Publications

2022

2021

Chromosome Level Genome Assembly and Annotation of Highly Invasive Japanese Stiltgrass (Microstegium vimineum)
Ramachandran D, et al., Genome Biology and Evolution, 2021, October 28

A chromosomal assembly of the soybean cyst nematode genome
Masonbrink R, et al., Mol Ecol Resour., 2021, October

The bowfin genome illuminates the developmental evolution of ray-finned fishes
Thompson AW, et al., Nature Genetics, 2021, August 30

Rootstocks influence the response of ripening grape berries to leafroll associated viruses
Vondras AM, et al., Mol Plant Pathol, 2021, August

Genome of the parasitoid wasp Dinocampus coccinellae reveals extensive duplications, accelerated evolution, and independent origins of thelytokous parthenogeny and solitary behavior
Sethuraman A, et al., bioRxiv, 2021, July 1

An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus
Saremi NF, et al., J Hered., 2021, June

Gene-rich UV sex chromosomes harbor conserved regulators of sexual development
Carey SB, et al., Science Advances, 2021, June 30

Chromosomal-level genome assembly of the painted sea urchin Lytechinus pictus, a genetically enabled model system for cell biology and embryonic development
Warner JF, et al., Genome Biology and Evolution, 2021, April 5

Towards complete and error-free genome assemblies of all vertebrate species
Rhie A, et al., Nature, 2021, April

Widespread recombination suppression facilitates plant sex chromosome evolution
Rifkin JL, et al., Mol Biol Evol., 2021, March 9

Chromosome-scale, haplotype-resolved assembly of human genomes
Garg S, et al., Nature biotechnology, 2021, March

A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
Liu J, et al., Genome Research, 2021, March

Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn
Hu Y, et al., Nature communications, 2021, February 23

Characterization of a pericentric inversion in plateau fence lizards (Sceloporus tristichus): evidence from chromosome-scale genomes
Bedoya AM, Leaché AD,, G3 (Bethesda), 2021, February 9

Genome assemblies for two Neotropical trees: Jacaranda copaia and Handroanthus guayacan
Burley JT, et al., G3 (Bethesda), 2021, February 9

Raw pacific biosciences and illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus
Guerrero FD, et al., Data in Brief, 2021, February 6

Structural and Functional Genomics of Chenopodium quinoa
Rey E, Jarvis DE,, The Quinoa Genome, 2021, February 5

Pigmentation Genes Show Evidence of Repeated Divergence and Multiple Bouts of Introgression in Setophaga Warblers
Baiz MD, et al., Current Biology, 2021, February

Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication
Nong W, et al., Communications Biology, 2021, January 19

A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina
Friis G, et al., G3 (Bethesda), 2021, January 18

Insights from the first genome assembly of Onion (Allium cepa)
Finkers R, et al., bioRxiv, 2021, January 1

De novo assemblies of Luffa acutangula and Luffa cylindrica genomes reveal an expansion associated with substantial accumulation of transposable elements
Pootakham W, et al., Molecular Ecology Resources, 2021, January

A chromosome‐scale assembly of the black gram (Vigna mungo) genome
Pootakham W, et al., Molecular Ecology Resources, 2021, January

2020

A low cost pipeline for soil microbiome profiling
Bollmann Giolai A, et al., MicrobiologyOpen, 2020, December

A Reference Genome Sequence for Giant Sequoia
Scott AD, et al., G3: Genes, Genomes, Genetics, 2020, November 5

A comparative genomics multitool for scientific discovery and conservation
Zoonomia Consortium,, Nature, 2020, November

Integrating genomics into conservation management
Latch EK; , Molecular ecology resources, 2020, November

Dense sampling of bird diversity increases power of comparative genomics
Feng S, et al., Nature, 2020, November

Genome biology of the paleotetraploid perennial biomass crop Miscanthus
Mitros T, et al., Nature communications, 2020, October 28

Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra
Winter S, et al., Gigabyte, 2020, October 20

Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome
Li Y, et al., BMC genomics, 2020, October 15

High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus
Harrop TWR, et al., G3: Genes, Genomes, Genetics, 2020, October 5

“Mind the Gap”: Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions
Acquadro A, et al., G3: Genes, Genomes, Genetics, 2020, October 5

Millipede genomes reveal unique adaptations during myriapod evolution
Qu Z, et al., PLoS biology, 2020, September 29

Early vertebrate origin of CTCFL, a CTCF paralog, revealed by proximity-guided shark genome scaffolding
Kadota M, et al., Scientific reports, 2020, September 3

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution
Mudd AB, et al., Communications biology, 2020, September 1

Advances in genomics of cashew tree: molecular tools and strategies for accelerated breeding
Savadi S, Muralidhara BM, Preethi P,, Tree Genetics & Genomes, 2020, August 5

Discovery and population genomics of structural variation in a songbird genus
Weissensteiner M, et al., Nature communications, 2020, July 7

Chromosomal level reference genome of the incense tree Aquilaria sinensis
Nong W, et al., Molecular ecology resources, 2020, July

Harnessing genomics to fast-track genetic improvement in aquaculture
Houston RD, et al., Nature Reviews Genetics, 2020, July

Analysis of global patents for the trend of synthetic biology inventions
Daming C, et al., Synthetic Biology Journal, 2020, June 30

Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing
Nong W, et al., Nature communications, 2020, June 19

A genome assembly of the barley ‘transformation reference’cultivar golden promise
Schreiber M, et al., G3: Genes, Genomes, Genetics, 2020, June 1

Deeply conserved synteny resolves early events in vertebrate evolution
Simakov O, et al., Nature ecology & evolution, 2020, June

Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation
Tigan, A, et al., Genome Biol Evol., 2020, June

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes
Uengwetwanit T, et al., bioRxiv [pre-print], 2020, May 16

The genomics of Cannabis and its close relatives
Kovalchuk I, et al., Annual review of plant biology, 2020, April 29

A pseudomolecule assembly of the Rocky Mountain elk genome reveals putative immune system gene loss near chromosomal fissions
Masonbrink R, et al., PLoS One, 2020, April 28

A high-quality genome assembly of the North American Song Sparrow, Melospiza melodia
Louha S, et al., G3: Genes, Genomes, Genetics, 2020, April 9

A genome assembly of the barley ‘transformation reference’ cultivar Golden Promise
Schreiber M, et al., G3: Genes, Genomes, Genetics. , 2020, April 3

Molluscan genomics: the road so far and the way forward
Gomes-dos-Santos A, et al., Hydrobiologia, 2020, April

Chromosome-level assembly of the Caenorhabditis remanei genome reveals conserved patterns of nematode genome organization
Teterina AA, Willis JH, Phillips PC,, Genetics, 2020, April

De novo assembly of the cattle reference genome with single-molecule sequencing
Rosen BD, et al., GigaScience., 2020, March 19

Chromosomal level reference genome of the incense tree Aquilaria sinensis
Nong W, et al.,  Molecular Ecology Resources., 2020, March 10

Chromosome-level assembly of the Caenorhabditis remanei genome reveals conserved patterns of nematode genome organization
Teterina AA, et al., Genetics., 2020, February 28

Characterization of a large pericentric inversion in Plateau Fence Lizards,(Sceloporus tristichus): evidence from chromosome-scale genomes
Bedoya, AM, Leaché AD,, G3 (Bethesda), 2020, February 11

Widespread recombination suppression facilitates plant sex chromosome evolution
Rifkin JL, et al., bioRxiv [pre-print], 2020, February 7

Genome Assembly and Analysis of the North American Mountain Goat (Oreamnos americanus) Reveals Species-Level Responses to Extreme Environments
Martchenko D, et al., G3, 2020, February 6

Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat
Nsabiyera V, et al., Front Plant Sci., 2020, February 4

