| 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, ... ... Schatz MC, et al. Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. Genome Research. PMID 39505490 DOI: 10.1101/gr.279334.124 |
0.807 |
|
| 2024 |
Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, ... ... Schatz MC, et al. High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation. Genome Research. PMID 39358015 DOI: 10.1101/gr.279273.124 |
0.481 |
|
| 2024 |
Ou S, Scheben A, Collins T, Qiu Y, Seetharam AS, Menard CC, Manchanda N, Gent JI, Schatz MC, Anderson SN, Hufford MB, Hirsch CN. Differences in activity and stability drive transposable element variation in tropical and temperate maize. Genome Research. PMID 39251347 DOI: 10.1101/gr.278131.123 |
0.804 |
|
| 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, ... ... Schatz MC, et al. Complete sequencing of ape genomes. Biorxiv : the Preprint Server For Biology. PMID 39131277 DOI: 10.1101/2024.07.31.605654 |
0.809 |
|
| 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 |
0.643 |
|
| 2024 |
Hwang S, Brown NK, Ahmed OY, Jenike KM, Kovaka S, Schatz MC, Langmead B. MEM-based pangenome indexing for -mer queries. Biorxiv : the Preprint Server For Biology. PMID 38826299 DOI: 10.1101/2024.05.20.595044 |
0.658 |
|
| 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, ... ... Schatz MC, et al. The complete sequence and comparative analysis of ape sex chromosomes. Nature. PMID 38811727 DOI: 10.1038/s41586-024-07473-2 |
0.568 |
|
| 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 |
0.644 |
|
| 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 |
0.54 |
|
| 2024 |
Jensen TD, Ni B, Reuter C, Gorzynski JE, Fazal S, Bonner DE, Ungar RA, Goddard PC, Natarajan Raja A, Ashley EA, Bernstein JA, Zuchner S, Greicius MD, Montgomery SB, Schatz MC, et al. Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease. Medrxiv : the Preprint Server For Health Sciences. PMID 38585781 DOI: 10.1101/2024.03.22.24304565 |
0.475 |
|
| 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, ... ... Schatz MC, 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 |
0.842 |
|
| 2024 |
Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, ... ... Schatz MC, et al. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. Medrxiv : the Preprint Server For Health Sciences. PMID 38496498 DOI: 10.1101/2024.03.05.24303792 |
0.48 |
|
| 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, ... ... Schatz MC, et al. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology. PMID 38278971 DOI: 10.1038/s41587-023-02100-3 |
0.656 |
|
| 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, ... ... Schatz MC, 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 |
0.585 |
|
| 2023 |
Scheben A, Mendivil Ramos O, Kramer M, Goodwin S, Oppenheim S, Becker DJ, Schatz MC, Simmons NB, Siepel A, McCombie WR. Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biology and Evolution. 15. PMID 37728212 DOI: 10.1093/gbe/evad148 |
0.334 |
|
| 2023 |
Stevenson DW, Ramakrishnan S, Alves CS, Coelho LA, Kramer M, Goodwin S, Ramos OM, Eshel G, Sondervan VM, Frangos S, Zumajo-Cardona C, Jenike K, Ou S, Wang X, Lee YP, ... ... Schatz M, et al. The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. Biorxiv : the Preprint Server For Biology. PMID 37662366 DOI: 10.1101/2023.08.24.554647 |
0.78 |
|
| 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, ... ... Schatz MC, et al. The complete sequence of a human Y chromosome. Nature. PMID 37612512 DOI: 10.1038/s41586-023-06457-y |
0.755 |
|
| 2023 |
Pinto BJ, O'Connor B, Schatz MC, Zarate S, Wilson MA. Concerning the eXclusion in human genomics: The choice of sex chromosome representation in the human genome drastically affects number of identified variants. G3 (Bethesda, Md.). PMID 37497639 DOI: 10.1093/g3journal/jkad169 |
0.444 |
|
| 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, ... ... Schatz MC, 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 |
0.712 |
|
| 2023 |
Yang X, Wang X, Zou Y, Zhang S, Xia M, Fu L, Vollger MR, Chen NC, Taylor DJ, Harvey WT, Logsdon GA, Meng D, Shi J, McCoy RC, Schatz MC, et al. Characterization of large-scale genomic differences in the first complete human genome. Genome Biology. 24: 157. PMID 37403156 DOI: 10.1186/s13059-023-02995-w |
