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Jie Liang - Publications

Affiliations: 
Bioengineering University of Illinois at Chicago, Chicago, IL, United States 
Area:
Bioinformatics Biology, General Biophysics, Biochemistry
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166 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
2023 Tian W, Lin M, Tang K, Barse M, Naveed H, Liang J. 3D-BMPP: 3D Beta-Barrel Membrane Protein Predictor. Methods in Molecular Biology (Clifton, N.J.). 2627: 321-328. PMID 36959455 DOI: 10.1007/978-1-0716-2974-1_17  0.674
2021 Sun Q, Perez-Rathke A, Czajkowsky DM, Shao Z, Liang J. High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis. Nature Communications. 12: 205. PMID 33420075 DOI: 10.1038/s41467-020-20490-9  0.49
2021 Perez-Rathke A, Fahie MAV, Chisholm CM, Chen M, Liang J. Simulation of pH-Dependent, Loop-Based Membrane Protein Gating Using Pretzel. Methods in Molecular Biology (Clifton, N.J.). 2186: 159-169. PMID 32918736 DOI: 10.1007/978-1-0716-0806-7_12  0.387
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  0.709
2020 Perez-Rathke A, Sun Q, Wang B, Boeva V, Shao Z, Liang J. CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells. Genome Biology. 21: 13. PMID 31948478 DOI: 10.1186/S13059-019-1904-Z  0.533
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  0.645
2020 Perez-Rathke A, Sun Q, Wang B, Boeva V, Shao Z, Liang J. Landscape of Multivalent Chromatin Interactions in Transcriptionally Active LOCI Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.3003  0.48
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  0.59
2019 Lei X, Wang B, Perez-Rathke A, Tian W, Chou CY, Tseng YY, Liang J. Predicting Oncogenic Missense Mutations. ... Ieee-Embs International Conference On Biomedical and Health Informatics. Ieee-Embs International Conference On Biomedical and Health Informatics. 2019. PMID 35261984 DOI: 10.1109/bhi.2019.8834553  0.588
2019 Wang Y, Sun Q, Liang J, Li H, Czajkowsky DM, Shao Z. Q-Nuc: a bioinformatics pipeline for the quantitative analysis of nucleosomal profiles. Interdisciplinary Sciences, Computational Life Sciences. PMID 31845186 DOI: 10.1007/S12539-019-00354-7  0.527
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  0.695
2019 Wang X, Tian W, Banh BT, Statler BM, Liang J, Stone DE. Mating yeast cells use an intrinsic polarity site to assemble a pheromone-gradient tracking machine. The Journal of Cell Biology. PMID 31570500 DOI: 10.1083/Jcb.201901155  0.324
2019 Sun Q, Perez-Rathke A, Czajkowsky D, Shao Z, Liang J. Uncovering a Novel Folding Landscape of the Drosophila Genome Through Hi-C Normalization via Fractal Monte Carlo Deep Sampling Biophysical Journal. 116: 69a. DOI: 10.1016/J.Bpj.2018.11.415  0.483
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  0.647
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  0.622
2019 Lei X, Tian W, Perez-Rathke A, Wang B, Chou C, Tseng J, Liang J. Predicting Candidate Onco-Genesis Mutations and Cooperative Units from Computed Protein Surface Pockets Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.2273  0.324
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  0.475
2018 Yang Y, Guo R, Gaffney K, Kim M, Muhammednazaar S, Tian W, Wang B, Liang J, Hong H. Folding-Degradation Relationship of a Membrane Protein Mediated by the Universally Conserved ATP-dependent Protease FtsH. Journal of the American Chemical Society. PMID 29528632 DOI: 10.1021/Jacs.8B00832  0.394
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  0.697
2017 Perez-Rathke A, Fahie MAV, Chisholm C, Liang J, Chen M. Mechanism of OmpG pH-dependent gating from loop ensemble and single channel studies. Journal of the American Chemical Society. PMID 29262680 DOI: 10.1021/Jacs.7B11979  0.379
2017 Tian W, Lei X, Kauffman LH, Liang J. A Knot Polynomial Invariant for Analysis of Topology of RNA Stems and Protein Disulfide Bonds. Molecular Based Mathematical Biology (Online). 5: 21-30. PMID 29201869 DOI: 10.1515/Mlbmb-2017-0002  0.3
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  0.686
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  0.67
2017 Lin M, Zhang G, Fahie M, Morgan LK, Chen M, Keiderling TA, Kenney LJ, Liang J. Engineering a Novel Porin OmpGF via Strand Replacement From Computational Analysis of Sequence Motif. Biochimica Et Biophysica Acta. PMID 28341438 DOI: 10.1016/J.Bbamem.2017.03.012  0.359
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  0.692
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  0.709
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  0.612
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  0.441
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  0.685
