Publications / Presentations

Peer Reviewed Journals

Published/Acepted

• Lu Y, Lau C, Ng L, Gong L, Kinahan P, Alessio A, Goldschneider J, and Pathak SD , “FusionViewer: An Open Source Toolkit for Viewing Multimodality Images,” The Insight Journal (open-source), Jan 2008.

• Lau C, Ng L, Thompson C, Pathak SD, Kuan L, Jones A, and Hawrylycz M, “Exploration and visualization of gene expression with neuroanatomy in adult mouse brain”, BMC Bioinformatics,vol 9, p 153, 2008. Highly Accessed

• Wisor J, Pasumarthi R, Geraschenko D, Thompson CL, Pathak SD, Sancar A, Franken P, Lein E and Kilduff T, “Sleep Deprivation Effects on Circadian Clock Gene Expression in the Cerebral Cortex Parallel Electroencephalographic Differences Among Mouse Strains”, J. Neuroscience, accepted April 2008.

• Lee CK, Sunkin SM, Kuan C, Thompson C, Pathak SD, Ng, L, Lau, C, Fishcer S, Mortrud, M, Slaughterbeck C, Jones A, Lein ES, and Hawrylycz M, “Quantitative methods for genome-scale analysis of in-situ hybridization and correlation with microarray data,” Genome Biology, vol. 9, R23, 2008.

• Tutar IB, Gong L, Narayanan S, Pathak SD Cho PS, Wallner K, and Kim Y, ”Seed-based transrectal ultrasound fluoroscopy registration method for intraoperative dosimetry analysis of prostate brachytherapy," Medical Physics, vol. 35, p 840, 2008.

• Lein ES, Hawrylycz M, Pathak SD (listed in alphabetical order with other 106 authors) et al.,”Refining cellular neuroanatomy through unbiased genome wide survey of gene expression in the brain”, Nature, vol 11, 168-76, 2007.

• Pathak SD, Lau C, and Hawrylycz, “ Non-negative matrix factorization framework for dimensionality reduction and unsupervised clustering,” The Insight Journal (open-source), Jun 2007.

• Ng L, Pathak SD, Kuan L, Lau C, Dong HW, Sodt A, Dang C, Gee J, Lein E, Jones A, and Hawrylycz M, “Genomics scale neuroinformatics for 3-D gene expression mapping”, IEEE/ACM Trans. Computational Biology and Bioinformatics, vol 4, 382-393, 2007.

• Tutar, I.B., Pathak SD, Gong L, Cho, PS, Wallner, K, and Kim, Y, “Semi-automatic 3D Prostate Segmentation from TRUS Images using Spherical Harmonics,” IEEE Transactions on Medical Imaging, vol. 25, pp. 1645-1654, 2006.

• Gong L, Pathak SD, Allesio A, and Kinahan P., “Automatic arm removal in PET and CT images for deformable registration,” Computerized Medical Imaging and Graphics, vol. 30, pp. 469-477, 2006.

• Gong L, Pathak SD, Haynor D, Cho P, and Kim Y, “Parametric shape modeling using deformable superellipse for prostate segmentation,” IEEE Transactions on Medical Imaging, vol. 23, no. 3, pp. 340-349, 2004.

• Haberman K, Pathak SD, and Kim Y, “Effects of Video Digitization in Pubic Arch Interference Assessment for Prostate Brachytherapy,” IEEE Transactions on Information Technology in Biomedicine, vol. 8, no. 10, pp. 451-458, 2003.

• Pathak SD, Wyman B, Ng L, Fogarasi S, Racki S, Oelund JC, Sparks BF, and Chalana V, “Quantitative image analysis: software systems in drug development trials,” Drug Discovery Today, vol. 8, no. 10, pp. 451-458, 2003.

• Tutar IB, Managuli R, Shamdasani V, Cho PS, Pathak SD, Kim Y., “Tomosynthesis-based localization of radioactive seeds in prostate brachytherapy,” Medical Physics, vol. 30, no. 12, pp. 3135-42, 2003.

• Gong L, Cho P, Han B, Wallner K, Sutlief S, Pathak SD, Haynor D, and Kim Y, “Ultrasound and fluoroscopy data fusion towards intraoperative dosimetry for prostate brachytherapy,” International Journal of Radiation Oncology, Biology, Physics, vol. 54, pp. 1322-1330, 2002.

• Pathak SD , Chalana V, Haynor DH, and Kim Y, “Edge-guided boundary delineation in prostate ultrasound,” IEEE Transactions on Medical Imaging, vol. 19, pp. 1211-1219, 2000.

• Pathak SD, Grimm PD, Chalana V, and Kim Y, “Pubic arch detection in transrectal ultrasound guided prostate cancer therapy,” IEEE Transactions on Medical Imaging, vol. 17, pp. 762-771, 1998.

