Publications 2025

Identification of protein biomarkers to differentiate between gram-negative and gram-positive infections in adults suspected of sepsis

Irani Shemirani M, Pernestig AK, Björkman J, ..., Ejdebäck M, Ståhlberg A

BMC Infect Dis 25 (1) 1576 [2025-11-14; online 2025-11-14]

Ultraprocessed Food Consumption and Risk of Early-Onset Colorectal Cancer Precursors Among Women

Wang C, Du M, Kim H, ..., Cao Y, Chan AT

JAMA Oncol - (-) - [2025-11-13; online 2025-11-13]

Clonal Hematopoiesis and Major Adverse Cardiac Events in People With HIV: Insights From the REPRIEVE Trial.

Xue L, Bhattacharya R, Uddin MM, ..., Grinspoon SK, Natarajan P

Arterioscler. Thromb. Vasc. Biol. - (-) - [2025-11-06; online 2025-11-06]

Longitudinal development of sex differences in the limbic system is associated with age, puberty and mental health.

Matte Bon G, Walther J, Comasco E, Derntl B, Kaufmann T

Commun Biol 8 (1) 1524 [2025-11-05; online 2025-11-05]

Clonal Hematopoiesis and Risk of New-Onset Myocarditis and Pericarditis.

Schuermans A, Flynn S, Niroula A, ..., Natarajan P, Honigberg MC

JAMA Cardiol 10 (11) 1147-1156 [2025-11-01; online 2025-09-01]

White Matter Regional Volumes in Relation to Menstrual Cycle Phase and Premenstrual Dysphoric Disorder.

Stenhammar E, Dubol M, Stiernman L, ..., Bixo M, Comasco E

Biol Psychiatry Glob Open Sci 5 (6) 100573 [2025-11-00; online 2025-07-28]

Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells

Schaepe JM, Fries T, Doughty BR, ..., Marklund E, Greenleaf WJ

Cell - (-) - [2025-11-00; online 2025-11-00]

Emil Marklund SciLifeLab Fellow

Proximity extension assay inflammatory profiling cannot distinguish the presence of residual C-peptide in patients with long-standing type 1 diabetes.

Anvari E, Lundkvist P, Singh K, Espes D

Acta diabetologica 62 (11) 1987-1996 [2025-11-00; online 2025-06-05]

Continuous Glucose Monitoring Data Analysis 2.0: Functional Data Pattern Recognition and Artificial Intelligence Applications.

Klonoff DC, Bergenstal RM, Cengiz E, ..., Ho CN, Healey E

J Diabetes Sci Technol 19 (6) 1515-1527 [2025-11-00; online 2025-08-14]

Tissue and cellular spatiotemporal dynamics in colon aging

Daly AC, Cambuli F, Äijö T, ..., Regev A, Vickovic S

Nat Biotechnol - (-) - [2025-10-22; online 2025-10-22]

Sanja Vickovic SciLifeLab Fellow

Association of estrogen receptor single nucleotide polymorphisms and perinatal depression.

Björvang RD, Gumbo LF, Årdahl A, ..., Fransson E, Skalkidou A

PLoS ONE 20 (10) e0334705 [2025-10-16; online 2025-10-16]

Artificial intelligence-assisted prostate cancer diagnosis for reduced use of immunohistochemistry

Blilie A, Mulliqi N, Ji X, ..., Eklund M, Kartasalo K

Commun Med (Lond) 5 (1) - [2025-10-15; online 2025-10-15]

Discovering the unseen: a performance comparison of taxonomic classification methods for unknown DNA barcodes

Orsholm J, Zito A, Somervuo P, ..., Roslin T, Furneaux B

- - (-) - [2025-10-14; online 2025-10-14]

DDLS Fellow Mariana Pires Braga

Genomic insights into a diarrheal outbreak in Bangladesh reveal novel ETEC lineages and expansion of CS23 colonization factor.

Rahman SIA, Jubair M, Akhtar M, ..., von Mentzer A, Chowdhury F

Microbiol Spectr 13 (10) e0331524 [2025-10-07; online 2025-09-10]

Electrospun PLGA fibers with calcium phosphate nanoparticles: effects of nanoparticle crystallinity and carbonate content on osteogenic activity.

