DDLS Fellow

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Primary: Shown in the list of current labels.

Year 2023

PubMed DOI Crossref
Diverticulosis is not associated with altered gut microbiota nor is it predictive of future diverticulitis: a population-based colonoscopy study.
Alexandersson BT, Hugerth LW, Hedin C, ..., Andreasson A, Schmidt PT
Scand. J. Gastroenterol. - (-) 1-8 [2023-03-29; online 2023-03-29]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Pre-pregnancy complications - associated factors and wellbeing in early pregnancy: a Swedish cohort study.
Gudnadottir U, Du J, Hugerth LW, ..., Fransson E, Brusselaers N
BMC Pregnancy Childbirth 23 (1) 153 [2023-03-08; online 2023-03-08]
DDLS Fellow Luisa Hugerth

Year 2022

PubMed DOI Crossref
Madagascar's extraordinary biodiversity: Threats and opportunities.
Ralimanana H, Perrigo AL, Smith RJ, ..., Zizka A, Antonelli A
Science (New York, N.Y.) 378 (6623) eadf1466 [2022-12-02; online 2022-12-02]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Madagascar's extraordinary biodiversity: Evolution, distribution, and use.
Antonelli A, Smith RJ, Perrigo AL, ..., Zizka A, Ralimanana H
Science (New York, N.Y.) 378 (6623) eabf0869 [2022-12-02; online 2022-12-02]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Salmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle.
Cohn AR, Orsi RH, Carroll LM, ..., Wiedmann M, Cheng RA
Front Microbiol 13 (-) 1005215 [2022-11-30; online 2022-11-30]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Genomic trajectories of a near-extinction event in the Chatham Island black robin.
von Seth J, van der Valk T, Lord E, ..., Robertson BC, Dussex N
BMC Genomics 23 (1) 747 [2022-11-10; online 2022-11-10]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Cohort profile: the Swedish Maternal Microbiome project (SweMaMi) - assessing the dynamic associations between the microbiome and maternal and neonatal adverse events.
Fransson E, Gudnadottir U, Hugerth LW, ..., Brusselaers N, Engstrand L
BMJ Open 12 (10) e065825 [2022-10-26; online 2022-10-26]
DDLS Fellow Luisa Hugerth
DOI Crossref
aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow
Pochon Z, Bergfeldt N, Kırdök E, ..., Unneberg P, Oskolkov N
- - (-) - [2022-10-05; online 2022-10-05]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic.
Rasmussen PU, Abrego N, Roslin T, ..., Hugerth LW, Tack AJM
New Phytol. 236 (2) 671-683 [2022-10-00; online 2022-07-15]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Of problems and opportunities-How to treat and how to not treat crystallographic fragment screening data.
Weiss MS, Wollenhaupt J, Correy GJ, ..., Thunissen M, Pearce NM
Protein Sci. 31 (9) e4391 [2022-09-00; online 2022-08-31]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery.
Wikström T, Abrahamsson S, Bengtsson-Palme J, ..., Valentin L, Hagberg H
Clin Transl Med 12 (9) e1023 [2022-09-00; online 2022-09-15]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Laboratory Misidentifications Resulting from Taxonomic Changes to Bacillus cereus Group Species, 2018-2022.
Carroll LM, Matle I, Kovac J, Cheng RA, Wiedmann M
Emerg Infect Dis 28 (9) 1877-1881 [2022-09-00; online 2022-08-24]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.
van der Valk T, Dehasque M, Chacón-Duque JC, ..., Díez-Del-Molino D, Dalén L
iScience 25 (8) 104826 [2022-08-19; online 2022-08-01]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
The origin and evolution of open habitats in North America inferred by Bayesian deep learning models.
Andermann T, Strömberg CAE, Antonelli A, Silvestro D
Nat Commun 13 (1) 4833 [2022-08-17; online 2022-08-17]
DDLS Fellow Tobias Andermann
DOI Crossref
Recent and local diversification of Central American understorey palms
Cano Á, Stauffer FW, Andermann T, ..., Perret M, Antonelli A
Global Ecol. Biogeogr. 31 (8) 1513-1525 [2022-08-00; online 2022-05-11]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Strains Associated with Two 2020 Welder Anthrax Cases in the United States Belong to Separate Lineages within Bacillus cereus sensu lato.
Carroll LM, Marston CK, Kolton CB, ..., Weiner ZP, Kovac J
Pathogens 11 (8) - [2022-07-29; online 2022-07-29]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Biosynthetic potential of the global ocean microbiome.
Paoli L, Ruscheweyh HJ, Forneris CC, ..., Piel J, Sunagawa S
Nature 607 (7917) 111-118 [2022-07-00; online 2022-06-22]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle.
Krog MC, Hugerth LW, Fransson E, ..., Schuppe-Koistinen I, Nielsen HS
Hum. Reprod. 37 (7) 1525-1543 [2022-06-30; online 2022-05-14]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking.
Carroll LM, Pierneef R, Mathole A, Atanda A, Matle I
Microbiol Spectr 10 (3) e0070022 [2022-06-29; online 2022-04-27]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.
Kutschera VE, Kierczak M, van der Valk T, ..., Dalén L, Díez-Del-Molino D
BMC Bioinformatics 23 (1) 228 [2022-06-13; online 2022-06-13]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
The vaginal microbiome and the risk of preterm birth: a systematic review and network meta-analysis.
Gudnadottir U, Debelius JW, Du J, ..., Fransson E, Brusselaers N
Sci Rep 12 (1) 7926 [2022-05-13; online 2022-05-13]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
The right bug in the right place: opportunities for bacterial vaginosis treatment.
Wu S, Hugerth LW, Schuppe-Koistinen I, Du J
NPJ Biofilms Microbiomes 8 (1) 34 [2022-05-02; online 2022-05-02]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Global Estimation and Mapping of the Conservation Status of Tree Species Using Artificial Intelligence.
Silva SV, Andermann T, Zizka A, Kozlowski G, Silvestro D
Front Plant Sci 13 (-) 839792 [2022-04-29; online 2022-04-29]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Estimating Alpha, Beta, and Gamma Diversity Through Deep Learning.
Andermann T, Antonelli A, Barrett RL, Silvestro D
Front Plant Sci 13 (-) 839407 [2022-04-19; online 2022-04-19]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies.
Pearce NM, Skyner R, Krojer T
Front Mol Biosci 9 (-) 861491 [2022-04-11; online 2022-04-11]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.
Ferreira PL, Batista R, Andermann T, ..., Bacon CD, Antonelli A
Mol. Phylogenet. Evol. 169 (-) 107432 [2022-04-00; online 2022-02-04]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Associations between Listeria monocytogenes genomic characteristics and adhesion to polystyrene at 8 °C.
Mahoney DBJ, Falardeau J, Hingston P, ..., Jang SS, Wang S
Food Microbiol 102 (-) 103915 [2022-04-00; online 2021-09-23]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
The microbiome in reproductive health: protocol for a systems biology approach using a prospective, observational study design.
Krog MC, Madsen ME, Bliddal S, ..., Schuppe-Koistinen I, Nielsen HS
Hum Reprod Open 2022 (2) hoac015 [2022-03-23; online 2022-03-23]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Mechanistic insights into the C55-P targeting lipopeptide antibiotics revealed by structure-activity studies and high-resolution crystal structures.
Wood TM, Zeronian MR, Buijs N, ..., Janssen BJC, Martin NI
Chem Sci 13 (10) 2985-2991 [2022-03-09; online 2022-02-21]
DDLS Fellow Nicholas Pearce
DOI Crossref
<i>IUCNN</i> – Deep learning approaches to approximate species' extinction risk
Zizka A, Andermann T, Silvestro D
Diversity and Distributions 28 (2) 227-241 [2022-02-00; online 2021-12-16]
DDLS Fellow Tobias Andermann
DOI Crossref
Meta-analysis reveals the global picture of antibiotic resistance gene prevalence across environments
Abramova A, Berendonk TU, Bengtsson-Palme J
bioRxiv preprint - (-) - [2022-01-30; online 2022-01-30]
DDLS Fellow Johan Bengtsson-Palme

