DDLS Fellow

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Primary: Shown in the list of current labels.

Year 2025

DOI Crossref
Strategies for taxonomic and functional annotation of metagenomes
Abramova A, Bengtsson-Palme J
- - (-) 57-81 [2025-00-00; online 2025-00-00]
DDLS Fellow Johan Bengtsson-Palme

Year 2024

DOI Crossref
Fish are poor sentinels for surveillance of riverine AMR
Tskhay F, Köbsch C, Elena AX, ..., Berendonk TU, Klümper U
- - (-) - [2024-10-22; online 2024-10-22]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Metagenomic assemblies tend to break around antibiotic resistance genes.
Abramova A, Karkman A, Bengtsson-Palme J
BMC Genomics 25 (1) 959 [2024-10-14; online 2024-10-14]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Genetic Adaptation to Amoxicillin inEscherichia coli: The Limited Role ofdinBandkatE
Teichmann L, Wenne M, Luitwieler S, ..., Bengtsson-Palme J, Kuile Bt
- - (-) - [2024-10-06; online 2024-10-06]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
The ACROBAT 2022 challenge: Automatic registration of breast cancer tissue.
Weitz P, Valkonen M, Solorzano L, ..., Ruusuvuori P, Rantalainen M
Med Image Anal 97 (-) 103257 [2024-10-00; online 2024-07-01]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
The 'queen of the Andes' (Puya raimondii) is genetically fragile and fragmented: a consequence of long generation time and semelparity?
Liu L, James J, Zhang Y, ..., Lascoux M, Ge X
New Phytol. 244 (1) 277-291 [2024-10-00; online 2024-08-12]
DDLS Fellow Jennifer James
DOI Crossref
The Organelle in the Ointment: improved detection of cryptic mitochondrial reads resolves many unknown sequences in cross-species microbiome analyses
Sonett D, Brown T, Bengtsson-Palme J, Padilla-Gamiño JL, Zaneveld JR
ISME Commun - (-) - [2024-09-24; online 2024-09-24]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder
Weibel CA, Wheeler AL, James JE, ..., McShea H, Masel J
Elife 12 (-) - [2024-09-06; online 2024-09-06]
DDLS Fellow Jennifer James
PubMed DOI Crossref
Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.
Doktorova M, Daum S, Ebenhan J, ..., Kenworthy AK, Levental I
bioRxiv - (-) - [2024-09-04; online 2024-09-04]
DDLS Fellow Milka Doktorova
PubMed DOI Crossref
Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach.
Sharma KD, Doktorova M, Waxham MN, Heberle FA
Biophys. J. 123 (17) 2877-2891 [2024-09-03; online 2024-04-30]
DDLS Fellow Milka Doktorova
DOI Crossref
Structure prediction of alternative protein conformations
Bryant P, Noé F
Nat Commun 15 (1) - [2024-08-26; online 2024-08-26]
DDLS Fellow Patrick Bryant
PubMed DOI Crossref
Mechanistic modeling of cell viability assays with in silico lineage tracing.
Mutsuddy A, Huggins JR, Amrit A, ..., Calhoun JC, Birtwistle MR
bioRxiv - (-) - [2024-08-26; online 2024-08-26]
Cemal Erdem DDLS Fellow
PubMed DOI Crossref
Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance, and antibiotic resistance to infer contamination or naturalization.
Erb IK, Suarez C, Frank EM, ..., Lindberg E, Paul CJ
FEMS Microbes 5 (-) xtae024 [2024-08-14; online 2024-08-14]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.
Leal JL, Milesi P, Hodková E, ..., Salojärvi J, Lascoux M
Syst. Biol. 73 (2) 392-418 [2024-07-27; online 2024-04-13]
DDLS Fellow Jennifer James Pascal Milesi SciLifeLab Fellow
DOI Crossref
Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
Bryant P, Noé F
PLoS Comput Biol 20 (7) e1012253 [2024-07-25; online 2024-07-25]
DDLS Fellow Patrick Bryant
DOI Crossref
Design of linear and cyclic peptide binders of different lengths from protein sequence information
Li Q, Vlachos EN, Bryant P
- - (-) - [2024-06-22; online 2024-06-22]
DDLS Fellow Patrick Bryant
DOI Crossref
Fluoroquinolone-Specific Resistance Trajectories inE. coliand their Dependence on the SOS-Response
Teichmann L, Luitwieler S, Bengtsson-Palme J, ter Kuile B
- - (-) - [2024-06-06; online 2024-06-06]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Structure prediction of protein-ligand complexes from sequence information with Umol
Bryant P, Kelkar A, Guljas A, Clementi C, Noé F
Nat Commun 15 (1) - [2024-05-28; online 2024-05-28]
DDLS Fellow Patrick Bryant
PubMed DOI Crossref
Effectiveness and Cost-effectiveness of Artificial Intelligence-assisted Pathology for Prostate Cancer Diagnosis in Sweden: A Microsimulation Study.
Du X, Hao S, Olsson H, ..., Eklund M, Clements M
Eur Urol Oncol - (-) - [2024-05-23; online 2024-05-23]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Efficient calculation of orientation-dependent lipid dynamics from membrane simulations.
Doktorova M, Khelashvili G, Brown MF
bioRxiv - (-) - [2024-04-15; online 2024-04-15]
DDLS Fellow Milka Doktorova
PubMed DOI Crossref
Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity.
Moraes Zenker M, Portella TP, Pessoa FAC, Bengtsson-Palme J, Galetti PM
Sci Rep 14 (1) 7432 [2024-03-28; online 2024-03-28]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice.
Jarquín-Díaz VH, Ferreira SCM, Balard A, ..., Forslund-Startceva SK, Heitlinger E
ISME Commun 4 (1) ycae053 [2024-01-00; online 2024-04-15]
DDLS Fellow Johan Bengtsson-Palme

