| Year |
Citation |
Score |
| 2024 |
Park J, Cook DE, Chang PC, Kolesnikov A, Brambrink L, Mier JC, Gardner J, McNulty B, Sacco S, Keskus A, Bryant A, Ahmad T, Shetty J, Zhao Y, Tran B, ... ... Paten B, et al. DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies. Biorxiv : the Preprint Server For Biology. PMID 39229187 DOI: 10.1101/2024.08.16.608331 |
0.372 |
|
| 2024 |
Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, ... ... Paten B, et al. Complete sequencing of ape genomes. Biorxiv : the Preprint Server For Biology. PMID 39131277 DOI: 10.1101/2024.07.31.605654 |
0.401 |
|
| 2024 |
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. Local read haplotagging enables accurate long-read small variant calling. Nature Communications. 15: 5907. PMID 39003259 DOI: 10.1038/s41467-024-50079-5 |
0.364 |
|
| 2024 |
Taylor DJ, Eizenga JM, Li Q, Das A, Jenike KM, Kenny EE, Miga KH, Monlong J, McCoy RC, Paten B, Schatz MC. Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References. Annual Review of Genomics and Human Genetics. PMID 38663087 DOI: 10.1146/annurev-genom-021623-081639 |
0.519 |
|
| 2024 |
Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen H, McNulty B, Porubsky D, Montague T, Lucas J, Condon C, Eizenga JM, Juul S, McKenzie S, Simmonds SE, Park J, ... ... Paten B, et al. Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Genome Research. PMID 38627094 DOI: 10.1101/gr.278268.123 |
0.39 |
|
| 2024 |
Keskus A, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, ... ... Paten B, et al. Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. Medrxiv : the Preprint Server For Health Sciences. PMID 38585974 DOI: 10.1101/2024.03.22.24304756 |
0.404 |
|
| 2024 |
Mirarab S, Rivas-González I, Feng S, Stiller J, Fang Q, Mai U, Hickey G, Chen G, Brajuka N, Fedrigo O, Formenti G, Wolf JBW, Howe K, Antunes A, Schierup MH, ... Paten B, et al. A region of suppressed recombination misleads neoavian phylogenomics. Proceedings of the National Academy of Sciences of the United States of America. 121: e2319506121. PMID 38557186 DOI: 10.1073/pnas.2319506121 |
0.394 |
|
| 2024 |
Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, ... ... Paten B, et al. Structurally divergent and recurrently mutated regions of primate genomes. Cell. PMID 38428424 DOI: 10.1016/j.cell.2024.01.052 |
0.447 |
|
| 2023 |
Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, ... ... Paten B, et al. Identification of constrained sequence elements across 239 primate genomes. Nature. PMID 38030727 DOI: 10.1038/s41586-023-06798-8 |
0.426 |
|
| 2023 |
Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline MS, Diekhans M, Fischer C, Navarro Gonzalez J, Hickey G, Hinrichs AS, Kuhn RM, Lee BT, Lee CM, Le Mercier P, ... ... Paten B, et al. The UCSC Genome Browser database: 2024 update. Nucleic Acids Research. PMID 37953330 DOI: 10.1093/nar/gkad987 |
0.494 |
|
| 2023 |
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. Local read haplotagging enables accurate long-read small variant calling. Biorxiv : the Preprint Server For Biology. PMID 37745389 DOI: 10.1101/2023.09.07.556731 |
0.375 |
|
| 2023 |
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, ... ... Paten B, et al. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nature Methods. PMID 37710018 DOI: 10.1038/s41592-023-01993-x |
0.366 |
|
| 2023 |
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, ... ... Paten B, et al. A draft human pangenome reference. Nature. 617: 312-324. PMID 37165242 DOI: 10.1038/s41586-023-05896-x |
0.384 |
|
| 2023 |
Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M, Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, et al. Increased mutation and gene conversion within human segmental duplications. Nature. 617: 325-334. PMID 37165237 DOI: 10.1038/s41586-023-05895-y |
0.326 |
|
| 2023 |
Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Marschall T, Li H, Paten B. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nature Biotechnology. PMID 37165083 DOI: 10.1038/s41587-023-01793-w |
0.466 |
|
| 2023 |
