VRL

Research

BioVis: Bioinformatics and Computational Biology Visualization

Projects People Videos Talks Publications Bibliography

Projects

Predictive Computational Models for Orthopaedics
Image-based Measurements and Models
RuleBender: Visual Debuggers for Diagram-Based Biological Models

People

Md. Abedul Haque
Liz Marai
Adam Smith
Yao Sun
Ashwin Venkataraman
John Wenskovitch
Wen Xu

Videos

 



Talks

 



 

Publications

2017

[al-2017-NTR]

H. Elhalawani et al, "Normal Tissue Radiomic Feature Kinetics in Oropharygeal Cancers Treated with Image-Guided Radiation Therapy: Assessment of Parotid Glands Textural Changes on Daily Non-contrast CT", Radiology Society of North America meeting RSNA 2017, pp. 0--0, 2017. (pdf) (bibtex: al-2017-NTR).
[al-2017-PTH]

H. Elhalawani et al, "Predicting the HPV P16 Status of Oropharyngeal Cancer Patients Using Radiomics and an Ensemble of Random Forests", Radiology Society of North America meeting RSNA 2017, pp. 0--0, 2017. (pdf) (bibtex: al-2017-PTH).
[Group-2017-CSA]
Multidisciplinary Larynx Cancer Working Group, "Conditional Survival Analysis of Patients With Locally Advanced Laryngeal Cancer: Construction of a Dynamic Risk Model and Clinical Nomogram", Nature Scientific Reports, Vol. 7(0), pp. 1--12, 2017. (pdf) (bibtex: Group-2017-CSA).
[Group-2017-MCT]
MD Anderson Head and Neck Cancer Quantitative Imaging Collaborative Group, "Matched computed tomography segmentation and demographic data for oropharyngeal cancer radiomics challenges", Nature Scientific Data, Vol. 4(0), pp. 1--14, 2017. (pdf) (bibtex: Group-2017-MCT).

2016

[al-2016-CEC]

A. Kanwar et al, "Contrast-enhanced CT (CE-CT) Texture Analysis Radiomic Analysis of Pretreatment Contrast-Enhanced CT Imaging Predicts Local Failure in Oropharyngeal Cancers Treated with Radiotherapy", ASTRO 2016, pp. 1--2, 2016. (pdf) (bibtex: al-2016-CEC).
[Kanwar-2016-DOA]
A Kanwar, AS Mohamed, LE Court, L Zhang, GE Marai, G Canahuate, JS Lee, S Perni, JA Messer, BH Pham, B Youssef, D Vock, A Rao, J Kalpathy-Cramer, GB Gunn, DI Rosenthal, CD Fuller, "Development of a Predictive Quantitative Contrast Computed Tomography-Based Feature (Radiomics) Profile for Local Recurrence in Oropharyngeal Cancers", International Journal of Radiation Oncology, Biology, Physics, Vol. 96(2), pp. 0--0, Feb 2016. (pdf) (bibtex: Kanwar-2016-DOA).

2015

[Aerts-2015-HFT]
J. Aerts, G.E. Marai, K. Nieselt, C. Nielsen, M. Streit, D. Weiskopf, "Highlights from the 5th Symposium on Biological Data Visualization: Part 1", BMC Bioinformatics, Vol. 16(0), pp. 1--2, 2015. (bibtex: Aerts-2015-HFT).
[Aerts2-2015-HFT]
J. Aerts2, G.E. Marai, K. Nieselt, C. Nielsen, M. Streit, D. Weiskopf, "Highlights from the 5th Symposium on Biological Data Visualization: Part 2", BMC Proceedings, Vol. 9(0), pp. 1--2, 2015. (bibtex: Aerts2-2015-HFT).
[Aurisano-2015-BAL]
J. Aurisano, K. Reda, A. Johnson, G.E. Marai, J. Leigh, "BactoGeNIE: A Large-Scale Comparative Genome Visualization for Big Displays", BMC Bioinformatics, Vol. 16(0), pp. 1--13, 2015. (pdf) (bibtex: Aurisano-2015-BAL).

