DDLS Fellow (500 publications)

Miller PG, Qiao D, Rojas-Quintero J, ..., Ebert BL, COPDGene Study Investigators, National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine Consortium

Blood 139 (3) 357-368 [2022-01-20; online 2021-12-03]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Functional dissection of inherited non-coding variation influencing multiple myeloma risk.

Ajore R, Niroula A, Pertesi M, ..., Houlston R, Nilsson B

Nat Commun 13 (1) 151 [2022-01-10; online 2022-01-10]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment.

Ruusuvuori P, Valkonen M, Kartasalo K, ..., Nykter M, Latonen L

Heliyon 8 (1) e08762 [2022-01-00; online 2022-01-14]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Artificial intelligence for diagnosis and Gleason grading of prostate cancer: the PANDA challenge.

Bulten W, Kartasalo K, Chen PC, ..., Eklund M, PANDA challenge consortium

Nat. Med. 28 (1) 154-163 [2022-01-00; online 2022-01-13]

DDLS Fellow Kimmo Kartasalo

DOI Crossref

Cholesterol stiffening of lipid membranes and drug interactions: Insights from neutron spin echo and deuterium NMR spectroscopy

Gupta S, Doole FT, Kumarage T, ..., Ashkar R, Brown MF

- - (-) 771-796 [2022-00-00; online 2022-00-00]

DDLS Fellow Milka Doktorova

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

Dnmt3a-mutated clonal hematopoiesis promotes osteoporosis.

Kim PG, Niroula A, Shkolnik V, ..., Natarajan P, Ebert BL

J. Exp. Med. 218 (12) - [2021-12-06; online 2021-10-26]

Abhishek Niroula DDLS Fellow

DOI Crossref

Smart3-ATAC: a highly sensitive method for joint accessibility and full-length transcriptome analysis in single cells

Cheng H, Pui Hp, Lentini A, ..., Deng Q, Enge M

- - (-) - [2021-12-03; online 2021-12-03]

Antonio Lentini DDLS Fellow

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

OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology.

Mulliqi N, Kartasalo K, Olsson H, ..., Eklund M, Ruusuvuori P

Bioinformatics 37 (21) 3995-3997 [2021-11-05; online 2021-08-07]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Vesicle Viewer: Online visualization and analysis of small-angle scattering from lipid vesicles.

Lewis-Laurent A, Doktorova M, Heberle FA, Marquardt D

Biophys. J. 120 (21) 4639-4648 [2021-11-02; online 2021-09-24]

DDLS Fellow Milka Doktorova

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

Distinction of lymphoid and myeloid clonal hematopoiesis.

Niroula A, Sekar A, Murakami MA, ..., Natarajan P, Ebert BL

Nat. Med. 27 (11) 1921-1927 [2021-11-00; online 2021-10-18]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration.

Liimatainen K, Latonen L, Valkonen M, Kartasalo K, Ruusuvuori P

BMC Cancer 21 (1) 1133 [2021-10-22; online 2021-10-22]

DDLS Fellow Kimmo Kartasalo

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

Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil.

Kipper D, Orsi RH, Carroll LM, ..., Wiedmann M, Lunge VR

Applied and environmental microbiology 87 (21) e0103621 [2021-10-14; online 2021-08-18]

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

Predicting Molecular Phenotypes from Histopathology Images: A Transcriptome-Wide Expression-Morphology Analysis in Breast Cancer.

Wang Y, Kartasalo K, Weitz P, ..., Hartman J, Rantalainen M

Cancer Res. 81 (19) 5115-5126 [2021-10-01; online 2021-08-02]

DDLS Fellow Kimmo Kartasalo

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

PubMed DOI Crossref

Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer.

Chelebian E, Avenel C, Kartasalo K, ..., Lundeberg J, Wählby C

Cancers (Basel) 13 (19) - [2021-09-28; online 2021-09-28]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations.

Huang X, Fortier AL, Coffman AJ, ..., Ragsdale AP, Gutenkunst RN

Mol. Biol. Evol. 38 (10) 4588-4602 [2021-09-27; online 2021-05-28]

DDLS Fellow Jennifer James

PubMed DOI Crossref

Using informative features in machine learning based method for COVID-19 drug repurposing.

Aghdam R, Habibi M, Taheri G

J Cheminform 13 (1) 70 [2021-09-20; online 2021-09-20]

DDLS Fellow Golnaz Taheri

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

PubMed DOI Crossref

Association of Diet Quality With Prevalence of Clonal Hematopoiesis and Adverse Cardiovascular Events.

Bhattacharya R, Zekavat SM, Uddin MM, ..., Bick A, Natarajan P

JAMA Cardiol 6 (9) 1069-1077 [2021-09-01; online 2021-06-10]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

ZBTB33 is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing.

Beauchamp EM, Leventhal M, Bernard E, ..., Jaiswal S, Ebert BL

Blood Cancer Discov 2 (5) 500-517 [2021-09-00; online 2021-07-14]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia.

Bensberg M, Rundquist O, Selimović A, ..., Lentini A, Nestor CE

Proc. Natl. Acad. Sci. U.S.A. 118 (34) - [2021-08-24; online 2021-08-21]

Antonio Lentini DDLS Fellow

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

The emerging role of artificial intelligence in the reporting of prostate pathology.

Egevad L, Delahunt B, Samaratunga H, ..., Kartasalo K, Eklund M

Pathology 53 (5) 565-567 [2021-08-00; online 2021-06-06]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Structure and Interdigitation of Chain-Asymmetric Phosphatidylcholines and Milk Sphingomyelin in the Fluid Phase.

