A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Filters
Single cell RNA-seq denoising using a deep count autoencoder
[article]
2018
bioRxiv
pre-print
Preserved Fulltext
We propose a deep count autoencoder network (DCA) to denoise scRNA-seq datasets. ...
Single-cell RNA sequencing (scRNA-seq) has enabled researchers to study gene expression at a cellular resolution. ...
This is a general issue of imputation methods and we propose a hyperparameter search in critical situations. ...
doi:10.1101/300681
fatcat:vw4m5vbdirctlbf7vamlq6na5i
Molecular Phylogeny of Daucus (Apiaceae)
2013
Systematic Botany
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
the above was a clade containing the remaining Daucus species. ...
Bayesian analyses of individual regions analyzed separately and averaged over multiple trees with *BEAST software (a coalescent approach), however, provided a phylogeny at variance with the concatenated ...
A. production. ...
doi:10.1600/036364413x670449
fatcat:bsj5corr3zfxlfrstbkcni3ffq
Gene discovery, annotation and orthology in the Asian citrus psyllid genome
2017
Figshare
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
The citrus industry is currently in a state of emergency due to the uncontrollable spread of Huanglongbing (citrus greening disease). ...
Since not much is known about the genetics and genomics of the psyllid, a multi- pronged approach was used to analyze the psyllid genome to identify genes that could be involved in pathogen transmission ...
Allison Izsak, Annie Kruse, Surya Saha, Michelle Cilia, Lukas Mueller Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14850 Further Research
• Analysis of psyllid gut proteome
using mass spectrometry ...
doi:10.6084/m9.figshare.4238924.v1
fatcat:3tzmc2qwqvctbaswzw6ybswbii
Advances in tomato research in the post-genome era
2013
Plant Biotechnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
The tomato (Solanum lycopersicum) draft genome, along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012, almost a decade after the International Tomato Genome project was ...
For these reasons, there has been a substantial effort for producing a high quality reference genome that will serve as an anchor for tomato species, and for closely related Solanaceae plants. ...
Genome-wide association mapping (GWAS) is a commonly used method to link phenotype data to genotype, and a large amount of SNP data has been generated as a result of the SolCAP project providing a valuable ...
doi:10.5511/plantbiotechnology.13.0904a
fatcat:qqpoqwgo7ncyran6mzsqbpvxqu
Real-time image processing with a 2D semiconductor neural network vision sensor
[article]
2019
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Usually, visual information is captured by a frame-based camera, converted into a digital format, and processed afterwards using a machine learning algorithm such as an artificial neural network (ANN). ...
Our device is based on a reconfigurable two-dimensional (2D) semiconductor photodiode array, with the synaptic weights of the network being stored in a continuously tunable photoresponsivity matrix. ...
As a substrate we used a silicon wafer with 280 nm-thick SiO2. First, we prepared a bottom metal layer by writing a design with electron-beam lithography (EBL) and evaporating Ti/Au (3/30 nm). ...
arXiv:1909.00205v1
fatcat:dulpok3ckjcq7ils27gsajjec4
Designing a transcriptome next-generation sequencing project for a nonmodel plant species1
2012
American Journal of Botany
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2012; you can also visit the original URL.
The file type is application/pdf.
Mainly, RNA-seq does not require a reference genome to gain useful transcriptomic information. In this review, the application of RNA-seq to nonmodel plant species will be addressed. ...
Species background information -Both variant alleles of a gene and gene duplications can complicate transcript assembly by making it diffi cult to distinguish between sequencing error, heterozygosity, ...
A method of determining whether a sequenced organism may be an appropriate reference was investigated with Pachycladon enysii using A. thaliana as a reference ( Collins et al., 2008 ) . ...
doi:10.3732/ajb.1100292
pmid:22268224
fatcat:ok6srj7mbjdadkaiw47xp2ypeq
Chitin Biosynthesis Genes in Diaphorina citri
[article]
2020
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Although most insects have two CHS genes, the presence of a single CHS gene is consistent with reports from other hemipteran genomes. ...
Chitin plays a crucial role in the development of the insect cuticle and exoskeleton, the peritrophic membrane of the midgut, and other structures such as the trachea, wing hinges and eggshell. ...
A
r
a
ú
j
o
S
J
,
A
s
l
a
m
H
,
T
e
a
r
G
,
C
a
s
a
n
o
v
a
J
. ...
doi:10.1101/2020.09.22.309211
fatcat:5hgpbkxx7vewnbzypc6k3hmgfq
A photosensor employing data-driven binning for ultrafast image recognition
[article]
2021
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
For a given pattern recognition task, its optimal shape is determined from training data using a machine learning algorithm. ...
Here, we push the concept of binning to its limit by combining a large fraction of the sensor elements into a single superpixel that extends over the whole face of the chip. ...
