Education

Pre- and postgraduate courses

photo of students in the labThe 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).

 

"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

 

  • 2nd 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.
  • 25th 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
  • 1st 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.
  • 19th 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).

 

 

  •  30th 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.

  • 6th 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.

  • 9th 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

  • 15th 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.

  • 14th 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.

  • 10th 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

 

 

 

 

 

 

 

 

  • 12th 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.
  • 20th Sept. 2018, Aiste Aleliunaite defended her PhD thesis: “Cellular response to site-specific replication blocks in mammalian cells”. Supervisor: Prof. Ian Hickson.
  • 25th Jun. 2018, Ireen Kooij passed her bachelor project: "Identification of Candidate Gene(s) Whose Mutation Predisposes to Radiation Sensitivity”.  Supervisor: Asso. Prof. Ying Liu. 
  • 10th 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.

 

 

 

 

  • 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.