Frewein MPK, Doktorova M, Heberle FA, ..., Porcar L, Pabst G

Symmetry (Basel) 13 (8) - [2021-08-00; online 2021-08-05]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

Model Membrane Systems Used to Study Plasma Membrane Lipid Asymmetry.

Scott HL, Kennison KB, Enoki TA, ..., Heberle FA, Katsaras J

Symmetry (Basel) 13 (8) - [2021-08-00; online 2021-07-26]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

Topological network based drug repurposing for coronavirus 2019.

Habibi M, Taheri G

PLoS ONE 16 (7) e0255270 [2021-07-29; online 2021-07-29]

DDLS Fellow Golnaz Taheri

PubMed DOI Crossref

Supplemental Association of Clonal Hematopoiesis With Incident Heart Failure.

Yu B, Roberts MB, Raffield LM, ..., Eaton CB, National Heart, Lung, and Blood Institute TOPMed Consortium

J. Am. Coll. Cardiol. 78 (1) 42-52 [2021-07-06; online 2021-07-03]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Artificial Intelligence for Diagnosis and Gleason Grading of Prostate Cancer in Biopsies-Current Status and Next Steps.

Kartasalo K, Bulten W, Delahunt B, ..., Egevad L, Eklund M

Eur Urol Focus 7 (4) 687-691 [2021-07-00; online 2021-08-12]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Prognostic implications of troponin T variations in inherited cardiomyopathies using systems biology.

Shakur R, Ochoa JP, Robinson AJ, ..., Vihinen M, Monserrat L

NPJ Genom Med 6 (1) 47 [2021-06-14; online 2021-06-14]

Abhishek Niroula DDLS Fellow

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

Interobserver reproducibility of perineural invasion of prostatic adenocarcinoma in needle biopsies.

Egevad L, Delahunt B, Samaratunga H, ..., Eklund M, Ruusuvuori P

Virchows Arch. 478 (6) 1109-1116 [2021-06-00; online 2021-02-03]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells.

Erdem C, Lee AV, Taylor DL, Lezon TR

PLoS Comput Biol 17 (6) e1009125 [2021-06-00; online 2021-06-30]

Cemal Erdem DDLS Fellow

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

Reply to Nagle et al.: The universal stiffening effects of cholesterol on lipid membranes.

Ashkar R, Doktorova M, Heberle FA, ..., Khelashvili G, Brown MF

Proc. Natl. Acad. Sci. U.S.A. 118 (20) - [2021-05-18; online 2021-05-07]

DDLS Fellow Milka Doktorova

DOI Crossref

Accuratede novoidentification of biosynthetic gene clusters with GECCO

Carroll LM, Larralde M, Fleck JS, ..., Cappio E, Zeller G

- - (-) - [2021-05-04; online 2021-05-04]

DDLS Fellow Laura Carroll

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

A SARS-CoV-2 (COVID-19) biological network to find targets for drug repurposing.

Habibi M, Taheri G, Aghdam R

Sci Rep 11 (1) 9378 [2021-04-30; online 2021-04-30]

DDLS Fellow Golnaz Taheri

PubMed DOI Crossref

Germline variants at SOHLH2 influence multiple myeloma risk.

Duran-Lozano L, Thorleifsson G, Lopez de Lapuente Portilla A, ..., Stefansson K, Nilsson B

Blood Cancer J 11 (4) 76 [2021-04-19; online 2021-04-19]

Abhishek Niroula DDLS Fellow

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

Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide.

Khelashvili G, Plante A, Doktorova M, Weinstein H

Biophys. J. 120 (6) 1105-1119 [2021-03-16; online 2021-02-23]

DDLS Fellow Milka Doktorova

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

PubMed DOI Crossref

Author Correction: Inherited causes of clonal haematopoiesis in 97,691 whole genomes.

Bick AG, Weinstock JS, Nandakumar SK, ..., Kathiresan S, Natarajan P

Nature 591 (7851) E27 [2021-03-00; online 2021-03-13]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Antibiotic Resistance in Shiga Toxigenic Escherichia coli Isolates from Surface Waters and Sediments in a Mixed Use Urban Agricultural Landscape.

Ma Y, Chen J, Fong K, ..., Delaquis P, Wang S

Antibiotics (Basel) 10 (3) - [2021-02-26; online 2021-02-26]

DDLS Fellow Laura Carroll

DOI Crossref

The Organelle in the Ointment: cryptic mitochondria account for many unknown sequences in cross-species microbiome comparisons

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

PubMed DOI Crossref

Accelerating target deconvolution for therapeutic antibody candidates using highly parallelized genome editing.

Mattsson J, Ekdahl L, Junghus F, ..., Teige I, Nilsson B

Nat Commun 12 (1) 1277 [2021-02-24; online 2021-02-24]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Continuous human uterine NK cell differentiation in response to endometrial regeneration and pregnancy.

Strunz B, Bister J, Jönsson H, ..., Ivarsson MA, Björkström NK

Sci Immunol 6 (56) - [2021-02-19; online 2021-02-19]

Antonio Lentini DDLS Fellow

PubMed DOI Crossref

Premature Menopause, Clonal Hematopoiesis, and Coronary Artery Disease in Postmenopausal Women.

Honigberg MC, Zekavat SM, Niroula A, ..., NHLBI Trans-Omics for Precision Medicine Program , Natarajan P

Circulation 143 (5) 410-423 [2021-02-02; online 2020-11-09]

Abhishek Niroula DDLS Fellow

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

Universal and taxon-specific trends in protein sequences as a function of age.

