Adam Kiezun
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Software toolsHampi: solver for string constraintsKaluza: constraint solver for multiple string variables of bounded length (builds on Hampi) jFuzz: whitebox fuzzer (testing tool) for Java Ardilla: automatic tool to find SQL injection and XSS attacks on PHP Web applications PolyPhen-HCM: predicting the effects of missense mutations in genes associated with Hypertrophic Cardiomyopathy R implementation of tests for association of rare variants with phenotypes: T1, T5, Madsen-Browning, variable threshold (VT) miRNAminer: microRNA homology search microRNAviewer: global view of miRNA conservation (using homology search) miRNAligner: conservation of human microRNAs in 44 vertebrates (using whole-genome alignments) AMI Calculator: risk calculator for heart attack PublicationsTrevor J Pugh, Olena Morozova, Edward F Attiyeh, Shahab Asgharzadeh, Jun S Wei, Daniel Auclair, Scott L Carter, Kristian Cibulskis, Megan Hanna, Adam Kiezun, Jaegil Kim, Michael S Lawrence, Lee Lichenstein, Aaron McKenna, Chandra Sekhar Pedamallu, Alex H Ramos, Erica Shefler, Andrey Sivachenko, Carrie Sougnez, Chip Stewart, Adrian Ally, Inanc Birol, Readman Chiu, Richard D Corbett, Martin Hirst, Shaun D Jackman, Baljit Kamoh, Alireza Hadj Khodabakshi, Martin Krzywinski, Allan Lo, Richard A Moore, Karen L Mungall, Jenny Qian, Angela Tam, Nina Thiessen, Yongjun Zhao, Kristina A Cole, Maura Diamond, Sharon J Diskin, Yael P Mosse, Andrew C Wood, Lingyun Ji, Richard Sposto, Thomas Badgett, Wendy B London, Yvonne MoyerThe genetic landscape of high-risk neuroblastoma In Nature Genetics (2013) David P. Nusinow, Adam Kiezun, Daniel J. O’Connell, Joel M. Chick, Yingzi Yue, Richard L. Maas, Steven P. Gygi and Shamil R. Sunyaev Network-based inference from complex proteomic mixtures using SNIPE In Bioinformatics (2012) 28 (23) 3115-3122 Adam Kiezun*, Kiran Garimella*, Ron Do*, Nathan O Stitziel*, Benjamin M Neale, Paul J McLaren, Namrata Gupta, Pamela Sklar, Patrick F Sullivan, Jennifer L Moran, Christina M Hultman, Paul Lichtenstein, Patrik Magnusson, Thomas Lehner, Yin Yao Shugart, Alkes L Price, Paul I W de Bakker, Shaun M Purcell & Shamil R Sunyaev Exome sequencing and the genetic basis of complex traits (* equal contribution) In Nature Genetics 2012, 44 pp. 623–630 Adam Kiezun*, Shay Artzi*, Shira Modai, Naama Volk, Ofer Isakov and Noam Shomron miRviewer: A multispecies microRNA homologous viewer (* equal contribution) In BMC Research Notes 2012, 5:92 (Note: the tool is now called microRNAviewer) Eun Bae Kim, Xiaodong Fang, Alexey A. Fushan, Zhiyong Huang, Alexei V. Lobanov, Lijuan Han, Stefano M. Marino, Xiaoqing Sun, Anton A. Turanov, Pengcheng Yang, Sun Hee Yim, Xiang Zhao, Marina V. Kasaikina, Nina Stoletzki, Chunfang Peng, Paz Polak, Zhiqiang Xiong, Adam Kiezun, Yabing Zhu, Yuanxin Chen, Gregory V. Kryukov, Qiang Zhang, Leonid Peshkin, Lan Yang, Roderick T. Bronson, Rochelle Buffenstein, Bo Wang, Changlei Han, Qiye Li, Li Chen, Wei Zhao, Shamil R. Sunyaev, Thomas J. Park, Guojie Zhang, Jun Wang & Vadim N. Gladyshev Genome sequencing reveals insights into physiology and longevity of the naked mole rat In Nature, October 2011 Raymond M Anchan, JL Eaton, Shane T Lipskind, Adam Kiezun, Daniel J O'Connell, Behzad Gerami-Naini