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Computational Analysis Of Cryptic Splice Sites, Remya Mohanan 2017 San Jose State University

Computational Analysis Of Cryptic Splice Sites, Remya Mohanan

Master's Projects

DNA in the nucleus of all eukaryotes is transcribed into mRNA where it is then translated into proteins. The DNA which is transcribed into mRNA is composed of coding and non-coding regions called exons and introns, respectively. It undergoes a post-trancriptional process called splicing where the introns or the non-coding regions are removed from the pre-mRNA to give the mature mRNA. Splicing of pre-mRNAs at 5 ́ and 3ˊ ends is a crucial step in the gene expression pathway. The mis-splicing by the spliceosome at different sites known as cryptic splice sites is caused by mutations which will affect the primary ...


Comparing Authentic And Cryptic 5’ Splice Sites Using Hidden Markov Models And Decision Trees, Pratikshya Mishra 2017 San Jose State University

Comparing Authentic And Cryptic 5’ Splice Sites Using Hidden Markov Models And Decision Trees, Pratikshya Mishra

Master's Projects

Splicing is the editing of the precursor mRNA produced during transcription. The mRNA contains a large number of nucleotides in the introns and exons which are spliced to remove the introns and bind the exons to produce the mature mRNA which is translated to generate proteins. Hence accurate splicing at 5’ and 3’ splice sites (authentic splice sites (AuthSS)) is of foremost importance. The 5’ and 3’ splice sites are characterized by consensus sequences. Eukaryotic genome also contains splice sites known as Cryptic Splice Sites (CSS) that match the consensus. But the CSS are activated only when there is a ...


Library For Writing Contracts For Java Programs Using Prolog, Yogesh Dixit 2017 San Jose State University

Library For Writing Contracts For Java Programs Using Prolog, Yogesh Dixit

Master's Projects

Today many large and complex software systems are being developed in Java. Although, software always has bugs, it is very important that these developed systems are more reliable despite these bugs.

One way that we can help achieve this is the Design by Contract (DbC) paradigm, which was first introduced by Bertrand Meyer, the creator of Eiffel. The concept of DbC was introduced for software developers so that they can produce more reliable software systems with a little extra cost. Using programming contracts allows developer to specify details such as input conditions and expected output conditions. Doing this makes it ...


Application Of Computational Methods To Study The Selection Of Authentic And Cryptic Splice Sites, Tapomay Dey 2017 San Jose State University

Application Of Computational Methods To Study The Selection Of Authentic And Cryptic Splice Sites, Tapomay Dey

Master's Projects

Proteins are building blocks of the bodies of eukaryotes, and the process of synthesizing proteins from DNA is crucial for the good health of an organism [13]. However, some mutations in the DNA may disrupt the selection of 5’ or 3’ splice sites by a spliceosome. An important research question is whether the disruptions have a stochastic relation to the position of nucleotides in the vicinity of the known authentic and cryptic splice sites. This can be achieved by proving that the authentic and cryptic splice sites are intrinsically different. However, the behavior of the spliceosome is not accurately known ...


A Ltihub For Composite Assignments, Sunita Rajain 2017 San Jose State University

A Ltihub For Composite Assignments, Sunita Rajain

Master's Projects

Learning management systems (LMS) such as Canvas and Blackboard use Learning Tool Interoperability (LTI) as their main integration point for external learning tools. Each external tool provider has to implement LTI specifications or follow LTI standards that is a time consuming and complex process as there is no easy to follow specification available. Through this project, I have developed a system that follows the LTI specifications and integrates the CodeCheck autograder and interactive exercises with any LMS. I developed a Java based web app named LTIHub that acts as a mediator between LMS and any Learning Tool Provider. The LTIHub ...


Headline Generation Using Deep Neural Networks, Dhruven Vora 2017 San Jose State University

Headline Generation Using Deep Neural Networks, Dhruven Vora

Master's Projects

News headline generation is one of the important text summarization tasks. Human generated news headlines are generally intended to catch the eye rather than provide useful information. There have been many approaches to generate meaningful headlines by either using neural networks or using linguistic features. In this report, we are proposing a novel approach based on integrating Hedge Trimmer, which is a grammar based extractive summarization system with a deep neural network abstractive summarization system to generate meaningful headlines. We analyze the results against current recurrent neural network based headline generation system.


Influence Detection And Spread Estimation In Social Networks, Madhura Kaple 2017 San Jose State University

Influence Detection And Spread Estimation In Social Networks, Madhura Kaple

Master's Projects

A social network is an online platform, where people communicate and share information with each other. Popular social network features, which make them di erent from traditional communication platforms, are: following a user, re-tweeting a post, liking and commenting on a post etc. Many companies use various social networking platforms extensively as a medium for marketing their products. A xed amount of budget is alloted by the companies to maximize the positive in uence of their product. Every social network consists of a set of users (people) with connections between them. Each user has the potential to extend its in ...