0.502 |
|
| 2023 |
Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, ... ... Schatz MC, et al. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell. 186: 1493-1511.e40. PMID 37001506 DOI: 10.1016/j.cell.2023.02.018 |
0.705 |
|
| 2023 |
Pinto BJ, O'Connor B, Schatz MC, Zarate S, Wilson MA. Concerning the eXclusion in human genomics: The choice of sex chromosome representation in the human genome drastically affects number of identified variants. Biorxiv : the Preprint Server For Biology. PMID 36865318 DOI: 10.1101/2023.02.22.529542 |
0.443 |
|
| 2023 |
Kirsche M, Prabhu G, Sherman R, Ni B, Battle A, Aganezov S, Schatz MC. Jasmine and Iris: population-scale structural variant comparison and analysis. Nature Methods. PMID 36658279 DOI: 10.1038/s41592-022-01753-3 |
0.363 |
|
| 2023 |
Kovaka S, Ou S, Jenike KM, Schatz MC. Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing. Nature Methods. 20: 12-16. PMID 36635537 DOI: 10.1038/s41592-022-01716-8 |
0.783 |
|
| 2022 |
Alonge M, Lebeigle L, Kirsche M, Jenike K, Ou S, Aganezov S, Wang X, Lippman ZB, Schatz MC, Soyk S. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology. 23: 258. PMID 36522651 DOI: 10.1186/s13059-022-02823-7 |
0.778 |
|
| 2022 |
Wagner J, Olson ND, Harris L, Khan Z, Farek J, Mahmoud M, Stankovic A, Kovacevic V, Yoo B, Miller N, Rosenfeld JA, Ni B, Zarate S, Kirsche M, Aganezov S, ... Schatz MC, et al. Benchmarking challenging small variants with linked and long reads. Cell Genomics. 2. PMID 36452119 DOI: 10.1016/j.xgen.2022.100128 |
0.42 |
|
| 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, ... ... Schatz MC, et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature. PMID 36261518 DOI: 10.1038/s41586-022-05325-5 |
0.789 |
|
| 2022 |
Fields PD, Waneka G, Naish M, Schatz MC, Henderson IR, Sloan DB. Complete sequence of a 641-kb insertion of mitochondrial DNA in the Arabidopsis thaliana nuclear genome. Genome Biology and Evolution. PMID 35446419 DOI: 10.1093/gbe/evac059 |
0.407 |
|
| 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, ... ... Schatz MC, 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 |
0.709 |
|
| 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, ... ... Schatz MC, 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 |
0.701 |
|
| 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, ... ... Schatz MC, et al. The complete sequence of a human genome. Science (New York, N.Y.). 376: 44-53. PMID 35357919 DOI: 10.1126/science.abj6987 |
0.795 |
|
| 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, ... Schatz MC, et al. Epigenetic patterns in a complete human genome. Science (New York, N.Y.). 376: eabj5089. PMID 35357915 DOI: 10.1126/science.abj5089 |
0.694 |
|
| 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, ... ... Schatz MC, et al. Complete genomic and epigenetic maps of human centromeres. Science (New York, N.Y.). 376: eabl4178. PMID 35357911 DOI: 10.1126/science.abl4178 |
0.722 |
|
| 2022 |
Gularte-Mérida R, Smith S, Bowman AS, da Cruz Paula A, Chatila W, Bielski CM, Vyas M, Borsu L, Zehir A, Martelotto LG, Shia J, Yaeger R, Fang F, Gardner R, Luo R, ... Schatz MC, et al. Same-Cell Co-Occurrence of RAS Hotspot and BRAF V600E Mutations in Treatment-Naive Colorectal Cancer. Jco Precision Oncology. 6: e2100365. PMID 35235413 DOI: 10.1200/PO.21.00365 |
0.52 |
|
| 2022 |
Krittanawong C, Johnson KW, Choi E, Kaplin S, Venner E, Murugan M, Wang Z, Glicksberg BS, Amos CI, Schatz MC, Tang WHW. Artificial Intelligence and Cardiovascular Genetics. Life (Basel, Switzerland). 12. PMID 35207566 DOI: 10.3390/life12020279 |
0.38 |
|
| 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, 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 |
0.375 |
|
| 2021 |
Kirsche M, Schatz MC. Democratizing long-read genome assembly. Cell Systems. 12: 945-947. PMID 34672955 DOI: 10.1016/j.cels.2021.09.010 |
0.502 |
|
| 2021 |
