Key publications
| mRNA Singletons Single mRNP Analysis Reveals that Small Cytoplasmic mRNP Granules Represent mRNA Singletons Cell Reports 29 (3): 736-748.e4 (2019) |
| Enhancers and Promoters Determinants of enhancer and promoter activities of regulatory elements Nat Rev Genet 337: 1–17 (2019) |
| Detection method for internal N7-methylguanosine Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing Nucleic Acids Res 47 (20) e126 (2019) |
| Ruminant Genomes Ruminants are a diverse group of mammals that includes families such as deer, cows, and goats. A large number of ruminant genomes were sequenced, and data analysis show large population reductions are coinciding with the migration of humans out of Africa. Also, authors found evidence for selection on cancer-related genes that may function in antler development in deer, and identified the genetic basis of adaptations that allow reindeer to survive in the harsh conditions of the Arctic. Adapted from abstract. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 364 (6446), eaav6202 (2019) |
| Signal Peptide Prediction SignalP 5.0 improves signal peptide predictions using deep neural networks Nature Biotechnology 37: 420–423 (2019) |
| Genetic Associations, Patterns of Viral Infections, and Chinese Population History 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) |
| Mechanism of Symmetric Inheritance MCM2 promotes symmetric inheritance of modified histones during DNA replication Science 361(6409): 1389-1392 (2018) |
| Improving Accuracy in Variant Genotyping Genotype estimates from short-read sequencing data are typically based on the alignment of reads to a linear reference, but reads originating from more complex variants often align poorly, resulting in biased genotype estimates. Here, we present a new method to efficiently perform unbiased, probabilistic genotyping across the variation spectrum. We also demonstrate that including a ‘variation-prior’ database containing already known variants significantly improves sensitivity. Adapted from abstract. Accurate genotyping across variant classes and lengths using variant graphs. Nature Genetics 50, 1054–1059 (2018) |
| Developmental Timing and Morphogenesis An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis Plant Cell 30(5): 952-967 (2018) |
| Enhancers and Promoters in Inflammatory Bowel Disease Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies Nature Communications 9: 1661 (2018) |
| Transcription Start Site Analysis Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities Nucleic Acids Res. 39: 311 (2018), |
| Demographic modelling to understand past phylogeography of the plains zebra A southern African origin and cryptic structure in the highly mobile plains zebra Nat Ecol Evol 2, 491–498 (2018) |
| Greenlandic Genetic Variation We show that a genetic mutation substantially increases the risk of type 2 diabetes for individuals who carry two copies of it. The mutation is common in native Greenlanders; hence, our finding has great potential to lead to better treatment of diabetes in this population. Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes. Nature Genetics 50, 172–174 (2018) |
| Native Americans and Migration Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans Nature 553: 203–207 (2018) |
| Cancers and Isoform Switches The Landscape of Isoform Switches in Human Cancers Mol Cancer Res 15(9): 1206-1220 (2017) |
| Genome Denmark We describe the construction of a reference genome based on high-coverage sequencing and de novo assemblies of 150 individuals with mate-pair libraries extending up to 20 kilobases. The reference genome is expected to strongly benefit precision medicine initiatives. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature 548, 87–91 (2017) |
| Protein Structure Evolution A generative angular model of protein structure evolution Mol Biol Evol. 34(8):2085-2100 (2017) |
| Protein Localization Prediction DeepLoc: prediction of protein subcellular localization using deep learning Bioinformatics 33(21): 3387–3395 (2017) |
| RNA Metabolism and Alternative Transcription Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters Nature Genetics 48: 984–994 (2016) |
| Coordinated Transcription Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells Science 27 (347): 1010-1014 (2015) |
| Promoter/Enhancer Atlas We present a collection of active enhancers instrumental in the pursuit to understand regulation of differentiation and homeostasis, as these enhancers control temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. We also present a comprehensive map over mammalian transcription start sites and their usage in human and mouse primary cells, cell lines and tissues. The functional annotation of mammalian cell-type-specific transcriptomes has wide applications in biomedical research. A promoter-level mammalian expression atlas. Nature 507, 462-70 (2014) |
| Rare Diseases Search FindZebra: A search engine for rare diseases International Journal of Medical Informatics 82(6): 528-538 (2013) |
| Bayesian Methods in Structural Bioinformatics This is the first field-defining book on Bayesian methods in structural bioinformatics. The book provides an introduction to Bayesian statistics and concepts in machine learning and statistical physics. Chapters include describtion of state-of-the-art statistical methods in structural bioinformatics with a particular focus on statistical methods that have a clear interpretation in the framework of statistical physics. Adapted from abstract. Bayesian Methods in Structural Bioinformatics, Statistics for Biology and Health. Springer-Verlag Berlin Heidelberg (2012) |
| Protein Structure Prediction Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized PLoS ONE 5(11): e13714 (2010) |
| Probabilistic Protein Structure Prediction Protein structure prediction requires efficient probabilistic exploration of the structural space that correctly reflects the relative conformational stabilities. We have developed a fully probabilistic, continuous model of local protein structure in atomic detail. The model represents a significant theoretical and practical improvement over the widely used fragment assembly technique. Adapted from abstract. A generative, probabilistic model of local protein structure. PNAS 105, 8932-8937 (2008) |
| Probabilistic Models of Proteins and Nucleic Acids In this landmark textbook, authors describe probabilistic models used in large-scale sequence analysis. Examples are hidden Markov models used for analysing biological sequences, linguistic-grammar-based probabilistic models used for identifying RNA secondary structure, and probabilistic evolutionary models used for inferring phylogenies of sequences from different organisms. Adapted from abstract. Biological sequence analysis. Probabilistic models of proteins and nucleic acids. Cambridge University Press (2008) |
| First detection of proteins regulated by miRNAs Identification of miRNA targets with stable isotope labeling by amino acids in cell culture Nucleic Acids Res 34, e107 (2006) |
| Cytoplasmic Protein Trafficking Cytoplasmic trafficking of IGF-II mRNA-binding protein by conserved KH domains Journal of Cell Science 115: 2087-2097 (2002) |
| H19 RNA H19 RNA Binds Four Molecules of Insulin-like Growth Factor II mRNA-binding Protein The Journal of Biological Chemistry 275, 29562-29569 (2000) |
| Translation Repression A Family of Insulin-Like Growth Factor II mRNA-Binding Proteins Represses Translation in Late Development Mol Cell Biol 19:1262–1270 (1999) |
| Termination of T7 RNA polymerase Intrinsic termination of T7 RNA polymerase mediated by either RNA or DNA EMBO J 15:4767-4774 (1996) |
| Translation of IGF-II mRNA Growth-dependent translation of IGF-II mRNA by a rapamycin-sensitive pathway Nature 377, 358–362 (1995) |