Nature news BigNeuron
Nature's 2015 News Highlight of the BigNeuron project. More news coverage of this project appeared in Science, NPR, NBC, etc.


Virtual Finger technique published in Nature Communications in July 2014. See the Allen Institute Press Release.

Mouse brain wiring map
A mouse brain wiring map generated at Allen Institute for Brain Science, and published in Nature in April 2014.

A new vehicle for biology
A SmartScope microimaging system being built in Peng Lab. This picture was used as the cover art of the 2012 Turning Images to Knowledge conference, Oct 28-31, 2012.

GAL4 resource
A collaboration project of the GAL4 resource with G. Rubin lab. My BrainAligner software (Nature Methods, 2011) is used as a critical element for this study, which is published as cover story of Cell Reports 2012.

High-throughut mapping of brains in 3D
High-throughput mapping of fruit fly brain circuit based on analyzing tens of thousands of 3D laser scanning microscopy image stacks of the adult Drosophila brain. This picture was used as the cover art of the 2011 Bioimage Informatics conference, Sept 18-21, 2011. Particularly, this work is based on a new 3D image registration method called BrainAligner (Nature Methods, 2011).

Brain wiring atlas of a fruit fly
A neuronal wiring atlas across brain compartments throughout a fruit fly's brain. I developed a pipeline (3D image registration/alignment, neuron tracing, pattern analysis and mining, atlas assembling and modeling) to produce this atlas. This picture was used as the cover art of the 2010 Cold Spring Harbor Neuronal Circuit conference, March 10-13, 2010. Particularly, I first produced a 3D neuronal image-pattern atlas by aligning thousands of 3D laser scanning microscopy image-stacks of fruit fly brains (from about 500 GAL4 lines) by using my BrainAligner system (Nature Methods, 2011); then I produced another 3D atlas of stereotyped (spatially invariant) neurite patterns using my Vaa3D-Neuron system (Nature Biotechnology, 2010).

The first post-embryonic 3D digital atlas of C. elegans
The cover picture of Nature Methods (Sept 2009 issue) highlighting the first single-cell resolution 3D digital nuclear atlas of a post-embryonic worm. This atlas documents cell identity of 357 nuclei as well as their statistics of spatial locations, sizes, etc. This atlas is important for single cell level gene expression analysis (with Liu, Long, et al, Cell, 2009) and automatic cell ablation/stimulation. (Read more about this atlas in our Nature Methods 2009 paper). This atlas can also be conveniently viewed/searched in 3D using my Vaa3D software. Indeed, this cover art was generated using Vaa3D as well.

3D reconstruction of fruit fly neurons
An artistic painting of a 3D reconstructed and rendered neuron model in adult fruit fly brains. You can download a full-size desktop picture here. This neuron was traced (reconstructed) conveniently using my Vaa3D software (published in Nature Biotechnology, 2010), from 3D confocal images of single neurons produced in Gerry Rubin lab. (Unpublished data. All rights reserved.)

Mapping single neurons to fruit fly brain atlas model
The cover art of the Proceedings of the 2009 Bioimage Informatics conference. This picture shows two single neuron reconstructions mapped to an adult fruit fly brain atlas model where various brain compartments are also displayed. The techniques used to trace these neurons and to build the digital atlas are implemented in my Vaa3D software. This picture was produced based on 3D confocal images and painted label-field generated in Julie Simpson, Tzumin Lee, and Gerry Rubin labs. Click here to download a desktop wallpaper picture. (Unpublished data. All rights reserved.)

Fly Brain Compartment Atlas

The cover art of the Proceedings of the 2008 Conference on Functional Anatomy of the Arthropod Central Complex and Motor System. This picture shows the compartmental atlas of a fruit fly's brain which I produced using the BrainAligner pipeline developed in my lab. The raw image data were produced in Julie Simpson lab.


Worm straightening scheme

Standardize 3D C. elegans image stacks by straightening the worm body. This technique is one of the critical steps in our project in building the entire digital cell atlas for developing C. elegans. For more information, read a new Bioinformatics paper here. BTW, don't get confused by the above animation: a C. elegans worm does not have eyes!