Porubsky D, Vollger MR, Harvey WT, Rozanski AN, Ebert P, Hickey G, Hasenfeld P, Sanders AD, Stober C, Korbel JO, Paten B, Marschall T, Eichler EE. Gaps and complex structurally variant loci in phased genome assemblies. Genome Research. 33: 496-510. PMID 37164484 DOI: 10.1101/gr.277334.122 |
0.388 |
|
| 2023 |
Porubsky D, Harvey WT, Rozanski AN, Ebler J, Höps W, Ashraf H, Hasenfeld P, Paten B, Sanders AD, Marschall T, Korbel JO, Eichler EE. Inversion polymorphism in a complete human genome assembly. Genome Biology. 24: 100. PMID 37122002 DOI: 10.1186/s13059-023-02919-8 |
0.397 |
|
| 2023 |
Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, ... ... Paten B, ... ... Paten B, et al. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science (New York, N.Y.). 380: eabn2937. PMID 37104612 DOI: 10.1126/science.abn2937 |
0.422 |
|
| 2023 |
Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, ... ... Paten B, ... ... Paten B, et al. Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.). 380: eabn3943. PMID 37104599 DOI: 10.1126/science.abn3943 |
0.44 |
|
| 2023 |
Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wallerman O, ... ... Paten B, et al. Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease. Biorxiv : the Preprint Server For Biology. PMID 36945512 DOI: 10.1101/2023.03.10.531987 |
0.465 |
|
| 2023 |
Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Gordon DS, Wei X, Logsdon GA, Haukness M, Dishuck PC, ... ... Paten B, et al. Structurally divergent and recurrently mutated regions of primate genomes. Biorxiv : the Preprint Server For Biology. PMID 36945442 DOI: 10.1101/2023.03.07.531415 |
0.503 |
|
| 2023 |
Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen H, McNulty B, Porubsky D, Montague T, Lucas J, Condon C, Eizenga J, Juul S, McKenzie S, Simmonds SE, Park J, ... ... Paten B, et al. Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Biorxiv : the Preprint Server For Biology. PMID 36865218 DOI: 10.1101/2023.02.21.529152 |
0.321 |
|
| 2023 |
Marco-Sola S, Eizenga JM, Guarracino A, Paten B, Garrison E, Moreto M. Optimal gap-affine alignment in O(s) space. Bioinformatics (Oxford, England). PMID 36749013 DOI: 10.1093/bioinformatics/btad074 |
0.318 |
|
| 2023 |
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, ... ... Paten B, et al. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Biorxiv : the Preprint Server For Biology. PMID 36711673 DOI: 10.1101/2023.01.12.523790 |
0.424 |
|
| 2023 |
Sibbesen JA, Eizenga JM, Novak AM, Sirén J, Chang X, Garrison E, Paten B. Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature Methods. 20: 239-247. PMID 36646895 DOI: 10.1038/s41592-022-01731-9 |
0.397 |
|
| 2022 |
Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, ... ... Paten B, et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Research. PMID 36420896 DOI: 10.1093/nar/gkac1071 |
0.496 |
|
| 2022 |
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, ... ... Paten B, et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature. PMID 36261518 DOI: 10.1038/s41586-022-05325-5 |
0.496 |
|
| 2022 |
Sirén J, Paten B. GBZ File Format for Pangenome Graphs. Bioinformatics (Oxford, England). PMID 36179091 DOI: 10.1093/bioinformatics/btac656 |
0.348 |
|
| 2022 |
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, ... ... Paten B, et al. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions. Cell Genomics. 2. PMID 35720974 DOI: 10.1016/j.xgen.2022.100129 |
0.469 |
|
| 2022 |
Markello C, Huang C, Rodriguez A, Carroll A, Chang PC, Eizenga J, Markello T, Haussler D, Paten B. A complete pedigree-based graph workflow for rare candidate variant analysis. Genome Research. PMID 35483961 DOI: 10.1101/gr.276387.121 |
0.417 |
|
| 2022 |
Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, ... ... Paten B, et al. The Human Pangenome Project: a global resource to map genomic diversity. Nature. 604: 437-446. PMID 35444317 DOI: 10.1038/s41586-022-04601-8 |
0.506 |
|
| 2022 |
