Erik Garrison

28 papers A 1B 1C 2Journal 20Unranked 4
YearRankTypeTitle / Venue / Authors
2025 — conf
Pangenome-Informed Language Models for Synthetic Genome Sequence Generation.
BIBM
Pengzhi Huang, François Charton, Jan-Niklas M. Schmelzle, Shelby S. Darnell, Pjotr Prins, Erik Garrison, G. Edward Suh
2025 — conf
PangenomicsBench: A Benchmark Suite and Characterization of Pangenomics.
IISWC
Noah Kaplan, Jan-Niklas Schmelzle, Yufeng Gu, Erik Garrison, Christopher Batten, Reetuparna Das
2024 J jnl
Cluster-efficient pangenome graph construction with nf-core/pangenome.
Bioinform.
Simon Heumos, Michael L. Heuer, Friederike Hanssen, Lukas Heumos, Andrea Guarracino, Peter Heringer, Philipp Ehmele, Pjotr Prins, Erik Garrison, Sven Nahnsen
2024 J jnl
Memory makes computation universal, remember?
CoRR
Erik Garrison
2024 J jnl
Panacus: fast and exact pangenome growth and core size estimation.
Bioinform.
Luca Parmigiani, Erik Garrison, Jens Stoye, Tobias Marschall, Daniel Doerr
2024 J jnl
Pangenome graph layout by Path-Guided Stochastic Gradient Descent.
Bioinform.
Simon Heumos, Andrea Guarracino, Jan-Niklas Schmelzle, Jiajie Li, Zhiru Zhang, Jörg Hagmann, Sven Nahnsen, Pjotr Prins, Erik Garrison
2024 J jnl
Popping Bubbles in Pangenome Graphs.
CoRR
Njagi Moses Mwaniki, Erik Garrison, Nadia Pisanti
2024 A conf
Rapid GPU-Based Pangenome Graph Layout.
SC
Jiajie Li, Jan-Niklas Schmelzle, Yixiao Du, Simon Heumos, Andrea Guarracino, Giulia Guidi, Pjotr Prins, Erik Garrison, Zhiru Zhang
2024 J jnl
Rapid GPU-Based Pangenome Graph Layout.
CoRR
Jiajie Li, Jan-Niklas Schmelzle, Yixiao Du, Simon Heumos, Andrea Guarracino, Giulia Guidi, Pjotr Prins, Erik Garrison, Zhiru Zhang
2023 — conf
Fast Exact String to D-Texts Alignments.
BIOINFORMATICS
Njagi Moses Mwaniki, Erik Garrison, Nadia Pisanti
2023 J jnl
Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.
Bioinform.
Bryce Kille, Erik Garrison, Todd J. Treangen, Adam M. Phillippy
2023 J jnl
Optimal gap-affine alignment in
Bioinform.
Santiago Marco-Sola, Jordan M. Eizenga, Andrea Guarracino, Benedict Paten, Erik Garrison, Miquel Moretó
2023 J jnl
Unbiased pangenome graphs.
Bioinform.
Erik Garrison, Andrea Guarracino
2022 J jnl
A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar.
PLoS Comput. Biol.
Erik Garrison, Zev N. Kronenberg, Eric T. Dawson, Brent S. Pedersen, Pjotr Prins
2022 J jnl
Fast Exact String to D-Texts Alignments.
CoRR
Njagi Moses Mwaniki, Erik Garrison, Nadia Pisanti
2022 J jnl
ODGI: understanding pangenome graphs.
Bioinform.
Andrea Guarracino, Simon Heumos, Sven Nahnsen, Pjotr Prins, Erik Garrison
2021 J jnl
Efficient dynamic variation graphs.
Bioinform.
Jordan M. Eizenga, Adam M. Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar, Simon Heumos, Glenn Hickey, Vincenza Colonna, Benedict Paten, Erik Garrison
2021 J jnl
GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
PLoS Comput. Biol.
Manuel Tognon, Vincenzo Bonnici, Erik Garrison, Rosalba Giugno, Luca Pinello
2020 J jnl
Haplotype-aware graph indexes.
Bioinform.
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
2019 — conf
Graph-Based Representations for Supporting Genome Data Analysis and Visualization: Opportunities and Challenges.
GbRPR
Vincenzo Carletti, Pasquale Foggia, Erik Garrison, Luca Greco, Pierluigi Ritrovato, Mario Vento
2019 J jnl
Viral coinfection analysis using a MinHash toolkit.
BMC Bioinform.
Eric T. Dawson, Sarah Wagner, David Roberson, Meredith Yeager, Joseph Boland, Erik Garrison, Stephen J. Chanock, Mark Schiffman, Tina Raine-Bennett, Thomas Lorey, Phillip E. Castle, Lisa Mirabello, Richard Durbin
2018 J jnl
A graph-based approach to diploid genome assembly.
Bioinform.
Shilpa Garg, Mikko Rautiainen, Adam M. Novak, Erik Garrison, Richard Durbin, Tobias Marschall
2018 C conf
Haplotype-aware graph indexes.
WABI
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
2018 J jnl
Haplotype-aware graph indexes.
CoRR
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
2018 J jnl
Superbubbles, Ultrabubbles, and Cacti.
J. Comput. Biol.
Benedict Paten, Jordan M. Eizenga, Yohei M. Rosen, Adam M. Novak, Erik Garrison, Glenn Hickey
2017 J jnl
A graph extension of the positional Burrows-Wheeler transform and its applications.
Algorithms Mol. Biol.
Adam M. Novak, Erik Garrison, Benedict Paten
2017 B conf
Superbubbles, Ultrabubbles and Cacti.
RECOMB
Benedict Paten, Adam M. Novak, Erik Garrison, Glenn Hickey
2016 C conf
A Graph Extension of the Positional Burrows-Wheeler Transform and Its Applications.
WABI
Adam M. Novak, Erik Garrison, Benedict Paten