Nagiza Samatova

Zhao, Y., Yang, X., Bolnykh, C., Harenberg, S., Korchiev, N., Yerramsetty, S. R., … Samatova, N. F. (2021, August 26). Predictive models with end user preference. STATISTICAL ANALYSIS AND DATA MINING, Vol. 8. https://doi.org/10.1002/sam.11545

Meleshko, S., & Samatova, N. F. (2020). Group classification of the two-dimensional shallow water equations with the beta-plane approximation of coriolis parameter in Lagrangian coordinates. COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION, 90. https://doi.org/10.1016/j.cnsns.2020.105337

Kaptsov, E., Meleshko, S., & Samatova, N. F. (2020). The one-dimensional Green-Naghdi equations with a time dependent bottom topography and their conservation laws. PHYSICS OF FLUIDS, 32(12). https://doi.org/10.1063/5.0031238

Yang, R., He, J., Xu, M., Ni, H., Jones, P., & Samatova, N. (2018). An Intelligent and Hybrid Weighted Fuzzy Time Series Model Based on Empirical Mode Decomposition for Financial Markets Forecasting. ADVANCES IN DATA MINING: APPLICATIONS AND THEORETICAL ASPECTS (ICDM 2018), Vol. 10933, pp. 104–118. https://doi.org/10.1007/978-3-319-95786-9_8

Xu, M., Yang, R., Ranshous, S., Li, S., & Samatova, N. F. (2018). Leveraging External Knowledge for Phrase-Based Topic Modeling. Proceedings - 2017 Conference on Technologies and Applications of Artificial Intelligence, TAAI 2017, 29–32. https://doi.org/10.1109/taai.2017.25

Xu, M., Yang, R., Jones, P., & Samatova, N. F. (2018). Mining Aspect-Specific Opinions from Online Reviews Using a Latent Embedding Structured Topic Model. COMPUTATIONAL LINGUISTICS AND INTELLIGENT TEXT PROCESSING, CICLING 2017, PT II, Vol. 10762, pp. 195–210. https://doi.org/10.1007/978-3-319-77116-8_15

Yang, R., Xu, M., Jones, P., & Samatova, N. (2018). Real time utility-based recommendation for revenue optimization via an adaptive online Top-K high utility itemsets mining model. ICNC-FSKD 2017 - 13th International Conference on Natural Computation, Fuzzy Systems and Knowledge Discovery, 1859–1866. https://doi.org/10.1109/fskd.2017.8393050

Sohn, D., Shpanskaya, K., Lucas, J. E., Petrella, J. R., Saykin, A. J., Tanzi, R. E., … Doraiswamy, P. M. (2018). Sex Differences in Cognitive Decline in Subjects with High Likelihood of Mild Cognitive Impairment due to Alzheimer's disease. SCIENTIFIC REPORTS, 8. https://doi.org/10.1038/s41598-018-25377-w

Chaudhary, M. S., Ranshous, S., & Samatova, N. F. (2017). A Community-Driven Graph Partitioning Method for Constraint-Based Causal Discovery. In C. Cherifi, H. Cherifi, M. Karsai, & M. Musolesi (Eds.), Complex Networks & Their Applications VI. COMPLEX NETWORKS 2017 (pp. 253–264). https://doi.org/10.1007/978-3-319-72150-7_21

Xu, M., Yang, R., Harenberg, S., & Samatova, N. F. (2017). A Lifelong Learning Topic Model Structured Using Latent Embeddings. 2017 11TH IEEE INTERNATIONAL CONFERENCE ON SEMANTIC COMPUTING (ICSC), pp. 260–261. https://doi.org/10.1109/icsc.2017.15

Yang, R., Xu, M., He, J., Ranshous, S., & Samatova, N. F. (2017). An Intelligent Weighted Fuzzy Time Series Model Based on a Sine-Cosine Adaptive Human Learning Optimization Algorithm and Its Application to Financial Markets Forecasting. ADVANCED DATA MINING AND APPLICATIONS, ADMA 2017, Vol. 10604, pp. 595–607. https://doi.org/10.1007/978-3-319-69179-4_42

