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Gibson RA, Mucha PJ. Finite-state parameter space maps for pruning partitions in modularity-based community detection. Sci Rep. 2022 Sep 23;12(1):15928. doi: 10.1038/s41598-022-20142-6. PubMed PMID: 36151268; PubMed Central PMCID: PMC9508178.
Weir WH, Mucha PJ, Kim WY. A bipartite graph-based expected networks approach identifies DDR genes not associated with TMB yet predictive of immune checkpoint blockade response. Cell Rep Med. 2022 May 17;3(5):100602. doi: 10.1016/j.xcrm.2022.100602. Epub 2022 Apr 18. PubMed PMID: 35584624; PubMed Central PMCID: PMC9133403.
Hinton AL, Mucha PJ. A Simultaneous Feature Selection and Compositional Association Test for Detecting Sparse Associations in High-Dimensional Metagenomic Data. Front Microbiol. 2022;13:837396. doi: 10.3389/fmicb.2022.837396. eCollection 2022. PubMed PMID: 35387076; PubMed Central PMCID: PMC8978828.
Gates KM, Fisher ZF, Arizmendi C, Henry TR, Duffy KA, Mucha PJ. Assessing the robustness of cluster solutions obtained from sparse count matrices. Psychol Methods. 2019 Dec;24(6):675-689. doi: 10.1037/met0000204. Epub 2019 Feb 11. PubMed PMID: 30742473; PubMed Central PMCID: PMC6689462.
Lee E, Emmons S, Gibson R, Moody J, Mucha PJ. Concurrency and reachability in treelike temporal networks. Phys Rev E. 2019 Dec;100(6-1):062305. doi: 10.1103/PhysRevE.100.062305. PubMed PMID: 31962508; PubMed Central PMCID: PMC6989038.
Trogdon JG, Weir WH, Shai S, Mucha PJ, Kuo TM, Meyer AM, Stitzenberg KB. Comparing Shared Patient Networks Across Payers. J Gen Intern Med. 2019 Oct;34(10):2014-2020. doi: 10.1007/s11606-019-04978-9. Epub 2019 Apr 3. PubMed PMID: 30945065; PubMed Central PMCID: PMC6816773.
Robinson JI, Weir WH, Crowley JR, Hink T, Reske KA, Kwon JH, Burnham CD, Dubberke ER, Mucha PJ, Henderson JP. Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections. J Clin Invest. 2019 Aug 12;129(9):3792-3806. doi: 10.1172/JCI126905. eCollection 2019 Aug 12. PubMed PMID: 31403473; PubMed Central PMCID: PMC6715368.
Emmons S, Mucha PJ. Map equation with metadata: Varying the role of attributes in community detection. Phys Rev E. 2019 Aug;100(2-1):022301. doi: 10.1103/PhysRevE.100.022301. PubMed PMID: 31574624.
Fisher JC. Social Space Diffusion: Applications of a Latent Space Model to Diffusion with Uncertain Ties. Sociol Methodol. 2019 Aug 1;49(1):258-294. doi: 10.1177/0081175018820075. Epub 2019 Feb 5. PubMed PMID: 33833476; PubMed Central PMCID: PMC8025911.
Lee HW, Malik N, Shi F, Mucha PJ. Social clustering in epidemic spread on coevolving networks. Phys Rev E. 2019 Jun;99(6-1):062301. doi: 10.1103/PhysRevE.99.062301. PubMed PMID: 31330685; PubMed Central PMCID: PMC6790070.
Li W, Cranmer SJ, Zheng Z, Mucha PJ. Infectivity enhances prediction of viral cascades in Twitter. PLoS One. 2019;14(4):e0214453. doi: 10.1371/journal.pone.0214453. eCollection 2019. PubMed PMID: 30995266; PubMed Central PMCID: PMC6469756.
Kirk JM, Kim SO, Inoue K, Smola MJ, Lee DM, Schertzer MD, Wooten JS, Baker AR, Sprague D, Collins DW, Horning CR, Wang S, Chen Q, Weeks KM, Mucha PJ, Calabrese JM. Functional classification of long non-coding RNAs by k-mer content. Nat Genet. 2018 Oct;50(10):1474-1482. doi: 10.1038/s41588-018-0207-8. Epub 2018 Sep 17. PubMed PMID: 30224646; PubMed Central PMCID: PMC6262761.
