Canary Center at Stanford Internship Projects

Faculty Mentor: Zhen Cheng, PhD
Internship Mentor:  Zhen Cheng, PhD, Hao Chen, PhD, Su Hyun Hong, PhD

Internship Positions: 3 positions available, High school or Undergraduates
Type of Laboratory Research: Wet lab

The main objective of Dr. Zhen Cheng's lab is to develop novel molecular imaging probesand techniques for non-invasive detection of cancer and its metastasis at the earliest stage,to cure cancer or transform it into a manageable disease.  Currently, Dr. Zhen Cheng's lab isactively studying several important topics in the cancer molecular imaging field.  Positronemission tomography (PET) is a very promising technology for non-invasively imaging, andDr. Zhen Cheng's lab focuses on developing novel peptides and small molecules based PET probes targeting melanoma associated receptors.  Many different types of platforms havebeen explored in molecular probe discovery. Among them protein scaffolds are the mostinteresting platforms due to their special features. Dr. Zhen Cheng's research group isespecially interested in studying two new emerging protein scaffolds for their diagnosticapplications: Affibody and Cystine knot miniproteins (knottins). Another exciting researchdirection in Dr. Zhen Cheng's lab is Cerenkov imaging. Recently, it has been discovered thata variety of radioactive materials could be detected by optical imaging techniques. This ismainly attributed to the ability of radioactive materials to produce low energy visiblephotons associated with Cerenkov radiation. This technique would be particularly useful inthe pre-clinical research, and may find applications in clinical cancer diagnosis.

Faculty Mentor: Utkan Demirci, PhD
Internship Mentor: Rami El Assal, DDS, Fatih Inci, PhD, Thomas Nieland, PhD

Internship Positions: 3 positions available, Undergraduates only

Type of Laboratory Research: Wet lab

The Demirci Bio-Acoustic MEMS in Medicine Labs (BAMM) laboratory specializes in applying microand nano-scale technologies to problems in medicine. We apply our cell printing, microfluidics andmicro patterning/monitoring/sorting expertise to several fields including cancer research, diagnostics,fertilization, stem cell engineering, and regenerative medicine. The project involves applyingadvanced MEMS, microfluidics, and imaging systems to: (1) Microfluidic and lab-on-a-chip techniques, (2) Localized Surface Plasmon Resonance biosensor research. Students involved inthese projects will have the unique opportunity to 1) develop physical understanding of optics and itsbiological applications, 2) learn performing research via MEMS, microfluidics and imaging.

Faculty Mentor: H. Tom Soh, PhD
Internship Mentors: Gurpreet Sekhon, PhD and Diana Wu

Internship Positions: 2 positions available, Undergraduates only
Type of Laboratory Research: Wet lab

The Soh Laboratory is interested in developing biosensor discovery technologies capable ofgenerating highly accurate and sensitive biosensors for simultaneous detection andreporting of disease biomarkers. As current technologies typically require long andcumbersome rational design schemes that often produce less than ideal sensitivity/accuracy, our approach streamlines this workflow by displaying nucleic acidcandidate libraries on bead particles and sorting the resulting populations with high-throughput FACS instrumentation.  The resulting biosensors isolated not only bind theircorresponding biomarkers with high affinity and specificity, but also simultaneously reportthe binding event through integrated signaling systems.   Thus we can produce highlyeffective, low-cost biosensor constructs that are directly translatable to a point-of-careclinical setting, as minimal post-discovery intervention is needed. To assist with this project, we are seeking a highly motivated and enthusiasticundergraduate research intern with a background in a relevant physical or life sciencesdiscipline.  The student will be exposed to wide spectrum of laboratory techniques rangingfrom bench work pipetting to assisting in running FACS instrumentation.  The student willgain knowledge on the fundamentals of nucleic acid and protein synthesis and chemicalmodification, solid-phase bio-conjugation chemistries, and working with DNA librariestailored for directed evolution.  Students with chemistry and/or biology lab experiencewould be preferred.

Faculty Mentor: Sanjiv Sam Gambhir, MD, PhD
Internship Mentors: Arutselvan Natarajan, PhD

Internship Positions: 1 position available, High School or Undergraduates
Type of Laboratory Research: Wet lab

Screening of novel protein binder from the yeast library for the imaging of activatedT cells. Including imaging of cancer and immune response against tumors. The internshipwill expose the individual to a number of sophisticated techniques that are relevant andrequisite for the fields of protein engineering, biomedical and molecular imaging research.

