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66 Documents
Journal Citation
Year Publication
Navale, V and McAuliffe, M. 2023. Implementing Informatics Tools with Data Management Plans for Disease Area Research. Data Science Journal, 22: 24, pp. 1–6. DOI: https://doi.org/10.5334/dsj-2023-024
Jamie McCusker, Leslie D. McIntosh, Chris Shaffer, Peter Boisvert, James Ryan, Vivek Navale, Umit Topaloglu, Rachel L. Richesson. Guiding principles for technical infrastructure to support computable biomedical knowledge. Learn Health Sys. Nov 2022;e10352. doi:10.1002/lrh2.10352
Vivek Navale, Matthew McAuliffe. The Integration of a Canonical Workflow Framework with an Informatics System for Disease Area Research. Data Intelligence 2022. 4 (2): 186–195. doi: https://doi.org/10.1162/dint_a_00125
Luby M, Merino JG, Davis R, Ansari S, Fisher M, Hsia AW, Kim Y, Latour LL, McCreedy ES, Sukhdeo Singh R, Wright CB, Lynch JK. "Association of Multiple Passes during Mechanical Thrombectomy with Incomplete Reperfusion and Lesion Growth." Cerebrovasc Dis. 2021 Dec 13:1-9. doi: https://doi.org/10.1159/000519796. (PMID: 34903681)
Ruida Cheng, Marion Crouzier, François Hug, Kylie Tucker, Paul Juneau, Evan McCreedy, William Gandler, Matthew J. McAuliffe, Frances T. Sheehan. Automatic Quadriceps and Patellae Segmentation of MRI with Cascaded U2-Net and SASSNet Deep Learning Model. Medical Physics. (2021). http://doi.org/10.1002/mp.15335
Navale, V., von Kaeppler, D. & McAuliffe, M. An overview of biomedical platforms for managing research data. J. of Data, Inf. and Manag. (2021). https://doi.org/10.1007/s42488-020-00040-0
Lin, D., Crabtree, J., Dillo, I. et al. The TRUST Principles for digital repositories. Sci Data 7, 144 (2020). https://doi.org/10.1038/s41597-020-0486-7
Clarke, Akanni, Philip G. McQueen, Hsiao Yu Fang, Ramakrishnan Kannan, Victor Wang, Evan McCreedy, Stephen Wincovitch, and Edward Giniger. "Abl signaling directs growth of a pioneer axon in Drosophila by shaping the intrinsic fluctuations of actin." Molecular biology of the cell 31, no. 6 (2020): 466-477. https://doi.org/10.1091/mbc.E19-10-0564 (PMID: 31967946)
Clarke, Akanni, Philip G. McQueen, Hsiao Yu Fang, Ramakrishnan Kannan, Victor Wang, Evan McCreedy, Tyler Buckley, Erika Johannessen, Stephen Wincovitch, and Edward Giniger. "Dynamic morphogenesis of a pioneer axon in Drosophila and its regulation by Abl tyrosine kinase." Molecular biology of the cell 31, no. 6 (2020): 452-465. https://doi.org/10.1091/mbc.E19-10-0563 (PMID: 31967935)
Luby, Marie, Yojan Shah, Evan McCreedy, Kyle Kern, Lawrence L. Latour, Richard Leigh, John K. Lynch, and Amie W. Hsia. "Abstract TP81: A Closer Look at MRI-Based Core in Patients With Large Vessel Occlusion Within 6 Hours From Onset." Stroke 51, no. Suppl_1 (2020): ATP81-ATP81. https://doi.org/10.1161/str.51.suppl_1.TP81
Ruida Cheng, Natalia A Alexandridi, Richard M Smith, Aricia Shen, William Gandler, Evan McCreedy, Matthew J McAuliffe, Frances T Sheehan. Fully automated patellofemoral MRI segmentation using holistically nested networks: Implications for evaluating patellofemoral osteoarthritis, pain, injury, pathology, and adolescent development. Magnetic resonance in medicine, 83(1), 139-153. https://doi.org/10.1002/mrm.27920
Navale V, Ji M, Vovk O et al. Development of an informatics system for accelerating biomedical research. [version 2; peer review: 2 approved]. F1000Research 2020, 8:1430 (https://doi.org/10.12688/f1000research.19161.2)
Ruida Cheng, Nathan S Lay, Holger R Roth, Baris Turkbey, Dakai Jin, William Gandler, Evan S McCreedy, Tom J Pohida, Peter A Pinto, Peter L Choyke, Matthew J McAuliffe, Ronald M Summers. Fully automated prostate whole gland and central gland segmentation on MRI using holistically nested networks with short connections. Journal of Medical Imaging, 6(2), 024007. https://doi.org/10.1117/1.JMI.6.2.024007
Nathan S Lay, Yohannes Tsehay, Ronald M Summers, Baris Turkbey, Matthew Greer, Ruida Cheng, Holger Roth, Matthew J McAuliffe, Sonia Gaur, Francesca Mertan, Peter Choyke. Detection of prostate cancer in multi-parametric mri using random forest with instance weighting & mr prostate segmentation by deep learning with holistically-nested networks. US Patent, 16488127, filed February 22, 2017, and issued May 12, 2019.
