMID: 39207756; PMCID: PMC11362867.
Hederman AP, Remmel CJ, Sharma S, Natarajan H, Weiner JA, Wrapp D, Donner C, Delforge ML, d’Angelo P, Furione M, Fornara C, McLellan JS, Lilleri D, Marchant A, Ackerman ME. Discrimination of primary and chronic cytomegalovirus infection based on humoral immune profiles in pregnancy. J Clin Invest. 2024 Aug 29:e180560. doi: 10.1172/JCI180560. Epub ahead of print. PMID: 39207860.
Yeum D, Renier TJ, Masterson TD, Carlson DD, Ballarino GA, Lansigan RK, Loos RJF, Emond JA, Gilbert-Diamond D. Genetic associations with consumption of palatable foods in the absence of hunger in response to food cues in children. Pediatr Obes. 2024 Aug 28:e13168. doi: 10.1111/ijpo.13168. Epub ahead of print. PMID: 39197865.
Dahl DM, Rodgers JP, Shipley WU, Michaelson MD, Wu CL, Parker W, Jani AB, Cury FL, Hudes RS, Michalski JM, Hartford AC, Song D, Citrin DE, Karrison TG, Sandler HM, Feng FY, Efstathiou JA. Bladder-Preserving Trimodality Treatment for High-Grade T1 Bladder Cancer: Results From Phase II Protocol NRG Oncology/RTOG 0926. J Clin Oncol. 2024 Sep 3:JCO2302510. doi: 10.1200/JCO.23.02510. Epub ahead of print. PMID: 39226514.
Sinicrope FA, Turk MJ. Immune checkpoint blockade: timing is everything. J Immunother Cancer. 2024 Aug 28;12(8):e009722. doi: 10.1136/jitc-2024-009722. PMID: 39209456; PMCID: PMC11409242.
Leyenaar JK, Arakelyan M, Schaefer AP, Freyleue SD, Austin AM, Simon TD, Van Cleave J, Ahuja N, Chien AT, Moen EL, O’Malley AJ, Goodman DC. Neurodevelopmental and Mental Health Conditions in Children With Medical Complexity. Pediatrics. 2024 Sep 1;154(3):e2024065650. doi: 10.1542/peds.2024-065650. PMID: 39099441; PMCID: PMC11350095.
Skandalakis GP, Neudorfer C, Payne CA, Bond E, Tavakkoli AD, Barrios-Martinez J, Trutti AC, Koutsarnakis C, Coenen VA, Komaitis S, Hadjipanayis CG, Stranjalis G, Yeh FC, Banihashemi L, Hong J, Lozano AM, Kogan M, Horn A, Evans LT, Kalyvas A. Establishing connectivity through microdissections of midbrain stimulation-related neural circuits. Brain. 2024 Sep 3;147(9):3083-3098. doi: 10.1093/brain/awae173. PMID: 38808482; PMCID: PMC11370807.
Sergent P, Pinto-Cárdenas JC, Carrillo AJA, Dávalos DL, Pérez MDG, Lechuga DAM, Alonso-Miguel D, Schaafsma E, Cuarenta AJ, Muñoz DC, Zarabanda Y, Palisoul SM, Lewis PJ, Kolling FW 4th, Affonso de Oliveira JF, Steinmetz NF, Rothstein JL, Lines L, Noelle RJ, Fiering S, Arias-Pulido H. An Abscopal Effect on Lung Metastases in Canine Mammary Cancer Patients Induced by Neoadjuvant Intratumoral Immunotherapy with Cowpea Mosaic Virus Nanoparticles and Anti-Canine PD-1. Cells. 2024 Sep 3;13(17):1478. doi: 10.3390/cells13171478. PMID: 39273048; PMCID: PMC11394642.
