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The field of computational and systems biology represents a synthesis of ideas and approaches from the life sciences, physical sciences, computer science, and engineering. Recent advances in biology, including the human genome project and massively parallel approaches to probing biological samples, have created new opportunities to understand biological problems from a systems perspective. Systems modeling and design are well established in engineering disciplines but are newer in biology. Advances in computational and systems biology require multidisciplinary teams with skill in applying principles and tools from engineering and computer science to solve problems in biology and medicine. To provide education in this emerging field, the Computational and Systems Biology (CSB) program integrates MIT's world-renowned disciplines in biology, engineering, mathematics, and computer science. Graduates of the program are uniquely prepared to make novel discoveries, develop new methods, and establish new paradigms. They are also well-positioned to assume critical leadership roles in both academia and industry, where this field is becoming increasingly important.

Computational and systems biology, as practiced at MIT, is organized around "the 3 Ds" of description, distillation, and design. In many research programs, systematic data collection is used to create detailed molecular- or cellular-level descriptions of a system in one or more defined states. Given the complexity of biological systems and the number of interacting components and parameters, system modeling is often conducted with the aim of distilling the essential or most important subsystems, components, and parameters, and of obtaining simplified models that retain the ability to accurately predict system behavior under a wide range of conditions. Distillation of the system can increase the interpretability of the models in relation to evolutionary and engineering principles such as robustness, modularity, and evolvability. The resulting models may also serve to facilitate rational design of perturbations to test understanding of the system or to change system behavior (e.g., for therapeutic intervention), as well as efforts to design related systems or systems composed of similar biological components.

More than 70 faculty members at the Institute participate in MIT's Computational and Systems Biology Initiative (CSBi). These investigators span nearly all departments in the School of Science and the School of Engineering, providing CSB students the opportunity to pursue thesis research in a wide variety of different MIT laboratories. It is also possible for students to arrange collaborative thesis projects with joint supervision by faculty members with different areas of expertise. Areas of active research include behavioral genetics and genomics; bioengineering and neuroengineering; biological networks and machine learning; cancer systems biology; cellular biophysics; chemical biology and metabolomics; evolutionary and computational biology; microbiology and systems ecology; molecular biophysics and structural biology; precision medicine and medical genomics; quantitative imaging; regulatory genomics, epigenomics, and proteomics; single cell manipulations and measurement; stem cell and developmental systems biology; synthetic biology and biological design; and systems immunology.

The CSB PhD program is an Institute-wide program that has been jointly developed by the Departments of Biology, Biological Engineering, and Electrical Engineering and Computer Science. The program integrates biology, engineering, and computation to address complex problems in biological systems, and CSB PhD students have the opportunity to work with CSBi faculty from across the Institute. The curriculum has a strong emphasis on foundational material to encourage students to become creators of future tools and technologies, rather than merely practitioners of current approaches. Applicants must have an undergraduate degree in biology (or a related field), bioinformatics, chemistry, computer science, mathematics, statistics, physics, or an engineering discipline, with dual-emphasis degrees encouraged.

All students pursue a core curriculum that includes classes in biology and computational biology, along with a class in computational and systems biology based on the scientific literature. Advanced electives in science and engineering enhance both the breadth and depth of each student's education. During their first year, in addition to coursework, students carry out rotations in multiple research groups to gain a broader exposure to work at the frontier of this field, and to identify a suitable laboratory in which to conduct thesis research. CSB students also serve as teaching assistants during one semester in the second year to further develop their teaching and communication skills and facilitate their interactions across disciplines. Students also participate in training in the responsible conduct of research to prepare them for the complexities and demands of modern scientific research. The total length of the program, including classwork, qualifying examinations, thesis research, and preparation of the thesis is roughly five years.

The CSB curriculum has two components. The first is a core that provides foundational knowledge of both biology and computational biology. The second is a customized program of electives that is selected by each student in consultation with members of the CSB graduate committee. The goal is to allow students broad latitude in defining their individual area of interest, while at the same time providing oversight and guidance to ensure that training is rigorous and thorough.

Core Curriculum

The core curriculum consists of three classroom subjects plus a set of three research rotations in different research groups. The classroom subjects are comprised of modern biology, computational biology, and a literature-based exploration of current research frontiers and paradigms, which is required of all first-year students in the program . Students also participate in three research rotations of one to two months' duration during their first year to expose them to a range of research activities in computation and systems biology, and to assist them in choosing a lab. Students are encouraged to gain experience in experimental and computational approaches taken across different disciplines at MIT.

Advanced Electives

To develop breadth and depth, add to the base of the diversified core, and contribute strength in areas related to their interest and research direction, students must take four advanced electives. Each student designs a program of advanced electives that satisfies the distribution and area requirements in close consultation with members of the graduate committee.

Additional Subjects

CSB PhD students may take classes beyond the required diversified core and advanced electives described above. These additional subjects can be used to add breadth or depth to the proposed curriculum, and might be useful to explore advanced topics relevant to the student's thesis research in later years. The CSB Graduate Committee works with each graduate student to develop a path through the curriculum appropriate for his or her background and research interests.

Training in the Responsible Conduct of Research

Throughout the program, students will be expected to attend workshops and other activities that provide training in the ethical conduct of research. This is particularly important in interdisciplinary fields such as computational and systems biology, where different disciplines often have very different philosophies and conventions. By the end of the fifth year, students will have had about 16 hours of training in the responsible conduct of research.

Qualifying Exams

In addition to coursework and a research thesis, each student must pass a written and an oral qualifying examination at the end of the second year or the beginning of the third year. The written examination involves preparing a research proposal based on the student's thesis research, and presenting the proposal to the examination committee. This process provides a strong foundation for the thesis research, incorporating new research ideas and refinement of the scope of the research project. The oral examination is based on the coursework taken and on related published literature. The qualifying exams are designed to develop and demonstrate depth in a selected area (the area of the thesis research) as well as breadth of knowledge across the field of computational and systems biology.

Thesis Research

Research will be performed under the supervision of a CSBi faculty member, culminating in the submission of a written thesis and its oral defense before the community and thesis defense committee. By the second year, a student will have formed a thesis advisory committee that they will meet with on an annual basis.

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Systems, Synthetic, and Quantitative Biology​

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Harvard was one of the first institutions to offer a program to explore this exciting new field. The program’s core curriculum includes courses on the methods and logic that shape research, how to conceptualize and present research, and an introduction to the faculty’s research.

The program has 48 faculty located in the Faculty of Arts and Sciences, Harvard Medical School, and Harvard-affiliated teaching hospitals including Dana-Farber Cancer Institute, Mass General, and Boston Children’s Hospital. SSQB is one of 14 PhD programs in the Harvard Integrated Life Sciences program that collectively gives you access to over 900 faculty research groups situated in the heart of Boston’s biotech hub. Our students are working on projects that range from fundamental problems in biology to translational research, whose goal is to directly affect medicine and global sustainability.

Graduates of the program have gone on to faculty positions at prestigious institutions such as MIT and Princeton University, while others are now industry leaders as startup founders or as decision-makers at companies including Boston Consulting Group, Yumanity Therapeutics, McKinsey & Company, and Regeneron.

Additional information on the graduate program is available from the Systems, Synthetic, and Quantitative Biology PhD Program , and requirements for the degree are detailed in Policies .

Admissions Requirements

Please review admissions requirements and other information before applying. You can find degree program-specific admissions requirements below and access additional guidance on applying from the Systems, Synthetic, and Quantitative Biology PhD Program .

Academic Background

Applicants typically have a background in biology, physics, chemistry, computer science, engineering, or mathematics and work to forge a new approach to biology that combines theoretical and experimental approaches. The typical student has a strong background in one of the disciplines relevant to systems biology and an interest in interdisciplinary research.

Standardized Tests

GRE General: Optional 

Contacting Faculty

Applicants should indicate their faculty of interest in the application. You are not required to contact any faculty in advance but are welcome to.

Applications are reviewed by the admissions committee during December and early January. Selected applicants are notified if they have been chosen for an on-campus interview. These visits provide students with the opportunity to meet with faculty and current students and to get a better feel for our community and the types of research conducted here. Applicants invited for an interview who reside overseas and cannot visit the Harvard campus may interview remotely.

Theses & Dissertations

Theses & Dissertations for Systems, Synthetic, and Quantitative Biology​

See list of Systems, Synthetic, and Quantitative Biology​ faculty

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Advances In Basic Science And Molecular Medicine

The Department of Chemical and Systems Biology explores the frontiers of basic science and molecular medicine, particularly at the crossroads of cellular, chemical, and computational biology. We train Ph.D. students to apply genetic, chemical, cell biological, and quantitative methods to decipher the complex regulatory systems associated with normal physiology and disease states.

Specific research areas include cell signaling pathways, cell cycle control, epigenetics, cell fate specification, and genomic stability. The Chemical and Systems Biology Ph.D. program also emphasizes collaborative learning, and our research community includes scientists trained in molecular biology, cell biology, chemistry, physics, and engineering.

Our Ph.D. program consistently ranks among the top graduate training programs in the world. Most recently the National Research Council named us the top pharmacology-related training program in the United States, based on students’ GRE scores, faculty publications, median time to degree, program requirements, and training resources. The Chemical and Systems Biology graduate program was especially commended for the quality of its research activities.

Why Chemical And Systems Biology?

How do cells achieve directed migration? Why doesn’t a skin cell become a neuron? How do drug-resistant cancers arise and how might they be prevented or overcome? Finding answers to these and other biomedical questions increasingly requires molecular, quantitative, and interdisciplinary approaches.

The Department of Chemical and Systems Biology is uniquely focused on understanding cell biology at the molecular and systems levels, and many of its faculty have expertise in biochemistry, chemistry, physics, and engineering. Developing novel technologies for basic research and translating discoveries into therapeutic strategies are also areas of special interest in the Chemical and Systems Biology community.

