Liang Lab Publications

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Ilyas Khan, Sunan Li, Lihong Tao, Chong Wang, Bowei Ye, Huiyu Li, Xiaoyang Liu, Iqbal Ahmad, Wenqiang Su, Gongxun Zhong, Zhiyuan Wen, Jinliang Wang, Rong-Hong Hua, Ao Ma, Jie Liang, Xiao-Peng Wan, Zhi-Gao Bu, Yong-Hui Zheng Tubeimosides are pan-coronavirus and filovirus inhibitors that can block their fusion protein binding to Niemann-Pick C1 Nature communications 15, 162 (2024). doi.org/10.1038/s41467-023-44504-4

Bowei Ye, Boshen Wang, Jie Liang Predicting Pathology of Missense Mutations through Protein-Specific Evolutionary Pattern 45th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2022, Sydney, Australia. doi.org/10.1109/EMBC40787.2023.10339993 (Supported by NIH grants R35 GM127084.)

Wei Tian, Meishan Lin, Ke Tang, Manisha Barse, Hammad Naveed, Jie Liang 3D-BMPP: 3D Beta-Barrel Membrane Protein Predictor Homology Modeling: Methods and Protocols 321-328. Springer US, 2023. PMC10593542 (Supported by R35 GM127084)

Khalid H Bhat, Saurabh Priyadarshi, Sarah Naiyer, Xinyan Qu, Hammad Farooq, Eden Kleiman, Jeffery Xu, Xue Lei, Jose F Cantillo, Robert Wuerffel, Nicole Baumgarth, Jie Liang, Ann J Feeney, Amy L Kenter An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation. Nature communications 14 (1), 1225 2023. doi.org/10.1038/s41467-023-36414-2 (Supported by R35 GM127084)

Boshen Wang, Xue Lei, Wei Tian, Alan Perez-Rathke, Yan-Yuan Tseng, Jie Liang Structure-based pathogenicity relationship identifier for predicting effects of single missense variants and discovery of higher-order cancer susceptibility clusters of mutations; Briefings in Bioinformatics bbad206 2023. doi.org/10.1093/bib/bbad206 (Supported by R35 GM127084)

Chen, S.-J., Hassan, M., Jernigan, R.L., Jia, K., Kihara, D., Kloczkowski, A., Kotelnikov, S., Kozakov, D., Liang, J., Liwo, A., Matysiak, S., Meller, J., Micheletti, C., Mitchell, J.C., Mondal, S., Nussinov, R., Okazaki, K., Padhorny, D., Skolnick, J., Sosnick, T.S., Stan, G., Vakser, I., Zou, X., Rose, G.D., Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proc Natl Acad Sci USA 2023. doi.org/10.1073/pnas.2214423119

Farid Manuchehrfar, Huiyu Li, Wei Tian, Ao Ma, Jie Liang Reactive vortexes in a naturally activated process: Non-diffusive rotational fluxes at transition state uncovered by persistent homology. J. Phys. Chem. B. 2022, 126, 45, 9297-9308 https://doi.org/10.1021/acs.jpcb.2c07015 (Supported by NIH grants R35 GM127084.)

Eva Hin Wa Leung, Kenneth Joves, Aydolun Petenkaya, Georgina Barham, Thomas G. Henderson, Jie Liang and Constantinos Chronis Reprogramming cell fates towards novel cancer immunotherapies Current Opinion in Pharmacology 2022, 67:102312.

Aydolun Petenkaya, Farid Manuchehrfar, Constantinos Chronis and Jie Liang Identifying transient cells during reprogramming via persistent homology 44th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2022, Glasgow, UK. https://doi.org/10.1109/EMBC48229.2022.9871358 (Supported by NIH grants R35 GM127084.) PMID: 36085927

Ke Tang, Jorjethe Roca, Rong Chen, Ajum Ansari, and Jie Liang Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse.grained loop.entropy model J Biological Physics In press https://doi.org/10.1007/s10867-022-09602-2 PMC9054998 (Supported by NIH grants R35 GM127084.)

Qing Cheng, Pourya Delafrouz, Jie Liang, Chun Liu, and Jie Shen Modeling and simulation of cell nuclear architecture reorganization process J Computational Physics 449(15):110808 https://doi.org/10.1016/j.jcp.2021.110808 PMC9524197 (Supported by NIH grants R35 GM127084.)

Hong Ming Shen, Robert Wuerffel, Jose F Cantillo, Saurabh Priyadarshi, Xue Lei, Jie Liang, Yee Ling Wu, Amy L Kenter Loop extrusion promotes an alternate pathway for isotype switching Cell Reports 37(8):110059. https://doi.org/10.1016/j.celrep.2021.110059 PMC8979556

Jie Liang and Alan Perez-Rathke Minimalistic 3D Chromatin Models: Sparse Interactions in Single Cells Drive the Chromatin Fold and Form Many-Body Units Current Opinion in Structural Biology 71:200-214 (2021). https://doi.org/10.1016/j.sbi.2021.06.017 PMC8967685 (Supported by NIH grants R35 GM127084.)

Yiyu Pang and Jie Liang. Inferring initial state of the ancestral network of cellular fate decision: a case study of phage lambda. 43rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Conf Proc IEEE Eng Med Biol Soc. , 2021., 2021 Nov; 2021:4436-4439. PMC8957294 (Supported by NIH R35GM127084)

Anna Terebus, Farid Manuchehrfar, Youfang Cao, Jie Liang Exact Probability Landscapes of Stochastic Phenotype Switching in Feed-Forward Loops: Phase Diagrams of Multimodality. Frontiers in Genetics https://doi.org/10.3389/fgene.2021.645640 (Supported by NIH grants R35 GM127084.)

Farid Manuchehrfar, Huiyu Li, Wei Tian, Ao Ma, and Jie Liang Exact Topology of the Dynamic Probability Surface of an Activated Process by Persistent Homology. Journal of Physical Chemistry B 125(18):4667-4680 (2021). https://doi.org/10.1021/acs.jpcb.1c00904 PMC8957293 (Supported by NIH grants R35 GM12708R01.) Cover Art.

Qiu Sun, Alan Perez-Rathke, Daniel M. Czajkowsky, Zhifeng Shao, and Jie Liang High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis. Nature Communications 205 (2021). https://doi.org/10.1038/s41467-020-20490-9 PMC7794469 (Supported by NIH grants R35 GM127084.)

Alan Perez-Rathke, Monifa A V Fahie, Christina M Chisholm, Min Chen, Jie Liang. Simulation of pH-Dependent, Loop-Based Membrane Protein Gating Using Pretzel. Methods Mol Biol. 2021. 2186:159-169. doi: 10.1007/978-1-0716-0806-7_12 (Supported by NIH grants loop R01-GM126558, R01-GM079804, and R35GM127084).

Jieling Zhao, Farid Manuchehrfar and Jie Liang Cell-substrate mechanics guide collective cell migration through intercellular adhesion: a dynamic finite element cellular model. Biomech Model Mechanobiol. 2020. doi.org/10.1007/s10237-020-01308-5 PMC7990038 (Supported by NIH grants R01 CA204962 and R35 GM12708R01.)

Alan Perez-Rathke, Qiu Sun, Boshen Wang, Valentina Boeva, Zhifeng Shao and Jie Liang. CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single-cells. Genome Biology. 21:13, 2020. doi.org/10.1186/s13059-019-1904-z. PMC6966897 PMC6966897 (Supported by NIH grants R21AI126308, R21AI137865, R01CA204962, and R35GM127084.)

Yuan Wang, Qiu Sun, Jie Liang, Hua Li, Daniel M. Czajkowsky, and Zhifeng Shao. Q-Nuc: A Bioinformatics Pipeline for the Quantitative Analysis of Nucleosomal Profiles. Interdisciplinary Sciences - Computational Life Sciences (INSC). 2020. INSC-D-19-00437. 12:69-81. doi.org/10.1007/s12539-019-00354-7. (Supported by NIH grants R01 CA204962 and R21AI126308.)

Thomas Bausewein, Hammad Naveed, Jie Liang and Stephan Nussberger. The structure of the TOM core complex in the mitochondrial outer membrane. Biological Chemistry. 2020. 401(6-7):687-697. doi: 10.1515/hsz-2020-0104

Anna Terebus, Chun Liu, and Jie Liang Discrete and continuous models of probability flux of switching dynamics: Uncovering stochastic oscillations in a toggle-switch system J. Chem. Phys, 2019. 151:185104 doi.org/10.1063/1.5124823 . PMC7043830 A preprint can be found here. PMC7043830 (Supported by NIH grant R35 GM127084 and R01 CA204962.)

