These publications are a subset of my scientific work that I consider to have contributed significantly towards. For a complete list of publications, check out my Google Scholar.



Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution

Kiefl E, Esen ÖC, Miller SE, Kroll KL, Willis AD, Rappé MS, Pan T, Eren AM
- A study that describes an approach to integrate environmental microbiology with recent advances in protein structure prediction, and illustrates the tight association between intra-population genetic variants, environmental selective pressures, and structural properties of proteins
- Demonstrates a quantifiable link between (1) the magnitude of selective pressures over key metabolic genes (e.g., glutamine synthase of the central nitrogen metabolism), (2) the availability of key nutrients in the environment (e.g., nitrate), and (3) the maintenance of nonsynonymous variants near protein active sites.
- Shows that the interplay between selective pressures and protein structures also maintains synonymous variants -- revealing a quantifiable link between translational accuracy and fluctuating selective pressures.
- Comes with a reproducible bioinformatics workflow that offers detailed access to computational steps used in the study that spans from metagenomic read recruitment and profiling to the integration of environmental variants and predicted protein structures.
Science Advances, 9(8):None.



Community-led, integrated, reproducible multi-omics with anvi'o

Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, Fink I, Pan JN, Yousef M, Fogarty EC, Trigodet F, Watson AR, Esen ÖC, Moore RM, Clayssen Q, Lee MD, Kivenson V, Graham ED, Merrill BD, Karkman A, Blankenberg D, Eppley JM, Sjödin A, Scott JJ, Vázquez-Campos X, McKay LJ, McDaniel EA, Stevens SLR, Anderson RE, Fuessel J, Fernandez-Guerra A, Maignien L, Delmont TO, Willis AD
- A summary of the progress of anvi'o during the past five years.
Nature Microbiology, 6(1):3:6.



Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade

Delmont TO, Kiefl E, Kilinc O, Esen ÖC, Uysal I, Rappé MS, Giovannoni S, Eren AM Co-first authors
- Introduces 'single-amino acid variants' (SAAVs) and demonstrates the use of SAAVs to tease apart evolutionary processes that shape the biogeography and genomic heterogeneity within a SAR11 population through metagenomics.
- A first attempt to link population genetics and the predicted protein structures to explore in silico the intersection beetween protein biochemistry and evolutionary processes acting on an environmental microbe.
- An application of metapangenomics to define subclades of SAR11 based on gene content and ecology.
- Reproducible bioinformatics workflow is here. Reviewer criticism and our responses are also available.
eLife, 8:e46497.



Evaluation of surface-enhanced Raman spectroscopy substrates from single-molecule statistics

Kiefl E, Kiefl RF, dos Santos DP, Brolo AG
- Demonstrates power-law statistics of surface-ehanced Raman spectroscopy (SERS) hotspots can be used to assess the quality of SERS substrates.
- Extends the theory of truncated Pareto-distributed single-molecule SERS statistics to multi-hotspot substrates.
The Journal of Physical Chemistry C, 121(45):25487-25493.



Robust Magnetic Properties of a Sublimable Single-Molecule Magnet

Kiefl E, Mannini M, Bernot K, Yi X, Amato A, Leviant T, Magnani A, Prokscha T, Suter A, Sessoli R, Salman Z
- Demonstrates an equivalence in the magnetic properties between bulk and nanofilm configurations of a single-molecule magnet (SMM) using muon spin spectroscopy
- Discovers a rare instance in which a single molecule magnet maintains its chemical structure and magnetic properties when sublimated into nanofilm, an important precursor for using SMMs for information storage.
ACS Nano, 10(6):5663-5669.

Intact telopeptides enhance interactions between collagens

Shayegan M, Altindal T, Kiefl E, Forde NR
- Uses optical tweezers-based microrheology to quantify the viscoelasticity of triple-helical collagen molecules, with and without non-helical flanking regions called telopeptides, which are known to be critical for self-assembly.
- This work suggests that telopeptides facilitate transient intermolecular interactions between collagen proteins
Biophysical journal, 111(11):2404-2416.