GBD 2021 Stroke Risk Factor Collaborators. Global, regional, and national burden of stroke and its risk factors, 1990-2021: a systematic analysis for the Global Burden of Disease Study 2021. Lancet Neurol. 2024 Oct;23(10):973-1003. doi: 10.1016/S1474-4422(24)00369-7. PMID: 39304265.
Leyenaar JK, Acquilano SC, Freyleue SD, Schaefer AP, McDaniel CE, Bode RS, Erdem G, Lauden S, Schmerge C, Choi SS, Felman K, Fleischer A, Houtrow AJ, Bruce ML, O’Malley AJ. Effectiveness of Direct Admission Compared to Admission Through the Emergency Department: A Stepped-Wedge Cluster-Randomized Trial. Pediatrics. 2024 Oct 1;154(4):e2024065776. doi: 10.1542/peds.2024-065776. PMID: 39301600.
Xu S, Kelkar NS, Ackerman ME. Positive-unlabeled learning to infer protection status and identify correlates in vaccine efficacy field trials. iScience. 2024 Feb 2;27(3):109086. doi: 10.1016/j.isci.2024.109086. PMID: 39295637; PMCID: PMC11409573.
Anderson EC, Foley HB, Levy JJ, Romano ME, Gui J, Bentz JL, Maldonado LE, Farzan SF, Bastain TM, Marsit CJ, Breton CV, Howe CG. Maternal glucose levels and late pregnancy circulating extracellular vesicle and particle miRNAs in the MADRES pregnancy cohort. Epigenetics. 2024 Dec;19(1):2404198. doi: 10.1080/15592294.2024.2404198. Epub 2024 Sep 18. PMID: 39292753.
Leyenaar JK, Freyleue SD, Arakelyan M, Schaefer AP, Moen EL, Austin AM, Goodman DC, O’Malley AJ. Rural-Urban Disparities in Hospital Services and Outcomes for Children With Medical Complexity. JAMA Netw Open. 2024 Sep 3;7(9):e2435187. doi: 10.1001/jamanetworkopen.2024.35187. PMID: 39316395; PMCID: PMC11423179.
Morris EA, Parvizi R, Orzechowski NM, Whitfield ML, Pioli PA. Mycophenolate mofetil directly modulates myeloid viability and pro-fibrotic activation of human macrophages. Rheumatology (Oxford). 2024 Sep 23:keae517. doi: 10.1093/rheumatology/keae517. Epub ahead of print. PMID: 39312626.
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 Oct 1;148(10):1119-1125. doi: 10.5858/arpa.2023-0163-OA. PMID: 38244086.
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 Oct;7(5):1024-1033. doi: 10.1016/j.euo.2024.01.004. Epub 2024 Feb 1. PMID: 38302323; PMCID: PMC11289167.
Sudo K, Delmas-Eliason A, Soucy S, Barrack KE, Liu J, Balasubramanian A, Shu CJ, James MJ, Hegner CL, Dionne HD, Rodriguez-Palacios A, Krause HM, O’Toole GA, Karpen SJ, Dawson PA, Schultz D, Sundrud MS. Quantifying Forms and Functions of Enterohepatic Bile Acid Pools in Mice. Cell Mol Gastroenterol Hepatol. 2024 Aug 22:101392. doi: 10.1016/j.jcmgh.2024.101392. Epub ahead of print. PMID: 39179177.
Bynum JPW, Benloucif S, Martindale J, O’Malley AJ, Davis MA. Regional variation in diagnostic intensity of dementia among older U.S. adults: An observational study. Alzheimers Dement. 2024 Aug 16. doi: 10.1002/alz.14092. Epub ahead of print. PMID: 39149970.
Schifferdecker KE, Yang CW, Mackwood MB, Rodriguez HP, Shortell SM, Akré ER, O’Malley AJ, Butler C, Berube AD, Andrews AO, Fisher ES. Safety Net Primary Care Capabilities After the COVID-19 Pandemic. JAMA Health Forum. 2024 Aug 2;5(8):e242547. doi: 10.1001/jamahealthforum.2024.2547. PMID: 39150731; PMCID: PMC11329874.