Year 2021

PubMed DOI Crossref
What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling Approach.
Bengtsson-Palme J, Jonsson V, Heß S
Environ. Sci. Technol. 55 (23) 15734-15743 [2021-12-07; online 2021-11-18]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.
G Ribeiro P, Torres Jiménez MF, Andermann T, ..., Bacon CD, Matos-Maraví P
Mol. Ecol. 30 (23) 6021-6035 [2021-12-00; online 2021-10-31]
DDLS Fellow Tobias Andermann
DOI Crossref
Genomic and niche divergence in an Amazonian palm species complex
Bacon CD, Roncal J, Andermann T, ..., Tunarosa N, Antonelli A
- 197 (4) 498-512 [2021-11-29; online 2021-05-10]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Improving sampling of crystallographic disorder in ensemble refinement.
Ploscariu N, Burnley T, Gros P, Pearce NM
Acta Crystallogr D Struct Biol 77 (Pt 11) 1357-1364 [2021-11-01; online 2021-10-20]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing.
Carroll LM, Buehler AJ, Gaballa A, ..., Cheng RA, Wiedmann M
Front Microbiol 12 (-) 763669 [2021-10-18; online 2021-10-18]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Characterization of Basal Transcriptomes Identifies Potential Metabolic and Virulence-Associated Adaptations Among Diverse Nontyphoidal Salmonella enterica Serovars.
Cohn AR, Orsi RH, Carroll LM, ..., Wiedmann M, Cheng RA
Front Microbiol 12 (-) 730411 [2021-10-13; online 2021-10-13]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa.
Carroll LM, Pierneef R, Mathole M, Matle I
Front Microbiol 12 (-) 748611 [2021-10-04; online 2021-10-04]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 9: Polymyxins: colistin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06861 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 8: Pleuromutilins: tiamulin and valnemulin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06860 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 7: Amphenicols: florfenicol and thiamphenicol.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06859 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 6: Macrolides: tilmicosin, tylosin and tylvalosin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06858 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 5: Lincosamides: lincomycin.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06856 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 4: β-Lactams: amoxicillin and penicillin V.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06855 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 3: Amprolium.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06854 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 2: Aminoglycosides/aminocyclitols: apramycin, paromomycin, neomycin and spectinomycin.
EFSA Panel on Biological Hazards (BIOHAZ) , Allende A, Koutsoumanis K, ..., Stella P, Peixe L
EFSA J 19 (10) e06853 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 1: Methodology, general data gaps and uncertainties.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06852 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 13: Diaminopyrimidines: trimethoprim.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06865 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 12: Tetracyclines: tetracycline, chlortetracycline, oxytetracycline, and doxycycline.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06864 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 11: Sulfonamides.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06863 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 10: Quinolones: flumequine and oxolinic acid.
EFSA Panel on Biological Hazards (BIOHAZ) , Koutsoumanis K, Allende A, ..., Stella P, Peixe L
EFSA J 19 (10) e06862 [2021-10-00; online 2021-10-26]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
A method for intuitively extracting macromolecular dynamics from structural disorder
Pearce NM, Gros P
Nat Commun 12 (1) - [2021-09-17; online 2021-09-17]
DDLS Fellow Nicholas Pearce
DOI Crossref
Microbial retention and resistances in stormwater quality improvement devices treating road runoff
Liguori R, Rommel SH, Bengtsson-Palme J, Helmreich B, Wurzbacher C
FEMS Microbes 2 (-) - [2021-08-03; online 2021-07-22]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Bicyclic β-Sheet Mimetics that Target the Transcriptional Coactivator β-Catenin and Inhibit Wnt Signaling.
Wendt M, Bellavita R, Gerber A, ..., Hennig S, Grossmann TN
Angew. Chem. Int. Ed. Engl. 60 (25) 13937-13944 [2021-06-14; online 2021-05-05]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source.
Douangamath A, Powell A, Fearon D, ..., Gorrie-Stone T, von Delft F
J Vis Exp - (171) - [2021-05-29; online 2021-05-29]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Microbial Community Interactions Are Sensitive to Small Changes in Temperature.
Burman E, Bengtsson-Palme J
Front Microbiol 12 (-) 672910 [2021-05-21; online 2021-05-21]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond.
Carroll LM, Cheng RA, Wiedmann M, Kovac J
Crit Rev Food Sci Nutr 62 (28) 7677-7702 [2021-05-03; online 2021-05-03]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar.
Bostanci N, Krog MC, Hugerth LW, ..., Nielsen HS, Schuppe-Koistinen I
Front. Cell. Infect. Microbiol. 11 (-) 625229 [2021-03-19; online 2021-03-19]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
No evidence for a placental microbiome in human pregnancies at term.
Sterpu I, Fransson E, Hugerth LW, ..., Wiberg-Itzel E, Schuppe-Koistinen I
Am J Obstet Gynecol 224 (3) 296.e1-296.e23 [2021-03-00; online 2020-08-29]
DDLS Fellow Luisa Hugerth
DOI Crossref
The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome Analysis
Sonett D, Brown T, Bengtsson-Palme J, Padilla-Gamiño JL, Zaneveld JR
bioRxiv preprint - (-) - [2021-02-24; online 2021-02-24]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Schneider JV, Jungcurt T, Cardoso D, ..., Berberich T, Zizka G
TAXON 70 (1) 48-71 [2021-02-00; online 2020-12-31]
DDLS Fellow Tobias Andermann
DOI Crossref
<i>iucn_sim</i> : a new program to simulate future extinctions based on IUCN threat status
Andermann T, Faurby S, Cooke R, Silvestro D, Antonelli A
Ecography 44 (2) 162-176 [2021-02-00; online 2020-11-10]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data.
Abramova A, Osińska A, Kunche H, Burman E, Bengtsson-Palme J
Bioinformatics - (-) - [2021-01-04; online 2021-01-04]
DDLS Fellow Johan Bengtsson-Palme

