| Year |
Citation |
Score |
| 2024 |
Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautiainen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, ... ... Phillippy AM, et al. Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. Genome Research. PMID 39505490 DOI: 10.1101/gr.279334.124 |
0.718 |
|
| 2024 |
Gomes de Lima L, Guarracino A, Koren S, Potapova T, McKinney S, Rhie A, Solar SJ, Seidel C, Fagen B, Walenz BP, Bouffard GG, Brooks SY, Peterson M, Hall K, Crawford J, ... ... Phillippy AM, et al. The formation and propagation of human Robertsonian chromosomes. Biorxiv : the Preprint Server For Biology. PMID 39386535 DOI: 10.1101/2024.09.24.614821 |
0.305 |
|
| 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, ... ... Phillippy AM, 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 |
0.508 |
|
| 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, ... ... Phillippy AM, et al. Complete sequencing of ape genomes. Biorxiv : the Preprint Server For Biology. PMID 39131277 DOI: 10.1101/2024.07.31.605654 |
0.783 |
|
| 2024 |
Sweeten AP, Schatz MC, Phillippy AM. ModDotPlot-rapid and interactive visualization of tandem repeats. Bioinformatics (Oxford, England). 40. PMID 39110522 DOI: 10.1093/bioinformatics/btae493 |
0.577 |
|
| 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, ... ... Phillippy AM, et al. The Ruminant Telomere-to-Telomere (RT2T) Consortium. Nature Genetics. PMID 39103649 DOI: 10.1038/s41588-024-01835-2 |
0.461 |
|
| 2024 |
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, ... ... Phillippy AM, et al. The complete sequence and comparative analysis of ape sex chromosomes. Nature. PMID 38811727 DOI: 10.1038/s41586-024-07473-2 |
0.466 |
|
| 2024 |
Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ. Parsnp 2.0: Scalable Core-Genome alignment for massive microbial datasets. Bioinformatics (Oxford, England). PMID 38724243 DOI: 10.1093/bioinformatics/btae311 |
0.76 |
|
| 2024 |
Sweeten AP, Schatz MC, Phillippy AM. ModDotPlot-Rapid and interactive visualization of complex repeats. Biorxiv : the Preprint Server For Biology. PMID 38712106 DOI: 10.1101/2024.04.15.589623 |
0.578 |
|
| 2024 |
Zhang S, Xu N, Fu L, Yang X, Li Y, Yang Z, Feng Y, Ma K, Jiang X, Han J, Hu R, Zhang L, de Gennaro L, Ryabov F, Meng D, ... ... Phillippy AM, et al. Comparative genomics of macaques and integrated insights into genetic variation and population history. Biorxiv : the Preprint Server For Biology. PMID 38645259 DOI: 10.1101/2024.04.07.588379 |
0.367 |
|
| 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, ... ... Phillippy AM, et al. The variation and evolution of complete human centromeres. Nature. PMID 38570684 DOI: 10.1038/s41586-024-07278-3 |
0.476 |
|
| 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, ... ... Phillippy AM, 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 |
0.718 |
|
| 2024 |
Bukhman YV, Morin PA, Meyer S, Chu LF, Jacobsen JK, Antosiewicz-Bourget J, Mamott D, Gonzales M, Argus C, Bolin J, Berres ME, Fedrigo O, Steill J, Swanson SA, Jiang P, ... ... Phillippy AM, et al. A high-quality blue whale genome, segmental duplications, and historical demography. Molecular Biology and Evolution. PMID 38376487 DOI: 10.1093/molbev/msae036 |
0.54 |
|
| 2024 |
Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ. Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets. Biorxiv : the Preprint Server For Biology. PMID 38352342 DOI: 10.1101/2024.01.30.577458 |
0.76 |
|
| 2024 |
Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Antunes A, Balacco JR, Chaisson MJP, Cheng H, Collins J, ... ... Phillippy AM, et al. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology. PMID 38278971 DOI: 10.1038/s41587-023-02100-3 |
0.605 |
|
| 2024 |
Benoit G, Raguideau S, James R, Phillippy AM, Chikhi R, Quince C. High-quality metagenome assembly from long accurate reads with metaMDBG. Nature Biotechnology. PMID 38168989 DOI: 10.1038/s41587-023-01983-6 |
0.477 |
|
| 2023 |
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, ... ... Phillippy AM, et al. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. Biorxiv : the Preprint Server For Biology. PMID 38077089 DOI: 10.1101/2023.11.30.569198 |
0.489 |
|
| 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 |
0.761 |
|
| 2023 |
Benoit G, Raguideau S, James R, Phillippy AM, Chikhi R, Quince C. Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs. Biorxiv : the Preprint Server For Biology. PMID 37786716 DOI: 10.1101/2023.07.07.548136 |
0.366 |
|
| 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, ... ... Phillippy AM, 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 |
0.392 |
|