Wei Tian, Hammad Naveed, Meishan Lin, and Jie Liang. GeTFEP: A general transfer free energy profile of transmembrane proteins. Protein Science, 2019. 29(2):469-479. DOI: 10.1002/pro.3763, PMC6954696 (Supported by NIH grants R01CA204962-01A1, R01GM079804, R21AI126308, R35GM127084.)

Xin Wang, Wei Tian, Bryan T. Banh, Bethanie-Michelle Statler, Jie Liang, David E. Stone. Mating yeast cells use an intrinsic polarity site to assemble a pheromone-gradient tracking machine J. Cell. Biol, 2019. DOI: 10.1083/jcb.201901155 doi.org/10.1063/1.5124823. PMC6829655 (Supported by NIH grant R35 GM127084, R01 CA204962, and R21AI126308.)

Anna Terebus, Youfang Cao, and Jie Liang. Sensitivities of Regulation Intensities in Feed-Forward Loops with Multistability. 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Conf Proc IEEE Eng Med Biol Soc. , 2019., pp. 1969-1972, doi: 10.1109/EMBC.2019.8856532. NIHMSID:1707459, PMID:31946285. (Supported by NSF MCB-1415589, NIH R35GM127084, R01CA204962-01A1, and R21 AI126308 are gratefully acknowledged.)

Alan Perez-Rathke, Samira Mali, Lin Du and Jie Liang. Alterations in Chromatin Folding Patterns in Cancer Variant-Enriched Loci IEEE EMBS International Conference on Biomedical & Health Informatics (BHI), 2019, pp. 1-4. , 2019:doi: 10.1109/BHI.2019.8834565. NIHMSID:1707446 PMC8172279 (Supported by NIH grants R21 AI126308, R35GM127084 and R01CA204962-01A1).

Boshen Wang, Wei Tian, Xue Lei, Alan Perez-Rathke, Yan Yuan Tseng and Jie Liang. Structure-based Method for Predicting Deleterious Missense SNPs IEEE EMBS International Conference on Biomedical & Health Informatics (BHI), , 2019 pp. 1-4, doi: 10.1109/BHI.2019.8834504. NIHMSID:1707462. PMC8204715 (Supported by NIH grants R01CA204962- 01A1, R35GM127084, and R21 AI126308).

Xue Lei Boshen Wang Alan Perez-Rathke Wei Tian Chia-Yi Chou Yan-Yuan Tseng Jie Liang. Predicting Oncogenic Missense Mutations. IEEE EMBS International Conference on Biomedical & Health Informatics (BHI), , 2019, pp. 1-4, doi: 10.1109/BHI.2019.8834553. NIHMSID:1707454 (Supported by NIH grants R01CA204962-01A1, R35GM127084 and R21AI126308).

Farid Manuchehrfar, Wei Tian, Tom Chou, and Jie Liang. Evolution of coagulation-fragmentation stochastic processes using accurate chemical master equation approach. Communications in Information and Systems 2019, 19(1):37-55. DOI: http://dx.doi.org/10.4310/CIS.2019.v19.n1.a3 PMC8378664 (Supported by NIH grants R35GM127084, R01CA204962-01A1, and R21 AI126308.)

Youfang Cao, Xue Lei, Ruy M. Ribeiro, Alan S. Perelson, and Jie Liang. Probabilistic control of HIV latency and transactivation by the Tat gene circuit. Proc Natl Acad Sci USA 2018. doi.org/10.1073/pnas.1811195115. (Supported by NIH grants R01 CA204962, R01 GM126558 and R35 GM127084.)

Anna Terebus, Chun Liu, and Jie Liang Discrete flux and velocity fields of probability and their global maps in reaction systems. J. Chem. Phys, 2018. 149:185101 (Supported by NIH grant R35 GM127084.)

Yiqing Yang, Ruiqiong Guo, Kristen Gaffney, Miyeon Kim, Shaima Muhammednazaar, Wei Tian, Boshen Wang, Jie Liang, Heedeok Hong. Folding-Degradation Relationship of a Membrane Protein Mediated by the Universally Conserved ATP-Dependent Protease FtsH. J Am Chem Soc, 2018. DOI: 10.1021/jacs.8b00832 (Supported by NIH grants R01GM079804 and R01GM126558 )

Wei Tian, Chang Chen, Xue Lei, Jieling Zhao, and Jie Liang. CASTp 3.0: computed atlas of surface topography of proteins Nucleic Acid Research, 2018. doi.org/10.1093/nar/gky473 PMC6031066 (Supported by NIH grant R01CA204962 and UIC ROAAP fund.)

Wei Tian, Meishan Lin, Ke Tang, Jie Liang, and Hammad Naveed. High-resolution structure prediction of β-barrel membrane proteins. Proc Natl Acad Sci USA 2018; 113(43):11991-11993. PMC5816179 [Supported by NIH grants NIH Grants R01GM079804, R01CA204962, R01GM126558, and R21AI126308).

Alan Perez-Rathke, Monifa A. Fahle, Christina Chisholm, Jie Liang and Min Chen. Mechanism of OmpG pH-Dependent Gating from Loop Ensemble and Single Channel Studies. J Am Chem Soc , 2018. 140(3):1105-1115 PMC5831328 (Supported by NIH grant R01-GM079804 and R01 GM126558).

Wei Tian and Jie Liang. On quantification of geometry and topology of protein pockets and channels for assessing mutation effects. IEEE EMBS Int Conf Biomed Health Inform , 2018: 263-266. PMC6157619, doi: [10.1109/BHI.2018.8333419] (Supported by NIH grants NIH grants R01CA204962).

Boshen Wang, Alan Perez-Rathke, Renhao Li, and Jie Liang. A General Method for Predicting Amino Acid Residues Experiencing Hydrogen Exchange IEEE EMBS Int Conf Biomed Health Inform , 2018:341-344. doi: [10.1109/BHI.2018.8333438], PMC5957487 PMC5957487 (Supported by NIH grants NIH grants R01GM079804, R01CA204962, R01GM126558, and R21AI126308).

Gamze Gursoy, Yun Xu, Amy Kenter, and Jie Liang Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data. Nucleic Acid Research, 2017. 45:11547-11558. doi.org/10.1093/nar/gkx784, PMC5714131 (Supported by NIH grants R01GM126558, R21AI126308, the Chicago Biomedical Consortium (with support from the Searle Funds at The Chicago Community Trust), and Research Open Access Publishing (ROAAP) Fund of the University of Illinois at Chicago).

Gamze Gursoy, Yun Xu, Jie Liang 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, 2017. 13(7): e1005658. https://doi.org/10.1371/journal.pcbi.1005658, PMC5714131, (Supported by NIH grant R01GM079804, R01GM126558, R21AI126308-01A1, the Chicago Biomedical Consortium (with support from the Searle Funds at The Chicago Community Trust), and the Research Open Access Publishing (ROAAP) Fund of the University of Illinois at Chicago).

Yun Xu, Changyu Hu, Yang Dai and Jie Liang. Global Nonlinear Fitness Function for Protein Structures. D. Xu et al. (eds.), Health Informatics Data Analysis, Health Information Science, , 2017. Springer International Publishing Switzerland, DOI 10.1007/978-3-319-44981-4_1

Wei Tian, Xue Lei, Louis H. Kauffman, and Jie Liang. A Knot Polynomial Invariant for Analysis of Topology of RNA Stems and Protein Disulfide Bonds Molecular Based Mathematical Biology , 2017. 5(1):21-30. DOI: https://doi.org/10.1515/mlbmb-2017-0002 (Supported by NIH grant GM079804).

Meishan Lin, Ge Zhang, Monifa Fahie, Leslie K Morgan, Min Chen, Timothy A Keiderling, Linda J Kenney and Jie Liang. Engineering a Novel Porin OmpGF Via Strand Replacement From Computational Analysis of Sequence Motif BBA - Biomembranes , 2017. 1859(7):1180-1189. doi: 10.1016/j.bbamem.2017.03.012. (Supported by NIH GM079804, AI123640, and VA 5IOBX099372).

Jieling Zhao, Youfang Cao, Luisa DiPietro, and Jie Liang. Dynamic cellular finite element method for modeling large scale cell migration and proliferation under the control of mechanical and biochemical cues: A study of re-epithelialization. Journal of the Royal Society Interface, 2017. 14:20160959, DOI: dx.doi.org/10.1098/rsif.2016.0959 (Supported by NIH GM079804, GM50875 and NSF MCB-1415589).

Wei Tian, Meishan Lin, Hammad Naveed, and Jie Liang. Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins Bioinformatics, 2017. 33 (11): 1664-1671. https://doi.org/10.1093/bioinformatics/btx053 (Supported by NIH GM079804).