Year 2023

PubMed DOI Crossref
Seeing the Membrane from Both Sides Now: Lipid Asymmetry and Its Strange Consequences.
Doktorova M, Levental I, Heberle FA
Cold Spring Harbor Perspectives in Biology 15 (12) - [2023-12-01; online 2023-12-01]
DDLS Fellow Milka Doktorova
PubMed DOI Crossref
CCR5 promoter region polymorphisms in systemic lupus erythematosus.
Schauren JDS, de Oliveira AH, Consiglio CR, ..., Ellwanger JH, Chies JAB
Int J Immunogenet - (-) - [2023-11-20; online 2023-11-20]
Camila Consiglio DDLS Fellow
PubMed DOI Crossref
Between but Not Within-Species Variation in the Distribution of Fitness Effects.
James J, Kastally C, Budde KB, ..., Consortium G, ,
Mol. Biol. Evol. 40 (11) - [2023-11-03; online 2023-10-14]
DDLS Fellow Jennifer James Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
SRCAP mutations drive clonal hematopoiesis through epigenetic and DNA repair dysregulation.
Chen CW, Zhang L, Dutta R, ..., Sperling AS, Goodell MA
Cell Stem Cell 30 (11) 1503-1519.e8 [2023-11-02; online 2023-10-19]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Functional and molecular profiling of hematopoietic stem cells during regeneration.
Rydström A, Grahn THM, Niroula A, ..., Larsson J, Karlsson S
Exp. Hematol. 127 (-) 40-51 [2023-11-00; online 2023-09-04]
Abhishek Niroula DDLS Fellow
DOI Crossref
aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow
Pochon Z, Bergfeldt N, Kırdök E, ..., Unneberg P, Oskolkov N
Genome Biol. 24 (1) - [2023-10-23; online 2023-10-23]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Functional imaging studies of acute administration of classic psychedelics, ketamine, and MDMA: Methodological limitations and convergent results.
Linguiti S, Vogel JW, Sydnor VJ, ..., Dworkin RH, Satterthwaite TD
Neurosci Biobehav Rev 154 (-) 105421 [2023-10-05; online 2023-10-05]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Connectome-based modelling of neurodegenerative diseases: towards precision medicine and mechanistic insight.
Vogel JW, Corriveau-Lecavalier N, Franzmeier N, ..., Jones DT, Ewers M
Nat Rev Neurosci 24 (10) 620-639 [2023-10-00; online 2023-08-24]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Genetic modification of inflammation- and clonal hematopoiesis-associated cardiovascular risk.
Yu Z, Fidler TP, Ruan Y, ..., Tall AR, Natarajan P
J. Clin. Invest. 133 (18) - [2023-09-15; online 2023-09-15]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
A Multi-Stain Breast Cancer Histological Whole-Slide-Image Data Set from Routine Diagnostics.
Weitz P, Valkonen M, Solorzano L, ..., Ruusuvuori P, Rantalainen M
Sci Data 10 (1) 562 [2023-08-24; online 2023-08-24]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?
Bengtsson-Palme J, Abramova A, Berendonk TU, ..., Wester AL, Zahra R
Environ Int 178 (-) 108089 [2023-08-00; online 2023-07-05]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments.
Abramova A, Berendonk TU, Bengtsson-Palme J
Environ Int 178 (-) 108084 [2023-08-00; online 2023-07-03]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Cell Membranes Sustain Phospholipid Imbalance Via Cholesterol Asymmetry
Doktorova M, Symons JL, Zhang X, ..., Levental KR, Levental I
- - (-) - [2023-07-31; online 2023-07-31]
DDLS Fellow Milka Doktorova
DOI Crossref
A new codon adaptation metric predicts vertebrate body size and tendency to protein disorder
