ICML 2021 publication: Efficient Generative Modelling of Protein Structure Fragments using a Deep Markov Model - a collaboration between researchers from Department of Computer Science and Department of Biology KU, and Evaxion Biotech
TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes - paper by Drs. Ivanov, Sandelin and Marquardt
Review in Genome Biology: Computational methods for chromosome-scale haplotype reconstruction - by Assistant Professor Garg
The SCARB Popgen group presents data analysis for the African leopard.
The leopard stands out as an elusive, versatile, and adaptable animal. Researchers from the University of Copenhagen publish the first genomic data for the African subspecies of the leopard in the acclaimed Cell Press journal Current Biology. The results show an exceptionally high genetic diversity and low differentiation.
Article in Nature co-authored by Patrícia Peènerová: Million-year-old DNA sheds light on the genomic history of mammoths
Multi-author review on autophagy: Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)
Center for Basic Machine Learning Research in Life Science: NNF awards DKK 29.984.002 Data Science Collaborative grant to PI Professor MSO Ole Winther and several collaborating research groups.
400.000 DKK grant to Assistant Professor Rasmus Heller for research expeditions to Africa from the Carlsberg Foundation in support of the project "Building the African biobank: a Noah s Ark of wildlife genetic resources".
Professor Peter Brodersen receives 450.000 DKK infrastructure grant from the Carlsberg Foundation for the project entitled "How a new layer of genetic control boosts plant seed germination".
Associate Professor Ida Moltke receives 4.984.858 DKK Carlsberg Foundation Young Researcher Fellowship Award for the project " Genome Greenland"
Cytoplasmic mRNPs revisited: Singletons and condensates. Assoc. Prof Jan Christiansen and colleagues co-author review in Wiley's BioAssays - Problems and Paradigms - Prospects and Overviews section
Professor Albrechtsen and Associate Professor Moltke are co-authors on Nature article: Population genomics of the Viking world.
Nature: 2020, 585(7825);390-396
Publication in the Journal "Cancers" from Prof. Sandelin and Colleagues: Cancer Cell Acid Adaptation Gene Expression Response Is Correlated to Tumor-Specific Tissue Expression Profiles and Patient Survival.
The RNA exosome shapes the expression of key protein-coding genes. Publication in Nucleic Acids Research from Prof. Sandelin and colleagues.
Cover art and research article in the Journal "Development" by Dr. Arribas-Hernandez, Professor Brodersen and colleagues: Recurrent requirement for the m6A-ECT2/ECT3/ECT4 axis in the control of cell proliferation during plant organogenesis.
No Evidence for N7-Methylation of Guanosine (m7G) in Human let-7e - Letter in Molecular Cell by Assoc. Prof. Jeppe Vinther.
Independent Research Fund Denmark (DFF) grant to Associate Professor Anders Albrechtsen: Models for human adaptation to identify and understand genetic variation affecting phenotypes and health. Award amount: DKK 2,870,488.
Genetic epidemiology seeks to identify genetic variants affecting human traits and diseases. Many traits have an impact on the health and survival of individuals thereby affecting the evolutionary fitness of the individual and the population. Here genome-wide data is used to create tree like structures, called drift trees, that seeks to capture changes in allele frequency in multiple populations given their population histories and they can be used to identify genetic variants affecting fitness by joint estimation of both genetic association to a phenotype and effects on individual fitness. This can be used to identify novel disease causing loci (genomic regions) or loci improving health that affects traits today and that have had a historical advantage or disadvantage on fitness. From the DFF website.
NNF grant to "Studies of metabolic health and disease in consanguineal relationships and small and historically isolated populations": Associate Professor Anders Albrechtsen is NNF Ascending Investigator within Endocrinology and Metabolism. Award size: DKK 9.957.358
NNF Hallas-Møller Ascending Investigator grant to Associate Professor Robin Andersson for the studies "Functional and topological redundancies in transcriptional regulation". Award size: DKK 9.994.444
"Cellular activities are controlled by specific processes during development and in response to environmental changes. Which genes are active and how much RNA is produced at a given timepoint in a cell is coordinated by specific regulatory elements encoded in the DNA that, via binding of dedicated proteins (transcription factors), determine the rate of transcription. These regulatory processes are essential for a cell and genetic disruptions of regulatory elements may therefore lead to disease. This project will investigate the mechanistic basis of how regulatory activities are conveyed via transcription factors and assess the occurrence of failsafe systems mediated via redundant regulatory elements that buffer the impact of possible mutations. Understanding these processes and the interplay of regulatory elements is of high importance to better understand transcriptional regulation and the genetic basis of disease, which may ultimately lead to better diagnostics and treatments." - Robin Andersson
NNF grant for Nuclear RNA degradation studies: Professor Albin Sandelin is NNF Distinguished Investigator and awarded funds for the project: "Deciphering the code of nuclear RNA degradation by deep learning and transcriptomics". Award size: DKK 9.995.004
"The most fundamental process in molecular biology is reading of genes in DNA into RNA (transcription), which is then translated into proteins. However, we also need systems to remove RNAs from cells – RNA degradation. Because RNA degradation rates vary between different RNAs, RNA transcription and degradation together shape the concentration of each RNA in the cell. Therefore, understanding RNA degradation systems is necessary to understand the cell. Our current understanding is not on the level where we can predict the RNA degradation rates of a specific RNA based on its sequence and chemical properties. In this project we will merge state of the art methods for profiling RNA properties with the latest development in computer science: deep learning. We will make methods that can predict RNA degradation rates and discover what biological signals that are important for RNA degradation. This will be important for cell biology, but also for RNA-based medicine and biotechnology." - Albin Sandelin
The Carlsberg Foundation has awarded an infrastructure grant (1.4 mDKK) to Professor Albin Sandelin and SCARB.
