Jie Liang - Publications

Affiliations: 
Bioengineering University of Illinois at Chicago, Chicago, IL, United States 
Area:
Bioinformatics Biology, General Biophysics, Biochemistry

134 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
2020 Bausewein T, Naveed H, Liang J, Nussberger S. The structure of the TOM core complex in the mitochondrial outer membrane. Biological Chemistry. PMID 32142473 DOI: 10.1515/Hsz-2020-0104  0.613
2020 Mali S, Perez-Rathke A, Sun Q, Gürsoy G, Liang J. Chromatin Folding under Different Nuclear Confinement Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.587  0.68
2020 Wang B, Lei X, Tian W, Perez-Rathke A, Tseng YY, Liang J. Atom Contact Profile by Alpha-Shape Improves Prediction of Effects of Missense Variant Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.2520  0.568
2019 Tian W, Naveed H, Lin M, Liang J. GeTFEP: A general transfer free energy profile of transmembrane proteins. Protein Science : a Publication of the Protein Society. PMID 31658402 DOI: 10.1002/Pro.3763  0.613
2019 Mali S, Perez-Rathke A, Sun Q, Gursoy G, Liang J. Roles of Nuclear Confinement, Excluded Volume, and Persistence on TAD Formations, Chromosome Territories, and Chromatin-Nuclear Envelope Interactions Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.3018  0.68
2019 Wang B, Lei X, Tian W, Perez-Rathke A, Tseng Y, Liang J. Structure-Based Method for Predicting Deleterious Missense SNPs Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.2280  0.568
2018 Wang B, Perez-Rathke A, Li R, Liang J. A General Method for Predicting Amino Acid Residues Experiencing Hydrogen Exchange. ... Ieee-Embs International Conference On Biomedical and Health Informatics. Ieee-Embs International Conference On Biomedical and Health Informatics. 2018: 341-344. PMID 29780972 DOI: 10.1109/BHI.2018.8333438  0.451
2018 Tian W, Lin M, Tang K, Liang J, Naveed H. High-resolution structure prediction of β-barrel membrane proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 29378944 DOI: 10.1073/Pnas.1716817115  0.586
2017 Gürsoy G, Xu Y, Kenter AL, Liang J. Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data. Nucleic Acids Research. PMID 28981716 DOI: 10.1093/Nar/Gkx784  0.684
2017 Gürsoy G, Xu Y, Liang J. Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model. Plos Computational Biology. 13: e1005658. PMID 28704374 DOI: 10.1371/Journal.Pcbi.1005658  0.669
2017 Tian W, Lin M, Naveed H, Liang J. Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins. Bioinformatics (Oxford, England). PMID 28158457 DOI: 10.1093/Bioinformatics/Btx053  0.625
2017 Tian W, Naveed H, Liang J. Improving 3D Structure Prediction of Beta-Barrel Membrane Proteins Biophysical Journal. 112: 55a. DOI: 10.1016/J.Bpj.2016.11.333  0.611
2016 Giirsoy G, Terebus A, Cao Y, Liang J, Gursoy G, Terebus A, Youfang Cao, Jie Liang, Gursoy G, Cao Y, Terebus A, Liang J. Mechanisms of stochastic focusing and defocusing in biological reaction networks: insight from accurate chemical master equation (ACME) solutions. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2016: 1480-1483. PMID 28226785 DOI: 10.1109/EMBC.2016.7590989  0.673
2016 Tang K, Zhang J, Liang J. Distance-Guided Forward and Backward Chain-Growth Monte Carlo Method for Conformational Sampling and Structural Prediction of Antibody CDR-H3 Loops. Journal of Chemical Theory and Computation. PMID 27996262 DOI: 10.1021/Acs.Jctc.6B00845  0.336
2016 Gürsoy G, Liang J. Three-dimensional chromosome structures from energy landscape. Proceedings of the National Academy of Sciences of the United States of America. 113: 11991-11993. PMID 27790979 DOI: 10.1073/Pnas.1614535113  0.684
2016 Cheng L, Liu HJ, Zhang J, Wei J, Liang JH, Jiang PH, Fan DD, Sun L, Shi J. High thermoelectric performance of the distorted bismuth(110) layer. Physical Chemistry Chemical Physics : Pccp. PMID 27302907 DOI: 10.1039/c6cp01958g  0.301
