Illinois Bio-Grid

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DePaul Bioinformatics Group

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Publications

The following documents have been published as part of the research associated with the Illinois Bio-Grid:

• K. G. Urie, D. Angulo, J. C. Lee, J. J. Kozak, H. B. Gray, J. R. Winkler, "Synchronous vs Asynchronous Chain Motion in alpha-Synuclein Contact Dynamics" J. Phys. Chem. B 2009, 113, 522-530.
• Kolbrun Kristjansdottir, Donald Wolfgeher, Nick Lucius, David Sigfredo Angulo, and Stephen J. Kron, "Phosphoprotein Profiling by PA-GeLC−MS/MS." Journal of Proteome Research May 2008. (Abstract and link to full text at ACS).

• Laurie Parker, Aaron Engel-Hall, Kevin Drew, George Steinhardt, Donald L. Helseth Jr, David Jabon, Timothy McMurry, David Sigfredo Angulo, Stephen J. Kron, "Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry." Journal of Mass Spectrometry. Volume 42 , Issue 12 (December 2007) pp. 1076. (Full Text at Wiley)

• Dennis Harman, Patrick Smyth, David Sigfredo Angulo. "A Database of Peak Annotations of Empirically Derived Mass Spectra." 1st Annual Midwest Symposium on Computational Biology & Bioinformatics. Northwestern University, Evanston, IL, October 18, 2007. (Abstract, Poster).

• Barry Dudek and David Sigfredo Angulo. "Metabolomic Analysis using R in a GRID Environment", DePaul CTI Research Symposium. Chicago, IL, May 5, 2007. (Abstract,Poster).

• Dennis Harman and David Sigfredo Angulo. "Annotation of Mass Spectrum Data", DePaul CTI Research Symposium. Chicago, IL, May 5, 2007. (Abstract, Poster).

• Donald L. Helseth Jr, Don Wolfgeher, Kolbrun Kristjánsdóttir, Stephen Kron and David Sigfredo Angulo. "Computational Analysis of Mass Spectrometry Isotopic Data", DePaul CTI Research Symposium. Chicago, IL, May 5, 2007. (Abstract, Poster).

• Mariellen Dwyer, Victoria Huang, Donald L. Helseth Jr and David Sigfredo Angulo. "Using Screencasts to Demonstrate the IBG Desktop", DePaul CTI Research Symposium. Chicago, IL, May 5, 2007. (Abstract, Poster).

• Kolbrun Kristjiansdottir, Donald Wolfgeher, Donald L. Helseth Jr., Nick Lucius, David Sigfredo Angulo and Stephen J. Kron. "Phosphoprotein profiling: Cell cycle regulated phosphoproteins and complexes in yeast. American Association for Cancer Research Special Conference: Advances in Proteomics in Cancer Research, Amelia Island, Florida, February 27 - March 2, 2007 (Poster)

• Fitzgerald, J.E., Jha, A.K., Sosnick, T.R., and Freed, K.F. (2007) Polypeptide Motions Are Dominated by Peptide Group Oscillations Resulting from Dihedral Angle Correlations between Nearest Neighbors. Biochemistry 46, 669-682.

• Puryear, Eric; Van Puymbrouck, Jennifer; Angulo, David Sigfredo; Drew, Kevin; Hollenbeck, Lee Ann; Battre, Dominic; Schilling, Alex; Jabon, David; von Laszewski, Gregor. "Achieving I/O Improvements in a Mass Spectral Database." ACM Crossroads Volume 13 , Issue 2 (December 2006) p. 11.

• Angulo, David Sigfredo. "The Bioinformatics Revolution," J. ACM Crossroads 13-1. Fall 2006.

• Angulo, David Sigfredo. "Challenges in Systems Biology: An Interview with Dr. Lee Hood, Inventor of the DNA Sequencer," J. ACM Crossroads 13-1. Fall 2006.

• Battré, Dominic; Angulo, David Sigfredo. "MPI Framework for Parallel Searching in Large Biological Databases," J. Parallel Distrib.Comput. (2006), doi: 10.1016/j.jpdc.2006.08.003

• Vogelbacher, Rob; Capraro, Benjamin; Sosnick, Tobin; Koide, Shohei; Angulo, David Sigfredo. IBG GeneDesigner: DNA Sequence Optimization for Designed Proteins BioMedical Informatics Workshop. Chicago, IL. October 13, 2006. (Abstract,Poster)
  • Awarded Best Bioinformatics Poster of Workshop

• David Sigfredo Angulo, Bryan Beaumont, David Kendall, Jonathan Gemmell, Michael Boyle, Gregory Zivich, Patrick Smyth, Frantz Gabeau, Anthony Jackson, Pelagic: A Bioinformatics Architecture in R, BioMedical Informatics Workshop. Chicago, IL. October 13, 2006. (Abstract, Poster)

