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1

Theory-guided Data Science: A New Paradigm for Scientific Discovery from Data

Karpatne, Anuj, Atluri, Gowtham, Faghmous, James, Steinbach, Michael, Banerjee, Arindam, Ganguly, Auroop, Shekhar, Shashi, Samatova, Nagiza, Kumar, Vipin

Journal:

IEEE Transactions on Knowledge and Data Engineering

Year:

2017

Language:

english

File:

PDF, 5.38 MB

english, 2017

2

A graph-based approach to find teleconnections in climate data

Kawale, Jaya, Liess, Stefan, Kumar, Arjun, Steinbach, Michael, Snyder, Peter, Kumar, Vipin, Ganguly, Auroop R., Samatova, Nagiza F., Semazzi, Fredrick

Journal:

Statistical Analysis and Data Mining

Year:

2013

Language:

english

File:

PDF, 7.16 MB

english, 2013

3

[IEEE 2012 IEEE International Conference on Cluster Computing (CLUSTER) - Beijing, China (2012.09.24-2012.09.28)] 2012 IEEE International Conference on Cluster Computing - Enabling Fast, Noncontiguous GPU Data Movement in Hybrid MPI+GPU Environments

Jenkins, John, Dinan, James, Balaji, Pavan, Samatova, Nagiza F., Thakur, Rajeev

Year:

2012

Language:

english

File:

PDF, 298 KB

english, 2012

4

[IEEE 2007 IEEE/ACS International Conference on Computer Systems and Applications - Amman, Jordan (2007.05.13-2007.05.16)] 2007 IEEE/ACS International Conference on Computer Systems and Applications - The Maximum Common Subgraph Problem: Faster Solutions via Vertex Cover

Abu-Khzam, Faisal N., Samatova, Nagiza F., Rizk, Mohamad A., Langston, Michael A.

Year:

2007

Language:

english

File:

PDF, 209 KB

english, 2007

5

[IEEE Distributed Processing Symposium (IPDPS) - Miami, FL, USA (2008.04.14-2008.04.18)] 2008 IEEE International Symposium on Parallel and Distributed Processing - Parallel, scalable, memory-efficient backtracking for combinatoria modeling of large-scale biological systems

Park, Byung-Hoon, Schmidt, Matthew, Thomas, Kevin, Karpinets, Tatiana, Samatova, Nagiza F.

Year:

2008

Language:

english

File:

PDF, 359 KB

english, 2008

6

[IEEE 2010 IEEE International Conference on Data Mining Workshops (ICDMW) - Sydney, TBD, Australia (2010.12.13-2010.12.13)] 2010 IEEE International Conference on Data Mining Workshops - Detecting and Tracking Community Dynamics in Evolutionary Networks

Chen, Zhengzhang, Wilson, Kevin A., Jin, Ye, Hendrix, William, Samatova, Nagiza F.

Year:

2010

Language:

english

File:

PDF, 397 KB

english, 2010

7

[IEEE Distributed Processing, Workshops and Phd Forum (IPDPSW) - Anchorage, AK, USA (2011.05.16-2011.05.20)] 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum - Sensitive and Specific Identification of Protein Complexes in "Perturbed" Protein Interaction Networks from Noisy Pull-Down Data

Hendrix, William, Karpinets, Tatiana, Park, Byung-Hoon, Schendel, Eric, Choudhary, Alok, Samatova, Nagiza F.

Year:

2011

Language:

english

File:

PDF, 872 KB

english, 2011

8

[IEEE 2007 IEEE International Parallel and Distributed Processing Symposium - Long Beach, CA, USA (2007.03.26-2007.03.30)] 2007 IEEE International Parallel and Distributed Processing Symposium - Automatic Parallelization of Scripting Languages: Toward Transparent Desktop Parallel Computing

Ma, Xiaosong, Li, Jiangtian, Samatova, Nagiza F.

Year:

2007

Language:

english

File:

PDF, 162 KB

english, 2007

9

Anomaly detection in dynamic networks: a survey

Ranshous, Stephen, Shen, Shitian, Koutra, Danai, Harenberg, Steve, Faloutsos, Christos, Samatova, Nagiza F.