Suárez-López YDC, Ramachandran RV, Platania V, ..., Chatzinikolaidou M, Sotiriou GA

Biomater Sci 13 (20) 5863-5873 [2025-10-07; online 2025-10-07]

Genetic variation of the estrogen receptor and its association with depression and anxiety symptoms in young females.

Musaoglu MN, Olofsdotter S, Vadlin S, ..., Nieratschker V, Comasco E

Prog Neuropsychopharmacol Biol Psychiatry 142 (-) 111485 [2025-10-02; online 2025-09-05]

Plasma Metabolome, Long-term Body Weight Change, and Type 2 Diabetes in U.S. Individuals.

Wu Z, Liu B, Li J, ..., Hu Y, Sun Q

Diabetes Care 48 (10) 1818-1826 [2025-10-01; online 2025-08-13]

Image based subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing.

Tampere M, H Le T, Asp E, ..., Östling P, Stadler C

Biomed. Pharmacother. 191 (-) 118447 [2025-10-00; online 2025-08-16]

DDLS Fellow Wei Ouyang

Hierarchical Vision Transformers for prostate biopsy grading: Towards bridging the generalization gap.

Grisi C, Kartasalo K, Eklund M, ..., van der Laak J, Litjens G

Med Image Anal 105 (-) 103663 [2025-10-00; online 2025-07-07]

Alterations of the pancreas in type 1 diabetes - from prior to diagnosis to long-standing disease.

Missima NG, Hill H, Aioanei CS, Liss P, Espes D

Endocrine 90 (1) 140-148 [2025-10-00; online 2025-07-12]

Maternal aggression driven by the transient mobilisation of a dormant hormone-sensitive circuit.

Stagkourakis S, Williams P, Spigolon G, ..., Fisone G, Broberger C

Nat Commun 16 (1) 8553 [2025-09-29; online 2025-09-29]

SciLifeLab Fellow Stefanos Stagkourakis

Liquid biomarkers associate with TGF-β Type I receptor and hypoxia in kidney cancer.

Mallikarjuna P, Erdem C, Beorlegui RI, ..., Kamali-Moghaddam M, Landström M

Signal Transduct Target Ther 10 (1) 309 [2025-09-26; online 2025-09-26]

Cemal Erdem DDLS Fellow

Tertiary lymphoid structures in Merkel cell carcinoma facilitate naïve and central memory T-cell infiltration linked to immunotherapy response.

Srinivas N, Spassova I, Lei KC, ..., Lui WO, Becker JC

J Immunother Cancer 13 (9) - [2025-09-23; online 2025-09-23]

Camilla Engblom SciLifeLab Fellow

Gene copy number variation (gCNV) contributes to adaptation along environmental gradient

Zhou Q, Lascoux M, Milesi P

- - (-) - [2025-09-16; online 2025-09-16]

Pascal Milesi SciLifeLab Fellow

Evolvability: progress and key questions

Pélabon C, Agudelo-Cantero GA, Araya Ajoy YG, ..., Walling C, Wright J

BioScience - (-) - [2025-09-09; online 2025-09-09]

DDLS Fellow Lisandro Milocco

Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data

Li T, Yang Q, Acs B, ..., Chen X, Hartman J

NPJ Precis Oncol 9 (1) 310 [2025-09-09; online 2025-09-09]

Camilla Engblom SciLifeLab Fellow

Thiazole-fused thiazoliniums with ketone warheads as covalent inhibitors targeting Cys44 of SARS-CoV-2 3CLpro.

Cao Q, Zhang Z, Zhu G, ..., Ge G, Li B

Chem. Biol. Interact. 418 (-) 111620 [2025-09-05; online 2025-06-24]

U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis.

Xu W, Cai H, Zhang Q, ..., Ouyang W, Cao G

Genome Biol. 26 (1) 261 [2025-09-01; online 2025-09-01]

DDLS Fellow Wei Ouyang

Understanding the transport of drugs across biomimetic barriers of various phospholipid compositions using a combined experimental and computational approach.