Heroy S, Taylor D, Shi FB, Forest MG, Mucha PJ. RIGID GRAPH COMPRESSION: MOTIF-BASED RIGIDITY ANALYSIS FOR DISORDERED FIBER NETWORKS. Multiscale Model Simul. 2018;16(3):1283-1304. doi: 10.1137/17M1157271. Epub 2018 Aug 21. PubMed PMID: 30450018; PubMed Central PMCID: PMC6234004.
Stanley N, Kwitt R, Niethammer M, Mucha PJ. Compressing Networks with Super Nodes. Sci Rep. 2018 Jul 18;8(1):10892. doi: 10.1038/s41598-018-29174-3. PubMed PMID: 30022035; PubMed Central PMCID: PMC6052167.
Granell C, Mucha PJ. Epidemic spreading in localized environments with recurrent mobility patterns. Phys Rev E. 2018 May;97(5-1):052302. doi: 10.1103/PhysRevE.97.052302. PubMed PMID: 29906863; PubMed Central PMCID: PMC6195814.
Trogdon JG, Chang Y, Shai S, Mucha PJ, Kuo TM, Meyer AM, Stitzenberg KB. Care Coordination and Multispecialty Teams in the Care of Colorectal Cancer Patients. Med Care. 2018 May;56(5):430-435. doi: 10.1097/MLR.0000000000000906. PubMed PMID: 29578953.
Li Z, Mucha PJ, Taylor D. NETWORK-ENSEMBLE COMPARISONS WITH STOCHASTIC REWIRING AND VON NEUMANN ENTROPY. SIAM J Appl Math. 2018;78(2):897-920. doi: 10.1137/17M1124218. Epub 2018 Mar 27. PubMed PMID: 30319156; PubMed Central PMCID: PMC6181241.
Lee HW, Malik N, Mucha PJ. Evolutionary prisoner's dilemma games coevolving on adaptive networks. J Complex Netw. 2018 Feb;6(1):1-23. doi: 10.1093/comnet/cnx018. Epub 2017 Jul 7. PubMed PMID: 29732158; PubMed Central PMCID: PMC5931405.
Taylor D, Caceres RS, Mucha PJ. Super-Resolution Community Detection for Layer-Aggregated Multilayer Networks. Phys Rev X. 2017 Jul-Sep;7(3). doi: 10.1103/PhysRevX.7.031056. Epub 2017 Sep 26. PubMed PMID: 29445565; PubMed Central PMCID: PMC5809009.
Weir WH, Emmons S, Gibson R, Taylor D, Mucha PJ. Post-Processing Partitions to Identify Domains of Modularity Optimization. Algorithms. 2017 Sep;10(3). doi: 10.3390/a10030093. Epub 2017 Aug 19. PubMed PMID: 29046743; PubMed Central PMCID: PMC5642987.
Taylor D, Myers SA, Clauset A, Porter MA, Mucha PJ. EIGENVECTOR-BASED CENTRALITY MEASURES FOR TEMPORAL NETWORKS(). Multiscale Model Simul. 2017;15(1):537-574. doi: 10.1137/16M1066142. Epub 2017 Mar 28. PubMed PMID: 29046619; PubMed Central PMCID: PMC5643020.
Malik N, Shi F, Lee HW, Mucha PJ. Transitivity reinforcement in the coevolving voter model. Chaos. 2016 Dec;26(12):123112. doi: 10.1063/1.4972116. PubMed PMID: 28039984; PubMed Central PMCID: PMC5848690.
Entwisle B, Williams NE, Verdery AM, Rindfuss RR, Walsh SJ, Malanson GP, Mucha PJ, Frizzelle BG, McDaniel PM, Yao X, Heumann BW, Prasartkul P, Sawangdee Y, Jampaklay A. Climate Shocks and Migration: An Agent-Based Modeling Approach. Popul Environ. 2016 Sep;38(1):47-71. doi: 10.1007/s11111-016-0254-y. Epub 2016 Jan 23. PubMed PMID: 27594725; PubMed Central PMCID: PMC5004973.
Taylor D, Shai S, Stanley N, Mucha PJ. Enhanced Detectability of Community Structure in Multilayer Networks through Layer Aggregation. Phys Rev Lett. 2016 Jun 3;116(22):228301. doi: 10.1103/PhysRevLett.116.228301. Epub 2016 Jun 2. PubMed PMID: 27314740; PubMed Central PMCID: PMC5125641.
Stanley N, Shai S, Taylor D, Mucha PJ. Clustering network layers with the strata multilayer stochastic block model. IEEE Trans Netw Sci Eng. 2016 Apr-Jun;3(2):95-105. doi: 10.1109/TNSE.2016.2537545. Epub 2016 Mar 25. PubMed PMID: 28435844; PubMed Central PMCID: PMC5400296.
