Publications

We list all our publications as follows. For some of the papers, we provided PDF files so that you can download them. For the rest papers, if you cannot download them from the publisher, please feel free to reach out to us.
Review
Perspective
Research Article:
In Press; Submitted; In Preparation; 2023; 2022; 2021; 2020; 2019; 2018; 2017; 2016; 2015; 2014; 2013; 2012; 2011; 2010; 2009; 2008; 2007; 2006; 2003; 2002; 2001.

Review

Liu YY. Controlling the human microbiome. Cell Systems 2023;14(2):135-159. PDF

D’Souza RM, Bernardo M, Liu YY, Controlling complex networks with complex nodes. Nature Review Physics 2023;5:250. PDF

Chen C, Liu YY. A survey on hyperlink prediction. IEEE Transactions on Neural Networks and Learning Systems (early access). Date of Publication: 26 June 2023. PDF

Ke S, Hartmann J, Ressler KJ, Liu YY, Koenen KC. The emerging role of the gut microbiome in posttraumatic stress disorder. Brain, Behavior, and Immunity. 2023;114:360-370. PDF

Liu YY, Barabási AL. Control Principles of Complex Systems. Reviews of Modern Physics 2016;88(3):053006. PDF

Perspective

Aparicio A, Liu YY. Distinct dynamic phases observed in bacterial microcosms. Engineering Microbiology 2023;3(1):100063.

Lee-Sarwar K, Liu YY, Litonjua AA, Weiss ST. Prenatal and perinatal influences on the microbiome: Clinical implications. J Allergy Clin Immunol. 2023;152(6):1414-1416.

Shakiba N, Li C, Garcia-Ojalvo J, Cho KH, Patil K, Walczak A, Liu YY, Kuehn S, Nie Q, Klein A, Deco G, Kringelbach M, Iyer-Biswas S. How can Waddington-like landscapes facilitate insights beyond developmental biology? Cell Systems 2022;13(1):4-9.

Ke S, Weiss ST, Liu YYRejuvenating the human gut microbiome. Trends in Molecular Medicine 2022;28(8):619-630. PDF

Liu YYTheoretical progress and practical challenges in controlling complex networks. National Science Review 2014;1(3):341-343.

Slotine JJ, Liu YYComplex networks: The missing link. Nature Physics 2012;8:512–513. 


Research Articles

In Press

Ma Q, Liu YY, Olshevsky A. Optimal Fixed Lockdown for Pandemic Control. IEEE Transactions on Automatic Control (In Press).

Guimond AJ, Ke S, Tworoger SS, Huang T, Chan AT, Kubzansky LD, Liu YY. Driven mind, healthy gut? Relationships of eudaimonic psychological well-being with the gut microbiome in older women. Psychosomatic Medicine (in press)

Submitted

Chen C*, Wang XW*, Liu YY. Stability of Complex Ecological Systems: A Theoretical Review. Submitted to SIAM Review.

Meng Y, Cornelius SP, Liu YY, Li A. Doubly heterogeneous networks enhance the emergence of cooperation. Submitted to Nature Communication.

Wang H, Wu HJ, Liu YY, Lü L. Higher-order interaction of brain microstructural and functional connectome. Submitted to PNAS Nexus (under review).  

Wang T, Li L, Figeys D, Liu YY. Pairing Metagenomics and Metaproteomics to Pinpoint Ecological Niches and Metabolic Essentiality of Microbial Communities. Submitted to The ISME Journal (under revision & resubmission).

Wang T, Holscher HD, Maslov S, Hu FB, Weiss ST, Liu YY. Predicting metabolic response to dietary intervention using deep learning.  Submitted to Nature Communications (under revision & resubmission).

Zhang Y, Ke S, Wang XW, Sun Y, Weiss ST, Liu YY. Association Rule Mining of the Human Gut Microbiome. Submitted to Bioinformatics Advances (under revision & resubmission).

In Preparation

Aparicio A, Sun Z, Gold DR, Litonjua AA, Weiss ST, Lee-Sarwar K, Liu YY. Genotype-microbiome-metabolome associations in early childhood, and their link to BMI and childhood obesity.