Ranshous, S., Chaudhary, M., & Samatova, N. F. (2017). Efficient Outlier Detection in Hyperedge Streams Using MinHash and Locality-Sensitive Hashing. In C. Cherifi, H. Cherifi, M. Karsai, & M. Musolesi (Eds.), Complex Networks & Their Applications VI. COMPLEX NETWORKS 2017 (pp. 105–116). https://doi.org/10.1007/978-3-319-72150-7_9

Ranshous, S., Joslyn, C. A., Kreyling, S., Nowak, K., Samatova, N. F., West, C. L., & Winters, S. (2017). Exchange Pattern Mining in the Bitcoin Transaction Directed Hypergraph. In Financial Cryptography and Data Security (pp. 248–263). https://doi.org/10.1007/978-3-319-70278-0_16

Karpatne, A., Atluri, G., Faghmous, J. H., Steinbach, M., Banerjee, A., Ganguly, A., … Kumar, V. (2017). Theory-Guided Data Science: A New Paradigm for Scientific Discovery from Data. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING, 29(10), 2318–2331. https://doi.org/10.1109/tkde.2017.2720168

Jones, P., Medd, D., Ramakrishnan, S., Shah, R., Keyton, J., & Samatova, N. (2017). Towards Automatic Linkage of Knowledge Worker's Claims with Associated Evidence from Screenshots. 2017 THIRD IEEE INTERNATIONAL CONFERENCE ON BIG DATA COMPUTING SERVICE AND APPLICATIONS (IEEE BIGDATASERVICE 2017), pp. 17–22. https://doi.org/10.1109/bigdataservice.2017.21

Zhang, W., Tang, H., Harenberg, S., Byna, S., Zou, X., Devendran, D., … Samatova, N. F. (2016). AMRZone: A Runtime AMR Data Sharing Framework For Scientific Applications. 2016 16TH IEEE/ACM INTERNATIONAL SYMPOSIUM ON CLUSTER, CLOUD AND GRID COMPUTING (CCGRID), pp. 116–125. https://doi.org/10.1109/ccgrid.2016.62

Chaudhary, M. S., Gonzalez, D. L., Bello, G. A., Angus, M. P., Desai, D., Harenberg, S., … Samatova, N. F. (2016). Causality-Guided Feature Selection. In Advanced Data Mining and Applications (pp. 391–405). https://doi.org/10.1007/978-3-319-49586-6_26

Bello, G. A., Harenberg, S., Agrawal, A., & Samatova, N. F. (2016). Community Detection in Dynamic Attributed Graphs. In Advanced Data Mining and Applications (pp. 329–344). https://doi.org/10.1007/978-3-319-49586-6_22

Zhang, W. Z., Tang, H. J., Ranshous, S., Byna, S., Martin, D. F., Wu, K. S., … Samatova, N. F. (2016). Exploring memory hierarchy and network topology for runtime AMR data sharing across scientific applications. 2016 IEEE International Conference on Big Data (Big Data), 1359–1366. https://doi.org/10.1109/bigdata.2016.7840743

Tang, H., Byna, S., Harenberg, S., Zhang, W., Zou, X., Martin, D. F., … Samatova, N. F. (2016). In situ Storage Layout Optimization for AMR Spatio-temporal Read Accesses. PROCEEDINGS 45TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING - ICPP 2016, pp. 406–415. https://doi.org/10.1109/icpp.2016.53

Harenberg, S., Seay, R. G., Bello, G. A., Chirkova, R. Y., Doraiswamy, P. M., & Samatova, N. F. (2016). Knowledge-Guided Maximal Clique Enumeration. In Advanced Data Mining and Applications (pp. 604–618). https://doi.org/10.1007/978-3-319-49586-6_43

Chen, W., Samatova, N. F., Stallmann, M. F., Hendrix, W., & Ying, W. (2016). On size-constrained minimum s-t cut problems and size-constrained dense subgraph problems. THEORETICAL COMPUTER SCIENCE, 609, 434–442. https://doi.org/10.1016/j.tcs.2015.10.031