Nathan Lay, Yohannes Tsehay, Yohan Sumathipala, Ruida Cheng, Sonia Gaur, Clayton Smith, Adrian Barbu, Le Lu, Baris Turkbey, Peter L Choyke, Peter Pinto, Ronald M Summers. A decomposable model for the detection of prostate cancer in multi-parametric MRI. International Conference on Medical Image Computing and Computer-Assisted Intervention.
Navale, V., & McAuliffe, M. (2018). Long-term preservation of biomedical research data. F1000Research, 7, 1353. https://doi.org/10.12688/f1000research.16015.1
Navale V, Bourne PE (2018) Cloud computing applications for biomedical science: A perspective. PLoS Comput Biol 14(6): e1006144. https://doi.org/10.1371/journal.pcbi.1006144
Cheng R, Roth H, Nathan Lay N, Lu L, Turkbey B, Gandler W, McCreedy E, Choyke P, Summers RM, McAuliffe MJ. Automatic MR Prostate Segmentation by Deep Learning with Holistically-Nested Networks, SPIE Medical Imaging, Vol. 10133, 101332H.
Bagci U, Celik H, Turkbey B, Cheng R, McCreedy E, Choyke P, McAuliffe MJ, Wood B. Developing Eye Tracking Environment for Prostate Cancer Diagnosis Using Multi-parametric MRI, ISMRM.
Cheng R, Lay N, Holger R, Lu L, Turkbey B, Mertan F, Gandler W, McCreedy ES, Choyke P, McAuliffe MJ, Summers R. Deep Learning with Orthogonal Volumetric HED Prostate Segmentation and 3D Surface Reconstruction Mo__del of Prostate M__RI IEEE ISBI.
Ting CY, McQueen PG, Pandya N, McCreedy ES, McAuliffe M, Lee CH. (March 2017). Analyzig Dendritic Morphology in Columns and Layers. J. Vis. Exp. (121). (PMID: 28362388)
Rosenthal LS, Drake D, Alcalay RN, Babcock D, Bowman FD, Chen-Plotkin A, Dawson TM, Dewey RB, German DC, Huang X, Landin B, McAuliffe M, Petyuk VA, Scherzer CR, Hillaire-Clarke CS, Sieber BA, Sutherland M, Tarn C, West A, Vaillancourt D, Zhang J, Gwinn K, PDBP consortium. The NINDS Parkinson's disease biomarkers program. Mov Disord 31:915-23. (PMID: 26442452)
Cheng R, Jackson JN, McCreedy ES, Gandler W, Eijkenboom JJFA, van Middelkoop M, McAuliffe, MJ, Sheehan FT. Patellar segmentation from 3D magnetic resonance images using guided recursive ray-tracing for edge pattern detection. Proc. SPIE Medical Imaging, Vol. 9788, 97880C.
Cheng R, Roth HR, Lu L, Wang S, Turkbey B, Gandler W, McCreedy ES, Agarwal HK, Choyke P, Summers RM, McAuliffe MJ. Active appearance model and deep learning for more accurate prostate segmentation on MRI. Proc. SPIE Medical Imaging, Vol. 9784, 97842I.
