Hearst Field Annex B-22
Berkeley CA 94720-2495
Phone: (510) 664-4182
Email: berkeleyconnect@berkeley.edu

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BERKELEY CONNECT IN
COMPUTATIONAL BIOLOGY

The Berkeley Connect program opens up the extraordinary resources of the University to you: the extraordinary students on our campus. By joining, you will become part of a community of like-minded faculty, mentors, and students that will provide a supportive environment in which to exchange and discuss ideas and goals. Berkeley Connect will help you make the most of your time at the University as you learn more about the emerging field of Computational Biology. We are excited to get to know you.

Message from the Director

Nir YosefThe future of biological innovation will be created by a new generation of biologists who are as competent at software engineering as they are at laboratory work. Berkeley Connect in Computational Biology is a mentoring program that accepts students from the biological or mathematical/computational sciences with a serious interest in computational biology.

Students joining the program will:

  • Become part of a community of active and engaged students with a serious interest in both computation and biology.
  • Become exposed to research, and get to meet researchers, in computational biology.
  • Receive mentoring and advice in how to structure an educational program combining computation and biology at UC Berkeley.
  • Get the opportunity to participate in special events and to join field trips to companies in the Bay Area that employ computational biologists.

In 2016-2017, Berkeley Connect in Computational Biology will be offered in the Fall semester only.

Nir Yosef
Faculty Director, Berkeley Connect in Computational Biology

Program Description

Berkeley Connect links undergraduate students with experienced mentors in Computational Biology. These mentors lead small groups (not more than 20) students in regular meetings; they also meet with students one-on-one to provide guidance and advice. The core of the Berkeley Connect program is a one-credit, pass-fail course that is designed to create a community of students with similar intellectual interests.There is no homework associated with Berkeley Connect: no exams, no papers, no quizzes. Instead, small group meetings focus on sharing ideas and learning new skills related to Computational Biology as a way to foster friendships and provide a supportive intellectual community for Berkeley undergraduates.There is not currently an undergraduate degree program in Computational Biology at UC Berkeley. Berkeley Connect in Computational Biology is designed for students with an intended or declared major in the biological or mathematical/computational sciences who have a serious interest in the interdisciplinary field of computational biology.

Every semester, Berkeley Connect sponsors a wide range of activities and events for participating studentsThey include:

  • small-group meetings led by your mentor;
  • one-on-one meetings with your mentor;
  • special events, including informal lectures by professors and guest speakers, and panels on career options, graduate school admissions, and other topics;
  • and visits to Berkeley resources.

At the heart of Berkeley Connect is the relationship between you and your mentor. The Berkeley Connect mentors are advanced graduate students or recent PhDs in Computational Biology, who are chosen both for their demonstrated commitment to undergraduates and for their scholarly achievement. They are dedicated to providing the kind of close-knit community and one-on-one attention that can be hard to find at a large university.

When you sign up for Berkeley Connect, you will join one of the small groups of participants in Computational Biology. Your small group will be led by your mentor, and will meet every other week during the semester for an hour-long dinner discussion sessions. Discussions will focus on key intellectual issues within Social Welfare as well as key skills you need to succeed in the major. Above all, the small groups will focus on building connections among students, so that each group becomes a supportive community for all participants.

You will also meet with your mentor one-on-one at least twice during the semester, once to get acquainted, and a second time just before Tele-Bears, to discuss your plans for completing your major. Your mentor also has office hours every other week, during which you are free to show up and ask questions, talk over your day or your week, discuss what you are learning in class, or just have an informal conversation.

Faculty

Nir YosefNir Yosef is an Assistant Professor of Computer Science and a core member at the Center of Computational Biology at UC Berkeley. He is also an associate member of the Ragon Institute of MGH, MIT and Harvard. His research focuses on studying how mRNA transcription is regulated in mammalian cells, by developing algorithms and software that integrate and make sense out of genome-scale data. The lab has two main areas of interest, the first is developing computational methodologies for the analysis of single­cell RNA sequencing data. This work focuses on questions related to normalization and visualization, inference of cellular sub­populations, and functional characterization of the cells’ transcriptional and metabolic programs. The second area of research is annotating and predicting the function of regulatory regions in the human or mouse genomes. This work focuses on questions related to data processing and normalization, identification of regulatory regions, and functional annotations of these regions by leveraging synthetic reporter assays. All of these tools are developed through close collaborations with experimental labs, with application to T cell development, HIV control, neural differentiation, and classification of cell types in the mouse brain. You can learn more about the Yosef research group here.

Berkeley Connect Mentors

Shaked AfikShaked Afik is a third-year graduate student in Computational Biology. He is interested in uncovering the regulatory mechanisms that control gene expression in the human immune system. Before coming to Berkeley, he studied computational biology at the Hebrew University of Jerusalem, Israel. Outside the lab he likes to hike and explore the Bay Area and the wonderful California scenery. He is excited to be a mentor of the Berkeley Connect program and help expose UC Berkeley undergraduates to the field of computational biology!


Syllabus

Schedule

To find sections in the upcoming semester, search the Schedule of Classes for Computational Biology 98BC (for first-year and sophomores) or 198BC (for juniors and seniors).

To help you meet other students who share your experiences and perspectives, Berkeley Connect sections are designated as lower division (first-year students and sophomores), new junior transfers, and upper division (juniors and seniors), but you can enroll in any section that fits your schedule and credit requirements.

To get on the Berkeley Connect in Computational Biology mailing list, please fill out this interest form.

How to Sign Up

To participate in Berkeley Connect in Computational Biology, you enroll in a section of Computational Biology 98BC or 198BC (one unit, taken on a Pass/Not Pass basis).The Berkeley Connect in Computational Biology pilot program is designed to serve students in biological or mathematical/computational science majors who have indicated their interest in this particular area of study. If you are interested in this field and would like to be added to our mailing list, please fill out this interest form.

Contact Us

Please see our FAQs.  If you have additional questions about Berkeley Connect in Computational Biology, please contact:  Nir Yosef, Faculty Director, Berkeley Connect in Computational Biology, niryosef@berkeley.edu.

Xuan Quach, Administrative Director, Center for Computational Biology,  xuquach@berkeley.edu

You can also contact the central Berkeley Connect office  at berkeleyconnect@berkeley.edu or (510)664-4182.

Links & Resources