| 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, ... ... Phillippy AM, et al. The complete sequence of a human Y chromosome. Nature. PMID 37612512 DOI: 10.1038/s41586-023-06457-y |
0.715 |
|
| 2023 |
Kille B, Garrison E, Treangen TJ, Phillippy AM. Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation. Bioinformatics (Oxford, England). 39. PMID 37603771 DOI: 10.1093/bioinformatics/btad512 |
0.613 |
|
| 2023 |
Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Balacco JR, Chaisson M, Cheng H, Collins J, Denisova A, ... ... Phillippy AM, et al. Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy. Biorxiv : the Preprint Server For Biology. PMID 37425881 DOI: 10.1101/2023.06.28.546576 |
0.676 |
|
| 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 |
0.399 |
|
| 2023 |
Kille B, Garrison E, Treangen TJ, Phillippy AM. Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation. Biorxiv : the Preprint Server For Biology. PMID 37325780 DOI: 10.1101/2023.05.16.540882 |
0.615 |
|
| 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, ... ... Phillippy AM, 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 |
0.341 |
|
| 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, ... ... Phillippy A, 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 |
0.371 |
|
| 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 |
0.498 |
|
| 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, ... ... Phillippy AM, 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 |
0.467 |
|
| 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, ... ... Phillippy AM, et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature. PMID 36261518 DOI: 10.1038/s41586-022-05325-5 |
0.766 |
|
| 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, ... ... Phillippy A, 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 |
0.577 |
|
| 2022 |
Kim J, Lee C, Ko BJ, Yoo DA, Won S, Phillippy AM, Fedrigo O, Zhang G, Howe K, Wood J, Durbin R, Formenti G, Brown S, Cantin L, Mello CV, et al. False gene and chromosome losses in genome assemblies caused by GC content variation and repeats. Genome Biology. 23: 204. PMID 36167554 DOI: 10.1186/s13059-022-02765-0 |
0.542 |
|
| 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, 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 |
0.521 |
|
| 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 |
0.387 |
|
| 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 |
0.395 |
|
| 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, ... ... Phillippy AM, 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 |
0.512 |
|
| 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, ... ... Phillippy AM, 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 |
0.653 |
|
| 2022 |
Hoyt SJ, Storer JM, Hartley GA, Grady PGS, Gershman A, de Lima LG, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Rhie A, Core LJ, Gerton JL, Makalowski W, ... ... Phillippy AM, et al. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science (New York, N.Y.). 376: eabk3112. PMID 35357925 DOI: 10.1126/science.abk3112 |
0.653 |
|
| 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, ... ... Phillippy AM, et al. The complete sequence of a human genome. Science (New York, N.Y.). 376: 44-53. PMID 35357919 DOI: 10.1126/science.abj6987 |
0.774 |
|
| 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, ... ... Phillippy AM, 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 |
0.538 |
|
| 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, ... ... Phillippy AM, et al. Epigenetic patterns in a complete human genome. Science (New York, N.Y.). 376: eabj5089. PMID 35357915 DOI: 10.1126/science.abj5089 |
0.635 |
|
| 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, ... ... Phillippy AM, et al. Complete genomic and epigenetic maps of human centromeres. Science (New York, N.Y.). 376: eabl4178. PMID 35357911 DOI: 10.1126/science.abl4178 |
0.675 |
|
| 2022 |
Mc Cartney AM, Anderson J, Liggins L, Hudson ML, Anderson MZ, TeAika B, Geary J, Cook-Deegan R, Patel HR, Phillippy AM. Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35042810 DOI: 10.1073/pnas.2115860119 |
0.304 |
|
| 2022 |
Lawniczak MKN, Durbin R, Flicek P, Lindblad-Toh K, Wei X, Archibald JM, Baker WJ, Belov K, Blaxter ML, Marques Bonet T, Childers AK, Coddington JA, Crandall KA, Crawford AJ, Davey RP, ... ... Phillippy AM, et al. Standards recommendations for the Earth BioGenome Project. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35042802 DOI: 10.1073/pnas.2115639118 |
0.321 |
|
| 2022 |
Vollger MR, Kerpedjiev P, Phillippy AM, Eichler EE. StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps. Bioinformatics (Oxford, England). PMID 35020798 DOI: 10.1093/bioinformatics/btac018 |