Weibel CA, Wheeler AL, James JE, Willis SM, Masel J
- - (-) - [2023-07-26; online 2023-07-26]
DDLS Fellow Jennifer James
PubMed DOI Crossref
A data-driven study of Alzheimer's disease related amyloid and tau pathology progression.
Aksman LM, Oxtoby NP, Scelsi MA, ..., Altmann A, ADNI
Brain - (-) - [2023-07-11; online 2023-07-11]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms.
Erdem C, Gross SM, Heiser LM, Birtwistle MR
Nat Commun 14 (1) 3991 [2023-07-06; online 2023-07-06]
Cemal Erdem DDLS Fellow
PubMed DOI Crossref
Birth Weight Is Associated With Clonal Hematopoiesis of Indeterminate Potential and Cardiovascular Outcomes in Adulthood.
Schuermans A, Nakao T, Ruan Y, ..., Natarajan P, Honigberg MC
J Am Heart Assoc 12 (13) e030220 [2023-07-04; online 2023-06-22]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Sex and gender in infection and immunity: addressing the bottlenecks from basic science to public health and clinical applications.
Pasin C, Consiglio CR, Huisman JS, ..., Kouyos RD, Bonhoeffer S
R Soc Open Sci 10 (7) 221628 [2023-07-00; online 2023-07-05]
Camila Consiglio DDLS Fellow
PubMed DOI Crossref
HLA Class I Genotype Is Associated with Relapse Risk after Allogeneic Stem Cell Transplantation for NPM1-Mutated Acute Myeloid Leukemia.
Narayan R, Niroula A, Wang T, ..., Spellman S, Lee SJ
Transplant Cell Ther 29 (7) 452.e1-452.e11 [2023-07-00; online 2023-03-29]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Building Asymmetric Lipid Bilayers for Molecular Dynamics Simulations: What Methods Exist and How to Choose One?
Chaisson EH, Heberle FA, Doktorova M
Membranes (Basel) 13 (7) - [2023-06-29; online 2023-06-29]
DDLS Fellow Milka Doktorova
PubMed DOI Crossref
RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy.
Øvrebø Ø, Ojansivu M, Kartasalo K, ..., Holme MN, Stevens MM
BMC Bioinformatics 24 (1) 237 [2023-06-05; online 2023-06-05]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Obesity-induced inflammation exacerbates clonal hematopoiesis.
Pasupuleti SK, Ramdas B, Burns SS, ..., Natarajan P, Kapur R
J. Clin. Invest. 133 (11) - [2023-06-01; online 2023-06-01]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments.
Bargheet A, Klingenberg C, Esaiassen E, ..., Bengtsson-Palme J, Pettersen VK
EBioMedicine 92 (-) 104613 [2023-06-00; online 2023-05-13]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Clonal Hematopoiesis of Indeterminate Potential Predicts Adverse Outcomes in Patients With Atherosclerotic Cardiovascular Disease.
Gumuser ED, Schuermans A, Cho SMJ, ..., Natarajan P, Honigberg MC
J. Am. Coll. Cardiol. 81 (20) 1996-2009 [2023-05-23; online 2023-05-18]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Data-driven neuropathological staging and subtyping of TDP-43 proteinopathies.
Young AL, Vogel JW, Robinson JL, ..., Lee EB, Hansson O
Brain - (-) - [2023-05-08; online 2023-05-08]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Comparison of Group-Level and Individualized Brain Regions for Measuring Change in Longitudinal Tau Positron Emission Tomography in Alzheimer Disease.
Leuzy A, Binette AP, Vogel JW, ..., Hansson O, Alzheimer’s Disease Neuroimaging Initiative
JAMA Neurol - (-) - [2023-05-08; online 2023-05-08]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
A practical approach to curate clonal hematopoiesis of indeterminate potential in human genetic data sets.