Malik N, Bookhagen B, Mucha PJ. Spatiotemporal patterns and trends of Indian monsoonal rainfall extremes. Geophys Res Lett. 2016 Feb 28;43(4):1710-1717. doi: 10.1002/2016GL067841. PubMed PMID: 27909349; PubMed Central PMCID: PMC5125774.
Verdery AM, Mouw T, Bauldry S, Mucha PJ. Correction: Network Structure and Biased Variance Estimation in Respondent Driven Sampling. PLoS One. 2016;11(1):e0148006. doi: 10.1371/journal.pone.0148006. eCollection 2016. PubMed PMID: 26799651; PubMed Central PMCID: PMC4723124.
Verdery AM, Mouw T, Bauldry S, Mucha PJ. Network Structure and Biased Variance Estimation in Respondent Driven Sampling. PLoS One. 2015;10(12):e0145296. doi: 10.1371/journal.pone.0145296. eCollection 2015. PubMed PMID: 26679927; PubMed Central PMCID: PMC4682989.
Parker KS, Wilson JD, Marschall J, Mucha PJ, Henderson JP. Network Analysis Reveals Sex- and Antibiotic Resistance-Associated Antivirulence Targets in Clinical Uropathogens. ACS Infect Dis. 2015 Nov 13;1(11):523-532. doi: 10.1021/acsinfecdis.5b00022. Epub 2015 Jul 24. PubMed PMID: 26985454; PubMed Central PMCID: PMC4788272.
Cranmer SJ, Menninga EJ, Mucha PJ. Kantian fractionalization predicts the conflict propensity of the international system. Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11812-6. doi: 10.1073/pnas.1509423112. Epub 2015 Sep 3. PubMed PMID: 26338977; PubMed Central PMCID: PMC4586843.
Taylor D, Klimm F, Harrington HA, Kramár M, Mischaikow K, Porter MA, Mucha PJ. Erratum: topological data analysis of contagion maps for examining spreading processes on networks. Nat Commun. 2015 Sep 4;6:8374. doi: 10.1038/ncomms9374. PubMed PMID: 26338078; PubMed Central PMCID: PMC4569840.
Taylor D, Klimm F, Harrington HA, Kramár M, Mischaikow K, Porter MA, Mucha PJ. Topological data analysis of contagion maps for examining spreading processes on networks. Nat Commun. 2015 Jul 21;6:7723. doi: 10.1038/ncomms8723. PubMed PMID: 26194875; PubMed Central PMCID: PMC4566922.
Chen A, McKinley SA, Shi F, Wang S, Mucha PJ, Harit D, Forest MG, Lai SK. Modeling of Virion Collisions in Cervicovaginal Mucus Reveals Limits on Agglutination as the Protective Mechanism of Secretory Immunoglobulin A. PLoS One. 2015;10(7):e0131351. doi: 10.1371/journal.pone.0131351. eCollection 2015. PubMed PMID: 26132216; PubMed Central PMCID: PMC4488843.
Jeub LG, Balachandran P, Porter MA, Mucha PJ, Mahoney MW. Think locally, act locally: detection of small, medium-sized, and large communities in large networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Jan;91(1):012821. doi: 10.1103/PhysRevE.91.012821. Epub 2015 Jan 26. PubMed PMID: 25679670; PubMed Central PMCID: PMC5125638.
Shi F, Mucha PJ. Nonaxisymmetric high-aspect-ratio ellipsoids under shear: lowest-order correction for finite aspect ratios. Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Jul;90(1):013005. doi: 10.1103/PhysRevE.90.013005. Epub 2014 Jul 8. PubMed PMID: 25122367.
McKinley SA, Chen A, Shi F, Wang S, Mucha PJ, Forest MG, Lai SK. Modeling neutralization kinetics of HIV by broadly neutralizing monoclonal antibodies in genital secretions coating the cervicovaginal mucosa. PLoS One. 2014;9(6):e100598. doi: 10.1371/journal.pone.0100598. eCollection 2014. PubMed PMID: 24967706; PubMed Central PMCID: PMC4072659.
Malik N, Marwan N, Zou Y, Mucha PJ, Kurths J. Fluctuation of similarity to detect transitions between distinct dynamical regimes in short time series. Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Jun;89(6):062908. doi: 10.1103/PhysRevE.89.062908. Epub 2014 Jun 10. PubMed PMID: 25019852; PubMed Central PMCID: PMC5125642.