Ke Tang, Jinfeng Zhang, and Jie Liang. Distance-Guided Forward and Backward Chain-Growth Monte Carlo Method for Conformational Sampling and Structural Prediction of Antibody CDR-H3 Loops. J Chemical Theory and Computation , 2016. 13 (1):380-388 DOI: 10.1021/acs.jctc.6b00845 (Supported by NIH GM079804 and GM115442, and NSF MCB-1415589).

C. Ma, T. Luciani, A. Terebus, J. Liang, and G. E. Marai. PRODIGEN: Visualizing the Probability Landscape of Stochastic Gene Regulatory Networks in State and Time Space. BMC Bioinformatics. , 2016. 18(Suppl 2):24. DOI 10.1186/s12859-016-1447-1. (Supported by NIH GM079804)

Gamze Gursoy and Jie Liang. Three-dimensional chromosome structures from energy landscape. Proc Natl Acad Sci USA 2016; 113(43):11991-11993. doi: 10.1073/pnas.1614535113 PMCID: PMC5087004 [Supported by: NIH GM079804, NSF MCB1415589, and the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust.].

Gamze Gursoy, Anna Terebus, Youfang Cao, and Jie Liang. Mechanisms of Stochastic Focusing and Defocusing in Biological Reaction Networks: Insight from Accurate Chemical Master Equation (ACME) Solutions. Conf Proc IEEE Eng Med Biol Soc. , 2016. DOI: 10.1109/EMBC.2016.7590989 . (Supported by NIH Grants GM079804, DMS0800257 and the Chicago Biomedical Consortium are gratefully acknowledged.)

Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA. Challenges in structural approaches to cell modeling. J Mol Biol , 2016. DOI:10.1016/j.jmb.2016.05.024 PMID:27255863 (supported by NIHR01 GM079804, NSFMCB1415589, and the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust).

Youfang Cao, Anna Terebus, and JieLiang. Chapter 3. Modeling stochastic gene regulatory networks using direct solutions of chemical master equation and rare event sampling. Emerging Research in the Analysis and Modeling of Gene Regulatory Networks , 2016. Ed. Ivanov, Qian, and Pal. IGI Global. Advances in Medical Technologies and Clinical Practice (AMTCP) Book Series. DOI: 10.4018/978-1-5225-0353-8.ch003

Amber Ismael, Wei Tian, Nicholas Waszczak, Xin Wang, Youfang Cao, Dmitry Suchkov, Eli Bar, Metodi V. Metodiev, Jie Liang, Robert A. Arkowitz, and David E. Stone Gb promotes pheromone receptor polarization and yeast chemotropism by inhibiting receptor phosphorylation Science Signaling , 2016. 9(423):ra38, DOI: 10.1126/scisignal.aad4376 (supported by NIH grant GM079804 and NSF grant DBI 1062328).

Youfang Cao, Anna Terebus, and Jie Liang. Accurate Chemical Master Equation solution using multi-finite buffers SIAM Multiscale Modeling and Simulation , 2016.14(2):923-963 DOI:10.1137/15M1034180 (supported by NIH grant GM079804, NSF grant MCB1415589, and the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust).

Jie Liang, Youfang Cao, Gamze Gursoy, Hammad Naveed, Anna Terebus, and Jieling Zhao. 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 , 2015. 43(4):323-346. DOI: 10.1615/CritRevBiomedEng.2016016559 (supported by NIH grant GM079804, NSF grant MCB1415589, and the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust).

Meishan Lin, Dennis Gessmann, Hammad Naveed, and Jie Liang Outer membrane protein folding and topology from a computational transfer free energy scale. J Am Chem Soc , 2016. 138(8):2592-601. http://dx.doi.org/10.1021/jacs.5b10307 PMCID: PMC4881743 [Supported by NIH grant GM079804, NSF grants DMS-0800257 and DBI- 1062328, and Chicago Community Trust grant Catalyst-2013-9. ]

Youfang Cao, Anna Terebus, and Jie Liang. State space truncation with quantified errors for accurate solutions to discrete Chemical Master Equation. Bulletin of Mathematical Biology , 2016. 78(4):617-661. PMCID: PMC4896403, DOI: 10.1007/s11538-016-0149-1. (supported by NIH grant GM079804, NSF grant MCB1415589, and the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust).

L Montefiori, R Wuerffel, D Roqueiro, B Lajoie, C Guo, T Gerasimova, S De, W Wood, KG Becker, J Dekker, J Liang, R Sen, AL Kenter. Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire. Cell Rep. , 2016. 14(4):896-906. doi: 10.1016/j.celrep.2015.12.083. Epub 2016 Jan 21. (supported by NIH grant GM079804, NSF grant MCB1415589, and the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust).

S.M. Camp, E. Ceco, C.L. Evenoski, S.M. Danilov, T. Zhou, E.T. Chiang, L. Moreno-Vinasco, B. Mapes, J. Zhao, G. Gursoy, M.E. Brown, D.M. Adyshev, S.S. Siddiqui, H. Quijada, S. Sammani, E. Letsiou, L. Saadat, M. Yousef, T. Wang, J. Liang, and J.G. Garcia. Unique Toll-like receptor 4 activation by NAMPT/PBEF Induces NFkB signaling and inflammatory lung injury. Scientific Report, 2015. doi: 10.1038/srep13135, PMCID: PMC4536637 (supported by NSF grant DBI 1062328.)

Sema Kachalo, Hammad Naveeed, Youfang Cao, Jieling Zhao, and Jie Liang. Mechanical model of geometric cell and topological algorithm for cell dynamics from single-cell to formation of monolayered tissues with pattern. PLoS ONE, 2015. DOI: 10.1371/journal.pone.0126484, PMCID:PMC4431879 (supported by NIH GM079804 and GM086145, and NSF DMS-0800257 and DBI 1062328. UIC Research Open Access Article Publishing (ROAAP) Fund).

Ke Tang, Samuel W.K. Wong, Jun S. Liu, Jinfeng Zhang, and Jie Liang. Conformational sampling and structure prediction of multiple interacting loops in soluble and beta-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method Bioinformatics, 2015. doi: 10.1093/bioinformatics/btv198, PMCID: PMC4528630 (supported by NIH grants GM079804 and GM101552, NSF grant MCB-1415589 and DBI 1062328, and the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust.)

Luisa Estrada Mallarino, Enguo Fan, Meike Odermatt, Matthias Muller, Meishan Lin, Jie Liang, Martin Heinzelmann, Fenja Fritsche, Hans-Jurgen Apell, and Wolfram Welte. TtOmp85, a beta-barrel assembly protein, functions by barrel augmentation Biochemistry, 2015. 54:844-852, DOI: 10.1021/bi5011305, PMCID: PMC4310625 (supported by NIH grants GM079804.)

Yun Xu, Changyu Hu, Yang Dai and Jie Liang. On simplified global nonlinear function for fitness landscape: a case study of inverse protein folding. PLoS ONE, 2014. DOI: 10.1371/journal.pone.0104403. PMCID: PMC4128808 (supported by NSF DBI 1062328 and DMS-0800257, NIH GM079804 and GM086145, the Chicago Biomedical Consortium with support from the Searle Funds at the Chicago Community Trust, UIC Research Open Access Article Publishing (ROAAP) Fund).

Wei Tian, Youfang Cao, Amber Ismael, David Stone, and Jie Liang. Roles of regulated internalization in the polarization of cell surface receptors. Conf Proc IEEE Eng Med Biol Soc. , 2014. 2014:1166-1169. doi: 10.1109/EMBC.2014.6943803 (Supported by NIH Grants GM079804, GM086145 and NSF Grants DBI 1062328, MCB-0453964 and DMS-0800257 are gratefully acknowledged.)

Anna Terebus, Youfang Cao and Jie Liang Exact computation of probability landscape of stochastic networks of single input and coupled toggle switch modules. Conf Proc IEEE Eng Med Biol Soc. , 2014. 2014:5228-31. doi: 10.1109/EMBC.2014.6944804 (Supported by Support from NIH Grants GM079804, GM086145 and NSF Grants DBI 1062328, MCB-0453964 and DMS-0800257 are gratefully acknowledged.)

Gamze Gursoy, Yun Xu and Jie Liang Computational predictions of structures of multichromosomes of budding yeast. Conf Proc IEEE Eng Med Biol Soc. , 2014. 3945-3948. doi: 10.1109/EMBC.2014.6944487. (Supported by NIH Grants GM079804, GM086145 and NSF Grants DBI 1062328 and DMS-0800257 and the Chicago Biomedical Consortium are gratefully acknowledged.)

