Papers authored or co-authored by RENCI staff are included in this archive. These papers were either published in academic/scientific journals or included in the proceedings of a professional conference. Please note that links to papers in online journals may be changed or removed by the journal and that passwords are sometimes required.
Fecho, K., Thessen, A.E., Baranzini, S.E., Bizon, C., Hadlock, J.J., Huang, S…The Biomedical Data Translator Consortium (2022). Progress toward a universal biomedical data translator. Clin Transl Sci. doi: 10.1111/cts.13301.
Unni, D.R., Moxon, S.A.T., Bada, M., Brush, M., Bruskiewich,R., Caufield, J.H…The Biomedical Data Translator Consortium (2022). Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci. doi: 10.1111/cts.13302.
Fecho, K., Ahalt, S.C., Appold, S., Arunachalam, S., Pfaff, E., Stillwell, L., …Peden, D.B. (2022). Development and Application of an Open Tool for Sharing and Analyzing Integrated Clinical and Environmental Exposures Data: Asthma Use Case. JMIR Formative Research. doi: 10.2196/32357.
Grossman, R.L., Boyles, R.R., Davis-Dusenbery, B.N., Haddock, A., Heath, A.P., Brian D O’Connor, …Ahalt. S. (2022). A Framework for the Interoperability of Cloud Platforms: Towards FAIR Data in SAFE Environments. arXiv (preprint).
Barnes, R.H, Golden, M.L., Borland, D., Heckert, R., Richardson, M., Creighton, R.A., Spang, J., Kamath, G. (2022). Computational metrics to quantify video quality in arthroscopic surgery. Arthroscopy. Available online 7 December 2021. https://doi.org/10.1016/j.asmr.2021.10.017
Kaul, S., Borland, D., Cao, N., Gotz, D. (2022). Improving visualization interpretation using counterfactuals. IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE VIS 2021). Early access. https://doi.org/10.1109/TVCG.2021.3114779
Thomas, A., Dietrich, J.C., Dawson, C., and Luettich, R.A. (2022). Effects of model resolution and coverage on storm-driven flooding predictions. Journal of Waterway, Port, Coastal, and Ocean Engineering, 148(1):04021046; DOI: 10.1061/(ASCE) WW.1943-5460.0000687.
Alves, V.M., Korn, D., Pervitsky, V., Thieme, A., Capuzzi, S.J., Baker, N., Chirkova, R., Ekins, S., Muratov, E.N., Hickey, A., & Tropsha, A. (2021). Knowledge-based approaches to drug discovery for rare diseases. Drug Discovery Today. https://doi.org/10.1016/j.drudis.2021.10.014
Fecho, K.,* Ahalt, S.C., Appold, S., Arunachalam, S., Pfaff, E., Stillwell, L., Valencia, A., Xu, H., & Peden, D. (2021). Factors influencing asthma exacerbations revealed through application of an open tool for sharing and exploring integrated clinical and environmental data. JMIR Formative Research. *Apart from the first/lead and last/senior author, all other authors are listed in alphabetical order.
Korn, D., Thieme, A.J., Yeakey, M., Alves, V.M., Borba, J.V.V.B., Capuzzi, S.J., Fecho, K., Bizon, C., Chirkova, R., Colvis, C.M., Southall, N.T., Austin, C.P., Muratov, E.N., & Tropsha, A. (2021). Defining clinical outcome pathways. Nat Rev Drug Discov, under peer review.
Fecho, K., Haaland, P., Krishnamurthy, A., Lan, B., Ramsey, S., Schmitt, P.L., Sharma, P., Sinha, M., & Xu H. (2021). An approach for open multivariate analysis of integrated clinical and environmental exposures data. Inform Med Unlocked 2021;26:100733. doi.org/10.1016/j.imu.2021.100733
Lan, B., Haaland, P., Krishnamurthy, A., Schmitt, P., Sharma, P., Sinha, M., Xu, H., & Fecho, K. (2021). Open application of statistical and machine learning models to explore the impact of environment exposures on health and disease: an asthma use case. Int J Environ Res Public Health, 18(21):11398 [published as part of a special issue titled “Application of Biostatistical Modelling in Public Health and Epidemiology”]. doi: 10.3390/ijerph182111398.
Borland, D., et al. (2021). Enabling exploratory longitudinal analysis of UNC Health Data on COVID. Conference paper, Proceedings of Visual Analytics in Healthcare 2021, in press. Preprint available at: ArXiv 2021:arXiv:2108.11476v1.
Fecho, K., Bizon, C., Miller, F.W., Schurman, S., Schmitt, C., Xue, W., Morton, K., Wang, P., & Tropsha, A. (2021). A biomedical knowledge graph system to propose mechanistic hypotheses for real-world environmental health observations: cohort study and informatics application. JMIR Medical Informatics, 9(7):e26714. doi: 10.2196/26714.
Fecho, K.,* Balhoff, J., Bizon, C., Byrd, W.E., Hang, S., Koslicki, D., Rensi, S.E., Schmitt, P., Wawer, M.J., Williams, M., & Ahalt, S.C. (2021). Application of MCAT questions as a testing tool and evaluation metric for knowledge graph–based reasoning systems. Clin Transl Sci 2021,14(5):1719–1724. doi: 10.1111/cts.13021 [online ahead of print]. *Apart from the first and last authors, all other authors are listed in alphabetical order.
Jackson, R., Matentzoglu, N., Overton, J.A., Vita, R., Balhoff, J.P., Buttigieg, P.L., Carbon, S., Courtot, M., Diehl, A.D., Dooley, D.M., Duncan, W.D., Harris, N.L., Haendel, M.A., Lewis, S.E., Natale, D.A., Osumi-Sutherland, D., Ruttenberg, A., Schriml, L.M., Smith, B., Stoeckert Jr., C.J., Vasilevsky, N.A., Walls, R.L., Zheng, J., Mungall, C.J., Peters, B. (Oct 2021). OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database. https://doi.org/10.1093/database/baab069
Patterson, J.R., Thomas, S.R., Shaw, D., Hayes, J.A., Daley, C.R., Knight, S., … and Krishnamurthy, A.K. (September 2021). COVID-19 data utilization in North Carolina: A qualitative analysis. JMIR Public Health and Surveillance, 7(9):e29310. doi: 10.2196/29310.
Papadimitriou, G., Wang, C., Vahi, K., Ferreira da Silva, R., Mandal, A., Liu, Z…Foster, I. (April 2021). End-to-end online performance data capture and analysis for scientific workflows. Future Generation Computer Systems, 117, 387-400. [Awarded 2021 Best paper for Elsevier Future Generation Computer Systems Journal]
Tu, H., Papadimitriou, G., Kiran, M., Wang, C., Mandal, A., Deelman, E., and Menzies, T. (May 2021). Mining workflows for anomalous data transfers. The 2021 Mining Software Repositories Conference.
Krawczuk, P., Papadimitriou, G., Nagarkar, S., Kiran, M., Mandal, A., and Deelman, E. (July 2021). Anomaly detection in scientific workflows using End-to-End Execution Gantt Charts and Convolutional Neural Networks. ACM Practice and Experience in Advanced Research Computing (PEARC 2021) Conference, Virtual.
Deelman, E., Mandal, A., Murillo, A.P., Nabrzyski, J., Pascucci, V., Ricci, R., Baldin, I., Sons, S., Christopherson, L., Vardeman, C., Ferreira da Silva, R., Wyngaard, J., Petruzza, S., Rynge, M., Vahi, K., Whitcup, W. R., Drake, J., and Scott, E. (Sept 2021). Blueprint: Cyberinfrastructure Center of Excellence. Zenodo. https://doi.org/10.5281/zenodo.4587866
Xie, B., Cao, Q., Kunjir, M., Wan, L., Chase, J., Mandal,A., & Rynge, M. (Sep 2021). WIRE: Resource-efficient Scaling with Online Prediction for DAG-based Workflows. The IEEE Cluster 2021 Conference (CLUSTER 2021), pp. 35-46, doi: 10.1109/Cluster48925.2021.00025.
Lyons, E., Seo, D., Kim, S., Habibi, H., Papadimitriou, G., Tanaka, R., Deelman, E., Zink, M., & Mandal, A. (Sept 2021). Predicting Flash Floods in the Dallas-Fort Worth Metroplex Using Workflows and Cloud Computing. The IEEE eScience 2021 Conference, Poster, Virtual, pp. 259-261, doi: 10.1109/eScience51609.2021.00050.
Brock, J., Christopherson, L., Deelman, E., Ferreira da Silva, R., Kee, K., Murillo, A…Whitcup, W. (Sept 2021). CI CoE and CI4Resilience’s Creating a Thriving Workplace Workshop Report. Zenodo, doi:10.5281/zenodo.5523235.
