Erik Kristiansson

Optimizing Gene-Based Testing for Antibiotic Resistance Prediction

2025

Unraveling the origins of mobile antibiotic resistance genes using random forest classification of large-scale genomic data

2025

Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes

2024

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

2024

Environmental concentrations of the fungicide tebuconazole alter microbial biodiversity and trigger biofilm-released transformation products

2024

20 years of bibliometric data illustrates a lack of concordance between journal impact factor and fungal species discovery in systematic mycology

2024

Transformers enable accurate prediction of acute and chronic chemical toxicity in aquatic organisms

Risk assessment of chemicals and their mixtures are hindered by scarcity and inconsistencies between different environmental exposure limits

2023

Dataset on aquatic ecotoxicity predictions of 2697 chemicals, using three quantitative structure-activity relationship platforms

2023

Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge

2023

Phenotypic and transcriptomic acclimation of the green microalga Raphidocelis subcapitata to high environmental levels of the herbicide diflufenican

2023

Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens

2023

How, not if, is the question mycologists should be asking about DNA-based typification

2023

Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes

2022

Economic interests cloud hazard reductions in the European regulation of substances of very high concern

Estimating the release of chemical substances from consumer products, textiles and pharmaceuticals to wastewater

2022

The curse of the uncultured fungus

2022

The impact of the ST131 clone on recurrent ESBL-producing E. coli urinary tract infection: a prospective comparative study

2022

Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes

2022

GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids

An updated phylogeny of the metallo-β-lactamases

2021

SMAD4 haploinsufficiency in small intestinal neuroendocrine tumors

2021

A framework for identifying the recent origins of mobile antibiotic resistance genes

2021

Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach

Patient-Tailored Measurable Residual Disease Monitoring in Peripheral Blood Using Deep Sequencing and Droplet Digital PCR for Early Detection of Relapse in Childhood Acute Myeloid Leukemia: A NOPHO-DBH Collaborative Study

2021

Does the scientific knowledge reflect the chemical diversity of environmental pollution? – A twenty-year perspective

2020

Triclosan changes community composition and selects for specific bacterial taxa in marine periphyton biofilms in low nanomolar concentrations

2020

Structural and biochemical characterization of the environmental MBLs MYO-1, ECV-1 and SHD-1

2020

Predicting clinical resistance prevalence using sewage metagenomic data

2020

The Association between Insertion Sequences and Antibiotic Resistance Genes

2020

MYO5B mutations in pheochromocytoma/paraganglioma promote cancer progression

2020

Phosphorylated CtIP bridges DNA to promote annealing of broken ends

MYO5B Mutations in Pheochromocytoma/Paraganglioma Promote Cancer Progression

2020

Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes

2020

Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping

2020

When mycologists describe new species, not all relevant information is provided (clearly enough)

2020

A comprehensive survey of integron-associated genes present in metagenomes

2020

Cultivation-Free Typing of Bacteria Using Optical DNA Mapping

2020

Long-term application of Swedish sewage sludge on farmland does not cause clear changes in the soil bacterial resistome

2019

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Modelling of zero-inflation improves inference of metagenomic gene count data

2019

177 Lu-octreotate therapy for neuroendocrine tumours is enhanced by Hsp90 inhibition

2019

Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes

PER extended-spectrum β-lactamases originate from Pararheinheimera spp

2019

The mobile FOX AmpC beta-lactamases originated in Aeromonas allosaccharophila

Sewage from Airplanes Exhibits High Abundance and Diversity of Antibiotic Resistance Genes

2019

mRNA Expression and Biomarker Responses in Perch at a Biomonitoring Site in the Baltic Sea - Possible Influence of Natural Brominated Chemicals

2019

Identification and reconstruction of novel antibiotic resistance genes from metagenomes

2019

Accurate and Sensitive Analysis of Minimal Residual Disease in Acute Myeloid Leukemia Using Deep Sequencing of Single Nucleotide Variations

2019

Pharmacology beyond the patient – The environmental risks of human drugs

2019

CMY-1/MOX-family AmpC β-lactamases MOX-1, MOX-2 and MOX-9 were mobilized independently from three Aeromonas species

2019

Introducing ribosomal tandem repeat barcoding for fungi

Bacterial identification by optical mapping of genomic DNA in nanofluidic channels

Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste

miRNA profiling of small intestinal neuroendocrine tumors defines novel molecular subtypes and identifies miR-375 as a biomarker of patient survival

Computational and Statistical Considerations in the Analysis of Metagenomic Data

2018

The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis

2018

Comparison of normalization methods for the analysis of metagenomic gene abundance data

2018

Environmental factors influencing the development and spread of antibiotic resistance

2018

The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines

2018

ECOdrug: A database connecting drugs and conservation of their targets across species

2018

Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics

2018

Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach

Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms

2017

Identification of 76 novel B1 metallo-beta-lactamases through large-scale screening of genomic and metagenomic data

2017

Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing

Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics

Using metagenomics to investigate human and environmental resistomes

Does antifouling paint select for antibiotic resistance?

