Sami Khuri's Master Thesis Students at SJSU

Major Advisor of:

[75] Shantanu Deshmukh. Detecting CRISPR Arrays using Long Short-Term Memory Networks. Defended in May 2019.

[74] Neha Atul Bhagwat. Designing Single Guide RNAs for CRISPR-Cas9. Defended in May 2019.

[73] Ishita Mathur. Predicting Off-Target Potential of CRISPR-Cas9 Single Guide RNA. Defended in May 2019.

[72] Pratik Surana. Benchmarking Optimization Algorithms for Capacitated Vehicle Routing Problems. Defended in May 2019.

[71] Aaron Kosmatin. Using Amino Acid Sequences to Generate Music. Defended in December 2018.

[70] Vandana Kannan. Feature Selection Using Genetic Algorithms. Defended in May 2018.

[69] Anuja Nandkumar. A Medical Price Prediction System. Defended in May 2018.

[68] Lavanya Abhinaya Koduri. A Convolutional Neural Network Based Approach for Visual Question Answering. Defended in May 2018.

[67] Divya Singh. Automated Lyrical Narrative Writing. Defended in May 2018.

[66] Remya Mohanan. Computational Analysis of Cryptic Splice Sites. Defended in May 2017.

[65] Tapomay Dey. Application of Computational Methods to Study the Selection of Authentic and Cryptic Splice Sites. Defended in May 2017.

[64] Pratikshya Mishra. Comparing Authentic and Cryptic 5' Splice Sites Using Hidden Markov Models and Decision Trees. Defended in May 2017.

[63] Shubhangi Rakhonde. Multiple Sequence Alignment with Profile Hidden Markov Models. Defended in May 2016.

[62] Li Miao. Comparative Analysis of Two Clustering Algorithms: K-Means and FSDP (Fast Search and Find of Density Peak). Defended in December 2015.

[61] Fengjiao (Jennifer) Wu. Using Probabilistic Graphical Models to Solve NP-Complete Puzzle Problems. Defended in May 2015.

[60] Shuang Wu. Comparative Analysis of Particle Swarm Optimization Algorithms for Text Feature Selection. Defended in May 2015.

[59] Santrupti Nerli. Using Hidden Markov Models to Detect DNA Motifs. Defended in May 2015.

[58] Sweta Shah. Masquerade Detection using Sigular Value Decomposition. Defended in December 2014.

[57] Sanya Valsan. Backward Sequential Feature Elimination and Joining Algorithms in Machine Learning. Defended in May 2014.

[56] Lakshmi Ananthagopal. Application of Message Passing and Sinkhorn Balancing Algorithms for Probabilistic Models. Defended in May 2014.

[55] Harini Padmanaban. Comparative Analysis of Naive Bayes and Tree Augmented Naive Bayes Models. Defended in May 2014.

[54] Mehal Patel. Bayesian Classifiers using Probabilistic Graphical Models. Defended in May 2014.

[53] Xiaohan Li. Attribute Selection Methods in Rough Set Theory. Defended in May 2014.

[52] Dhivya Srinivasan. Higher Order PWM for Modeling Transcription Factor Binding Sites. Defended in December 2013.

[51] Shuang Wang. Algorithms for Solving the Reducts Problem in Rough Sets. Defended in December 2012.

[50] Hardik Shah. Algorithms for Predicting Secondary Structures of Human Viruses. Defended in December 2012.

[49] Miaoer (Miao) Yu. Computational Modeling of Protein Dynamics with Gromacs and Java. Defended in December 2012.

[48] Vanessa Gaeke. A Database-Driven Website of Beta Thalassemia. Defended in October 2012.

[47] Sheetal Gosrani. Metagenome - Processing and Analysis. Defended in May 2012.

[46] Li Wen. Promoter Prediction Based on E.Coli Characteristics. Defended in December 2011.

[45] Manisha Gaikwad. EC2Lab: SaaS using Amazon Elastic Cloud Compute. Defended in December 2011.

[44] Maciej Kicinski. Ab Initio Protein Structure Prediction Algorithms. Defended in May 2011.

[43] Meenakshi Mali. RNA Secondary Structure Prediction Tool. Defended in May 2011.

[42] Emily Howe. STOP using just GO: A Multi-Ontology Enrichment Analysis Tool. Defended in May 2011.