Angulo MT, Lippner G, Liu YY, Barabási AL. Sensitivity of Complex Networks

Gibson TE, Carey V, Bashan A, Hohmann EL, Weiss ST, Liu YYOn the Stability Landscape of the Human Gut Microbiome: Implications for Microbiome-based Therapies.

Levy O, Tripathi S, Pope SD, Liu YY#, Medzhitov R#. Gene regulatory interactions limit the gene expression diversity.

Li A, Cornelius S, Liu YY, Wang L, Barabási AL. Control energy scaling in temporal networks.

Martino M, Dunne C, Liu Y-Y. CACTI: Visualizing the Skeleton of a Network.

Schich M, Huemer C, Adamczyk P, Manovich L, Liu YYNetwork Dimensions in the Getty Provenance Index.

Wang T, Fu Y, Shuai M, Zheng JS, Zhu L, Sun Q, Chan AT, Hu FB, Weiss ST, Liu YY. Microbiome-based correction of nutrient profiles derived from self-reported dietary assessments.

Wang XW, Liu YYCharacterizing scaling laws in gut microbial dynamics from time series data: caution is warranted

2024

Long C, Deng J, Nguyen J, Liu YY, Alm EJ, Solé R, Saavedra S. Structured community transitions explain the switching capacity of microbial systems. PNAS 2024;121(6):e2312521121.

2023

Aparicio A, Gold DR, Weiss ST, Litonjua AA, Lee-Sarwar K, Liu YY. Association of Vitamin D Level and Maternal Gut Microbiome during Pregnancy: Findings from a Randomized Controlled Trial of Antenatal Vitamin D Supplementation. Nutrients 2023;15(9):2059.

Aparicio A, Wang T, Saavedra S, Liu YY. Feasibility in MacArthur’s consumer-resource model. Theoretical Ecology 2023;16:225–238.

Chen C, Liao C, Liu YY. Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning. Nature Communications 2023;14:2375.

Chen C, Weiss ST, Liu YY, Graph Convolutional Network-based Feature Selection for High-dimensional and Low-sample Size Data, Bioinformatics 2023;39(4):btad135.

Fan C, Shen M, Nussinov Z, Liu Z, Sun Y, Liu YY. Searching for spin glass ground states through deep reinforcement learning. Nature Communications 2023;14:725.

Fan C, Shen M, Nussinov Z, Liu Z, Sun Y, Liu YY. Reply to: Deep reinforced learning heuristic tested on spin-glass ground states: The larger picture. Nature Communications 2023;14:5659.

Hobbs BD, Morrow JD, Wang XW, Liu YY, DeMeo DL, Hersh CP, Celli BR, Bueno R, Criner GJ, Silverman EK, Cho MH. Identifying Chronic Obstructive Pulmonary Disease from Integrative Omics and Clustering in Lung Tissue. BMC Pulmonary Medicine 2023;23:115.

Ke S, Guimond AJ, Tworoger SS, Huang T, Chan AT, Liu YY, Kubzansky LD. Gut feelings: associations of emotions and emotion regulation with the gut microbiome in women. Psychological Medicine 2023;Mar 21:1-10.

Ke S, Xiao Y, Weiss ST, Chen X, Kelly CP, Liu YY. A computational method to dissect colonization resistance of the gut microbiota against pathogens. Cell Reports Methods 2023;3:100576.

Ke S, Wang XW, Ratanatharathorn AD, Huang T, Roberts A, Grodstein F, Kubzansky LD, Koenen KC, Liu YY. Association of Post-Traumatic Stress Disorder with Dietary Pattern and Gut Microbiome in a Cohort of Women. Nature Mental Health 2023 (published: 19 October 2023).

Li L, Wang T, Ning Z, Zhang X, Butcher J, Serrana JM, Simopoulos C, Mayne J, Stintzi A, Mack DR, Liu YY, Figeys D. Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics. Nature Communications 2023;14:3428.