Fu Y, Winter PW, Rojas R, Wang V, McAuliffe M, Patterson GH Axial superresolution via multiangle TIRF microscopy with sequential imaging and photobleaching. Proc Natl Acad Sci U S A 113:4368-73.
Christensen RP, Bokinsky A, Santella A, Wu, Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colon-Ramos DA, Bao Z, Shroff H. Untwisting the Caenorhabditis elegans Embryo. Elife. (PMID: 26633880)
Cheng R., Turkbey B, Gandler W, Agarwal HK, Shah VP, Bokinsky A, McCreedy, ES, Wang S, Sankineni S, Bernardo M, Pohida T, Choyke P, McAuliffe MJ. Atlas Based AAM and SVM Model for Fully Automatic MRI Prostate Segmentation. IEEE EMBC. (PMID: 25570593)
Kumar A, Wu Y, Christensen R, Chandris P, Gandler W, McCreedy E, Bokinsky A, Colon-Ramos DA, Bao Z, McAuliffe M, Rondeau G, Shroff H. Dual-view Plane Illumination Microscopy for Rapid and Spatially Isotropic Imaging. Nature Protocols.(PMID: 25299154)
Cheng R, Xu S, Bokinsky A, McCreedy E, Wood BJ, McAuliffe M. GPU-based Multi-histogram Volume Navigation for Virtual Bronchoscopy. IEEE EMBC.(PMID: 25570698)
Cheng R, Turkbey B, Gandler, W, Agarwal HK, Shah, VP, Bokinsky A., McCreedy ES, Wang S, Sankineni S, Bernardo, M, Pohida, T, Choyke P, McAuliffe MJ. Atlas Based AAM and SVM Model for Fully Automatic MRI Prostate Segmentation. IEEE EMBC. (PMID: 25570593)
Ting CY, McQueen PG, Pandya N, Lin TY, Yang M, Reddy OV, O Connor MB, McAuliffe M, Lee CH. Photoreceptor-Derived Activin Promotes Dendritic Termination and Restricts the Receptive Fields of First-Order Interneurons in Drosophila Neuron. Neuron. 19; 81(4):830-46.
Wu Y, Wawrzusin P, Senseney J, Fischer RS, Christensen R, Santella A, York AG, Winter PW, Waterman CM, Bao Z, Colon-Ramos DA, McAuliffe M, Shroff H. Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Nat Biotechnol. 31(11):1032-8.
Shroff H, Wu Y, Wawrzusin P, Senseney J., Fischer R., Christensen R, Santella A, York A, Winter P, Waterman C, Bao Z, Colon-Ramos D, & McAuliffe, M. DiSPIM: time to leave your confocal behind presented in International Worm Meeting.
Cheng R, Marcelino B, Senseney J, Bokinsky A, Gandler W, Turkbey B, Pohida T, Choyke P, McAuliffe MJ. Segmentation and surface reconstruction model of prostate MRI. IEEE ISBI, 185-9.
Cheng R, Turkbey B, Senseney J, Bokinsky A, Gandler W, McCreedy E, Pohida T, Choyke P, McAuliffe M. 2D Registration Guided Models for Semi-automatic MRI Prostate Segmentation, SPIE Medical Imaging, DOI: 10.1117/12.2006225.
Senseney J, Bokinsky A, Cheng R, McCreedy E, McAuliffe M. Java Multi-histogram Volume Rendering Framework for Medical Images, SPIE Medical Imaging, DOI: 10.1117/12.2006980.
Hall D, Huerta MF, McAuliffe MJ, Farber GK. Sharing Heterogeneous Data: The National Database for Autism Research. Neuroinformatics, Volume 10, Issue 4, 331-339.
Cheng R, Bokinsky A, Senseney J, Pandya N, McCreedy E, McAuliffe M. A flexible Java GPU-enhanced visualization framework and its applications, IEEE CBMS, DOI: 10.1109/CBMS.2012.6266300.
