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Jianhua Xing, Ph.D. - Publications

Affiliations: 
1998-2002 University of California, Berkeley, Berkeley, CA, United States 
 2015- Computational and Systems Biology University of Pittsburgh, Pittsburgh, PA, United States 
Area:
theoretical chemistry, statistical physics, quantitative biology, biophysics, systems biology
Website:
http://www.csb.pitt.edu/jianhua-xing/
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57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Wang H, Ardila C, Jindal A, Aggarwal V, Wang W, Vande Geest J, Jiang Y, Xing J, Sant S. Protrusion force and cell-cell adhesion play a critical role in collective tumor cluster migration. Biorxiv : the Preprint Server For Biology. PMID 39345581 DOI: 10.1101/2024.09.18.613706  0.577
2022 Wang W, Poe D, Yang Y, Hyatt T, Xing J. Epithelial-to-mesenchymal transition proceeds through directional destabilization of multidimensional attractor. Elife. 11. PMID 35188459 DOI: 10.7554/eLife.74866  0.607
2022 Qiu X, Zhang Y, Martin-Rufino JD, Weng C, Hosseinzadeh S, Yang D, Pogson AN, Hein MY, Hoi Joseph Min K, Wang L, Grody EI, Shurtleff MJ, Yuan R, Xu S, Ma Y, ... ... Xing J, et al. Mapping transcriptomic vector fields of single cells. Cell. PMID 35108499 DOI: 10.1016/j.cell.2021.12.045  0.458
2021 Teekakirikul P, Zhu W, Gabriel GC, Young CB, Williams K, Martin LJ, Hill JC, Richards T, Billaud M, Phillippi JA, Wang J, Wu Y, Tan T, Devine W, Lin JH, ... ... Xing J, et al. Common deletion variants causing protocadherin-α deficiency contribute to the complex genetics of BAV and left-sided congenital heart disease. Hgg Advances. 2. PMID 34888534 DOI: 10.1016/j.xhgg.2021.100037  0.326
2021 Zhang Y, Zhang S, Xing J, Bahar I. Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis. The Journal of Chemical Physics. 154: 195102. PMID 34240914 DOI: 10.1063/5.0046710  0.39
2021 Tripathi S, Xing J, Levine H, Jolly MK. Mathematical Modeling of Plasticity and Heterogeneity in EMT. Methods in Molecular Biology (Clifton, N.J.). 2179: 385-413. PMID 32939734 DOI: 10.1007/978-1-0716-0779-4_28  0.392
2020 Chen YJ, Cheng YY, Wang W, Tian XJ, Lefever DE, Taft DA, Zhang J, Xing J. Erratum to: Rapid, modular, and cost-effective generation of donor DNA constructs for CRISPR-based gene knock-in. Biology Methods & Protocols. 5: bpaa021. PMID 33241121 DOI: 10.1093/biomethods/bpaa021  0.722
2020 Wang W, Douglas D, Zhang J, Kumari S, Enuameh MS, Dai Y, Wallace CT, Watkins SC, Shu W, Xing J. Live-cell imaging and analysis reveal cell phenotypic transition dynamics inherently missing in snapshot data. Science Advances. 6. PMID 32917609 DOI: 10.1126/Sciadv.Aba9319  0.665
2020 Zhang Y, Krieger J, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I. State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. Progress in Biophysics and Molecular Biology. PMID 32866476 DOI: 10.1016/J.Pbiomolbio.2020.08.006  0.466
2020 Chen YJ, Cheng YY, Wang W, Tian XJ, Lefever DE, Taft DA, Zhang J, Xing J. Rapid, modular, and cost-effective generation of donor DNA constructs for CRISPR-based gene knock-in. Biology Methods & Protocols. 5: bpaa006. PMID 32411820 DOI: 10.1093/Biomethods/Bpaa006  0.752
2020 Tian XJ, Zhou D, Fu H, Zhang R, Wang X, Huang S, Liu Y, Xing J. Sequential Wnt Agonist Then Antagonist Treatment Accelerates Tissue Repair and Minimizes Fibrosis. Iscience. 23: 101047. PMID 32339988 DOI: 10.1016/J.Isci.2020.101047  0.638
