Pubs
Arcadia Pubs
Arcadia Science is reimagining scientific publishing and does not publish work in traditional peer-reviewed journals. We are experimenting with sharing more modular pieces of work in a timely fashion. You can check out our projects and pubs at research.arcadiascience.com. See pubs that I’ve specifically contributed to here, with a select few pubs listed below that I’ve led:
Discovering shared protein structure signatures connected to polyphosphate accumulation in diverse bacteria. pub code data Avasthi P, Celebi FM, McDaniel EA. 2023. DOI: 10.57844/arcadia-ac10-23e7
Quickly processing and profiling microbial community sequencing data with a Nextflow workflow for metagenomics. pub workflow Dutton RJ, McDaniel EA. 2023. DOI: 10.57844/arcadia-7etp-pj24
Creating reproducible workflows for complex computational pipelines. pub Celebi FM, McDaniel EA, Reiter T. 2023. DOI: 10.57844/arcadia-cc5j-a519
Academic Publications
# Denotes equal contribution.
15. Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium. publication code data McDaniel E.A, Scarborough M., Mulat D.G., Lin X., Sampara P.S., Olson H.M., Young R.P., Eder E.K., Attah I.K., Markillie L.M., Hoyt D.W., Lipton M.S., Hallam S.J., Ziels R.M. ISMEJ. Oct. 2023. DOI: 10.1038/s41396-023-01542-6.
14. Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria. preprint publication #Tran P.Q., #Bachand S.C., #Hotvedt J.C., Kieft K, McDaniel E.A., McMahon K.D., Anantharaman K. mSystems. June 2023. DOI: 10.1138/msystems.00201-23.
13. Environmental predictors of electroactive bacterioplankton in small boreal lakes. preprint publication Olmsted C.N., Ort R., Tran P.Q., McDaniel E.A., Robert E.E., Bond D.R., He S., McMahon K.D. Environmental Microbiology. Dec. 2022. DOI: 10.1111/1462-2920.16314.
12. TbasCO: Trait-Based Comparative ’Omics Identifies Ecosystem-Level and Niche-Differentiating Adaptations in an Engineered Microbiome. preprint publication software code BioProject data #McDaniel E.A., #van Steenbrugge, J.J.M, Noguera D.R., McMahon K.D., Raaijmakers J.M., Medema M.H., Oyserman B.O. ISME Communications. Nov 2022. DOI: 10.1038/s43705-022-00189-2
11. Signatures of Microbial Diversity at Multiple Scales of Resolution within Engineered Enrichment Communities. preprint code Abigail supplementary data R1 supplementary data Abigail BioProject R1 BioProject McDaniel E.A., Moya-Flores F., Mendez D., Weathersby C., Oyserman B.O., Flowers J., He S., Petriglieri F., Singleton C.M., Nielsen P.H., McMahon K.D. bioRxiv. October 2022. DOI: 10.1101/2022.10.01.510452
10. Expanded diversity of tfdA harboring bacteria across the natural and built environment. preprint data #White A.M., #Gonzalez Vasquez A., McDaniel E.A., Peterson B.D., Koch P.L, Remucal C.K., McMahon K.D. bioRxiv. September 2022. DOI: 10.1101/2022.09.28.509959
9. Re-evaluation of the phylogenetic diversity and global distribution of the lineage Candidatus Accumulibacter. preprint publication Petriglieri F., Singleton C.M., Kondrotaite Z., Dueholm M.S., McDaniel E.A., McMahon K.D., Nielsen P.H. mSystems. April 2022. DOI: 10.1128/msystems.00016-22.
8. Prospects for Multi-omics in the Microbial Ecology of Water Engineering. preprint publication McDaniel E.A., Wahl S.A., Ishii S., Pinto A., Ziels R., Nielsen P.H., McMahon K.D., Williams R.B.H. Water Research. Oct. 2021. DOI: 10.1016/j.waterres.2021.117608
7. Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics. preprint publication code BioProject data #McDaniel E.A., #Moya-Flores F., Keene Beach N., Camejo P.Y., Oyserman B.O., Kizaric M., Khor E.H., Noguera D.R., McMahon K.D. mSystems. July 2021, 6 (4) e00474-21; DOI: 10.1128/mSystems.00474-21
6. Genome-Resolved Metagenomics of a Photosynthetic Bioreactor Performing Biological Nutrient Removal. publication code BioProject data McDaniel E.A., Wever R., Oyserman B.O., Noguera D.R., McMahon K.D. Microbiology Resource Announcements. May 2021, 10 (18) e00244-21; DOI: 10.1128/MRA.00244-21
5. Community-led, integrated, reproducible multi-omics with anvi’o. publication Eren A.M., Kiefl E., Shaiber A., Veseli I., Miller S.E., Schecter M.S., Fink I., Pan J.N., Yousef M., Fogarty E.C., Trigodet F., Watson A.R., Esen O.C., Moore R.M., Clayssen Q., Lee M.D., Kivenson V., Graham E.D., Merrill B.D., Karkman A., Blankenberg D., Eppley J.M., Sjoden A., Scott J.J., Vazquez-Campos X., McKay L.J, McDaniel E.A., Stevens S.L.R., Anderson R., Fuessel J., Fernandez-Guerra A., Maignien L., Delmont T.O., Willis A.D. Nature Microbiology (Commentary). Jan. 2021, 6, 3-6. DOI: 10.1038/s41564-020-00834-3.
4. Mercury methylation genes identified across diverse anaerobic microbial guilds in a eutrophic sulfate-enriched lake. preprint publication data Peterson B.D., McDaniel E.A., Schmidt A.G., Lepak R.F., Tran P.Q., Marick R.A., Ogorek J.M., DeWild J.F., Krabbenhoft D.P., McMahon K.D. Environmental Science and Technology. Nov. 2020, 54 (24), 15840-15851; DOI: 10.1021/acs.est.0c05435
3. Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms. preprint publication code data McDaniel E.A., Peterson B., Stevens S.L.R., Tran P.Q., Anantharaman K., McMahon K.D. mSystems. Aug 2020, 5 (4) e00299-20; DOI: 10.1128/mSystems.00299-20
2. metabolisHMM: Phylogenomic analysis for exploration of microbial phylogenies and metabolic pathways. preprint software McDaniel E.A., Anantharaman, K., McMahon K.D. bioRxiv. Dec. 2019, DOI: 10.1101/2019.12.20.884627.
1. Independent Mechanisms for Acquired Salt Tolerance versus Growth Resumption Induced by Mild Ethanol Pretreatment in Saccharomyces cerevisiae. preprint publication McDaniel E.A., Stuecker T.N., Veluvolu M., Gasch A.P., Lewis J.A. mSphere. Editors Pick. Nov 2018, 3 (6) e0057418; DOI: 10.1128/mSphere.00574-18