2014

[Marai-2014-BBB]
G.E. Marai, S. O’Donoghue, C. Bartlett and J. Aerts (editors), "BMC Bioinformatics Biological Data Visualization Series", BioMed Central, Vol. 0(0), pp. 1--100, 2014. (bibtex: Marai-2014-BBB).
[Wenskovitch-2014-MAT]
J. Wenskovitch, L.A. Harris, J.J. Tapia, J.R. Faeder, G.E. Marai, "MOSBIE: A Tool for Comparison and Analysis of Rule-Based Biochemical Models", BMC Bioinformatics Journal 15:316, Vol. 15(0), pp. 1--22, 2014. (pdf) (bibtex: Wenskovitch-2014-MAT).

2013

[Haque-2013-ASA]

Md. A. Haque, G. E. Marai, "A Semi-Automated Method for Subject-Specific Modeling of the Spinal Canal from Computed Tomography Images and Dynamic Radiographs", The 18th International Workshop on Vision, Modeling and Visualization, pp. 1--8, Sep 2013. (pdf) (bibtex: Haque-2013-ASA).
[Haque-2013-ITM]

Md. A. Haque, G. E. Marai, "Image to Mesh: Spinal Ligament 3D Surface Models from Bone Volume Images and Dynamic Radiographs", MeshMed: Workshop on Mesh Processing in Medical Imaging, Medical Image Computing and Computer Assisted Intervention (MICCAI) 2013, pp. 1--12, Sep 2013. (pdf) (bibtex: Haque-2013-ITM).

2012

[Smith-2012-IMS]
A. M. Smith, "INTEGRATED MODELING, SIMULATION, AND VISUALIZATION FOR RULE-BASED INTRACELLULAR BIOCHEMISTRY", Master's Thesis, Vol. 0(4), pp. 0--0, Apr 2012. (pdf) (bibtex: Smith-2012-IMS).
[Smith-2012-RIM]
A.M. Smith, W. Xu, Y. Sun, J.R. Faeder, G.E. Marai, "RuleBender: Integrated Modeling, Simulation and Visualization for Rule-Based Intracellular Biochemistry", BMC Journal of Bioinformatics, Vol. 13(6), pp. 1--16, Jun 2012. (pdf) (bibtex: Smith-2012-RIM).

2011

[Smith-2011-RIV]
IEEE BioVis'11 Best Paper Award
A.M. Smith, W. Xu, Y. Sun, J.R. Faeder, G.E. Marai, "RuleBender: Integrated Visualization for Biochemical Rule-Based Modeling", IEEE Visualization 2011, IEEE BioVIs: Symposium on Biological Data Visualization, pp. 1--8, Oct 2011. (pdf) (bibtex: Smith-2011-RIV).
[Smith-2011-SGV]

A. Smith, W. Xu, J.R. Faeder, G.E. Marai, "Scalable Global Views for Biological Rule-Based Modeling", IEEE Visualization 2011, Information Visualization, Poster Abstracts with System Demonstration, pp. 1--2, Oct 2011. (pdf) (bibtex: Smith-2011-SGV).
[Xu-2011-RAV]
W. Xu, A. Smith, J.R. Faeder, G.E. Marai, "RuleBender: A Visual Interface for Rule-Based Modeling", Bioinformatics Journal, Vol. 27(4), pp. 1721--2, Apr 2011. (pdf) (bibtex: Xu-2011-RAV).

2010

[A.M. Smith-2010-VTF]

A.M. Smith, W. Xu, Y. Sun, J.R. Faeder, G.E. Marai, "Visual Tools for Modeling and Simulation of Cell Signaling Networks ", Carnegie Mellon University Bioimaging Informatics Symposium, pp. 1--1, Sep 2010. (pdf) (bibtex: A.M. Smith-2010-VTF).

2009

[Marai-2009-DOA]

G.E. Marai, J.J. Crisco, D.H. Laidlaw, "Development of a Kinematic 3D Carpal Model to Analyze In Vivo Soft-Tissue Interaction Across Multiple Static Postures", The 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'09), pp. 0--0, Sep 2009. (pdf) (bibtex: Marai-2009-DOA).
[Marai-2009-EOO]

G.E. Marai, J.J. Crisco, D.H. Laidlaw, "Estimation of Optimal Carpal Contact in the Human Wrist from Multiple Static Articulation Postures", BMES (Biomedical Engineering Society) 2009 Annual Fall Scientific Meeting, pp. 0--0, Oct 2009. (pdf) (bibtex: Marai-2009-EOO).

