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Publications


2013
Rasheed Z, Rangwala H. "A Map-Reduce Framework for Clustering Metagenomes.". In: Proceedings of the 12th IEEE International Workshop on High Performance Computational Biology (HiCOMB). Boston, MA: IEEE; 2013:. Download: HICOMB2013-06.pdf (229.89 KB)
Blasiak S, Sudarshan S, Rangwala H. "Joint Segmentation and Clustering in Text Corpuses.". In: SIAM International Conference in Data Mining. Austin, TX: SIAM; 2013:. Abstract  Download: 217.pdf (1.27 MB)
Rasheed Z, Rangwala H. "MC-MinH: Metagenome Clustering using Minwise based Hashing.". In: SIAM International Conference in Data Mining. Austin, TX: SIAM; 2013:. Abstract  Download: 277.pdf (379.42 KB)
Saha T, Rangwala H, Domeniconi C. "Sparsification and Sampling of Networks for Collective Classification.". In: The 2013 International Conference on Social Computing, Behavioral-Cultural Modeling, & Prediction (SBP). Washington, DC: Springer; 2013:. Abstract  Download: 10.1007_978-3-642-37210-0_32.pdf (217.95 KB)
Bajaj JS, DM H, AJ S, et al. "Modulation of the Metabiome by Rifaximin in Patients with Cirrhosis and Minimal Hepatic Encephalopathy." PLoS ONE . 2013;8(4). Download: journal.pone_.0060042.pdf (1.72 MB)
2012
Saha T, Rangwala H, Domeniconi C. "Multi-label Classification using Adaptive Neighborhoods.". In: Eleventh International Conference on Machine Learning and Applications (ICMLA). Boca Raton, FL: IEEE; 2012:. Download: ICMLA_Rank.pdf (259.52 KB)
Charuvaka A, Rangwala H. "Multi-task learning for classifying proteins with dual hierarchies.". In: IEEE International Conference on Data Mining (ICDM). Brussels, Belgium: IEEE; 2012:. Download: 4905a834.pdf (276.15 KB)
Rasheed Z, Rangwala H, Barbara D. "LSH-Div: Species Diversity Estimation using Locality Sensitive Hashing.". In: IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Philadelphia, USA: IEEE; 2012:. Download: OTU_BIBM2012.pdf (344.53 KB)
Blasiak S, Rangwala H, Laskey KB. "A Family of Feed-forward Models for Protein Sequence Classification.". In: Proceedings of the European Conference on Machine Learning and Principles of Knowledge Discovery and Data Mining (ECML-PKDD). Bristol, UK: ECML; 2012:. Download: ecml2012.pdf (450.15 KB)
Yu G, Domeniconi C, Rangwala H, Zhang G, Yu Z. "Transductive multi-label ensemble classification for protein function prediction.". In: Proceedings of the 18th ACM SIGKDD international conference on Knowledge discovery and data mining. Beijing, China: ACM; 2012:. KDD '12. Download: p1077-yu.pdf (557.57 KB)
Blasiak S, Rangwala H, Laskey KB. "Beam Methods for the Profile Hidden Markov Model.". In: 2012 SIAM International Conference in Data Mining. Anaheim, CA: SIAM; 2012:. Download: sam2012.pdf (1.04 MB)
Rasheed Z, Rangwala H, Barbara D. "Efficient Clustering of Metagenomic Sequences using Locality Sensitive Hashing.". In: SIAM International Conference in Data Mining. Anaheim, CA: SIAM; 2012:. Abstract  Download: mclsh_sdm2012.pdf (604.91 KB)
Mutlu EA, Gillevet PM, Rangwala H, et al. "Colonic microbiome is altered in alcoholism." American Journal of Physiology - Gastrointestinal and Liver Physiology. 2012. Abstract  Download: Liver Physiol-2012ajpgi.pdf (462.89 KB)
Wang P, Domeniconi C, Rangwala H, Laskey KB. "Feature Enriched Nonparametric Bayesian Co-clustering.". In: PAKDD (1).; 2012:. Download: FE-DPCC.pdf (288.04 KB)
Hiremagalore S, Liang C, Stavrou A, Rangwala H. "Improving network response times using social information." Social Network Analysis and Mining. 2012:1-12. Abstract  Download: SNAM_J_Sharath_2012.pdf (939.6 KB)
Yavvari C, Tokhtabayev AG, Rangwala H, Stavrou A. "Malware Characterization Using Behavioral Components." In: Kotenko IV, Skormin VA, eds. MMM-ACNS. St. Petersburg, Russia; 2012:.
Rasheed Z, Rangwala H. "Metagenomic Taxonomic Classification using Extreme Learning Machines. ." Journal of Bioinformatics and Computational Biology. 2012;10:1250015. Download: S0219720012500151.pdf (300.48 KB)
Yu G, Zhang G, Rangwala H, Domeniconi C, Yu Z. "Protein function prediction using weak-label learning.". In: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM; 2012:.
2011
Saha T, Domeniconi C, Rangwala H. "Detection of Communities and Bridges in Weighted Networks.". In: MLDM.; 2011:.
Charuvaka A, Rangwala H. "Evaluation of short read metagenomic assembly." BMC Genomics. 2011;12 Suppl 2:S8. Abstract
Mahmood SF, Rangwala H. "GPU-Euler: Sequence Assembly Using GPGPU.". In: HPCC.; 2011:.
Blasiak S, Rangwala H. "A Hidden Markov Model Variant for Sequence Classification.". In: IJCAI.; 2011:.
Li S, Rangwala H. "An Information Theoretic Approach for the Analysis of RNA and DNA Binding Sites.". In: BICoB.; 2011:.
