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Computer Science

D-Index
34
Citations
6109
World Ranking
12044
National Ranking
106

Overview

Veli Mäkinen is a researcher affiliated with the University of Helsinki in Finland. Their work spans multiple fields, primarily focusing on biochemistry, genetics, molecular biology, and computer science. Mäkinen's research encompasses various subfields such as molecular biology, artificial intelligence, genetics, hardware and architecture, and plant science.

The scientist has published extensively on topics related to algorithms and data compression, genomics and phylogenetic studies, DNA and biological computing, network packet processing and optimization, genome rearrangement algorithms, RNA and protein synthesis mechanisms, and machine learning and algorithms.

Recent publication venues for Mäkinen's work include:

  • arXiv (Cornell University)
  • Bioinformatics
  • bioRxiv (Cold Spring Harbor Laboratory)
  • Leibniz-Zentrum für Informatik (Schloss Dagstuhl)
  • ACM Transactions on Algorithms

Some of the recent papers authored by or closely related to Mäkinen's research interests are:

  • Accurate spliced alignment of long RNA sequencing reads, 2021, Bioinformatics
  • Bacterial genomic epidemiology with mixed samples, 2021, Microbial Genomics
  • Chaining for accurate alignment of erroneous long reads to acyclic variation graphs, 2023, Bioinformatics
  • On the Complexity of String Matching for Graphs, 2023, ACM Transactions on Algorithms
  • Founder reconstruction enables scalable and seamless pangenomic analysis, 2021, Bioinformatics

Mäkinen's list of frequent co-authors includes:

  • Nicola Rizzo
  • Massimo Equi
  • Manuel Cáceres
  • Alexandru I. Tomescu
  • Tuukka Norri

In addition to articles, Mäkinen has contributed to book publications. One notable publication is titled Genome-Scale Algorithm Design, published by Cambridge University Press in 2023.

Best Publications

  • Compressed full-text indexes

    Gonzalo Navarro;Veli Mäkinen

  • Compressed representations of sequences and full-text indexes

    Paolo Ferragina;Giovanni Manzini;Veli Mäkinen;Gonzalo Navarro

  • Computational pan-genomics: status, promises and challenges.

    Tobias Marschall;Manja Marz;Manja Marz;Thomas Abeel;Louis Dijkstra

  • Indexing graphs for path queries with applications in genome research

    Jouni Siren;Niko Valimaki;Veli Makinen

  • Succinct suffix arrays based on run-length encoding

    Veli Mäkinen;Gonzalo Navarro

  • Storage and Retrieval of Highly Repetitive Sequence Collections

    Veli Mäkinen;Gonzalo Navarro;Jouni Sirén;Niko Välimäki

  • Rank and select revisited and extended

    Veli Mäkinen;Gonzalo Navarro

  • Dynamic entropy-compressed sequences and full-text indexes

    Veli Mäkinen;Gonzalo Navarro

  • An Alphabet-Friendly FM-Index

    Paolo Ferragina;Giovanni Manzini;Veli Mäkinen;Gonzalo Navarro

  • Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing

    Veli Antti Tapani Mäkinen;Djamal Belazzougui;Fabio Cunial;Alexandru Ioan Tomescu

  • A novel min-cost flow method for estimating transcript expression with RNA-Seq

    Alexandru I Tomescu;Anna Kuosmanen;Romeo Rizzi;Veli Mäkinen

  • Faster entropy-bounded compressed suffix trees

    Johannes Fischer;Veli Mäkinen;Gonzalo Navarro

  • Geometric Algorithms for Transposition Invariant Content-Based Music Retrieval

    Esko Ukkonen;Kjell Lemström;Veli Mäkinen

  • Fast scaffolding with small independent mixed integer programs

    Leena Salmela;Veli Mäkinen;Niko Välimäki;Johannes Ylinen

  • Position-restricted substring searching

    Veli Makinen;Gonzalo Navarro

  • Space-Efficient Algorithms for Document Retrieval

    Niko Välimäki;Veli Mäkinen

  • Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections

    Jouni Sirén;Niko Välimäki;Veli Mäkinen;Gonzalo Navarro

  • Implicit compression boosting with applications to self-indexing

    Veli Mäkinen;Gonzalo Navarro

  • Approximate matching of run-length compressed strings

    Veli Mäkinen;Gonzalo Navarro;Esko Ukkonen

  • Detection of Viruses in Sweetpotato from Honduras and Guatemala Augmented by Deep-Sequencing of Small-RNAs

    M. Kashif;S. Pietilä;K. Artola;R. A. C. Jones

  • Compact Suffix Array — A Space-Efficient Full-Text Index

    Veli Mäkinen

Frequent Co-Authors

gonzalo navarro
gonzalo navarro University of Chile
Esko Ukkonen
Esko Ukkonen University of Helsinki
Juha Kärkkäinen
Juha Kärkkäinen University of Helsinki
Tobias Marschall
Tobias Marschall Heinrich Heine University Düsseldorf
Simon J. Puglisi
Simon J. Puglisi University of Helsinki
Jukka Corander
Jukka Corander University of Oslo
Sebastian Böcker
Sebastian Böcker Friedrich Schiller University Jena
Paolo Ferragina
Paolo Ferragina University of Pisa
Robert M. Waterhouse
Robert M. Waterhouse Swiss Institute of Bioinformatics
Evan E. Eichler
Evan E. Eichler University of Washington

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