Aleksey photo

Aleksey V. Zimin

Associate Research Scientist

Center for Computational Biology
Department of Biomedical Engineering

Johns Hopkins University

Welch Medical Library, 1900 E. Monument St., Rm 105
Baltimore, MD 21205

Phone: (443) 287 4815    E-mail: alekseyz jhu edu

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 directions of my research are (i) development of algorithms and software for de novo genome assembly of the latest generation sequencing data, and (ii) application of the software to produce de novo assemblies for the most challenging genomes. I lead the development of the MaSuRCA genome assembly package, which is currently able to produce high quality assemblies from data produced by Illumina, PacBio, and Oxford Nanopore instruments. I maintain a blog dedicated to assembler development and results at masurca.blogspot.com. I have played a leading role in producing assemblies for many challenging genome projects, including the 22 Gbp genome of loblolly pine (Pinus taeda), the 16 Gbp genome of bread wheat (Triticum aestivum), the 3Gbp Atlantic salmon (Salmo salar), and others.

My current research is aimed at development of MaSuRCA assembler, creating assemblies of large challneging genomes (such as 8Gbp genome of Sequoia and 26Gbp genome of Coast Redwood -- the largest tree on Earth) from hybrid short and long read data sets, development of synteny-guided assembly approach, and correction of Oxford Nanopore direct RNA sequencing data with Illumina reads.


Funding
My research is supported in part by NSF award IOS-1744309 and USDA-NIFA award 2018-67015-28199.