Publications

  • Kjellin, Jonas; Avesson, Lotta; Reimegård, Johan; Liao, Zhen et al.

    Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas

    Part of Genome Research, p. 436-447, 2021.

    Open access
  • Zaghlool, Ammar; Niazi, Adnan; Björklund, Åsa K.; Orzechowski Westholm, Jakub et al.

    Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts

    Part of Scientific Reports, 2021.

    Open access
  • Gawryluk, Ryan M. R.; Stairs, Courtney W.

    Diversity of electron transport chains in anaerobic protists

    Part of Biochimica et Biophysica Acta - Bioenergetics, 2021.

    Open access
  • Martinez, Julien; Klasson, Lisa; Welch, John J.; Jiggins, Francis M.

    Life and Death of Selfish Genes: Comparative Genomics Reveals the Dynamic Evolution of Cytoplasmic Incompatibility

    Part of Molecular biology and evolution, p. 2-15, 2021.

    Open access
  • Strawbridge, Rona J.; Johnston, Keira J. A.; Bailey, Mark E. S.; Baldassarre, Damiano et al.

    The overlap of genetic susceptibility to schizophrenia and cardiometabolic disease can be used to identify metabolically different groups of individuals

    Part of Scientific Reports, 2021.

    Open access
  • Huang, Zhaobin; Petersen, Jillian M.; Martijn, Joran; Ettema, Thijs J. G. et al.

    A novel alphaproteobacterium with a small genome identified from the digestive gland of multiple species of abalone

    Part of Environmental Microbiology Reports, p. 387-395, 2020.

  • Svensson, Daniel; Rentoft, Matilda; Dahlin, Anna M.; Lundholm, Emma et al.

    A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences

    Part of PLoS ONE, 2020.

    Open access
  • Onsbring, Henning; Tice, Alexander K.; Barton, Brandon T.; Brown, Matthew W. et al.

    An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells

    Part of BMC Genomics, 2020.

    Open access
  • Garnica, Sigisfredo; Rosenstein, Ronja; Schön, Max Emil

    Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems

    Part of PeerJ, 2020.

    Open access
  • Montoliu-Nerin, Merce; Sanchez-Garcia, Marisol; Bergin, Claudia; Grabherr, Manfred et al.

    Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei

    Part of Scientific Reports, 2020.

    Open access
  • Patriarca, Claudia; Sedano Núñez, Vicente T.; Garcia, Sarahi L; Bergquist, Jonas et al.

    Character and environmental lability of cyanobacteria-derived dissolved organic matter

    Part of Limnology and Oceanography, 2020.

    Open access
  • Stairs, Courtney W.; Dharamshi, Jennah; Tamarit, Daniel; Eme, Laura et al.

    Chlamydial contribution to anaerobic metabolism during eukaryotic evolution

    Part of Science Advances, 2020.

    Open access
  • Hosseini, Sara; Meunier, Cécile; Nguyen, Diem; Reimegård, Johan et al.

    Comparative analysis of genome-wide DNA methylation in Neurospora

    Part of Epigenetics, 2020.

    Open access
  • Reysenbach, Anna-Louise; St John, Emily; Meneghin, Jennifer; Flores, Gilberto E. et al.

    Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities

    Part of Proceedings of the National Academy of Sciences of the United States of America, p. 32627-32638, 2020.

    Open access
  • Lewis, William H; Lind, Anders E.; Sendra, Kacper M.; Onsbring Gustafson, Henning et al.

    Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss

    Part of Molecular biology and evolution, p. 524-539, 2020.

    Open access
  • Mahajan, Mayank; Seeger, Christian; Yee, Benjamin; Andersson, Siv G. E.

    Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum

    Part of Genome Biology and Evolution, p. 1528-1548, 2020.

    Open access
  • Almeida, Pedro; Proux-Wera, Estelle; Churcher, Allison; Soler, Lucile et al.

    Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion

    Part of BMC Biology, 2020.

    Open access
  • Martijn, Joran; Schön, Max Emil; Lind, Anders E.; Vosseberg, Julian et al.

    Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition

    Part of Nature Communications, 2020.

    Open access
  • Halvorsen, Matthew; Huh, Ruth; Oskolkov, Nikolay; Wen, Jia et al.

    Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia

    Part of Nature Communications, 2020.

    Open access
  • Dharamshi, Jennah E.; Tamarit, Daniel; Eme, Laura; Stairs, Courtney W. et al.

    Marine Sediments Illuminate Chlamydiae Diversity and Evolution

    Part of Current Biology, p. 1032-1048.e7, 2020.

  • Jimenez-Gonzalez, Alejandro; Andersson, Jan O.

    Metabolic reconstruction elucidates the lifestyle of the last Diplomonadida common ancestor

    Part of MSYSTEMS, 2020.

  • Sjöberg, Susanne; Stairs, Courtney W.; Allard, Bert; Homa, Felix et al.

    Microbiomes in a manganese oxide producing ecosystem in the Ytterby mine, Sweden: impact on metal mobility

    Part of FEMS Microbiology Ecology, 2020.

    Open access
  • Morrow, Jennifer L.; Schneider, Daniela, I; Klasson, Lisa; Janitz, Caroline et al.

    Parallel Sequencing of Wolbachia wCer2 from Donor and Novel Hosts Reveals Multiple Incompatibility Factors and Genome Stability after Host Transfers

    Part of Genome Biology and Evolution, p. 720-735, 2020.

    Open access
  • Mahajan, Mayank; Yee, Benjamin; Hägglund, Emil; Guy, Lionel et al.

    Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures

    Part of Molecular biology and evolution, p. 1020-1040, 2020.

  • Schön, Max Emil; Eme, Laura; Ettema, Thijs J. G.

    PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics

    Part of Bioinformatics, p. 1718-1724, 2020.

    Open access
  • Lord, Edana; Dussex, Nicolas; Kierczak, Marcin; Diez-del-Molino, David et al.

    Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros

    Part of Current Biology, p. 3871-3879, 2020.

    Open access
  • Klimovich, Alexander; Giacomello, Stefania; Björklund, Åsa; Faure, Louis et al.

    Prototypical pacemaker neurons interact with the resident microbiota

    Part of Proceedings of the National Academy of Sciences of the United States of America, p. 17854-17863, 2020.

    Open access
  • Nordlund, Jessica; Marincevic-Zuniga, Yanara; Cavelier, Lucia; Raine, Amanda et al.

    Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing

    Part of Scientific Reports, 2020.

    Open access
  • Tamarit, Daniel; Andersson, Siv G. E.

    Rethinking microbial symbioses

    Part of FEMS Microbiology Letters, 2020.

    Open access
  • Murray, Alison E.; Freudenstein, John; Gribaldo, Simonetta; Hatzenpichler, Roland et al.

    Roadmap for naming uncultivated Archaea and Bacteria

    Part of Nature Microbiology, p. 987-994, 2020.

    Open access
  • Tiklova, Katarina; Nolbrant, Sara; Fiorenzano, Alessandro; Björklund, Åsa K. et al.

    Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson's disease

    Part of Nature Communications, 2020.

    Open access
  • Wallén-Mackenzie, Åsa; Dumas, Sylvie; Papathanou, Maria; Martis Thiele, Michaela et al.

    Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures

    Part of Communications Biology, 2020.

    Open access
  • Najdrova, Vladimira; Stairs, Courtney W.; Vinopalova, Martina; Voleman, Lubos et al.

    The evolution of the Puf superfamily of proteins across the tree of eukaryotes

    Part of BMC Biology, 2020.

    Open access
  • Tengvall, Katarina; Bergvall, K; Olsson, M; Ardesjö-Lundgren, Brita et al.

    Transcriptomes from German shepherd dogs reveal differences in immune activity between atopic dermatitis affected and control skin

    Part of Immunogenetics, p. 315-323, 2020.

    Open access
  • Dombrowski, Nina; Williams, Tom A.; Sun, Jiarui; Woodcroft, Benjamin J. et al.

    Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution

    Part of Nature Communications, 2020.

    Open access
  • Hess, Sebastian; Eme, Laura; Roger, Andrew J.; Simpson, Alastair G. B.

    A natural toroidal microswimmer with a rotary eukaryotic flagellum

    Part of Nature Microbiology, p. 1620-1626, 2019.

  • Schwank, Katrin; Bornemann, Till L., V; Dombrowski, Nina; Spang, Anja et al.

    An archaeal symbiont-host association from the deep terrestrial subsurface

    Part of The ISME Journal, p. 2135-2139, 2019.

  • Seitz, Kiley W.; Dombrowski, Nina; Eme, Laura; Spang, Anja et al.

    Asgard archaea capable of anaerobic hydrocarbon cycling

    Part of Nature Communications, 2019.

    Open access
  • Clark, David W.; Karlsson, Torgny; Sennblad, Bengt; Gyllensten, Ulf B. et al.

    Associations of autozygosity with a broad range of human phenotypes

    Part of Nature Communications, 2019.

    Open access
  • Bysani, Madhusudhan; Agren, Rasmus; Davegardh, Cajsa; Volkov, Petr et al.

    ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes

    Part of Scientific Reports, 2019.

    Open access
  • Fritzell, Peter; Welinder-Olsson, Christina; Jönsson, Bodil; Melhus, Åsa et al.

    Bacteria: back pain, leg pain and Modic sign-a surgical multicentre comparative study

    Part of European spine journal, p. 2981-2989, 2019.

    Open access
  • Johansson, Henrik J.; Socciarelli, Fabio; Vacanti, Nathaniel M.; Haugen, Mads H. et al.

    Breast cancer quantitative proteome and proteogenomic landscape

    Part of Nature Communications, 2019.

    Open access
  • Tiukova, Ievgeniia A.; Pettersson, Mats; Höppner, Marc P.; Olsen, Remi-Andre et al.

    Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis

    Part of PLoS ONE, 2019.

    Open access
  • Hård, Joanna; Al Hakim, Ezeddin; Kindblom, Marie; Björklund, Åsa K. et al.

    Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing

    Part of Genome Biology, 2019.

    Open access
  • Martijn, Joran; Lind, Anders E.; Schön, Max E.; Spiertz, Ian et al.

    Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon

    Part of Environmental Microbiology, p. 2485-2498, 2019.

    Open access
  • Shebanits, Kateryna; Günther, Torsten; Johansson, Anna C. V.; Maqbool, Khurram et al.

    Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.

    Part of BMC Biotechnology, 2019.

    Open access
  • Morris, Julia; Bailey, Mark E. S.; Baldassarre, Damiano; Cullen, Breda et al.

    Genetic variation in CADM2 as a link between psychological traits and obesity

    Part of Scientific Reports, 2019.

    Open access
  • Kampfraath, A. A.; Klasson, Lisa; Anvar, S. Y.; Vossen, R. H. A. M. et al.

    Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model

    Part of BMC Genomics, 2019.

    Open access
  • Morales, Hernan E.; Faria, Rui; Johannesson, Kerstin; Larsson, Tomas et al.

    Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast

    Part of Science Advances, 2019.

    Open access
  • Jimenez-Gonzalez, Alejandro; Xu, Feifei; Andersson, Jan O.

    Lateral Acquisitions Repeatedly Remodel the Oxygen Detoxification Pathway in Diplomonads and Relatives

    Part of Genome Biology and Evolution, p. 2542-2556, 2019.