Our goal is to train a new generation of scientists with the interdisciplinary skills and creative thinking required to tackle emerging challenges in biomedical research. We invite all interested students to apply to the Chemical and Systems Biology Ph.D. program through the Stanford Biosciences online application form. Applicants whose research interests match well with our scientific mission are encouraged to select Chemical and Systems Biology as their primary home program.

We have 189 systems biology PhD Projects, Programmes & Scholarships

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systems biology PhD Projects, Programmes & Scholarships

Doctoral researcher (m/f/div) in microbiome systems biology, phd research project.

PhD Research Projects are advertised opportunities to examine a pre-defined topic or answer a stated research question. Some projects may also provide scope for you to propose your own ideas and approaches.

Funded PhD Project (Students Worldwide)

This project has funding attached, subject to eligibility criteria. Applications for the project are welcome from all suitably qualified candidates, but its funding may be restricted to a limited set of nationalities. You should check the project and department details for more information.

Projects in mathematical systems and control theory

Self-funded phd students only.

This project does not have funding attached. You will need to have your own means of paying fees and living costs and / or seek separate funding from student finance, charities or trusts.

Systems immunology and multi-omics approaches to understand protective immunity to human malaria

Phd student positions at international max planck research school for molecules of life, munich, funded phd programme (students worldwide).

Some or all of the PhD opportunities in this programme have funding attached. Applications for this programme are welcome from suitably qualified candidates worldwide. Funding may only be available to a limited set of nationalities and you should read the full programme details for further information.

Germany PhD Programme

A German PhD usually takes 3-4 years. Traditional programmes focus on independent research, but more structured PhDs involve additional training units (worth 180-240 ECTS credits) as well as placement opportunities. Both options require you to produce a thesis and present it for examination. Many programmes are delivered in English.

Max Planck Research Programme

Max Planck Research Programmes are structured PhD opportunities set up by the Max Planck Society, an independent non-profit German research organisation. Max Planck Institutes and universities collaborate to offer interdisciplinary and international PhD opportunities providing high standards of training and support as well as generous funding.

15 fully funded PhD positions in molecular technologies and systems medicine

Austria phd programme.

An Austrian PhD usually takes 3-4 years. Most students complete their projects within broader PhD programmes incorporating a curriculum of courses and training worth a certain number of ECTS credits as well as research towards an original thesis. This will be presented for a public examination by two academic experts. Most programmes are delivered in German, but some universities offer English-language teaching.

Biozentrum PhD Fellowships in life sciences

Switzerland phd programme.

A Swiss PhD usually takes 3-5 years. Traditional doctorates focus on independent research; more structured programmes include additional training and sometimes involve two or more universities working in partnership. Both types of PhD require you to produce an original thesis and present it for a public examination. Some programmes are delivered in English, with others offered in German, French or Italian.

Data-driven optimal prediction of bacteria growth

Competition funded phd project (students worldwide).

This project is in competition for funding with other projects. Usually the project which receives the best applicant will be successful. Unsuccessful projects may still go ahead as self-funded opportunities. Applications for the project are welcome from all suitably qualified candidates, but potential funding may be restricted to a limited set of nationalities. You should check the project and department details for more information.

Self funded MSc by research or PhD in Biology: Paratransgenesis for leishmania

Understanding the evolution of gene regulatory networks through biophysical modelling and machine learning, 12 fully funded ph.d. positions at the cologne graduate school of ageing research, phd position in antiviral immunity and vaccinology (m/f/d), investigating the impact of inflammation on cardiovascular disease, international ph.d. programs in the life sciences, gene regulation in cancer metastasis.

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2023-24 edition, mathematical, computational, and systems biology, ph.d..

The graduate program in Mathematical, Computational, and Systems Biology (MCSB) is designed to meet the interdisciplinary training challenges of modern biology and function in concert with existing departmental programs (Departmental option) or as an individually tailored program (stand-alone option) leading to a Ph.D. degree.

The degree program provides students with both opportunity for rigorous training toward research careers in areas related to systems biology and flexibility through individualized faculty counseling on curricular needs, and access to a diverse group of affiliated faculty and research projects from member departments. Current member departments include Biomedical Engineering, Biological Chemistry, Computer Science, Developmental and Cell Biology, Ecology and Evolutionary Biology, Mathematics, Microbiology and Molecular Genetics, Molecular Biology and Biochemistry, Chemistry, and Physics.

If you have any questions or would like to learn more about the MCSB Program, please email [email protected] .

Students interested in the MCSB Program apply to the Office of Graduate Studies (OGS). Applicants must specify that they wish to pursue the M.S. or Ph.D. Upon completion of the M.S., students who may wish to pursue a Ph.D. may request to be evaluated together with the pool of prospective Ph.D. candidates for admission to the Ph.D. program.

Applicants are expected to hold a Bachelor’s degree in one of the Science, Technology, Engineering, and Mathematics (STEM) fields. Applicants are evaluated on the basis of their prior academic record and their potential for creative research and teaching, as demonstrated in submitted application materials (official university transcripts, letters of recommendation, GRE scores, and statement of purpose).

Required Core Courses

Enrolled students participate in a common first-year “gateway” program and must complete the seven required core courses (listed above). Students are assigned an MCSB Advisory Committee consisting of two participating faculty members to oversee course and laboratory work. Subsequently, students select a thesis advisor and choose between the Departmental or Interdisciplinary (Stand-Alone) options for the remainder of their Ph.D. training.

Departmental Option

For students who select the Departmental option, a faculty member in a participating department must agree to serve as the student’s thesis advisor. Completion of the Ph.D. is subject to the degree requirements of the departmental Ph.D. program in which the student enrolls. Participating departments accept both the course work and research conducted during the “gateway” year in partial fulfillment of such requirements. Students are encouraged to consult with the department of choice for specific information on additional requirements. All department student advisory committees are established according to the rules of the participating department. In addition, the student’s MCSB Advisory Committee meets annually to follow progress and provide additional guidance. The normative time to degree for students in the Departmental option is five years.

To complete the coursework requirements for the Departmental option, students must:

• Attend first-year bootcamp
• Perform at least two laboratory rotations; one in an experimental (wet) lab and one in a computational (dry) lab
• Complete the seven required core courses, in addition to any departmental requirements.

Interdisciplinary (Stand-Alone) Option

For students who select the stand-alone option, the student’s thesis advisor assumes the role of the Committee Chair when a participating MCSB faculty member agrees to accept that role. Adjustments to the MCSB Advisory Committee may be made based on the area of the student’s research, or by request of the student, thesis advisor, or committee members. The student meets biannually with the Advisory Committee until an Advancement to Candidacy Committee has formed, which then assumes the duties until the M.S. or Ph.D. defense. The normative time to degree for students in the Stand-Alone option is five years.

To complete the coursework requirements for the Stand-Alone option, students must:

• Complete the seven required core courses, plus five elective courses selected from Breadth Categories I and II.

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2023-2024 Catalogue

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Interdisciplinary PhD Program Systems Biology

Main content, phd program systems biology.

The aim of this highly interdisciplinary PhD program of systems biological researchers of the University of Zurich and ETH in Zurich and Basel is to train students from various disciplines and departments including Computer Science and (Bio)Informatics, Biological Sciences, and Engineering to become future leaders in Systems Biology.

Systems Biology aims at the quantitative analysis and predictive mathematical modeling at all levels of biological organization. The PhD program “Systems Biology” provides students with the generic skills for working in this new scientific field as well as training in project-specific (biological and/or computational) aspects of their PhD work.

Life Science Zurich Graduate School

The PhD program Systems Biology is associated with the external page Life Science Zurich Graduate School call_made . The Life Science Zurich Graduate School consists of several highly competitive PhD programs, jointly run by the ETH Zurich and the University of Zurich.  

Research Groups

Find out about the research groups that are part of the Systems Biology program.

University of Colorado Denver | Anschutz Denver | Anschutz Medical Campus

2024-2025 academic catalog, integrative and systems biology, phd.

Graduate Program Director:  Michael Wunder Website:   https://clas.ucdenver.edu/integrative-biology/academics/graduate-programs

Introduction

Please click  here  to see Integrative Biology department information.

The PhD program in Integrative and Systems Biology at the University of Colorado Denver is a multidisciplinary, dual campus program that offers students opportunities to address complex questions in biology using computational, laboratory and field approaches. The more than 40 program faculty members allow students to participate on a diversity of projects at all levels of biological organization, ranging from ecology and environmental microbiology to biochemistry, developmental biology and neuroscience. Depending on the track an incoming student chooses, the approach will either be to explore the problem at multiple levels of biological organization (integrative biology) or to explore the multi-component nature of a biological system (systems biology).

The PhD program is research-based. Applicants to the program must have a declared area of specialization that aligns with the research focus of a program graduate faculty member. Faculty expertise can be found undergraduate faculty profiles on the Department of Integrative Biology website (clas.ucdenver.edu/biology/). Students must contact prospective faculty advisors to determine if openings are available within the faculty member’s research group.

These program requirements are subject to periodic revision by the academic department, and the College of Liberal Arts and Sciences reserves the right to make exceptions and substitutions as judged necessary in individual cases. Therefore, the College strongly urges students to consult regularly with their Biology advisor to confirm the best plans of study before finalizing them.

Graduate Education Policies and Procedures apply to this program.