• Gil D. Kwak, Donald L. Helseth, Jr., Alex Schilling and David Sigfredo Angulo, Hypothetical Sequence Analyzer, BioMedical Informatics Workshop. Chicago, IL. October 13, 2006. (Abstract, Poster)

• Donald L. Helseth, Jr., Laurie Parker, Kolbrun Kristjánsdóttir, Kevin Drew, Don Wolfgeher, Alex Schilling and David Sigfredo Angulo, Developing Post-Translational Modification MS Tools, BioMedical Informatics Workshop. Chicago, IL. October 13, 2006. (Abstract, Poster)

• Rob Vogelbacher, Benjamin Capraro, Tobin Sosnick, Shohei Koide, David Sigfredo Angulo, IBG GeneDesigner: DNA Sequence Optimization for Designed Proteins Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006. (Abstract,Poster)

• Gemmell, Jonathan; Kohn, Stephen; Angulo, David; Sosnick, Tobin; Freed, Karl; Jha, Abhishek; DeBartolo, Joseph. The Illinois Bio-Grid Rama Map (Poster). Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006. ( Abstract, Poster ).

• David Sigfredo Angulo, Bryan Beaumont, David Kendall, Jonathan Gemmell, Michael Boyle, Gregory Zivich, Patrick Smyth, Frantz Gabeau, Anthony Jackson, Pelagic: A Bioinformatics Architecture in R, Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006. (Abstract, Poster)

• Donald L. Helseth, Jr., Laurie Parker, Kolbrun Kristjánsdóttir, Kevin Drew, Don Wolfgeher, Alex Schilling and David Sigfredo Angulo, Developing Post-Translational Modification MS Tools, Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006. (Abstract, Poster)

• Gil D. Kwak, Donald L. Helseth, Jr., Alex Schilling and David Sigfredo Angulo, Hypothetical Sequence Analyzer, Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006. (Abstract, Poster)

• Laurie Parker, Aaron Engel-Hall, Kevin Drew, George Steinhardt, Donald L. Helseth, Jr., David Sigfredo Angulo, Alex Schilling and Stephen J. Kron, Quantifying peptide phosphorylation using MALDI-TOF mass spectrometry, Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006. (Abstract, Poster)

• Gemmell, Jonathan; Kohn, Stephen; Angulo, David; Sosnick, Tobin; Freed, Karl; Jha, Abhishek; DeBartolo, Joseph. The Illinois Bio-Grid Protein Map (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006. ( Abstract, Poster ).

• Harman, Dennis; Angulo, David; Drew, Kevin; Schilling, Alex. A Data Model for Annotating the Peaks of Mass Spectrum Data (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006. ( Abstract, Poster ).

• Kwak, Gil; Angulo, David; Shilling, Alexander. Hypothetical Sequence Analyzer (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006. (Abstract, Poster ).
  • Awarded Best of Conference Poster

• Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Enhancing a Mass Spectrometry I/O Framework. Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

• Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Comparing Mass Spectra (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

• Van Puymbrouck, Jennifer; Puryear, Eric; Angulo, David; Schilling,Alex; Drew, Kevin; Jabon,David; von Laszewski, Gregor. Mass Spectrometry Database Infrastructure and Data Import Module (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

• McElhaney, Renee; Angulo, David Sigfredo; Frank, Ed; Siwamutita, Paiboon; Stejerean, Cosmin. Developing MSLauncher as Analysis Tool (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006. (Abstract, Poster).

• Ala Eldeen, Hussam; Angulo, David; Drew, Kevin; Battre, Dominic; Schilling, Alex; Puryear, Eric; Van Puymbrouck, Jennifer; Jabon, David; von Laszewski, Gregor. Implementing Spectral Similarity Algorithms for Protein Identification. Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

• Stejerean, Cosmin; Siwamutita, Paiboon; Frank, E. D.; Giometti, Carol S; Babnigg, Gyorgy; Angulo, David; Drew, Kevin; von Laszewski, Gregor. An End-to-End System for Organizing and Sharing Raw and Derived Mass Spectrometry Data. Proceedings of the 2006 DePaul CTI Research Symposium. April 2006.

• Van Puymbrouck, Jennifer; Angulo, David; Drew, Kevin; Hollenbeck, Lee Ann; Battre, Dominic; Schilling, Alex; Jabon, David; von Laszewski, Gregor. A Batch Import Module for an Emprically Derived Mass Spectral Database. Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

• Vogelbacher, Rob; Angulo, David; and Koide, Shohei. Sequence Optimization for Synthetic Genes Using a Genetic Algorithm. Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

• Gemmell, Jonathan; Angulo, David; Sosnick, Tobin; Freed, Karl; Jha, Abhishek; Colubri, Andres; DeBartolo, Joseph; Kendall, David and von Laszewski, Gregor. Inverse Protein Folding of Ubiquitin on the Illinois Bio-Grid. Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

• von Laszewski, Gregor; Bone, Matthew; Fatima, Ishrath; Sosonkin, Mikhail; Winch, Robert; Vijayakumar, Nithya; Sahasrabudhe, Pankaj; Amin, Kaizar; Hategan, Mihael; DiCarlo, Jonathan; and Angulo, David. Towards the Development of a Bioinformatics Grid Desktop. Preprint ANL/MCS-ANL/MCS-P1189-0804, Mathematics and Computer Science Division, Argonne National Laboratory August 2004.