Discovery of a new TLR gene and gene expansion event through improved desert tortoise genome assembly with chromosome-scale scaffolds
Dolby GA, et al., Genome biology and evolution, 2020, February 1

Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes
Bray MS, et al., Environmental microbiology reports, 2020, February

DoveTail Genomics-Advances in De Novo Genome Assembly with Dovetail Genomics–Methods, Applications, and Some Pretty Cool Science!
Holder N,, Plant and Animal Genome XXVIII Conference, 2020, January 15

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data
Armstrong EE, et al., BMC biology, 2020, January 8

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins
Suryamohan S, et al., Nature Genetics., 2020, January 6

Three-dimensional Genome Organization Maps in Normal Haematopoietic Stem Cells and Acute Myeloid Leukemia
Wang B, et al., bioRxiv, 2020, January 1

A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference
Wang C, et al., bioRxiv, 2020, January 1

Population genomics of North American northern pike: variation and sex-specific signals from a chromosome-level, long read genome assembly
Johnson HA, et al., bioRxiv, 2020, January 1

A Solanum lycopersicoides reference genome facilitates biological discovery in tomato
Powell AF, et al., BioRxiv, 2020, January 1

The giant sequoia genome and proliferation of disease resistance genes
Scott AD, et al., bioRxiv, 2020, January 1

A high-quality reference genome assembly of the saltwater crocodile, Crocodylus porosus, reveals patterns of selection in Crocodylidae
Ghosh A, et al., Genome Biol Evol., 2020, January 1

A draft genome sequence of the elusive giant squid, Architeuthis dux
da Fonseca RR, et al., GigaScience. , 2020, January 1

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?
Kadota M, et al., GigaScience. , 2020, January 1

Genome Assembly of the Dogface Butterfly Zerene cesonia
Rodriguez-Caro L, et al., Genome Biol Evol., 2020, January 1

Accurate chromosome-scale haplotype-resolved assembly of human genomes
Garg S, et al., bioRxiv, 2020, January

Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar’s hibernating dwarf lemurs
Williams RC, et al., Heredity (Edinb.), 2020, January

2019

Genetic architecture drives seasonal onset of hibernation in the 13-lined ground squirrel
Grabek KR, et al., Communications Biology., 2019, December 20

The mitochondrial transcriptome of the anglerfish Lophius piscatorius
Dubin A, et al., BMC Res Notes., 2019, December 10

Dichotomy of dosage compensation along the neo Z chromosome of the monarch butterfly
Gu L, et al., Current Biology., 2019, December 2

A highly contiguous reference genome for northern bobwhite (Colinus virginianus)
Salter JF, et al., G3 (Bethesda), 2019, December 1

Contemporary Demographic Reconstruction Methods Are Robust to Genome Assembly Quality: A Case Study in Tasmanian Devils
Patton AH, et al., Mol Biol Evol., 2019, December 1

Sex-dependent dominance maintains migration supergene in rainbow trout
Pearse DE, et al., Nat Ecol Evl., 2019, December

Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species
Maughan PJ, et al., BMC Biology, 2019, November 22

Towards an adaptive and genomic understanding of an exaggerated secondary sexual trait in water striders
Toubiana W, Biodiversity. Université de Lyon, 2019, November 12

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts
Burkhardt AK, et al., BMC Genomics, 2019, November 4

Genome sequence and analysis of the eggplant (Solanum melongena L.)
Li D, et al., bioRxiv [pre-print], 2019, October 31

Complete loss of the MHC II pathway in an anglerfish, Lophius piscatorius
Dubin A, et al., Bio Lett., 2019, October 31

De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri
Udal JA, et al., G3, 2019, October 7

The major histocompatibility complex of old world camels-a synopsis
Plasil M, et al., Cells, 2019, October 5

Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
Kuon J, et al., BMC Biology, 2019, September 18

Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition
Kalbfleisch TS, et al., Nature Communications, 2019, September 11

