The purpose of the study program is to provide the students with advanced theoretical and practical knowledge in various areas of molecular and cell biology, genetics and virology, as well as to familiarize them with modern methodical and technical approaches utilized in these scientific fields and with the possibilities of such approaches for problem-solving in current biological and biomedical science (including interdisciplinary research). The main scope of the program can be characterized as the study of biological processes at molecular and cell level, focusing particularly on complex interactions between cells and environment or between various information macromolecules (DNA, RNA, proteins) and using the most modern approaches of molecular biology and bioinformatics.

Study Duties

Doctoral students must complete at least one specialized lecture/course selected among the subjects taught at the Faculty of Science, Charles University, or the Faculties of Medicine, Charles University (including courses provided by cooperating institutions). This lecture/course should be related to the topic of their doctoral thesis and correspond to their professional needs (it should be chosen in consultation with their supervisor). It is possible to enroll in and complete more specialized courses as needed and recommended by the supervisor. The lecture/course must be a genuinely scientific subject (so-called soft-skills courses are not accepted as a required study duty, although students may, of course, enroll in and complete them if deemed appropriate by them or by the faculty they are studying at).

Additional study duties may be set by the faculty’s internal regulations, and their fulfillment may be binding for doctoral students of the respective faculty, provided this is explicitly stated in those regulations (e.g., an English language examination).

Participation in Conferences

The Subject Area Board requires doctoral students to take an active part (i.e., by presenting a poster or giving a lecture) in national and, in particular, international scientific conferences in order to gain important and highly useful experience for further scientific work. Such active participation in at least one national/international conference during doctoral study is a mandatory component of the Individual Study Plan (ISP), and the doctoral student must provide evidence of it (by submitting a copy of the confirmation of active participation in the conference and the abstract as an attachment uploaded to SIS during the relevant annual ISP evaluation). Doctoral students should also attend various types of regular doctoral conferences organized by their faculty or supervisory institution; participation in this type of conference may form another part of the ISP if required by the internal regulations of the faculty. However, these „internal“ conferences do not count towards fulfilling the above-mentioned requirement of an active participation of doctoral student in a „standard“ national/international scientific conference.

Discussion on the Doctoral Dissertation Topic

Doctoral students studying in the full-time form of doctoral study must register for this course at such a time that the Discussion takes place either during the second year or (in justified cases) in the winter semester of the third year of their study. Doctoral students studying in the part-time form of doctoral study may complete the course also in the summer semester of their third year. Each academic year, the Discussion will be held during one of the following three periods: January/February, June, and September. The doctoral students will be notified about the exact time and place well in advance of the relevant period.

The doctoral students will have to give a presentation about their doctoral project, followed by a discussion with a committee. For this purpose, students must prepare a PowerPoint or PDF presentation including, in particular, the project’s objectives and rationale, a brief overview of methodological approaches and main results already achieved, future prospects, current state of their publication activity, etc., which they will present to the committee. The presentation of the current state of work on the doctoral project should last approx. 15, at most 20 minutes. The presentation must be in English and the subsequent discussion between the students and the committee will also be conducted in English.

Students must demonstrate in their interaction with the committee a detailed and up-to-date knowledge and understanding of various issues directly related to their doctoral project, including associated topics, and an awareness of the principles, possibilities, and limitations of the methodological approaches relevant to their research. They are expected to clearly demonstrate the ability to grasp the essence of the problem, place it in a broader context, and, above all, show critical and creative thinking. During this discussion, the committee will also provide feedback on the project. A summary of the questions, comments, recommendations, and suggestions arising from the discussion will subsequently be sent in writing (by e-mail) to the students and their supervisors. It is strongly recommended that either the supervisor or another representative of the supervising Laboratory attend the Discussion in person.

In the event of serious objections of the committee to the progress of the project, or findings of significant gaps in the students’ knowledge based on this discussion, the Subject Area Board reserves the right to request that it be repeated within a defined timeframe.

