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BIT Undergraduate Summer Research

BIOMEDICAL INFORMATICS TRAINING UNDERGRADUATE SUMMER RESEARCH (BIT-SR) PROGRAM 2015

Description

The Biomedical Informatics Training Undergraduate Summer Research (BIT-SR) Program will provide community college students with the opportunity to explore and learn about research approaches to problems in biochemistry and drug discovery, genomics, proteomics, structural biology, and systems biology using biomedical informatics and computational biology.

Based on their research interests, each BIT-SR Program student will be assigned to a faculty-advisor in his/her area of interest and teamed with a BIT graduate student in that advisors laboratory who will serve as the student’s immediate research mentor and collaborator. Throughout their summer research experience, each BIT-SR Program student will participate in all individual laboratory activities such as laboratory meeting presentations, departmental seminar attendance, etc. At the end of the summer research period, each student will prepare a written paper of their work and present their results at a BIT Undergraduate Summer Research Program Symposium attended by the UCI Institute for Genomics and Bioinformatics (UCI/IGB) research community.

The summer research experience will begin and last for 10 weeks during the summer. The Program will start June 15, 2015 and will end with a symposium on August 21. 2015. Student will be expected to participate in the program full time. There will be additional work before June 9th to help you prepare for your research experience at UCI. In addition, there will you will need to do a presentation after the research experience.

Description of Summer Program Activities

Orientation: Based on the student’s personal statement, an appropriate faculty advisor and BIT student lab mentor will be assigned to each student. The first day will be devoted to getting acquainted, familiarizing the students with their assigned laboratories, and learning basic laboratory procedures, schedules, and activities. During this time each student will meet, together and separately, with their faculty advisor and BIT student mentor for an explanation of the research project they will be involved in and for reading and laboratory assignments. The next day the students will receive formal instruction in the responsible conduct of research and in laboratory safety.

Research: The goal of the BIT Undergraduate Summer Research Program is to provide each student with a high-quality research experience. We believe this is best accomplished by personal supervision in a one-on-one active research laboratory environment. In this scenario, the faculty advisor will spend time discussing the student’s research strategies and methods and providing supporting advice and literature references. This learning experience will be reinforced by side-by-side working and collaboration with the BIT student lab mentor and the inclusion and participation of the student in laboratory activities such as research meetings, departmental and IGB seminars, and daily interactions with other laboratory personnel.

Activities: In addition to their everyday research activities, each student will be encouraged to participate in the social and intellectual environment associated with a university research experience. For example, they will participate in weekly laboratory meetings where they will present their research results in an informal setting for critique and advice. This important training experience will be used for their preparation of more formal presentations.

At the end of the summer, each student will submit a scientific paper to be included in a “Journal of the BIT Undergraduate Summer Research Program” which will be published by the IGB and provided to the summer program students. In addition, a “BIT Undergraduate Summer Research Program Symposium” will be organized for the final day of the program to be presented in the auditorium of Bren Hall for Computer Sciences. This symposium will be attended by the faculty and laboratory personnel of the BIT Undergraduate Summer Research Program and will be open to the faculty and laboratory personnel of the IGB and the UCI community at large. Students will be asked to present a poster or presentation at their community college for their family and peers in the fall semester. Dr. Debra Mauzy-Melitz will be available to help students prepare their paper and poster.

Admission: Students will be selected based on several criteria. Perspective student participants will be asked to submit a personal statement of their career goals. Based upon their academic records and personal statements, selected students will be invited to UCI to interview with the program directors, Drs. Hatfield and Baldi.