Zhang Z, Christensen BC, Salas LA. Recalibrate concepts of epigenetic aging clocks in human health. Aging (Albany NY). 2024 Jul 17;16(14):11125-11127. doi: 10.18632/aging.206027. Epub 2024 Jul 17. PMID: 39028368; PMCID: PMC11315393.
Yu X, Song L, Cen L, Cao B, Tao R, Shen Y, Abate-Daga D, Rodriguez PC, Conejo-Garcia JR, Wang X. A pan-cancer gamma delta T cell repertoire. bioRxiv [Preprint]. 2024 Jul 22:2024.07.18.604205. doi: 10.1101/2024.07.18.604205. PMID: 39091790; PMCID: PMC11291071.
Vaickus LJ, Kerr DA, Velez Torres JM, Levy J. Artificial Intelligence Applications in Cytopathology: Current State of the Art. Surg Pathol Clin. 2024 Sep;17(3):521-531. doi: 10.1016/j.path.2024.04.011. Epub 2024 May 30. PMID: 39129146.
Sanville J, O’Toole GA, Madan J, Coker M. Premodulator microbiome alterations associated with postmodulator growth outcomes in pediatric cystic fibrosis: Can we predict outcomes? J Pediatr Gastroenterol Nutr. 2024 Aug 9. doi: 10.1002/jpn3.12350. Epub ahead of print. PMID: 39118488.
Levis M, Levy J, Dimambro M, Dufort V, Ludmer DJ, Goldberg M, Shiner B. Using natural language processing to evaluate temporal patterns in suicide risk variation among high-risk Veterans. Psychiatry Res. 2024 Sep;339:116097. doi: 10.1016/j.psychres.2024.116097. Epub 2024 Jul 27. PMID: 39083961.
Alsup A, Nissen E, Salas LA, Molinaro AM, Reiner A, Liu S, Madsen TE, Liu L, Auer PL, Christensen BC, Wiencke JK, Kelsey KT, Koestler DC. An assessment of compositional methods for the analysis of DNA methylation-based deconvolution estimates. Epigenomics. 2024 Aug 2:1-14. doi: 10.1080/17501911.2024.2379242. Epub ahead of print. PMID: 39093129.
Leyenaar JK, Arakelyan M, Schaefer AP, Freyleue SD, Austin AM, Simon TD, Van Cleave J, Ahuja N, Chien AT, Moen EL, O’Malley AJ, Goodman DC. Neurodevelopmental and Mental Health Conditions in Children With Medical Complexity. Pediatrics. 2024 Aug 5:e2024065650. doi: 10.1542/peds.2024-065650. Epub ahead of print. PMID: 39099441.
Dutta R, Cabral DGA, Lyu N, Vu NP, Wang Y, Allen B, Dan X, Cortiñas RG, Khazaei P, Schäfer M, Albornoz ACCD, Smart SE, Nie S, Devoret MH, Mazziotti DA, Narang P, Wang C, Whitfield JD, Wilson AK, Hendrickson HP, Lidar DA, Pérez-Bernal F, Santos LF, Kais S, Geva E, Batista VS. Simulating Chemistry on Bosonic Quantum Devices. J Chem Theory Comput. 2024 Aug 13;20(15):6426-6441. doi: 10.1021/acs.jctc.4c00544. Epub 2024 Jul 28. PMID: 39068594.
Hill-Batorski L, Weiner JA, Ackerman ME, Hatta Y, Hoft DF, Herber R, Moser MJ, Bilsel P. Intranasal M2SR (M2-deficient Single Replication) Influenza Vaccine Induces Broadly Reactive Mucosal Antibody Production in Adults. J Infect Dis. 2024 Jul 16:jiae361. doi: 10.1093/infdis/jiae361. Epub ahead of print. PMID: 39012796.