Involvement in International Cooperation and Grant Activities

During their study, doctoral students should undertake a research internship abroad (with a total duration of at least one month). Its inclusion in the individual study plan is decided primarily by the supervisor, and its implementation depends on the possibilities of the respective research institution. If an internship cannot be arranged, doctoral students should engage in international collaboration in another manner in accordance with the Standards of Study Programmes at Charles University.

Doctoral students are also encouraged to take an active part in the preparation of grant projects at their supervising Laboratory. It is also highly recommended that they prepare and submit their own project proposals in the annual competition for grant allocation at Charles University (Charles University Grant Agency).

Creative Work and the Publication Activity

The main requirement for creative work is the independent execution of original, high-quality scientific work, the outcome of which should be at least one original scientific publication related to the topic of the doctoral project and published or accepted for publication during the doctoral study. This publication must appear in a peer-reviewed journal indexed in databases generally recognized by the international scientific community (Web of Science, i.e. journals with an impact factor). It should be an „original paper“, and the doctoral student must be the first author and must make a significant contribution to its creation (specified both in the publication itself, if the journal allows this, and in the Ph.D. thesis - see below). For unpublished manuscripts, confirmation that the manuscript has been accepted for publication by the respective journal must be provided. Shared first authorship may be accepted as first authorship, but only with the prior approval of the programme guarantor. It is not desirable for the same shared-first-author publication to serve as the primary basis for several different Ph.D. theses.

Case reports are acceptable as first-author papers only when they represent a substantial scientific contribution (e.g., the description of a novel gene in the pathogenesis of a disease, a new biological mechanism explaining gene function, a new therapeutic approach, or a novel diagnostic method). In such cases, functional experiments should be included. A case report providing only a clinical description of symptoms and patient phenotype cannot be accepted as the required publication.

If the first-author publication has not yet been definitively accepted by a journal but is under peer review (and the journal is of a sufficiently high quality), doctoral students may request an exemption from the publication requirements described above. The same applies if the first-author publication is of a type other than an „original paper“; however, it must be based on experimental work by the doctoral student within the doctoral project (e.g., not a review article or a book chapter - these do not count as a first-author publication meeting the requirements; video publications are also not accepted unless accompanied by a full-text paper). The supervisor must approve such a request, which must be submitted at least one month before the thesis is due to be submitted for its defense. Further information about the proper form of such a request, its attachments and the required form of the Ph.D. thesis in these cases will be provided to students by the programme guarantor, to whom the request should then be sent by e-mail. The Subject Area Board will review the request and may, but is not obliged to, grant it. Such exemptions are expected to be rare and well-justified. If the Subject Area Board does not approve the request, doctoral students must wait to submit the thesis until the publication is accepted by the respective journal.

The purpose of the Subject Area Board’s requirement for a first-author publication is primarily: 1) to ensure that doctoral students learn how to independently prepare such a paper based on the results of their experiments, and 2) to familiarize them with the processes involved in publishing it in a scientific journal recognized by the international scientific community. It is therefore expected that doctoral students (in consultation with their supervisor and possibly other members of the research team) will draft the first version of the publication (particularly the Introduction and Discussion sections, as well as those parts of Materials and Methods and Results that directly relate to their own experiments or to experiments in which they were substantially involved, including preparation of the relevant figures or other documentation). This initial draft may be further revised by the students themselves, their supervisors, and possibly other co-authors before submission to the journal. Revisions not made directly by the students (especially more substantial changes) should always be discussed with them.

Doctoral students do not necessarily need to be the corresponding or submitting authors, but they should, in cooperation with their supervisor (or the submitting author), take part in the entire process of submitting the article to a scientific journal and in everything related to the subsequent peer-review process (response to reviewers’ comments, resubmission, etc.). All significant revisions to a paper which should serve as the basis for the doctoral thesis, that arise during the review process, should also, as far as possible, be discussed by supervisors/submitting authors with the respective student.

In addition to the required first-author publication, doctoral students may of course be co-authors of other scientific publications, whether arising directly from the doctoral project or from other projects of their supervising Laboratory (the Subject Area Board welcomes active involvement of doctoral students in various scientific collaborations). However, only publications directly related to the doctoral project and produced during the doctoral study may be included in the thesis itself (and may partly replace certain parts of it - see below).