Xin, Y., Fu, S.W., Mandal, A., Baldin, I., Tanaka, R., Rynge, M…Welch, V. (Oct 2021). Root cause analysis of data integrity errors in networked systems with incomplete information. The 12th International Conference on Information and Communication Technology Convergence (ICTC 2021), Jeju Island, South Korea.
Krawczuk, P., Papadimitriou, G., Tanaka, R., Do, T.M.A., Subramanya, S., Nagarkar, S…Deelman, E. (Nov 2021). A data-oriented characterization of scientific machine learning workflows. The 16th Workshop on Workflows in Support of Large-Scale Science (WORKS ’21), St. Louis, MO.
Lyons, E., Wang, S., Thareja, K., Qu, C., Papadimitriou, G., Tanaka, R…Zink, M. (Dec 2021). FlyNet: A platform to support scientific workflows from the edge to the core for UAV applications. 2021 IEEE/ACM 14th International Conference on Utility and Cloud Computing (UCC 2021), Leicester, UK.
Richelle, A., Kellman, B.P., Wenzel, A.T., Chiang, A.W.T., Reagan, T., Gutierrez, J.M…, Robasky, K., Lewis, N.E. (2021). What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data. Cell Reports Methods, 1(3). https://doi.org/10.1016/j.crmeth.2021.100040
Borland, D., McCormick, C.M., Patel, N.K., Krupa, O., Mory, J.T., Beltran, A.A…Stein, J.L. (2021). Segmentor: a tool for manual refinement of 3D microscopy annotations. BMC Bioinformatics. 22(260). https://doi.org/10.1186/s12859-021-04202-8
Ma, J., Krupa, O., Glass, M.R., McCormick, C.M., Borland, D…Wu, G. (2021). 3D nucleus instance segmentation for whole-brain microscopy images. Information Processing in Medical Imaging (IPMI). Lecture Notes in Computer Science. 12729:504-516. http://dx.doi.org/10.1007/978-3-030-78191-0_39
Good, B.M., Auken, K.V., Hill, D.P., Mi, H., Carbon, S., Balhoff, J.P…D’Eustachio, P. (2021). Reactome and the Gene Ontology: Digital convergence of data resources. Bioinformatics https://doi.org/10.1093/bioinformatics/btab325
Filer, D.L., Kuo, F., Brandt, A.T., Tilley , C.R., Mieczkowski, P.A., Berg, J.S., Robasky, K., Li, Y., Bizon, C., Tilson, J.L., Powell, B.C., Bost D.M., Jeffries, C.D., Wilhelmsen, K.C. (2021). Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing. BMC Bioinformatics. (accepted, not yet published)
Filer, D.L., Mieczkowski, P.A., Brandt, A., Gilmore, K.L., Powell, B.C., Berg, J.S., Wilhelmsen, K.C., Vora, N.L. (2021). Noninvasive prenatal exome sequencing diagnostic utility limited by sequencing depth and fetal fraction. Prenatal Diagnosis. (accepted, not yet published)
Rahouti, M., Xiong, K., and Xin, Y. (2021). Secure software-defined networking communication systems for smart cities: Current status, challenges, and trends. IEEE Access, 9, 12083-12113. doi: 10.1109/ACCESS.2020.3047996.
Choi, Y-D., Goodall, J.L., Sadler, J.M., Castronova, A.M., Bennett, A., Li, Z., Nijssen, B. …Tarboton, G. (January 2021). Toward open and reproducible environmental modeling by integrating online data repositories, computational environments, and model Application Programming Interfaces. Environmental Modelling & Software, 135, 233-240. DOI: 10.1016/j.envsoft.2020.104888.
Reese, J.T., Unni, D., Callahan, T.J., Cappelletti, L., Ravanmehr, V., Carbon, S. …Mungall, C.J. (2021). KG-COVID-19: A framework to produce customized knowledge graphs for COVID-19 response. Patterns. https://doi.org/10.1016/j.patter.2020.100155.
Qi, K., Borland, D., Brunsen, E., Minogue, J., Peck, T. (2021). The impact of prior knowledge on the effectiveness of haptic feedback and visual modalities for teaching forces. Proceedings of the 2021 International Conference on Multimodal Interaction (ICMI ’21). 203-211. https://dl.acm.org/doi/abs/10.1145/3462244.3479915
The Gene Ontology Consortium (including Balhoff, J.P.). (2021). The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa1113.
Borland, D., Zhang, J., Kaul, S., and Gotz, D. (2021). Selection-bias-corrected visualization via dynamic reweighting. IEEE Transactions on Visualization and Computer Graphics (Proceedings of Visual Analytics Science and Technology 2020), 27(2), 1481-1491. https://doi.org/10.1109/TVCG.2020.3030455
Fecho, K., Garantziotis, S., Krishnamurthy, A., Pfaff, E., Schmitt, C., Schurman, S., Shuptrine, S., Xu, H., and Ahalt, S. (2021). Open integrated analysis of multi-institutional data using ICEES. AMIA 2021 Informatics Summit. [conference proceedings].
Stemerman, R., Arguello, J., Brice, J., Krishnamurthy, A., Houston, M., and Kitzmiller, R. (February 2021). Identification of social determinants of health using multi-label classification of electronic health record clinical notes. JAMIA Open. doi: https://doi.org/10.1093/jamiaopen/ooaa069.
Agarwal, M., Calloway, C., Niederhut, D., Shupe, D., editors. (2021). Proceedings of the 20th Python in Science Conference. http://doi.org/10.25080/majora-1b6fd038-02b
M. Rahouti, K. Xiong, Y. Xin, N. Ghani (Oct. 2021). QoSP: A Priority-Based Queueing Mechanism in Software-Defined Networking Environments. 40th IEEE International Performance Computing and Communications Conference.
Yi, H., Bizon, C., Borland, D., Matthew, W., Matthew, S., Rittmuller, R., Ranwan, R., Srinivasan, R., and Krishnamurthy, A, AI Tool with Active Learning for Detection of Rural Roadside Safety Features, IEEE Machine Learning on Big Data special session of IEEE BigData 2021, Dec., 2021. (accepted, to be published in Dec. 2021)
Vaidya, G., Cellinese, N. and Lapp, H. (2021) JPhyloRef: a tool for testing and resolving phyloreferences. Journal of Open Source Software, 6(64), 3374, https://doi.org/10.21105/joss.03374
Bao, B., Gazestani, V. H., Xiao, Y., Kim, R., Chiang, A. W., Nalabolu, S., Pierce, K., Robasky, K., Lewis, N.E., Courchesne, E. (2021). A Highly Accurate Ensemble Classifier for the Molecular Diagnosis of ASD at Ages 1 to 4 Years. medRxiv.
Robasky, K., Kim, R., Yi, H., Xu, H., Bao, B., Chiang, A. W., … & Lewis, N. E. (2021). Transfer learning improves outcome predictions for ASD from gene expression in blood. bioRxiv.
Waldrop, A.M., Cheadle, J.B, Bradford, K., Braswell, N., Watson, M., Crerar, A…Cox S. (2021). Dug: A semantic search engine leveraging peer-reviewed literature to span biomedical data repositories. bioRxiv. 2021.07.07.451461; doi: https://doi.org/10.1101/2021.07.07.451461
Vaidya, G., Cellinese, N., Lapp, H. (2021) A new phylogenetic data standard for computable clade definitions: The Phyloreference Exchange Format (Phyx). PeerJ, accepted.
Russell, T. (2021). iRODS User Group Meeting 2021 Proceedings. https://irods.org/ugm2021/.
Aikaterini, P.K., Taflanidis, A.A., Plumlee, M., Asher, T.G., Spiller, E., Luettich, Jr…Shmied, L. (2021). Improvements in storm surge surrogate modeling for synthetic storm parameterization, node condition classification and implementation to small size databases. Natural Hazards. DOI: 10.1007/s11069-021-04881-9.
Rucker, C.A.,Tull, N., Dietrich, J.C., Langan, T.E., Mitasova, H., Blanton, B.O…Luettich, R.A. (2021). Downscaling of real-time coastal flooding predictions for decision support. Natural Hazards. DOI: 10.1007/s11069-021-04634-8.
Evensen, G., Amezcua, J., Bocquet, M., Carrassi, A., Farchi, A., Fowler, A… Vossepoel, F.C. (2021). An international initiative of predicting the SARS-CoV-2 pandemic using ensemble data assimilation. Foundation of Data Science Conference (FODS 2021), 3(3): 413-477. doi: 10.3934/fods.2021001.
