Kun Huang's Publications

·                   Peer-reviewed journal papers

1.    Schwartzbaum J, Huang K, Lawler S, Ding B, Yu J. Allergy and inflammatory transcriptome is predominantly negatively correlated with CD133 expression, accepted to Neuro-Oncology, 2009.

2.    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, accepted to Bioinformatics, 2009.

3.    Cooper L, Sertel O, Kong J, Huang K, Gurcan M. Feature-based registration of distinct stained histopathology images: an application for computerized follicular lymphoma prognosis, accepted to Computer Methods and Programs in Biomedicine, 2009.

4.    Yu J, Ershler M, Yu L, Wei M, Hackanson B, Yokohama A, Mitsui T, Liu C, Mao C, Liu S, Liu Z, Liu C-G, Liu X, Huang K, Visser J, Guido M, Plass C, Belyavsky A, Caligiuri M. TSC-22 contributes to hematopoietic stem cell proliferation and repopulation and is epigenetically silenced in large granular lymphocyte leukemia, accepted to Blood, 2009.

5.    Rybaczyk L, Circle K, Grants I, Cooke H, Needleman B, Wunderlich JE, Huang K, Christofi FL. A New Comparative Analysis of Gene Expression and Selection (CAGES) Reveals Unique Purine Gene Dysregulation Profiles that Distinguish between Crohn’s and Ulcerative Colitis, accepted to Inflammatory Bowel Diseases, 2009.

6.    Mosaliganti K, Cooper L, Sharp R, Machiraju R, Leone G, Huang K, Saltz J. Reconstruction of Cellular Biological Structures from Optical Microscopy Data, accepted to IEEE Transactions on Visualization and Computer Graphics, 2008.

7.    Mosaliganti K, Sharp R, Machiraju R, Huang K, Leone G. Geometry-driven Visualization of Microscopic Structures in Biology, accepted to Computer Graphics Forum, the International Journal of the Eurographics Association, 2008.

8.    Mosaliganti K, Janoos F, Irfanoglu O, Ridgway R, Machiraju R, Huang K, Saltz J, Leone G, Ostrowski M. Tensor Classification of N-point Correlation Function features for Histology Tissue Segmentation, accepted to Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis, 2008.

9.    Janoos F, Mosaliganti K, Xu X, Machiraju R, Wong S, Huang K. Robust 3D Reconstruction and Identification of Dendritic Spines from Optical Microscopy Imaging, accepted to Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis, 2008.

10.           Mosaliganti K, Pan T, Ridgway R, Sharp R, Cooper L, Culacy A, Sharma A, Irfanoglu O, Machiraju R, Kurc T, Wenzel P, deBruin A, Leone G, Saltz J, Huang K. An Imaging Workflow for Characterizing Phenotypical Change in Terabyte Sized Mouse Model Datasets, accepted to Journal of Biomedical Informatics, 2008.

11.           Rybaczyk L, Bashaw M, Pathak D, Huang K. An Indicator of Cancer: Downregulation of Monoamine Oxidase-A in Multiple Organs and Species, accepted to BMC Genomics, 2008.

12.           Ruiz A, Ujaldon M, Cooper L, Huang K. Non-rigid Registration for Large Sets of Microscopic Images on Graphics Processors, accepted to Journal of Signal Processing Systems, 2008.

13.           Mosaliganti K, Janoos F, Sharp R, Ridgway R, Machiraju R, Huang K, Wenzel P, deBruin A, Leone G, Saltz J. Detection and visualization of surface-pockets to enable phenotyping studies. IEEE Transactions on Medical Imaging, 26(9):1283-1290, 2007.

14.           Wenzel PL, Wu L, de Bruin A, Chong JL, Chen WY, Dureska G, Sites E, Pan T, Sharma A, Huang K, Ridgway R, Mosaliganti K, Sharp R, Machuraju R, Saltz J, Yamamoto H, Cross JC, Robinson ML, Leone G. Rb is Critical in a Mammalian Tissue Stem Cell Population. Genes and Development, 21:85-97, 2007.