Year 2020

PubMed DOI Crossref
Ileocolonic Histopathological and Microbial Alterations in the Irritable Bowel Syndrome: A Nested Community Case-Control Study.
Talley NJ, Alexander JL, Walker MM, ..., Powell N, Andreasson A
Clin Transl Gastroenterol 12 (1) e00296 [2020-12-22; online 2020-12-22]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Microbial model communities: To understand complexity, harness the power of simplicity.
Bengtsson-Palme J
Comput Struct Biotechnol J 18 (-) 3987-4001 [2020-12-02; online 2020-12-02]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome.
Hugerth LW, Pereira M, Zha Y, ..., Schuppe-Koistinen I, Engstrand L
mSphere 5 (6) - [2020-11-18; online 2020-11-18]
DDLS Fellow Luisa Hugerth
DOI Crossref
Implications for tetraspanin-enriched microdomain assembly based on structures of CD9 with EWI-F
Oosterheert W, Xenaki KT, Neviani V, ..., van Bergen en Henegouwen PM, Gros P
Life Sci. Alliance 3 (11) e202000883 [2020-11-00; online 2020-09-21]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Genome sequence of segmented filamentous bacteria present in the human intestine.
Jonsson H, Hugerth LW, Sundh J, Lundin E, Andersson AF
Commun Biol 3 (1) 485 [2020-09-04; online 2020-09-04]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
The past and future human impact on mammalian diversity.
Andermann T, Faurby S, Turvey ST, Antonelli A, Silvestro D
Sci Adv 6 (36) - [2020-09-00; online 2020-09-04]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population.
Hugerth LW, Andreasson A, Talley NJ, ..., Agreus L, Engstrand L
Gut 69 (6) 1076-1084 [2020-06-00; online 2019-10-10]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.
Andermann T, Torres Jiménez MF, Matos-Maraví P, ..., Bacon CD, Antonelli A
Front Genet 10 (-) 1407 [2020-02-21; online 2020-02-21]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Phylogenomics and biogeography of the world's thrushes (Aves, Turdus): new evidence for a more parsimonious evolutionary history.
Batista R, Olsson U, Andermann T, ..., Ribas CC, Antonelli A
Proc. Biol. Sci. 287 (1919) 20192400 [2020-01-29; online 2020-01-22]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Evidence of altered mucosa-associated and fecal microbiota composition in patients with Irritable Bowel Syndrome.
Sundin J, Aziz I, Nordlander S, ..., Simrén M, Öhman L
Sci Rep 10 (1) 593 [2020-01-17; online 2020-01-17]
DDLS Fellow Luisa Hugerth

