| A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling R D’Amore, UZ Ijaz, M Schirmer, JG Kenny, R Gregory, AC Darby, ... BMC genomics 17, 1-20, 2016 | 440 | 2016 |
| Advances and challenges in metatranscriptomic analysis M Shakya, CC Lo, PSG Chain Frontiers in genetics 10, 904, 2019 | 353 | 2019 |
| A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees M Shakya, N Gottel, H Castro, ZK Yang, L Gunter, J Labbé, W Muchero, ... PloS one 8 (10), e76382, 2013 | 291 | 2013 |
| Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities M Shakya, C Quince, JH Campbell, ZK Yang, CW Schadt, M Podar Environmental microbiology 15 (6), 1882-1899, 2013 | 227 | 2013 |
| Inter‐field variability in the microbial communities of hydrothermal vent deposits from a back‐arc basin GE Flores, M Shakya, J Meneghin, ZK Yang, JS Seewald, C Geoff Wheat, ... Geobiology 10 (4), 333-346, 2012 | 106 | 2012 |
| Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life M Shakya, SA Ahmed, KW Davenport, MC Flynn, CC Lo, PSG Chain Scientific reports 10 (1), 1723, 2020 | 94 | 2020 |
| Hi-C deconvolution of a human gut microbiome yields high-quality draft genomes and reveals plasmid-genome interactions. MO Press, AH Wiser, ZN Kronenberg, KW Langford, M Shakya, CC Lo, ... bioRxiv, 198713, 2017 | 88 | 2017 |
| Functional and evolutionary characterization of a gene transfer agent’s multilocus “genome” AP Hynes, M Shakya, RG Mercer, MP Grüll, L Bown, F Davidson, ... Molecular Biology and Evolution 33 (10), 2530-2543, 2016 | 58 | 2016 |
| Insights into origin and evolution of α-proteobacterial gene transfer agents M Shakya, SM Soucy, O Zhaxybayeva Virus evolution 3 (2), vex036, 2017 | 53 | 2017 |
| The national microbiome data collaborative: Enabling microbiome science EM Wood-Charlson, Anubhav, D Auberry, H Blanco, MI Borkum, ... Nature Reviews Microbiology 18 (6), 313-314, 2020 | 51 | 2020 |
| Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition MBN Albright, LV Gallegos-Graves, KL Feeser, K Montoya, JB Emerson, ... ISME communications 2 (1), 24, 2022 | 36 | 2022 |
| The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource EA Eloe-Fadrosh, F Ahmed, M Babinski, J Baumes, M Borkum, L Bramer, ... Nucleic Acids Research 50 (D1), D828-D836, 2022 | 35 | 2022 |
| Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments RA Hurt Jr, MS Robeson, M Shakya, JG Moberly, TA Vishnivetskaya, B Gu, ... PLoS One 9 (7), e102826, 2014 | 33 | 2014 |
| Machine-learning classification suggests that many alphaproteobacterial prophages may instead be gene transfer agents R Kogay, TB Neely, DP Birnbaum, CR Hankel, M Shakya, O Zhaxybayeva Genome Biology and Evolution 11 (10), 2941-2953, 2019 | 24 | 2019 |
| Remedial Treatment of Corroded Iron Objects by Environmental Aeromonas Isolates WM Kooli, T Junier, M Shakya, M Monachon, KW Davenport, ... Applied and environmental microbiology 85 (3), e02042-18, 2019 | 16 | 2019 |
| EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts CC Lo, M Shakya, R Connor, K Davenport, M Flynn, AM Gutiérrez, B Hu, ... Bioinformatics 38 (10), 2700-2704, 2022 | 14 | 2022 |
| NCBI’s virus discovery Hackathon: Engaging research communities to identify cloud infrastructure requirements R Connor, R Brister, JP Buchmann, W Deboutte, R Edwards, ... Genes 10 (9), 714, 2019 | 13 | 2019 |
| Brief protocol for EDGE bioinformatics: analyzing microbial and metagenomic NGS data C Philipson, K Davenport, L Voegtly, CC Lo, PE Li, Y Xu, M Shakya, ... Bio-protocol 7 (23), e2622-e2622, 2017 | 9 | 2017 |
| A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays PE Li, A Myers y Gutiérrez, K Davenport, M Flynn, B Hu, CC Lo, ... Bioinformatics 37 (7), 1024-1025, 2021 | 7 | 2021 |
| A gene cluster that encodes histone deacetylase inhibitors contributes to bacterial persistence and antibiotic tolerance in Burkholderia thailandensis SN Micheva-Viteva, M Shakya, SH Adikari, CD Gleasner, N Velappan, ... Msystems 5 (1), 10.1128/msystems. 00609-19, 2020 | 7 | 2020 |
Patrick S. G. ChainLos Alamos National Laboratory在 lanl.gov 的电子邮件经过验证