There, a substantial fraction of pixels are combined into a "superpixel" that extends over the whole face of the chip, thus forming a large-area photodetector with a complex geometrical structure that ...
arXiv:2111.10612v1
fatcat:mnnukjbpfjh2fae267dvnmhqjm
AN9, a Petunia GlutathioneS-Transferase Required for Anthocyanin Sequestration, Is a Flavonoid-Binding Protein
2000
Plant Physiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
We conclude that AN9 is a flavonoid-binding protein, and propose that in vivo it serves as a cytoplasmic flavonoid carrier protein. ...
For many xenobiotics it is well established that a covalent glutathione (GSH) tag mediates recognition of molecules destined for vacuolar sequestration by a tonoplast-localized ATP-binding cassette pump ...
Mueller, unpublished data). ...
doi:10.1104/pp.123.4.1561
pmid:10938372
pmcid:PMC59113
fatcat:upjuls3vrrbb3b4bpacp7bqqxa
solGS: a web-based tool for genomic selection
2014
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Results: We have developed a web-based tool, called solGS, for predicting genomic estimated breeding values (GEBVs) of individuals, using a Ridge-Regression Best Linear Unbiased Predictor (RR-BLUP) model ...
Raw data is stored in a generic database schema, Chado Natural Diversity, co-developed by multiple database groups. ...
Acknowledgements This work was supported by the NEXTGEN Cassava project, through a grant to Cornell University by the Bill & Melinda Gates Foundation and the UK Department for International Development ...
doi:10.1186/s12859-014-0398-7
pmid:25495537
pmcid:PMC4269960
fatcat:5ui43mfl5zgw7misyoctzvli3y
ImageBreed: Open‐access plant breeding web–database for image‐based phenotyping
2020
tppj
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
Summary-statistic phenotypic values are extracted for every observed plot-polygon image using a structured ontology. ...
To this end, ImageBreed provides a software solution for end-to-end image-based phenotyping integrated into the Breedbase plant breeding system. ...
In addition to assigning a spectral category, users must provide a name and a description for each uploaded imaging campaign. ...
doi:10.1002/ppj2.20004
fatcat:xiu73ee47ndtphkswgqb3igqky
Rapid and independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)
[article]
2019
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Closely related species shared similar cardenolide traits, but not glucosinolate traits, likely as a result of specific selective pressures acting on distinct molecular diversification mechanisms. ...
We sequenced and assembled the genome of E. cheiranthoides and foliar transcriptomes of 47 additional Erysimum species to construct a highly resolved phylogeny, revealing that cardenolide diversity increased ...
of defense compounds 399 Glucosinolates consist of a β-D-glucopyranose residue linked via a sulfur atom to a (Z)-N-400 hydroximinosulfate ester and a variable R group (Halkier and Gershenzon 2006) . ...
doi:10.1101/761569
fatcat:5wwqar64v5cqhhh26kxzaedui4
Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective
2012
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Conclusions: Polyploidization is a powerful mechanism for plant speciation that can occur during one generation; however millions of generations may be necessary for duplicate genes to acquire a new function ...
With Whole Genome Duplication (WGD) events, polyploid genomes usually maintain a high percentage of gene duplicates. ...
., a wholly owned subsidiary of BAT. ...
doi:10.1186/1471-2164-13-406
pmid:22900718
pmcid:PMC3582432
fatcat:omhfcb7w5ndrti2yr243onqkd4
A Prospective Injury Surveillance Study on Ski Touring
2019
Orthopaedic Journal of Sports Medicine
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
A total of 27 injury-events were reported, of which 18 (67%) were classified as mild, 7 (26%) as moderate, and 2 (7%) as severe. ...
Methods: Between November 2015 and May 2016, a total of 191 participants from the Alps region were prospectively tracked via personalized online questionnaires. ...
b
Mueller et al The Orthopaedic Journal of Sports Medicine ...
doi:10.1177/2325967119867676
pmid:31548973
pmcid:PMC6743203
fatcat:oi7tsqhejvd7bbunblsjak6r74
The Tomato Expression Atlas
2017
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Using tomato fruit as a model, we have developed the Tomato Expression Atlas to facilitate effective data analysis, allowing the simultaneous visualization of groups of genes at a cell/tissue level of ...
This work has been supported by a grant from the US National Science Foundation (Plant Genome Research Program; IOS-1339287) and a Grant-in-Aid for JSPS Fellows from the Japan Society for the Promotion ...
Introduction Large-scale transcriptome profiling has become widely adopted as a means to characterize the status and diversity of biological samples, and as a platform for functional genomic studies. ...
doi:10.1093/bioinformatics/btx190
pmid:28379331
pmcid:PMC5860121
fatcat:2zudeh5z4bfvhhgonifeuixr4u
« Previous
Showing results 1 — 15 out of 3,186 results