Baslan T, Kovaka S, Sedlazeck FJ, Zhang Y, Wappel R, Tian S, Lowe SW, Goodwin S, Schatz MC. High resolution copy number inference in cancer using short-molecule nanopore sequencing. Nucleic Acids Research. PMID 34551429 DOI: 10.1093/nar/gkab812 |
0.442 |
|
| 2021 |
Yan SM, Sherman RM, Taylor DJ, Nair DR, Bortvin AN, Schatz MC, McCoy RC. Local adaptation and archaic introgression shape global diversity at human structural variant loci. Elife. 10. PMID 34528508 DOI: 10.7554/eLife.67615 |
0.415 |
|
| 2021 |
Ahmed O, Rossi M, Kovaka S, Schatz MC, Gagie T, Boucher C, Langmead B. Pan-genomic matching statistics for targeted nanopore sequencing. Iscience. 24: 102696. PMID 34195571 DOI: 10.1016/j.isci.2021.102696 |
0.717 |
|
| 2021 |
Hulse-Kemp AM, Bostan H, Chen S, Ashrafi H, Stoffel K, Sanseverino W, Li L, Cheng S, Schatz MC, Garvin T, du Toit LJ, Tseng E, Chin J, Iorizzo M, Van Deynze A. An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids. The Plant Genome. e20101. PMID 34109759 DOI: 10.1002/tpg2.20101 |
0.478 |
|
| 2021 |
Fouks B, Brand P, Nguyen HN, Herman J, Camara F, Ence D, Hagen D, Hoff KJ, Nachweide S, Romoth L, Walden KK, Guigo R, Stanke M, Narzisi G, Yandell M, ... ... Schatz MC, et al. The genomic basis of evolutionary differentiation among honey bees. Genome Research. PMID 33947700 DOI: 10.1101/gr.272310.120 |
0.374 |
|
| 2021 |
Ranallo-Benavidez TR, Lemmon Z, Soyk S, Aganezov S, Salerno WJ, McCoy RC, Lippman ZB, Schatz MC, Sedlazeck FJ. Optimized sample selection for cost-efficient long-read population sequencing. Genome Research. PMID 33811084 DOI: 10.1101/gr.264879.120 |
0.356 |
|
| 2021 |
Thielen PM, Wohl S, Mehoke T, Ramakrishnan S, Kirsche M, Falade-Nwulia O, Trovão NS, Ernlund A, Howser C, Sadowski N, Morris CP, Hopkins M, Schwartz M, Fan Y, Gniazdowski V, ... ... Schatz MC, et al. Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area. Jci Insight. 6. PMID 33749660 DOI: 10.1172/jci.insight.144350 |
0.44 |
|
| 2020 |
Palatnick A, Zhou B, Ghedin E, Schatz MC. iGenomics: Comprehensive DNA sequence analysis on your Smartphone. Gigascience. 9. PMID 33284326 DOI: 10.1093/gigascience/giaa138 |
0.429 |
|
| 2020 |
Kovaka S, Fan Y, Ni B, Timp W, Schatz MC. Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. Nature Biotechnology. PMID 33257863 DOI: 10.1038/s41587-020-0731-9 |
0.394 |
|
| 2020 |
Chin CS, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A, Rautiainen M, Aganezov S, Kirsche M, Zarate S, Schatz MC, Xiao C, Rowell WJ, Markello C, Farek J, et al. A diploid assembly-based benchmark for variants in the major histocompatibility complex. Nature Communications. 11: 4794. PMID 32963235 DOI: 10.1038/s41467-020-18564-9 |
0.474 |
|
| 2020 |
Aganezov S, Goodwin S, Sherman RM, Sedlazeck FJ, Arun G, Bhatia S, Lee I, Kirsche M, Wappel R, Kramer M, Kostroff K, Spector DL, Timp W, McCombie WR, Schatz MC. Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. Genome Research. PMID 32887686 DOI: 10.1101/Gr.260497.119 |
0.429 |
|
| 2020 |
Thielen PM, Wohl S, Mehoke T, Ramakrishnan S, Kirsche M, Falade-Nwulia O, Trovao NS, Erlund A, Howser C, Sadowski N, Morris P, Hopkins M, Schwartz M, Fan Y, Gniazdowski V, ... ... Schatz MC, et al. Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region. Medrxiv : the Preprint Server For Health Sciences. PMID 32817965 DOI: 10.1101/2020.08.13.20174136 |
0.314 |
|
| 2020 |
Nattestad M, Aboukhalil R, Chin CS, Schatz MC. Ribbon: Intuitive visualization for complex genomic variation. Bioinformatics (Oxford, England). PMID 32766814 DOI: 10.1093/Bioinformatics/Btaa680 |
0.405 |
|
| 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, ... ... Schatz MC, 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 |
0.49 |
|
| 2020 |
Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, Levy Y, Harel TH, Shalev-Schlosser G, Amsellem Z, Razifard H, ... ... Schatz MC, et al. Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell. PMID 32553272 DOI: 10.1016/J.Cell.2020.05.021 |
0.341 |
|
| 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, ... ... Schatz MC, et al. A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32541955 DOI: 10.1038/S41587-020-0538-8 |
0.704 |
|
| 2020 |