• Aarnink RG, Pathak SD, de la Rosette JJ, Debruyne FMJ, Kim Y, and Wijkstra H, “Edge detection in prostatic ultrasound images using integrated edge maps,” Ultrasonics, vol. 36, pp. 637-644, 1998.

• Pathak SD, Chalana V and Kim Y, “Interactive automatic fetal head measurements from ultrasound Images,” Ultrasound in Medicine and Biology, vol. 23, pp. 665-673, 1997.

Submitted / In preparation

• Pathak SD, Haynor DR, Thompson CL and Hawrylycz, M, “Non-negative Matrix Factorization with Markov Random Fields: Analysis of Spatial Data with Applications to Gene Expression in the Brain,” ACM Knowledge Discovery and Data Mining , submitted 2008.

• Thompson CL, MacPherson C, Pathak SD, Ng L, Cusick A, Schmeier S, Hoffman O, Kaur M, Riley Z, Hide WA, Sunkin S, Bernard S, Puchalski S, Gage FH, Hawrylycz M, Jones A, Bajic V, and Lein ES, “Molecular partitioning of the hippocampus into novel subdomains with implications for functional architecture and transcriptional regulation,” Neuron, submitted 2007.

• Ng L, Bernard A, Lau C, Dong HW, Kuan L, Pathak SD, Sunkin S, Dang C, Hohmann J, Lein E, Jones A and Hawrylycz M, “AGEA: An Anatomic Gene Expression Atlas of the C57BL\6J Adult Mouse Brain,” in preparation, Journal to be Decided.

• Pathak SD, Sunkin S, Lein ES and Hawrylycz M, “Spatio-genomic brainwide unsupervised exploration of the mouse brain gene co-expression network discovery,” in preparation, Journal To Be Decided (possibley PLOS Computational Biology).

Invited Talks

• Co-expression networks in the C57Bl/6J mouse brain.
  Pathak S, Howell M, Sunkin S, Jones A and Hawrylycz M, Invited talk at Systems Biology: Global Regulation of Gene Expression Meeting, Cold Spring Harbor Lab, New York, March 2008.

• Computational challenges in mapping the mammalian brainscape.
  Invited speaker in a workshop on Solving Computational Challenges in Medical Imaging, Univ. of Washington, Seatle , July 2007.

• Informatics of the mouse brain via machine learning
  Invited speaker at National Brain Research Center, New Delhi, India, Feb 2006.

• Computational methods for gene expression analysis in neuroscience.
  Organizer of a day long workshop on neuroinformatics at NIPS, Whistler, Canada, Dec 2005.

• Image processing research at Insightful.
  Molecular Imaging Seminar, Mass General Hospital, Boston, MA, March 2004.

• Medical image segmentation and registration with ITK.
  Medical Imaging Seminar Series, University of Washington, Seattle, WA, Fall 2002.

• On-line Dosimetry: The Horizon in Prostate Brachytherapy
  Medical Imaging Seminar Series, University of Washington, Seattle, WA, Fall 2002.

• Pubic Arch Interference (PAI) Assessment using Transrectal Ultrasound (TRUS) for Prostate Brachytherapy
  Radiology Society of North America (RSNA), Dec 1998.

• New Method to Determine Pubic Arch Interference in Prostate Brachytherapy
  Medical Imaging Seminar Series, University of Washington, Seattle, WA, Fall 1998.

• Quantitative three-dimensional trans-rectal ultrasound for prostate imaging
  Medical Imaging Seminar Series, University of Washington, Seattle, WA, Winter 1998.

• Near Real Time Automatic Fetal Head Measurements from Ultrasound Image
  Radiology Society of North America (RSNA), Chicago, IL, Dec 1996.

Conference Papers

• Dang C, Sodt A, Lau C, Youngstrom B, Ng L, Kuan L, Pathak SD, Jones A, and Hawrylycz M, "The Allen Brain Atlas: Delivering Neuroscience to the Web on a Genome Wide Scale.", DILS, pp.17-26 2007.

• Hohman, J, Ng. L. Kuan L, Pathak SD, Lein E, Jones A, and Hawrylycz, M, “Identification of genes with enriched expression in the arcuate nucleus of the hypothalamus using high-throughput in situ hybridization,” Society for Neuroscience Meeting, Washington DC, Oct 2006.

• Pathak SD, Lau C, Ng L., Kuan L, Lein E, and Hawrylycz, M, “Three dimensional mouse brain gene expression visualization and image based genomic level expression search,” Computational Neuroscience Meeting 2006, Edinburgh U.K., July 2006.

• Pathak SD, Lau C, Ng L, Kuan L, Sodt A, Kawal R and Hawrylycz M, “Mouse brain gene expression analysis using model based clustering,” IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Arlington VA, April 2006.

