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List of works by Daniel S. Rokhsar

A 34K SNP genotyping array forPopulus trichocarpa: Design, application to the study of natural populations and transferability to otherPopulusspecies

scientific article published on 11 January 2013

A Chromosome-scale Reference Genome of Trifoliate Orange (Poncirus trifoliata) Provides Insights into Disease Resistance, Cold Tolerance and Genome Evolution in Citrus

scientific article published on 27 September 2020

A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis

scientific article

A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans

scientific article published on 10 January 2019

A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis

scientific article published on 10 April 2019

A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes

scientific article

A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy

scientific article

A genome-wide survey of switchgrass genome structure and organization

scientific article

A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors

scientific article published on 8 May 2003

A genomewide survey of developmentally relevant genes in Ciona intestinalis. II. Genes for homeobox transcription factors

scientific article published on 8 May 2003

A genomewide survey of developmentally relevant genes in Ciona intestinalis. III. Genes for Fox, ETS, nuclear receptors and NFkappaB.

scientific article published on 13 May 2003

A large CRISPR-induced bystander mutation causes immune dysregulation

scientific article published on 18 February 2019

A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation

article

A proposal to sequence the amphioxus genome submitted to the Joint Genome Institute of the US Department of Energy

article

A reference genome for common bean and genome-wide analysis of dual domestications

scientific article published on 8 June 2014

A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis

scientific article

A segmental genomic duplication generates a functional intron

scientific article

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

scientific article

Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis

scientific article published on 25 July 2007

Acoel genome reveals the regulatory landscape of whole-body regeneration

scientific article published on 01 March 2019

Adaptation to heavy-metal contaminated environments proceeds via selection on pre-existing genetic variation

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution

scientific article published on 01 September 2020

Anatomy and development of the nervous system of Nematostella vectensis, an anthozoan cnidarian

scientific article published in March 2009

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).

scientific article

Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta

scientific article published on 21 June 2019

Assemblathon 1: a competitive assessment of de novo short read assembly methods

scientific article

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

scientific article

Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

scientific article

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes

scientific article published on 28 March 2018

Beware of 46-Fold Symmetry: The Classification of Two-Dimensional Quasicrystallographic Lattices

scientific article published in Physical Review Letters

Beyond “living fossils”: Can comparative genomics finally reveal novelty?

scientific article published in 2021

Bogoliubov quasiparticles, spinons, and spin-charge decoupling in superconductors

scientific article published on 01 June 1990

Chlamydomonas reinhardtii at the crossroads of genomics

scientific article published on December 2003

Chordate evolution and the three-phylum system

scientific article

Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis

scientific article

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

scientific article published on 14 April 2022

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage ⬇️

scientific article published on 4 February 2016

Collective Excitations of a Confined Bose Condensate

scientific article published in Physical Review Letters

Community structure and metabolism through reconstruction of microbial genomes from the environment

scientific article (publication date: 4 March 2004)

Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes.

scientific article published in January 2007

Condensates in a twist

scientific article published in Nature

Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs

scientific article

Constrained spin model of phason dynamics in quasicrystals

scientific article published on 01 November 1990

Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta

scientific article published on 09 August 2019

Correction to: Current status and impending progress for cassava structural genomics

scientific article published in 2021

Current status and impending progress for cassava structural genomics

scientific article published in 2021

Deeply conserved synteny and the evolution of metazoan chromosomes

scientific article published on 02 February 2022

Deeply conserved synteny resolves early events in vertebrate evolution

scientific article published on 20 April 2020

Development and initial characterization of a HAPPY panel for mapping the X. tropicalis genome

scientific article

Development of a toolbox to dissect host-endosymbiont interactions and protein trafficking in the trypanosomatid Angomonas deanei

scientific article

Disordered bosons: Condensate and excitations

scientific article published on 01 April 1994

Diversification of mandarin citrus by hybrid speciation and apomixis

scientific article published in 2021

Domain shuffling and the evolution of vertebrates

scientific article published on 14 May 2009

Dynamic processes shape spatiotemporal properties of retinal waves.

scientific article published in August 1997

Early evolution of the LIM homeobox gene family.

scientific article

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals

scientific article (publication date: October 2008)

