Group picture, September 2019
Anthony Mathelier, PhD – Group leader
email@example.com; @AMathelier; office: (+47) 228-40-561
Mailing address: NCMM, P.O. Box 1137 Blindern, 0318 Oslo, Norway
Anthony Mathelier is a computer scientist by background who completed his PhD under the supervision of Dr. Alessandra Carbone at the University Pierre and Marie Curie, Paris, France, in 2010. His PhD research aimed at the development of computational tools to predict miRNAs in eukaryotes. He joined Dr. Wyeth Wasserman in 2011 at the University of British Columbia, Vancouver, Canada, as a postdoctoral fellow. He became the deputy group leader in Dr. Wasserman lab in 2013. He focused on gene regulation at the transcriptional level during his postdoc. In particular, understanding how transcription factors (TFs) bind in a sequence specific manner to the DNA and how the alteration of transcriptional regulation contributes to cancer. He is the group leader of the Computational Biology & Gene Regulation team at the Centre for Molecular Medicine Norway, part of the Nordic EMBL partnership, since May 2016.
Jaime Castro-Mondragon, PhD – Postdoctoral fellow
Jaime Castro-Mondragòn completed his PhD in Bioinformatics under the supervision of Dr. Jacques van Helden at the Aix-Marseille Université, Marseille, France, in 2017. His PhD work was mainly focused on the development of tools to analyze Transcription Factor Binding Motifs, mainly on the clustering of motifs to reduce motif redundancy and to group TF motifs from the same TF Families. He is interested in gene expression regulation, computational biology, and data visualization. His current project is focused on finding mutations altering miRNA expression on diseases, for example, cancer. He joined the lab as a Postdoctoral fellow on October 2017.
Roza Berhanu Lemma, PhD – Postdoctoral fellow
Roza Berhanu Lemma completed her PhD in molecular biology from the Department of Biosciences, University of Oslo, under the supervision of Prof. Odd Stokke Gabrielsen in Dec. 2018. Her PhD thesis is entitled ‘Novel mechanisms controlling the interplay between SUMOylation, chromatin remodelling and transcription — A study of the functional interaction between the SUMO-protease SENP1, the chromatin remodeler CHD3 and the pioneer transcription factor c-Myb’. Although Roza is a molecular biologist by training, she developed an increasing interest in bioinformatics and computational biology. As a result, she joined the group in Jan. 2019. She is interested in transcriptional regulation and dysregulation, epigenetics, and their implications in cancer. Her current project is on the interplay between DNA methylation and TF-binding.
Vipin Kumar, PhD – Postdoctoral fellow
Vipin Kumar completed his PhD in Bioinformatics under the supervision of Pr. Albin Sandelin and Dr. Yuichi Taniguchi as part of a joint program between the University of Copenhagen, Denmark and the RIKEN BDR center in Osaka, Japan, in 2019. His PhD work was mainly focused on the development of algorithms to analyze Hi-C sequencing data, mainly to delineate of chromatin structures through clustering. He is interested in the articulation of multiple omics technologies to better grasp the progression of genomic processes. His current work is focused on characterizing the functional role played by low-affinity transcription factors binding sites through the integration of Hi-C data with more conventional TFBS analysis.
Rafael Riudavets Puig – PhD student
Rafael Riudavets Puig studied a Bachelor in Biomedicine at the University of Barcelona followed by a Master in Bioinformatics and Biostatistics at the Open University of Catalunya. The title of his Master thesis was “Identification of highly altered genes in Breast Cancer Patients through the integration of multiple omics data”. The objective of this thesis was to identify genes showing DNA mutations and/or Copy Number Alterations, Hyper/Hypomethylations and Over/underexpression when comparing paired Tumor vs Normal Breast Cancer samples from The Cancer Genome Atlas. This would be followed by integration of gene alterations together with pathway information to also identify highly altered pathways. Rafael joined the lab in August 2019 as a PhD candidate.
Ieva Rauluseviciute – PhD student
Ieva has a BSc in Genetics from Vilnius University, Lithuania and MSc in Molecular medicine from NTNU, Trondheim, Norway. Her MSc thesis entitled “Computational analysis of DNA methylation and gene expression patterns in prostate cancer” focused on non-canonical DNA methylation and gene expression patterns. Ieva joined the lab in April 2020 as a PhD candidate.
Katalin Ferenc – PhD student
Kata has a BSc in Biology from the Eotvos Lorand University of Budapest (Hungary) and a MSc in Biomedicine from Karolinska Institute (Sweden). Her thesis was titled “Investigating the intersection of double strand breaks and mutational processes in ovarian cancer”. To gain a deeper understanding of data analysis methods, she completed a MSc in Applied Data Science from the University of Gothenburg (Sweden). Her second thesis was titled “Computational analysis and data mining of drug-induced transcriptional changes”, focusing on building a toxicity prediction model and exploring the scope of the DRUG-seq method. To follow her original interest in cancer genetics and epigenetics, Kata joined the lab in August 2021 as a PhD candidate.
Hallvard Wæhler – PhD student
Hallvard has a Master degree in molecular biology from the University of Oslo. The title of his thesis was “Investigating the Effects of Paracetamol on Neuronal Differentiation using High Throughput Imaging and Analysis”. This project focused on tool development for analysis from high-throughput imaging experiments. Today Hallvard is a PhD-student supervised by Ragnhild Eskeland and co-supervised by Anthony Mathelier and Sigve Nakken in a project focusing on retrotransposable elements and non-coding RNA in disease and development.
Paul Boddie – Software developer
Paul is a software developer with a Bachelor (Honours) degree in Computer Science from Heriot-Watt University, Edinburgh, Scotland. He has worked in a range of organisations and previously spent several years at the Biotechnology Centre at the University of Oslo, having positions in the Donaldson (bioinformatics) and Thiede (proteomics) groups, where he worked on biomedical literature text mining and more generally on database, application and tool development.
Peter Arnesen – Master student
Peter Arnesen is a Master student from the Faculty of Mathematics and Natural Science at the University of Oslo. Peter is working on using topic modeling and deep learning methods to study DNA methylation in cancer patients.
- Aziz Khan – Postdoctoral fellow (2016-2019), then research scientist in Christina Curtis’ lab, Stanford Cancer Institute, Stanford University, USA
- Marius Gheorghe – PhD student (2016-2019), then senior bioinformatician at NEC OncoImmunity, Oslo, Norway
- Solveig Klokkerud – Master student (2019-2020), then engineer at the Institute for Cancer Research, Oslo, Norway.
- Timothée Launay – Master student (2020), then continued his Master studies.
- Kübra Altinel – Master student (2017-2018), then PhD student at the University of Copenhagen, Denmark.
- Arnaud Stigliani – visiting PhD student (2017), PhD student at the CEA, Grenoble, France.
- Victor Laigle – Master student (2017), then continued his Master studies.
- Eleftherios Pavlos – Master student (2016-2017)