0.402 |
|
| 2021 |
Dussex N, van der Valk T, Morales HE, Wheat CW, Díez-Del-Molino D, von Seth J, Foster Y, Kutschera VE, Guschanski K, Rhie A, Phillippy AM, Korlach J, Howe K, Chow W, Pelan S, et al. Population genomics of the critically endangered kākāpō. Cell Genomics. 1: 100002. PMID 36777713 DOI: 10.1016/j.xgen.2021.100002 |
0.429 |
|
| 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 |
0.424 |
|
| 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, ... ... Phillippy AM, 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 |
0.445 |
|
| 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, ... ... Phillippy AM, 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 |
0.597 |
|
| 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 |
0.396 |
|
| 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, ... ... Phillippy AM, et al. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome Biology. 22: 120. PMID 33910595 DOI: 10.1186/s13059-021-02336-9 |
0.429 |
|
| 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, ... ... Phillippy AM, et al. Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature. PMID 33910227 DOI: 10.1038/s41586-021-03535-x |
0.528 |
|
| 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, ... ... Phillippy AM, et al. The structure, function and evolution of a complete human chromosome 8. Nature. PMID 33828295 DOI: 10.1038/s41586-021-03420-7 |
0.414 |
|
| 2021 |
Kim JH, Noskov VN, Ogurtsov AY, Nagaraja R, Petrov N, Liskovykh M, Walenz BP, Lee HS, Kouprina N, Phillippy AM, Shabalina SA, Schlessinger D, Larionov V. The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning. Scientific Reports. 11: 2997. PMID 33542373 DOI: 10.1038/s41598-021-82565-x |
0.433 |
|
| 2021 |
Zhou Y, Shearwin-Whyatt L, Li J, Song Z, Hayakawa T, Stevens D, Fenelon JC, Peel E, Cheng Y, Pajpach F, Bradley N, Suzuki H, Nikaido M, Damas J, Daish T, ... ... Phillippy AM, et al. Platypus and echidna genomes reveal mammalian biology and evolution. Nature. PMID 33408411 DOI: 10.1038/s41586-020-03039-0 |
0.523 |
|
| 2020 |
Green ED, Gunter C, Biesecker LG, Di Francesco V, Easter CL, Feingold EA, Felsenfeld AL, Kaufman DJ, Ostrander EA, Pavan WJ, Phillippy AM, Wise AL, Dayal JG, Kish BJ, Mandich A, et al. Strategic vision for improving human health at The Forefront of Genomics. Nature. 586: 683-692. PMID 33116284 DOI: 10.1038/s41586-020-2817-4 |
0.488 |
|
| 2020 |
Morin PA, Archer FI, Avila CD, Balacco JR, Bukhman YV, Chow W, Fedrigo O, Formenti G, Fronczek JA, Fungtammasan A, Gulland FMD, Haase B, Heide-Jorgensen MP, Houck ML, Howe K, ... ... Phillippy A, et al. Reference genome and demographic history of the most endangered marine mammal, the vaquita. Molecular Ecology Resources. PMID 33089966 DOI: 10.1111/1755-0998.13284 |
0.494 |
|
| 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 |
0.443 |
|
| 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, ... ... Phillippy AM, et al. Improved reference genome of the arboviral vector Aedes albopictus. Genome Biology. 21: 215. PMID 32847630 DOI: 10.1186/S13059-020-02141-W |
0.385 |
|
| 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 |
0.566 |
|
| 2020 |
Scott MJ, Benoit JB, Davis RJ, Bailey ST, Varga V, Martinson EO, Hickner PV, Syed Z, Cardoso GA, Torres TT, Weirauch MT, Scholl EH, Phillippy AM, Sagel A, Vasquez M, et al. Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs. Communications Biology. 3: 424. PMID 32753684 DOI: 10.1038/s42003-020-01152-4 |
0.381 |
|
| 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. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32699374 DOI: 10.1038/S41587-020-0640-Y |
0.366 |
|
| 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, ... ... Phillippy A, 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 |
0.645 |
|
| 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, ... ... Phillippy AM, et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. PMID 32663838 DOI: 10.1038/S41586-020-2547-7 |
0.485 |
|
| 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 |
0.496 |
|
| 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, ... ... Phillippy AM, et al. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience. 9. PMID 32543654 DOI: 10.1093/Gigascience/Giaa051 |
0.537 |
|
| 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 |
0.653 |
|
| 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, ... ... Phillippy AM, 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 |
0.521 |
|
| 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, ... ... Phillippy AM, 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 |
0.54 |
|
