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Single cell RNA-seq denoising using a deep count autoencoder [article]

Gökcen Eraslan, Lukas M. Simon, Maria Mircea, Nikola S. Mueller, Fabian J. Theis
2018 bioRxiv   pre-print
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)

David Spooner, Percy Rojas, Meredith Bonierbale, Lukas A. Mueller, Manish Srivastav, Douglas Senalik, Philipp Simon
2013 Systematic Botany  
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

Allison Izsak, Annie Kruse, Surya Saha, Michelle Cilia, Lukas A Mueller
2017 Figshare  
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

Naama Menda, Susan R. Strickler, Lukas A. Mueller
2013 Plant Biotechnology  
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]

Lukas Mennel, Joanna Symonowicz, Stefan Wachter, Dmitry K. Polyushkin, Aday J. Molina-Mendoza, Thomas Mueller
2019 arXiv   pre-print
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

Susan R. Strickler, Aureliano Bombarely, Lukas A. Mueller
2012 American Journal of Botany  
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]

Sherry Miller, Blessy Tamayo, Teresa Shippy, Prashant S Hosmani, Mirella Flores-Gonzalez, Lukas A Mueller, Wayne B Hunter, Tom D'elia, Susan J Brown, Surya Saha
2020 bioRxiv   pre-print
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]

Lukas Mennel, Aday J. Molina-Mendoza, Matthias Paur, Dmitry K. Polyushkin, Dohyun Kwak, Miriam Giparakis, Maximilian Beiser, Aaron Maxwell Andrews, Thomas Mueller
2021 arXiv   pre-print
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

Lukas A. Mueller, Christopher D. Goodman, Rebecca A. Silady, Virginia Walbot
2000 Plant Physiology  
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

Isaak Y Tecle, Jeremy D Edwards, Naama Menda, Chiedozie Egesi, Ismail Y Rabbi, Peter Kulakow, Robert Kawuki, Jean-Luc Jannink, Lukas A Mueller
2014 BMC Bioinformatics  
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

Nicolas Morales, Nicholas S. Kaczmar, Nicholas Santantonio, Michael A. Gore, Lukas A. Mueller, Kelly R. Robbins
2020 tppj  
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]

Tobias Züst, Susan R. Strickler, Adrian F. Powell, Makenzie E Mabry, Hong An, Mahdieh Mirzaei, Thomas York, Cynthia K. Holland, Pavan Kumar, Matthias Erb, Georg Petschenka, José-María Gomez (+5 others)
2019 bioRxiv   pre-print
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

Aureliano Bombarely, Kieron D Edwards, Juan Sanchez-Tamburrino, Lukas A Mueller
2012 BMC Genomics  
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

Taina Mueller, Gerhard Ruedl, Matthaeus Ernstbrunner, Fabian Plachel, Stefan Fröhlich, Thomas Hoffelner, Herbert Resch, Lukas Ernstbrunner
2019 Orthopaedic Journal of Sports Medicine  
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

Noe Fernandez-Pozo, Yi Zheng, Stephen I Snyder, Philippe Nicolas, Yoshihito Shinozaki, Zhangjun Fei, Carmen Catala, James J Giovannoni, Jocelyn K.C Rose, Lukas A Mueller, Janet Kelso
2017 Bioinformatics  
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
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