Author

J. Dekker

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Cell Biology· 6 Ecology· 2 Evolutionary Biology· 1 Immunology· 1 Microbiology· 1

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Research Focus:chromatin & epigenetic regulation· 7 Approach:experimental assay· 7 Approach:statistical model· 5 Research Focus:cell type annotation· 4 Assay:ChIP-seq· 3 Assay:Hi-C· 3 Organism:human· 3 Organism:multiple species· 3

Frequent Co-Authors

A. H. Ali· 2 shared A. T. Ford· 2 shared B. Dekker· 2 shared C. Fichtel· 2 shared C. H. Fleming· 2 shared J. L. Belant· 2 shared L. Yang· 2 shared M. J. Noonan· 2 shared

Activity by Year

2019-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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Curved chords = mutual co-authorship

2 shared papersEcology

A. H. Ali

Mutual co-authors in cluster

Author profile →

11 papers

Recent·Most cited

Enhancer-driven local 3D chromatin domain folding modulates transcription in human mammary tumor cells

S. Kocanova, F. Raynal, I. Goiffon, B. A. Oksuz, D. Bau, A. Kamgoue, S. Cantaloube, Y. Zhan, B. Lajoie, M. A. Marti-Renom, J. Dekker, K. Bystricky

The paper investigates how enhancer-driven 3D chromatin domain folding regulates transcription in human mammary tumor cells following estradiol stimulation.

bioRxiv · Oct 17, 2023Cell Biology

High number of HPAI H5 Virus Infections and Antibodies in Wild Carnivores in the Netherlands, 2020-2022

I. Chestakova, A. van der Linden, B. Bellido Martin, V. Caliendo, O. Vuong, S. Thewessen, T. Hartung, T. Bestebroer, J. Dekker, B. Jonge Poerink, A. Grone, M. Koopmans, R. Fouchier, J. van den Brand, R. S. Sikkema

The paper reports HPAI H5 virus infections and antibodies in wild carnivores in the Netherlands from 2020-2022, showing increasing infection rates and mammalian adaptation markers.

bioRxiv · May 12, 2023Microbiology

The search behavior of terrestrial mammals

M. J. Noonan, R. Martinez-Garcia, C. H. Fleming, B. Garcia De Figueiredo, A. H. Ali, N. Attias, J. L. Belant, D. E. Beyer, D. Berteaux, L. R. Bidner, R. B. Boone, S. Boutin, J. Brito, M. Brown, A. Carter, , M. Lashley

This study analyzes GPS data from 1,396 terrestrial mammals across 62 species to show how predator-prey dynamics influence movement strategies and resource search efficiency.

bioRxiv · Dec 31, 2022 · PreprintEcology

Mitotic chromosomes scale to nucleo-cytoplasmic ratio and cell size in Xenopus

C. Y. Zhou, B. Dekker, Z. Liu, H. Cabrera, J. Ryan, J. Dekker, R. Heald

This study shows mitotic chromosomes scale with cell size and nucleo-cytoplasmic ratio in Xenopus, distinct from other subcellular structures, through mechanisms involving condensin I and importin pathways.

bioRxiv · Oct 20, 2022Cell Biology

Clarifying space use concepts in ecology: range vs. occurrence distributions

J. M. Alston, C. H. Fleming, M. J. Noonan, M. A. Tucker, I. Silva, C. Folta, T. S. Akre, A. H. Ali, J. L. Belant, D. Beyer, N. Blaum, K. Boehning-Gaese, R. Cunha de Paula, J. Dekker, J. Drescher-Lehman, , W. F. Fagan

This paper distinguishes between range and occurrence distributions in ecology, showing that conflating them can lead to incorrect ecological inferences and conservation practices.

bioRxiv · Sep 29, 2022Ecology

The little skate genome and the evolutionary emergence of wing-like fin appendages

F. Marletaz, E. de la Calle-Mustienes, R. D. Acemel, T. Nakamura, C. Paliou, S. Naranjo, P. M. Martinez-Garcia, I. Cases, V. A. Sleight, C. Hirschberger, M. Marcet-Houben, D. Navon, A. Andrescavage, K. Skvortsova, P. E. Duckett, , J. L. Gomez-Skarmeta

This study identifies genomic rearrangements and regulatory changes in the little skate that contribute to the evolution of wing-like fin appendages.

bioRxiv · Mar 21, 2022 · PreprintEvolutionary Biology

pmTR database: population matched (PM) germline allelic variants of T-cell receptor (TR) loci

J. Dekker, J. J. M. van Dongen, M. Reinders, I. Khatri

The paper introduces the pmTR database, which provides population-specific germline T-cell receptor alleles from 26 human populations, enhancing research on population-specific immune responses.

bioRxiv · Dec 23, 2020Immunology

Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome length and individualization

P. Choppakatla, B. Dekker, E. Cutts, A. Vannini, J. Dekker, H. Funabiki

This study shows H1.8 inhibits condensins and topo II to regulate chromosome length and individualization during mitosis.

bioRxiv · Dec 20, 2020Cell Biology

SPATIAL ORGANIZATION OF TRANSCRIBED EUKARYOTIC GENES

S. Leidescher, J. Ribisel, S. Ullrich, Y. Feodorova, E. Hildebrand, S. Bultmann, S. Link, K. Thanisch, C. B. Mulholland, J. Dekker, H. Leonhardt, L. Mirny, I. Solovei

This study investigates how transcription shapes genome spatial organization by analyzing long highly expressed genes and demonstrating the formation of transcription loops with polymerases and nascent RNAs.

bioRxiv · May 20, 2020Cell Biology

Large domains of heterochromatin direct the formation of short mitotic chromosome loops

M. H. Fitz-James, P. Tong, A. L. Pidoux, H. Ozadam, L. Yang, S. A. White, J. Dekker, R. C. Allshire

The paper shows that heterochromatin in mouse and human cells forms smaller chromatin loops during mitosis compared to euchromatic regions.

bioRxiv · Apr 1, 2020Cell Biology

Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control

A. D. Viny, R. L. Bowman, Y. Liu, V.-P. Lavallee, S. E. Redlich, W. Xiao, B. H. Durham, A. Navitski, J. Park, S. Braunstein, E. Azizi, M. Witkin, T. Baslan, C. J. Ott, D. Pe'er, , R. L. Levine

The paper shows Stag2 loss in HSPCs impairs B-cell lineage commitment by reducing chromatin accessibility, while Stag1 cannot restore this function despite rescuing topological domains.

bioRxiv · Mar 18, 2019 · PreprintCell Biology