Old world camels in a modern world – a balancing act between conservation and genetic improvement
Burger PA, et al., Animal Genetics. , 2019, September 18

The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters
van Hoek ML, et al., BMC Genomics, 2019, August 30

Integrating Hi-C links with assembly graphs for chromosome-scale assembly
Ghurye J, et al., PLoS Comput Biol., 2019, August 21

De novo genome sequence assembly of dwarf coconut (Cocos nucifera L. ‘Catigan Green Dwarf’) provides insights into genomic variation between coconut types and related palm species
Lantican DV, et al., G3 (Bethesda), 2019, August 9

Impacts of obesity, maternal obesity and nicotinamide mononucleotide supplementation on sperm quality in mice
Youngson NA, et al., Reproduction, 2019, August 1

An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)
Farre M, et al., GigaScience, 2019, July 30

The caribou (Rangifer tarandus) genome
Taylor RS, et al., Genes, 2019, July 17

A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality
Carballo J, et al., Scientific Reports., 2019, July 15

Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary
Elbers JP, et al., Mol Ecol Resour., 2019, July

Chromosome-level alpaca reference genome VicPac3.1 improves genomic insight into the biology of new world camelids
Richardson MF, et al., Front. Genet, 2019, June 21

Aquatic adaptation and depleted diversity: A deep dive into the genomes of the sea otter and giant otter
Beichman AC, et al., Molecular Biology and Evolution. , 2019, June 18

Genomic signatures of heterokaryosis in the oomycete pathogen Bremia lactucae
Fletcher K, et al.,  Nat Commun., 2019, June 14

Gene family evolution in the pea aphid based on chromosome-level genome asssembly
Lin Y, et al., Molecular Biology and Evolution. , 2019, June 7

Modern technologies and algorithms for scaffolding assembled genomes
Ghurye J, Pop M, PLOS Computational Biology, 2019, June 5

The draft genome of eggplant
Hirakawa H, The Eggplant Genome, 2019, May 31

Structural variation detection by proximity ligation from formalin-fixed, paraffin-embedded tumor tissue
Troll CJ, et al., J Mol Diagn, 2019, May

Improving Illumina assemblies with Hi‐C and long reads: An example with the North African dromedary
Elbers JP, et al., Molecular Ecology Resources, 2019, April 11

Origin and evolution of the octoploid strawberry genome
Edgar PP, et al., Nat Genet., 2019, April

A reference-grade wild soybean genome
Xie M, et al., Nature Communications. , 2019, March 14

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry
Colle M, et al., GigaScience, 2019, March 1

A critical comparison of technologies for a plant genome sequencing project
Paajanen P, et al., GigaScience, 2019, March

The new bovine reference genome assembly provides new insight into genomic organization of the bovine major histocompatibility complex
Zorc M, et al., Journal of Central European Agriculture, 2019, March

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods
Belcaid M, et al., PNAS, 2019, February 19

New approaches for genome assembly and scaffolding
Rice ES, Green RE. , Annu Rev Anim Biosci., 2019, February 15

New approaches for genome assembly and scaffolding
Farre M, Green RE. , Gigascience, 2019, February 1

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
Low WY, et al., Nature Communications., 2019, January 16

Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution
Chaw S-M, et al., Nat Plants, 2019, January

2018

Evaluation of genome scaffolding tools using pooled clone sequencing
Dal E, et al., Turk J Biol., 2018, December 10

Current Strategies of Polyploid Plant Genome Sequence Assembly
Kyriakidou M, et al., Front Plant Sci., 2018, November 21

Comparative analysis of the Pocillopora damiconis genome highlights roles of immune system in coral evolution
Cunning R, et al., Scientific Reports., 2018, October 31

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci
Lilue J, et al., Nature Genetics., 2018, October 1

Genomic approaches for studying crop evolution
Schreiber M, et al., Genome Biol., 2018, September 21

The Molecular Genetic Basis of Herbivory between Butterflies and their Host-Plants
Nallu S, et al., Nature Ecology & Evolution, 2018, September