2008

[Marai-2008-AKB]

G.E. Marai, J.J. Crisco, D.H. Laidlaw, "A Kinematics-Based Method for Evaluating the Stabilizing Role of Ligaments in the Carpal Joint", 16th Annual Symposium on Computational Methods in Orthopaedic Biomechanics, pp. 0--0, Mar 2008. (pdf) (bibtex: Marai-2008-AKB).

2007

[Crisco-2007-EOD]
J.J. Crisco, D. Moore, G.E. Marai, D.H. Laidlaw, E. Akelman, A. C. Weiss, S.W. Wolfe, "Effects of Distal Radius Malunion on Distal Radioulnar Joint Mechanics -- An In-Vivo Study", Journal of Orthopedic Research, Vol. 25(1), pp. 547--555, Jan 2007. (pdf) (bibtex: Crisco-2007-EOD).
[Marai-2007-DDP]
G.E. Marai, "Data-driven Predictive Modeling of Diarthrodial Joints", Ph.D. Dissertation, Brown University, Vol. 0(5), pp. 0--0, May 2007. (pdf) (bibtex: Marai-2007-DDP).

2006

[Marai-2006-AKB]

G.E. Marai, J.J. Crisco, D.H. Laidlaw, "A Kinematics-Based Method for Generating Cartilage Maps and Deformations in the Multi-Articulating Wrist Joint From CT Images", IEEE 2006 Conference of the Engineering in Medicine and Biology Society (EMBC'06), pp. 2079--2082, Sep 2006. (pdf) (bibtex: Marai-2006-AKB).

2004

[Marai-2004-JAI]

G. E. Marai, C. Demiralp, S. Andrews, D. H. Laidlaw, "JointViewer -- an interactive system for exploring orthopedic data", IEEE Visualization 2004 Poster Compendium, pp. 0--0, 2004. (pdf) (bibtex: Marai-2004-JAI).

2003

[Crisco-2003-KAM]

J.J. Crisco, G.E. Marai, D.H. Laidlaw, D. Moore, E. Akelman, "Kinematic and mechanical changes in the distal radioulnar joint (druj) of patients with malunited distal radius fractures", 49th Annual Meeting of the Orthopaedic Research Society, pp. 0--0, 2003. (pdf) (bibtex: Crisco-2003-KAM).
[Marai-2003-A3M]

G.E. Marai, D.H. Laidlaw, J.J. Coburn, M.A. Upal, J.J. Crisco, "A 3D Method for Segmenting and Registering Carpal Bones from CT Volume Images", Annual Meeting of the American Society of Biomechanics, pp. 0--0, 2003. (pdf) (bibtex: Marai-2003-A3M).
[Marai-2003-EJC]
G.E. Marai, D.H. Laidlaw, C. Demiralp, S. Andrews, C.M. Grimm, J.J. Crisco, "Estimating Joint Contact Areas and Ligament Lengths from Bone Kinematics and Surfaces", IEEE Transactions on Biomedical Engineering, Vol. 51(5), pp. 790--799, May 2003. (pdf) (bibtex: Marai-2003-EJC).

2002

[Marai-2002-CAA]

G.E. Marai, D.H. Laidlaw, C. Demiralp, C. Grimm, J.J. Crisco, D. Moore, A.E. Akelman, "Contact Areas and Ligament Lengths are Abnormal in Patients with Malunited Distal Radius Fracture Despite Normal Radioulnar Kinematics", 4th World Congress Biomechanics, pp. 0--0, Aug 2002. (pdf) (bibtex: Marai-2002-CAA).

2001

[Demiralp-2001-MAV]
C. Demiralp, G.E. Marai, S. Andrews, D.H. Laidlaw, J.J. Crisco, C. Grimm, "Modeling and Visualization of Inter-Bone Distances in Joints", IEEE Visualization 2001, Work in Progress Proc., Vol. 0(0), pp. 0--0, 2001. (pdf) (bibtex: Demiralp-2001-MAV).
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