Applications can be submitted online at:
https://eee.uci.edu/survey/BIT2015

Potential Mentors

  1. Bogi Andersen MD, Professor, Departments of Medicine and Biological Chemistry. Dr. Andersen’s laboratory uses quantitative genomic and high-throughput DNA sequencing methods to study pathways and transcriptional mechanisms that regulate development and homeostasis of epithelial tissues, with a focus on stratified epithelia, hair follicles and mammary glands. One of the main goals of the laboratory is to investigate at a genomic level the relationship between regulation of normal and aberrant (cancer) organ development.
  2. Lee Bardwell, Professor, Department of Developmental and Cell Biology. The goal of Dr. Bardwell’s research effort is to elucidate the molecular mechanisms by which intracellular signal transduction cascades execute a diverse repertoire of responses with efficiency and specificity. His group uses computational and biological methods to study conserved signaling pathways controlling growth and development in yeast and mammalian cells.
  3. James Hall, Professor, Department of Physiology and Biophysics. The Hall laboratory uses structural biology and computational methods to study the development and homeostatic maintenance of the optical lens. The overall goal of this research is to understand the role of water channels and gap junction channels in the fluid balance of the ocular lens. A second focus of the Hall lab is the interaction of amyloid oligomers, long suspected a causative agent for Alzheimer’s disease, with lipid membranes in both artificial and in living cells.
  4. Lan Huang, Associate Professor, Developmental and Cell Biology; Physiology and Biophysics. Dr. Huang laboratory employs quantitative methods focused on developing and employing novel integrated mass spectrometry-based proteomic approaches to decipher the dynamics of the 26S proteasome interacting networks under different biological conditions in order to gain a better understanding of the pathways required for ubiquitinated substrate recognition and transport prior to degradation by the proteasome.
  5. Anthony A. James, Professor, Department of Microbiology and Molecular Genetics, Department of Molecular Biology and Biochemistry. The James laboratory is working on novel genetic methods for controlling the transmission of vector-borne diseases and thedevelopment of vaccines and drug targets for these infectious diseases. This laboratory was the first to develop transgenesis procedures for mosquitoes and has developed computational methods to engineer single-chain antibodies that interfere with malaria parasite development in the mosquito.
  6. Arthur Lander, M.D., Ph.D., Professor, Developmental and Cell Biology. Dr. Arthur Lander is Professor of Developmental and Cell Biology and Biomedical Engineering and Director of the UCI Center for Complex Biological Systems (CCBS), and the UCI NIGMS National Center for Systems Biology.  Research in the Lander lab is focused on the use of computational modeling to elucidate the performance objectives of complex signaling networks and transport systems in growth and patterning.  This includes studying how feedback circuitry in morphogen gradients facilitates robust patterning, sharp border formation, and suppression of gene expression noise; and how feedback effects in cellular proliferation and differentiation facilitate rapid and accurate regeneration. 
  7. Richard H. Lathrop, Ph.D., Professor, Information and Computer Science. Dr. Lathrop has broad interests in computational molecular biology, including current research interests in protein structure prediction from sequence, protein-DNA interactions and genetic regulation, rational drug design and discovery, and other molecular structure/function relationships. Together with Prof. Hatfield he is the co-inventor of the Computational Optimized DNA Assembly (CODA) technology, the core technology of the IGB Computational Biology Research Laboratory. CODA also is the core technology of Verdezyne Inc., a top-ten synthetic biology company founded by Lathrop and Hatfield located in Carlsbad, CA.
  8. Haoping Liu, Professor, Department of Biological Chemistry. The Liu lab uses a combination of molecular genetics and genomics approaches to identify components of the hyphal signaling pathways that are important for yeast infections. She uses a protein microarray develoed in her lab to profile humoral immune responses to Candida albicans infections. Computational and statistical analyses of this study are performed in collaboration with the group of Dr. Baldi.
  9. Hartmut Luecke, Professor, Department of Molecular Biology and Biochemistry; Physiology and Biophysics. The main focus of the Luecke laboratory is the use of X-ray crystallography and computational analysis to study structure-function proerties of integral membrane proteins. 
  10. Eric D. Mjolsness, Professor, Department of Computer Science. Research activities and interests in the Mjolsness include scientific inference systems, using techniques from machine learning, pattern recognition, nonlinear optimization, statistical physics and other mathematical disciplines to further research into computational biology. Specific projects include modeling plant development (www.computableplant.org), informatics of mathematical models (www.sigmoid.org), and in collabora tion with Prof. Hatfield, mathematical modeling of gene/signaling regulatory networks.
  11. Qing Nie, Professor, Department of Mathematics; Biomedical Engineering; Center for Complex Biological Systems; Mathematical and Computational Biology. Dr. Nie works in the area of mathematical and computational biology with applications to cell signalling and morphogen systems.