Kabedev A, Tønning MH, Teleki A, Bauer-Brandl A, Jacobsen AC

Colloids Surf B Biointerfaces 253 (-) 114706 [2025-09-00; online 2025-04-21]

Genomic profiling of enterotoxigenic Escherichia coli toxins and adhesins in livestock isolates from Kenya.

Njoroge SM, Kulohoma BW, Falzon LC, ..., von Mentzer A, Fèvre EM

Microb Genom 11 (9) - [2025-09-00; online 2025-09-25]

Gene and pathway analysis of genome-wide genetic associations of bladder cancer.

Shi M, Meng X, Xu X, Wang Q

Curr Urol 19 (5) 321-330 [2025-09-00; online 2025-06-05]

Contextualizing Telomere Biology Through Biopsychological Plasticity: Insights From the Differential Susceptibility Hypothesis.

Comasco E

Biol Psychiatry Glob Open Sci 5 (5) 100548 [2025-09-00; online 2025-06-07]

A Base-Mediated Rearrangement of the Benzylic 1,5-Hexadipyridynyl Moiety.

Remmerswaal WA, Nguyen TT, Han Z, ..., Zhu W, Erdelyi M

Chempluschem 90 (9) e202500252 [2025-09-00; online 2025-08-04]

Colchicine and Longitudinal Dynamics of Clonal Hematopoiesis: An Exploratory Substudy of the LoDoCo2 Trial.

Mohammadnia N, Xue L, Vestjens LTW, ..., El Messaoudi S, Honigberg MC

J. Am. Coll. Cardiol. - (-) - [2025-08-29; online 2025-08-29]

NAIP/NLRC4 inflammasome dynamics in murine enteroids are tuned by NAIP ligand concentration and epithelial cell differentiation.

Andreassen PR, Ernst C, Pimentel Mendes M, ..., Hardt WD, Vorholt JA

Cell Reports 44 (8) 116143 [2025-08-26; online 2025-08-20]

Flame-made nanoparticles for magnetic hyperthermia and MRI in colorectal cancer theranostics.

Zhang Y, Paraskeva C, Chen Q, ..., Koliaraki V, Teleki A

Nanoscale Adv 7 (17) 5284-5299 [2025-08-19; online 2025-07-16]

Matrix-M adjuvant triggers inflammasome activation and enables antigen cross-presentation through induction of lysosomal membrane permeabilization.

Zarnegar B, Carow B, Eriksson J, ..., Stertman L, Lunderius Andersson C

NPJ Vaccines 10 (1) 184 [2025-08-05; online 2025-08-05]

Risk of atherosclerotic cardiovascular disease after cancer diagnosis: findings from 3 prospective cohort studies.

Liu Q, Wang Q, Wang K, ..., Song M, Giovannucci E

J. Natl. Cancer Inst. 117 (8) 1707-1716 [2025-08-01; online 2025-05-30]

Mechanistic modeling of cell viability assays with in silico lineage tracing.

Mutsuddy A, Huggins JR, Amrit AK, ..., Calhoun JC, Birtwistle MR

PLoS Comput Biol 21 (8) e1013156 [2025-08-00; online 2025-08-29]

Cemal Erdem DDLS Fellow

Mast Cell Phenotypic Heterogeneity Impacts the Interplay with Pathogenic Salmonella Typhimurium Bacteria.

von Beek C, Prensa GI, Andersson JHM, Pejler G, Sellin ME

Eur. J. Immunol. 55 (8) e70040 [2025-08-00; online 2025-08-21]

Germline genetic variation impacts clonal hematopoiesis landscape and progression to malignancy.

Liu J, Tran D, Xue L, ..., Natarajan P, Bolton KL

Nat. Genet. 57 (8) 1872-1880 [2025-08-00; online 2025-07-15]

cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads.

Petri AJ, Thi-Huyen Nguyen M, Rajwar A, Benson E, Sahlin K

PLoS ONE 20 (7) e0321246 [2025-07-24; online 2025-07-24]

Erik Benson Kristoffer Sahlin SciLifeLab Fellow

Transcription of GABAA receptor subunits in circulating monocytes and association to emotional brain function in premenstrual dysphoric disorder.

