Sotabase

Career

· Professor, University of Helsinki2010–
· Academy Research Fellow, University of Helsinki2007–2009
· Postdoctoral Researcher, University of Helsinki2005–2007
· Postdoctoral Visit, Bielefeld University2004–2005
· PhD Student, University of Helsinki2003–
· Visitor, Aalto University

Publications (165)

Compressed full-text indexes
CSUR · 2007
769
cited
Compressed representations of sequences and full-text indexes
TALG · 2007
371
cited
Indexing Graphs for Path Queries with Applications in Genome Research
IEEE/ACM Transactions on Computational Biology & Bioinformatics · 2014
271
cited
Storage and Retrieval of Highly Repetitive Sequence Collections
J. Comput. Biol. · 2010
232
cited
Succinct Suffix Arrays based on Run-Length Encoding
Nordic Journal of Computing · 2005
224
cited
The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
Nature Communications · 2014
219
cited
PRACTICAL IMPLEMENTATION OF RANK AND SELECT QUERIES
2005
195
cited
Dynamic entropy-compressed sequences and full-text indexes
TALG · 2006
161
cited
Rank and select revisited and extended
Theoretical Computer Science · 2007
147
cited
An Alphabet-Friendly FM-Index
SPIRE · 2004
119
cited
Faster entropy-bounded compressed suffix trees
Theoretical Computer Science · 2009
100
cited
A novel min-cost flow method for estimating transcript expression with RNA-Seq
BMC Bioinformatics · 2013
96
cited
Geometric algorithms for transposition invariant content based music retrieval
International Society for Music Information Retrieval Conference · 2003
96
cited
Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections
SPIRE · 2008
85
cited
Space-Efficient Algorithms for Document Retrieval
Annual Symposium on Combinatorial Pattern Matching · 2007
83
cited
Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing
2015
81
cited
Implicit Compression Boosting with Applications to Self-indexing
SPIRE · 2007
75
cited
On the Complexity of String Matching for Graphs
International Colloquium on Automata, Languages and Programming · 2023
72
cited
Bit-parallel sequence-to-graph alignment
bioRxiv · 2018
69
cited
Position-Restricted Substring Searching
Latin American Symposium on Theoretical Informatics · 2006
68
cited
Sotabase