Publications - Data Mining for Biomedical Informatics Group

Books

Gaurav Pandey, Chad L. Meyers, Michael Steinbach, and Vipin Kumar. Computational Approaches to Protein Function Prediction. Wiley-Interscience, 2012. [Info]

Book Chapters

Chandrika Kamath, Nikhil Wale, George Karypis, Gaurav Pandey, Vipin Kumar et al. Scientific Data Analysis in Scientific Data Management: Challenges, Existing Technology, and Deployment. Editors Arie Shoshani and Doron Rotem, CRC Press, 2009. [Info]

Refereed Journal Articles

Casey Dorr, Callie Janik, Madison Weg, Raha A. Been, Justin Bader, Ryan Kang, Brandon Ng, Lindsey Foran, Sean R. Landman, M. Gerard O'Sullivan, Michael Steinbach, Aaron L. Sarver, Kevin A. T. Silverstein, David A. Largaespada, and Timothy K. Starr. Transposon mutagenesis screen identifies potential lung cancer drivers and CUL3 as a tumor suppressor. Molecular Cancer Research 13, no. 8 (2015): 1238-1247. [DOI]
Gowtham Atluri, Michael Steinbach, Kelvin O. Lim, Vipin Kumar, and Angus MacDonald. Connectivity cluster analysis for discovering discriminative subnetworks in schizophrenia. Human brain mapping (2014). [DOI]
Maneesh Bhargava, Trisha L. Becker, Kevin J. Viken, Pratik D. Jagtap, Sanjoy Dey, Michael S. Steinbach, Baolin Wu et al. Proteomic Profiles in Acute Respiratory Distress Syndrome Differentiates Survivors from Non-Survivors. PloS one 9, no. 10 (2014): e109713. [DOI]
Raha A. Been, Michael A. Linden, Courtney J. Hager, Krista J. DeCoursin, Juan E. Abrahante, Sean R. Landman, Michael Steinbach, Aaron L. Sarver, David A. Largaespada, and Timothy K. Starr. Genetic Signature of Histiocytic Sarcoma Revealed by a Sleeping Beauty Transposon Genetic Screen in Mice. PloS one 9, no. 5 (2014): e97280. [DOI]
Sean R. Landman, Tae Hyun Hwang, Kevin A.T. Silverstein, Yingming Li, Scott M. Dehm, Michael Steinbach, and Vipin Kumar. SHEAR: sample heterogeneity estimation and assembly by reference. BMC genomics 15, no. 1 (2014): 84. (Highly Accessed) [DOI] [Software]
Michael Steinbach, Haoyu Yu, Sean R. Landman, and Vipin Kumar. Identification of co-occurring insertions in cancer genomes using association analysis. International Journal of Data Mining and Bioinformatics 10, no. 1 (2014): 65-82. [DOI]
Maneesh Bhargava, Sanjoy Dey, Trisha Becker, Michael Steinbach, Baolin Wu, Sang Mee Lee, LeeAnn Higgins et al. Protein expression profile of rat type two alveolar epithelial cells during hyperoxic stress and recovery. American Journal of Physiology-Lung Cellular and Molecular Physiology 305, no. 9 (2013): L604-L614. [DOI]
Andrew B. Poppe, Krista Wisner, Gowtham Atluri, Kelvin O. Lim, Vipin Kumar, and Angus W. MacDonald III. Toward a neurometric foundation for probabilistic independent component analysis of fMRI data. Cognitive, Affective, & Behavioral Neuroscience 13, no. 3 (2013): 641-659. [DOI]
Gowtham Atluri, Kanchana Padmanabhan, Gang Fang, Michael Steinbach, Jeffrey R. Petrella, Kelvin Lim, Angus MacDonald III, Nagiza F. Samatova, P. Murali Doraiswamy, and Vipin Kumar. Complex biomarker discovery in neuroimaging data: Finding a needle in a haystack. NeuroImage: Clinical 3 (2013): 123-131. (Highly Accessed) [DOI]
