department menu

Semester-In-Residence Projects

Biotech SIR Brochure

The Semester-In-Residence (SIR) program is a unique part of the California State University San Marcos’ Professional Science Master’s in Biotechnology. The program provides students with the opportunity to work in a biotechnology or related life sciences business to address a real-world issue, project or problem by integrating new skills and information gained from their coursework.

The project functions as a capstone experience in lieu of a Master’s thesis, and runs for approximately 15 weeks requiring 300 hours of work. It is similar to a structured internship with a very specific, comprehensive schedule of deliverables established by the student, in consultation with the CSUSM Biotechnology Advisory Committee and the community partner.

Company Listings

Abbott Vascular  |  Active Motif  |   Ajinomoto Althea Inc.   |   Alere, Inc.  |  Althea Technologies  |  Ambryx, Inc.  |  Ardea Biosciences  |  Autogenomics  |  BioLegend Inc.   |   Bioresearch, Inc.  |  BD Biosciences  |  Carlsbad Aquafarm  |  Cliniqa Corporation  |  CSUSM  |  Dramm & Echter  |  Eco Feedstock   |   Encina Waste  |  Exeligen  |  Genentech  |  Genmark Diagnostics, Inc.  |  Genoptix  |  Howard Hughes Medical Institute  |  Ibis Biosciences, an Abbott Company  |  Illumina Inc.  |  Imgenex Corporation  |  Life Technologies  |  MaVax Therapeutics  |  Media. Genentech, Inc.  |  Millipore  |  Myron L Company  |  Neuropore Therapies, Inc  |  Point Loma Wastewater Treatment Plant  |  Promethean Biofuels Cooperative Corp.  |  Quidel Corporation  |  San Diego Zoo Global Institute for Conservation Research  |  San Diego Sheriffs Department, Crime Lab  |  Sapphire Energy  |  The Scripps Research Institute  |  Seacoast Science, Inc.  |  Sirigen/BDB  |  Syntron Bioresearch, Inc.  |  T2 Energy  |  ThermoFisher Scientific  |  Time Logic  |  Valicor Renewables   |  Water Authority 


Research and Development

Endoplasmic Reticulum Stress in Rodent Models: Interface with Metabolic Disease

Vivianite Investigation at the Point Loma Wastewater Treatment Plant by Phosphate Fractionation

Determining the Membrane Topology of CsgG Protein in Escherichia Coli

Gene Regulation Using Transcription Activator-like Effectors in Mammalian Cell Lines

Comparison of Four Bioanalystical Methods for the Quantitation of a PEGylated Therapeutic

Evaluation of Glutaraldehyde Crosslinking Reactions to Enhance the Efficiency of an Anti-Streptolysin O Purification Column  Christopher Heisinger

Effects of Zinc on Ethanol Drinking, Behavior, and Oxidative Stress Following Chronic Intermittent Ethanol Exposure  Chelsea Cates-Gatto

Improving Photophysical Properties of Brilliant VioletTM Polymers Via Structural Modifications  Lan Tran

A Target Enrichment and Fast PCR Method for Rapid Detection of Infectious Pathogens  Joseph Musmacker

Piecing Together the Visual Corticothalamic Retinotopic Map of the Mouse  Jamie Evora

Evaluation of Pollen Tube Growth from Liliaceae Flowers  Harika Sokkam

Characterization of Stem Cells Using CDy 1 a Stem Cell-Specific Dye  Rhoda Mondeh-Lowor

Epigenetics and Exercise in Relation to Atherosclerosis  Sukhdeep Sandhu

Chicken Fibroblast Cell Fusion with Avian Germline Stem Cells: A Model for Conservation of Exotic Bird Germplasm  Madhawi Alohali

Creating and Screening Mutant Populations to Enhance Astaxanthin Production in Haematococcus Pluvialis  Rohit Patel

Engineering a Cell Line for Analysis of Type I Interferon Signaling  Nahn Nguyen

Direct Conversion of Human Fibroblasts into Defined Neuronal Subtypes Using Lineage-Specific Factors  Nina Rander

The Effects of Aurintricarboxylic Acid in CHO Cultures in Chemically Defined  Elaine Lee

Gene Regulation Using Transcription Activator-Like Effectors in Mammalian Cell Lines  Vinita Kapur

Optimizing Adsorption Capacity of Activated Carbon: A Study of Effects of Arene Concentration Nana Banafon  Alicia Smith

