The aim of studying and bibliography

The main aim of study: Gain knowledge and skills in computer-aided analysis of the genome

The general information about the module: The module is realized in the form of lectures (15 h) and problem exercises in computer laboratory (30 h)

Teaching materials: Materiały dydaktyczne dostepne on-line w portalu ZICh PRz oraz www.e-chemia.pl

Bibliography required to complete the module

Bibliography used during lectures

1	T. Stubblebine	Wyrażenia regularne. Leksykon kieszonkowy	Helion.	2008
2	R. L. Schwartz, T. Phoenix, B. d foy	Perl. Wprowadzenie	Helion.	2006
3	B.Dębska, G.Fic	Konspekty do wykładów opublikowane na stronie Zakładu Informatyki Chemicznej	ZICh PRz.	2012

Bibliography used during classes/laboratories/others

1

B. Dębska, G. Fic

Bioinformatyka w analizie genomu. Instrukcje do ćwiczeń laboratoryjnych

ZICh PRz.

2012

Bibliography to self-study

1	A. D. Baxevanis, B. F. F. Ouellette	Bioinformatyka . Podręcznik do analizy genów i białek	PWN Warszawa.	2004
2	P. G. Higgs, T. K. Attwood	Bioinformatyka i ewolucja molekularna	PWN Warszawa.	2008
3	J.Xiong	Podstawy bioinformatyki	Wydawnictwa Uniwersytetu Warszawskiego.	2009

Basic requirements in category knowledge/skills/social competences

Formal requirements:

Basic requirements in category knowledge: basic knowledge of organic chemistry, molecular biology

Basic requirements in category skills: computer skills - Windows

Basic requirements in category social competences: Ability to work individually and in a team of 2-3 persons.

Module outcomes

MEK	The student who completed the module	Types of classes / teaching methods leading to achieving a given outcome of teaching	Methods of verifying every mentioned outcome of teaching	Relationships with KEK	Relationships with PRK
01	can test and modify computer programs in Perl to solve simple problems in molecular biology and biotechnology	lecture, laboratory	test, observation of the task performance, project report,	K_W02++ K_W06+ K_U07++	P7S_UW P7S_WG
02	knows the basics of programming in Perl	lecture, laboratory	written exam, test, observation of the task performance, project report	K_W02++ K_U07++	P7S_UW P7S_WG
03	is able to use specialized computer programs for searching and for analysis of sequential information.	laboratory	test, observation of the task performance, project report	K_W02++ K_W06++ K_U01+ K_U07++	P7S_UW P7S_WG
04	can use the selected artificial intelligence methods to support engineering tasks and scientific research in the field of molecular biology and biotechnology	lecture, laboratory	test, written report	K_W02+++ K_W06+ K_U07++	P7S_UW P7S_WG
05	is able to visualize complex 3D models of protein systems - DNA / RNA	laboratory, laboratory at which the student solves the problems	yest, written report	K_W02+ K_W06+ K_U07++	P7S_UW P7S_WG
06	knows the computer programs for creation of phylogenetic trees	lecture, laboratory	written exam, test, written report	K_W02++ K_W06+ K_U07++	P7S_UW P7S_WG

Attention: Depending on the epidemic situation, verification of the achieved learning outcomes specified in the study program, in particular credits and examinations at the end of specific classes, can be implemented remotely (real-time meetings).

The syllabus of the module

Sem.	TK	The content	realized in	MEK
2	TK01	Artificial intelligence techniques for computer-assisted diagnosis genome. Artificial neural networks	W01	MEK04
2	TK02	Graph theory and decision trees. Methods of presentation and interpretation of decision trees. Methods for generating phylogenetic trees	W02	MEK04 MEK06
2	TK03	Application of hidden Markov model to searching similarities between sequences of genomes. Sequence matching algorithms	W03-W04	MEK03 MEK04
2	TK04	Beginner’s introduction to PERL Programming Language	W05-W06	MEK01 MEK02
2	TK05	Regular expression and their application in bioinformatics	W07	MEK01
2	TK06	Genetic and physical maps	L03	MEK03
2	TK07	Searching similarities between genomes sequences	L01	MEK03
2	TK08	Construction of philogenetic trees	L02	MEK06
2	TK09	Gene prediction	L09	MEK03 MEK04
2	TK10	Analysis and visualisation of DNA-protein complexes in restriction and ligation processes	L10	MEK05
2	TK11	PERL programming language in genome analysis	L05-L08	MEK01 MEK02 MEK04
2	TK12	Sequence assembly	L04	MEK03

The student's effort

The type of classes	The work before classes	The participation in classes	The work after classes
Lecture (sem. 2)		contact hours: 15.00 hours/sem.	complementing/reading through notes: 2.00 hours/sem. Studying the recommended bibliography: 2.00 hours/sem.
Laboratory (sem. 2)	The preparation for a Laboratory: 8.00 hours/sem. The preparation for a test: 10.00 hours/sem.	contact hours: 30.00 hours/sem.	Finishing/Making the report: 5.00 hours/sem.
Advice (sem. 2)		The participation in Advice: 2.00 hours/sem.
Credit (sem. 2)	The preparation for a Credit: 10.00 hours/sem.	The written credit: 2.00 hours/sem.

