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List of works by Sofia K. Forslund

A novel exploratory method for visual recombination detection

scientific article

A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation

scientific article

Antibiotics-induced monodominance of a novel gut bacterial order

scientific article published on 18 January 2019

B-cell lymphoma/leukaemia 10 and angiotensin II-induced kidney injury

scientific article published on 01 April 2020

Benchmarking homology detection procedures with low complexity filters

scientific article published on 20 July 2009

Benchmarking the next generation of homology inference tools

scientific article published on June 2016

Biggest challenges in bioinformatics

scientific article (publication date: April 2013)

Country-specific antibiotic use practices impact the human gut resistome

scientific article published on 08 April 2013

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

scientific article published on 2 December 2015

Domain architecture conservation in orthologs

scientific article

Domain tree-based analysis of protein architecture evolution

scientific article published on 19 November 2007

Dynamic Changes in Microbiome Composition Following Mare's Milk Intake for Prevention of Collateral Antibiotic Effect

scientific article published on 21 April 2021

Evolution of protein domain architectures

scientific article published on January 2012

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

scientific article published on 29 April 2017

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

article

Fasting alters the gut microbiome reducing blood pressure and body weight in metabolic syndrome patients

scientific article published on 30 March 2021

Gearing up to handle the mosaic nature of life in the quest for orthologs

scientific article published on 30 August 2017

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis

scientific article published on 30 December 2016

Human gut microbes impact host serum metabolome and insulin sensitivity

scientific article

Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

scientific article

Individuality and temporal stability of the human gut microbiome.

scientific article published in January 2013

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children

scientific article published on 26 January 2016

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes

scientific article published on 01 April 2022

MOCAT2: a metagenomic assembly, annotation and profiling framework

scientific article

Metagenomic analysis of gut microbial communities from a Central Asian population

article

Metagenomic insights into the human gut resistome and the forces that shape it.

scientific article published on 29 January 2014

Microbiome and metabolome features of the cardiometabolic disease spectrum

scientific article published on 17 February 2022

OrthoDisease: tracking disease gene orthologs across 100 species

scientific article published on 12 May 2011

Orthology confers intron position conservation

scientific article

Predicting protein function from domain content

scientific article published on 30 June 2008

Protein Intake, Metabolic Status and the Gut Microbiota in Different Ethnicities: Results from Two Independent Cohorts

QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets

scientific article published on 21 November 2006

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

scientific article published in July 2015

RTK: efficient rarefaction analysis of large datasets

scientific article published on 7 April 2017

Recovery of gut microbiota of healthy adults following antibiotic exposure

scientific article published on 22 October 2018

STRING v10: protein-protein interaction networks, integrated over the tree of life

scientific article (publication date: 2015)

Salt Transiently Inhibits Mitochondrial Energetics in Mononuclear Phagocytes

scientific article published on 28 April 2021

Salt-responsive gut commensal modulates TH17 axis and disease

scientific article published on 15 November 2017

Shared and Distinct Gut Microbiota in Spondyloarthritis, Acute Anterior Uveitis, and Crohn's Disease

scientific article published on 19 October 2023

Short-Chain Fatty Acid Propionate Protects From Hypertensive Cardiovascular Damage.

scientific article published in March 2019

Similarity of the dog and human gut microbiomes in gene content and response to diet.

scientific article published on 19 April 2018

Standardized benchmarking in the quest for orthologs

scientific article (publication date: 4 April 2016)

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

scientific article published on 06 May 2020

Structure and function of the global topsoil microbiome

scientific article published in Nature

Subspecies in the global human gut microbiome.

scientific article published on 14 December 2017

The Pfam protein families database

scientific article (publication date: 2012)

The Pfam protein families database

scientific article (published 2010-01-01)

The Pfam protein families database ⬇️

scientific article

Towards the biogeography of prokaryotic genes

scientific article published in 2021

Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines

scientific article published on 05 November 2018

VisRD--visual recombination detection

scientific article published on 9 July 2004

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

scientific article (publication date: 17 November 2015)

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

scientific article published on 01 January 2019

eggNOG v4.0: nested orthology inference across 3686 organisms

scientific article (publication date: December 2013)

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

scientific article published on 01 January 2020

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

scientific article

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