Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation

Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds

(2021) Phuong T. N. Hoang et al.   CHROMOSOMA

A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era

(2021) Wenxi Jiang et al.   BMC PLANT BIOLOGY

Chorus2: design of genome‐scale oligonucleotide‐based probes for fluorescence in situ hybridization

(2021) Tao Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Advances in Chromatin Imaging at Kilobase-Scale Resolution

(2020) Alistair Boettiger et al.   TRENDS IN GENETICS

A universal chromosome identification system for maize and wild Zea species

(2020) Guilherme T. Braz et al.   CHROMOSOME RESEARCH

OligoMinerApp: a web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment

(2020) Marco Passaro et al.   NUCLEIC ACIDS RESEARCH

An efficient Oligo‐FISH painting system for revealing chromosome rearrangements and polyploidization in Triticeae

(2020) Guangrong Li et al.   PLANT JOURNAL

ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization

(2020) Mengwei Hu et al.   Scientific Reports

Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships

(2019) Patrice S. Albert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluorescence in situ hybridization in plants: recent developments and future applications

(2019) Jiming Jiang   CHROMOSOME RESEARCH

Nondisjunction and unequal spindle organization accompany the drive of Aegilops speltoides B chromosomes

(2019) DanDan Wu et al.   NEW PHYTOLOGIST

iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

(2019) Eleni Gelali et al.   Nature Communications

Dual‐color oligo‐FISH can reveal chromosomal variations and evolution in Oryza species

(2019) Xiaoyu Liu et al.   PLANT JOURNAL

Meiotic crossovers characterized by haplotype-specific chromosome painting in maize

(2019) Lívia do Vale Martins et al.   Nature Communications

Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana (Musa Spp.)

(2019) Denisa Šimoníková et al.   Frontiers in Plant Science

Kmasker plants – a tool for assessing complex sequence space in plant species

(2019) Sebastian Beier et al.   PLANT JOURNAL

Snakemake—a scalable bioinformatics workflow engine

(2018) Johannes Köster et al.   BIOINFORMATICS

Chromosome painting and comparative physical mapping of the sex chromosomes in Populus tomentosa and Populus deltoides

(2018) Haoyang Xin et al.   CHROMOSOMA

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Oli2go: an automated multiplex oligonucleotide design tool

(2018) Michaela Hendling et al.   NUCLEIC ACIDS RESEARCH

OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes

(2018) Brian J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana

(2018) Mao-Lun Weng et al.   GENETICS

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

(2018) Guy Nir et al.   PLoS Genetics

Comparative Oligo-FISH Mapping: An Efficient and Powerful Methodology To Reveal Karyotypic and Chromosomal Evolution

(2017) Guilherme T. Braz et al.   GENETICS

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

Comparative Oligo-FISH Mapping: An Efficient and Powerful Methodology To Reveal Karyotypic and Chromosomal Evolution

(2017) Guilherme T. Braz et al.   GENETICS

Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides

(2015) Yonghua Han et al.   GENETICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

Oligonucleotide Probes for ND-FISH Analysis to Identify Rye and Wheat Chromosomes

(2015) Shulan Fu et al.   Scientific Reports

Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides

(2015) Yonghua Han et al.   GENETICS

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Expanding probe repertoire and improving reproducibility in human genomic hybridization

(2013) Stephanie N. Dorman et al.   NUCLEIC ACIDS RESEARCH

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH

(2012) Magda Bienko et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Comprehensive FISH Probe Design Tool Applied to Imaging Human Immunoglobulin Class Switch Recombination

(2012) Jakub Nedbal et al.   PLoS One

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

(2012) B. J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Visualization of Fine-Scale Genomic Structure by Oligonucleotide-Based High-Resolution FISH

(2011) N.A. Yamada et al.   CYTOGENETIC AND GENOME RESEARCH

Random BAC FISH of monocot plants reveals differential distribution of repetitive DNA elements in small and large chromosome species

(2011) Go Suzuki et al.   PLANT CELL REPORTS

mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models forIn SilicoEvaluation of Oligonucleotide Probes for FluorescenceIn SituHybridization

(2010) L. Safak Yilmaz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Chromosomal detection of simple sequence repeats (SSRs) using nondenaturing FISH (ND-FISH)

(2010) Ángeles Cuadrado et al.   CHROMOSOMA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A novel, simple and rapid nondenaturing FISH (ND-FISH) technique for the detection of plant telomeres. Potential used and possible target structures detected

(2009) Ángeles Cuadrado et al.   CHROMOSOME RESEARCH