Mc Cartney AM, Shafin K, Alonge M, Bzikadze AV, Formenti G, Fungtammasan A, Howe K, Jain C, Koren S, Logsdon GA, Miga KH, Mikheenko A, Paten B, Shumate A, Soto DC, et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nature Methods. PMID 35361931 DOI: 10.1038/s41592-022-01440-3 |
0.424 |
|
| 2022 |
Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, ... ... Paten B, et al. A complete reference genome improves analysis of human genetic variation. Science (New York, N.Y.). 376: eabl3533. PMID 35357935 DOI: 10.1126/science.abl3533 |
0.478 |
|
| 2022 |
Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, ... ... Paten B, et al. The complete sequence of a human genome. Science (New York, N.Y.). 376: 44-53. PMID 35357919 DOI: 10.1126/science.abj6987 |
0.673 |
|
| 2022 |
Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, ... ... Paten B, et al. Complete genomic and epigenetic maps of human centromeres. Science (New York, N.Y.). 376: eabl4178. PMID 35357911 DOI: 10.1126/science.abl4178 |
0.465 |
|
| 2022 |
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, ... ... Paten B, et al. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nature Biotechnology. PMID 35347328 DOI: 10.1038/s41587-022-01221-5 |
0.449 |
|
| 2022 |
Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, Culotti A, Ellrott K, Goecks J, Grossman RL, Hall IM, Hansen KD, Lawson J, Leek JT, Luria AO, ... ... Paten B, et al. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genomics. 2. PMID 35199087 DOI: 10.1016/j.xgen.2021.100085 |
0.413 |
|
| 2022 |
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, ... ... Paten B, et al. Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. The New England Journal of Medicine. PMID 35020984 DOI: 10.1056/NEJMc2112090 |
0.412 |
|
| 2021 |
Sirén J, Monlong J, Chang X, Novak AM, Eizenga JM, Markello C, Sibbesen JA, Hickey G, Chang PC, Carroll A, Gupta N, Gabriel S, Blackwell TW, Ratan A, Taylor KD, ... ... Paten B, et al. Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science (New York, N.Y.). 374: abg8871. PMID 34914532 DOI: 10.1126/science.abg8871 |
0.436 |
|
| 2021 |
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. Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nature Methods. PMID 34725481 DOI: 10.1038/s41592-021-01299-w |
0.406 |
|
| 2021 |
Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, ... Paten B, et al. Erratum to: Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution. PMID 34015138 DOI: 10.1093/molbev/msab100 |
0.373 |
|
| 2021 |
Mao Y, Catacchio CR, Hillier LW, Porubsky D, Li R, Sulovari A, Fernandes JD, Montinaro F, Gordon DS, Storer JM, Haukness M, Fiddes IT, Murali SC, Dishuck PC, Hsieh P, ... ... Paten B, et al. A high-quality bonobo genome refines the analysis of hominid evolution. Nature. PMID 33953399 DOI: 10.1038/s41586-021-03519-x |
0.525 |
|
| 2021 |
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, ... ... Paten B, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 592: 737-746. PMID 33911273 DOI: 10.1038/s41586-021-03451-0 |
0.681 |
|
| 2021 |
Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, ... ... Paten B, et al. Author Correction: Dense sampling of bird diversity increases power of comparative genomics. Nature. PMID 33833441 DOI: 10.1038/s41586-021-03473-8 |
0.318 |
|
| 2021 |
Garg P, Martin-Trujillo A, Rodriguez OL, Gies SJ, Hadelia E, Jadhav B, Jain M, Paten B, Sharp AJ. Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression. American Journal of Human Genetics. PMID 33794196 DOI: 10.1016/j.ajhg.2021.03.016 |
0.341 |
|
| 2020 |
Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, ... ... Paten B, et al. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science (New York, N.Y.). 370. PMID 33335035 DOI: 10.1126/science.abc6617 |
0.487 |
|
| 2020 |
Porubsky D, Ebert P, Audano PA, Vollger MR, Harvey WT, Marijon P, Ebler J, Munson KM, Sorensen M, Sulovari A, Haukness M, Ghareghani M, Lansdorp PM, Paten B, et al. Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nature Biotechnology. PMID 33288906 DOI: 10.1038/s41587-020-0719-5 |
0.436 |
|
| 2020 |
Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, ... ... Paten B, et al. GENCODE 2021. Nucleic Acids Research. PMID 33270111 DOI: 10.1093/nar/gkaa1087 |
0.752 |
|
| 2020 |
Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, ... ... Paten B, et al. Dense sampling of bird diversity increases power of comparative genomics. Nature. 587: 252-257. PMID 33177665 DOI: 10.1038/s41586-020-2873-9 |
0.532 |
|
| 2020 |
Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, ... ... Paten B, et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 587: 246-251. PMID 33177663 DOI: 10.1038/s41586-020-2871-y |
0.556 |
|
| 2020 |
Eizenga JM, Novak AM, Kobayashi E, Villani F, Cisar C, Heumos S, Hickey G, Colonna V, Paten B, Garrison E. Efficient dynamic variation graphs. Bioinformatics (Oxford, England). PMID 33040146 DOI: 10.1093/Bioinformatics/Btaa640 |
0.468 |
|
| 2020 |
Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, ... Paten B, et al. Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution. PMID 32946576 DOI: 10.1093/Molbev/Msaa240 |
0.479 |
|
| 2020 |
Garg P, Jadhav B, Rodriguez OL, Patel N, Martin-Trujillo A, Jain M, Metsu S, Olsen H, Paten B, Ritz B, Kooy RF, Gecz J, Sharp AJ. A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions. American Journal of Human Genetics. PMID 32937144 DOI: 10.1016/J.Ajhg.2020.08.019 |
0.46 |
|
| 2020 |
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, ... ... Paten B, et al. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology. PMID 32686750 DOI: 10.1038/S41587-020-0503-6 |
0.564 |
|
| 2020 |
Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, ... ... Paten B, et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. PMID 32663838 DOI: 10.1038/S41586-020-2547-7 |
0.502 |
|
| 2020 |
Chang X, Eizenga J, Novak AM, Sirén J, Paten B. Distance indexing and seed clustering in sequence graphs. Bioinformatics (Oxford, England). 36: i146-i153. PMID 32657356 DOI: 10.1093/Bioinformatics/Btaa446 |
0.562 |
|
| 2020 |
Ding H, Bailey AD, Jain M, Olsen H, Paten B. Gaussian Mixture Model-Based Unsupervised Nucleotide Modification Number Detection Using Nanopore Sequencing Readouts. Bioinformatics (Oxford, England). PMID 32597959 DOI: 10.1093/Bioinformatics/Btaa601 |
0.39 |
|
| 2020 |
Krasheninnikova K, Diekhans M, Armstrong J, Dievskii A, Paten B, O'Brien S. halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments. Gigascience. 9. PMID 32463100 DOI: 10.1093/Gigascience/Giaa047 |
0.595 |
|
| 2020 |
Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G, Chang X, Seaman JD, Rounthwaite R, Ebler J, Rautiainen M, Garg S, Paten B, Marschall T, Sirén J, et al. Pangenome Graphs. Annual Review of Genomics and Human Genetics. PMID 32453966 DOI: 10.1146/annurev-genom-120219-080406 |
0.549 |
|
| 2020 |
Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, ... ... Paten B, et al. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000research. 9: 136. PMID 32308977 DOI: 10.12688/F1000Research.18236.1 |
0.341 |
|
| 2020 |
Hickey G, Heller D, Monlong J, Sibbesen JA, Sirén J, Eizenga J, Dawson ET, Garrison E, Novak AM, Paten B. Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biology. 21: 35. PMID 32051000 DOI: 10.1186/S13059-020-1941-7 |
0.418 |
|
| 2020 |
Burton AS, Stahl SE, John KK, Jain M, Juul S, Turner DJ, Harrington ED, Stoddart D, Paten B, Akeson M, Castro-Wallace SL. Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing. Genes. 11. PMID 31936690 DOI: 10.3390/Genes11010076 |
0.405 |
|
| 2019 |
Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, ... ... Paten B, et al. A strategy for building and using a human reference pangenome. F1000research. 8: 1751. PMID 34386196 DOI: 10.12688/f1000research.19630.1 |
0.366 |
|
| 2019 |
Workman RE, Tang AD, Tang PS, Jain M, Tyson JR, Razaghi R, Zuzarte PC, Gilpatrick T, Payne A, Quick J, Sadowski N, Holmes N, de Jesus JG, Jones KL, Soulette CM, ... ... Paten B, et al. Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome. Nature Methods. PMID 31819268 DOI: 10.1038/S41592-019-0697-Z |
0.327 |
|
| 2019 |
