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 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)