Journal:

Wiley Interdisciplinary Reviews: Computational Statistics

Year:

2015

Language:

english

File:

PDF, 538 KB

english, 2015

10

Data-driven, data-intensive computing for modelling and analysis of biological networks: application to bioethanol production

Park, Byung-Hoon, Samatova, Nagiza F, Karpinets, Tatiana, Jallouk, Andrew, Molony, Scott, Horton, Scott, Arcangeli, Steven

Journal:

Journal of Physics Conference Series

Year:

2007

Language:

english

File:

PDF, 502 KB

english, 2007

11

[IEEE 2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid) - Cartagena, Colombia (2016.5.16-2016.5.19)] 2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid) - Usage Pattern-Driven Dynamic Data Layout Reorganization

Tang, Houjun, Byna, Suren, Harenberg, Steve, Zou, Xiaocheng, Zhang, Wenzhao, Wu, Kesheng, Dong, Bin, Rubel, Oliver, Bouchard, Kristofer, Klasky, Scott, Samatova, Nagiza F.

Year:

2016

Language:

english

File:

PDF, 534 KB

english, 2016

12

The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior

James M. McCollum, Gregory D. Peterson, Chris D. Cox, Michael L. Simpson, Nagiza F. Samatova

Journal:

Computational Biology and Chemistry

Year:

2006

Language:

english

File:

PDF, 896 KB

english, 2006

13

Sampling streaming data with replacement

Byung-Hoon Park, George Ostrouchov, Nagiza F. Samatova

Journal:

Computational Statistics & Data Analysis

Year:

2007

Language:

english

File:

PDF, 345 KB

english, 2007

14

Transparent runtime parallelization of the R scripting language

Jiangtian Li, Xiaosong Ma, Srikanth Yoginath, Guruprasad Kora, Nagiza F. Samatova

Journal:

Journal of Parallel and Distributed Computing

Year:

2011

Language:

english

File:

PDF, 720 KB

english, 2011

15

On parameterized complexity of the Multi-MCS problem

Wenbin Chen, Matthew C. Schmidt, Nagiza F. Samatova

Journal:

Theoretical Computer Science

Year:

2009

Language:

english

File:

PDF, 556 KB

english, 2009

16

Theoretical underpinnings for maximal clique enumeration on perturbed graphs

William Hendrix, Matthew C. Schmidt, Paul Breimyer, Nagiza F. Samatova

Journal:

Theoretical Computer Science

Year:

2010

Language:

english

File:

PDF, 2.07 MB

english, 2010

17

DENSE: efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules

Willam Hendrix, Andrea M Rocha, Kanchana Padmanabhan, Alok Choudhary, Kathleen Scott, James R Mihelcic, Nagiza F Samatova

Journal:

BMC Systems Biology

Year:

2011

Language:

english

File:

PDF, 376 KB

english, 2011

18

On the parameterized complexity of the Multi-MCT and Multi-MCST problems

Wenbin Chen, Matthew C. Schmidt, Nagiza F. Samatova

Journal:

Journal of Combinatorial Optimization

Year:

2011

Language:

english

File:

PDF, 244 KB

english, 2011

19

A scalable, parallel algorithm for maximal clique enumeration

Matthew C. Schmidt, Nagiza F. Samatova, Kevin Thomas, Byung-Hoon Park

Journal:

Journal of Parallel and Distributed Computing

Year:

2009

Language:

english

File:

PDF, 3.92 MB

english, 2009

20

Vector space model for the generalized parts grouping problem

Nagiza F. Samatova, Thomas E. Potok, Michael R. Leuze

Journal:

Robotics and Computer-Integrated Manufacturing

Year:

2001

Language:

english

File:

PDF, 128 KB

english, 2001

21

Cultivation and quantitative proteomic analyses of acidophilic microbial communities

VerBerkmoes, Nathan C, Power, Mary E, Samatova, Nagiza F, Carver, Rudolf L, Hettich, Robert L, Banfield, Jillian F, Belnap, Christopher P, Pan, Chongle