Patient-tailored analysis of minimal residual disease in acute myeloid leukemia using next generation sequencing.

2017

Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

2017

Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory

Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes.

2017

Discovery of the fourth mobile sulfonamide resistance gene

Integrative analysis of omics data

2017

Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics

2017

HirBin: High-resolution identification of differentially abundant functions in metagenomes

2017

Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F

Detailed characterization of plasmids carrying resistance genes using optical DNA mapping

2016

Top 50 most wanted fungi

New Ph.D. students in the empirical sciences should be recruited into ongoing scientific studies right from the start

Expression profiling of small intestinal neuroendocrine tumors identifies subgroups with clinical relevance, prognostic markers and therapeutic targets.

Biomarker responses in eelpouts from four coastal areas in Sweden, Denmark and Germany

HattCI: Fast and Accurate attC site Identification Using Hidden Markov Models.

Proteotyping: Tandem Mass Spectrometry Shotgun Proteomic Characterization and Typing of Pathogenic Microorganisms

Malignant pheochromocytomas/paragangliomas harbor mutations in transport and cell adhesion genes.

2016

Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.

2016

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics

2016

Draft genome sequence of extended-spectrum-β-lactamase-producing Escherichia coli strain CCUG 62462, isolated from a urine sample

2016

Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules

2016

The structure and diversity of human, animal and environmental resistomes

2016

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)

2016

Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping.

2016

Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.

Proteotyping of Streptococcus pneumoniae, using tandem mass spectrometry for identification of biomarkers for species and strain differentiation

Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics

Optical mapping of single DNA molecules in nanochannels: A novel method for identification and characterization of antibiotic resistance

2015

Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities

2015

Tentacle: distributed quantification of genes in metagenomes

2015

Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India

Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake

Proteotyping: Proteomic characterization, classification and identification of microorganisms--A prospectus

Patient-Tailored Analysis of Minimal Residual Disease in Acute Myeloid Leukemia Using Next Generation Sequencing

The human gut microbiome as a transporter of antibiotic resistance genes between continents

2015

A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts

Waterborne beclomethasone dipropionate affects the physiology of fish while its metabolite beclomethasone is not taken up

2015

Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential

2015

Resistance Mutations in gyrA and parC are Common in Escherichia Communities of both Fluoroquinolone-Polluted and Uncontaminated Aquatic Environments

2014

BacMet: antibacterial biocide and metal resistance genes database

Assessing variation in the potential susceptibility of fish to pharmaceuticals, considering evolutionary differences in their physiology and ecology

Genetic Copy Number Variations in Colon Mucosa Indicating Risk for Colorectal Cancer.

Fluoroquinolones and qnr genes in sediment, well water, soil and human fecal flora in an Indian environment polluted by drug manufacturing

2014

Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India

2013

A novel method for cross-species gene expression analysis

Acquired genetic mechanisms of a multiresistant bacterium isolated from a treatment plant receiving wastewater from antibiotic production.

Incorporating molecular data in fungal systematics: a guide for aspiring researchers

High levels of quinolone resistance genes found near a waste water treatment plant serving antibiotic manufacturers

Gastrointestinal stromal tumors (GISTs) express somatostatin receptors and bind radiolabeled somatostatin analogs.

2013

Hepatic transcriptome profiling indicates differential mRNA expression of apoptosis and immune related genes in eelpout (Zoarces viviparus) caught at Göteborg harbor, Sweden

2013

Functional verification of computationally predicted qnr genes

2013

ERBB3 is a marker of a ganglioneuroblastoma/ganglioneuroma-like expression profile in neuroblastic tumours.

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

Oral exposure to industrial effluent with exceptionally high levels of drugs does not indicate acute toxic effects in rats

Expression of the glucocorticoid receptor is decreased in experimental Staphylococcus aureus sepsis.

Global hepatic gene expression in rainbow trout exposed to sewage effluents: A comparison of different sewage treatment technologies

2012

A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Does ketoprofen or diclofenac pose the lowest risk to fish?