Fleurantin, E., Sampson, C., Maes, D.P., Bennett, J., Fernandes-Nunez, T., Marx, S., and Evensen, G. (2021). A study of disproportionately affected populations by race/ethnicity during the SARS-CoV-2 pandemic using multi-population SEIR modeling and ensemble data assimilation. Foundation of Data Science Conference (FODS 2021), 3(3): 479-541. doi: 10.3934/fods.2021022.
Gotz, D., Zhang, J., Wang, W., Shrestha, J., & Borland, D. (2020). Visual analysis of high-dimensional event sequence data via dynamic hierarchical aggregation. IEEE Transactions on Visualization and Computer Graphics (Proceedings of Visual Analytics Science and Technology 2019). 26(1):440-450. https://doi.ieeecomputersociety.org/10.1109/TVCG.2019.2934661.
Gotz, D., Zhang, J., Kaul, S., Bobashev, G., and Borland, D. (2020). Visual analytics to combat selection bias in retrospective EHR data analyses. American Medical Informatics Association (AMIA) Annual Symposium Podium Abstract.
Aliverti, E., Tilson, J.L., Filer, D.L., Babcock, B., Colaneri, A., Ocasio, J., … Dunson, D.B. (2020). Projected t-SNE for batch correction. Bioinformatics, 36(11), 3522–3527. https://doi.org/10.1093/bioinformatics/btaa189.
Cox, S., Ahalt, S.C., Balhoff, J., Bizon, C., Fecho, K., Kebede, Y. …Xu, H. (2020). TranQL: An interactive query and visualization environment for federated knowledge graphs. JMIR Preprints, 17964. doi: 10.2196/preprints.17964.
Feng, Y., Judi, D.R., and Rakowski, C.L. (2020). An assessment of the influence of uncertainty in temporally evolving streamflow forecasts on riverine inundation modeling. Water, 12(3), 911. https://doi.org/10.3390/w12030911.
Gan, T., Tarboton, D.G., Horsburgh, J.S., Dash, P., Idaszak, R., and Yi, H. (2020). Collaborative sharing of multidimensional space-time data in a next generation hydrologic information system. Environmental Modelling & Software, 129, 104706. https://doi.org/10.1016/j.envsoft.2020.104706
Gonzalez-Liencres, C., Zapata, L.E., Iruretagoyena, G., Seinfeld, S., Perez-Mendez, L., Arroyo-Palacios, J., … Sanchez-Vives, M.V. (2020). Being the victim of intimate partner violence in virtual reality: First- versus third-person perspective. Frontiers in Psychology, 11. https://doi.org/10.3389/fpsyg.2020.00820
Jeffries, C., Ford, J., Tilson, J., Perkins, D., Bost, D., Filer, D., and Wilhelmsen, K. (March 2020). Frisky CALF outruns LASSO. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.03.27.011700
Kiran, M., Wang, C., Papadimitriou, G., Mandal, A., and Deelman, E. (2020). Detecting Anomalous Packets in Network Transfers: Investigations using PCA, Autoencoder and Isolation Forest. TCP, Machine Learning. https://doi.org/10.1007/s10994-020-05870-y
Peng, Q., Wilhelmsen, K.C., and Ehlers, C.L. (2020). Common genetic substrates of alcohol and substance use disorder severity revealed by pleiotropy detection against GWAS catalog in two populations. Addict Biol, e12877. doi: 10.1111/adb.12877.
Robasky, K., Boyles, R., Bradford, K. C., Gold, M., Lenhardt, W. C., McKeen, S., … Ahalt, S. (2020). How to Launch Transdisciplinary Research Communication. RTI Press. https://doi.org/10.3768/rtipress.2020.rb.0022.2004.
Vora, N.L., Gilmore, K., Brandt, A., Gustafson, C., Strande, N., Ramkissoon, L., Hardisty, E., Foreman, A.K.M., Wilhelmsen, K., Owen, P., Weck, K. E., Berg, J.S., Powell, C.M., and Powell, B.C. (2020). An approach to integrating exome sequencing for fetal structural anomalies into clinical practice. Genetics in medicine: official journal of the American College of Medical Genetics. doi: 10.1038/s41436-020-0750-4.
Xu, H., Cox, S., Stillwell, L., Pfaff, E., Champion, J., Ahalt, S.C., and Fecho, K. (March 2020). FHIR PIT: an open software application for spatiotemporal integration of clinical data and environmental exposures data. BMC Medical Informatics and Decision Making, 20(53). doi: 10.1186/s12911-020-1056-9.
Agarwal, M., Calloway, C., Niederhut, D., Shupe, D., editors. (2020). Proceedings of the 19th Python in Science Conference. http://doi.org/10.25080/Majora-342d178e-02b
Bizon, C., Fecho, K., Cox, S., Balhoff, J., Kebede, Y., Wang, P., Morton, K., Ahalt, S.C., and Tropsha, A. (November 2020). Application of a biomedical question-answering system to support reasoning on MCAT questions. AMIA 2020 Annual Symposium, conference paper [proceedings are in press].
Fecho, K., Bizon, C., Miller, F.W., Schurman, S., Schmitt, C., Xue, W., Wang, P., Morton, K., Cox, S., Tropsha, A. (November 2020). Use of the open ROBOKOP knowledge graph–based application to provide mechanistic explanations for observed associations between environmental exposures and immune-mediated diseases. AMIA 2020 Annual Symposium, conference paper [proceedings are in press].
Cox, S., Dong, X., Rai, R., Christopherson, L., Zheng, W., Tropsha, A., and Schmitt, C. (2020). A semantic similarity based methodology for predicting protein-protein interactions: Evaluation with P53-interacting kinases. J Biomed Inform, 111:103579. doi: 10.1016/j.jbi.2020.103579.
Thessen, A.E., Walls, R.L., Vogt, L., Singer, J., Warren, R., Buttigieg, P.L. …Haendel, M.A. (2020). Transforming the study of organisms: Phenomic data models and knowledge bases. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1008376.
Valencia, A., Stillwell, L., Appold, S., Arunachalam, S., Cox, S., Xu, H. …Fecho, K. (July 21, 2020). Translator Exposure APIs: Open access to data on airborne pollutant exposures, roadway exposures, and socio-environmental exposures and use case application. Int. J. Environ. Res. Public Health, 17(14), 5243. doi: 10.3390/ijerph17145243.
Cox, S., Ahalt, S.C., Balhoff, J., Bizon, C., Fecho, K., Kebede, Y., …Xu, H. (November 23, 2020). Visualization environment for federated knowledge graphs: Development of an interactive biomedical query language and web application interface. JMIR Med Inform, 8(11). doi: 10.2196/17964. PMID: 33226347; PMCID: PMC7721550.
Russell, T. (2020). iRODS User Group Meeting 2020 Proceedings. https://irods.org/ugm2020/.
Gan, T., Tarboton, D., Horsburgh, J., Dash, P., Idaszak, R., and Yi, H. (July 2020). Collaborative sharing of multidimensional space-time data in a next generation hydrologic information system. Environmental Modelling & Software, 129. DOI: 10.1016/j.envsoft.2020.104706.
Perkins, D.O., Jeffries, C.D., Do, K.Q. (August 15, 2020). Potential roles of redox dysregulation in the development of schizophrenia. Biol Psychiatry, 88(4), 326-336. doi: 10.1016/j.biopsych.2020.03.016. Epub 2020 Apr 2. PMID: 32560962 Review.
Korn, D., Bobrowski, T., Li, M., Kebede, Y., Wang, P., Owen, P. …Tropsha, A. (November 11, 2020). COVID-KOP: Integrating emerging COVID-19 data with the ROBOKOP database. Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa718.
Korn, D., Pervitsky, V., Bobrowski, T., Alves, V., Schmitt, C., Bizon, C. …Tropsha, A. (2020): COVID-19 Knowledge Extractor (COKE): A tool and a web portal to extract drug-target protein associations from the CORD-19 Corpus of Scientific Publications on COVID-19. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.13289222.v
Aliverti, E., Tilson, J.L., Filer, D.L., Babcock, B., Colaneri, A., Ocasio, J. …David B Dunson. (June 2020). Projected t-SNE for batch correction. Bioinformatics, 36(11), 3522–3527. https://doi.org/10.1093/bioinformatics/btaa189.
Yang, Y., Li, G., Qian, H., Wilhelmsen, K.C., Shen, Y., and Li, Y. (2020). SMNN: Batch effect correction for single-cell RNA-seq data via supervised mutual nearest neighbor detection. Bioinformatics. https://doi.org/10.1093/bib/bbaa097.
Vora, N.L., Gilmore, K., Brandt, A., Gustafson, C., Strande, N., Ramkissoon, L. …Powell, B.C. (2020). Correction: An approach to integrating exome sequencing for fetal structural anomalies into clinical practice. Genet Med, 22, 1426. https://doi.org/10.1038/s41436-020-0870-x.
