Recent Accomplishments:  
(1) RIMI student scholar, Alex Pankov, accepted into the bioinformatics Ph.D. program at RIMI partner instituation, UCSF. [Read more...]
(2) Dr. Mariel Vazquez receives an NSF CAREER award, one of only two awarded by the Mathematical Biology Program. [Read more...]

RIMI Student Scholars



Reyka Jayasinghe
B.S. in Cell and Molecular Biology

Breast cancer is the most common cancer among women worldwide and statistics show there were 1.6 million new cases during the year 2010 alone. After initial treatment, breast cancer can recur in a patient either in the same place or in a distant region of the body, a phenomenon. Mr. R. Cavalcante, a former graduate student in Dr. Arsuaga’s group, created a topological space for multidimensional data to understand similarities among breast cancer patient Copy Number Aberration (CNA) profiles. The main focus of the study was to find regions of CNA’s associated with recurrence of breast cancer among patients. Reyka’s research involved testing which genes, within these aberrations, drive tumor recurrence by growing cell lines at Lawrence Berkeley National Lab and performing gene knockdowns on these regions to understand how each of the specific chromosomal aberrations effects the mechanisms of the cell lines. In another related project, Reyka used a simulated contact probability algorithm, to compare contacts within various space filled curves to experimentally observed contact interactions to understand chromatin structure within the nucleus. Reyka is currently working towards her Ph.D. at Washington University in St Louis.

Mentor: Dr. Javier Arsuaga

 

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Shea Feeney
Pursuing B.S. in Biochemistry, with a secondary major in Cell and Molecular Biology

Shea’s project concerns the study of the neural tube, the precursor to the central nervous system, and its closure in early stage chicken embryos. Abnormal neural tube closure causes neural tube defects (NTD) which are one of the most common birth defects. These include spina bifida, where the spinal cord and the tissues overlying it will protrude through the back and anencephaly, which can result in partial or complete absence of the brain and skull. Shea specifically works on characterizing the role of Porcupine in neural tube closure by inhibiting Porcupine’s protein function. Shea plans to pursue a Ph.D. and eventually work in industry as a researcher.

Mentor: Dr. Laura Burrus

 

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Tsebaot "Mimi" Beraki
M.S. in Biochemistry

Mimi's research project investigated altered nitrite reductase activity in diabetes. The objective of her research was to determine how increased non-enzymatically glycated hemoglobin disrupts normal nitric oxide physiology. Determining whether the glycation of Hb alters its fundamental nitric oxide chemistry may clarify the underlying connection between diabetes and cardiovascular dysfunction. Mimi is currently working towards a Ph.D. at the University of Texas Southwestern Medical Center.

Mentor: Dr. Raymond Esquerra

 

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Gregory Ho
M.S. in Biology

Greg's research focus was the enzyme nitric oxide synthase. This enzyme catalyzes the production of the gaseotransmitter nitric oxide from L-arginine. Nitric oxide production in the body is important for vasodilation and as a cellular messenger but has gained enormous attention for being implicated in numerous diseases. Greg studied the enzyme using magnetic circular dichorism to explore the catalytic heme active site during metal interactions and electron transfer. He is interested in communicating and presenting scientific ideas to a general audience and is currently applying to Ph.D. programs.

Mentor: Dr. Raymond Esquerra

 

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Abriti Sharma
B.S. in Biochemistry

The purpose of Abriti’s SFSU research project was to investigate the role of phenylalanine-41 in substrate/inhibitor binding and recognition in trypsin-fold serine proteases. The specific interaction observed between this residue and macromolecular inhibitors in co-crystal structures of trypsin suggest that it may be critical in substrate and inhibitor binding. Proteases play a direct and significant role in many biological processes, including disease states such as Alzheimer’s disease and cancer. Consequently, proteases are attractive targets for drug design. A better understanding of the molecular determinants of substrate/inhibitor binding and recognition may facilitate the development of specific inhibitors of proteases. Abriti is currently working towards a Ph.D. at Washington University in St. Louis.

Mentor: Dr. Teaster Baird, Jr.

 

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Raymond Cavalcante
M.A. in Mathematics

While at SFSU Raymond’s research involved locating regions of genomic instability that are characteristic to various cancers. Specifically, his measure of genomic instability is related to copy number variations; when a segment of DNA in the genome appears more or less than is normal. Variations, such as these, have been shown to be present in various cancer tissues. At this time Raymod is focusing on Glioblastoma and breast cancer, but the methodologies using mathematics can be applied broadly. Raymond is employed two primary branches of investigation: (1) utilizes computational homology methods to understand the aCGH data, and (2) uses graph theoretic methods to augment the computational homology methods. Raymond is currently working towards his Ph.D. in Bioinformatics at the University of Michigan.

Mentor: Dr. Javier Arsuaga

 

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Mousa Rebouh
M.A. in Mathematics

While at SFSU Mousa’s research project involved using a novel approach with metrics and tangles to analyze cancer patient data. Cancerous cells want to multiply, and so they amplify chromosomal areas that help them regenerate, and they delete areas that suppress them. Clustering methods are widely used to identify copy number deletions and amplifications, but these methods involve metrics that do not remember location. This new method allows for the identification of location along the chromosome where copy number deletions and amplifications occur. The aim is to find chromosomal regions that drive tumor growth.

