Funding
The study programme is being established with the support of the Czech Recovery Plan, project NPO_UK_MSMT-16602/2022.
Bioinformatics and computational biology are multidisciplinary disciplines on the interface of computer science (especially algorithms and software development, data engineering), mathematics (especially probability, statistics, and mathematical modeling), and biology (especially molecular and evolutionary) aimed at the development and implementation of algorithms, software tools, and mathematical models for processing, analyzing, and modeling biological data and processes at the molecular and cellular level.
The common denominator of bioinformatics and computational biology, which encompasses diverse areas such as systems biology, neuroinformatics, bioimaging, and computational drug design, is the development of analytical procedures and software tools for processing and analyzing large, domain-specific, and heterogeneous data to understand cellular processes at the molecular level, to learn from the evolution of given processes and eventually apply this knowledge in various fields, especially in medicine and biotechnology.
Pursuing a PhD in bioinformatics offers an opportunity to become an expert in a rapidly evolving field that plays a critical role in advancing our understanding of complex biological systems.
As a bioinformatics PhD student, you will learn cutting-edge techniques for analyzing and interpreting large-scale genomic, proteomic, and metabolomic data, as well as develop computational tools to facilitate data analysis. You will also have the opportunity to collaborate with experts in other fields, such as biology, medicine, and engineering, and work on projects with real-world applications, such as drug discovery and personalized medicine.
Furthermore, pursuing a PhD in bioinformatics can lead to diverse career opportunities, including academia, industry, government, and healthcare. With the growing demand for data-driven solutions in biology and medicine, bioinformatics PhD graduates are highly sought after in both the public and private sectors.
Although there is no widely accepted categorization of the domain, for the purpose of our study program, we partition the field into the following non-exclusive categories.
Unlike Bachelor's or Master's studies, doctoral studies which are more oriented towards on obtaining foundational knowledge and skills and are therefore more course-oriented, PhD studies are highly specialized. To earn a PhD degree you are expected to develop expertise in a specific area of the discipline, to make original contributions to your field of study through independent research, publish the results of your research, write a dissertation about the results, and defend your work. The following sections describe various aspects of the study program.
As we strongly believe that the primary focus of a PhD studies should be on research rather than coursework. Therefore, there is only one obligatory course in the programme, the Doctoral Bioinformatics Seminar. The idea of the seminar is for students from different fields of bioinformatics and computational biology to share their insights and knowledge, mutually broadening their views and enriching their research with new insights from related areas which are not directly within their direct field of expertise.
Additionally, in their first one or two years of the programme, students are expected to take 1-2 courses, which should be chosen to complement their research focus. This will enable them to develop a deeper understanding of their research area and provide them with the necessary tools to conduct high-quality research.
We compiled a list of courses that you might find usefull here. Some are beneficial for those comming from the biology background while others for those coming from the computer science background.
A soft skills course which we recommend the students to take is Presentation Skills for Bioinformaticians.In order to be allowed to defend doctoral thesis, the student needs to fulfill the following criteria. A deviation from those criteria is possible but will be considered on an ad-hoc basis. The student needs to have least 2 impacted (WOS or SJR) journal publications, with at least one having the student as the first (joint first authorship is fine) or corresponding author. In the case of an exceptionally important article in a top journal such as Nature or Science, one publication is sufficient. This requirement can be replaced in exceptional cases by peer-reviewed conferences (a typical publication format in some fields such as computer science), which must be top conferences in the field (on the order of A or A* conferences according to CORE rating) and quite exceptionally by several manuscripts in Bioarxiv. These results will be recognized ad-hoc.
It is expected that the exam will be taken no later than during the 5th semester since starting the doctoral studies. The aim of the examination is to evaluate the work done so far and the progress on the dissertation. The aim is therefore not to test knowledge on the basis of a curriculum of a group of courses or fixed lists of topics. There are 2 reasons for this:
Therefore, the exam will consist of 2 parts:
Bioinformatics and computational biology is an interdisciplinary programme with each research topic relying on contributions from both computer science/mathematics and biology. The exam will thus cover these two areas, with a particular focus on the student's specific research interests. The supervisor will propose the specific topic, which will be presented to the subject area board. As the topic may be far from the expertise of all subject area board members, two experts in relevant fields will also be proposed for the examination. These experts may be members of the subject area board or external specialists.