Tae Hyun Hwang, Gowtham Atluri, Rui Kuang, Vipin Kumar, Timothy Starr, Kevin AT Silverstein, Peter M. Haverty, Zemin Zhang, and Jinfeng Liu. Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers. BMC genomics 14, no. 1 (2013): 440. [DOI]
Eric E. Schadt, Onureena Banerjee, Gang Fang, Zhixing Feng, Wing H. Wong, Xuegong Zhang, Andrey Kislyuk et al. Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome research 23, no. 1 (2013): 129-141. [DOI]
Gang Fang, Diana Munera, David I. Friedman, Anjali Mandlik, Michael C. Chao, Onureena Banerjee, Zhixing Feng et al. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nature biotechnology 30, no. 12 (2012): 1232-1239. [DOI]
Tae Hyun Hwang, Gowtham Atluri, MaoQiang Xie, Sanjoy Dey, Changjin Hong, Vipin Kumar, and Rui Kuang. Co-clustering phenome-genome for phenotype classification and disease gene discovery. Nucleic acids research 40, no. 19 (2012): e146-e146. [DOI]
Gang Fang, Majda Haznadar, Wen Wang, Haoyu Yu, Michael Steinbach, Timothy R. Church, William S. Oetting, Brian Van Ness, and Vipin Kumar. High-order SNP combinations associated with complex diseases: efficient discovery, statistical power and functional interactions. PloS one 7, no. 4 (2012): e33531. [DOI]
Gang Fang, Gaurav Pandey, Wen Wang, Manish Gupta, Michael Steinbach, and Vipin Kumar. Mining low-support discriminative patterns from dense and high-dimensional data. Knowledge and Data Engineering, IEEE Transactions on 24, no. 2 (2012): 279-294. [DOI] [Software]
Rohit Gupta, Navneet Rao, and Vipin Kumar. Discovery of error-tolerant biclusters from noisy gene expression data. BMC bioinformatics 12, no. Suppl 12 (2011): S1. [DOI]
Jeremy Bellay, Gowtham Atluri, Tina L. Sing, Kiana Toufighi, Michael Costanzo, Philippe Souza Moraes Ribeiro, Gaurav Pandey et al. Putting genetic interactions in context through a global modular decomposition. Genome research 21, no. 8 (2011): 1375-1387. [DOI]
Bonnie L. Westra, Sanjoy Dey, Gang Fang, Michael Steinbach, Vipin Kumar, Cristina Oancea, Kay Savik, and Mary Dierich. Interpretable predictive models for knowledge discovery from home-care electronic health records. Journal of Healthcare Engineering 2, no. 1 (2011): 55-74. [DOI]
Gaurav Pandey, Bin Zhang, Aaron N. Chang, Chad L. Myers, Jun Zhu, Vipin Kumar, and Eric E. Schadt. An integrative multi-network and multi-classifier approach to predict genetic interactions. PLoS computational biology 6, no. 9 (2010): e1000928. [DOI]
Gaurav Pandey, Chad L. Myers, and Vipin Kumar. Incorporating functional inter-relationships into protein function prediction algorithms. BMC bioinformatics 10, no. 1 (2009): 142. (Highly Accessed) [DOI]
Brian Van Ness, Christine Ramos, Majda Haznadar, Antje Hoering, Jeff Haessler, John Crowley, Susanna Jacobus, Martin Oken, Vincent Rajkumar, Philip Greipp, Bart Barlogie, Brian Durie, Michael Katz, Gowtham Atluri, Gang Fang, Rohit Gupta, Michael Steinbach, Vipin Kumar, Richard Mushlin, David Johnson and Gareth Morgan. Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival. BMC medicine 6, no. 1 (2008): 26. [DOI]
Hui Xiong, Gaurav Pandey, Michael Steinbach, and Vipin Kumar. Enhancing data analysis with noise removal. Knowledge and Data Engineering, IEEE Transactions on 18, no. 3 (2006): 304-319. [DOI]