• von Laszewski, Gregor; Trieu, Tan; Zimny, Phillip; Angulo, David. The Java CoG Kit Experiment Manager. Tech-Report, Argonne National Laboratories, 2006.

• Battre, Dominic. Distributed Searching in Biological Databases. Masters Dissertation, Tech-Report 05-018, DePaul University. November 18, 2005.

• Drew, Kevin. Computationally Analyzing Mass Spectra of Hydrogen Deuterium Exchange Experiments. Masters Dissertation, Tech-Report TR-2005-12, University of Chicago. April 10, 2005.

• Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Developing a Distributed and Scalable Foundation for Mass Spectrometry Data. 19th annual National Conference on Undergraduate Research. Lexington, VA April 21-23, 2005.

• Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Mass Spectrometry in the Illinois BioGrid 19th annual National Conference on Undergraduate Research. Lexington, VA April 21-23, 2005.

• Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Mass Spectrometry in the Illinois BioGrid^? (Poster). Annual DePaul^? Science Showcase for Guidance Counselors. Chicago, IL December 10, 2004.

• Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Mass Spectrometry in the Illinois BioGrid^?. (Poster) Proceedings of 2004 DePaul^? CTI Research Symposium. November 2004

• Gemmell, Jonathan; Angulo, David; Colubri, Andres; Sosnick, Tobin; Freed, Karl; Koide, Shohei; von Laszewski, Gregor. Steering Monte-Carlo Protein Folding Simulations With Data From Nuclear Magnetic Resonance Experiments On The Illinois Bio-Grid (Poster). Proceedings of 2004 DePaul CTI Research Symposium. November 2004.

• Drew, Kevin; Angulo, David; Schilling, Alex; Freeman, Tim. Mass Spectra Analysis on the Illinois BioGrid (Poster). Proceedings of 2004 Midwest Software Engineering Conference, Chicago. June, 2004.
  • Awarded Best of Conference Student Poster
  • abstract

• Colubri, Andrés; Raddatz, Jessica Lyn; Angulo, David. !AIfold: A Statistical Potential for Protein Folding. (Poster) Proceedings of the 12th International Conference on Intelligent Systems for Molecular Biology and 3rd European Conference on Computational Biology (ISMB/ECCB). Glasgow, Scotland, UK. July 31 - August 4, 2004.

• Angulo, David; Schilling, Alex; Drew, Kevin; Freeman, Tim. Mass Spectra Analysis on the Illinois BioGrid. (Poster) Proceedings of NETTAB 2004 (Network Tools and Applications in Biology) Conference, Camerino, Italy. September 5-7, 2004.

• Gregor von Laszewski, Kaizar Amin, Matt Bone, Mike Hategan, Pankaj Sahasrabudhe, Mike Sosonkin, Robert Winch, Nithya Vijayakumar, David Angulo. Building Grid Workflows from Legacy Applications. Proceedings of SC2004 Conference, Pittsburgh, PA. Nov. 6-12, 2004.
  • Awarded Best of Conference Poster

• Angulo, David S.; Parsad, Nigel M.; Goodale, Tom; Allen, Gabrielle; Seidel, Ed. Computing the Smith-Waterman Algorithm on the Illinois Bio Grid (Poster). Proceedings of 2003 Midwest Software Engineering Conference, Chicago

• Sickel, Jeff; Angulo, David S.; Steele, Adam. Enhancing Dynamic Fluid Flow Analysis With Computational Grids (Poster). Proceedings of 2003 Midwest Software Engineering Conference, Chicago

• Finkelman, Steve; Angulo, David S.; Steele, Adam; Hackett, Shannon. Phylogenetics on the Illinois Bio-Grid (Poster). Proceedings of 2003 Midwest Software Engineering Conference, Chicago

• Steele, Adam; Angulo, David S. The Illinois BioGrid: A Prototype for Industry-Academe Collaboration. Proceedings of 2003 Midwest Software Engineering Conference, Chicago
  • Powerpoint presentation

-- BarryDudek - 14 May 2007
-- LarryHelseth - 06 May 2007
-- LarryHelseth - 27 Feb 2007
-- LarryHelseth - 15 Oct 2006
-- LarryHelseth - 03 Oct 2006
-- DaveAngulo - 28 Jan 2006
-- DaveAngulo - 28 Jan 2005
-- DaveAngulo - 28 Jan 2004
-- DaveAngulo - 28 Jan 2003