Wilkins OM, Campbell R, Yosufzai Z, Doe V, Soucy SM. Cloud-based introduction to BASH programming for biologists. Brief Bioinform. 2024 Jul 23;25(Supplement_1):bbae244. doi: 10.1093/bib/bbae244. PMID: 39041911; PMCID: PMC11264290.
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 Mar;10(2):271-278. doi: 10.1016/j.euf.2024.01.008. Epub 2024 Feb 1. PMID: 38307806; PMCID: PMC11257781.
Bouley SJ, Grassetti AV, Allaway RJ, Wood MD, Hou HW, Burdon Dasbach IR, Seibel W, Wu J, Gerber SA, Dragnev KH, Walker JA, Sanchez Y. Chemical genetic screens reveal defective lysosomal trafficking as synthetic lethal with NF1 loss. J Cell Sci. 2024 Aug 1;137(15):jcs262343. doi: 10.1242/jcs.262343. Epub 2024 Aug 14. PMID: 39016685.
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 Jul;51(7):5109-5118. doi: 10.1002/mp.17031. Epub 2024 Mar 17. PMID: 38493501; PMCID: PMC11316970.
Isaacs JF, Degefu HN, Chen T, Kleist SA, Musial SC, Ford MA, Searles TG, Lin CC, Skorput AGJ, Shirai K, Turk MJ, Zanazzi GJ, Rosato PC. CD39 Is Expressed on Functional Effector and Tissue-resident Memory CD8+ T Cells. J Immunol. 2024 Sep 1;213(5):588-599. doi: 10.4049/jimmunol.2400151. PMID: 38975728; PMCID: PMC11333163.
McCoy KM, Ackerman ME, Grigoryan G. A Comparison of Antibody-Antigen Complex Sequence-to-Structure Prediction Methods and their Systematic Biases. bioRxiv [Preprint]. 2024 Jun 28:2024.03.15.585121. doi: 10.1101/2024.03.15.585121. PMID: 38979267; PMCID: PMC11230293.
Isaacs JF, Degefu HN, Chen T, Kleist SA, Musial SC, Ford MA, Searles TG, Lin CC, Skorput AGJ, Shirai K, Turk MJ, Zanazzi GJ, Rosato PC. CD39 Is Expressed on Functional Effector and Tissue-resident Memory CD8+ T Cells. J Immunol. 2024 Sep 1;213(5):588-599. doi: 10.4049/jimmunol.2400151. PMID: 38975728; PMCID: PMC11333163.
Pachucki MC, Hong CS, O’Malley AJ, Levy DE, Thorndike AN. Network spillover effects associated with the ChooseWell 365 workplace randomized controlled trial to promote healthy food choices. Soc Sci Med. 2024 Aug;355:117033. doi: 10.1016/j.socscimed.2024.117033. Epub 2024 Jun 27. PMID: 38981183.
Ran X, Morden NE, Meara E, Moen EL, Rockmore DN, O’Malley AJ. Exploiting relationship directionality to enhance statistical modeling of peer-influence across social networks. Stat Med. 2024 Sep 20;43(21):4073-4097. doi: 10.1002/sim.10169. Epub 2024 Jul 9. PMID: 38981613; PMCID: PMC11338714.
Ramirez-Velandia F, Ranawaka KH, Wadhwa A, Salih M, Fodor TB, Lau TS, Pacheco-Barrios N, Enriquez-Marulanda A, Khan IS, Vega RA, Stippler M, Taussky P, Hong J, Ogilvy CS. Comparison of Postoperative Seizures Between Burr-Hole Evacuation and Craniotomy in Patients With Nonacute Subdural Hematomas: A Bi-Institutional Propensity Score-Matched Analysis. Neurosurgery. 2024 Jul 5. doi: 10.1227/neu.0000000000003046. Epub ahead of print. PMID: 38967423.
