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Genomics / Proteomics

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IDTitleSection/TopicAuthorsKeywords
562A de novo detection pipeline for alternative splicing based on single-molecule long-read isoforms using Amborella trichopoda
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Genomics / ProteomicsLiu, Xiaoxian; Barbazuk, William B.; Soltis, Pamela S.; Soltis, Douglas E..RNA alternative splicing
de novo pipeline
Amborella trichopoda
Transcriptome
42A functional genomics approach (PIPE, Protein-protein Interaction Prediction Engine) to identify new early maturity alleles in soybean for Western Canada
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Genomics / ProteomicsSamanfar, Bahram; Cober, Elroy; Charette, Martin; Schoenrock, Andrew; Dehne, Frank; Golshani, Ashkan; Molnar, Steve.Soybean
Early maturity
Flowering pathway
E10
SSR
SNP
Bioinformatics
PPI
PIPE
Functional genomics
147Changes in DNA methylation and the domestication of tomato
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Genomics / ProteomicsLira-Medeiros, Catarina; Voloch, Carolina; Litt, Amy.epigenetcs
cytosine methylation
tomato
domestication
792Comparative genomic analysis of Apocynaceae plastomes: Pseudogenes, repeat content, and molecular evolution
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Genomics / ProteomicsWalter, Lauren; Livshultz, Tatyana; Straub, Shannon C.K..Apocynaceae
Carissa
Plastome
accD
634Comparative Genomics of Disease Resistance Genes in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris)
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Genomics / ProteomicsNepal, Madhav P.; Neupane, Surendra; Mathew, Febina; Ma, Qin; Varenhorst, Adam; Andersen, Ethan J.; Reese, R. Neil.Comparative Genomics 
Disease Resistance Genes 
legumes
Fabaceae
Gene Clustering
Selection Pressure
Synteny
TNL Genes
488Comparative genomics of Parasitaxus usta, a podocarp conifer with a unique form of heterotrophy
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Genomics / ProteomicsGerelle, Wesley; Lam, Vivienne K. Y.; Graham, Sean W..mycoheterotrophy
heterotrophy
Transcriptome
evolution
1kp
gene ontology
Gene loss
180Comparative transcriptome analysis of beach morning glory reveals important salt adaptation mechanisms
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Genomics / ProteomicsLuo, Yan; Freese, Daniella; Reid, Robert; Zhang, Heng-You; Miller, Thomas E.; Loraine, Ann; Song, Bao-Hua.comparative transcriptome
halophyte
glycophyte
salt tolerance
Ipomoea
380Comparative transcriptomics of Crassulacean acid metabolism in Yucca
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Genomics / ProteomicsHeyduk, Karolina; Ray, Jeremy; Leebens-Mack, Jim.photosynthesis
Transcriptomics
comparative transcriptome
RNAseq
870Comparative transcriptomics of the genus Cuscuta
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Genomics / ProteomicsMcNeal, Joel R..Cuscuta
Transcriptome
polyploidy
Molecular evolution
806Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns
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Genomics / ProteomicsGuo, Wenhu; Mower, Jeff.ferns
mitochondrial genome
repetitive DNA
introns
RNA editing
Ophioglossum
Psilotum
375De novo transcriptome assembly and gene expression profiling of the desiccation-tolerant desert green alga Scenedesmus rotundus during desiccation and rehydration
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Genomics / ProteomicsPeredo, Elena L; Cardon, Zoe; Thomas, Suzanne; Bruce, Douglas.desiccation tolerance
Transcriptomics
green algae
land colonization
photoprotection
508Differences in population genetic structure of hawkmoth- and bee-pollinated species of Oenothera (Onagraceae)
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Genomics / ProteomicsLewis, Emily Marie; Fant, Jeremie; Moore, Michael; Skogen, Krissa.gene flow
pollination biology
fragmentation
635Examination of the molecular genetic basis of andromonoecy in Aneilema (Commelinaceae)
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Genomics / ProteomicsEvans, Timothy; Weitzel, Alexander; Faden, Robert.Aneilema
Commelinaceae
Transcriptome
differential expression
898Functional and spatial heterogeneity of gene family evolution in non-model species: three strategies using Caryophyllales as an example
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Genomics / ProteomicsYang, Ya; Moore, Michael; Brockington, Samuel; Smith, Stephen.Transcriptome
genome
Caryophyllales
betalain
242Gene expression and mycoheterotrophy: an exploratory analysis of green vs. non-green Corallorhiza (Orchidaceae)
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Genomics / ProteomicsBarrett, Craig; Perez, Leticia.Transcriptome
mycoheterotroph
orchid
photosynthesis
parasite
RNAseq
gene expression
177Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae)
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Genomics / ProteomicsLuo, Yan; Hu, Jin-Yong; Song, Bao-Hua.RNA-seq
Transcriptome
cleistogamy
cleistogamous flowers
chasmogamous flowers
environmental response
181Genome-wide association study of soybean cyst nematode (Heterodera glycines Ichinohe) HG type 2.5.7 (race 1) resistance in wild soybean (Glycine soja Sieb. & Zucc.)