The exam topic proposal should include
The preferred form of the thesis is an article-based thesis of papers linked by an overarching research question or theme. The thesis should include an overview introduction of approximately 30-50 pages setting the publications in a broader context. The purpose of the introduction is to provide an overview of the research domain and a summary/discussion of the results and own contributions, which are then detailed in the accompanying papers.
The thesis will be reviewed by two oponnents with at least one being from abroad. The thesis defense will include thesis presentation and discussion.
We strongly believe that pursuing an internship abroad can provide PhD students with numerous benefits, including international experience, exposure to different research methods, a professional network, cultural immersion, and enhanced career prospects. It is an excellent opportunity for students to broaden their horizons, gain new perspectives, and develop a set of skills that will be valuable in their future careers.
For the above reasons, we strongly advise at least a 3-month internship at an abroad institution. If the student does not undergo an internship it needs, the reasons for such a decision need to be explained during the thesis defense.
The following text is based on the "Methodology for Collaboration with Foreign Institutions within the Bioinformatics and Computational Biology Study Program at Charles University" available in Czech here.
We aim for active involvement on the international stage, particularly in collaboration with European universities. The goal of these collaborations is to enable students and academic staff to gain knowledge and experience that are not sufficiently covered within the domestic study program due to the breadth of the field. International collaboration contributes to the personal and professional growth of students and provides new incentives for academic staff to improve teaching.
The main benefits of international cooperation include:
4EU+ is an alliance of European universities aimed at strengthening cooperation between member institutions in education and research.
Erasmus+ is a European Union program supporting educational, teaching, and research activities for students and academic staff at European universities.
In addition to Erasmus+ and 4EU+, there are other opportunities for international collaboration through specific projects and bilateral agreements with prestigious research institutions.
The following text is based on the "Methodology for Involving Companies in the Doctoral Study Program" available in Czech here.
We actively develop and maintain cooperation with companies that have bioinformatics or cheminoformatics research divisions. These include companies starting from small academic start-ups up to large pharmaceutical companies. There currently exist three formal channels via which we, and the students of our study programme, interact with the industry: academia-industry meet-ups, partnership programme of Faculty of Mathematics and Physics, and industrial PhD.
Before you apply for the doctoral study programme in Bioinforamtics and computational biology, we strongly advice you to first find an advisor and agree with them on the prospective PhD project. Although it is technically possible to submit an admission application without having an agreed upon supervisor we strongly discourage from taking such path. In order to get accepted for the study programme, you need to apply for the PhD programme either at the Faculty of Mathematics and Physics or Faculty of Science. The choice is basically given by the affiliation of your advisor. Should your advisor not be affiliated with either of the faculties, we suggest to pick Faculty of Mathematics and Physics if the prospective doctoral project is more computationally oriented and Faculty of Science in case of more application oriented project. In any case, you will be pursuing the Ph.D. under the same study board with exactly the same rules, irrespective on the faculty under which you will be officially enrolled. The choice of faculty determines whether you submit your application at the Faculty of Mathematics and physics (following this set of intructions) or at the Faculty of Science (following this set of intructions). After you provide all the required documents you will need to pass the entrance interview (the same irrespective of the faculty you applied to). Befor the interview, you will need to prepare and attaches a written (approximately 250-500 words) proposal for a doctoral project (part of the application form). Then, the inteview will be held in English and will have two parts. In the first part, you will present yourself and your doctoral project in a short (max 10 minutes) presentation. In the second part of the examination, the committee will ask three questions. One question will focus on the project itself, and the other two questions will test the orientation in the field regarding the proposed your project's topic and your previous field of study. The committee will evaluate each answer with a Pass/Fail statement. You must receive a Pass for all three answers in order to be accepted for the programme. Additionally you need to demonstrate English language profficiency by passing language examination. This can be waived as described in the admission procedure materials linked above.
The study programme is being established with the support of the Czech Recovery Plan, project NPO_UK_MSMT-16602/2022.