| 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 |
0.54 |
|
| 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, ... ... Phillippy AM, et al. De novo assembly of the cattle reference genome with single-molecule sequencing. Gigascience. 9. PMID 32191811 DOI: 10.1093/Gigascience/Giaa021 |
0.563 |
|
| 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, ... ... Phillippy AM, 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 |
0.577 |
|
| 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 |
0.548 |
|
| 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 |
0.42 |
|
| 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, ... Phillippy AM, 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 |
0.651 |
|
| 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 |
0.466 |
|
| 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 |
0.539 |
|
| 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 |
0.314 |
|
| 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 |
0.337 |
|
| 2018 |
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature Communications. 9: 5114. PMID 30504855 DOI: 10.1038/S41467-018-07641-9 |
0.564 |
|
| 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, ... ... Phillippy AM, et al. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature. PMID 30429615 DOI: 10.1038/S41586-018-0692-Z |
0.433 |
|
| 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 |
0.513 |
|
| 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 |
0.642 |
|
| 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 |
0.557 |
|
| 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 |
0.454 |
|
| 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, ... ... Phillippy AM, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology. PMID 29431738 DOI: 10.1038/Nbt.4060 |
0.55 |
|
| 2018 |
Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome alignment system. Plos Computational Biology. 14: e1005944. PMID 29373581 DOI: 10.1371/Journal.Pcbi.1005944 |
0.746 |
|
| 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 |
0.737 |
|
| 2017 |
Phillippy AM. New advances in sequence assembly. Genome Research. 27: xi-xiii. PMID 28461322 DOI: 10.1101/gr.223057.117 |
0.396 |
|
| 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, ... ... Phillippy AM, 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 |
0.557 |
|
| 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 |
0.524 |
|
| 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, ... ... Phillippy AM, 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 |
0.465 |
|
| 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 |
0.352 |
|
| 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 |
0.679 |
|
| 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, ... ... Phillippy AM, 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 |
0.524 |
|
| 2016 |
Treangen TJ, Schoeler G, Phillippy AM, Bergman NH, Turell MJ. Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru. Plos Neglected Tropical Diseases. 10: e0004440. PMID 27074162 DOI: 10.1371/Journal.Pntd.0004440 |
0.641 |
|
| 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, ... ... Phillippy AM, 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 |
0.33 |
|
| 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 |
0.314 |
|
| 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 |
0.581 |
|
| 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 |
0.58 |
|
| 2014 |
Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DE, Celniker SE, Phillippy AM, Bergman CM, Landolin JM. Long-read, whole-genome shotgun sequence data for five model organisms. Scientific Data. 1: 140045. PMID 25977796 DOI: 10.1038/Sdata.2014.45 |
0.549 |
|
| 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 |
0.78 |
|
| 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 |
0.678 |
|
| 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, ... ... Phillippy AM, et al. High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience. 3: 11. PMID 25061512 DOI: 10.1186/2047-217X-3-11 |
0.642 |
|
| 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 |
0.775 |
|
| 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 |
0.567 |
|
| 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 |
0.501 |
|
| 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 |
0.53 |
|
| 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, ... ... Phillippy AM, 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 |
0.815 |
|
| 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 |
0.437 |
|
| 2013 |
Harrington R, Ondov BD, Radune D, Friss MB, Klubnik J, Diviak L, Hnath J, Cendrowski SR, Blank TE, Karaolis D, Friedlander AM, Burans JP, Rosovitz MJ, Treangen T, Phillippy AM, et al. Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis. Genome Announcements. 1. PMID 23405332 DOI: 10.1128/Genomea.00067-12 |