Melnik S, Porter MA, Mucha PJ, Gleeson JP. Dynamics on modular networks with heterogeneous correlations. Chaos. 2014 Jun;24(2):023106. doi: 10.1063/1.4869983. PubMed PMID: 24985420; PubMed Central PMCID: PMC4000391.
Chen A, McKinley SA, Wang S, Shi F, Mucha PJ, Forest MG, Lai SK. Transient antibody-mucin interactions produce a dynamic molecular shield against viral invasion. Biophys J. 2014 May 6;106(9):2028-36. doi: 10.1016/j.bpj.2014.02.038. PubMed PMID: 24806935; PubMed Central PMCID: PMC4017286.
Klimm F, Bassett DS, Carlson JM, Mucha PJ. Resolving structural variability in network models and the brain. PLoS Comput Biol. 2014 Mar;10(3):e1003491. doi: 10.1371/journal.pcbi.1003491. eCollection 2014 Mar. PubMed PMID: 24675546; PubMed Central PMCID: PMC3967917.
Bassett DS, Wymbs NF, Porter MA, Mucha PJ, Grafton ST. Cross-linked structure of network evolution. Chaos. 2014 Mar;24(1):013112. doi: 10.1063/1.4858457. PubMed PMID: 24697374; PubMed Central PMCID: PMC4108627.
Shi F, Mucha PJ, Durrett R. Multiopinion coevolving voter model with infinitely many phase transitions. Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Dec;88(6):062818. doi: 10.1103/PhysRevE.88.062818. Epub 2013 Dec 30. PubMed PMID: 24483522; PubMed Central PMCID: PMC5131864.
Malik N, Mucha PJ. Role of social environment and social clustering in spread of opinions in coevolving networks. Chaos. 2013 Dec;23(4):043123. doi: 10.1063/1.4833995. PubMed PMID: 24387562; PubMed Central PMCID: PMC4108632.
Bassett DS, Wymbs NF, Rombach MP, Porter MA, Mucha PJ, Grafton ST. Task-based core-periphery organization of human brain dynamics. PLoS Comput Biol. 2013;9(9):e1003171. doi: 10.1371/journal.pcbi.1003171. Epub 2013 Sep 26. PubMed PMID: 24086116; PubMed Central PMCID: PMC3784512.
Walsh SJ, Malanson GP, Entwisle B, Rindfuss RR, Mucha PJ, Heumann BW, McDaniel PM, Frizzelle BG, Verdery AM, Williams N, Xiaozheng Y, Ding D. Design of an Agent-Based Model to Examine Population-Environment Interactions in Nang Rong District, Thailand. Appl Geogr. 2013 May;39. doi: 10.1016/j.apgeog.2012.12.010. PubMed PMID: 24277975; PubMed Central PMCID: PMC3838637.
Bassett DS, Porter MA, Wymbs NF, Grafton ST, Carlson JM, Mucha PJ. Robust detection of dynamic community structure in networks. Chaos. 2013 Mar;23(1):013142. doi: 10.1063/1.4790830. PubMed PMID: 23556979; PubMed Central PMCID: PMC3618100.
Onnela JP, Fenn DJ, Reid S, Porter MA, Mucha PJ, Fricker MD, Jones NS. Taxonomies of networks from community structure. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Sep;86(3 Pt 2):036104-36104. doi: 10.1103/physreve.86.036104. Epub 2012 Sep 10. PubMed PMID: 23030977; PubMed Central PMCID: PMC4144942.
Wymbs NF, Bassett DS, Mucha PJ, Porter MA, Grafton ST. Differential recruitment of the sensorimotor putamen and frontoparietal cortex during motor chunking in humans. Neuron. 2012 Jun 7;74(5):936-46. doi: 10.1016/j.neuron.2012.03.038. PubMed PMID: 22681696; PubMed Central PMCID: PMC3372854.
Durrett R, Gleeson JP, Lloyd AL, Mucha PJ, Shi F, Sivakoff D, Socolar JE, Varghese C. Graph fission in an evolving voter model. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3682-7. doi: 10.1073/pnas.1200709109. Epub 2012 Feb 21. PubMed PMID: 22355142; PubMed Central PMCID: PMC3309720.
Gleeson JP, Melnik S, Ward JA, Porter MA, Mucha PJ. Accuracy of mean-field theory for dynamics on real-world networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Feb;85(2 Pt 2):026106. doi: 10.1103/PhysRevE.85.026106. Epub 2012 Feb 7. PubMed PMID: 22463278.
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