Tang, H., Byna, S., Harenberg, S., Zou, X., Zhang, W., Wu, K., … Samatova, N. F. (2016). Usage Pattern-Driven Dynamic Data Layout Reorganization. 2016 16TH IEEE/ACM INTERNATIONAL SYMPOSIUM ON CLUSTER, CLOUD AND GRID COMPUTING (CCGRID), pp. 356–365. https://doi.org/10.1109/ccgrid.2016.15

Chen, W., Schmidt, M., Tian, W., Samatova, N. F., & Zhang, S. (2015). An efficient algorithm for pairwise local alignment of protein interaction networks. JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 13(2). https://doi.org/10.1142/s0219720015500031

Ranshous, S., Shen, S., Koutra, D., Harenberg, S., Faloutsos, C., & Samatova, N. F. (2015). [Review of Anomaly detection in dynamic networks: a survey]. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL STATISTICS, 7(3), 223–247. https://doi.org/10.1002/wics.1347

Zhang, W., Tang, H., Zou, X., Harenberg, S., Liu, Q., Klasky, S., & Samatova, N. F. (2015). Exploring Memory Hierarchy to Improve Scientific Data Read Performance. 2015 IEEE INTERNATIONAL CONFERENCE ON CLUSTER COMPUTING - CLUSTER 2015, pp. 66–69. https://doi.org/10.1109/cluster.2015.18

Gonzalez, D. L., II, Angus, M. P., Tetteh, I. K., Bello, G. A., Padmanabhan, K., Pendse, S. V., … Samatova, N. F. (2015). On the data-driven inference of modulatory networks in climate science: an application to West African rainfall. NONLINEAR PROCESSES IN GEOPHYSICS, 22(1), 33–46. https://doi.org/10.5194/npg-22-33-2015

Zou, X., Wu, K., Boyuka, D. A., Martin, D. F., Byna, S., Tang, H., … Samatova, N. F. (2015). Parallel In Situ Detection of Connected Components in Adaptive Mesh Refinement Data. 2015 15TH IEEE/ACM INTERNATIONAL SYMPOSIUM ON CLUSTER, CLOUD AND GRID COMPUTING, pp. 302–312. https://doi.org/10.1109/ccgrid.2015.154

Bello, G. A., Angus, M., Pedemane, N., Harlalka, J. K., Semazzi, F. H. M., Kumar, V., & Samatova, N. F. (2015). Response-Guided Community Detection: Application to Climate Index Discovery. In Machine Learning and Knowledge Discovery in Databases (pp. 736–751). https://doi.org/10.1007/978-3-319-23525-7_45

Boyuka, D. A., II, Tang, H., Bansal, K., Zou, X., Klasky, S., & Samatova, N. F. (2015). The Hyperdyadic Index and Generalized Indexing and Query with PIQUE. PROCEEDINGS OF THE 27TH INTERNATIONAL CONFERENCE ON SCIENTIFIC AND STATISTICAL DATABASE MANAGEMENT. https://doi.org/10.1145/2791347.2791374

Harenberg, S., Bello, G., Gjeltema, L., Ranshous, S., Harlalka, J., Seay, R., … Samatova, N. (2014). Community detection in large-scale networks: a survey and empirical evaluation. Wiley Interdisciplinary Reviews: Computational Statistics, 6(6), 426–439. https://doi.org/10.1002/WICS.1319

Lakshminarasimhan, S., Zou, X., Boyuka, D. A., II, Pendse, S. V., Jenkins, J., Vishwanath, V., … Samatova, N. F. (2014). DIRAQ: scalable in situ data- and resource-aware indexing for optimized query performance. CLUSTER COMPUTING-THE JOURNAL OF NETWORKS SOFTWARE TOOLS AND APPLICATIONS, 17(4), 1101–1119. https://doi.org/10.1007/s10586-014-0358-z

Liess, S., Kumar, A., Snyder, P. K., Kawale, J., Steinhaeuser, K., Semazzi, F. H. M., … Kumar, V. (2014). Different Modes of Variability over the Tasman Sea: Implications for Regional Climate. JOURNAL OF CLIMATE, 27(22), 8466–8486. https://doi.org/10.1175/jcli-d-13-00713.1

