Publications

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Journal Articles
Perlis D.  2006.  Theory and Application of Self-Reference: Logic and Beyond. Self-reference. 178:121-121.
Perlis D.  1990.  Thing and Thought. Knowledge Representation and Defeasible Reasoning. Kluwer.
Nirkhe M, Kraus S, Perlis D.  1995.  Thinking takes time: a modal active-logic for reasoning in time. Proc. of BISFAI-95.
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al..  2009.  Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.. Appl Environ Microbiol. 75(7):2046-56.
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al..  2009.  Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.. Appl Environ Microbiol. 75(7):2046-56.
Plaisant C, Sears A.  1992.  Touchscreen interfaces for alphanumeric data entry. Human Factors and Ergonomics Society Annual Meeting Proceedings. 36(4):293-297.
Marchionini G, Haas S, Plaisant C, Shneiderman B, Hert C.  2005.  Toward a Statistical Knowledge Network (2004). Institute for Systems Research Technical Reports.
Regier JC, Zwick A, Cummings MP, Kawahara AY, Cho S, Weller S, Roe A, Baixeras J, Brown JW, Parr C et al..  2009.  Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol Biol. 9:280-280.
Martin, M.P, Weirs G, Candler GV, Piomelli U, Johnson H, Nompelis I.  2000.  Toward the large-eddy simulation over a hypersonic elliptical cross-section cone. AIAA Paper No. 00-2311.
Yoon I, Sussman A, Memon AM, Porter A.  2011.  Towards incremental component compatibility testing. Proceedings of the 14th international ACM Sigsoft symposium on Component based software engineering, CBSE. 11:119-128.
Brough J, Schwartz M, Gupta SK, Anand D, Kavetsky R, Pettersen R.  2007.  Towards the development of a virtual environment-based training system for mechanical assembly operations. Virtual Reality. 11(4):189-206.
Dingermann T, Sharp S, Appel B, DeFranco D, Mount SM, Heiermann R, Pongs O, Söll D.  1981.  Transcription of cloned tRNA and 5S RNA genes in a Drosophila cell free extract. Nucleic Acids ResearchNucl. Acids Res.. 9(16):3907-3918.
Hannenhalli S, Putt ME, Gilmore JM, Wang J, Parmacek MS, Epstein JA, Morrisey EE, Margulies KB, Cappola TP.  2006.  Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure. Circulation. 114(12):1269-1276.
Hannenhalli S, Putt ME, Gilmore JM, Wang J, Parmacek MS, Epstein JA, Morrisey EE, Margulies KB, Cappola TP.  2006.  Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure. Circulation. 114(12):1269-1276.
Hannenhalli S, Pevzner PA.  1999.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACM. 46(1):1-27.
Kelly W, Pugh W, Rosser E, Shpeisman T.  1996.  Transitive closure of infinite graphs and its applications. Languages and Compilers for Parallel Computing. :126-140.
Lee B, Parr CS, Plaisant C, Bederson BB, Veksler VD, Gray WD, Kotfila C.  2006.  TreePlus: Interactive Exploration of Networks with Enhanced Tree Layouts. Visualization and Computer Graphics, IEEE Transactions on. 12(6):1414-1426.
Lee B, Parr CS, Plaisant C, Bederson BB, Veksler VD, Gray WD, Kotfila C.  2006.  TreePlus: Interactive Exploration of Networks with Enhanced Tree Layouts. Visualization and Computer Graphics, IEEE Transactions on. 12(6):1414-1426.
Phang KY, Foster JS, Hicks MW, Sazawal V.  2009.  Triaging Checklists: a Substitute for a PhD in Static Analysis. Evaluation and Usability of Programming Languages and Tools (PLATEAU) PLATEAU 2009.
Perlis D.  1989.  Truth and meaning (research note). Artificial intelligence. 39(2):245-250.
Cleaveland R, Panangaden P.  1988.  Type theory and concurrency. International Journal of Parallel Programming. 17(2):153-206.
Miller M, Perlis D.  1991.  Typicality constants and range defaults: Some pros and cons of a cognitive model of default reasoning. Methodologies for Intelligent Systems. :560-569.
Mount SM, Pettersson I, Hinterberger M, Karmas A, Steitz JA.  1983.  The U1 small nuclear RNA-protein complex selectively binds a 5′ splice site in vitro. Cell. 33(2):509-518.
Verma R, Peters NR, D'Onofrio M, Tochtrop GP, Sakamoto KM, Varadan R, Zhang M, Coffino P, Fushman D, Deshaies RJ et al..  2004.  Ubistatins Inhibit Proteasome-Dependent Degradation by Binding the Ubiquitin Chain. Science. 306(5693):117-120.
Langmead B, Trapnell C, Pop M, Salzberg SL.  2009.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 10(3):R25-R25.

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