Year 2019

PubMed DOI Crossref
Enrichment of oral microbiota in early cystic precursors to invasive pancreatic cancer.
Gaiser RA, Halimi A, Alkharaan H, ..., Del Chiaro M, Sällberg Chen M
Gut 68 (12) 2186-2194 [2019-12-00; online 2019-03-14]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Effects of sampling strategy and DNA extraction on human skin microbiome investigations.
Bjerre RD, Hugerth LW, Boulund F, ..., Johansen JD, Engstrand L
Sci Rep 9 (1) 17287 [2019-11-21; online 2019-11-21]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.
Bengtsson-Palme J, Milakovic M, Švecová H, ..., Grabic R, Udikovic-Kolic N
Water Res 162 (-) 437-445 [2019-10-01; online 2019-07-04]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Strategies to Reduce or Eliminate Resistant Pathogens in the Environment
Bengtsson‐Palme J, Heß S
Antibiotic Drug Resistance - (-) 637-673 [2019-09-09; online 2019-08-23]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data
Magesh S, Jonsson V, Bengtsson-Palme J
MBMG 3 (-) - [2019-09-04; online 2019-09-04]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Insights Into Enhanced Complement Activation by Structures of Properdin and Its Complex With the C-Terminal Domain of C3b.
van den Bos RM, Pearce NM, Granneman J, Brondijk THC, Gros P
Front Immunol 10 (-) 2097 [2019-09-04; online 2019-09-04]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Investigation of the skin microbiome: swabs vs. biopsies.
Prast-Nielsen S, Tobin AM, Adamzik K, ..., Engstrand L, Fry L
Br. J. Dermatol. 181 (3) 572-579 [2019-09-00; online 2019-05-06]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Colitis-induced colorectal cancer and intestinal epithelial estrogen receptor beta impact gut microbiota diversity.
Ibrahim A, Hugerth LW, Hases L, ..., Engstrand L, Williams C
Int. J. Cancer 144 (12) 3086-3098 [2019-06-15; online 2019-01-11]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Mucosal-associated invariant T cells and oral microbiome in persistent apical periodontitis.
Davanian H, Gaiser RA, Silfverberg M, ..., Engstrand L, Sällberg Chen M
Int J Oral Sci 11 (2) 16 [2019-05-09; online 2019-05-09]
DDLS Fellow Luisa Hugerth
DOI Crossref
<scp>CoordinateCleaner</scp> : Standardized cleaning of occurrence records from biological collection databases
Zizka A, Silvestro D, Andermann T, ..., Zizka V, Antonelli A
Methods Ecol Evol 10 (5) 744-751 [2019-05-00; online 2019-02-24]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia.
Guzman-Otazo J, Gonzales-Siles L, Poma V, ..., Iñiguez V, Sjöling Å
PLoS ONE 14 (1) e0210735 [2019-01-14; online 2019-01-14]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.
Nilsson RH, Larsson KH, Taylor AFS, ..., Kõljalg U, Abarenkov K
Nucleic Acids Res. 47 (D1) D259-D264 [2019-01-08; online 2018-10-30]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Large expert-curated database for benchmarking document similarity detection in biomedical literature search.
Brown P, RELISH Consortium , Zhou Y
Database (Oxford) 2019 (-) - [2019-01-01; online 2019-01-01]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements.
Andermann T, Fernandes AM, Olsson U, ..., Faircloth BC, Antonelli A
Syst. Biol. 68 (1) 32-46 [2019-01-01; online 2018-05-18]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Introducing ribosomal tandem repeat barcoding for fungi.
Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Nilsson RH
Mol Ecol Resour 19 (1) 118-127 [2019-01-00; online 2018-10-24]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Assessment and Management of Risks Associated With Antibiotic Resistance in the Environment
Bengtsson-Palme J
Management of Emerging Public Health Issues and Risks: Multidisciplinary Approaches to the Changing Environment - (-) 243-263 [2019-00-00; online 2019-00-00]
DDLS Fellow Johan Bengtsson-Palme

Year 2018

PubMed DOI Crossref
Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.
Bengtsson-Palme J, Richardson RT, Meola M, ..., Hartmann M, Nilsson RH
Bioinformatics 34 (23) 4027-4033 [2018-12-01; online 2018-06-19]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb.
Rasmussen PU, Hugerth LW, Blanchet FG, ..., Lindahl BD, Tack AJM
New Phytol. 220 (4) 1248-1261 [2018-12-00; online 2018-03-24]
DDLS Fellow Luisa Hugerth