Program Requirements

• The PhD degree requirements comprise six phases. First, students must complete a minimum of 60 credits, including 30 dissertation credits. Up to 30 hours of graduate level courses from other programs may be transferred and counted toward the degree.
• Students must also form an Advisory Committee and an Examination Committee, pass the Preliminary Exam, meet the academic residency requirement, pass the comprehensive exam, and write and orally defend a dissertation.
• Students must earn a minimum grade of B- (2.7) in all courses that apply to the degree and must achieve a minimum cumulative GPA of 3.0. Courses taken using P+/P/F or S/U grading cannot apply to degree. requirements

Research-based PhD degree program requires :

• Completing 60 credits including 30 of dissertation
• Meeting minimum academic residency requirements
• Forming Advisory and Examination committees
• Passing the Preliminary Exam
• Writing and defending research proposal
• Passing the Comprehensive Exam
• Writing and defending dissertation (including >one publishable unit)

Master's Thesis ( BIOL 6950 )  credits will not apply to the PhD.

To learn more about the Student Learning Outcomes for this program, please visit our website.

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Center for Computational Biology

Computational Biology PhD

The main objective of the Computational Biology PhD is to train the next generation of scientists who are both passionate about exploring the interface of computation and biology, and committed to functioning at a high level in both computational and biological fields.

The program emphasizes multidisciplinary competency, interdisciplinary collaboration, and transdisciplinary research, and offers an integrated and customizable curriculum that consists of two semesters of didactic course work tailored to each student’s background and interests, research rotations with faculty mentors spanning computational biology’s core disciplines, and dissertation research jointly supervised by computational and biological faculty mentors.

The Computational Biology Graduate Group facilitates student immersion into UC Berkeley’s vibrant computational biology research community. Currently, the Group includes over 46 faculty from across 14 departments of the College of Letters and Science, the College of Engineering, the College of Natural Resources, and the School of Public Health. Many of these faculty are available as potential dissertation research advisors for Computational Biology PhD students, with more available for participation on doctoral committees.

The First Year

The time to degree (normative time) of the Computational Biology PhD is five years. The first year of the program emphasizes gaining competency in computational biology, the biological sciences, and the computational sciences (broadly construed). Since student backgrounds will vary widely, each student will work with faculty and student advisory committees to develop a program of study tailored to their background and interests. Specifically, all first-year students must:

• Perform three rotations with Core faculty (one rotation with a non-Core faculty is acceptable with advance approval)
• Complete course work requirements (see below)
• Complete a course in the Responsible Conduct of Research
• Attend the computational biology seminar series
• Complete experimental training (see below)

Laboratory Rotations

Entering students are required to complete three laboratory rotations during their first year in the program to seek out a Dissertation Advisor under whose supervision dissertation research will be conducted. Students should rotate with at least one computational Core faculty member and one experimental Core faculty member. Click here to view rotation policy. 

Course Work & Additional Requirements

Students must complete the following coursework in the first three (up to four) semesters. Courses must be taken for a grade and a grade of B or higher is required for a course to count towards degree progress:

• Fall and Spring semester of CMPBIO 293, Doctoral Seminar in Computational Biology
• A Responsible Conduct of Research course, most likely through the Department of Molecular and Cell Biology.
• STAT 201A & STAT 201B : Intro to Probability and Statistics at an Advanced Level. Note: Students who are offered admission and are not prepared to complete STAT 201A and 201B will be required to complete STAT 134 or PH 142 first.
• CS61A : The Structure and Interpretation of Computer Programs. Note: students with the equivalent background can replace this requirement with a more advanced CS course of their choosing.
• 3 elective courses relevant to the field of Computational Biology , one of which must be at the graduate level (see below for details).
• Attend the computational biology invited speaker seminar series. A schedule is circulated to all students by email and is available on the Center website. Starting with the 2023 entering class, CCB PhD students must enroll in CMPBIO 275: Computational Biology Seminar , which provides credit for this seminar series.
• 1) completion of a laboratory course at Berkeley with a minimum grade of B,
• 2) completion of a rotation in an experimental lab (w/ an experimental project), with a positive evaluation from the PI,
• a biological sciences undergraduate major with at least two upper division laboratory-based courses,
• a semester or equivalent of supervised undergraduate experimental laboratory-based research at a university,
• or previous paid or volunteer/internship work in an industry-based experimental laboratory.

Students are expected to develop a course plan for their program requirements and to consult with the Head Graduate Advisor before the Spring semester of their first year for formal approval (signature required). The course plan will take into account the student’s undergraduate training areas and goals for PhD research areas.

Satisfactory completion of first year requirements will be evaluated at the end of the spring semester of the first year. If requirements are satisfied, students will formally choose a Dissertation advisor from among the core faculty with whom they rotated and begin dissertation research.

Waivers: Students may request waivers for the specific courses STAT 201A, STAT 201B, and CS61A. In all cases of waivers, the student must take alternative courses in related areas so as to have six additional courses, as described above. For waiving out of STAT 201A/B, students can demonstrate they have completed the equivalent by passing a proctored assessment exam on Campus. For waiving out CS61A, the Head Graduate Advisor will evaluate student’s previous coursework based on the previous course’s syllabus and other course materials to determine equivalency.

Electives: Of the three electives, students are required to choose one course in each of the two following cluster areas:

• Cluster A (Biological Science) : These courses are defined as those for which the learning goals are primarily related to biology. This includes courses covering topics in molecular biology, genetics, evolution, environmental science, experimental methods, and human health. This category may also cover courses whose focus is on learning how to use bioinformatic tools to understand experimental data.
• Cluster B (Computational Sciences): These courses are defined as those for which the learning goals involve computing, inference, or mathematical modeling, broadly defined. This includes courses on algorithms, computing languages or structures, mathematical or probabilistic concepts, and statistics. This category would include courses whose focus is on biological applications of such topics.

In the below link we give some relevant such courses, but students can take courses beyond this list; for courses not on this list, the Head Graduate Advisor will determine to which cluster a course can be credited. For classes that have significant overlap between these two clusters, the department which offers the course may influence the decision of the HGA as to whether the course should be assigned to cluster A or B.

See below for some suggested courses in these categories:

Suggested Coursework Options

Second Year & Beyond

At the beginning of the fall of the second year, students begin full-time dissertation research in earnest under the supervision of their Dissertation advisor. It is anticipated that it will take students three (up to four) semesters to complete the 6 course requirement. Students are required to continue to participate annually in the computational biology seminar series.

Qualifying Examination

Students are expected to take and pass an oral Qualifying Examination (QE) by the end of the spring semester (June 15th) of their second year of graduate study. Students must present a written dissertation proposal to the QE committee no fewer than four weeks prior to the oral QE. The write-up should follow the format of an NIH-style grant proposal (i.e., it should include an abstract, background and significance, specific aims to be addressed (~3), and a research plan for addressing the aims) and must thoroughly discuss plans for research to be conducted in the dissertation lab. Click here for more details on the guidelines and format for the QE. Click here to view the rules for the composition of the committee and the form for declaring your committee.

Advancement to Candidacy

After successfully completing the QE, students will Advance to Candidacy. At this time, students select the members of their dissertation committee and submit this committee for approval to the Graduate Division. Students should endeavor to include a member whose research represents a complementary yet distinct area from that of the dissertation advisor (ie, biological vs computational, experimental vs theoretical) and that will be integrated in the student’s dissertation research. Click here to view the rules for the composition of the committee and the form for declaring your committee.

Meetings with the Dissertation Committee

After Advancing to Candidacy, students are expected to meet with their Dissertation Committee at least once each year.

Teaching Requirements

Computational Biology PhD students are required to teach at least two semesters (starting with Fall 2019 class), but may teach more. The requirement can be modified if the student has funding that does not allow teaching. Starting with the Fall 2019 class: At least one of those courses should require that you teach a section. Berkeley Connect or CMPBIO 293 can count towards one of the required semesters.

The Dissertation

Dissertation projects will represent scholarly, independent and novel research that contributes new knowledge to Computational Biology by integrating knowledge and methodologies from both the biological and computational sciences. Students must submit their dissertation by the May Graduate Division filing deadline (see Graduate Division for date) of their fifth–and final–year.

Special Requirements

Students will be required to present their research either orally or via a poster at the annual retreat beginning in their second year.

• Financial Support

The Computational Biology Graduate Group provides a competitive stipend (the stipend for 2023-24 is $43,363) as well as full payment of fees and non-resident tuition (which includes health care). Students maintaining satisfactory academic progress are provided full funding for five to five and a half years. The program supports students in the first year, while the PI/mentor provides support from the second year on. A portion of this support is in the form of salary from teaching assistance as a Graduate Student Instructor (GSI) in allied departments, such as Molecular and Cell Biology, Integrative Biology, Plant and Microbial Biology, Mathematics, Statistics or Computer Science. Teaching is part of the training of the program and most students will not teach more than two semesters, unless by choice.

Due to cost constraints, the program admits few international students; the average is two per year. Those admitted are also given full financial support (as noted above): stipend, fees and tuition.

Students are also strongly encouraged to apply for extramural fellowships for the proposal writing experience. There are a number of extramural fellowships that Berkeley students apply for that current applicants may find appealing. Please note that the NSF now only allows two submissions – once as an undergrad and once in grad school. The NSF funds students with potential, as opposed to specific research projects, so do not be concerned that you don’t know your grad school plans yet – just put together a good proposal! Although we make admissions offers before the fellowships results are released, all eligible students should take advantage of both opportunities to apply, as it’s a great opportunity and a great addition to a CV.

• National Science Foundation Graduate Research Fellowship (app deadlines in Oct)
• Hertz Foundation Fellowship (app deadline Oct)
• National Defense Science and Engineering Graduate Fellowship (app deadline in mid-Fall)
• DOE Computational Science Graduate Fellowship (Krell Institute) (app deadline in Jan)

CCB no longer requires the GRE for admission (neither general, nor subject). The GRE will not be seen by the review committee, even if sent to Berkeley.