Darby CA, Gaddipati R, Schatz MC, Langmead B. Vargas: heuristic-free alignment for assessing linear and graph read aligners. Bioinformatics (Oxford, England). PMID 32321164 DOI: 10.1093/Bioinformatics/Btaa265 |
0.646 |
|
| 2020 |
Wang L, Lu Z, delaBastide M, Van Buren P, Wang X, Ghiban C, Regulski M, Drenkow J, Xu X, Ortiz-Ramirez C, Marco CF, Goodwin S, Dobin A, Birnbaum KD, Jackson DP, ... ... Schatz MC, et al. Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science. 11: 289. PMID 32296450 DOI: 10.3389/Fpls.2020.00289 |
0.31 |
|
| 2020 |
Ranallo-Benavidez TR, Jaron KS, Schatz MC. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications. 11: 1432. PMID 32188846 DOI: 10.1038/s41467-020-14998-3 |
0.477 |
|
| 2020 |
Xu Z, Green B, Benoit N, Schatz M, Wheelan S, Cormack B. De novo genome assembly of Candida glabrata reveals cell wall protein complement and structure of dispersed tandem repeat arrays. Molecular Microbiology. PMID 32068314 DOI: 10.1111/Mmi.14488 |
0.47 |
|
| 2019 |
Chen S, Krusche P, Dolzhenko E, Sherman RM, Petrovski R, Schlesinger F, Kirsche M, Bentley DR, Schatz MC, Sedlazeck FJ, Eberle MA. Paragraph: a graph-based structural variant genotyper for short-read sequence data. Genome Biology. 20: 291. PMID 31856913 DOI: 10.1186/s13059-019-1909-7 |
0.437 |
|
| 2019 |
Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. Bmc Bioinformatics. 20: 641. PMID 31842730 DOI: 10.1186/s12859-019-3208-4 |
0.416 |
|
| 2019 |
Souza GM, Van Sluys MA, Lembke CG, Lee H, Margarido GRA, Hotta CT, Gaiarsa JW, Diniz AL, Oliveira MM, Ferreira SS, Nishiyama MY, Ten-Caten F, Ragagnin GT, Andrade PM, de Souza RF, ... ... Schatz MC, et al. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. Gigascience. 8. PMID 31782791 DOI: 10.1093/Gigascience/Giz129 |
0.482 |
|
| 2019 |
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biology. 20: 224. PMID 31661016 DOI: 10.1186/S13059-019-1829-6 |
0.516 |
|
| 2019 |
Chen LY, VanBuren R, Paris M, Zhou H, Zhang X, Wai CM, Yan H, Chen S, Alonge M, Ramakrishnan S, Liao Z, Liu J, Lin J, Yue J, Fatima M, ... ... Schatz MC, et al. The bracteatus pineapple genome and domestication of clonally propagated crops. Nature Genetics. PMID 31570895 DOI: 10.1038/S41588-019-0506-8 |
0.434 |
|
| 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, ... ... Schatz MC, 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 |
0.711 |
|
| 2019 |
Darby CA, Fitch JR, Brennan PJ, Kelly BJ, Bir N, Magrini V, Leonard J, Cottrell CE, Gastier-Foster JM, Wilson RK, Mardis ER, White P, Langmead B, Schatz MC. Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads. Iscience. 18: 1-10. PMID 31271967 DOI: 10.1016/J.Isci.2019.05.037 |
0.717 |
|
| 2019 |
Soyk S, Lemmon ZH, Sedlazeck FJ, Jiménez-Gómez JM, Alonge M, Hutton SF, Van Eck J, Schatz MC, Lippman ZB. Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nature Plants. 5: 471-479. PMID 31061537 DOI: 10.1038/S41477-019-0422-Z |
0.354 |
|
| 2019 |
Luo R, Sedlazeck FJ, Lam TW, Schatz MC. A multi-task convolutional deep neural network for variant calling in single molecule sequencing. Nature Communications. 10: 998. PMID 30824707 DOI: 10.1038/S41467-019-09025-Z |
0.67 |
|
| 2019 |
Schatz MC, Cosgrove A. Graph genomes article collection. Genome Biology. 20: 25. PMID 30709357 DOI: 10.1186/s13059-019-1636-0 |
0.324 |
|
| 2018 |
Wirthlin M, Lima NCB, Guedes RLM, Soares AER, Almeida LGP, Cavaleiro NP, Loss de Morais G, Chaves AV, Howard JT, Teixeira MM, Schneider PN, Santos FR, Schatz MC, Felipe MS, Miyaki CY, et al. Parrot Genomes and the Evolution of Heightened Longevity and Cognition. Current Biology : Cb. PMID 30528582 DOI: 10.1016/J.Cub.2018.10.050 |
0.365 |
|
| 2018 |
Dennenmoser S, Sedlazeck FJ, Schatz MC, Altmüller J, Zytnicki M, Nolte AW. Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish. Molecular Ecology. PMID 30520198 DOI: 10.1111/mec.14969 |
0.5 |
|
| 2018 |
Zhang J, Zhang X, Tang H, Zhang Q, Hua X, Ma X, Zhu F, Jones T, Zhu X, Bowers J, Wai CM, Zheng C, Shi Y, Chen S, Xu X, ... ... Schatz MC, et al. Publisher Correction: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nature Genetics. PMID 30425353 DOI: 10.1038/S41588-018-0293-7 |
0.396 |
|
| 2018 |