MSTCUT for fly image clustering
MSTCUT clustering of fly gene expression patterns in the eigen-embryo space. Read the ISBI2006 paper on the MinMaxPartition MSTCUT method for image clustering and the RECOMB2004 paper on hybrid Gaussian mixture model (GMM) to retrieve genes that have similar expression pattern images.
mRMR feature selection
Minimum Redundancy Maximum Relevance (mRMR) gene selection scheme which is promising in detecting highly discriminant gene markers for cancer classification and is very efficient in optimizing the Max-Dependency/Min-Error feature selection criterion. Read a theory-paper on IEEE Transactions on Pattern Analysis and Machine Intelligence (2005), and a result-paper on Journal of Bioinformatics and Computational Biology (2005). You can run the program here.
BMA for brain images
Automatical detection of brain regions in 3D MR images corresponding to clinical function deficits such as mild cognitive impairment (MCI) and Alzheimer's Disease. Read the Bayesian Morphometry paper in IEEE Transactions on Medical Imaging (2004) and an application study for real MCI data.

 

Selected publications

[Highly Downloaded | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 and Earlier]

DISCLAIMER: These materials are presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder. Also note that the software posted below cannot be re-distributed in any form without explicit permission from me.

Highly Downloaded Papers

"Automatic tracing of ultra-volumes of neuronal images"

Peng, H., Zhou Z., Meijering, E., Zhao, T., Ascoli, G., and Hawrylycz, M.
Nature Methods,
Vol. 14, pp. 332-333, DOI: 10.1038/nmeth.4233, 2017. [Journal version | Preprint]

"TeraFly: real-time 3D visualization and 3D annotation of terabytes of multidimensional volumetric images"

Bria, A., Iannello, G., Onofri, L., and Peng, H.
Nature Methods,
Vol. 13, pp. 192-194, DOI: 10.1038/nmeth.3767, 2016. [Journal version]

"BigNeuron: large-scale 3D neuron reconstruction from optical microscopy images"

Peng, H., Hawrylycz, M., Roskams, J., Hill, S., Spruston, N., Meijering, E., Ascoli, G.A
Neuron,
DOI: http://dx.doi.org/10.1016/j.neuron.2015.06.036, Vol. 87, No. 2, pp. 252-256, 2015. [ Journal web version | PDF]

"Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis"

Peng, H., Tang, J., Xiao, H., Bria, A., et al.,
Nature Communications,
DOI: 10.1038/ncomms5342, 2014. [Open Access paper | Press Release | Software ]

"Extensible visualization and analysis for multidimensional images using Vaa3D"

Peng, H., Bria, A., Zhou, Z., Iannello, G., and Long, F.,
Nature Protocols,
Vol. 9, No. 1, pp. 193-208, 2014. [PDF | Software ]

"V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets"

Peng, H., Ruan, Z., Long, F., Simpson, J.H., and Myers, E.W.
Nature Biotechnology,
Vol.28, No.4, pp.348-353, DOI:10.1038/nbt.1612, 2010. [ PDF | Journal version | HHMI Press Release | Nature Methods Highlight | Software ]

"BrainAligner: 3D registration atlases of Drosophila brains"

Peng, H., Chung, P., Long, F., Qu, L., Jenett, A., Seeds, A., Myers, E.W., and Simpson, J.H.
Nature Methods,
Vol. 8, No. 6, pp.493-498, DOI: 10.1038/nmeth.1602, 2011. [PDF | Journal version with Supplements | Nature Methods News and Views: 'Bringing fly brains in line' | BrainAligner Software]

"A 3D digital atlas of C. elegans and its application to single-cell analyses"

Long, F.*, Peng, H.*, Liu, X., Kim, S. and Myers, E.W. (*equal contribution)
Nature Methods,
Vol. 6, No. 9, pp. 667-672, DOI:10.1038/nmeth.1366, 2009. [ PDF | Supplements | CellExplorer Software | Nature Methods News and Views: 'Google earthworm']

"Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy,"

Peng, H., Long, F., and Ding, C.
IEEE Transactions on Pattern Analysis and Machine Intelligence,
Vol. 27, No. 8, pp.1226-1238, 2005. [ PDF]

(Run the mRMR program.)

