The development and integration of computational tools into life sciences research
My main interest is developing and integrating computational tools into life sciences research. I have designed, created and managed data analysis procedures while supervising and advising graduate students and postdoctoral researchers. I actively participate in all levels of the research enterprise from experimental design, hypothesis testing, and student supervision to publication and grant writing.
- Bioinformatics coordinator of the Penn State Genome Cartography Project (http://atlas.bx.psu.edu). I co-mentor and supervising several doctoral candidates to establishing the proper data analysis protocols for processing high throughput sequencing data. The project is a collaboration with Prof. Frank Pugh from the Department of Biochemistry and Molecular Biology
- GeneTrack (http://genetrack.googlecode.com) is a web based data visualization site that can retrieve and display genome wide experimental data at very high speeds (the project that this software is part of has been funded by NIH). The project is a collaboration with Prof. Frank Pugh from the Department of Biochemistry and Molecular Biology. Role: primary author of the software.
- BooleanNet (http://booleannet.googlecode.com) is a software tool that provides intuitive and accessible tools for simulating biological regulatory networks in a Boolean formalism. The project is a collaboration with Prof. Reka Albert from the Physics Department. Role: primary author of the software.
- Galaxy (http://g2.trac.bx.psu.edu), in operation since 2006, is a website for large throughput genomic analyses. The project has been funded by NSF, served originally as Co-PI on the first funded grant. The project was a collaboration with Prof. Anton Nekrutenko from the Department of Biochemistry and Molecular Biology.
- LionDB (http://www.liondb.org) in continuous operation since 2004, is a web based data exchange conduit that developed to facilitate data transfer between the microarray facility, statisticians and end-users at Penn State. The project is a collaboration with Dr. Craig Praul, Director of Genomics Core Facility and Prof. Naomi Altman from the Statistics Department. Role: primary author of the software.
I have published in three distinct scientific fields, Physics, Computer Science and Biology. In each of these fields I have co-authored works published in the most highly rated and selective journals or conferences of that scientific domain such as: Physical Review Letters, Conference on Human Factors in Computing Systems, Bioinformatics, Genome Research and Nature.
- Attractor analysis of asynchronous Boolean models of signal transduction networks Assieh Saadatpour, Istvan Albert, Reka Albert Journal of Theoretical Biology (in press, 2010)
- Disease dynamics in a dynamic social network
- C. Christensen, I. Albert, B. Grenfell, R. Albert Physica A (in press)
- Nucleosome organization in the Drosophila genome Travis N. Mavrich,, Cizhong Jiang, Ilya P. Ioshikhes, Xiaoyong Li, Bryan J. Venters, Sara J. Zanton, Lynn P. Tomsho, Ji Qi, Robert Glaser, Stephan C. Schuster, David S. Gilmour, Istvan Albert, and B. Franklin Pugh Nature (2008)
- A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome Travis N. Mavrich, Ilya P. Ioshikhes, Bryan J. Venters, Cizhong Jiang, Lynn P. Tomsho, Ji Qi, Stephan C. Schuster, Istvan Albert, and B. Franklin Pugh Genome Research (2008)
- Boolean network simulations for life scientist Istvan Albert, Juilee Thakar, Song Li, Ranran Zhang , Reka Albert Source Code for Biology and Medicine (2008)
- GeneTrack - a genomic data processing and visualization framework Istvan Albert, Shinichiro Wachi, Cizhong Jiang, and B. Franklin Pugh Bioinformatics (2008)
- Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome Istvan Albert, Travis N. Mavrich, Lynn P. Tomsho, Ji Qi, Sara J. Zanton , Stephan C. Schuster, and B. Franklin Pugh Nature 446, 572-576, (2007)