2016 Liang J, Cheng L, Zhang J, Liu H, Zhang Z. Maximizing the thermoelectric performance of topological insulator Bi2Te3 films in the few-quintuple layer regime. Nanoscale. PMID 27071548 DOI: 10.1039/C6Nr00724D  0.305
2016 Ni C, Yan M, Zhang J, Cheng R, Liang J, Deng D, Wang Z, Li M, Yao Z. A novel mutation in TRPV3 gene causes atypical familial Olmsted syndrome. Scientific Reports. 6: 21815. PMID 26902751 DOI: 10.1038/srep21815  0.318
2016 Lin M, Gessmann D, Naveed H, Liang J. Outer membrane protein folding and topology from a computational transfer free energy scale. Journal of the American Chemical Society. PMID 26860422 DOI: 10.1021/Jacs.5B10307  0.606
2016 Gürsoy G, Xu Y, Liang J. The NC-SAC: Computational Pipeline for Predicting Structures of 3D Chromatin Chains from Experimental Data: Origin of Scaling Properties, Emergence of Chromosome Territories and Discovery of Novel Loci Interactions Associated with Differential Gene Expression Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.423  0.69
2016 Tian W, Liang J, Naveed H. Improved 3D Structure Prediction of Beta-Barrel Membrane Proteins by using Evolutionary Coupling Constraints, Reduced State Space and an Empirical Potential Function Biophysical Journal. 110: 56a. DOI: 10.1016/J.Bpj.2015.11.370  0.624
2016 Gürsoy G, Terebus A, Cao Y, Liang J. Stochastic Focusing and Defocusing in Biological Reaction Networks: Lessons Learned from Accurate Chemical Master Equation (ACME) Solutions Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.1695  0.673
2015 Liang J, Cao Y, Gursoy G, Naveed H, Terebus A, Zhao J. Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells. Critical Reviews in Biomedical Engineering. 43: 323-46. PMID 27480462 DOI: 10.1615/Critrevbiomedeng.2016016559  0.786
2015 Guo J, Qin S, Liang J, Lin T, Si L, Chen X, Chi Z, Cui C, Du N, Fan Y, Gu K, Li F, Li J, Li Y, Liang H, et al. Chinese Guidelines on the Diagnosis and Treatment of Melanoma(2015 Edition). Chinese Clinical Oncology. PMID 27164849 DOI: 10.21037/cco.2015.12.02  0.329
2015 Guo J, Qin S, Liang J, Lin T, Si L, Chen X, Chi Z, Cui C, Du N, Fan Y, Gu K, Li F, Li J, Li Y, Liang H, et al. Chinese Guidelines on the Diagnosis and Treatment of Melanoma (2015 Edition). Annals of Translational Medicine. 3: 322. PMID 26734632 DOI: 10.3978/j.issn.2305-5839.2015.12.23  0.329
2015 Zhang J, Zhao J, Xu Y, Liang J, Chang P, Yan F, Li M, Liang Y, Zou Z. Genome-Wide Association Mapping for Tomato Volatiles Positively Contributing to Tomato Flavor. Frontiers in Plant Science. 6: 1042. PMID 26640472 DOI: 10.3389/fpls.2015.01042  0.319
2015 Zhan X, Yang Y, Liang J, Zou D, Zhang J, Feng L, Shi T, Li X. In-line mixing states monitoring of suspensions using ultrasonic reflection technique. Ultrasonics. PMID 26548526 DOI: 10.1016/j.ultras.2015.10.024  0.316
2015 Yao S, Zhang J, Shen D, Xiao R, Gu S, Zhao M, Liang J. Removal of Pb(II) from water by the activated carbon modified by nitric acid under microwave heating. Journal of Colloid and Interface Science. 463: 118-127. PMID 26520818 DOI: 10.1016/j.jcis.2015.10.047  0.315
2015 Zhang J, Yan M, Cheng R, Ni C, Liang J, Li M, Yao Z. A rare RECQL4 indel mutation in a Chinese patient with Rothmund-Thomson syndrome. Journal of the European Academy of Dermatology and Venereology : Jeadv. PMID 26515231 DOI: 10.1111/jdv.13466  0.329
2015 Li M, Wang J, Zhang J, Ni C, Li X, Liang J, Cheng R, Li Z, Yao Z. Genome-wide linkage and exome sequencing analyses identify a initiation codon mutation of KRT5 in a unique Chinese generalized Dowling-Degos disease family. The British Journal of Dermatology. PMID 26440693 DOI: 10.1111/bjd.14178  0.329
2015 Jiang PH, Liu HJ, Fan DD, Cheng L, Wei J, Zhang J, Liang JH, Shi J. Enhanced thermoelectric performance of carbon nanotubes at elevated temperature. Physical Chemistry Chemical Physics : Pccp. PMID 26426972 DOI: 10.1039/c5cp04282h  0.308
2015 Liang J, Yang Y, Zhang J, Wu J, Dong P, Yuan J, Zhang G, Lou J. Metal diselenide nanoparticles as highly active and stable electrocatalysts for the hydrogen evolution reaction. Nanoscale. PMID 26290364 DOI: 10.1039/C5Nr03724G  0.304