Journal:

The ISME Journal

Year:

2009

Language:

english

File:

PDF, 545 KB

english, 2009

22

Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions

Belnap, Christopher P, Pan, Chongle, Denef, Vincent J, Samatova, Nagiza F, Hettich, Robert L, Banfield, Jillian F

Journal:

The ISME Journal

Year:

2011

Language:

english

File:

PDF, 526 KB

english, 2011

23

RACHET: An Efficient Cover-Based Merging of Clustering Hierarchies from Distributed Datasets

Nagiza F. Samatova, George Ostrouchov, Al Geist, Anatoli V. Melechko

Journal:

Distributed and Parallel Databases

Year:

2002

Language:

english

File:

PDF, 465 KB

english, 2002

24

ISABELA for effective in situ compression of scientific data

Sriram Lakshminarasimhan, Neil Shah, Stephane Ethier, Seung-Hoe Ku, C.S. Chang, Scott Klasky, Rob Latham, Rob Ross, Nagiza F. Samatova

Journal:

Concurrency and Computation: Practice and Experience

Year:

2012

Language:

english

File:

PDF, 3.70 MB

english, 2012

25

Community-based anomaly detection in evolutionary networks

Zhengzhang Chen, William Hendrix, Nagiza F. Samatova

Journal:

Journal of Intelligent Information Systems

Year:

2012

Language:

english

File:

PDF, 734 KB

english, 2012

26

A high-throughputde novosequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

Chongle Pan, Byung H Park, William H McDonald, Patricia A Carey, Jillian F Banfield, Nathan C VerBerkmoes, Robert L Hettich, Nagiza F Samatova

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.37 MB

english, 2010

27

Efficientα,β-motif finder for identification of phenotype-related functional modules

Matthew C Schmidt, Andrea M Rocha, Kanchana Padmanabhan, Zhengzhang Chen, Kathleen Scott, James R Mihelcic, Nagiza F Samatova

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 517 KB

english, 2011

28

BioDEAL: community generation of biological annotations

Paul Breimyer, Nathan Green, Vinay Kumar, Nagiza F Samatova

Journal:

BMC Medical Informatics and Decision Making

Year:

2009

Language:

english

File:

PDF, 2.21 MB

english, 2009

29

In-silicoidentification of phenotype-biased functional modules

Padmanabhan, Kanchana, Wilson, Kevin, Rocha, Andrea M, Wang, Kuangyu, Mihelcic, James R, Samatova, Nagiza F

Journal:

Proteome Science

Year:

2012

Language:

english

File:

PDF, 610 KB

english, 2012

30

Detecting Differential and Correlated Protein Expression in Label-Free Shotgun Proteomics

Zhang, Bing, VerBerkmoes, Nathan C., Langston, Michael A., Uberbacher, Edward, Hettich, Robert L., Samatova, Nagiza F.

Journal:

Journal of Proteome Research

Year:

2006

Language:

english

File:

PDF, 494 KB

english, 2006

31

In silico Discovery of Enzyme–Substrate Specificity-determining Residue Clusters

Gong-Xin Yu, Byung-Hoon Park, Praveen Chandramohan, Rajesh Munavalli, Al Geist, Nagiza F. Samatova

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 427 KB

english, 2005

32

Spice: discovery of phenotype-determining component interplays

Zhengzhang Chen, Kanchana Padmanabhan, Andrea M Rocha, Yekaterina Shpanskaya, James R Mihelcic, Kathleen Scott, Nagiza F Samatova

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 3.92 MB

english, 2012

33

Discovery of extreme events-related communities in contrasting groups of physical system networks

Chen, Zhengzhang, Hendrix, William, Guan, Hang, Tetteh, Isaac K., Choudhary, Alok, Semazzi, Fredrick, Samatova, Nagiza F.

