My Bibliography

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Mia Jovanova, Ovidia Stanoi, Christin Scholz, Bruce Doré, Danielle Cosme, Yoona Kang, Nicole Cooper, Zachary M. Boyd, Dani S. Bassett, Peter J. Mucha, David M. Lydon-Staley, Kevin N. Ochsner, Emily B. Falk. Neural responses to peers moderate conversation-drinking associations in daily life. Scientific Reports. 2025 July. doi: 10.1038/s41598-025-05846-9.

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Xie He, Philip S. Chodrow, Peter J. Mucha. Edge correlations and link prediction in growing hypergraphs. Physical Review E. 2025 August. doi: 10.1103/4lkd-mtzq.

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Tyler M. Barrett, Charles Kevin Tiu, Kayla Kauffman, Michelle Pender, Jean Yves Rabezara, Prisca Rahary, Lin-Fa Wang, Randall A. Kramer, Voahangy Soarimalala, Peter J. Mucha, James Moody, Charles L. Nunn. Identifying Social-Epidemiological Roles Associated with Viral Exposure Using Regular Equivalence Blockmodeling. 2025 November. DOI: 10.1101/2025.11.05.25339611.

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Masuda N, Boyd ZM, Garlaschelli D, Mucha PJ. Introduction to correlation networks: Interdisciplinary approaches beyond thresholding. Phys Rep. 2025 Aug 21;1136:1-39. doi: 10.1016/j.physrep.2025.06.002. Epub 2025 Jun 30. PubMed PMID: 40814354; PubMed Central PMCID: PMC12345407.

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Tom Wolff, Jonathan H. Morgan, Gabriel Varela, Kieran Lele, Ethan Bhojani, Emily Heraty, Dana K Pasquale, Peter Mucha, James Moody. ideanet: Integrating Data Exchange and Analysis for Networks ('ideanet'). 2024 December. DOI: 10.32614/cran.package.ideanet.

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Xie He, Amir Ghasemian, Eun Lee, Alice C. Schwarze, Aaron Clauset, Peter J. Mucha. Link prediction accuracy on real-world networks under non-uniform missing-edge patterns. PLOS ONE. 2024 July. doi: 10.1371/journal.pone.0306883.

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Tom Wolff, Jonathan Howard Morgan, Gabriel Varela, Kieran Lele, Ethan Bhojani, Emily Heraty, Dana Pasquale, Peter Mucha, James Moody. ideanet: Integrating Data Exchange and Analysis for Networks ('ideanet'). 2024 December. DOI: 10.32614/cran.package.ideanet.

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William Stanford, Peter J. Mucha, Eran Dayan. Age-related differences in network controllability are mitigated by redundancy in large-scale brain networks. Communications Biology. 2024 June. doi: 10.1038/s42003-024-06392-2.

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Xie He, Amir Ghasemian, Eun Lee, Aaron Clauset, Peter J. Mucha. Sequential stacking link prediction algorithms for temporal networks. Nature Communications. 2024 February. doi: 10.1038/s41467-024-45598-0.

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Anna Vasenina, Yu Fu, George A. O'Toole, Peter J. Mucha. Local control: a hub-based model for the c-di-GMP network. mSphere. 2024 May. doi: 10.1128/msphere.00178-24.

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Tyler M. Barrett, Georgia C. Titcomb, Mark M. Janko, Michelle Pender, Kayla Kauffman, Alma Solis, Maheriniaina Toky Randriamoria, Hillary S. Young, Peter J. Mucha, James Moody, Randall A. Kramer, Voahangy Soarimalala, Charles L. Nunn. Disentangling social, environmental, and zoonotic transmission pathways of a gastrointestinal protozoan (Blastocystis spp.) in northeast Madagascar. American Journal of Biological Anthropology. 2024 November. doi: 10.1002/ajpa.25030.

