UCLA Bioinformatics: The Philosophy of the Undergraduate Program

Bioinformatics is an important interdisciplinary research area with tremendous opportunities in graduate training and industry employment.  Yet, few academic institutions offer undergraduate programs designed to prepare students for opportunities in Bioinformatics.

The UCLA Undergraduate Bioinformatics Minor is an academic program established in Fall 2012 at UCLA.  Undergraduates in any Major can obtain a Bioinformatics Minor by completing an additional 8 courses. Since Fall 2012, approximately 80 students have joined the Minor program. These students represent Majors in over a dozen UCLA departments, including: Computer Science; Chemistry; Molecular, Cell, & Developmental Biology; Microbiology, Immunology, and Molecular Genetics; Ecology and Evolutionary Biology; and Computational and Systems Biology.

Over 45 faculty specializing in computational and experimental biology are associated with the Bioinformatics Minor, spanning the fields of biology, mathematics, engineering, and medicine. Course offerings from more than 12 unique departments allow the Minor program to encompass the breadth of the growing Bioinformatics field.

Here we describe the principles and philosophy that guided the design of our Minor.

  1. Our Core Bioinformatics Courses Teach Interdisciplinary Computation. The foundation of our program is the cluster of three integrated core courses in Bioinformatics. These courses are truly interdisciplinary; they satisfy elective requirements in multiple departments and recruit students from different Majors to the Minor program. These core courses build upon the philosophy that students must first learn fundamental concepts in computation in order to later explore problems in Bioinformatics.  These courses offer basic skills and appeal to many students beyond those interested in Bioinformatics.
  1. Rigorous Background in Computation. To be successful in Bioinformatics, students must have a solid background in both computation and Biology. Our core courses require as prerequisites a substantial background in computation and statistics. To enter the Minor, we require that students have completed one year of programming and one upper division Statistics course.  To complete the Minor, our students take Linear Algebra and one upper division course on Algorithms taught by the Computer Science or Math Department.  Our students also take a Molecular Biology course taught by the Life Sciences Department. We believe that it is important for faculty in Computer Science and Program in Computing to teach programming, and for faculty in the Life Sciences to teach Biology. Further, it is important for students to take the same programming classes as do their peers in Engineering majors, and for students to take the same Biology classes alongside their peers in Life Sciences.
  1. The Bioinformatics Minor Builds upon the Students’ Major. Every student graduating from UCLA with a Bioinformatics Minor also completes an academic Major program. While we do adjust the Minor curriculum to help students efficiently complete both their Major and Minor requirements within 4 years, each of our graduates has exactly the same amount of training in their Major as fellow Majors who are not in the Minor.  This avoids a common pitfall in interdisciplinary education: students only receive a superficial background in each academic area.
  1. Bioinformatics is a Research Oriented Field. Our Minor is closely integrated with our undergraduate research program, which places students in the labs of Bioinformatics faculty. Most of the Bioinformatics Minors at UCLA are working in a research lab.  Undergraduates are strongly encouraged to engage in research. The Minor allows for a substantial amount of research credits, an allowance that helps students complete their Major and Minor requirements in four years.  In addition, many of our undergraduates participate in the Bruins-in-Genomics Summer (B.I.G. Summer) program or similar undergraduate education experience summer programs.
  1. Bioinformatics is an Increasingly Diverse Field. The core courses in Bioinformatics are designed to be interesting and accessible to students from a wide variety of educational backgrounds. Each course typically has enrollment approaching 100. Far more students who are not in the Bioinformatics Minor take these courses as electives to fulfill their Major requirements. Student enthusiasm is high for these accessible interdisciplinary courses that combine computational sciences and Biology. We find that this approach boosts broader undergraduate engagement in the field and encourages students from traditionally underrepresented groups to pursue research, graduate school, or careers in STEM fields.
  1. Let Excitement Foster Program Growth. Bioinformatics is an exciting area, and specialized training is critical for the next generation of biomedical researchers. However, undergraduate Bioinformatics programs, when offered by a college or university, are typically quite small.  Such programs are often limited in size and engagement as students are unaware of the field or become aware of Bioinformatics late in their college career. We strategized the Bioinformatics Minor program at UCLA specifically to attract students at any stage of their college career and to maximize curricular flexibility so students can easily complete Minor requirements. Many students are attracted to the Minor when they enroll in Bioinformatics core courses to fulfill elective requirements for their Major; some develop a keen interest in the field and then join the Minor. Even students who are unable to complete all Minor requirements benefit from our program; they complete key coursework and join a research lab, gaining knowledge and experience crucial for gaining employment or admission to graduate school.