DOI Crossref
Quantifying point-mutations in shotgun metagenomic data
Magesh S, Jonsson V, Bengtsson-Palme J
bioRxiv preprint - (-) - [2018-10-11; online 2018-10-11]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Conceptual and empirical advances in Neotropical biodiversity research.
Antonelli A, Ariza M, Albert J, ..., Zizka A, Edwards SV
PeerJ 6 (-) e5644 [2018-10-04; online 2018-10-04]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Bacteriophages Synergize with the Gut Microbial Community To Combat Salmonella.
Hu YOO, Hugerth LW, Bengtsson C, ..., Du J, Engstrand L
mSystems 3 (5) - [2018-10-02; online 2018-10-02]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.
Alneberg J, Karlsson CMG, Divne AM, ..., Andersson AF, Pinhassi J
Microbiome 6 (1) 173 [2018-09-28; online 2018-09-28]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements.
Pärnänen K, Karkman A, Hultman J, ..., Satokari R, Virta M
Nat Commun 9 (1) 3891 [2018-09-24; online 2018-09-24]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Structure and function of the global topsoil microbiome.
Bahram M, Hildebrand F, Forslund SK, ..., Tedersoo L, Bork P
Nature 560 (7717) 233-237 [2018-08-00; online 2018-08-01]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance.
Larsson DGJ, Andremont A, Bengtsson-Palme J, ..., Wellington EM, Wernersson AS
Environ Int 117 (-) 132-138 [2018-08-00; online 2018-05-07]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea.
Alneberg J, Sundh J, Bennke C, ..., Labrenz M, Andersson AF
Sci Data 5 (-) 180146 [2018-07-31; online 2018-07-31]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
SECAPR-a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments.
Andermann T, Cano Á, Zizka A, Bacon C, Antonelli A
PeerJ 6 (-) e5175 [2018-07-13; online 2018-07-13]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always.
Bengtsson-Palme J
Microbiome 6 (1) 125 [2018-07-07; online 2018-07-07]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms.
Kraupner N, Ebmeyer S, Bengtsson-Palme J, ..., Flach CF, Larsson DGJ
Environ Int 116 (-) 255-268 [2018-07-00; online 2018-04-25]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data
Richardson RT, Bengtsson-Palme J, Gardiner MM, Johnson RM
PeerJ 6 (-) e5126 [2018-06-26; online 2018-06-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.
Keedy DA, Hill ZB, Biel JT, ..., Wells JA, Fraser JS
Elife 7 (-) - [2018-06-07; online 2018-06-07]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+ site.
Wahlgren WY, Dunevall E, North RA, ..., Ramaswamy S, Friemann R
Nat Commun 9 (1) 1753 [2018-05-01; online 2018-05-01]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies.
Hagen O, Andermann T, Quental TB, Antonelli A, Silvestro D
Syst. Biol. 67 (3) 458-474 [2018-05-01; online 2017-10-27]
DDLS Fellow Tobias Andermann
DOI Crossref
Introducing ribosomal tandem repeat barcoding for fungi
Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Henrik Nilsson R
bioRxiv preprint - (-) - [2018-04-28; online 2018-04-28]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies.
Angers-Loustau A, Petrillo M, Bengtsson-Palme J, ..., Venturi V, Van den Eede G
F1000Res 7 (-) 459 [2018-04-13; online 2018-04-13]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Protection goals must guide risk assessment for antibiotics.
Bengtsson-Palme J, Larsson DGJ
Environ Int 111 (-) 352-353 [2018-02-00; online 2017-10-31]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK).
Nilsson RH, Taylor AFS, Adams RI, ..., Kõljalg U, Abarenkov K
MycoKeys - (28) 65-82 [2018-01-08; online 2018-01-08]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Environmental factors influencing the development and spread of antibiotic resistance.
Bengtsson-Palme J, Kristiansson E, Larsson DGJ
FEMS Microbiol Rev 42 (1) - [2018-01-01; online 2017-10-27]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing?
Bengtsson-Palme J, Gunnarsson L, Larsson DGJ
Journal of Cleaner Production 171 (-) 137-146 [2018-01-00; online 2018-01-00]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Strategies for Taxonomic and Functional Annotation of Metagenomes
Bengtsson-Palme J
Metagenomics: Perspectives, Methods, and Applications - (-) 55-79 [2018-00-00; online 2018-00-00]
DDLS Fellow Johan Bengtsson-Palme