15.           Sharp R, Ridgway R, Mosalignati K, Wenzel P, Pan T, de Bruin A, Machuraju R, Huang K, Leone G, Saltz J. Volume rendering phenotype differences in mouse placenta microscopy data. Computing in Science & Engineering, 9(1):38-47, 2007.

16.           Hong W, Wright J, Huang K, Ma Y. A multi-scale hybrid linear model for lossy image representation. IEEE Transaction on Image Processing, 15(12):3655-3671, 2006.

17.           Yang AY, Rao S, Huang K, Hong W, Ma Y. Symmetry-based 3-D reconstruction from perspective images, Computer Vision and Image Understanding (CVIU), 99(2):210-240, August 2005.

18.           Hastings S, Ribeiro M, Langella S, Oster S, Catalyurek U, Pan T, Huang K, Ferreira R, Saltz J, Kurc T, XML database support for distributed execution of data-intensive scientific workflows, ACM SIGMOD Record, 34(3): 50-55, 2005.

19.           Huang K, Hong W, Ma Y. Symmetry-based photo editing, Pattern Recognition, 38(6): 825-834, 2004.

20.           Hong W, Yang AY, Huang K, Ma Y. On symmetry and multiple view geometry: structure, pose, and calibration from a single image, International Journal Computer of Vision, 60(3): 241-265, 2004.

21.           Ma Y, Huang K, Vidal R, Kosecka J, Sastry S. Rank conditions of the multiple-view matrix in multiple-view geometry, International Journal of Computer Vision, 59(2):115-137, 2004.

 

·       Peer-reviewed conference papers

22.           Ruan N, Jin R, Lee V, Huang K. A Sparsification Approach for Temporal Graphical Model Decomposition, to appear in Proceedings of the IEEE International Conference on Data Minding (ICDM), 2009.

23.           Kundu A, Ozer HG, Borlawsky T, Circle K, Huang K, Payne P. Clinical Attribute Network for Chronic Lymphocytic Leukemia, to appear in Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine (BIBM), 2009.

24.           Camerlengo T, Ozer HG, Teng M, Perez F, Yan P, Li L, Parvin J, Huang T, Kurc T, Liu Y, Huang K. Enabling Data Analysis on High-throughput Data in Large Data Depository Using Web-based Analysis Platform – A Case Study on Integrating QUEST with GenePattern in Epigenetics Research, to appear in Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine (BIBM), 2009.

25.           Kong J, Boyer K, Dunham P, Saltz J, Huang K. A new model-based estimation of ellipses for object representation, to appear in Proceedings of the IEEE Engineering in Medicine and Biology Conference (EMBC), 2009.

26.           Zhang J, Xiang Y, Jin R, Huang K. Using Frequent Co-expression Network to Identify Gene Clusters for Breast Cancer Prognosis, to appear in Proceedings of the ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing, 428-434, IEEE Press, 2009.

27.           Camerlengo T, Ozer HG, Zhang G, Joobeur T, Meulia T, Trgovcich J, Huang K. Computational challenges and solutions to the analysis of microRNA
profiles in virally-infected cells derived by massively parallel sequencing, to appear in Proceedings of the Ohio Collaborative Conference on Bioinformatics (OCCBIO), IEEE Press, 2009.

28.           Ozer HG, Camerlengo T, Huang T, Parvin J, Huang K. A new method for mapping short DNA sequencing reads by using quality scores, to appear in Proceedings of the Ohio Collaborative Conference on Bioinformatics (OCCBIO), IEEE Press, 2009.

29.           Parvin J, Kais Z, Arora M, Kotian S, Zha A, Ransburgh D, Bozdag D, Catalyurek U, Huang K. Identification of a breast cancer associated regulatory network, to appear in Proceedings of the Ohio Collaborative Conference on Bioinformatics (OCCBIO), IEEE Press, 2009.

30.           Ozer H, Bozdag D, Camerlengo T, Wu J, Huang Y-W, Hartley T, Parvin J, Huang T, Catalyurek U, Huang K. A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments, to appear in Proceedings of the First International Conference on Bioinformatics and Computational Biology, Lecture Notes in Computer Science, Springer-Verlag, 2009.