Haendel, M.A., Chute, C.G., and Gersing. K. The national COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. JAMIA 2020. https://doi.org/10.1093/jamia/ocaa196. [Fecho, K., author collaborator]
Christopherson, L., Mandal, A., Scott, E., and Baldin, I. (July 2020). Toward a data lifecycle model for NSF large facilities. PEARC ’20: Practice and Experience in Advanced Research Computing, 168-175. https://doi.org/10.1145/3311790.3396636.
Tavares, M. (August 2020). Converging data privacy and security. ISSA Journal 2020. https://www.issa.org/journal/august-2020/.
Lyons, E., Westbrook, D., Grote, A., Papadimitriou, G., Thareja, K., Wang, C. …Ruth, P. (November 2020). An on-demand weather avoidance system for small aircraft flight path routing. Darema, F., Blasch, E., Ravela, S., and Aved, A. (eds). Dynamic Data Driven Applications Systems (DDDAS 2020). Lecture Notes in Computer Science, 12312. Springer, Cham. https://doi.org/10.1007/978-3-030-61725-7_36.
Papadimitriou, G., Lyons, E., Wang, C., Thareja, K., Tanaka, R., Ruth, P. …Mandal, A. (November 2020). Application aware software defined flows of workflow ensembles. 2020 IEEE/ACM Innovating the Network for Data-Intensive Science (INDIS). doi: 10.1109/INDIS51933.2020.00007.
Cutcher‐Gershenfeld, J., Baker, K.S., Berente, N., Berkman, P.A., Canavan, P., Feltus, F. A., … Veazey, P. (2020). Negotiated sharing of pandemic data, models, and resources. Negotiation Journal, 36(4), 497-534. https://doi.org/10.1111/nejo.12340.
Vaidya, G., Lapp, H., and Cellinese, N. (October 2020). Enabling machines to integrate biodiversity data with evolutionary knowledge. Biodiversity Information Science and Standards, 4:e59088. https://doi.org/10.3897/biss.4.59088.
Pfaff, E.R., Crosskey, M., Morton, K., Krishnamurthy, A. (2020). Clinical Annotation Research Kit (CLARK): Computable phenotyping using machine learning. JMIR Med Inform 2020, 8(1):e16042. doi: 10.2196/16042.
Mohamed Rahouti, Kaiqi Xiong, Yufeng Xin (Nov. 2020). Prototyping an SDN Control Framework for QoS Guarantees. International Conference on Testbeds and Research Infrastructures.
Borland, D., Wang, W., Zhang, J., Shrestha, J., & D. Gotz. (2019). Selection bias tracking and detailed subset comparison for high-dimensional data. IEEE Transactions on Visualization and Computer Graphics (Proceedings of Visual Analytics Science and Technology 2019). 26(1):429-439. 2020. https://doi.ieeecomputersociety.org/10.1109/TVCG.2019.2934209
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Bandaragoda, C., Castronova, A., Istanbulluoglu, E., Strauch, R., Nudurupati, S., Phuong, J.,…Adams, J.M. (2019). Enabling collaborative numerical modeling in earth sciences using knowledge infrastructure. Environmental Modelling & Software, 120, 104424. doi: 10.1016/j.envsoft.2019.03.020.
The Biomedical Data Translator Consortium (2019). Toward a universal biomedical data translator. Clinical and Translation Science, 12(2), 86-90. doi:10.1111/cts.12591.
The Biomedical Data Translator Consortium (2019). The Biomedical Data Translator Program: Conception, culture, and community. Clinical and Translational Science, 12(2), 91-94. doi: 10.1111/cts.12592.
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Borland, D., Christopherson, L., and Schmitt, C. (2019). Ontology-based interactive visualization of patient-generated research questions. Applied Clinical Informatics, 10(03), 377–386. doi: 10.1055/s-0039-1688938.
Calloway, C., Lippa, D., Niederhut, D., and Shupe, D. (2019). Proceedings of the 18th Python in Science Conference (SciPy 2019). Austin, TX. doi:10.25080/Majora-7ddc1dd1-026.
Berente, N., Brunson, D., King, J.L., Wilkins-Diehr, N., Ahalt, S.C., Cutcher-Gershenfeld, J., …Neeman, H. (2019). The professionalization of cyberinfrastructure personnel. PEARC19.
Daniel, J.B., Clarke, L.W., Jones, A., Wojciechowicz, M.L., Torre, D., Jagodnik, K.M.,…Jenkins, S.L. (2019). FAIRshake: Toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources. BioRxiv. doi: 10.1101/657676.
Das, S., Werner, J., Antonakakis, M., Polychronakis, M., and Monrose, F. (2019). SoK: The challenges, pitfalls, and perils of using hardware performance counters for security. 2019 IEEE Symposium on Security and Privacy (SP). doi: 10.1109/sp.2019.00021.
Erhardt, R., Bell, J., Blanton, B., Nutter, F., Robinson, M., and Smith, R. (2019). Stronger climate resilience with insurance. Bulletin of the American Meteorological Society, 100(8), 1549-1552. doi: 10.1175/bams-d-19-0073.1.
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The Gene Ontology Consortium (including Balhoff, J.P.). (2019). The Gene Ontology Resource: 20 years and still going strong. Nucleic Acids Research, 47(D1), D330-D338. doi: 10.1093/nar/gky1055.
Gotz, D., Zhang, J., Wang, W., Shrestha, J., and Borland, D. (2019). Visual analysis of high-dimensional event sequence data via dynamic hierarchical aggregation. IEEE Transactions on Visualization and Computer Graphics, 26(1), 1. doi: 10.1109/tvcg.2019.2934661.
Gotz, D., Wang, W., Chen, A.T., and Borland, D. (2019). Visualization model validation via inline replication. Information Visualization, 18(4), 405-425. doi: 10.1177/1473871618821747.
Jackson, R.C., Balhoff, J.P., Douglass, E., Harris, N.L., Mungall, C.J., and Overton, J. A. (2019). ROBOT: A tool for automating ontology workflows. BMC Bioinformatics, 20(407). doi: 10.1186/s12859-019-3002-3.
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Lander, H., Alpert, K., Rajasekar, A., Turner, J., and Wang, L. (2019). Data discovery for case studies: The DataBridge for Neuroscience project. Proceedings of the 13th International Multi-Conference on Society, Cybernetics and Informatics, 1, 19-25.
Mabee, P.M., Balhoff, J.P., Dahdul, W.M., Lapp, H., Mungall, C.J., and Vision, T.J. (2019). A logical model of homology for comparative biology. Systematic Biology. doi: 10.1093/sysbio/syz067.
Morton, K., Wang, P., Bizon, C., Cox, S., Balhoff, J., Kebede, Y., Fecho, K., and Tropsha, A. (2019). ROBOKOP: An abstraction layer and user interface for knowledge graphs to support question answering. Bioinformatics. doi: 10.1093/bioinformatics/btz604.
Peng, Q., Bizon, C., Gizer, I.R., Wilhelmsen, K.C., and Ehlers, C.L. (2019). Genetic loci for alcohol-related life events and substance-induced affective symptoms: indexing the “dark side” of addiction. Translational Psychiatry, 9(1). doi: 10.1038/s41398-019-0397-6.
Stucky, B.J., Balhoff, J.P., Barve, N., Barve, V., Brenskelle, L., Brush, M.H.,…Dahlem, G.A. (2019). Developing a vocabulary and ontology for modeling insect natural history data: Example data, use cases, and competency questions. Biodiversity Data Journal, 7. doi: 10.3897/bdj.7.e33303.
Thomas, P.D., Hill, D.P., Mi, H., Osumi-Sutherland, D., Auken, K.V., Carbon, S.,…Balhoff, J.P. (2019). Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. Nature Genetics, 51(10), 1429–1433. doi: 10.1038/s41588-019-0500-1.
Thomas, A., Dietrich, J.C., Asher, T.G., Bell, M., Blanton, B.O., Copeland, J.H.,…Cox, A.T. (2019). Influence of storm timing and forward speed on tides and storm surge during Hurricane Matthew. Ocean Modelling, 137, 1-19. doi: 10.1016/j.ocemod.2019.03.004.
Werner, J., Mason, J., Antonakakis, M., Polychronakis, M., and Monrose, F. (2019). The SEVerESt of them all. Proceedings of the 2019 ACM Asia Conference on Computer and Communications Security – Asia CCS 19, 73-85. doi: 10.1145/3321705.3329820.
