Saturday, September 26, 2015

Date: Dec 7, 2015. Susan Strickler: Long read assembly and annotation strategies for complex plant genomes

Susan Strickler is a Research Associate in the Mueller lab at the Boyce Thompson Institute on Cornell University campus.

Plant genome assembly can be notoriously difficult due to such challenges as heterozygosity, polyploidy, and repeats.  The long read technology provided by PacBio sequencing can help to overcome some of these obstacles to result in more complete and accurate assembly and annotation.  In this talk, I will discuss de novo genome assembly tools and methods for processing PacBio genome and transcriptome data to generate high quality plant genomes and gene models.

Date: Dec 07, 2015
Time: 11:00 AM
Location: Weill hall, Room 221

Slides

Date: Oct 19, 2015. Katie Wilkins: Population Diversity of Xanthomonas oryzae pv oryzicola TAL Effectors and their Candidate Targets

Katie Wilkins is a Computational Biology PhD Candidate in the Bogdanove lab in the Plant Pathology and Plant-Microbe Biology section of the School of Integrative Plant Science at Cornell University.

Xanthomonas oryzae pv oryzicola is the causal agent of bacterial leaf streak of rice, a disease that can lead to up to 30% yield loss in this staple crop. Disease progression is mediated in part by the secretion of transcription activator-like (TAL) effectors that upregulate host genes by binding to corresponding promoter regions. Genes upregulated by TAL effectors can confer host resistance or enhance host susceptibility. Knowledge of these important TAL effector-target pairs informs breeding of resistant rice varieties. To determine the distribution of TAL effectors and their candidate targets at the population level, we sequenced 10 strains of Xanthomonas oryzae pv oryzicola and performed RNA-Seq of rice inoculated with each strain. We also used population level conservation to evaluate potential importance of the identified TAL effectors and their candidate targets.


Date: Oct 19, 2015
Time: 11:00 AM
Location: Weill hall, Room 221

Tuesday, April 28, 2015

Date: May 4, 2015. Kevin Panke-Buisse: Rhizosphere Microbiome: Manipulation and Investigation

Kevin Panke-Buisse is a PhD Candidate in the Kao-Kniffin Lab in the Horticulture section of the School of Integrative Plant Science at Cornell University.

Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. This talk will outline some of the ways we can manipulate the rhizosphere microbiome and look at shifts across treatments via 16s sequencing.

Date: May 04, 2015
Time: 10:30 AM
Location: Weill hall, Room 321
Paper
Slides

Monday, April 13, 2015

Date: Apr 20, 2015. Jeff Glaubitz: The Maize Rare Alleles Project: Biology & Bioinformatics

Jeff Glaubitz is a Senior Research Associate and the Project Manager of Panzea - the NSF Maize Diversity Project.

The NSF project Biology Of Rare Alleles In Maize And Its Wild Relatives (Ed Buckler, PI) is combining the power of population genetic and molecular models with quantitative genetics to elucidate the relative contributions of rare versus common alleles to phenotypic variation and evolution. We are taking advantage of recent advances in high-throughput genotyping and phenotyping methodologies to identify the key biological attributes of variants (genome annotations) that will allow us to better predict the functional effects of rare alleles in Zea. This information will then be used to accelerate crop improvement either through more accurate genomic selection or via future genome editing approaches. We hope to enhance the effectiveness of plant breeding by improving our ability to identify, predict, and select on the effects of rare variants, both deleterious and beneficial. In this talk I will give an overview of the biological goals of this project and the various bioinformatic tools that are being developed to achieve these goals, with an emphasis on TASSEL.

Date: April 20, 2015
Time: 11:00 AM
Location: Weill hall, Room 321
Slides

Thursday, February 26, 2015

Date: Mar 2, 2015. Minghui Wang: Genome-wide crossover distribution in the population of maize B73 and Mo17

Minghui Wang is a Postdoctoral Associate at the BRC Bioinformatics Facility on campus.

Crossovers (COs) are essential for the accurate segregation of homologous chromosomes at the first meiotic division. However, CO are not evenly distributed across genome. Their number and location are tightly regulated. Here, we report a detailed, genome-wide characterization of the rate and localization of COs in maize, in male and female meiosis.

Date: Mar 2, 2015
Time: 11:00 AM
Location: Weill hall, Room 321
Slides

Tuesday, January 27, 2015

Date: Feb 2, 2015. Zehong Ding: Comparison of leaf gradient transcriptomics in multiple C3 and C4 species

Zehong Ding is a Postdoctoral Associate at the BRC Bioinformatics Facility on campus.

Transferring C4 photosynthesis into C3 crops has been proposed as one of the most promising ways to increase the yield ceiling and hence global productivity. To better understand the function of C4 photosynthesis, and to identify candidate genes that associated with C4 pathway, comparative transcriptomes were conducted along a leaf developmental gradient in maize, viridis, sorghum and rice. In total 478 C4 candidate genes were identified. Besides the classical C4 genes, many function well characterized genes that associated with light reaction, starch and sucrose metabolism, hormone, TFs, and transporters were included. These findings will provide important insights into the gene differentiation between C3 and C4 species. In addition, the C4 candidate genes that identified in our approach would be a useful gene resource that could be used for C4 engineering of C3 crops.

Date: Feb 2, 2015
Time: 11:00 AM
Location: Weill hall, Room 321
Slides


Thursday, December 4, 2014

Date: Dec 8, 2014. Brandon Barker: Autosave for Research: Checkpoint and Restart Computational Workloads

Brandon Barker is a Computational Scientist working at the Cornell Center for Advanced Computing with research interests in safety-critical programming, parallel computing and linear modelling of metabolic systems.

It is not uncommon to have computational analyses running for many days or weeks. Software, hardware, and power failures all present the possibility that a significant amount of work could be lost. In some cases, the programmer can incrementally save data at specific intervals, but this is an error-prone process, and it is time-consuming to implement for each application. If a failure occurs, all data not saved will need to be regenerated again, and the researcher can only hope that another failure won't occur.

There is general solution known as Checkpoint/Restart (C/R) that can work for serial and a large variety of parallel programming applications. The primary advantage of all C/R implementations is the automation of saving program state at specified increments and allowing the program to be resumed. There are numerous C/R frameworks and implementations, each offering various advantages and disadvantages; despite some implementations being very mature, C/R remains an area of open and active research as no single solution covers every application type. By knowing the capabilities and drawbacks of each C/R solution, as well as the requirements and specifications of your application, it should be straightforward to choose a C/R framework that is right for you.

In this talk, we discuss in more detail what checkpointing is, and several scenarios where one would and would not want to use it. Next we discuss several popular checkpointing solutions, giving examples when pertinent of software that would not work well with each solution. Finally, we give some simple examples of how checkpointing can be implemented on your own system (Linux currently required).

Date: Dec 8, 2014
Time: 11:00 AM
Location: Weill hall, Room 121
Webex (webcast)
Slides