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Core Faculty

Jianlin Cheng, Ph.D.

Associate Professor

Office: 109 Naka Hall

Phone: (573) 882-7306


Lab URL:

Home Department: Electrical Engineering and Computer Science

Concentration: Bioinformatics

Education: PhD, University of California Irvine

Dr. Jianlin Cheng’s research is focused on bioinformatics, systems biology, machine learning and data mining. To date, his group has designed and developed a variety of cutting-edge computational methods for protein structure and function prediction, proteomics, genomics, biological network simulation, and general machine learning. His protein structure prediction methods were ranked among the best in the last three consecutive biannual Critical Assessment of Techniques for Protein Structure Prediction (CASP7, CASP8, and CASP9), from 2006 to 2010. The bioinformatics tools and web services produced by Dr. Cheng’s research are publicly available and used by life scientists from around the world.

Selected Publications

61 entries « 1 of 7 »


Juan Cai, W; Yin, L; Kang, Q; Chen Zeng, Z; Liang Wang, S; Cheng, J

The Serum Pepsinogen Test as a Predictor of Kazakh Gastric Cancer (Journal Article)

Sci Rep, 7 , pp. 43536, 2017, ISSN: 2045-2322 (Electronic) 2045-2322 (Linking).

(Links | BibTeX)


Adhikari, B; Cheng, J

Protein Residue Contacts and Prediction Methods (Journal Article)

Methods Mol Biol, 1415 , pp. 463-76, 2016, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking).

(Links | BibTeX)

Bhattacharya, D; Adhikari, B; Li, J; Cheng, J

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling (Journal Article)

Bioinformatics, 32 (13), pp. 2059-61, 2016, ISSN: 1367-4811 (Electronic) 1367-4803 (Linking).

(Links | BibTeX)

Bhattacharya, D; Cao, R; Cheng, J

UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling (Journal Article)

Bioinformatics, 32 (18), pp. 2791-9, 2016, ISSN: 1367-4811 (Electronic) 1367-4803 (Linking).

(Links | BibTeX)

Bhattacharya, D; Nowotny, J; Cao, R; Cheng, J

3Drefine: an interactive web server for efficient protein structure refinement (Journal Article)

Nucleic Acids Res, 44 (W1), pp. W406-9, 2016, ISSN: 1362-4962 (Electronic) 0305-1048 (Linking).

(Links | BibTeX)

Cao, R; Bhattacharya, D; Adhikari, B; Li, J; Cheng, J

Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11 (Journal Article)

Proteins, 84 Suppl 1 , pp. 247-59, 2016, ISSN: 1097-0134 (Electronic) 0887-3585 (Linking).

(Links | BibTeX)

Cao, R; Bhattacharya, D; Hou, J; Cheng, J

DeepQA: improving the estimation of single protein model quality with deep belief networks (Journal Article)

BMC Bioinformatics, 17 (1), pp. 495, 2016, ISSN: 1471-2105 (Electronic) 1471-2105 (Linking).

(Links | BibTeX)

Cao, R; Cheng, J

Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks (Journal Article)

Methods, 93 , pp. 84-91, 2016, ISSN: 1095-9130 (Electronic) 1046-2023 (Linking).

(Links | BibTeX)

Cao, R; Cheng, J

Protein single-model quality assessment by feature-based probability density functions (Journal Article)

Sci Rep, 6 , pp. 23990, 2016, ISSN: 2045-2322 (Electronic) 2045-2322 (Linking).

(Links | BibTeX)

Cui, S; Ji, T; Li, J; Cheng, J; Qiu, J

What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment (Journal Article)

Stat Appl Genet Mol Biol, 15 (2), pp. 87-105, 2016, ISSN: 1544-6115 (Electronic) 1544-6115 (Linking).

(Links | BibTeX)

61 entries « 1 of 7 »