James JE, Willis SM, Nelson PG, ..., Kosinski LJ, Masel J

Elife 10 (-) - [2021-01-08; online 2021-01-08]

DDLS Fellow Jennifer James

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

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

Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes.

James J, Eyre-Walker A

Genome Biol Evol 12 (12) 2441-2449 [2020-12-06; online 2020-10-24]

DDLS Fellow Jennifer James

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

Structural and functional consequences of reversible lipid asymmetry in living membranes.

Doktorova M, Symons JL, Levental I

Nat. Chem. Biol. 16 (12) 1321-1330 [2020-12-00; online 2020-11-16]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

S100A6 is a critical regulator of hematopoietic stem cells.

Grahn THM, Niroula A, Végvári Á, ..., Zubarev RA, Karlsson S

Leukemia 34 (12) 3323-3337 [2020-12-00; online 2020-06-19]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Identification of areas of grading difficulties in prostate cancer and comparison with artificial intelligence assisted grading.

Egevad L, Swanberg D, Delahunt B, ..., Clements M, Eklund M

Virchows Arch. 477 (6) 777-786 [2020-12-00; online 2020-06-15]

DDLS Fellow Kimmo Kartasalo

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

PubMed DOI Crossref

The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19.

Consiglio CR, Cotugno N, Sardh F, ..., Palma P, Brodin P

Cell 183 (4) 968-981.e7 [2020-11-12; online 2020-09-06]

Camila Consiglio DDLS Fellow

PubMed DOI Crossref

DNA methylation in infants with low and high body fatness.

Henriksson P, Lentini A, Altmäe S, ..., Nestor CE, Löf M

BMC Genomics 21 (1) 769 [2020-11-09; online 2020-11-09]

Antonio Lentini DDLS Fellow

PubMed DOI Crossref

Genomic Characterization of Salmonella Minnesota Clonal Lineages Associated with Poultry Production in Brazil.

Kipper D, Carroll LM, Mascitti AK, ..., Ikuta N, Lunge VR

Animals (Basel) 10 (11) - [2020-11-05; online 2020-11-05]

DDLS Fellow Laura Carroll

PubMed DOI Crossref

Novel Effective Bacillus cereus Group Species "Bacillus clarus" Is Represented by Antibiotic-Producing Strain ATCC 21929 Isolated from Soil.

Méndez Acevedo M, Carroll LM, Mukherjee M, ..., Dudley EG, Kovac J

mSphere 5 (6) - [2020-11-04; online 2020-11-04]

DDLS Fellow Laura Carroll

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

Androgen Receptor Signaling Positively Regulates Monocytic Development.

Consiglio CR, Gollnick SO

Front Immunol 11 (-) 519383 [2020-10-15; online 2020-10-15]

Camila Consiglio DDLS Fellow

PubMed DOI Crossref

ANHIR: Automatic Non-Rigid Histological Image Registration Challenge.

Borovec J, Kybic J, Arganda-Carreras I, ..., Zhao S, Munoz-Barrutia A

IEEE Trans Med Imaging 39 (10) 3042-3052 [2020-10-00; online 2020-04-07]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR.

Smyrlaki I, Ekman M, Lentini A, ..., Högberg B, Reinius B

Nat Commun 11 (1) 4812 [2020-09-23; online 2020-09-23]

Antonio Lentini DDLS Fellow

PubMed DOI Crossref

No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods.

Carroll LM, Cheng RA, Kovac J

Front Microbiol 11 (-) 580691 [2020-09-22; online 2020-09-22]

DDLS Fellow Laura Carroll

PubMed DOI Crossref

How cholesterol stiffens unsaturated lipid membranes.

Chakraborty S, Doktorova M, Molugu TR, ..., Brown MF, Ashkar R

Proc. Natl. Acad. Sci. U.S.A. 117 (36) 21896-21905 [2020-09-08; online 2020-08-25]

DDLS Fellow Milka Doktorova

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

Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State.

Carroll LM, Huisman JS, Wiedmann M

Sci Rep 10 (1) 14428 [2020-09-02; online 2020-09-02]

DDLS Fellow Laura Carroll

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

Enzalutamide, an Androgen Receptor Antagonist, Enhances Myeloid Cell-Mediated Immune Suppression and Tumor Progression.

Consiglio CR, Udartseva O, Ramsey KD, Bush C, Gollnick SO

Cancer Immunol Res 8 (9) 1215-1227 [2020-09-00; online 2020-07-13]

Camila Consiglio DDLS Fellow

PubMed DOI Crossref

Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19.

Rodriguez L, Pekkarinen PT, Lakshmikanth T, ..., Kekäläinen E, Brodin P

Cell Rep Med 1 (5) 100078 [2020-08-25; online 2020-08-05]

Camila Consiglio DDLS Fellow

PubMed DOI Crossref

Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group III Bacillus cereus Sensu Lato Facilitate the Transition between Emetic and Diarrheal Foodborne Pathogens.

Carroll LM, Wiedmann M

MBio 11 (4) - [2020-08-25; online 2020-08-25]

DDLS Fellow Laura Carroll

PubMed DOI Crossref

Mapping DNA Methylation in Mammals: The State of the Art.

Lentini A, Nestor CE

Methods in molecular biology (Clifton, N.J.) 2198 (-) 37-50 [2020-08-22; online 2020-08-22]

Antonio Lentini DDLS Fellow

PubMed DOI Crossref

Analyzing DNA-Immunoprecipitation Sequencing Data.

Lentini A, Nestor CE

Methods in molecular biology (Clifton, N.J.) 2198 (-) 431-439 [2020-08-22; online 2020-08-22]

Antonio Lentini DDLS Fellow

PubMed DOI Crossref

Natural killer cell immunotypes related to COVID-19 disease severity.