Stiernman L, Comasco E, Johansson M, Bixo M

Transl Psychiatry 15 (1) 255 [2025-07-23; online 2025-07-23]

ApoB-containing lipoproteins: count, type, size, and risk of coronary artery disease.

Morze J, Melloni GEM, Wittenbecher C, ..., Sabatine MS, Marston NA

Eur. Heart J. 46 (27) 2691-2701 [2025-07-14; online 2025-04-28]

Determinants of divergent Salmonella and Shigella epithelial colonization strategies resolved in human enteroids and colonoids.

Geiser P, Di Martino ML, Lopes ACC, ..., Eriksson J, Sellin ME

MBio 16 (7) e0091125 [2025-07-09; online 2025-05-30]

Optimized Artificial Colonic Mucus Enabling Physiologically Relevant Diffusion Studies of Drugs, Particles, and Delivery Systems.

Tjakra M, Chakrapeesirisuk N, Jacobson M, ..., Teleki A, Bergström CAS

Mol. Pharm. 22 (7) 4032-4045 [2025-07-07; online 2025-06-10]

Alexandra Teleki Mikael Sellin SciLifeLab Fellow

Development and retrospective validation of an artificial intelligence system for diagnostic assessment of prostate biopsies: study protocol.

Mulliqi N, Blilie A, Ji X, ..., Kartasalo K, Eklund M

BMJ Open 15 (7) e097591 [2025-07-07; online 2025-07-07]

High-throughput DNA melt measurements enable improved models of DNA folding thermodynamics.

Ke Y, Sharma E, Wayment-Steele HK, ..., Marklund E, Greenleaf WJ

Nat Commun 16 (1) 5572 [2025-07-01; online 2025-07-01]

Emil Marklund SciLifeLab Fellow

A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins.

Sharapov S, Timoshchuk A, Zaytseva O, ..., Lauc G, Aulchenko YS

Nat Commun 16 (1) 5525 [2025-07-01; online 2025-07-01]

When numbers matter: Rethinking the role of gene duplication on short evolutionary timescales.

Lindstedt F, Zhou Q, Milesi P

American journal of botany 112 (7) e70072 [2025-07-00; online 2025-07-09]

Pascal Milesi SciLifeLab Fellow

The value of mental science: we publish what matters.

Malhi GS, Adlington K, Al-Diwani A, ..., Zisman-Ilani Y, Fernandez-Egea E

Br J Psychiatry 227 (1) 429-433 [2025-07-00; online 2025-06-09]

Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: implications for conservation and management

Söderquist L, Joffard N, Scofield DG, ..., Karrenberg S, Sletvold N

Ecography 2025 (7) - [2025-07-00; online 2025-03-19]

Pascal Milesi SciLifeLab Fellow

Bending the Course of Evolution: How Mutualistic Interactions Affect Macroevolutionary Dynamics of Diversification in Mimetic Ithomiini Butterflies.

Chazot N, Braga MP, Aubier TG, ..., Willmott KR, Elias M

Am Nat 206 (1) 1-15 [2025-07-00; online 2025-05-21]

DDLS Fellow Mariana Pires Braga

A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen.

Di Martino ML, Jenniches L, Bhetwal A, ..., Barquist L, Sellin ME

Nat. Genet. 57 (7) 1730-1741 [2025-07-00; online 2025-06-12]

Accelerating Simulation-Based Inference with Variational Autoencoders

Nautiyal M, Shternshis A, Hellander A, Singh P

- - (-) 1-10 [2025-06-30; online 2025-06-30]

Prashant Singh SciLifeLab Fellow

Flame-Made Doped Iron Oxide Nanoparticles as Tracers for Magnetic Particle Imaging.

Ansari SR, Imhoff ED, Suárez-López YDC, ..., Rinaldi-Ramos CM, Teleki A

Chem Mater 37 (11) 4071-4084 [2025-06-10; online 2025-05-20]

Emotion generation and regulation in premenstrual dysphoric disorder: dysregulation of large-scale brain networks across the menstrual cycle.