Analysis of differential gene expression during mouse follicular development In Fertility and Sterility 96 (3), S126-S126 (ASRM 2011 Abstract) Adam Kiezun*, Vijay Ganesh*, Shay Artzi, Philip Guo, Pieter Hooimeijer, Michael D. Ernst HAMPI: A Solver for Word Equations over Strings, Regular Expressions and Context-Free Grammars (* equal contribution) In ACM Transactions on Software Engineering and Methodology (TOSEM) (in press) 2011 Nathan O. Stitziel*, Adam Kiezun*, Shamil R. Sunyaev Computational and Statistical Approaches to Analyzing Variants Identified by Exome Sequencing (* equal contribution) In Genome Biology Special Issue on Exome Sequencing, September, 2011 Vijay Ganesh, Adam Kiezun, Shay Artzi, Philip Guo, Pieter Hooimeijer, Michael D. Ernst HAMPI: A Solver for Testing, Analysis, and Vulnerability Detection In Proceedings of International Conference on Computer Aided Verification (CAV) (Snowbird, Utah, USA), July 2011 (Invited Tutorial Paper at CAV 2011) Daniel M. Jordan*, Adam Kiezun*, Samantha M. Baxter*, Vineeta Agarwala, Robert C. Green, Michael F. Murray, Trevor Pugh, Matthew S. Lebo, Heidi L. Rehm, Birgit H. Funke, Shamil R. Sunyaev Development and Validation of a Computational Method for Assessment of Missense Variants in Hypertrophic Cardiomyopathy, (* equal contribution) In The American Journal of Human Genetics, February 2011 Frank Tip, Robert M. Fuhrer, Adam Kiezun, Michael D. Ernst, Ittai Balaban, Bjorn de Sutter Refactoring Using Type Constraints, In ACM Transactions on Programming Languages and Systems (TOPLAS), 2011 Shay Artzi, Adam Kiezun, Julian Dolby, Frank Tip, Daniel Dig, Amit Paradkar, Michael D. Ernst Finding Bugs in Web Applications Using Dynamic Test Generation and Explicit State Model Checking, In IEEE Transactions on Software Engineering (TSE), 2009 Adam Kiezun, Vijay Ganesh, Philip J. Guo, Pieter Hooimeijer, Michael D. Ernst HAMPI: A Solver for String Constraints, In ISSTA 2009 --- International Symposium on Testing and Analysis, (Chicago, Illinois, USA), July 19-23, 2009. ACM SIGSOFT Distinguished Paper Award (Previous version appeared as a technical report). Hampi website Karthick Jayaraman, David Harvison, Vijay Ganesh, Adam Kiezun*, jFuzz: a concolic whitebox fuzzer for Java, In NFM 2009 --- NASA Formal Methods Symposium (Moffett Field, California, USA), April 6-8, 2009. (*corresponding author) Adam Kiezun, Angelina Lee, Noam Shomron, Evaluation of optimization techniques for variable selection in logistic regression applied to diagnosis of myocardial infarction, In Bioinformation 3(7), 311-313 (2009) Adam Kiezun, Philip J. Guo, Karthick Jayaraman, Michael D. Ernst, Automatic Creation of SQL Injection and Cross-site Scripting Attacks, In ICSE 2009 --- IEEE International Conference on Software Engineering, (Vancouver, Canada), May 16-24, 2009. (Previous version appeared as a technical report). Shay Artzi, Adam Kiezun, Jaime Quinonez, Michael D. Ernst, Parameter Reference Immutability: Formal Definition, Inference Tool, and Comparison. In International Journal of Automated Software Engineering, Vol. 16 Issue 1 (2009). Shay Artzi, Adam Kiezun, Julian Dolby, Frank Tip, Danny Dig, Amit Paradkar, Michael D. Ernst, Finding Bugs in Dynamic Web Applications, In ISSTA 2008 --- ACM International Symposium on Software