2015 Shen J, Zhang J, Wang Z, Ni C, Li H, Cheng R, Liang J, Li M, Yao Z. Gene diagnosis and prenatal genetic diagnosis of a case of dystrophic epidermolysis bullosa family caused by gonadosomatic mosaicism for the COL7A1 mutation p.Gly2043Arg in the pregnant mother. Journal of the European Academy of Dermatology and Venereology : Jeadv. PMID 26289024 DOI: 10.1111/jdv.13229  0.329
2015 Camp SM, Ceco E, Evenoski CL, Danilov SM, Zhou T, Chiang ET, Moreno-Vinasco L, Mapes B, Zhao J, Gursoy G, Brown ME, Adyshev DM, Siddiqui SS, Quijada H, Sammani S, ... ... Liang J, et al. Unique Toll-Like Receptor 4 Activation by NAMPT/PBEF Induces NFκB Signaling and Inflammatory Lung Injury. Scientific Reports. 5: 13135. PMID 26272519 DOI: 10.1038/Srep13135  0.675
2015 Zhang J, Liu Z, Liang J, Wu J, Cheng F, Wang X. Three genes encoding AOP2, a protein involved in aliphatic glucosinolate biosynthesis, are differentially expressed in Brassica rapa. Journal of Experimental Botany. PMID 26188204 DOI: 10.1093/Jxb/Erv331  0.344
2015 Zhang J, Liu HJ, Cheng L, Wei J, Liang JH, Fan DD, Shi J, Tang XF, Zhang QJ. Erratum: Phosphorene nanoribbon as a promising candidate for thermoelectric applications. Scientific Reports. 5: 11175. PMID 26161904 DOI: 10.1038/srep11175  0.329
2015 Zhang J, Tong H, Fu X, Zhang Y, Liu J, Cheng R, Liang J, Peng J, Sun Z, Liu H, Zhang F, Lu W, Li M, Yao Z. Molecular Characterization of NF1 and Neurofibromatosis Type 1 Genotype-Phenotype Correlations in a Chinese Population. Scientific Reports. 5: 11291. PMID 26056819 DOI: 10.1038/srep11291  0.311
2015 Wang HL, Fan SS, Pang M, Liu YH, Guo M, Liang JB, Zhang JL, Yu BF, Guo R, Xie J, Zheng GP. The Ankyrin Repeat Domain 49 (ANKRD49) Augments Autophagy of Serum-Starved GC-1 Cells through the NF-κB Pathway. Plos One. 10: e0128551. PMID 26043108 DOI: 10.1371/journal.pone.0128551  0.32
2015 Kachalo S, Naveed H, Cao Y, Zhao J, Liang J. Mechanical model of geometric cell and topological algorithm for cell dynamics from single-cell to formation of monolayered tissues with pattern. Plos One. 10: e0126484. PMID 25974182 DOI: 10.1371/Journal.Pone.0126484  0.609
2015 Tan K, Zhang J, Teng X, Liang J, Wang X, Yuan X, Tian M, Fan X. High level of IFN-γ released from whole blood of human tuberculosis infections following stimulation with Rv2073c of Mycobacterium tuberculosis. Journal of Microbiological Methods. 114: 57-61. PMID 25959099 DOI: 10.1016/j.mimet.2015.05.007  0.317
2015 Tang K, Wong SW, Liu JS, Zhang J, Liang J. Conformational sampling and structure prediction of multiple interacting loops in soluble and β-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method. Bioinformatics (Oxford, England). PMID 25861965 DOI: 10.1093/Bioinformatics/Btv198  0.341
2015 Li J, Zeng G, Qi Y, Tang X, Zhang J, Wu Z, Liang J, Shi L, Liu H, Zhang P. Xenotransplantation of human adipose-derived stem cells in zebrafish embryos. Plos One. 10: e0123264. PMID 25849455 DOI: 10.1371/journal.pone.0123264  0.307
2015 Du X, Yang XH, Wu YF, Liang J, Zhang J, Huang ZC, Zhu ZP, Lin W, Zou MX, Wen JY, Wu SJ, Guo R, Zhang XM, Lahn BT, He F, et al. Distribution of the cytoskeletal protein, Nestin, in acute leukemia. Biotechnic & Histochemistry : Official Publication of the Biological Stain Commission. 90: 384-94. PMID 25839093 DOI: 10.3109/10520295.2014.988751  0.32
2015 Wang X, Zhang J, Liang J, Zhang Y, Teng X, Yuan X, Fan X. Protection against Mycobacterium tuberculosis infection offered by a new multistage subunit vaccine correlates with increased number of IFN-γ+ IL-2+ CD4+ and IFN-γ+ CD8+ T cells. Plos One. 10: e0122560. PMID 25822536 DOI: 10.1371/Journal.Pone.0122560  0.305
2015 Zhang J, Cheng R, Ni C, Liang J, Li M, Yao Z. First Mal de Meleda report in Chinese Mainland: two families with a recurrent homozygous missense mutation in SLURP-1. Journal of the European Academy of Dermatology and Venereology : Jeadv. PMID 25763536 DOI: 10.1111/jdv.13038  0.329
