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List of works by Lukas A Mueller

A community-based annotation framework for linking solanaceae genomes with phenomes

scientific article (publication date: August 2008)

A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research

scientific article

A dynamic interface for capsaicinoid systems biology.

scientific article published on 24 June 2009

A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz)

scientific article published on 07 December 2021

A quick guide for student-driven community genome annotation

scientific article published on 03 April 2019

An Endophyte Constructs Fungicide-Containing Extracellular Barriers for Its Host Plant.

scientific article

An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita

scientific article

An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells

scientific article published on 19 February 2007

Analysis of Ultra Low Genome Conservation in Clostridium difficile ⬇️

scientific article published on December 8, 2010

Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins

scientific article

Asian citrus psyllid stylet morphology and applicability to the model for inter-instar stylet replacement in the potato psyllid

scientific article published on 14 August 2018

Association analysis for disease resistance to Fusarium oxysporum in cape gooseberry (Physalis peruviana L).

scientific article

BrAPI-an application programming interface for plant breeding applications

scientific article published on 01 October 2019

Breedbase: a digital ecosystem for modern plant breeding

scientific article published in 2022

Can Cross-Country Genomic Predictions Be a Reasonable Strategy to Support Germplasm Exchange? – A Case Study With Hydrogen Cyanide in Cassava

scientific article published in 2021

Capsidiol-related genes are highly expressed in response to Colletotrichum scovillei during Capsicum annuum fruit development stages

scientific article published on 21 July 2020

Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts

scientific article (publication date: December 2005)

Combining 'omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut.

scientific article

Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade

scientific article

Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato

scientific article

Comparative analysis of Cucurbita pepo metabolism throughout fruit development in acorn squash and oilseed pumpkin

scientific article published on 21 September 2016

Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

scientific article published on 26 February 2015

Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression

scientific article published on 13 August 2020

Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

scientific article published in 2021

Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening

scientific article

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

scientific article published in 2021

Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants

scientific article published on 03 June 2010

Current status and impending progress for cassava structural genomics

scientific article published in 2021

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

scientific article published on 08 August 2019

De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus.

scientific article published on 7 November 2017

De-novo assembly of zucchini genome reveals a whole genome duplication associated with the origin of theCucurbitagenus

article published in 2017

Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective

scientific article

Development on Citrus medica infected with 'Candidatus Liberibacter asiaticus' has sex-specific and -nonspecific impacts on adult Diaphorina citri and its endosymbionts

scientific article published on 06 October 2020

Differential regulation of caffeine metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta).

scientific article published on 24 September 2014

Dissecting Tissue-Specific Transcriptomic Responses from Leaf and Roots under Salt Stress in Petunia hybrida Mitchell.

scientific article published on 3 August 2017

Diversification of R2R3-MYB Transcription Factors in the Tomato Family Solanaceae

scientific article published on 30 June 2016

Draft Genome Sequence Resource of the Citrus Stem-End Rot Fungal Pathogen Lasiodiplodia theobromae CITRA15

scientific article published on 15 November 2020

Dynamic Maize Responses to Aphid Feeding Are Revealed by a Time Series of Transcriptomic and Metabolomic Assays

scientific article published on 16 September 2015

EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot

scientific article published on 17 August 2006

Enabling proteomic studies with RNA‐Seq: The proteome of tomato pollen as a test case ⬇️

scientific article published on March 1, 2012

Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome

scientific article

Exploiting the diversity of tomato: the development of a phenotypically and genetically detailed germplasm collection

scientific article published on 01 May 2020

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

article

Floral gene resources from basal angiosperms for comparative genomics research

scientific article

From manual curation to visualization of gene families and networks across Solanaceae plant species

scientific article published on 15 May 2013

Genes conserved for arbuscular mycorrhizal symbiosis identified through phylogenomics.

