Research Interests:
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Pattern Recognition and Machine Learning
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Intelligent Data Analysis
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Bioimage informatics
Selected Publications
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Akiko Terauchi, Patricia Yee, Mariel P. Seiglie, Lisa Kim, Julia C. Pitino, Eli Kritzer, Qiyu Zhang, Jie Zhou, Yulong Li, David D. Ginty, Wei-Chung A. Lee, Hisashi Umemori. "The projection-specific signals that establish functionally segregated dopaminergic synapses".
Cell, in press. (Cell impact factor in 2023: 66.85)
- L. Manubens-Gil et al., "BigNeuron: A resource to benchmark and predict best-performing algorithms for automated reconstruction of neuronal morphology", Nature Methods. April 2023 Link
- Y. Hu et al. "LabGym: A versatile computational tool for automatic quantification of user-defined animal behaviors". Cell Reports Methods. Feb. 2023. Link
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T. Kaneko, A. M. Macara, R. Li, Y. Hu, K. Iwasaki, Z. Dunnings, E. Firestone, S. Horvatic, A. Guntur, O. T. Shafer, C-H. Yang, J. Zhou, B. Ye, "Serotonergic modulation enables pathway-specific plasticity in a developing sensory circuit in Drosophila", Neuron. 95: 623-638. 2017. Link
- R. Santos, et al., "Machine learning techniques in searches for tth in the h →bb decay channel",
Journal of Instrumentation 12, April 2017, arXiv:1610.03088
- H. Peng, J. Zhou, Z. Zhou, A. Bria, Y. Li, D. M. Kleissas, N. G. Drenkow, B. Long, X. Liu, and H. Chen, "Bioimage Informatics for Big Data", Advances in Anatomy, Embryology and Cell Biology, 2016;219:263-72. doi: 10.1007/978-3-319-28549-8_10. Link
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A. Esktrom, R. Suvanto, T. Yang, B. Ye, and J. Zhou, “Robust Neuron Counting based on Fusion of Shape Map and Multi-cue Learning”, 2016 International Conference on Brain Informatics and Health (BIH 2016), Oct 12-16. Omaha, Nebraska.
- J. Sanders, A. Singh, G. Sterne, B. Ye and J. Zhou,
"Learning-guided automatic three dimensional synapse quantification for drosophila neurons", BMC Bioinformatics 2015, 16:177. doi:10.1186/s12859-015-0616-y Link to paper.
- T. Smafield, V. Pasupuleti, K. Sharma, R. L. Huganir, B. Ye, J. Zhou, "Automatic Dendritic Length Quantification for High Throughput Screening of Mature Neurons", Neuroinformatics, 13:4, pp.443-458, 2015. doi:10.1007/s12021-015-9267-4. Link to paper. Link to software
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N. Japkowicz, V. Barnabe-Lortie, S. Horvatic,and J. Zhou, "Multi-class Learning using Data Driven ECOC with Deep Search and Re-Balancing", IEEE Intl. Conference on Data Science and Advanced Analytics (IEEE DSAA'2015), Oct 19-21, Paris, 2015.
Main track long presentation acceptance rate: 9%.
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J. Zhou, L. Yang and B. Ye, "QTIP: Quantifier for Topographic Index of Presynaptic-terminal using 3D Confocal Imaging", Bioimage Informatics Conference, Gaithersburg, MD, Oct 2015. pdf Link to software.
- L. Yang, R. Li, T. Kaneko,, K. Takle, R. K. Morikawa, L. Essex, X. Wang, J. Zhou, K. Emoto, Y. Xiang, B. Ye, "Trim9 Regulates Activity-Dependent Fine-Scale Topography in Drosophila", Current Biology, 2014, DOI:http://dx.doi.org/10.1016/j.cub.2014.03.041
- J. Zhou, S. Lamichhane, G. Sterne, B. Ye, H. C. Peng, "BIOCAT: a Pattern Recognition Platform for Customizable Biological Image Classification and Annotation", BMC Bioinformatics, 2013, 14:291 doi:10.1186/1471-2105-14-291.Link to paper. Highly Accessed.
- J. Zhou, A. Brunson, J. Winans, K. Duffin and N. Karonis, "Performance Model Selection for Learning-based Biological Image Analysis on a Cluster", ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB 2013) Washington D.C. Sept. 2013. pp324-332. preprint
- S. Lamichhane and J. Zhou, "Automatic Analysis of Dendritic Territory for Neuronal Images", International Symposium on Bioinformatics Research and Applications, Dallas, Texas, May 21-23, 2012.
- J. Zhou and H. C. Peng, "Counting cells in 3D confocal
images based on discriminative models",
ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB 2011). pp399-403.
