2024

• From Models to Practice: Enhancing OSS Project Sustainability with Evidence-Based Advice
  N. Khan, V Filkov
  ACM International Conference on the Foundations of Software Engineering, IVR, 2024
  
  
• Do We Run How We Say We Run? Formalization and Practice of Governance in OSS Communities
  M Chakraborti, C Atkisson, Ş Stănciulescu, V Filkov, S Frey
  Proceedings of the CHI Conference on Human Factors in Computing Systems, 1-26
  
  

2023

• GitHub OSS Governance File Dataset
  Y Yan, S Frey, A Zhang, V Filkov, L Yin
  2023 IEEE/ACM 20th International Conference on Mining Software Repositories
  
  
• On the Self-Governance and Episodic Changes in Apache Incubator Projects: An Empirical Study
  Yin, L., Zhang, X., Filkov, V.
  ICSE 2023
  
  

2022

• Code, Quality, and Process Metrics in Graduated and Retired ASFI Projects
  Stanciulescu, S., Yin, L., Filkov, V.
  FSE 2022
  
  
• Open Source Software Sustainability: Combining Institutional Analysis and Socio-Technical Networks
  Yin, L., Chakraborti, M., Yan, Y.,Schweik, C., Frey, S., Filkov, V.
  CSCW 2022
  
  
• Exploring Apache Incubator Project Trajectories with APEX
  Ramchandran, A., Yin,L., Filkov, V.
  MSR 2022, Tool track
  
  
• Evolution and differentiation of the cybersecurity communities in three social question and answer sites: A mixed-methods analysis
  Wu, M., Aranovich, R., Filkov, V.
  PLOS One
  
  

2021

• Beyond NVD: Cybersecurity meets the Semantic Web
  Aranovich, L., Wu, M., Yu, Yu, D., Katsy, K., Ahmadnia, B., Bishop, M., Filkov, V., Sagae, K.
  NSPW 2021
  
  
• Sustainability Forecasting for Apache Incubator Projects
  Yin, L., Chen, Z., Xuan, Q., Filkov, V.
  ESEC/SIGSOFT FSE 2021
  
  
• Apache Software Foundation Incubator Project Sustainability Dataset
  Yin, L., Chen, Z., Xuan, Q., Filkov, V.
  MSR 2021, Data track
  
  

2020

• Team Discussions and Dynamics During DevOps Tool Adoptions in OSS Projects
  Yin, L., Filkov, V.
  ASE 2020
  ACM Distinguished Paper Award
  
  
• Evolutionary network genomics of wood formation in a phylogenetic survey of angiosperm forest trees
  Zinkgraf, M., Zhao, S., Gerttula, S., Canning, C.; Lu, M-Z. Filkov, V., Groover, A.
  New Phytologist
  
  
• Software Visualization and Deep Transfer Learning for Effective Software Defect Prediction
  Chen, J. Hu, K. , Yu, Y., Chen, Z., Xuan, Q., Liu, Y., Filkov, V.
  ICSE 2020, Seoul, South Korea
  
  

2019

• Whom Are You Going to Call? Determinants of @-Mentions in GitHub Discussions. Preprint is here.
  Kavaler, D., Devanbu, P., Filkov, V.
  ESE 2019
  
  
• Status, Identity, and Language: A Study of Issue Discussions in GitHub
  Liao, J., Kavaler, D., Yang, G., Filkov, V., Devanbu, P.
  PLOS One 2019
  
  
• Socio-Technical Work-Rate Increase Associates With Changes in Work Patterns in Online Projects
  Sarker, F., Vasilescu, B., Blincoe, K., and Filkov, V.
  International Conference on Software Engineering, ICSE, IEEE (2019)
  
  
• Tool Choice Matters: JavaScript Quality Assurance Tools and Usage Outcomes in GitHub Projects
  Kavaler, D., Trockman, A., Vasilescu, B., and Filkov, V.
  International Conference on Software Engineering, ICSE, IEEE (2019)
  
  
• Studying Android App Popularity by Cross-Linking GitHub and Google Play Store
  J Businge, M Openja, D Kavaler, E Bainomugisha, F Khomh, V Filkov
  26th IEEE International Conference on Software Analysis, Evolution and Reengineering, SANER, 2019
  
  

2018

• Cross-Project Code Clones in GitHub
  M. Gharehyazie, B. Ray, V. Filkov
  Empirical Software Engineering journal, 2019
  