2020 Yang J, Antin P, Berx G, Blanpain C, Brabletz T, Bronner M, Campbell K, Cano A, Casanova J, Christofori G, Dedhar S, Derynck R, Ford HL, Fuxe J, García de Herreros A, ... ... Xing J, et al. Guidelines and definitions for research on epithelial-mesenchymal transition. Nature Reviews. Molecular Cell Biology. PMID 32300252 DOI: 10.1038/S41580-020-0237-9  0.305
2019 Fujimaki K, Li R, Chen H, Della Croce K, Zhang HH, Xing J, Bai F, Yao G. Graded regulation of cellular quiescence depth between proliferation and senescence by a lysosomal dimmer switch. Proceedings of the National Academy of Sciences of the United States of America. PMID 31636214 DOI: 10.1073/Pnas.1915905116  0.574
2019 Igoshin OA, Chen J, Xing J, Liu J, Elston TC, Grabe M, Kim KS, Nirody JA, Rangamani P, Sun SX, Wang H, Wolgemuth C. Biophysics at the coffee shop: lessons learned working with George Oster. Molecular Biology of the Cell. 30: 1882-1889. PMID 31322997 DOI: 10.1091/Mbc.E19-02-0107  0.679
2019 Wang W, Taft DA, Chen YJ, Zhang J, Wallace CT, Xu M, Watkins SC, Xing J. Learn to segment single cells with deep distance estimator and deep cell detector. Computers in Biology and Medicine. 108: 133-141. PMID 31005005 DOI: 10.1016/J.Compbiomed.2019.04.006  0.638
2019 Singh M, Tian XJ, Donnenberg VS, Watson AM, Zhang J, Stabile LP, Watkins SC, Xing J, Sant S. Targeting the temporal dynamics of hypoxia-induced tumor-secreted factors halts tumor migration. Cancer Research. PMID 30952634 DOI: 10.1158/0008-5472.Can-18-3151  0.688
2019 Zhang J, Chen H, Li R, Taft DA, Yao G, Bai F, Xing J. Spatial clustering and common regulatory elements correlate with coordinated gene expression. Plos Computational Biology. 15: e1006786. PMID 30822341 DOI: 10.1371/Journal.Pcbi.1006786  0.596
2019 Xing J, Tian X. Investigating epithelial-to-mesenchymal transition with integrated computational and experimental approaches. Physical Biology. PMID 30665206 DOI: 10.1088/1478-3975/Ab0032  0.697
2018 Zhang J, Tian XJ, Chen YJ, Wang W, Watkins S, Xing J. Pathway crosstalk enables cells to interpret TGF-β duration. Npj Systems Biology and Applications. 4: 18. PMID 29872541 DOI: 10.1038/s41540-018-0060-5  0.76
2018 Zhou D, Fu H, Xiao L, Mo H, Zhuo H, Tian X, Lin L, Xing J, Liu Y. Fibroblast-Specific β-catenin Signaling Dictates the Outcome of AKI. Journal of the American Society of Nephrology : Jasn. PMID 29343518 DOI: 10.1681/Asn.2017080903  0.657
2017 Kwon JS, Everetts NJ, Wang X, Wang W, Della Croce K, Xing J, Yao G. Controlling Depth of Cellular Quiescence by an Rb-E2F Network Switch. Cell Reports. 20: 3223-3235. PMID 28954237 DOI: 10.1016/J.Celrep.2017.09.007  0.704
2017 Xing J. Quantitative Systems Biology Studies Reveal a Nested Relay Mechanism for TGF-Beta Signaling Biophysical Journal. 112: 38a. DOI: 10.1016/J.Bpj.2016.11.243  0.394
2016 Tian XJ, Zhang H, Zhang J, Xing J. Reciprocal Regulation Between mRNA and miRNA Enables a Bistable Switch That Directs Cell Fate Decisions. Febs Letters. PMID 27578189 DOI: 10.1002/1873-3468.12379  0.699
2016 Tian XJ, Zhang H, Sannerud J, Xing J. Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design. Proceedings of the National Academy of Sciences of the United States of America. PMID 27162367 DOI: 10.1073/Pnas.1601722113  0.689
2016 Zhang J, Tian XJ, Xing J. Signal Transduction Pathways of EMT Induced by TGF-β, SHH, and WNT and Their Crosstalks. Journal of Clinical Medicine. 5. PMID 27043642 DOI: 10.3390/Jcm5040041  0.705
2014 Zhang J, Tian XJ, Zhang H, Teng Y, Li R, Bai F, Elankumaran S, Xing J. TGF-β-induced epithelial-to-mesenchymal transition proceeds through stepwise activation of multiple feedback loops. Science Signaling. 7: ra91. PMID 25270257 DOI: 10.1126/Scisignal.2005304  0.748