Maucourant C, Filipovic I, Ponzetta A, ..., Björkström NK, Karolinska COVID-19 Study Group

Sci Immunol 5 (50) - [2020-08-21; online 2020-08-23]

Antonio Lentini DDLS Fellow

PubMed DOI Crossref

Direct label-free imaging of nanodomains in biomimetic and biological membranes by cryogenic electron microscopy.

Heberle FA, Doktorova M, Scott HL, ..., Waxham MN, Levental I

Proc. Natl. Acad. Sci. U.S.A. 117 (33) 19943-19952 [2020-08-18; online 2020-08-05]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica.

Liao J, Orsi RH, Carroll LM, Wiedmann M

Environ. Microbiol. 22 (7) 2811-2828 [2020-07-00; online 2020-04-27]

DDLS Fellow Laura Carroll

PubMed DOI Crossref

Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data.

Doktorova M, Kučerka N, Kinnun JJ, ..., Katsaras J, Heberle FA

J Phys Chem B 124 (25) 5186-5200 [2020-06-25; online 2020-06-16]

DDLS Fellow Milka Doktorova

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

Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis.

Nilsson A, Haanstra JR, Engqvist M, ..., Teusink B, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 117 (19) 10294-10304 [2020-05-12; online 2020-04-27]

Avlant Nilsson DDLS Fellow

PubMed DOI Crossref

The utility of artificial intelligence in the assessment of prostate pathology.

Egevad L, Ström P, Kartasalo K, ..., Delahunt B, Eklund M

Histopathology 76 (6) 790-792 [2020-05-00; online 2020-05-14]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Identification of germline variants in adults with hemophagocytic lymphohistiocytosis.

Miller PG, Niroula A, Ceremsak JJ, ..., Berliner N, Ebert BL

Blood Adv 4 (5) 925-929 [2020-03-10; online 2020-03-10]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Stressful Beginnings with Long-Term Consequences.

Consiglio CR, Brodin P

Cell 180 (5) 820-821 [2020-03-05; online 2020-03-07]

Camila Consiglio DDLS Fellow

PubMed DOI Crossref

Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins.

Khelashvili G, Cheng X, Falzone ME, ..., Accardi A, Weinstein H

J Comput Chem 41 (6) 538-551 [2020-03-05; online 2019-11-21]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

No evidence for DNA N 6-methyladenine in mammals.

Douvlataniotis K, Bensberg M, Lentini A, Gylemo B, Nestor CE

Sci Adv 6 (12) eaay3335 [2020-03-00; online 2020-03-18]

Antonio Lentini DDLS Fellow

PubMed DOI Crossref

Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes.

Carroll LM, Wiedmann M, Kovac J

MBio 11 (1) - [2020-02-25; online 2020-02-25]

DDLS Fellow Laura Carroll

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

Regulation of lipid saturation without sensing membrane fluidity.

Ballweg S, Sezgin E, Doktorova M, ..., Hummer G, Ernst R

Nat Commun 11 (1) 756 [2020-02-06; online 2020-02-06]

DDLS Fellow Erdinc Sezgin Milka Doktorova SciLifeLab Fellow

PubMed DOI Crossref

Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation.

Moest M, Van Belleghem SM, James JE, ..., Steiner FM, Jiggins CD

PLoS Biol. 18 (2) e3000597 [2020-02-00; online 2020-02-06]

DDLS Fellow Jennifer James

PubMed DOI Crossref

Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study.

Ström P, Kartasalo K, Olsson H, ..., Egevad L, Eklund M

Lancet Oncol 21 (2) 222-232 [2020-02-00; online 2020-01-08]

DDLS Fellow Kimmo Kartasalo

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

Paenibacillus odorifer, the Predominant Paenibacillus Species Isolated from Milk in the United States, Demonstrates Genetic and Phenotypic Conservation of Psychrotolerance but Clade-Associated Differences in Nitrogen Metabolic Pathways.

Beno SM, Cheng RA, Orsi RH, ..., Martin NH, Wiedmann M

mSphere 5 (1) - [2020-01-22; online 2020-01-22]

DDLS Fellow Laura Carroll

PubMed DOI Crossref

On the Long and Winding Road to a Perfect Membrane Model.

Doktorova M

Biophys. J. 118 (2) 273-275 [2020-01-21; online 2019-11-28]

DDLS Fellow Milka Doktorova

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

PubMed DOI Crossref

MPRAscore: robust and non-parametric analysis of massively parallel reporter assays.

Niroula A, Ajore R, Nilsson B

Bioinformatics 35 (24) 5351-5353 [2019-12-15; online 2019-07-31]

Abhishek Niroula DDLS Fellow

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

Complex I is bypassed during high intensity exercise.

Nilsson A, Björnson E, Flockhart M, Larsen FJ, Nielsen J

Nat Commun 10 (1) 5072 [2019-11-07; online 2019-11-07]

Avlant Nilsson DDLS Fellow

PubMed DOI Crossref

ProTstab - predictor for cellular protein stability.

Yang Y, Ding X, Zhu G, ..., Lv Q, Vihinen M

BMC Genomics 20 (1) 804 [2019-11-04; online 2019-11-04]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

The importance of study design in the application of artificial intelligence methods in medicine.

Eklund M, Kartasalo K, Olsson H, Ström P

NPJ Digit Med 2 (-) 101 [2019-10-18; online 2019-10-18]

DDLS Fellow Kimmo Kartasalo

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

PubMed DOI Crossref

Peptide-Induced Lipid Flip-Flop in Asymmetric Liposomes Measured by Small Angle Neutron Scattering.

