Victoria Stodden

20042019
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Research Output 2004 2019

2019

Computing environments for reproducibility: Capturing the “Whole Tale”

Brinckman, A., Chard, K., Gaffney, N., Hategan, M., Jones, M. B., Kowalik, K., Kulasekaran, S., Ludaescher, B., Mecum, B. D., Nabrzyski, J., Stodden, V., Taylor, I. J., Turk, M. J. & Turner, K., May 2019, In : Future Generation Computer Systems. 94, p. 854-867 14 p.

Research output: Contribution to journalArticle

Data mining
Big data

Implementing computational reproducibility in the Whole Tale environment

Chard, K., Gaffney, N., Jones, M. B., Kowalik, K., Ludaescher, B., Nabrzyski, J., Stodden, V., Taylor, I., Turk, M. J. & Willis, C., Jun 17 2019, P-RECS 2019 - Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems, co-located with HPDC 2019. Association for Computing Machinery, Inc, p. 17-22 6 p. (P-RECS 2019 - Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems, co-located with HPDC 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Transparency
Pipelines
Experiments

Initial thoughts on cybersecurity and reproducibility

Deelman, E., Stodden, V., Taufer, M. & Welch, V., Jun 17 2019, P-RECS 2019 - Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems, co-located with HPDC 2019. Association for Computing Machinery, Inc, p. 13-15 3 p. (P-RECS 2019 - Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems, co-located with HPDC 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Computer systems

Scientific tests and continuous integration strategies to enhance reproducibility in the scientific software context

Krafczyk, M., Shi, A., Bhaskar, A., Marinov, D. & Stodden, V., Jun 17 2019, P-RECS 2019 - Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems, co-located with HPDC 2019. Association for Computing Machinery, Inc, p. 23-28 6 p. (P-RECS 2019 - Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems, co-located with HPDC 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Software testing
Physics
Testing
Open source software
2018

AIM: AN ABSTRACTION for IMPROVING MACHINE LEARNING PREDICTION

Stodden, V., Wu, X. & Sochat, V., Aug 17 2018, 2018 IEEE Data Science Workshop, DSW 2018 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 150-154 5 p. 8439914. (2018 IEEE Data Science Workshop, DSW 2018 - Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Learning systems
Machine Learning
Prediction
Pipelines
prediction

An empirical analysis of journal policy effectiveness for computational reproducibility

Stodden, V., Seiler, J. & Ma, Z., Mar 13 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 11, p. 2584-2589 6 p.

Research output: Contribution to journalArticle

workflow
random sample
artifact
communication
science

Enabling the verification of computational results

Stodden, V., Krafczyk, M. S. & Bhaskar, A., Jun 11 2018, Proceedings of the 1st International Workshop on Practical Reproducible Evaluation of Computer Systems, P-RECS 2018. Association for Computing Machinery, Inc, 3. (Proceedings of the 1st International Workshop on Practical Reproducible Evaluation of Computer Systems, P-RECS 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Deposits
Physics
Availability
Specifications

Realizing the potential of data science

Berman, F., Rutenbar, R., Hailpern, B., Christensen, H., Davidson, S., Estrin, D., Franklin, M., Martonosi, M., Raghavan, P., Stodden, V. & Szalay, A. S., Apr 2018, In : Communications of the ACM. 61, 4, p. 67-72 6 p.

Research output: Contribution to journalArticle

Reproducibility and replicability of rodent phenotyping in preclinical studies

Kafkafi, N., Agassi, J., Chesler, E. J., Crabbe, J. C., Crusio, W. E., Eilam, D., Gerlai, R., Golani, I., Gomez-Marin, A., Heller, R., Iraqi, F., Jaljuli, I., Karp, N. A., Morgan, H., Nicholson, G., Pfaff, D. W., Richter, S. H., Stark, P. B., Stiedl, O., Stodden, V. & 6 others, Tarantino, L. M., Tucci, V., Valdar, W., Williams, R. W., Würbel, H. & Benjamini, Y., Apr 2018, In : Neuroscience and Biobehavioral Reviews. 87, p. 218-232 15 p.

Research output: Contribution to journalReview article

Information Dissemination
Rodentia
Genotype
Research Personnel
Health

Reproducibility of research: Issues and proposed remedies

Allison, D. B., Shiffrin, R. M. & Stodden, V., Mar 13 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 11, p. 2561-2562 2 p.