2015 Gürsoy G, Xu Y, Liang J. Effect of Architecture of Cell Nucleus on the Folding Principles of 3D Genome of Budding Yeast Biophysical Journal. 108: 538. DOI: 10.1016/J.Bpj.2014.11.2953  0.674
2014 Gürsoy G, Xu Y, Kenter AL, Liang J. Spatial confinement is a major determinant of the folding landscape of human chromosomes. Nucleic Acids Research. 42: 8223-30. PMID 24990374 DOI: 10.1093/Nar/Gku462  0.672
2014 Tang K, Zhang J, Liang J. Fast protein loop sampling and structure prediction using distance-guided sequential chain-growth Monte Carlo method. Plos Computational Biology. 10: e1003539. PMID 24763317 DOI: 10.1371/Journal.Pcbi.1003539  0.346
2014 Li Y, Naveed H, Kachalo S, Xu LX, Liang J. Mechanisms of regulating tissue elongation in Drosophila wing: impact of oriented cell divisions, oriented mechanical forces, and reduced cell size. Plos One. 9: e86725. PMID 24504016 DOI: 10.1371/Journal.Pone.0086725  0.596
2014 Naveed H, Liang J. Weakly stable regions and protein-protein interactions in beta-barrel membrane proteins. Current Pharmaceutical Design. 20: 1268-73. PMID 23713778 DOI: 10.2174/13816128113199990071  0.615
2014 Gürsoy G, Xu Y, Kenter A, Liang J. Population Properties and Complex Folding Behavior of Chromosome Arise from Spatial Confinement of Self-Avoiding Chromatin Chains Biophysical Journal. 106: 78a. DOI: 10.1016/J.Bpj.2013.11.506  0.679
2014 Gürsoy G, Xu Y, Kenter A, Liang J. Three-Dimensional Chromatin Model of α-Globin Gene Locus in Differentially Activated States Biophysical Journal. 106: 78a. DOI: 10.1016/J.Bpj.2013.11.505  0.69
2014 Tang K, Zhang J, Liang J. Conformational Sampling and Structure Prediction of Multi-Loops in Proteins using Distance-Guided Sequential Chain-Growth Monte Carlo Method Biophysical Journal. 106: 53a. DOI: 10.1016/J.Bpj.2013.11.374  0.361
2013 Cao Y, Naveed H, Liang C, Liang J. Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesis. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2013: 5550-3. PMID 24110994 DOI: 10.1109/EMBC.2013.6610807  0.601
2013 Zhao J, Naveed H, Kachalo S, Cao Y, Tian W, Liang J. Dynamic mechanical finite element model of biological cells for studying cellular pattern formation. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2013: 4517-20. PMID 24110738 DOI: 10.1109/EMBC.2013.6610551  0.608
2013 Gursoy G, Xu Y, Kenter A, Liang J. Population Properties of Self-Avoiding Polymer Chain Models of Chromosomes in a Confined Space of Nucleus Biophysical Journal. 104: 581a. DOI: 10.1016/J.Bpj.2012.11.3229  0.685
2013 Lin M, Naveed H, Liang J. Statistical Mechanical Model for the Transfer Free Energy of Amino Acids in the Context of Membrane Protein OmpLA Biophysical Journal. 104: 401a. DOI: 10.1016/J.Bpj.2012.11.2236  0.611
2012 Li Y, Naveed H, Kachalo S, Xu LX, Liang J. Mechanisms of regulating cell topology in proliferating epithelia: impact of division plane, mechanical forces, and cell memory. Plos One. 7: e43108. PMID 22912800 DOI: 10.1371/Journal.Pone.0043108  0.607
2012 Naveed H, Jimenez-Morales D, Tian J, Pasupuleti V, Kenney LJ, Liang J. Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding. Journal of Molecular Biology. 419: 89-101. PMID 22391420 DOI: 10.1016/J.Jmb.2012.02.043  0.613
2012 Naveed H, Xu Y, Jackups R, Liang J. Predicting three-dimensional structures of transmembrane domains of β-barrel membrane proteins. Journal of the American Chemical Society. 134: 1775-81. PMID 22148174 DOI: 10.1021/Ja209895M  0.751
2012 Geula S, Naveed H, Liang J, Shoshan-Barmatz V. Structure-based analysis of VDAC1 protein: defining oligomer contact sites. The Journal of Biological Chemistry. 287: 2179-90. PMID 22117062 DOI: 10.1074/Jbc.M111.268920  0.606
2012 Liang J, Naveed H, Jimenez-Morales D, Adamian L, Lin M. Computational studies of membrane proteins: models and predictions for biological understanding. Biochimica Et Biophysica Acta. 1818: 927-41. PMID 22051023 DOI: 10.1016/J.Bbamem.2011.09.026  0.619
