Ben Langmead

According to our database, Ben Langmead authored at least 24 papers between 2011 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests.

Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, Gonzalo Navarro

CoRR, 2024

2023

Pangenomic genotyping with the marker array.

Taher Mun, Naga Sai Kavya Vaddadi, Ben Langmead

Algorithms Mol. Biol., December, 2023

r-indexing without backward searching.

Omar Ahmed, Andrej Baláz, Nathaniel K. Brown, Lore Depuydt, Adrián Goga, Alessia Petescia, Mohsen Zakeri, Jan Fostier, Travis Gagie, Ben Langmead, Gonzalo Navarro, Nicola Prezza

CoRR, 2023

Minimizing Reference Bias: The Impute-First Approach for Personalized Genome Analysis.

Naga Sai Kavya Vaddadi, Taher Mun, Benjamin Thomas Langmead

Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2022

MONI: A Pangenomic Index for Finding Maximal Exact Matches.

Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher

J. Comput. Biol., 2022

Finding Maximal Exact Matches Using the r-Index.

Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher

J. Comput. Biol., 2022

KATKA: A KRAKEN-Like Tool with k Given at Query Time.

Travis Gagie, Sana Kashgouli, Ben Langmead

Proceedings of the String Processing and Information Retrieval, 2022

2021

LevioSAM: fast lift-over of variant-aware reference alignments.

Taher Mun, Nae-Chyun Chen, Ben Langmead

Bioinform., November, 2021

Megadepth: efficient coverage quantification for BigWigs and BAMs.

Christopher Wilks, Omar Ahmed, Daniel N. Baker, David Zhang, Leonardo Collado-Torres, Ben Langmead

Bioinform., 2021

Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing.

Dominik Kempa, Ben Langmead

Proceedings of the 29th Annual European Symposium on Algorithms, 2021

PHONI: Streamed Matching Statistics with Multi-Genome References.

Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi

Proceedings of the 31st Data Compression Conference, 2021

Fast and memory-efficient scRNA-seq <i>k</i>-means clustering with various distances.

Daniel N. Baker, Nathan Dyjack, Vladimir Braverman, Stephanie C. Hicks, Ben Langmead

Proceedings of the BCB '21: 12th ACM International Conference on Bioinformatics, 2021

2020

Matching Reads to Many Genomes with the r-Index.

Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini

J. Comput. Biol., 2020

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.

Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini

J. Comput. Biol., 2020

Vargas: heuristic-free alignment for assessing linear and graph read aligners.

Charlotte A. Darby, Ravi Gaddipati, Michael C. Schatz, Ben Langmead

Bioinform., 2020

2019

Scaling read aligners to hundreds of threads on general-purpose processors.

Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles

Bioinform., 2019

Prefix-free parsing for building big BWTs.

Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini, Taher Mun

Algorithms Mol. Biol., 2019

2018

Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.

Christopher Wilks, Phani Gaddipati, Abhinav Nellore, Ben Langmead

Bioinform., 2018

2017

Rail-RNA: scalable analysis of RNA-seq splicing and coverage.

Abhinav Nellore, Leonardo Collado-Torres, Andrew E. Jaffe, José Alquicira-Hernández, Christopher Wilks, Jacob Pritt, James Morton, Jeffrey T. Leek, Ben Langmead

Bioinform., 2017

2016

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.

Abhinav Nellore, Christopher Wilks, Kasper D. Hansen, Jeffrey T. Leek, Ben Langmead

Bioinform., 2016

2015

<i>Polyester</i>: simulating RNA-seq datasets with differential transcript expression.

Alyssa C. Frazee, Andrew E. Jaffe, Ben Langmead, Jeffrey T. Leek

Bioinform., 2015

2013

Practical software for big genomics data.

Ben Langmead

Proceedings of the IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, 2013

2012

Algorithms and High Performance Computing Approaches for sequencing-based Comparative genomics.

Benjamin Thomas Langmead

PhD thesis, 2012

2011

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets.

Alyssa C. Frazee, Ben Langmead, Jeffrey T. Leek

BMC Bioinform., 2011