SCIENTIFIC FOCUS AREAS

transcriptional regulation, enhancers, promoters, genomics, transcriptomics, machine learning, variant-to-function

RESEARCH VISION

The Andersson lab focuses on modeling gene regulation to gain insights into molecular mechanisms by which enhancer or promoter dysregulation contributes to disease risk.

We take an interdisciplinary approach and combine machine learning, statistical learning, genetics, and molecular biology to:

1. determine which noncoding sequences act as enhancers, which genes they regulate and in which cell types
2. learn how the human genome encodes regulatory activity
3. characterize the mechanisms that control gene expression variation

Learn more about our research (lab website), software (GitHub), or browse our publications (Google scholar).

Name:             Robin Andersson
Title:               Associate Professor of Computational Biology, PhD
Nationality:      Swedish
ORCID:           0000-0003-1516-879X
Lab website:    https://anderssonlab.org
Lab GitHub:     https://github.com/anderssonlab

SCIENTIFIC FOCUS AREAS

transcriptional regulation, enhancers, promoters, genomics, transcriptomics, machine learning, variant-to-function

EDUCATION

Nov 2010         Awarded PhD in Bioinformatics at the Linnaeus Centre for Bioinformatics, Uppsala University, Sweden. PhD supervisors: Prof. Jan Komorowski, Prof. Jan Dumanski and Prof. Claes Wadelius. Research focused on computational analyses of chromatin and chromosomal aberrations. PhD studies resulted in 18 publications in scientific journals.

Jun 2004          Awarded Master of Science in Computer Science, Institute of Technology, Linköping University, Sweden. Main study profile was theoretical Computer Science with a focus on Machine Learning.

CURRENT POSITIONS

Sep 2024 -        Associate professor (UCPH promotion programme to professor) at the Section for Computational and RNA Biology, Department of Biology, University of Copenhagen. The lab focuses on modeling gene regulation to gain insights into molecular mechanisms by which enhancer or promoter dysregulation contributes to disease risk.

2021 -              Visiting researcher at Broad Institute of MIT and Harvard, Cambridge, MA, USA

PREVIOUS POSITIONS

2020 – 2024     Associate professor at Department of Biology, University of Copenhagen, Denmark.

2015 – 2020     Tenure-track assistant professor at Department of Biology, University of Copenhagen, Denmark.

2010 – 2015     Postdoctoral research fellow at Department of Biology, University of Copenhagen, Denmark, in the group of Prof. Albin Sandelin. Research primarily focused on transcriptional regulation via enhancers and the biogenesis and decay of enhancer RNAs. Research resulted in 22 primary research publications in scientific journals.

2004                Research Assistant at The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden. Work mainly focused on development of a functional genomics toolkit for machine learning and creating a new undergraduate course in Artificial Intelligence for Bioinformatics.

AWARDS

2015                  ERC Horizon 2020 starting grant award

2016                  Sapere Aude Research leader award

2020                  Hallas-Møller Ascending Investigator award

SUPERVISION AND TEACHING

17 graduated MSc students and 5 graduated PhDs from the lab. Current group: 1 Assistant professor, 2 Postdocs, 3 PhD students, 1 lab technician.

2015 –              Lecturer – Genome Sequence Analysis, University of Copenhagen, Denmark. Course responsible since 2016.

2019 –              Lecturer – Advanced Bioinformatics for Next Generation Sequencing, University of Copenhagen, Denmark.

INSTITUTIONAL RESPONSIBILITIES

2022 –              PhD coordinator at the Department of Biology, University of Copenhagen, Denmark.

2018 – 2021     Member of BIO-SFU (chair as of September 2019), the strategic research board at the Department of Biology, University of Copenhagen, Denmark.

2017 – 2023     Representative of Section for Computational and RNA Biology in the Biocenter Office Committee at the Department of Biology, University of Copenhagen, Denmark.

REVIEWING ACTIVITIES

2016-2024       Member of 6 PhD assessment commitees in Denmark and Sweden.

2015-2024       External referee for H2020 European Research Council, French National Research Agency (ANR), Medical Research Council UK.

Referee for >30 manuscripts in scientific journals including: Nature Genetics, EMBO Journal, Genetics, Genome Biology, Bioinformatics, Nucleic Acids Research, Trends in Biochemical Sciences, Nature Communications, Genome Research, Transcription, RNA Biology, BioEssays, Oncogene.

