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Semester-In-Residence Projects

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.

Biotech SIR Brochure

Past Projects

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 protothecoidesAndre Domingo & Jennifer Zarzoso
  • Characterization of the interation of CsgF and Human Islet Amyloid PolypeptideMaryAm 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