Ameet SoniAssistant Professor
Computer Science Department
500 College Ave
Swarthmore, PA 19081
phone: (610) 957-6288
office: 253 Science Center
|Fall 2013 Schedule|
|CS35 Data Structures and Algorithms|
|Lecture||1:15-2:30pm Tuesday, Thursday||128 Sci Ctr|
|Lab||1:15-2:45pm Monday||240 Sci Ctr|
|Office Hours||3:00pm-5:00pm Thursday, and by appointment||253 Sci Ctr|
|Research Hours||9:00am-noon Monday, Wednesday|
Most recently, I worked on ACMI (Automated Crystallographic Map Interpretation). The task of determining protein structures has been a central one to the biological community for several decades. The structure allows biologists to extract information about the underlying biology of a protein, and has implications for various applications such as disease treatment, drug design, and protein design. The most popular method for producing protein structures is by interpreting an electron-density map - a three-dimensional image of a molecule produced through X-ray crystallography. This process, however, remains a resource- intensive and time-consuming task, stunting basic biological research. Thus, the main objective of the project is:
Probabilistic Ensembles for Improved Inference in Protein-Structure Determination.
Ameet Soni, Jude Shavlik.
Journal of Bioinformatics and Computational Biology, 10(1), 2012.
An extended version of this paper can be found here.
Techniques for Improved Probabilistic Inference In Protein-Structure Determination via X-Ray Crystallography
PhD Thesis, Department of Computer Sciences, University of Wisconsin-Madison, 2011.
Also appears as UW Technical Report CS-TR-11-1703
Probabilistic ensembles for improved inference in protein-structure determination
Ameet Soni, Jude Shavlik
BCB '11 Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2011
Slides (PPT/PPTX). Abstract.
Structural characterization of human Uch37.
E. Sethe Burgie, Craig Bingman, S. Leigh Grundhoefer, Ameet Soni, George Phillips
Proteins: Structure, Function, and Bioinformatics, 80: 649-654, 2011.
Guiding belief propagation using domain knowledge for protein-structure determination
Ameet Soni, Craig Bingman, Jude Shavlik
BCB '10 Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010
Slides (PPT/PPTX). Abstract.
Spherical-Harmonic Decomposition for Molecular Recognition in Electron-Density Maps.
Frank DiMaio, Ameet Soni, George Phillips, Jude Shavlik.
International Journal of Data Mining and Bioinformatics, 3: 205-227, 2009.
doi: 10.1504/IJDMB.2009.024852; NIHMSID: NIHMS68171; PMCID: PMC2696052
(The paper is in pre-publication form. It is an extension to: DiMaio et al. (BIBM 2007))
Machine Learning in Structural Biology: Interpreting 3D Protein Images.
Frank DiMaio, Ameet Soni, Jude Shavlik.
In S. Mitra, S. Datta, T. Perkins & G. Michailidis, editors,
Introduction to Machine Learning and Bioinformatics, 237-276, 2008. Chapman & Hall/CRC Press
Creating Protein Models from Electron-Density Maps using Particle-Filtering Methods.
Frank DiMaio, Dmitry Kondrashov, Eduard Bitto, Ameet Soni, Craig Bingman, George Phillips, Jude Shavlik.
Bioinformatics, 23: 2851-2858, 2007.
doi: 10.1093/bioinformatics/btm480; PMCID: PMC2567142
Improved Methods for Template-Matching in Electron-Density Maps Using Spherical Harmonics.
Frank DiMaio, Ameet Soni, George Phillips, and Jude Shavlik.
BIBM' 07 Proceedings of the First IEEE International Conference on Bioinformatics and Biomedicine, 2007
Code. Data. Abstract.