Lee HM, Kisicki MD, Hong J, Knight JC. Importance of Multispecialty Coordination of Care in an Electroconvulsive Therapy Patient With Musculoskeletal, Neurological, and Vascular Injuries: A Case Report. J ECT. 2024 Jun 28. doi: 10.1097/YCT.0000000000001037. Epub ahead of print. PMID: 38968434.
Miller JA, Hammad M, Amini E, Andrianne R, Burnett AL, Gross K, Gross MS, Hatzichristodoulou G, Hotaling J, Hsieh TC, Jenkins LC, Jones JM, Lentz A, Levy J, Modgil V, Osmonov D, Park SH, Pearce I, Perito P, Sadeghi-Nejad H, Sempels M, Simhan J, Suarez-Sarmiento A Jr, van Renterghem K, Warner JN, Yafi FA, Ziegelmann M, Barham DW. Factors Affecting Implant Length in Primary Inflatable Penile Prosthesis Placement. Urology. 2024 Jul 5:S0090-4295(24)00546-6. doi: 10.1016/j.urology.2024.06.068. Epub ahead of print. PMID: 38972393.
Smulowitz PB, O’Malley AJ, McWilliams JM, Zaborski L, Landon BE. Emergency Department Visits And Hospital Capacity In The US: Trends In The Medicare Population During The COVID-19 Pandemic. Health Aff (Millwood). 2024 Jul;43(7):970-978. doi: 10.1377/hlthaff.2023.01153. PMID: 38950291.
Walsh SR, Gay CL, Karuna ST, Hyrien O, Skalland T, Mayer KH, Sobieszczyk ME, Baden LR, Goepfert PA, Del Rio C, Pantaleo G, Andrew P, Karg C, He Z, Lu H, Paez CA, Baumblatt JAG, Polakowski LL, Chege W, Anderson MA, Janto S, Han X, Huang Y, Dumond J, Ackerman ME, McDermott AB, Flach B, Piwowar-Manning E, Seaton K, Tomaras GD, Montefiori DC, Gama L, Mascola JR; HVTN 127/HPTN 087 Study Team. Safety and pharmacokinetics of VRC07-523LS administered via different routes and doses (HVTN 127/HPTN 087): A Phase I randomized clinical trial. PLoS Med. 2024 Jun 24;21(6):e1004329. doi: 10.1371/journal.pmed.1004329. PMID: 38913710; PMCID: PMC11251612.
Connor RI, Sakharkar M, Rappazzo CG, Kaku CI, Curtis NC, Shin S, Wieland-Alter WF, Wentworth J, Mielcarz DW, Weiner JA, Ackerman ME, Walker LM, Lee J, Wright PF. Characteristics and Functions of Infection-enhancing Antibodies to the N-terminal Domain of SARS-CoV-2. Pathog Immun. 2024 Jun 18;9(2):1-24. doi: 10.20411/pai.v9i2.679. PMID: 38933606; PMCID: PMC11197847.
Rogers RR, Kesthely CA, Jean-Pierre F, El Hafi B, O’Toole GA. Dpr-mediated H2O2 resistance contributes to streptococcus survival in a cystic fibrosis airway model system. J Bacteriol. 2024 Jul 25;206(7):e0017624. doi: 10.1128/jb.00176-24. Epub 2024 Jun 28. PMID: 38940597; PMCID: PMC11270861.
Wang B, Adamo ME, Zhou X, Wang Z, Gerber SA, Kettenbach AN, Dunlap JC. Acetylation of WCC is dispensable for the core circadian clock but differentially regulates acute light responses in Neurospora. J Biol Chem. 2024 Jun 27;300(8):107508. doi: 10.1016/j.jbc.2024.107508. Epub ahead of print. PMID: 38944116; PMCID: PMC11325773.
Xu S, Ackerman ME. Leveraging permutation testing to assess confidence in positive-unlabeled learning applied to high-dimensional biological datasets. BMC Bioinformatics. 2024 Jun 19;25(1):218. doi: 10.1186/s12859-024-05834-2. PMID: 38898392; PMCID: PMC11186207.