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Robinson JI, Marks LR, Hinton AL, O'Halloran JA, Goss CW, Mucha PJ, Henderson JP. Development of a metabolome-based respiratory infection prognostic during COVID-19 arrival. mBio. 2025 Jan 8;16(1):e0334323. doi: 10.1128/mbio.03343-23. Epub 2024 Nov 22. PubMed PMID: 39576111; PubMed Central PMCID: PMC11708037.

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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. PubMed PMID: 38591888; PubMed Central PMCID: PMC11237430.

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He X, Ghasemian A, Lee E, Clauset A, Mucha PJ. Sequential stacking link prediction algorithms for temporal networks. Nat Commun. 2024 Feb 14;15(1):1364. doi: 10.1038/s41467-024-45598-0. PubMed PMID: 38355612; PubMed Central PMCID: PMC10866871.

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Zongsen Zou, Robert F. Potter, William H. McCoy, 4th, John A. Wildenthal, George L. Katumba, Peter J. Mucha, Gautam Dantas, Jeffrey P. Henderson. E. coli catheter-associated urinary tract infections are associated with distinctive virulence and biofilm gene determinants. JCI Insight. 2023 January. doi: 10.1172/jci.insight.161461.

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Xie He, Amir Ghasemian, Eun Lee, Aaron Clauset, Peter Mucha. Sequential Stacking Link Prediction Algorithms for Temporal Networks. 2023 February. DOI: 10.21203/rs.3.rs-2535525/v1.

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Amanda L. McGowan, Zachary M. Boyd, Yoona Kang, Logan Bennett, Peter J. Mucha, Kevin N. Ochsner, Dani S. Bassett, Emily B. Falk, David M. Lydon-Staley. Within-Person Temporal Associations Among Self-Reported Physical Activity, Sleep, and Well-Being in College Students. Psychosomatic Medicine. 2023 February. doi: 10.1097/PSY.0000000000001159.

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Zou Z, Potter RF, McCoy WH 4th, Wildenthal JA, Katumba GL, Mucha PJ, Dantas G, Henderson JP. E. coli catheter-associated urinary tract infections are associated with distinctive virulence and biofilm gene determinants. JCI Insight. 2023 Jan 24;8(2). doi: 10.1172/jci.insight.161461. PubMed PMID: 36512427; PubMed Central PMCID: PMC9977300.

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Zhou D, Kang Y, Cosme D, Jovanova M, He X, Mahadevan A, Ahn J, Stanoi O, Brynildsen JK, Cooper N, Cornblath EJ, Parkes L, Mucha PJ, Ochsner KN, Lydon-Staley DM, Falk EB, Bassett DS. Mindful attention promotes control of brain network dynamics for self-regulation and discontinues the past from the present. Proc Natl Acad Sci U S A. 2023 Jan 10;120(2):e2201074119. doi: 10.1073/pnas.2201074119. Epub 2023 Jan 3. PubMed PMID: 36595675; PubMed Central PMCID: PMC9926276.

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Weiyan Yin, Tengfei Li, Peter J. Mucha, Jessica R. Cohen, Hongtu Zhu, Ziliang Zhu, Weili Lin. Altered neural flexibility in children with attention-deficit/hyperactivity disorder. Molecular Psychiatry. 2022 November. doi: 10.1038/s41380-022-01706-4.

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Ryan Gibson, Peter Mucha. Finite-State Parameter Space Maps for Pruning Partitions in Modularity-Based Community Detection. 2022 April. doi: 10.21203/rs.3.rs-1551680/v1.

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William H. Weir, Peter J. Mucha, William Y. Kim. A bipartite graph-based expected networks approach identifies DDR genes not associated with TMB yet predictive of immune checkpoint blockade response. Cell Reports Medicine. 2022 May; 3(5):100602. doi: 10.1016/j.xcrm.2022.100602.

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William C. Stanford, Peter J. Mucha, Eran Dayan. A robust core architecture of functional brain networks supports topological resilience and cognitive performance in middle- and old-aged adults. Proceedings of the National Academy of Sciences. 2022 November. doi: 10.1073/pnas.2203682119.