Vlasschaert C, Mack T, Heimlich JB, ..., Jaiswal S, Bick AG
Blood 141 (18) 2214-2223 [2023-05-04; online 2023-01-19]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Prediction of risk for myeloid malignancy in clonal hematopoiesis.
Weeks LD, Niroula A, Neuberg D, ..., Natarajan P, Ebert BL
NEJM Evid 2 (5) - [2023-05-00; online 2023-04-25]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Interobserver reproducibility of cribriform cancer in prostate needle biopsies and validation of International Society of Urological Pathology criteria.
Egevad L, Delahunt B, Iczkowski KA, ..., Eklund M, Kartasalo K
Histopathology 82 (6) 837-845 [2023-05-00; online 2023-01-25]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Development of top-down cortical propagations in youth.
Pines A, Keller AS, Larsen B, ..., Fair DA, Satterthwaite TD
Neuron 111 (8) 1316-1330.e5 [2023-04-19; online 2023-02-17]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends.
James JE, Nelson PG, Masel J
Mol. Biol. Evol. 40 (4) - [2023-04-04; online 2023-03-23]
DDLS Fellow Jennifer James
PubMed DOI Crossref
Gray matter hypoperfusion is a late pathological event in the course of Alzheimer's disease.
Ahmadi K, Pereira JB, Berron D, ..., Mutsaerts HJ, Hansson O
J. Cereb. Blood Flow Metab. 43 (4) 565-580 [2023-04-00; online 2022-11-22]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Clonal haematopoiesis and risk of chronic liver disease.
Wong WJ, Emdin C, Bick AG, ..., Ebert BL, Natarajan P
Nature 616 (7958) 747-754 [2023-04-00; online 2023-04-12]
Abhishek Niroula DDLS Fellow
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. 58 (10) 1131-1138 [2023-03-29; online 2023-03-29]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format.
Mutsuddy A, Erdem C, Huggins JR, ..., Feltus FA, Birtwistle MR
Bioinform Adv 3 (1) vbad039 [2023-03-23; online 2023-03-23]
Cemal Erdem DDLS Fellow
PubMed DOI Crossref
Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics.
Doktorova M, Khelashvili G, Ashkar R, Brown MF
Biophys. J. 122 (6) 984-1002 [2023-03-21; online 2022-12-05]
DDLS Fellow Milka Doktorova
DOI Crossref
MEMMAL: A tool for expanding large-scale mechanistic models with machine learned associations and big datasets
Erdem C, Birtwistle MR
Front. Syst. Biol. 3 (-) - [2023-03-09; online 2023-03-09]
Cemal Erdem DDLS Fellow
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
PubMed DOI Crossref
Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes.
Inda-Díaz JS, Lund D, Parras-Moltó M, ..., Bengtsson-Palme J, Kristiansson E
Microbiome 11 (1) 44 [2023-03-08; online 2023-03-08]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Clonal Hematopoiesis and Risk of Incident Lung Cancer.
Tian R, Wiley B, Liu J, ..., Bolton KL, Cao Y
J Clin Oncol 41 (7) 1423-1433 [2023-03-01; online 2022-12-08]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
TP53-mediated clonal hematopoiesis confers increased risk for incident atherosclerotic disease.
Zekavat SM, Viana-Huete V, Matesanz N, ..., Fuster JJ, Klarin D
Nat Cardiovasc Res 2 (-) 144-158 [2023-01-16; online 2023-03-24]
Abhishek Niroula DDLS Fellow
DOI Crossref
A Risk Management Framework for Emergence of Novel Antibiotic Resistance Determinants
Heß S, Bengtsson-Palme J
- - (-) - [2023-00-00; online 2023-00-00]
DDLS Fellow Johan Bengtsson-Palme