31.           Mosaliganti K, Machiraju R, Huang K. Geometry-driven visualization of microscopic structures, in Proceedings of the IEEE International Symposium of Biomedical Imaging (ISBI’08), 2008.

32.           Ruiz A, Ujaldon M,  Andrades JA, Becerra J, Huang K, Pan T, Saltz J. The GPU on biomedical image processing for color and phenotype analysis, in Proceedings of IEEE 7th Intl. Symposium on BioInformatics & BioEngineering (BIBE'07), Cambridge, Massachussets, October 2007.

33.           Mosaliganti K, Chen J, Janoos F, Machiraju R, Xia W, Huang K.  Automated quantification of colony growth in clonogenic assays, in Proceedings of International Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB’07), New Jersey, September 2007.

34.           Cooper L, Naidu S, Leone G, Saltz J, Huang K. Registering high resolution microscopic images with different histochemical stainings - a tool for mapping gene expression with cellular structures, in Proceedings of International Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB’07), New Jersey, September 2007.

35.           Janoos F, Irfanoglu O, Mosaliganti K, Machiraju R, Huang K, Wenzel P, de Bruin A, Leone G. Multiple-resolution image segmentation using the 2-point correlation functions, in Proceedings of the IEEE International Symposium on Biomedical Imaging, Washington, DC, April 2007

36.           Mosaliganti K, Jonoos F, Xu X, Machuraju R, Wong STC, Huang K, Temporal matching of dentritic spines in confocal microscopy images of neuronal tissue, in Proceedings of the Microscopic Image Analysis with Applications in Biology (MIAAB) Workshop in MICCAI, October 2006.

37.           Ridgeway R, Irfanoglu O, Machuraju R, Huang K. Image segmentation with tensor-based classification of N-point correlation functions, in Proceedings of the Microscopic Image Analysis with Applications in Biology (MIAAB) Workshop in MICCAI, October 2006.

38.           Cooper L, Huang K, Sharma A, Mosaliganti R, Pan T. Registration vs. reconstruction: Building 3-D models from 2-D microscopy images, in Proceedings of the Bioimage Informatics Workshop, September 2006.

39.           Huang K, Cooper L, Sharma A, Pan T. Fast automatic registration algorithm for large microscopy images, in Proceedings of the IEEE/NLM Life Science Systems & Applications Workshop, 128-129, July 2006.

40.           Sharp R, Ridgway R, Mosalignati K, Irfanoglu O, Wenzel P, Machiraju R, Pan T, de Bruin A, Machuraju R, Leone G, Huang K, Saltz J. Examining Phenotype Differences in Mouse Placenta with Volume Rendering and Segmentation, in Proceedings of the IEEE/NLM Life Science Systems & Applications Workshop, 70-71, July 2006.

41.           Prescott J, Clary M, Wiet G, Pan T, Huang K. Automatic registration of large set of microscopic images using high-level features, in Proceedings of the IEEE International Symposium on Medical Imaging, Arlington, VA, April 2006.

42.           Mosaliganti R, Pan T, Sharp R, Ridgway R, Iyengar S, Gulacy A, Wenzel P, de Bruin A, Machiraju R, Huang K, Leone G, Saltz J. Registration and 3D visualization of large microscopy images, in Proceedings of the SPIE Annual  Medical Imaging Meetings, February 2006.

43.           Cooper L, Liu J, Huang K. Spatial segmentation of temporal texture using mixture linear models, in Proceedings of the Dynamical Vision Workshop in the International Conference of Computer Vision, Beijing, China, October 2005.

44.           Hong W, Wright J, Huang K, Ma Y. A multi-scale hybrid linear model for lossy image representation, in Proceedings of the IEEE International Conference on Computer Vision (ICCV), 1:764-771, Beijing, China, October 2005.

45.           Pan T, Huang K. Virtual mouse placenta: tissue layer segmentation, in Proceedings of the IEEE EMBC, September 2005.

46.           Huang K, Wagner A, Ma Y. Hybrid linear system identification via subspace embedding and segmentation, in Proceedings of the 43th IEEE Conference on Decision and Control, December 2004.

