Tom van der Valk

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DDLS Fellow: Evolution and biodiversity

Primary: Shown in the list of current labels.

Year 2026

PubMed DOI Crossref
Ancient RNA expression profiles from the extinct woolly mammoth.
Mármol-Sánchez E, Fromm B, Oskolkov N, ..., Friedländer MR, Dalén L
Cell 189 (1) 52-69.e22 [2026-01-08; online 2025-11-14]
DDLS Fellow Marc Friedländer SciLifeLab Fellow Tom van der Valk

Year 2025

PubMed DOI Crossref
Ancient host-associated microbes obtained from mammoth remains.
Guinet B, Oskolkov N, Moreland K, ..., Dalén L, van der Valk T
Cell 188 (23) 6606-6619.e24 [2025-11-13; online 2025-09-02]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Reticulate and Hybrid Speciation is Promoted by Environmental Instability in an Indo-Pacific Species Complex of Whistlers (Aves: Pachycephala).
Irestedt M, Müller IA, Thörn F, ..., van der Valk T, Jønsson KA
Mol. Ecol. 34 (21) e70018 [2025-11-00; online 2025-07-12]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Small Bugs, Big Data: Metagenomics for Arthropod Biodiversity Monitoring.
López Clinton S, Iwaszkiewicz-Eggebrecht E, Miraldo A, ..., Ronquist F, van der Valk T
Ecol Evol 15 (9) e72163 [2025-09-00; online 2025-09-16]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Genomic and morphological analysis reveals long-term mammoth hybridization in British Columbia, Canada.
Dehasque M, van der Valk T, Chacón-Duque JC, ..., Lister A, Dalén L
Biol. Lett. 21 (9) 20250305 [2025-09-00; online 2025-09-24]
DDLS Fellow Tom van der Valk
DOI Crossref
The Impact of Reference Genome Divergence on Ancient DNA Damage Detection in Metagenomic Contexts
Guinet B, Sharif BM, van der Valk T
- - (-) - [2025-07-20; online 2025-07-20]
DDLS Fellow Tom van der Valk
DOI Crossref
1000 conifer genomes: Genome innovation, organisation and diversity
Nilsson O, Kalman TA, Delhomme N, ..., Nystedt B, Street N
- - (-) - [2025-05-26; online 2025-05-26]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Metagenomic biodiversity assessment within an offshore wind farm.
Serivichyaswat PT, Scholte T, Wilms T, Stranddorf L, van der Valk T
Sci Rep 15 (1) 16786 [2025-05-14; online 2025-05-14]
DDLS Fellow Tom van der Valk
DOI Crossref
Disinfecting eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data
Oskolkov N, Jin C, Clinton SL, ..., Heintzman PD, van der Valk T
- - (-) - [2025-03-19; online 2025-03-19]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.
Oskolkov N, Jin C, Clinton SL, ..., Heintzman PD, van der Valk T
Gigascience 14 (-) - [2025-01-06; online 2025-10-03]
DDLS Fellow Tom van der Valk

Year 2024

PubMed DOI Crossref
Temporal dynamics of woolly mammoth genome erosion prior to extinction.
Dehasque M, Morales HE, Díez-Del-Molino D, ..., Vartanyan S, Dalén L
Cell 187 (14) 3531-3540.e13 [2024-07-11; online 2024-06-27]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Unravelling reference bias in ancient DNA datasets.
Dolenz S, van der Valk T, Jin C, ..., Dalén L, Heintzman PD
Bioinformatics 40 (7) - [2024-07-01; online 2024-07-04]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
From genomic threat assessment to conservation action.
van der Valk T, Dalèn L
Cell 187 (5) 1038-1041 [2024-02-29; online 2024-03-02]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species.
Estravis Barcala M, van der Valk T, Chen Z, ..., Nilsson O, Wu HX
Plant J. 117 (3) 944-955 [2024-02-00; online 2023-11-10]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Comparative genomic analyses provide new insights into evolutionary history and conservation genomics of gorillas.
van der Valk T, Jensen A, Caillaud D, Guschanski K
BMC Ecol Evol 24 (1) 14 [2024-01-26; online 2024-01-26]
DDLS Fellow Tom van der Valk