Faculty Mentor: Sanjiv Sam Gambhir, MD, PhD
Internship Mentor: Edwin Chang, PhD

Internship Positions: 1 position available, High school or undergraduate
Type of Laboratory Research: Wet lab

Glioblastoma multiforme (GBM) is an exceptionally aggressive class of brain cancer. Unfortunately, it is also the main type of primary tumor that patients suffering from brain cancer will encounter. GBM is not only extremely proliferative but it is genomically and phenotypically heterogeneous. These characteristics are encapsulated with the nomenclature of “multiforme”. The diversity of subgroups within a GBM makes therapy difficult and consequently, there are few therapeutic and diagnostic tools that can be used to combat the disease. In this internship, the intern will participate in finding such new tools by screening promising drugs against glioblastoma cell cultures of human origin. Once we have identified the leaders, we will then validate them in preclinical models of human GBM.

The internship will expose the individual to a number of techniques that are relevant and requisite for the fields of biomedical and molecular imaging research. Since, GBM lines grow as suspension cell cultures (i.e. the cells float and grow in liquid suspension as opposed to sticking to the bottom of the plate); the intern will learn both adherent and 3-dimensional cell cultures for several glioblastoma lines. To monitor the therapeutic impact of our screened drugs, standardized bioassays for cellular activity (cell counts, alamar blue and MTT proliferation assays, neurospheres size distribution, bioluminescence activity) will be introduced and mastered. If time permits, the intern will be shown the fundamentals of preclinical model development. The models will then be employed to validate drugs that have passed the initial screen from cellular culture. Such investigations will also introduce the intern to established bioluminescence assays of cancer cell growth and development.

Faculty Mentor: Sanjiv Sam Gambhir, MD, PhD
Internship Mentor:  Frezghi Habte, PhD

Internship Positions: 1 position available, High school or undergraduate
Type of Laboratory Research: Dry lab

Development of advanced image quantitation methods for preclinical molecularimaging. Imaging is currently an essential tool in the early cancer detectionresearch conducted by various investigators in the canary center at Stanford. Inparticular, radionuclide and optical imaging techniques have emerged as the mostutilized approaches frequently used in various preclinical research with smallanimal models to determine signal uptake in target organs in vivo. Accurate quantification of signal uptakes of various diseases in vivo can play a vital role invarious research studies including understanding the tumor biology, developmentof effective drug for diagnosis and treatment and also for developing advanceimaging techniques. Compared to a simple qualitative analysis (e.g., visualinspection), which is highly subjective, it is understood that quantitative imageanalysis has superior advantage in characterizing biological processes in moreobjective and repeatable manner. However, due to the complexity of the imaginginstrument and associated analysis tools, there is still significant variability inquantitative imaging, which makes the development of standardized methodsdifficult that requires further development. This project will involve assessing theexiting overall image data analysis methods and developing new imagingacquisition strategies and/or analysis software tools that improve the accuracy andefficiency of quantification preclinical imaging techniques. The task of the projectwill require an interest and basic knowledge of molecular biology, the physics ofmedical imaging and programming preferably in Matlab and/or C++.

Faculty Mentor: Sanjiv Sam Gambhir, MD, PhD
Internship Mentor: Sharon Hori, PhD

Internship Positions: 1 position available, Undergraduates only
Type of Laboratory Research: Mixture of wet and dry lab

Most cancers can be more effectively treated if they are discovered early.  Dr. Hori is studying thedetectability of early-stage cancers using secreted cancer-specific biomarkers – proteins or moleculesreleased from cancer cells into the blood. The purpose of this internship is to use integrative biologicaland mathematical modeling techniques to study the relationship between a growing tumor and theamount of biomarker it secretes, with the overall goal of identifying better strategies to detect small, early-stage cancers from a blood sample.The internship applicant should be a highly-motivated undergraduate with a basic background inmolecular/cellular biology and mathematics (single-variable calculus required), and have a strong desireto learn and integrate biological and mathematical modeling techniques. Computer programming andmathematical modeling skills preferred but not required. The intern will have the opportunity to learn how to culture cancer cells, treat cancer cells with chemotherapeutic drugs, perform assays to assess cellviability and measure secreted biomarker levels, image cells using fluorescence and bioluminescencetechniques, develop basic mathematical/computational models for tumor growth and biomarker secretion,and/or use mathematical modeling approaches to study or make predictions about cancer state. Thissummer internship will provide a unique opportunity to gain hands-on experience in biological andcomputational research, and is ideal for students interested in molecular/cellular biology, cancer research,medicine, computational and systems biology, biomedical engineering and related fields. Minimum 40hr/week required.