  
• Reconstructing Gene Networks of Forest Trees from Gene Expression Data: Toward Higher-Resolution Approaches (invited)
  M. Zinkgraf, A. Groover, V. Filkov
  ICT Innovations 2018, CCIS 940, Springer
  
  
• Within-Ecosystem Issue Linking: A Large-Scale Study of Rails"
  Y. Zhang, Y. Yu, H. Wang, B. Vasilescu, V. Filkov
  Proceedings of the 7th ACM/IEEE International Workshop on Software Mining
  
  
• Whom Are You Going to Call?: Determinants of @-Mentions in GitHub Discussions
  D. Kavaler, P. Devanbu, V. Filkov
  arXiv:1806.08457, 2018
  
  
• Multiple feedback loops of the Arabidopsis circadian clock provide rhythmic robustness across environmental conditions
  A. Shalit-Kaneh, R.W. Kumimoto, V. Filkov, S.L. Harmer
  PNAS June 18, 2018. 201805524
  
  
• One Size Does Not Fit All: An Empirical Study of Containerized Continuous Deployment Workflows
  Y. Zhang, B. Vasilescu, H. Wang, V. Filkov
  FSE 2018, accepted
  
  
• Modern Food Foraging Patterns: Geography and Cuisine Choices of Restaurant Patrons on Yelp
  Q. Xuan, M. Zhou, Z. Zhang, C. Fu, Y. Xiang, Z. Wu, V. Filkov
  IEEE Transactions on Computational Social Systems, vol. 5, no. 2, pp. 508-517, June 2018. doi: 10.1109/TCSS.2018.2819659
  
  
• A Clustering-based Approach for Mining Dockerfile Evolutionary Trajectories
  Y. Zhang, H. Wang, V. Filkov
  SCIS
  
  
• Determinants of quality, latency, and amount of Stack Overflow answers about recent Android APIs
  D. Kavaler, V. Filkov
  PLOS One, March 2018, https://doi.org/10.1371/journal.pone.0194139
  
  
• Transcriptional and temporal response of Populus stems to gravi-stimulation
  M. Zinkgraf, S. Gertulla, S. Zhao, V. Filkov, A. Groover
  Journal of Integrative Plant Biology (JIPB), https://doi.org/10.1111/jipb.12645

2017

• A Large Scale Study of Programming Languages and Code Quality in Github
  B. Ray, D. Posnett, P. Devanbu, V. Filkov
  CACM, 60 (10), p.91-100, 2017
  CACM also ran a Technical Perspective article about our article. It is available here.
  
  
• How Do Software Engineering Practices Change Following Adoption of Continuous Integration?
  Y. Zhao, Y. Zhou, A. Serebrenik, V. Filkov, B. Vasilescu
  32nd IEEE/ACM International Conference on Automated Software Engineering, 2017
  
  
• Perceived Language Complexity in GitHub Issue Discussions and Their Effect on Issue Resolution
  D. Kavaler, S. Sirovica, V. Helendoorn, R. Aranovich, V. Filkov
  32nd IEEE/ACM International Conference on Automated Software Engineering, 2017
  
  
• Social synchrony on complex networks (preprint.)
  Q. Xuan, Z.-Y. Zhang, C. Fu, H.-. Hu, V. Filkov
  IEEE Transactions on Cybernetics, PP(99), p.1-12, 2017
  
  
• Some From Here, Some From There: Cross-Project Code Reuse in GitHub
  Mohammad Gharehyazie, Baishakhi Ray and Vladimir Filkov
  MSR 2017
  ACM Distinguished Paper Award
  
  
• Identifying gene coexpression networks underlying the dynamic regulation of wood forming tissues in Populus under diverse environmental conditions (offprint).
  M. Zinkgraf, L. Liu, A. Groover, V. Filkov
  New Phytologist 2017 Mar 1. doi: 10.1111/nph.14492.

2016

• Tracing distributed collaborative development in apache software foundation projects
  Mohammad Gharehyazie, Vladimir Filkov
  Empirical Software Engineering, 2016, doi:10.1007/s10664-016-9463-3
  
  
• Initial and Eventual Software Quality Relating to Continuous Integration in GitHub
  Yue Yu, Bogdan Vasilescu, Huaimin Wang, Vladimir Filkov, Premkumar Devanbu
  arXiv:1606.00521, 2016
  
  
• Converging Work-Talk Patterns in Online Task-Oriented Communities
  Qi Xuan, Premkumar Devanbu, and Vladimir Filkov
  PLOS One 11(5): e0154324. doi:10.1371/journal.pone.0154324, 2016
  