Research output: Contribution to journalEditorial

2017

Four simple recommendations to encourage best practices in research software

Jiménez, R. C., Kuzak, M., Alhamdoosh, M., Barker, M., Batut, B., Borg, M., Capella-Gutierrez, S., Chue Hong, N., Cook, M., Corpas, M., Flannery, M., Garcia, L., Gelpí, J. L., Gladman, S., Goble, C., González Ferreiro, M., Gonzalez-Beltran, A., Griffin, P. C., Grüning, B., Hagberg, J. & 29 others, Holub, P., Hooft, R., Ison, J., Katz, D. S., Leskošek, B., López Gómez, F., Oliveira, L. J., Mellor, D., Mosbergen, R., Mulder, N., Perez-Riverol, Y., Pergl, R., Pichler, H., Pope, B., Sanz, F., Schneider, M. V., Stodden, V., Suchecki, R., Svobodová Vařeková, R., Talvik, H. A., Todorov, I., Treloar, A., Tyagi, S., van Gompel, M., Vaughan, D., Via, A., Wang, X., Watson-Haigh, N. S. & Crouch, S., Jan 1 2017, In : F1000Research. 6, 876.

Research output: Contribution to journalArticle

Practice Guidelines
Software
Research
Sustainable development
Software engineering

Structuring supplemental materials in support of reproducibility

Greenbaum, D., Rozowsky, J., Stodden, V. & Gerstein, M., Apr 5 2017, In : Genome biology. 18, 1, 64.

Research output: Contribution to journalArticle

Genomics
reproducibility
branching
genomics
material
2016

Enhancing reproducibility for computational methods

Stodden, V., McNutt, M., Bailey, D. H., Deelman, E., Gil, Y., Hanson, B., Heroux, M. A., Ioannidis, J. P. A. & Taufer, M., Dec 9 2016, In : Science. 354, 6317, p. 1240-1241 2 p.

Research output: Contribution to journalReview article

Making massive computational experiments painless

Monajemi, H., Donoho, D. L. & Stodden, V., Jan 1 2016, Proceedings - 2016 IEEE International Conference on Big Data, Big Data 2016. Ak, R., Karypis, G., Xia, Y., Hu, X. T., Yu, P. S., Joshi, J., Ungar, L., Liu, L., Sato, A-H., Suzumura, T., Rachuri, S., Govindaraju, R. & Xu, W. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2368-2373 6 p. 7840870. (Proceedings - 2016 IEEE International Conference on Big Data, Big Data 2016).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Program processors
Experiments
Cluster computing
Taxonomies
Design of experiments
2015

Facilitating Reproducibility in Scientific Computing: Principles and Practice

Bailey, D. H., Borwein, J. M. & Stodden, V., Jan 1 2015, Reproducibility: Principles, Problems, Practices, and Prospects. Wiley, p. 205-231 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Scientific Computing
Reproducibility
Tide
workflow
Wake

Reproducing statistical results

Stodden, V., Apr 10 2015, In : Annual Review of Statistics and Its Application. 2, p. 1-19 19 p.

Research output: Contribution to journalArticle

Disclosure
Reproducibility
Statistical test
Incentives
Reward

ResearchCompendia.org: Cyberinfrastructure for reproducibility and collaboration in computational science

Stodden, V., Miguez, S. & Seiler, J., Jan 1 2015, In : Computing in Science and Engineering. 17, 1, p. 12-19 8 p., 7030302.

Research output: Contribution to journalArticle

Transparency
Demonstrations
Pipelines

Self-correction in science at work: Improve incentives to support research integrity

Alberts, B., Cicerone, R. J., Fienberg, S. E., Kamb, A., McNutt, M., Nerem, R. M., Schekman, R., Shiffrin, R., Stodden, V., Suresh, S., Zuber, M. T., Pope, B. K. & Jamieson, K. H., Jun 26 2015, In : Science. 348, 6242, p. 1420-1422 3 p.

Research output: Contribution to journalShort survey

Scientific Misconduct
educational development
Organizational Policy
education policy
health education
2014

Implementing reproducible research

Stodden, V., Leisch, F. & Peng, R. D., Jan 1 2014, CRC Press. 419 p.

Research output: Book/ReportBook

Computational Science
Reproducibility
Software
Open Source Software
Cloud Computing
Leishmania major
amastigotes
promastigotes
antimicrobial peptides
Parasites

RunMyCode.Org: A research-reproducibility tool for computational sciences

Hurlin, C., Pérignon, C. & Stodden, V., Jan 1 2014, Implementing Reproducible Research. CRC Press, p. 367-382 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Computational Science
Reproducibility
Local System
Web-based
Availability

The reproducible research movement in statistics

Stodden, V., 2014, In : Statistical Journal of the IAOS. 30, 2, p. 91-93 3 p.