PLEASE NOTE: The application deadline is Wednesday, November 30 , 2023, 8:59 PST/11:59 EST

If you would like to learn more about our program, you can watch informational YouTube videos from the past two UC Berkeley Graduate Diversity Admissions Fairs: 2021 recording & 2020 recording .

We invite applications from students with distinguished academic records, strong foundations in the basic biological, physical and computational sciences, as well as significant computer programming and research experience. Admission for the Computational Biology PhD is for the fall semester only, and Computational Biology does not offer a Master’s degree.

We are happy to answer any questions you may have, but please be sure to read this entire page first, as many of your questions will be answered below or on the Tips tab.

IMPORTANT : Please note that it is not possible to select a specific PhD advisor until the end of the first year in the program, so contacting individual faculty about openings in their laboratories will not increase your chances of being accepted into the program. You will have an opportunity to discuss your interests with relevant faculty if you are invited to interview in February.

Undergraduate Preparation

Minimum requirements for admission to graduate study:

• A bachelor’s degree or recognized equivalent from an accredited institution.
• Minimum GPA of 3.0.
• Undergraduate preparation reflecting a balance of training in computational biology’s core disciplines (biology, computer science, statistics/mathematics), for example, a single interdisciplinary major, such as computational biology or bioinformatics; a major in a core discipline and a combination of interdisciplinary course work and research experiences; or a double major in core disciplines.
• Basic research experience and aptitude are key considerations for admission, so evidence of research experience and letters of recommendation from faculty mentors attesting to the applicant’s research experience are of particular interest.
• GRE – NOT required or used for review .
• TOEFL scores for international students (see below for details).

Application Requirements

ALL materials, including letters, are due November 30, 2023 (8:59 PST). More information is provided and required as part of the online application, so please create an account and review the application before emailing with questions (and please set up an account well before the deadline):

• A completed graduate application: The online application opens in early or mid-September and is located on the Graduate Division website . Paper applications are not accepted. Please create your account and review the application well ahead of the submit date , as it will take time to complete and requests information not listed here.
• A nonrefundable application fee: The fee must be paid using a major credit card and is not refundable. For US citizens and permanent residents, the fee is $135; US citizens and permanent residents may request a fee waiver as part of the online application. For all other students (international) the fee is $155 (no waivers, no exceptions). Graduate Admissions manages the fee, not the program, so please contact them with questions.
• Three letters of recommendation, minimum (up to five are accepted): Letters of recommendation must be submitted online as part of the Graduate Division’s application process. Letters are also due November 30, so please inform your recommenders of this deadline and give them sufficient advance notice. It is your responsibility to monitor the status of your letters of recommendation (sending prompts, as necessary) in the online system.
• Transcripts: Unofficial copies of all relevant transcripts, uploaded as part of the online application (see application for details). Scanned copies of official transcripts are strongly preferred, as transcripts must include applicant and institution name and degree goal and should be easy for the reviewers to read (print-outs from online personal schedules can be hard to read and transcripts without your name and the institution name cannot be used for review). Do not send via mail official transcripts to Grad Division or Computational Biology, they will be discarded.
• Essays: Follow links to view descriptions of what these essays should include ( Statement of Purpose [2-3 pages], Personal Statement [1-2 pages]). Also review Tips tab for formatting advice.
• (Highly recommended) Applicants should consider applying for extramural funding, such as NSF Fellowships. These are amazing opportunities and the application processes are great preparation for graduate studies. Please see Financial Support tab.
• Read and follow all of the “Application Tips” listed on the last tab. This ensures that everything goes smoothly and you make a good impression on the faculty reviewing your file.

The GRE general test is not required. GRE subject tests are not required. GRE scores will not be a determining factor for application review and admission, and will NOT be seen by the CCB admissions committee. While we do not encourage anyone to take the exam, in case you decide to apply to a different program at Berkeley that does require them: the UC Berkeley school code is 4833; department codes are unnecessary. As long as the scores are sent to UC Berkeley, they will be received by any program you apply to on campus.

TOEFL/IELTS

Adequate proficiency in English must be demonstrated by those applicants applying from countries where English is not the official language. There are two standardized tests you may take: the Test of English as a Foreign Language (TOEFL), and the International English Language Testing System (IELTS). TOEFL minimum passing scores are 90 for the  Internet-based test (IBT) , and 570 for the paper-based format (PBT) . The TOEFL may be waived if an international student has completed at least one year of full-time academic course work with grades of B or better while in residence at a U.S. university (transcript will be required). Please click here for more information .

Application Deadlines

The Application Deadline is 8:59 pm Pacific Standard Time, November 30, 2023 . The application will lock at 9pm PST, precisely. All materials must be received by the deadline. While rec letters can continue to be submitted and received after the deadline, the committee meets in early December and will review incomplete applications. TOEFL tests should be taken by or before the deadline, but self-reported scores are acceptable for review while the official scores are being processed. All submitted applications will be reviewed, even if materials are missing, but it may impact the evaluation of the application.

It is your responsibility to ensure and verify that your application materials are submitted in a timely manner. Please be sure to hit the submit button when you have completed the application and to monitor the status of your letters of recommendation (sending prompts, as necessary). Please include the statement of purpose and personal statement in the online application. While you can upload a CV, please DO NOT upload entire publications or papers. Please DO NOT send paper résumés, separate folders of information, or articles via mail. They will be discarded unread.

The Computational Biology Interview Visit dates will be: February 25-27, 2024

Top applicants who are being considered for admission will be invited to visit campus for interviews with faculty. Invitations will be made by early January. Students are expected to stay for the entire event, arriving in Berkeley by 5:30pm on the first day and leaving the evening of the final day. In the application, you must provide the names of between 7-10 faculty from the Computational Biology website with whom you are interested in conducting research or performing rotations. This helps route your application to our reviewers and facilitates the interview scheduling process. An invitation is not a guarantee of admission.

International students may be interviewed virtually, as flights are often prohibitively expensive.

Tips for the Application Process

Uploaded Documents: Be sure to put your name and type of essay on your essays ( Statement of Purpose [2-3 pages], Personal Statement [1-2 pages]) as a header or before the text, whether you use the text box or upload a PDF or Word doc. There is no minimum length on either essay, but 3 pages maximum is suggested. The Statement of Purpose should describe your research and educational background and aspirations. The Personal Statement can include personal achievements not necessarily related to research, barriers you’ve had to overcome, mentoring and volunteering activities, things that make you unique and demonstrate the qualities you will bring to the program.

Letters of Recommendation: should be from persons who have supervised your research or academic work and who can evaluate your intellectual ability, creativity, leadership potential and promise for productive scholarship. If lab supervision was provided by a postdoc or graduate student, the letter should carry the signature or support of the faculty member in charge of the research project. Note: the application can be submitted before all of the recommenders have completed their letters. It is your responsibility to keep track of your recommender’s progress through the online system. Be sure to send reminders if your recommenders do not submit their letters.

Extramural fellowships: it is to your benefit to apply for fellowships as they may facilitate entry into the lab of your choice, are a great addition to your CV and often provide higher stipends. Do not allow concerns about coming up with a research proposal before joining a lab prevent you from applying. The fellowships are looking for research potential and proposal writing skills and will not hold you to specific research projects once you have started graduate school.

Calculating GPA: Schools can differ in how they assign grades and calculate grade point averages, so it may be difficult for this office to offer advice. The best resource for calculating the GPA for your school is to check the back of the official transcripts where a guide is often provided or use an online tool. There are free online GPA conversion tools that can be found via an internet search.

Faculty Contact/Interests: Please be sure to list faculty that interest you as part of the online application. You are not required to contact any faculty in advance, nor will it assist with admission, but are welcome to if you wish to learn more about their research.

Submitting the application: To avoid the possibility of computer problems on either side, it is NOT advisable to wait until the last day to start and/or submit your application. It is not unusual for the application system to have difficulties during times of heavy traffic. However, there is no need to submit the application too early. No application will be reviewed before the deadline.

Visits: We only arrange one campus visit for recruitment purposes. If you are interested in visiting the campus and meeting with faculty before the application deadline, you are welcome to do so on your own time (we will be unable to assist).

Name: Please double check that you have entered your first and last names in the correct fields. This is our first impression of you as a candidate, so you do want to get your name correct! Be sure to put your name on any documents that you upload (Statement of Purpose, Personal Statement).

California Residency: You are not considered a resident if you hope to enter our program in the Fall, but have never lived in California before or are here on a visa. So, please do not mark “resident” on the application in anticipation of admission. You must have lived in California previously, and be a US citizen or Permanent Resident, to be a resident.

Faculty Leadership Head Graduate Advisor and Chair for the PhD & DE John Huelsenbeck ( [email protected] )

Associate Head Graduate Advisor for PhD & DE Liana Lareau ( [email protected] )

Equity Advisor Rasmus Nielsen ( [email protected] )

Director of CCB Elizabeth Purdom ( [email protected] )

Core PhD & DE Faculty ( link )

Staff support Student Services Advisor (GSAO): Kate Chase ( [email protected] )

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Education & Training

Phd in bioinformatics and systems biology with emphasis in biomedical informatics.

The PhD curriculum for our trainees consists of formal instruction to provide the intellectual framework for conducting research.

Biomedical Informatics Core

• Informatics in Clinical Environments (MED 265): 1 Students are introduced to the basics of healthcare systems and clinical information needs through direct observation and classroom discussion. Students are introduced to medical language, disease processes, and health care practices to provide context prior to direct patient observation at primary, specialty, emergency, and inpatient sites in conjunction with clinical faculty affiliated with the training program. Students examine how clinicians use history-taking, physical examination and diagnostic testing to establish diagnoses and prognoses. Medical decision-making is introduced in the context of available informatics tools and clinical documentation and communication processes. Post-observation classroom discussions encourage students to think critically of the processes they observed and formulate hypotheses about how informatics solutions can modify the processes.
• Modeling Clinical Data and Knowledge for Computation (MED 267): This course describes existing methods for representing and communicating biomedical knowledge. The course describes existing health care standards and modeling principles required for implementing data standards, including biomedical ontologies, standardized terminologies, and knowledge resources.

