Haploid to diploid alignment for variation calling assessment

por Mäkinen, Veli, Rahkola, Jani
Publicado 2013

Recombination-aware alignment of diploid individuals

por Mäkinen, Veli, Valenzuela, Daniel
Publicado 2014

Accurate spliced alignment of long RNA sequencing reads

por Sahlin, Kristoffer, Mäkinen, Veli
Publicado 2021

Normalized N50 assembly metric using gap-restricted co-linear chaining

por Mäkinen, Veli, Salmela, Leena, Ylinen, Johannes
Publicado 2012

Variant genotyping with gap filling

por Walve, Riku, Salmela, Leena, Mäkinen, Veli
Publicado 2017

Evaluating approaches to find exon chains based on long reads

por Kuosmanen, Anna, Norri, Tuukka, Mäkinen, Veli
Publicado 2017

Bit-parallel sequence-to-graph alignment

por Rautiainen, Mikko, Mäkinen, Veli, Marschall, Tobias
Publicado 2019

Combinatorial algorithms: 27th international workshop, IWOCA 2016, Helsinki, Finland, August 17-19, 2016, proceedings

por Mäkinen, Veli, Puglisi, Simon J, Salmela, Leena
Publicado 2016

On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly

por Rizzi, Romeo, Tomescu, Alexandru I, Mäkinen, Veli
Publicado 2014

A framework for space-efficient read clustering in metagenomic samples

por Alanko, Jarno, Cunial, Fabio, Belazzougui, Djamal, Mäkinen, Veli
Publicado 2017

A safe and complete algorithm for metagenomic assembly

por Obscura Acosta, Nidia, Mäkinen, Veli, Tomescu, Alexandru I.
Publicado 2018

Linear time minimum segmentation enables scalable founder reconstruction

por Norri, Tuukka, Cazaux, Bastien, Kosolobov, Dmitry, Mäkinen, Veli
Publicado 2019

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

por Tomescu, Alexandru I, Kuosmanen, Anna, Rizzi, Romeo, Mäkinen, Veli
Publicado 2013

Fast scaffolding with small independent mixed integer programs

por Salmela, Leena, Mäkinen, Veli, Välimäki, Niko, Ylinen, Johannes, Ukkonen, Esko
Publicado 2011

Towards pan-genome read alignment to improve variation calling

por Valenzuela, Daniel, Norri, Tuukka, Välimäki, Niko, Pitkänen, Esa, Mäkinen, Veli
Publicado 2018

Founder reconstruction enables scalable and seamless pangenomic analysis

por Norri, Tuukka, Cazaux, Bastien, Dönges, Saska, Valenzuela, Daniel, Mäkinen, Veli
Publicado 2021

Chaining for accurate alignment of erroneous long reads to acyclic variation graphs

por Ma, Jun, Cáceres, Manuel, Salmela, Leena, Mäkinen, Veli, Tomescu, Alexandru I
Publicado 2023

Distributed hybrid-indexing of compressed pan-genomes for scalable and fast sequence alignment

por Maarala, Altti Ilari, Arasalo, Ossi, Valenzuela, Daniel, Mäkinen, Veli, Heljanko, Keijo
Publicado 2021

MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP

por Husić, Edin, Li, Xinyue, Hujdurović, Ademir, Mehine, Miika, Rizzi, Romeo, Mäkinen, Veli, Milanič, Martin, Tomescu, Alexandru I
Publicado 2019

Bacterial genomic epidemiology with mixed samples

por Mäklin, Tommi, Kallonen, Teemu, Alanko, Jarno, Samuelsen, Ørjan, Hegstad, Kristin, Mäkinen, Veli, Corander, Jukka, Heinz, Eva, Honkela, Antti
Publicado 2021