Shadid I, Lee-Sarwar K, Lu Z, Yadama A, Laranjo N, Carey V, O’Connor GT, Zeiger RS, Bacharier L, Guchelaar HJ, Liu YY, Litonjua AA, Weiss ST, Mirzakhani H. Early life gut microbiome in children following spontaneous preterm birth and maternal preeclampsia. iScience 2023;26(12):108311.

Sun Z, Lee-Sarwar K, Kelly RS, Lasky-Su JA, Litonjua AA, Weiss ST, Liu YY. Revealing the importance of prenatal gut microbiome in offspring neurodevelopment in humans. eBioMedicine 2023;90:104491.

Sun Z, Liu J, Zhang M, Wang T, Huang S, Weiss ST, Liu YY. Eliminate false positives in metagenomic profiling via targeting type IIB restriction sites. Nature Communications 2023;14:5321.

Wang T, Wang XW, Lee-Sarwar K, Litonjua AA, Weiss ST, Sun Y, Maslov S, Liu YY. Predicting metabolomic profiles from microbial composition through neural ordinary differential equations. Nature Machine Intelligence 2023;5:284.

Wang XW, Hu Y, Menichetti G, Grodstein F, Bhupathiraju SN, Sun Q, Zhang X, Hu F, Weiss ST, Liu YYNutritional redundancy in the human diet and its application in phenotype association studies. Nature Communications 2023;14:4316.

Wang XW, Liu YY. Origins of scaling laws in microbial dynamics. Physical Review Research 2023; 5:013004.

Wang XW, Madeddu L, Spirohn K, Martini L, Fazzone A, Becchetti L, Wytock TP, Kovács IA, Balogh OM, Benczik B, Pétervári M, Ágg B, Ferdinandy P, Vulliard L, Menche J, Colonnese S, Petti M, Scarano G, Cuomo F, Hao T, Laval F, Willems L, Twizere JC, Calderwood MA, Petrillo E, Barabási AL, Silverman EK, Loscalzo J, Velardi P, Liu YY. Assessment of community efforts to advance computational prediction of protein-protein interactions. Nature Communications 2023;14:1582.

Wang XW, Wang T, Schaub DP, Chen C, Sun Z, Ke S, Hecker J, Maaser-Hecker A, Zeleznik OA, Zeleznik R, Litonjua AA, DeMeo DL, Lasky-Su J, Silverman EK, Liu YY, Weiss ST. Benchmarking omics-based prediction of asthma development in children. BMC Respiratory Research 2023;24:63.

Wang XW, Wu L, Dai L, Yin X, Zhang T, Weiss ST, Liu YYEcological Dynamics Imposes Fundamental Challenges in Microbial Source Tracking. iMeta 2023;2(1):e75. 

Wang XW, Sun Z, Jia H, Michel-Mata S, Angulo MT, Dai L, He X, Weiss ST, Liu YY. Identifying keystone species in microbial communities using deep learning. Nature Ecology & Evolution 2023 (published: 16 November 2023).

Yin X, Li L, Chen X, Liu YY, Lam T, Topp E, Zhang T. Global environmental resistome: Distinction and connectivity across diverse habitats benchmarked by metagenomic analyses. Water Research 2023;235:119875.

2022

Cao Y, Wang L, Ke S, Kelly CP, NR P, Pollock NR, Gálvez JAV, Daugherty K, Xu H, Yao J, Chen Y, Liu YY, Chen X. Analysis of Intestinal Mycobiota of Patients with Clostridioides difficile Infection among a Prospective Inpatient Cohort. Microbiology Spectrum 2022;10(4):e01362-22.

Hu H, Tan Y, Li C, Chen J, Kou Y, Xu Z, Liu YY, Tan Y, Dai L. StrainPanDA: linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data. iMeta 2022;1(3):e41.

Ke S, Weiss ST, Liu YYDissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes. Nature Communications 2022;13:5235.

Lee-Sarwar K, Dedrick S, Momeni B, Kelly RS, Zeiger RS, O’Connor GT, Sandel MT, Bacharier LB, Beigelman A, Laranjo N, Gold DR, Lasky-Su J, Litonjua AA, Liu YY, Weiss ST. Association of the Gut Microbiome and Metabolome with Wheeze Frequency in Childhood Asthma. The Journal of Allergy and Clinical Immunology 2022;150(2):325-336.