2016 Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA. Challenges in structural approaches to cell modeling. Journal of Molecular Biology. PMID 27255863 DOI: 10.1016/J.Jmb.2016.05.024  0.386
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  0.688
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  0.697
2016 Perez-Rathke A, Chisholm C, Chen M, Liang J. Computational Models of Interacting Loop Regions in pH-Dependent Gating of OmpG Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.380  0.329
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  0.722
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  0.641
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  0.772
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  0.649
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  0.37
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  0.309
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  0.631
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  0.528
2015 Estrada Mallarino L, Fan E, Odermatt M, Müller M, Lin M, Liang J, Heinzelmann M, Fritsche F, Apell HJ, Welte W. TtOmp85, a β-barrel assembly protein, functions by barrel augmentation. Biochemistry. 54: 844-52. PMID 25537637 DOI: 10.1021/Bi5011305  0.375
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  0.678
2014 Gürsoy G, Xu Y, Liang J. Computational predictions of structures of multichromosomes of budding yeast. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2014: 3945-8. PMID 25570855 DOI: 10.1109/EMBC.2014.6944487  0.658
2014 Xu Y, Hu C, Dai Y, Liang J. On simplified global nonlinear function for fitness landscape: a case study of inverse protein folding. Plos One. 9: e104403. PMID 25110986 DOI: 10.1371/Journal.Pone.0104403  0.409
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  0.668
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  0.499
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  0.615
2014 Jimenez-Morales D, Adamian L, Shi D, Liang J. Lysine carboxylation: unveiling a spontaneous post-translational modification. Acta Crystallographica. Section D, Biological Crystallography. 70: 48-57. PMID 24419378 DOI: 10.1107/S139900471302364X  0.367
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  0.7
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  0.683
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  0.691
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  0.545
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  0.58
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  0.601
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  0.674
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  0.681
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  0.62
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  0.704
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  0.805
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  0.678
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  0.723
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  0.734
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  0.682
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  0.614
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  0.719
2012 Naveed H, Liang J. Engineering Biological Nanopores with Enhanced Properties Biophysical Journal. 102: 188a-189a. DOI: 10.1016/J.Bpj.2011.11.1028  0.696
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  0.452
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  0.59
2011 Jimenez-Morales D, Liang J. Pattern of Amino Acid Substitutions in Transmembrane Domains of β-Barrel Membrane Proteins for Detecting Remote Homologs in Bacteria and Mitochondria Plos One. 6. PMID 22069449 DOI: 10.1371/Journal.Pone.0026400  0.406
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  0.716
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  0.757
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  0.676
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  0.594
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  0.69
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  0.729
2011 Zhao J, Dundas J, Kachalo S, Ouyang Z, Liang J. Improving Accuracy of Functional Surfaces of Protein Structures Modeled From Sequences Biophysical Journal. 100: 48a. DOI: 10.1016/J.Bpj.2010.12.459  0.407
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  0.743
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  0.565
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  0.76
2011 Xu Y, Adamian L, Liang J. Vectorial Network Model (VNM) for Protein Dynamics: An Analytical Tool for Protein Fluctuations Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.3118  0.337
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  0.494
