2024
2023
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
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
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 –
Fügenschuh M, Fu F. Overcoming vaccine hesitancy by multiplex social networktargeting: an analysis of targeting algorithms and implications. Appl Netw Sci.2023;8(1):67. doi: 10.1007/s41109-023-00595-y. Epub 2023 Sep 21. PMID: 37745797;PMCID: PMC10514145.
Chen X, Fu F. Outlearning extortioners: unbending strategies can fosterreciprocal fairness and cooperation. PNAS Nexus. 2023 May 25;2(6):pgad176. doi:10.1093/pnasnexus/pgad176. PMID: 37287707; PMCID: PMC10244001.
Song L, Bai G, Liu XS, Li B and Li H, Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data, Genome Res. 2023 Jun;33(6):923-931. PMID: 37169596 PMCID: PMC10519407
Sheehan S, Mawe S, Chen M, Klug J, Ladiges W, Korstanje R, Mahoney JM. A machine learning approach for quantifying age-related histological changes in the mouse kidney. bioRxiv [Preprint]. 2023 Jul 7:2023.07.07.548002. doi: 10.1101/2023.07.07.548002. PMID: 37461572; PMCID: PMC10350062.
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.
Valdivia, G., Alonso-Miguel, D., Perez-Alenza, M.D., Zimmermann, A.B.E., Schaafsma, E., Kolling, F.W., Barreno, L., Alonso-Diez, A., Beiss, V., Affonso de Oliveira, J.F., Suárez-Redondo, M., Fiering, S., Steinmetz, N.F., vom Berg, J., Peña, L., Arias-Pulido, H., 2023. Neoadjuvant Intratumoral Immunotherapy with Cowpea Mosaic Virus Induces Local and Systemic Antitumor Efficacy in Canine Mammary Cancer Patients. Cells 12, 2241. PMID: 37759464 PMCID: PMC10527658
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;
PubMed Central PMCID: PMC10153261
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
PMCID: PMC10055145
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.