47.           Huang K, Yang AY, Ma Y. Image representation with hybrid and adaptive linear models, in Proceedings of the International Conference on Image Processing, October 2004.

48.           Huang K, Ma Y. Robust GPCA algorithm with applications in video segmentation via hybrid system identification, in Proceedings of the Sixteenth International Symposium on Mathematical Theory of Networks and Systems (MTNS2004), Leuven, Belgium, July 2004.

49.           Huang K, Vidal R, Ma Y. Minimum effective dimension for mixtures of subspaces: a robust GPCA algorithm and its applications, in Proceedings of the IEEE International Conference on Computer Vision and Pattern Recognition (CVPR'04), June 2004.

50.           Huang K, Hong W, Yang AY, Ma Y. Large baseline matching and reconstruction from symmetry cells, in Proceedings of the IEEE International Conference on Robotics and Automation (ICRA'04), 2:1418-1423, New Orleans, USA, April 2004.

51.           Yang AY, Rao S, Huang K, Hong W, Ma Y. Geometric segmentation of perspective images based on symmetry groups, in Proceedings of the International Conference on Computer Vision, 2:1251-1258, Nice, France, October, 2003.

52.           Huang K, Hong W, Ma Y. Symmetry-based photoediting, in the International Conference on Computer Vision, Workshop on Higher Level Knowledge, 21-28, Nice, France, October, 2003..

53.           Brand M, Huang K. A unifying theorem for spectral embedding and clustering, in Proceedings of the 9th International Conference on Artificial Intelligence and Statistics, Key West, Florida, January, 2003.

54.           Huang K, Fossum R, Ma Y. Generalized rank conditions in multiple view geometry with application to dynamic scenes, in Proceedings of the 6th European Conference on Computer Vision, Copenhagen, Denmark, May 2002.

55.           Ma Y, Huang K, Yang Y. Classification of rank conditions for multiple views of dynamical scenes, in 6th European Conference on Computer Vision, Workshop on Vision and Modeling of Dynamic Scenes, Copenhagen, Denmark, May 2002.

56.           Ma Y, Kosecka J, Huang K. Rank deficiency condition of the multiple view matrix for mixed point and line features, in Proceeding of the 5th Asian Conference on Computer Vision, Melbourne, Australia, January 2002.

57.           Huang K, Kumar PR. Hierarchical and integrated algorithms: comparison and applications in motion estimation and recognition, in Proceedings of the 39th IEEE Conference on Decision and Control, pp.674-9 vol.1, Sydney, Australia, December 2000.

 

·       Book chapters

58.           Huang K, Mosaliganti K, Cooper L, Machiraju R. Quantitative phenotyping using microscopic images, in Microscopic Image Analysis for Life Science Applications, Artech House Publishers, 2008.

59.           Cooper L, Ruiz A, Ujaldon M, Huang K. Scalable Image Registration and 3D Reconstruction at Microscopic Resolution, in High Throughput Image Reconstruction and Analysis, Artech House Publishers, 2008.

60.           Huang K, Ma Y. A survey on geometric vision, in Handbook of Robotics, CRC Press, 2004.

 

·       Peer reviewed abstracts

61.           Xiang Y, Zhang J, Ruan N, Jin R, Parvin J, Huang K. A study on frequent co-expression networks in cancers, AMIA Annual Summit on Translational Bioinformatics, San Francisco, March 2009.

62.           Huang K, Wu J, Zhang J, Huang T, Parvin J. GenomeScape: a universal 3D visualization tool for genomic data, AMIA Annual Summit on Translational Bioinformatics, San Francisco, March 2009.

63.           Cooper L, Wright J, Singh S, Bluestein E, Ma Y, Huang K. GeneSubspace - a tool for clustering the gene expression profiles using mixture linear models, AMIA Annual Summit on Translational Bioinformatics, San Francisco, March 2009.

64.           Rybaczyk L, Pathak D, Cooper L, Circle K, Huang K. Four common gene expression changes across multiple cancers in multiple species. AACR annual meeting (Abstract#4266), 2008.

