| Year |
Citation |
Score |
| 2024 |
Henglin M, Ghareghani M, Harvey WT, Porubsky D, Koren S, Eichler EE, Ebert P, Marschall T. Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing. Genome Biology. 25: 265. PMID 39390579 DOI: 10.1186/s13059-024-03409-1 |
0.389 |
|
| 2024 |
Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D, Paisie CA, Harvey WT, Zhao X, Martino GV, Henglin M, ... ... Koren S, et al. Complex genetic variation in nearly complete human genomes. Biorxiv : the Preprint Server For Biology. PMID 39372794 DOI: 10.1101/2024.09.24.614721 |
0.486 |
|
| 2024 |
Olagunju TA, Rosen BD, Neibergs HL, Becker GM, Davenport KM, Elsik CG, Hadfield TS, Koren S, Kuhn KL, Rhie A, Shira KA, Skibiel AL, Stegemiller MR, Thorne JW, Villamediana P, et al. Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content. Nature Communications. 15: 8277. PMID 39333471 DOI: 10.1038/s41467-024-52384-5 |
0.358 |
|
| 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, ... ... Koren S, et al. Complete sequencing of ape genomes. Biorxiv : the Preprint Server For Biology. PMID 39131277 DOI: 10.1101/2024.07.31.605654 |
0.429 |
|
| 2024 |
Kalbfleisch TS, McKay SD, Murdoch BM, Adelson DL, Almansa-Villa D, Becker G, Beckett LM, Benítez-Galeano MJ, Biase F, Casey T, Chuong E, Clark E, Clarke S, Cockett N, Couldrey C, ... ... Koren S, et al. The Ruminant Telomere-to-Telomere (RT2T) Consortium. Nature Genetics. PMID 39103649 DOI: 10.1038/s41588-024-01835-2 |
0.432 |
|
| 2024 |
Luan T, Cepeda V, Liu B, Bowen Z, Ayyangar U, Almeida M, Hill CM, Koren S, Treangen TJ, Porter A, Pop M. MetaCompass: Reference-guided Assembly of Metagenomes. Arxiv. PMID 38903742 |
0.483 |
|
| 2024 |
Conlan S, Subramanian P, Plata Barril B, Youn J-H, Thomas PJ, Koren S, Dotson GA, Park M, Rhie A, Segre JA, Dekker JP, Zelazny AM. Whole-genome sequence of NIH1002, a strain associated with disseminated disease. Microbiology Resource Announcements. e0006224. PMID 38899875 DOI: 10.1128/mra.00062-24 |
0.505 |
|
| 2024 |
Fodor E, Okendo J, Szabó N, Szabó K, Czimer D, Tarján-Rácz A, Szeverényi I, Low BW, Liew JH, Koren S, Rhie A, Orbán L, Miklósi Á, Varga M, Burgess SM. The reference genome of Macropodus opercularis (the paradise fish). Scientific Data. 11: 540. PMID 38796485 DOI: 10.1038/s41597-024-03277-1 |
0.47 |
|
| 2024 |
Cheng H, Asri M, Lucas J, Koren S, Li H. Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nature Methods. PMID 38730258 DOI: 10.1038/s41592-024-02269-8 |
0.501 |
|
| 2024 |
Smith T, Olagunju T, Rosen B, Neibergs H, Becker G, Davenport K, Elsik C, Hadfield T, Koren S, Kuhn K, Rhie A, Shira K, Skibiel A, Stegemiller M, Thorne J, et al. The first complete T2T Assemblies of Cattle and Sheep Y-Chromosomes uncover remarkable divergence in structure and gene content. Research Square. PMID 38712074 DOI: 10.21203/rs.3.rs-4033388/v1 |
0.366 |
|
| 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, ... ... Koren S, et al. Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Genome Research. PMID 38627094 DOI: 10.1101/gr.278268.123 |
0.428 |
|
| 2024 |
Logsdon GA, Rozanski AN, Ryabov F, Potapova T, Shepelev VA, Catacchio CR, Porubsky D, Mao Y, Yoo D, Rautiainen M, Koren S, Nurk S, Lucas JK, Hoekzema K, Munson KM, et al. The variation and evolution of complete human centromeres. Nature. PMID 38570684 DOI: 10.1038/s41586-024-07278-3 |
0.445 |
|
| 2024 |
Henglin M, Ghareghani M, Harvey W, Porubsky D, Koren S, Eichler EE, Ebert P, Marschall T. Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing. Biorxiv : the Preprint Server For Biology. PMID 38529499 DOI: 10.1101/2024.02.15.580432 |
0.386 |
|
| 2024 |
Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautianinen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, et al. Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. Biorxiv : the Preprint Server For Biology. PMID 38529488 DOI: 10.1101/2024.03.15.585294 |
0.577 |
|
| 2023 |
Oppert B, Dossey AT, Chu FC, Šatović-Vukšić E, Plohl M, Smith TPL, Koren S, Olmstead ML, Leierer D, Ragan G, Johnston JS. The Genome of the Yellow Mealworm, : It's Bigger Than You Think. Genes. 14. PMID 38137031 DOI: 10.3390/genes14122209 |
0.377 |
|
| 2023 |
Chen NC, Paulin LF, Sedlazeck FJ, Koren S, Phillippy AM, Langmead B. Improved sequence mapping using a complete reference genome and lift-over. Nature Methods. PMID 38036856 DOI: 10.1038/s41592-023-02069-6 |
0.512 |
|
| 2023 |
Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, et al. The complete sequence of a human Y chromosome. Nature. PMID 37612512 DOI: 10.1038/s41586-023-06457-y |
0.431 |
|
| 2023 |
Fodor E, Okendo J, Szabó N, Szabó K, Czimer D, Tarján-Rácz A, Szeverényi I, Low BW, Liew JH, Koren S, Rhie A, Orbán L, Miklósi Á, Varga M, Burgess SM. The reference genome of the paradise fish ( ). Biorxiv : the Preprint Server For Biology. PMID 37609174 DOI: 10.1101/2023.08.10.552018 |
0.469 |
|
| 2023 |
Logsdon GA, Rozanski AN, Ryabov F, Potapova T, Shepelev VA, Mao Y, Rautiainen M, Koren S, Nurk S, Porubsky D, Lucas JK, Hoekzema K, Munson KM, Gerton JL, Phillippy AM, et al. The variation and evolution of complete human centromeres. Biorxiv : the Preprint Server For Biology. PMID 37398417 DOI: 10.1101/2023.05.30.542849 |
0.368 |
|
| 2023 |
Cheng H, Asri M, Lucas J, Koren S, Li H. Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Arxiv. PMID 37332563 |
0.495 |
|
| 2023 |
Dossey AT, Oppert B, Chu FC, Lorenzen MD, Scheffler B, Simpson S, Koren S, Johnston JS, Kataoka K, Ide K. Genome and Genetic Engineering of the House Cricket (): A Resource for Sustainable Agriculture. Biomolecules. 13. PMID 37189337 DOI: 10.3390/biom13040589 |
0.331 |
|
| 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, ... ... Koren S, et al. A draft human pangenome reference. Nature. 617: 312-324. PMID 37165242 DOI: 10.1038/s41586-023-05896-x |
0.406 |
|
| 2023 |
Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C, Gerton JL, Phillippy AM, Colonna V, Garrison E. Recombination between heterologous human acrocentric chromosomes. Nature. 617: 335-343. PMID 37165241 DOI: 10.1038/s41586-023-05976-y |
0.325 |
|
| 2023 |
Waldbieser GC, Liu S, Yuan Z, Older CE, Gao D, Shi C, Bosworth BG, Li N, Bao L, Kirby MA, Jin Y, Wood ML, Scheffler B, Simpson S, Youngblood RC, ... ... Koren S, et al. Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. Bmc Biology. 21: 67. PMID 37013528 DOI: 10.1186/s12915-023-01556-8 |
0.328 |
|
| 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, ... ... Koren S, 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 |
0.367 |
|
| 2023 |
Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nature Biotechnology. PMID 36797493 DOI: 10.1038/s41587-023-01662-6 |
0.494 |
|
| 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, ... ... Koren S, et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature. PMID 36261518 DOI: 10.1038/s41586-022-05325-5 |
0.541 |
|
| 2022 |
McGrath JM, Funk A, Galewski P, Ou S, Townsend B, Davenport K, Daligault H, Johnson S, Lee J, Hastie A, Darracq A, Willems G, Barnes S, Liachko I, Sullivan S, ... Koren S, et al. A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.). Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 36208288 DOI: 10.1093/dnares/dsac033 |
0.537 |
|
| 2022 |
Jain C, Rhie A, Hansen NF, Koren S, Phillippy AM. Long-read mapping to repetitive reference sequences using Winnowmap2. Nature Methods. PMID 35365778 DOI: 10.1038/s41592-022-01457-8 |
0.383 |
|
| 2022 |
