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List of works by Sofia K. Forslund

A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links

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

Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice

scientific article published in January 2024

Abstract P2072: Integrative Network Analysis Of Microbiome-Immune Axis In Metabolic Syndrome Patients During A Fasting Intervention

scholarly article

Advances and Applications in the Quest for Orthologs

scientific article published on 01 October 2019

An altered plasma lipidome–phenome network characterizes heart failure with preserved ejection fraction

scholarly article published on 19 January 2024

Antibiotics-induced monodominance of a novel gut bacterial order

scientific article published on 18 January 2019

Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology

scientific article published on 21 December 2020

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)

Blood Pressure Changes Correlate with Short-Chain Fatty Acids Production Shifts Under a Synbiotic Intervention

scientific article published on 31 March 2020

Constructing Phylogenetic Supernetworks from Quartets

scholarly article published in Lecture Notes in Computer Science

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

scientific article published in Nature

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

Domainoid: domain-oriented orthology inference

scientific article published on 28 October 2019

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

scientific article published on 21 April 2021

Elevated aldosterone and blood pressure in a mouse model of familial hyperaldosteronism with ClC-2 mutation

scientific article published on 14 November 2019

Enhanced Ca2+ signaling, mild primary aldosteronism, and hypertension in a familial hyperaldosteronism mouse model (Cacna1hM1560V/+)

scientific article published on 27 April 2021

Evolution of Protein Domain Architectures

scientific article published on 01 January 2019

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

Hitchhiker's guide to microbiome studies

scientific article published on 01 March 2020

Human gut microbes impact host serum metabolome and insulin sensitivity

scientific article

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology

scientific article published on 18 November 2020

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

Phosphodiesterase 3A and Arterial Hypertension

scientific article published on 11 June 2020

Precarious Symbiosis Between Host and Microbiome in Cardiovascular Health

scientific article published on 01 May 2019

Predicting protein function from domain content

scientific article published on 30 June 2008

Propionic Acid Shapes the Multiple Sclerosis Disease Course by an Immunomodulatory Mechanism

scientific article published on 10 March 2020

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

Quantifying Technical Confounders in Microbiome Studies

scientific article published on 06 May 2020

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

S100A8 and S100A9 are Important for Postnatal Development of Gut Microbiota and Immune System in Mice and Infants

scientific article published on 14 August 2020

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

Spondyloarthritis, acute anterior uveitis, and Crohn’s disease have both shared and distinct gut microbiota

scientific article published on 16 May 2022

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

Studies of the bugs within: telling sickness from cure

scientific article published in 2018

Subspecies in the global human gut microbiome.

scientific article published on 14 December 2017

Ten Years of Collaborative Progress in the Quest for Orthologs

scientific article published on 2 April 2021

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

Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.

scientific article published on 2 March 2018

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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