65.           Rybaczyk L, Wunderlich J, Circle K, Needleman B, Melvin S, Cardounel A, Grants I, Huang K, Christofi F: Differential Dysregulation of ADORA3, ADORA2A, ADORA2B, and P2RY14 Expression Profiles from 37 Purine Genes in Mucosal Biopsies and Peripheral Blood Mononuclear Cells in IBD,  Gastroenterology 132: Suppl. 2, A-246, 2007.

66.           Circle K, Rybaczyk L, Grants I, Wunderlich J, Huang K, Christofi F: A new comparative analysis of gene expression and selection (CAGES) reveals purine gene signature profiles that distinguish between crohn's and ulcerative colitis. 6th Annual Advances in the Inflammatory Bowel Diseases, 2007.

67.           Huang K, Sharma A, Cooper L, Pan T, Gurcan M, Saltz J. A novel image registration pipeline for 3-D reconstruction from microscopy images, Advancing Practice, Instruction and Innovation Through Informatics (APIII), Vancouver, Canada, August 2006.

68.           Sharma A, Huang K, Pan T, Gurcan M, Saltz J. A parallel image registration framework for terabyte sized microscopy datasets, Advancing Practice, Instruction and Innovation Through Informatics (APIII), Vancouver, Canada, August 2006.

69.           Pan T, Sharma A, Gurcan M, Huang K, Leone G, Saltz J. GridCAD Microscopy: A caBIG based system for image processing and quantitative analysis, Advancing Practice, Instruction and Innovation Through Informatics (APIII), Vancouver, Canada, August 2006.

70.           Huang K, Iyengar S, Radecki R, Mahmoud AM, Twa MD, Lembach RG, Roberts CJ. Comparison of Corneal Scattering Properties Pre- and Post-LASIK Using Orbscan Images, in Proceedings of the 2006 Annual Meeting for Research in Vision and Ophthalmology (ARVO), Fort Lauderdale, FL, April 2006.

71.           Pan T, Masaliganti K, Sharp R, Ridgeway R, Huang K, Machuraju R, Saltz J. Virtual placenta: computational phenotyping through image analysis, Advancing Practice, Instruction and Innovation Through Informatics (APIII), Vancouver, Canada, August 2005.

 

·       Technical reports

72.           Huang K, Hong W, Yang AY, Rao S, Ma Y. Symmetry-Based 3-D Reconstruction from Perspective Images (Part I and II), Technical Report, UILU-ENG-03-2204, April,2003.

73.           Brand M, Huang K. A Unifying Theorem for Spectral Embedding and Clustering, Technical Report of Mitsubishi Electric Research Laboratory, TR2002-42, October, 2002.

74.           Fossum R, Huang K, Ma Y. General Rank Conditions in Multiple View Geometry, Technical Report, UILU-ENG-01-2222, October 8,2001.

75.           Ma Y, Huang K, Vidal R, Kosecka J, Sastry S. New Rank Conditions of the Multiple View Matrix in Multiple View Geometry, Technical Report, UILU-ENG-01-2214 (DC-220), June 18, 2001.

76.           Ma Y, Vidal R, Huang K, Sastry S. New Rank Deficiency Condition for Multiple View Geometry of Point Features, Technical Report, UILU-ENG-01-2208 (DC-200), May 8, 2001.

77.           Ma Y, Huang K, Kosecka J. New Rank Deficiency Condition for Multiple View Geometry of Line Features, Technical Report, UILU-ENG-01-2209 (DC-201), May 8, 2001.

78.           Huang K, Moroz LL, Sudlow L, Gillette R. Nitric Oxide and 5-HT May Regulate Feeding Network Arousal State via Intracellular Ca2+ and H+ in Pleurobranchae Californica, in Abstracts of 28th Annual Meeting of Society for Neuroscience, Los Angeles, USA, October 1998.

 

·       Thesis and dissertations

79.           Huang K, Geometric principles of visual sensor networks, Ph.D. Dissertation, University of Illinois, 2004.

80.           Huang K, Hierarchical and integrated algorithms: comparison and applications in motion estimation and recognition, Master Thesis, University of Illinois, 2000.

81.           Huang K, Computer-aided analysis of electrophysiological signals, Bachelor Degree Thesis, Tsinghua University, 1996.