Author

Nicole Shapiro

Joint Genome InstituteORCID 0000-0002-5405-7761Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Assay:metagenomics· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Organism:chicken / avian· 1 Research Focus:chromatin & epigenetic regulation· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1

Frequent Co-Authors

Nikos C. KyrpidesiD· 2 shared Tanja WoykeiD· 2 shared A. Elizabeth Arnold· 1 shared Aaron E. DarlingiD· 1 shared Adrian FritziD· 1 shared Alexander SczyrbaiD· 1 shared Alexey A. GurevichiD· 1 shared Alice Carolyn McHardyiD· 1 shared

Activity by Year

2016-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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2 shared papersBioinformatics

Nikos C. KyrpidesORCID

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3 papers

Recent·Most cited

Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria

Pengfan Zhang, Breanna Michell Roque, Pedro Romero, Nicole Shapiro, Emiley A. Eloe‐Fadrosh, Ermias Kebreab, Spencer Diamond, Matthias Hess

This study investigates how Asparagopsis supplementation affects rumen microbiota, finding reduced methane production and changes in microbial gene expression and function.

Microbiome · Nov 13, 2025Peer-reviewedMicrobiology

Critical Assessment of Metagenome Interpretation - a benchmark of computational metagenomics software

Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Rubén Garrido‐Oter, Tue Sparholt Jørgensen, Nicole Shapiro, , Alice Carolyn McHardy

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.

Nature Methods · Oct 2, 2017Peer-reviewedBioinformatics

Absence of Genome Reduction In Diverse, Facultative Endohyphal Bacteria

David A Baltrus, Kevin Dougherty, Kayla R Arendt, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T.B.K. Reddy, Chew Yee Ngan, Chris Daum, Nicole Shapiro, Victor Markowitz, , A. Elizabeth Arnold

The paper analyzes genome sequences of facultative endohyphal bacteria from diverse fungi, finding no genome reduction and no universal pathways for host interaction.

bioRxiv · Mar 25, 2016Microbiology