2014 Mondal D, Dougherty E, Mukhopadhyay A, Carbo A, Yao G, Xing J. Systematic reverse engineering of network topologies: a case study of resettable bistable cellular responses. Plos One. 9: e105833. PMID 25170839 DOI: 10.1371/Journal.Pone.0105833  0.745
2014 Wang P, Song C, Zhang H, Wu Z, Tian XJ, Xing J. Epigenetic state network approach for describing cell phenotypic transitions. Interface Focus. 4: 20130068. PMID 24904734 DOI: 10.1098/Rsfs.2013.0068  0.773
2014 Chen C, Baumann WT, Xing J, Xu L, Clarke R, Tyson JJ. Mathematical models of the transitions between endocrine therapy responsive and resistant states in breast cancer. Journal of the Royal Society, Interface / the Royal Society. 11: 20140206. PMID 24806707 DOI: 10.1098/Rsif.2014.0206  0.615
2014 Zhang H, Tian XJ, Mukhopadhyay A, Kim KS, Xing J. Statistical mechanics model for the dynamics of collective epigenetic histone modification. Physical Review Letters. 112: 068101. PMID 24580708 DOI: 10.1103/Physrevlett.112.068101  0.711
2014 Xing J, Mather W, Hong C. Computational cell biology: past, present and future Interface Focus. 4: 20140027. DOI: 10.1098/Rsfs.2014.0027  0.335
2013 Hu Y, Ru N, Xiao H, Chaturbedi A, Hoa NT, Tian XJ, Zhang H, Ke C, Yan F, Nelson J, Li Z, Gramer R, Yu L, Siegel E, Zhang X, ... ... Xing J, et al. Tumor-specific chromosome mis-segregation controls cancer plasticity by maintaining tumor heterogeneity. Plos One. 8: e80898. PMID 24282558 DOI: 10.1371/Journal.Pone.0080898  0.691
2013 Tian XJ, Zhang H, Xing J. Coupled reversible and irreversible bistable switches underlying TGFβ-induced epithelial to mesenchymal transition. Biophysical Journal. 105: 1079-89. PMID 23972859 DOI: 10.1016/J.Bpj.2013.07.011  0.711
2012 Fu Y, Jiang X, Zhang H, Xing J. A strategy to study pathway cross-talks of cells under repetitive exposure to stimuli. Bmc Systems Biology. 6: S6. PMID 23282371 DOI: 10.1186/1752-0509-6-S3-S6  0.555
2012 Wu Z, Xing J. Functional roles of slow enzyme conformational changes in network dynamics. Biophysical Journal. 103: 1052-9. PMID 23009855 DOI: 10.1016/J.Bpj.2012.08.008  0.75
2012 Wu Z, Nogales E, Xing J. Comparative studies of microtubule mechanics with two competing models suggest functional roles of alternative tubulin lateral interactions. Biophysical Journal. 102: 2687-96. PMID 22735518 DOI: 10.1016/J.Bpj.2012.05.003  0.774
2012 Hong T, Xing J, Li L, Tyson JJ. A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells. Bmc Systems Biology. 6: 66. PMID 22697466 DOI: 10.1186/1752-0509-6-66  0.632
2012 Bai F, Minamino T, Wu Z, Namba K, Xing J. Coupling between switching regulation and torque generation in bacterial flagellar motor. Physical Review Letters. 108: 178105. PMID 22680910 DOI: 10.1103/Physrevlett.108.178105  0.74
2012 Fu Y, Glaros T, Zhu M, Wang P, Wu Z, Tyson JJ, Li L, Xing J. Network topologies and dynamics leading to endotoxin tolerance and priming in innate immune cells. Plos Computational Biology. 8: e1002526. PMID 22615556 DOI: 10.1371/Journal.Pcbi.1002526  0.755
2012 Glaros T, Fu Y, Xing J, Li L. Molecular mechanism underlying persistent induction of LCN2 by lipopolysaccharide in kidney fibroblasts. Plos One. 7: e34633. PMID 22514649 DOI: 10.1371/Journal.Pone.0034633  0.438
2011 Hong T, Xing J, Li L, Tyson JJ. A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells. Plos Computational Biology. 7: e1002122. PMID 21829337 DOI: 10.1371/Journal.Pcbi.1002122  0.64