Stiernman L, Dubol M, Comasco E, ..., Stiernman L, Bixo M

Biol. Psychiatry - (-) - [2025-06-06; online 2025-06-06]

Differentially expressed transcripts associated with depressive symptoms during pregnancy and postpartum.

Björvang RD, Vrettou M, Bujanda Cundin X, ..., Comasco E, Skalkidou A

Mol. Psychiatry - (-) - [2025-06-05; online 2025-06-05]

Trajectories and dimensional phenotypes of depressive symptoms throughout pregnancy and postpartum in relation to prior premenstrual symptoms.

Schleimann-Jensen E, Sundström-Poromaa I, Meltzer-Brody S, ..., Skalkidou A, Comasco E

Br J Psychiatry 226 (6) 401-409 [2025-06-00; online 2025-06-20]

Subjective, behavioural and physiological correlates of stress in women using hormonal contraceptives.

Bürger Z, Kordowich C, Kübbeler J, ..., Derntl B, Kogler L

Br J Psychiatry 226 (6) 392-400 [2025-06-00; online 2025-06-13]

Psychiatric symptoms on the ovarian hormone roller-coaster.

Comasco E, Epperson CN, Kulkarni J

Br J Psychiatry 226 (6) 329-330 [2025-06-00; online 2025-06-18]

Postdiagnosis physical activity and dietary inflammatory and insulinemic potential with overall survival in men with nonmetastatic prostate cancer.

Lee DH, Rezende LFM, Ferrari G, ..., Mucci LA, Giovannucci EL

Eur. J. Epidemiol. 40 (6) 669-679 [2025-06-00; online 2025-05-28]

Magnetic microfiber hyperthermia for synergistic antimicrobial activity against methicillin-resistant Staphylococcus aureus.

Ansari SR, Grimm D, Ramachandran RV, ..., Sotiriou GA, Teleki A

Mater Today Bio 32 (-) 101862 [2025-06-00; online 2025-05-12]

Fish are poor sentinels for surveillance of riverine antimicrobial resistance.

Tskhay F, Köbsch C, Elena AX, ..., Berendonk TU, Klümper U

One Health 20 (-) 101026 [2025-06-00; online 2025-04-01]

Emerging multi-drug resistant and extended-spectrum β-lactamase (ESBL)-positive enterotoxigenic E. coli (ETEC) clones circulating in aquatic environments and in patients.

Joffré E, Martín-Rodríguez AJ, Justh de Neczpal A, von Mentzer A, Sjöling Å

One Health 20 (-) 100968 [2025-06-00; online 2025-01-10]

Environmental reservoir of resistance genes for the last resort antibiotic Cefiderocol

Gschwind R, Bonnet M, Abramova A, ..., Bengtsson-Palme J, Ruppe E

- - (-) - [2025-05-26; online 2025-05-26]

Library-based single-cell analysis of CAR signaling reveals drivers of in vivo persistence.

Perez CR, Garmilla A, Nilsson A, ..., Lauffenburger DA, Birnbaum ME

Cell Syst 16 (5) 101260 [2025-05-21; online 2025-04-10]

Avlant Nilsson DDLS Fellow

Gender differences in global antimicrobial resistance

Salehi M, Laitinen V, Bhanushali S, ..., Pärnänen K, Lahti L

NPJ Biofilms Microbiomes 11 (1) 79 [2025-05-19; online 2025-05-19]

Cell shapes decode molecular phenotypes in image-based spatial proteomics.

Le T, Leineweber WD, Viana MP, ..., Rafelski SM, Lundberg E

bioRxiv - (-) - [2025-05-16; online 2025-05-16]

DDLS Fellow Wei Ouyang

Community-promoted antibiotic resistance genes show increased dissemination among pathogens

Lund D, Johnning A, Holmström M, ..., Bengtsson-Palme J, Kristiansson E

- - (-) - [2025-05-15; online 2025-05-15]

Evaluation of unsupervised learning algorithms for the classification of behavior from pose estimation data.

Mlost J, Dawli R, Liu X, Costa AR, Pollak Dorocic I

Patterns (N Y) 6 (5) 101237 [2025-05-09; online 2025-04-22]

Iskra Pollak Dorocic SciLifeLab Fellow

De novo clustering of large long-read transcriptome datasets with isONclust3.

