Publications

Articles

[ LINK ]: Pinskiy V, Jones J, Tolpygo A, Franciotti N, Weber K, Mitra PP (2015). High-throughput method of whole-brain sectioning, using the tape-transfer technique. PLoS ONE 10(7): e0102363. doi: 10.1371/journal.pone.0102363.

LINK ]: Pinskiy V, Tolpygo AS, Jones J, Weber K, Franciotti N, Mitra PP (2013). A low-cost technique to cryo-protect and freeze rodent brains, precisely aligned to stereotaxic coordinates for whole-brain cryosectioning. Journal Neuroscience Methods 218(2), 206-213.

LINK ]: Menashe I, Grange P, Larsen EC, Banerjee-Basu S,  Mitra PP (2013). Co-expression Profiling of Autism Genes in the Mouse Brain. PLOS Computational Biology9(7): e1003128.

[ PDF ]: Grange P, Hawrylycz M, Mitra PP (2012). Computational Neuroanatomy and Co-expression of Genes in the Adult Mouse Brain, Analysis Tools for the Allen Brain Atlas. Quantitative Biology 0002 (2012).

[ PDF ]: Grange P, Mitra PP (2012). Computational Neuroanatomy and Gene Expression: Optimal Sets of Marker Genes for Brain Regions. IEEE, 46th annual Conference on Information Sciences and Systems, Princeton 2012.

[ PDF ] : Bohland JW, Bokil H, Pathak SD, Lee CK, Ng L, Lau C, Kuan C, Hawrylycz M, Mitra PP (2010). Clustering of Spatial Gene Expression Patterns in the Mouse Brain, and Comparison with Classical Neuroanatomy. Methods 50 (2010) 105–112.

[ PDF LINK]: Bohland JW, Wu C, Barbas H, Bokil H, Cline HT, Freed PJ, Greenspan RJ, Haber SN, Hawrylycz M, Herrera DG, Hilgetag CC, Huang ZJ, Jones A, Jones EG, Karten HJ, Kleinfeld D, Kotter R, Lester HA, Lin JM, Mikula S, Panksepp J, Safdieh J, Saper CB, Schiff ND, Stillman BW, Svoboda K, Swanson LW, Toga AW, Watson JD, Mitra PP (2009). A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale. PLoS Computational Biology. 5(3): e1000334.

[ PDF | LINK ] : Bohland JW, Bokil H, Allen CB, Mitra PP. The brain atlas concordance problem: quantitative comparison of anatomical parcellations. PLoS One. 2009 Sep 29;4(9):

[ PDF ] : Ng L, Bernard A, Lau C, Overly CC, Dong HW, Kuan C, Pathak S, Sunkin SM, Dang C, Bohland JW, Bokil H, Mitra PP, Puelles L, Hohmann J, Anderson DJ, Lein ES, Jones AR & Hawrylycz M (2009). An Anatomic Atlas of the Adult Mouse Brain. Nature Neuroscience 12(3), 356-362.

LINK ] : Lin JM, Bohland JW, Andrews P, Burns GA, Allen CB, Mitra PP (2008). An analysis of the abstracts presented at the annual meetings of the Society for Neuroscience from 2001 to 2006. PLoS One, 3(4): e2052.

Conference Posters

2014

PDF ] : Carmel, J. B., Mechler, F., Mukherjee, A., Wen, T., Tolpygo, A., Mitra, P., Whole rat brain analysis of anterograde tracers from motor cortex and retrograde tracers from cervical spinal cord: Validation of an efficient, automated method with stereology (2014). Meeting of the Society for Neuroscience, Washington, D.C.

PDF ] : Giese, G., Scherbarth, A., Pinskiy, V., Tolpygo, A., Mechler, F., Mitra, P., Combining brain clearing and light-sheet fluorescence microscopy with tape-transfer assisted sectioning and histochemistry for whole mouse brain and spinal cord imaging (2014). Meeting of the Society for Neuroscience, Washington, D.C.

PDF ] : Geyer, S., Reimann, K., Weiss, M., Rose, D., Silva, A. C., Rosa, M. G. P., Pinskiy, V., Tolpygo, A., Mitra, P. P., Turner, R., The microanatomical origin of the high-field magnetic resonance imaging signal in the marmoset cerebral cortex: myelin sheaths or cell bodies? (2014). Meeting of the Society for Neuroscience, Washington, D.C.

Previous years

PDF ] : Shewcraft, R., Pinskiy, V., Tolpygo, A., Mukherjee, A., Putrino, D., Wong, Y. T., Mitra, P. P., Pesaran, B. Dissecting long-range circuits in macaque cortex by registering optogenetically driven neural activity with anatomical connectivity (2013). Meeting of the Society for Neuroscience, San Diego, CA. 