Zou, X., Lakshminarasimhan, S., Boyuka, D. A., II, Ranshous, S., Tang, H., Klasky, S., & Samatova, N. F. (2014). Fast Set Intersection through Run-Time Bitmap Construction over PForDelta-Compressed Indexes. In Lecture Notes in Computer Science (pp. 668–679). https://doi.org/10.1007/978-3-319-09873-9_56

Liu, Q., Logan, J., Tian, Y., Abbasi, H., Podhorszki, N., Choi, J. Y., … Yu, W. (2014). Hello ADIOS: the challenges and lessons of developing leadership class I/O frameworks. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 26(7), 1453–1473. https://doi.org/10.1002/cpe.3125

Tang, H., Zou, X., Jenkins, J., Boyuka, D. A., II, Ranshous, S., Kimpe, D., … Samatova, N. F. (2014). Improving Read Performance with Online Access Pattern Analysis and Prefetching. In Lecture Notes in Computer Science (pp. 246–257). https://doi.org/10.1007/978-3-319-09873-9_21

Jenkins, J., Dinan, J., Balaji, P., Peterka, T., Samatova, N. F., & Thakur, R. (2014). Processing MPI Derived Datatypes on Noncontiguous GPU-Resident Data. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 25(10), 2627–2637. https://doi.org/10.1109/tpds.2013.234

Jenkins, J., Zou, X., Tang, H., Kimpe, D., Ross, R., & Samatova, N. F. (2014). RADAR: Runtime Asymmetric Data-Access Driven Scientific Data Replication. In Lecture Notes in Computer Science (pp. 296–313). https://doi.org/10.1007/978-3-319-07518-1_19

Chen, W., Chen, Z., Samatova, N. F., Peng, L., Wang, J., & Tang, M. (2014). Solving the maximum duo-preservation string mapping problem with linear programming. THEORETICAL COMPUTER SCIENCE, 530, 1–11. https://doi.org/10.1016/j.tcs.2014.02.017

Faghmous, J. H., Banerjee, A., Shekhar, S., Steinbach, M., Kumar, V., Ganguly, A. R., & Samatova, N. (2014). Theory-Guided Data Science for Climate Change. COMPUTER, 47(11), 74–78. https://doi.org/10.1109/mc.2014.335

Boyuka, D. A., II, Lakshminarasimhan, S., Zou, X., Gong, Z., Jenkins, J., Schendel, E. R., … Samatova, N. F. (2014). Transparent In Situ Data Transformations in ADIOS. 2014 14TH IEEE/ACM INTERNATIONAL SYMPOSIUM ON CLUSTER, CLOUD AND GRID COMPUTING (CCGRID), pp. 256–266. https://doi.org/10.1109/ccgrid.2014.73

Schendel, E. R., Harenberg, S., Tang, H. J., Vishwanath, V., Papka, M. E., & Samatova, N. F. (2013). A generic high-performance method for deinterleaving scientific data. Euro-par 2013 parallel processing, 8097, 571–582. https://doi.org/10.1007/978-3-642-40047-6_58

Kawale, J., Liess, S., Kumar, A., Steinbach, M., Snyder, P., Kumar, V., … Semazzi, F. (2013). A graph-based approach to find teleconnections in climate data. Statistical Analysis and Data Mining, 6(3), 158–179. https://doi.org/10.1002/SAM.11181

Jenkins, J., Arkatkar, I., Lakshminarasimhan, S., Boyuka, D. A., II, Schendel, E. R., Shah, N., … Samatova, N. F. (2013). ALACRITY: Analytics-Driven Lossless Data Compression for Rapid In-Situ Indexing, Storing, and Querying. In Transactions on Large-Scale Data- and Knowledge-Centered Systems X (pp. 95–114). https://doi.org/10.1007/978-3-642-41221-9_4

Atluri, G., Padmanabhan, K., Fang, G., Steinbach, M., Petrella, J. R., Lim, K., … Kumar, V. (2013). Complex biomarker discovery in neuroimaging data: Finding a needle in a haystack. NeuroImage: Clinical, 3, 123–131. https://doi.org/10.1016/J.NICL.2013.07.004