Our current goal for the Bioinformatics Minor is to graduate 50 students per year.  We hope that 10 to 20 of them will enter graduate studies in Bioinformatics.  We are not there yet, but are growing. This year, around 10 graduates applied to Ph.D. programs in Bioinformatics.  Many of our students recently began or are applying to Ph.D. programs in Bioinformatics and related areas.  We expect that they will do very well in the admissions process and have great backgrounds for starting Ph.D. study in Bioinformatics.

bioinformatics-minor-graphical-element-the-minor

Read more about the Bioinformatics Minor on the official website:
http://bioinformatics.ucla.edu/undergradute-bioinformatics-minor/

Check out a list of research opportunities available for undergrads at UCLA:
http://bioinformatics.ucla.edu/undergraduate-research/

Learn more about 2016 undergraduate research and B.I.G. Summer activities at ZarLab:
zarlab.cs.ucla.edu/b-i-g-summer-in-zarlab/

Applications to the 2017 B.I.G. Summer program are due January 27:
http://qcb.ucla.edu/big-summer/

UCLA Launches CGSI with Inaugural Summer Programs

In 2015, Profs. Eleazar Eskin (UCLA), Eran Halperin (UCLA), John Novembre (The University of Chicago), and Ben Raphael (Brown University) created the Computational Genomics Summer Institute (CGSI). A collaboration with the Institute for Pure and Applied Mathematics (IPAM) led by Russ Caflisch, CGSI aims to develop a flexible program for improving education and enhancing collaboration in Bioinformatics research. In summer 2016, the inaugural program included a five-day short course (July 18-22) followed by a three-week long course (July 22 to August 12).

Over the past two decades, technological developments have substantially changed research in Bioinformatics. New methods in DNA sequencing technologies are capable of performing large-scale measurements of cellular states with a lower cost and higher efficiency of computing time. These improvements have revolutionized the potential application of genomic studies toward clinical research and development of novel diagnostic tools and treatments for human disease.

Modern genomic data collection creates an enormous need for mathematical and computational infrastructures capable of analyzing datasets that are increasingly larger in scale and resolution. This poses several unique challenges to researchers in Bioinformatics, an interdisciplinary field that cuts across traditional academic fields of math, statistics, computer science, and biology—and includes private-industry sequence technology developers. Innovation depends on seamless collaboration among scientists with different skill sets, communication styles, and institution-driven career goals. Therefore, impactful Bioinformatics research requires an original framework for doing science that bridges traditional discipline-based academic structures.

The summer 2016 courses combined formal research talks and tutorials with informal interaction and mentorship in order to facilitate exchange among international researchers. Participants in the short program attended five full days packed with lectures, tutorials, and journal clubs covering a variety of cutting-edge techniques. Senior trainees, including advanced graduate students and post-docs, underwent additional training through the long program’s residence program. The extended program enabled these scientists to interact with leading researchers through a mix of structured training programs and flexible time for collaboration with fellow participants and other program faculty.

Collaboration on a wide variety of problem types and research themes facilitated cross-disciplinary communication and networking. During both courses, CGSI participants shared technical skills in coding and data analysis relevant to genetic and epigenetic imputation, fine-mapping of complex traits, linear mixed models, and Bayesian statistics in human, canine, mouse, and bacteria datasets. Scholars at different stages of their careers explored application of these methods, among others, to emerging themes such as cancer, neuropsychiatric disorders, evolutionary adaptation, early human origins, and data privacy.

CGSI instructors and participants established mentor-mentee relationships in computational genomics labs at UCLA, including the ZarLab and Bogdan Lab, while tackling practical problems and laying groundwork for future publications. In addition, participants developed comradery and professional connections while enjoying a full schedule of social activities, including dinners at classic Los Angeles area restaurants, volleyball tournaments in Santa Monica, bike rides along the beach, morning runs around UCLA campus, and even an excursion to see a live production of “West Side Story” at the Hollywood Bowl.