Research output: Contribution to journalArticle

Statistics
Movement
Open science
Science policy

What computational scientists need to know about intellectual property law: A primer

Stodden, V., Jan 1 2014, Implementing Reproducible Research. CRC Press, p. 325-340 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Intellectual Property
Computational Science
Data Sharing
Output
Citations
2013

editors’ introduction

Lane, J., Stodden, V., Bender, S. & Nissenbaum, H., Jan 1 2013, Privacy, Big Data, and the Public Good: Frameworks for Engagement. Cambridge University Press, p. xi-xix

Research output: Chapter in Book/Report/Conference proceedingForeword/postscript

Privacy
Confidentiality
Likely
Requirements
Costs

Enabling Reproducibility in Big Data Research: Balancing onfidentiality and Scientific Transparency

Stodden, V., Jan 1 2013, Privacy, Big Data, and the Public Good: Frameworks for Engagement. Cambridge University Press, p. 112-132 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Reproducibility
Transparency
Balancing
Digitization
Privacy

Privacy, big data, and the public good: Frameworks for engagement

Lane, J., Stodden, V., Bender, S. & Nissenbaum, H., Jan 1 2013, Cambridge University Press. 322 p.

Research output: Book/ReportBook

Privacy
Confidentiality
Maximise
Framework
Engagement

Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals

Stodden, V., Guo, P. & Ma, Z., Jun 21 2013, In : PloS one. 8, 6, e67111.

Research output: Contribution to journalArticle

Empirical Research
data analysis
Availability
Information Dissemination
2012

Reproducible research: Tools and strategies for scientific computing

Stodden, V., Jul 30 2012, In : Computing in Science and Engineering. 14, 4, p. 11-12 2 p., 6241363.

Research output: Contribution to journalEditorial

Natural sciences computing

Reproducible research for scientific computing: Tools and strategies for changing the culture

Leveque, R., Mitchell, I. & Stodden, V., Jul 30 2012, In : Computing in Science and Engineering. 14, 4, p. 13-17 5 p., 6171147.

Research output: Contribution to journalArticle

Natural sciences computing

RunMyCode.org: A novel dissemination and collaboration platform for executing published computational results

Stodden, V., Hurlin, C. & Pérignon, C., Dec 1 2012, 2012 IEEE 8th International Conference on E-Science, e-Science 2012. 6404455. (2012 IEEE 8th International Conference on E-Science, e-Science 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Websites
Availability
2010
science policy
Lead
Innovation
innovation
science

Reproducible research concepts and tools for cancer bioinformatics

Carey, V. J. & Stodden, V., 2010, Biomedical Informatics for Cancer Research. Springer US, p. 149-175 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Computational Biology
Research
Neoplasms
Earth Sciences
Software
2009

A global empirical evaluation of new communication technology use and democratic tendency

Stodden, V. & Meier, P., Dec 1 2009, 2009 International Conference on Information and Communication Technologies and Development, ICTD 2009 - Proceedings. p. 3-16 14 p. 5426719. (2009 International Conference on Information and Communication Technologies and Development, ICTD 2009 - Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Internet
Communication
Regression analysis
Time series

Reproducible research in computational harmonic analysis

Donoho, D. L., Maleki, A., Shahram, M., Rahman, I. U. & Stodden, V., Jan 1 2009, In : Computing in Science and Engineering. 11, 1, p. 8-18 11 p., 4720218.

Research output: Contribution to journalArticle

Harmonic analysis
Atomizers
2007

Virtual northern analysis of the human genome

Hurowitz, E. H., Drori, I., Stodden, V., Donoho, D. L. & Brown, P. O., May 23 2007, In : PloS one. 2, 5, e460.

Research output: Contribution to journalArticle

Human Genome
Genes
Messenger RNA
genome
Untranslated Regions
2006

Breakdown point of model selection when the number of variables exceeds the number of observations

Donoho, D. & Stodden, V., Dec 1 2006, International Joint Conference on Neural Networks 2006, IJCNN '06. p. 1916-1921 6 p. 1716344. (IEEE International Conference on Neural Networks - Conference Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Linear regression
Recovery

Fast ℓ1 minimization for genomewide analysis of mRNA lengths

Drori, I., Stodden, V. & Hurowitz, E. H., 2006, 2006 IEEE International Workshop on Genomic Signal Processing and Statstics, GENSIPS 2006. p. 19-20 2 p. 4161756

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Messenger RNA
Genes
Gene
Complementary DNA
Nonnegative Solution
2005

Multiscale representations for manifold-valued data

Rahman, I. U., Drori, I., Stodden, V., Donoho, D. L. & Schröder, P., Dec 1 2005, In : Multiscale Modeling and Simulation. 4, 4, p. 1201-1232 32 p.

Research output: Contribution to journalArticle

wavelet
compression
Wavelet Coefficients
software
matrix
2004

When does non-negative matrix factorization give a correct decomposition into parts?

Donoho, D. & Stodden, V., Jan 1 2004, Advances in Neural Information Processing Systems 16 - Proceedings of the 2003 Conference, NIPS 2003. Neural information processing systems foundation, (Advances in Neural Information Processing Systems).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Factorization
Decomposition
Cones
Sampling