Jackson TL, Desai R, Wafa HA, Wang Y, Peacock J, Peto T, Chakravarthy U, Dakin H, Wordsworth S, Lewis C, Clinch P, Ramazzotto L, Neffendorf JE, Lee CN, O’Sullivan JM, Reeves BC; STAR study group. Stereotactic radiotherapy for neovascular age-related macular degeneration (STAR): a pivotal, randomised, double-masked, sham-controlled device trial. Lancet. 2024 Jul 6;404(10447):44-54. doi: 10.1016/S0140-6736(24)00687-1. Epub 2024 Jun 11. PMID: 38876132.
McCoy KM, Ackerman ME, Grigoryan G. A comparison of antibody-antigen complex sequence-to-structure prediction methods and their systematic biases. Protein Sci. 2024 Sep;33(9):e5127. doi: 10.1002/pro.5127. PMID: 39167052; PMCID: PMC11337930.
Sudo K, Delmas-Eliason A, Soucy S, Barrack KE, Liu J, Balasubramanian A, Shu CJ, James MJ, Hegner CL, Dionne HD, Rodriguez-Palacios A, Krause HM, O’Toole GA, Karpen SJ, Dawson PA, Schultz D, Sundrud MS. Quantifying forms and functions of enterohepatic bile acid pools in mice. Cell Mol Gastroenterol Hepatol. 2024 Aug 21:101392. doi: 10.1016/j.jcmgh.2024.101392. Epub ahead of print. PMID: 39179177.
Holt JD, Schultz D, Nadell CD. Dispersal of a dominant competitor can drive multispecies coexistence in biofilms. Curr Biol. 2024 Aug 12:S0960-9822(24)01017-0. doi: 10.1016/j.cub.2024.07.078. Epub ahead of print. PMID: 39163856.
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 Jun;20(6):787-796. doi: 10.1200/OP.23.00690. Epub 2024 Feb 22. PMID: 38386962.
Lee MK, Zhang Z, Sehgal K, Butler R, Stolrow H, Ramush G, Shirai K, Koestler DC, Salas LA, Wiencke JK, Haddad R, Kelsey KT, Christensen BC. Immunomethylomic profiles of long-term head and neck squamous cell carcinoma survivors on immune checkpoint inhibitors. Epigenomics. 2024 May 21:1-9. doi: 10.1080/17501911.2024.2343274. Epub ahead of print. PMID: 38869472.
Schiebout C, Frost HR. CAraCAl: CAMML with the integration of chromatin accessibility. BMC Bioinformatics. 2024 Jun 13;25(1):212. doi: 10.1186/s12859-024-05833-3. PMID: 38872103; PMCID: PMC11170880.
Zhou Y, Song L, Li H. Full resolution HLA and KIR gene annotations for human genome assemblies. Genome Res. 2024 Jun 5:gr.278985.124. doi: 10.1101/gr.278985.124. Epub ahead of print. PMID: 38839374.
Taton M, Willems F, Widomski C, Georges D, Martin C, Jiang Y, Renard K, Konopnicki D, Cogan A, Necsoi C, Matagne A, De Wit S, Ackerman ME, Marchant A, Dauby N. HIV-related immune activation attenuates polyfunctional IgG and memory B-cell responses to Tdap immunization during pregnancy. EBioMedicine. 2024 Jun;104:105179. doi: 10.1016/j.ebiom.2024.105179. Epub 2024 Jun 7. PMID: 38848615; PMCID: PMC11192781.
Sun P, Li C, Yang C, Sun M, Hou H, Guan Y, Chen J, Liu S, Chen K, Ma Y, Huang Y, Li X, Wang H, Wang L, Chen S, Cheng H, Xiong W, Sheng X, Zhang M, Peng J, Wang S, Wang Y, Yin L. A biodegradable and flexible neural interface for transdermal optoelectronic modulation and regeneration of peripheral nerves. Nat Commun. 2024 Jun 3;15(1):4721. doi: 10.1038/s41467-024-49166-4. PMID: 38830884; PMCID: PMC11148186.
