Software tools

    Hampi: solver for string constraints
    Kaluza: 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

Publications

Trevor 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 Moyer
The 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.



Dirk Baeumer, Erich Gamma and Adam Kiezun,
Integrating refactoring support into a Java development tool
In OOPSLA'01 Companion (October 2001).

Theses

Adam 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 Reports

Shay Artzi, Adam Kiezun, Julian Dolby, Frank Tip, Danny Dig, Amit Paradkar, and Michael D. Ernst
Finding 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

  

Demos

Adam Kiezun, Robert Fuhrer, Frank Tip and Markus Keller,
Generics-related Refactorings in Eclipse,
Demo at OOPSLA'05, San Diego, USA

Robert Fuhrer, Frank Tip, Adam Kiezun and Markus Keller,
Generics-related Refactorings in Eclipse,
Demo at ECOOP'05, Glasgow, UK

Robert Fuhrer, Frank Tip and Adam Kiezun,
Advanced Refactorings in Eclipse,
In OOPSLA'04 Companion (November 2004), Vancouver, Canada  

Robert Fuhrer, Frank Tip and Adam Kiezun,
Advanced Refactorings in Eclipse,
Demo at ECOOP'04, Oslo, Norway

Invited Talks and Presentations

Dagstuhl Seminar ''Types for Tools: Applications of Type Theoretic Techniques'', Refactoring for Parameterization of Java Classes, Dagstuhl, Germany, 2005

COMARCH Research Lab, Refactoring and code manipulation support in Eclipse, Warsaw, Poland, April 2004

Polish Java User's Group meeting, Refactoring and code manipulation support in Eclipse, Warsaw, Poland, April 2004

Dagstuhl Seminar ''Program Analysis for Object-Oriented Evolution'', Refactoring support in Eclipse, Dagstuhl, Germany, 2003

IBM Developer's day, Extending Eclipse, Heidelberg, Germany, 2002

Belgian Java Users' Group Seminar, 3-day tutorial about Eclipse, Brussels, Belgium, 2003