The way of giving the component module grades and the final grade

The type of classes	The way of giving the final grade
Lecture
Laboratory	Credit all the laboratory (test, execution of exercises, report)
The final grade	Final grade (K): K= 0.5w L +0.5wW, L- positive evaluation of the lab; W - positive evaluation of the lecture, w - factor related to the time of credit, w= 1,0 first term, w = 0,9 second term , w = 0,8 third term.

Sample problems

Required during the exam/when receiving the credit
(-)

Realized during classes/laboratories/projects
(-)

Others
(-)

Can a student use any teaching aids during the exam/when receiving the credit : no

The contents of the module are associated with the research profile: yes

1	B. Bakera; M. Rakoczy-Trojanowska; M. Szeliga; M. Święcicka; M. Tyrka	Identification of candidate genes responsible for chasmogamy in wheat	2023
2	P. Bednarek; A. Dorczyk; T. Drzazga; D. Jasińska; P. Krajewski; B. Ługowska; R. Martofel; P. Matysik; M. Niewińska; D. Ratajczak; K. Rączka; T. Sikora; D. Tyrka; M. Tyrka; E. Witkowski; U. Woźna-Pawlak	Genome-wide association mapping in elite winter wheat breeding for yield improvement	2023
3	M. Dyda; G. Gołębiowska; M. Rapacz; M. Szechyńska-Hebda; M. Tyrka; I. Wąsek; M. Wędzony	Quantitative trait loci and candidate genes associated with freezing tolerance of winter triticale (× Triticosecale Wittmack)	2022
4	M. Dyda; G. Gołębiowska; M. Rapacz; M. Tyrka; M. Wędzony	Genetic mapping of adult-plant resistance genes to powdery mildew in triticale	2022
5	M. Dyda; G. Gołębiowska; M. Rapacz; M. Tyrka; M. Wędzony	Mapping of QTL and candidate genes associated with powdery mildew resistance in triticale (× Triticosecale Wittm.)	2022
6	P. Krajewski; R. Marcinkowski; R. Martofel; P. Matysik; M. Mokrzycka; M. Rakoczy-Trojanowska; M. Rokicki; S. Stojałowski; M. Tyrka; U. Woźna-Pawlak; B. Żmijewska	Genome-Wide Association Analysis for Hybrid Breeding in Wheat	2022
7	A. Pietrusińska; M. Tyrka	Linkage of Lr55 wheat leaf rust resistance gene with microsatellite and DArT-based markers	2021
8	B. Bakera; P. Krajewski; M. Mokrzycka; M. Rakoczy-Trojanowska; M. Szeliga; M. Święcicka; M. Tyrka	Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses	2021
9	B. Bakera; P. Krajewski; P. Matysik; M. Mokrzycka; M. Rakoczy-Trojanowska; M. Rokicki; S. Stojałowski; M. Szeliga; D. Tyrka; M. Tyrka	Evaluation of genetic structure in European wheat cultivars and advanced breeding lines using high-density genotyping-by-sequencing approach	2021
10	J. Buczkowicz; T. Drzazga; B. Ługowska; P. Matysik; K. Rubrycki; M. Semik; D. Tyrka; M. Tyrka; E. Witkowski	Identyfikacja efektywnych genów odporności na wybrane choroby wirusowe i grzybowe pszenicy zwyczajnej	2021
11	J. Buczkowicz; T. Drzazga; G. Fic; M. Jaromin; P. Krajewski; P. Matysik; R. Mazur; P. Milczarski; T. Sikora; M. Szeliga; D. Tyrka; M. Tyrka; E. Witkowski	Selekcja genomowa pszenicy ozimej	2021
12	E. Ciszkowicz; E. Kaznowska; P. Porzycki; M. Semik; M. Tyrka	MiR-93/miR-375: Diagnostic Potential, Aggressiveness Correlation and Common Target Genes in Prostate Cancer	2020
13	G. Czajowski; M. Karbarz; M. Pojmaj; A. Strzembicka; D. Tyrka; M. Tyrka; A. Wardyńska; M. Wędzony	Quantitative trait loci mapping of adult-plant resistance to powdery mildew in triticale	2020
14	J. Ciura; M. Szeliga; M. Tyrka	Representational Difference Analysis of Transcripts Involved in Jervine Biosynthesis	2020
15	J. Ciura; M. Grzesik; M. Szeliga; M. Tyrka	Identification of candidate genes involved in steroidal alkaloids biosynthesis in organ-specific transcriptomes of Veratrum nigrum L.	2019
16	M. Dyda; M. Szechyńska-Hebda; M. Tyrka; I. Wąsek; M. Wędzony	Local and systemic regulation of PSII efficiency in triticale infected by the hemibiotrophic pathogen Microdochium nivale	2019
17	M. Dziurka; K. Hura; T. Hura; A. Ostrowska; M. Tyrka	Participation of Wheat and Rye Genome in Drought Induced Senescence in Winter Triticale (X Triticosecale Wittm.)	2019
18	Z. Banaszak; A. Fiust; Z. Nita; W. Orłowska-Job; M. Pojmaj; M. Rapacz; M. Tyrka; M. Wójcik-Jagła	Sposób selekcji mrozoodpornych genotypów jęczmienia ozimego	2019