Research

My Research

I have been working in the field of Bioinformatics since 2002, beginning with my collaborations with The Institute for Genomic Research (TIGR) and Celera Genomics. The main goals of my research are:
1. developing algorithms and software for de novo genome assembly and annotation for the latest generation sequencing data, and
2. applying the software to produce high quality annotated assemblies for the most challenging genomes.

I lead the development of the open-source MaSuRCA genome assembly package, which is currently able to produce accurate high-quality assemblies from sequencing data produced by Illumina, PacBio, and Oxford Nanopore instruments.  As of today, MaSuRCA was used to assemble over 2600 eukaryotic genomes submitted to NCBI GenBank. I played a leading role in producing assemblies for many challenging genome projects, including the 22 Gbp genome of Loblolly pine (Pinus taeda), the 17 Gbp genome of bread wheat (Triticum aestivum), the 3Gbp Atlantic salmon (Salmo salar), and many other plants and animals. In the recent years, I was the leading author of several widely used bioinformatic software titles such as MUMmer4 sequence aligner, POLCA and JASPER assembly polishers, and SAMBA scaffolder. Most recently the focus of my research has encompassed transcriptome assembly, protein alignment and genome annotation algorithms.  My most recent work includes a novel automated genome annotation package called EviAnn, which surpasses all published annotation software when tested with the same input data.

Funding

My research is currently supported by NIH grants R01-HG006677 (PI Steven Salzberg) and R35-GM130151 (PI Steven Salzberg).
In the past my research has been supported in part by NSF award IOS-1744309 (PI Steven Salzberg) and USDA-NIFA award 2018-67015-28199 (PI Aleksey Zimin), and NSF award ABR-PG 1444893 (PI Aldwinckle, Cornell University, Zimin was PI on subcontract to University of Maryland).