Yingzi Li, Hammad Naveed, Jie Liang, and Lisa X. Xu. Effects of mechanical properties on tumor invasion: Insights from a cellular Model. Conf Proc IEEE Eng Med Biol Soc. , 2014. 6818-21. doi: 10.1109/EMBC.2014.6945194. (Supported by NIH GM079804 and GM086145, NSF DBI-1062328 and DMS-0800257, the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust)

Gamze Gursoy, Yun Xu, Amy Kenter, and Jie Liang Spatial confinement is a major determinant of the folding landscape of human chromosomes Nucleic Acid Research, 2014. DOI:10.1093/nar/gku462. PMCID: PMC4117743 (supported by NSF DBI 1062328 and DMS- 0800257, NIH 1R21GM101552, GM079804, GM086145, and the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust. )

Ke Tang, Jinfeng Zhang, and Jie Liang Fast protein loop sampling and structure prediction using distance-guided sequential chain-growth Monte Carlo method PLoS Computational Biology, 2014. DOI: 10.1371/journal.pcbi.1003539. PMCID: PMC3998890 (supported by NSF DBI 1062328 and DMS- 0800257, NIH 1R21GM101552, GM079804, GM086145, and the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust. )

David Jimenez-Morales, Larisa Adamian, Dashuang Shi and Jie Liang. Lysine carboxylation: Unveiling the prevalence of a spontaneous posttranslational modification Acta Crystallographica Section D, 2014. 70(Pt 1):48-57. doi: 10.1107/S139900471302364X. Epub 2013 Dec 24. PMCID: PMC3919261 (supported by NSF DBI 1062328 and DMS-0800257, and NIH GM079804 and GM086145, and by a grant form the CBC/Searle Family and Chicago Community Trust fund)

Yingzi Li, Hammad Naveed, Sema Kachalo, Lisa X Xu and Jie Liang. Mechanisms of regulating tissue elongation in drosophila wing: Impact of oriented cell divisions, oriented mechanical forces, and reduced cell size. PLoS ONE, 2014. DOI: 10.1371/journal.pone.0086725. PMCID: PMC3913577 (supported by NSF DBI 1062328 and DMS-0800257, and NIH GM079804 and GM086145, and by a grant form the CBC/Searle Family and Chicago Community Trust fund)

Bhaskar DasGupta, Joe Dundas and Jie Liang Chapt 15. Algorithmic methodologies for discovery of nonsequential protein structure similarities. In Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics , 2013. (Eds.) Y. Pan, J. Wang, and M. Li. IEEE and Wiley book series on Bioinformatics. Pages 299-316.

Youfang Cao and Jie Liang. Adaptively Biased Sequential Importance Sampling for Rare Events in Reaction Networks with Comparison with Exact Solutions from Finite Buffer dCME Method. J. Chem. Phys., 2013. 139(2):025101. doi: 10.1063/1.4811286. PMCID: PMC3724789 (supported by NSF DBI 1062328 and DMS-0800257, and NIH GM079804 and GM086145)

David Mowrey, Qiang Chen, Yuhe Liang, Jie Liang, Yan Xu, Pei Tang. Signal Transduction Pathways in the Pentameric Ligand-Gated Ion Channels. PLoS ONE, 2013. 8(5):e64326. doi: 10.1371/journal.pone.0064326. PMCID: PMC3648548

Hammad Naveed and Jie Liang. Weakly Stable Regions and Protein-Protein Interactions in Beta-Barrel Membrane Proteins. Current Pharmaceutical Design, 2014. 20(8):1268ॆआ ॆअ ॆआ ॆअ ॆआ ॆअ ॆआ ॆअ 1273. PMCID: PMC4127314 (Supported by NIH GM079804, NSF DMS-0800257 and DBI-1062328, and ONR N00014-09-1-002)

Youfang Cao, Hammad Naveed, Claire Liang, and Jie Liang. Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesis. Conf Proc IEEE Eng Med Biol Soc. , 2013. 2013:5550-3. PMCID: PMC4148915. (Supported by NSF DBI 1062328 and DMS- 0800257, and NIH GM079804 and GM086145)

Jieling Zhao, Hammad Naveed, Sema Kachalo, Youfang Cao, Wei Tian, and Jie Liang. Dynamic Mechanical Finite Element Model of Biological Cells for Studying Cellular Pattern Formation. Conf Proc IEEE Eng Med Biol Soc. , 2013.2013:4517-20. PMCID: PMC4148913. (Supported by NIH GM079804, GM081682, GM086145, GM055876-13 and NSF DMS-0800257, DBI 1062328)

Marco Maggioni, Tanya Berger-Wolf, and Jie Liang GPU-based Steady-State Solution of the Chemical Master Equation IEEE 27th International Symposium on Parallel & Distributed Processing Workshops (HiCOMB) , 2013. 2013:579-588. DOI:10.1109/IPDPSW.2013.271

Bin He., Richard Baird, Robert Butera, Aniruddha Datta, Steven George, Bruce Hecht, Alfred Hero, Gianluca Lazzi, Raphael C. Lee, Jie Liang, Michael Neuman, Grace C. Y. Peng, Eric J. Perreault, Melur Ramasubramanian, May D. Wang, John Wikswo, Guang-Zhong Yang, and Yuan-Ting Zhang. Grand Challenges in Interfacing Engineering With Life Sciences and Medicine IEEE Transactions on Biomedical Engineering , 2013 doi:10.1109/TBME.2013.2244886. PMID: 23380847.

Yingzi Li, Hammad Naveed, Sema Kachalo, Lisa X. Xu, and Jie Liang Mechanisms of Regulating Cell Topology in Proliferating Epithelia: Impact of Division Plane, Mechanical Forces, and Cell Memory PLoS ONE , 2012 7(8): e43108. doi:10.1371/journal.pone.0043108. PMCID: PMC3422310 [Supported by NIH GM079804 and GM086145, and the NSF DBI 1062328 and DMS-0800257. ]

David Jimenez-Morales, Jie Liang and Bob Eisenberg Ionizable side chains at catalytic active sites of enzymes Eur J Biophys , 2012 41:449-460, DOI 10.1007/s00249-012-0798-4. PMCID: PMC3360948 [Supported by NIH GM079804 and GM086145, and the NSF DBI 1062328 and DMS-0800257. D.J.-M. is supported by the Becas Talentia Excellence Grant (Junta de Andalucia, Spain)]

Hammad Naveed, David Jimenez-Morales, Jun Tian, Volga Pasupuleti, Linda J Kenney, and Jie Liang Engineered Oligomerization State of OmpF Protein through Computational Design Decouples Oligomer Dissociation from Unfolding. J Mol Biol , 2012 419:89-101, dx.doi.org/10.1016/j.jmb.2012.02.043. PMCID: PMC3772668 [Supported by NIH GM079804, GM-058746, NSF DMS-0800257 and DBI-1062328. H.N. is supported by the Fulbright Fellowship and the Higher Education Commission of Pakistan, D.J.-M. is supported by the Becas Talentia Excellence Grant (Junta de Andalucia, Spain)]

Hammad Naveed, Yun Xu, Ronald Jackups, Jr., and Jie Liang Predicting Three-Dimensional Structures of Transmembrane Domains of b-Barrel Membrane Proteins J Am Chem Soc , 2012 134 (3), pp 1775-1781, DOI: 10.1021/ja209895m. PMCID: PMC3415959 [Supported by NIH GM079804, NSF DMS-0800257 and DBI-1062328, and ONR N00014-09-1-0028. H.N. is supported by the Fulbright Fellowship and the Higher Education Commission of Pakistan.]

Jie Liang, Hammad Naveed, David Jimenez-Morales, Larisa Adamian, and Meishan Lin Computational Studies of Membrane Proteins: Models and Predictions for Biological Understanding. Biochimica et Biophysica Acta (BBA) - Biomembranes. , 2012 1818(4):927-41 http://dx.doi.org/10.1016/j.bbamem.2011.09.026. PMCID: PMC3737997 [Supported by NIH GM079804, GM086145 and NSF DBI 1062328, BMS0800257, and ONR N00014-09-1-0028].

Shay Geula, Hammad Naveed, Jie Liang, and Varda Shoshan-Barmatz. Structure-based Analysis of VDAC1 Protein: Definging oligomer contact sites J Biol Chem , 2012 287(3):2179-90. dx.doi.org/10.1074/jbc.M111.268920. PMCID: PMC3265896 [Supported by NIH GM079804, NSF DMS-0800257 and DBI-1062328, and ONR N00014-09-1-0028. H.N. is supported by the Fulbright Fellowship and the Higher Education Commission of Pakistan.]

