References

Crustacean leg regeneration restores complex microanatomy and cell diversity

10.1126/sciadv.abn9823 · 2022 · External reference

Genome-wide quantitative enhancer activity maps identified by STARR-seq

10.1126/science.1232542 · 2013 · External reference

The crustacean Parhyale

10.1038/s41592-022-01596-y · 2022 · External reference

Predicting gene expression from DNA sequence using deep learning models

10.1038/s41576-025-00841-2 · 2025 · External reference

High-resolution profiling of histone methylations in the human genome

10.1016/j.cell.2007.05.009 · 2007 · External reference

Hi-C: a comprehensive technique to capture the conformation of genomes

10.1016/j.ymeth.2012.05.001 · 2012 · External reference

Discovery of regulatory elements by a computational method for phylogenetic footprinting

10.1101/gr.6902 · 2002 · External reference

AMAS: a fast tool for alignment manipulation and computing of summary statistics

10.7717/peerj.1660 · 2016 · External reference

H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex

10.7554/elife.02833 · 2014 · External reference

Stages of embryonic development in the amphipod crustacean, Parhyale hawaiensis

10.1002/gene.20145 · 2005 · External reference

Knockout of crustacean leg patterning genes suggests that insect wings and body walls evolved from ancient leg segments

10.1038/s41559-020-01349-0 · 2020 · External reference

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

10.1038/nmeth.2688 · 2013 · External reference

Single-cell chromatin accessibility reveals principles of regulatory variation

10.1038/nature14590 · 2015 · External reference

Gone with Gondwana: Amphipod diversification in freshwaters followed the breakup of the supercontinent

10.1016/j.ympev.2022.107464 · 2022 · External reference

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

10.1038/nmeth.4396 · 2017 · External reference

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing

10.1126/science.aab1601 · 2015 · External reference

Twelve years of SAMtools and BCFtools

10.1093/gigascience/giab008 · 2021 · External reference

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

10.1038/s41588-022-01048-5 · 2022 · External reference

Searching for regulatory elements in human noncoding sequences

10.1016/s0959-440x(97)80058-9 · 1997 · External reference

Early and late periodic patterns of even skipped expression are controlled by distinct regulatory elements that respond to different spatial cues

10.1016/0092-8674(89)90916-1 · 1989 · External reference

Promoter architectures and developmental gene regulation

10.1016/j.semcdb.2016.01.014 · 2016 · External reference

Dictionary learning for integrative, multimodal and scalable single-cell analysis

10.1038/s41587-023-01767-y · 2024 · External reference

Parhyale plumicornis (Crustacea: Amphipoda: Hyalidae): is this an anti-lessepsian mediterranean species? morphological remarks, molecular markers and ecological notes as tools for future records

10.1080/14772000.2016.1248519 · 2017 · External reference

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

10.1101/gr.214346.116 · 2017 · External reference

The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion

10.7554/elife.20062 · 2016 · External reference

Targeting the cell membrane in established and emerging model organisms

10.1242/dev.205415 · 2026 · External reference

BigWig and BigBed: enabling browsing of large distributed datasets

10.1093/bioinformatics/btq351 · 2010 · External reference

ChIP-Seq: technical considerations for obtaining high-quality data

10.1038/ni.2117 · 2011 · External reference

A versatile strategy for gene trapping and trap conversion in emerging model organisms

10.1242/dev.066324 · 2011 · External reference

Transgenesis in non-model organisms: the case of Parhyale

10.1007/978-1-4939-1242-1_10 · 2014 · External reference

Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum

10.1242/dev.160663 · 2018 · External reference

Fast gapped-read alignment with Bowtie 2

10.1038/nmeth.1923 · 2012 · External reference

Transcriptional coupling of distant regulatory genes in living embryos

10.1038/s41586-022-04680-7 · 2022 · External reference

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

10.1093/bioinformatics/btt656 · 2014 · External reference

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

10.1126/science.1181369 · 2009 · External reference

pyGenomeTracks: reproducible plots for multivariate genomic datasets

10.1093/bioinformatics/btaa692 · 2021 · External reference

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

10.1186/s13059-014-0550-8 · 2014 · External reference

Parhyale darvishi, a new widely distributed amphipod species, in the Persian Gulf and the Gulf of Oman (Crustacea, Amphipoda, Hyalidae)