"Bioimage informatics: a new area of engineering biology"

Peng, H.
Bioinformatics,
Vol. 24, No. 17, pp. 1827-1836, 2008. [PDF]

2017 Papers

"Automatic tracing of ultra-volumes of neuronal images"

Peng, H., Zhou Z., Meijering, E., Zhao, T., Ascoli, G., and Hawrylycz, M.
Nature Methods,
Vol. 14, pp. 332-333, DOI: 10.1038/nmeth.4233, 2017. [Journal version | Preprint]

"Fast assembling of neuron fragments in serial 3D sections"

Chen, H., Iascone, D.M., da Costa, N., Lein, E., Liu, T., and Peng, H.,
Brain Informatics,
DOI: 10.1007/s40708-017-0063-9, 2017. [Journal Open Access version]

"Ensemble neuron tracer for 3D neuron reconstruction"

Wang, C.W., Lee, Y., Pradana, H., Zhou, Z., and Peng, H..
Neuroinformatics,
doi:10.1007/s12021-017-9325-1, 2017. [Preprint]

"3D neuron tip detection in volumetric microscopy images using an adaptive ray-shooting model"

Liu, M., Gong, R., Chen, W., and Peng, H.
Pattern Recognition,
DOI: 10.1016/j.patcog.2017.02.010, 2017. [Preprint]

2016 Papers

"TeraFly: real-time 3D visualization and 3D annotation of terabytes of multidimensional volumetric images"

Bria, A., Iannello, G., Onofri, L., and Peng, H.
Nature Methods,
Vol. 13, pp. 192-194, DOI: 10.1038/nmeth.3767, 2016. [Journal version]

"Imagining the future of bioimage analysis"

Meijering, E., Carpenter, A., Peng, H., Hamprecht, F., and Olivo-Marin, J.C.
Nature Biotechnology,
Vol. 34, pp. 1250-1255, DOI: 10.1038/nbt.3722, 2016. [Journal version]

"To the cloud! A grassroots proposal to accelerate brain science discovery"

Neuro Cloud Consortium
Neuron,
http://dx.doi.org/10.1016/j.neuron.2016.10.033, 2016. [Journal version]

"Inferring cortical function in the mouse visual system through large-scale systems neuroscience"

Hawrylycz, M., Anastassiou, C., ..., Peng, H., ...
PNAS,
Vol. 113, no. 27, pp. 7337-7344, 2016.

"Deep models for brain EM image segmentation: novel insights and improved performance"

Fakhry, A., Peng, H., and Ji, S.
Bioinformatics,
DOI: 10.1093/bioinformatics/btw165, 2016. [Journal version]

"Rivulet: 3D Neuron Morphology Tracing with Iterative Back-Tracking"

Liu, S.Q., Zhang, D., Li, S.D., Feng, D., Peng, H., and Cai, W.D.
Neuroinformatics,
DOI: 10.1007/s12021-016-9302-0, 2016.

"Reconstructing the brain: from image stacks to neuron synthesis"

Shillcock , J.C., Hawrylycz, M., Hill, S., and Peng, H.
Brain Informatics,
DOI: 10.1007/s40708-016-0041-7, 2016. [Open access journal version]

"Bioimage informatics for big data"

Peng, H., Zhou, J., Zhou, Z., Bria, A., Li, Y., Kleissas, D.M., Drenkow, N.G., Long, B., Liu, X., and Chen, H.
Advances in Anatomy, Embryology and Cell Biology,
Vol. 219, pp. pp 263-272, DOI: 10.1007/978-3-319-28549-8_10, 2016. [Journal version]

"TReMAP: automatic 3d neuron reconstruction based on tracing, reverse mapping and assembling of 2d projections"

Zhou, Z, Liu, X., Long, B., and and Peng, H.
Neuroinformatics,
Vol. 14, No. 1, pp. 41-50. DOI: 10.1007/s12021-015-9278-1, 2016. [Preprint PDF]

2015 Papers

"3D Image-guided automatic pipette positioning for single cell experiments in vivo"