MEMBERSHIPS OF SCIENTIFIC SOCIETIES

2021 –             Partner in the Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute (https://www.broadinstitute.org/nnfc), a Novo Nordisk Foundation bridgehead center between the Broad Institute and Danish researchers investigating the genetics and gene regulation of common complex diseases.

2020 –             Member of ENHPATHY (https://www.enhpathy.eu/), an ERC MCSA-ITN bringing together expertise on enhancer biology, epigenomics, bioinformatics and medical genetics to increase scientific knowledge on the molecular basis of human enhanceropathies and to open new diagniostic and therapeutic avenues for patients.

2015 –             Member of FANTOM5 and FANTOM6 consortia (https://fantom.gsc.riken.jp/), worldwide collaborative projects aiming at identifying all functional elements in mammalian genomes.

INVITED KEYNOTE TALKS AT SCIENTIFIC CONFERENCES

• ISMB/ECCB meeting (https://www.iscb.org/ismbeccb2019) in the Regulatory & Systems Genomics COSI (RegSys), Basel, Switzerland, July 22-23, 2019. Title: Insights into gene regulatory elements from transcription start site sequencing. YouTube video of the talk: https://youtu.be/4-6RtyqjqEo
• European Human Genetics Conference ESHG2021 (https://2021.eshg.org/programme-2021/), virtual, August 28-31, 2021. Title: Determinants of promoter and enhancer activities of regulatory elements.

GRANTS

• Novo Nordisk Foundation, Hallas-Møller Ascending Investigator (PI: Robin Andersson): 01/2021 – 12/2025, 10M DKK
  Functional and topological redundancies in transcriptional regulation. The aim of this project is to investigate the mechanisms underlying regulatory robustness.
• Novo Nordisk Foundation, Center grant (Coordinator: Todd Golub, Co-PI: Robin Andersson): 09/2021 – ongoing, beneficiary grant, 3.3M DKK
  Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute. A Novo Nordisk Foundation bridgehead center (https://www.broadinstitute.org/nnfc) between the Broad Institute and Danish researchers investigating the genetics and gene regulation of common complex diseases.
• Marie Skłodowska-Curie actions (MSCA)-ITN-ETN European Training Network (Coordinator: Salvatore Spicuglia, Co-PI: Robin Andersson): 03/2020 – 02/2024, beneficiary grant, 2.2M DKK
  Molecular basis of human enhanceropathies (ENHPATHY).An ERC ITN bringing together experts on enhancer biology, epigenomics, bioinformatics and medical genetics to increase scientific knowledge on the molecular basis of human enhanceropathies and to open new diagnostic and therapeutic avenues for patients.
• Novo Nordisk Foundation Project Grant in Bioscience and Basic Biomedicine (PI: Andersson): 03/2019 – 02/2022, 1.5M DKK
  Understanding the impact of genetic variants on transcriptional activities using deep learning. The aim of this project was todevelop deep learning methods for studying how DNA sequence determine cell-type specific regulatory activities.
• Independent Research Fund Denmark Sapere Aude Forskningsleder (PI: Andersson): 09/2015 – 12/2020, 7.1M DKK
  A systematic characterization of the impact of human regulatory variation. This grant aimed to understandthe impact of genetic variants on transcriptional activities, to establish deeplearning methods for analyzing genetic variants, and to study how redundant promoters confer robustness to genetic variants.
• H2020 European Research Council starting grant (PI: Andersson): 05/2015 – 04/2020, 1.4M EUR
  A systematic characterization of regulatory architectures and their determinants of regulatory activities. This grant established my independent lab and focused on transcriptional analyses of enhancers and regulatory domains.

BIBLIOMETRICS

Metrics according to Google Scholar as of 2024-09-16:

• Number of peer-reviewed publications: 65
• Number of citations: 11,362
• h-index: 40
• Number of first author publications: 11
• Number of corresponding author publications: 15

Google Scholar page: https://scholar.google.com/citations?user=D8RKCXsAAAAJ

MAJOR COLLABORATIONS

• Anja Groth, chromatin replication and epigenetic inheritance, University of Copenhagen
• Joshua Brickman, stem cell biology and enhancer regulation, University of Copenhagen
• Prof. Jesse Engreitz, enhancer-promoter communication, Stanford University
• Ray Jones, single-cell eQTL analyses, Broad Institute of MIT and Harvard
• Prof. Alvaro Rada Iglesias, developmental biology and enhancer regulation, University of Cantabria