Bhaskar DasGupta, Joseph Dundas and Jie Liang, Algorithmic Methodologies for Discovery of Non-sequential Protein Structure Similarities
Y. Pan, J. Wang and M. Li (editors): Algorithmic and AI Methods for Protein Bioinformatics, , 2012 In press Wiley book series on Bioinformatics © Wiley, 2012

David Jimenez-Morales and Jie Liang. Pattern of Amino Acid Substitutions in Transmembrane Domains of beta-Barrel Membrane Proteins for Detecting Remote Homologs in Bacteria and Mitochondria. PLoS ONE , 2011 6(11):e26400. doi:10.1371/journal.pone.0026400. PMCID: PMC3206045 [Supported by NIH GM079804, GM081682, GM086145 and NSF BMS0800257, ONR N00014-09-1-0028, and Becas Talentia Excellence Grant of Spain]

Dennis Gessmann, Frauke Mager, Hammad Naveed, Thomas Arnold, Sara Weirich, Dirk Linke, Jie Liang, and Stephan Nussberger. Improving the Resistance of a Eukaryotic &B-Barrel Protein to Thermal and Chemical Perturbations J. Mol. Biol. , 2011:413:150-161. PMCID: PMC3782296 [Supported by NIH GM079804, GM086145 and NSF BMS0800257]

Yingzi Li, Hammad Naveed, Sema Kachalo, Lisa X. Xu, and Jie Liang. Mechanical Forces Mediate Localized Topological Change in Epithelia. Conf Proc IEEE Eng Med Biol Soc. 2011, 2011 2011:178-81. PMCID: PMC3725274 [Supported by NIH GM079804, GM081682, and GM086145; NSF DMS-0800257; and 985 phase II grant of SJTU T226208001. Y.L. was also supported by the China Scholarship Council. H.N. was supported by the Fulbright Fellowship and the Higher Education Commission of Pakistan].

Jieling Zhao, Joe Dudnas, Sema Kachalo, Zheng Ouyang, and Jie Liang. Accuracy of functional surfaces on comparatively modeled protein structures. J Struct Funct Genomics 2011,12(2):97-107. DOI 10.1007/s10969-011-9109-z. PMCID: PMC3415962 [Supported by: NIH GM079804, GM081682, GM086145, GM055876-13 and NSF DMS-0800257].

Marco Maggioni, Marco Domenico Santambrogio, and Jie Liang GPU-accelerated chemical similarity assessment for large scale databases. Internatonal Conference on Computational Science, ICCS 2011, Singapore, June 1-3. [Supported by: NIH GM079804 and GM086145].

Jiayue Cui, Jason Hao, Olesya A. Ulanovskaya, Joseph Dundas, Jie Liang, and Sergei A. Kozmin. Creation and manipulation of common functional groups en route to a skeletally diverse chemical library. Proc Natl Acad Sci USA 2011 Apr 26; 108(17):6763-8. Epub 2011 Mar 7. PMCID: PMC3084086 [Supported by: NIH GM086145 and the Chicago Biomedical Consortium].

Joe Dundas, Bhaskar DasGupta, and Jie Liang. Sequence order independent comparison of protein global backbone structures and local binding surfaces. Protein function prediction for omics era, D. Kihara ed., Chapter 7, Springer, 2011, In press [Supported by: NIH GM079804, GM081682, GM086145; NSF DBI-0646035, DMS-0800257; and ONR N00014-09-1-0028].

Larisa Adamian, Hammad Naveed, and Jie Liang. Lipd-binding surfaces of membrane proteins: Evidence from evolutionary and structural analysis. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1808(2011):1092-1102. PMCID: PMC3381425 [Supported by: NIH GM079804, GM081682, GM086145; NSF DBI-0646035, DMS-0800257; and ONR N00014-09-1-0028]

Joseph M. Dundas, Larisa Adamian, and Jie Liang. Structural signatures of enzyme binding pockets from order-independent surface alignment: A study of metalloendopeptidase and NAD binding proteins. Journal of Molecular Biology. 2011 Mar 11;406(5):713-29. Epub 2010 Dec 9, doi:10.1016/j.jmb.2010.12.005. PMCID: PMC3061237 [Supported by: NIH GM079804, GM081682, GM086145; NSF DMS-0800257; and ONR N00014-09-1-0028].

Ming Lin, Jian Zhang, Hsiao-Mei Lu, Rong Chen, and Jie Liang. Constrained proper sampling of conformations of transition state ensemble during protein folding. Journal of Chemical Physics. 2011 Feb 21;134(7):075103. PMCID: PMC3071304 [Supported by NIH grants GM079804, GM081682, NSF grant DBI-0646035, and DMS-0800257, DMS-0800183, DMS-0915139 and DMS-0905763].

Ronald Jackups, Jr and Jie Liang. Combinatorial analysis for sequence and spatial motif discovery in short sequence fragments. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010, 7(3):524-536.,
An appendix describing an alternative positional null model is here. PMCID: PMC3417775 [Supported by NSF DBI0646035, DMS0800257, and NIH GM079804, GM081682].

Youfang Cao and Jie Liang. Nonlinear Langevin model with product stochasticity for biological networks: The case of the Schnakenberg model Journal of Systems Science and Complexity. 23(5):896-905, DOI: 10.1007/s11424-010-0213-0 [Supported by Phase II 985 Project under Grant No. T226208001, NIH Grants GM079804, GM081682, NSF Grants DBI-0646035, DMS-0800257, and ONR Grant N00014-09-1-0028].

Youfang Cao, Hsiao-Mei Lu, and Jie Liang. Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda. Proc Natl Acad Sci USA 2010, Oct 11 2010 Oct 26;107(43):18445-50. Epub 2010 Oct 11 doi:10.1073/pnas.1001455107 PMCID: PMC2972968 [Supported by Phase II 985 Project, 973 Grant 2007CB914703, NIH GM079804, GM081682, NSF DMS-0800257, and a grant from the Chicago Biomedical Consortium].

Hammad Naveed, Yingzi Li, and Jie Liang. Geometric order in proliferating epithelia: Impact of rearr angements and cleavage plane orientation. Conf Proc IEEE Eng Med Biol Soc. 2010, 2010:3808-11. PMCID: PMC3746753 [Supported by NIH GM079804, GM081682, and ONR N00014-09-1-0028].

Jie Liang and Hong Qian. Computational cellular dynamics based on the chemical master equation: A challange for understanding complexity. Journal of Computer Science and Technology. 2010, 25(1):154-168, PMCID: PMC4079062 [Supported by NIH GM079804, GM081682, GM086145, GM068610, NSF DBI-0646035, DMS-0800257, 985/ Phase II Grant under Grant No. T226208001].

Jie Liang, Sema Kachalo, Xiang Li, Zheng Ouyang, Yan-Yuan Tseng, and Jinfeng Zhang. Geometric structures of proteins for understanding folding, discriminating natives and predicting biochemical functions The Word Is a Jigsaw (Ed. Rien van de Weygaert), 2009, Springer. Accepted . [Supported by grants from NSF (DBI-0646035 and DMS-0800257), NIH (GM079804, GM081682, and GM086145) and ONR (N00014-09-1-0028)].

Jie Liang. Geometry of protein shape and its evolutionary pattern for function prediction and characterization Conf Proc IEEE Eng Med Biol Soc. 2009, 2009:2324-7. PMCID: PMC3744228 [Supported by grants from NSF (DBI-0646035 and DMS-0800257), NIH (GM079804, GM081682, and GM086145) and ONR (N00014-09-1-0028)].

Youfang Cao and Jie Liang. Nonlinear coupling for improved stochastic network model: A study of Schnakenberg model The Third International Symposium on Optimization and Systems Biology (OSB'09) 2009, 2009 ORSC & APORC, pp. 379-386. [Supported by a phase II 985 Project (Sub-Project: T226208001 at Shanghai Jiao Tong University, Shanghai, China), NIH grants GM079804-01A1, GM081682, NSF grants DBI-0646035 and DMS- 0800257, and ONR N00014-09-1-0028].

Larisa Adamian, Helene A. Gussin, Yan Yuan Tseng, Niraj J. Muni, Feng Feng, Haohua Qian, David R. Pepperberg, and Jie Liang. Structural model of rho1 GABAc receptor based on evolutionary analysis: Testing of predicted protein-protein interactions involved in receptor assembly and function Protein Science 2009, 18(11):2371-2383. PMCID: PMC2788291 [Grant sponsor: NIH; Grant numbers: GM079804, GM068958, EY016094, EY013693, EY001792; Grant sponsor: NSF; Grant number: DBI0646035; Grant sponsors: Daniel F. and Ada L. Rice Foundation (Skokie, IL); Macular Degeneration Research Program of the American Health Assistance Foundation (Clarksburg, MD); Research to Prevent Blindness (New York, NY); Hope for Vision (Washington, DC); Sigma Xi.]

