Search | Virtual Health Library

1.

CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification.

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.

Cell ; 176(1-2): 254-267.e16, 2019 01 10.

Article in English | MEDLINE | ID: mdl-30633905

2.

Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

Qi, Lei S; Larson, Matthew H; Gilbert, Luke A; Doudna, Jennifer A; Weissman, Jonathan S; Arkin, Adam P; Lim, Wendell A.

Cell ; 184(3): 844, 2021 Feb 04.

Article in English | MEDLINE | ID: mdl-33545038

3.

Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

Qi, Lei S; Larson, Matthew H; Gilbert, Luke A; Doudna, Jennifer A; Weissman, Jonathan S; Arkin, Adam P; Lim, Wendell A.

Cell ; 152(5): 1173-83, 2013 Feb 28.

Article in English | MEDLINE | ID: mdl-23452860

4.

Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages.

Piya, Denish; Nolan, Nicholas; Moore, Madeline L; Ramirez Hernandez, Luis A; Cress, Brady F; Young, Ry; Arkin, Adam P; Mutalik, Vivek K.

PLoS Biol ; 21(12): e3002416, 2023 Dec.

Article in English | MEDLINE | ID: mdl-38048319

5.

Redefining fundamental concepts of transcription initiation in bacteria.

Mejía-Almonte, Citlalli; Busby, Stephen J W; Wade, Joseph T; van Helden, Jacques; Arkin, Adam P; Stormo, Gary D; Eilbeck, Karen; Palsson, Bernhard O; Galagan, James E; Collado-Vides, Julio.

Nat Rev Genet ; 21(11): 699-714, 2020 11.

Article in English | MEDLINE | ID: mdl-32665585

6.

Network news: innovations in 21st century systems biology.

Arkin, Adam P; Schaffer, David V.

Cell ; 144(6): 844-9, 2011 Mar 18.

Article in English | MEDLINE | ID: mdl-21414475

7.

Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins.

Adler, Benjamin A; Chamakura, Karthik; Carion, Heloise; Krog, Jonathan; Deutschbauer, Adam M; Young, Ry; Mutalik, Vivek K; Arkin, Adam P.

Nat Chem Biol ; 19(6): 759-766, 2023 06.

Article in English | MEDLINE | ID: mdl-36805702

8.

Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics.

Price, Morgan N; Deutschbauer, Adam M; Arkin, Adam P.

PLoS Genet ; 18(4): e1010156, 2022 04.

Article in English | MEDLINE | ID: mdl-35417463

9.

Evaluating E. coli genome-scale metabolic model accuracy with high-throughput mutant fitness data.

Bernstein, David B; Akkas, Batu; Price, Morgan N; Arkin, Adam P.

Mol Syst Biol ; 19(12): e11566, 2023 Dec 06.

Article in English | MEDLINE | ID: mdl-37888487

10.

Eliminating genes for a two-component system increases PHB productivity in Cupriavidus basilensis 4G11 under PHB suppressing, nonstress conditions.

Sander, Kyle; Abel, Anthony J; Friedline, Skyler; Sharpless, William; Skerker, Jeffrey; Deutschbauer, Adam; Clark, Douglas S; Arkin, Adam P.

Biotechnol Bioeng ; 121(1): 139-156, 2024 01.

Article in English | MEDLINE | ID: mdl-37638652

11.

Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide.

Hunt, Kristopher A; Carr, Alex V; Otwell, Anne E; Valenzuela, Jacob J; Walker, Kathleen S; Dixon, Emma R; Lui, Lauren M; Nielsen, Torben N; Bowman, Samuel; von Netzer, Frederick; Moon, Ji-Won; Schadt, Christopher W; Rodriguez, Miguel; Lowe, Kenneth; Joyner, Dominique; Davis, Katherine J; Wu, Xiaoqin; Chakraborty, Romy; Fields, Matthew W; Zhou, Jizhong; Hazen, Terry C; Arkin, Adam P; Wankel, Scott D; Baliga, Nitin S; Stahl, David A.