2012 Gursoy G, Adamian L, Lu H, Liang J. Predicting Allosteric Pathways for Activation of K+ Channels by Perturbation Based Markovian Transmission Model Biophysical Journal. 102: 686a. DOI: 10.1016/J.Bpj.2011.11.3729  0.741
2012 Lin M, Naveed H, Liang J. Computational Free Energy Scale of Amino Acid Residues in Membrane Protein from Statistical Mechanics Biophysical Journal. 102: 59a. DOI: 10.1016/J.Bpj.2011.11.349  0.61
2012 Li Y, Naveed H, Kachalo S, Xu LX, Liang J. On Mechanisms of Regulation of Tissue Elongation in Drosophila Wing Biophysical Journal. 102: 593a. DOI: 10.1016/J.Bpj.2011.11.3234  0.593
2012 Naveed H, Liang J. TMBB-Explorer: A Webserver to Predict the Structure, Oligomerization State, Ppi Interface, and Thermodynamic Properties of the Transmembrane Domains of Outer Membrane Proteins Biophysical Journal. 102: 469a. DOI: 10.1016/J.Bpj.2011.11.2573  0.618
2012 Naveed H, Liang J. Engineering Biological Nanopores with Enhanced Properties Biophysical Journal. 102: 188a-189a. DOI: 10.1016/J.Bpj.2011.11.1028  0.624
2012 Tang K, Zhang J, Liang J. Efficient Protein Loop Generation using Distance-Guided Sequential Monte Carlo Method Biophysical Journal. 102: 185a. DOI: 10.1016/J.Bpj.2011.11.1007  0.338
2011 Li Y, Naveed H, Kachalo S, Xu LX, Liang J. Mechanical forces mediate localized topological change in epithelia. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2011: 178-81. PMID 22254279 DOI: 10.1109/IEMBS.2011.6089923  0.612
2011 Gessmann D, Mager F, Naveed H, Arnold T, Weirich S, Linke D, Liang J, Nussberger S. Improving the resistance of a eukaryotic β-barrel protein to thermal and chemical perturbations. Journal of Molecular Biology. 413: 150-61. PMID 21835183 DOI: 10.1016/J.Jmb.2011.07.054  0.617
2011 Zhao J, Dundas J, Kachalo S, Ouyang Z, Liang J. Accuracy of functional surfaces on comparatively modeled protein structures. Journal of Structural and Functional Genomics. 12: 97-107. PMID 21541664 DOI: 10.1007/S10969-011-9109-Z  0.673
2011 Cui J, Hao J, Ulanovskaya OA, Dundas J, Liang J, Kozmin SA. Creation and manipulation of common functional groups en route to a skeletally diverse chemical library. Proceedings of the National Academy of Sciences of the United States of America. 108: 6763-8. PMID 21383124 DOI: 10.1073/Pnas.1015253108  0.657
2011 Lin M, Zhang J, Lu HM, Chen R, Liang J. Constrained proper sampling of conformations of transition state ensemble of protein folding. The Journal of Chemical Physics. 134: 075103. PMID 21341875 DOI: 10.1063/1.3519056  0.498
2011 Adamian L, Naveed H, Liang J. Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis. Biochimica Et Biophysica Acta. 1808: 1092-102. PMID 21167813 DOI: 10.1016/J.Bbamem.2010.12.008  0.604
2011 Dundas J, Adamian L, Liang J. Structural signatures of enzyme binding pockets from order-independent surface alignment: a study of metalloendopeptidase and NAD binding proteins. Journal of Molecular Biology. 406: 713-29. PMID 21145898 DOI: 10.1016/J.Jmb.2010.12.005  0.661
2011 Gursoy G, Adamian L, Lu H, Liang J. Effects of Electric Field on Channel Proteins Through Dipole Perturbation and Network of Signal Transmission Biophysical Journal. 100: 567a. DOI: 10.1016/J.Bpj.2010.12.3287  0.741
2011 Liu LT, Li M, Mowrey D, Lu H, Liang J, Xu Y, Tang P. Anesthetic Modulation of Signal Transduction Pathways in the α4β2 nAchR Revealed by the Perturbation-Based Markovian Transmission Model Biophysical Journal. 100: 548a. DOI: 10.1016/J.Bpj.2010.12.3193  0.477
2011 Gursoy G, Lu H, Liang J. Predicting Sequence of Events upon Ligand Binding Using PMT Model: A Case Study of Adenylate Kinase Biophysical Journal. 100: 537a. DOI: 10.1016/J.Bpj.2010.12.3134  0.747
2011 Tang K, Zhang J, Liang J. Protein Loop Modeling using Distance-Guided Sequential Monte Carlo Method Biophysical Journal. 100: 215a. DOI: 10.1016/J.Bpj.2010.12.1386  0.346
2011 Naveed H, Xu Y, Jackups R, Liang J. Intertwined Coil Inspired Modeling of β-Barrel Membrane Protein Structures using Predicted Interstrand Interaction Constraints Biophysical Journal. 100: 206a. DOI: 10.1016/J.Bpj.2010.12.1335  0.749
