Education

Pre- and postgraduate courses

photo of students in the lab The CCS aims to provide a dynamic and friendly research environment for students at various levels both within our dedicated laboratories and on our university courses.

The CCS group leaders, postdocs and PhD students are participating in teaching on courses including: Molecular Biology, Medical Cell and Tissue Biology (Block D), Medical Genetics, Human Genetics, Molecular biology and Genetics , Advanced Live Cell Imaging, Reproductive Biology Course, and regular teaching seminars in genomics for embryologists (Region H).

Courses provided by CCS members

"Analysis of genome-wide enrichment data"

(PhD course; supervised and lectured by Mads Lerdrup)

A wealth of new methods based on high-throughput sequencing of enriched DNA or RNA subpopulations have been developed. These new capabilities have transformed the focus from one or a few genomic loci to more abstract and genome-wide system-level interpretations. ChIP-seq, ChIP-exo, Cut&Run, Cut&Tag, ATAC-seq, Repli-seq, MiDAS-seq, and many similar methods have been applied in thousands of studies of functional properties, such as chromatin accessibility, DNA replication, replication stress, and DNA-repair pathways as well as transcriptional regulation in normal development and many diseases.

This course will enable attendees to perform their own processing, analysis, and interpretation of such data. The emphasis will be on step-wise expansion of capabilities through hands-on exercises, with the end goal being that attendees autonomously can reproduce published figures from deposited raw data. In addition, the course will provide a theoretical background understanding of data structures, workflows, visualization, and limitations as well as present real-life use cases where these types of analyses have been the core of scientific studies.

More details of this course could be found at: https://phdcourses.ku.dk/DetailKursus.aspx?id=110329&sitepath=SUND

Bachelor project, MSc and PhD defenses

2024

28^th June 2024, Veronika Baráth, will defend her PhD thesis “Visualization and Characterization of Loop Extrusion Activity by PICH Using Optical Tweezers”. Main supervisor: Prof. Ian D. Hickson. Co-supervisor: Asso. Prof. Héctor Herranz Muñoz.
23^rd April 2024, Ernest Lim, defended his PhD thesis “Characterising the Organismal Role of ZGRF1 in Mus Musculus”. Main supervisor: Prof. Michael Lisby. Co-supervisor: CCS affiliated Asso. Prof. Andrés López-Contreras.
22^nd March 2024, Yiqing Wang, defended her PhD thesis ’’Towards defining the essential role of mammalian Topoisomerase IIIα’’. Main supervisor: Prof. Ian David Hickson. Co-supervisors: Asso. Prof. Anna Hélène Bizard, CCS affiliated Asso. Prof. Andrés López-Contreras.
6^th February 2024, Szymon Aleksander Barwacz, defended his PhD thesis “Analysis of factors contributing to mitotic DNA synthesis”. Main supervisor: Prof. Ying Liu. Co-supervisor: Prof. Michael Lisby.

2023

2^nd October 2023, Judith Bello Rodríguez, defended her PhD thesis “Identification of mechanisms that affect aneuploidy in human oocytes”. Main supervisor: Prof. Eva R. Hoffmann. Co-supervisors: Prof. Jakob Nilsson, Asso. Prof. Anna Hélène Bizard and Assi. Prof. Jennifer Rose Gruhn.
25^th September 2023, Daniela Alosi, defended her PhD thesis “Chromosome instability at fragile sites in human cells”. Main supervisor: Prof. Ian Hickson. Co-supervisors: Asso. Profs Thomas Bentin & Anna Hélène Bizard
1^st August. 2023, Ajuna Azad, defended her PhD thesis “Transcriptomic analysis of human female germ cells to investigate factors governing genomic instability and reproductive ageing in women”. Main supervisor: Prof. Eva Ran Hoffmann. Co-supervisor: Asso. Prof. Mads Lerdrup.
19^th Jun. 2023, Marina Stenbek passed her master thesis: “Establishment of an advanced protocol for generation of fetal ovarian somatic cell-like cells (FOSLC) for in vitro gametogenesis”. Main supervisor: Michael Lisby (SCIENCE). Co-supervisor: Dr. Jason Alexander Halliwell (SUND).