[41] Rupinder Singh. A MicroRNA Target Prediction Algorithm. Defended in December 2010.

[40] Leyan Tang. Computational MicroRNA Target Prediction in Animals. Defended in December 2010.

[39] Sarbinder Kallar. Clustering and Validation of Microarray Data Using Consensus Clustering. Defended in May 2010.

[38] David Shao. Open Source Analysis of Biomedical Figures. Defended in May 2010.

[37] Steve Ikeoka. Analysis of Machine Learning Based Mehods for Identifying Micro RNA (MiRNA) Precursors. Defended in December 2009.

[36] Lakshmi Radhakrishnan. Robust Identification and Annotation of Disease-Causing SNPs in the Human Genome. Defended in December 2009.

[35] Manju Hari Hara Prasad. Compressing DNA sequences. Defended in May 2009.

[34] Phil Heller. A Gap-Oriented Genetic Algorithm for Multiple Sequence Alignment. Defended in May 2009.

[33] Rupali Khabiya. A Predictive Algorithm for MicroRNA Target Sites. Defended in May 2009.

[32] Medha Pradhan. Motif Discovery in Biological Sequences. Defended in December 2008.

[31] Ryan Pham. A Seeded Genetic Algorithm for RNA Secondary Structure Prediction with Pseudoknots. Defended in December 2008.

[30] Euna Park. Exact and Approximation Algorithms for Computing Reversal Distances in Genome Rearrangement. Defended in May 2008.

[29] Ching Chia Li. DNA Fragment Assembly Algorithms: Towards a Solution for Long Repeats. Defended in May 2008.

[28] Amie Radenbaugh. Applications of Genetic Algorithms in Bioinformatics. Defended in April 2008.

[27] George Shalu. Creating an Internet-Based Database of Beta Thalassemia Mutations. Defended in April 2008.

[26] Prafulla Basavaraja. Visualization of Mutations in the Beta Globin Gene that cause Beta Thalassemia. Defended in November 2007.

[25] Douglas Simmons. Prediction of Alternative Splice Sites in Human Genes. Defended in May 2007.

[24] Lisa Yu. RNA Secondary Structure Prediction Algorithms. Defended in Decenber 2006.

[23] Anannya Sengupta. Clustering Algorithms for Microarray Analysis. Defended in Decenber 2006.

[22] Brandon Hunter. Visualization of RNA Secondary Structure Prediction Algorithms. Defended in Decenber 2006.

[21] Nikhila Rao. Operon Prediction in Cyanobacteria using Comparative Genomics. Defended in May 2005.

[20] Priya Mathew. An Integrative Bioinfomatics Tool for Protein Sequence Analysis. Defended in December 2004.

[19] Jimmy Yu. Design and Analysis of Linear Discriminant Analysis and Hidden Markov Models as Gene Prediction Algorithms. Defended in December 2003.

[18] Ananth Prasad. Visualization of BLAST and PSI-BLAST in Bioinformatics. Defended in November 2003.

[17] Elo Leung. Using the Fuzzy C-Means Algorithm to Cluster Microarray Data. Defended in November 2003.

[16] Vidyagauri Nadkarni. Assembling DNA Fragments with Genetic Algorithms. Defended in May 2003.

[15] Lishan Li. Computational Techniques for the DNA Fragment Assembly Problem. Defended in May 2003.

[14] Chen Yang. Visualization of Phylogenetic Tree Construction Algorithms. Defended in May 2003.

[13] Yimin Jing. Exact and Heuristic Algorithms for the DNA Fragment Assembly Problem. Defended in May 2003.

[12] Radhika Ravirala. Multiple Sequence Alignment using Genetic Algorithms. Defended in January 2003.

[11] Eleanor Zhou. Java Visualization of Dynamic Programming Algorithms for Protein and Genomic Sequence Alignment Problems. Defended in December 2002.

[10] Radhika Madaan. Generic Framework for Web Applications using XML. Defended in December 2001.

[9] Tristan Marly. DNA Fragment Assembly Using Genetic Algorithms. Defended in May 1999.

[8] Hsiu-Chin Hsu. Visualization of Algorithms from Data Compression and Operating Systems. Defended in April 1999.

[7] Ping Wu. Java Implementation of Concurrent Programming Applications from Operating Systems. Defended in April 1999.

[6] Barbara Vendelin. An Algorithm for the Network Design Problem. Defended in April 1999.