2011 Li Y, Naveed H, Kachalo S, Liang J. Topological Properties and Variations of Cells in Proliferating Epithelia: Impact of Mechanical Force and Division Orientation Biophysical Journal. 100: 166a. DOI: 10.1016/J.Bpj.2010.12.1123  0.607
2010 Naveed H, Li Y, Kachalo S, Liang J. Geometric order in proliferating epithelia: impact of rearrangements and cleavage plane orientation. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2010: 3808-11. PMID 21097056 DOI: 10.1109/IEMBS.2010.5627601  0.616
2010 Cao Y, Lu HM, Liang J. Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda. Proceedings of the National Academy of Sciences of the United States of America. 107: 18445-50. PMID 20937911 DOI: 10.1073/Pnas.1001455107  0.499
2010 Jackups R, Liang J. Combinatorial analysis for sequence and spatial motif discovery in short sequence fragments. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 7: 524-36. PMID 20671322 DOI: 10.1109/Tcbb.2008.101  0.606
2010 Naveed H, Jackups R, Liang J. Accurate Ab Initio Prediction of Three Dimensional Structures of Beta-Barrel Membrane Proteins from Sequences Biophysical Journal. 98: 644a. DOI: 10.1016/J.Bpj.2009.12.3529  0.746
2010 Tang K, Zhang J, Zhang J, Liang J. Accurate Loop Generation of Protein Structures using Distance-Guided Sequential Monte Carlo Sampling Method Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.2509  0.354
2010 Lu H, Liang J. Identification of Signal Transmission Pathways in F-Box Proteins Using Perturbation-Based Markovian Transmission (PMT) Model Biophysical Journal. 98: 442a. DOI: 10.1016/J.Bpj.2009.12.2401  0.508
2009 Zhang J, Dundas J, Lin M, Chen R, Wang W, Liang J. Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation. Rna (New York, N.Y.). 15: 2248-63. PMID 19864433 DOI: 10.1261/Rna.1723609  0.654
2009 Lu HM, Liang J. Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES. Plos Computational Biology. 5: e1000526. PMID 19798437 DOI: 10.1371/Journal.Pcbi.1000526  0.514
2009 Adamian L, Gussin HA, Tseng YY, Muni NJ, Feng F, Qian H, Pepperberg DR, Liang J. Structural model of rho1 GABAC receptor based on evolutionary analysis: Testing of predicted protein-protein interactions involved in receptor assembly and function. Protein Science : a Publication of the Protein Society. 18: 2371-83. PMID 19768800 DOI: 10.1002/Pro.247  0.566
2009 Naveed H, Jackups R, Liang J. Predicting weakly stable regions, oligomerization state, and protein-protein interfaces in transmembrane domains of outer membrane proteins. Proceedings of the National Academy of Sciences of the United States of America. 106: 12735-40. PMID 19622743 DOI: 10.1073/Pnas.0902169106  0.751
2009 Tseng YY, Dundas J, Liang J. Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. Journal of Molecular Biology. 387: 451-64. PMID 19154742 DOI: 10.1016/J.Jmb.2008.12.072  0.767
2009 Naveed H, Jackups R, Liang J. Predicting Strained Regions for Folding and Protein-Protein Interaction in Bacterial Outer Membranes Biophysical Journal. 96: 339a. DOI: 10.1016/J.Bpj.2008.12.3824  0.748
2009 Lu H, Cao Y, Liang J. A Study of Cro's Role in the Induction of Phage Lambda Switch by Stochastic Probability Landscape Model Biophysical Journal. 96: 306a. DOI: 10.1016/J.Bpj.2008.12.1526  0.478
2008 Liang J, Tseng YY, Dundas J, Binkowski TA, Joachimiak A, Ouyang Z, Adamian L. Chapter 4. Predicting and characterizing protein functions through matching geometric and evolutionary patterns of binding surfaces. Advances in Protein Chemistry and Structural Biology. 75: 107-41. PMID 20731991 DOI: 10.1016/S0065-3233(07)75004-0  0.784
2008 Cao Y, Lu HM, Liang J. Stochastic probability landscape model for switching efficiency, robustness, and differential threshold for induction of genetic circuit in phage lambda. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2008: 611-4. PMID 19162730 DOI: 10.1109/IEMBS.2008.4649227  0.5
2008 Lin M, Lu HM, Chen R, Liang J. Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints. The Journal of Chemical Physics. 129: 094101. PMID 19044859 DOI: 10.1063/1.2968605  0.515