Efficient and accurate clustering for large-scale genetic mapping

Electronic pairing mechanism in fullerenes: Interactions and correlations

scientific article published on 01 August 1993

Erratum

scientific article published on 26 September 2009

Erratum: Corrigendum: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

scholarly article published in Nature Biotechnology

Evidence for a microRNA expansion in the bilaterian ancestor

scientific article

Exact diagonalization of finite frustrated spin-(1/2 Heisenberg models

scientific article published on 01 March 1990

Exact solutions of frustrated ordinary and chiral eight-site Hubbard models

scientific article published on 01 July 1991

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

scientific article

Folding pathway of a lattice model for proteins

scientific article

Fungal genome sequencing and bioenergy

article

Genesis and expansion of metazoan transcription factor gene classes

scientific article published on 21 February 2008

Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing

scientific article published on 3 June 2015

Genome biology of the paleotetraploid perennial biomass crop Miscanthus

scientific article published on 28 October 2020

Genome evolution in the allotetraploid frog Xenopus laevis

scientific article

Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis.

scientific article

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

scientific article published on 3 August 2012

Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78

scientific article

Genome sequences of two Phytophthora species responsible for Sudden Oak Death and Soybean Root Rot provide novel insights into their evolutionary origins and mechanisms of pathogenesis

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

scientific article

Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: “waiting for Godot”

article

Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri

scientific article

Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses

scientific article published on 3 February 2010

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

scientific article published on 27 January 2021

Genomics of the origin and evolution of Citrus.

scientific article published on 7 February 2018

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

scientific article published on 29 July 2020

Gutzwiller projection for bosons

scientific article published on 01 November 1991

Gutzwiller projection with embedded clusters

scientific article published on 01 April 1992

Hemichordate genomes and deuterostome origins

scientific article

HipMer

Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution

scientific article

Identical genomic organization of two hemichordate hox clusters

scientific article

Identification of candidate genes encoding the core components of the cell death machinery in the Ciona intestinalis genome

article

Insights into bilaterian evolution from three spiralian genomes

scientific article

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)

scientific article

Is the molten globule a third phase of proteins?

scientific article

Isothermal strand-displacement amplification applications for high-throughput genomics

scientific article published in December 2002

Isotopic disorder and the electronic pairing mechanism in superconducting fullerenes

scientific article published on 01 July 1993

Isotopic disorder in superconducting fullerenes

scientific article published on 01 August 1993

Mechanical unfolding of a beta-hairpin using molecular dynamics

scientific article

Meraculous: de novo genome assembly with short paired-end reads

scientific article (publication date: 2011)

Metallic Screening and Correlation Effects in Superconducting Fullerenes

scientific article published in Physical Review Letters

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

scientific article

Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G

scientific article

New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis

scientific article published on 11 December 2019

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans.

scientific article published on 11 July 2010

Old can be new again: HAPPY whole genome sequencing, mapping and assembly

scientific article published on 15 April 2009

Pairing in alkaline-earth-metal-doped fullerenes

scientific article published on 01 December 1995

Pairing in doped spin liquids: Anyon versusd-wave superconductivity

scientific article published in Physical Review Letters

Parallel De Bruijn Graph Construction and Traversal for De Novo Genome Assembly

Parallel evolution of nacre building gene sets in molluscs

scientific article

Pathways for protein folding: is a new view needed?

scientific article published on February 1998

Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida)

scientific article published on 29 June 2021

Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

scientific article

Phytozome: a comparative platform for green plant genomics

scientific article (publication date: 2012)

Populus resequencing: towards genome-wide association studies.

scientific article

Predicted signatures of rotating Bose–Einstein condensates

scientific article published in Nature

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo

scholarly article

Publisher correction: Young inversion with multiple linked QTLs under selection in a hybrid zone

scientific article published on 01 October 2017

QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii

scientific article

QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert

scientific article published on 13 July 2017

Quadratic quantum antiferromagnets in the fermionic large-Nlimit

scientific article published on 01 August 1990

Quasicrystalline textures of cholesteric liquid crystals: Blue phase III?