Comprehensive Analysis of Antibiotic Resistance Genes Using Metagenomic DNA Sequencing: Studies of Contaminated River Sediment, Well Water and Soil Microbial Communities

2012

Estradiol ameliorates arthritis and protects against systemic bone loss in Staphylococcus aureus infection in mice

Comprehensive Analysis of Antibiotic Resistance Genes Using Metagenomic DNA Sequencing: Studies of Contaminated River Sediment, Well Water and Soil Microbial Communities

Environmental Comparative Pharmacology: Theory and application

Antibiotika i miljön tros öka risken för spridning av resistensgener mellan arter.

2011

Pyrosequencing of Antibiotic-Contaminated River Sediments Reveals High Levels of Resistance and Gene Transfer Elements

Exploring the metagenomes of environmental antibiotic hotspots to identify resistance factors that we may face in the clinic tomorrow

Expression profiling of GIST: CD133 is associated with KIT exon 11 mutations, gastric location, and poor prognosis.

Physiology and mRNA expression in rainbow trout (Oncorhynchus mykiss) after long-term exposure to the new antifoulant medetomidine.

Environmental microbial communities living under very high antibiotic selection pressure

The genome of an extensively drug-resistant bacterium isolated from a wastewater treatment plant receiving effluent from antibiotic manufacturing

Diclofenac in fish: Blood plasma levels similar to human therapeutic levels affect global hepatic gene expression.

An open source chimera checker for the fungal ITS region

Hypoxia stimulates CXCR4 signalling in ileal carcinoids.

Whole genome sequencing of a multiresistant bacterium isolated from a wastewater treatment plant receiving effluent from antibiotic drug manufactureing

Environmental biomonitoring of Zoarces viviparus in combination with large scale gene expression profiling

Exploring the microbial resistome in river sediments exposed to extraordinary high levels of antibiotics

An open source chimera checker for the fungal ITS region

An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology

Antibiotic-contaminated effluent promotes mobile resistance in environmental baceria

Genes with relevance for early to late progression of colon carcinoma based on combined genomic and transcriptomic information from the same patients.

Colour and melanophore function in rainbow trout after long term exposure to the new antifoulant medetomidine

Monitoring of the viviparous fish species eelpout (Zoarces viviparus) indicates environmental changes in coastal waters.

Genetic basis of arsenite and cadmium tolerance in Saccharomyces cerevisiae.

A software pipeline for processing and identification of fungal ITS sequences

Release of fluoroquinolones and other active pharmaceutical ingredients from Indian bulk drug manufacture – environmental fate and effects on antibiotic resistance development, microbial ecosystems and aquatic vertebrates. Invited platform presentation.

Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing

identification of novel biomarkers - a framework for cross-species gene expression analysis

Short-term oral exposure to effluent from bulk drug industries does not indicate acute toxic effects in rat

Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing

The ITS region as a target for characterization of fungal communities using emerging sequencing technologies

2009

Predicting functional upstream open reading frames in Saccharomyces cerevisiae

Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing.

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing

Multi-endpoint studies on the eelpout (Zoarces viviparus), using gene expression oligonucleotide microarray

An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity

Evolutionary Forces Act on Promoter Length: Identification of Enriched Cis-Regulatory Elements

Multi-endpoint studies on the eelpout (Zoarces viviparus), using gene expression oligonucleotide microarray

Large-scale gene expression analysis in non-model organisms – de novo transcriptome sequencing and microarray design.

Establishing the barnacle Balanus improvisus as a potent invertebrate monitoring system in marine ecotoxicogenomics

Pharmaceutical Industry Effluent Diluted 1:500 Affects Global Gene Expression, Cytochrome P4501A Activity and Plasma Phosphate in Fish.

Pharmaceutical industry effluent diluted 1:500 affects global hepatic gene expression, CYP1A activity and plasma phosphate in fish

Dose-response effects on global hepatic gene expression in rainbow trout exposed to diclofenac

Evolutionary conservation of human drug targets in organisms used for environmental risk assessments.

Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing

Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota)

Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

Sensitive and robust gene expression changes in fish exposed to estrogen – a microarray approach

Statistical analysis of gene expression data

Quantitative transcriptome, proteome and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite

Weighted Analysis of General Microarray Experiments

Quantitative transcriptome, proteome and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite

2007

Weighted Analysis of General Microarray Experiments

Taxonomic reliability of DNA sequences in public sequence databases: A fungal perspective

Quality Optimised Analysis of General Paired Microarray Experiments

Quality Optimised Analysis of General Paired Microarray Experiments

Weighted Analysis of Paired Microarray Experiments

Weighted Analysis of Paired Microarray Experiments

A new Method for Analysis of microarray Gene Expression Assays

2005

Approaching the taxonomic affiliation of unidentified sequences in public databases : an example from the mycorrhizal fungi

2005

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals

Identifying factors involved in the cellular response to arsenic

Identifying factors involved in the cellular response to arsenic