[5] Annapoorani Ganesan. Algorithms for the Job Shop Scheduling Problem. Defended in December 1998.

[4] Sowmya Miryala. Heuristic Techniques for the Open Shop Scheduling Problem. Defended in November 1998.

[3] Srilatha Moturi. Performance of Decoding Algorithms for Group Codes. Defended in December 1997.

[2] Flora Ai-Hua Chung. Heuristic Algorithms for Graph Coloring Problems. Defended in September 1997.

[1] Teresa Li-Pei Chiu. Heuristic Algorithms for the Terminal Assignment Problem. Defended in May 1996.

MS Thesis Committee Member of:

[105] Benjamin Strauss. Predicting Switch-Like Behavior in Proteins using Logistic Regression on Sequence-Based Descriptors. Defended in July 2019.

[104] Mrudula Murali. Online Local Communities. Defended in May 2019.

[103] Shishir Kulkarni. GloVeNoR - Global Vectors for Node Representations. Defended in May 2019.

[102] Monica Golahalli Seenappa. Graph Classification Using Machine Learning Algorithms. Defended in May 2019.

[101] Neeraj Kulkarni. Learning to Play the Trading Game. Defended in May 2019.

[100] Saurabh Mithe. Deep Learning on Graphs Using Graph Convolutional Networks. Defended in May 2019.

[99] Ishan Shinde. Nitrogenase Iron Protein Detection using Neural Network. Defended in May 2019.

[98] Deepthi Vishwanath. Validating Key-Value Based Implementations of the Raft Consensus Algorithm for Distributed Systems. Defended in May 2018.

[97] Riya Prem Suchdev. Subtopics in Yelp Reviews. Defended in May 2018.

[96] Saily Ghodke. Load Balancing and VM Allocation in Cloud Based Data Centers. Defended in May 2018.

[95] Neethu Sundarprasad. Speech Emotion Detection Using Machine Learning Techniques. Defended in May 2018.

[94] Nishanth Reddy Pinnapareddy. Deep Learning Based Recommendation Systems. Defended in May 2018.

[93] Nitisha Raut. Facial Emotion Recognition Using Machine Learning. Defended in May 2018.

[92] Roshni Velluva Puthanidam. Time-Efficient Hybrid Approach for Facial Expression Recognition. Defended in December 2017.

[91] Becky Lee. Novel phosphate solubilizing bacteria lineages as potential bio-fertilizer in coffee farming. Defended in December 2017.

[90] Ketki Kulkarni. Community Detection in Social Networks. Defended in May 2017.

[89] Madhura Kaple. Influence Detection and Spread Estimation in Social Networks. Defended in May 2017.

[88] Behrooz Shahriari. Generic Online Learning for Partial Visible and Dynamic Environment with Delayed Feedback. Defended in May 2017.

[87] Jyoti Phatak. Structure-function relationship between quercetin, its methylated derivatives and cytotoxicity in triple negative breast cancer cells. Defended in July 2016.

[86] Radha Kotipalli. Processing Posting Lists Using OpenCL.
Defended in May 2016.

[85] Sreenidhi Pundi Muralidharan. On-the-Fly Map Generator for Openstreetmap Data using Webgl.
Defended in December 2015.

[84] Aparna Shikhare. Cryptanalysis of the Purple Cipher using Random Restarts.
Defended in December 2015.

[83] Jingjing (Lola) Young. Mining Concept in Big Data.
Defended in May 2015.

[82] Pooja Mishra. A Scalable Search Engine Aggregator.
Defended in May 2015.

[81] Pushkar Umaranikar. An Open Source Advertisement Server.
Defended in May 2015.

[80] Nikitha Ganesh. Static Analysis for Malicious Java Applets.
Defended in May 2015.

[79] Anusha Damodaran. Combining Dynamic and Static Analysis for Malware Detection.
Defended in May 2015.

[78] Eve Zheng. Musicological N-Gram Approach in Genre Classification.
Defended in May 2015.

[77] Vicky Na Zhao. Weighted Switching Hybrid Context-Aware (W-SHCA) Recommended System.
Defended in May 2015.

[76] Liang Wu. Twitter Opinion Mining for Adverse Drug Events.
Defended in May 2015.

[75] Jing Huang. Energy Aware Dynamic Virtual Machine Migration Algorithms in Green Cloud Data Centers.
Defended in December 2014.