Long, B., Li, L., Knoblich, U., Zeng, H., and Peng, H.
Scientific Reports,
doi:10.1038/srep18426, 2015. [Open Access paper]

"BigNeuron: large-scale 3D neuron reconstruction from optical microscopy images"

Peng, H., Hawrylycz, M., Roskams, J., Hill, S., Spruston, N., Meijering, E., Ascoli, G.A
Neuron,
DOI: http://dx.doi.org/10.1016/j.neuron.2015.06.036, Vol. 87, No. 2, pp. 252-256, 2015. [ Journal web version | PDF]

"From DIADEM to BigNeuron"

Peng, H., Meijering, E., Ascoli, G.,
NeuroInformatics,
DOI: 10.1007/s12021-015-9270-9, 2015, [Open Access Paper]

"Blastneuron for automated comparison, retrieval and clustering of 3d neuron morphologies"

Wan, Y., Long, F., Qu, L., Xiao, H., Hawrylycz, M., Myers, E., Peng, H.,
NeuroInformatics,
DOI 10.1007/s12021-015-9272-7, 2015. [Preprint PDF]

"SmartTracing: self-learning based neuron reconstruction"

Chen, H., Xiao, H., Liu, T., and Peng, H.
Brain Informatics,
DOI: 10.1007/s40708-015-0018-y, 2015. [Open Access paper]

"3-D registration of biological images and models: registration of microscopic images and its uses in segmentation and annotation"

Qu, L., Long, F., Peng, H.,
IEEE Signal Processing Magazine,
Vol. 32, No. 1, pp.70-77, 2015. [PDF]

"Interactive exemplar-based segmentation toolkit for biomedical image analysis"

Li, X., Zhou, Z., Keller, P., Zeng, H., Liu, T., and Peng, H.,
ISBI-2015,
pp.168-171, 2015. [PDF]

2014 Papers

"Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis"

Peng, H., Tang, J., Xiao, H., Bria, A., et al.,
Nature Communications,
DOI: 10.1038/ncomms5342, 2014. [Open Access paper | Press Release | Software ]

"Extensible visualization and analysis for multidimensional images using Vaa3D"

Peng, H., Bria, A., Zhou, Z., Iannello, G., and Long, F.,
Nature Protocols,
Vol. 9, No. 1, pp. 193-208, 2014. [PDF | Software ]

"Adaptive image enhancement for tracing 3d morphologies of neurons and brain vasculatures"

Zhou, Z., Sorensen, S., Zeng, H., Hawrylycz, M., and Peng, H.,
NeuroInformatics,
DOI: 10.1007/s12021-014-9249-y, 2014. [PDF]

"LittleQuickWarp: an ultrafast image warping tool"

Qu, L., Peng, H.,
Methods,
DOI: 10.1016/j.ymeth.2014.09.002, 2014. [Paper]

"A mesoscale connectome of the mouse brain"

Oh, S.W., Harris, J.A., Ng, L., ..., Peng, H., ..., Zeng, H.,
Nature,
doi:10.1038/nature13186, 2014. [Paper]

"Constructing 5D developing gene expression patterns without live animal imaging"

Peng, H., Myers, E.W.,
Biomedical Engineering Letters,
Vol. 4, No. 4, pp. 338-346, 2014. [paper]

"Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience"

Heckscher, E.S., Long, F., ..., Peng, H., Myers, E.W., Doe, C.,
Development,
Vol. 141, pp. 2524-2532, 2014. [PDF]

"Wiring economy can account for cell body placement across species and brain areas"

Rivera-Alba, M., Peng, H., de Polavieja G.G., and Chklovskii, D.B.,
Current Biology,
Vol. 24, No. 3, R109-R110, 2014. [Paper]

2013 Papers

"Automated image computing reshapes computational neuroscience"

Peng, H., Roysam, B., and Ascoli, G.,
BMC Bioinformatics,
Vol. 14, No. 293, doi:10.1186/1471-2105-14-293, 2013. [Open Access Paper]

"APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of gray-weighted image distance-trees"

Xiao, H., and Peng, H.,
Bioinformatics,
Vol. 29, No. 11, pp. 1448-1454, 2013. [PDF | Supplement]