Johnson SB, Whitney G, McAuliffe M, Wang H, McCreedy E, Leon Rozenblit L, Evans CC. Using Global Unique Identifiers to Link Autism Collections. J. Am. Med. Inform. Assoc., Vol. 17, No. 6, 689-695. (PMID: 20962132)
Senseney J, Hemler P, and McAuliffe MJ, Automated Segmentation of Computed Tomography Images, 22nd IEEE International Symposium on Computer-Based Medical Systems (CBMS), DOI: 10.1109/CBMS.2009.5255342.
Young L, Tu SW, Tennakoon L, Vismer D, Astakhov V, Gupta A, Grethe JS, Martone ME, Das AK, McAuliffe MJ. Ontology Driven Data Integration for Autism Research. 22nd IEEE International Symposium on Computer-Based Medical Systems (CBMS), DOI: 10.1109/CBMS.2009.5255362.
Giesel FL, Mehndiratta A, Locklin J, McAuliffe MJ, White S, Haberkorn U, Choyke PL, Knopp MV, Wood BJ, von Tengg-Kobligk H. Image Fusion for Treatment Planning, Navigation and Follow Up in Percutaneous Radiofrequency Ablation using MRI, CT and PET. Experimental Oncology 31(2), 106-14.
Calabrese M, De Stefano N, Atzori M, Bernardi B, Mattisi I, Barachino L, Rinaldi L, Morra A, McAuliffe MJ, Perini P, Battistini L, Gallo P. Extensive cortical inflammation is associated with epilepsy in multiple sclerosis. Journal of Neurology. Electronic publication: (http://www.springerlink.com/content/5q58136m44m20v71/).
Cheng R, Bokinsky A, Hemler PF, McCreedy ES, McAuliffe, MJ. Java Based Volume Rendering Frameworks. International Symposium on Medical Imaging, SPIE. Volume 6918, 6911804.
Wood BJ, MD, Locklin JK, Viswanathan A, Kruecker J, Haemmerich D, Cebral J, Sofer A, Cheng R, McCreedy E, Cleary K, McAuliffe MJ, Glossop N, Yanof J. Technologies for Guidance of Radiofrequency Ablation in the Multimodality Interventional Suite of the Future. Journal of Vascular and Interventional Radiology _ JVIR 18(1). (PMID: 17296700)
Monzon A, Hemler PF, Nalls M, Manini T, Clark BC, Harris TB, McAuliffe MJ. Segmentation of magnetic resonance images of the thighs for a new National Institutes of Health initiative. International Symposium on Medical Imaging (SPIE), Vol. 6512, 65123L.
Calabrese M, Atzori M, Bernardi V, Morra A, Romualdi C, Rinaldi L, McAuliffe MJ, Barachino L, Perini P, Fischl B, Battistin L, Gallo P. Cortical atrophy is relevant in multiple sclerosis at clinical onset. Journal of Neurology, Vol 254, Number 9.
Bazin PL, Cuzzocreo JL, Yassa MA, Gandler W, McAuliffe MJ, Bassett SS, Pham DL. Volumetric neuroimage analysis extensions for the MIPAV software package Journal of Neuroscience Methods; 165 (1), 111-21.
Griffith C, Bagnato F, Gupta S, Calabrese A, Oh U, Chiu A, Ohayon JM, McAuliffe MJ, Tasciyan TA, Jacobson S. Brain volume measurements in patients with HTLV-1 associated tropical spastic paraparesis. Journal of Neurovirology 12 (5), 349-55.
Liepinsh DJ, Grivennikov SI, Klarmann KD, Lagarkova MA, Drutskaya MS, Lockett SJ, Tessarollo L, McAuliffe M, Keller JR, Kuprash DV, Nedospasov SA. Novel Lymphotoxin Alpha (LT{alpha}) Knockout Mice with Unperturbed Tumor Necrosis Factor Expression: Reassessing LT{alpha} Biological Functions. Mol Cell Biol. 26 (11), 4214-25.
McCreedy ES, Cheng R, Hemler P, Viswanathan A, Wood B, McAuliffe MJ. Radio Frequency Ablation Registration, Segmentation, and Fusion Tool. IEEE Transaction on Information Technology in Biomedicine, Vol. 10, No. 3, ISSN 1089-7771, 490 _ 496.(PMID: 16871716)
Hemler PF, McCreedy ES, Cheng R, Wood B, McAuliffe MJ. Vasculature segmentation for radio frequency ablation of non-resectable hepatic tumors. International Symposium on Medical Imaging (SPIE), Vol. 6144, 1134-1141.