Nguyen MHL, DiPasquale M, Rickeard BW, ..., Katsaras J, Marquardt D

Langmuir 35 (36) 11735-11744 [2019-09-10; online 2019-08-27]

DDLS Fellow Milka Doktorova

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

A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases.

Gawel DR, Serra-Musach J, Lilja S, ..., Gustafsson M, Benson M

Genome Med 11 (1) 47 [2019-07-30; online 2019-07-30]

Antonio Lentini DDLS Fellow

PubMed DOI Crossref

3D-Printed Whole Prostate Models with Tumor Hotspots Using Dual-Extruder Printer.

Liimatainen K, Latonen L, Kartasalo K, Ruusuvuori P

Annu Int Conf IEEE Eng Med Biol Soc 2019 (-) 2867-2871 [2019-07-00; online 2020-01-18]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica.

Liao J, Orsi RH, Carroll LM, ..., Zhang H, Wiedmann M

BMC Evol Biol BMC Evolutionary Biology 19 (1) 132 [2019-06-21; online 2019-06-21]

DDLS Fellow Laura Carroll

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

Assembly and Characterization of a Pathogen Strain Collection for Produce Safety Applications: Pre-growth Conditions Have a Larger Effect on Peroxyacetic Acid Tolerance Than Strain Diversity.

Harrand AS, Kovac J, Carroll LM, ..., Kent DJ, Wiedmann M

Front Microbiol 10 (-) 1223 [2019-05-31; online 2019-05-31]

DDLS Fellow Laura Carroll

PubMed DOI Crossref

Sex differences in IL-17 contribute to chronicity in male versus female urinary tract infection.

Zychlinsky Scharff A, Rousseau M, Lacerda Mariano L, ..., Duffy D, Ingersoll MA

JCI Insight 5 (13) - [2019-05-30; online 2019-05-30]

Camila Consiglio DDLS Fellow

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

PubMed DOI Crossref

Identification of Novel Mobilized Colistin Resistance Gene mcr-9 in a Multidrug-Resistant, Colistin-Susceptible Salmonella enterica Serotype Typhimurium Isolate.

Carroll LM, Gaballa A, Guldimann C, ..., Henderson LO, Wiedmann M

MBio 10 (3) - [2019-05-07; online 2019-05-07]

DDLS Fellow Laura Carroll

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

Deep Learning in Image Cytometry: A Review.

Gupta A, Harrison PJ, Wieslander H, ..., Sintorn I, Wählby C

Cytometry A 95 (4) 366-380 [2019-04-00; online 2018-12-19]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Gramicidin Increases Lipid Flip-Flop in Symmetric and Asymmetric Lipid Vesicles.

Doktorova M, Heberle FA, Marquardt D, ..., Weinstein H, Andersen OS

Biophys. J. 116 (5) 860-873 [2019-03-05; online 2019-01-25]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges.

Carroll LM, Wiedmann M, Mukherjee M, ..., Cole JA, Kovac J

Front Microbiol 10 (-) 144 [2019-02-12; online 2019-02-12]

DDLS Fellow Laura Carroll

PubMed DOI Crossref

A New Computational Method for Membrane Compressibility: Bilayer Mechanical Thickness Revisited.

Doktorova M, LeVine MV, Khelashvili G, Weinstein H

Biophys. J. 116 (3) 487-502 [2019-02-05; online 2019-01-03]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

How good are pathogenicity predictors in detecting benign variants?

Niroula A, Vihinen M

PLoS Comput Biol 15 (2) e1006481 [2019-02-00; online 2019-02-11]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

TCF/LEF dependent and independent transcriptional regulation of Wnt/β-catenin target genes.

Doumpas N, Lampart F, Robinson MD, ..., Cantù C, Basler K

EMBO J. 38 (2) - [2019-01-15; online 2018-11-13]

Antonio Lentini DDLS Fellow

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

Next-Generation Sequencing

Wiedmann M, Carroll LM

- - (-) 376-383 [2019-00-00; online 2019-00-00]

DDLS Fellow Laura Carroll

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

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

PubMed DOI Crossref

Accurate In Silico Modeling of Asymmetric Bilayers Based on Biophysical Principles.

Doktorova M, Weinstein H

Biophys. J. 115 (9) 1638-1643 [2018-11-06; online 2018-09-15]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

Nearly Neutral Evolution across the Drosophila melanogaster Genome.

Castellano D, James J, Eyre-Walker A

Mol. Biol. Evol. 35 (11) 2685-2694 [2018-11-01; online 2018-11-13]

DDLS Fellow Jennifer James

PubMed DOI Crossref

First report of an mcr-1-harboring Salmonella enterica subsp. enterica serotype 4,5,12:i:- strain isolated from blood of a patient in Switzerland.

Carroll LM, Zurfluh K, Jang H, ..., Stephan R, Guldimann C

Int. J. Antimicrob. Agents 52 (5) 740-741 [2018-11-00; online 2018-08-10]

DDLS Fellow Laura Carroll

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

Focal Adhesion Kinase and ROCK Signaling Are Switch-Like Regulators of Human Adipose Stem Cell Differentiation towards Osteogenic and Adipogenic Lineages.

Hyväri L, Ojansivu M, Juntunen M, ..., Miettinen S, Vanhatupa S

Stem Cells Int 2018 (-) 2190657 [2018-09-12; online 2018-09-12]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Comparative analysis of tissue reconstruction algorithms for 3D histology.