Refereed Conference and Workshop Articles

Vanja Paunić, Michael Steinbach, Abeer Madbouly, and Vipin Kumar. Amb-EM: a SNP-based prediction of HLA alleles using ambiguous HLA data. In Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 104-113. ACM, 2014.
Gowtham Atluri, Michael Steinbach, Kelvin O. Lim, Angus MacDonald III, and Vipin Kumar. Discovering Groups of Time Series with Similar Behavior in Multiple Small Intervals of Time. In Proceedings of the 2014 SIAM International Conference on Data Mining, pp. 1055-1063. SIAM, 2014.
Sanjoy Dey, Gyorgy Simon, Bonnie Westra, Michael Steinbach, and Vipin Kumar. Mining Interpretable and Predictive Diagnosis Codes from Multi-source Electronic Health Records. In Proceedings of the 2014 SIAM International Conference on Data Mining, pp. 1001-1009. SIAM, 2014.
Vanja Paunić, Michael Steinbach, Abeer Madbouly, and Vipin Kumar. Evaluation of Label Dependency for the Prediction of HLA Genes. In Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, p. 296. ACM, 2013.
Vanja Paunić, Michael Steinbach, Vipin Kumar, and Martin Maiers. Prediction of HLA genes from SNP data and HLA haplotype frequencies. In Data Mining Workshops (ICDMW), 2012 IEEE 12th International Conference on, pp. 964-971. IEEE, 2012.
Sanjoy Dey, Kelvin Lim, Gowtham Atluri, Angus MacDonald III, Michael Steinbach, and Vipin Kumar. A pattern mining based integrative framework for biomarker discovery. In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pp. 498-505. ACM, 2012.
Michael Steinbach, Haoyu Yu, Gang Fang, and Vipin Kumar. Using constraints to generate and explore higher order discriminative patterns. In Advances in Knowledge Discovery and Data Mining, pp. 338-350. Springer Berlin Heidelberg, 2011.
Gowtham Atluri, Jeremy Bellay, Gaurav Pandey, Chad Myers, and Vipin Kumar. Discovering coherent value bicliques in genetic interaction data. In Proceedings of 9th International Workshop on Data Mining in Bioinformatics (BIOKDD’10), 2010. [PDF]
Rohit Gupta, Navneet Rao, and Vipin Kumar. Discovery of Error-tolerant Biclusters from Noisy Gene Expression Data. In Proceedings of 9th International Workshop on Data Mining in Bioinformatics (BIOKDD’10), 2010. [PDF]
Rohit Gupta, Smita Agrawal, Navneet Rao, Ze Tian, Rui Kuang, and Vipin Kumar. Integrative Biomarker Discovery for Breast Cancer Metastasis from Gene Expression and Protein Interaction Data Using Error-tolerant Pattern Mining. In Proceedings of the International Conference on Bioinformatics and Computational Biology (BICoB), 2010. [PDF]
Gang Fang, Rui Kuang, Gaurav Pandey, Michael Steinbach, Chad L. Myers, and Vipin Kumar. Subspace differential coexpression analysis: problem definition and a general approach. In Proceedings of the 15th Pacific Symposium on Biocomputing (PSB), vol. 15, pp. 145-56. 2010. [PDF] [Software]
Gowtham Atluri, Rohit Gupta, Gang Fang, Gaurav Pandey, Michael Steinbach, and Vipin Kumar. Association analysis techniques for bioinformatics problems. In Proceedings of the International Conference on Bioinformatics and Computational Biology (BICoB), pp. 1-13. 2009. (Invited Paper) [PDF]
Rohit Gupta, Michael Steinbach, Karla V. Ballman, Vipin Kumar, and Petrus C. de Groen. Colorectal Cancer Despite Colonoscopy: Critical Is the Endoscopist, Not the Withdrawal Time. Abstract in Gastroenterology 136, no. 5, A-55, 2009. (Selected for presentation in clinical science plenary session in DDW 2009) (Recipient of Student Abstract Prize) [PDF]