Jian Zhang, Joseph Dundas, Ming Lin, Rong Chen, Wei Wang, and Jie Liang Prediction of geometrically feasible three dimensional structures of pseudoknotted RNA through free energy estimation RNA 2009, 15: 2248-2263, doi: 10.1261/rna.1723609. PMCID: PMC2779689 [Supported by grants from the US National Science Foundation (DMS-0800183 and DMS-0800257 ), National Institute of Health (GM68958 and GM079804), and Office of Naval Research (N00014-06-1-0100). J.Z. and W.W. acknowledge the National Natural Science Foundation of China (90403120, 10504012, and 10704033) and the National Basic Research Program of China (2006CB910302). This research is supported in part by the Project of Knowledge Innovation Pro- gram (PKIP) of Chinese Academy of Sciences, Grant No.KJCX2.YW.W10. We also acknowledge Shanghai Super-computer Center for providing computing resources.]

Hsiao-Mei Lu and Jie Liang Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: A study of GroEL-GroES PLoS Computational Biol 2009, 5(10): e1000526. doi:10.1371/journal.pcbi.1000526. PMCID: PMC2741606 [Supported by NIH grants GM079804, GM081682, GM086145, NSF grants DBI-0646035 and DMS-0800257, and ONR grant N00014-09-1-0028].

Hammad Naveed, Ronald Jackups, Jr, and Jie Liang. Predicting weakly stable regions, oligomerization state, and protein.protein interfaces in transmembrane domains of outer membrane proteins. Proc Natl Acad Sci USA 2009, 106(31):12735-12740 doi: 10.1073/pnas.0902169106. PMCID: PMC2722334 [Supported by National Institutes of Health Grants GM079804-01A1 and GM081682, National Science Foundation Grants DBI-0646035 and DMS-0800257, and Office of Naval Research Grant N00014-09-1-0028. H.N. was supported by a Fulbright Fellowship and the Higher Education Commission of Pakistan].

Soundararajan Krishnaswamy, Rajani Kanteti, Jonathan Duke-Cohan, Sivakumar Loganathan, Wanqing Liu, Patrick Ma, Martin Sattler, Patrick Singleton, Nithya Ramnath, Federico Innocenti, Dan Nicolae, Zheng Ouyang, Jie Liang, John Minna, Mark Kozloff, Mark Ferguson, Viswanathan Natarajan, Yi-Ching Wang, Joe Garcia, Everett Vokes, Ravi Salgia Ethnic Differences and Functional Analysis of MET Mutations in Lung Cancer Clinical Cancer Research, 2009, 15(18):5714-5723. PMCID: PMC2767337 [Supported by NIH/National Cancer Institute R01 grants, CA100750-04, CA129501-01A1, and CA-125541-01; V-Foundation/Guy Geleerd Memorial; MARF/Jeffrey P. Hayes Memorial Grant; Cancer Research Foundation/Goldblatt Award (R. Salgia); Lung Cancer Specialized Programs of Research Excellence P50CA70907 (J. Minna); and P01HL058064-13 (J. Garcia)]

Jerry O. Ebalunode, Xialan Dong, Zheng Ouyang, Jie Liang, Roderic G. Eckenhoff, and Weifan Zheng. Structure-based shape pharmacophore modeling for the discovery of novel anesthetic compounds Bioorganic and Medicinal Chemistry, 2009, 17(14):5133-5138. PMID: 19520579

Yan-Yuan Tseng, Joseph Dundas, and Jie Liang. Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns J. Mol. Biol. 2009, 387(2) 451-464. PMCID: PMC2670802 [Supported by grants from the NSF (DBI-0646035 and DMS-0800257), NIH (GM079804-01A1 and GM081682), and ONR (N000140310329)].

Jie Liang, Yan-Yuan Tseng, Joseph Dundas, Andrewn Binkowski, Andrzej Joachimiak, Zheng Ouyang, and Larisa Adamian. Chapter 4: Predicting and characterizing protein functions through matching geometric and evolutionary patterns of binding surfaces, Advances in protein chemistry. 2008, 75:107-141. PMCID: PMC2882714 [Supported by grants from National Science Foundation (CAREER DBI0133856, DBI0078270, DBI0646035,and DMSॆआ ॆअ ॆआ ॆअ ॆआ ॆअ ॆआ ॆअ 0800257), National Institute of Health (GM68958, GM079804, and GM081682), Office of Naval Research (N000140310329), and Whitaker Foundation (TFॆआ ॆअ ॆआ ॆअ ॆआ ॆअ ॆआ ॆअ 04ॆआ ॆअ ॆआ ॆअ ॆआ ॆअ ॆआ ॆअ 0023)].

Ming Lin, Hsiao-Mei Lu, Rong Chen, and Jie Liang. Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints J Chem Phys. 2008, 129(094101):1-13. PMCID: PMC2640457 [Supported by NIH Grant Nos.GM079804-01A1 and GM081682 and by NFS Grant Nos.DBI-0646035 and DMS-0800257]

Youfang Cao, Hsiao-Mei Lu, and Jie Liang. Stochastic probability landscape model for switching efficiency, robustness, and differential threshold for induction of genetic circuit in phage lambda Conf Proc IEEE Eng Med Biol Soc. 2008, 30:611-614. PMCID: PMC2630505 [Supported by 985 phase II grant of Shanghai Jiao Tong University (T226208001), and by NIH grants GM079804-01A1, GM081682, NSF grants DBI-0646035 and DMS-0800257].

David Jimenez-Morales, Larisa Adamian, and Jie Liang. Detecting Remote Homologues Using Scoring Matrices Calculated from the Estimation of Amino Acid Substitution Rates of Beta-Barrel Membrane Proteins Conf Proc IEEE Eng Med Biol Soc. 2008, 30:1347-1350. PMCID: PMC2630510 [Support from NIH GM-079804, GM081682 and NSF DBI-0646035].

Zheng Ouyang and Jie Liang. Predicting protein folding rates from geometric contact and amino acid sequence. Protein Science, 2008, 17(7):1256-63. PMCID: PMC2441995 [Supported by grants from the National Science Foundation (DBI-0646035) and the National Institutes of Health (GM079804-01A1 and GM081682 GM68958)].

Youfang Cao and Jie Liang. Optimal enumeration of state space of finitely buffered stochastic molecular networks and accurate computation of steady state landscape probability BMC Systems Biology, 2008, 2:30:1-13 doi:10.1186/1752-0509-2-30. PMCID: PMC2375859 [Supported by a phase II 985 Project (Sub-Project:T226208001) at Shanghai Jiao Tong University, Shanghai, China].

Jerry Osagie Ebalunode, Zheng Ouyang, Jie Liang, and Weifan Zheng. A novel approach to structure-based pharmacophore search using computational geometry and shape matching techniques J Chemical Information and Modeling, 2008, 48(4):889-901. PMID: 18396858

Jian Zhang, Ming Lin, Rong Chen, Wei Wang, and Jie Liang. Discrete state model and accurate estimation of loop entropy of RNA secondary structures J Chem Phys. 2008, 128(125107):1-10, DOI:10.1063/1.2895050. PMCID: PMC2494904 Abstract. [Supported by grants from National Science Foundation (DBI-0646035), National Institute of Health (GM68958 and GM079804), and Office of Naval Research (N00014-06-1-0100). J.Z. and W.W. are also supported by the National Natural Science Foundation of China (90403120, 10504012, and 10704033) and the National Basic Research Program of China (2006CB910302)].

Ming Lin, Rong Chen, and Jie Liang. Statistical geometry of lattice chain polymers with voids of defined shapes: Sampling with strong constraints J Chem Phys. 2008, 128(084903):1-12 DOI:10.1063/1.2831905. P

Hsiao-Mei Lu and Jie Liang. A model study of protein nascent chain and cotranslational folding using hydrophobic-polar residues. Proteins, 2008, 70(2):442-449. PMID: 17680696 [Grant sponsor: National Science Foundation; Grant number: CAREER DB10133856; Grant sponsor: National Institute of Health; Grant numbers: GM68958 and GM079804; Grant sponsor: Office of Naval Research; Grant number: N00014-06-1-0100.]

Joe Dundas, T Andrew Binkowski, Bhaskar DasGupta, and Jie Liang. Topology independent protein structural alignment BMC Bioinformatics, 2007, 8:388, doi:10.1186/1471-2105-8-388. PMCID: PMC2096629 [Bhaskar DasGupta was supported by NSF grants IIS-0346973, IIS-0612044 and DBI-0543365. Joe Dundas was partially supported by NSF grant IIS-0612044. Jie Liang was supported by NSF grant DBI-0133856 and NIH grants GM68958 and GM079804].

Youfang Cao and Jie Liang. An optimal algorithm for enumerating state space of stochastic molecular networks with small copy numbers of molecules Conf Proc IEEE Eng Med Biol Soc. 2007, 29:4599-4602. PMID: 18003030 [Supported by a phase II 985 Project (Sub-Project:T226208001) at Shanghai Jiaotong University, Shanghai, China].

Hsiao-Mei Lu and Jie Liang. Perturbation-based Markovian Transmission Model for Macromolecular Machinery in Cell Conf Proc IEEE Eng Med Biol Soc. 2007, 29:5029-5034. PMID: 18003136 [Supported by grants from NSF (CAREER DBI0133856), NIH (GM68958 and GM079804), and ONR (N000140310329)].

Zheng Ouyang and Jie Liang. Detecting Positively Selected Sites From Amino Acid Sequences: An Implicit Codon Model Conf Proc IEEE Eng Med Biol Soc. 2007, 29:5302-5306. PMCID: PMC3406752 [Supported by grants from NSF (CAREER DBI0133856), NIH (GM68958 and GM079804), and ONR (N000140310329)].

Joe Dundas, T.A. Binkowski, Bhaskar DasGupta and Jie Liang. Topology Independent Protein Structural Alignment 7th Workshop on Algorithms in Bioinformatics, R. Giancarlo and S. Hannenhalli (Eds.), 2007, LNBI 4645:171-182. PMCID: PMC2096629 [Supported by NSF grant IIS-0346973.NSF grants IIS-0346973, IIS-0612044 and DBI-0543365. Supported by NSF grant DBI-0133856 and NIH grants GM68958 and GM079804].

Yan Yuan Tseng and Jie Liang. Predicting enzyme functional surfaces and locating key residues automatically from structures. Annals of Biomedical Engineering, 2007, 35(6):1037-1042. PMID: 17294116 [Supported by grants from NSF (CAREER DBI0133856), NIH (GM68958), and ONR (N000140310329)].

Jinfeng Zhang, Ming Li, Rong Chen, Jie Liang, and Jun Liu. Monte Carlo sampling of near-native structures of proteins with applications. Proteins, 2007, 66(1):61-68. PMID: 17039507 [Grant sponsor: National Institute of Health; Grant number: GM68958; Grant sponsor: National Science Foundation; Grant numbers: DBI-0133856, DMS-0244541, DMS-0244638; Grant sponsor: NSF China; Grant number: 10228102; Grant sponsor: Whitaker Foundation; Grant number: TF-04-0023].

Larisa Adamian, Zheng Ouyang, Yan Yuan Tseng, Jie Liang. Evolutionary Patterns of Retinal-Binding Pockets of Type I Rhodopsins and Their Functions Photochem Photobiol. 2006, 82(6):1426-1435. PMID: 16922602.

Ronald Jackups, Jr. Sarah Cheng and Jie Liang. Sequence motifs and antimotifs in beta-barrel membrane proteins from a genome-wide analysis: the Ala-Tyr dichotomy and chaperone binding motifs J Mol Biol. 2006, 363(2):611-23. PMID: 16973175.
Data: ( Supplementary data of various propensities are here.)

Larisa Adamian and Jie Liang. Prediction of transmembrane helix orientation in polytopic membrane proteins BMC Structural Biology, 2006, 6(13):1-17, doi:10.1186/1472-6807-6-13. PMCID: PMC1540425.

Joe Dundas, Zheng Ouyang, Jeffery Tseng, Andrew Binkowski, Yaron Turpaz and Jie Liang. CASTp: computer atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues Nucleic Acids Research, 2006, 34:W116-118, doi:10.1093/nar/gkl282. PMCID: PMC1538779.

Sema Kachalo, Hsiao-Mei Lu and Jie Liang. Protein folding dynamics via quantification of kinematic energy landscape Physical Review Letters, 2006, 96:058105:1-4. PMID: 16487000.

Xiang Li and Jie Liang. Chapt 3. Knowledge-based energy functions for computational studies of proteins.
Ying Xu, Dong Xu, Jie Liang: Computational Methods for Protein Structure Prediction and Modeling, Volume 1:Basic Characterization, 2006 pg. 71-124. Editor-in-Chief: Elias Greenbaum, © 2007 Springer Science, 233 Spring Street, New York, NY 10013, USA: ISBN 10:0-387-33319-3

Yan-Yuan Tseng and Jie Liang. Automated method for predicting enzyme functional surfaces and locating key residues with accuracy and specificity Conf Proc IEEE Eng Med Biol Soc. 2006, 1:4552-4555. PMID: 17947099.

Jie Liang. Chapt 6. Computation of protein geometry and its applications: Packing and function prediction
Ying Xu, Dong Xu, Jie Liang: Computational Methods for Protein Structure Prediction and Modeling, Volume 1:Basic Characterization, 2006 pg. 181-206. Editor-in-Chief: Elias Greenbaum, © 2007 Springer Science, 233 Spring Street, New York, NY 10013, USA: ISBN 10:0-387-33319-3

Larisa Adamian and Jie Liang. Prediction of buried helices in multispan alpha helical membrane proteins Proteins, 2006, 63:1-5. PMID: 16419070.

Yan Yuan Tseng and Jie Liang. Estimation of amino acid residue substitution rates at local spatial regions and application in protein function inference: A Bayesian Monte Carlo approach Mol Biol Evo. 2006, 23:421-436. PMID: 16251508.

Ronald Jackups, Jr. and Jie Liang. Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction J Mol Biol. 2005, 354:979-993. PMID: 16277990.
A more useful description of the techniques is in the Supplementary Material .
See also the Editor's Choice of the Science magazine.

Jinfeng Zhang, Rong Chen and Jie Liang. Empirical potential function for simplified protein models: Combining contact and local sequence-structure descriptors Proteins, 2005, 63(4):949-960. PMID: 16477624.
See data files for supplimentary data and program files for Perl scripts and C++ program source code.

T. Andrew Binkowski, Andrzej Joachimiak, and Jie Liang. Protein surface analysis for function annotation in high-throughput structural genomics pipeline Protein Science, 2005, 14:2972-2981. PMCID: PMC2253251.

Xiang Li, and Jie Liang. Geometric cooperativity and anti-cooperativity of three-body interactions in native proteins. Proteins, 2005, 60:46-65. PMID: 15849756.

Jie Liang, Larisa Adamian, and Ronald Jackups, Jr. The membrane-water interface region of membrane proteins: structural bias and the anti-snorkeling effect. Trends in Biochemical Sciences, 2005, 30(7):355-357. PMID: 15935679.

Larisa Adamian, Vikas Nanda, William F. DeGrado, and Jie Liang. Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins Proteins, 2005, 59:496-509. PMID: 15789404.

Xiang Li, and Jie Liang. Computational design of combinatorial peptide library for modulating protein-protein interactions. Pacific Symposium on Biocomputing, 2005, 28-39. PMID: 15759611.

Xiang Li, Ozlem Keskin, Buyong Ma, Ruth Nussinov and Jie Liang. Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that are pre-organized in the unbound states. Implications to docking J Mol Biol. 2004, 344:781-795. PMID: 15533445.

Jeffrey Tseng and Jie Liang. Estimating evolutionary rate of local protein binding surfaces: a Bayesian Monte Carlo approach Conf Proc IEEE Eng Med Biol Soc. 2004, 27:739-742. PMID: 17282289.

Sema Kachalo, Hsiao-Mei Lu, and Jie Liang. Protein folding dynamics in lattice model with physical movement Conf Proc IEEE Eng Med Biol Soc. 2004, 27:4449-4452. PMID: 17281224.

Nathan Stitziel, Brenton G. Mar, Jie Liang, and Carol Westbrook. Membrane-associated and secreted genes in breast cancer. Cancer Research, 2004 64:8682-8687. PMID: 15574777.

Jinfeng Zhang, Rong Chen, and Jie Liang. Potential function of simplified protein models for discriminating native proteins from decoys: Combining contact interaction and local sequence-dependent geometry. Conf Proc IEEE Eng Med Biol Soc. 2004, 26:2976 - 2979 Vol.4 DOI 10.1109/IEMBS.2004.1403844. PMID: 17270903.

T. Andrew Binkowski, Bhaskar DasGupta, and Jie Liang. Order independent structural alignment of circularly permuted proteins. Conf Proc IEEE Eng Med Biol Soc. 2004, 26:2781 -2784 Vol.4 DOI 10.1109/IEMBS.2004.1403795. PMID: 17270854.

Changyu Hu, Xiang Li, and Jie Liang. Developing optimal nonlinear scoring function for protein design Bioinformatics, 2004, 20(17):3080-3098. PMID: 15217818.

Moon Jung Song, Seungmin Hwang, Wendy Wong, June Round, DeeAnn Martinez-Guzman1, Yaron Turpaz, Jie Liang, Ben Wong, Reid C. Johnson, Michael Carey, and Ren Sun. The DNA architectural protein HMGB1 facilitates RTAmediated viral gene expression in gamma2 herpesviruses. J. Virology. 2004, 78(23):12940-12950. PMCID: PMC524970.