Year 2022

PubMed DOI Crossref
Obesity-Associated Neurodegeneration Pattern Mimics Alzheimer's Disease in an Observational Cohort Study.
Morys F, Potvin O, Zeighami Y, ..., Dagher A, Alzheimer’s Disease Neuroimaging Initiative
J. Alzheimers Dis. 91 (3) 1059-1071 [2022-12-25; online 2022-12-25]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Linking Individual Differences in Personalized Functional Network Topography to Psychopathology in Youth.
Cui Z, Pines AR, Larsen B, ..., Fan Y, Satterthwaite TD
Biol. Psychiatry 92 (12) 973-983 [2022-12-15; online 2022-05-18]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction.
Olsson H, Kartasalo K, Mulliqi N, ..., Spjuth O, Eklund M
Nat Commun 13 (1) 7761 [2022-12-15; online 2022-12-15]
DDLS Fellow Kimmo Kartasalo
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
DOI Crossref
The global groundwater resistome: core antibiotic resistance genes, their dynamics and drivers
Kampouris ID, Bengtsson-Palme J, Babin D, ..., Berendonk TU, Klümper U
- - (-) - [2022-11-15; online 2022-11-15]
DDLS Fellow Johan Bengtsson-Palme
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
Curation of BIDS (CuBIDS): A workflow and software package for streamlining reproducible curation of large BIDS datasets.
Covitz S, Tapera TM, Adebimpe A, ..., Cieslak M, Satterthwaite TD
NeuroImage 263 (-) 119609 [2022-11-00; online 2022-09-03]
DDLS Fellow Jacob W Vogel
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
PubMed DOI Crossref
Cholesterol's balancing act: Defying the status quo.
Doktorova M, Levental I
Biophys. J. 121 (20) 3771-3773 [2022-10-18; online 2022-08-30]
DDLS Fellow Milka Doktorova
PubMed DOI Crossref
A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.
Gross SM, Dane MA, Smith RL, ..., Gray JW, Heiser LM
Commun Biol 5 (1) 1066 [2022-10-07; online 2022-10-07]
Cemal Erdem DDLS Fellow
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
TET2-mutant clonal hematopoiesis and risk of gout.
Agrawal M, Niroula A, Cunin P, ..., Rao DA, Ebert BL
Blood 140 (10) 1094-1103 [2022-09-08; online 2022-06-18]
Abhishek Niroula DDLS Fellow
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
Mesowestern Blot: Simultaneous Analysis of Hundreds of Submicroliter Lysates.
Zadeh CO, Huggins JR, Sarmah D, ..., Erdem C, Birtwistle MR
ACS Omega 7 (33) 28912-28923 [2022-08-23; online 2022-08-11]
Cemal Erdem DDLS Fellow
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
PubMed DOI Crossref
nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.
Dang CC, Minh BQ, McShea H, ..., Vinh LS, Lanfear R
Syst. Biol. 71 (5) 1110-1123 [2022-08-10; online 2022-02-10]
DDLS Fellow Jennifer James
PubMed DOI Crossref
Local molecular and global connectomic contributions to cross-disorder cortical abnormalities.
Hansen JY, Shafiei G, Vogel JW, ..., Dagher A, Misic B
Nat Commun 13 (1) 4682 [2022-08-10; online 2022-08-10]
DDLS Fellow Jacob W Vogel
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
Issues and recommendations for the residual approach to quantifying cognitive resilience and reserve.
Elman JA, Vogel JW, Bocancea DI, ..., Kremen WS, Alzheimer’s Disease Neuroimaging Initiative
Alzheimers Res Ther 14 (1) 102 [2022-07-25; online 2022-07-25]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Detection of perineural invasion in prostate needle biopsies with deep neural networks.
Kartasalo K, Ström P, Ruusuvuori P, ..., Eklund M, Egevad L
Virchows Arch. 481 (1) 73-82 [2022-07-00; online 2022-04-21]
DDLS Fellow Kimmo Kartasalo
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
Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression-based convolutional neural networks.
Weitz P, Wang Y, Kartasalo K, ..., Eklund M, Rantalainen M
Bioinformatics 38 (13) 3462-3469 [2022-06-27; online 2022-05-21]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.
Erdem C, Mutsuddy A, Bensman EM, ..., Feltus FA, Birtwistle MR
Nat Commun 13 (1) 3555 [2022-06-21; online 2022-06-21]
Cemal Erdem DDLS Fellow
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
Probing the Link between Pancratistatin and Mitochondrial Apoptosis through Changes in the Membrane Dynamics on the Nanoscale.
Castillo SR, Rickeard BW, DiPasquale M, ..., Kelley EG, Marquardt D
Mol. Pharm. 19 (6) 1839-1852 [2022-06-06; online 2022-05-13]
DDLS Fellow Milka Doktorova
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
Genetics of smoking and risk of clonal hematopoiesis.
Levin MG, Nakao T, Zekavat SM, ..., Damrauer SM, Natarajan P
Sci Rep 12 (1) 7248 [2022-05-04; online 2022-05-04]
Abhishek Niroula DDLS Fellow
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
Subtypes of Alzheimer's disease: questions, controversy, and meaning.
Vogel JW, Hansson O