A Chatbot Framework For Yioop, Harika Nukala 2017 San Jose State University

A Chatbot Framework For Yioop, Harika Nukala

Master's Projects

Over the past few years, messaging applications have become more popular than Social networking sites. Instead of using a specific application or website to access some service, chatbots are created on messaging platforms to allow users to interact with companies’ products and also give assistance as needed. In this project, we designed and implemented a chatbot Framework for Yioop. The goal of the Chatbot Framework for Yioop project is to provide a platform for developers in Yioop to build and deploy chatbot applications. A chatbot is a web service that can converse with users using artificial intelligence in messaging platforms ...


Uncovering Functional Relationships In Leukemia, Reginald McGee 2017 Mathematical Biosciences Institute

Uncovering Functional Relationships In Leukemia, Reginald Mcgee

Biology and Medicine Through Mathematics Conference

No abstract provided.


Exploring An Autoimmune Hair Loss Condition Through Mathematical Modeling And Sensitivity Analysis, Atanaska Dobreva, Ralf Paus, Nick Cogan 2017 Florida State University

Exploring An Autoimmune Hair Loss Condition Through Mathematical Modeling And Sensitivity Analysis, Atanaska Dobreva, Ralf Paus, Nick Cogan

Biology and Medicine Through Mathematics Conference

No abstract provided.


Modeling Hiv Dynamics Following 3bnc117 Antibody Infusion, Samantha Erwin 2017 Virginia Polytechnic Institute and State University

Modeling Hiv Dynamics Following 3bnc117 Antibody Infusion, Samantha Erwin

Biology and Medicine Through Mathematics Conference

No abstract provided.


A Deterministic Model Of The Effect Of Electric Field On Chemotherapeutics Delivery Into A Tumor, Maryam Moarefian, Luke Achenie 2017 Virginia Polytechnic Institute and State University

A Deterministic Model Of The Effect Of Electric Field On Chemotherapeutics Delivery Into A Tumor, Maryam Moarefian, Luke Achenie

Biology and Medicine Through Mathematics Conference

No abstract provided.


Simulating The Evolution Of Skin Melanoma Using Heat Transfer, Ephraim Agyingi 2017 Rochester Institute of Technology

Simulating The Evolution Of Skin Melanoma Using Heat Transfer, Ephraim Agyingi

Biology and Medicine Through Mathematics Conference

No abstract provided.


A Mathematical Model Of The Effects Of Resistance Training On Body Composition, Marcella Torres, Angela Reynolds, Eric Trexler, Abbie Smith-Ryan 2017 Virginia Commonwealth University

A Mathematical Model Of The Effects Of Resistance Training On Body Composition, Marcella Torres, Angela Reynolds, Eric Trexler, Abbie Smith-Ryan

Biology and Medicine Through Mathematics Conference

No abstract provided.


Modeling Original Antigenic Sin In Dengue Viral Infection, Ryan Nikin-Beers 2017 Virginia Polytechnic Institute and State University

Modeling Original Antigenic Sin In Dengue Viral Infection, Ryan Nikin-Beers

Biology and Medicine Through Mathematics Conference

No abstract provided.


Interaction Of The Tear Film With The Ocular Surface, Richard J. Braun, Amy Janett, Nicholas Gewecke, Spencer Walker 2017 University of Delaware

Interaction Of The Tear Film With The Ocular Surface, Richard J. Braun, Amy Janett, Nicholas Gewecke, Spencer Walker

Biology and Medicine Through Mathematics Conference

No abstract provided.


Adaptive Therapy: Modeling Evolutionary Principles In Anticancer Therapy, Jeffrey B. West 2017 University of Southern California

Adaptive Therapy: Modeling Evolutionary Principles In Anticancer Therapy, Jeffrey B. West

Biology and Medicine Through Mathematics Conference

No abstract provided.


Incorporating Vessel Wall Remodeling Into 1d Cardiovascular Network Models Of Pulmonary Hypertension, Mansoor A. Haider, Nicholas A. Hill, Mette S. Olufsen 2017 University of Glasgow

Incorporating Vessel Wall Remodeling Into 1d Cardiovascular Network Models Of Pulmonary Hypertension, Mansoor A. Haider, Nicholas A. Hill, Mette S. Olufsen

Biology and Medicine Through Mathematics Conference

No abstract provided.


Immuno-Kinetics Of Immunotherapy: Dosing With Dcs, Elizabeth Zollinger 2017 St. Joseph's College, Brooklyn

Immuno-Kinetics Of Immunotherapy: Dosing With Dcs, Elizabeth Zollinger

Biology and Medicine Through Mathematics Conference

No abstract provided.


An Improved Algorithm For Learning To Perform Exception-Tolerant Abduction, Mengxue Zhang 2017 Washington University in St. Louis

An Improved Algorithm For Learning To Perform Exception-Tolerant Abduction, Mengxue Zhang

Engineering and Applied Science Theses & Dissertations

Abstract

Inference from an observed or hypothesized condition to a plausible cause or explanation for this condition is known as abduction. For many tasks, the acquisition of the necessary knowledge by machine learning has been widely found to be highly effective. However, the semantics of learned knowledge are weaker than the usual classical semantics, and this necessitates new formulations of many tasks. We focus on a recently introduced formulation of the abductive inference task that is thus adapted to the semantics of machine learning. A key problem is that we cannot expect that our causes or explanations will be perfect ...


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