[74] Lok Kei (Luisa) Leong. Analyzing Big Data with Decision Trees.
Defended in May 2014.

[73] Akash Patel. Incorporating Privacy and Security Features in an Open Source Search Engine.
Defended in May 2014.

[72] Mangesh Dahale. Text Summarization for Compressed Inverted Indexes and Snippets.
Defended in May 2014.

[71] Shailesh Padave. Incorporating WordNet in an Information Retrieval System.
Defended in May 2014.

[70] Mangesh Musale. Hunting for Metamorphic JavaScript Malware.
Defended in May 2014.

[69] Kalbhor Ashwin. A Tiered Approach to Detect Metamorphic Malware with Hidden Markov Models.
Defended in May 2014.

[68] Chetan Sharma. Big Data Analysis using Neural Networks.
Defended in May 2014.

[67] Lokmanyathilak Govindan Sankar Selvan. Opinion Mining on Twitter Data Stream to give Companies an up-to-date Feedback on their Free Products.
Defended in May 2014.

[66] Snigdha Rao Parvatneni. Adding a Source Code Searching Capability to Yioop.
Defended in December 2013.

[65] Mallika Perepa. Access Control in a Social Networking Environmnet.
Defended in December 2013.

[64] Jared Lee. Compression-Based Analysis of Metamorphic Malware.
Defended in December 2013.

[63] Arshi Agrawal. User Profiling in GUI-Based Windows Systems for Intrusion Detection.
Defended in May 2013.

[62] Teja Tamboli. Metamorphic Code Generation from LLVM IR Bytecode.
Defended in May 2013.

[61] Sandhya Vissapragada. Yioop! Introducing Autosuggest and Spell Check.
Defended in December 2012.

[60] Sampada Kathare. Easier Debugging of Multithreaded Software.
Defended in December 2012.

[59] Sayali Deshpande. Eigenvalue Analysis for Metamorphic Detection.
Defended in December 2012.

[58] Tanmayee Potluri. Extendig Yioop! Abilities to Search the Invisible Web.
Defended in December 2012.

[57] Xiu Guo. An Evaluation of the X10 Programming Language.
Defended in December 2012.

[56] Rafael Alvarez-Horine. Video in Cloud TCP Congestion Control Optimization for Cloud Computing.
Defended in November 2012.

[54] Parin Mukeshkumar Shah. Face Detection from Images using Support Vector Machine. Defended in May 2012.

[53] Sachin Kamath. Stock Market Analysis based on the Technical Indicators. Defended in May 2012.

[52] Ashutosh Singh. Social Networks for Botnet Command and Control. Defended in May 2012.

[51] Sivanaga Prasad Shola. Identifying Influential Bloggers. Defended in May 2012.

[50] Shabana Kazi. Hidden Markov Models for Software Piracy Detection. Defended in May 2012.

[49] Annie Hii Toderici. Chi-Squared Distance and Metamorphic Virus Detection. Defended in March 2012.

[48] Xinjun Zhang. ActiBot: A Botnet to Evade Active Detection. Defended in December 2011.

[47] Amrapali Dhavare. Efficient Attacks on Homophonic Substitution Ciphers. Defended in December 2011.

[46] Chao-Hsin Shih. Augmented-Life Phone Organizer. Defended in December 2011.

[45] Neha Runwal. Graph Technique for Metamorphic Virus Detection. Defended in December 2011.

[44] Mausami Mungale. Robust Watermarking using Hidden Markov Models. Defended in May 2011.

[43] Trusha Parikh. Bioinformatics, Immunology, and Viriology. Defended in May 2011.

[42] Rashmi Muralidhar. Substitution Cipher with Non-Prefix Codes. Defended in May 2011.

[41] Abhishek Shah. Approximate Disassembly using Dynamic Programming. Defended in December 2010.

[40] Swathi Vegesna. View Component of the Web-Based IDE to develop Web Applications on CakePHP. Defended in December 2010.

[39] Sugiharto Widjaja. Web-Based IDE to create Model and Controller Components for MVC-Based Web Applications on CakePHP. Defended in December 2010.

[38] Chi-Wen Fu. Bioinformatics, Immunology, and Biology Safety. Defended in December 2010.