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Stanford WC, Mucha PJ, Dayan E. A robust core architecture of functional brain networks supports topological resilience and cognitive performance in middle- and old-aged adults. Proc Natl Acad Sci U S A. 2022 Nov;119(44):e2203682119. doi: 10.1073/pnas.2203682119. Epub 2022 Oct 25. PubMed PMID: 36282912; PubMed Central PMCID: PMC9636938.

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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.

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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.

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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.

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Stephanie Langella, Peter J. Mucha, Kelly S. Giovanello, Eran Dayan. The association between hippocampal volume and memory in pathological aging is mediated by functional redundancy. Neurobiology of Aging. 2021 December. doi: 10.1016/j.neurobiolaging.2021.09.002.

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Stephanie Langella, Muhammad Usman Sadiq, Peter J. Mucha, Kelly S. Giovanello, Eran Dayan. Lower functional hippocampal redundancy in mild cognitive impairment. Translational Psychiatry. 2021 January. doi: 10.1038/s41398-020-01166-w.

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Muhammad Usman Sadiq, Stephanie Langella, Kelly S. Giovanello, Peter J. Mucha, Eran Dayan. Accrual of functional redundancy along the lifespan and its effects on cognition. NeuroImage. 2021 April; 229:117737. doi: 10.1016/j.neuroimage.2021.117737.

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Keith A. Kroma-Wiley, Peter J. Mucha, Danielle S. Bassett. Synchronization of coupled Kuramoto oscillators under resource constraints. Physical Review E. 2021 July; 104(1). doi: 10.1103/PhysRevE.104.014211.

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Daniel A. Paydarfar, David Paydarfar, Peter J. Mucha, Joshua Chang. Optimizing Emergency Stroke Transport Strategies Using Physiological Models. Stroke. 2021 December; 52(12):4010--4020. doi: 10.1161/STROKEAHA.120.031633.

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Smeekens JM, Johnson-Weaver BT, Hinton AL, Azcarate-Peril MA, Moran TP, Immormino RM, Kesselring JR, Steinbach EC, Orgel KA, Staats HF, Burks AW, Mucha PJ, Ferris MT, Kulis MD. Fecal IgA, Antigen Absorption, and Gut Microbiome Composition Are Associated With Food Antigen Sensitization in Genetically Susceptible Mice. Front Immunol. 2020;11:599637. doi: 10.3389/fimmu.2020.599637. eCollection 2020. PubMed PMID: 33542716; PubMed Central PMCID: PMC7850988.

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Jackson JC, Watts J, Henry TR, List JM, Forkel R, Mucha PJ, Greenhill SJ, Gray RD, Lindquist KA. Emotion semantics show both cultural variation and universal structure. Science. 2019 Dec 20;366(6472):1517-1522. doi: 10.1126/science.aaw8160. PubMed PMID: 31857485.

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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.

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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.

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Lee E, Karimi F, Wagner C, Jo HH, Strohmaier M, Galesic M. Homophily and minority-group size explain perception biases in social networks. Nat Hum Behav. 2019 Oct;3(10):1078-1087. doi: 10.1038/s41562-019-0677-4. Epub 2019 Aug 12. PubMed PMID: 31406337; PubMed Central PMCID: PMC6839769.

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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.

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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.

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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.

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Copeland M, Siennick SE, Feinberg ME, Moody J, Ragan DT. Social Ties Cut Both Ways: Self-Harm and Adolescent Peer Networks. J Youth Adolesc. 2019 Aug;48(8):1506-1518. doi: 10.1007/s10964-019-01011-4. Epub 2019 Apr 15. PubMed PMID: 30989471; PubMed Central PMCID: PMC6640100.

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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.

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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.

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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.

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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.

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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.

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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.

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Copeland M, Fisher JC, Moody J, Feinberg ME. Different Kinds of Lonely: Dimensions of Isolation and Substance Use in Adolescence. J Youth Adolesc. 2018 Aug;47(8):1755-1770. doi: 10.1007/s10964-018-0860-3. Epub 2018 May 17. PubMed PMID: 29774451; PubMed Central PMCID: PMC6045973.

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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.

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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.