- A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly Daniel Blankerberg, James Taylor, Ian Schenk, Jianbin He, Yi Zhang, Matthew Ghent, Narayan Veeraraghavan, Istvan Albert, Webb Miller, Kateryna Makova, Ross C. Hardison, and Anton Nekrutenko Genome Research 17:960-964, (2007)
- Nucleosome positions predicted by comparative genomics Ilya P. Ioshikhes, Istvan Albert, Sara J. Zanton, and B. Franklin Pugh, Nature Genetics 38 , 1210 - 1215 (2006)
- Rapid and Asymmetric Divergence of Duplicate Genes in the Human Gene Coexpression Network Wen-Yu Chung, Reka Albert, Istvan Albert, Anton Nekrutenko and Kateryna D. Makova BMC Bioinformatics, 7 : 46 (2006)
- Galaxy: A platform for interactive large-scale genome analysis Belinda Giardine, Cathy Riemer, Ross Hardison, Richard Burnharns, Laura Elnitski, Prachi Shah, Yi Zhang, Daniel Blankerberg, Istvan Albert, Webb Miller, James Kent and Anton Nekrutenko Genome Research 15:1451-1455, 2005
- Conserved network motifs allow protein-protein interaction prediction Istvan Albert and Reka Albert Bioinformatics, 12 December 2004; Vol. 20, No. 18
- HyBrow - A Prototype System for Computer Aided Hypothesis Evaluation Stephen Racunas , Nigam Shah, Istvan Albert and Nina Fedoroff Bioinformatics 4 Aug 2004; Vol 20, Suppl 1:I257-I264
- Structural Vulnerability of the North American Power Grid Reka Albert, Istvan Albert and Gary L. Nakarado Physical Review E, 69, 025103(R) (2004)
- Experiences with a Recommender System on Four Mobile Devices Brad Miller, Istvan Albert, Shyong Lam, Joe Konstan & John Riedl 17th Annual Human-Computer Interaction Conference (HCI‘03), Bath, England, 8-12 September 2003
- Is Seeing Believing? How Recommender Systems Influence Users’ Opinions Cosley, D., Lam, S.K., Albert, I., Konstan, J., & Riedl, J. Proceedings of CHI 2003 Conference on Human Factors in Computing Systems (CHI‘03) , Fort Lauderdale, FL, pp. 585-592
- MovieLens Unplugged: Experiences with an Occasionally Connected Recommender System Bradley N. Miller, Istvan Albert, Shyong K. Lam, Joseph A. Konstan, John Riedl Proceedings of ACM 2003 International Conference on Intelligent User Interfaces (IUI‘03)
- Getting to Know You: Learning New User Preferences in Recommender Systems Rashid, A.M., Albert, I., Cosley, D., Lam, S.K., McNee, S., Konstan, J.A., & Riedl, J. Proceedings of the 2002 International Conference on Intelligent User Interfaces (IUI‘02) , San Francisco, CA, pp. 127-134.
- On the Recommending of Citations for Research Papers McNee, S., Albert, I., Cosley, D., Gopalkrishnan, P., Lam, S.K., Rashid, A.M., Konstan, J.A., & Riedl, J. Proceedings of ACM 2002 Conference on Computer Supported Cooperative Work (CSCW‘02), New Orleans, LA, pp. 116-125.
- Modeling relaxation and jamming in granular media B. Kahng, I. Albert, P. Schiffer, and A.-L. Barabasi Physical Review E 64, 051303 (2001)
- Granular Drag on a Discrete Object: Shape Effects on Jamming I. Albert, J. G. Sample, A. J. Morss, S. Rajagopalan, A.-L. Barabasi, and P. Schiffer Physical Review E 64, 061303-1 - 061303-4 (2001)
- The Drag Force in Granular Media P. Schiffer, I. Albert, J. G. Sample, and A.-L. Barabasi Proceedings of Fourth International Conference on Micromechanics of Granular Media, ed. Y. Kishino, (A. A. Balkema, Lisse, 2001)
- Stick-Slip Fluctuations in Granular Drag I. Albert, P. Tegzes, R. Albert, J. G. Sample, A.-L. Barabasi, T.Vicsek, and P. Schiffer Physical Review E 64, 031307-1- 031307-9 (2001)
- An Experimental Study of the Fluctuations in Granular Drag by Istvan Albert, Pal Tegzes, Reka Albert, John Sample, Albert-Laszlo Barabasi, Tamas Vicsek, B. Kahng and Peter Schiffer Proc. Materials Research Society Symposium Series 627, ed. S. Sen, M. Hunt (2000)
- Jamming and Fluctuations in Granular Drag I. Albert, P. Tegzes, B. Kahng, R. Albert, J. Sample, M. Pfiefer, A.-L. Barabasi, T. Vicsek, and P. Schiffer, Physical Review Letters 84, 5122-5 (2000)
- Maximum Angle of Stability in Wet and Dry Spherical Granular Media R. Albert, I. Albert, D. J. Hornbaker, P. Schiffer, and A.-L. Barabasi Physical Review E 56, R6271 (1997)
- What Keeps Sandcastles Standing D. J. Hornbaker, R. Albert, I. Albert, A.-L. Barabasi, and P. Schiffer Nature 387, 765 (1997)