Testing and Analysis, (Seattle, Washington, USA), July 20-24, 2008. (Previous version appeared as a technical report). Patrice Godefroid, Adam Kiezun*, Michael Y. Levin, Grammar-based Whitebox Fuzzing, In PLDI 2008 --- ACM Conference on Programming Languages Design and Implementation, (Tuscon, Arizona, USA), June 7-13, 2008. (*principal author, names sorted alphabetically) (Previous version appeared as a technical report). Shay Artzi, Adam Kiezun, Noam Shomron, miRNAminer: a tool for homologous microRNA gene search, In BMC Bioinformatics 2008, 9:39 Designated as "Highly Accessed" article on BioMed Central The miRNAminer tool Shay Artzi, Adam Kiezun, David Glasser, Michael Ernst, Combined Static and Dynamic Mutability Analysis, In ASE 2007 --- International Conference on Automated Software Engineering, (Atlanta, Georgia, USA), November 5-7, 2007. (Previous version, containing additional material, appeared as a technical report). Best Paper Selection Robert Fuhrer, Adam Kiezun, Markus Keller, Refactoring in the Eclipse JDT: Past, Present, and Future (position paper), In WRT 2007 --- Workshop on Refactoring Tools at ECOOP 2007, (Berlin, Germany), July, 2007. Yoav Zibin, Alex Potanin, Mahmood Ali, Shay Artzi, Adam Kiezun, Michael Ernst, Object and reference immutability using Java generics, In ESEC/FSE 2007 --- European Software Engineering Conference and ACM Symposium on the Foundations of Software Engineering, (Dubrovnik, Croatia), September 5-7, 2007. ACM SIGSOFT Distinguished Paper Award Adam Kiezun, Michael Ernst, Frank Tip, Robert Fuhrer Refactoring for parameterizing Java classes, In ICSE'07 --- International Conference on Software Engineering, (Minneapolis, MN, USA), May 20-26, 2007 (for additional examples material, see also the technical report) ACM SIGSOFT Distinguished Paper Award Shay Artzi, Michael Ernst, Adam Kiezun, Carlos Pacheco and Jeff Perkins, Finding the needles in the haystack: Generating legal test inputs for object-oriented programs, In MTOOS 2006 --- Workshop on Model-Based Testing and Object-Oriented Systems, (Portland, Oregon, USA), October 23, 2006. Robert Fuhrer, Frank Tip, Adam Kiezun, Julian Dolby and Markus Keller, Efficiently Refactoring Java Applications to Use Generic Libraries, In ECOOP 2005 --- Object-Oriented Programming, 19th European Conference, (Glasgow, Scotland), July 25-29, 2005. Alan Donovan, Adam
Kiezun, Matthew S. Tschantz and Michael Ernst,
Converting Java programs to use generic libraries, In Object-Oriented Programming Systems, Languages, and Applications (OOPSLA 2004), (Vancouver, BC, Canada), October 26-28, 2004, pp. 15-34 Frank Tip, Adam Kiezun,
and Dirk Baeumer,
Refactoring for generalization using type constraints, In Object-Oriented Programming Systems, Languages, and Applications (OOPSLA 2003), (Anaheim, CA, USA), November 6-8, 2003, pp. 13-26. Dirk Baeumer, Erich Gamma and Adam Kiezun, Integrating refactoring support into a Java development tool In OOPSLA'01 Companion (October 2001). ThesesAdam Kiezun,Effective Software Testing with a String-Constraint Solver MIT, May 2009, PhD Thesis My defense slides Adam Kiezun, Refactoring Java Programs (orig. Refaktoryzacja programow w jezyku Java, html version), MIMUW, Warsaw, September 2001, MSc Thesis (in Polish) (awarded 3rd prize in the 18th