A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. - Alexandru I. Tomescu; Anna Kuosmanen; Romeo Rizzi; Veli Mäkinen (WABI, 2013)

A novel min-cost flow method for estimating transcript expression with RNA-Seq. - Alexandru I. Tomescu; Anna Kuosmanen; Romeo Rizzi; Veli Mäkinen (BMC Bioinform., 2013)

Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly. - Alexandru I. Tomescu; Travis Gagie; Alexandru Popa 001; Romeo Rizzi; Anna Kuosmanen; Veli Mäkinen (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy. - Anna Kuosmanen; Ahmed Sobih; Romeo Rizzi; Veli Mäkinen; Alexandru I. Tomescu (BIOINFORMATICS, 2016)

Speeding up Dynamic Programming on DAGs through a Fast Approximation of Path Cover. - Anna Kuosmanen; Topi Paavilainen; Travis Gagie; Rayan Chikhi; Alexandru I. Tomescu; Veli Mäkinen (CoRR, 2017)

Third-generation RNA-sequencing analysis: graph alignment and transcript assembly with long reads. - Anna Kuosmanen (2017)

Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. - Anna Kuosmanen; Topi Paavilainen; Travis Gagie; Rayan Chikhi; Alexandru I. Tomescu; Veli Mäkinen (RECOMB, 2018)

Evaluating approaches to find exon chains based on long reads. - Anna Kuosmanen; Tuukka Norri; Veli Mäkinen (Briefings Bioinform., 2018)

Sparse Dynamic Programming on DAGs with Small Width. - Veli Mäkinen; Alexandru I. Tomescu; Anna Kuosmanen; Topi Paavilainen; Travis Gagie; Rayan Chikhi (ACM Trans. Algorithms, 2019)