Kartasalo K, Latonen L, Vihinen J, ..., Nykter M, Ruusuvuori P

Bioinformatics 34 (17) 3013-3021 [2018-09-01; online 2018-04-24]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Preparation of asymmetric phospholipid vesicles for use as cell membrane models.

Doktorova M, Heberle FA, Eicher B, ..., Pabst G, Marquardt D

Nat Protoc 13 (9) 2086-2101 [2018-09-00; online 2018-09-08]

DDLS Fellow Milka Doktorova

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

DNA methylation as a genomic marker of exposure to chemical and environmental agents.

Meehan RR, Thomson JP, Lentini A, Nestor CE, Pennings S

Curr Opin Chem Biol 45 (-) 48-56 [2018-08-00; online 2018-03-02]

Antonio Lentini DDLS Fellow

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 reassessment of DNA-immunoprecipitation-based genomic profiling.

Lentini A, Lagerwall C, Vikingsson S, ..., Benson M, Nestor CE

Nat. Methods 15 (7) 499-504 [2018-07-00; online 2018-06-25]

Antonio Lentini DDLS Fellow

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

Metabolite Depletion Affects Flux Profiling of Cell Lines.

Nilsson A, Haanstra JR, Teusink B, Nielsen J

Trends Biochem. Sci. 43 (6) 395-397 [2018-06-00; online 2018-04-12]

Avlant Nilsson DDLS Fellow

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 multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression.

Ali M, Ajore R, Wihlborg AK, ..., Weinhold N, Nilsson B

Nat Commun 9 (1) 1649 [2018-04-25; online 2018-04-25]

Abhishek Niroula DDLS Fellow

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

PON-tstab: Protein Variant Stability Predictor. Importance of Training Data Quality.

Yang Y, Urolagin S, Niroula A, ..., Shen B, Vihinen M

Int J Mol Sci 19 (4) - [2018-03-28; online 2018-03-28]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Recon3D enables a three-dimensional view of gene variation in human metabolism.

Brunk E, Sahoo S, Zielinski DC, ..., Thiele I, Palsson BO

Nat. Biotechnol. 36 (3) 272-281 [2018-03-00; online 2018-02-19]

Avlant Nilsson DDLS Fellow

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

Impacts of feeding preweaned calves milk containing drug residues on the functional profile of the fecal microbiota.

Pereira RVV, Carroll LM, Lima S, ..., Bicalho RC, Warnick LD

Sci Rep 8 (1) 554 [2018-01-11; online 2018-01-11]

DDLS Fellow Laura Carroll

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

PubMed DOI Crossref

Metabolic Models of Protein Allocation Call for the Kinetome.

Nilsson A, Nielsen J, Palsson BO

Cell Systems 5 (6) 538-541 [2017-12-27; online 2017-12-29]

Avlant Nilsson DDLS Fellow

PubMed DOI Crossref

Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer.

Ehteshami Bejnordi B, Veta M, Johannes van Diest P, ..., Racoceanu D, Venâncio R

JAMA 318 (22) 2199-2210 [2017-12-12; online 2017-12-14]

DDLS Fellow Kimmo Kartasalo

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

Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties.

Doktorova M, Heberle FA, Kingston RL, ..., Vogt VM, Dick RA

Biophys. J. 113 (9) 2004-2015 [2017-11-07; online 2017-11-09]

DDLS Fellow Milka Doktorova

DOI Crossref

Precision food safety: A systems approach to food safety facilitated by genomics tools

Kovac J, Bakker Hd, Carroll LM, Wiedmann M

TrAC Trends in Analytical Chemistry 96 (-) 52-61 [2017-11-00; online 2017-11-00]

DDLS Fellow Laura Carroll

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

DOI Crossref

Dual Structured Convolutional Neural Network with Feature Augmentation for Quantitative Characterization of Tissue Histology

Valkonen M, Kartasalo K, Liimatainen K, ..., Latonen L, Ruusuvuori P

- - (-) 27-35 [2017-10-00; online 2017-10-00]

DDLS Fellow Kimmo Kartasalo

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

Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data.

Carroll LM, Kovac J, Miller RA, Wiedmann M

Applied and environmental microbiology 83 (17) - [2017-09-01; online 2017-08-17]

DDLS Fellow Laura Carroll

PubMed DOI Crossref

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

Daneshjou R, Wang Y, Bromberg Y, ..., Brenner SE, Morgan AA

Hum. Mutat. 38 (9) 1182-1192 [2017-09-00; online 2017-07-07]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.

Carraro M, Minervini G, Giollo M, ..., Moult J, Tosatto SCE

Hum. Mutat. 38 (9) 1042-1050 [2017-09-00; online 2017-05-16]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned.

Niroula A, Vihinen M

Hum. Mutat. 38 (9) 1085-1091 [2017-09-00; online 2017-05-02]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Genome scale metabolic modeling of cancer.

Nilsson A, Nielsen J

Metab. Eng. 43 (Pt B) 103-112 [2017-09-00; online 2016-11-04]

Avlant Nilsson DDLS Fellow

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

p16(Ink4a) and senescence-associated β-galactosidase can be induced in macrophages as part of a reversible response to physiological stimuli.

Hall BM, Balan V, Gleiberman AS, ..., Chernova OB, Gudkov AV

Aging (Albany NY) 9 (8) 1867-1884 [2017-08-02; online 2017-08-05]

Camila Consiglio DDLS Fellow

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

A durable and biocompatible ascorbic acid-based covalent coating method of polydimethylsiloxane for dynamic cell culture.

Leivo J, Virjula S, Vanhatupa S, ..., Miettinen S, Kallio P

J R Soc Interface 14 (132) - [2017-07-00; online 2017-07-28]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations.