scientific article published on 18 January 2016

Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex

scientific article published in March 2014

Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

scientific article published on 16 November 2020

Genome sequencing and analysis of the model grass Brachypodium distachyon

scientific article

Graph pangenome captures missing heritability and empowers tomato breeding

scientific article published on 08 June 2022

High density genotype storage for plant breeding in the Chado schema of Breedbase

scientific article published on 11 November 2020

High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening.

scientific article

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

scientific article published in January 2017

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

scientific article published on 01 January 2019

Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)

scientific article published on 07 April 2020

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida.

scientific article published on 27 May 2016

Large-scale GWAS using historical data identifies a conserved genetic architecture of cyanogenic glucosides content in cassava (Manihot esculenta Crantz.) root

scientific article published on 08 November 2020

Linkage between the I-3 gene for resistance to Fusarium wilt race 3 and increased sensitivity to bacterial spot in tomato

scientific article published on 6 October 2017

Linking the potato genome to the conserved ortholog set (COS) markers

scientific article

Longitudinal Transcriptomic, Proteomic, and Metabolomic Analyses of Citrus sinensis (L.) Osbeck Graft-Inoculated with "Candidatus Liberibacter asiaticus"

scientific article published on 15 January 2020

Longitudinal transcriptomic, proteomic, and metabolomic analysis of Citrus limon response to graft inoculation by 'Candidatus Liberibacter asiaticus'

scientific article published on 27 April 2020

MetaCyc and AraCyc. Metabolic pathway databases for plant research

scientific article published on May 2005

MetaCyc: a multiorganism database of metabolic pathways and enzymes.

scientific article

Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook

scientific article published on 14 July 2020

Metabolic profiles of six African cultivars of cassava (Manihot esculenta Crantz) highlight bottlenecks of root yield

scientific article published on 17 January 2020

Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum)

scientific article published on 30 September 2019

Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

scientific article published on 23 August 2017

PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

scientific article published on 12 November 2019

Plant Metabolic Pathways in MetaCyc and SolCyc

article

Querying and computing with BioCyc databases

scientific article

Rapid defense responses in maize leaves induced by Spodoptera exigua caterpillar feeding.

scientific article published in July 2017

Reinterpretation of 'sperm pump' or 'sperm syringe' function with notes on other male internal reproductive organs in the Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae)

scientific article published on 01 January 2020

Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection

scientific article published on 01 March 2019

Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota) ⬇️

scientific article published on May 24, 2012

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases.

scientific article

Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions.

scientific article published on 15 February 2018

The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits

scientific article

The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community

scientific article

The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data

scientific article

The Genome Database for Rosaceae (GDR): year 10 update

scientific article

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

scientific article published on 12 November 2013

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

scientific article

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases ⬇️

scientific article (publication date: 2012)

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

scientific article

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems

scientific article published on 25 September 2020

The SGN VIGS tool: user-friendly software to design virus-induced gene silencing (VIGS) constructs for functional genomics.

scientific article published on 30 December 2014

The SGN comparative map viewer

scientific article published on 17 January 2008

The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond

scientific article published on July 2005

The Sol Genomics Network (SGN)--from genotype to phenotype to breeding

scientific article

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

scientific article

The Tomato Expression Atlas.

scientific article published on 30 March 2017

The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL).

scientific article published on January 2005

The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

scientific article published on 14 April 2021

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

scientific article published on 25 November 2012

The tomato kinome and the tomato kinase library ORFeome: novel resources for the study of kinases and signal transduction in tomato and solanaceae species

scientific article

TobEA: an atlas of tobacco gene expression from seed to senescence

scientific article

Transcriptomic Analysis of L. Roots during the Early Infection Process.

scientific article published on March 2017

Transcriptomic analysis of cultivated cotton Gossypium hirsutum provides insights into host responses upon whitefly-mediated transmission of cotton leaf curl disease

article

Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum

scientific article

solGS: a web-based tool for genomic selection

scientific article

solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database ⬇️

scientific article published on October 21, 2010

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