Formenti G, Rhie A, Walenz BP, Thibaud-Nissen F, Shafin K, Koren S, Myers EW, Jarvis ED, Phillippy AM. Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation. Nature Methods. PMID 35361932 DOI: 10.1038/s41592-022-01445-y |
0.402 |
|
| 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 |
0.51 |
|
| 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, ... ... Koren S, 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 |
0.472 |
|
| 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, et al. The complete sequence of a human genome. Science (New York, N.Y.). 376: 44-53. PMID 35357919 DOI: 10.1126/science.abj6987 |
0.521 |
|
| 2022 |
Vollger MR, Guitart X, Dishuck PC, Mercuri L, Harvey WT, Gershman A, Diekhans M, Sulovari A, Munson KM, Lewis AP, Hoekzema K, Porubsky D, Li R, Nurk S, Koren S, et al. Segmental duplications and their variation in a complete human genome. Science (New York, N.Y.). 376: eabj6965. PMID 35357917 DOI: 10.1126/science.abj6965 |
0.481 |
|
| 2022 |
Gershman A, Sauria MEG, Guitart X, Vollger MR, Hook PW, Hoyt SJ, Jain M, Shumate A, Razaghi R, Koren S, Altemose N, Caldas GV, Logsdon GA, Rhie A, Eichler EE, et al. Epigenetic patterns in a complete human genome. Science (New York, N.Y.). 376: eabj5089. PMID 35357915 DOI: 10.1126/science.abj5089 |
0.431 |
|
| 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, ... ... Koren S, et al. Complete genomic and epigenetic maps of human centromeres. Science (New York, N.Y.). 376: eabl4178. PMID 35357911 DOI: 10.1126/science.abl4178 |
0.497 |
|
| 2022 |
Oppert B, Muszewska A, Steczkiewicz K, Šatović-Vukšić E, Plohl M, Fabrick JA, Vinokurov KS, Koloniuk I, Johnston JS, Smith TPL, Guedes RNC, Terra WR, Ferreira C, Dias RO, Chaply KA, ... ... Koren S, et al. The Genome of (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success. Genes. 13. PMID 35328000 DOI: 10.3390/genes13030446 |
0.469 |
|
| 2021 |
McCartney MA, Auch B, Kono T, Mallez S, Zhang Y, Obille A, Becker A, Abrahante JE, Garbe J, Badalamenti JP, Herman A, Mangelson H, Liachko I, Sullivan S, Sone ED, ... Koren S, et al. The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Comparative Genomics, Invasion Genetics, and Biocontrol. G3 (Bethesda, Md.). PMID 34897429 DOI: 10.1093/g3journal/jkab423 |
0.491 |
|
| 2021 |
Tan M, Redmond AK, Dooley H, Nozu R, Sato K, Kuraku S, Koren S, Phillippy AM, Dove AD, Read T. The whale shark genome reveals patterns of vertebrate gene family evolution. Elife. 10. PMID 34409936 DOI: 10.7554/eLife.65394 |
0.373 |
|
| 2021 |
Palatini U, Masri RA, Cosme LV, Koren S, Thibaud-Nissen F, Biedler JK, Krsticevic F, Johnston JS, Halbach R, Crawford JE, Antoshechkin I, Failloux AB, Pischedda E, Marconcini M, Ghurye J, et al. Author Correction: Improved reference genome of the arboviral vector Aedes albopictus. Genome Biology. 22: 205. PMID 34253230 DOI: 10.1186/s13059-021-02431-x |
0.403 |
|
| 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, 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 |
0.554 |
|
| 2021 |
Kronenberg ZN, Rhie A, Koren S, Concepcion GT, Peluso P, Munson KM, Porubsky D, Kuhn K, Mueller KA, Low WY, Hiendleder S, Fedrigo O, Liachko I, Hall RJ, Phillippy AM, et al. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nature Communications. 12: 1935. PMID 33911078 DOI: 10.1038/s41467-020-20536-y |
0.384 |
|
| 2021 |
Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R, Houde P, Koren S, Oliver K, Smith M, Skelton J, et al. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome Biology. 22: 120. PMID 33910595 DOI: 10.1186/s13059-021-02336-9 |
0.419 |
|
| 2021 |
Yang C, Zhou Y, Marcus S, Formenti G, Bergeron LA, Song Z, Bi X, Bergman J, Rousselle MMC, Zhou C, Zhou L, Deng Y, Fang M, Xie D, Zhu Y, ... ... Koren S, et al. Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature. PMID 33910227 DOI: 10.1038/s41586-021-03535-x |