Rohit Gupta, Michael Steinbach, Karla V. Ballman, Vipin Kumar, and Petrus C. de Groen. Colorectal Cancer Despite Colonoscopy: Estimated Size of the Truly Missed Lesions. Abstract in Gastroenterology 136, no. 5, A-764, 2009. (Presented in DDW 2009) [PDF]
Gaurav Pandey, Gowtham Atluri, Michael Steinbach, Chad L. Myers, and Vipin Kumar. An association analysis approach to biclustering. In Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining, pp. 677-686, ACM, 2009. [PDF]
Gaurav Pandey, Gowtham Atluri, Gang Fang, Rohit Gupta, Michael Steinbach, and Vipin Kumar. Association analysis techniques for analyzing complex biological data sets. In Proceedings of the IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), pp. 1-4, IEEE, 2009. [PDF]
Gaurav Pandey, Lakshmi Naarayanan Ramakrishnan, Michael Steinbach, and Vipin Kumar. Systematic Evaluation of Scaling Methods for Gene Expression Data. In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 376-381. 2008. [PDF]
Rohit Gupta, Gang Fang, Blayne Field, Michael Steinbach, and Vipin Kumar. Quantitative evaluation of approximate frequent pattern mining algorithms. In Proceedings of the 14th ACM SIGKDD international conference on Knowledge discovery and data mining, pp. 301-309. ACM, 2008. [PDF] [Software]
Gaurav Pandey, Gowtham Atluri, Michael Steinbach, and Vipin Kumar. Association analysis techniques for discovering functional modules from microarray data. In Proceedings of the ISMB satellite meeting on Automated Function Prediction. 2008. (Also published in Nature Precedings) [PDF]
Rohit Gupta, Brian Brownlow, Robert Domnick, Gavin Harewood, Michael Steinbach, Vipin Kumar, and Piet de Groen. Colon cancer not prevented by colonoscopy. American College of Gastroenterology (ACG) Annual Meeting, 2008. (Recipient of the 2008 ACG Olympus Award and the 2008 ACG Presidential Award) [PDF]
Gaurav Pandey, Michael Steinbach, Rohit Gupta, Tushar Garg, and Vipin Kumar. Association analysis-based transformations for protein interaction networks: a function prediction case study. In Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining, pp. 540-549. ACM, 2007. (Also selected for a Highlight talk at ISMB 2008) [PDF]
Gaurav Pandey and Vipin Kumar. Incorporating Functional Inter-relationships into Algorithms for Protein Function Prediction. In Proceedings of the ISMB satellite meeting on Automated Function Prediction, 2007. [PDF]
Rohit Gupta, Tushar Garg, Gaurav Pandey, Michael Steinbach, and Vipin Kumar. Comparative study of various genomic data sets for protein function prediction and enhancements using association analysis. In SIAM Workshop on Data Mining for Biomedical Informatics, 2007. [PDF]
Hui Xiong, X. He, Chris Ding, Ya Zhang, Vipin Kumar, and Stephen R. Holbrook. Identification of Functional Modules in Protein Complexes via Hyperclique Pattern Discovery. In Pacific symposium on biocomputing, pp. 221-232. 2005. [PDF]
Benjamin W. Mayer, Huzefa S. Rangwala, Rohit Gupta, Jaideep Srivastava, George Karypis, Vipin Kumar, and Piet C. de Groen. Feature mining for prediction of degree of liver fibrosis. In AMIA Annual Symposium Proceedings, vol. 2005, p. 1048, American Medical Informatics Association, 2005. [Poster]