Decreasing product heterogeneity by removal of the heavy chain terminal lysine from Mab1  Jennipher Rose Jose

Characterization of crude glycerol transesterfication methods and their effects on the growth of Chlorella vulgaris and Chlorella protothecoides  Andre Domingo & Jennifer Zarzoso

Characterization of the interation of CsgF and Human Islet Amyloid Polypeptide  MaryAm Alshulah

Monitoring Sendai viral backbone clearance in newly established induced pluripotent stem cells  Akili Tcha Binidi

Using Peptide Nucleic Acid Capture Probes to Identify 16s rRNA Gene of Sepsis causing Bacteria in Whole Blood Specimens  Soujanya Mamidi

Determining the regions involved in CsgE interation with HIAPP  Ashwag Binmahfooz

Evaluation of Enhancers that Increase Generation of Induced Pluripotent Stem Cells Under Xeno-Free Culture Conditions  Nikki Wetton

Translocation of Cell-Penetrating Peptides into  Emiliania huxleyi: Developing Novel Methods for Genome-Editing in Algae  Ryan Wallace

Identification of oogonial stem cells in adult quail ovaries: A model for conservation research of endangered avian species  Sara Jabalameli

Efficient Genome Editing Through Identification of a Universal Cell-Penetrating Peptide Conjugated to CRISPR/Cas9 System  Trae Reighert & Hirak Chavada



Comparison Evaluation of Various Software Tools and Methodologies for Chromatin-Immunoprecipitation (ChIP) Data Analysis

A Methodology for the Analysis of Metagenomics Data Using DeCypher System

A Comparative Analysis of the Tera-BLAST™ Algorithm

Efficient and Multiplex Genome Editing Using GeneArt CRISPR Nuclease mRNA.  Johan Garza

Functional Annotation of the Emiliana Huxleyi, Isochrysis Galbana, and Gephyrocapsa Oceanica Genomes  Jonathan Dy Albay



Commercialization of Biopellet Fertilizer: Marketing Plan for Encina Waste Water Authority

Increasing the Knowledge Base for Neutrophil Gelatinase-Associated Lipocalin (NGAL) as a Biomarker for Acute Renal Injury and Cardiorenal Syndrome

Development and Market Analysis of an Educational Mini-Bioreactor  Christopher Kensinger and Eric Gudorf

Online Market Survey to Assess the Need for an Educational High Performance Liquid Chromatograph (HPLC)  Jennifer Cunningham

Research and Analysis of the Market’s Interest for the Pollen Grwoth Cell Fertilization Kit  Minh Huynh

Developing Trial-Size Products to Offer More Effective Solutions for Experimental Design  Matt Miceli

Optimizing Website Design to Enhance Company Visibility  Kyle LeBlanc

FermSys Marketing Plan


Business Development

A Business Plan: Bioinformatic Services

Becoming a CRO: A Business Plan   

Increasing Efficiency in Complaint Handling by Implementation of Investigation Report  Denisse Reyes

Advancing Operation and Internal Capabilities through Documentation

Phase Zero Research for Market Feasibility of a New Diagnostic Test in the Biotechnology Industry  Jillian Lai


Product/Assay Development

Use of Oligonucleotide Capture Probes to Increase Bacterial Sensitivity on the Ibis PLEX-ID BAC Assay in Whole Blood Specimens

Optimizing TnT and TnC Cross-Linking to Increase Antibody Affinity and TnT, Yield, and Stability

Novel Multiplex PCR Technology Using Universal Primer in a Statin Assay  Perna Singh

Detection of Toxin Producing Clostridium Difficile Using Multiplex PCR  Jaya Ramrakhyani

Mouse Global LINE Methylation Assay  Patty Valesco

Optimizing the Asymmetric Primer Extension Assay Using the Infiniti Platform Kathleen Borst

Development of Cost-Effective Multiplex PCR Detection of MRSA  Abhisek A. Naik

Detection of Cancer Variants in Clinical Studies of a Next-Generation Sequencing Based Assay  Foram Rathi

Introducing an initialization step to optimize the signal to noise ratio on the eSenor Chip  Vanessa Mendez

Development of a multiplex PCR assay to detect drug resistant Helicobacter pylori  Abdullah Althuwaybi

Screening of anti-human VEGFR-1 and anti-human VEGFR-2 antibodies with different in-house clones, for flow cytometry and immunohistochemistry applications  Tannaz Rafizadeh