Journal:

Data Mining and Knowledge Discovery

Year:

2013

Language:

english

File:

PDF, 1.14 MB

english, 2013

34

ProRata: A Quantitative Proteomics Program for Accurate Protein Abundance Ratio Estimation with Confidence Interval Evaluation

Pan, Chongle, Kora, Guruprasad, McDonald, W. Hayes, Tabb, David L., VerBerkmoes, Nathan C., Hurst, Gregory B., Pelletier, Dale A., Samatova, Nagiza F., Hettich, Robert L.

Journal:

Analytical Chemistry

Year:

2006

Language:

english

File:

PDF, 502 KB

english, 2006

35

[IEEE 2012 IEEE International Conference on Data Engineering (ICDE 2012) - Arlington, VA, USA (2012.04.1-2012.04.5)] 2012 IEEE 28th International Conference on Data Engineering - ISOBAR Preconditioner for Effective and High-throughput Lossless Data Compression

Schendel, Eric R., Jin, Ye, Shah, Neil, Chen, Jackie, Chang, C.S., Ku, Seung-Hoe, Ethier, Stephane, Klasky, Scott, Latham, Robert, Ross, Robert, Samatova, Nagiza F.

Year:

2012

Language:

english

File:

PDF, 1.04 MB

english, 2012

36

Solving the maximum duo-preservation string mapping problem with linear programming

Chen, Wenbin, Chen, Zhengzhang, Samatova, Nagiza F., Peng, Lingxi, Wang, Jianxiong, Tang, Maobin

Journal:

Theoretical Computer Science

Year:

2014

Language:

english

File:

PDF, 285 KB

english, 2014

37

THE WAR.

Atluri, Gowtham, Padmanabhan, Kanchana, Fang, Gang, Steinbach, Michael, Petrella, Jeffrey R., Lim, Kelvin, MacDonald, Angus, Samatova, Nagiza F., Doraiswamy, P. Murali, Kumar, Vipin

Journal:

Year:

1914

Language:

english

File:

PDF, 1008 KB

english, 1914

38

Complex biomarker discovery in neuroimaging data: Finding a needle in a haystack

Atluri, Gowtham, Padmanabhan, Kanchana, Fang, Gang, Steinbach, Michael, Petrella, Jeffrey R., Lim, Kelvin, MacDonald, Angus, Samatova, Nagiza F., Doraiswamy, P. Murali, Kumar, Vipin

Journal:

NeuroImage: Clinical

Year:

2013

Language:

english

File:

PDF, 856 KB

english, 2013

39

DIRAQ: scalable in situ data- and resource-aware indexing for optimized query performance

Lakshminarasimhan, Sriram, Zou, Xiaocheng, Boyuka, David A., Pendse, Saurabh V., Jenkins, John, Vishwanath, Venkatram, Papka, Michael E., Klasky, Scott, Samatova, Nagiza F.

Journal:

Cluster Computing

Year:

2014

Language:

english

File:

PDF, 1.44 MB

english, 2014

40

[IEEE 2009 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Washington, D.C., USA (2009.11.1-2009.11.4)] 2009 IEEE International Conference on Bioinformatics and Biomedicine - An Algorithm for the Discovery of Phenotype Related Metabolic Pathways

Schmidt, Matthew C., Samatova, Nagiza F.

Year:

2009

Language:

english

File:

PDF, 208 KB

english, 2009

41

Robust Estimation of Peptide Abundance Ratios and Rigorous Scoring of Their Variability and Bias in Quantitative Shotgun Proteomics

Pan, Chongle, Kora, Guruprasad, Tabb, David L., Pelletier, Dale A., McDonald, W. Hayes, Hurst, Gregory B., Hettich, Robert L., Samatova, Nagiza F.

Journal:

Analytical Chemistry

Year:

2006

Language:

english

File:

PDF, 514 KB

english, 2006

42

Processing MPI Derived Datatypes on Noncontiguous GPU-Resident Data

Jenkins, John, Dinan, James, Balaji, Pavan, Peterka, Tom, Samatova, Nagiza F., Thakur, Rajeev

Journal:

IEEE Transactions on Parallel and Distributed Systems

Year:

2014

Language:

english

File:

PDF, 776 KB

english, 2014

43

Coordinating Computation and I/O in Massively Parallel Sequence Search

Lin, Heshan, Ma, Xiaosong, Feng, Wuchun, Samatova, Nagiza F.

