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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

75 entries « 1 of 8 »


Adhikari, B; Cheng, J

CONFOLD2: improved contact-driven ab initio protein structure modeling (Journal Article)

BMC Bioinformatics, 19 (1), pp. 22, 2018, ISSN: 1471-2105 (Electronic) 1471-2105 (Linking).

(Links | BibTeX)

Adhikari, B; Hou, J; Cheng, J

Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning (Journal Article)

Proteins, 86 Suppl 1 , pp. 84-96, 2018, ISSN: 1097-0134 (Electronic) 0887-3585 (Linking).

(Links | BibTeX)

Oluwadare, O; Zhang, Y; Cheng, J

A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data (Journal Article)

BMC Genomics, 19 (1), pp. 161, 2018, ISSN: 1471-2164 (Electronic) 1471-2164 (Linking).

(Links | BibTeX)


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

Assessing Predicted Contacts for Building Protein Three-Dimensional Models (Journal Article)

Methods Mol Biol, 1484 , pp. 115-126, 2017, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking).

(Links | BibTeX)

Cheng, J

DNCON2: Improved protein contact prediction using two-level deep convolutional neural networks (Journal Article)

Bioinformatics, 2017.


Hou, J; Adhikari, B; Cheng, J

DeepSF: deep convolutional neural network for mapping protein sequences to folds (Journal Article)

Bioinformatics, 2017, ISSN: 1367-4811 (Electronic) 1367-4803 (Linking).

(Links | BibTeX)

Jiang, L; Wan, Y; Anderson, J C; Hou, J; Islam, S M; Cheng, J; Peck, S C

Genetic dissection of Arabidopsis MAP kinase phosphatase 1-dependent PAMP-induced transcriptional responses (Journal Article)

J Exp Bot, 68 (18), pp. 5207-5220, 2017, ISSN: 1460-2431 (Electronic) 0022-0957 (Linking).

(Links | BibTeX)

Cai, Juan W; Yin, L; Kang, Q; Zeng, Chen Z; Wang, Liang 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)

Li, H; Hou, J; Adhikari, B; Lyu, Q; Cheng, J

Deep learning methods for protein torsion angle prediction (Journal Article)

BMC Bioinformatics, 18 (1), pp. 417, 2017, ISSN: 1471-2105 (Electronic) 1471-2105 (Linking).

(Links | BibTeX)

Oluwadare, O; Cheng, J

ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data (Journal Article)

BMC Bioinformatics, 18 (1), pp. 480, 2017, ISSN: 1471-2105 (Electronic) 1471-2105 (Linking).

(Links | BibTeX)

75 entries « 1 of 8 »