Wu, D.T.Y., Chen, A.T., Manning, J.D., Levy-Fix, G., Backonja, U., Borland, D.,…Caban, J.J. (2019). Evaluating visual analytics for health informatics applications: A systematic review from the American Medical Informatics Association Visual Analytics Working Group Task Force on Evaluation. Journal of the American Medical Informatics Association, 26(4), 314-323. doi: 10.1093/jamia/ocy190.
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Yang, K., Davidson, R.A., Vergara, H., Kolar, R.L., Dresback, K.M., Colle, B.A.,…Blanton, B. (2019). Incorporating inland flooding into hurricane evacuation decision support modeling. Natural Hazards, 96(2), 857–878. doi: 10.1007/s11069-019-03573-9.
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Borland, D., Wang, W., & Gotz, D. Contextual visualization: making the unseen visible to combat bias during visual analysis. (2018). IEEE Computer Graphics and Applications. Accepted for publication.
Borland, D., Yi, H., Grant, G.D., Kedziora, K.M., Chao, H.X., Haggerty, R.A., Kumar, J., Wolff, S.C., Cook, J.G., & Purvis, J.E. (2018). The Cell Cycle Browser: an interactive tool for visualizing, simulating, and perturbing cell cycle progression. Cell Systems. Accepted for publication.
Borland, D. Visualizing Information. Duke Center for Health Informatics Short Course. U.S. Food and Drug Administration. March 16, 2018.
Blanton, B., Dresback, K., Colle, B., Kolar, R., Vergara, H., Hong, Y., Leonardo, N., Davidson, R., Nozick, L. & Wachtendorf, T. (2018). An integrated scenario ensemble-based framework for hurricane evacuation modeling: Part 2-Hazard Modeling. Risk Analysis.
Cyriac, R., Dietrich, J., Fleming, J., Blanton, B., Kaiser, C., Dawson, C., & Luettich, R. (2018). Variability in coastal flooding predictions due to forecast errors during Hurricane Arthur. Coastal Engineering, 137, 59 – 78.
Davidson, R., Nozick, L., Wachtendorf, T, Blanton, B., Colle, B., Kolar, R., DeYoung, S., Dresback, K., Yi, W., Yang, K., & Leonardo, N. (2018). An integrated scenario ensemble-based framework for hurricane evacuation modeling: Part 1-Hazard Modeling. Risk Analysis.
Fang, J., Castillo, C., & Ahalt, S. (2018, April). Cachalot: A network-aware, cooperative cache network for geo-distributed, data-intensive applications. IEEE/IFIP Network Operations and Management Symposium. Taipei, Taiwan.
Fellinger, D. (2018, February). Coping with “Big Data” in research computing. eResearch New Zealand. Queenstown, New Zealand.
Gao, S., Shrivastava, S., Ogan, K., Baldin, I., & Xin, Y. (2018, June). Evaluating path query mechanisms as a foundation for SDN network control. IEEE Conference on Network Softwarization (Netsoft). Montreal, Canada.
Idaszak, R, Tarboton, D.G. (PI), Yi, H., Calloway, C., Wang, S., Horsburgh, J., Ames, D., Clark, M., Goodall, J., Couch, A., Castronova., T., Bandaragoda, C., Seul, M., Henderson, M., & Doan, P. (2018, June). HydroShare and iRODS: How iRODS manages data for a hydrology community of 1000’s of users. iRODS User Group Meeting. Durham, NC.
Jackson, L.M., Fernando, P.C., Hanscom, J.S., Balhoff, J.P., & Mabee, P.M. (2018). Automated integration of trees and traits: A case study using paired fin loss across teleost fishes. Systematic Biology, 67, 559–575.
Jeffries, C.D., Perkins, D.O., Fournier, M., Do, K.Q., Cuenod, M., Khadimallah, I., Domenici, E., Addington, J., Bearden, C.E., Cadenhead, K.S., Cannon, T.D., Cornblatt, B.A., Mathalon, D.H., McGlashan, T.H., Seidman, L.J., Tsuang, M., Walker, E.F., & Woods, S.W. (2018). Networks of blood proteins in the neuroimmunology of schizophrenia. Translational Psychiatry, 8(1), 112. doi: 10.1038/s41398-018-0158-y.
Katz, D. S., Niemeyer, K. E., Gesing, S., Hwang, L., Bangerth, W., Hettrick, S., … Lago, P. (2018). Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4). Journal of Open Research Software, 6(1), 10. DOI: http://doi.org/10.5334/jors.184.
Karancia, A., Stillwell, L., Lenhardt, W.C., & Dietrich, C. (2018, June). Cyberinfrastructure for enhancing interdisciplinary engagement in coastal risk management research. iEMSs 2018. Fort Collins, CO.
Kiran, M., Wang, C., Rao, N.S.V. & Mandal, A. (2018, July). Detecting outliers in network transfers with feature extraction. DISE1: Joint Workshop on Deep (or Machine) Learning for Safety-Critical Applications in Engineering, co-located with 35th International Conference on Machine Learning. Stockholm, Sweden.
Lenhardt, W. C., & Blanton. B. (2018). NC Policy Collaboratory Project Report: Increasing Access to Certain North Carolina Environmental Monitoring and Natural Resource Data (pp. 1-42, Rep.). Chapel Hill, NC: RENCI, UNC-Chapel Hill.
Morton, M., Werner, J., Kintis, P., Snow, K., Antonakakis, M., Polychronakis, M., & Monrose, F. (2018, April). Security risks in asynchronous web servers: When performance optimizations amplify the impact of data-oriented attacks. 3rd IEEE European Symposium on Security and Privacy. London, United Kingdom.
Ni, H., Rahouti, M., Chakrabortty, A., Xiong, K., & Xin, Y. (2018, August). Routing path optimization for regulating delays in wide-area controllers implemented over cloud networks. IEEE PES General Meeting. Portland, OR.
Rajasekar, A., Lander, H, & Lenhardt, W.C. (2018, January). Analytics for earth science data discovery: Applying DataBridge to long-tail and large data collections in the earth and environmental sciences. ESIP Winter Meeting. Bethesda, MD.
Ramirez, G., Sarino, F., Tilson, J.L., & Ermler, W.C. Spin-Orbit configuration interaction calculations of electronic transition energies and spectral properties of PbO. Journal of Chemistry (under review).
Schmitt, C. Chase, J., Baldin, I., Coposky, J., Shoffner, M., Lamm, B., & Mostafa, J. (2018). US Patent No. 9984245B2. Chapel Hill, NC.
Yi, H., Idaszak, R., Stealey, M., Calloway, C., Couch, A.L., & Tarboton, D.G. (2018). Advancing distributed data management for the HydroShare hydrologic information system. Elsevier Environmental Modelling & Software, 102, 233–240.
Seinfeld,,S. Arroyo-Palacios, J., Iruretagoyena, G., Hortensius, R., Zapata, L.E., Borland, D., de Gelder, B., Slater, M., & Sanchez-Vives, M.V. (2018). Offenders become the victim in virtual reality: impact of changing perspective in domestic violence. Scientific Reports, 8(1), 2692.
Smith, J. L. (2018). Probabilistic Hurricane Track Generation for Storm Surge Prediction (Master’s thesis, UNC-Chapel Hill, 2018) (pp. 1-31). Chapel Hill: 2017.
Yao, Y., Cao, Q., Farias, R., Chase, J., Orlikowski, V., Ruth, P., Cevik, M., Wang, C., & Buraglio, N. (2018, April). Toward live inter-domain network services on the ExoGENI testbed. IEEE International Conference on Computer Communications. Honolulu, HI.
Zhang, T. & Xin, Y. (2018, April). A truthful online auction mechanism for deadline-aware cloud resource allocation. IEEE/IFIP Network Operations and Management Symposium (NOMS) 2018. Taipei, Taiwan.
Zheutlin, A.B., Jeffries, C.D., Perkins, D.O., Chung, Y., Chekroud, A.M., Addington, J., Bearden, C.E., Cadenhead, K.S., Cornblatt, B.A., Mathalon, D.H., McGlashan, T.H., Seidman, L.J., Walker, E.F., Woods, S.W., Tsuang, M., & Cannon, T.D. (2018). The Role of microRNA Expression in Cortical Development During Conversion to Psychosis. Neuropsychopharmacology: official publication of the American College of Neuropsychopharmacology, 42(11), 2188-2195.
Ahalt, S. (2017). DCRI data solutions all hands meeting. Invited Presentation (Speaker). Durham, NC.
Aikat, J., Carsey, T.M., Fecho, K., Jeffay, K., Krishnamurthy, A., Mucha, P.J., Rajasekar, A., & Ahalt, S.C. (2017). Scientific training in the era of big data: A new pedagogy for graduate education. Big Data, 5(1), 12-18. doi:10.1089/big.2016.0014.