2008 Lu HM, Liang J. A model study of protein nascent chain and cotranslational folding using hydrophobic-polar residues. Proteins. 70: 442-9. PMID 17680696 DOI: 10.1002/Prot.21575  0.503
2007 Lu HM, Liang J. Perturbation-based Markovian Transmission Model for macromolecular machinery in cell. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2007: 5029-34. PMID 18003136 DOI: 10.1109/IEMBS.2007.4353470  0.509
2007 Dundas J, Binkowski TA, DasGupta B, Liang J. Topology independent protein structural alignment. Bmc Bioinformatics. 8: 388. PMID 17937816 DOI: 10.1186/1471-2105-8-388  0.789
2007 Tseng YY, Liang J. Predicting enzyme functional surfaces and locating key residues automatically from structures. Annals of Biomedical Engineering. 35: 1037-42. PMID 17294116 DOI: 10.1007/S10439-006-9241-2  0.584
2007 Zhang J, Lin M, Chen R, Liang J, Liu JS. Monte Carlo sampling of near-native structures of proteins with applications. Proteins. 66: 61-8. PMID 17039507 DOI: 10.1002/Prot.21203  0.37
2006 Tseng YY, Liang J. Automated method for predicting enzyme functional surfaces and locating key residues with accuracy and specificity. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 1: 4552-5. PMID 17947099 DOI: 10.1109/IEMBS.2006.259540  0.579
2006 Jackups R, Liang J. Combinatorial model for sequence and spatial motif discovery in short sequence fragments: examples from beta-barrel membrane proteins. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 1: 3470-3. PMID 17947032 DOI: 10.1109/IEMBS.2006.259727  0.604
2006 Jackups R, Cheng S, Liang J. Sequence motifs and antimotifs in beta-barrel membrane proteins from a genome-wide analysis: the Ala-Tyr dichotomy and chaperone binding motifs. Journal of Molecular Biology. 363: 611-23. PMID 16973175 DOI: 10.1016/J.Jmb.2006.07.095  0.605
2006 Adamian L, Ouyang Z, Tseng YY, Liang J. Evolutionary patterns of retinal-binding pockets of type I rhodopsins and their functions. Photochemistry and Photobiology. 82: 1426-35. PMID 16922602 DOI: 10.1562/2006-02-14-Ra-802  0.559
2006 Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Research. 34: W116-8. PMID 16844972 DOI: 10.1093/Nar/Gkl282  0.788
2006 Kachalo S, Lu HM, Liang J. Protein folding dynamics via quantification of kinematic energy landscape. Physical Review Letters. 96: 058106. PMID 16487000 DOI: 10.1103/Physrevlett.96.058106  0.491
2006 Zhang J, Chen R, Liang J. Empirical potential function for simplified protein models: combining contact and local sequence-structure descriptors. Proteins. 63: 949-60. PMID 16477624 DOI: 10.1002/Prot.20809  0.364
2006 Tseng YY, Liang J. Estimation of amino acid residue substitution rates at local spatial regions and application in protein function inference: a Bayesian Monte Carlo approach. Molecular Biology and Evolution. 23: 421-36. PMID 16251508 DOI: 10.1093/Molbev/Msj048  0.584
2005 Kachalo S, Lu HM, Liang J. Protein folding dynamics in lattice model with physical movement. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 4: 4449-52. PMID 17281224 DOI: 10.1109/IEMBS.2005.1615454  0.501
2005 Binkowski TA, Joachimiak A, Liang J. Protein surface analysis for function annotation in high-throughput structural genomics pipeline. Protein Science : a Publication of the Protein Society. 14: 2972-81. PMID 16322579 DOI: 10.1110/Ps.051759005  0.705
2005 Jackups R, Liang J. Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction. Journal of Molecular Biology. 354: 979-93. PMID 16277990 DOI: 10.1016/J.Jmb.2005.09.094  0.601
2005 Liang J, Adamian L, Jackups R. The membrane-water interface region of membrane proteins: structural bias and the anti-snorkeling effect. Trends in Biochemical Sciences. 30: 355-7. PMID 15935679 DOI: 10.1016/J.Tibs.2005.05.003  0.617
2004 Zhang J, Chen R, Liang J. Potential function of simplified protein models for discriminating native proteins from decoys: combining contact interaction and local sequence-dependent geometry. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 4: 2976-9. PMID 17270903 DOI: 10.1109/IEMBS.2004.1403844  0.367