Project name: Computer storage for state-of-the-art bioinformatics and high-throughput biology. The funds will be used to buy new storage capacity.
DTU, ITU and KU collaboration to recieve status as the Copenhagen ELLIS Unit - a key center for machine learning
The European Laboratory for Learning and Intelligent Systems (ELLIS) is a European network in AI. The Copenhagen unit is one of the first appointed ELLIS Units and one of 17 ELLIS units in 10 European countries.
The Novo Nordisk Foundation awards grant for the project "A new generation of microfluidics-based methods to study genetic and functional effects of complex spatiotemporal gradients in tumor microenvironments"
Professors Stine Falsig Pedersen and Albin Sandelin receives DKK 4,987,214 from the Novo Nordisk Foundation Exploratory Interdisciplinary Synergy Programme.
Professor Sandelin receives 2.2 mDKK award from Novo Nordisk Foundation for the project "Cell selection and gene regulation underlying chronic acid adaptation in cancer cells". Professors Falsig Pedersen and Sandelin also recieves 4.987.214 DKK grant (Exploratory Interdisciplinary Synergy Programme) for the project:" A new generation of microfluidics-based methods to study genetic and functional effects of complex spatiotemporal gradients in tumor microenvironments"
Occurrence and functions of m6A and other covalent modifications in plant mRNA.
Publication by Professor Peter Brodersen and post doc Laura Arribas-Hernández summarizes current knowledge on the biochemistry, molecular mechanisms, and biological functions of mRNA modifications in plants. Plant Physiol. 2019 Nov 20. pii: pp.01156.2019.
Cell Reports publication: "Single mRNP Analysis Reveals that Small Cytoplasmic mRNP Granules Represent mRNA Singletons"
Using super-resolution microscopy and fluorescence correlation spectroscopy to analyze the molecular composition and dynamics of single cytoplasmic mRNP granules in live cells, the authors conclude, that cytoplasmic mRNP granules are mRNA singletons.
Nature Genetics review article: "Determinants of enhancer and promoter activities of regulatory elements"
Professor Sandelin and Assistant Professor Andersson review the role of regulatory elements with a particular focus on the factors that determine the promoter and/or enhancer activity.
2 new grants from Independent Research Fund Denmark (DFF) to Assoc. Prof. Hamelryck and Prof. Winther
Assoc. Prof. Hamelryck and Prof. Winther both receive grants from DFF for the projects entitled “Deep Probabilistic Programming for Protein Structure” (DKK 5,903,016) and “Few-shot generative models” (DKK 2,616,792), respectively
Assistant Professor Ida Moltke is co-editor of a new edition of Handbook of Statistical Genomics (2-volume set, Fourth Edition)
The 4th edition of Handbook of Statistical Genomics by co-editors Ida Moltke, David Balding and John Marioni is now available. More than 75% is new material.
ERC Starting Grant to Assistant Professor Rasmus Heller
Assistant Professor Rasmus Heller has been awarded a Starting Grant worth €1.5 million from the European Research Council (ERC).
Ruminants’ Genes are a Treasure Trove
A large-scale research project has focused on mapping the genomes of 44 ruminant species - a group of animals that have intrigued researchers for years because of their biological diversity and their huge importance as domestic animals. The results have recently been published in three articles in the top-ranked journal Science. Assistant Professor Rasmus Heller is part of the research team and a co-author on the Science articles.
Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing - new paper in Nucleic Acids Research
Associate Professors Jeppe Vinther and Anders Albrechtsen with co-authors publish paper in Nucleic Acids Research
Accelerating vaccine development through a deep learning and probabilistic programming approach to protein structure prediction
Associate Professor Thomas Hamelryck (BIO/DIKU) and the Copenhagen-based company Evaxion have obtained funding from the Innovation Foundation for an Industrial PhD project. DIKU will receive a part of the approx 2.5 mDKK grant, namely 360.000 DKK to cover supervision, courses, evaluation etc. throughout the project period.