Bhalachandra, S., Porterfield, A., Olivier, S.L., & Prins, J.F. (2017). An adaptive core-specific runtime for energy efficiency. IEEE Parallel and Distributed Processing Symposium (IPDPS).
Culbertson, Goel, S., Madden, M.B., Safaenili, N., Jackson, K.L., Carton, T., Waitman, R., et al. (2017). The building blocks of interoperability: A multisite analysis of patient demographic attributes available for matching. Applied Clinical Informatics, 8(2), 322-336. DOI: https://doi.org/10.4338/ACI-2016-11-RA-0196
Gadepally, V., Krishnamurthy, A., & Ozguner, U. (2017). A framework for estimating long term driven behavior. Journal of Advanced Transportation, 2017, 11 pages. DOI:10.1155/2017/3080859
Gizer, I.R., Bizon, C., Gilder, D.A., Ehlers, C.L., & Wilhelmson, K.C. (2017). Whole genome sequence study of cannabis dependence in two independent cohorts. Addiction Biology, doi: 10.1111/adb.12489
Grunninger, C., Shanley, L., Rawlings-Goss, R., Miller, J.S., Khan, F.R., Turner, C., & Hubbard, M. (2017). Legal issues in big data. Hosted by the University of Georgia, School of Law, Athens, GA.
Hassmiller Lich, K.M., Cornejo, D.A., Mayorga, M.E., Pignone, M., Tangka, F.K.L., Richardson, L.C., Kuo, T-M., et al. (2017). Cost-effectiveness analysis of four stimulated colorectal cancer screening interventions, North Carolina. Preventing Chronic Disease, 14(18).
Katz, D.S., Niemeyer, K.E., Gesing, S., Hwang, L., Bangerth, W., Hettrick, S., Idaszak, R., et al. (2017). Report on the fourth workshop on sustainable software for science: Practice and experiences. (WSSSPE4)
Mandal, A., Ruth, P., Baldin, I., Ferreira de Silva, R., & Deelman, E. (2017). Data flow prioritization for scientific workflows using a virtual SDX on ExoGENI (poster). 25th GENI Engineering Conference, Miami, FL.
Otto, J.M., Gizer, I.R., Ellingson, J.M., & Wilhelmsen, K.C. (2017). Genetic variation in the exome: Associations with alcohol and tobacco co-use. Psychology of Addictive Behaviors: Journal of the Society of Psychologists in Addictive Behaviors, 31(3), 354-366. doi: 10.1037/adb0000270
Patel, R.Y., Shah, N., Jackson, A.R., Ghosh, R., Pawliczek, P., Paithankar, S., Baker, A., et al. (2017). ClinGen pathogenicity calculator: A configurable system for assessing pathogenicity of genetic variants. Genome Medicine, 9(1).
Peng, Q., Schork, N.J., Wilhelmson, K.C., & Ehlers, C.L. (2017). Whole genome sequence association and ancestry-informed polygenic profile of EEG alpha in a Native American population. Neuropsychiatric Genetics, doi: 10.1002/ajmg.b.32533
Qian, T., Mueller, F., & Xin, Y. (2017). A linux real-time packet scheduler for reliable static SDN routing. Euromicro conference on real-time systems (ECRTS).
Qian, T., Xu, H., Mueller, F., Chakraborty, A., & Xin, Y. (2017). A resilient and distributed so ware infrastructure for wide-area measurement CPS systems. ACM Transaction on CPS, submitted.
Richmond-Rakerd, L.S., Otto, J.M., Slutske, W.S., Ehlers, C.L., Wilhelmsen, K.C., & Gizer, I.R. (2017). A novel tobacco use phenotype suggests the 15q25 and 19q13 loci may be differentially associated with cigarettes per day and tobacco-related problems. Nicotine & Tobacco Research, 19(4), 426-434. doi: 10.1093/ntr/ntw260.
Shanley, L.A. (2017). Aspen institute dialogue series on sharing and integrating data for water sustainability. Invited Presentation, Aspen, Colorado.
Shanley, L.A. (2017). Earth observation big data. Space Studies Board of the National Academies of Science, Engineering and Medicine. Invited Presentation. Washington, D.C.
Shanley, L.A. (2017). Gates foundation open imagery network convening. Invited Presentation. Seattle, Washington.
Shanley, L.A., Bouazzi, V., Dennis, S., Duffy, D., & Morgan, D. (2017). Federal big data research challenges. NSF Big Data PI Workshop. Washington, DC.
Tarboton, D., Idaszak, R., Horsburgh, J., Ames, D., Goodall, J., Band, L., Merwade, V., et al. (2017). Hydroshare- Advancing hydrology through collaborative data and model sharing. Poster presented at 2017 NSF SI2 PI meeting.
Yao, Y., Cao, Q., Chase, J., Ruth, P., Baldin, I., Xin, Y., & Mandal, A. (2017). Slice-based network transit service: Inter-domain L2 networking on ExoGENI. INFOCOM17 workshop on Distributed Cloud Computing (DCC ’17).
Yin, X., Lin, Y., Shen, C., Wang, L., Zuo, X., Zheng, X., Yang, S., et al. (2017). Integration of expression quantitative trait loci and pleiotropy identifies a novel psoriasis susceptibility gene, PTPN1. The Journal of Gene Medicine, 19(1-2), doi: 10.1002/jgm.2939.
Yin, X., Bizon, C., Tilson, J., Lin, Y., Gizer, I.R., Ehlers, C.L., & Wilhelmson, K.C. (2017). Genome-wide meta-analysis identifies a novel susceptibility signal at CACNA2D3 for nicotine dependence. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. doi: 10.1002/ajmg.b.32540
Zheutlin, A.B., Jeffries, C.D., Perkins, D.O., Chung, Y., Chekroud, A.M., Addington, J., et al. (2017). The role of microRNA expression in cortical development during conversion to psychosis. Neuropsychopharmacology, doi: 10.1038/npp.2017.34.
Ahalt, S., Berriman, B., Brown, M., Carver, J., Hong, N.C., Fish, A., Idaszak, R., Newman, G., Panda, D., Patra, A., Puckett, E.G., Roland, C., Thain, D., Uluagac, S., & Zhang, B. (2016) Toward a Framework for Evaluating Software Success: A Proposed First Step. Poster at the 2016 NSF SI2 PI Workshop.
Aikat, J., Carsey, T., Fecho, K., Jeffay, K., Krishnamurthy, A., Mucha, P., Rajasekar, A., Ahalt, S. (2016) Scientific Training in the Era of Big Data: A new Pedagogy for Graduate Education.
Allen, G., Chen, E., Idaszak, R., Katz, D. (2016) Report on software metrics for research software. http://ceur-ws.org/Vol-1686/.
Baldin, I., Chase, J., Xin, Y., Mandal, A., Ruth, P, Cstillo, C., Orlikowski, V., Heermann, C., and Mills, J. (2016) The GENI Book: ExoGENI: A Multi-Domain Infrastructure-As-A-Service Testbed.
Barber, R.C., Phillips, N.R., Tilson, J.L., Huebinger, R.M., Shewale, S.J., Koenig, J.L., Mitchel, J.S., O’Bryant, S.E., Waring, S.C., Diaz-Arrastia, R., Chasse, S., Wilhelmsen, K.C. (2015) Can Genetic Analysis of Putative Blood Alzheimer’s Disease Biomarkers Lead to Identification of Susceptibility Loci? Alzheimer’s Disease Neuroimaging Initiative; Texas Alzheimer’s Research and Care Consortium.
Berg, J.S., Foreman, A.K., O’Daniel, J.M., Booker, J.K., Boshe, L., Carey, T., Crooks, K.R., Jensen, B.C., Juengst, E.T., Lee, K., Nelson, D.K., Powell, B.C., Powell, C.M., Roche, M.I., Skrzynia, C., Strande, N.T., Weck, K.E., Wilhelmsen, K.C., & Evans, J.P. (2016) A semiquantitative metric for evaluating clinical actionability of incidental or secondary findings from genome-scale sequencing. Genetics of Medicine, 18(5), 467-475.
Bizon, C., Spiegel, M., Chasse, S.A., Gizer, I.R., Li, Y., Malc, E.P., Mieczkowski, P.A., Sailsbery, J.K., Wang, X., Ehlers, C.L, Wilhelmsen, K.C. (2016) Variant calling in low-coverage whole genome sequencing of a Native American population sample. BMC Genomics.
Blanton, B., Dresback, K., Colle, B., Kolar, B., Vergara, H., Hong, Y., Leonardo, N., Davidson, R., Nozick, L., & Wachtendorf, T. (2016) An integrated scenario ensemble- based framework for hurricane evacuation modeling: Part 2- Hazard modeling. Risk Analysis.