Workman RE, Tang AD, Tang PS, Jain M, Tyson JR, Razaghi R, Zuzarte PC, Gilpatrick T, Payne A, Quick J, Sadowski N, Holmes N, de Jesus JG, Jones KL, Soulette CM, ... ... Paten B, et al. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nature Methods. PMID 31740818 DOI: 10.1038/S41592-019-0617-2 |
0.376 |
|
| 2019 |
Sirén J, Garrison E, Novak AM, Paten B, Durbin R. Haplotype-aware graph indexes. Bioinformatics (Oxford, England). PMID 31406990 DOI: 10.1093/Bioinformatics/Btz575 |
0.513 |
|
| 2019 |
Beyer W, Novak AM, Hickey G, Chan J, Tan V, Paten B, Zerbino DR. Sequence tube maps: making graph genomes intuitive to commuters. Bioinformatics (Oxford, England). PMID 31368484 DOI: 10.1093/Bioinformatics/Btz597 |
0.773 |
|
| 2019 |
Ebler J, Haukness M, Pesout T, Marschall T, Paten B. Haplotype-aware diplotyping from noisy long reads. Genome Biology. 20: 116. PMID 31159868 DOI: 10.1186/S13059-019-1709-0 |
0.439 |
|
| 2019 |
Sarsani VK, Raghupathy N, Fiddes IT, Armstrong J, Thibaud-Nissen F, Zinder O, Bolisetty M, Howe K, Hinerfeld D, Ruan X, Rowe L, Barter M, Ananda G, Paten B, Weinstock GM, et al. The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain. G3 (Bethesda, Md.). PMID 30996023 DOI: 10.1534/G3.119.400071 |
0.545 |
|
| 2019 |
Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin C, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, ... ... Paten B, et al. A strategy for building and using a human reference pangenome F1000research. 8: 1751. DOI: 10.12688/F1000Research.19630.1 |
0.468 |
|
| 2018 |
Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R, Dlott CC, Dolman L, et al. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. Plos Genetics. 14: e1007752. PMID 30586411 DOI: 10.1371/Journal.Pgen.1007752 |
0.372 |
|
| 2018 |
Armstrong J, Fiddes IT, Diekhans M, Paten B. Whole-Genome Alignment and Comparative Annotation. Annual Review of Animal Biosciences. PMID 30379572 DOI: 10.1146/Annurev-Animal-020518-115005 |
0.614 |
|
| 2018 |
Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, ... ... Paten B, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. PMID 30357393 DOI: 10.1093/Nar/Gky955 |
0.753 |
|
| 2018 |
Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S. Chromosome assembly of large and complex genomes using multiple references. Genome Research. PMID 30341161 DOI: 10.1101/Gr.236273.118 |
0.563 |
|
| 2018 |
Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, ... ... Paten B, et al. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nature Genetics. PMID 30275530 DOI: 10.1038/S41588-018-0223-8 |
0.669 |
|
| 2018 |
Garrison E, Sirén J, Novak AM, Hickey G, Eizenga JM, Dawson ET, Jones W, Garg S, Markello C, Lin MF, Paten B, Durbin R. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nature Biotechnology. PMID 30125266 DOI: 10.1038/Nbt.4227 |
0.681 |
|
| 2018 |
Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Research. PMID 29884752 DOI: 10.1101/Gr.233460.117 |
0.614 |
|
| 2018 |
Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, ... ... Paten B, et al. High-resolution comparative analysis of great ape genomes. Science (New York, N.Y.). 360. PMID 29880660 DOI: 10.1126/Science.Aar6343 |
0.552 |
|
| 2018 |
Tunstall T, Kock R, Vahala J, Diekhans M, Fiddes I, Armstrong J, Paten B, Ryder OA, Steiner CC. Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells. Genome Research. 28: 780-788. PMID 29798851 DOI: 10.1101/Gr.227603.117 |
0.393 |
|
| 2018 |
Haussler D, Smuga-Otto M, Eizenga JM, Paten B, Novak AM, Nikitin S, Zueva M, Miagkov D. A Flow Procedure for Linearization of Genome Sequence Graphs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 29792514 DOI: 10.1089/Cmb.2017.0248 |
0.51 |
|
| 2018 |
Dang LT, Tondl M, Chiu MHH, Revote J, Paten B, Tano V, Tokolyi A, Besse F, Quaife-Ryan G, Cumming H, Drvodelic MJ, Eichenlaub MP, Hallab JC, Stolper JS, Rossello FJ, et al. TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets. Bmc Genomics. 19: 238. PMID 29621972 DOI: 10.1186/S12864-018-4630-0 |
0.544 |
|
| 2018 |
Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, ... ... Paten B, et al. Repeat associated mechanisms of genome evolution and function revealed by theandgenomes. Genome Research. PMID 29563166 DOI: 10.1101/Gr.234096.117 |
0.543 |
|
| 2018 |
Jain M, Olsen HE, Turner DJ, Stoddart D, Bulazel KV, Paten B, Haussler D, Willard HF, Akeson M, Miga KH. Linear assembly of a human centromere on the Y chromosome. Nature Biotechnology. PMID 29553574 DOI: 10.1038/Nbt.4109 |
0.43 |
|
| 2018 |
Paten B, Eizenga JM, Rosen YM, Novak AM, Garrison E, Hickey G. Superbubbles, Ultrabubbles, and Cacti. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 29461862 DOI: 10.1089/Cmb.2017.0251 |
0.539 |
|
| 2018 |
Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, ... ... Paten B, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology. PMID 29431738 DOI: 10.1038/Nbt.4060 |
0.545 |
|
| 2018 |
Marschall T, Marz M, Abeel T, Dijkstra L, Dutilh BE, Ghaffaari A, Kersey P, Kloosterman WP, Makinen V, Novak AM, Paten B, Porubsky D, Rivals E, Alkan C, Baaijens JA, et al. Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics. 19: 118-135. PMID 27769991 DOI: 10.1093/Bib/Bbw089 |
0.579 |
|
| 2017 |
Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes I, Armstrong J, Laayouni H, Gordon D, Huddleston J, Perez RG, Povolotskaya I, Armero AS, Garrido JG, Ho D, Ribeca P, ... ... Paten B, et al. A 3-way hybrid approach to generate a new high quality chimpanzee reference genome (Pan_tro_3.0). Gigascience. PMID 29092041 DOI: 10.1093/Gigascience/Gix098 |
0.594 |
|
| 2017 |
Rosen Y, Eizenga J, Paten B. Modelling haplotypes with respect to reference cohort variation graphs. Bioinformatics (Oxford, England). 33: i118-i123. PMID 28881971 DOI: 10.1093/Bioinformatics/Btx236 |
0.334 |
|
| 2017 |
Novak AM, Garrison E, Paten B. A graph extension of the positional Burrows-Wheeler transform and its applications. Algorithms For Molecular Biology : Amb. 12: 18. PMID 28702075 DOI: 10.1186/S13015-017-0109-9 |
0.501 |
|
| 2017 |
Jagodnik KM, Koplev S, Jenkins S, Ohno-Machado L, Paten B, Schurer SC, Dumontier M, Verborgh R, Bui A, Ping P, McKenna NJ, Madduri R, Pillai A, Ma'ayan A. Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons: Report from the Commons Framework Pilots Workshop. Journal of Biomedical Informatics. PMID 28501646 DOI: 10.1016/J.Jbi.2017.05.006 |
0.324 |
|
| 2017 |
Paten B, Novak AM, Eizenga JM, Garrison E. Genome graphs and the evolution of genome inference. Genome Research. PMID 28360232 DOI: 10.1101/Gr.214155.116 |
0.577 |
|
| 2017 |
O'Connor BD, Yuen D, Chung V, Duncan AG, Liu XK, Patricia J, Paten B, Stein L, Ferretti V. The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. F1000research. 6: 52. PMID 28344774 DOI: 10.12688/F1000Research.10137.1 |
0.541 |
|
| 2017 |
Rand AC, Jain M, Eizenga JM, Musselman-Brown A, Olsen HE, Akeson M, Paten B. Mapping DNA methylation with high-throughput nanopore sequencing. Nature Methods. PMID 28218897 DOI: 10.1038/Nmeth.4189 |
0.425 |
|
| 2017 |
Rice ES, Kohno S, St John J, Pham S, Howard J, Lareau L, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN, Gresham C, McCarthy F, Kern C, ... ... Paten B, et al. Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Research. PMID 28137821 DOI: 10.1101/Gr.213595.116 |
0.438 |
|
| 2017 |
Dawson ET, Garrison E, Novak A, Paten B, Eizinga J, Hickey G, Chanock S, Durbin R. Abstract 3570: Germline structural variant detection with variation graphs Cancer Research. 77: 3570-3570. DOI: 10.1158/1538-7445.Am2017-3570 |
0.589 |
|
| 2016 |
Jain M, Olsen HE, Paten B, Akeson M. Erratum to: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biology. 17: 256. PMID 27964738 DOI: 10.1186/S13059-016-1122-X |
0.505 |
|
| 2016 |
Jain M, Olsen HE, Paten B, Akeson M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biology. 17: 239. PMID 27887629 DOI: 10.1186/S13059-016-1103-0 |
0.494 |
|
| 2016 |
Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D. Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. Bmc Bioinformatics. 17: 400. PMID 27687569 DOI: 10.1186/S12859-016-1258-4 |
0.762 |
|
| 2016 |
Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, et al. Long-read sequence assembly of the gorilla genome. Science (New York, N.Y.). 352: aae0344. PMID 27034376 DOI: 10.1126/Science.Aae0344 |
0.607 |
|
| 2016 |
Lincoln SE, Cline M, Yang S, Kobayashi Y, Zhang M, O'Leary E, Topper S, Paten B, Nussbaum R. Variant classifications in BRCA1 and BRCA2: A systematic analysis of interlaboratory concordance Journal of Clinical Oncology. 34: 1592-1592. DOI: 10.1200/Jco.2016.34.15_Suppl.1592 |
0.388 |
|
| 2016 |
Novak AM, Garrison E, Paten B. A graph extension of the positional burrows-wheeler transform and its applications Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9838: 246-256. DOI: 10.1007/978-3-319-43681-4_20 |
0.406 |
|
| 2015 |
Ip CL, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, et al. MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000research. 4: 1075. PMID 26834992 DOI: 10.12688/F1000Research.7201.1 |
0.575 |
|
| 2015 |
Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, et al. The UCSC Genome Browser database: 2016 update. Nucleic Acids Research. PMID 26590259 DOI: 10.1093/Nar/Gkv1275 |
0.59 |
|
| 2015 |
Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, ... ... Paten B, et al. The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery. Human Mutation. 36: 915-21. PMID 26295439 DOI: 10.1002/Humu.22858 |
0.354 |
|
| 2015 |
Novak AM, Rosen Y, Haussler D, Paten B. Canonical, stable, general mapping using context schemes. Bioinformatics (Oxford, England). 31: 3569-76. PMID 26220960 DOI: 10.1093/Bioinformatics/Btv435 |
0.426 |
|
| 2015 |
Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, James Kent W, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, et al. The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association : Jamia. PMID 26174866 DOI: 10.1093/Jamia/Ocv047 |
0.511 |
|
| 2015 |
Koepfli KP, Paten B, O'Brien SJ. The Genome 10K Project: a way forward. Annual Review of Animal Biosciences. 3: 57-111. PMID 25689317 DOI: 10.1146/Annurev-Animal-090414-014900 |
0.568 |
|
| 2015 |
Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M. Improved data analysis for the MinION nanopore sequencer. Nature Methods. 12: 351-6. PMID 25686389 DOI: 10.1038/Nmeth.3290 |
0.467 |
|
| 2015 |
Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Building a pan-genome reference for a population. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 387-401. PMID 25565268 DOI: 10.1089/Cmb.2014.0146 |
0.784 |
|
| 2015 |
Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, ... ... Paten B, et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Research. 43: D670-81. PMID 25428374 DOI: 10.1093/Nar/Gku1177 |
0.624 |
|
| 2015 |
Ballinger TJ, Zerbino D, Paten B, Haussler D. Abstract B1-11: Application of the CN-AVG method to reconstruct the evolutionary history of glioblastoma multiforme Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-11 |
0.738 |
|
| 2015 |
Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Building a pan-genome reference for a population Journal of Computational Biology. 22: 387-401. DOI: 10.1089/cmb.2014.0146 |
0.713 |
|
| 2014 |
Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, ... ... Paten B, et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science (New York, N.Y.). 346: 1254449. PMID 25504731 DOI: 10.1126/Science.1254449 |
0.576 |
|
| 2014 |
Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature. 516: 242-5. PMID 25274305 DOI: 10.1038/Nature13760 |
0.42 |
|
| 2014 |
Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, ... ... Paten B, et al. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Research. 24: 2077-89. PMID 25273068 DOI: 10.1101/Gr.174920.114 |
0.504 |
|
| 2014 |
Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. Comparative assembly hubs: web-accessible browsers for comparative genomics. Bioinformatics (Oxford, England). 30: 3293-301. PMID 25138168 DOI: 10.1093/Bioinformatics/Btu534 |
0.557 |
|
| 2014 |
Paten B, Zerbino DR, Hickey G, Haussler D. A unifying model of genome evolution under parsimony Bmc Bioinformatics. 15. PMID 24946830 DOI: 10.1186/1471-2105-15-206 |