1  Students with a clinical background will replace MED 265 with an additional course: Bioinformatics Applications to Human Disease (MED 263).

Bioinformatics Core

The core courses provide foundations in the biological basis of human health and disease and the statistical discovery of medical knowledge from biological experimentation. These classes are taken during the first year.

• Bioinformatics II (BENG 202) :  Introduction to methods for sequence analysis, applications to genome and proteome sequences, and protein structure and sequence-structure analysis.
• Principles of Biomedical Informatics (MED 264) : students are introduced to the fundamental principles of BMI and to the problems that define modern healthcare. The extent to which BMI can address healthcare problems is explored. Topics covered include structuring of data, computing with phenotypes, integration of molecular, image and other non-traditional data types into electronic medical records, clinical decision support systems, biomedical ontologies, data and communication standards, data aggregation, and knowledge discovery.
• Bioinformatics IV (MATH 283):  Analysis of modern genomic data, sequence analysis, gene expression/functional genomics analysis, and gene mapping/applied population genetics. The course focuses on statistical modeling and inference.

For the fourth core class, choose one of the following. In the event that a student completes two or more of these with suitable grades, one will count as core and the other(s) as electives.

• Algorithms in Computational Biology (CSE 280A): (Formerly CSE 206B) The course focuses on algorithmic aspects of modern bioinformatics and covers the following topics: computational gene hunting, sequencing, DNA arrays, sequence comparison, pattern discovery in DNA, genome rearrangements, molecular evolution, computational proteomics, and others. Prerequisites: CSE202 preferred or consent of instructor. 
• Algorithms for Biological Data Analysis (ECE 208): This course introduces a series of general algorithmic techniques but uses computational evolutionary biology as the context. The course motivates each algorithmic concept using a specific biological application related to evolution and focuses the discussion on specific types of (big) data available in modern biological studies. Note: The instructor and the BISB program are in the process of getting approval from the Graduate Council to introduce this as a course and to allow it as a core option. While we await approval, the course is offered under a temporary course number, ECE 286, by Prof. Siavash Mirarab, with the title "Algorithms for Biological Data Analysis." The course code ECE 286 may be used by other special topics courses as well, so be sure to enroll in the correct one.
• Genomics, Proteomics, and Network Biology (Bioinformatics III, BENG 203/CSE283): This is core in the BISB track. In the BMI track, it may be taken as the 4th core class or as an elective. Anotating genomes, characterizing functional genes, profiling, reconstructioning pathways.  Prerequisites: Pharm 201, BENG 202/CSE282, or consent of instructor. 

All students in years 1 and 2 must take both seminars in fall, winter, and spring quarters.

• Current Trends in Biomedical Informatics (MED 262): Weekly talks by researchers introduce students to current research topics within BMI. Speakers are drawn from academia, health care organizations, industry, and government.
• Bioinformatics Student Research Talks (BNFO 283) : Weekly presentations by Bioinformatics and Systems Biology students about Research Projects that are proposed or completed. Faculty mentors are present to contribute critiques and suggestions.

All students must take one of the two ethics courses by the end of second year. However, funding sources may require that it be taken first year, so we recommend taking it the first year.

• Scientific Ethics (SOMI 226): see below description
• Ethics in Scientific Research (BIOM 219): Overview of ethical issues in scientific research, conflicts of interest; national, statewide and campus issues and requirement; ethical issues in publications; authorship; retention of research records; tracing of research records; attribution; plagiarism; copyright considerations; primary, archival and meeting summary publications; ethical procedures and policies; NIH, NSF, California and UC San Diego; case studies and precedents in ethics.

Research and Teaching

During the academic year, all students must be enrolled in the appropriate research course for their level. Students typically do three rotations in year 1 (BNFO 298) and then do research units (BNFO 299) with their thesis advisor in years 2 and later. BNFO 299 units may be varied to meet the full-time enrollment requirement of 12 units per quarter in fall, winter, and spring.

• Teaching Assistantship (TA) (BNFO 500) :  Students will be a TA for two quarters during second or third year. To prepare for this teaching, students will receive training through the Center for Teaching Development at UCSD.
• Research Rotation (BNFO 298) : Taken each quarter during first year to help determine the thesis adviser.
• Graduate Research (BNFO 299): Independent work by graduate students engaged in research and writing theses. S/U grades only. May be taken for credit fifteen times.

Students must take 16 units of elective courses, including 8 units from the BMI series and 4 units from the CS series. The final 4 units can be taken from any series. The two BMI core courses MED 265 (or MED 263 for students with a clinical background) and MED 267 count as electives. Please check this  BISB curriculum page  for the list of all approved electives and elective series. 

Formal Progress to Degree

There are three formal evaluations that students must complete prior to being awarded a PhD degree: 

• Qualifying Examination:  This examination must be passed prior to the end of the student’s second year of study. The written portion of the exam consists of the student preparing an NIH or NSF-style research proposal. This proposal is then defended in an oral examination. Once the student passes the oral portion of the exam, the student is deemed to be qualified for advancing into PhD thesis research.
• Advancement to PhD Candidacy:  Upon completion of formal course requirements, each student is required to take a written and oral qualifying examination that admits the student to the candidacy of the PhD Program. The exam is administered by the dissertation committee, which consists of five faculty members.
• Final Examination:  All students defend their thesis in a final oral examination.

How to Apply

Application for admission to graduate studies is made directly through the Bioinformatics and Systems Biology website.

To be considered for the NLM fellowship, in addition to submitting your application and documentation to the degree program of your choice, please send the following to dbmi fellowship at ucsd dot edu:

• Personal Statement- explaining why you are a good candidate for the fellowship and what you hope to accomplish as an NLM trainee, the specific kind of research and topics you are interested in studying and what your goals are after completing the fellowship.
• A current and up to date CV; and
• In the body of your email please indicate which degree program you are applying to.

Leroy Hood, MD, PhD

Science transforming health.

Co-founder, Professor and Chief Strategy Officer, ISB; Emeritus Science Advisor, Providence

Send Email [email protected], [email protected]

Lab Website: Visit Lab Website http://hood-price.isbscience.org

A world-renowned scientist and recipient of the National Medal of Science in 2011, Dr. Leroy Hood co-founded the Institute for Systems Biology (ISB) in 2000, served as its first President from 2000-2017 and is a Professor and Chief Strategy Officer. In 2016, ISB affiliated with Providence where Dr. Hood now serves as Emeritus Science Advisor.

He is a member of the National Academy of Sciences, the National Academy of Engineering, and the National Academy of Medicine. Of the more than 6,000 scientists worldwide who belong to one or more of these academies, Dr. Hood is one of only 20 people elected to all three.

He received his MD from Johns Hopkins University School of Medicine and his PhD in biochemistry from Caltech. Dr. Hood was a faculty member at Caltech from 1967-1992, serving for 10 years as the Chair of Biology. During this period, he and his colleagues developed four sequencer and synthesizer instruments that paved the way for the Human Genome Project’s successful mapping and understanding of the human genome. He and his students also deciphered many of the complex mechanisms of antibody diversification. In 1992, Dr. Hood founded and chaired the Department of Molecular Biotechnology at the University of Washington, the first academic department devoted to cross-disciplinary biology.

Dr. Hood is currently carrying out studies in Alzheimer’s Disease, cancer, and wellness. He is pioneering a 1 million patient genome/phenome project, and is bringing scientific (quantitative) wellness to the contemporary U.S. health care system.

Dr. Hood has played a role in founding 15 biotechnology companies including Amgen, Applied Biosystems, Arivale, and Nanostring. He has co-authored textbooks in biochemistry, immunology, molecular biology, genetics, and systems biology.

In addition to having received 18 honorary degrees from prestigious universities in the U.S. and abroad, Dr. Hood has published more than 850 peer-reviewed articles and currently holds 36 patents.

Dr. Hood is the recipient of numerous national and international awards, including the Lasker Award for Studies of Immune Diversity (1987), the Kyoto Prize in advanced technology (2002), the Heinz Award for pioneering work in Systems Biology (2006), the National Academy of Engineering Fritz J. and Delores H. Russ Prize for developing automated DNA sequencing (2011), and the National Academy of Science Award for Chemistry in Service to Society (2017).

