Publications | MLBio+ Laboratory

Publications

Below is a list of my publications. Currently, I do not have the pdfs for these papers but will have them up shortly. If you are interested in them please don't feel shy to contact me. You can also get them from link.

Ph. D. Thesis
Huzefa Rangwala Protein Structure and Function Prediction using Kernel Methods. University of Minnesota, Minneapolis (2008). [PDF]

BOOK CHAPTERS
Huzefa Rangwala, Kevin DeRonne, George Karypis. Protein Structure Prediction using String Kernels in Knowledge Discovery in Bioinformatics: Techniques, Methods and Applications, published by John Wiley and Sons (2006).
Huzefa Rangwala, George Karypis. Predicting Local Structure and Function of Proteins in Biological Data Mining, to be published by CRC Press (2008).

JOURNAL PAPERS
Huzefa Rangwala, George Karypis. Profile-based Direct Kernels for Remote Homology Detection and Fold Recognition in BIOINFORMATICS, 21(23):4239-4247 (2005).
Huzefa Rangwala, George Karypis. . Building Multiclass Classifiers for Remote Homology Detection and Fold Recognition in BMC Bioinformatics, 7(455) (2006).
Huzefa Rangwala, George Karypis. Incremental Window-based Protein Sequence Alignments in BIOINFORMATICS, 23(2):e17-e23 (2007).
Huzefa Rangwala, George Karypis. fRMSDPred: Predicting Local Rmsd between Structural Fragments using Sequence Information in PROTEINS: Structure, Function and Bioinformatics (Accepted. In Press).

CONFERENCE/ WORKSHOP PAPERS
Huzefa Rangwala, Eric Lantz, Roy Musselman, Kurt Pinnow, Brian Smith, Brian Wallenfelt. Massively Parallel BLAST for the Blue Gene/L. Presented at the High Availability and Performance Computing Workshop held in conjunction with the 6th Los Alamos Computer Science Institute Symposium, Santa Fe, New Mexico (October, 2005).
Benjamin Mayer, Huzefa Rangwala, Rohit Gupta, Jaideep Srivastava, George Karypis, Vipin Kumar and Piet C de Groen Feature Mining for Prediction of Degree of Liver Fibrosis. Poster session at the American Medical Informatics Association Annual Symposium, Washington, DC (October, 2005).
Huzefa Rangwala, George Karypis. Incremental Window-based Protein Sequence Alignments. Presented at the 5th European Conference in Computational Biology, Eilat, Israel (January 2007).
Huzefa Rangwala, George Karypis. fRMSDPred: Predicting Local Rmsd between Structural Fragments using Sequence Information. Presented at Computational Systems Biology Conference, Sand Deigo, CA (August 2007).
Huzefa Rangwala, George Karypis. fRMSDAlign: Protein Sequence Alignment using predicted local structure information at the 6th Asia Pacific Bioinformatics Conference, Kyoto, Japan (January 2008).
Huzefa Rangwala, Christopher Kauffman, George Karypis. A generalized framework for Protein Sequence Annotation at the Machine Learning in Computational Biology Workshop, Whistler, Canada (December 2007).
Christopher Kauffman, Huzefa Rangwala, George Karypis. Improving Homology Models for Protein-Ligand Binding Sites at Computational Systems Biology Conference, Stanford, CA (August 2008).
Salim Charaniya, Huzefa Rangwala, Keri Mills, Kevin Johnson, George Karypis, Wei-Shou Hu. Mining cell culture process data to unveil high productivity characteristics at the 236th ACS National Meeting in Philadelphia, PA (August 2008).
Rezwan Ahmed, Huzefa Rangwala, George Karypis. TOPTMH: Topology Predictor for Transmembrane Alpha-Helices at the ECML-PKDD 2008 Conference in Antwerp, Belgium (September 2008).
Xia Ning, Huzefa Rangwala, George Karypis. Improved SAR Models- Exploiting Target-Ligand Relationships. (Submitted).
Ruinan Zhang, Huzefa Rangwala, George Karypis. Whole genome alignments using MPI-LAGAN. (Submitted).