Technical Reports

Gowtham Atluri, Michael Steinbach, Kelvin Lim, Angus MacDonald, and Vipin Kumar. Discovering the Longest Set of Distinct Maximal Correlated Intervals in Time Series Data. Technical Report 14-025, September 2014, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gowtham Atluri, Michael Steinbach, Kelvin Lim, Angus MacDonald, and Vipin Kumar. Discovering Groups of Time Series with Similar Behavior in Multiple Small Intervals of Time. Technical Report 14-005, January 2014, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Sanjoy Dey, Rohit Gupta, Michael Steinbach, and Vipin Kumar. Integration of Clinical and Genomic data: a Methodological Survey. Technical Report 13-005, February 2013, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Michael Steinbach, Hayou Yu, Gang Fang, Vanja Paunic, and Vipin Kumar. The Nature and Limits of Discriminative Patterns. Technical Report 12-025, December 2012, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Sanjoy Dey, Gowtham Atluri, Michael Steinbach, Angus MacDonald, Kelvin Lim, and Vipin Kumar. A pattern mining based integrative framework for biomarker discovery. Technical Report 12-002, February 2012, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gaurav Pandey, Sahil Manocha, Gowtham Atluri, and Vipin Kumar. Enhancing the functional content of protein interaction networks. Technical Report 12-001, February 2012, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gang Fang, Wen Wang, Benjamin Oatley, Brian Van Ness, Michael Steinbach, and Vipin Kumar. Characterizing Discriminative Patterns. Technical Report 11-005, February 2011, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gang Fang, Wen Wang, Vanja Paunic, Benjamin Oatley, Majda Haznadar, Michael Steinbach, Brian Van Ness, Chad L. Myers, and Vipin Kumar. Construction and Functional Analysis of Human Genetic Interaction Networks with Genome-wide Association Data. Technical Report 11-001, January 2011, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gang Fang, Majda Haznadar, Wen Wang, Michael Steinbach, Brian Van Ness, and Vipin Kumar. A Computationally Efficient and Statistically Powerful Framework for Searching High-order Epistasis with Systematic Pruning and Gene-set Constraints. Technical Report 10-013, June 2010, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gang Fang, Michael Steinbach, Chad L. Myers, and Vipin Kumar. Integration of Differential Gene-combination Search and Gene Set Enrichment Analysis: A General Approach. Technical Report 09-031, December 2009, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Rohit Gupta, Smita Agrawal, Navneet Rao, Ze Tian, Rui Kuang, and Vipin Kumar. Integrative Biomarker Discovery for Breast Cancer Metastasis from Gene Expression and Protein Interaction Data Using Error-tolerant Pattern Mining. Technical Report 09-029, November 2009, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Rohit Gupta, Navneet Rao, and Vipin Kumar. A Novel Error-Tolerant Frequent Itemset Model for Binary and Real-Valued Data. Technical Report 09-026, October 2009, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gang Fang, Rui Kuang, Gaurav Pandey, Michael Steinbach, Chad L. Myers, and Vipin Kumar. Subspace Differential Coexpression Analysis: Problem Definition and a General Approach. Technical Report 09-021, July 2009, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gowtham Atluri, Jeremy Bellay, Gaurav Pandey, Chad L. Myers, and Vipin Kumar. Two-Dimensional Association Analysis For Finding Constant Value Biclusters In Real-Valued Data. Technical Report 09-020, July 2009, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gang Fang, Gaurav Pandey, Wen Wang, Manish Gupta, Michael Steinbach, and Vipin Kumar. Mining Low-Support Discriminative Patterns from Dense and High-Dimensional Data. Technical Report 09-011, April 2011, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Rohit Gupta, Gang Fang, Blayne Field, Michael Steinbach, and Vipin Kumar. Quantitative Evaluation of Approximate Frequent Pattern Mining Algorithms. Technical Report 09-005, February 2009, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gaurav Pandey, Gowtham Atluri, Michael Steinbach, Chad L. Myers, and Vipin Kumar. Association Analysis for Real-valued Data: Definitions and Application to Microarray Data. Technical Report 08-007, March 2008, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF] [Software]
Gaurav Pandey, Chad L. Myers, and Vipin Kumar. Incorporating Functional Inter-relationships into Protein Function Prediction Algorithms. Technical Report 08-001, Januay 2008, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gaurav Pandey, Lakshmi Naarayanan Ramakrishnan, Michael Steinbach, and Vipin Kumar. Systematic Evaluation of Scaling Methods for Gene Expression Data. Technical Report 07-015, June 2007, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gaurav Pandey, Michael Steinbach, Rohit Gupta, Tushar Garg, and Vipin Kumar. Association Analysis-based Transformations for Protein Interaction Networks: A Function Prediction Case Study. Technical Report 07-007, March 2007, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Gaurav Pandey, Vipin Kumar, and Michael Steinbach. Computational Approaches for Protein Function Prediction: A Survey. Technical Report 06-028, October 2006, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]
Hui Xiong, Gaurav Pandey, Michael Steinbach, and Vipin Kumar. Enhancing Data Analysis with Noise Removal. Technical Report 05-020, May 2005, Department of Computer Science and Engineering, Univesity of Minnesota. [PDF]