Liu H, Liao C, Tang J, Chen J, Lei C, Zheng L, Wu L, Zhang C, Liu YY, Xavier J, Dai L. Ecological dynamics of the gut microbiome in response to dietary fiber. The ISME Journal 2022;16:2040.

Michel-Mata S, Wang XW, Liu YY, Angulo MT. Predicting microbiome compositions through deep learning. iMeta 2022;1(1):e3.

Wang XW, Qiao D, Cho M, DeMeo DL, Silverman EK, Liu YYA Statistical Physics Approach for Disease Module Detection. Genome Research 2022;32:1918-1929.

Wang Y, Tang J, Lv Q, Tan Y, Dong X, Liu H, Zhao N, He Z, Kou Y, Tan Y, Liu XA, Wang L, Liu YY, Dai L. Establishment and Resilience of Transplanted Gut Microbiota in Aged Mice. iScience 2022;25(1):103654.

2021

Aparicio A, Velasco JX, Moog CH, Liu YY, Angulo MT. Identifying sensor species to predict critical transitions in complex ecosystems. PNAS 2021;118(51):e2104732118.

Cao Y, Wang L, Ke S, Gálvez JAV, Pollock NR, Barret C, Sprague R, Daugherty K, Xu H, Lin Q, Yao J, Chen Y, Kelly CP, Liu YY, Chen X. Fecal Mycobiota Combined with Host Immune Factors Distinguish Clostridioides difficile Infection from Asymptomatic Carriage. Gastroenterology 2021;160(7):2328-2339.

Dedrick S, Akbari MJ, Dyckman S, Zhao N, Liu YY, Momeni B. Impact of temporal pH fluctuations on the coexistence of nasal bacteria. Frontiers in Microbiology 2021;12:144.

Deng Y, Huang Y, Che Y, Yang Y, Yin X, Yan A, Dai L, Liu YY, Polz M, Zhang T. Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants. The ISME Journal 2021;15:2817.

Huang S, Jiang S, Huo D, Allaband C, Estaki M, Cantu V, Ferre P, Vázquez-Baeza Y, Zhu Q, Ma C, Li W, Zarrinpar A, Li C, Liu YY, Knight R, Zhang J. Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut, but differentially influence the resident microbiome. Microbiome 2021;9:151.

Ke S, Mitchell SJ, MacArthur MR, Kane AE, Sinclair DA, Venable EM, Chadaideh KS, Carmody RN, Grodstein F, Mitchell JR, Liu YYGut Microbiota predicts Healthy Late-life Aging in Male Mice. Nutrients 2021;13(9):3290.

Ke S, Pollock NP, Wang X-W, Chen X, Daugherty K, Lin Q, Xu H, Garey KW, Gonzales-Luna AJ, Kelly CP, Liu YYIntegrating gut microbiome and host immune markers to understand the pathogenesis of Clostridioides difficile infection. Gut Microbes 2021;13(1):18.

Morrow JD, Castaldi P, Chase R, Yun J, Lee S, Liu YY, Hersh C. Peripheral blood microbial signatures in current and former smokers. Scientific Reports 2021;11:19875.

Sun Z, Huang S, Zhang M, Zhu Q, Haiminen N, Carrieri AP, Vazquez-Baeza Y, Parida L, Kim HC, Knight R, Liu YYChallenges in Benchmarking Metagenomic Profilers. Nature Methods 2021;18:618-626.

Zhao N, Saavedra S, Liu YYThe impact of colonization history on the composition of ecological systems. Physical Review E 2021;103:052403.

2020

Aceituno PV, Yan G, Liu YYTailoring Echo State Networks for Optimal Learning. iScience 2020;23(9):101440.

Coutinho BC, Wu AK, Zhou HJ, Liu YYCovering problems and core percolations on hypergraphs. Physical Review Letters 2020;124(24):248301.

