Mikko Rautiainen, MSc
PhD student (alum)
Mikko received his BSc and MSc from the University of Helsinki in computer science. He started his PhD at the Max Planck Institute for Computer Science supervised by Tobias Marschall. His research focuses on pangenomics, graph based methods and genome assembly.
MBG
Minimizer based sparse de Bruijn Graph constructor
GraphAligner
A tool to align long reads to genome graphs.
The complete sequence of a human genome
MBG: Minimizer-based Sparse de Bruijn Graph Construction
Bioinformatics, January 21, 2021
GraphAligner: rapid and versatile sequence-to-graph alignment
Genome Biol, September 24, 2020
A diploid assembly-based benchmark for variants in the major histocompatibility complex
Nat Commun, September 22, 2020
Chin C, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A, Rautiainen M, Aganezov S, Kirsche M, Zarate S, Schatz MC, Xiao C, Rowell WJ, Markello C, Farek J, Sedlazeck FJ, Bansal V, Yoo B, Miller N, Zhou X, Carroll A, Barrio AM, Salit M, Marschall T, Dilthey AT, Zook JM
Haplotype threading: accurate polyploid phasing from long reads
Genome Biol, September 21, 2020
Schrinner SD, Serra Mari R, Ebler J, Rautiainen M, Seillier L, Reimer JJ, Usadel B, Marschall T, Klau GW
Pangenome Graphs
Annu Rev Genomics Hum Genet, May 26, 2020
Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G, Chang X, Seaman JD, Rounthwaite R, Ebler J, Rautiainen M, Garg S, Paten B, Marschall T, Siren J, Garrison E
Bit-parallel sequence-to-graph alignment
Bioinformatics, March 9, 2019
Legend: * joint first author; † joint last author