- J. Zhou and J. Zhang, "Pointwise regression and
clustering analysis
for 3D gene expression in the Drosophila blastoderm", Workshop on Microscopic Image Analysis with Applications to Biology (MIAAB 2011).
- B. S. Divakaruni and J. Zhou, "Image categorization using
codebooks built from scored and selected local features",
The 2011 International Conference on Image Processing, Computer Vision and Pattern Recognition
(IPCV 2011). Paper Website (with implementation, powerpoint slides and more)
- J. Zhou, J. Yao, J. Deng and J. Dewald,
"EEG-based classification for elbow versus shoulder torque intentions
involving stroke subjects
", Computers in Biology and Medicine. 39:443-452. 2009.
- J. Zhou, H. C. Peng, and C. Y. Suen, "Data driven
decomposition for multi-class classification", Pattern Recognition, 41:67-76, 2008.
- J. Zhou and H. C. Peng, "Automatic
recognition and annotation of gene expression patterns of fly embryos", Bioinformatics, 23(5):589-596, 2007.
- H. C. Peng, F. H. Long, J. Zhou, G. Leung,
M. Eisen, and E. Myers, "Automatic image analysis for gene expression patterns
of fly embryos", BMC Cell Biology, vol. 8. 2007. Link
to paper.
- J. Zhou and S. Yedida, "Channel selection in EEG-based
prediction of shoulder/elbow movement intentions: a computational approach",
IEEE Symposium on Computational Intelligence in Bioinformatics and Computational
Biology (CIBCB2007), pp.455-460,
2007.
- J. Zhou and H. C. Peng, "Automatic recognition and annotation of gene
expression patterns of fly embryos", Workshop on Multiscale Biological
Imaging, Data Mining & Informatics (Bioimage Informatics 2006),
pp.49-50, 2006.
- L. Sun and J. Zhou, "Developing multiregime
speed-density relationships using cluster analysis", J. of the
Transportation Research Board, 1934:64-71, 2005.
- J. Zhou, J. Yao, J. Deng and J. Dewald,
"EEG-based discrimination of elbow/shoulder torques using Brain
Computer Interface algorithms: implications for rehabilitation", the
27th Intl Conf of the IEEE Engineering in Medicine and Biology
(EMBC05). pp.4134-4137. (Invited speaker for mini-symposium on
neuro-rehabilitation engineering.)
- J. Zhou and C. Y. Suen, "Unconstrained numeral pair
recognition using enhanced error correcting output coding: a holistic approach",
International Conference on Document Analysis and Recognition, (ICDAR'2005)
pp.484-488.
- J. Zhou and H. C. Peng, "Toward Automatic Annotation of
in situ mRNA Expression Patterns of Drosophila Embryos",
Computational Systems Bioinformatics Conference (CSB2005), Workshop on
Bioimage Data Mining and Informatics. pp.395. August 12, 2005 Stanford, CA (abstract).
- J. Zhou and G. Pasteris, "Data
driven approach to designing minimum Hamming distance polychotomizer",
ACM Symposium on Applied Computing (SAC 2005). pp.27-31.
- L. Sun and J. Zhou,
"Developing multi-regime Speed-density relationships using cluster analysis",
Transportation Research Board Annual Meeting 2005. Selected for publication in the Journal of the Transportation Research Board.
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J. Zhou, "Comparing regularized B-spline neural
network, multilayer perceptron and boosted-CART on two problems of
heart arrhythmia diagnosis", the 26th International Conference of the
IEEE Engineering in Medicine and Biology. pp. 3601-3604, 2004.
- J. Zhou and L. Li, "Using genetic algorithm
trained perceptrons with adaptive structure for the detection of
premature ventricular contraction", Computers in Cardiology, pp
353-356, 2004.
- J. Zhou and L. Li, "Regularized B-spline network and its
application to heart arrhythmia classification", ACM Symposium on Applied
Computing (SAC 2004). pp. 291-295, 2004.
- J. Zhou, "Automatic detection of premature ventricular contraction using
quantum neural networks", 3rd IEEE Symposium on Bioinformatics and
Bioengineering (BIBE2003), pp.169-173, 2003.
- J. Zhou, A. Krzyzak and, C. Y. Suen, "Verification -- a method of enhancing
the recognizers of isolated and touching handwritten numerals",
Pattern Recognition Journal,
35(5):1179-1189, 2002
- J. Zhou, A. Krzyzak, C. Y. Suen, "Recognition and verification of
touching handwritten numerals", Proc. of Int. Workshop on Frontiers
in Handwriting Recognition, pp.179-188, 2000.
- J. Zhou, Q. Gan, A. Krzyzak, and C. Y. Suen. "Recognition of handwritten
numerals by quantum neural network with fuzzy features", Intl.
