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Search life-sciences literature (45,100,050 articles, preprints and more)

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Exposure levels and target attainment of piperacillin/tazobactam in adult patients admitted to the intensive care unit: a prospective observational study.
El-Haffaf I, Marsot A, Hachemi D, Pesout T, Williams V, Smith MA, Albert M, Williamson D
Can J Anaesth, 71(4):511-522, 19 Jan 2024
Cited by: 1 article | PMID: 38243099
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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Alvarez Jerez P, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, [...] Paten B
Nat Methods, 20(10):1483-1492, 14 Sep 2023
Cited by: 41 articles | PMID: 37710018 | PMCID: PMC11222905
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Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.
Lee H, Greer SU, Pavlichin DS, Zhou B, Urban AE, Weissman T, Human Pangenome Reference Consortium, Ji HP
Cell Rep Methods, 3(8):100543, 02 Aug 2023
Cited by: 2 articles | PMID: 37671027 | PMCID: PMC10475782
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Gaps and complex structurally variant loci in phased genome assemblies.
Porubsky D, Vollger MR, Harvey WT, Rozanski AN, Ebert P, Hickey G, Hasenfeld P, Sanders AD, Stober C, Human Pangenome Reference Consortium, Korbel JO, Paten B, Marschall T, Eichler EE
Genome Res, 33(4):496-510, 01 Apr 2023
Cited by: 21 articles | PMID: 37164484 | PMCID: PMC10234299
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Increased mutation and gene conversion within human segmental duplications.
Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M, Human Pangenome Reference Consortium, Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh P, Eichler EE
Nature, 617(7960):325-334, 10 May 2023
Cited by: 32 articles | PMID: 37165237 | PMCID: PMC10172114
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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, [...] Paten B
Nature, 617(7960):312-324, 10 May 2023
Cited by: 263 articles | PMID: 37165242 | PMCID: PMC10172123
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Recombination between heterologous human acrocentric chromosomes.
Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C, Human Pangenome Reference Consortium, Gerton JL, Phillippy AM, Colonna V, Garrison E
Nature, 617(7960):335-343, 10 May 2023
Cited by: 37 articles | PMID: 37165241 | PMCID: PMC10172130
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Pangenome graph construction from genome alignments with Minigraph-Cactus.
Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Human Pangenome Reference Consortium, Marschall T, Li H, Paten B
Nat Biotechnol, 42(4):663-673, 10 May 2023
Cited by: 45 articles | PMID: 37165083 | PMCID: PMC10638906
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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PA, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, North American Brain Expression Consortium (NABEC), [...] Paten B
bioRxiv, 15 Jan 2023
Cited by: 0 articles | PPR: PPR597038
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Semi-automated assembly of high-quality diploid human reference genomes.
Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, Chin CS, Cody S, Collins J, Ebert P, [...] Human Pangenome Reference Consortium
Nature, 611(7936):519-531, 19 Oct 2022
Cited by: 85 articles | PMID: 36261518 | PMCID: PMC9668749
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A Draft Human Pangenome Reference
Liao W, 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, [...] Paten B
bioRxiv, 09 Jul 2022
Cited by: 0 articles | PPR: PPR516455
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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, [...] Zook JM
Cell Genom, 2(5):S2666-979X(22)00058-1, 27 Apr 2022
Cited by: 84 articles | PMID: 35720974 | PMCID: PMC9205427
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Automated assembly of high-quality diploid human reference genomes
Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJ, Chin C, Cody S, Collins J, Ebert P, [...] Human Pangenome Reference Consortium
bioRxiv, 06 Mar 2022
Cited by: 0 articles | PPR: PPR464906
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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, [...] Ashley EA
Nat Biotechnol, 40(7):1035-1041, 28 Mar 2022
Cited by: 27 articles | PMID: 35347328 | PMCID: PMC9287171
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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, [...] Ashley EA
N Engl J Med, 386(7):700-702, 12 Jan 2022
Cited by: 71 articles | PMID: 35020984
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Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic Shock.
Gorzynski JE, Goenka SD, Shafin K, Jensen TD, Fisk DG, Grove ME, Spiteri E, Pesout T, Monlong J, Bernstein JA, Ceresnak S, Chang PC, Christle JW, Chubb H, Dunn K, Garalde DR, Guillory J, Ruzhnikov MRZ, Wright C, [...] Ashley EA
Circ Genom Precis Med, 15(2):e003591, 08 Feb 2022
Cited by: 1 article | PMID: 35133172
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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, 18(11):1322-1332, 01 Nov 2021
Cited by: 116 articles | PMID: 34725481 | PMCID: PMC8571015
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Towards complete and error-free genome assemblies of all vertebrate species.
Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, [...] Jarvis ED
Nature, 592(7856):737-746, 28 Apr 2021
Cited by: 954 articles | PMID: 33911273 | PMCID: PMC8081667
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Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks
Shafin K, Pesout T, Chang P, Nattestad M, Kolesnikov A, Goel S, Baid G, Eizenga JM, Miga KH, Carnevali P, Jain M, Carroll A, Paten B
bioRxiv, 05 Mar 2021
Cited by: 0 articles | PPR: PPR293005
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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, [...] Zook JM
bioRxiv, 15 Nov 2020
Cited by: 0 articles | PPR: PPR238244
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Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, [...] Paten B
Nat Biotechnol, 38(9):1044-1053, 04 May 2020
Cited by: 247 articles | PMID: 32686750 | PMCID: PMC7483855
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Towards complete and error-free genome assemblies of all vertebrate species
Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Lee C, Ko BJ, Kim J, Bista I, Smith M, Haase B, [...] Jarvis ED
bioRxiv, 23 May 2020
Cited by: 0 articles | PPR: PPR166664
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Efficientde novoassembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit
Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, [...] Paten B
bioRxiv, 26 Jul 2019
Cited by: 1 article | PPR: PPR86911
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Haplotype-aware diplotyping from noisy long reads.
Ebler J, Haukness M, Pesout T, Marschall T, Paten B
Genome Biol, 20(1):116, 03 Jun 2019
Cited by: 36 articles | PMID: 31159868 | PMCID: PMC6547545
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Haplotype-aware genotyping from noisy long reads
Ebler J, Haukness M, Pesout T, Marschall T, Paten B
bioRxiv, 03 Apr 2018
Cited by: 1 article | PPR: PPR14664
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