Year 2017

PubMed DOI Crossref
The relation between Blastocystis and the intestinal microbiota in Swedish travellers.
Forsell J, Bengtsson-Palme J, Angelin M, ..., Evengård B, Granlund M
BMC Microbiol. 17 (1) 231 [2017-12-11; online 2017-12-11]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data.
Berglund F, Marathe NP, Österlund T, ..., Larsson DGJ, Kristiansson E
Microbiome 5 (1) 134 [2017-10-12; online 2017-10-12]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Using metagenomics to investigate human and environmental resistomes.
Bengtsson-Palme J, Larsson DGJ, Kristiansson E
J Antimicrob Chemother 72 (10) 2690-2703 [2017-10-01; online 2017-07-05]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
In Vivo Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis.
Thorell K, Bengtsson-Palme J, Liu OH, ..., Lundin SB, Sjöling Å
Infect. Immun. 85 (10) - [2017-10-00; online 2017-09-20]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.
Hugerth LW, Andersson AF
Front Microbiol 8 (-) 1561 [2017-09-04; online 2017-09-04]
Affiliated researcher DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets.
Boulund F, Berglund F, Flach CF, ..., Larsson DGJ, Kristiansson E
BMC Genomics 18 (1) 682 [2017-09-02; online 2017-09-02]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The complete mitochondrial genome of the copepod Calanus glacialis.
Choquet M, Alves Monteiro HJ, Bengtsson-Palme J, Hoarau G
Mitochondrial DNA B Resour 2 (2) 506-507 [2017-08-06; online 2017-08-06]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Does antifouling paint select for antibiotic resistance?
Flach CF, Pal C, Svensson CJ, ..., Tysklind M, Larsson DGJ
Sci. Total Environ. 590-591 (-) 461-468 [2017-07-15; online 2017-03-08]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Mineral Type Structures Soil Microbial Communities
Ahmed E, Hugerth LW, Logue JB, ..., Andersson AF, Holmström SJM
Geomicrobiology Journal 34 (6) 538-545 [2017-07-03; online 2016-11-22]
Affiliated researcher DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data.
Richardson RT, Bengtsson-Palme J, Johnson RM
Mol Ecol Resour 17 (4) 760-769 [2017-07-00; online 2016-11-21]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life.
Wampach L, Heintz-Buschart A, Hogan A, ..., de Beaufort C, Wilmes P
Front Microbiol 8 (-) 738 [2017-05-02; online 2017-05-02]
Affiliated researcher DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Ten simple rules for surviving an interdisciplinary PhD.
Demharter S, Pearce N, Beattie K, ..., Deane CM, Knapp B
PLoS Comput Biol 13 (5) e1005512 [2017-05-00; online 2017-05-25]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites.
Pearce NM, Bradley AR, Krojer T, ..., Deane CM, von Delft F
Struct Dyn 4 (3) 032104 [2017-05-00; online 2017-02-28]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Pearce NM, Krojer T, Bradley AR, ..., Deane CM, von Delft F
Nat Commun 8 (-) 15123 [2017-04-24; online 2017-04-24]
DDLS Fellow Nicholas Pearce
DOI Crossref
Antibiotic resistance in the food supply chain: where can sequencing and metagenomics aid risk assessment?
Bengtsson-Palme J
Current Opinion in Food Science 14 (-) 66-71 [2017-04-00; online 2017-04-00]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination.
Krojer T, Talon R, Pearce N, ..., Marsden B, von Delft F
Acta Crystallogr D Struct Biol 73 (Pt 3) 267-278 [2017-03-01; online 2017-02-24]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Proper modelling of ligand binding requires an ensemble of bound and unbound states.
Pearce NM, Krojer T, von Delft F
Acta Crystallogr D Struct Biol 73 (Pt 3) 256-266 [2017-03-01; online 2017-03-06]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Gentle, fast and effective crystal soaking by acoustic dispensing.
Collins PM, Ng JT, Talon R, ..., Pearce NM, von Delft F
Acta Crystallogr D Struct Biol 73 (Pt 3) 246-255 [2017-03-01; online 2017-03-06]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers.
Lindh MV, Sjöstedt J, Ekstam B, ..., Legrand C, Pinhassi J
Environ. Microbiol. 19 (3) 1222-1236 [2017-03-00; online 2017-02-06]
Affiliated researcher DDLS Fellow Luisa Hugerth

