Publications by authors named "Adam M Novak"

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Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.
Xian Chang, Adam M Novak, Jordan M Eizenga, Jouni Sirén, Jean Monlong

bioRxiv· October 2025

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Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.
Xian Chang, Adam M Novak, Jordan M Eizenga, Jouni Sirén, Jean Monlong

Res Sq· October 2025

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Pangenome-aware DeepVariant.
Mobin Asri, Pi-Chuan Chang, Juan Carlos Mier, Jouni Sirén, Parsa Eskandar, Adam M Novak

bioRxiv· June 2025

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Personalized pangenome references.
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak

Nat Methods· November 2024

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Efficient indexing and querying of annotations in a pangenome graph.
Adam M Novak, Dickson Chung, Glenn Hickey, Sarah Djebali, Toshiyuki T Yokoyama

bioRxiv· October 2024

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Pangenome graph construction from genome alignments with Minigraph-Cactus.
Glenn Hickey, Jean Monlong, Jana Ebler, Adam M Novak, Jordan M Eizenga

Nat Biotechnol· April 2024

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Personalized Pangenome References.
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak

bioRxiv· December 2023

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A draft human pangenome reference.
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Adam M Novak

Nature· May 2023

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Haplotype-aware pantranscriptome analyses using spliced pangenome graphs.
Jonas A Sibbesen, Jordan M Eizenga, Adam M Novak, Jouni Sirén, Xian Chang

Nat Methods· February 2023

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The Human Pangenome Project: a global resource to map genomic diversity.
Ting Wang, Lucinda Antonacci-Fulton, Kerstin Howe, Heather A Lawson, Julian K Lucas, Adam M Novak

Nature· April 2022

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Pangenomics enables genotyping of known structural variants in 5202 diverse genomes.
Jouni Sirén, Jean Monlong, Xian Chang, Adam M Novak, Jordan M Eizenga

Science· December 2021

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Efficient dynamic variation graphs.
Jordan M Eizenga, Adam M Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar

Bioinformatics· January 2021

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Progressive Cactus is a multiple-genome aligner for the thousand-genome era.
Joel Armstrong, Glenn Hickey, Mark Diekhans, Ian T Fiddes, Adam M Novak

Nature· November 2020

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Pangenome Graphs.
Jordan M Eizenga, Adam M Novak, Jonas A Sibbesen, Simon Heumos, Ali Ghaffaari

Annu Rev Genomics Hum Genet· August 2020

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Distance indexing and seed clustering in sequence graphs.
Xian Chang, Jordan Eizenga, Adam M Novak, Jouni Sirén, Benedict Paten

Bioinformatics· July 2020

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Genotyping structural variants in pangenome graphs using the vg toolkit.
Glenn Hickey, David Heller, Jean Monlong, Jonas A Sibbesen, Jouni Sirén, Adam M Novak

Genome Biol· February 2020

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Haplotype-aware graph indexes.
Jouni Sirén, Erik Garrison, Adam M Novak, Benedict Paten, Richard Durbin

Bioinformatics· January 2020

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Sequence tube maps: making graph genomes intuitive to commuters.
Wolfgang Beyer, Adam M Novak, Glenn Hickey, Jeffrey Chan, Vanessa Tan

Bioinformatics· December 2019

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A strategy for building and using a human reference pangenome.
Bastien Llamas, Giuseppe Narzisi, Valerie Schneider, Peter A Audano, Evan Biederstedt, Adam M Novak

F1000Res· October 2019

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Variation graph toolkit improves read mapping by representing genetic variation in the reference.
Erik Garrison, Jouni Sirén, Adam M Novak, Glenn Hickey, Jordan M Eizenga

Nat Biotechnol· October 2018

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Superbubbles, Ultrabubbles, and Cacti.
Benedict Paten, Jordan M Eizenga, Yohei M Rosen, Adam M Novak, Erik Garrison

J Comput Biol· July 2018

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A Flow Procedure for Linearization of Genome Sequence Graphs.
David Haussler, Maciej Smuga-Otto, Jordan M Eizenga, Benedict Paten, Adam M Novak

J Comput Biol· July 2018

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A graph-based approach to diploid genome assembly.
Shilpa Garg, Mikko Rautiainen, Adam M Novak, Erik Garrison, Richard Durbin

Bioinformatics· July 2018

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Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis.
Ian T Fiddes, Gerrald A Lodewijk, Meghan Mooring, Colleen M Bosworth, Adam D Ewing, Adam M Novak

Cell· May 2018

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TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.
Yulia Newton, Adam M Novak, Teresa Swatloski, Duncan C McColl, Sahil Chopra

Cancer Res· November 2017

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