Gonzalez, D. L., II, Pendse, S. V., Padmanabhan, K., Angus, M. P., Tetteh, I. K., Srinivas, S., … Samatova, N. F. (2013). Coupled Heterogeneous Association Rule Mining (CHARM): Application toward Inference of Modulatory Climate Relationships. 2013 IEEE 13TH INTERNATIONAL CONFERENCE ON DATA MINING (ICDM), pp. 1055–1060. https://doi.org/10.1109/icdm.2013.142

Chen, Z., Hendrix, W., Guan, H., Tetteh, I. K., Choudhary, A., Semazzi, F., & Samatova, N. F. (2013). Discovery of extreme events-related communities in contrasting groups of physical system networks. DATA MINING AND KNOWLEDGE DISCOVERY, 27(2), 225–258. https://doi.org/10.1007/s10618-012-0289-3

Tian, W., & Samatova, N. F. (2013). Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns. INTERNATIONAL JOURNAL OF GENOMICS, 2013. https://doi.org/10.1155/2013/670623

Lakshminarasimhan, S., Shah, N., Ethier, S., Ku, S.-H., Chang, C. S., Klasky, S., … Samatova, N. F. (2013). ISABELA for effective in situ compression of scientific data. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 25(4), 524–540. https://doi.org/10.1002/cpe.2887

Gong, Z., Boyuka, D. A., II, Zou, X., Liu, Q., Podhorszki, N., Klasky, S., … Samatova, N. F. (2013). PARLO: PArallel Run-time Layout Optimization for Scientific Data Explorations with Heterogeneous Access Patterns. PROCEEDINGS OF THE 2013 13TH IEEE/ACM INTERNATIONAL SYMPOSIUM ON CLUSTER, CLOUD AND GRID COMPUTING (CCGRID 2013), pp. 343–351. https://doi.org/10.1109/ccgrid.2013.58

Jenkins, J., Arkatkar, I., Lakshminarasimhan, S., Shah, N., Schendel, E. R., Ethier, S., … Samatova, N. F. (2012). Analytics-Driven Lossless Data Compression for Rapid In-situ Indexing, Storing, and Querying. In Lecture Notes in Computer Science (pp. 16–30). https://doi.org/10.1007/978-3-642-32597-7_2

Jenkins, J., Schendel, E. R., Lakshminarasimhan, S., Boyuka, D. A., Rogers, T., Ethier, S., … Samatova, N. F. (2012). Byte-precision level of detail processing for variable precision analytics. International conference for high performance computing networking. https://doi.org/10.1109/sc.2012.26

Chen, Z. Z., Hendrix, W., & Samatova, N. F. (2012). Community-based anomaly detection in evolutionary networks. Journal of Intelligent Information Systems, 39(1), 59–85. https://doi.org/10.1007/s10844-011-0183-2

Padmanabhan, K., Wang, K., & Samatova, N. F. (2012). Functional Annotation of Hierarchical Modularity. PLOS ONE, 7(4). https://doi.org/10.1371/journal.pone.0033744

Meleshko, S. V., Samatova, N. F., & Melechko, A. V. (2012). Group analysis of the thin film dewetting equation. INTERNATIONAL JOURNAL OF NON-LINEAR MECHANICS, 47(1), 9–13. https://doi.org/10.1016/j.ijnonlinmec.2011.08.005

Gonzalez, D. L., II, Chen, Z., Tetteh, I. K., Pansombut, T., Semazzi, F., Kumar, V., … Samatova, N. F. (2012). Hierarchical Classifier-Regression Ensemble for Multi-Phase Non-Linear Dynamic System Response Prediction: Application to Climate Analysis. 12TH IEEE INTERNATIONAL CONFERENCE ON DATA MINING WORKSHOPS (ICDMW 2012), pp. 781–788. https://doi.org/10.1109/icdmw.2012.133

Schendel, E. R., Jin, Y., Shah, N., Chen, J., Chang, C. S., Ku, S.-H., … Samatova, N. F. (2012). ISOBAR Preconditioner for Effective and High-throughput Lossless Data Compression. 2012 IEEE 28TH INTERNATIONAL CONFERENCE ON DATA ENGINEERING (ICDE), pp. 138–149. https://doi.org/10.1109/icde.2012.114

