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Alexandru I. Tomescu
- > Home > Persons > Alexandru I. Tomescu
Publications
- 2023
- [b4]Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, Alexandru I. Tomescu:
Genome-Scale Algorithm Design: Bioinformatics in the Era of High-Throughput Sequencing (2nd edition). Cambridge University Press 2023, ISBN 9781009341233 - [j48]Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen:
Algorithms and Complexity on Indexing Founder Graphs. Algorithmica 85(6): 1586-1623 (2023) - [j47]Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu:
Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. Bioinform. 39(8) (2023) - [j45]Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu, Roberto Grossi:
On the Complexity of String Matching for Graphs. ACM Trans. Algorithms 19(3): 21:1-21:25 (2023) - [j43]Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu:
Graphs cannot be indexed in polynomial time for sub-quadratic time string matching, unless SETH fails. Theor. Comput. Sci. 975: 114128 (2023) - 2021
- [c25]Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen:
Algorithms and Complexity on Indexing Elastic Founder Graphs. ISAAC 2021: 20:1-20:18 - [c24]Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu:
Graphs Cannot Be Indexed in Polynomial Time for Sub-quadratic Time String Matching, Unless SETH Fails. SOFSEM 2021: 608-622 - [i24]Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen:
Algorithms and Complexity on Indexing Founder Graphs. CoRR abs/2102.12822 (2021) - 2020
- [c21]Veli Mäkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri, Alexandru I. Tomescu:
Linear Time Construction of Indexable Founder Block Graphs. WABI 2020: 7:1-7:18 - [i21]Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu:
Conditional Indexing Lower Bounds Through Self-Reducibility. CoRR abs/2002.00629 (2020) - [i19]Veli Mäkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri, Alexandru I. Tomescu:
Linear Time Construction of Indexable Founder Block Graphs. CoRR abs/2005.09342 (2020) - 2019
- [j36]Edin Husic, Xinyue Li, Ademir Hujdurovic, Miika Mehine, Romeo Rizzi, Veli Mäkinen, Martin Milanic, Alexandru I. Tomescu:
MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP. Bioinform. 35(5): 769-777 (2019) - [j34]Veli Mäkinen, Alexandru I. Tomescu, Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi:
Sparse Dynamic Programming on DAGs with Small Width. ACM Trans. Algorithms 15(2): 29:1-29:21 (2019) - [j32]Romeo Rizzi, Massimo Cairo, Veli Mäkinen, Alexandru I. Tomescu, Daniel Valenzuela:
Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics. IEEE ACM Trans. Comput. Biol. Bioinform. 16(1): 23-30 (2019) - [c19]Massimo Equi, Roberto Grossi, Veli Mäkinen, Alexandru I. Tomescu:
On the Complexity of String Matching for Graphs. ICALP 2019: 55:1-55:15 - [i14]Massimo Equi, Roberto Grossi, Alexandru I. Tomescu, Veli Mäkinen:
On the Complexity of Exact Pattern Matching in Graphs: Determinism and Zig-Zag Matching. CoRR abs/1902.03560 (2019) - 2018
- [j30]Nidia Obscura Acosta, Veli Mäkinen, Alexandru I. Tomescu:
A safe and complete algorithm for metagenomic assembly. Algorithms Mol. Biol. 13(1): 3:1-3:12 (2018) - [c18]Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen:
Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. RECOMB 2018: 105-121 - 2017
- [j27]Veli Mäkinen, Valeria Staneva, Alexandru I. Tomescu, Daniel Valenzuela, Sebastian Wilzbach:
Interval scheduling maximizing minimum coverage. Discret. Appl. Math. 225: 130-135 (2017) - [i12]Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen:
Speeding up Dynamic Programming on DAGs through a Fast Approximation of Path Cover. CoRR abs/1705.08754 (2017) - 2016
- [j24]Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu:
Gap Filling as Exact Path Length Problem. J. Comput. Biol. 23(5): 347-361 (2016) - [c15]Anna Kuosmanen, Ahmed Sobih, Romeo Rizzi, Veli Mäkinen, Alexandru I. Tomescu:
On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy. BIOINFORMATICS 2016: 272-277 - [c14]Ahmed Sobih, Alexandru I. Tomescu, Veli Mäkinen:
MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows. RECOMB 2016: 111-121 - 2015
- [b2]Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, Alexandru I. Tomescu:
Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing. Cambridge University Press 2015, ISBN 9781107078536 - [j22]Karen E. van Rens, Veli Mäkinen, Alexandru I. Tomescu:
SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP. Bioinform. 31(7): 1133-1135 (2015) - [j18]Alexandru I. Tomescu, Travis Gagie, Alexandru Popa, Romeo Rizzi, Anna Kuosmanen, Veli Mäkinen:
Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly. IEEE ACM Trans. Comput. Biol. Bioinform. 12(6): 1345-1354 (2015) - [c12]Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu:
Gap Filling as Exact Path Length Problem. RECOMB 2015: 281-292 - [i9]Veli Mäkinen, Valeria Staneva, Alexandru I. Tomescu, Daniel Valenzuela:
Interval scheduling maximizing minimum coverage. CoRR abs/1508.07820 (2015) - 2014
- [j17]Romeo Rizzi, Alexandru I. Tomescu, Veli Mäkinen:
On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly. BMC Bioinform. 15(S-9): S5 (2014) - 2013
- [j11]Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen:
A novel min-cost flow method for estimating transcript expression with RNA-Seq. BMC Bioinform. 14(S-5): S15 (2013) - [c5]Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen:
A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. WABI 2013: 85-98 - [i5]Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen:
A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. CoRR abs/1307.7811 (2013)
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