Mentors: Dr. Javier Arsuaga and Dr. Mariel Vazquez

 

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Anna Batt
Pursuing M.S. in Biochemistry

As a graduate student Anna’s research focuses on the investigation of the modification of primary selectivity in the influence of amino aid identities N-terminal to the scissile bond. To pursue her research interests she worked in Dr. Teaster Baird’s lab on a project with three specific aims; (1) to construct S1’ binding site variants of anionic rat trypsin, (2) to construct a P1’ peptide library, and (3) to kinetically and structurally characterize the S1’ binding site variants of rat trypsin. In the future, Anna would like to focus her research on enzymatic bioremediation. She believes that the use of enzymes over chemicals or microorganisms to degrade harmful pollutants could provide many possible environmental advantages. Anna hopes to enter into a Ph.D. program where she can continue her research and work towards her eventual goal of becoming a college professor.

Mentor: Dr. Teaster Baird, Jr.

 

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Meghann Shorrock
M.S. in Cell and Molecular Biology

Meghann completed her program at SFSU and has continued her studies at UC Davis where she is a Ph.D. candidate.

Mentor: Dr. Diana Chu.

 

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Angel Ku
B.S. in Cell and Molecular Biology

Angel’s focus of study was on identifying the barriers for recruitment and biospecimen accrual within clinical research in minority populations. Influenced by his mother’s own trials and tribulations within the health care industry, he hopes to create a culturally and linguistically appropriate clinical trial workshop that discusses the importance of minority participation. As a career goal, Angel hopes to one day, work as a researcher within certain minority communities to address the community-specific issues in a culturally appropriate way. Angel's dream is to have a direct influence on making health equity a reality. Angel is currently working towards a Ph.D. at UC San Francisco.

Mentor: Dr. Leticia Márquez-Magaña

 

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Christina Lorimer
M.A. in English, with a concentration in TESOL

While pursuing her MA at SFSU, Christina actively collaborated on projects, such as “Harnessing English as a Second Language and Adult Literacy Instruction for Diabetes Prevention”, a collaboration between SFSU and the California Diabetes Program and “Growing old, staying healthy: Stories of immigrant elders in the Bay Area”, a project directed by Project SHINE staff at SFSU. These projects helped her better understand health issues in vulnerable minority populations as she developed teaching methods that best provide students with the language skills necessary to navigate through complex systems in a new culture. She hopes to build a base of behavioral research expertise necessary to carry out future research internships and her doctoral dissertation. Christina was accepted into the Fulbright Program to continue her research in Brazil beginning March 2012. When she returns, she hopes to begin applying to Ph.D. programs.

Mentor: Dr. Maricel Santos

 

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Alex Pankov
B.S. in Statistics and Applied Math

While at SFSU, Alex focused on the identification of copy number changes across patient cohorts. He is developing a statistical approach that compares available algorithms that are used to identify copy number changes in Comparative Genomic Hybridization arrays. In particular his aims were at developing a platform that can be used for finding a consensus list of copy number changes associated with breast cancer recurrence. Alex is currently working towards his Ph.D. in Bioinformatics at UCSF.

Mentors: Dr. Mariel Vazquez and Dr. Javier Arsuaga

 

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Jenny Shao
M.S. in Chemistry

As a graduate student Jenny’s focus of study was on the design and synthesis of potential porphyrinic photodrugs with biomedical applications. She hopes to continue her research while moving on to pursue a Ph.D. While pursuing her Ph.D. she will further her study into development of more effective cancer treatments in an attempt to better understand the mechanism of cancer cell proliferation and apoptosis. Jenny is currently applying to Ph.D. programs.

Mentor: Dr. Usrula Simonis

 

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Sarah Dovi
M.A. in Psychology, with a concentration in Developmental Psychology

Sarah's studies at SFSU focused on imitation and symbolic play in children with autism while they participate in integrated playgroups. Her focus is on social learning through peer modeling and cognitive development of children with autism. She uses naturalistic observation methods to look for biological markers, such as the presence of imitative behaviors that may indicate mirror neuron activity in the neocortex that may help to better understand the origin of the developmental disorder. She hopes to better understand how children operate in contextually relevant situations and how observable behaviors may act as indicators of cognitive and neurological development. She hopes to continue her research while moving on to pursue a Ph.D.

Mentors: Dr. Pamela Wolfberg and Dr. Jeff Cookston

 

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Juan Castellón
M.S. in Microbiology

As a graduate student Juan’s focus of study was on the diversity of adaptive behaviors shown in clonal cultures of the soil bacterium Bacillus subtilis when starved for nutrients. Like many other bacteria, B. subtilis, becomes highly motile or enters into a non-motile state leading to biofilm formation about starvation. Juan is studying the molecular control of this population heterogeneity. Juan plans to use his microbial genetics training while pursuing a PhD in Microbiology. In his doctoral work he hopes to study how virulence is developed in pathogenic bacteria so as to better understand how particular diseases arise and can be combated. Juan is currently working torwards his Ph.D. at UC Santa Cruz.

Mentor: Dr. Leticia Márquez-Magaña

 

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