Trends Neurosci 45 (5) 342-345 [2022-05-00; online 2022-02-25]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Clonal Hematopoiesis and CKD Progression.
Niroula A, Belizaire R
J. Am. Soc. Nephrol. 33 (5) 878-879 [2022-05-00; online 2022-04-06]
Abhishek Niroula DDLS Fellow
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
Multiple Cortical to Striatal Accumulation Trajectories of β-Amyloid: Do All Roads Lead to Rome?
Vogel JW, Tosun D
Neurology 98 (17) 695-696 [2022-04-26; online 2022-03-25]
DDLS Fellow Jacob W Vogel
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
Differentiating amyloid beta spread in autosomal dominant and sporadic Alzheimer's disease.
Levitis E, Vogel JW, Funck T, ..., Dominantly Inherited Alzheimer Network , Alzheimer’s Disease Neuroimaging Initiative
Brain Commun 4 (3) fcac085 [2022-04-13; online 2022-04-13]
DDLS Fellow Jacob W Vogel
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
Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of indeterminate potential.
Nakao T, Bick AG, Taub MA, ..., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium , Natarajan P
Sci Adv 8 (14) eabl6579 [2022-04-08; online 2022-04-06]
Abhishek Niroula DDLS Fellow
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
Brain charts for the human lifespan.
Bethlehem RAI, Seidlitz J, White SR, ..., Bullmore ET, Alexander-Bloch AF
Nature 604 (7906) 525-533 [2022-04-00; online 2022-04-06]
DDLS Fellow Jacob W Vogel
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
Genome-wide association study on 13 167 individuals identifies regulators of blood CD34+cell levels.
Lopez de Lapuente Portilla A, Ekdahl L, Cafaro C, ..., Stefansson K, Nilsson B
Blood 139 (11) 1659-1669 [2022-03-17; online 2022-01-11]
Abhishek Niroula DDLS Fellow
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
PubMed DOI Crossref
Clonal Hematopoiesis Is Associated With Higher Risk of Stroke.
Bhattacharya R, Zekavat SM, Haessler J, ..., Natarajan P, Reiner AP
Stroke 53 (3) 788-797 [2022-03-00; online 2021-11-08]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Biomarker-Based Prediction of Longitudinal Tau Positron Emission Tomography in Alzheimer Disease.
Leuzy A, Smith R, Cullen NC, ..., Stomrud E, Hansson O
JAMA Neurol 79 (2) 149-158 [2022-02-01; online 2021-12-21]
DDLS Fellow Jacob W Vogel
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
PubMed DOI Crossref
Association of clonal hematopoiesis with chronic obstructive pulmonary disease.
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

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
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
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
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
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
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
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
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
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
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
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

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
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
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
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
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
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
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
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
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
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

Year 2019

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
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
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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

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
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
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
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
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
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
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
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

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
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
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
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
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
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
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
SciLifeLab Data Centre
Publications 9.5.1