Tamma PD, Fan Y, Bergman Y, Pertea G, Kazmi A, Lewis S, Carroll KC, Schatz MC, Timp W, Simner PJ. Applying Rapid Whole Genome Sequencing to Predict Phenotypic Antimicrobial Susceptibility Testing Results Among Carbapenem-Resistant Clinical Isolates. Antimicrobial Agents and Chemotherapy. PMID 30373801 DOI: 10.1128/AAC.01923-18 |
0.31 |
|
| 2018 |
Zhang J, Zhang X, Tang H, Zhang Q, Hua X, Ma X, Zhu F, Jones T, Zhu X, Bowers J, Wai CM, Zheng C, Shi Y, Chen S, Xu X, ... ... Schatz MC, et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nature Genetics. PMID 30297971 DOI: 10.1038/S41588-018-0237-2 |
0.37 |
|
| 2018 |
Kent CF, Dey A, Patel H, Tsvetkov N, Tiwari T, MacPhail VJ, Gobeil Y, Harpur BA, Gurtowski J, Schatz MC, Colla SR, Zayed A. Conservation Genomics of the Declining North American Bumblebee Reveals Inbreeding and Selection on Immune Genes. Frontiers in Genetics. 9: 316. PMID 30147708 DOI: 10.3389/Fgene.2018.00316 |
0.424 |
|
| 2018 |
Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck F, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin J, Beck T, Sundaravadanam Y, Kramer M, ... ... Schatz MC, et al. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Research. PMID 29954844 DOI: 10.1101/Gr.231100.117 |
0.455 |
|
| 2018 |
Gómez-Romero L, Palacios-Flores K, Reyes J, García D, Boege M, Dávila G, Flores M, Schatz MC, Palacios R. Precise detection of de novo single nucleotide variants in human genomes. Proceedings of the National Academy of Sciences of the United States of America. PMID 29735690 DOI: 10.1073/Pnas.1802244115 |
0.481 |
|
| 2018 |
Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC. Accurate detection of complex structural variations using single-molecule sequencing. Nature Methods. PMID 29713083 DOI: 10.1038/S41592-018-0001-7 |
0.358 |
|
| 2018 |
Sedlazeck FJ, Lee H, Darby CA, Schatz MC. Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nature Reviews. Genetics. PMID 29599501 DOI: 10.1038/S41576-018-0003-4 |
0.392 |
|
| 2018 |
Hulse-Kemp AM, Maheshwari S, Stoffel K, Hill TA, Jaffe D, Williams SR, Weisenfeld N, Ramakrishnan S, Kumar V, Shah P, Schatz MC, Church DM, Van Deynze A. Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library. Horticulture Research. 5: 4. PMID 29423234 DOI: 10.1038/S41438-017-0011-0 |
0.536 |
|
| 2017 |
Luo R, Sedlazeck FJ, Darby CA, Kelly SM, Schatz MC. LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning. Computational and Structural Biotechnology Journal. 15: 478-484. PMID 29213995 DOI: 10.1016/J.Csbj.2017.10.002 |
0.744 |
|
| 2017 |
Roberts RJ, Carneiro MO, Schatz MC. Erratum to: The advantages of SMRT sequencing. Genome Biology. 18: 156. PMID 28814314 DOI: 10.1186/S13059-017-1295-Y |
0.374 |
|
| 2017 |
Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, ... Schatz MC, et al. Hybrid assembly with long and short reads improves discovery of gene family expansions. Bmc Genomics. 18: 541. PMID 28724409 DOI: 10.1186/S12864-017-3927-8 |
0.497 |
|
| 2017 |
Luo R, Schatz MC, Salzberg SL. 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model. Gigascience. PMID 28637275 DOI: 10.1093/Gigascience/Gix045 |
0.724 |
|
| 2017 |
Feigin ME, Garvin T, Bailey P, Waddell N, Chang DK, Kelley DR, Shuai S, Gallinger S, McPherson JD, Grimmond SM, Khurana E, Stein LD, Biankin AV, Schatz MC, Tuveson DA. Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. Nature Genetics. PMID 28481342 DOI: 10.1038/Ng.3861 |
0.462 |
|
| 2017 |
Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC. GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics (Oxford, England). PMID 28369201 DOI: 10.1093/Bioinformatics/Btx153 |
0.472 |
|
| 2017 |
Schatz MC. Nanopore sequencing meets epigenetics. Nature Methods. 14: 347-348. PMID 28362434 DOI: 10.1038/nmeth.4240 |
0.349 |
|
| 2016 |
Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, ... ... Schatz MC, et al. Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. Plos Genetics. 12: e1006500. PMID 27935956 DOI: 10.1371/journal.pgen.1006500 |
0.427 |
|
| 2016 |