  
• Stochastic actor-oriented modeling for studying homophily and social influence in OSS projects (offprint).
  David Kavaler, Vladimir Filkov
  Empirical Software Engineering, p.1-29, 2016, doi:10.1007/s10664-016-9431-y
  
  
• The Sky is Not the Limit: Multitasking Across GitHub Projects
  Bogdan Vasilescu, Kelly Blincoe, Qi Xuan, Casey Casalnuovo, Daniela Damian, Premkumar Devanbu, and Vladimir Filkov
  ICSE 2016
  
  
• Transcriptional and Hormonal Regulation of Gravitropism of Woody Stems in Populus
  Suzanne Gerttula, Matthew Zinkgraf, Gloria Muday, Daniel Lewis, Farid M Ibatullin, Harry Brumer, Foster Hart, Shawn D Mansfield, Vladimir Filkov, Andrew Groover
  Plant Cell, October 2015
  An "In Brief" article about our article: When a Tree Falls in the Woods: The Gravitropic Response in Poplar
  The article was featured on the journal's cover page.

2015

• Developer Onboarding in GitHub: The Role of Prior Social Links and Language Experience
  Casey Casalnuovo, Bogdan Vasilescu, Prem Devanbu and Vladimir Filkov
  ESEC/FSE 2015
  
  
• Quality and Productivity Outcomes Relating to Continuous Integration in GitHub
  Bogdan Vasilescu, Yu Yue, Huaimin Wang, Premkumar Devanbu and Vladimir Filkov
  ESEC/FSE 2015
  
  
• Temporal motifs reveal collaboration patterns in online task-oriented networks
  Qi Xuan, Huiting Fang, Chenbo Fu, Vladimir Filkov
  Physical Revue E 91, 052813 (2015)
  
  
• A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus
  Liu, Lijun; Ramsay, Trevor; Zinkgraf, Matthew; Sundell, David; Street, Nathaniel; Filkov, Vladimir; Groover, Andrew
  The Plant Journal 82(5): 887-898 (2015)
  
  
• Wait For It: Determinants of Pull Request Evaluation Latency on GitHub.
  Yu, Y., Wang, H., Filkov, V., Devanbu, P., and Vasilescu, B.
  12th Working Conference on Mining Software Repositories, MSR, IEEE (2015).
  
  
• A Data Set for Social Diversity Studies of GitHub Teams.
  Vasilescu, B., Serebrenik, A., and Filkov, V.
  12th Working Conference on Mining Software Repositories, Data Track, MSR, IEEE (2015).
  
  
• Perceptions of Diversity on GitHub: A User Survey.
  Vasilescu, B., Filkov, V., and Serebrenik, A.
  8th International Workshop on Cooperative and Human Aspects of Software Engineering, CHASE, IEEE (2015).
  
  
• Gender and Tenure Diversity in GitHub Teams Erratum.
  Bogdan Vasilescu, Daryl Posnett, Baishakhi Ray, Mark van den Brand, Alexander Serebrenik, Premkumar Devanbu, Vladimir Filkov
  International Conference on Human Factors in Computing Systems, ACM CHI 2015.
  
  
• Assert Use in GitHub Projects
  Casey Casalnuovo, Prem Devanbu, Abilio Oliveira, Vladimir Filkov, Baishakhi Ray
  The 37th International Conference on Software Engineering, ICSE 2015.
  
  
• The Populus ARBORKNOX1 homeobox transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function
  Lijun Liu, Matthew Zinkgraf, H. Earl Petzold, Eric P. Beers, Vladimir Filkov, and Andrew Groover
  New Phytologist, 205(2): 682-694, 2015
  
  

2014

• Converging Work-Talk Patterns in Online Task-Oriented Communities
  Qi Xuan, Prem Devanbu, Vladimir Filkov
  CoRR abs/1404.5708 (2014)
  
  
• Focus-Shifting Patterns of OSS Developers and Their Congruence with Call Graphs
  Qi Xuan, Aaron Okano, Prem Devanbu, Vladimir Filkov Nominee: ACM Distinguished Paper Award
  ACM SIGSOFT FSE 2014
  
  
• A Large Scale Study of Programming Languages and Code Quality in Github
  Baishakhi Ray, Daryl Posnett, Vladimir Filkov, Prem Devanbu
  ACM SIGSOFT FSE 2014
  
  This is slightly updated from the version available in the ACM digital library. Due to a bug in GitHub Linguist, our TypeScript data was incorrect. This version corrects the errors. Some of the findings (concerning TypeScript) changed, and are highlighted in the PDF. We are requesting a change to the ACM DL version.
  
