Yana Safonova
Assistant Professor at Penn State University
State College, Pennsylvania, United States
Summary
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Senior🎓
Top SchoolYana Safonova is an assistant professor and computational biologist with 12 years of experience studying adaptive immunity and translating computational methods into biological insight. She combines academic leadership at Penn State and prior faculty and postdoctoral roles at Johns Hopkins and UC San Diego with hands-on algorithm development for genome assembly. Her open-source contributions include substantive back-end improvements to the widely used SPAdes assembler, optimizing haplotype assembly and redundant contig removal—skills that bridge algorithm design and practical bioinformatics pipelines. Trained in Russian institutions and seasoned in U.S. research environments, she brings a cross-cultural perspective to collaborative, interdisciplinary projects. Her work is notable for integrating rigorous computational methods with immunology questions, enabling clearer interpretation of complex immune repertoires.
12 years of coding experience
2 years of employment as a software developer
Степень магистра, Степень магистра at Нижегородский Государственный Университет им. Н.И. Лобачевского (ННГУ)
Github Skills (14)
sequencer10
assembly10
c-language10
cprogramming-language10
assemble10
assembler10
genome-assembly10
data-structure9
bioinformatics9
biom9
algorithm9
data-structures9
algorithms9
python8
Programming languages (2)
Github contributions (5)
ablab/spades
Dec 2013 - Jan 2017
SPAdes Genome Assembler
Role in this project:
Back-end Developer
Back-end DeveloperContributions:47 commits in 3 years 2 months
Contributions summary:Yana primarily focused on enhancing the SPAdes genome assembler, making improvements to the core functionality. Their commits indicate modifications to the consensus contigs constructor, particularly within the `dipspades` module. They implemented features such as improved redundant contig removal, and optimized overlap search and haplotype assembly. The user also addressed bugs and added informative output to the console.
bioinformaticsgenomeassemblerspadesgenome-assembly
Immunotools/immunotools
Oct 2018 - Aug 2022
Tools for processing immunosequencing data
Contributions:69 commits, 5 PRs, 80 pushes in 3 years 10 months
bioinformaticsgenomics
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