2011 Xing J, Kim KS. Application of the projection operator formalism to non-hamiltonian dynamics. The Journal of Chemical Physics. 134: 044132. PMID 21280712 DOI: 10.1063/1.3530071  0.312
2011 Bai F, Minamino T, Xing J, Berry R, Namba K. 1SA-01 Theoretical and experimental approaches to analyze the mechanism of rotational switching in bacterial flagellar motor(1SA Dynamics and Robustness in Biological networks,The 49th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 51. DOI: 10.2142/Biophys.51.S1_1  0.329
2011 Wu Z, Nogales E, Xing J. Is an Alternative Model for Microtubule Assembly Needed? Biophysical Journal. 100: 449a. DOI: 10.1016/J.Bpj.2010.12.2645  0.775
2010 Fu Y, Zhu M, Xing J. Resonant activation: a strategy against bacterial persistence. Physical Biology. 7: 16013. PMID 20147776 DOI: 10.1088/1478-3975/7/1/016013  0.469
2009 Wu Z, Wang HW, Mu W, Ouyang Z, Nogales E, Xing J. Simulations of tubulin sheet polymers as possible structural intermediates in microtubule assembly. Plos One. 4: e7291. PMID 19806219 DOI: 10.1371/Journal.Pone.0007291  0.754
2009 Wu Z, Elgart V, Qian H, Xing J. Amplification and detection of single-molecule conformational fluctuation through a protein interaction network with bimodal distributions. The Journal of Physical Chemistry. B. 113: 12375-81. PMID 19691265 DOI: 10.1021/Jp903548D  0.744
2009 Bai F, Lo CJ, Berry RM, Xing J. Model studies of the dynamics of bacterial flagellar motors. Biophysical Journal. 96: 3154-67. PMID 19383460 DOI: 10.1016/J.Bpj.2009.01.023  0.304
2007 Xing J. Nonequilibrium dynamic mechanism for allosteric effect. Physical Review Letters. 99: 168103. PMID 17995300 DOI: 10.1103/Physrevlett.99.168103  0.31
2006 Xing J, Bai F, Berry R, Oster G. Torque-speed relationship of the bacterial flagellar motor. Proceedings of the National Academy of Sciences of the United States of America. 103: 1260-5. PMID 16432218 DOI: 10.1073/Pnas.0507959103  0.518
2005 Xing J, Liao JC, Oster G. Making ATP. Proceedings of the National Academy of Sciences of the United States of America. 102: 16539-46. PMID 16217018 DOI: 10.1073/Pnas.0507207102  0.656
2005 Xing J, Wang H, Oster G. From continuum Fokker-Planck models to discrete kinetic models. Biophysical Journal. 89: 1551-63. PMID 15994886 DOI: 10.1529/Biophysj.104.055178  0.558
2004 Xing J, Wang H, von Ballmoos C, Dimroth P, Oster G. Torque generation by the Fo motor of the sodium ATPase. Biophysical Journal. 87: 2148-63. PMID 15454418 DOI: 10.1529/Biophysj.104.042093  0.553
2001 Xing J, Coronado EA, Miller WH. Some new classical and semiclassical models for describing tunneling processes with real-valued classical trajectories Journal of Physical Chemistry B. 105: 6574-6578. DOI: 10.1021/Jp0046086  0.436
2001 Coronado EA, Xing J, Miller WH. Ultrafast non-adiabatic dynamics of systems with multiple surface crossings: A test of the Meyer-Miller Hamiltonian with semiclassical initial value representation methods Chemical Physics Letters. 349: 521-529. DOI: 10.1016/S0009-2614(01)01242-8  0.447
2000 Kim Y, Corchado JC, Villà J, Xing J, Truhlar DG. Multiconfiguration molecular mechanics algorithm for potential energy surfaces of chemical reactions The Journal of Chemical Physics. 112: 2718-2735. DOI: 10.1063/1.480846  0.369
1999 Li J, Xing J, Cramer CJ, Truhlar DG. Accurate dipole moments from Hartree–Fock calculations by means of class IV charges The Journal of Chemical Physics. 111: 885-892. DOI: 10.1063/1.479199  0.507
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