| Year |
Citation |
Score |
| 2024 |
Connor R, Shakya M, Yarmosh DA, Maier W, Martin R, Bradford R, Brister JR, Chain PSG, Copeland CA, di Iulio J, Hu B, Ebert P, Gunti J, Jin Y, Katz KS, et al. Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses. 16. PMID 38543795 DOI: 10.3390/v16030430 |
0.325 |
|
| 2022 |
Albright MBN, Gallegos-Graves V, Feeser KL, Montoya K, Emerson JB, Shakya M, Dunbar J. Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition. Isme Communications. 2: 24. PMID 37938672 DOI: 10.1038/s43705-022-00109-4 |
0.34 |
|
| 2022 |
Xiaoli L, Hagey JV, Park DJ, Gulvik CA, Young EL, Alikhan NF, Lawsin A, Hassell N, Knipe K, Oakeson KF, Retchless AC, Shakya M, Lo CC, Chain P, Page AJ, et al. Benchmark datasets for SARS-CoV-2 surveillance bioinformatics. Peerj. 10: e13821. PMID 36093336 DOI: 10.7717/peerj.13821 |
0.306 |
|
| 2020 |
Shakya M, Ahmed SA, Davenport KW, Flynn MC, Lo CC, Chain PSG. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. Scientific Reports. 10: 1723. PMID 32015354 DOI: 10.1038/S41598-020-58356-1 |
0.415 |
|
| 2019 |
Shakya M, Lo CC, Chain PSG. Advances and Challenges in Metatranscriptomic Analysis. Frontiers in Genetics. 10: 904. PMID 31608125 DOI: 10.3389/Fgene.2019.00904 |
0.578 |
|
| 2019 |
Kogay R, Neely TB, Birnbaum DP, Hankel CR, Shakya M, Zhaxybayeva O. Machine-learning classification suggests that many alphaproteobacterial prophages may instead be gene transfer agents. Genome Biology and Evolution. PMID 31560374 DOI: 10.1093/Gbe/Evz206 |
0.381 |
|
| 2019 |
Domman D, Ruis C, Dorman MJ, Shakya M, Chain PSG. Novel Insights Into the Spread of Enteric Pathogens Using Genomics. The Journal of Infectious Diseases. PMID 31538189 DOI: 10.1093/Infdis/Jiz220 |
0.341 |
|
| 2019 |
Connor R, Brister R, Buchmann JP, Deboutte W, Edwards R, Martí-Carreras J, Tisza M, Zalunin V, Andrade-Martínez J, Cantu A, D'Amour M, Efremov A, Fleischmann L, Forero-Junco L, Garmaeva S, ... ... Shakya M, et al. NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements. Genes. 10. PMID 31527408 DOI: 10.3390/Genes10090714 |
0.41 |
|
| 2017 |
Shakya M, Soucy SM, Zhaxybayeva O. Insights into origin and evolution of α-proteobacterial gene transfer agents. Virus Evolution. 3: vex036. PMID 29250433 DOI: 10.1093/Ve/Vex036 |
0.353 |
|
| 2016 |
Hynes AP, Shakya M, Mercer RG, Grüll MP, Bown L, Davidson F, Steffen E, Matchem H, Peach ME, Berger T, Grebe K, Zhaxybayeva O, Lang AS. Functional and evolutionary characterization of a gene transfer agent's multi-locus "genome". Molecular Biology and Evolution. PMID 27343288 DOI: 10.1093/Molbev/Msw125 |
0.32 |
|
| 2016 |
D'Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. Bmc Genomics. 17: 55. PMID 26763898 DOI: 10.1186/S12864-015-2194-9 |
0.663 |
|
| 2013 |
Shakya M, Gottel N, Castro H, Yang ZK, Gunter L, Labbé J, Muchero W, Bonito G, Vilgalys R, Tuskan G, Podar M, Schadt CW. A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees. Plos One. 8: e76382. PMID 24146861 DOI: 10.1371/Journal.Pone.0076382 |
0.629 |
|
| 2013 |
Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environmental Microbiology. 15: 1882-99. PMID 23387867 DOI: 10.1111/1462-2920.12086 |
0.647 |
|
| 2012 |
Flores GE, Shakya M, Meneghin J, Yang ZK, Seewald JS, Geoff Wheat C, Podar M, Reysenbach AL. Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin. Geobiology. 10: 333-46. PMID 22443386 DOI: 10.1111/J.1472-4669.2012.00325.X |
0.647 |
|
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