publications

2024

1. 

   Exact global alignment using A* with seed heuristic and match pruning

   Ragnar Groot Koerkamp, and Pesho Ivanov

   Oxford Bioinformatics, 2024

   Bib PDF Code Slides

   @article{koerkamp2022exact,
     title = {Exact global alignment using A* with seed heuristic and match pruning},
     author = {Groot Koerkamp, Ragnar and Ivanov, Pesho},
     journal = {Oxford Bioinformatics},
     year = {2024},
     publisher = {Cold Spring Harbor Laboratory},
     addendum1 = {\\\emph{Extends the seed heuristic with inexact seed matching and match chaining to align sequences with high error rates.}},
   }

2023

1. 

   Optimal Sequence Alignment using A*

   Petar Ivanov

   ETH Zurich, 2023

   Bib PDF Code Slides

   @phdthesis{ivanov2023optimal,
     title = {Optimal Sequence Alignment using {A*}},
     author = {Ivanov, Petar},
     year = {2023},
     school = {ETH Zurich},
   }

2022

1. 

   Fast and Optimal Sequence-to-Graph Alignment Guided by Seeds

   Pesho Ivanov, Benjamin Bichsel, and Martin Vechev

   In RECOMB, 2022

   Bib PDF Code Slides

   @inproceedings{ivanov2022fast,
     title = {Fast and {O}ptimal {S}equence-to-{G}raph {A}lignment {G}uided by {S}eeds},
     author = {Ivanov, Pesho and Bichsel, Benjamin and Vechev, Martin},
     booktitle = {RECOMB},
     year = {2022},
     addendum1 = {\\\emph{Improves upon the previous paper by a seed heuristic for A* to map long sequences in near-linear time with sequence length.}},
   }

2020

1. 

   AStarix: Fast and Optimal Sequence-to-Graph Alignment

   Pesho Ivanov, Benjamin Bichsel, Harun Mustafa, André Kahles, Gunnar Rätsch, and Martin Vechev

   In RECOMB, 2020

   Bib PDF Code Slides

   @inproceedings{ivanov2020astarix,
     title = {{AStarix}: {F}ast and {O}ptimal {S}equence-to-{G}raph {A}lignment},
     author = {Ivanov, Pesho and Bichsel, Benjamin and Mustafa, Harun and Kahles, Andr{\'e} and R{\"a}tsch, Gunnar and Vechev, Martin},
     booktitle = {RECOMB},
     year = {2020},
     addendum1 = {\\\emph{Suggests \A for optimal mapping, demonstrates that a trie index enables sub-linear mapping with reference size, introduces the sequence-to-graph mapper AStarix.}},
   }