CGSI organizers thank the National Institutes of Health grant GM112625, UCLA Clinical and Translational Science Institute grant UL1TR000124, and IPAM for making this unique program possible. We look forward to fostering more collaboration between mathematicians, computer scientists, biologists, and sequencing technology developers in both industry and academia with future CGSI programs.

Visit the CGSI website for an up-to-date archive of program videos, slides, papers, and more:
http://computationalgenomics.bioinformatics.ucla.edu/

Enrollment in 2017 CGSI programs opens this fall with a registration deadline of February 1.

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B.I.G. Summer in ZarLab

This summer, six young adults engaged in a unique eight-week learning experience with ZarLab, learning practical skills in genomics and bioinformatics while conducting research on large-scale human genetic datasets. These four undergraduate students participated in the Bruins-In-Genomics (B.I.G.) Summer Program, an intensive laboratory and seminar program aimed at providing real-world experience for students who are interested in pursuing interdisciplinary graduate education in the quantitative and biological sciences. In addition, two Los Angeles-area high school students participated in laboratory activities as volunteer researchers.

Eleazar Eskin, co-organizer of the summer program, and Serghei Mangul, post-doctoral scholar, hosted the young scholars in ZarLab, a UCLA computational genetics group affiliated with both the Computer Science Department and the Human Genetics Department. Mangul supervised a group of students who collaborated on a project aimed at developing computational methods for the study of the human immune system and microbiome. Working with data from one of the largest sequencing projects in the world, the Genotype-Tissue Expression (GTEx) study, the students analyzed more than 8,000 samples obtained from 544 individuals and representing 53 different tissue types. In doing so, they gained familiarization with current approaches to studying how changes in our genes contribute to common human diseases.

During a poster session on August 12, 2016, the B.I.G. participants presented the results of their work on GTEx:

  • Jeremy Rotman: “Studying the microbiome by analyzing the coverage of sequencing reads mapped to viruses, eukaryotes, and bacteria”
  • Benjamin Statz: “An improved method for analysis of variable domain of B and T cell receptors”
  • William Van Der Wey: “Functional profiling of microbial communities across multiple human tissues”
  • Kevin Wesel: “Profiling repeat elements across multiple human tissues”

In addition to mentoring B.I.G. Program students in ZarLab, Mangul developed and presented a three-part series of workshops introducing students to UNIX earlier during the program.

Eskin and Mangul also hosted a B.I.G. Program student, Samantha Jenson, who collaborated with Jonathan Flint, a world-renowned authority on the genetics of depression and co-director of UCLA’s Depression Grand Challenge. This year, Eskin facilitated a Neurogenetics working group and weekly neurogenetics seminar series for the B.I.G. Program. Participants in this group gained first-hand experience in the process of developing methods for mapping the underlying genetic causes of Major Depression Disorder. Jenson presented her work on “Structural variant discovery in Major Depression Disorder” during the August 12th poster session.

The annual B.I.G. Program is a collaboration between multiple labs and includes next generation sequencing analysis workshops, weekly science talks by researchers, a weekly student journal club, professional development seminars, social activities, concluding poster sessions, and an optional GRE test prep course. Participants also benefited from relevant workshops and research talks presented during the UCLA Computational Genomics Summer Institute (CGSI).

Congratulations to Benjamin, Jeremy, Kevin, Samantha, and William on their acceptance to and success in the B.I.G. Summer Program!

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We thank the following generous institutions that made this year’s B.I.G. Summer Program a big success:

  • National Institutes of Health grant MH109172
  • UCOP for a UC-HBCU partnership Program in Genomics and Systems
  • NIH NIBIB for NGS Data Analysis Skills for the Biosciences Pipeline  R25EB022364
  • NIH NIMH for Undergraduate Research Experience in Neuropsychiatric Genomics R25MH109172-01

Learn more about the B.I.G. Program:
UCLA Newsroom: UCLA hosts summer program for future biosciences leaders
http://newsroom.ucla.edu/releases/ucla-hosts-summer-program-for-future-biosciences-leaders