2017      NAS Award for Chemistry in Service to Society 2016      The UCD Ulysses Medal 2015      The Johns Hopkins University Alumni Association Global Achievement Award 2014      Institute of Electrical and Electronics Engineers Medal for Innovations in Healthcare Technology 2014      Geoffrey Beene Builders of Science award presented by Research!America 2013      Alvin J. Thompson Award for Leadership in K-12 education and science (awarded by NW Association for Biomedical Research) 2013      Future in Review, CEO of the Year 2012      Elected as a Fellow to the American Association for Cancer Research 2011      National Medal of Science 2011      Fritz and Dolores Russ Prize, National Academy of Engineering 2007      Elected Member, National Academy of Engineering 2007      Elected Member, Inventors Hall of Fame for the automated DNA sequencer 2006      Heinz Award for pioneering work in systems biology 2005      AACR-Irving Weinstein Foundation Distinguished Lecturer Award 2003      Elected Member, Institute of Medicine of the National Academy of Science 2003      Lemelson-MIT Prize for Innovation and Invention 2002      Kyoto Prize in Advanced Technology 2000      Elected Member, American Philosophical Society 1993      Scientist of the Year, Research and Development Magazine 1987      Albert Lasker Basic Medical Research Award 1982      Elected Member, National Academy of Science 1982      Elected Fellow, American Academy of Arts and Sciences

2018-present Chief Strategy Officer and Professor, Institute for Systems Biology 2016-present Chief Science Officer and Senior Vice President, Providence St. Joseph Health 2000-2017 President, Co-founder and Professor, Institute for Systems Biology 1992-2000 Chairman and Founder of the Department of Molecular Biotechnology at University of Washington 1970-1992 Caltech Faculty Member — Chair of Biology for 10 years 1967-1970 Senior Investigator, National Cancer Institute, National Institutes of Health 1967 PhD Caltech 1964 MD The Johns Hopkins School of Medicine 1960 BS Caltech

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Hood, L. 2000. “The Human Genome Project–Launch Pad for Human Genetic Engineering.” In Engineering the Human Germline (1st Edition) , edited by J. Campbell, 17–24. New York: Oxford University Press. Cite Ideker, T., V. Thorsson, A. F. Siegel, and L. E. Hood. 2000. “Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data.” J Comput Biol 7 (6): 805–17. Cite Chaudhary, P. M., M. T. Eby, A. Jasmin, A. Kumar, L. Liu, and L. Hood. 2000. “Activation of the NF-KappaB Pathway by Caspase 8 and Its Homologs.” Oncogene 19 (39): 4451–60. Cite Deng, Y., A. Madan, A. B. Banta, C. Friedman, B. J. Trask, L. Hood, and L. Li. 2000. “Characterization, Chromosomal Localization, and the Complete 30-Kb DNA Sequence of the Human Jagged2 (JAG2) Gene.” Genomics 63 (1): 133–38. Cite Nelson, P. S., N. Clegg, B. Eroglu, V. Hawkins, R. Bumgarner, T. Smith, and L. Hood. 2000. “The Prostate Expression Database (PEDB): Status and Enhancements in 2000.” Nucleic Acids Res 28 (1): 212–13. Cite Lin, B., J. T. White, C. Ferguson, R. Bumgarner, C. Friedman, B. Trask, W. Ellis, P. Lange, L. Hood, and P. S. Nelson. 2000. “PART-1: A Novel Human Prostate-Specific, Androgen-Regulated Gene That Maps to Chromosome 5q12.” Cancer Res 60 (4): 858–63. Cite Goode, E. L., J. L. Stanford, L. Chakrabarti, M. Gibbs, S. Kolb, R. A. McIndoe, V. A. Buckley, et al. 2000. “Linkage Analysis of 150 High-Risk Prostate Cancer Families at 1q24-25.” Genet Epidemiol 18 (3): 251–75. Cite Aebersold, R., L. E. Hood, and J. Watts. 2000. “Equipping Scientists for the New Biology.” Nat Biotechnol 18 (4): 359. Cite Brewster, J. L., S. L. Martin, J. Toms, D. Goss, K. Wang, K. Zachrone, A. Davis, G. Carlson, L. Hood, and J. D. Coffin. 2000. “Deletion of Dad1 in Mice Induces an Apoptosis-Associated Embryonic Death.” Genesis 26 (4): 271–78. Cite Nelson, P. S., D. Han, Y. Rochon, G. L. Corthals, B. Lin, A. Monson, V. Nguyen, et al. 2000. “Comprehensive Analyses of Prostate Gene Expression: Convergence of Expressed Sequence Tag Databases, Transcript Profiling and Proteomics.” Electrophoresis 21 (9): 1823–31. Cite Baliga, N. S., Y. A. Goo, W. V. Ng, L. Hood, C. J. Daniels, and S. DasSarma. 2000. “Is Gene Expression in Halobacterium NRC-1 Regulated by Multiple TBP and TFB Transcription Factors?” Mol Microbiol 36 (5): 1184–85. Cite Gibbs, M., J. L. Stanford, G. P. Jarvik, M. Janer, M. Badzioch, M. A. Peters, E. L. Goode, et al. 2000. “A Genomic Scan of Families with Prostate Cancer Identifies Multiple Regions of Interest.” Am J Hum Genet 67 (1): 100–109. Cite Allen, E. E., and L. Hood. 2000. “Biotechnology, Inquiry, and Public Education.” Trends Biotechnol 18 (8): 329–30. Cite Cameron, R. A., G. Mahairas, J. P. Rast, P. Martinez, T. R. Biondi, S. Swartzell, J. C. Wallace, et al. 2000. “A Sea Urchin Genome Project: Sequence Scan, Virtual Map, and Additional Resources.” Proc Natl Acad Sci U S A 97 (17): 9514–18. Cite Rowen, L., G. K. Wong, R. P. Lane, and L. Hood. 2000. “Intellectual Property. Publication Rights in the Era of Open Data Release Policies.” Science 289 (5486): 1881. Cite Siegel, A. F., G. van den Engh, L. Hood, B. Trask, and J. Roach. 2000. “Modeling the Feasibility of Whole Genome Shotgun Sequencing Using a Pairwise End Strategy.” Genomics 68 (3): 237–46. Cite Ng, W. V., S. P. Kennedy, G. G. Mahairas, B. Berquist, M. Pan, H. D. Shukla, S. R. Lasky, et al. 2000. “Genome Sequence of Halobacterium Species NRC-1.” Proc Natl Acad Sci U S A 97 (22): 12176–81. Cite Anderson, J. P., A. G. Rodrigo, G. H. Learn, A. Madan, C. Delahunty, M. Coon, M. Girard, S. Osmanov, L. Hood, and J. I. Mullins. 2000. “Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type 1 Subtype E.” J Virol 74 (22): 10752–65. Cite Rampazzo, A., F. Pivotto, G. Occhi, N. Tiso, S. Bortoluzzi, L. Rowen, L. Hood, A. Nava, and G. A. Danieli. 2000. “Characterization of C14orf4, a Novel Intronless Human Gene Containing a Polyglutamine Repeat, Mapped to the ARVD1 Critical Region.” Biochem Biophys Res Commun 278 (3): 766–74. Cite Hood, L. 2001. “Melanoma Techniques and Protocols: Molecular Diagnosis, Treatment, and Monitoring.” In Methods in Molecular Medicine , 61:Forward by Hood, L. Totowa, NJ: Humana Pr Inc. Cite Ideker, T., T. Galitski, and L. Hood. 2001. “A New Approach to Decoding Life: Systems Biology.” Annu Rev Genomics Hum Genet 2: 343–72. Cite Baliga, N. S., S. P. Kennedy, W. V. Ng, L. Hood, and S. DasSarma. 2001. “Genomic and Genetic Dissection of an Archaeal Regulon.” Proc Natl Acad Sci U S A 98 (5): 2521-5. Cite DasSarma, S., S. P. Kennedy, B. Berquist, W. Victor Ng, N. S. Baliga, J. L. Spudich, M. P. Krebs, J. A. Eisen, C. H. Johnson, and L. Hood. 2001. “Genomic Perspective on the Photobiology of Halobacterium Species NRC-1, a Phototrophic, Phototactic, and UV-Tolerant Haloarchaeon.” Photosynth Res 70 (1): 3–17. Cite Hood, L. 2001. “Deciphering Heredity.” In The Alfred Deakin Lectures: Ideas for the Future of a Civil Society , 164–76. Sydney, Australia: Australian Broadcasting Corporation. Cite Peters, M. A., G. P. Jarvik, M. Janer, L. Chakrabarti, S. Kolb, E. L. Goode, M. Gibbs, et al. 2001. “Genetic Linkage Analysis of Prostate Cancer Families to Xq27-28.” Hum Hered 51 (1–2): 107–13. Cite Park, I. K., C. A. Klug, K. Li, L. Jerabek, L. Li, M. Nanamori, R. R. Neubig, L. Hood, I. L. Weissman, and M. F. Clarke. 2001. “Molecular Cloning and Characterization of a Novel Regulator of G-Protein Signaling from Mouse Hematopoietic Stem Cells.” J Biol Chem 276 (2): 915–23. Cite Wang, K., L. Gan, T. Kunisada, I. Lee, H. Yamagishi, and L. Hood. 2001. “Characterization of the Japanese Pufferfish (Takifugu Rubripes) T-Cell Receptor Alpha Locus Reveals a Unique Genomic Organization.” Immunogenetics 53 (1): 31–42. Cite Chen, F., L. Rowen, L. Hood, and E. V. Rothenberg. 2001. “Differential Transcriptional Regulation of Individual TCR V Beta Segments before Gene Rearrangement.” J Immunol 166 (3): 1771–80. Cite Lin, B., J. T. White, C. Ferguson, S. Wang, R. Vessella, R. Bumgarner, L. D. True, L. Hood, and P. S. Nelson. 2001. “Prostate Short-Chain Dehydrogenase Reductase 1 (PSDR1): A New Member of the Short-Chain Steroid Dehydrogenase/Reductase Family Highly Expressed in Normal and Neoplastic Prostate Epithelium.” Cancer Res 61 (4): 1611–18. Cite McPherson, J. D., M. Marra, L. Hillier, R. H. Waterston, A. Chinwalla, J. Wallis, M. Sekhon, et al. 2001. “A Physical Map of the Human Genome.” Nature 409 (6822): 934–41. Cite Bruls, T., G. Gyapay, J. L. Petit, F. Artiguenave, V. Vico, S. Qin, A. M. Tin-Wollam, et al. 2001. “A Physical Map of Human Chromosome 14.” Nature 409 (6822): 947–48. Cite Lander, E. S., L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody, J. Baldwin, K. Devon, et al. 2001. “Initial Sequencing and Analysis of the Human Genome.” Nature 409 (6822): 860–921. Cite Peck, R. F., C. Echavarri-Erasun, E. A. Johnson, W. V. Ng, S. P. Kennedy, L. Hood, S. DasSarma, and M. P. Krebs. 2001. “Brp and Blh Are Required for Synthesis of the Retinal Cofactor of Bacteriorhodopsin in Halobacterium Salinarum.” J Biol Chem 276 (8): 5739–44. Cite Aderem, A., and L. Hood. 2001. “Immunology in the Post-Genomic Era.” Nat Immunol 2 (5): 373–75. Cite Meyer, A. L., J. Benson, F. Song, N. Javed, I. E. Gienapp, J. Goverman, T. A. Brabb, L. Hood, and C. C. Whitacre. 2001. “Rapid Depletion of Peripheral Antigen-Specific T Cells in TCR-Transgenic Mice after Oral Administration of Myelin Basic Protein.” J Immunol 166 (9): 5773–81. Cite Ideker, T., V. Thorsson, J. Ranish, R. Christmas, J. Buhler, J. K. Eng, R. Bumgarner, D. R. Goodlett, R. Aebersold, and L. Hood. 2001. “Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network.” Science 292 (5518): 929–34. Cite Lane, R. P., T. Cutforth, J. Young, M. Athanasiou, C. Friedman, L. Rowen, G. Evans, R. Axel, L. Hood, and B. J. Trask. 2001. “Genomic Analysis of Orthologous Mouse and Human Olfactory Receptor Loci.” Proc Natl Acad Sci U S A 98 (13): 7390–95. Cite Anderson, J. P., A. G. Rodrigo, G. H. Learn, Y. Wang, H. Weinstock, M. L. Kalish, K. E. Robbins, L. Hood, and J. I. Mullins. 2001. “Substitution Model of Sequence Evolution for the Human Immunodeficiency Virus Type 1 Subtype B Gp120 Gene over the C2-V5 Region.” J Mol Evol 53 (1): 55–62. Cite Terskikh, A. V., M. C. Easterday, L. Li, L. Hood, H. I. Kornblum, D. H. Geschwind, and I. L. Weissman. 2001. “From Hematopoiesis to Neuropoiesis: Evidence of Overlapping Genetic Programs.” Proc Natl Acad Sci U S A 98 (14): 7934–39. Cite Hood, L. 2001. “Computing Life: The Challenge Ahead.” IEEE Eng Med Biol Mag 20 (4): 20. Cite Glusman, G., L. Rowen, I. Lee, C. Boysen, J. Roach, A. Smit, K. Wang, B. F. Koop, and L. Hood. 2001. “Comparative Genomics of the Human and Mouse T Cell Receptor Loci.” Immunity 15 (3): 337–49. Cite Goode, E. L., J. L. Stanford, M. A. Peters, M. Janer, M. Gibbs, S. Kolb, M. D. Badzioch, L. Hood, E. A. Ostrander, and G. P. Jarvik. 2001. “Clinical Characteristics of Prostate Cancer in an Analysis of Linkage to Four Putative Susceptibility Loci.” Clin Cancer Res 7 (9): 2739–49. Cite Kennedy, S. P., W. V. Ng, S. L. Salzberg, L. Hood, and S. DasSarma. 2001. “Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence.” Genome Res 11 (10): 1641–50. Cite Moore, R. C., P. Mastrangelo, E. Bouzamondo, C. Heinrich, G. Legname, S. B. Prusiner, L. Hood, D. Westaway, S. J. Dearmond, and P. Tremblay. 2001. “Doppel-Induced Cerebellar Degeneration in Transgenic Mice.” Proc Natl Acad Sci U S A 98 (26): 15288–93. Cite Futter, N. Wade, H. Varmus, E. Green, C. Venter, L. Hood, R. Bazell, et al. 2002. “After the Genome: Where Should We Go?” In The Genomic Revolution: Unveiling the Unity of Life , 64–73. Joseph Henry Press, Washington, D.C. with the American Museum of Natural History. Cite Foltz, G., A. Madan, and L. Hood. 2002. Cancer Proteomics: Methodologies for the Selection of Immunotherapy Targets. Principles and Practice of Biologic Therapy of Cancer Updates, Third Edition . New York: Lippincott Williams & Wilkins, A Wolters Kluwer Company. Cite Lane, R. P., J. C. Roach, I. Lee, C. Boysen, A. Smit, B. J. Trask, and L. Hood. 2002. “Genomic Analysis of the Olfactory Receptor Region of the Mouse and Human T-Cell Receptor Alpha/Delta Loci.” Genome Research 12 (1): 81–87. Cite Lane, R. P., T. Cutforth, R. Axel, L. Hood, and B. J. Trask. 2002. “Sequence Analysis of Mouse Vomeronasal Receptor Gene Clusters Reveals Common Promoter Motifs and a History of Recent Expansion.” Proc Natl Acad Sci U S A 99 (1): 291–96. Cite Park, I. K., Y. He, F. Lin, O. D. Laerum, Q. Tian, R. Bumgarner, C. A. Klug, et al. 2002. “Differential Gene Expression Profiling of Adult Murine Hematopoietic Stem Cells.” Blood 99 (2): 488–98. Cite Liu, A. Y., P. S. Nelson, G. van den Engh, and L. Hood. 2002. “Human Prostate Epithelial Cell-Type CDNA Libraries and Prostate Expression Patterns.” Prostate 50 (2): 92–103. Cite