scientific article published in April 1986

Quasiparticle Statistics in Time-Reversal Invariant States

scientific article published in Physical Review Letters

Rapid whole-genome mutational profiling using next-generation sequencing technologies

scientific article published on 4 September 2008

Real-space renormalization study of disordered interacting bosons

scientific article published on 01 August 1992

Reference genome sequence of the model plant Setaria

scientific article

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

scientific article published in December 2012

Reply to ‘‘Neutral-fermion-soliton statistics in the short-range resonating-valence-bond state: A reevaluation’’

scientific article published on 01 October 1989

Retinal waves are governed by collective network properties

scientific article published on May 1999

Reverse methanogenesis: testing the hypothesis with environmental genomics

scientific article published in September 2004

Rosaceaous Genome Sequencing: Perspectives and Progress

Rudimentary quasicrystallography: The icosahedral and decagonal reciprocal lattices

scientific article published on 01 April 1987

Scale equivalence of quasicrystallographic space groups

scientific article published on 01 May 1988

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization

scientific article

Self-organization in prebiological systems: simulations of a model for the origin of genetic information

scientific article published in January 1986

Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism

scientific article

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

scientific article (publication date: July 2014)

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

scientific article published on 18 April 2016

Simple theory of exchange coupling in transition-metal magnetic multilayers

scientific article published on 01 September 1991

Solitons in chiral-spin liquids

scientific article published in Physical Review Letters

Stacking quasicrystallographic lattices

scientific article published on 01 May 1990

StellaBase: the Nematostella vectensis Genomics Database

scientific article

Suboptimization of developmental enhancers

scientific article

Superconductivity and the Quantum Hard-Core Dimer Gas

scientific article published in Physical Review Letters

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods

scientific article published on 11 January 2019

Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers

scientific article published on 06 May 2016

Terabase-scale metagenome coassembly with MetaHipMer

scientific article published on 01 July 2020

The Amphimedon queenslandica genome and the evolution of animal complexity ⬇️

scientific article

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

scientific article

The Cassava Genome: Current Progress, Future Directions

scientific article published on 5 January 2012

The Chlamydomonas genome reveals the evolution of key animal and plant functions

scientific article

The DNA sequence and biology of human chromosome 19

scientific article

The DNA sequence and comparative analysis of human chromosome 5

scientific article

The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins

scientific article

The Eucalyptus grandis Genome Project: Genome and transcriptome resources for comparative analysis of woody plant biology

scientific article

The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

scientific article

The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility

scientific article

The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism

scientific article

The NK homeobox gene cluster predates the origin of Hox genes

scientific article published on 22 March 2007

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

scientific article

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants

scientific article

The Sorghum bicolor genome and the diversification of grasses

scientific article

The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle

scientific article

The Trichoplax genome and the nature of placozoans

scientific article

The amphioxus genome and the evolution of the chordate karyotype

scientific article

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

scientific article

The deuterostome context of chordate origins.

scientific article published on April 2015

The dynamic genome of Hydra

scientific article

The early ANTP gene repertoire: insights from the placozoan genome

scientific article

The evolutionary origin of hedgehog proteins

scientific article

The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii

scientific article

The genome of Eucalyptus grandis

scientific article

The genome of the Western clawed frog Xenopus tropicalis

scientific article

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

scientific article

The genome portal of the Department of Energy Joint Genome Institute

scientific article published on 22 November 2011

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

scholarly article

The genomic landscape of molecular responses to natural drought stress in Panicum hallii

scientific article published in Nature Communications

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

scientific article

The information content of spontaneous retinal waves

scientific journal article

The octopus genome and the evolution of cephalopod neural and morphological novelties

scientific article

The sequence and analysis of duplication-rich human chromosome 16

scientific article

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

scientific article

Topology and nematic ordering

scientific article published in Physical Review Letters

Topology and nematic ordering. I. A gauge theory

article

Topology and nematic ordering. II. Observable critical behavior

scientific article published on 01 August 1995

Topology of the resonating valence-bond state: Solitons and high- T c superconductivity

scientific article

Transcription factor binding site identification using the self-organizing map.

scientific article published on 12 January 2005

Variational evidence for spin liquids in frustrated lattices

article

Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies

scientific article

Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

scientific article

Young inversion with multiple linked QTLs under selection in a hybrid zone

scientific article

merAligner: A Fully Parallel Sequence Aligner

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