Liang C, Hiremagalore S, Stavrou A, Rangwala H. "Predicting Network Response Times Using Social Information.". In: ASONAM.; 2011:.
Wisittipanit N, Rangwala H, Sikaroodi M, Keshavarzian A, Mutlu EA, Gillevet P. "Profiling Microbial Communities using SSU rRNA Sequence and LH-PCR Data.". In: BICoB.; 2011:.
Dixon E, Clubb C, Pittman S, et al. "Solid-phase microextraction and the human fecal VOC metabolome." PLoS One. 2011;6:e18471. Abstract
Rasheed Z, Rangwala H. "TAC-ELM: Metagenomic Taxonomic Classification with Extreme Learning Machines.". In: BICoB.; 2011:.
2010
Naqvi A, Rangwala H, Spear G, Gillevet P. "Analysis of multitag pyrosequence data from human cervical lavage samples." Chem Biodivers. 2010;7:1076-1085. Abstract
Rangwala H, Jamali S. "Co-Participation Networks Using Comment Information.". In: ICWSM.; 2010.
Rangwala H, Jamali S. "Defining a Coparticipation Network Using Comments on Digg." IEEE Intelligent Systems. 2010;25:36-45.
Charuvaka A, Rangwala H. "Evaluation of short read metagenomic assembly.". In: BIBM.; 2010:.
Rangwala H, Karypis G. Introduction to protein structure prediction : methods and algorithms. Vol. 14. Hoboken, N.J.: Wiley; 2010. Wiley series on bioinformatics 14. Abstract
Rangwala H, Karypis G. "Introduction to Protein Structure Prediction: Methods and Algorithms." In: Rangwala H, Karypis G, eds. Wiley; 2010:.
Rangwala H. "Introduction to Protein Structure Prediction: Methods and Algorithms." In: Rangwala H, Karypis G, eds. Wiley; 2010:.
Charaniya S, Le H, Rangwala H, et al. "Mining manufacturing data for discovery of high productivity process characteristics." J Biotechnol. 2010;147:186-197. Abstract
Rangwala H. "Multiple Kernel Learning for Fold Recognition.". In: BICoB.; 2010:.
Naqvi A, Rangwala H, Keshavarzian A, Gillevet P. "Network-based modeling of the human gut microbiome." Chem Biodivers. 2010;7:1040-1050. Abstract
Wisittipanit N, Rangwala H, Gillevet P, Sikaroodi M, Mutlu EA, Keshavarzian A. "SVM-based classification and feature selection methods for the analysis of Inflammatory Bowel disease microbiome data." In: Huan J, Chen J, Zaki M, eds. Proceedings of the 9th International Workshop on Data Mining in Bioinformatics.; 2010:.
Ahmed R, Rangwala H, Karypis G. "TOPTMH: topology predictor for transmembrane alpha-helices." J Bioinform Comput Biol. 2010;8:39-57. Abstract
2009
Rangwala H, Karypis G. "Biological Data Mining." In: Chen J, Lonardi S, eds. CRC Press; 2009.
Jamali S, Rangwala H. "Digging Digg: Comment Mining, Popularity Prediction, and Social Network Analysis." Web Information Systems and Mining, International Conference on. 2009:32-38.
Rangwala H, Kauffman C, Karypis G. "A Kernel Framework for Protein Residue Annotation.". In: PAKDD.; 2009:. Abstract
Ning X, Rangwala H, Karypis G. "Multi-assay-based structure-activity relationship models: improving structure-activity relationship models by incorporating activity information from related targets." J Chem Inf Model. 2009;49:2444-2456. Abstract
Rangwala H, Kauffman C, Karypis G. "svmPRAT: SVM-based protein residue annotation toolkit." BMC Bioinformatics. 2009;10:439. Abstract
2008
Rangwala H, Karypis G. "fRMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information for Pairs with Low Sequence Identity.". In: APBC.; 2008:.
Rangwala H, Karypis G. "fRMSDPred: predicting local RMSD between structural fragments using sequence information." Proteins. 2008;72:1005-1018. Abstract
Zhang R, Rangwala H, Karypis G. "Genome Alignments Using MPI-LAGAN.". In: BIBM.; 2008:.
Kauffman C, Rangwala H, Karypis G. "Improving homology models for protein-ligand binding sites." Comput Syst Bioinformatics Conf. 2008;7:211-222. Abstract
Ahmed R, Rangwala H, Karypis G. "TOPTMH: Topology Predictor for Transmembrane alpha-Helices.". In: ECML/PKDD (1).; 2008:. Abstract
2007
Rangwala H, Karypis G. "fRMSDPred: predicting local RMSD between structural fragments using sequence information." Comput Syst Bioinformatics Conf. 2007;6:311-322. Abstract
Rangwala H, Karypis G. "Incremental window-based protein sequence alignment algorithms." Bioinformatics. 2007;23:e17-23. Abstract
Rangwala H, DeRonne K, Karypis G. "Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications." In: Hu X, Pan Y, eds. Knowledge Discovery in Bioinformatics. John Wiley & Sons, Inc.; 2007:.
2006
Rangwala H, Karypis G. "Building multiclass classifiers for remote homology detection and fold recognition." BMC Bioinformatics. 2006;7:455. Abstract
2005
Mayer BW, Rangwala HS, Gupta R, et al. "Feature mining for prediction of degree of liver fibrosis." AMIA Annu Symp Proc. 2005:1048.
Rangwala H, Lantz E, Musselman R, Pinnow K, Smith B, Wallenfelt B. "Massively parallel BLAST for the Blue Gene/L.". In: In High Availability and Performance Computing Workshop.; 2005.
Rangwala H, Karypis G. "Profile-based direct kernels for remote homology detection and fold recognition." Bioinformatics. 2005;21:4239-4247. Abstract
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