List of works - Hana Šimková

A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat

scientific article published on 27 October 2011

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

scientific article published on 22 April 2013

A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies

scientific article published on 5 April 2014

A chromosome conformation capture ordered sequence of the barley genome

scientific article

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R.

scientific article

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

scientific article

A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B.

scientific article

A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome

scientific article

A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat

scientific article published on 11 February 2021

A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS).

scientific article

A physical map of the short arm of wheat chromosome 1A.

scientific article

A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus

scientific article

Advanced resources for plant genomics: a BAC library specific for the short arm of wheat chromosome 1B.

scientific article published on 15 August 2006

Advances in plant chromosome genomics

scientific article published on 07 January 2014

An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

article by María Muñoz-Amatriaín et al published 2011 in The plant genome

An efficient approach to BAC based assembly of complex genomes

scientific article published on 20 January 2016

BAC libraries from wheat chromosome 7D: efficient tool for positional cloning of aphid resistance genes

scientific article

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

scientific article published in July 2016

Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene

scientific article published on 11 April 2015

Chromosome Genomics in the Triticeae

Chromosome analysis and sorting using flow cytometry

scientific article

Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat

scientific article

Chromosome identification for the carnivorous plant Genlisea margaretae

scientific article published on 7 May 2016

Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata

scientific article

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

scientific article published on 18 March 2021

Chromosomes in the flow to simplify genome analysis

scientific article

Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

article

Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes

article

Construction of BAC Libraries from Flow-Sorted Chromosomes

scientific article

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L

scientific article

Construction of a subgenomic BAC library specific for chromosomes 1D, 4D and 6D of hexaploid wheat

scientific article

Correction: Chromosome Isolation by Flow Sorting in Aegilops umbellulata and Ae. comosa and Their Allotetraploid Hybrids Ae. biuncialis and Ae. geniculata

scientific article published on 27 December 2011

Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

scientific article

Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.)

article

Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1.

scientific article

Dispersion and domestication shaped the genome of bread wheat

scientific article published on 24 January 2013

Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat

scientific article

Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species

scientific article

Features of the organization of bread wheat chromosome 5BS based on physical mapping

scientific article published on 9 February 2018

Fine mapping, phenotypic characterization and validation of non-race-specific resistance to powdery mildew in a wheat-Triticum militinae introgression line

scientific article published on 26 April 2012

First survey of the wheat chromosome 5A composition through a next generation sequencing approach

scientific article

Flow Analysis and Sorting of Plant Chromosomes

scientific article published on 10 October 2016

Flow cytometric chromosome sorting from diploid progenitors of bread wheat, T. urartu, Ae. speltoides and Ae. tauschii

scientific article published on 20 February 2014

Flow cytometric chromosome sorting in plants: the next generation

scientific article published on 14 March 2012

Flow sorting and sequencing meadow fescue chromosome 4F.

scientific article published on 4 October 2013

Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives

scientific article published on 27 May 2011

Functional features of a single chromosome arm in wheat (1AL) determined from its structure

scientific article

Gene content and virtual gene order of barley chromosome 1H.

scientific article published on 19 August 2009

Genotype-specific SNP map based on whole chromosome 3B sequence information from wheat cultivars Arina and Forno

scientific article published on 10 October 2012

Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies

scientific article published in January 2019

Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes

scientific article

Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat

scientific article

Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat

scientific article

LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome

scientific article

Long-read sequence assembly: a technical evaluation in barley

scientific article published on 01 July 2021

Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus

scientific article

Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications

scientific article published on 9 December 2014

One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are ⬇️

article

Physical Map of the Short Arm of Bread Wheat Chromosome 3D.

scientific article published on July 2017

Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A.

scientific article

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

scientific article

Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences.

scientific article

Sequence composition and gene content of the short arm of rye (Secale cereale) chromosome 1.

scientific article

Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS.

scientific article

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

scientific article published on 07 August 2015

Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation

scientific article

Shifting the limits in wheat research and breeding using a fully annotated reference genome

scientific article

Syntenic relationships between the U and M genomes of Aegilops, wheat and the model species Brachypodium and rice as revealed by COS markers

scientific article

The Enigma of Progressively Partial Endoreplication: New Insights Provided by Flow Cytometry and Next-Generation Sequencing

scientific article published on 19 June 2016

The Wheat Black Jack: Advances Towards Sequencing the 21 Chromosomes of Bread Wheat

The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat

scientific article published on 18 September 2019

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line

scientific article published on 11 August 2016

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

scientific article

The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements

scientific article published on 13 June 2015

The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus

scientific article published on 30 November 2015

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

scientific article published on 14 July 2013

Unlocking the barley genome by chromosomal and comparative genomics

scientific article published on 5 April 2011

Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A.

scientific article published on 19 June 2014

List of works by Hana Šimková

A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies

A chromosome conformation capture ordered sequence of the barley genome

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R.

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B.

A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome

A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat

A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS).

A physical map of the short arm of wheat chromosome 1A.

A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus

Advanced resources for plant genomics: a BAC library specific for the short arm of wheat chromosome 1B.

Advances in plant chromosome genomics

An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

An efficient approach to BAC based assembly of complex genomes

BAC libraries from wheat chromosome 7D: efficient tool for positional cloning of aphid resistance genes

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene

Chromosome Genomics in the Triticeae

Chromosome analysis and sorting using flow cytometry

Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat

Chromosome identification for the carnivorous plant Genlisea margaretae

Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

Chromosomes in the flow to simplify genome analysis

Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes

Construction of BAC Libraries from Flow-Sorted Chromosomes

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L

Construction of a subgenomic BAC library specific for chromosomes 1D, 4D and 6D of hexaploid wheat

Correction: Chromosome Isolation by Flow Sorting in Aegilops umbellulata and Ae. comosa and Their Allotetraploid Hybrids Ae. biuncialis and Ae. geniculata

Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.)

Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1.

Dispersion and domestication shaped the genome of bread wheat

Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat

Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species

Features of the organization of bread wheat chromosome 5BS based on physical mapping

Fine mapping, phenotypic characterization and validation of non-race-specific resistance to powdery mildew in a wheat-Triticum militinae introgression line

First survey of the wheat chromosome 5A composition through a next generation sequencing approach

Flow Analysis and Sorting of Plant Chromosomes

Flow cytometric chromosome sorting from diploid progenitors of bread wheat, T. urartu, Ae. speltoides and Ae. tauschii

Flow cytometric chromosome sorting in plants: the next generation

Flow sorting and sequencing meadow fescue chromosome 4F.

Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives

Functional features of a single chromosome arm in wheat (1AL) determined from its structure

Gene content and virtual gene order of barley chromosome 1H.

Genotype-specific SNP map based on whole chromosome 3B sequence information from wheat cultivars Arina and Forno

Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies

Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes

Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat

Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat

LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome

Long-read sequence assembly: a technical evaluation in barley

Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus

Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications

One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are ⬇️

Physical Map of the Short Arm of Bread Wheat Chromosome 3D.

Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A.

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences.

Sequence composition and gene content of the short arm of rye (Secale cereale) chromosome 1.

Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS.

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Syntenic relationships between the U and M genomes of Aegilops, wheat and the model species Brachypodium and rice as revealed by COS markers

The Enigma of Progressively Partial Endoreplication: New Insights Provided by Flow Cytometry and Next-Generation Sequencing

The Wheat Black Jack: Advances Towards Sequencing the 21 Chromosomes of Bread Wheat

The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements

The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

Unlocking the barley genome by chromosomal and comparative genomics

Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A.