Journal:

IEEE Transactions on Parallel and Distributed Systems

Year:

2011

Language:

english

File:

PDF, 2.64 MB

english, 2011

44

[IEEE 2012 SC - International Conference for High Performance Computing, Networking, Storage and Analysis - Salt Lake City, UT, USA (2012.11.10-2012.11.16)] 2012 International Conference for High Performance Computing, Networking, Storage and Analysis - Byte-precision level of detail processing for variable precision analytics

Jenkins, John, Schendel, Eric R., Lakshminarasimhan, Sriram, Boyuka, David A., Rogers, Terry, Ethier, Stephane, Ross, Robert, Klasky, Scott, Samatova, Nagiza F.

Year:

2012

Language:

english

File:

PDF, 1.31 MB

english, 2012

45

[IEEE 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007) - Fremont, CA, USA (2007.11.2-2007.11.4)] 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007) - Multi-stage Framework to Infer Protein Functional Modules from Mass Spectrometry Pull-Down Data with Assessment of Biological Relevance

Park, Byung-Hoon, Zhang, Bing, Karpinets, Tatiana, Samatova, Nagiza F.

Year:

2007

Language:

english

File:

PDF, 414 KB

english, 2007

46

[IEEE 2010 IEEE International Conference on Data Mining Workshops (ICDMW) - Sydney, TBD, Australia (2010.12.13-2010.12.13)] 2010 IEEE International Conference on Data Mining Workshops - The Multiple Alignment Algorithm for Metabolic Pathways without Abstraction

Chen, Wenbin, Rocha, Andrea M., Hendrix, William, Schmidt, Matthew, Samatova, Nagiza F.

Year:

2010

Language:

english

File:

PDF, 338 KB

english, 2010

47

A Multi-Level Cache Model for Run-Time Optimization of Remote Visualization

Sisneros, Robert, Jones, Chad, Huang, Jian, Gao, Jinzhu, Park, Byung-Hoon, Samatova, Nagiza

Journal:

IEEE Transactions on Visualization and Computer Graphics

Year:

2007

Language:

english

File:

PDF, 2.51 MB

english, 2007

48

[IEEE 2008 IEEE/ACS International Conference on Computer Systems and Applications (AICCSA) - Doha, Qatar (2008.03.31-2008.04.4)] 2008 IEEE/ACS International Conference on Computer Systems and Applications - Rapid and robust ranking of text documents in a dynamically changing corpus

Park, Byung-Hoon, Samatova, Nagiza F., Munavalli, Rajesh, Krishnamurthy, Ramya, Kettani, Houssain, Geist, Al

Year:

2008

Language:

english

File:

PDF, 422 KB

english, 2008

49

[IEEE 2012 IEEE 12th International Conference on Data Mining Workshops - Brussels, Belgium (2012.12.10-2012.12.10)] 2012 IEEE 12th International Conference on Data Mining Workshops - Hierarchical Classifier-Regression Ensemble for Multi-phase Non-linear Dynamic System Response Prediction: Application to Climate Analysis

Gonzalez, Doel L., Chen, Zhengzhang, Tetteh, Isaac K., Pansombut, Tatdow, Semazzi, Fredrick, Kumar, Vipin, Melechko, Anatoli, Samatova, Nagiza F.

Year:

2012

Language:

english

File:

PDF, 2.44 MB

english, 2012

50

[IEEE 2012 IEEE International Symposium on Parallel & Distributed Processing (IPDPS) - Shanghai, China (2012.05.21-2012.05.25)] 2012 IEEE 26th International Parallel and Distributed Processing Symposium - Multi-level Layout Optimization for Efficient Spatio-temporal Queries on ISABELA-compressed Data

Gong, Zhenhuan, Lakshminarasimhan, Sriram, Jenkins, John, Kolla, Hemanth, Ethier, Stephane, Chen, Jackie, Ross, Robert, Klasky, Scott, Samatova, Nagiza F.

Year:

2012

Language:

english

File:

PDF, 871 KB

english, 2012