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Genomics / ProteomicsZhang, Heng-You; Song, Qijian; Luo, Yan; Nelson, Randall L.; Song, Bao-Hua.Soybean cyst nematode
Genome-wide association study
Glycine soja
single nucleotide polymorphisms
resistance
560Genome-wide Identification of the CNL Disease Resistance Genes in Barley (Hordeum vulgare L.) and Their Evolutinary Divergence
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Genomics / ProteomicsAndersen, Ethan J.; Nepal, Madhav P.; Ali, Shaukat; Yen, Yang; Reese, R. Neil; Neupane, Surendra.Grass Phylogenetics
Disease Resistance Genes 
Coiled-coil Nucleotide-binding site
NBS-LRRs
gene duplication
Purifying Selection
616Genomic Consequences of Reciprocal Polyploidization in Tragopogon
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Genomics / ProteomicsShan, Shengchen; Soltis, Douglas; Soltis, Pamela S..polyploidy
Transcriptomics
Tragopogon miscellus
Reciprocal cross
732Identifying diagnostic plastid polymorphisms for the non-fertile vetiver grass ‘Sunshine’ (Chrysopogon zizanioides)
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Genomics / ProteomicsSigmon, Brandi; Adams, Robert; Mower, Jeffrey.vetiver
Chrysopogon zizanioides
chloroplast
plastid
genome
polymorphism
444Karyotypic Diversity and Pollen Viability in Resynthesized allopolyploids Tragopogon mirus and T. miscellus.
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Genomics / ProteomicsSpoelhof, Jonathan; Chester, Micahel; Rodriguez, Roseana; Geraci, Blake; Heo, Kweon; Mavrodiev, Evgeny; Soltis, Douglas E; Soltis, Pamela S..polyploidy
chromosomal rearrangement
Tragopogon
fertility
334Lectins (haemagglutinins) from the Red Alga Acanthophora spicifera (vahl)Boergesen: Isolation, partial purification and characterization
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Genomics / ProteomicsRavirajan, Mangaiyarkarasi; Natesanpayer, Nadimuthu.Seaweeds
Acanthophora spicifera
Haemagglutinin
Lectin
Column Chromatography
720Organ-specific transcriptomes of Oenothera harringtonii (Onagraceae) and associated variation in floral scent
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Genomics / ProteomicsBechen, Lindsey; Overson, Rick; Johnson, Matthew; Fant, Jeremie; Levin, Rachel; Robert, Raguso; Skogen, Krissa; Wickett, Norm.transcriptomes
differential expression
Genomics
gene expression
floral volatiles
pollination
RNA-seq
onagraceae
230Patterns of cyto-nuclear disequilibrium and the influence of heteroplasmy in wild carrot, Daucus carota (Apiaceae)
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Genomics / ProteomicsRamsey, Adam Joseph; Mandel, Jennifer R.Genetic diversity
Genomes
Mitochondria
SNPs
SSRs
Paternal Leakage
plastid
393Patterns of homoeologue usage within and among three Glycine allopolyploid species
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Genomics / ProteomicsCoate, Jeremy; Powell, Adrian; Koenig, Max; Doyle, Jeff.polyploidy
Homoeologue-specific expression
RNA-seq
gene duplication
Gene loss
463Sexual dimorphic expression patterns in the transcriptome of juvenile tissue of Ceratodon purpureus
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Genomics / ProteomicsLandis, Jacob Brian; Carey, Sarah B.; Payton, Adam C.; Woodruff, Emily D.; Conrad, Roth E.; Barry, Kerrie; Jenkins, Jerry; Grimwood, Jane; Schmutz, Jeremy; McDaniel, Stuart F..comparative transcriptome
RNAseq
de novo
Trinity
moss
sex-specific expression
881Significant genetic structure and variation among domesticated Brassica rapa subspecies uncovered by transcriptomics
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Genomics / ProteomicsQi, Xinshuai; An, Hong; Hall, Tara; Pires, Joseph Chris; Barker, Michael S.domestication
Transcriptomics
phylogenomics
Phylogeography
polyploidy
520Testing hypotheses on the repeated origination of polyploidy in plants
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Genomics / ProteomicsWitherup, Colby; Johnson, Matthew; Wickett, Norm.polyploidy
meiosis
443The Mitochondrial Genome of Eleusine indica
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Genomics / ProteomicsHall, Nathan; Zhang, Hui; McElroy, J. Scott; Goertzen, Leslie.Mitochondria
Eleusine indica
Poaceae
694The origin and diversity of Brassica napus
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Genomics / ProteomicsAn, Hong; Qi, Xinshuai; Barker, Michael S; Pires, Joseph Chris.Brassica napus
genetic structure
RNA-seq
Allopolyploidy
760The phylogenies and evolutionary history of the Portullugo Clade (Caryophyllales)
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Genomics / ProteomicsMoore, Abigail J; Hancock, Lillian Pine; De Vos, Jurriaan; Edwards, Erika.Portulacineae
Caryophyllales
Portullugo
sequence capture
gene family evolution
536The Story of Stresses: A look at transcriptomic variation of a single cultivated sunflower genotype across five abiotic stresses
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Genomics / ProteomicsMasalia, Rishi R.; Burke, John.Transcriptomics
Abiotic Stress
Cultivated Sunflower
drought
Salt
differential expression
RNAseq
178Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae)
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Genomics / ProteomicsEgan, Ashley N.; Vatanparast, Mohammad; Shetty, Prateek; Chopra, Ratan; Doyle, Jeff; Sathyanarayana, N..Fabaceae
Psophocarpus tetragonolobus
Transcriptomics
Roche 454 pyrosequencing
genetic resources
219Tremendous Transfer – Intracellular Gene Transfer in the Basal Angiosperm Amborella trichopoda
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Genomics / ProteomicsNaumann, Julia; Wafula, Eric K.; Palmer, Jeffrey D.; dePamphilis, Claude W..Mitochondrial DNA
Plastid DNA
Nuclear Genome
Gene Transfer
Intracellular Gene Transfer
genome evolution
704Weighted Gene Correlation Network Analysis of Morphine Biosynthesis in Opium Poppy (Papaver somniferum)
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Genomics / ProteomicsLane, Amanda; Kerry, John; Augustin, Megan; Kutchan, Toni; Leebens-Mack, Jim.Transcriptomics
Benzylisoquinoline Alkaloids
network analysis
RNAseq
Papaver somniferum

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