"BIOCAT: a pattern recognition platform for customizable biological image classification and annotation"

Zhou, J., Lamichhane, S., Sterne, G., Ye, B., and Peng, H.,
BMC Bioinformatics,
Vol. 14, No. 291, doi:10.1186/1471-2105-14-291, 2013. [Open Access Paper]

"Micron-scale resolution optical tomography of entire mouse brains with confocal light sheet microscopy"

Silvestri, L., Bria, A., Costantini, I., Sacconi, L., Peng, H., Iannello, G., and Pavone, F.S.,
Journal of Visualized Experiments (JoVE),
Vol. 80, e50696, doi:10.3791/50696, 2013. [Paper]

"Eight pairs of descending visual neurons in the dragonfly give wing motor centers accurate population vector of prey direction"

Gonzalez-Bellido, P., Peng, H., Yang, J., Georgopoulos, A.P., and Olberg, R.M.,
PNAS,
Vol. 110, No. 2, pp. 696-701, 2013. [PDF | Commentary by Nordstrom | PNAS Annual Paper Award ]

"A distance-field based automatic neuron tracing method"

Yang, J., Gonzalez-Bellido, P., and Peng, H.
BMC Bioinformatics,
Vol. 14, No. 93, doi:10.1186/1471-2105-14-93, 2013. [Open Access Paper]

"Automated cellular annotation for high resolution images of adult C. elegans"

Aerni, SJ., Liu, X., Do, CB, Gross, SS, Nguyen, A., Guo, SD, Long, F., Peng, H., Kim, SS, and Batzoglou, S.,
Bioinformatics,
Vol. 29, No. 13, pp. i18-i26, 2013. [PDF]

"Clonal development and organization of the adult Drosophila central brain"

Yu, H.H., Awasaki, T., Schroeder, M., Long, F., Yang, J.S., He, Y., Ding, P. Kao J., W. G., Peng, H., Myers, G., and Lee, T.,
Current Biology,
Vol. 23, pp. 1-11, http://dx.doi.org/10.1016/j.cub.2013.02.057, 2013. [PDF]

2012 Papers

"Visualization and analysis of 3D microscopic images"

Long, F., Zhou, J., and Peng, H.
PLoS Computational Biology,
Vol. 8, No. 6, pp. e1002519. doi:10.1371/journal.pcbi.1002519, 2012. [PDF]

"A GAL4-driver line resource for Drosophila neurobiology"

Jenett, A., Rubin, G., ..., Peng, H., ..., and Zugates, C.
Cell Reports,
Vol. 2, pp. 1-11. 2012. [PDF]

"Biological imaging software tools"

Eliceiri, K.W., Berthold, M.R., Goldberg, I.G., Ibanez, L., Manjunath, B.S., Martone, M.E., Murphy, R.F., Peng, H., Plant, A.L., Roysam, B., Stuurmann, N., Swedlow, J.R., Tomancak, P., and Carpenter, A.E.
Nature Methods,
Vol. 9., No. 7, pp. 697-710, 2012.

"mGRASP enables mapping mammalian synaptic connectivity with light microscopy"

Kim, J., Zhao, T., Petralia, R.S., Yu, Y., Peng, H., Myers, E.W., and Magee, J.C.,
Nature Methods,
Vol. 9., No. 1, pp. 96-102, 2012. [PDF]

"Bioimage informatics: a new category in Bioinformatics"

Peng, H., Bateman, A., Valencia, A., and Wren, J.D.
Bioinformatics,
Vol. 28, No. 8, pp. 1057, 2012. [PDF]

2011 Papers

"BrainAligner: 3D registration atlases of Drosophila brains"

Peng, H., Chung, P., Long, F., Qu, L., Jenett, A., Seeds, A., Myers, E.W., and Simpson, J.H.
Nature Methods,
Vol. 8, No. 6, pp.493-498, DOI: 10.1038/nmeth.1602, 2011. [PDF | Journal HTML version with Supplements | Nature Methods News and Views: 'Bringing fly brains in line' | BrainAligner Software]

"Simultaneous recognition and segmentation of cells: application in C. elegans"