Fan C, Zeng L, Sun Y, Liu YYFinding key players in complex networks through deep reinforcement learning. Nature Machine Intelligence 2020;2:317-324.

Levy O, Amit G, Vaknin D, Snir T, Efroni S, Castaldi P, Liu YY, Cohen HY, Bashan A. Age-related loss of gene-to-gene transcriptional coordination among single cells. Nature Metabolism 2020;2:1305-1315.

Li A, Zhou L, Su Q, Cornelius SP, Liu YY, Wang L, Levin SA. Evolution of Cooperation on Temporal Networks. Nature Communications 2020;11:2259.

Tian L, Wang XW, Wu AK, Fan Y, Friedman J, Dahlin A, Waldor MK, Weinstock GM, Weiss ST, Liu YY. Deciphering Functional Redundancy in the Human Microbiome. Nature Communications 2020;11:6217.

Vila JCC, Liu YY, Sanchez A. Dissimilarity-Overlap Analysis of Replicate Enrichment Communities. The ISME Journal 2020;14:2505.

Wang X, Liu YYOvercome Competitive Exclusion in Ecosystems. iScience (cover story) 2020;23(4):101009.

Wang XW, Liu YYComparative study of classifiers for human microbiome data. Medicine in Microecology 2020;4:100013.

Wang XW, Chen Y, Liu YYLink Prediction through Deep Generative Model. iScience 2020;23(10):101626.

Wu AK, Tian L, Coutinho BC, Omar Y, Liu YYStructural vulnerability of quantum networks. Physical Review A 2020;101(5):052315.

Xiao Y, Angulo MT, Lao S, Weiss ST, Liu YYAn Ecological Framework to Understand the Efficacy of Fecal Microbiota Transplantation. Nature Communications 2020;11:3329.

2019

Angulo MT, Moog CH, Liu YYA theoretical framework for controlling complex microbial communities. Nature Communications 2019;10:1045.

Chen Y, Angulo MT, Liu YYRevealing complex ecological dynamics via symbolic regression. BioEssays (cover story) 2019;41(12):1970121.

Li A, Liu YYControlling network dynamics. Advances in Complex Systems 2019;22:1950021.

Li P, Zhang T, Xiao Y, Tian L, Cui B, Ji G, Liu YY, Zhang F. Timing for the second fecal microbiota transplantation to maintain the long-term benefit from the first treatment for Crohn’s disease. Applied Microbiology and Biotechnology 2019;103(1):349-60.

Sonawane AR, Tian L, Chu C, Qiu X, Wang L, Holden-Wiltse J, Grier A, Gill SR, Caserta MT, Walsh EE, Mariani TJ, Weiss ST, Silverman EK, Glass K, Liu YYMicrobiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection. Scientific Reports 2019;9:13824.

Wu M, He S, Zhang Y, Chen J, Sun Y, Liu YY, Zhang J, Poor HV. A Tensor-Based Framework for Studying Eigenvector Multicentrality in Multilayer Networks. PNAS 2019;116(31):15407.

Xiao Y, Song C, Tian L, Liu YYAccelerating the Emergence of Order in Swarming Systems. Advances in Complex Systems 2019;22:1950015.

2018

Fan Y, Xiao Y, Momeni B, Liu YYHorizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Systems. Journal of Theoretical Biology 2018;454:53-59.

Sharma A, Halu A, Decano JL, Menche J, Liu YY, Fadista J, Santolini M, Padi M, Weiss ST, Vidal M, Silverman EK, Aikawa M, Barabási AL, Groop L, Loscalzo J. Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes. npj Systems Biology and Applications 2018;4:25. 

Wu AK, Tian L, Liu YYBridges in Complex Networks. Physical Review E 2018;97:012307. 

2017

Angulo MT, Moreno JA, Barabási AL, Liu YYFundamental limitations of network reconstruction from temporal data. Journal of the Royal Society Interface 2017;14(127):20160966.

Cao HT, Gibson T, Bashan A, Liu YYInferring Human Microbial Dynamics from Temporal Metagenomics Data: Pitfalls and Lessons. BioEssays 2017;39(2):1600188.

