Peer-reviewed publications

1. Accurate human genome analysis with element avidity sequencing

   Carroll A, Kolesnikov A, Cook DE, Brambrink L, Wiseman KN, Billings SM, Kruglyak S, Lajoie BR, Zhao J, Levy SE, McLean CY, Shafin K, Nattestad M, Chang PC.
   BMC Bioinformatics. 2025 Jul 25;26(1):194. doi: 10.1186/s12859-025-06191-4.

2. Highly accurate assembly polishing with DeepPolisher

   Mastoras M, Asri M, Brambrink L, Hebbar P, Kolesnikov A, Cook DE, Nattestad M, Lucas J, Won TS, Chang PC, Carroll A, Paten B, Shafin K; and the Human Pangenome Reference Consortium.
   Genome Res. 2025 Jul 1;35(7):1595-1608. doi: 10.1101/gr.280149.124.

3. Local read haplotagging enables accurate long-read small variant calling

   Kolesnikov A, Cook D, Nattestad M, Brambrink L, McNulty B, Gorzynski J, Goenka S, Ashley EA, Jain M, Miga KH, Paten B, Chang PC, Carroll A, Shafin K.
   Nat Commun. 2024 Jul 13;15(1):5907. doi: 10.1038/s41467-024-50079-5.

4. A draft human pangenome reference

   Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H, Paten B.
   Nature. 2023 May;617(7960):312-324. doi: 10.1038/s41586-023-05896-x. Epub 2023 May 10.

5. DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer

   Baid G, Cook DE, Shafin K, Yun T, Llinares-López F, Berthet Q, Belyaeva A, Töpfer A, Wenger AM, Rowell WJ, Yang H, Kolesnikov A, Ammar W, Vert JP, Vaswani A, McLean CY, Nattestad M, Chang PC, Carroll A.
   Nat Biotechnol. 2023 Feb;41(2):232-238. doi: 10.1038/s41587-022-01435-7. Epub 2022 Sep 1.

6. Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting

   Gorzynski JE, Goenka SD, Shafin K, Jensen TD, Fisk DG, Grove ME, Spiteri E, Pesout T, Monlong J, Baid G, Bernstein JA, Ceresnak S, Chang PC, Christle JW, Chubb H, Dalton KP, Dunn K, Garalde DR, Guillory J, Knowles JW, Kolesnikov A, Ma M, Moscarello T, Nattestad M, Perez M, Ruzhnikov MRZ, Samadi M, Setia A, Wright C, Wusthoff CJ, Xiong K, Zhu T, Jain M, Sedlazeck FJ, Carroll A, Paten B, Ashley EA.
   N Engl J Med. 2022 Feb 17;386(7):700-702. doi: 10.1056/NEJMc2112090. Epub 2022 Jan 12.

7. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing

   Goenka SD, Gorzynski JE, Shafin K, Fisk DG, Pesout T, Jensen TD, Monlong J, Chang PC, Baid G, Bernstein JA, Christle JW, Dalton KP, Garalde DR, Grove ME, Guillory J, Kolesnikov A, Nattestad M, Ruzhnikov MRZ, Samadi M, Sethia A, Spiteri E, Wright CJ, Xiong K, Zhu T, Jain M, Sedlazeck FJ, Carroll A, Paten B, Ashley EA.
   Nat Biotechnol. 2022 Jul;40(7):1035-1041. doi: 10.1038/s41587-022-01221-5. Epub 2022 Mar 28.

8. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

   Olson ND, Wagner J, McDaniel J, Stephens SH, Westreich ST, Prasanna AG, Johanson E, Boja E, Maier EJ, Serang O, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, Kyriakidis K, Malousi A, Shafin K, Pesout T, Jain M, Paten B, Chang PC, Kolesnikov A, Nattestad M, Baid G, Goel S, Yang H, Carroll A, Eveleigh R, Bourgey M, Bourque G, Li G, Ma C, Tang L, Du Y, Zhang S, Morata J, Tonda R, Parra G, Trotta JR, Brueffer C, Demirkaya-Budak S, Kabakci-Zorlu D, Turgut D, Kalay Ö, Budak G, Narcı K, Arslan E, Brown R, Johnson IJ, Dolgoborodov A, Semenyuk V, Jain A, Tetikol HS, Jain V, Ruehle M, Lajoie B, Roddey C, Catreux S, Mehio R, Ahsan MU, Liu Q, Wang K, Sahraeian SME, Fang LT, Mohiyuddin M, Hung C, Jain C, Feng H, Li Z, Chen L, Sedlazeck FJ, Zook JM.
   Cell Genom. 2022 May 11;2(5):100129. doi: 10.1016/j.xgen.2022.100129. Epub 2022 Apr 27.

9. Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

   Shafin K, Pesout T, Chang PC, Nattestad M, Kolesnikov A, Goel S, Baid G, Kolmogorov M, Eizenga JM, Miga KH, Carnevali P, Jain M, Carroll A, Paten B.
   Nat Methods. 2021 Nov;18(11):1322-1332. doi: 10.1038/s41592-021-01299-w. Epub 2021 Nov 1.