Journal on Document Analysis and Recognition, 2(1):30-36,
1999.
- J. Zhou, Q. Gan, A. Krzyzak, C. Y. Suen, "Quantum neural network in
recognition of handwritten numerals", Proc. of Intl.
Workshop on Frontiers in Handwriting Recognition (IWFHR'98), pp.305-314, 1998
- J. Zhou, Q. Gan, C. Y. Suen, "A high performance hand-printed numeral
recognition system with verification module," Proc. of Int. Conference of
Document Analysis and Recognition (ICDAR), vol. 1, pp.293-297, 1997.
Chapters in books:
- J. Zhou, H. C. Peng, "Automatic Annotation of Biological Images",
in "Handbook of Pattern Recognition and Computer Vision", volume 4,
edited by C. H. Chen. World Scientific. 2011.
- J. Zhou, Q. Gan, A. Krzyzak, C. Y. Suen, "Quantum neural network in
recognition of handwritten numerals", in "Advances in handwriting
recognition", edited by Seong-Whan Lee, pp368-377. World Scientific. 1999.
- J. Zhou, Q. Gan, "Invariant pattern representation and recognition
methods based on size transformation", in "New Advances in Theory
and Application of Electronics and Information", edited by Mingyi He,
Press of Northwestern Polytechnic University, China, September 1995
Posters and Demo Presentations:
- Bioimage Informatics Sept. 2010, Carnegie Mellon University, Pittsburgh, PA;
Bioimage Informatics 2009, Janelia Farm Research Campus, HHMI, Ashburn, VA.
- Computer Vision For Neuroscience and Vice Versa, Sept. 2008, HHMI
Janelia Farm, Ashburn, VA.
- 16th International Conference on Intelligent Systems for
Molecular Biology
(ISMB 2008),
July 2008, Toronto, Canada.
- Computer Vision and Pattern Recognition
2010, San Francisco, CA.
Services / Talks
- Editorial Board Member for Pattern Recognition Journal since 2010
- Associate Editor for Pattern Recognition Journal since 2006
- Program Committee Members for conferences such as
Workshop on
Microscopic Image Analysis with Applications to Biology (MIAAB 2011); International Symposium on
Computational Models for Life Sciences (CMLS-11) 2011; IEEE Intl
Conf on Granular Computing 2011; IEEE Intl
Conf on Granular Computing 2006
- Reviewer for Plos Computational Biology
- Reviewer for Bioinformatics
- Reviewer for BMC Bioinformatics
- Reviewer for Optical Engineering
- Reviewer for International Journal of Pattern Recognition and Artificial Intelligence
- Reviewer for Pattern Recognition Letters Journal
- Reviewer for Neurocomputing Journal
- Reviewer for IEEE Transactions on Knowledge and Data Engineering
- Reviewer for IEEE Transactions on Neural Networks.
- Reviewer for Image and Vision Computing Journal.
- Reviewer for Soft Computing Journal.
- Reviewer for various conferences such as Workshop on
Microscopic Image Analysis with Applications to Biology (MIAAB 2011); International Symposium on Bioinformatics and
BioEngineering, 2007; IEEE
Intl Conf on Granular Computing 2006; Intl Conf. on Document Analysis
and Recognition 2005
- Invited talk: July 30, 2004 Concordia University, Montreal, Canada
- Invited talk: Sept 3, 2004 Lawrence Berkeley National Lab, Berkeley, CA
- Invited talk: Oct 20, 2005 Lawrence Berkeley National Lab, Berkeley, CA
Grants, Awards, Honors
- National Institutes of Health NIH/NIMH R15MH099569, PI. 2013-2017
- Burroughs Wellcome Fund (BWF) Collaborative Research Travel Grant (CRTG) 2012-2013. PI. "Automatic Image Analysis for Identifying Regulators of Subcellular Synapse Distribution."
- Faculty for Undergraduate Research Assistantship, Office of Student Engagement and Experiential Learning, Northern Illinois University, summer 2012, fall 2013.
"Computational Algorithms and Tools for High-dimensional Neuronal Image Analysis"
- Great Journeys Research Grant, Research and Graduate Studies Development
Council, Northern Illinois University, 2011-2012, 2013-2014
- Graduate School Summer Research and Artistry Grants, Northern Illinois University,
2003, 2005, 2006, 2011
- Undergraduate Research Apprenticeship Program (URAP), Northern Illinois University, 2003, 2004, 2005.
- Undergradaute Research Appreticeship Program (URAP), Northern Illinois University 2012-2013, fall 2013
- IBM Team Success Award 2000
- Recipient of FONDS F.C.A.R. (Fonds pour la Formation de Chercheurs et l'Aide a la Recherche, Fund for Training of Researchers and Research Support), Quebec, Canada 1998-1999