Fang H, Bergmann EA, Arora K, Vacic V, Zody MC, Iossifov I, O'Rawe JA, Wu Y, Jimenez Barron LT, Rosenbaum J, Ronemus M, Lee YH, Wang Z, Dikoglu E, Jobanputra V, ... ... Schatz MC, et al. Indel variant analysis of short-read sequencing data with Scalpel. Nature Protocols. 11: 2529-2548. PMID 27854363 DOI: 10.1038/Nprot.2016.150 |
0.452 |
|
| 2016 |
Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, ... ... Schatz MC, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods. PMID 27749838 DOI: 10.1038/Nmeth.4035 |
0.53 |
|
| 2016 |
Vembar SS, Seetin M, Lambert C, Nattestad M, Schatz MC, Baybayan P, Scherf A, Smith ML. Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 27345719 DOI: 10.1093/dnares/dsw022 |
0.545 |
|
| 2016 |
Nattestad M, Schatz MC. Assemblytics: a web analytics tool for the detection of variants from an assembly. Bioinformatics (Oxford, England). 32: 3021-3. PMID 27318204 DOI: 10.1093/bioinformatics/btw369 |
0.483 |
|
| 2016 |
Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS, Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D'Agostino N, Davies K, Druege U, Dudareva N, ... ... Schatz MC, et al. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature Plants. 2: 16074. PMID 27255838 DOI: 10.1038/Nplants.2016.74 |
0.495 |
|
| 2016 |
Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, ... ... Schatz MC, et al. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. Plos Genetics. 12: e1005954. PMID 27082250 DOI: 10.1371/Journal.Pgen.1005954 |
0.48 |
|
| 2016 |
Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, et al. Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nature Communications. 7: 10164. PMID 26836631 DOI: 10.1038/Ncomms10164 |
0.348 |
|
| 2015 |
Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, et al. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. 47: 1435-42. PMID 26523774 DOI: 10.1038/Ng.3435 |
0.415 |
|
| 2015 |
Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P, Schatz MC, McCombie WR. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Research. 25: 1750-6. PMID 26447147 DOI: 10.1101/Gr.191395.115 |
0.486 |
|
| 2015 |
Schatz MC. Biological data sciences in genome research. Genome Research. 25: 1417-22. PMID 26430150 DOI: 10.1101/gr.191684.115 |
0.425 |
|
| 2015 |
Wences AH, Schatz MC. Metassembler: merging and optimizing de novo genome assemblies. Genome Biology. 16: 207. PMID 26403281 DOI: 10.1186/s13059-015-0764-4 |
0.467 |
|
| 2015 |
Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M. Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proceedings of the National Academy of Sciences of the United States of America. 112: 12462-7. PMID 26392545 DOI: 10.1073/Pnas.1516718112 |
0.504 |
|
| 2015 |
Stephens ZD, Lee SY, Faghri F, Campbell RH, Zhai C, Efron MJ, Iyer R, Schatz MC, Sinha S, Robinson GE. Big Data: Astronomical or Genomical? Plos Biology. 13: e1002195. PMID 26151137 DOI: 10.1371/Journal.Pbio.1002195 |
0.447 |
|
| 2015 |
Narzisi G, Schatz MC. The challenge of small-scale repeats for indel discovery. Frontiers in Bioengineering and Biotechnology. 3: 8. PMID 25674564 DOI: 10.3389/Fbioe.2015.00008 |
0.49 |
|
| 2015 |
Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P. Extending reference assembly models. Genome Biology. 16: 13. PMID 25651527 DOI: 10.1186/S13059-015-0587-3 |
0.515 |
|
| 2014 |
Schatz MC, Maron LG, Stein JC, Hernandez Wences A, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biology. 15: 506. PMID 25468217 DOI: 10.1186/S13059-014-0506-Z |
0.532 |
|
| 2014 |
Fang H, Wu Y, Narzisi G, O'Rawe JA, Barrón LT, Rosenbaum J, Ronemus M, Iossifov I, Schatz MC, Lyon GJ. Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Medicine. 6: 89. PMID 25426171 DOI: 10.1186/S13073-014-0089-Z |
0.44 |
|
| 2014 |
Marcus S, Lee H, Schatz MC. SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips. Bioinformatics (Oxford, England). 30: 3476-83. PMID 25398610 DOI: 10.1093/Bioinformatics/Btu756 |
0.496 |
|
| 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, et al. High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience. 3: 11. PMID 25061512 DOI: 10.1186/2047-217X-3-11 |
0.719 |
|
| 2014 |
Blood PD, Marcus S, Schatz MC. Large-scale sequencing and assembly of cereal genomes using blacklight Acm International Conference Proceeding Series. DOI: 10.1145/2616498.2616502 |