Training/Process Development

Optimizing Clean In Place Procedures for Oceanside Manufacturing

Chromatograghy DeltaV Overview: Creating an E-learning Module

Lean Manufacturing Principles: Optimization of Workflow and Production Lead Time Reduction

Implementation of the BenchPro 2100 for the Production of Low Demand Plasmids

Developing Mammalian Cell Culture Capabilities for Process Science at Ajinomoto Althea, Inc.  Berlin Siador

Cleanroom Training to Decrease Deviations Related to Process Error and Operator Error  Jaycee Nguen

Establishing amplicon monitoring program and implementing improved cleaning procedures to reduce contamination in pre- and post-PCR laboratories  Mayur Jain

Implementing a Curriculum for Improving Accuracy of Real-time Comments in Electronic Batch Records for Genentech, Inc. Kirstie Hunt


Advancing Operations and Internal Capabilities through Documentation

Performance Improvement and Outcome Monitoring for Urinalysis Drug Test Breaking  Zeena Jahani 

Manufacturing Bottlenecks: A Document Control Project  Brian Pizano

An Enabling High Throughput Process for Discovery of Specific Peptide Drug  Ross Fellows

Creation, Implementation and Assessment of a Mastery-Level Curriculum for Bioprocess Technicians  Martha James

Identifying the Competitive Landscape and End-User Requirements for the Development of a Novel GMP 500L Single-Use Bioreactor System

Implementartion of Lean Principles for the Re-Organization of the Quality Control Laboratories for Optimizing Associate Efficiency, Eliminating Waste and Controlling Inventory  Germalaine Arenas

The Advantages of Single Use Bioreactors and its Use as an Inoculum Seed Reactor  Bayan Awwad

Reducing HiSeq Setup Times in Sequencing Services Laboratory with 5S: Implications for Productivity and Quality  Ashley Ginbey

Chemical Utilization Analysis Used in DNA Sequencing: A Proposal for Optimization and Cost Reduction  Wallace Keau Wong

Bringing Gracilaria From Tank to Market: Optimization of Growth and Dehydration Methods  Thomas Pillsworth

Flow Cytometry Workflow Optimization through Implementation of Lean/Six Sigma Methodologies  Robert Andrews

Developing Addiction/Pain Management Genotyping Panel using Technology Platform  Azadeh Farahmand

Developing a Device for Self-Monitoring of Progesterone During In- Vitro Fertilization (IVF)  Marziyeh Tehraniyekta

A Web-Based Training Module for Manufacturing Process Comment Writing  Natalie Mabrey

Lean Manufacturing Principles: Optimization of Workflow and Production Lead Time Reduction  Manuel A. Perez



Determining the Trans Fat Content of Cakes and Doughnuts Sold in San Diego Grocery Store Bakeries

Guidelines for a Companion Diagnostic in a Regulated Environment

Microbial Survey of Althea Technologies 2011/2012 Environmental Isolates  Gabriel Rodriguez

Development of a Universal Contamination Testing Protocol for Index Adaptors used for Multiple Platforms  Rita Pitts

Equipment Validation of the 3 mm Bioprocess System  Joey Stark

Ensuring Genoptix Compliance with FDA Guidelines for Laboratory Developed Tests  Kevin Nguyen

Cost Analysis of Terminal Sterilization and Aseptic Processing Methods of Sensitive Implantable Combination Drug Device Products  Zenabu Bawa-Mamudu

Optimizing Adsorption Capacity of Activated Carbon  Alicia Smith

A Study of Effect of Arene Concentration  Nana Banafon

Development of a Real Time Molecular Surveillance Tool for Algal Pond Contaminants  Hee Cheol Kim

Quality Manual for Employees  Jeffery Ly



Communication: The Driving Force for Continuous Improvement Wave Reactor Proof of Concept

Evaluating Communication Channels and Practices Within and Across the Ardea Phase 3 Clinical Program  Kathy Truong

Development and Pilot Experiment of a Project Portfolio Management Tool for Supplier Quality  Jessie Wood

Installation of a Fertigation Monitoring System to Control the Nutritional Flow of Hydroponic Plants  Mike Vo

Optimizing Metabolic Efficiency through Manipulation of Surfboard Design  Taylor Frazee

Calibration and Testing of Electrodes for Use in a Hydroponic System  Jack Hattaway