Qu, L., Long, F., Liu, X., Kim, S., Myers, E.W., and Peng, H.
Bioinformatics,
Vol. 27, No. 20, pp.2895-2902, 2011. [Open Access journal version | Supplement Figures/Data]

"Automatic 3D neuron tracing using all-path pruning"

Peng, H., Long, F., and Myers, E.W.
Bioinformatics,
Vol. 27, No. 13, pp.i239-i247, DOI: 10.1093/bioinformatics/btr237, 2011. [PDF]

"Proof-editing is the bottleneck of 3D neuron reconstruction: the problem and solutions"

Peng, H., Long, F., Zhao, T., and Myers, E.W.
Neuroinformatics,
Vol. 9, No. 2-3, pp.103-105, 2011. [PDF]

"Automated high speed stitching of large 3D microscopic images"

Yu, Y., and Peng, H.
Proc. of IEEE 2011 International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'2011),
pp.238-241, 2011. [PDF ]

2010 and Earlier

"V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets"

Peng, H., Ruan, Z., Long, F., Simpson, J.H., and Myers, E.W.
Nature Biotechnology,
Vol.28, No.4, pp.348-353, DOI:10.1038/nbt.1612, 2010. [ PDF | Journal version | HHMI Press Release | Nature Methods, Research Highlight | Software ]

"Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model"

Peng, H., Ruan, Z., Atasoy, D., and Sternson, S.
Bioinformatics,
Vol.26, pp. i38-i46, 2010. [PDF]

"A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems "

Qu, L. and Peng, H.
Bioinformatics,
Vol.26, No.8, pp.1091-1097, 2010. [ PDF | Supplementary Videos, Figures, Programs, and Data ]

"Segmentation of center brains and optic lobes in 3D confocal images of adult fruit fly brains"

Lam, S.C.B., Ruan, Z., Zhao, T., Long, F., Jenett, A., Simpson, J.H., Myers, E.W., and Peng, H.
Methods,
Vol.50, No.2, pp.63-69, 2010. [PDF ]

"A 3D digital atlas of C. elegans and its application to single-cell analyses"

Long, F.*, Peng, H.*, Liu, X., Kim, S., and Myers, E.W. (*equal contribution)
Nature Methods,
Vol. 6, No. 9, pp. 667-672, doi:10.1038/nmeth.1366, 2009. [ PDF | Supplements | CellExplorer Software | Nature Methods News and Views: 'Google earthworm']

"Analysis of cell fate from single-cell gene expression profiles in C. elegans"

Liu, X., Long, F., Peng, H., Aerni, S.J., Jiang, M., Sanchez-Blanco, A., Murray, J.I., Preston, E., Mericle, B., Batzoglou, S., Myers, E.W., and Kim, S.
Cell,
Vol. 139, pp. 623-633, 2009. [PDF]

"VANO: a volume-object image annotation system"

Peng, H., Long, F., and Myers, E.W.
Bioinformatics,
Vol. 25, No. 5, pp. 695-697, 2009. [ PDF | software]

"Bioimage informatics: a new area of engineering biology"

Peng, H.
Bioinformatics,
Vol. 24, No. 17, pp. 1827-1836, 2008. [PDF]

"Automatic recognition of cells (ARC) for 3D images of C. elegans"

Long, F., Peng, H., Liu, X., Kim, S., and Myers, E.W.
Lecture Notes in Computer Science: Research in Computational Molecular Biology (Proc. of RECOMB 2008, Singapore, March 30 - April 2, 2008),
Springer Berlin / Heidelberg, pp. 128-139, 2008. [Preprint]

"Straightening C. elegans images"

Peng, H., Long, F., Liu, X., Kim, S., and Myers, E.W.
Bioinformatics,
Vol. 24, No. 2, pp. 234-242, 2008. [Preprint in color | Open-access journal version | Demo program]

"Data driven decomposition for multi-class classification"

Zhou, J., Peng, H., and Suen, C.Y.
Pattern Recognition,
Vol. 41, pp. 67-76, 2008. [PDF]

"Automatic image analysis for gene expression patterns of fly embryos"