Year 2016

PubMed DOI Crossref
FARAO: the flexible all-round annotation organizer.
Hammarén R, Pal C, Bengtsson-Palme J
Bioinformatics 32 (23) 3664-3666 [2016-12-01; online 2016-08-04]
Affiliated researcher DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics.
Bengtsson-Palme J, Hammarén R, Pal C, ..., Tysklind M, Larsson DGJ
Sci. Total Environ. 572 (-) 697-712 [2016-12-01; online 2016-08-17]
Affiliated researcher DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The structure and diversity of human, animal and environmental resistomes.
Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG
Microbiome 4 (1) 54 [2016-10-07; online 2016-10-07]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
An introduction to plant phylogenomics with a focus on palms
Barrett CF, Bacon CD, Antonelli A, Cano Á, Hofmann T
Bot. J. Linn. Soc. 182 (2) 234-255 [2016-10-00; online 2016-03-18]
DDLS Fellow Tobias Andermann
DOI Crossref
Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
Abarenkov K, Adams RI, Laszlo I, ..., Schriml L, Nilsson RH
MykoKeys 16 (-) 1-15 [2016-09-26; online 2016-09-26]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Strategies to improve usability and preserve accuracy in biological sequence databases.
Bengtsson-Palme J, Boulund F, Edström R, ..., Sanli K, Thorell K
Proteomics 16 (18) 2454-2460 [2016-09-00; online 2016-08-17]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.
Lundström SV, Östman M, Bengtsson-Palme J, ..., Flach CF, Larsson DGJ
Sci. Total Environ. 553 (-) 587-595 [2016-05-15; online 2016-03-22]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2
Bengtsson-Palme J, Thorell K, Wurzbacher C, Sjöling Å, Nilsson RH
Ecological Informatics 33 (-) 45-50 [2016-05-00; online 2016-05-00]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation.
Bengtsson-Palme J, Larsson DG
Environ Int 86 (-) 140-149 [2016-01-00; online 2015-11-17]
DDLS Fellow Johan Bengtsson-Palme