Hemler PF, McCreedy ES, Cheng R, Wood B, McAuliffe MJ. Assessment of radio frequency treatment of hepatic tumors. International Symposium on Medical Imaging (SPIE), Vol. 6141, 717-723.
Yim PJ, Vora AV, Raghavan D, Prasad R, McAuliffe MJ, Ohman-Strickland P, Nosher JL. Volumetric Analysis of Liver Metastases in Computed Tomography with the Fuzzy C-Means Algorithm, Journal of Computer Assisted Tomography, Volume 30, 212-220.
Baggett D, Nakaya M, McAuliffe M, Lockett S. Whole Cell Segmentation in Solid Tissue Sections. International Society for Analytical Cytology, Vol. 67A,137-143.
Muanza TM, Cotrim A, McAuliffe MJ, Sowers AL, Baum BJ, Cook JA, Feldchtein F, Amazeen PG, Colman CN, Mitchell JB. Evaluation of Radiation-Induced Oral Mucositis by Optical Coherence Tomography. Clinical Cancer Research Vol. 11, 5221-5127.
McCreedy ES, Cheng R, Hemler P, Viswanathan A, Wood B, McAuliffe MJ. Radio Frequency Ablation Registration, Segmentation, and Fusion Tool. IEEE Computer-Based Medical Systems (CBMS), 259 _ 264.
Jia, G, Baudendistel KT, von Tengg-Kobligk H, Heverhagen JT, Polzer H, Henry H, McAuliffe MJ, Levine AL, Rosol TJ, Knopp MV. Assessing Prostate Volume by Magnetic Resoance Imaging, A Comparison of Different Measurement Approaches for Organ Volume Analysis. Investigative Radiology, Volume 40, 243-248.
Bazin PL, Gandler W, McAuliffe MJ, Pham DL. A Software Tool for Atlas-based Volumetric Neuroimage Analysis. International Symposium on Medical Imaging, SPIE. Volume 5747, 1824-1833.
Hemler P, McCreedy E, McAuliffe MJ. Performance comparison of a new liver vessel segmentation algorithm, International Symposium on Medical Imaging (SPIE), Vol. 5370, 1785-1794.
McAuliffe MJ, Lalonde FM, McGarry D, Gandler W, Csaky K, Trus BL. Medical Image Processing, Analysis & Visualization In Clinical Research. IEEE Computer-Based Medical Systems (CBMS), 381-386.
Yim PJ, Marcos HB, McAuliffe MJ, McGarry D, Heaton Ian, Choyke PL. Registration of Time-Series Contrast Enhancement Magnetic Resonance Images for Renography. IEEE Computer-Based Medical Systems (CBMS), 516-520.
Zito MA, Koennecke LA, McAuliffe MJ, Rooijen NV, and Heyes MP. Depletion of systemic macrophages by liposome-encapsulated clodronate attenuates parenchymal macrophage invasion and neurodegeneration following local endotoxin infusion. Brain Research I.
Summers RM, Agcaoili CML, McAuliffe MJ, Dalal SS, Yim PJ, Choyke PL, Walther MM, Linehan WM. Helical CT of von Hippel-Lindau: Semi-automated Segmentation of Renal Lesions. Proceedings of the IEEE International Conference on Image Processing, 293-296.
McAuliffe MJ, Eberly D, Fritsch DS, Chaney EL, and Pizer SM: Scale-Space Boundary Evolution Initialized by Cores. Proceedings of the Fourth International Conference on Visualization in Biomedical Computing, Lecture Notes in Comp Sci Vol 1131, KH Hohne and R Kikinis (eds), Springer, 173-182.
Fritsch DS, Chaney EL, Boxwala A, McAuliffe MJ, Raghavan S, Thall A, and Earnhart JD. Core-based Registration for Automatic Radiotherapy Treatment Verification. International Journal of Radiation Oncology, Biology, Physics. 33 (5). 1287-1300.