HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families. - Paul I. W. de Bakker; Alex Bateman; David F. Burke; Ricardo Núñez Miguel; Kenji Mizuguchi; Jiye Shi; Hiroki Shirai; Tom L. Blundell (Bioinform., 2001)

DDBASE2.0: updated domain database with improved identification of structural domains. - A. Vinayagam; Jiye Shi; Ganesan Pugalenthi; B. Meenakshi 004; Tom L. Blundell; Ramanathan Sowdhamini (Bioinform., 2003)

iMembrane: homology-based membrane-insertion of proteins. - Sebastian Kelm; Jiye Shi; Charlotte M. Deane (Bioinform., 2009)

MEDELLER: homology-based coordinate generation for membrane proteins. - Sebastian Kelm; Jiye Shi; Charlotte M. Deane (Bioinform., 2010)

Environment specific substitution tables improve membrane protein alignment. - Jamie R. Hill; Sebastian Kelm; Jiye Shi; Charlotte M. Deane (Bioinform., 2011)

Mobile computing - A green computing resource. - He Ba; Wendi Rabiner Heinzelman; Charles-Antoine Janssen; Jiye Shi (WCNC, 2013)

Memoir: template-based structure prediction for membrane proteins. - Jean-Paul Ebejer; Jamie R. Hill; Sebastian Kelm; Jiye Shi; Charlotte M. Deane (Nucleic Acids Res., 2013)

Use of Network Latency Profiling and Redundancy for Cloud Server Selection. - Minseok Kwon; Zuochao Dou; Wendi B. Heinzelman; Tolga Soyata; He Ba; Jiye Shi (IEEE CLOUD, 2014)

Improving B-cell epitope prediction and its application to global antibody-antigen docking. - Konrad Krawczyk; Xiaofeng Liu; Terry Baker; Jiye Shi; Charlotte M. Deane (Bioinform., 2014)

Crowdsourcing Yields a New Standard for Kinks in Protein Helices. - Henry R. Wilman; Jean-Paul Ebejer; Jiye Shi; Charlotte M. Deane; Bernhard Knapp (J. Chem. Inf. Model., 2014)

SAbDab: the structural antibody database. - James Dunbar; Konrad Krawczyk; Jinwoo Leem; Terry Baker; Angelika Fuchs; Guy Georges; Jiye Shi; Charlotte M. Deane (Nucleic Acids Res., 2014)

Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design. - James Dunbar; Bernhard Knapp; Angelika Fuchs; Jiye Shi; Charlotte M. Deane (PLoS Comput. Biol., 2014)

The Cloudlet Accelerator: Bringing Mobile-Cloud Face Recognition into Real-Time. - Nathaniel Powers; Alexander Alling; Kiara Osolinsky; Tolga Soyata; Meng Zhu; Haoliang Wang; He Ba; Wendi B. Heinzelman; Jiye Shi; Minseok Kwon (GLOBECOM Workshops, 2015)

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction. - Claire Marks; Jaroslaw Nowak; Stefan Klostermann; Guy Georges; James Dunbar; Jiye Shi; Sebastian Kelm; Charlotte M. Deane (Bioinform., 2017)

Comparing co-evolution methods and their application to template-free protein structure prediction. - Saulo Henrique Pires de Oliveira; Jiye Shi; Charlotte M. Deane (Bioinform., 2017)

Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank. - Qian Zhang 003; Zhijian Xu; Jiye Shi; Weiliang Zhu (J. Chem. Inf. Model., 2017)

Predicting loop conformational ensembles. - Claire Marks; Jiye Shi; Charlotte M. Deane (Bioinform., 2018)

Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction. - Saulo Henrique Pires de Oliveira; Eleanor C. Law; Jiye Shi; Charlotte M. Deane (Bioinform., 2018)

D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics. - Zhaoqiang Chen; Xinben Zhang; Cheng Peng; Jinan Wang; Zhijian Xu; Kaixian Chen; Jiye Shi; Weiliang Zhu (J. Chem. Inf. Model., 2019)

Underestimated Noncovalent Interactions in Protein Data Bank. - Zhijian Xu; Qian Zhang 003; Jiye Shi; Weiliang Zhu (J. Chem. Inf. Model., 2019)

TCRBuilder: multi-state T-cell receptor structure prediction. - Wing Ki Wong; Claire Marks; Jinwoo Leem; Alan P. Lewis; Jiye Shi; Charlotte M. Deane (Bioinform., 2020)

Thera-SAbDab: the Therapeutic Structural Antibody Database. - Matthew I. J. Raybould; Claire Marks; Alan P. Lewis; Jiye Shi; Alexander Bujotzek; Bruck Taddese; Charlotte M. Deane (Nucleic Acids Res., 2020)

Co-evolutionary distance predictions contain flexibility information. - Dominik Schwarz; Guy Georges; Sebastian Kelm; Jiye Shi; Anna Vangone; Charlotte M. Deane (Bioinform., 2021)

The Promise of AI for DILI Prediction. - Andreu Vall; Yogesh Sabnis; Jiye Shi; Reiner Class; Sepp Hochreiter; Günter Klambauer (Frontiers Artif. Intell., 2021)

Public Baseline and shared response structures support the theory of antibody repertoire functional commonality. - Matthew I. J. Raybould; Claire Marks; Aleksandr Kovaltsuk; Alan P. Lewis; Jiye Shi; Charlotte M. Deane (PLoS Comput. Biol., 2021)

Mechano-fluorescence actuation in single synaptic vesicles with a DNA framework nanomachine. - Jiangbo Liu; Xinxin Jing; Mengmeng Liu; Fan Li; Min Li; Qian Li; Jiye Shi; Jiang Li; Lihua Wang; Xiuhai Mao; Xiaolei Zuo; Chunhai Fan (Sci. Robotics, 2022)