Environ Sci Technol ; 58(16): 7056-7065, 2024 Apr 23.

Article in English | MEDLINE | ID: mdl-38608141

12.

Mutant phenotypes for thousands of bacterial genes of unknown function.

Price, Morgan N; Wetmore, Kelly M; Waters, R Jordan; Callaghan, Mark; Ray, Jayashree; Liu, Hualan; Kuehl, Jennifer V; Melnyk, Ryan A; Lamson, Jacob S; Suh, Yumi; Carlson, Hans K; Esquivel, Zuelma; Sadeeshkumar, Harini; Chakraborty, Romy; Zane, Grant M; Rubin, Benjamin E; Wall, Judy D; Visel, Axel; Bristow, James; Blow, Matthew J; Arkin, Adam P; Deutschbauer, Adam M.

Nature ; 557(7706): 503-509, 2018 05.

Article in English | MEDLINE | ID: mdl-29769716

13.

Four families of folate-independent methionine synthases.

Price, Morgan N; Deutschbauer, Adam M; Arkin, Adam P.

PLoS Genet ; 17(2): e1009342, 2021 02.

Article in English | MEDLINE | ID: mdl-33534785

14.

Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone.

Wu, Xiaoqin; Gushgari-Doyle, Sara; Lui, Lauren M; Hendrickson, Andrew J; Liu, Yina; Jagadamma, Sindhu; Nielsen, Torben N; Justice, Nicholas B; Simmons, Tuesday; Hess, Nancy J; Joyner, Dominique C; Hazen, Terry C; Arkin, Adam P; Chakraborty, Romy.

Appl Environ Microbiol ; 89(6): e0050023, 2023 06 28.

Article in English | MEDLINE | ID: mdl-37272792

15.

Data-driven flow-map models for data-efficient discovery of dynamics and fast uncertainty quantification of biological and biochemical systems.

Makrygiorgos, Georgios; Berliner, Aaron J; Shi, Fengzhe; Clark, Douglas S; Arkin, Adam P; Mesbah, Ali.

Biotechnol Bioeng ; 120(3): 803-818, 2023 03.

Article in English | MEDLINE | ID: mdl-36453664

16.

High-throughput mapping of the phage resistance landscape in E. coli.

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.

PLoS Biol ; 18(10): e3000877, 2020 10.

Article in English | MEDLINE | ID: mdl-33048924

17.

Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products.

Adams, Jeremy David; Sander, Kyle B; Criddle, Craig S; Arkin, Adam P; Clark, Douglas S.

Microb Cell Fact ; 22(1): 69, 2023 Apr 12.

Article in English | MEDLINE | ID: mdl-37046248

18.

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.

Seaver, Samuel M D; Liu, Filipe; Zhang, Qizhi; Jeffryes, James; Faria, José P; Edirisinghe, Janaka N; Mundy, Michael; Chia, Nicholas; Noor, Elad; Beber, Moritz E; Best, Aaron A; DeJongh, Matthew; Kimbrel, Jeffrey A; D'haeseleer, Patrik; McCorkle, Sean R; Bolton, Jay R; Pearson, Erik; Canon, Shane; Wood-Charlson, Elisha M; Cottingham, Robert W; Arkin, Adam P; Henry, Christopher S.

Nucleic Acids Res ; 49(D1): D575-D588, 2021 01 08.

Article in English | MEDLINE | ID: mdl-32986834

19.

Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments.

Goff, Jennifer L; Szink, Elizabeth G; Thorgersen, Michael P; Putt, Andrew D; Fan, Yupeng; Lui, Lauren M; Nielsen, Torben N; Hunt, Kristopher A; Michael, Jonathan P; Wang, Yajiao; Ning, Daliang; Fu, Ying; Van Nostrand, Joy D; Poole, Farris L; Chandonia, John-Marc; Hazen, Terry C; Stahl, David A; Zhou, Jizhong; Arkin, Adam P; Adams, Michael W W.

Environ Microbiol ; 24(11): 5546-5560, 2022 11.

Article in English | MEDLINE | ID: mdl-36053980

20.

Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes.

Sanchez, