My Google Scholar Page

2013

• Jose Laborde, Daniel Robinson, Anuj Srivastava, Eric Klassen and Jinfeng Zhang, RNA global alignment in the joint sequence-structure space using Elastic Shape Analysis, Nucleic Acid Research, accepted.

2012

• Leif Ellingson, Jinfeng Zhang, Protein Surface Matching by Combining Local and Global Geometric Information , PLoS ONE, 2012, 7(7): e40540.
• Chi Zhang, Rajesh Chowdhary, Jinfeng Zhang, Biological pathway discovery through text mining and data integration, IEEE-EMBS, 2012, accepted.
• Shreyas Karnik, Sin Lam Tan, Bess Berg, Ingrid Glurich, Humberto J Vidaillet, C. David Page, Jinfeng Zhang, Rajesh Chowdhary, Predicting Atrial Fibrillation and Flutter using Electronic Health Records, IEEE-EMBS, 2012, accepted.
• Tingting Zhao, Lindsey Bell, Mark W. Horner, John Sulik, Jinfeng Zhang, Consumer Responses towards Home Energy Financial Incentives: A Survey-Based Study , Energy policy, (2012), 47:291-297.
• Rajesh Chowdhary, Sin Lam Tan, Jinfeng Zhang, Vladimir B. Bajic and Jun S. Liu, Context-specific Protein Network Miner - an online system for exploring context-specific protein interaction networks from the literature , PLoS One, 2012, 7(4): e34480. doi:10.1371/journal.pone.0034480.
• Sentil Balaji, Charles Mcclendon, Rajesh Chowdhary, Jun S Liu and Jinfeng Zhang, IMID: Integrated molecular interaction database , Bioinformatics, (2012) 28 (5): 747-749.
• Rajesh Chowdhary, Jinfeng Zhang, Sin Lam Tan, Daniel Osborne, Vladimir B Bajic, Jun S Liu, PIMiner: a web tool for extraction of protein interactions from biomedical literature, IJDMB, accepted.

2011

• Jose Laborde, Anuj Srivastava, Jinfeng Zhang. Structure-based RNA function prediction using elastic shape analysis, IEEE-BIBM, 2011, 16-21.
• Tyrone Ryba, Ichiro Hiratani, Dana Battaglia, Micheal Kulik, Jinfeng Zhang, Stephen Dalton, and David M Gilbert. Replication timing: a fingerprint for cell identity and pluripotency, PLoS Computational Biology, 2011, 7(10): e1002225.
• Zhiyong Cheng, Jinfeng Zhang, David P Ballou, Charles H Williams, Jr, Reactivity of thioredoxin as a protein thiol-disulfide oxidoreductase , Chemical Review, 2011, 111 (9), 5768-5783.
• Lindsey Bell, Rajesh Chowdhary, Jun S Liu, Xufeng Niu, Jinfeng Zhang. Integrated bio-entity network: a system for biological knowledge discovery. PLoS ONE, 2011, 6(6): e21474, doi:10.1371/journal.pone.0021474.
• Lindsey Bell, Jinfeng Zhang, Xufeng Niu. Mixture of logistic models and an ensemble approach for extracting protein-protein interactions. ACM-BCB, 371-375, (2011).
• Leif Ellingson, Jinfeng Zhang. An efficient algorithm for matching protein binding sites for protein function prediction. ACM-BCB, 289-293, (2011).
• Wei Liu, Anuj Srivastava, Jinfeng Zhang. A mathematical framework for protein structure comparison, PLoS Computational Biology 7(2), (2011): e1001075. doi:10.1371/journal.pcbi.1001075

2010

• Yue Li, Gary Tyson, Jinfeng Zhang. Effect of sequences on the shape of protein energy landscapes , ACM-BCB, 35-42, (2010).
• Wei Liu, Anuj Srivastava, Jinfeng Zhang. Protein structure alignment using elastic shape analysis, ACM-BCB, 62-70, (2010).
• Tyrone Ryba, Ichiro Hiratani, Junjie Lu, Mari Itoh, Michael Kulik, Jinfeng Zhang, Stephen Dalton, David M. Gilbert. Evolutionarily conserved replication timing profiles distinguish closely related cell types and predict long range chromatin interactions , Genome Research, 20(6):761-70 (2010).

2009

• Rajesh Chowdhary, Jinfeng Zhang, Jun S Liu. Bayesian Inference of Protein-protein Interactions from Biological Literature , Bioinformatics, 25(12), 1536-1542 (2009).

• Jie Liang, Sema Kachalo, Xiang Li, Zheng Ouyang, Yan-Yuan Tseng, Jinfeng Zhang. Geometric structures of proteins for understanding folding, discriminating natives and predicting biochemical functions . The World Is a Jigsaw (Ed. Rien van de Weygaert), 2009, Springer.

2007

• Jinfeng Zhang, Sam C Kou, Jun S Liu. Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo Journal of Chemical Physics, 126, 225101 (2007).

• Jinfeng Zhang, Ming Lin, Rong Chen, Jie Liang, Jun S Liu. Monte Carlo sampling of near-native structures of proteins and applications, Proteins, 66, 61-68, (2007)

-2006

• Jinfeng Zhang, Jun S Liu. On side-chain conformational entropy of proteins. PLoS Computational Biology, (2006) 2(12): e168. doi:10.1371/journal.pcbi.0020168.

• Jinfeng Zhang, Rong Chen, Jie Liang. Empirical Potential Function for Simplified Protein Models: Combining Contact and Local Sequence-Structure Descriptors. Proteins. 63(4), 949-960, (2006)

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

• Jinfeng Zhang, Rong Chen, Chao Tang, Jie Liang. Origin of scaling behavior of protein packing density: A sequential Monte Carlo study of compact long chain polymers. J. Chem. Phys. 118(13):6102-6109, (2003).

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