Thu, 21 Aug 2008 14:21:47 BST CiteULike: tmmurali's Kumar http://www.citeulike.org/user/tmmurali/author/Kumar CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/tmmurali/article/3006750 <i>(2007), pp. 540-549.</i> Association analysis-based transformations for protein interaction networks: a function prediction case study Gaurav Pandey Michael Steinbach Rohit Gupta Tushar Garg Vipin Kumar doi:10.1145/1281192.1281251 (2007), pp. 540-549. 2008-07-15T19:13:01-00:00 2007 540 549 ACM gene-function-prediction ppi_network_quality ppi-prediction http://www.citeulike.org/user/tmmurali/article/554250 <i>Cell Biol Educ, Vol. 4, No. 4. (2005), pp. 323-329.</i><br /><br />With genomics well established in modern molecular biology, recent studies have sought to further the discipline by integrating complementary methodologies into a holistic depiction of the molecular mechanisms underpinning cell function. This genomic subdiscipline, loosely termed "systems biology," presents the biology educator with both opportunities and obstacles: The benefit of exposing students to this cutting-edge scientific methodology is manifest, yet how does one convey the breadth and advantage of systems biology while still engaging the student? Here, I describe an active-learning approach to the presentation of systems biology. In graduate classes at the University of Michigan, Ann Arbor, I divided students into small groups and asked each group to interpret a sample data set (e.g., microarray data, two-hybrid data, homology-search results) describing a hypothetical signaling pathway. Mimicking realistic experimental results, each data set revealed a portion of this pathway; however, students were only able to reconstruct the full pathway by integrating all data sets, thereby exemplifying the utility in a systems biology approach. Student response to this cooperative exercise was extremely positive. In total, this approach provides an effective introduction to systems biology appropriate for students at both the undergraduate and graduate levels. Teaching systems biology: an active-learning approach. A Kumar doi:10.1187/cbe.04-12-0057 Cell Biol Educ, Vol. 4, No. 4. (2005), pp. 323-329. 2006-03-16T13:00:25-00:00 2005 Cell Biol Educ 1536-7509 4 4 323 329 systems-biology-education http://www.citeulike.org/user/tmmurali/article/2799757 <i>Autophagy, Vol. 2, No. 1. (r 2006), pp. 12-23.</i><br /><br />With its relevance to our understanding of eukaryotic cell function in the normal and disease state, autophagy is an important topic in modern cell biology; yet, few textbooks discuss autophagy beyond a two- or three-sentence summary. Here, we report an undergraduate/graduate class lesson for the in-depth presentation of autophagy using an active learning approach. By our method, students will work in small groups to solve problems and interpret an actual data set describing genes involved in autophagy. The problem-solving exercises and data set analysis will instill within the students a much greater understanding of the autophagy pathway than can be achieved by simple rote memorization of lecture materials; furthermore, the students will gain a general appreciation of the process by which data are interpreted and eventually formed into an understanding of a given pathway. As the data sets used in these class lessons are largely genomic and complementary in content, students will also understand first-hand the advantage of an integrative or systems biology study: No single data set can be used to define the pathway in full-the information from multiple complementary studies must be integrated in order to recapitulate our present understanding of the pathways mediating autophagy. In total, our teaching methodology offers an effective presentation of autophagy as well as a general template for the discussion of nearly any signaling pathway within the eukaryotic kingdom. A systems biology approach to learning autophagy. DJ Klionsky A Kumar Autophagy, Vol. 2, No. 1. (r 2006), pp. 12-23. 2008-05-14T18:46:51-00:00 2006 Autophagy 1554-8627 2 1 12 23 systems-biology-education http://www.citeulike.org/user/tmmurali/article/343247 <i>(2005), pp. 721-732.</i> Discovering large dense subgraphs in massive graphs David Gibson Ravi Kumar Andrew Tomkins doi:10.1109/FOCS.2004.48 (2005), pp. 721-732. 2005-10-07T07:08:02-00:00 2005 721 732 VLDB Endowment csb_survey_network_modules http://www.citeulike.org/user/tmmurali/article/400051 <i>Nat Rev Genet, Vol. 6, No. 8. (2005), pp. 654-662.</i> MOLECULAR CLOCKS: FOUR DECADES OF EVOLUTION Sudhir Kumar doi:10.1038/nrg1659 Nat Rev Genet, Vol. 6, No. 8. (2005), pp. 654-662. 2005-11-18T15:43:56-00:00 2005 Nat Rev Genet 6 8 654 662 molecular_clock