10.11646/zootaxa.4132.3.4 · 2016 · External reference

BAC library for the amphipod crustacean, Parhyale hawaiensis

10.1016/j.ygeno.2010.03.005 · 2010 · External reference

The crustacean model Parhyale hawaiensis

10.1016/bs.ctdb.2022.02.001 · 2022 · External reference

Establishing genetic transformation for comparative developmental studies in the crustacean Parhyale hawaiensis

10.1073/pnas.0501101102 · 2005 · External reference

Probing the evolution of appendage specialization by Hox gene misexpression in an emerging model crustacean

10.1073/pnas.0902804106 · 2009 · External reference

The bithorax complex: control of segmental identity

10.1101/gad.1.9.891 · 1987 · External reference

In vivo enhancer analysis of human conserved non-coding sequences

10.1038/nature05295 · 2006 · External reference

Tools for neuroanatomy and neurogenetics in Drosophila

10.1073/pnas.0803697105 · 2008 · External reference

Using translational enhancers to increase transgene expression in Drosophila

10.1073/pnas.1204520109 · 2012 · External reference

The Toxicogenome of Hyalella azteca: a model for sediment ecotoxicology and evolutionary toxicology

10.1021/acs.est.8b00837 · 2018 · External reference

BEDTools: a flexible suite of utilities for comparing genomic features

10.1093/bioinformatics/btq033 · 2010 · External reference

deepTools2: a next generation web server for deep-sequencing data analysis

10.1093/nar/gkw257 · 2016 · External reference

Analysis of the genetically tractable crustacean Parhyale hawaiensis reveals the organisation of a sensory system for low-resolution vision

10.1186/s12915-019-0676-y · 2019 · External reference

MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons

10.1093/molbev/msy159 · 2018 · External reference

EMBOSS: the european molecular biology open software suite

10.1016/s0168-9525(00)02024-2 · 2000 · External reference

The long-range interaction landscape of gene promoters

10.1038/nature11279 · 2012 · External reference

Comprehensive analysis of Hox gene expression in the amphipod crustacean Parhyale hawaiensis

10.1016/j.ydbio.2015.10.029 · 2016 · External reference

Distinct gene expression dynamics in developing and regenerating crustacean limbs

10.1073/pnas.2119297119 · 2022 · External reference

Comprehensive integration of single-cell data

10.1016/j.cell.2019.05.031 · 2019 · External reference

Single-cell chromatin state analysis with Signac

10.1038/s41592-021-01282-5 · 2021 · External reference

Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis

10.1242/dev.200793 · 2022 · External reference

OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes

10.1093/nar/gkae987 · 2025 · External reference

10.1007/978-3-319-24277-4

10.1007/978-3-319-24277-4 · 2016 · External reference

Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb

10.7554/elife.34410 · 2018 · External reference

IQ-TREE 3: phylogenomic inference software using complex evolutionary models

10.32942/x2p62n · 2025 · External reference

Highly conserved non-coding sequences are associated with vertebrate development

10.1371/journal.pbio.0030007 · 2005 · External reference

Model-based analysis of chIP-seq (MACS)

10.1186/gb-2008-9-9-r137 · 2008 · External reference

Genome-wide discovery of cis-regulatory elements in a large genome [bulk ATAC-seq]

2026 · External reference

Genome-wide discovery of cis-regulatory elements in a large genome [scATAC-seq]

2026 · External reference

Short genomic reads from a Parhyale aquilina individual

2026 · External reference

Short genomic reads from a Parhyale darvishi individual

2026 · External reference

Short genomic reads from a Parhyale plumicornis individual

2026 · External reference

Supplementary data for 'Genome-wide discovery of cis-regulatory elements in a large genome'

10.5281/zenodo.19020963 · 2026 · External reference