Kun Huang, PhD
Associate Professor, College of Medicine
Phone number: (614) 292-5607
Email:
kun.huang@osumc.edu
Raghu Machiraju, PhD
Associate Professor, College of Engineering and College of Medicine
Phone number: (614) 292-6730
Email:
machiraju.1@osu.edu
Our collective laboratory works on problems of computational biology while leveraging methods from bioinformatics, visualization, and image analysis. Our group has engineered several workflows for processing and analyzing images for problems in cancer, neuro, and wound biology and immunology. We have developed algorithms that have been adapted for exploration in the laboratory at the microscopic scale (confocal, brightfield, histology, etc.) and in radiology clinics (diffusion tensor MR, fMRI, etc.). Our algorithms are derived from the fields of computer vision and machine learning. In addition, we are also developing tools for processing sequence data (micro array, RNA-seq, CHiP-seq). Kun Huang is also a Co-director of the Bioinformatics Share Resource facility in the Comprehensive Cancer Center. This combined focus of image informatics and bio informatics is serving us well and we collaborate with several groups on campus and elsewhere.
Team Members
Hatice Gulcin Ozer, Postdoctoral Researcher, Comprehensive Cancer Center (CCC)
Yang Xiang, CIFellow, Biomedical Informatics (BMI)
Cenny Taslim, Postdoctoral Researcher, Comprehensive Cancer Center (CCC)
Jie Zhang, Postdoctoral Researcher, Comprehensive Cancer Center (CCC)
Amy Webb, Postdoctoral Researcher, Biomedical Informatics (BMI)
David Liebner, Postdoctoral Fellow, Oncology (CCC)
Thierry Pecot, Pelatonia Fellow, Comprehensive Cancer Center (CCC)
Terry Camerlengo, Research Specialist, Comprehensive Cancer Center (CCC)
Ayse Selen Yilmaz, Research Specialist, Comprehensive Cancer Center (CCC)
Onti Raghuram Srinivasan, Graduate Student, Computer Science and Engineering (CSE)
Nan Meng, Graduate Student, Computer Science and Engineering (CSE)
Hao Ding, Graduate Student, Computer Science and Engineering (CSE)
Chao Wang, Graduate Student, Electrical and Computer Engineering (ECE)
Qihang Li, Graduate Student, Computer Science and Engineering (CSE)
Sundaresan Raman, Pelatonia Graduate Student, Computer Science and Engineering (CSE), and Comprehensive Cancer Center (CCC)
Andrew Yates, Graduate Student, Computer Science and Engineering (CSE)
Brian Arand, Fellow, Computer Science and Engineering (CSE)
June Kaewprag, Graduate Student, Computer Science and Engineering (CSE)
Zhiwei Ma, Graduate Student, Biophysics Program
Jinchao Di, Graduate Student, Electrical and Computer Engineering (ECE)
Research Interests
Bio-informatics, computational biology, bioimaging informatics and data visualization, machine learning and computer vision
Selected Publications
Han Z, Tian L, Pécot T, Huang T, Machiraju R, Huang K. A Signal Processing Approach for Enriched Region Detection in RNA Polymerase II ChIP-seq Data, BMC Bioinformatics (accepted).
Ouseph M, Li J, Chen H-Z, Pécot T, Wenzel P, Thompson JC, Comstock G, Chokshi V, Byrne M, Forde B, Chong J-L, Huang K, Machiraju R, de Bruin A, Leone G. Atypical E2F Repressors and Activators Coordinate Placental Development. Developmental Cell (accepted).
Ozer HG, Parvin J, Huang K. DFI: gene feature discovery in RNA-seq experiments from multiple sources, accepted to Special Issue for ICIBM Conference, BMC Genomics, 2012
Brown KN, Chen S, Han Z, Lu C-H, Tan X, Ding L, Zhang X-J, Cruz AL, Saur D, Anderson SA, Huang K, Shi S-H. Clonal production and organization of inhibitory interneurons in the neocortex, accepted to Science, 2011.
Rink C, Christoforidis G, Khanna S, Peterson L, Patel Y, Khanna S, Abduljalil A, Irfanoglu O, Machiraju R, Bergdall V, Sen C. Tocotrienol Vitamin E Protects Against Pre-clinical Canine Ischemic Stroke by Inducing Arteriogenesis, Nature Journal of Cerebral Blood Flow & Metabolism (2011), June, pp. 1–13.
Janoos F, Machiraju R, Singh S, Morocz I, Spatio-Temporal Models of Mental Processes from fMRI. NeuroImage 2011, Jul 15;57(2):362-77.
Janoos F, Mosaliganti K, Xu X, Machiraju R, Wong S. Robust 3D Reconstruction and Identification of Dendritic Spines from Optical Microscopy Imaging. Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis, (13)1:167-179, 2009.
Taslim C, Wu J, Yan P, Singer G, Parvin J, Huang T, Lin S, Huang K. Comparative study on ChIP-seq data: normalization and binding pattern characterization, Bioinformatics, 25(18): 2334-2340, 2009.
Mosaliganti K, Cooper L, Sharp R, Machiraju R, Huang K, Leone G. Visualization of Cellular Biology Structures from Optical Microscopy Data. IEEE Transactions on Visualization and Computer Graphics, (14)4:863-76, 2008.
Mosaliganti K, Janoos F, Sharp R, Ridgway R, Machiraju R, Huang K, Wenzel P, de Bruin A, Leone G Saltz J. Detection and Visualization of Surface-Pockets to enable Phenotyping Studies, Special Issue on Mathematical Methods in Biomedical Image Analysis, IEEE Transactions on Medical Imaging, 26(9):1283-90, 2007.