Geiger CJ, Wong GCL, O’Toole GA. A bacterial sense of touch: T4P retraction motor as a means of surface sensing by Pseudomonas aeruginosa PA14. J Bacteriol. 2024 Jul 25;206(7):e0044223. doi: 10.1128/jb.00442-23. Epub 2024 Jun 4. PMID: 38832786; PMCID: PMC11270903.
Wang Y, Gui J, Howe CG, Emond JA, Criswell RL, Gallagher LG, Huset CA, Peterson LA, Botelho JC, Calafat AM, Christensen B, Karagas MR, Romano ME. Association of diet with per- and polyfluoroalkyl substances in plasma and human milk in the New Hampshire Birth Cohort Study. Sci Total Environ. 2024 Jul 10;933:173157. doi: 10.1016/j.scitotenv.2024.173157. Epub 2024 May 11. PMID: 38740209; PMCID: PMC11247473.
Caverly LJ, Ross BD, Dickson RP. From gut to lung and back again: early life microbiota in cystic fibrosis. Eur Respir J. 2024 May 9;63(5):2400595. doi: 10.1183/13993003.00595-2024. PMID: 38724179.
Gidding SS, Ballantyne CM, Cuchel M, de Ferranti S, Hudgins L, Jamison A, McGowan MP, Peterson AL, Steiner RD, Uveges MK, Wang Y. It is Time to Screen for Homozygous Familial Hypercholesterolemia in the United States. Glob Heart. 2024 May 3;19(1):43. doi: 10.5334/gh.1316. PMID: 38708402; PMCID: PMC11067975.
Frost HR. Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error. PLoS Comput Biol. 2024 Apr 29;20(4):e1012084. doi: 10.1371/journal.pcbi.1012084. PMID: 38683883; PMCID: PMC11081506.
Pastora AB, Rzasa KM, O’Toole GA. Multiple pathways impact the swarming motility of Pseudomonas fluorescens Pf0-1. Microbiol Spectr. 2024 Jun 4;12(6):e0016624. doi: 10.1128/spectrum.00166-24. Epub 2024 Apr 30. PMID: 38687073; PMCID: PMC11237744.
Murray MA, Noronha KJ, Wang Y, Friedman AP, Paradkar S, Suh HW, Sundaram RK, Brenner C, Saltzman WM, Bindra RS. Exploiting Metabolic Defects in Glioma with Nanoparticle-Encapsulated NAMPT Inhibitors. Mol Cancer Ther. 2024 Aug 1;23(8):1176-1187. doi: 10.1158/1535-7163.MCT-24-0012. PMID: 38691846; PMCID: PMC11292319.
Li X, Mara AB, Musial SC, Kolling FW, Gibbings SL, Gerebtsov N, Jakubzick CV. Coordinated chemokine expression defines macrophage subsets across tissues. Nat Immunol. 2024 Jun;25(6):1110-1122. doi: 10.1038/s41590-024-01826-9. Epub 2024 May 2. PMID: 38698086.
Frost HR. A generalized eigenvector centrality for multilayer networks with inter-layer constraints on adjacent node importance. Appl Netw Sci. 2024;9(1):14. doi: 10.1007/s41109-024-00620-8. Epub 2024 Apr 30. PMID: 38699246; PMCID: PMC11060970.
Lee MK, Azizgolshani N, Shapiro JA, Nguyen LN, Kolling FW, Zanazzi GJ, Frost HR, Christensen BC. Identifying tumor type and cell type-specific gene expression alterations in pediatric central nervous system tumors. Nat Commun. 2024 Apr 30;15(1):3634. doi: 10.1038/s41467-024-47712-8. PMID: 38688897; PMCID: PMC11061189.