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• PhD SYBB Application Process

PhD in Systems Biology and Bioinformatics Application Process

• SYBB Application
• SYBB Student Handbook
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How to Apply to the SYBB PhD Program

Students interested in earning a PhD in Systems Biology and Bioinformatics may enter the program through two mechanisms:

Biomedical Sciences Training Program (BSTP)

Apply for admission to the BSTP program at Case Western Reserve University with Systems Biology and Bioinformatics as your Priority Program of Interest (or PPI). The School of Graduate Studies processes the application and includes a nonrefundable application fee. Priority will be given to applications received by October 15. We will continue to review applications received after the priority deadline, but not beyond the final application deadline of January 1. Your application will be reviewed by the Admissions Committee as soon as it is complete.

Please note that our program has limited financial resources for supporting students who are not citizens or permanent residents of the United States.

Medical Scientist Training Program (MSTP) 

Apply for the PhD in SYBB program as a result of acceptance into the Medical Scientist Training Program (MSTP) . The MSTP program is a highly selective combined MD/PhD program. Students in the MSTP Program take PhD course work in conjunction with MD course work. The MSTP students have 20 different PhD programs available to them including Nutrition. Upon completion of their PhD course work, the students will work full time on their PhD and then upon completion of the PhD return to traditional medical school to complete their MD.  

• Nebraska Medicine
• Current Students
• Current Faculty

Peng Xiao, PhD

Assistant Professor, Department of Genetics, Cell Biology, and Anatomy Operational Director, Bioinformatics and Systems Biology Core

Phone: 402-559-2083

• PhD, Biomedical Sciences, Creighton University
• BS, Biochemistry and Molecular Biology, Hunan Normal University
• Dai HD, Doucet GE, Wang Y, Puga T, Samson K, Xiao P, Khan AS. Longitudinal Assessments of Neurocognitive Performance and Brain Structure Associated With Initiation of Tobacco Use in Children, 2016 to 2021. JAMA Netw Open. 2022. 5:e2225991. PMID: 35947383; PMCID: PMC9366547.
• Liu B, Kong Y, Shi W, Kuss M, Liao K, Hu G, Xiao P, Sankarasubramanian J, Guda C, Wang X, Lei Y, Duan B. Exosomes derived from differentiated human ADMSC with the Schwann cell phenotype modulate peripheral nerve-related cellular functions. Bioact Mater. 2021. 14:61-75. PMID: 35310346; PMCID: PMC8892082.
• Wu S, Kumar V, Xiao P, Kuss M, Lim JY, Guda C, Butcher J, Duan B. Age related extracellular matrix and interstitial cell phenotype in pulmonary valves. Sci Rep. 2020. 10:21338. PMID: 33288823; PMCID: PMC7721746.

985145 Nebraska Medical Center Omaha, NE 68198-5145

Publications

Curriculum & Core Subjects

The CSB Ph.D. curriculum has two components: the core subjects and advanced electives. Core subjects provide foundational knowledge of both biology and computational biology. Advanced electives are chosen by each student to generate a customized program of study, in close consultation with members of the CSB Ph.D. Graduate Committee and the student's thesis advisor. The goal is to allow students broad latitude in defining their individual area of interest, but at the same time to provide oversight and guidance to ensure that they receive rigorous and thorough training.

Core Subjects

The core curriculum consists of three classroom subjects plus a set of three two-month rotations in different research groups. The classroom subjects fall into three areas:

Topics in Computational and Systems Biology (One Subject): All first-year students in the program are required to participate in this literature-based exploration of current research frontiers and paradigms. Papers for discussion are selected from a broad range of topics in computational and systems biology, with an emphasis on the integration of experimental and computational approaches to understanding complex biological systems. This subject is limited to students in the CSB Ph.D. Program in order to build a strong community among the class. It is the only subject in the program with such a limitation. 