0.496 |
|
| 2013 |
Schatz MC, Langmead B. The DNA Data Deluge: Fast, efficient genome sequencing machines are spewing out more data than geneticists can analyze. Ieee Spectrum. 50: 26-33. PMID 24920863 DOI: 10.1109/Mspec.2013.6545119 |
0.699 |
|
| 2013 |
Saw JH, Schatz M, Brown MV, Kunkel DD, Foster JS, Shick H, Christensen S, Hou S, Wan X, Donachie SP. Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. nov., from a lava cave in KÄ«lauea Caldera, Hawai'i. Plos One. 8: e76376. PMID 24194836 DOI: 10.1371/Journal.Pone.0076376 |
0.513 |
|
| 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, ... ... Schatz MC, 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 |
0.823 |
|
| 2013 |
Roberts RJ, Carneiro MO, Schatz MC. The advantages of SMRT sequencing. Genome Biology. 14: 405. PMID 23822731 DOI: 10.1186/gb-2013-14-6-405 |
0.442 |
|
| 2013 |
Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, et al. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology. 14: R41. PMID 23663246 DOI: 10.1186/Gb-2013-14-5-R41 |
0.373 |
|
| 2013 |
Doolittle WF, Fraser P, Gerstein MB, Graveley BR, Henikoff S, Huttenhower C, Oshlack A, Ponting CP, Rinn JL, Schatz MC, Ule J, Weigel D, Weinstock GM. Sixty years of genome biology. Genome Biology. 14: 113. PMID 23651518 DOI: 10.1186/Gb-2013-14-4-113 |
0.413 |
|
| 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 |
0.782 |
|
| 2013 |
Roberts RJ, Carneiro MO, Schatz MC. The advantages of SMRT sequencing Genome Biology. 405. DOI: 10.1186/Gb-2013-14-7-405 |
0.442 |
|
| 2012 |
Schatz MC, Phillippy AM. The rise of a digital immune system. Gigascience. 1: 4. PMID 23587178 DOI: 10.1186/2047-217X-1-4 |
0.533 |
|
| 2012 |
Gurtowski J, Schatz MC, Langmead B. Genotyping in the cloud with Crossbow. Current Protocols in Bioinformatics. Unit15.3. PMID 22948728 DOI: 10.1002/0471250953.Bi1503S39 |
0.586 |
|
| 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 |
0.491 |
|
| 2012 |
Lee H, Schatz MC. Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score. Bioinformatics (Oxford, England). 28: 2097-105. PMID 22668792 DOI: 10.1093/Bioinformatics/Bts330 |
0.426 |
|
| 2012 |
Schatz MC, Witkowski J, McCombie WR. Current challenges in de novo plant genome sequencing and assembly. Genome Biology. 13: 243. PMID 22546054 DOI: 10.1186/Gb-2012-13-4-243 |
0.488 |
|
| 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 |
0.847 |
|
| 2012 |
Schatz MC, Witkowski J, McCombie WR. Current challenges in de novo plant genome sequencing and assembly Genome Biology. 13: 243. DOI: 10.1186/gb-2012-13-4-243 |
0.468 |
|
| 2012 |
Titmus MA, Gurtowski J, Schatz MC. Answering the demands of digital genomics Concurrency and Computation: Practice and Experience. 26: 917-928. DOI: 10.1002/cpe.2925 |
0.456 |
|
| 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 |
0.584 |
|
| 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, ... ... Schatz MC, 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 |
0.822 |
|
| 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, ... Schatz MC, 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 |
0.805 |
|
| 2010 |
Kelley DR, Schatz MC, Salzberg SL. Quake: quality-aware detection and correction of sequencing errors. Genome Biology. 11: R116. PMID 21114842 DOI: 10.1186/gb-2010-11-11-r116 |
0.679 |
|
| 2010 |
Cornman SR, Schatz MC, Johnston SJ, Chen YP, Pettis J, Hunt G, Bourgeois L, Elsik C, Anderson D, Grozinger CM, Evans JD. Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera. Bmc Genomics. 11: 602. PMID 20973996 DOI: 10.1186/1471-2164-11-602 |
0.467 |
|
| 2010 |
Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, ... ... Schatz MC, et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. Plos Biology. 8. PMID 20838655 DOI: 10.1371/Journal.Pbio.1000475 |
0.712 |
|
| 2010 |
Schatz MC. The missing graphical user interface for genomics. Genome Biology. 11: 128. PMID 20804568 DOI: 10.1186/gb-2010-11-8-128 |
0.323 |
|
| 2010 |
Schatz MC, Langmead B, Salzberg SL. Cloud computing and the DNA data race Nature Biotechnology. 28: 691-693. PMID 20622843 DOI: 10.1038/Nbt0710-691 |
