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List of works by Thomas Sicheritz-Ponten

A draft genome sequence of the elusive giant squid, Architeuthis dux

scientific article published on 01 January 2020

A first glimpse into the pattern and scale of gene transfer in Apicomplexa

scientific article published on March 2004

A human gut microbial gene catalogue established by metagenomic sequencing

scientific article

A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults

scientific article published in Nature Communications

A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection

scientific article

A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae.

scientific article published in July 1998

An Aboriginal Australian genome reveals separate human dispersals into Asia

scientific article (publication date: 7 October 2011)

Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome

scientific article

Ancient human genome sequence of an extinct Palaeo-Eskimo

scientific article

Arctic-adapted dogs emerged at the Pleistocene-Holocene transition

scientific article published on 01 June 2020

Author Correction: Dense sampling of bird diversity increases power of comparative genomics

Bacterial diversity in snow on North Pole ice floes.

scientific article

Bacterial natural transformation by highly fragmented and damaged DNA ⬇️

scientific article (publication date: 3 December 2013)

Benchmarking of methods for genomic taxonomy

scientific article published on 26 February 2014

BioWish: a molecular biology command extension to Tcl/Tk

scientific article

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

scientific article

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut.

scientific article published on 27 June 2016

Comparative Genomics Sheds Light On Niche Differentiation And The Evolutionary History Of ComammoxNitrospira

Comparative Genomics of Four Pseudomonas Species

scientific article (publication date: 2004)

Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira

scientific article published on 7 March 2018

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

scientific article

Complete genes may pass from food to human blood.

scientific article

Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae)

scholarly article by Nizar Jamal Haddad et al published January 2017 in Mitochondrial DNA. Part B, Resources

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

scientific article published on 04 May 2019

Correction: MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

scientific article published on 12 June 2017

Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia

Dense sampling of bird diversity increases power of comparative genomics

scientific article published on 11 November 2020

Distinct life histories impact dikaryotic genome evolution in the rust fungus Puccinia striiformis causing stripe rust in wheat

scientific article published on 09 April 2020

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

scientific article

Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago

scientific article

Enterotypes of the human gut microbiome

scientific article

Enterotypes of the human gut microbiome

scientific article published in Nature

Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses

scientific article

Erratum: Addendum: Enterotypes of the human gut microbiome

scientific article published in Nature

Erratum: Corrigendum: The microbiome of New World vultures

scientific article published in Nature Communications

Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse

scientific article published on 22 September 2015

Evolutionary history of the extinct Sardinian dhole

scientific article published in 2021

GRS: a graphic tool for genome retrieval and segment analysis.

scientific article

GenePublisher: Automated analysis of DNA microarray data

scientific article

Genome Sequence of Talaromyces atroroseus, Which Produces Red Colorants for the Food Industry

scientific article

Genome update: distribution of two-component transduction systems in 250 bacterial genomes

scientific article published on 01 November 2005

Genome update: prediction of secreted proteins in 225 bacterial proteomes

scientific article

Genome update: sigma factors in 240 bacterial genomes

scientific article published on 01 October 2005

Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages

scientific article published on 27 October 2020

Genomic analyses of the extinct Sardinian dhole ( Cynotherium sardous ) reveal its evolutionary history

Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India

article

Genomic profiling of thousands of candidate polymorphisms predicts risk of relapse in 778 Danish and German childhood acute lymphoblastic leukemia patients

scientific article

Global features of the Alcanivorax borkumensis SK2 genome

scientific article published on 12 December 2007

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

scientific article published on 08 March 2019

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach

scientific article published on 01 September 2019

Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)

scientific article published in 2021

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

scientific article published on 19 February 2018

Horizontal Gene Transfer in Eukaryotic Parasites: A Case Study of Entamoeba histolytica and Trichomonas vaginalis

article

Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank)

scientific article

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

scientific article published on 6 July 2014

Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

scientific article

Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry

scientific article

Influence of Oenococcus oeni and Brettanomyces bruxellensis on Aged Wine Microbial Taxonomic and Functional Profiles

scholarly article published 8 November 2017

InterMap3D: predicting and visualizing co-evolving protein residues.

scientific article

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

article

Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing

scientific article published on 19 August 2015

Kouprey (<i>Bos sauveli</i>) genomes unveil polytomic origin of wild Asian <i>Bos</i>

scientific article published on 06 October 2021

Linear Motif Atlas for Phosphorylation-Dependent Signaling

scientific article (publication date: 2 September 2008)

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

scientific article

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance

scientific article published on 10 July 2015

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.

scientific article

Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene.

scientific article

Microbiota in foods from Inuit traditional hunting

scientific article published on 14 January 2020

Mitochondrial genome of the North African Sahara Honeybee, Apis mellifera sahariensis (Hymenoptera: Apidae)

scholarly article by Nizar Jamal Haddad et al published 2 January 2017 in Mitochondrial DNA. Part B, Resources

Molecular markers for tracking the origin and worldwide distribution of invasive strains of Puccinia striiformis ⬇️

scientific article published on 20 March 2016

Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus

scientific article published on 05 October 2020

Multilocus sequence typing of total-genome-sequenced bacteria

scientific article

Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data.

scientific article published on 21 November 2017

Palaeogenomic insights into the origins of French grapevine diversity

scientific article published on 10 June 2019

Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes

scientific article

Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins

scientific article

Population genomics of Bronze Age Eurasia

scientific article published on June 2015

Population genomics of grey wolves and wolf-like canids in North America

scientific article published on 12 November 2018

Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence

scientific article (publication date: June 2004)

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

scientific article

Protective role of the vulture facial and gut microbiomes aid adaptation to scavenging

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples.

scientific article published in August 2014

Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples

scientific article published on 30 October 2013

Reads2Type: a web application for rapid microbial taxonomy identification

scientific article published on 25 November 2015

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

scientific article

Richness of human gut microbiome correlates with metabolic markers

scientific article (publication date: 29 August 2013)

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

scientific article published in Nature

Speciation with gene flow in equids despite extensive chromosomal plasticity

scientific article

Targeted Metabolic Engineering Guided by Computational Analysis of Single-Nucleotide Polymorphisms (SNPs)

scientific article published on 01 January 2013

The chemical interactome space between the human host and the genetically defined gut metabotypes

scientific article published on 22 November 2012

The evolutionary history of extinct and living lions

scientific article published on 04 May 2020

The genome of a Late Pleistocene human from a Clovis burial site in western Montana

scientific article

The genome of the protist parasite Entamoeba histolytica

scientific article

The genome sequence of Rickettsia prowazekii and the origin of mitochondria

scientific article

The genus burkholderia: analysis of 56 genomic sequences.

scientific article published on 19 August 2009

The microbial composition of dried fish prepared according to Greenlandic Inuit traditions and industrial counterparts

scientific article published on 13 August 2019

The microbiome of New World vultures

scientific article

The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

scientific article

Traces of ATCV-1 associated with laboratory component contamination

scientific article published on 5 February 2015

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

scientific article

Transcriptional interactions suggest niche segregation among microorganisms in the human gut.

scientific article

Transcriptome and genome size analysis of the Venus flytrap

scientific article

Trichomonas vaginalis surface proteins: a view from the genome.

scientific article published on 24 October 2007

Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics

scientific article

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

scientific article

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

scientific article

Upstream Freshwater and Terrestrial Sources Are Differentially Reflected in the Bacterial Community Structure along a Small Arctic River and Its Estuary

scientific article

Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial.

scientific article published in November 2017

Whole-genome analyses resolve early branches in the tree of life of modern birds

scientific article

Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group

scientific article published on 14 April 2008

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