Search Results - "ARKIN, Adam P"

A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming by Ning, Daliang, Yuan, Mengting, Wu, Linwei, Zhang, Ya, Guo, Xue, Zhou, Xishu, Yang, Yunfeng, Arkin, Adam P., Firestone, Mary K., Zhou, Jizhong

“…Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal,…”
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FastTree 2--approximately maximum-likelihood trees for large alignments by Price, Morgan N, Dehal, Paramvir S, Arkin, Adam P

“…We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements…”
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Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression by Qi, Lei S., Larson, Matthew H., Gilbert, Luke A., Doudna, Jennifer A., Weissman, Jonathan S., Arkin, Adam P., Lim, Wendell A.

“…Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating, perturbing, and engineering cellular systems. Here, we develop a…”
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Deciphering microbial interactions in synthetic human gut microbiome communities by Venturelli, Ophelia S, Carr, Alex V, Fisher, Garth, Hsu, Ryan H, Lau, Rebecca, Bowen, Benjamin P, Hromada, Susan, Northen, Trent, Arkin, Adam P

“…The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model‐guided framework…”
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Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics by Price, Morgan N, Deutschbauer, Adam M, Arkin, Adam P

“…To discover novel catabolic enzymes and transporters, we combined high-throughput genetic data from 29 bacteria with an automated tool to find gaps in their…”
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Stochasticity, succession, and environmental perturbations in a fluidic ecosystem by Zhou, Jizhong, Deng, Ye, Zhang, Ping, Xue, Kai, Liang, Yuting, Van Nostrand, Joy D, Yang, Yunfeng, He, Zhili, Wu, Liyou, Stahl, David A, Hazen, Terry C, Tiedje, James M, Arkin, Adam P

“…Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping…”
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Precise and reliable gene expression via standard transcription and translation initiation elements by Mutalik, Vivek K, Guimaraes, Joao C, Cambray, Guillaume, Lam, Colin, Christoffersen, Marc Juul, Mai, Quynh-Anh, Tran, Andrew B, Paull, Morgan, Keasling, Jay D, Arkin, Adam P, Endy, Drew

“…By using a bicistronic design, with a leader peptide that overlaps with and contains the Shine-Dalgarno site for a downstream gene of interest, the authors…”
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A fast comparative genome browser for diverse bacteria and archaea by Price, Morgan N, Arkin, Adam P

“…Genome sequencing has revealed an incredible diversity of bacteria and archaea, but there are no fast and convenient tools for browsing across these genomes…”
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Composability of regulatory sequences controlling transcription and translation in Escherichia coli by Kosuri, Sriram, Goodman, Daniel B., Cambray, Guillaume, Mutalik, Vivek K., Gao, Yuan, Arkin, Adam P., Endy, Drew, Church, George M.

“…The inability to predict heterologous gene expression levels precisely hinders our ability to engineer biological systems. Using well-characterized regulatory…”
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Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation by Zhang, Shuyan, Ito, Masakazu, Skerker, Jeffrey M., Arkin, Adam P., Rao, Christopher V.

“…Natural lipids can be used to make biodiesel and many other value-added compounds. In this work, we explored a number of different metabolic engineering…”
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Quantifying the local adaptive landscape of a nascent bacterial community by Ascensao, Joao A., Wetmore, Kelly M., Good, Benjamin H., Arkin, Adam P., Hallatschek, Oskar

“…The fitness effects of all possible mutations available to an organism largely shape the dynamics of evolutionary adaptation. Yet, whether and how this…”
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Engineering Rhodosporidium toruloides for increased lipid production by Zhang, Shuyan, Skerker, Jeffrey M., Rutter, Charles D., Maurer, Matthew J., Arkin, Adam P., Rao, Christopher V.

“…ABSTRACT Oleaginous yeast are promising organisms for the production of lipid‐based chemicals and fuels from simple sugars. In this work, we explored…”
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A method for achieving complete microbial genomes and improving bins from metagenomics data by Lui, Lauren M, Nielsen, Torben N, Arkin, Adam P

“…Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from…”
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High-throughput mapping of the phage resistance landscape in E. coli by Mutalik, Vivek K, Adler, Benjamin A, Rishi, Harneet S, Piya, Denish, Zhong, Crystal, Koskella, Britt, Kutter, Elizabeth M, Calendar, Richard, Novichkov, Pavel S, Price, Morgan N, Deutschbauer, Adam M, Arkin, Adam P

“…Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical…”
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The essential gene set of a photosynthetic organism by Rubin, Benjamin E., Wetmore, Kelly M., Price, Morgan N., Diamond, Spencer, Shultzaberger, Ryan K., Lowe, Laura C., Curtin, Genevieve, Arkin, Adam P., Deutschbauer, Adam, Golden, Susan S.

“…Synechococcus elongatusPCC 7942 is a model organism used for studying photosynthesis and the circadian clock, and it is being developed for the production of…”
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Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) by Lucks, Julius B, Mortimer, Stefanie A, Trapnell, Cole, Luo, Shujun, Aviran, Sharon, Schroth, Gary P, Pachter, Lior, Doudna, Jennifer A, Arkin, Adam P

“…New regulatory roles continue to emerge for both natural and engineered noncoding RNAs, many of which have specific secondary and tertiary structures essential…”
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CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification by Oakes, Benjamin L., Fellmann, Christof, Rishi, Harneet, Taylor, Kian L., Ren, Shawn M., Nadler, Dana C., Yokoo, Rayka, Arkin, Adam P., Doudna, Jennifer A., Savage, David F.

“…The ability to engineer natural proteins is pivotal to a future, pragmatic biology. CRISPR proteins have revolutionized genome modification, yet the…”
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Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons by Wetmore, Kelly M, Price, Morgan N, Waters, Robert J, Lamson, Jacob S, He, Jennifer, Hoover, Cindi A, Blow, Matthew J, Bristow, James, Butland, Gareth, Arkin, Adam P, Deutschbauer, Adam

“…Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq…”
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Versatile RNA-sensing transcriptional regulators for engineering genetic networks by Lucks, Julius B, Qi, Lei, Mutalik, Vivek K, Wang, Denise, Arkin, Adam P

“…The widespread natural ability of RNA to sense small molecules and regulate genes has become an important tool for synthetic biology in applications as diverse…”
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Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity by Tian, Renmao, Ning, Daliang, He, Zhili, Zhang, Ping, Spencer, Sarah J, Gao, Shuhong, Shi, Weiling, Wu, Linwei, Zhang, Ya, Yang, Yunfeng, Adams, Benjamin G, Rocha, Andrea M, Detienne, Brittny L, Lowe, Kenneth A, Joyner, Dominique C, Klingeman, Dawn M, Arkin, Adam P, Fields, Matthew W, Hazen, Terry C, Stahl, David A, Alm, Eric J, Zhou, Jizhong

“…The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment,…”
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