Padmanabhan, K., Wilson, K., Rocha, A. M., Wang, K., Mihelcic, J. R., & Samatova, N. F. (2012). In-silico identification of phenotype-biased functional modules. PROTEOME SCIENCE, 10. https://doi.org/10.1186/1477-5956-10-s1-s2

Gong, Z., Lakshminarasimhan, S., Jenkins, J., Kolla, H., Ethier, S., Chen, J., … Samatova, N. F. (2012). Multi-level Layout Optimization for Efficient Spatio-temporal Queries on ISABELA-compressed Data. 2012 IEEE 26TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS), pp. 873–884. https://doi.org/10.1109/ipdps.2012.83

Schmidt, M. C., Rocha, A. M., Padmanabhan, K., Shpanskaya, Y., Banfield, J., Scott, K., … Samatova, N. F. (2012). NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems. PLOS COMPUTATIONAL BIOLOGY, 8(5). https://doi.org/10.1371/journal.pcbi.1002490

Lakshminarasimhan, S., Kumar, P., Liao, W. K., Choudhary, A., Kumar, V., & Samatova, N. F. (2012). On the path to sustainable, scalable, and energy-efficient data analytics: Challenges, promises, and future directions. 2012 International Green Computing Conference (IGCC). https://doi.org/10.1109/igcc.2012.6322265

Lakshminarasimhan, S., Shah, N., Ethier, S., Klasky, S., Latham, R., Ross, R., & Samatova, N. F. (2011). Compressing the Incompressible with ISABELA: In-situ Reduction of Spatio-temporal Data. In Euro-Par 2011 Parallel Processing (pp. 366–379). https://doi.org/10.1007/978-3-642-23400-2_34

Lin, H., Ma, X., Feng, W., & Samatova, N. F. (2011). Coordinating Computation and I/O in Massively Parallel Sequence Search. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 22(4), 529–543. https://doi.org/10.1109/tpds.2010.101

Hendrix, W., Rocha, A. M., Padmanabhan, K., Choudhary, A., Scott, K., Mihelcic, J. R., & Samatova, N. F. (2011). DENSE: efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules. BMC SYSTEMS BIOLOGY, 5. https://doi.org/10.1186/1752-0509-5-172

Schmidt, M. C., Rocha, A. M., Padmanabhan, K., Chen, Z., Scott, K., Mihelcic, J. R., & Samatova, N. F. (2011). Efficient alpha, beta-motif finder for identification of phenotype-related functional modules. BMC BIOINFORMATICS, 12. https://doi.org/10.1186/1471-2105-12-440

Jenkins, J., Arkatkar, I., Owens, J. D., Choudhary, A., & Samatova, N. F. (2011). Lessons Learned from Exploring the Backtracking Paradigm on the GPU. In Euro-Par 2011 Parallel Processing (pp. 425–437). https://doi.org/10.1007/978-3-642-23397-5_42

Chen, W., Schmidt, M. C., & Samatova, N. F. (2011). On the parameterized complexity of the Multi-MCT and Multi-MCST problems. JOURNAL OF COMBINATORIAL OPTIMIZATION, 21(2), 151–158. https://doi.org/10.1007/s10878-009-9220-2

Belnap, C. P., Pan, C., Denef, V. J., Samatova, N. F., Hettich, R. L., & Banfield, J. F. (2011). Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions. The ISME Journal, 5(7), 1152–1161. https://doi.org/10.1038/ismej.2010.200

Li, J., Ma, X., Yoginath, S., Kora, G., & Samatova, N. F. (2011). Transparent runtime parallelization of the R scripting language. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 71(2), 157–168. https://doi.org/10.1016/j.jpdc.2010.08.013

Pan, C., Park, B. H., McDonald, W. H., Carey, P. A., Banfield, J. F., VerBerkmoes, N. C., … Samatova, N. F. (2010). A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. BMC Bioinformatics, 11.

