Genomics and Proteomics program
National Centre for Biomolecular Research
Guarantor: Assoc. Prof. Jan Paleček, PhD, jpalecek@sci.muni.cz, room C02-214
FGP seminar – 12th of September 2022
(seminar for supervisors in October)1
Evaluation of Science & PhD at SCI MUNI – September 20222
I will talk about:
̶ Our program basics and specifics
̶ board, statistics, roadmap, deadlines,
̶ Thesis advisory committee (TAC)
̶ state exam, thesis defense
̶ awards
̶ University level
̶ Info hubs
̶ MUNI PhD news
GenPro PhD program Scientific board
Assoc. Prof. Jan Palecek, Ph.D. (Chair)
Prof. RNDr. Jiří Fajkus, CSc (Vicechair)
Prof. Mgr. Martin Lysák, Ph.D., DSc.
Prof. RNDr. Zbyněk Zdráhal, Dr.
Assoc. Prof. Mgr. Miloslava Fojtová, CSc.
Assoc. Prof. RNDr. Lenka Fajkusová, CSc.
Assoc. Prof. Jan Hejátko, Ph.D.
Assoc. Prof. Jan Havliš, Dr.
Assoc. Prof. Miroslav Fojta, CSc.
Assoc. Prof. Ctirad Hofr, Ph.D.
External members
Assoc. Prof. Eduard Kejnovský, CSc. (Inst. of Biophysics, ASCR, Brno)
RNDr. Roman Hobza, Ph.D. (Inst. of Biophysics, ASCR, Brno)
Prof. Mgr. Marek Šebela, Ph.D. (Palacky University, Olomouc)
Assoc. Prof. RNDr. Petr Pečinka, CSc. (University of Ostrava)
Objectives:The aim of the Genomics and
Proteomics program is to train top class
specialists in these subjects …
… under the supervision of highly
experienced researchers/supervisors.
Statistics
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Degree programme
Number
of
current
students*
Biomolecular Chemistry and Bioinformatics 32
Animal Physiology, Immunology and
Developmental Biology
41
Mathematics and Statistics 49
Biochemistry 40
Geology 53
Ecological and Evolutionary Biology 57
Molecular and Cell Biology and Genetics 65
Genomics and Proteomics 63
Environmental Health Sciences 69
Chemistry 69
Life Sciences 70
Physics 73
Total 784
~10 in/~10 out
4+1 is standard
Drop rate ~25%
As PhD you should:
• understand theories, concepts, and methods that represent
current trends in Genomics and Proteomics field … become
independent expert
• independently design and conduct research in all its stages
• interpret research outcomes and present them at international
conferences
• write a research paper and publish it in an impacted international
scientific journal
• be competitive at job market (e.g. as postdoctoral fellow in a
foreign laboratory)
• supervise students … to once become a science leader5
Studies roadmap – Mandatory duties
6
• (FGP) seminars during whole regular study (not in combined study)
• Semesters 1-4 (first 2 years of study) - research project + theoretical courses,
preparing for state doctoral exam and project topics
• Semesters 5 + – main focus on research project
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FGP seminar
̶ Every 1st lecture in Autumn semester dedicated to program
updates
̶ FGP seminar serves to PhD students (NCBR-FGP group, 7th and
8th year students, those outside MU etc.)
̶ 2 students only – presentation skills training, project overviews …
(20 minutes, intro, results, major conclusions – as for PhD defense)
̶ Those registered but having their own seminar platform – talk to
prof. Fajkus (send him PPT from your seminar presebtation)
Milestones and deadlines
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1. 6. 2022 – 20. 9. 2022 Student’s semestral plan
15. 6. 2022 – 30. 9. 2022 Supervisor approves
1. 9. 2022 – 7. 10. 2022 Scientific board/chair approves
1. 12. 2022 – 31. 1. 2023 Student’s feedback
15. 12. 2022 – 15. 2. 2023 Supervisor evaluates
Anytime Scientific board/chair evaluates
• Research project plan – 1st year
(max 1 page describing background, objectives, methods, and timeline).