Faculty Mentor: Parag Mallick, PhD

Internship Positions: 3 positions available, High school or undergraduate
Type of Laboratory Research: Dry lab

Blood-based biomarkers are of significant clinical interest for their potential to detect cancers earlier and personalize treatment.   Unfortunately, despite decades of work, few biomarkers are currently in clinical practice.  Our group is working to develop a novel platform for biomarker discovery in which large-scale data analytics and mathematical modeling are used in tandem to inform biomarker discovery studies.   Recently we developed a resource (Markerville) for holding information about biomarkers including how they were discovered, what the cohort sizes were, etc.  Though manual curation of this resource is possible, there are tens-of-thousands of journal articles on biomarkers.  Consequently, it is intractable for a manual process to capture the current knowledge.  To overcome this barrier, we hope to develop a natural language processing approach to automatically discover and then 'read' the thousands of papers on biomarkers. The extracted data will be used to populate Markerville and improve the processes by which biomarkers are developed.

Faculty Mentor: Ramasamy Paulmurugan, PhD
Internship Mentors: Kira Foygel, PhD and Thillai Sekar Veerapazham, PhD

Internship Positions: 2 positions available, Undergraduates only
Type of Laboratory Research: Mixture of wet and dry lab

The main focuses of our lab are 1) to understand the molecular mechanism of tamoxifen resistance in breast cancer, 2) to develop non-invasive molecular imaging assays to study histone methylations, 3) to study Nrf2-Keap1 interaction to monitor antioxidant chemoresistance in cancer therapies and, 4) to develop ultrasound-microbubbles mediated targeted delivery of microRNAs for advanced cancer therapy. Breast cancer is a highly heterogeneous disease, and there is a growing body of evidence that this heterogeneity occurs at both genetic and phenotypic levels. Our lab mainly focuses on developing strategies to improve breast cancer therapy while understanding the molecular mechanism of drug resistance to circumvent the problem and to improve the therapeutic efficacy. We are mainly interested in studying the pathways regulated by estrogen receptors (ERα and ERβ) and Nrf2 (Nuclear factor (erythroid- derived 2)-like 2) to develop our therapeutic interventions. MicroRNAs are small regulatory RNAs expressed by cells to control gene expression. MicroRNA expression is completely dysregulated in cancer. Inhibition or restoration of microRNA functions have been reported to play significant roles in cancer- related events in cell, thus potentially heralding a powerful approach to create a new generation of molecularly targeted anti-cancer therapies. The finding that individual microRNAs target several hundred genes and regulate cellular pathways associated with pathogenesis, targeting microRNAs for the functional maintenance of cellular genes further underscores the emerging importance of microRNA-mediated regulation in breast cancer. Ultrasound can be used for image-guided delivery of drugs and microRNAs for therapeutic interventions in cancers. Our lab is developing microRNA mediated targeted therapy specifically for triple negative breast cancers. The epigenetic mechanisms, including DNA-methylation, histone acetylation, and histone methylation, are important for cellular development, differentiation, proliferation, and apoptosis. In addition to their roles in normal cellular processes, epigenetic mechanisms are believed to be capable of responding to different chemical and physical agents, possibly leading to altered biological pathways associated with cellular diseases. Considering the importance, we are currently working on developing molecular imaging assays to study histone methylation in living animals.

Faculty Mentor: Sharon Pitteri, PhD

Internship Positions: 2 positions available, Undergraduates only
Type of Laboratory Research: Mixture of wet and dry lab

The Pitteri Laboratory is focused on the discovery and validation of proteins and other types of molecules in the blood that can be used as indicators of risk, diagnosis, progression, and recurrence of cancer. We specialize in molecular analysis of clinical and biological samples to detect cancer and understand biology. We utilize state-of-the art technologies to identify, quantify, and characterize molecules, particularly, proteins of interest.