Li A, Cornelius S, Liu YY, Wang L, Barabási AL. The Fundamental Advantages of Temporal Networks. Science 2017;358(6366):1042-1046. 

Liu H, Zhao R, Fang H, Cheng F, Fu Y, Liu YYEntropy-based consensus clustering for patient stratification. Bioinformatics 2017;33(17):2691-2698.

Tian L, Bashan A, Shi DN, Liu YYArticulation Points in Complex Networks. Nature Communications 2017;8:14223. 

Xiao Y, Angulo MT, Friedman J, Waldor MK, Weiss ST, Liu YYMapping the ecological networks of microbial communities. Nature Communications 2017;8:2042.

Yan G, Martinez ND, Liu YYStability of Degree Heterogeneous Ecological Networks. Journal of the Royal Society Interface 2017;14(131):20170189.

2016

Bashan A, Gibson TE, Friedman J, Carey VJ, Weiss ST, Hohmann EL, Liu YYUniversality of Human Microbial Dynamics. Nature 2016;534:259-262.

Basler G, Nikoloski Z, Larhlimi A, Barabási AL, Liu YYControl of Fluxes in Metabolic Networks. Genome Research (featured as a cover story) 2016;26:956-968.

Cao HT, Gibson TE, Mou S, Liu YYImpacts of Network Topology on the Performance of a Distributed Algorithm Solving Linear Equations. 2016 IEEE 55th Conference on Decision and Control (CDC), Las Vegas, NV, USA, 2016, pp. 1733-1738.

Chang Y, Glass K, Liu YY, Silverman EK, Crapo J, Tal-Singer R, Bowler RP, Dy J, Cho MH, Castaldi PJ. COPD Subtypes Identified by Network-Based Clustering of Blood Gene Expression. Genomics (featured as a cover story) 2016;107(2-3):51-58.

Garmaroudi FS, Handy DE, Liu YY, Loscalzo J. Systems Pharmacology and Rational Polypharmacy: Nitric Oxide−Cyclic GMP Signaling Pathway as an Illustrative Example and Derivation of the General Case. PloS Computational Biology 2016;12(3):e1004822.

Gibson TE, Bashan A, Cao HT, Weiss ST, Liu YYOn the Origins and Control of Community Types in the Human Microbiome. PloS Computational Biology 2016;12(2):e1004688.

McGeachie MJ, Sordillo JE, Gibson T, Weinstock GM, Liu YY, Gold DR, Weiss ST, Litonjua A. Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks. Scientific Reports 2016;6:20369.

Vinayagam A, Gibson TE, Lee H-J, Yilmazel B, Roesel C, Hu Y, Kwon Y, Sharma A, Liu YY, Perrimon N, Barabási AL. Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets. PNAS 2016;113(18):4976-4981.

2015

Angulo MT, Liu YY, Slotine JJ. Network motifs emerge from interconnections that favor stability. Nature Physics 2015;11:848-852.

Barzel B, Liu YY, Barabási AL. Constructing minimal models for complex system dynamics. Nature Communications 2015;6:7186.

Inoue H, Liu YYRevealing the intricate effect of collaboration on innovation. PLoS ONE 2015;10(3):e0121973.

Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Kamburov A, Krykbaeva I, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova A, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill BE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M. Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders. Cell 2015;161(3):647-660.

Yan G, Tsekenis G, Barzel B, Slotine JJ, Liu YY, Barabási AL. Spectrum of Controlling and Observing Complex Networks. Nature Physics 2015;11:779-786.

Zhao C, Wang WX, Liu YY, Slotine JJ. Individual dynamics induces symmetry in network controllability. Scientific Reports 2015;5(8422):1-5. 

2014

Gao J, Liu YY, D’Souza R, Barabási AL. Target Control of Complex Networks. Nature Communications 2014;5:5415.

Liu YY, Nacher J, Ochiai T, Martino M, Altshuler Y. Prospect Theory for Online Financial Trading. PLoS ONE 2014;9(10):e109458.