2022

30^th Sept. 2022, Gijs Zonderland, defended his PhD thesis “Exploring a new role of the TRESLIN-MTBP complex in cell cycle control”. Main supervisor: Asso. Prof. Luis Ignacio Toledo Lazaro. Co-supervisor: Prof. Jiri Lukas.
6^th Sept. 2022, Sampath Amitash Gadi, defended his PhD thesis “Analysis of DNA replication in human cells: Revisiting origin firing and the replisome”. Main supervisor: Asso. Prof. Luis Ignacio Toledo Lazaro. Co-supervisor: Asso. Prof. Julien Duxin.
9^th Aug. 2022, Jazib Hussein defended his PhD thesis “DNA damage as a molecular timer for reproductive lifespan in women”. Main supervisor: Prof. Eva Ran Hoffmann. Co-supervisor: affiliated researcher Andres Joaquin Lopez Contreras
15^th Jun. 2022, Thomas René Simonsen passed his bachelor thesis: “The role of PARP1 in early germ cell differentiation”. Main supervisor: Prof. Eva R. Hoffmann. Co-supervisor: Dr. Jason Alexander Halliwell.
14^th Jun. 2022, Lea Jerman-Plesec passed her master thesis: “Analysis of whole chromosome aneuploidies in human preimplantation embryos”. Main supervisor: Prof. Eva R. Hoffmann. Co-supervisor: Dr. Ivan Vogel.
10^th Jun. 2022, Philipp Harald Richter defended his PhD thesis “DNA double strand break end-resection factors play an essential role in mitotic DNA synthesis in human cells”. Main supervisor: Asso. Prof. Ying Liu. Co-supervisor: Prof. Ian D. Hickson

2021

26^th Feb. 2021, David Pladevall-Morera defended his PhD thesis “Exploring the role of ATRX in genome stability and cancer”. Main supervisor: Asso. Prof. Andres Lopez-Contreras. Co-supervisor: Prof. Simon Bekker-Jensen.
12^th Feb. 2021, Joaquim Ollé López passed his master thesis: “Single-cell RNAseq analysis of human oocytes”. Supervisors: Prof. Eva R. Hoffmann (SUND) and Prof Prof. Michael Lisby (SCIENCE).
11^th Feb. 2021, Indre Pauraite passed her master thesis: “Understanding how Treslin controls cell cycle progression in mammalian cells”. Supervisor: Asso. Prof. Luis Ignacio Toledo Lazaro.

2020

29^th Oct. 2020, Marisa Maria Goncalves Dinis passed her master thesis: “The Identification Of Proteins Facilitating The Replication At FRAXA, A Locus Affected By Folate Deficiency”. Main Supervisor: Asso. Prof. Ying Liu. Co-supervisor: Dr. Lorenza Garribba.
28^th Sept. 2020, Andreas Ingham passed his master thesis: “Identification of novel regulators of Common Fragile Site (CFS) stability”. Main Supervisor: Asso. Prof. Andres J Lopez-Contreras. Co-supervisor: David Pladevall-Morera.