  
• Developer initiation and social interactions in OSS: A case study of the Apache Software Foundation
  Mohammad Gharehyazie, Daryl Posnett, Bogdan Vasilescu, Vladimir Filkov
  Empirical Software Engineering (this is a much extended version of our ICSM 2013 paper below)
  
  
• Building It Together: Synchronous Development in OSS
  Qi Xuan, Vladimir Filkov
  ACM/IEEE 36th International Conference on Software Engineering, ICSE 2014
  
  
• Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
  Lijun Liu, Victor Missirian, Matthew Zinkgraf, Andrew Groover and Vladimir Filkov
  BMC Genomics
  
  
• How Social Q&A Sites are Changing Knowledge Sharing in Open Source Software Communities
  Bogdan Vasilescu, Alexander Serebrenik, Prem Devanbu, Vladimir Filkov
  17th ACM Conference on Computer Supported Cooperative Work and Social Computing (CSCW 2014)
  

2013

• Modeling transcriptional networks regulating secondary growth and wood formation in forest trees
  Lijun Liu, Vladimir Filkov, Andrew Groover
  Physiologia Plantarum, 2013
  
  
• StackOverflow and GitHub: Associations Between Software Development and Crowdsourced Knowledge
  Bogdan Vasilescu, Vladimir Filkov, Alexander Serebrenik
  IEEE International Conference on Social Computing (SocialCom 2013)
  
  
• Synchrony in Social Groups and Its Benefits
  Qi Xuan, Vladimir Filkov
  Chapter in Handbook of Human Computation, Michelucci P. (ed.), Springer 2013
  
  
• Social Activities Rival Patch Submission For Prediction of Developer Initiation in OSS Projects Nominee: ACM Distinguished Paper Award
  Mohammad Gharehyazie, Daryl Posnett, Vladimir Filkov
  29th IEEE International Conference on Software Maintenance, Eindhoven, The Netherlands 2013
  
  
• Asking for (and about) Permissions Used by Android Apps
  Ryan Stevens, Jonathan Ganz, Vladimir Filkov, Hao Chen, Premkumar Devanbu
  IEEE/ACM 10th Working Conference on Mining Software Repositories, MSR 2013
  
  
• Janus: prediction and ranking of mutations required for functional interconversion of enzymes
  Addington TA, Mertz RW, Siegel JB, Thompson JM, Fisher AJ, Filkov V, Fleischman NM, Suen AA, Zhang C, Toney MD
  Journal of Molecular Biology, 425(8): 1378-1389, 2013
  
  
• Dual Ecological Measures of Focus for Software Development Winner: ACM Distinguished Paper Award
  Daryl Posnett, Raissa D'Souza, Prem Devanbu, Vladimir Filkov
  ACM/IEEE 35th International Conference of Software Engineering, ICSE 2013
  
  
• Using and Asking: APIs Used in the Android Market and Asked About in StackOverflow Best Paper Runner-Up (top 5%)
  David Kavaler, Daryl Posnett, Clint Gibler, Hao Chen, Prem Devanbu, Vladimir Filkov
  The 5th International Conference on Social Informatics (SocInfo2013)
  

• Ecological inference in empirical software engineering. Winner: Best Paper Award and ACM Distinguished Paper Award
  D. Posnett, V. Filkov, P. Devanbu.
  Proceedings of the 26th IEEE/ACM International Conference on Automated Software Engineering (ASE), 2011
  
  
• Discovery of Rare Mutations in Populations: TILLING by Sequencing
  H. Tsai, T. Howell, R. Nitcher, V. Missirian, B. Watson, K. Ngo, M. Lieberman, J. Fass, C. Uauy, R. Tran, A. Khan, V. Filkov, T. Tai, J. Dubcovsky, L. Comai.
  Plant Physiology, 156(3), 1257-1268, 2011
  
  
• Statistical Mutation Calling from Sequenced Overlapping DNA Pools in TILLING Experiments
  V. Missirian, L. Comai, V. Filkov.
  BMC Bioinformatics, 12:287, 2011
  
  
• Validity of Network Analyses in Open Source Projects
  R. Nia, C. Bird, P. Devanbu, V. Filkov.
  Proceedings of the Seventh Working Conference on Mining Software Repositories, 2010
  
  
• Strong associations between microbe phenotypes and their network architecture
  S. Roy, V. Filkov
  Physical Review E 80, 040902(R), 2009 (rapid communication) 
  