Petri AJ, Sahlin K

Bioinformatics 41 (5) - [2025-05-06; online 2025-04-23]

Kristoffer Sahlin SciLifeLab Fellow

Gene regulatory networks linked to GABA signalling emerge as relevant for glioblastoma pathogenesis

Nissen I, Dakhel S, Chakraborty C, ..., Erdem C, Remeseiro S

- - (-) - [2025-05-05; online 2025-05-05]

Cemal Erdem DDLS Fellow

The Role of Artificial Intelligence in the Evaluation of Prostate Pathology.

Egevad L, Camilloni A, Delahunt B, ..., Eklund M, Kartasalo K

Pathol Int 75 (5) 213-220 [2025-05-00; online 2025-04-14]

Reply to the Letter to the Editor regarding "Early detection of pancreatic cancer: Study design and analytical considerations in biomarker discovery and early phase validation studies".

Mahoney DM, Smith LM, Wang QL, ..., Oberg AL, PCDC Biostatistics Subcommittee

Pancreatology 25 (3) 487-488 [2025-05-00; online 2025-05-10]

Precision nutrition for cardiometabolic diseases.

Guasch-Ferré M, Wittenbecher C, Palmnäs M, ..., Sargent JL, Merino J

Nat. Med. 31 (5) 1444-1453 [2025-05-00; online 2025-04-30]

Physical Color Calibration of Digital Pathology Scanners for Robust Artificial Intelligence-Assisted Cancer Diagnosis.

Ji X, Salmon R, Mulliqi N, ..., Eklund M, Kartasalo K

Mod. Pathol. 38 (5) 100715 [2025-05-00; online 2025-01-16]

The overlooked trio: sleep duration, sampling time and physical exercise alter levels of olink-assessed blood biomarkers of cardiovascular risk.

Brandão LEM, Zhang L, Grip A, ..., Benedict C, Cedernaes J

Biomark Res 13 (1) 67 [2025-04-29; online 2025-04-29]

Sex differences in DNMT3A-mutant clonal hematopoiesis and the effects of estrogen.

Stomper J, Niroula A, Belizaire R, ..., Bandaru TS, Ebert BL

Cell Reports 44 (4) 115494 [2025-04-22; online 2025-04-02]

Omics Approach for Personalised Prevention of Type 2 Diabetes Mellitus for African and European Populations (OPTIMA): a protocol paper.

Goedecke JH, Danquah I, Abidha CA, ..., Landberg R, Olsson T

BMJ Open 15 (4) e099108 [2025-04-22; online 2025-04-22]

Long-term gamma-aminobutyric acid (GABA) treatment fails to regain beta-cell function in longstanding type 1 diabetes in a randomized trial.

Hill H, Lundkvist P, Tsatsaris G, ..., Espes D, Carlsson PO

Sci Rep 15 (1) 11530 [2025-04-04; online 2025-04-04]

Putting cancer immunotherapy into spatial context in the clinic.

Engblom C, Lundeberg J

Nat. Biotechnol. 43 (4) 471-476 [2025-04-00; online 2025-04-15]

Camilla Engblom SciLifeLab Fellow

Occurrence and spread of carbapenemase‐producing Enterobacterales (CPE) in the food chain in the EU/EFTA. Part 1: 2025 update

Allende A, Álvarez‐Ordóñez A, Bortolaia V, ..., Rabbås H, Peixe L

EFSA J 23 (4) - [2025-04-00; online 2025-04-00]

Seal milk oligosaccharides rival human milk complexity and exhibit functional dynamics during lactation

Jin C, Lundstrøm J, Cori CR, ..., Khoo KH, Bojar D

- - (-) - [2025-03-20; online 2025-03-20]

Survival and adaptative strategies of Enterotoxigenic E. coli (ETEC) to the freshwater environment.