McDonald M-L, Mattheisen M, Cho M, Liu YY, Harshfield B, Hersh C, Bakke P, Gulsvik A, Lange C, Beaty T, Silverman E. Beyond GWAS in COPD: Probing the Landscape between Gene-Set Associations, Genome-Wide Associations and Protein-Protein Interaction Networks. Human Heredity 2014;78(3):131-139.

2013

Jia T, Liu YY, Csóka E, Pósfai M, Slotine JJ, Barabási AL. Emergence of bimodality in controlling complex networks. Nature Communications. 2013;4:2002.

Liu YY, Slotine JJ, Barabási AL. Observability of complex systems. PNAS (featured as a cover story) 2013;110:2460–2465. 

Pósfai M, Liu YY, Slotine JJ, Barabási AL. Effect of correlations on network controllability. Scientific Reports. 2013;3:1067.

Zhao JH, Zhou HJ, Liu YYInducing effect on the percolation transition in complex networks. Nature Communications. 2013;4:2412.

2012

Liu YY, Slotine JJ, Barabási AL. Control Centrality and Hierarchical Structure in Complex Networks. PloS ONE 2012;7:e44459. 

Liu YY, Csóka E, Zhou H, Pósfai M. Core percolation on complex networks. Physical Review Letters. 2012;109:205703. 

2011

Liu YY, Slotine JJ, Barabási AL. Controllability of complex networks. Nature (featured as a cover story) 2011;473:167–173.

Liu YY, Slotine JJ, Barabási AL. Few inputs can reprogram biological networks (Liu et al. Reply). Nature 2011;478:E4–E5.

2010

Hovorka O, Liu Y, Dahmen KA, Berger A. On the ability to determine intrinsic switching field distributions from hysteresis loops in the partially correlated magnetization reversal regime. Journal of Magnetism and Magnetic Materials. 2010;322:459–468. 

Hovorka O, Evans RFL, Chantrell RW, Liu Y, Dahmen KA, Berger A. Validation of ΔH(M, ΔM)-technique for identification of switching field distributions in the presence of thermal relaxation. Journal of Applied Physics. 2010;108:123901.

Liu Y, Park J, Dahmen KA, Chemla YR, Ha T. A comparative study of multivariate and univariate hidden Markov modelings in time-binned single-molecule FRET data analysis. The Journal of Physical Chemistry B. 2010;114:5386–5403.

2009

Hovorka O, Liu Y, Dahmen KA, Berger A. Simultaneous determination of intergranular interactions and intrinsic switching field distributions in magnetic materials. Applied Physics Letters. 2009;95:192504.

Liu Y, Dahmen KA. Unexpected universality in static and dynamic avalanches. Physical Review E. 2009;79:061124.

Liu Y, Hovorka O, Berger A, Dahmen KA. Effects of nonuniform exchange and magnetostatic interactions on the determination of intrinsic switching field distributions. Journal of Applied Physics. 2009;105:123905.

Liu Y, Dahmen KA. Random-field Ising model in and out of equilibrium. Europe Physics Letters. 2009;86:56003.

White RA, Liu Y, Dahmen KA. Thermal effects on crackling noise. Europe Physics Letters. 2009;86:50001.

2008

Liu Y, Dahmen KA, Berger A. Determination of intrinsic switching field distributions in perpendicular recording media: Numerical study of the ΔH(M, ΔM) method. Physical Review B. 2008;77:054422.

Liu Y, Dahmen KA, Berger A. The role of dipolar interactions for the determination of intrinsic switching field distributions. Applied Physics Letters 2008;92:222503. 

Liu Y, Dahmen KA, Berger A. A comparative study of the ΔH(M, ΔM) method reliability for square and triangular lattices. Journal of Applied Physics. 2008;103:07F504.

2007

Liu Y, Dahmen KA. No-passing rule in the ground state evolution of the random-field Ising model. Physical Review E. 2007;76:031106.

2006

Xu XB, Liu Y, Fangohr H, Zhang L, Ding SY, Wang ZH, Liu SL, Wu GJ, Shao HM. Metastable behavior of vortex matter in the electronic transport processes of homogenous superconductors. Physical Review B. 2006;73:214521.