CSB.100 Topics in Computational and Systems Biology  

Modern Biology (One Subject):

A semester of modern graduate-level biology at MIT strengthens the biology base of all students in the program. Subjects in molecular biology, neurobiology, biochemistry, or genetics fulfill this requirement. The particular course taken by each student will depend on his or her background and will be determined in consultation with members of the CSB Ph.D. Graduate Committee. Subjects that can fulfill the biology requirement for the CSB Ph.D. degree include: (choose one) 

• Principles of Biochemical Analysis (7.51)  
• Genetics for Graduate Students (7.52)  
• Molecular Biology (7.58)  
• Eukaryotic Cell Biology: Principles and Practice (7.61/20.561J)  
• Immunology (7.63)
• Molecular and Cellular Neuroscience Core II (7.68/9.013J)  

Computational Biology (One Subject): 

1.        6.8700/HST.507 J Advanced Computational Biology: Genomes, Networks, Evolution . This course additionally examines recent publications in the areas covered, with research-style assignments. A more substantial final project is expected, which can lead to a thesis and publication, 

2.       7.81/8.591 J Systems Biology   This graduate-level course explores more in-depth cellular and population-level systems with an emphasis on synthetic biology, modeling of genetic networks, cell-cell interactions, and evolutionary dynamics.  

3.     20.490 Computational Systems Biology: Deep Learning in the Life Sciences   Presents innovative approaches to computational problems in the life sciences, focusing on deep learning-based approaches with comparisons to conventional methods. Topics include protein-DNA interaction, chromatin accessibility, regulatory variant interpretation, medical image understanding, medical record understanding, therapeutic design, and experiment design (the choice and interpretation of interventions). Focuses on machine learning model selection, robustness, and interpretation. Teams complete a multidisciplinary final research project using TensorFlow or other framework. Provides a comprehensive introduction to each life sciences problem, but relies upon students understanding probabilistic problem formulations. Students taking graduate version complete additional assignments.

4.       Both a and b below:                   

a.       6.C51Modeling with Machine Learning: from Algorithms to Applications  focuses on modeling with machine learning methods with an eye towards applications in engineering and sciences. Introduction to modern machine learning methods, from supervised to unsupervised models, with an emphasis on newer neural apporaches. Emphasis on the understanding of how and why the methods work from the point of view of modeling, and when they are applicable. Unsing concrete examples, covers formulation of machine learning tasks, adapting and extending methods to given problems, and how the methods can and should be evaluated. Students taking graduate version complete additonal assignments. Students cannot receive credit without simultaneous completion of a 6-unit disciplinary module. Enrollment may be limited. 

b.       20.C51/3.C51/10.C51J Machine Learning for Molecular Engineering  Building on core material in 6.C51, provides an introduction to the use of machine learning to solve problems arising int he science and engineering of biology, chemistry, and materials. Equips students to design and implement achine learning approaches to challenges such as analysis of omics (genomics, transcriptomics, proteomics, etc.) microscopy, spectroscopy, or crystallography data and design of new molecules and materials such as drugs, catalysts, polymer, alloys, ceramics, and proteins. Students taking graduat version complete addiitonal assignments. Students cannot receive credit with simultaneous completion of 6.CS1.          

                                         6.C51 & 20.C51 MUST BE TAKEN TOGETHER IN THE SAME SEMESTER

Brian Trippe arrives as Assistant Professor of Statistics

A new appointment will join our department on July 1. Brian comes to us from a postdoctoral stint with the Columbia University Department of Statistics as well as a visiting researcher post with the University of Washington's Institute for Protein Design in Seattle. He earned his PhD in Computational and Systems Biology from MIT where he was a founding co-organizer of the Machine Learning for Protein Engineering Seminar Series.

Brian's recent research develops and applies statistical machine learning methods to solve challenges that arise in biotechnology and medicine. Through work on computational protein design over the past two years, he and his collaborators have synthesized hundreds of new molecules that have been subsequently validated in laboratory experiments. His future work aims to develop these machine learning methods to enable biotechnology solutions to challenges ranging from disease eradication to climate change-robust agriculture, with a long-term goal of building statistical foundations for data-driven genetic engineering.

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Integrated Physiology

Graduate program.

Integrated Physiology faculty are associated with multiple departments, representing diverse research interests and scientific approaches, but sharing common interests in understanding how complex physiological systems are regulated. In addition, the faculty all share a deep commitment to quality graduate education and are actively engaged in mentoring and supporting students as they progress toward their PhD. 

Faculty research fall into one of more of the research tracks below:

Major Research Tracks

Reproductive biology.

Reproductive Biology was founded in 2004 as an interdepartmental Graduate Program. The basic science and clinical faculty are drawn from 10 different Departments and Divisions, allowing students to take an integrated, translational, multidisciplinary approach to the study of reproductive biology and pathophysiology. Students in the Reproductive Biology Track have opportunities to investigate research areas including:

• Signal transduction and transcriptional regulation
• Reproductive Endocrinology and Metabolism
• Neuroendocrinology
• Breast, Ovarian and Uterine cancers
• Epidemiology
• Complications of Pregnancy
• Development and function of the reproductive system
• Mammary gland development and lactation
• Placental development and function
• Obesity and fetal developmental programming

Cellular Physiology

Training in Cellular Physiology prepares graduate PhD students for independent careers in biomedical research through grounding in the fundamental principles of physiology and biophysics, and their application to important problems of cellular systems regulation. Students in the Cellular Physiology track have a broad array of research projects from which to choose, and access to an equally broad assortment of cutting edge techniques and instrumentation for their projects, including advanced electrophysiology, high-resolution imaging, and novel biochemical (including photochemical) tools.

Research projects in Cellular Physiology cover problems such as recycling of synaptic vesicles, transduction and modulation of signals in the olfactory bulb, mechanisms of sound localization in mammals, the role of glia and spontaneous secretion of transmitter in the brain, characterization of sodium channel isoforms in excitable cells, regulation of potassium channel expression during development, excitation-contraction coupling, molecular physiology of cardiac pacemaking, processing of sound information in the auditory brainstem, neurophysiology of making decision and initiating actions, and neurophysiology of the cerebellum.

Molecular Nutrition and Metabolic Systems

Research in molecular nutrition and metabolic systems underpins advances in many areas of medicine and physiology, and is essential for understanding complex diseases and disorders of human biology, such as obesity, diabetes and cardiovascular disease. Students in the Molecular Nutrition and Metabolic Systems (MNMS) track have opportunities to investigate how nutrients are metabolized by cells, organs and higher systems, and how defects in metabolic systems contribute to human disease.

Research projects in the MNMS track employ state of the art techniques in metabolism, cell and molecular biology, imaging, genomics and proteomics that provide students with capabilities of generating sophisticated mechanistic insight into metabolic disorders and disease processes. Students that successfully complete MNMS training and research programs are prepared for independent careers in biomedical research in academic, industry and government laboratories.

Cardiovascular/Pulmonary/Renal/GI Physiology

Cardiovascular/Pulmonary/Renal/GI Physiology research seeks to uncover mechanisms, and integrating principals, regulating fundamental cardiac, pulmonary, renal, and GI systems. Investigators in this track pursue mechanistic research related to how hormones, metabolism, ion channel properties, exercise, and diseases, regulate, or disrupt, multiple physiological systems.

Research projects in this track focus on serious human health problems related to cardiac function, pulmonary disorders, renal abnormalities, endothelial biology, obesity, and diabetes. These projects employs cutting-edge molecular biology, imaging, genomics, ion channel and modeling approaches in cellular, organ, and higher-order experimental systems. Students in this track will have opportunities to integrate many of these experimental approaches in the pursuit of understanding cardiac, pulmonary, renal, and GI systems biology.

Curtis Henry PhD

• Immunology Microbiology (SOM)

Email Address: [email protected]

C. Henry Faculty Profile

Research Interest

• Adaptive Immunity
• Basic Sciences - Immunology
• Cancer Biology
• Cellular Structure
• Immunotherapy
• Innate Immunity

Faculty Diversity, Equity, and Inclusion Training Reporting

• Send me more information
• Summer Research Programs
• PIKE-PREP (Postbac Program)

Biological Sciences

• Mellon College of Science

M.S. in Quantitative Biology and Bioinformatics

The study of Biology is undergoing a revolution driven by new technologies that enable scientists to generate extensive amounts of data.  For example, the costs of sequencing nucleic acids have dropped dramatically, resulting in unprecedented amounts of genomic, transcriptomic, and proteomic data.  Advances in imaging extend from the nano to the macro scale to probe function and generate enormous amounts of data that describe behaviours of cells from subcellular to organ-levels.  The new datasets cut across all subdisciplines in biology and enable scientists to ask questions in new ways to reveal the fundamental rules of life.

The M.S. in Quantitative Biology and Bioinformatics (MS-QBB) will prepare students for new careers bioinformatics and related fields. Our mission is to provide students who have background in life sciences skills to prepare for careers in bioinformatics. This program allows student to choose a 2-semester or a 3-semester program of study. If you are interested in applying, learn more about the application process on our admissions page or e-mail us .

Program Mission

To provide students who have a background in biology and other sciences with a practical and focused educational experience to prepare them for careers in bioinformatics and quantitative biological science.

2-semester M.S. in QBB

Our 2-semester option allows students to quickly gain the most relevant skills in bioinformatics. Students will begin study in late August and graduate in late May.

3-semester M.S. in QBB - Advanced Study

The 3-semester option allows students to spend a third semester gaining additional experience and some more advanced coursework. Students will begin study in late August, have the option to earn course credit with optional summer internships (interested students may apply to these in the first year), then students will complete their third semester in the following Fall and graduate in late December.

Students are encouraged to seek external internships after their first year and pursue this degree full-time, completing the program in 3 semesters.

Related programs

Students who are interested in this program may also want to consider the M.S. in Computational Biology and M.S. in Automated Science programs . Those programs expect a higher level of quantitative background & skills to enter and are designed to engage students with a more in-depth focus computational machine learning competencies and the application of machine learning to biological research.

How to Apply

The CMU Rales Fellow Program is dedicated to developing a diverse community of STEM leaders from underrepresented and underresourced backgrounds by eliminating cost as a barrier to education. Learn more about this program for master's and Ph.D. students. Learn more

Join our growing network of prospective students!

Fill in the form below to connect with a program advisor

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