0.484 |
|
| 2021 |
Logsdon GA, Vollger MR, Hsieh P, Mao Y, Liskovykh MA, Koren S, Nurk S, Mercuri L, Dishuck PC, Rhie A, de Lima LG, Dvorkina T, Porubsky D, Harvey WT, Mikheenko A, et al. The structure, function and evolution of a complete human chromosome 8. Nature. PMID 33828295 DOI: 10.1038/s41586-021-03420-7 |
0.402 |
|
| 2020 |
Rhie A, Walenz BP, Koren S, Phillippy AM. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology. 21: 245. PMID 32928274 DOI: 10.1186/S13059-020-02134-9 |
0.514 |
|
| 2020 |
Palatini U, Masri RA, Cosme LV, Koren S, Thibaud-Nissen F, Biedler JK, Krsticevic F, Johnston JS, Halbach R, Crawford JE, Antoshechkin I, Failloux AB, Pischedda E, Marconcini M, Ghurye J, et al. Improved reference genome of the arboviral vector Aedes albopictus. Genome Biology. 21: 215. PMID 32847630 DOI: 10.1186/S13059-020-02141-W |
0.452 |
|
| 2020 |
Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Research. PMID 32801147 DOI: 10.1101/Gr.263566.120 |
0.625 |
|
| 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, 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 |
0.624 |
|
| 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, et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. PMID 32663838 DOI: 10.1038/S41586-020-2547-7 |
0.533 |
|
| 2020 |
Jain C, Rhie A, Zhang H, Chu C, Walenz BP, Koren S, Phillippy AM. Weighted minimizer sampling improves long read mapping. Bioinformatics (Oxford, England). 36: i111-i118. PMID 32657365 DOI: 10.1093/Bioinformatics/Btaa435 |
0.532 |
|
| 2020 |
Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, ... ... Koren S, et al. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience. 9. PMID 32543654 DOI: 10.1093/Gigascience/Giaa051 |
0.563 |
|
| 2020 |
Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, et al. A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32541955 DOI: 10.1038/S41587-020-0538-8 |
0.55 |
|
| 2020 |
Ou S, Liu J, Chougule KM, Fungtammasan A, Seetharam AS, Stein JC, Llaca V, Manchanda N, Gilbert AM, Wei S, Chin CS, Hufnagel DE, Pedersen S, Snodgrass SJ, Fengler K, ... ... Koren S, et al. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications. 11: 2288. PMID 32385271 DOI: 10.1038/S41467-020-16037-7 |
0.593 |
|
| 2020 |
Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, et al. Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nature Communications. 11: 2071. PMID 32350247 DOI: 10.1038/S41467-020-15848-Y |
0.561 |
|
| 2020 |
Rice ES, Koren S, Rhie A, Heaton MP, Kalbfleisch TS, Hardy T, Hackett PH, Bickhart DM, Rosen BD, Ley BV, Maurer NW, Green RE, Phillippy AM, Petersen JL, Smith TPL. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. Gigascience. 9. PMID 32242610 DOI: 10.1093/Gigascience/Giaa029 |
0.573 |
|
| 2020 |
Rosen BD, Bickhart DM, Schnabel RD, Koren S, Elsik CG, Tseng E, Rowan TN, Low WY, Zimin A, Couldrey C, Hall R, Li W, Rhie A, Ghurye J, McKay SD, et al. De novo assembly of the cattle reference genome with single-molecule sequencing. Gigascience. 9. PMID 32191811 DOI: 10.1093/Gigascience/Giaa021 |
0.585 |
|
| 2020 |
Waterhouse RM, Aganezov S, Anselmetti Y, Lee J, Ruzzante L, Reijnders MJMF, Feron R, Bérard S, George P, Hahn MW, Howell PI, Kamali M, Koren S, Lawson D, Maslen G, et al. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies. Bmc Biology. 18: 1. PMID 31898513 DOI: 10.1186/S12915-019-0728-3 |
0.611 |
|
| 2019 |
Liu R, Low WY, Tearle R, Koren S, Ghurye J, Rhie A, Phillippy AM, Rosen BD, Bickhart DM, Smith TPL, Hiendleder S, Williams JL. New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes. Bmc Genomics. 20: 1000. PMID 31856728 DOI: 10.1186/S12864-019-6364-Z |
0.318 |
|
| 2019 |
Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM. Mash Screen: high-throughput sequence containment estimation for genome discovery. Genome Biology. 20: 232. PMID 31690338 DOI: 10.1186/S13059-019-1841-X |
0.558 |
|
| 2019 |
Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. Plos Computational Biology. 15: e1007273. PMID 31433799 DOI: 10.1371/Journal.Pcbi.1007273 |
0.503 |
|
| 2019 |
Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, ... ... Koren S, et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature Biotechnology. PMID 31406327 DOI: 10.1038/S41587-019-0217-9 |
0.575 |
|
| 2019 |
Bickhart DM, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, et al. Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome Biology. 20: 153. PMID 31375138 DOI: 10.1186/S13059-019-1760-X |
0.416 |
|
| 2019 |
Dilthey AT, Jain C, Koren S, Phillippy AM. Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps. Nature Communications. 10: 3066. PMID 31296857 DOI: 10.1038/S41467-019-10934-2 |
0.523 |
|
| 2019 |
Chen Z, Omori Y, Koren S, Shirokiya T, Kuroda T, Miyamoto A, Wada H, Fujiyama A, Toyoda A, Zhang S, Wolfsberg TG, Kawakami K, Phillippy AM, Mullikin JC, et al. De novo assembly of the goldfish () genome and the evolution of genes after whole-genome duplication. Science Advances. 5: eaav0547. PMID 31249862 DOI: 10.1126/Sciadv.Aav0547 |
0.562 |
|
| 2019 |
Ghurye J, Koren S, Small ST, Redmond S, Howell P, Phillippy AM, Besansky NJ. A chromosome-scale assembly of the major African malaria vector Anopheles funestus. Gigascience. 8. PMID 31157884 DOI: 10.1093/Gigascience/Giz063 |
0.411 |
|
| 2019 |
Dilthey AT, Mentzer AJ, Carapito R, Cutland C, Cereb N, Madhi SA, Rhie A, Koren S, Bahram S, McVean G, Phillippy AM. HLA*LA - HLA typing from linearly projected graph alignments. Bioinformatics (Oxford, England). PMID 30942877 DOI: 10.1093/Bioinformatics/Btz235 |
0.412 |
|
| 2019 |
Koren S, Phillippy AM, Simpson JT, Loman NJ, Loose M. Reply to 'Errors in long-read assemblies can critically affect protein prediction'. Nature Biotechnology. PMID 30670797 DOI: 10.1038/S41587-018-0005-Y |
0.315 |
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| 2018 |
Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, et al. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature. PMID 30429615 DOI: 10.1038/S41586-018-0692-Z |
0.499 |
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| 2018 |
Jain C, Koren S, Dilthey A, Phillippy AM, Aluru S. A fast adaptive algorithm for computing whole-genome homology maps. Bioinformatics (Oxford, England). 34: i748-i756. PMID 30423094 DOI: 10.1093/Bioinformatics/Bty597 |
0.531 |
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| 2018 |
Nasko DJ, Koren S, Phillippy AM, Treangen TJ. RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification. Genome Biology. 19: 165. PMID 30373669 DOI: 10.1186/S13059-018-1554-6 |
0.4 |
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| 2018 |
Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM. De novo assembly of haplotype-resolved genomes with trio binning. Nature Biotechnology. PMID 30346939 DOI: 10.1038/Nbt.4277 |
0.603 |
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| 2018 |
Kim JH, Dilthey AT, Nagaraja R, Lee HS, Koren S, Dudekula D, Wood Iii WH, Piao Y, Ogurtsov AY, Utani K, Noskov VN, Shabalina SA, Schlessinger D, Phillippy AM, Larionov V. Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing. Nucleic Acids Research. PMID 29788454 DOI: 10.1093/Nar/Gky442 |
0.516 |
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| 2018 |
Miller JR, Koren S, Dilley KA, Harkins DM, Stockwell TB, Shabman RS, Sutton GG. A draft genome sequence for the cell line, ISE6. F1000research. 7: 297. PMID 29707202 DOI: 10.12688/F1000Research.13635.1 |
0.608 |