Jinfeng Zhang, Yu Chen, Rong Chen and Jie Liang. Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models. J. Chem. Phys. 2004, 121:592-603. PMID: 15260581.

T. Andrew Binkowski, Patrick Freeman and Jie Liang. pvSOAR: Detecting similar surface patterns of Pocket and Void Surfaces of Amino Acid Residues on proteins. Nucleic Acid Research, 2004, 32:W555-W558. PMCID: PMC441528.

Yan Yuan Tseng and Jie Liang. Are residues in a protein folding nucleus evolutionarily conserved? J. Mol. Biol. 2004, 335:869-880. PMID: 14698285.

Nathan O. Stitziel, T. Andrew Binkowski, Yan Yuan Tseng, Simon Kasif and Jie Liang. topoSNP: A topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acid Research, 2004, 32:D520-D522. PMCID: PMC308838.

Changyu Hu, Xiang Li and Jie Liang. Optimal nonlinear scoring function for global fitness landscape of protein design. Conf Proc IEEE Eng Med Biol Soc. 2004, 26:2828-2831 Vol.4 DOI 10.1109/IEMBS.2004.1403807. PMID: 17270866.

Sema Kachalo, Zarema Arbieva and Jie Liang. Assessing effect of cross-hybridization on oligonucleotide microarrays. Methods of microarray data analysis III, 2003, CAMDA' 02:185-198. DOI 10.1007/b105346

Xiang Li, Changyu Hu, and Jie Liang. Simplicial edge representation of protein structures and alpha contact potential with confidence measure. Proteins, 2003, 53:792-805. PMID: 14635122.

T. Andrew Binkowski, Larisa Adamian and Jie Liang. Inferring functional relationship of proteins from local sequence and spatial surface patterns. J Mol Biol. 2003, 332:505-526. PMID: 12948498.

T. Andrew Binkowski, Shapor Naghibzadeh, and Jie Liang. CASTp: computed atlas of surface topography of proteins. Nucleic Acid Research, 2003, 31(13):3352-3355. PMCID: PMC168919. Abstract

Nathan O. Stitziel, Yan Yuan Tseng, Dimitri Pervouchine, David Goddeau, Simon Kasif, and Jie Liang. Structural location of disease-associated single nucleotide polymorphisms. J Mol Biol. 2003, 327:1021-1030. PMID: 12662927.

J. D. Lear, H. Gratkowski, L. Adamian, J. Liang, and W.F. DeGrado Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles. Biochemistry, 2003, 42(21):6400-6407. PMID: 12767221.

Larisa Adamian, and Jie Liang. Interhelical hydrogen bonds in transmembrane region are important for function and stability of Ca2+-transporting ATPase. Cell Biochemistry and Biophysics, 2003, 39:1-12. PMID: 12835525.

Larisa Adamian, Ronald Jackups, Jr, T. Andrew Binkowski, and Jie Liang. Higher order interhelical spatial interactions inmembrane proteins. J Mol Biol. 2003, 327:251-272. PMID: 12614623.

Jinfeng Zhang, Rong Chen, Chao Tang, and Jie Liang. Origin of scaling behavior of protein packing density: A sequential Monte Carlo study of compact long chain polymers. J Chem Phys. 2003, 118(13):6102-6109. (eprint in arxiv)
Data: (SAWs in pdb format and Z_alpha data are here.)

Jie Liang. Experimental and computational studies of the determinants of membrane protein folding. Current Opinion in Chemical Biology, 2002, 6:878-884. PMID: 12470745.

Jie Liang, Jinfeng Zhang and Rong Chen. Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method. J Chem Phys. 2002, 117:3511-3521. PMCID: PMC3689594.

Jie Liang and Sema Kachalo. Computational Analysis of Microarray Gene Expression Profiles Clustering, Classification, and Beyond. Chemometrics and Intelligent Laboratory Systems, 2002, 62:199-216.

Larisa Adamian, and Jie Liang. Interhelical hydrogen bonds and spatial motif in membrane proteins: Polar clamps and serine zippers. Proteins, 2002, 47:209-218. PMID: 11933067.

Maria P. McGee, Jie Liang, and J. Luba. Hydration effects of heparin on antithrombin probed by osmotic stress. Biophys J. 2002, 82:1040-1049. PMCID: PMC1301910.

M. P. McGee and J. Liang. Factor X, Coagulation. Wiley Encyclopedia of Molecular Medicine, 2002

L. Adamian and J. Liang. Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins. J Mol Biol. 2001, 311:891-907. PMID: 11518538.

J. Liang and K.A. Dill. Are proteins well-packed? Biophys J. 2001, 81:751-766. PMCID: PMC1301551.

M. P. McGee and J. Liang. Regulation of glycosaminoglycan function by osmotic potentials. Measurement of water transfer during antithrombin activation by heparin. J Biol Chem. 2001, 276:49275-49282. PMID: 11677228.

I. Gomes, T. L. Sharma, J. D. Kapp, S. Edassery, N. Fulton, J. Liang, R. Hoffman, and C.A. Westbrook. Highly abundant genes in the transcriptosome of human and baboon CD34 antigen-positive bone marrow cells. Blood, 2001, 98:93-99. PMID: 11418467.

C. Yuan, O. Kuwata, J. Liang, S. Misra, S.P. Balashov, T.G. Ebrey. Chloride binding regulates the Schiff base pK in gecko P521 cone-type visual pigment. Biochemistry, 1999, 38:4649-4654. PMID: 10194387.

M.P. McGee, H. Teuschler and J. Liang. Electrostatic interactions during activation of coagulation factor IX via the tissue factor pathway: effect of univalent salts. Biochim Biophys Acta. 1999, 1453:239-253. PMID: 10036322.

J. Liang, H. Edelsbrunner, and C. Woodward. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science, 1998, 7:1884-1897. PMCID: PMC2144175.

H. Edelsbrunner, M. Facello and J. Liang. On the definition and the construction of pockets in macromolecules. Disc Appl Math. 1998, 88:83-102. PMID: 9390238.

J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar and S. Subramaniam. Analytical shape computing of macromolecules II: identication and computation of inaccessible cavities inside proteins. Proteins, 1998, 33:18-29. PMID: 9741841.

J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar and S. Subramaniam. Analytical shape computing of macromolecules I: molecular area and volume through alpha shape. Proteins, 1998, 33:1-17. PMID: 9741840.

J. Liang and M.P. McGee. Mechanisms of coagulation factor Xa inhibition by antithrombin. Correlation between hydration structure and water transfer during reactive loop insertion. Biopys J. 1998, 75:573-582. PMCID: PMC1299733.

M.P. McGee, H. Teuschler, and J. Liang. 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. Biochemistry, 1998, 330:533-539. PMCID: PMC1219170.

J. Liang and S. Subranmaniam. Computation of molecular electrostatics with boundary element methods. Biophys J. 1997, 73:1830-1841. PMCID: PMC1181083.

S. Kim, J. Liang, and B.A. Barry. Chemical complementation identies a proton acceptor for redox-active tyrosine D in photosystem II. Proc Natl Acad Sci. 1997, 94:14406-14411. PMCID: PMC24999.

J.W. Lewis, J. Liang, T.G. Ebrey, M. Sheves, N. Livnah, O. Kuwata, S. Jager, and D.S. Kliger. Early photolysis intermediates of gecko and bovine articial visual pigments. Biochemistry, 1997, 36:14593-14600. PMID: 9398178.

H. Edelsbrunner, M. Facello, P. Fu and J. Liang. Measuring proteins and voids in proteins. Proc 28th Ann Hawaii Intl Conf System Sci. 1995, 5:256-264

T.G. Ebrey and J. Liang. The bleaching of visual pigments. Handbook of organic photochemistry and photobiology, 1995, 1484-1491

J. Lewis, J. Liang, T.G. Ebrey, M. Sheves and D.S. Kliger. Chloride effect on the early photolysis intermediates of a gecko cone-type visual pigment. Biochemistry, 1995, 34:5817-5823. PMID: 7727442.

J. Liang, G. Steinberg, N. Livnah, M. Sheves and T.G. Ebrey. The pKa of the protonated Schiff base of gecko cone and octopus visual pigments. Biophys J. 1994, 67:848-854. PMCID: PMC1225427.

J. Liang, R. Govindjee, and T.G. Ebrey. Metarhodopsin intermediates of the gecko cone pigment P521. Biochemistry, 1993, 32(51):14187-14193. PMID: 8260505.

W. Lin, C. Ma, Z. Luo, W. Fan, Y. Chen and J. Liang. Study on the radiosensitization of AT1727 on human lung adenocarcinoma cell line SPC-A-1. J Rad Res Rad Pro. 1987, 5:58-62.


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