Chen, Z., Wilson, K. A., Jin, Y., & Samatova, N. F. (2010). Detecting and Tracking Community Dynamics in Evolutionary Networks. The 10th IEEE International Conference on Data Mining Workshops, 318–327. https://doi.org/10.1109/icdmw.2010.32

Hendrix, W., Schmidt, M. C., Breimyer, P., & Samatova, N. F. (2010). Theoretical underpinnings for maximal clique enumeration on perturbed graphs. THEORETICAL COMPUTER SCIENCE, 411(26-28), 2520–2536. https://doi.org/10.1016/j.tcs.2010.03.011

Schmidt, M. C., Samatova, N. F., Thomas, K., & Park, B.-H. (2009). A scalable, parallel algorithm for maximal clique enumeration. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 69(4), 417–428. https://doi.org/10.1016/j.jpdc.2009.01.003

Breimyer, P., Green, N., Kumar, V., & Samatova, N. F. (2009). BioDEAL: community generation of biological annotations. BMC Medical Informatics and Decision Making, 9.

Chang, C. S., Ku, S., Diamond, P. H., Lin, Z., Parker, S., Hahm, T. S., & Samatova, N. (2009, May). Compressed ion temperature gradient turbulence in diverted tokamak edge. PHYSICS OF PLASMAS, Vol. 16. https://doi.org/10.1063/1.3099329

Belnap, C. P., Pan, C., VerBerkmoes, N. C., Power, M. E., Samatova, N. F., Carver, R. L., … Banfield, J. F. (2009). Cultivation and quantitative proteomic analyses of acidophilic microbial communities. The ISME Journal, 4(4), 520–530. https://doi.org/10.1038/ismej.2009.139

Awekar, A., & Samatova, N. F. (2009). Fast matching for all pairs similarity search. 2009 IEEE/WIC/ACM International Joint Conferences on Web Intelligence (WI) and Intelligent Agent Technologies (IAT), vol 1, 295–300. https://doi.org/10.1109/wi-iat.2009.52

Yang, S., Pappas, K. M., Hauser, L. J., Land, M. L., Chen, G.-L., Hurst, G. B., … Brown, S. D. (2009). Improved genome annotation for Zymomonas mobilis. Nature Biotechnology, 27(10), 893–894. https://doi.org/10.1038/nbt1009-893

Chen, W., Schmidt, M. C., & Samatova, N. F. (2009). On parameterized complexity of the Multi-MCS problem. THEORETICAL COMPUTER SCIENCE, 410(21-23), 2024–2032. https://doi.org/10.1016/j.tcs.2008.12.060

Lin, H., Ma, X., Li, J., Yu, T., & Samatova, N. (2008). Adaptive Request Scheduling for Parallel Scientific Web Services. In Lecture Notes in Computer Science (pp. 276–294). https://doi.org/10.1007/978-3-540-69497-7_19

Pan, C., Oda, Y., Lankford, P. K., Zhang, B., Samatova, N. F., Pelletier, D. A., … Hettich, R. L. (2008). Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics. MOLECULAR & CELLULAR PROTEOMICS, 7(5), 938–948. https://doi.org/10.1074/mcp.M700147-MCP200

Zhang, B., Park, B.-H., Karpinets, T., & Samatova, N. F. (2008). From pull-down data to protein interaction networks and complexes with biological relevance. BIOINFORMATICS, 24(7), 979–986. https://doi.org/10.1093/bioinformatics/btn036

Abu-Khzam, F. N., Rizk, M. A., Abdallah, D. A., & Samatova, N. F. (2008). The Buffered Work-Pool Approach for Search-Tree Based Optimization Algorithms. In Parallel Processing and Applied Mathematics (pp. 170–179). https://doi.org/10.1007/978-3-540-68111-3_19

Park, B.-H., Ostrouchov, G., & Samatova, N. F. (2007). Sampling streaming data with replacement. Computational Statistics & Data Analysis, 52(2), 750–762. https://doi.org/10.1016/j.csda.2007.03.010

Zhang, B., VerBerkmoes, N. C., Langston, M. A., Uberbacher, E., Hettich, R. L., & Samatova, N. F. (2006). Detecting Differential and Correlated Protein Expression in Label-Free Shotgun Proteomics. Journal of Proteome Research, 5(11), 2909–2918. https://doi.org/10.1021/pr0600273