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| 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, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology. PMID 29431738 DOI: 10.1038/Nbt.4060 |
0.622 |
|
| 2018 |
Miller JR, Koren S, Dilley KA, Puri V, Brown DM, Harkins DM, Thibaud-Nissen F, Rosen B, Chen XG, Tu Z, Sharakhov IV, Sharakhova MV, Sebra R, Stockwell TB, Bergman NH, et al. Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation. Gigascience. PMID 29329394 DOI: 10.1093/Gigascience/Gix135 |
0.382 |
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| 2018 |
Eccles D, Chandler J, Camberis M, Henrissat B, Koren S, Le Gros G, Ewbank JJ. De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads. Bmc Biology. 16: 6. PMID 29325570 DOI: 10.1186/S12915-017-0473-4 |
0.576 |
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| 2017 |
Schmidt MH, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat RT, Maumus F, Aury JM, Koren S, et al. De novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing. The Plant Cell. PMID 29025960 DOI: 10.1105/Tpc.17.00521 |
0.606 |
|
| 2017 |
Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Briefings in Bioinformatics. PMID 28968737 DOI: 10.1093/Bib/Bbx098 |
0.585 |
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| 2017 |
Venkateswaran K, Checinska Sielaff A, Ratnayake S, Pope RK, Blank TE, Stepanov VG, Fox GE, van Tongeren SP, Torres C, Allen J, Jaing C, Pierson D, Perry J, Koren S, Phillippy A, et al. Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station. Genome Announcements. 5. PMID 28798168 DOI: 10.1128/Genomea.00680-17 |
0.353 |
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| 2017 |
Ghurye J, Pop M, Koren S, Bickhart D, Chin CS. Scaffolding of long read assemblies using long range contact information. Bmc Genomics. 18: 527. PMID 28701198 DOI: 10.1186/S12864-017-3879-Z |
0.475 |
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| 2017 |
Wilson WH, Gilg IC, Moniruzzaman M, Field EK, Koren S, LeCleir GR, Martínez Martínez J, Poulton NJ, Swan BK, Stepanauskas R, Wilhelm SW. Genomic exploration of individual giant ocean viruses. The Isme Journal. PMID 28498373 DOI: 10.1038/Ismej.2017.61 |
0.424 |
|
| 2017 |
Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, ... ... Koren S, et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Research. PMID 28396521 DOI: 10.1101/Gr.213611.116 |
0.617 |
|
| 2017 |
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research. PMID 28298431 DOI: 10.1101/Gr.215087.116 |
0.607 |
|
| 2017 |
Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, Lee J, Lam ET, Liachko I, Sullivan ST, Burton JN, Huson HJ, Nystrom JC, Kelley CM, Hutchison JL, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nature Genetics. PMID 28263316 DOI: 10.1038/Ng.3802 |
0.57 |
|
| 2017 |
Schwartz JC, Gibson MS, Heimeier D, Koren S, Phillippy AM, Bickhart DM, Smith TP, Medrano JF, Hammond JA. The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation. Immunogenetics. PMID 28180967 DOI: 10.1007/S00251-017-0973-Y |
0.44 |
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| 2017 |
Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marcais G, Yorke JA, Dvorak J, Salzberg SL. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm. Genome Research. PMID 28130360 DOI: 10.1101/Gr.213405.116 |
0.583 |
|
| 2017 |
Ghurye J, Pop M, Koren S, Bickhart D, Chin C. Chromosome scale de novo assembly of genomes using chromatin interaction data F1000research. 6. DOI: 10.7490/F1000Research.1114160.1 |
0.473 |
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| 2017 |
Olson ND, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Treangen TJ, Pop M. Metagenomic assembly through the lens of validation: a review of recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes. Briefings in Bioinformatics. DOI: 10.1002/Https://Doi.Org/10.1093/Bib/Bbx098 |