Doktorova M, Harries D, Khelashvili G

Phys Chem Chem Phys 19 (25) 16806-16818 [2017-06-28; online 2017-06-20]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations.

Carroll LM, Wiedmann M, den Bakker H, ..., Warnick LD, Pereira RV

Applied and environmental microbiology 83 (12) - [2017-06-15; online 2017-05-31]

DDLS Fellow Laura Carroll

PubMed DOI Crossref

Metastasis detection from whole slide images using local features and random forests.

Valkonen M, Kartasalo K, Liimatainen K, ..., Latonen L, Ruusuvuori P

Cytometry A 91 (6) 555-565 [2017-06-00; online 2017-04-20]

DDLS Fellow Kimmo Kartasalo

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

Temporal Genomic Phylogeny Reconstruction Indicates a Geospatial Transmission Path of Salmonella Cerro in the United States and a Clade-Specific Loss of Hydrogen Sulfide Production.

Kovac J, Cummings KJ, Rodriguez-Rivera LD, ..., Thachil A, Wiedmann M

Front Microbiol 8 (-) 737 [2017-05-01; online 2017-05-01]

DDLS Fellow Laura Carroll

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

PubMed DOI Crossref

Direct evidence for a polygenic etiology in familial multiple myeloma.

Halvarsson BM, Wihlborg AK, Ali M, ..., Hansson M, Nilsson B

Blood Adv 1 (10) 619-623 [2017-04-11; online 2017-04-07]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Predicting Severity of Disease-Causing Variants.

Niroula A, Vihinen M

Hum. Mutat. 38 (4) 357-364 [2017-04-00; online 2017-01-24]

Abhishek Niroula DDLS Fellow

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

Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models.

Valkonen M, Ruusuvuori P, Kartasalo K, ..., Visakorpi T, Latonen L

Sci Rep 7 (-) 44831 [2017-03-20; online 2017-03-20]

DDLS Fellow Kimmo Kartasalo

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

PubMed DOI Crossref

Potential Involvement of Type I Interferon Signaling in Immunotherapy in Seasonal Allergic Rhinitis.

Mattson L, Lentini A, Gawel DR, ..., Xiang Z, Zhang H

J Immunol Res 2016 (-) 5153184 [2016-12-19; online 2016-12-19]

Antonio Lentini DDLS Fellow

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

Bacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments.

Miller RA, Beno SM, Kent DJ, ..., Boor KJ, Kovac J

Int. J. Syst. Evol. Microbiol. 66 (11) 4744-4753 [2016-11-00; online 2016-08-12]

DDLS Fellow Laura Carroll

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

Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways.

Erdem C, Nagle AM, Casa AJ, ..., Lee AV, Lezon TR

Mol. Cell Proteomics 15 (9) 3045-3057 [2016-09-00; online 2016-06-30]

Cemal Erdem DDLS Fellow

DOI Crossref

Benchmarking of algorithms for 3D tissue reconstruction

Kartasalo K, Latonen L, Visakorpi T, Nykter M, Ruusuvuori P

- - (-) 2360-2364 [2016-09-00; online 2016-09-00]

DDLS Fellow Kimmo Kartasalo

DOI Crossref

A software tool for studying the size and shape of human cardiomyocytes

Rasku J, Ojala M, Pölönen RP, ..., Aalto-Setälä K, Juhola M

Biomedical Signal Processing and Control 30 (-) 134-139 [2016-09-00; online 2016-09-00]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Production of hemolysin BL by Bacillus cereus group isolates of dairy origin is associated with whole-genome phylogenetic clade.

Kovac J, Miller RA, Carroll LM, ..., Beno SM, Wiedmann M

BMC Genomics 17 (-) 581 [2016-08-09; online 2016-08-09]

DDLS Fellow Laura Carroll

PubMed DOI Crossref

5-Hydroxymethylcytosine Remodeling Precedes Lineage Specification during Differentiation of Human CD4(+) T Cells.

Nestor CE, Lentini A, Hägg Nilsson C, ..., Zhang H, Benson M

Cell Reports 16 (2) 559-570 [2016-07-12; online 2016-06-23]

Antonio Lentini DDLS Fellow

PubMed DOI Crossref

PON-Sol: prediction of effects of amino acid substitutions on protein solubility.

Yang Y, Niroula A, Shen B, Vihinen M

Bioinformatics 32 (13) 2032-2034 [2016-07-01; online 2016-02-19]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Application of a Nonlinear Model to Transcript Levels of Upregulated Stress Response Gene ibpA in Stationary-Phase Salmonella enterica Subjected to Sublethal Heat Stress.

Carroll LM, Bergholz TM, Hildebrandt IM, Marks BP

J Food Prot 79 (7) 1089-1096 [2016-07-00; online 2016-07-01]

DDLS Fellow Laura Carroll

PubMed DOI Crossref

Variation Interpretation Predictors: Principles, Types, Performance, and Choice.

Niroula A, Vihinen M

Hum. Mutat. 37 (6) 579-597 [2016-06-00; online 2016-04-15]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Subnanometer Structure of an Asymmetric Model Membrane: Interleaflet Coupling Influences Domain Properties.

Heberle FA, Marquardt D, Doktorova M, ..., London E, Pabst G

Langmuir 32 (20) 5195-5200 [2016-05-24; online 2016-05-16]

DDLS Fellow Milka Doktorova

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

PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations.

Niroula A, Vihinen M

Nucleic Acids Res. 44 (5) 2020-2027 [2016-03-18; online 2016-02-03]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase.