  
• Fair and Balanced? Bias in bug-fix Datasets
  C. Bird, A. Bachmann, E. Aune, J. Duffy, A. Bernstein, V. Filkov, P. Devanbu
  Proceedings of SIGSOFT FSE 2009
  
  
• Modeling and verifying a broad array of network properties
  V. Filkov, Z. M. Saul, S. Roy, R. M. D'Souza, P. T. Devanbu
  EPL (Europhysics Letters) 2009 April; 86(2), 28003
  
  
• From Architecture to Function (and Back) in Bio-networks (Invited)
  V. FIlkov
  Proceedings of 1st International Conference on Bioinformatics and Computational Bilogy (BICoB) 2009
  
  
• Evolution of Apache Open Source Software
  H.-R. Wen, R.M. D'Souza, Z. M. Saul, V. Filkov
  chapter in Dynamics On and Of Complex Networks, Birkhauser, Springer. 2009
  
  
• Structure and Dynamics of Research Collaboration in Computer Science
  C. Bird, E. Barr, A. Nash, P. Devanbu, V. Filkov, and Z. Su.
  Proceedings of SIAM International Conference on Data Mining (SDM), 2009, 826-837.
  
  
• A Simple Model of the Modular Structure of Transcriptional Regulation in Yeast
  V. Filkov, N. Shah
  Journal of Computational Biology 2008 May; 15(4): 393-405.
  
  
• Latent Social Structure in Open Source Projects
  C. Bird, D. Pattison, R. D'Souza, V. Filkov, P. Devanbu
  Proceedings of SIGSOFT FSE 2008, 24-35.
  
  
• Consensus Clustering Algorithms: Comparison and Refinement
  A. Goder, V. Filkov
  Proceedings of ALENEX 2008, 109-117.
  
  
• Exploring Biological Network Structure Using Exponential Random Graph Models
  Z. M. Saul; V. Filkov
  Bioinformatics 2007 Oct 1;23(19):2604-11. 
  
  
• Recommending Random Walks Nominee: ACM Distinguished Paper Award
  Z. M. Saul, V. Filkov, P. Devanbu, C. Bird
  Proceedings of ESEC/SIGSOFT FSE 2007, 15-24.
  
  
• Methods for Random Modularization of Biological Networks
  Z. M. Saul, V. Filkov
  Proceedings of BIBE 2006: 285-288.
  
  
• A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem
  Z. Ding, V. Filkov, D. Gusfield
  Journal of Computational Biology 2006 Mar;13(2):522-553
  (a shorter version appeared at RECOMB 2005). 
  
  
• Identifying Gene Regulatory Networks from Gene Expression Data
  V. Filkov
  chapter in Handbook of Computational Molecular Biology (S. Aluru editor), Chapman&Hall/CRC Press 2005.
  
  
• Microarray Data Integration and Top-Down Modeling of Gene Regulation
  V. Filkov (invited)
  Proceedings of 4th Int.Conf. on Informatics and IT, 2004, 423-432. (2004).
  
  
• Regulation Hierarchies from Expression Data
  V. Filkov, N. Shah
  Proceedings of RECOMB Satellite Workshop on Regulatory Genomics, 88-97, 2004.
  
  
• Heterogeneous Data Integration with the Consensus Clustering Formalism
  V. Filkov,  S. Skiena
  Proceedings of DILS'04, 110-123, 2004.
  
  
• Integrating Microarray Data by Consensus Clustering
  V. Filkov, S. Skiena
  International Journal on Artificial Intelligence Tools, 13(4): 863-880, 2004 
  
  
• GeneBox: Interactive Visualization of Microarray Data Sets
  N. Shah, V. Filkov, B. Hamann, K. Joy
  Proceedings of METMBS'03, 10-16, 2003.
  
  
• Computational Understanding of Cis-Regions
  V. Filkov, S. Istrail (invited)
  Genome Informatics 13:236-239, 2002.
  
  
• Computational Understanding of Gene Regulation
  Vladimir Filkov
  PhD Thesis, Stony Brook University
  
  
• Analysis Techniques for Microarray Time-Series Data
  V. Filkov, S. Skiena, J. Zhu
  Journal of Computational Biology 9:317-330, 2002
  (a shorter version appeared at RECOMB 2001).
  
  
• Covering Points on a Circle with Circular Arcs
  V. Filkov
  Proceedings of CCCG 2000.
  
  
• Identifying Gene Regulatory Networks from Experimental Data
  T. Chen, V. Filkov, S. Skiena
  Proceedings of RECOMB 1999
  (extended version appeared in Parallel Computing, 27(1-2): 141-162, 2001).