Year 2023

PubMed DOI Crossref
aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.
Pochon Z, Bergfeldt N, Kırdök E, ..., Unneberg P, Oskolkov N
Genome Biol. 24 (1) 242 [2023-10-23; online 2023-10-23]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Ghost admixture in eastern gorillas.
Pawar H, Rymbekova A, Cuadros-Espinoza S, ..., Marques-Bonet T, Kuhlwilm M
Nat Ecol Evol 7 (9) 1503-1514 [2023-09-00; online 2023-07-27]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Genomics of adaptive evolution in the woolly mammoth.
Díez-Del-Molino D, Dehasque M, Chacón-Duque JC, ..., van der Valk T, Dalén L
Curr. Biol. 33 (9) 1753-1764.e4 [2023-05-08; online 2023-04-07]
DDLS Fellow Tom van der Valk

Year 2022

DOI Crossref
Ghost admixture in eastern gorillas
Pawar H, Rymbekova A, Cuadros S, ..., Marques-Bonet T, Kuhlwilm M
- - (-) - [2022-12-19; online 2022-12-19]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Genomic trajectories of a near-extinction event in the Chatham Island black robin.
von Seth J, van der Valk T, Lord E, ..., Robertson BC, Dussex N
BMC Genomics 23 (1) 747 [2022-11-10; online 2022-11-10]
DDLS Fellow Tom van der Valk
DOI Crossref
aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow
Pochon Z, Bergfeldt N, Kırdök E, ..., Unneberg P, Oskolkov N
- - (-) - [2022-10-05; online 2022-10-05]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.
van der Valk T, Dehasque M, Chacón-Duque JC, ..., Díez-Del-Molino D, Dalén L
iScience 25 (8) 104826 [2022-08-19; online 2022-08-01]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.
Kutschera VE, Kierczak M, van der Valk T, ..., Dalén L, Díez-Del-Molino D
BMC Bioinformatics 23 (1) 228 [2022-06-13; online 2022-06-13]
DDLS Fellow Tom van der Valk
DOI Crossref
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
Kutschera VE, Kierczak M, van der Valk T, ..., Dalén L, Díez-del-Molino D
- - (-) - [2022-03-07; online 2022-03-07]
DDLS Fellow Tom van der Valk

Year 2021

PubMed DOI Crossref
Population genomics of the critically endangered kākāpō.
Dussex N, van der Valk T, Morales HE, ..., Robertson BC, Dalén L
Cell Genom 1 (1) 100002 [2021-10-13; online 2021-09-08]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.
Liu S, Westbury MV, Dussex N, ..., Dalén L, Gilbert MTP
Cell 184 (19) 4874-4885.e16 [2021-09-16; online 2021-08-24]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Mammuthus sp. (Early and Middle Pleistocene Mammoths).
Pečnerová P, Díez-Del-Molino D, van der Valk T, ..., Götherström A, Dalén L
Trends in Genetics 37 (7) 682-683 [2021-07-00; online 2021-05-11]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.
von Seth J, Dussex N, Díez-Del-Molino D, ..., Götherström A, Dalén L
Nat Commun 12 (1) 2393 [2021-04-26; online 2021-04-26]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Million-year-old DNA sheds light on the genomic history of mammoths.
van der Valk T, Pečnerová P, Díez-Del-Molino D, ..., Götherström A, Dalén L
Nature 591 (7849) 265-269 [2021-03-00; online 2021-02-17]
DDLS Fellow Tom van der Valk

Year 2020

PubMed DOI Crossref
Moose genomes reveal past glacial demography and the origin of modern lineages.
Dussex N, Alberti F, Heino MT, ..., Dalén L, Díez-Del-Molino D
BMC Genomics 21 (1) 854 [2020-12-02; online 2020-12-02]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.
van der Valk T, Vezzi F, Ormestad M, Dalén L, Guschanski K
Mol Ecol Resour 20 (5) 1171-1181 [2020-09-00; online 2019-05-05]
DDLS Fellow Tom van der Valk

Year 2019

PubMed DOI Crossref
Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.
Hooper R, Brealey JC, van der Valk T, ..., Foote AD, Guschanski K
Mol. Ecol. 28 (2) 484-502 [2019-01-00; online 2018-10-24]
DDLS Fellow Tom van der Valk

Year 2018

DOI Crossref
Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
Hooper R, Brealey JC, van der Valk T, ..., Foote AD, Guschanski K
- - (-) - [2018-03-14; online 2018-03-14]
DDLS Fellow Tom van der Valk
SciLifeLab Data Centre
Publications 9.5.1