Nilsson A, Nielsen J

Sci Rep 6 (-) 22264 [2016-03-01; online 2016-03-01]

Avlant Nilsson DDLS Fellow

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

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

Classification of Amino Acid Substitutions in Mismatch Repair Proteins Using PON-MMR2.

Niroula A, Vihinen M

Hum. Mutat. 36 (12) 1128-1134 [2015-12-00; online 2015-09-22]

Abhishek Niroula DDLS Fellow

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

A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases.

Gustafsson M, Gawel DR, Alfredsson L, ..., Nestor CE, Benson M

Sci Transl Med 7 (313) 313ra178 [2015-11-11; online 2015-11-13]

Antonio Lentini DDLS Fellow

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

CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels.

Kartasalo K, Pölönen R, Ojala M, ..., Aalto-Setälä K, Kallio P

BMC Bioinformatics 16 (-) 344 [2015-10-26; online 2015-10-26]

DDLS Fellow Kimmo Kartasalo

PubMed DOI Crossref

Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer.

Ylipää A, Kivinummi K, Kohvakka A, ..., Visakorpi T, Nykter M

Cancer Res. 75 (19) 4026-4031 [2015-10-01; online 2015-08-17]

DDLS Fellow Kimmo Kartasalo

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

Harmful somatic amino acid substitutions affect key pathways in cancers.

Niroula A, Vihinen M

BMC Med Genomics 8 (-) 53 [2015-08-19; online 2015-08-19]

Abhishek Niroula DDLS Fellow

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

DOI Crossref

MATHEMATICAL MODELING OF BEHÇET'S DISEASE: A DYNAMICAL SYSTEMS APPROACH

ERDEM C, BOZKURT Y, ERMAN B, GÜL A, DEMIR A

J. Biol. Syst. 23 (02) 231-257 [2015-06-00; online 2015-05-28]

Cemal Erdem DDLS Fellow

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

Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2 -containing membranes.

Khelashvili G, Doktorova M, Sahai MA, ..., Shi L, Weinstein H

Proteins 83 (5) 952-969 [2015-05-00; online 2015-03-25]

DDLS Fellow Milka Doktorova

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

PubMed DOI Crossref

Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems.

Nestor CE, Ottaviano R, Reinhardt D, ..., Benson M, Meehan RR

Genome Biol. 16 (1) 11 [2015-02-04; online 2015-02-04]

Antonio Lentini DDLS Fellow

PubMed DOI Crossref

PON-P2: prediction method for fast and reliable identification of harmful variants.

Niroula A, Urolagin S, Vihinen M

PLoS ONE 10 (2) e0117380 [2015-02-03; online 2015-02-03]

Abhishek Niroula DDLS Fellow

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

PubMed DOI Crossref

Computational prediction of hinge axes in proteins.

Shamsuddin R, Doktorova M, Jaswal S, Lee-St John A, McMenimen K

BMC Bioinformatics 15 Suppl 8 (Suppl 8) S2 [2014-07-14; online 2014-07-14]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

A dedicated database system for handling multi-level data in systems biology.

Pornputtapong N, Wanichthanarak K, Nilsson A, Nookaew I, Nielsen J

Source Code Biol Med 9 (-) 17 [2014-07-10; online 2014-07-10]

Avlant Nilsson DDLS Fellow

PubMed DOI Crossref

SIRT1 promoter polymorphisms as clinical modifiers on systemic lupus erythematosus.

Consiglio CR, Juliana da Silveira S, Monticielo OA, ..., Brenol JC, Chies JA

Mol. Biol. Rep. 41 (7) 4233-4239 [2014-07-00; online 2014-02-26]

Camila Consiglio DDLS Fellow

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

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.

Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, ..., Nookaew I, Nielsen J

Nucleic Acids Res. 42 (Web Server issue) W175-W181 [2014-07-00; online 2014-05-03]

Avlant Nilsson DDLS Fellow

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

DNA methylation changes separate allergic patients from healthy controls and may reflect altered CD4+ T-cell population structure.

Nestor CE, Barrenäs F, Wang H, ..., Gustafsson M, Benson M

PLoS Genet 10 (1) e1004059 [2014-01-00; online 2014-01-02]

Antonio Lentini DDLS Fellow

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

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

PubMed DOI Crossref

Hybrid and nonhybrid lipids exert common effects on membrane raft size and morphology.

Heberle FA, Doktorova M, Goh SL, ..., Katsaras J, Feigenson GW

Journal of the American Chemical Society 135 (40) 14932-14935 [2013-10-09; online 2013-09-26]

DDLS Fellow Milka Doktorova

PubMed DOI Crossref

Profiling of human CD4+ T-cell subsets identifies the TH2-specific noncoding RNA GATA3-AS1.

Zhang H, Nestor CE, Zhao S, ..., Benson M, Wang H

J. Allergy Clin. Immunol. 132 (4) 1005-1008 [2013-10-00; online 2013-07-16]

Antonio Lentini DDLS Fellow

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

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

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

PubMed DOI Crossref

Association of the HLA-G gene +3142C>G polymorphism with systemic lupus erythematosus.

Consiglio CR, Veit TD, Monticielo OA, ..., Brenol JC, Chies JA

Tissue Antigens 77 (6) 540-545 [2011-06-00; online 2011-03-14]

Camila Consiglio DDLS Fellow

DDLS Fellow

Year 2025

Year 2024

Year 2023

Year 2022

Year 2021

Year 2020

Year 2019

Year 2018

Year 2017

Year 2016

Year 2015

Year 2014

Year 2013

Year 2012

Year 2011