• Kinahan RE, MacDonald L, Ng L, Alessio A, Segars P, Tsui BMW, and Pathak SD, "Compensating for patient respiration in PET/CT imaging with the registered and summed phases (RASP) procedure, ISBI, pp. 1104-1107, 2006.

• Hawrylycz M, Chen L, Dang C, Dong H, Jones A, Kawal R, Kuan L, Larsen K, Lau C, Lein E, Ng. L, Pathak SD, Teemer C, Thompson C, Sodt A, Sunkin S and Wohnoutka P, “An automated informatics pipeline for computing 3D gene-expression atlases,” Soc. For Neuroscience, Washington DC, Nov. 2005.

• Pathak SD, Lein E, Smith S, Haynor DR, and Hawrylycz M, “Gene expression detection and expression visualization in in-situ hybridized cross-sectional images of the mouse brain.” SPIE Medical Imaging, vol. 5747, pp. 1112-1119, 2005.

• Lau C, Pathak SD, Gong L, Kinahan P, Cheng P, and Ng L, “Advanced PET/CT fusion workstation for oncology imaging,” SPIE Medical Imaging, vol. 5744, pp. 670-676, 2005.

• Gong L, Ng L, Pathak SD, Tutar I, Cho PS, Haynor DR and Kim Y, “Prostate ultrasound image segmentation using level set based region flow with shape guidance,” SPIE Medical Imaging, vol. 5747, pp. 1648-1657, 2005.

• Cho P, Narayanan S, Lam S, Pathak SD, Tutar I, Gong L, Kim Y, and Wallner K, “Dynamic brachytherapy: intra-operative dose optimization using dual-modality imaging,” The 14th International Conference on the Use of Computers in Radiation Therapy, 2004.

• Gong L, Pathak SD, Haynor D, Cho P, and Kim Y, “Prostate segmentation in ultrasound images with deformable shape priors,” SPIE Medical Imaging, vol. 5029, pp. 535-543, 2003.

• Gong L, Cho P, Han B, Pathak SD, Haynor D, Wallner K, Sutlief S, and Kim Y, “Registration of prostate brachytherapy seeds with prostate anatomy for improved post-implant dosimetry,” SPIE Medical Imaging, vol. 4681, pp. 567-575, 2002.

• Gong L, S. Pathak SD, and Y. Kim, “Selective contrast enhancement of prostate ultrasound images using sticks with high-level information,” SPIE Medical Imaging, vol. 4319, pp. 615-622, 2001.

• Haberman K, Pathak SD, Grimm PD, Moran BJ and Kim Y, “JPEG compression of ultrasound images and its effects in predicting pubic arch interference for prostate brachytherapy,” SPIE Medical Imaging, vol. 3976: 552-562, 2000.

• Haberman K, Pathak SD and Kim Y, “Effects of video digitization of ultrasound images in predicting pubic arch interference for prostate brachytherapy,” SPIE Medical Imaging, vol. 3976, pp. 196-207, 2000.

• Pathak SD, and Kim Y, “Improving contrast of edges in ultrasound images using a priori transducer position information,” SPIE Medical Imaging, vol. 3976, pp. 563-572, 2000.

• Pathak SD, Chalana V, Haynor DH and Kim Y, “Edge guided delineation of the prostate in transrectal ultrasound images,” IEEE EMBS, vol. 2, p. 1056, 1999.

• Pathak SD, Grimm PD, Chalana V, and Kim Y, “Predicting pubic arch interference using multiplanar transrectal ultrasound (TRUS) for prostate brachytherapy,” SPIE Medical Imaging, vol. 3658, pp. 48-57, 1999.

• Pathak SD, Stoknes K, Grimm PD, Estlund J, and Kim Y, “Interactive tool for visualization and segmentation of radioactive seeds in post-operative prostate brachytherapy CT images,” SPIE Medical Imaging, vol. 3568, pp. 2-8, 1999.

• Pathak SD, Aarnink RG, de la Rosette JJ, Chalana V, Wijkstra H, Debruyne FMJ and Kim Y, "Quantitative three-dimensional trans-rectal ultrasound for prostate imaging," SPIE Medical Imaging, vol. 3335, pp. 83-92, 1998.

• Managuli R, Basoglu C, Pathak SD, and Kim Y, “Fast convolution on programmable microprocessor and application in unsharp masking,” SPIE Medical Imaging, vol. 3335, pp. 675-685, 1998.

• Pathak SD, Chalana V and Kim Y, “Multimedia systems in ultrasound image boundary detection and measurements,” SPIE Medical Imaging, vol. 3031, pp. 397-408, 1997.

• Mancuso ME, Pathak SD and Kim Y, "Platform independent software for medical image processing on the Internet,” SPIE Medical Imaging, vol. 3031, pp. 844-850, 1997.

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Last Modified: October 6, 2007 by Sayan Pathak - sayanpathak at hotmail.com