A distance and orientation dependent potential energy function with cluster energy. - Lin Chen 007; Jing He 002 (BIBM Workshops, 2011)

Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions. - Kamal Al-Nasr; Lin Chen 007; Dong Si; Desh Ranjan; Mohammad Zubair; Jing He 002 (BCB, 2012)

A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps. - Kamal Al-Nasr; Lin Chen 007; Desh Ranjan; Mohammad Zubair; Dong Si; Jing He 002 (BCB, 2013)

Solving the Secondary Structure MatchingProblem in Cryo-EM De Novo ModelingUsing a Constrained $K$-Shortest Path Graph Algorithm. - Kamal Al-Nasr; Desh Ranjan; Mohammad Zubair; Lin Chen 007; Jing He 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Using Combined Features to Analyze Atomic Structures derived from Cryo-EM Density Maps. - Lin Chen 007; Jing He 002 (BCB, 2018)

A Histogram-based Outlier Profile for Atomic Structures Derived from Cryo-Electron Microscopy. - Lin Chen 007; Jing He 002 (BCB, 2019)