Sjöling Å, Ashokkumar E, Bjurnemark C, ..., Zhu B, Joffré E

Res Sq - (-) - [2025-03-19; online 2025-03-19]

Early gonadotoxic effects of cyclophosphamide on the prepubertal testis and the feasibility of reducing toxicity through combined antioxidant therapy

Eskafinoghani A, Reyes Palomares A, Hao X, ..., Lundberg A, Rodriguez-Walberg KA

- - (-) - [2025-03-19; online 2025-03-19]

Arian Lundberg DDLS Fellow

Abstract 072: Plasma Metabolome Predicts Long-term Body Weight Gain and Type 2 Diabetes in Non-Obese Individuals

Wu Z, Liu B, Li J, ..., Hu Y, Sun Q

Circulation 151 (Suppl_1) - [2025-03-11; online 2025-03-11]

Predicting allergy and postpartum depression from an incomplete compositional microbiome

Shternshis A, Tong B, Skalkidou A, ..., Hugerth LW, Singh P

- - (-) - [2025-03-06; online 2025-03-06]

Prashant Singh SciLifeLab Fellow

Androgen Receptor Inhibition Increases MHC Class I Expression and Improves Immune Response in Prostate Cancer.

Chesner LN, Polesso F, Graff JN, ..., Feng FY, Moran AE

Cancer Discov 15 (3) 481-494 [2025-03-03; online 2024-12-09] Open Access

Arian Lundberg DDLS Fellow

Recent advances in precision nutrition and cardiometabolic diseases.

Martínez-González MA, Planes FJ, Ruiz-Canela M, ..., Razquin C, Hu FB

Rev Esp Cardiol (Engl Ed) 78 (3) 263-271 [2025-03-00; online 2024-09-30]

Click Chemistry-Based Bioconjugation of Iron Oxide Nanoparticles.

Asad S, Ahl D, Suárez-López YDC, ..., Phillipson M, Teleki A

Small 21 (11) e2407883 [2025-03-00; online 2025-02-09]

Avances en nutrición de precisión y enfermedades cardiometabólicas

Martínez-González MA, Planes FJ, Ruiz-Canela M, ..., Razquin C, Hu FB

Revista Española de Cardiología 78 (3) 263-271 [2025-03-00; online 2025-03-00]

Applying 3D cultures and high-throughput technologies to study host-pathogen interactions.

De Martinis ECP, Alves VF, Pereira MG, ..., Dannborg M, Bengtsson-Palme J

Front Immunol 16 (-) 1488699 [2025-02-20; online 2025-02-20]

Genetic adaptation to amoxicillin in Escherichia coli: The limited role of dinB and katE.

Teichmann L, Wenne M, Luitwieler S, ..., Bengtsson-Palme J, Ter Kuile B

PLoS ONE 20 (2) e0312223 [2025-02-19; online 2025-02-19]

PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity

Larralde M, Zeller G, Carroll LM

- - (-) - [2025-02-17; online 2025-02-17]

DDLS Fellow Laura Carroll

Towards an interpretable deep learning model of cancer.

Nilsson A, Meimetis N, Lauffenburger DA

NPJ Precis Oncol 9 (1) 46 [2025-02-14; online 2025-02-14]

Avlant Nilsson DDLS Fellow

Rapid Evolution of Host Repertoire and Geographic Range in a Young and Diverse Genus of Montane Butterflies.

Mo S, Zhu Y, Braga MP, ..., Zhang P, Wang H

Syst. Biol. 74 (1) 141-157 [2025-02-10; online 2024-11-01]

DDLS Fellow Mariana Pires Braga

The business case for investing in biodiversity data

Hasan F, Nyström J, Andersson C, ..., Johansson V, Andermann T

- - (-) - [2025-02-04; online 2025-02-04]

DDLS Fellow Tobias Andermann

Ceftazidime-avibactam tolerance and persistence among difficult-to-treat KPC-producing Klebsiella pneumoniae clinical isolates from bloodstream infections.

Abichabki N, Gaspar GG, Bortolato LR, ..., Darini ALC, Andrade LN

Eur. J. Clin. Microbiol. Infect. Dis. 44 (2) 343-353 [2025-02-00; online 2024-11-30]

Adaptation of Escherichia coli to ciprofloxacin and enrofloxacin: Differential proteomics of the SOS response and RecA-independent mechanisms.