Borland, D., West, V.L., & Hammond, W.E. (2016) Multivariate visualization of longitudinal clinical data. Proceedings of the IEEE VIS 2016 Workshop on Temporal and Sequntial Event Analysis.
Borland, D., Chartier, T., and Peck, T. (2016) Pixar’s Linear Algebra. The Bulletin of the International Linear Algebra Society.
Buchkovich, M.L., Brown, C.C., Robasky, K. (2016) Novel, allele sequence signature approach enables HLA-typing for biomarker identification using gene expression data. ASHG 2016 Annual Meeting. Vancouver, British Columbia.
Chase, J. and Baldin, I. (2016) The GENI Book: A Retrospective on ORCA: Open Resource Control Architecture.
Couser, N.L., Masood, M.M., Strande, N.T., Foreman, A.K., Crooks, K., Weck, K.E., Lu, M., Wilhelmsen, K.C., Roche, M., Evans, J.P., Berg, J.S., Powell, C.M. (2016) The phenotype of multiple congenital anomalies-hypotonia-seizures syndrome 1: report and review. Med Genet A.
Cutcher-Gershenfeld, J., Baker, K.S., Berente, N., Carter, D.R., DeChurch, L.A., Flint, C.C., Gershenfeld, G., Haberman, M., King, J.L., Kirkpatrick, C., Knight, E., Lawrence, B., Lewis, S., Lenhardt, W.C., Lopez, P., Mayernik, M.S., McElroy, C., Mittleman, B., Nichol, V., Nolan, M., Shin, N., Thompson, C.A., Winter, S., Zaslavsky, I. (2016) Build It, But Will They Come? A Geoscience Cyberinfrastructure Baseline Analysis. Data Science Journal.
Davidson, R., Nozick, L., Wachtendorf, T., Blanton, B., Colle, B., Kolar, R., DeYoung, S., Dresback, K., Yi, W., Yang, K., & Leonardo, N. (2016) An integrated scenario ensemble- based framework for hurricane evacuation modeling: Part 1- Evacuation modeling. Risk Analysis.
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Minogue, J., Borland, D., Russo, M., Chen, S.T., Grady, R. Investigating the influence of haptic technology on upper elementary students’ reasoning about sinking & floating. National Association of Research in Science Teaching (NARST) Annual International Conference. April 2015.
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Reilly, J., Ahalt, S., McGee, J., Owen, P., Schmitt, C., Wilhelmsen, K. MaPSeq, A Service-Oriented Architecture for Genomics Research within an Academic Biomedical Research Institution. 2015.
Ahalt, S., Carsey, T., Couch, A., Hooper, R., Ibanz, L., Idaszak, R., Jones, M.B., Lin, J., Robinson, E. NSF Workshop on Supporting Scientific Discovery through Norms and Practices for Software and Data Citation and Attribution. April 2015.
Deelman, E., Carothers, C., Mandal, A., Tierney, B., Vetter, J.S., Bladin, I., Castillo, C., Juve, G., Krol, D., Lynch, V., Mayer, B., Meredith, J., Proffen, T., Ruth, P., Silva, R. PANORAMA: An Approach to Performance Modeling and Diagnosis of Extreme Scale Workflows. International Journal of High Performance Computing Applications. July 14, 2015.
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Fellinger, D., Moore, R., Xu, H. Policy-based Data Management: The Future of Reproducible Data-Driven Research. American Laboratory. March 18, 2015.
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Lenhardt, W., Reference Data Layers for Earth and Environmental Science: History, Frameworks, Science Needs, Approaches, and New Technologies. 2015 Fall Meeting, AGU. San Francisco, CA. December 14-18, 2015.
Thakur, S., Schmitt, C., Feldman, M., Lowe, N.J. RTP-Vis: Visualizing Ecosystem of Companies and Founders in Research Triangle Area. BusinessVis Workshop 2015 at IEEE Vis conference. October 2015.
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Xin, Y., Shayman, M., La, R. Reconfiguration of Survivable IP over WDM Networks. Journal of Optical Switching and Networking. 2015.
Lenhardt, W. Reference Data Layers for Earth and Environmental Science: History, Frameworks, Science Needs, Approaches, and New Technologies. 2015 Fall Meeting, AGU. San Francisco, CA. December 14-18 2015.
Thakur, S., Schmitt, C., Feldman, M., Lowe, N.J. RTP-Vis: Visualizing Ecosystem of Companies and Founders in Research Triangle Area. BusinessVis Workshop 2015 at IEEE Vis conference. October 2015.
Schmitt, C., Cox, S., Fecho, K., Idaszak, R., Lander, H., Rajasekar, A., Thakur, S. Scientific Discovery in the Era of Big Data: More than the Scientific Method. RENCi, University of North Carolina at Chapel Hill. 2015.
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Lenhardt, W.C., Ahalt, S., Jones, M., Aukema, J., Hampton, S., Hespanh, S.R., Idaszak, R., Schildhauer, M. ISEES-WSSI Lessons for sustainable science software from an early career training institute on open science synthesis. 2nd Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2). New Orleans, LA, USA, November 16. 2014.
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Borland, D., West, V.L., Hammond, W.E. Multivariate visualization of system-wide National Health Service data using radial coordinates. Proceedings of the 2014 Workshop on Visual Analytics in Healthcare (VAHC 2014). Washington, DC, USA, November 15, 2014.
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Li, A., Chall, S., Lu, W., Vorderstrasse, A., Johnson, C. The challenges of disparate data formats: Analysis and visualization in the SLIDES project. American Medical Informatics Association (AMIA) 2014 Annual Symposium. Washington, DC, USA, November 15-19, 2014.
Sankaran, S., Yi, H., Cherry, M. The REACH NC Resource Finder: A multi-institutional, statewide implementation of eagle-i. VIVO/SciTS 2014 Conference. Austin, TX, USA, August 6-8.
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Blanton, B. and Lenhardt, C. A user perspective on sustainable scientific software. First Workshop on Sustainable Software for Science: Practice and Experiences, in conjunction with SC13. Sunday, November 17, 2013, Denver, CO.
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Mandal, A., Ruth, P., Baldin, I., Xin, Y., Castillo, C., Rynge, M., Deelman, E. Evaluating I/O aware network management for scientific workflows on networked clouds. Proceedings of 3rd IEEE/ACM International Workshop on Network-Aware Data Management (co-located with SC’13). November 2013, Denver, CO.
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Tilson, J.L., Fowler, R., Ermler, W. Comparative analysis of the electronic structures of RuO2+ and OsO2+ using the spin-orbit configuration interaction method. National meeting of the American Chemical Society, PHYS division. New Orleans, LA, April 7-11, 2013.
Blanton, B., Fleming, J., Luettich, R. Data management for coastal storm surge forecasts using THREDDS, OPeNDAP, and CF-UGRID community-driven standards. Presented at 13th International Conference on Estuarine and Coastal Modeling. San Diego, CA, Nov. 2013.
Mane, K., Phillips, O., Schmitt, C., Wilhelmsen, K., Gersing, K., Pietrobon, R., Akushevich, I. Visual analytics to optimize patient-population evidence delivery for personalized care. 4th ACM International Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (ACM BCB 2013). Washington, DC, Sept. 2013.
Mane, K., Carrasco, V., Mostafa, J. Visual-based interactive clinical decision support tools: Developing user-centric approaches. 2013 Workshop on Visual Analytics in Healthcare, American Medical Informatics Association. Washington, DC, Nov. 25, 2013.
West, V., Borland, D., Hammond, W.E. Visualization of EHR and health related data for information discovery. 2013 Workshop on Visual Analytics in Healthcare, American Medical Informatics Association. Washington, DC, Nov. 25, 2013.
Tateosian, L., Mitasova, H., Thakur, S., Russ, E., Hardin, E. (2013). Visualizations of coastal terrain time-series. Information Visualization Journal.
Thakur, S., & Chakrabortty, A. Multi-Dimensional wide-area visualization of power system dynamics using synchrophasors. IEEE Power and Energy Society General Meeting (PESGM). Vancouver, British Columbia, Canada, July 21-25, 2013.
Huck, K., Shende, S., Malony, A., Kaiser, H., Porterfield, A., Fowler, R., Brightwell, R. An early prototype of an autonomic performance environment for exascale. International Workshop on Runtime and Operating Systems for Supercomputers (ROSS2013). in conjunction with the International Conference on Supercomputining, Eugene, Oregon. June 10, 2013
Weiss, M., Xin, Y., Chakrabortty, A. A multi-user network testbed for wide-area monitoring and control of power systems using distributed synchrophasors. ACM eEnergy 2013 (eEnergy13). Poster Session, Berkeley, CA, May 2013.