Lee MK, Azizgolshani N, Zhang Z, Perreard L, Kolling FW, Nguyen LN, Zanazzi GJ, Salas LA, Christensen BC. Associations in cell type-specific hydroxymethylation and transcriptional alterations of pediatric central nervous system tumors. Nat Commun. 2024 Apr 30;15(1):3635. doi: 10.1038/s41467-024-47943-9. PMID: 38688903; PMCID: PMC11061294.
Chacko R, Davis MJ, Levy J, LeBoeuf M. Integration of a deep learning basal cell carcinoma detection and tumor mapping algorithm into the Mohs micrographic surgery workflow and effects on clinical staffing: A simulated, retrospective study. JAAD Int. 2024 Mar 1;15:185-191. doi: 10.1016/j.jdin.2024.02.014. PMID: 38651039; PMCID: PMC11033206.
Jennings EB, Percarpio RB, Tafe LJ, Demidenko E, Levy J, Gutmann EJ, Marotti JD. Does ROSE matter? Evaluation of final diagnostic, PD-L1 immunohistochemistry, and molecular testing yields of CT-guided lung biopsies performed before and after the onset of the COVID-19 pandemic. J Am Soc Cytopathol. 2024 Jul-Aug;13(4):263-271. doi: 10.1016/j.jasc.2024.03.004. Epub 2024 Mar 29. PMID: 38677893.
Song L, Langmead B. Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification. Genome Biol. 2024 Apr 25;25(1):106. doi: 10.1186/s13059-024-03244-4. PMID: 38664753; PMCID: PMC11046777.
Bratches RWR, Freundlich NZ, Odom JN, O’Malley AJ, Barr PJ. Communicating visit information to family caregivers: How does method matter? A national survey. Palliat Support Care. 2024 Apr 24:1-8. doi: 10.1017/S1478951524000427. Epub ahead of print. PMID: 38654707.
Gerber S, Silver RE, Das SK, Greene SS, Dix SR, Ramirez I, Morcos CL, Dao MC, Ceglia L, Roberts SB. Development and Feasibility of an eHealth Diabetes Prevention Program Adapted for Older Adults-Results from a Randomized Control Pilot Study. Nutrients. 2024 Mar 23;16(7):930. doi: 10.3390/nu16070930. PMID: 38612963; PMCID: PMC11154527.
O’Toole GA. It’s time to write a minireview. J Bacteriol. 2024 May 23;206(5):e0011324. doi: 10.1128/jb.00113-24. Epub 2024 Apr 16. PMID: 38624220; PMCID: PMC11112987.
Goity A, Dovzhenok A, Lim S, Hong C, Loros J, Dunlap JC, Larrondo LF. kTranscriptional rewiring of an evolutionarily conserved circadian clock. EMBO J. 2024 May;43(10):2015-2034. doi: 10.1038/s44318-024-00088-3. Epub 2024 Apr 16. PMID: 38627599; PMCID: PMC11099105.
Vasenina A, Fu Y, O’Toole GA, Mucha PJ. Local control: a hub-based model for the c-di-GMP network. mSphere. 2024 May 29;9(5):e0017824. doi: 10.1128/msphere.00178-24. Epub 2024 Apr 9. PMID: 38591888; PMCID: PMC11237430.
Bagheri M, Mohamed GA, Mohamed Saleem MA, Ognjenovic NB, Lu H, Kolling FW, Wilkins OM, Das S, LaCroix IS, Nagaraj SH, Muller KE, Gerber SA, Miller TW, Pattabiraman DR. Pharmacological induction of chromatin remodeling drives chemosensitization in triple-negative breast cancer. Cell Rep Med. 2024 Apr 16;5(4):101504. doi: 10.1016/j.xcrm.2024.101504. Epub 2024 Apr 8. PMID: 38593809; PMCID: PMC11031425.
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
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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.
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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.
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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.