0.5 |
|
| 2016 |
Davison M, Treangen TJ, Koren S, Pop M, Bhaya D. Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers. Plos One. 11: e0160574. PMID 27611571 DOI: 10.1371/Journal.Pone.0160574 |
0.409 |
|
| 2016 |
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology. 17: 132. PMID 27323842 DOI: 10.1186/S13059-016-0997-X |
0.447 |
|
| 2016 |
Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Wang R, Zhang Y, Zhou T, Zeng Q, Fu Q, Gao S, Li N, ... Koren S, et al. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature Communications. 7: 11757. PMID 27249958 DOI: 10.1038/Ncomms11757 |
0.542 |
|
| 2016 |
Hall AB, Papathanos PA, Sharma A, Cheng C, Akbari OS, Assour L, Bergman NH, Cagnetti A, Crisanti A, Dottorini T, Fiorentini E, Galizi R, Hnath J, Jiang X, Koren S, et al. Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. Proceedings of the National Academy of Sciences of the United States of America. PMID 27035980 DOI: 10.1073/Pnas.1525164113 |
0.417 |
|
| 2016 |
Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, et al. Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nature Communications. 7: 10507. PMID 26856261 DOI: 10.1038/Ncomms10507 |
0.439 |
|
| 2015 |
Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. Corrigendum: Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature Biotechnology. 33: 1109. PMID 26448093 DOI: 10.1038/Nbt1015-1109C |
0.416 |
|
| 2015 |
Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature Biotechnology. 33: 623-30. PMID 26006009 DOI: 10.1038/Nbt.3238 |
0.637 |
|
| 2015 |
Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, Sullivan MB, Woyke T, Eric Wommack K, Stepanauskas R. Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. The Isme Journal. PMID 25848873 DOI: 10.1038/Ismej.2015.48 |
0.453 |
|
| 2015 |
Johnson SL, Baker AL, Chain PS, Currie BJ, Daligault HE, Davenport KW, Davis CB, Inglis TJ, Kaestli M, Koren S, Mayo M, Merritt AJ, Price EP, Sarovich DS, Warner J, et al. Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia pseudomallei. Genome Announcements. 3. PMID 25676747 DOI: 10.1128/Genomea.01282-14 |
0.505 |
|
| 2015 |
Koren S, Phillippy AM. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Current Opinion in Microbiology. 23: 110-20. PMID 25461581 DOI: 10.1016/J.Mib.2014.11.014 |
0.623 |
|
| 2014 |
Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology. 15: 524. PMID 25410596 DOI: 10.1186/S13059-014-0524-X |
0.585 |
|
| 2014 |
Treangen TJ, Maybank RA, Enke S, Friss MB, Diviak LF, Karaolis DK, Koren S, Ondov B, Phillippy AM, Bergman NH, Rosovitz MJ. Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923. Genome Announcements. 2. PMID 25377701 DOI: 10.1128/Genomea.01110-14 |
0.419 |
|
| 2014 |
Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, Xiong Y, Zhang Y, Zhou S, Schwartz DC, Schatz M, Aboukhalil R, Fedrigo O, Bukovnik L, Wang T, ... ... Koren S, et al. High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience. 3: 11. PMID 25061512 DOI: 10.1186/2047-217X-3-11 |
0.536 |
|
| 2014 |
Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. Automated ensemble assembly and validation of microbial genomes. Bmc Bioinformatics. 15: 126. PMID 24884846 DOI: 10.1186/1471-2105-15-126 |
0.617 |
|
| 2014 |
Swan BK, Chaffin MD, Martinez-Garcia M, Morrison HG, Field EK, Poulton NJ, Masland ED, Harris CC, Sczyrba A, Chain PS, Koren S, Woyke T, Stepanauskas R. Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. Plos One. 9: e95380. PMID 24743558 DOI: 10.1371/Journal.Pone.0095380 |
0.436 |
|
| 2014 |