Choi, J.W., Bedard, D., Fowler, R., Vuduc, R. A roofline model of energy. Proceedings of International Parallel and Distributed Processing Symposium. Boston, MA, May 2013.
Ahalt, S., Band, L., Minsker, B., Palmer, M., Tiemann, M., Idaszak, R., Lenhardt, C., Whitton, M. Water Science Software Institute: An open source engagement process. 2013 International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE13). San Francisco, California, May 18, 2013.
Porterfield, A., Olivier, S., Bhalachandra, S., Prins, J. Power measurement and concurrency throttling for energy reduction on OpenMP programs. IEEE Workshop on High-Performance, Power-Aware Computing. Boston MA, May 2013.
Russell, T., Coposky, J., Johnson, H., Idaszak, R., Schmitt, C. e-IRODS Composable Resources. 2013 iRODS User Group Meeting. Max Planck Institute for Plasma Physics (IPP), Garching, Germany, Feb 28-Mar 1, 2013.
Russell, T., & Stillwell, L. Scotty: iRODS administration interface. iRODS User Group Meeting. Max Planck Institute for Plasma Physics (IPP), Garching, Germany, Feb 28-Mar 1, 2013.
Greenberg, J., Rowell, C., Rajavi, K., Conway, M., Lander, H. HIVEing Across U.S. DataNets. Research Data Management Implementations Workshop. Arlington Gateway, Arlington, VA, March 13-14, 2013.
Tilson, J., Ruth, P., Fowler, R., Ermler, W. Parallel spin-orbit configuration interaction method: A performance co-design inspired implementation for high performance computation. National meeting of the American Chemical Society, COMP Division. New Orleans, LA, April 7-11, 2013.
Chakrabortty, A., & Xin, Y. Hardware-in-the-Loop simulations and verifications of smart power systems over an Exo-GENI testbed. The Second GENI Research and Educational Experiment Workshop (GREE2013). Salt Lake City, Utah, March 2013.
Kohli, L., Whitton, M., Brooks, F. (2013). Redirected touching: Training and adaptation in warped virtual spaces. Proceedings of 2013 IEEE Symposium on 3D User Interfaces (3DUI). pp.79-86
Kum, H.C., Pathak, D., Krisnamurthy, A., Reiter, M., Ahalt, S. Secure decoupled linkage (CDLink) for building a social genome. 2013 IEEE International Conference on Big Data. Santa Clara, CA, USA, Oct. 6-9, 2013.
Kum, H.C., Pathak, D., Sanka, G., Ahalt, S. Privacy beyond anonymity: Decoupling data using encryption. 2013 American Medical Informatics Association Joint Summit on Translation Science: Clinical Research Informatics. San Francisco, CA, USA, March 20-22, 2013.
Kum, H.C., Ahalt, S. Privacy by design: Understanding data access models for secondary data. 2013 American Medical Informatics Association Joint Summit on Translation Science: Clinical Research Informatics. San Francisco, CA, USA, March 20-22, 2013.
Xin, Y., Baldin, I., Huang, S. Recursive cross-layer network virtualization and flexible optical burst switching SDN. OSA Incubator and NSF Workshop on Scaling Terabit Networks. Washington, DC, Sept. 19-20, 2013.
Whitton, M.C. and Peck, T.C. (2013). Stepping-Driven Locomotion Interfaces. In Steinicke, F., Visell, Y., Campos, J., Lécuyer, A. (Eds.), In human walking in virtual environments: Perception, technology, and applications. Springer-Verlag.
Mane, K., Loddenkemper, T., Sánchez Fernández, I., Mikati, M., Tennison, M., Schmitt, C., Wilhelmsen, K., Leviton, A. (2013) Visual aids to medical data and computational diagnostics: New frontiers in pediatric neurology. Epilepsy and Behavior Journal.
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Lenhardt, C., Ahalt, S., Blanton, B., Christopherson, L., Idaszak, R. Data management lifecycle and software lifecycle management in the context of conducting science. Workshop on Sustainable Software for Science at Supercomputing 2013. Denver, CO, USA, Nov. 17-22, 2013.
Christopherson, L., Idaszak, R., Ahalt, S. Developing scientific software through the open community engagement process. Workshop on Sustainable Software for Science at Supercomputing 2013. Denver, CO, USA, Nov. 17-22, 2013.
Dresback, K.M., Fleming, J.G., Blanton, B.O., Gourly, J.J., Tromble, E.M., Luettich, R.A., Kolar, R.L., Hong, Y., Van Cooten, S., Bergara, H.J., Flamig, Z.L., Lander, H.M., Kelleher, K.E., Nemunaitis-Monroe, K.L. Skill assessment of a real-time forecast system utilizing a coupled hydrologic and coastal hydrodynamic model during Hurricane Irene. (2011). Continental Shelf Research 71. 78-94. doi:10.1016/j.csr.2013.10.007.
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Rajasekar, A., Kum, H., Crosas, M., Crabtree, J., Sankaran, S., Lander, H., Carsey, T., King, G., Zhan, J. The data bridge. Science Journal. 2(1).
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Chakrabortty, A., Michailidis, G., Xin, Y. A decentralized ID algorithm for detecting slow-fast oscillations in power systems from overwhelming volumes of phasor data. 51st IEEE Conference on Decision and Control (CDC). Maui, HI, Dec. 2012.
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Zhang, R., Mandal, A., Koelbel, C., Cooper, K. Combined fault tolerance and scheduling techniques for workflow applications on computational grids. Proceedings of the IEEE International Symposium on Cluster Computing and the Grid (CCGrid). Shanghai, China, May 18-21, 2009.
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Buneci, Emma and D. Reed. Analysis of Application Heartbeats: Learning Structural and Temporal Features in Time Series Data for Identification of Performance Problems Under submission: Supercomputing Conference Nov 2008 http://portal.acm.org/citation.cfm?id=1413370.1413423&dl=ACM&coll=ACM
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Fowler, Robert J., Todd Gamblin, Gopi Kandaswamy, Anirban Mandal, Alan K. Porterfield, Lavanya Ramakrishnan, and Daniel Reed. Challenges of scale: When all computing becomes grid computing. In Lucio Grandinetti, editor, High Performance Computing and Grids in Action, Advances in Parallel Computing. IOS Press, Amsterdam, March 2008. http://www.booksonline.iospress.nl/Content/View.aspx?piid=8556
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Baldine, I. and M. Vellala and A. Wang and G. N. Rouskas and R. Dutta and D. Stevenson “A Unified Software Architecture to Enable Cross-Layer Design in the Future Internet” in Proceedings of IEEE ICCCN 2007. http://www.csc.ncsu.edu/faculty/rouskas/Publications/Conferences/ICCCN-SILO-2007.pdf
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McGee, J., J. L. Tilson, S. McLean. “Gateway to the TeraGrid for Bio-Scientists: A Tutorial. What does it do? How is it used in course curricula? How was it constructed?”, TeraGrid 2007, Madison, WI, June, 2007.
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Zhang, Y., R. Fowler, K. Huck, A., Malony, A. Porterfield, D. Reed, S. Shende, V. Taylor, and X. Wu. US QCD computational performance studies with PERI. J. Phys: Conf. Ser, 78(012083):5pp, August 2007.
Froyd, Nathan, Nathan Tallent, John Mellor-Crummey, and Rob Fowler. Call path profiling for unmodified, optimized binaries. In Proceedings of the GCC and GNU Toolchain Developers’ Summit, Ottawa, Canada, June 2006.
Gamblin, Todd, Rob Fowler, and Daniel A. Reed. Runtime methods for automatic behavioral stratification of scientific codes. In Proceedings of the Los Alamos Computer Science Institute 7th Annual Symposium, Santa Fe, MN, October 2006. Best Poster Award.
Nurmi, D., A. Mandal, J. Brevik, K, C. Koelbel, R. Wolski and K. Kennedy, “Evaluation of a Workflow Scheduler Using Integrated Performance Modeling and Batch Queue Wait Time Prediction,” in Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC), pp. 29-, November 2006. http://vgrads.rice.edu/papers/batch-queue-sc06.pdf
Ramakrishnan, Lavanya, Brian O. Blanton, Howard M. Lander, Richard A. Luettich, Jr, Daniel A. Reed, Steven R. Thorpe, “Real-time Storm Surge Ensemble Modeling in a Grid Environment”, Second International Workshop on Grid Computing Environments (GCE), Workshop at SC|06, November 2006, Tampa, Florida.
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“Planning for Cyberinfrastructure Software” NSF SCI workshop, February 2005.
Ruckenstein, E. Shulgin, J. L. Tilson, “Treatment of Dilute Clusters of Methanol and Water by ab Initio Quantum Mechanical Calculations”, E, J. Phys. Chem. A. 109(5); 807-815. (2005)
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