The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves 
Powell D, et al., DNA Research, 2018, August 31

Chicago® and Dovetail™ Hi-C proximity ligation yield chromosome length scaffolds of Ixodes scapularis genome
Nuss AB, et al., bioRxiv [pre-print], 2018, August 15

High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)
Autenrieth M, et al., Molecular Ecology Resources, 2018, July 23

Stout camphor tree genome fills gaps in understanding of flowering plant genome and gene family evolution
Chaw SM, et al., bioRxiv [pre-print], 2018, July 18

Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars
Thind AK, et al.,  BMC Genome Biology, 2018, July 10

Decimation by sea star wasting disease and rapid genetic change in keystone species, Pisaster ochracceus 
Schiebelhut LM, et al., Proc Natl Acad Sci U S A, 2018, July 3

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers
Coombe L, et al., BMC Bioinformatics, 2018, June 20

A high-quality reference genome for the invasive mosquitofish Gambusia affinis using a chicago library
Hoffberg SL, et al., G3 (Bethesda)., 2018, May 31

The African Bullfrog (Pyxicephalus adspersus) genome unites the two ancestral ingredients for making vertebrate sex chromosomes
Denton RD, et al., bioRxiv [pre-print], 2018, May 24

Improved genome assembly and annotation for the rock pigeon (Columba livia)
Holt C, et al., G3 (Bethesda). , 2018, May 4

Fast-SG: an alignment-free algorithm for hybrid assembly
Genova AD, et al., Gigascience , 2018, May 1

Improved de novo genomic assembly for the domestic donkey
Renaud G, et al., Sci Rep., 2018, April 4

Intact DNA purified from flow-sorted nuclei unlocks the potential of next-generation genome mapping and assembly in Solanum species
Gaiero P, et al., MethodsX., 2018, April 10

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat
Medoza MLZ, et al., Nat Ecol Evol, 2018, April

EquCab3, an updated reference genome for the domestic horse
Kalbfleisch TS, et al., bioRxiv [pre-print], 2018, April

A guide to sequence your favorite plant genomes
Li F-W, et al., Appl Plant Sci., 2018, March 30

The sea lamprey germline provides insights into programmed genome rearrangements and vertebrate evolution
Smith JJ, et al., Nat Genet., 2018, February

Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)
Fernandez-Silva I, et al., Sci Rep. , 2018, January 28

Single-Cell mRNA-Seq Using the Fluidigm C1 System and Integrated Fluidics Circuits
Gong H, et al., Methods Mol Biol., 2018, January 1

2017

Genome Sequencing and Assembly by Long Reads in Plants
Li C, et al., Genes, 2017, December 28

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)
Larsen PA, et al., BMC Biol., 2017, November 16

A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)
Kuderna LFK, et al., Sci Rep., 2017, November 1

The draft genome of tropical fruit durian (Durio zibethinus)
Teh BT, et al., Nat Genet, 2017, November

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
Varshney RK, et al., Nat Biotechnol.,, 2017, October 1

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula
Moll KM, et al., BMC Genomics, 2017, August 14

An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance
Kaur P, et al., Plant Biotechnology Journal , 2017, August 1

The impact of third generation genomic technologies on plant genome assembly
Thind AK, et al., Nat Biotechnol. , 2017, August

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
Schwager EE, et al., BMC Biol, 2017, July 31

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
Rice ES, et al., Genome Res. , 2017, May

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data
Jiao WB, et al., Genome Res., 2017, May

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
Reyes-Chin-Wo S, et al., Nat Commun., 2017, April 12

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
Laio WB, Schneeberger K, Current Opinion in Plant Biology, 2017, April

The genome of Chenopodium quinoa
Jarvis DE, et al., Nature, 2017, February 16

De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species
Pootakham W, et al., Sci Rep, 2017, February 2

Discovery of large genomic inversions using long range information
Razekh ME, et al., BMC Genomics, 2017, January 10

2016