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  0.803
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  0.633
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  0.602
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  0.554
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  0.676
2010 Zhao J, Kachalo S, Ouyang Z, Liang J. Identification of Functional Surfaces of Proteins from Sequences Biophysical Journal. 98: 760a. DOI: 10.1016/J.Bpj.2009.12.4173  0.424
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  0.795
2010 Xu Y, Hu C, Dai Y, Liang J. Simplified Global Nonlinear Function for Fitness Landscape of Protein Design Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.3481  0.378
2010 Adamian LA, Liang J. Evolutionary Conservation of Phospholipid-Binding Sites in Membrane Proteins Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.284  0.426
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  0.503
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  0.618
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  0.7
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  0.596
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  0.651
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  0.806
2009 Ebalunode JO, Dong X, Ouyang Z, Liang J, Eckenhoff RG, Zheng W. Structure-based shape pharmacophore modeling for the discovery of novel anesthetic compounds. Bioorganic & Medicinal Chemistry. 17: 5133-8. PMID 19520579 DOI: 10.1016/J.Bmc.2009.05.060  0.347
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  0.821
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  0.8
2009 Ouyang Z, Liang J, Kachalo S. Inferring Protein-protein Interface From Geometry Of Unbound Structures Biophysical Journal. 96: 598a. DOI: 10.1016/J.Bpj.2008.12.3131  0.431
2009 Zhang J, Dundas J, Lin M, Chen R, Wang W, Liang J. A New Free Energy Rule Toward Psuedo-knotted RNA Structure Prediction Biophysical Journal. 96: 579a. DOI: 10.1016/J.Bpj.2008.12.3025  0.317
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  0.553
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  0.802
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  0.49
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  0.61
2008 Ouyang Z, Liang J. Predicting protein folding rates from geometric contact and amino acid sequence. Protein Science : a Publication of the Protein Society. 17: 1256-63. PMID 18434498 DOI: 10.1110/Ps.034660.108  0.405
2008 Ebalunode JO, Ouyang Z, Liang J, Zheng W. Novel approach to structure-based pharmacophore search using computational geometry and shape matching techniques. Journal of Chemical Information and Modeling. 48: 889-901. PMID 18396858 DOI: 10.1021/Ci700368P  0.315
2008 Zhang J, Lin M, Chen R, Wang W, Liang J. Discrete state model and accurate estimation of loop entropy of RNA secondary structures. The Journal of Chemical Physics. 128: 125107. PMID 18376982 DOI: 10.1063/1.2895050  0.313
2008 Lin M, Chen R, Liang J. Statistical geometry of lattice chain polymers with voids of defined shapes: sampling with strong constraints. The Journal of Chemical Physics. 128: 084903. PMID 18315083 DOI: 10.1063/1.2831905  0.405
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  0.626
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  0.536
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  0.815
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  0.674
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  0.536
2007 Saidel GM, Liang J. ABME Special Issue: Systems Biology, Bioinformatics, and Computational Biology Annals of Biomedical Engineering. 35: 861-862. DOI: 10.1007/S10439-007-9325-7  0.374
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  0.643
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  0.659
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  0.693
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  0.647
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  0.757
2006 Adamian L, Liang J. Prediction of transmembrane helix orientation in polytopic membrane proteins. Bmc Structural Biology. 6: 13-13. PMID 16792816 DOI: 10.1186/1472-6807-6-13  0.422
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  0.594
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  0.522
2006 Adamian L, Liang J. Prediction of buried helices in multispan alpha helical membrane proteins Proteins. 63: 1-5. PMID 16419070 DOI: 10.1002/Prot.20874  0.418
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  0.683
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  0.577
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  0.781
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  0.682