Harhay GP, Murray RW, Lubbers B, Griffin D, Koren S, Phillippy AM, Harhay DM, Bono J, Clawson ML, Heaton MP, Chitko-McKown CG, Smith TP. Complete Closed Genome Sequences of Four Mannheimia varigena Isolates from Cattle with Shipping Fever. Genome Announcements. 2. PMID 24526648 DOI: 10.1128/Genomea.00088-14 |
0.57 |
|
| 2014 |
Harhay GP, McVey DS, Koren S, Phillippy AM, Bono J, Harhay DM, Clawson ML, Heaton MP, Chitko-McKown CG, Korlach J, Smith TP. Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever. Genome Announcements. 2. PMID 24526647 DOI: 10.1128/Genomea.00084-14 |
0.536 |
|
| 2013 |
Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology. 14: R101. PMID 24034426 DOI: 10.1186/Gb-2013-14-9-R101 |
0.591 |
|
| 2013 |
Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M. De novo likelihood-based measures for comparing genome assemblies. Bmc Research Notes. 6: 334. PMID 23965294 DOI: 10.1186/1756-0500-6-334 |
0.634 |
|
| 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, ... ... Koren S, 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 |
0.638 |
|
| 2013 |
Harhay GP, Koren S, Phillippy AM, McVey DS, Kuszak J, Clawson ML, Harhay DM, Heaton MP, Chitko-McKown CG, Smith TP. Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle. Genome Announcements. 1. PMID 23682137 DOI: 10.1128/Genomea.00188-13 |
0.49 |
|
| 2013 |
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biology. 14: R2. PMID 23320958 DOI: 10.1186/Gb-2013-14-1-R2 |
0.548 |
|
| 2013 |
Vacek G, Hornung B, Bolding J, Koren S. Accelerating error correction and assembly of single-molecule sequencing reads F1000research. 4. DOI: 10.7490/F1000Research.1093938.1 |
0.439 |
|
| 2012 |
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Adam M Phillippy. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology. 30: 693-700. PMID 22750884 DOI: 10.1038/Nbt.2280 |
0.59 |
|
| 2012 |
Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, et al. The bonobo genome compared with the chimpanzee and human genomes. Nature. 486: 527-31. PMID 22722832 DOI: 10.1038/Nature11128 |
0.522 |
|
| 2012 |
Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research. 22: 557-67. PMID 22147368 DOI: 10.1101/Gr.131383.111 |
0.639 |
|
| 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, ... ... Koren S, 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 |
0.59 |
|
| 2011 |
Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics (Oxford, England). 27: 2964-71. PMID 21926123 DOI: 10.1093/Bioinformatics/Btr520 |
0.423 |
|
| 2011 |
Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M. Next generation sequence assembly with AMOS. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 11.8. PMID 21400694 DOI: 10.1002/0471250953.Bi1108S33 |
0.554 |
|
| 2011 |
Koren S, Treangen T, Pop M. ScaffViz: visualizing metagenome assemblies Genome Biology. 12: P8. DOI: 10.1186/Gb-2011-12-S1-P8 |
0.302 |
|
| 2011 |
Treangen TJ, Koren S, Astrovskaya I, Sommer D, Liu B, Pop M. MetAMOS: a metagenomic assembly and analysis pipeline for AMOS Genome Biology. 12: P25. DOI: 10.1186/Gb-2011-12-S1-P25 |
0.412 |
|
| 2010 |
Koren S, Miller JR, Walenz BP, Sutton G. An algorithm for automated closure during assembly. Bmc Bioinformatics. 11: 457. PMID 20831800 DOI: 10.1186/1471-2105-11-457 |
0.542 |
|
| 2010 |
Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 95: 315-27. PMID 20211242 DOI: 10.1016/J.Ygeno.2010.03.001 |
0.545 |
|
| 2009 |
Rausch T, Koren S, Denisov G, Weese D, Emde AK, Döring A, Reinert K. A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics (Oxford, England). 25: 1118-24. PMID 19269990 DOI: 10.1093/Bioinformatics/Btp131 |
0.521 |
|
| 2008 |
Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics (Oxford, England). 24: 2818-24. PMID 18952627 DOI: 10.1093/Bioinformatics/Btn548 |
0.565 |
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