Austin, D. W., Allen, M. S., McCollum, J. M., Dar, R. D., Wilgus, J. R., Sayler, G. S., … Simpson, M. L. (2006). Gene network shaping of inherent noise spectra. Nature, 439(7076), 608–611. https://doi.org/10.1038/nature04194

Pan, C., Kora, G., McDonald, W. H., Tabb, D. L., VerBerkmoes, N. C., Hurst, G. B., … Hettich, R. L. (2006). ProRata:  A Quantitative Proteomics Program for Accurate Protein Abundance Ratio Estimation with Confidence Interval Evaluation. Analytical Chemistry, 78(20), 7121–7131. https://doi.org/10.1021/ac060654b

Pan, C., Kora, G., Tabb, D. L., Pelletier, D. A., McDonald, W. H., Hurst, G. B., … Samatova, N. F. (2006). Robust Estimation of Peptide Abundance Ratios and Rigorous Scoring of Their Variability and Bias in Quantitative Shotgun Proteomics. Analytical Chemistry, 78(20), 7110–7120. https://doi.org/10.1021/ac0606554

McCollum, J. M., Peterson, G. D., Cox, C. D., Simpson, M. L., & Samatova, N. F. (2006). The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior. Computational Biology and Chemistry, 30(1), 39–49. https://doi.org/10.1016/j.compbiolchem.2005.10.007

Suters, W. H., Abu-Khzam, F. N., Zhang, Y., Symons, C. T., Samatova, N. F., & Langston, M. A. (2005). A New Approach and Faster Exact Methods for the Maximum Common Subgraph Problem. In Lecture Notes in Computer Science (pp. 717–727). https://doi.org/10.1007/11533719_73

Yu, G.-X., Park, B.-H., Chandramohan, P., Munavalli, R., Geist, A., & Samatova, N. F. (2005). In silico Discovery of Enzyme–Substrate Specificity-determining Residue Clusters. Journal of Molecular Biology, 352(5), 1105–1117. https://doi.org/10.1016/j.jmb.2005.08.008

Jenkins, J., Arkatkar, I., Lakshminarasimhan, S., Boyuka, D. A., Schendel, E. R., Shah, N., … Samatova, N. F. ALACRITY: Analytics-driven lossless data compression for rapid in-situ indexing, storing, and querying. Transactions on large-scale data- and knowledge- centered systems x: special issue on database- and expert-systems applications, 8220, 95–114.

Ranshous, S., Shen, S., Koutra, D., Faloutsos, C., & Samatova, N. F. Anomaly detection in dynamic networks: A survey. In Technical Report- Not held in TRLN member libraries.

Padmanabhan, K., Nudelman, K., Harenberg, S., Bello, G., Sohn, D., Shpanskaya, K., … Samatova, N. F. Characterizing gene and protein crosstalks in subjects at risk of developing Alzheimer's disease: A new computational approach. Processes, 5(3).

Harenberg, S., Bello, G. A., Gjeltema, L., Ranshous, S., Harlalka, J., Seay, R., … Samatova, N. Community detection in large-scale networks: A Survey and empirical evaluation. In Technical Report- Not held in TRLN member libraries (p. 2014).

Lakshminarasimhan, S., Shah, N., Ethier, S. J., Klasky, S., Latham, R., Ross, R., & N.F., S. Compressing the Incompressible with ISABELA:
In-situ Reduction of Spatio-Temporal Data. In Technical Report- Not held in TRLN member libraries.

Samatova, N. F., Schmidt, M. C., Hendrix, W., Breimyer, P., Thomas, K., & Park, B. H. Coupling graph perturbation theory with scalable parallel algorithms for large-scale enumeration of maximal cliques in biological graphs - art. no. 012053. Scidac 2008: Scientific discovery through advanced computing, 125, 12053–12053.

Chen, Z., Pansombut, T., Hendrix, W., Gonzalez, D., Semazzi, F., Choudhary, A., … Samatova, N. F. Forecaster: Forecast Oriented Feature Elimination-based Classification of Adverse Spatio-Temporal Extremes.

Jenkins, J. P., Zou, X., Tang, H., Kimpe, D., Ross, R., & Samatova, N. F. Parallel data layout optimization of scientific data through access-driven replication. In Technical Report- Not held in TRLN member libraries.