2003

Ding SY, Leng X, Qiu L, Wang ZH, Liu Y, Zhang H. Effect of Na doping on flux pinning of YBa1.9Na0.1Cu3O7-δ. Physica C: Superconductivity. 2003;385(3):368–372. 

Ding SY, Leng X, Luo H, Liu Y, Xiao L, Reng HT, Jiao YL, Zheng MH. Second peak effect in SmBa2Cu3Oy. Physica C: Superconductivity. 2003;386:73–76.

Leng X, Ding SY, Liu Y, Wang ZH, Liu HK, Dou SX. Dip effect in ac susceptibility due to surface barrier with flux creep. Physical Review B. 2003;68:214511. 

Leng X, Luo H, Qiu L, Liu Y, Wang ZH, Ding SY, Zhang H. Second peak and critical current for YBa1.9Na0.1Cu3Oy. Physica C: Superconductivity. 2003;386:245–248.

Leng X, Luo H, Liu Y, Ding SY, Xiao L, Reng HT, Jiao YL, Zheng MH. Influence of process on flux pinning for MTG SmBa2Cu3Oy. Physica C: Superconductivity. 2003;386:85–88.

Leng X, Qiu L, Wang ZH, Luo H, Liu Y, Ding SY, Zhang H, Lin JW. Flux pinning energy of YBa1.9Na0.1Cu3O7- δ. Physica C: Superconductivity. 2003;386:10–13.

Liu Y, Ding SY, Luo H, Leng X, Xiao L, Reng HT, Jiao YL, Zheng MH, Lin JW. Field sweeping rate dependent tail of magnetization curve. Physica C: Superconductivity. 2003;386:77–80.

Liu Y, Ding SY, Luo H, Leng X, Lin JW. Study on the limiting factor of critical current in Ag–Bi2223 tapes. Physica C: Superconductivity. 2003;386:190–193.

Luo H, Liu Y, Leng X, Wang ZH, Ding SY, Wang XL, Dou SX. Flux motion in new superconductor MgB2. Physica C: Superconductivity. 2003;387:307–312.

Luo H, Lin JW, Leng X, Liu Y, Qiu L, Ding SY. Determination of critical current density in flux creep state for MgB2. Physica C: Superconductivity. 2003;388:171–172.

2002

Liu Y, Luo H, Yang T, Leng X, Wu XF, Lin JW, Wang ZH, Luo HM, Ding SY. Transport properties in Tl-2212 film. Superconductor Science and Technology. 2002;15(3):375-380. 

Liu Y, Luo H, Leng X, Wang ZH, Qiu L, Ding SY, Lin LZ. Historical critical current in inhomogeneous system. Chinese Journal of Low Temperature Physics. 2002;24(4):241.

Liu Y, Luo H, Leng X, Wang ZH, Qiu L, Ding SY, Lin LZ. History effect in inhomogeneous superconductors. Physical Review B. 2002;66:144510. 

Luo H, Wu XF, Lee CM, Yang T, Leng X, Liu Y, Qiu L, Luo HM, Wang ZH, Ding SY. AC losses of superconductor MgB2. Superconductor Science and Technology. 2002;15(3):370-374.

Wu XF, Luo H, Luo HM, Liu Y, Yang T, Leng X, Qiu L, Ding SY. Peak effect of a La0.9Pr0.1Ba2Cu2.62Al0.38O7-ysingle crystal. Superconductor Science and Technology. 2002;15(3):385–389. 

2001

Ding SY, Liu Y, Wu XF, Lin FY, Wang ZH, Qiu L. The effect of the geometric factor on the VI curve of Tl-2212 film. Journal of Physics: Condensed Matter 2001;13(30):6509.

Ding SY, Liu Y, Wang ZH, Luo HM. Study of VI curve of Tl-2212 film. Physica C: Superconductivity and its Applications 2001;364-365:504–506.

Wu XF, Luo H, Ding SY, ZHANG YH, Yang T, Liu Y, Wang ZH, Luo HM. Study of History Effect of Vortex Matter by AC Susceptibility. Journal of Superconductivity 2001;14:501–507.