Paul Medvedev

Algorithms Mol. Biol., December, 2024

Compression algorithm for colored de Bruijn graphs.

[BibT_eX]

[DOI]

Yoann Dufresne

Algorithms Mol. Biol., December, 2024

Fast Context-Aware Analysis of Genome Annotation Colocalization.

[BibT_eX]

[DOI]

J. Comput. Biol., 2024

Applying the Safe-And-Complete Framework to Practical Genome Assembly.

[BibT_eX]

[DOI]

Proceedings of the 24th International Workshop on Algorithms in Bioinformatics, 2024

PLA-index: A k-mer Index Exploiting Rank Curve Linearity.

[BibT_eX]

[DOI]

Md. Hasin Abrar

Proceedings of the 24th International Workshop on Algorithms in Bioinformatics, 2024

Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2024

2023

Theoretical Analysis of Edit Distance Algorithms.

[BibT_eX]

[DOI]

Commun. ACM, December, 2023

Theoretical Analysis of Sequencing Bioinformatics Algorithms and Beyond.

[BibT_eX]

[DOI]

Commun. ACM, July, 2023

Exact Sketch-Based Read Mapping.

[BibT_eX]

[DOI]

Tizian Schulz

Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

2022

The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches.

[BibT_eX]

[DOI]

J. Comput. Biol., 2022

Data Structures to Represent a Set of k-long DNA Sequences.

[BibT_eX]

[DOI]

Jan Holub

ACM Comput. Surv., 2022

The limitations of the theoretical analysis of applied algorithms.

[BibT_eX]

[DOI]

CoRR, 2022

Theoretical analysis of edit distance algorithms: an applied perspective.

[BibT_eX]

[DOI]

CoRR, 2022

The K-mer File Format: a standardized and compact disk representation of sets of k-mers.

[BibT_eX]

[DOI]

Bioinform., 2022

Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT).

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2022

2021

What do Eulerian and Hamiltonian cycles have to do with genome assembly?

[BibT_eX]

[DOI]

Mihai Pop

PLoS Comput. Biol., 2021

Disk compression of k-mer sets.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2021

GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping.

[BibT_eX]

[DOI]

Gulsum Gudukbay

Jashwant Raj Gunasekaran

Proceedings of the IEEE International Parallel and Distributed Processing Symposium Workshops, 2021

2020

Bipartite graphs of small readability.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2020

Ten Simple Rules for writing algorithmic bioinformatics conference papers.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2020

De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm.

[BibT_eX]

[DOI]

Kristoffer Sahlin

J. Comput. Biol., 2020

Improved representation of sequence bloom trees.

[BibT_eX]

[DOI]

Robert S. Harris

Bioinform., 2020

Representation of k-mer Sets Using Spectrum-Preserving String Sets.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2020

2019

An Optimal O(nm) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph.

[BibT_eX]

[DOI]

ACM Trans. Algorithms, 2019

Data structures to represent sets of k-long DNA sequences.

[BibT_eX]

[DOI]

Jan Holub

CoRR, 2019

Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

[BibT_eX]

[DOI]

Chen Sun

Bioinform., 2019

Modeling biological problems in computer science: a case study in genome assembly.

[BibT_eX]

[DOI]

Briefings Bioinform., 2019

2018

AllSome Sequence Bloom Trees.

[BibT_eX]

[DOI]

J. Comput. Biol., 2018

RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly.

[BibT_eX]

[DOI]

Bioinform., 2018

Introduction to HiCOMB 2018.

[BibT_eX]

[DOI]

Srinivas Aluru

David A. Bader

Proceedings of the 2018 IEEE International Parallel and Distributed Processing Symposium Workshops, 2018

Parallel Read Partitioning for Concurrent Assembly of Metagenomic Data.

[BibT_eX]

[DOI]

Proceedings of the 25th IEEE International Conference on High Performance Computing, 2018

2017

Safe and Complete Contig Assembly Through Omnitigs.

[BibT_eX]

[DOI]

Alexandru I. Tomescu

J. Comput. Biol., 2017

VarMatch: robust matching of small variant datasets using flexible scoring schemes.

[BibT_eX]

[DOI]

Chen Sun

Bioinform., 2017

TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes.

[BibT_eX]

[DOI]

Ilya Minkin

Son K. Pham

Bioinform., 2017

Parallel and Memory-Efficient Preprocessing for Metagenome Assembly.

[BibT_eX]

[DOI]

Vasudevan Rengasamy

Kamesh Madduri

Proceedings of the 2017 IEEE International Parallel and Distributed Processing Symposium Workshops, 2017

Optimal Omnitig Listing for Safe and Complete Contig Assembly.

[BibT_eX]

[DOI]

Proceedings of the 28th Annual Symposium on Combinatorial Pattern Matching, 2017

2016

On the readability of overlap digraphs.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2016

Compacting de Bruijn graphs from sequencing data quickly and in low memory.

[BibT_eX]

[DOI]

Antoine Limasset

Bioinform., 2016

Safe and Complete Contig Assembly Via Omnitigs.

[BibT_eX]

[DOI]

Alexandru I. Tomescu

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB).

[BibT_eX]

[DOI]

Farhad Hormozdiari

Fereydoun Hormozdiari

Carl Kingsford

Fabio Vandin

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015

On the Representation of De Bruijn Graphs.

[BibT_eX]

[DOI]

J. Comput. Biol., 2015

2014

Informed and automated k-mer size selection for genome assembly.

[BibT_eX]

[DOI]

Bioinform., 2014

2013

Using state machines to model the Ion Torrent sequencing process and to improve read error rates.

[BibT_eX]

[DOI]

David Golan

Bioinform., 2013

2012

Complexity of independent set reconfigurability problems.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2012

2011

Genome Graphs.

[BibT_eX]

[DOI]

PhD thesis, 2011

Shortest paths between shortest paths.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2011

The plane-width of graphs.

[BibT_eX]

[DOI]

J. Graph Theory, 2011

Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers.

[BibT_eX]

[DOI]

J. Comput. Biol., 2011

Error correction of high-throughput sequencing datasets with non-uniform coverage.

[BibT_eX]

[DOI]

Bioinform., 2011

2010

Rearrangement Models and Single-Cut Operations.

[BibT_eX]

[DOI]

Anne Bergeron

Jens Stoye

J. Comput. Biol., 2010

Shortest Paths between Shortest Paths and Independent Sets.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Algorithms - 21st International Workshop, 2010

2009

Maximum Likelihood Genome Assembly.

[BibT_eX]

[DOI]

J. Comput. Biol., 2009

A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG).

[BibT_eX]

[DOI]

Jens Stoye

Francisco M. de la Vega

Bioinform., 2009

Rearrangement Models and Single-Cut Operations.

[BibT_eX]

[DOI]

Jens Stoye

Proceedings of the Comparative Genomics, International Workshop, 2009

2008

The relative worst order ratio applied to seat reservation.

[BibT_eX]

[DOI]

Joan Boyar

ACM Trans. Algorithms, 2008

Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2008

2007

Computability of Models for Sequence Assembly.

[BibT_eX]

[DOI]

Konstantinos Georgiou

Gene Myers