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  0.691
2005 Li X, Liang J. Geometric cooperativity and anticooperativity of three-body interactions in native proteins. Proteins. 60: 46-65. PMID 15849756 DOI: 10.1002/Prot.20438  0.39
2005 Adamian L, Nanda V, DeGrado WF, Liang J. Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins. Proteins. 59: 496-509. PMID 15789404 DOI: 10.1002/Prot.20456  0.365
2005 Li X, Keskin O, Ma B, Nussinov R, Liang J. Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. Journal of Molecular Biology. 344: 781-95. PMID 15533445 DOI: 10.1016/J.Jmb.2004.09.051  0.432
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  0.451
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  0.751
2004 Song MJ, Hwang S, Wong W, Round J, Martinez-Guzman D, Turpaz Y, Liang J, Wong B, Johnson RC, Carey M, Sun R. The DNA architectural protein HMGB1 facilitates RTA-mediated viral gene expression in gamma-2 herpesviruses. Journal of Virology. 78: 12940-50. PMID 15542646 DOI: 10.1128/Jvi.78.23.12940-12950.2004  0.302
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  0.441
2004 Hu C, Li X, Liang J. Developing optimal non-linear scoring function for protein design Bioinformatics. 20: 3080-3098. PMID 15217818 DOI: 10.1093/Bioinformatics/Bth369  0.38
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  0.776
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  0.669
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  0.802
2003 Li X, Hu C, Liang J. Simplicial edge representation of protein structures and alpha contact potential with confidence measure. Proteins. 53: 792-805. PMID 14635122 DOI: 10.1002/Prot.10442  0.362
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  0.773
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  0.746
2003 Lear JD, Gratkowski H, Adamian L, Liang J, DeGrado WF. Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles. Biochemistry. 42: 6400-7. PMID 12767221 DOI: 10.1021/Bi020573J  0.389
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  0.661
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  0.818
2003 Zhang J, Chen R, Tang C, Liang J. Origin of scaling behavior of protein packing density: A sequential Monte Carlo study of compact long chain polymers Journal of Chemical Physics. 118: 6102-6109. DOI: 10.1063/1.1554395  0.391
2002 Adamian L, Liang J. Interhelical hydrogen bonds and spatial motifs in membrane proteins: Polar clamps and serine zippers Proteins. 47: 209-218. PMID 11933067 DOI: 10.1002/Prot.10071  0.329
2002 McGee MP, Liang J, Luba J. Hydration effects of heparin on antithrombin probed by osmotic stress. Biophysical Journal. 82: 1040-9. PMID 11806943 DOI: 10.1016/S0006-3495(02)75463-5  0.302
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  0.43
2001 McGee MP, Liang J. Regulation of glycosaminoglycan function by osmotic potentials. Measurement of water transfer during antithrombin activation by heparin. The Journal of Biological Chemistry. 276: 49275-82. PMID 11677228 DOI: 10.1074/Jbc.M104413200  0.306
2001 Adamian L, Liang J. Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins. Journal of Molecular Biology. 311: 891-907. PMID 11518538 DOI: 10.1006/Jmbi.2001.4908  0.412
2001 Liang J, Dill KA. Are proteins well-packed? Biophysical Journal. 81: 751-66. PMID 11463623 DOI: 10.1016/S0006-3495(01)75739-6  0.365
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  0.701
1999 McGee MP, Teuschler H, Liang J. Electrostatic interactions during activation of coagulation factor IX via the tissue factor pathway: effect of univalent salts. Biochimica Et Biophysica Acta. 1453: 239-53. PMID 10036322 DOI: 10.1016/S0925-4439(98)00108-2  0.306
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  0.733
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  0.655
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  0.56
1998 Liang J, McGee MP. Hydration structure of antithrombin conformers and water transfer during reactive loop insertion. Biophysical Journal. 75: 573-82. PMID 9675160 DOI: 10.1016/S0006-3495(98)77548-4  0.306
1998 McGee MP, Teuschler H, Liang J. Effective electrostatic charge of coagulation factor X in solution and on phospholipid membranes: implications for activation mechanisms and structure-function relationships of the Gla domain. The Biochemical Journal. 330: 533-9. PMID 9461553 DOI: 10.1042/Bj3300533  0.328
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  0.591
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  0.514
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  0.509
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  0.52
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  0.51
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