Peng, H., Long, F., Zhou, J., Leung, G., Eisen, M.B., and Myers, E.W.
BMC Cell Biology,
Vol. 8, No. Supp.1, pp.S7, 2007. [Open-access journal version | Preprint | a simple fly embryonic pattern browser]

"Automatic recognition and annotation of gene expression patterns of fly embryos"

Zhou, J.*, and Peng. H.* (*equal contribution)
Bioinformatics,
Vol. 23, No. 5, pp. 589-596, 2007. [PDF | Supplementary Materials]

"Phenotype clustering of breast epithelial cells in confocal images based on nuclear protein distribution analysis"

Long, F., Peng, H., Sudar, D., Lelievre, S., and Knowles, D.
BMC Cell Biology,
Vol. 8, No. Supp.1, pp.S3, 2007. [Open-access journal version]

"Transitive closure and metric inequality of weighted graphs - detecting protein interaction modules using cliques,"

Ding, C., He, X., Xiong, H., Peng, H., and Holbrook, S.R.
International Journal of Data Mining and Bioinformatics,
Vol. 1, No. 2, pp.162-177, 2006. [Paper]

"Clustering gene expression patterns of fly embryos,"

Peng, H., Long, F., Eisen, M.B., and Myers, E.W.
Proc. IEEE 2006 International Symposium on Biomedical Imaging (ISBI 2006),
pp.1144-1147, Washington DC, April 6-9, 2006. [PDF]

"Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy,"

Peng, H., Long, F., and Ding, C.
IEEE Transactions on Pattern Analysis and Machine Intelligence,
Vol. 27, No. 8, pp.1226-1238, 2005. [PDF]

(Run the mRMR program.)

"Minimum redundancy maximum relevance feature selection,"

Peng, H., Ding, C., and Long, F.
IEEE Intelligent Systems,
Vol. 20, No. 6, pp.70-71, November/December, 2005. [PDF]

"Minimum redundancy feature selection from microarray gene expression data,"

Ding, C., and Peng, H.
Journal of Bioinformatics and Computational Biology,
Vol. 3, No. 2, pp.185-205, 2005. [PDF]

(A conference version with a different set of results, but the same title, also appeared on:
Proc. 2nd IEEE Computational Systems Bioinformatics Conference (CSB 2003),
pp.523-528, Stanford, CA, Aug, 2003. [PDF])

"Comparing in situ mRNA expression patterns of Drosophila embryos,"

Peng, H., and Myers, E.W.
Proc. 8th Annual Int. Conf. on Research in Computational Molecular Biology (RECOMB 2004),
pp.157-166, San Diego, USA, Mar, 2004. [PDF]

"A Bayesian morphometry algorithm,"

Herskovits, E., Peng, H., and Davatzikos, C.
IEEE Transactions on Medical Imaging,
Vol.24, No.6, pp.723-737, 2004. [PDF]

(This is an extended journal version of the following earlier ISBI paper.)

"Bayesian clustering methods for morphological analysis of MR images,"

Peng, H., Herskovits, E.H., and Davatzikos, C.,
Int. Symp. on Biomedical Imaging: from Nano to Macro,
pp.485-488, Washington, D.C., July, 2002. [PDF]

An electronic demo were also given at 2002 NIH Human Brain Project Annual Meeting,
Washington, D.C., May, 2002. [HTML])

A study using real BLSA Mild Cognitive Impairment data is the following report:

"Bayesian analysis of morphological changes associated with mild cognitive impairment: a cross-sectional study,"

Peng, H., Shen, D., Davatzikos, C., Resnick, S., and Herskovits, E.H.
Technical Report,
Johns Hopkins University, School of Medicine, Dept. of Radiology, 2002. [PDF]

"Structural search and stability enhancement of Bayesian networks,"

Peng, H., and Ding, C.
Proc. 3rd IEEE Int. Conf. Data Mining (ICDM 2003),
pp.621-624, Melbourne, Florida, USA, Nov, 2003. [PDF]

"Document image recognition based on template matching of component block projections,"

Peng, H., Long, F., and Chi, Z.
IEEE Transactions on Pattern Analysis and Machine Intelligence,
Vol.25, No.9, pp.1188-1192, 2003. [PDF]

 
 
   
           
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