national annual contest for best Master's Theses in Computer Science in Poland, 2001) Technical ReportsShay Artzi, Adam Kiezun, Julian Dolby, Frank Tip, Danny Dig, Amit Paradkar, and Michael D. ErnstFinding Bugs in Web Applications Using Dynamic Test Generation and Explicit State Model Checking, MIT CSAIL Tech Report MIT-CSAIL-TR-2009-010, March 2009 Adam Kiezun, Vijay Ganesh, Philip J. Guo, Pieter Hooimeijer, Michael D. Ernst HAMPI: A Solver For String Constraints, MIT CSAIL Tech Report MIT-CSAIL-TR-2009-004, February 2009 Adam Kiezun, Philip J. Guo, Karthick Jayaraman, Michael D. Ernst Automatic Creation of SQL Injection and Cross-site Scripting Attacks, MIT CSAIL Tech Report MIT-CSAIL-TR-2008-054, September 2008 Shay Artzi, Adam Kiezun, Julian Dolby, Frank Tip, Danny Dig, Amit Paradkar, Michael Ernst Finding bugs in dynamic Web applications, MIT CSAIL Tech Report MIT-CSAIL-TR-2008-006, February 2008 Patrice Godefroid, Adam Kiezun, Michael Y. Levin Grammar-based whitebox fuzzing, Microsoft Research Tech Report MSR-TR-2007-154, November 2007 Shay Artzi, Adam Kiezun, David Glasser, Michael D. Ernst Combined Static and Dynamic Mutability Analysis, MIT CSAIL Tech Report MIT-CSAIL-TR-2007-020, MIT, March 2007 Adam Kiezun, Michael Ernst, Frank Tip, Robert Fuhrer Refactoring for parameterizing Java classes, MIT CSAIL Tech Report MIT-CSAIL-TR-2006-61, MIT, September 2006 Shay Artzi, Michael Ernst, Adam Kiezun, Carlos Pacheco, Jeff Perkins Finding the needles in the haystack: Generating legal test inputs for object-oriented programs, MIT CSAIL Tech Report MIT-CSAIL-TR-2006-056, MIT, September 2006 Shay Artzi, Michael D. Ernst, David Glasser, and Adam Kiezun Combined Static and Dynamic Mutability Analysis, MIT CSAIL Tech Report MIT-CSAIL-TR-2006-065, MIT, September 2006 This work is superseded by the new technical report. Shay Artzi, Adam Kiezun, Calvin Newport and David Schultz Encrypted Keyword Search in a Distributed Storage System, MIT CSAIL Tech Report MIT-CSAIL-TR-2006-010, MIT, February 2006 Frank Tip, Robert
Fuhrer, Julian Dolby, and Adam Kiezun,
Refactoring techniques for migrating applications to generic Java container classes, IBM T.J. Watson Research Center IBM Research Report RC 23238, (Yorktown Heights, NY, USA), June 2, 2004. Frank Tip, Adam Kiezun,
and Dirk Bauemer,
Refactoring for generalization using type constraints, IBM Research Report 22662, December 4, 2002. MIT class projectsAdam KiezunApplying Binary Particle Swarm Optimization to Select Variables in Logistic Regression for Diagnosis of Myocardial Infarction, Project report in Medical Decision Support (HST951), MIT, December 2007 Shay Artzi and Adam Kiezun Analysis of Phylogenetic Distribution of microRNAs in Several Metazoan Species, Project report in Computational Biology (6.895), MIT, December 2006 Shay Artzi, Adam Kiezun, Carlos Pacheco, and Jeff Perkins Automatic Generation of Unit Regression Tests, Project report in Program Analysis (6.883), MIT, December 2005 Shay Artzi, Adam Kiezun, Calvin Newport and David Schultz Encrypted Keyword Search in a Distributed Storage System, (NOTE: if you want to cite it, please refer to the technical report) Project report in Distributed Computer Systems (6.824), MIT, May 2005 Demos
Adam Kiezun, Robert Fuhrer, Frank Tip and Markus Keller, |