Year 2015

PubMed DOI Crossref
Metagenome-assembled genomes uncover a global brackish microbiome.
Hugerth LW, Larsson J, Alneberg J, ..., Pinhassi J, Andersson AF
Genome Biol. 16 (-) 279 [2015-12-14; online 2015-12-14]
Affiliated researcher DDLS Fellow Luisa Hugerth
DOI Crossref
The European technical report on aquatic effect-based monitoring tools under the water framework directive
Wernersson AS, Carere M, Maggi C, ..., Kammann U, Kase R
Environ Sci Eur 27 (1) - [2015-12-00; online 2015-03-11]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential.
Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG
BMC Genomics 16 (-) 964 [2015-11-17; online 2015-11-17]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.
Bengtsson-Palme J, Hartmann M, Eriksson KM, ..., Larsson DG, Nilsson RH
Mol Ecol Resour 15 (6) 1403-1414 [2015-11-00; online 2015-03-23]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.
Sanli K, Bengtsson-Palme J, Nilsson RH, ..., Blanck H, Eriksson KM
Front Microbiol 6 (-) 1192 [2015-10-30; online 2015-10-30]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents.
Bengtsson-Palme J, Angelin M, Huss M, ..., Larsson DG, Johansson A
Antimicrob. Agents Chemother. 59 (10) 6551-6560 [2015-10-00; online 2015-08-10]
Affiliated researcher DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling.
Lindh MV, Sjöstedt J, Andersson AF, ..., Legrand C, Pinhassi J
Environ. Microbiol. 17 (7) 2459-2476 [2015-07-00; online 2015-01-27]
Affiliated researcher DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Antibiotic resistance genes in the environment: prioritizing risks.
Bengtsson-Palme J, Larsson DG
Nat. Rev. Microbiol. 13 (6) 396 [2015-06-00; online 2015-04-27]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
ITS1: a DNA barcode better than ITS2 in eukaryotes?
Wang XC, Liu C, Huang L, ..., Cai D, Li JQ
Mol Ecol Resour 15 (3) 573-586 [2015-05-00; online 2014-09-24]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts.
Nilsson RH, Tedersoo L, Ryberg M, ..., Edgar RC, Abarenkov K
Microbes Environ 30 (2) 145-150 [2015-03-19; online 2015-03-19]
DDLS Fellow Johan Bengtsson-Palme

Year 2014

PubMed DOI Crossref
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India.
Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DG
Front Microbiol 5 (-) 648 [2014-12-02; online 2014-12-02]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.
Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A
BMC Genomics 15 (-) 749 [2014-09-01; online 2014-09-01]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies.
Hugerth LW, Wefer HA, Lundin S, ..., Engstrand L, Andersson AF
Applied and environmental microbiology 80 (16) 5116-5123 [2014-08-00; online 2014-06-13]
Affiliated researcher DDLS Fellow Luisa Hugerth
DOI Crossref
Improving ITS sequence data for identification of plant pathogenic fungi
Nilsson RH, Hyde KD, Pawłowska J, ..., Kõljalg U, Abarenkov K
Fungal Diversity 67 (1) 11-19 [2014-07-00; online 2014-05-15]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.
Hugerth LW, Muller EE, Hu YO, ..., Wilmes P, Andersson AF
PLoS ONE 9 (4) e95567 [2014-04-22; online 2014-04-22]
Affiliated researcher DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
BacMet: antibacterial biocide and metal resistance genes database.
Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DG
Nucleic Acids Res. 42 (Database issue) D737-D743 [2014-01-00; online 2013-12-03]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Metaxa, Overview
Bengtsson-Palme J, Hartmann M, Eriksson KM, Nilsson RH
Encyclopedia of Metagenomics - (-) 1-5 [2014-00-00; online 2014-04-16]
DDLS Fellow Johan Bengtsson-Palme

Year 2013

PubMed DOI Crossref
Towards a unified paradigm for sequence-based identification of fungi.
Kõljalg U, Nilsson RH, Abarenkov K, ..., Weiss M, Larsson KH
Mol. Ecol. 22 (21) 5271-5277 [2013-11-00; online 2013-09-24]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
Bengtsson-Palme J, Ryberg M, Hartmann M, ..., Veldre V, Nilsson RH
Methods Ecol Evol - (-) n/a-n/a [2013-07-00; online 2013-07-19]
DDLS Fellow Johan Bengtsson-Palme

Year 2012

DOI Crossref
Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
Nilsson RH, Tedersoo L, Abarenkov K, ..., Larsson E, Kõljalg U
MykoKeys 4 (-) 37-63 [2012-09-05; online 2012-09-05]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets.
Bengtsson J, Hartmann M, Unterseher M, ..., Eriksson KM, Nilsson RH
Res. Microbiol. 163 (6-7) 407-412 [2012-07-00; online 2012-07-21]
DDLS Fellow Johan Bengtsson-Palme

Year 2011

PubMed DOI Crossref
Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.
Bengtsson J, Eriksson KM, Hartmann M, ..., Rosenblad MA, Nilsson RH
Antonie Van Leeuwenhoek 100 (3) 471-475 [2011-10-00; online 2011-06-15]
DDLS Fellow Johan Bengtsson-Palme
SciLifeLab Data Centre
Publications 9.5.0