2019

2^nd Dec. 2019, Divya Achuthankutty defended her PhD thesis: “Dissecting replication stress signaling: New regulatory mechanisms and experimental approaches”. Main supervisor: Prof. Niels Mailand. Co- supervisor: Prof. Ian Hickson.
21^st Nov. 2019, Andrés José Bueno Venegas defended his PhD thesis: “Towards Defining the Essential Role of the SMC5/6 Complex in Human Cells”. Supervisor: Prof. Ian Hickson.
29^th Aug. 2019, Karina Gaardahl passed her master thesis: “Investigating functional interactions between BRCA1 and RASAL2 in breast cancer cell lines”. Main Supervisor: Asso. Prof. Andres J Lopez-Contreras. Co-supervisor: Dr. Eliene Albers.
30^th Aug. 2019, Smaragdi Kompocholi passed her master thesis: “Further unravelling the role of ZGRF1”. Supervisor: Prof. Michael Lisby
14^th Aug. 2019, Keerthana Stine Viswalingam passed her maser thesis: “Characterization and Epistasis Analysis of a Novel Human Helicase ZGRF”. Supervisor: Prof. Michael Lisby
4^th Jul. 2019, Lorenza Garribba defended her PhD thesis: “Analysis of folate deficiency-induced genome instability in human cells”. Main Supervisor: Asso. Prof. Ying Liu. Co-supervisor: Prof. Ian Hickson.
28^th Jun. 2019,
26^th Jun. 2019, Ditte Marie Storm passed her bachelor project: "The effect of Topoisomerase II inhibition in chromosome stability”. Supervisor: Prof. Eva Hoffmann.
21^st May 2019, Wei Wu defended his PhD thesis: “RTEL1 resolves conflicts between DNA replication and Transcription”. Main Supervisor: Asso. Prof. Ying Liu. Co-supervisor: Prof. Ian Hickson
29^th Mar. 2019, Eliene Albers defended her PhD thesis: “Generation and characterization of a PICH deficient mouse model.” Main Supervisor: Asso. Prof. Andres J Lopez-Contreras. Co-supervisor: Prof. Ian Hickson
21^st Mar. 2019, André Brannvoll defended his PhD thesis: “Guardians of the genome”. Main Supervisor: Prof. Michael Lisby. Co-supervisors: Asso. Profs Hocine W. Mankouri and Andrés López-Contreras.

2018

12^th Dec. 2018, Amruta Shrikhande defended her PhD thesis: "Understanding the regulation of endogenous mutagenesis”.(Brighton, University of Sussex) Main supervisor: Prof. Eva Hoffmann. Co-supervisor: Dr Francis Pearl.
20^th Sept. 2018, Aiste Aleliunaite defended her PhD thesis: “Cellular response to site-specific replication blocks in mammalian cells”. Supervisor: Prof. Ian Hickson.
25^th Jun. 2018, Ireen Kooij passed her bachelor project: "Identification of Candidate Gene(s) Whose Mutation Predisposes to Radiation Sensitivity”. Supervisor: Asso. Prof. Ying Liu.
10^th May 2018, Robert Blanshard defended his PhD thesis: "An investigation of genome stability in human female meiosis by genome wide chromosome fingerprinting and copy number analysis”. (Brighton, University of Sussex) Main supervisor: Prof. Eva Hoffmann. Co-supervisor: Prof Tony Carr.
17th Apr. 2018, Signe Winther Jørgensen defended her PhD thesis "Analysis of DNA replication stress at a telomeric region". Main Supervisor: Prof. Ian David Hickson. Co-supervisor: Asso. Prof. Hocine William Mankouri.

2017

29^th Sept. 2017, Victoria Alexandra Bjerregaard defended her PhD thesis "Folate deficiency drives missegregation of the FRAXA locus". Main Supervisor: Asso. Prof. Ying Liu. Co-supervisor: Prof. Ian David Hickson.
13^th Sept. 2017, Özgun Özer defended her PhD thesis ”Telomere Instability in Human Cells - replication stress-induced mitotic DNA synthesis at difficult-to-replicate loci”. Main Supervisor: Prof. Ian David Hickson, Co-supervisors: Asso. Profs. Ying Liu, Hocine William Mankouri and Claus Storgaard Sørensen

2016

31st May 2016, Ganesha Pitchai, defended his PhD thesis "Biophysical and Structural Characterization of the Interaction Between PICH and BEND3". Main Supervisor: Prof. Ian Hickson. Co-supervisors: Dr. Werner W. Streicher and Prof. Guillermo Montoya.

2015

28^th Apr. 2015, Christian Friberg Nielsen, defended his PhD thesis "PICH Stimulates Topoisomerase IIa to Promote Sister Chromatid Disjunction in Mitosis” Main PhD supervisor: Prof. Ian Hickson. Co-supervisor: Asso. Prof. Ying Liu