Peter Brodersen receives 10 mDKK Hallas-Møller Ascending Investigators award
Project title: 'Mechanistic basis of post-transcriptional gene regulation via N6-methyladenosine-modified messenger RNA'. The grant allows Peter Brodersen´s group to pursue research into how gene regulation affects plant growth and development. The study of gene regulation is central to biology, because it explains why cells within an organism acquire very different properties despite the fact that they contain the same genes.
Associate Professor Peter Brodersen receives funding of 6.189.953 DKK from Danish Council for Independent Research
Epitranscriptomic control of plant stem cell behaviour
New publication in J Biol Chem by Associate Professor Peter Brodersen & co-authors
Farnesylated Heat Shock Protein 40 is a component of membrane-bound RISC in Arabidopsis.
Albrectsen Group members co-author Cell publication
Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. Cell: 175(2);347-359.e14 (2018)
Scientists create new technology and solve a key puzzle for cellular memory
With a new groundbreaking technique, researchers from University of Copenhagen, including Assistant Professor Robin Andersson, have managed to identify a protein that is responsible for cellular memory being transmitted when cells divide. The finding is crucial for understanding development from one cell to a whole body.
ERC Starting Grant to Assistant Professor Ida Moltke
Associate Professor Peter Brodersen and team publish paper in Plant Cell
An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis.
Paper from the Sandelin Group: Boyd et al. Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies.
This study characterises enhancer and promoters in nearly 100 inflammatory bowl disease patients, showing that SNPs over-represented in the disease are highly overrepresented in regulatory regions, and that such data can be used for disease classification
Cell publication co-authored by Assistant Professor Ida Moltke
Physiological and Genetic Adaptations to Diving in Sea Nomads.
Ida Moltke receives a Villum Young Investigator Grant
DKK 153 million for 18 young research talents - Assistant Professor Ida Moltke is one of these talents
Assistant Professor Ida Moltke is joint first author on a publication in Nature Genetics. Assoc. Professor Anders Albrechtsen is co-author.
The paper shows the presence of a loss-of-function mutation in the gene ADCY3 in Greenland which increases risk of obesity and type 2 diabetes
Professor Sandelin co-authors Nucleic Acids Research paper. Khan et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.
A large update to the widely used JASPAR database which holds models for DNA binding proteins.
Publication in Nature - co-authored by Assoc. Professor Anders Albrectsen
Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans.
Professor Sandelin receives 4 mDKK funding from the Danish Cancer Society
Characterization of the interplay between environmental and genetic drivers of pancreatic ductal adenocarcinoma
Peter Brodersen and co-authors publish article in Genes & Development
Heat-shock protein 40 is the key farnesylation target in meristem size control, abscisic acid signaling, and drought resistance.
Yet another Science publication co-authored by Anders Albrechtsen
Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers
New publication from Vittig-Seerup and Sandelin: The landscape of isoform switches in human cancers.
This study shows a method to assess isoform switching in disease, and makes a global analysis of isoform switching in large cancer RNA-seq data sets.
Robin Andersson receives a Sapere Aude Award from The Danish Council for Independent Research
Assistant Professor Robin Andersson receives DKK 7 million from Sapere Aude, DFF's research leader grant. Robin's research project fokuses on variation in gene regulation.
Professor Sandelin receives DKK 5,888,616 from the Independent Research Fund Denmark
Characterization of inflammatory stress transfer between mother and fetus in pregnancy
Assoc. Professor Anders Albrectsen is co-author on Science publication
Ancient genomic changes associated with domestication of the horse
The first study of enhancer and promoter response to carbon nanotube exposure - from the Sandelin Group
Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo
Associate Professor Peter Brodersen receives an ERC Consolidator Grant 2016
Associate Professor Peter Brodersen receives the prestigious ERC Consolidator Grant (approx 2 mEuro) from the European Research Council (ERC)
2016 Award from The Lundbeck Foundation to Anders Albrechtsen
Associate Professor Anders Albrechtsen receives a 5-year fellowship (10 mDKK) from the Lundbeck Foundation
Ida Moltke receives the Women in Science Award from L’Oréal-UNESCO
Assistant Professor Ida Moltke receives one of the three L'Oréal-UNESCO For Women In Science Awards that each year are awarded to outstanding female researchers in the natural sciences in Denmark.
Albin Sandelin receives DKK 2,538,927 from Danish Council for Independent Research - Medical Sciences - Research Project 1
Localization of causal cis-regulatory SNPs within enhancer regions active in inflammatory bowel disease
Robin Andersson »My Science is both high risk and high gain«
Assistant Professor Robin Andersson receives 10,9 mDKK from the EU