We are looking for a highly motivated undergraduate student looking for an internship to work on a summer research project focused on cancer early detection. The internship is well-suited for students with interests in biology, applied physical science, and/or medical research. You will gain hands-on experience with biochemistry and analytical chemistry techniques and data analysis. A positive attitude, willingness to learn and contribute, and meticulous attention to details are a must. Undergraduate level coursework in chemistry and/or biology are required. Strong computer skills, particularly in computer programming, are desirable. This internship is a full time (8 hours per day), eight week minimum commitment.

Faculty Mentor: Juergen K. Willmann, MD
Internship Mentors: Lotfi Kacem, PhD, Sayan Chowdhury, PhD, Ahmed El Kaffas, PhD

Internship Positions: 3 positions available, Undergraduates only
Type of Laboratory Research: Wet lab

In Translational Molecular Imaging Laboratory there is opportunity to explore imaging of novel targets that are expressed on the vascular endothelial cells in various diseases. This laboratory emphasizes on the development and clinical translation of novel molecular and functional imaging biomarkers with special focus on imaging cancer including pancreatic, liver, renal, ovarian, and prostate cancer and inflammation. The main focus of our lab involves diagnosis, therapy and monitoring of mouse models of inflammation and cancer and ultrasound guided nanoparticle delivery. We further advance clinically available radiological imaging modalities such as ultrasound and magnetic resonance imaging (MRI), as promising imaging tools for early detection and treatment monitoring of abdominal and pelvic diseases. Our mission is to integrate novel molecular and functional imaging strategies into clinical protocols for improved patient care in the near future.

Faculty Mentor: Jeremy Dahl, PhD
Internship Mentor:Jeremy Dahl, PhD and Dongwoon Hyun

Internship Positions: 1 position available, Undergraduates only

Type of Laboratory Research: Mixture of Wet & Dry lab

Development of coherence-based ultrasound imaging techniques for molecularimaging. Ultrasound molecular imaging is an attractive modality for early cancer detectionbecause it does not use ionizing radiation, has real-time imaging capabilities, and can beused to target specific cancers.   In ultrasound molecular imaging, gas-filled echogenicmicrobubbles are modified by adding coatings to the microbubble shell that make themfirmly attach to molecular markers.   These gas-filled bubbles act as reflectors of ultrasonic wave to generate high-contrast signals that indicate the location of the molecular marker,and thus the cancer.  Technical challenges remain, however, in the ability to detect thesetargeted microbubbles with ultrasound imaging techniques used to identify thesemicrobubbles.  Microbubbles are sensitive to the amplitude of the ultrasonic pressurewave, and the rate at which they are dissolved or destroyed increases with pressure.  Thus,the pressures required to image the microbubbles must be kept to several orders ofmagnitude below that of conventional diagnostic B-mode to prevent significant loss of themicrobubbles that would provide localization of tumors. The low pressures required forthis type of imaging creates a low signal-to-noise ratio, because the echoes are notsignificantly greater than the ultrasound system’s thermal noise. While a largeconcentration of microbubbles generates sufficient reflections to overcome noise, a lowconcentration, such as the case of targeted microbubbles and small cancers, can beoverwhelmed by thermal or other sources of noise.  In this project, we will continue todevelop a real-time imaging modality, based on the coherence of microbubble signals, toimprove the sensitivity of ultrasound molecular imaging.  Tasks of the project will involveprogramming in Matlab and/or CUDA, imaging and data acquisition with ultrasound, andmicrobubble creation.  Knowledge of medical imaging or ultrasound physics and familiaritywith Fourier Transforms and basic signal & systems concepts will be helpful.

Faculty Mentor: Tanya Stoyanova, PhD

Internship Positions: 2 positions available, Undergraduates only

Type of Laboratory Research: Wet lab

Our research focuses on understanding fundamental molecular mechanisms underlyingcancer development. Currently, we study signaling cascades initiated by cell surface receptors.We are interested in how these receptors signal to drive prostate cancer initiation and how theyregulate the transition from indolent to aggressive disease. The long term goal of our laboratoryis to improve the stratification of indolent from aggressive prostate cancer and aid thedevelopment of better therapeutic strategies for the advanced disease.

Additionally, we are interested in understanding molecular mechanism that govern theself-renewal activity of adult stem cells and cancer stem cells. We use molecular biologytechniques, cell culture based adult stem cell assay and in vivo tissue regeneration models of cancer.