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.