·
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.