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Displaying 1 - 7 of 7

Functional Profiling of Thousands of Sequence-Diverse Protease Homologs with GROQ-seq

May 12, 2026

Author(s)

James McLellan, Svetlana Ikonomova, Shwetha Sreenivasan, Alan Amin, Catherine Baranowski, Amanda Reider Apel, Peter Kelly, David Ross, Aviv Spinner

High-quality datasets that span broad sequence diversity are essential for understanding protein sequence–function relationships beyond local mutational landscapes. Here, we applied Growth-based Quantitative Sequencing (GROQ-seq) to measure function across

A mathematical framework to correct for compositionality in microbiome datasets

January 6, 2026

Author(s)

Samuel Forry, Stephanie Servetas, Jason Kralj, Monique Hunter, Jennifer Dootz

The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease

Toward a common standard for data and specimen provenance in life sciences

April 18, 2023

Author(s)

Rudolf Wittner, Petr Holub, Cecilia Mascia, Francesca Frexia, Heimo Muller, Markus Plass, Clare M Allocca, Fay Betsou, Tony Burdett, Ibon Cancio, Adriane Chapman, Martin Chapman, Melanie Courtot, Vasa Curcin, Johann Eder, Mark Elliot, Katrina Exter, Carole Goble, Martin Golebiewski, Bron Kisler, Andreas Kremer, Simone Leo, Sheng Lin-Gibson, Anna Marsano, Marco Mattavelli, Josh Moore, Hiroki NAKAE, Isabelle PERSEIL, Ayat Salman, James Sluka, Stian Soiland-Reyes, Caterina Strambio De Castillia, michael sussman, Jason Swedlow, Kurt Zatloukal, Joerg Geiger

Open and practical exchange, dissemination, and reuse of specimens and data have become a fundamental requirement for life sciences research. The quality of the data obtained and thus the findings and knowledge derived is thus significantly influenced by

Effects of DNA Template Preparation on Variability in Cell-Free Protein Production

August 13, 2022

Author(s)

Eugenia Romantseva, Nina Alperovich, David Ross, Steven Lund, Elizabeth Strychalski

DNA templates for protein expression remain an unexplored source of variability in the performance of cell-free expression (CFE) systems for protein production. To characterize this variability, we investigated the effects of two common DNA extraction

Method for reproducible automated bacterial cell culture and measurement

August 8, 2022

Author(s)

David Ross, Peter Tonner, Olga Vasilyeva

Microbial cell culture is one of the most commonly performed protocols for synthetic biology, and laboratories are increasingly using 96-well plates and laboratory automation systems for cell culture. Here we describe a method for reproducible microbial

Interpretable modeling of genotype-phenotype landscapes with state-of-the-art predictive power

June 21, 2022

Author(s)

Peter Tonner, Abe Pressman, David Ross

Large-scale measurements linking genetic background to biological function have drivena need for models that can incorporate these data for reliable predictions and insightinto the underlying biophysical system. Recent modeling efforts, however, prioritize

THE GUT MICROBIOME AND XENOBIOTICS: IDENTIFYING KNOWLEDGE GAPS

July 1, 2020

Author(s)

Vicki L. Sutherland, Charlene A. McQueen, donna Mendrick, donna gulezian, Carl Cerniglia, Steven Foley, Samuel Forry, Sangeeta Khare, Xue Liang, Jose E. Manautou, Donald Tweedie, howard young, Alexander Aleksenkyo, frank burns, Rod Dietert, Katherine Karberg, alan wilson, connie chen

There is an increasing awareness that the gut microbiome plays a critical role in human health and disease, but mechanistic insights are often lacking. In June 2018, the Health and Environmental Sciences Institute (HESI) held a workshop, "The Gut