In recent years, technological advances in fields such as sequencing have transformed certain aspects of biology into an information-based discipline.
To make this abundance of data—often called Big Data—useful to researchers and breeders, it needs to be organized and made accessible. Towards this goal, the Mueller lab designs and implements databases that assist scientists in their research and plant breeders in more efficient crop improvement.
Our databases and software make transcriptomic, genotypic and phenotypic data from thousands of experiments accessible to the public, often focusing on under-researched staple crops from food-insecure regions. A method called Genomic Selection that uses high-throughput genotyping technologies, such as genotyping-by-sequencing (GBS), and large phenotyping data sets allows for rapid prediction of desirable traits in new plant crosses.
Based on these tools, the Mueller laboratory collaborates on a variety of different projects. With the Nextgen Cassava project, we have created Cassavabase, a database specifically designed for cassava breeders in Africa. We coordinate the Solanaceae Genomics Network—a compilation of all the genetic information known about solanaceous plants, such as tomato, petunia and Nicotiana. We are also developing breeding databases for yam, sweet potato and the cooking banana and we work with the Genomic and Open-source Breeding Informatics Initiative (GOBII) to streamline crop breeding for five staple crops—wheat, rice, maize, sorghum and chickpea. Finally, the Mueller group is involved in multiple genome sequencing projects, including tomato, coffee, petunia and Nicotania benthamiana.
Citrus Greening Solutions
A systems-based pipeline approach for delivering commercial, grove-deployable solutions using a novel therapeutic delivery strategy and citrus transgenics.
Access to data and tools for breeders and researchers, including genomic selection algorithms and analysis capacity, a cassava genome browser, cassava ontology tools, phenotyping tools, and social networking.
A breeding database designed for advanced breeding methods in banana breeding.
A collection of Root Tubers & Banana Databases, which hold genomic and phenotypic information for next generation breeding applications.
A database about breeding data for Yam (genus Dioscorea). Yam species that are being used for breeding include , Dioscorea rotundata, Dioscorea cayenensis (both are native to Africa and the major cultivated species), Dioscorea aleata (native to Southeast Asia), and Dioscorea praehensilis, as well as several other species.
- As genome sequencing becomes cheaper and faster, resulting in an exponential increase in data, the need for efficiency in predicting gene function is growing, as is the need to train the next generation of scientists in bioinformatics. Researchers in the lab of Lukas Mueller, a faculty member of the Boyce Thompson Institute (BTI), have developed […] Read more »
- It’s a dietary staple for millions of Africans, but cassava has traditionally received little attention from scientists and plant breeders in comparison to cash crops such as wheat and maize. However, researchers have recently been working to find cassava a scientific “home.” Around 100 cassava breeders, experts, and scientists from around the world, including BTI’s […] Read more »
- The new S. lycopersicoides genome sequence offers the opportunity for innovative breeding programs that may hold the ability to confer desirable traits to marketable tomato varieties. Read more »
- Cornell University and BTI will expand international efforts to deliver improved varieties of cassava to smallholder farmers in sub-Saharan Africa with $35 million in new funding from the Bill & Melinda Gates Foundation and UK aid in the United Kingdom. Read more »
- Researchers at BTI, Cornell and USDA published a spatiotemporal map of gene expression across all tissues and developmental stages of the tomato fruit – the genetic information underlying how a fruit changes from inside to out as it ripens. Their data is available in the new Tomato Expression Atlas (TEA). Read more »
- More than 70 participants joined in on the training sessions provided by members of BTI's Mueller Lab, October-December 2017. Read more »
- During June and July at BTI, visiting scholars from crop breeding programs in Nigeria, Nairobi, and Uganda have been working closely with researchers in Lukas Mueller’s group to discuss ways to improve the development of online resources related to two of Africa’s most important staple crops: cassava and banana. Read more »
- The offices of data scientists at BTI emptied out earlier this month as a contingent of researchers flew to San Diego for the 25th annual Plant and Animal Genome Conference. Read more »
- The collaboration works with breeding centers around the world to develop tools to make the process of adding a trait into an existing, high-yield crop variety more efficient. Read more »
- Many BTI researchers will present their latest research at the 13th annual SolGenomics Conference, Sept. 12-16 in Davis, California. Read more »
- An international group of computer programmers gathered at BTI to create a single interface that will connect databases from breeding programs worldwide Read more »
- A group of students and experts work together through video conferencing to identify the genes in the genome of the newly sequenced Asian citrus psyllid, the insect that spreads the bacterium that causes citrus greening disease. Read more »
- An international consortium of researchers has sequenced the two wild parent species of the domesticated petunia Read more »
- Tompkins County has awarded Gomes Selman, a 2015 high school intern at BTI, its Distinguished Youth award for his numerous academic and volunteer commitments. Read more »
- BTI researchers used a genome comparison approach to identify genes necessary for beneficial plant-fungal relationships, which may lead to better crop plants that require less fertilizer input. Read more »
- The GOBII project gathered researchers from breeding centers around the world to make a plan to develop the architecture for a genomics database for five staple crops. Read more »
- BTI Researchers pinpointed which genes are important at different stages of tomato fruit development by monitoring how gene expression changed in the first four days after a flower becomes pollinated. Read more »
- BTI Professor Lukas Mueller will participate in an international collaboration to expedite crop breeding for five worldwide staple crops—wheat, rice, maize, sorghum and chickpea. Read more »
- "Biology is becoming a data science," said Ruiz. "Biologists need to learn to use bioinformatics tools." Read more »
- Jocelyn Rose, professor of plant biology and director of Cornell’s Institute of Biotechnology, with BTI co-PI's Carmen Catala, Zhangjun Fei, James Giovannoni, and Lukas Mueller will research ripening mechanisms & drought tolerance. Read more »
- BTI researchers led team that pioneered international tomato gene sequencing and genetic basis of fruit ripening. Congrats to Vrebalov, Van Eck, Mueller, Giovannoni, Fei. Read more »
- This Nicotiana benthamiana web site shares papers, results, tools, protocols, and other materials from researchers using NB as a study plant. Read more »
- The genome of an experimentally important relative of tobacco has been sequenced by US and Canadian researchers. Read more »
- Cassava, a rough and ready root crop that has long been the foundation of food security in Africa is finally getting the respect it deserves. Read more »
- Are juicier, sweeter, more disease-resistant watermelons on the way? Read more »
- For the first time, the genome of the tomato, Solanum lycopersicum, has been decoded. Read more »
Interns in the Mueller lab work on a variety of bioinformatics and genomics projects and gain experience in the following areas: genome assembly, structural and functional annotation, biochemical pathways, comparative genomics, ontology development and data presentation and visualization.
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