0.67 |
|
| 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 |
0.505 |
|
| 2010 |
Schatz MC, Delcher AL, Salzberg SL. Assembly of large genomes using second-generation sequencing Genome Research. 20: 1165-1173. PMID 20508146 DOI: 10.1101/gr.101360.109 |
0.699 |
|
| 2010 |
Kingsford C, Schatz MC, Pop M. Assembly complexity of prokaryotic genomes using short reads. Bmc Bioinformatics. 11: 21. PMID 20064276 DOI: 10.1186/1471-2105-11-21 |
0.736 |
|
| 2010 |
Kelley D, Schatz M, Salzberg S. Quality-aware error correction of sequencing reads F1000research. 1. DOI: 10.7490/F1000Research.274.1 |
0.683 |
|
| 2009 |
Trapnell C, Schatz MC. Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment. Parallel Computing. 35: 429-440. PMID 20161021 DOI: 10.1016/j.parco.2009.05.002 |
0.612 |
|
| 2009 |
Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology. 10: R134. PMID 19930550 DOI: 10.1186/Gb-2009-10-11-R134 |
0.714 |
|
| 2009 |
Cornman RS, Chen YP, Schatz MC, Street C, Zhao Y, Desany B, Egholm M, Hutchison S, Pettis JS, Lipkin WI, Evans JD. Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. Plos Pathogens. 5: e1000466. PMID 19503607 DOI: 10.1371/journal.ppat.1000466 |
0.49 |
|
| 2009 |
Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 10: R42. PMID 19393038 DOI: 10.1186/Gb-2009-10-4-R42 |
0.78 |
|
| 2009 |
Schatz MC. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics (Oxford, England). 25: 1363-9. PMID 19357099 DOI: 10.1093/bioinformatics/btp236 |
0.417 |
|
| 2009 |
Navlakha S, Schatz MC, Kingsford C. Revealing biological modules via graph summarization. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 253-64. PMID 19183002 DOI: 10.1089/Cmb.2008.11Tt |
0.569 |
|
| 2008 |
Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fadrosh DW, Fuester RW, Pedroni MJ, Haas BJ, Schatz MC, Jones KM, Crabtree J, Forberger H, Nene V. Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps. Genome Biology. 9: R183. PMID 19116010 DOI: 10.1186/gb-2008-9-12-r183 |
0.448 |
|
| 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 |
0.823 |
|
| 2008 |
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, ... ... Schatz M, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 452: 991-6. PMID 18432245 DOI: 10.1038/Nature06856 |
0.759 |
|
| 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 |
0.69 |
|
| 2007 |
Schatz MC, Trapnell C, Delcher AL, Varshney A. High-throughput sequence alignment using Graphics Processing Units. Bmc Bioinformatics. 8: 474. PMID 18070356 DOI: 10.1186/1471-2105-8-474 |
0.683 |
|
| 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, ... ... Schatz MC, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341 |
0.766 |
|
| 2007 |
Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, ... ... Schatz M, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science (New York, N.Y.). 317: 1756-60. PMID 17885136 DOI: 10.1126/Science.1145406 |
0.815 |
|
| 2007 |
Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fuester RW, Schatz MC, Pedroni MJ, Fadrosh DW, Haas BJ, Toms BS, Chen D, Nene V. Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus. Bmc Microbiology. 7: 61. PMID 17594494 DOI: 10.1186/1471-2180-7-61 |
0.377 |
|
| 2007 |
Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, ... ... Schatz M, et al. Genome sequence of Aedes aegypti, a major arbovirus vector. Science (New York, N.Y.). 316: 1718-23. PMID 17510324 DOI: 10.1126/Science.1138878 |
0.78 |
|
| 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 |
0.767 |
|
| 2007 |
Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, et al. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (New York, N.Y.). 315: 207-12. PMID 17218520 DOI: 10.1126/Science.1132894 |
0.786 |
|
| 2005 |
Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, ... ... Schatz MC, et al. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. Plos Biology. 3: e15. PMID 15660156 DOI: 10.1371/Journal.Pbio.0030015 |
0.32 |
|
| 2004 |
Gajer P, Schatz M, Salzberg SL. Automated correction of genome sequence errors. Nucleic Acids Research. 32: 562-9. PMID 14744981 DOI: 10.1093/Nar/Gkh216 |
0.717 |
|
| Show low-probability matches. |