Before submitting the thesis for defense, doctoral students must send the programme guarantor by e-mail a link to their first-author publication and (if applicable) a list of other publications intended to serve as the basis for the thesis, so that the guarantor can check that the publication requirements set by the Subject Area Board have been met.

Ph.D. Thesis

Before submitting the thesis for defense, doctoral students must fulfill all outstanding requirements listed in their ISP, successfully pass the Discussion on the Doctoral Dissertation Topic, and have at least one first-author original scientific publication related to their doctoral project and produced during their doctoral study (see above).

The thesis should be the doctoral student’s own original text, enabling the reviewers and the defense committee to assess the student’s ability to conduct independent scientific work in the relevant field. In the thesis, students should be able to present the scientific problem comprehensively and formulate independent opinions and questions arising from the results of their experiments.

In addition to the parts required by the faculty (title page, author’s declaration, abstracts in Czech and English, etc.) and accompanying sections such as Table of contents, Reference list, and possibly a List of abbreviations, the thesis must include: 1) Theoretical introduction (a review of the current state of knowledge in the literature related to the project topic); 2) clearly defined Objectives of the Project; 3) Experimental section (a description of the initial hypotheses and the experiments used to test them, i.e., the overall concept of the experiments, materials, methodological approaches, and results, including relevant figures and tables); 4) Discussion; 5) Summary/Conclusions. These parts may be titled and subdivided appropriately according to the nature of the doctoral project and in accordance with faculty regulations. Certain modifications to the structure (e.g., combining the Experimental section and Discussion in the case of bioinformatics theses) are allowed but must be consulted in advance with the programme guarantor.

The thesis may be written as a traditional monograph, or original scientific publications by the doctoral student (related to the topic of the doctoral project, produced during the doctoral study, and by the time of submission already published, accepted for publication, or under peer review in an impact-factor journal with proof of acceptance or ongoing review) may be incorporated into the Experimental section (thus replacing parts of the results and materials/methodological approaches). Only publications in which the doctoral student made a substantial contribution should be included. For each included publication, the student must provide a concise (1-2 pages) summary of the results and conclusions presented in the paper and explain how it relates to the main topic of the doctoral project. This summary must also contain a clear and detailed statement of the student’s contribution to obtaining the results and preparing the manuscript.

If multiple publications are included, they must form a logical sequence and be linked by the student’s original text, explaining their interrelations and placing them in the overall context of the doctoral project. It is not acceptable simply to insert publications without such explanatory or connecting text. Nor is it appropriate to include publications that are only marginally related to the project and with each other, giving the thesis an incoherent character.

All as-yet unpublished experiments by the doctoral student relevant to the research problem and their results should be described in full in the Experimental section.

If doctoral students choose to incorporate their publication(s) into the thesis, this must be done either directly within the main text of the thesis or as the Supplementary section (with the full publication(s) attached). Merely citing links to websites where the publication(s) can be found is not allowed. Students are also responsible for ensuring that the publication(s) or their manuscripts are presented in the thesis in a manner consistent with the license terms of the relevant publisher or the journal where the manuscript is under review.

Including publications in the thesis can never substitute for the Theoretical introduction or the overall Discussion of the results. The text in these sections must not be copied (or translated) directly from the student’s publications or other sources; it must be an original text by the student. In the Discussion, it is not sufficient merely to summarize results - the students must provide a full-fledged discussion of the topic in an appropriately broad context, offering their own possible explanations of observed phenomena and comparing their findings with relevant publications, including both supporting and potentially contradictory results.

The thesis may be submitted in Czech, Slovak, or English (English is particularly recommended).

The Subject Area Board does not require the preparation and submission of a separate „Summary of the Ph.D. Thesis“ unless explicitly required by faculty regulations.

Detailed information on the course of SDZ and requirements for doctoral students can be found here.

Important Information, Dates, Rules and Documents here.

Further information regarding the DSP Molecular and Cellular Biology, Genetics, and Virology program is available here.