0.721 |
|
| 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 |
0.713 |
|
| 2013 |
Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings in Bioinformatics. 14: 213-24. PMID 22199379 DOI: 10.1093/Bib/Bbr074 |
0.771 |
|
| 2012 |
Schatz MC, Phillippy AM. The rise of a digital immune system. Gigascience. 1: 4. PMID 23587178 DOI: 10.1186/2047-217X-1-4 |
0.422 |
|
| 2012 |
Treangen TJ, Phillippy AM. Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone. Genome Biology. 13: 181. PMID 23270611 DOI: 10.1186/gb-2012-13-12-181 |
0.619 |
|
| 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 |
0.839 |
|
| 2011 |
Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW. Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proceedings of the National Academy of Sciences of the United States of America. 108: E1423-32. PMID 22123943 DOI: 10.1073/Pnas.1111712108 |
0.507 |
|
| 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, ... ... Phillippy AM, 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 |
0.806 |
|
| 2011 |
Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, et al. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology. 193: 5450-64. PMID 21784931 DOI: 10.1128/Jb.05262-11 |
0.796 |
|
| 2011 |
Sahl JW, Johnson JK, Harris AD, Phillippy AM, Hsiao WW, Thom KA, Rasko DA. Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity. Bmc Genomics. 12: 291. PMID 21639920 DOI: 10.1186/1471-2164-12-291 |
0.343 |
|
| 2011 |
Rasko DA, Worsham PL, Abshire TG, Stanley ST, Bannan JD, Wilson MR, Langham RJ, Decker RS, Jiang L, Read TD, Phillippy AM, Salzberg SL, Pop M, Van Ert MN, Kenefic LJ, et al. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of Sciences of the United States of America. 108: 5027-32. PMID 21383169 DOI: 10.1073/Pnas.1016657108 |
0.688 |
|
| 2010 |
Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W. Probing the pan-genome of Listeria monocytogenes: New insights into intraspecific niche expansion and genomic diversification Bmc Genomics. 11. PMID 20846431 DOI: 10.1186/1471-2164-11-500 |
0.671 |
|
| 2010 |
Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL, Ravel J. Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray. Applied and Environmental Microbiology. 76: 5636-8. PMID 20581189 DOI: 10.1128/Aem.00303-10 |
0.396 |
|
| 2009 |
Phillippy AM, Deng X, Zhang W, Salzberg SL. Efficient oligonucleotide probe selection for pan-genomic tiling arrays Bmc Bioinformatics. 10: 293. PMID 19758451 DOI: 10.1186/1471-2105-10-293 |
0.722 |
|
| 2009 |
Phillippy AM, Ayanbule K, Edwards NJ, Salzberg SL. Insignia: a DNA signature search web server for diagnostic assay development. Nucleic Acids Research. 37: W229-34. PMID 19417071 DOI: 10.1093/Nar/Gkp286 |
0.638 |
|
| 2008 |
Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. Bmc Genomics. 9: 204. PMID 18452608 DOI: 10.1186/1471-2164-9-204 |
0.817 |
|
| 2008 |
Phillippy AM, Schatz MC, Pop M. Genome assembly forensics: finding the elusive mis-assembly. Genome Biology. 9: R55. PMID 18341692 DOI: 10.1186/Gb-2008-9-3-R55 |
0.658 |
|
| 2007 |
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Phillippy AM, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341 |
0.742 |
|
| 2007 |
Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL. Comprehensive DNA signature discovery and validation. Plos Computational Biology. 3: e98. PMID 17511514 DOI: 10.1371/Journal.Pcbi.0030098 |
0.687 |
|
| 2007 |
Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL. Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biology. 8: R34. PMID 17349036 DOI: 10.1186/Gb-2007-8-3-R34 |
0.75 |
|
| 2005 |
Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, et al. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science (New York, N.Y.). 307: 105-8. PMID 15637277 DOI: 10.1126/Science.1102226 |
0.404 |
|
| 2004 |
Pop M, Phillippy A, Delcher AL, Salzberg SL. Comparative genome assembly. Briefings in Bioinformatics. 5: 237-48. PMID 15383210 DOI: 10.1093/Bib/5.3.237 |
0.773 |
|
| 2004 |
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biology. 5: R12. PMID 14759262 DOI: 10.1186/Gb-2004-5-2-R12 |
0.688 |
|
| 2003 |
Delcher AL, Salzberg SL, Phillippy AM. Using MUMmer to identify similar regions in large sequence sets. Current Protocols in Bioinformatics. Unit 10.3. PMID 18428693 DOI: 10.1002/0471250953.bi1003s00 |
0.617 |
|
| 2002 |
Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Research. 30: 2478-83. PMID 12034836 DOI: 10.1093/Nar/30.11.2478 |
0.75 |
|
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