Teichmann L, Pasman R, Luitwieler S, ..., Bengtsson-Palme J, Ter Kuile B

Int. J. Antimicrob. Agents 65 (2) 107420 [2025-02-00; online 2024-12-30]

Probing the Hidden Photoisomerization of a Symmetric Phosphaalkene Switch

Deka R, Steen JD, Hilbers MF, ..., Orthaber A, Crespi S

Angewandte Chemie 137 (5) - [2025-01-27; online 2024-12-13]

Telomemore enables single-cell analysis of cell cycle and chromatin condensation.

Yakovenko I, Mihai IS, Selinger M, ..., Forsell M, Henriksson J

Nucleic Acids Res. 53 (3) - [2025-01-24; online 2025-01-29]

DDLS Fellow Laura Carroll

Emotion regulation-based internet-delivered cognitive behavioural therapy for premenstrual dysphoric disorder: study protocol for a randomised controlled trial in Sweden.

Hoppe JM, Weise C, Kleinstaeuber M, ..., Andersson G, Buhrman M

BMJ Open 15 (1) e091649 [2025-01-22; online 2025-01-22]

Fluoroquinolone-specific resistance trajectories in E. coli and their dependence on the SOS-response.

Teichmann L, Luitwieler S, Bengtsson-Palme J, Ter Kuile B

BMC Microbiol. 25 (1) 37 [2025-01-21; online 2025-01-21]

Protocol to infer off-target effects of drugs on cellular signaling using interactome-based deep learning.

Meimetis N, Lauffenburger DA, Nilsson A

STAR Protoc 6 (1) 103573 [2025-01-16; online 2025-01-16]

Avlant Nilsson DDLS Fellow

Liquid crystal nanoparticles for oral combination antibiotic therapies: A strategy towards protecting commensal gut bacteria during treatment.

He X, Karlsson PA, Xiong R, ..., Bergström CAS, Hubert M

J Colloid Interface Sci 678 (Pt B) 287-300 [2025-01-15; online 2024-08-31]

White matter integrity upon progesterone antagonism in individuals with premenstrual dysphoric disorder: A randomized placebo-controlled diffusion tensor imaging study.

Kaltsouni E, Gu X, Wikström J, ..., Sundström-Poromaa I, Comasco E

Prog Neuropsychopharmacol Biol Psychiatry 136 (-) 111179 [2025-01-10; online 2024-10-23]

DTPPI: predicting drug interactions using a weighted drug-protein network

Szydlik S, Taheri G

- - (-) - [2025-01-08; online 2025-01-08]

DDLS Fellow Golnaz Taheri

Progestagens and progesterone receptor modulation: Effects on the brain, mood, stress, and cognition in females.

Bencker C, Gschwandtner L, Nayman S, ..., Bixo M, Comasco E

Front Neuroendocrinol 76 (-) 101160 [2025-01-00; online 2024-11-06]

Unveiling Driver Modules in Lung Cancer: A Clustering-Based Gene-Gene Interaction Network Analysis

Taheri G, Szalai M, Habibi M, Papapetrou P

- - (-) 41-58 [2025-00-00; online 2025-01-01]

DDLS Fellow Golnaz Taheri

The Utility of Deep Learning for Modeling Seasonal Biodiversity Changes Across the Landscape

Baggström A, Goodsell R, van Dijk L, ..., Tack A, Andermann T

- - (-) - [2025-00-00; online 2025-00-00]

DDLS Fellow Tobias Andermann

Strategies for taxonomic and functional annotation of metagenomes

Abramova A, Bengtsson-Palme J

- - (-) 57-81 [2025-00-00; online 2025-00-00]

Menstrual cycle-related changes in the human brain

Pletzer B, Comasco E, Hidalgo-Lopez E, ..., Sundström-Poromaa I, Derntl B

- - (-) 604-623 [2025-00-00; online 2024-02-12]

Limited Effects of Tetracycline and Ciprofloxacin on Soil Bacterial Communities

Wenne M, Abramova A, Bengtsson-Palme J

- - (-) - [2025-00-00; online 2025-00-00]