• State Doctoral Exam (SDE/SDZ) – 2nd to 4th year (award)
• Thesis defense – 4th to 5th year (award) = standard time (4+1)
or later … extended = 8+1 (9th year only exceptions – dean must approve)
I am watching you ;-)
Introducing TAC!!
Supervisor guides you best
9
Thesis Advisory Committee (TAC)
̶ Scientific board decided to implement TAC in December 2021 to help students to:
̶ 1st year: set up your doctoral project plan (1 meeting during 1st year)
̶ 4th/5th year: get your thesis finished in the standard study time of 4+1 years
(1 meeting before the end of 4th year or beginning of 5th year)
̶ 6th year: get your thesis finished as soon as possible (1 meeting during 6th year)
̶ TAC extended by 1 member of the Scientific board
̶ 7th/8th year: get your thesis finished as soon as possible (meeting every semester)
̶ mediate disagreements between students and supervisors … (you can organize TAC
anytime you need)
student + supervisor + 2 independent scientists
State Doctoral Exam (SDE)
• prove student's professional orientation in the following areas
• prove sufficient general knowledge in the field studied and indepth
knowledge in areas related to the Ph.D. thesis
Areas:
Example:
• 5 min PPT and questions from (~7) committee members
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Genomics and molecular biology
Proteomics and structural biochemistry
Methods in genomics or proteomics
Hormonal regulation
Posttranscriptional regulation
Primary sequence analysis
Thesis defense
• student must be the first author on at least one publication (WoS
IF above the subject median)
• student’s contribution must be stated
• If the student co-authored at least 3 papers - comprehensive
introduction and commentary on papers
• If there are less than 3 publications - monography.
Defense: supervisor introduces student, student gives 20 min
lecture on major results/achievments, reviewers report and discuss
SDE and defense applications via IS (Iva Klimova)
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Awards
̶ NCBR director (continually):
̶ SDE in time (2nd to 4th year) – 5000CZK
̶ Defense in time before the end of 5th year – 10000CZK
̶ Poster presentation, oral presentation
̶ dean (deadlines)
̶ Best student in doctoral program
̶ vicerector (deadlines)
̶ Excelent results in doctoral studies
̶ rector (deadlines)
̶ Best student in doctoral program
̶ Outstanding Doctoral Thesis
New MUNI PhD standards – since 2021
https://portal.muni.cz/  Research
https://is.muni.cz/auth/do/mu/Uredni_deska/Predpisy_MU/Masarykova_univerzita/Ostatni_doku
menty/Metodika/odbor_vyzkumu/metodicky_list_c_1_2021_zasady_a_doporuceni_pro_efektivni_a_kvalitni_doktorske_s/
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NEWS:
MUNI MENDEL DOCTORANDUS programme
https://mendel200.muni.cz/en
Setting higher PhD
standards at MUNI
- Kick off 14/9/2022
- https://mmd.muni.cz
- Coordinated by SCI
MUNI
- Guaranteed minimum
income of students
- Focus on
interdisciplinary and soft
skill trainings
- European Doctorate
standards
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On-site visit programme – Chemistry (1st day)
Thursday 15-09-2022, University Campus MU, Brno-Bohunice, room 432/B17
14 –14.20 Welcome, introduction of MU and the Faculty of Science, evaluation panel, programme
14.20–15 Presentation of the National Centre for Biomolecular Research and its research areas
15–15.40 Presentation of the Department of Chemistry and its research areas
15.40–16 Coffee break
16–16.40 Presentation of the Department of Biochemistry and its research areas
16.50–17.20
Meeting with PhD students of Biomolecular chemistry and bioinformatics,
Genomics and proteomics, Life Sciences
17.25–17.55 Meeting with PhD students of Analytical geochemist, Chemistry
18–18.30 Meeting with PhD students of Bioanalytical chemistry, Biochemistry
19.30 Joint dinner
Information hub for PhD students
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https://www.sci.muni.cz/en/students/phd  Research