10. Ribbon: intuitive visualization for complex genomic variation

    Nattestad M, Aboukhalil R, Chin CS, Schatz MC.
    Bioinformatics. 2021 Apr 20;37(3):413-415. doi: 10.1093/bioinformatics/btaa680.

11. BigTop: a three-dimensional virtual reality tool for GWAS visualization

    Westreich ST, Nattestad M, Meyer C.
    BMC Bioinformatics. 2020 Jan 31;21(1):39. doi: 10.1186/s12859-020-3373-5.

12. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

    Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck FJ, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin CS, Beck T, Sundaravadanam Y, Kramer M, Antoniou E, McPherson JD, Hicks J, McCombie WR, Schatz MC.
    Genome Res. 2018 Aug;28(8):1126-1135. doi: 10.1101/gr.231100.117. Epub 2018 Jun 28.

13. Accurate detection of complex structural variations using single-molecule sequencing

    Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC.
    Nat Methods. 2018 Jun;15(6):461-468. doi: 10.1038/s41592-018-0001-7. Epub 2018 Apr 30.

14. GenomeScope: fast reference-free genome profiling from short reads

    Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC.
    Bioinformatics. 2017 Jul 15;33(14):2202-2204. doi: 10.1093/bioinformatics/btx153.

15. Phased diploid genome assembly with single-molecule real-time sequencing

    Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC.
    Nat Methods. 2016 Dec;13(12):1050-1054. doi: 10.1038/nmeth.4035. Epub 2016 Oct 17.

16. Assemblytics: a web analytics tool for the detection of variants from an assembly

    Nattestad M, Schatz MC.
    Bioinformatics. 2016 Oct 1;32(19):3021-3. doi: 10.1093/bioinformatics/btw369. Epub 2016 Jun 17.

17. Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing

    Vembar SS, Seetin M, Lambert C, Nattestad M, Schatz MC, Baybayan P, Scherf A, Smith ML.
    DNA Res. 2016 Aug;23(4):339-51. doi: 10.1093/dnares/dsw022. Epub 2016 Jun 26.

18. The effect of α-mating factor secretion signal mutations on recombinant protein expression in Pichia pastoris

    Lin-Cereghino GP, Stark CM, Kim D, Chang J, Shaheen N, Poerwanto H, Agari K, Moua P, Low LK, Tran N, Huang AD, Nattestad M, Oshiro KT, Chang JW, Chavan A, Tsai JW, Lin-Cereghino J.
    Gene. 2013 May 1;519(2):311-7. doi: 10.1016/j.gene.2013.01.062. Epub 2013 Feb 21.

19. Analysis of the 5' untranslated region (5'UTR) of the alcohol oxidase 1 (AOX1) gene in recombinant protein expression in Pichia pastoris

    Staley CA, Huang A, Nattestad M, Oshiro KT, Ray LE, Mulye T, Li ZH, Le T, Stephens JJ, Gomez SR, Moy AD, Nguyen JC, Franz AH, Lin-Cereghino J, Lin-Cereghino GP.
    Gene. 2012 Apr 1;496(2):118-27. doi: 10.1016/j.gene.2012.01.006. Epub 2012 Jan 25.

Preprints

1. Highly accurate assembly polishing with DeepPolisher

   Mastoras M, Asri M, Brambrink L, Hebbar P, Kolesnikov A, Cook DE, Nattestad M, Lucas J, Won TS, Chang PC, Carroll A, Paten B, Shafin K.
   bioRxiv [Preprint]. 2024 Sep 19:2024.09.17.613505. doi: 10.1101/2024.09.17.613505.

2. Local read haplotagging enables accurate long-read small variant calling

   Kolesnikov A, Cook D, Nattestad M, McNulty B, Gorzynski J, Goenka S, Ashley EA, Jain M, Miga KH, Paten B, Chang PC, Carroll A, Shafin K.
   bioRxiv [Preprint]. 2023 Sep 12:2023.09.07.556731. doi: 10.1101/2023.09.07.556731.

3. DeepTrio: variant calling in families using deep learning

   Kolesnikov A, Goel S, Nattestad M, Yun T, Baid G, Yang H, McLean CY, Chang PC, Carroll A
   bioRxiv [Preprint]. 2021 Apr 06. doi: 10.1101/2021.04.05.438434

4. SplitThreader: Exploration and analysis of rearrangements in cancer genomes

   Nattestad M, Alford MC, Sedlazeck FJ, Schatz MC
   bioRxiv [Preprint]. 2016 Nov 15. doi: 10.1101/087981.

5. Third-generation sequencing and the future of genomics

   Lee H, Gurtowski J, Yoo S, Nattestad M, Marcus S, Goodwin S, McCombie WR, Schatz MC

Blog Posts

1. DeepVariant over the years

   Gunjan Baid, Maria Nattestad, Alexey Kolesnikov, Daniel Cook, Howard Yang, Pi-Chuan Chang, Andrew Carroll
   Google DeepVariant Blog. 2021

2. Looking Through DeepVariant's Eyes

   Maria Nattestad, Gunjan Baid, Andrew Carroll, Pi-Chuan Chang
   Google DeepVariant Blog. 2020

3. One Genome Browser to Rule Them All?

   Maria Nattestad
   Medium. 2018

4. Making genomic data come alive with circos plots

   Maria Nattestad
   Medium. 2017