2004 Binkowski TA, DasGupta B, Liang J. Order independent structural alignment of circularly permuted proteins. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 4: 2781-4. PMID 17270854 DOI: 10.1109/IEMBS.2004.1403795  0.704
2004 Zhang J, Chen Y, Chen R, Liang J. Importance of chirality and reduced flexibility of protein side chains: a study with square and tetrahedral lattice models. The Journal of Chemical Physics. 121: 592-603. PMID 15260581 DOI: 10.1063/1.1756573  0.327
2004 Binkowski TA, Freeman P, Liang J. pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins. Nucleic Acids Research. 32: W555-8. PMID 15215448 DOI: 10.1093/Nar/Gkh390  0.703
2004 Tseng YY, Liang J. Are residues in a protein folding nucleus evolutionarily conserved? Journal of Molecular Biology. 335: 869-80. PMID 14698285 DOI: 10.1016/J.Jmb.2003.11.007  0.576
2004 Stitziel NO, Binkowski TA, Tseng YY, Kasif S, Liang J. topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Research. 32: D520-2. PMID 14681472 DOI: 10.1093/Nar/Gkh104  0.775
2003 Binkowski TA, Adamian L, Liang J. Inferring functional relationships of proteins from local sequence and spatial surface patterns. Journal of Molecular Biology. 332: 505-26. PMID 12948498 DOI: 10.1016/S0022-2836(03)00882-9  0.703
2003 Binkowski TA, Naghibzadeh S, Liang J. CASTp: Computed Atlas of Surface Topography of proteins. Nucleic Acids Research. 31: 3352-5. PMID 12824325 DOI: 10.1093/Nar/Gkg512  0.687
2003 Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, Liang J. Structural location of disease-associated single-nucleotide polymorphisms. Journal of Molecular Biology. 327: 1021-30. PMID 12662927 DOI: 10.1016/S0022-2836(03)00240-7  0.585
2003 Adamian L, Jackups R, Binkowski TA, Liang J. Higher-order interhelical spatial interactions in membrane proteins. Journal of Molecular Biology. 327: 251-72. PMID 12614623 DOI: 10.1016/S0022-2836(03)00041-X  0.784
2002 Liang J, Zhang J, Chen R. Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method The Journal of Chemical Physics. 117: 3511-3521. DOI: 10.1063/1.1493772  0.336
1999 Yuan C, Kuwata O, Liang J, Misra S, Balashov SP, Ebrey TG. Chloride binding regulates the schiff base pK in gecko P521 cone-type visual pigment Biochemistry. 38: 4649-4654. PMID 10194387 DOI: 10.1021/Bi9828977  0.683
1998 Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Science : a Publication of the Protein Society. 7: 1884-97. PMID 9761470 DOI: 10.1002/Pro.5560070905  0.682
1998 Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins. 33: 18-29. PMID 9741841 DOI: 10.1002/(Sici)1097-0134(19981001)33:1<18::Aid-Prot2>3.0.Co;2-H  0.515
1998 Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins. 33: 1-17. PMID 9741840 DOI: 10.1002/(Sici)1097-0134(19981001)33:1<1::Aid-Prot1>3.0.Co;2-O  0.491
1998 Edelsbrunner H, Facello M, Liang J. On the definition and the construction of pockets in macromolecules Discrete Applied Mathematics. 88: 83-102. DOI: 10.1016/S0166-218X(98)00067-5  0.493
1997 Lewis JW, Liang J, Ebrey TG, Sheves M, Livnah N, Kuwata O, Jäger S, Kliger DS. Early photolysis intermediates of gecko and bovine artificial visual pigments. Biochemistry. 36: 14593-600. PMID 9398178 DOI: 10.1021/Bi9712908  0.454
1995 Lewis JW, Liang J, Ebrey TG, Sheves M, Kliger DS. Chloride effect on the early photolysis intermediates of a gecko cone-type visual pigment. Biochemistry. 34: 5817-23. PMID 7727442 DOI: 10.1021/Bi00017A013  0.467
1994 Liang J, Steinberg G, Livnah N, Sheves M, Ebrey TG, Tsuda M. The pK(a) of the protonated Schiff bases of gecko cone and octopus visual pigments Biophysical Journal. 67: 848-854. PMID 7948697 DOI: 10.1016/S0006-3495(94)80544-2  0.45
1993 Liang J, Govindjee R, Ebrey TG. Metarhodopsin intermediates of the Gecko cone pigment P521 Biochemistry. 32: 14187-14193. PMID 8260505 DOI: 10.1021/Bi00214A018  0.457
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