0.75 |
|
| 2014 |
Kolmogorov M, Raney B, Paten B, Pham S. Ragout - A reference-assisted assembly tool for bacterial genomes Bioinformatics. 30: I302-I309. PMID 24931998 DOI: 10.1093/bioinformatics/btu280 |
0.525 |
|
| 2014 |
Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser Bioinformatics. 30: 1003-1005. PMID 24227676 DOI: 10.1093/Bioinformatics/Btt637 |
0.537 |
|
| 2014 |
Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. Comparative assembly hubs: Web-accessible browsers for comparative genomics Bioinformatics. 30: 3293-3301. DOI: 10.1093/bioinformatics/btu534 |
0.442 |
|
| 2014 |
Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Haussler D, Paten B. Building a pangenome reference for a population Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8394: 207-221. DOI: 10.1007/978-3-319-05269-4-17 |
0.574 |
|
| 2013 |
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, ... ... Paten B, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2: 10. PMID 23870653 DOI: 10.1186/2047-217X-2-10 |
0.716 |
|
| 2013 |
Hickey G, Paten B, Earl D, Zerbino D, Haussler D. HAL: A hierarchical format for storing and analyzing multiple genome alignments Bioinformatics. 29: 1341-1342. PMID 23505295 DOI: 10.1093/Bioinformatics/Btt128 |
0.787 |
|
| 2012 |
Westesson O, Lunter G, Paten B, Holmes I. Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. Plos One. 7: e34572. PMID 22536326 DOI: 10.1371/Journal.Pone.0034572 |
0.368 |
|
| 2012 |
Zerbino DR, Paten B, Haussler D. Integrating genomes Science. 336: 179-182. PMID 22499938 DOI: 10.1126/science.1216830 |
0.749 |
|
| 2011 |
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, ... ... Paten B, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21: 2224-41. PMID 21926179 DOI: 10.1101/Gr.126599.111 |
0.778 |
|
| 2011 |
Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: Algorithms for genome multiple sequence alignment Genome Research. 21: 1512-1528. PMID 21665927 DOI: 10.1101/Gr.123356.111 |
0.752 |
|
| 2011 |
Roskin KM, Paten B, Haussler D. Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization Bmc Bioinformatics. 12. PMID 21569267 DOI: 10.1186/1471-2105-12-144 |
0.353 |
|
| 2011 |
Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D. Cactus graphs for genome comparisons Journal of Computational Biology. 18: 469-481. PMID 21385048 DOI: 10.1089/Cmb.2010.0252 |
0.518 |
|
| 2010 |
Haudry Y, Ramialison M, Paten B, Wittbrodt J, Ettwiller L. Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation. Nature Protocols. 5: 323-34. PMID 20134431 DOI: 10.1038/Nprot.2009.158 |
0.704 |
|
| 2009 |
Paten B, Herrero J, Beal K, Birney E. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics (Oxford, England). 25: 295-301. PMID 19056777 DOI: 10.1093/Bioinformatics/Btn630 |
0.698 |
|
| 2008 |
Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Research. 18: 1829-43. PMID 18849525 DOI: 10.1101/Gr.076521.108 |
0.689 |
|
| 2008 |
Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Research. 18: 1814-28. PMID 18849524 DOI: 10.1101/Gr.076554.108 |
0.711 |
|
| 2007 |
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, ... ... Paten B, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/Nature06340 |
0.481 |
|
| 2007 |
Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J. Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nature Methods. 4: 563-5. PMID 17589518 DOI: 10.1038/Nmeth1061 |
0.705 |
|
| 2007 |
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Paten B, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874 |
0.688 |
|
| 2007 |
Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Paten B, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307 |
0.686 |
|
| 2005 |
Ettwiller L, Paten B, Souren M, Loosli F, Wittbrodt J, Birney E. The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biology. 6: R104. PMID 16356267 DOI: 10.1186/Gb-2005-6-12-R104 |
0.681 |
|
| 2004 |
Ettwiller L, Paten B. Guilt by multiple association Heredity. 92: 481-482. DOI: 10.1038/Sj.Hdy.6800452 |
0.754 |
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