[37] Ellen Stuart. Privacy and Security in Biomedical Applications of Radio Frequency Identification (RFID) and Wireless Sensor Networks . Defended in May 2010.

[36] Ronak Shah. Metamorphic Viruses with Built-In Buffer Overflow. Defended in May 2010.

[35] Cathy Lee. Bioinformatics, Immunology, and Molecular Biology. Defended in March 2010.

[34] Tom Chien. Bioinformatics, Molecular Biology, and Microbiology. Defended in February 2010.

[33] Pallavi Kanagalakatte Basavaraju. Heuristic Search Cryptoanalysis of the Zodiac 340 Cipher. Defended in December 2009.

[32] BingChun Chang. A Detailed Investigation of the Two Thresholds Two Divisor (TTTD) Algorithm and a New Improvement. Defended in December 2009.

[31] Swathi Venugopal. Priority Based Routing for Mobile Peer-to-Peer (MP2P) Communications. Defended in June 2009.

[30] Ken Chan. Error-Sensitive Adaptive Frame Aggregation in 802.11n WLANs. Defended in June 2009.

[29] Glenn Jahnke. MrCraig: Distributed Gene Prediction with MapReduce and Ensemble Classifiers. Defended in May 2009.

[28] Ashish Kaul. Visualized Architecture Knowledge Management Collaboration Services. Defended in May 2009.

[27] Barath Kuppuswamy. Priority Based Power Management and Reduced Downtime in Data Centers. Defended in May 2009.

[26] Nancy Fong. Bioinformatics, Molecular Biology, and Immunology. Defended in May 2009.

[25] Derrik Dela Cruz. Procedural Modeling of Plant Life using L-Systems. Defended in May 2009.

[24] Rajdheep Jandir. Event Based Propagation Approach to Constraint Configuration Problems. Defended in April 2009.

[23] Heather Kwong. Cryptanalysis of the SIGABA Cipher. Defended in December 2008.

[22] Supraja Swarna. Semantic Categorization of Online Video. Defended in December 2008.

[21] Nora Pakulis. Bioinformatics, Microbial Physiology, and Immunology. Defended in June 2007.

[20] Khoi Vu Nguyen. A hierarchical trusted third-party system for secure peer-to-peer transactions. Defended in April 2007.

[19] Sudhanthira Shanmugam. Bioinformatics, Genetics and Immunology. Defended in March 2007.

[18] Narayana Kashyap. A meaningful MD5 collision attack. Defended in September 2006.

[17] Sabrina Qian Li. ASH - A Scheduler for HOAs. Defended in September 2005.

[16] Hemlata Arcot. Perception-Based Fuzzy Information Retrieval. Defended in November 2003.

[15] Bo Chen. Dynamic Site Map Visualization. Defended in May 2003.

[14] Hong Li. Reliable Multicast Congestion Control for TCP/IP in Heterogeneous Wired/Wireless/Mobile Networks. Defended in May 2002.

[13] Yifan Gao. Protecting Digital Images with Invisible Digital Watermarks. Defended in May 1999.

[12] Suhair Halteh. A Distributive Alarm Notification System. Defended in May 1999.

[11] Otto Leung. Seashell Patterns With Cellular Automata. Defended in April 1999.

[10] Hua Mei. Supporting TCP via Unicast and Multicast GFR over ATM Networks. Defended in April 1999.

[9] Terrance Bing-Parks. A Visualization of a Quantum Mechanical Search Algorithm. Defended in April 1999.

[8] John Swapceinski. Java Implementation of the Knuth-Bendix Algorithm. Defended in April 1999.

[7] Ashima Verma. Modeling and Evaluation of High Speed LAN Switches. Defended in December 1998.

[6] Asha Kalyur. Process Migration in Sparta. Defended in December 1998.

[5] Surekha Nidamarty. Workflow Framework. Defended in October 1998.

[4] Bennett Niizawa. Multicasting ABR Rate Control Protocols for Hybrid Wired/Wireless ATM Networks. Defended in May 1998.

[3] Savitha S. Rao. Instruction Scheduling, RISC Machines and Code Optimization. Defended in August 1997.

[2] Martin F. Schlapfer. A Comparison of Genetic and Other Algorithms for the Traveling Salesman Problem. Defended in May 1997.

[1] Sandeep Shenoy. ATM ABR Protocol: Validation and Performance Evaluation. Defended in May 1997.

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Last updated on May 8, 2015