  12. Suzanne Sandmeyer, Professor, Department of Biological Chemistry and Department of Microbiology and Molecular Genetics; Director, Genomics/High-throughput Facility and Associate Director, Institute for Genomics and Bioinformatics. The Sandmeyer laboratory studies Ty3, a retrovirus like element in S. cerevisiae, as a model system for understanding the interactions of retroviruses and their host cells.  Retroviruses are not only of interest as the causative agent of acquired immunodeficiency syndrome and some cancers, but also for their potential applications in gene therapy. The Sandmeyer laboratory is also using yeast for metabolic engineering. In this area they have worked to develop S. cerevisiae strains competent for metabolism of plant sugars xylose and arabinose. The Sandmeyer and Baldi groups are working to establish high throughput sequencing in the IGB High-throughput Genomics Facility.
  13. Padhraic J. Smyth, Professor, Department of Computer Science. Dr. Smyth's research includes machine learning, pattern recognition, applied statistics, data mining, information theory and artificial intelligence. His work focuses on how to automatically extract information from large and complex data sets. His research group works on the basic theory of inference from data as well as on a variety of applications of data analytic algorithms to problems in medicine, biology, climate modeling, astronomy, planetary science and analysis of Web and text data. He has enjoyed successful collaborations with Prof. Bogi Anderson.
  14. Kevin Thornton, Assistant Professor, Department of Ecology and Evolutionary Biology. The Thornton laboratory works in several areas of populations genetics. First, members of the laboratory develop statistical methods for the analysis of SNP data, particularly on the detection of natural selection effects in resequencing data, using HTS technologies. Second, members of the laboratory are performing whole-genome resequencing of wild-type lines from Drosophila species related to D. melanogaster. The main aim of this project is the computational detection, and experimental validation, of structural variation within these genomes. Finally, members of the laboratory are modeling human genetic diseases in an effort to understand the results of "GWAS" studies, and are exploring means to improve the ability to uncover the causal mutations underlying human disease.
  15. Douglas J. Tobias, Professor, Department of Chemistry. In collaboration with the experimental group of Prof. Stephen White in the Department of Physiology and Biophysics in the School of Medicine, and BIT Program trainees researchers in the Tobias laboratory are performing molecular dynamics simulations of several large integral membrane proteins of known structure in explicit membrane environments, with the goal of cataloging protein-membrane interactions that stabilize complex membrane protein folds. These researchers also are using molecular dynamics simulations to explore the structural and thermodynamic aspects of burying polar and charged residues in membranes. The predictions of these simulations are being correlated with integration/translocation experiments developed by White and von Heijne.  In the end, a comprehensive biological hydrophobicity scale that accounts for both residue polarity and location will emerge for more accurate prediction of membrane protein structures.
  16. Rahul Warrior, Associate Professor, Department of Developmental & Cell Biology. Prof. Warrior uses experimental and computationally modeling methods to study nuclear protein trafficking and architecture abnormalities of developmental disease.
  17. Stephen H. White, Professor, Department of Physiology and Biophysics. Dr. White's laboratory is dedicated to understanding membrane proteins through studies of the interactions of polypeptides with fluid lipid bilayers.  His work involves five broad areas: (1) structural determinations of the location of peptides and proteins in bilayers and their effects on bilayer structure, (2) physicochemical studies of peptide and protein partitioning into bilayer systems, (3) the development of web-based structure prediction tools, and (4) molecular biological studies of translocon-assisted folding of membrane proteins, and (5) molecular dynamics simulations of membrane proteins related to translocon-assisted folding and ion-channel gating.
  18. Xiaohui, Xie, Assistant Professor, Department of Computer Science. Dr. Xie’s group was the first to use comparative genomics for discovering regulatory elements in the promoter and 3'-untranslated regions of the human genome. His recent work has been focused on expanding the earlier analysis from the gene-proximal regions to the entire human genome, using 25 recently available mammalian genomes. In addition to sequence analysis, the Xie laboratory is also interested in discovering gene signatures for cancer diagnosis and prognosis using high-throughput genomic data.
  19. Kyoko Yokomori, Professor, Department of Biological Chemistry. Dr. Yokomori’s group studies the role of nuclear scaffolding protein complexes in chromosome dynamics, DNA repair and developmental gene regulation, and their roles in developmental diseases in humans.

For more information on the BIT-SR Program, please contact
Debra Mauzy-Melitz at This e-mail address is being protected from spambots. You need JavaScript enabled to view it '; document.write( '' ); document.write( addy_text23491 ); document.write( '<\/a>' ); //--> This e-mail address is being protected from spambots. You need JavaScript enabled to view it