MAKER annotations complete!

March 15, 2016

We have completed annotation of our rosid de novo genome assemblies with MAKER. This is a fairly complete package of tools that does repeat masking, aligns transcript/protein evidence, produces ab initio predictions, and synthesizes results into annotations with evidence-based quality values. Beyond evidence from alignment with transcript/protein evidence, confidence in annotations can be boosted with matches to a Pfam domain or the Uni/SwissProt database.

Here is a look at our Malus ioensis annotations. There are ~62k annotations, and over 60% of these...

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New ddRAD-seq manuscript submitted

January 6, 2016

Collaborator Jeff Peters (Wright State University) has submitted a manuscript that develops a conceptual framework for using ddRAD-seq data to define units for conservation, which was applied to two populations of mottled ducks, one of which is of conservation concern. I assisted in data collection, ddRAD-seq genotyping, and data analyses.

Teaching at Boston University

September 1, 2015

In addition to my postdoc research at Harvard University, this fall I am serving as a Lecturer in the College of General Studies (CGS) at Boston University. The CGS offers a two-year interdisciplinary curriculum designed to give students a challenging and comprehensive liberal arts foundation upon which to build a specialized field of study. I am teaching lecture and labs for a biology course (NS201) that gives students an introduction to the scientific method and how it has been used to enhance our understanding of the natural world.

7 de novo genome assemblies complete!

August 15, 2015

For my postdoc research on comparative genomics of Maleae, de novo assemblies of seven species (five Maleae and two outgroups) have been completed! These assemblies were generated with data from short insert and mate-pair libraries and the AllPaths-LG software. These assemblies contain a similar number of eukaryote BUSCOs found in published rosid genomes, and will be used to study gene fate following a whole genome duplication event in the common ancestor of Maleae.

BUSCO results for Maleae genomes. Searches for single-copy plant orthologs (n = 956) were conducted...

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ddRAD-seq phylogenetics manuscript submitted!

February 9, 2015

This manuscript describes phylogenetic analyses of two avian genera (Lagonosticta finches and Vidua parasitic finches) using thousands of loci derived from ddRAD-seq. We conducted these analyses using a variety of concatenated data sets (i.e., sequence, indel, and presence-absence characters), and also using numerous species tree methods based on gene trees and single nucleotide polymorphisms.

This work is the product of an NSF Doctoral Dissertation Improvement Grant.

Two ddRAD-seq manuscripts with collaborators submitted!

January 20, 2015

Collaborations on the collection and analysis of ddRAD-seq data are starting to generate manuscripts for publications!

Emily Ebel (Boston University, Stanford University) submitted a manuscript describing a phylogenetic analysis of Adelpha butterflies, which also includes analyses of diversification rates and mapping of host preference and wing patterning characters.

Phil Lavretsky (Wright State University, University of Miami) submitted a manuscript describing population structure of Mexican ducks, which is highlighted by the finding of elevated divergence between Mexican...

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Illumina Synthetic Long Read data collected

December 30, 2014

We have now successfully generated long read data for two species using Illumina's new Synthetic Long Read kit. This kit size selects 8-10kb fragments, spreads them in low concentrations across 384 (barcoded) wells, and completes a Nextera-like tagmentation of molecules in each well. Short reads are generated with a HiSeq, and long reads are synthesized in BaseSpace.

One lane of sequencing per sample generated ~500Mb of long read data, with an N50 for longer reads (those ≥1500bp) of ~6500. Now on to exploring the best practices for using these data to increase our scaffold...

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Invited speaker at UMass Lowell

September 17, 2014

I was an invited speaker for a departmental seminar at UMass Lowell, and presented my dissertation research on indigobirds. Thanks to Jessica Garb for the invitation, and for chatting about the exciting spider silk and venom research in your lab!