Jin Chen
Assistant Professor
MSU-DOE Plant Research Laboratory
Department of Computer Science & Engineering

Michigan State University

Tel: (517) 355-5015 (office)
Tel: (517) 353-0697 (lab)
Fax: (517) 353-9168
Email: jinchen@msu.edu
Office: Plant Biology Building 232

Address:
MSU-DOE Plant Research Laboratory
Michigan State University
106 Plant Biology Building
East Lansing, MI 48824-1312 USA


[Research]     [Teaching]     [Publications]    [People]    [Professional Activites]

 

Dr. Jin Chen is an Assistant Professor in the MSU-DOE Plant Research Laboratory and the Department of Computer Science & Engieering at Michigan State University. He received his Ph.D. in Computer Science from the National University of Singapore (NUS) under the supervision of Dr. Wynne Hsu, Dr. Mong Li Lee and Dr. See-Kiong Ng in 2007. He received his Bachelor degree in Computer Science from Southeast University in China in 1997. Before joining MSU, he was a postdoctoral research associate in the bioinformatics laboratory of Dr. Seung Y. Rhee at the Carnegie Institution for Science at Stanford University from December 2006 to August 2009. Before starting his PhD study, he was a software developer and then team leader in the Information Center at the Jiangsu Electric Power Company from July 1997 to April 2002.

His research focused on the application of data mining and computer vision algorithms to solve basic biological problems in plant biology. His group develops new computational software packages to address a range of topics, which can be divided into two broad categories. In category 1 plant phenotype data modeling, his research focus is on 2D and 3D leaf alignment, phenotype heterogeneity test, phenotype ontology construction, and phenotype data clustering. In category 2 reconstructing gene networks with omics data, he is interested in high-dimensional subspace clustering on gene expression and protein-protein interaction data, regulatory interaction modeling, biological network reconstruction, and plant organelle function inference. Recently, he is working on the integration of the research lines in the two categories.

 

 

[Software]

Pheno-informatics

High-throughput Plant growth Analysis (HPGA)

High-throughput Plant growth Analysis 2.0 (HPGA 2.0)

Leaf Alignment

Leaf Tracking

Gene Ontology

Cross-category GO Term Similarity Measurement (CroGO)

Integrative Gene Functional Similarity Measurement (InteGO)

Network based GO term Similarity (NETSIM)

Gene Expression Data Analysis

Optimal Timepoint Selection (OTS)

Transcriptional Regulatory Interaction Model (TRIM)

Transcriptional Regulatory Interaction Model v2 (mTRIM)

Pattern Recomposition for the Isolation of Independent Signals (PRIISM)

Protein Interaction Data Analysis

Interaction Reliability by Alternative Path (IRAP*)

 

 


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