[PDF ] : Mukherjee, A., Mechler, F., Pinsksiy, V., Tolpygo, A., Grange, P., Mitra, P. Software tools for reconstruction of 3D projection patterns for injection-based tractography (2013). Meeting of the Society for Neuroscience, San Diego, CA.

[ PDF ] : Grange, P., Mukherjee, A., Pinskiy, V., Tolpygo, A., Zheng, L., Uchida, N., Watabe-Uchida, M., Mitra, P. Automated analysis of the density of monosynaptic inputs to VTA dopamine neurons (2013). Meeting of the Society for Neuroscience, San Diego, CA. 

[ PDF ] : Sorooshyari, S., Pinskiy, V., Tolpygo, A., Mitra, P.  Quantitative modeling of tracer injections into brain tissue (2013). Meeting of the Society for Neuroscience, San Diego, CA.

[ PDF ] : Pinskiy, V., Mukherjee, A., Tolpygo, A., Badea, A., Johnson, A.G., Mitra, P. P. Combining high resolution mri and dti with dense whole-brain histology for mouse (2013). Meeting of the Society for Neuroscience, San Diego, CA.

PDF ] : Grange P., Bohland J. W., Hawrylycz, M., Mitra, P. P. A software suite for multivariate analysis of brain-wide gene-expression maps (2012). Meeting of the Society for Neuroscience, New Orleans, LA.

PDF ] : Pinskiy V, Tolpygo AS, Franciotti N, Weber K, Mitra PP. Whole Skull and Spinal Cord Cryosectioning of Adult Mouse (2012). Meeting of the Society for Neuroscience, New Orleans, LA.

PDF ] : Grange P, Okaty BW, Nelson SB, Hawrylycz M, Mitra PP, Distribution of cell types in the mouse brain from the Allen Atlas of the adult mouse brain (2012). Society for Neuroscience Meeting, Washington, DC.

PDF ] : Mukhopadhyay S, Grange P, Sengupta A, Mitra PP, Inferences about brain evolution from brain-wide gene-expression maps (2012). Society for Neuroscience Meeting, Washington, DC.

PDF ] : Pinskiy V, Krishnan K, Mukhopadhyay S, Collins Z, Tolpygo AS, Huang JZ, Mitra PP, High-Throughput Whole Brain Neuroanatomical mapping of GABAergic cell types in C57BL/6 mice (2011). Society for Neuroscience Meeting, Washington, DC.

PDF ] : Pinskiy V, Jones J, Wang H, Cox H, Mitra PP. Tape-transfer assisted cryosectioning for the Mouse Brain Architecture Project (2010). Meeting of the Society for Neuroscience, San Diego, CA.

PDF ] : Grange P, Pologruto T, Pinskiy V, Wang H, Khabbaz A, Spring S, Yu L, Germann J, Henkelman M, Mitra PP. Computer-guided stereotactic injections for the Mouse Brain Architecture Project (2010). Meeting of the Society for Neuroscience, San Diego, CA.

PDF ] : Grange P and Mitra PP.  Marker genes and the anatomy of the mouse brain (2010). Meeting of the Society for Neuroscience, San Diego, CA.

PDF ] : Bohland JW, Bokil, H Pathak S, Lin JM, Lee CK, Ng L, Osorio-Duque F, Lau C, Herrera D, Hawrylycz M, Mitra PP. Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy (2008). Meeting of the Society for Neuroscience, Washington, D.C.

PDF ] : Bokil H, Bohland JW, Pathak S, Lin JM, Lee CK, Ng L, Osorio-Duque F, Lau C, Herrera D, Hawrylycz M, Mitra PP. Spatial correlation and localization patterns of gene expression in the mouse brain (2008). Meeting of the Society for Neuroscience, Washington, D.C.

[ PDF ] : Lin JM, Bohland JW, Andrews PA, Iossifov I, Yankama B, Kulkarni J, Wu C, Berwick RC, Di Sciullo AM, Mitra PP. A literature mining and curation system for neuroscience knowledge discovery (2008). Meeting of the Society for Neuroscience, Washington, D.C.

[ PDF ] : Bohland JW, Bokil H, Wu C, Breiter HC, Makris N, Kennedy DN, Allen CB, Mitra PP. Quantitative comparison of anatomical parcellation schemes for MRI (2007). Meeting of the Society for Neuroscience, San Diego, CA.

[ PDF ] : Lin JM, Andrews PA, Burns GA, Bohland JW, Allen CB, Mitra PP. Community structure of neuroscience research: inferences from a co-authorship graph of Society for Neuroscience meeting abstracts (2007). Meeting of the Society for Neuroscience, San Diego, CA.

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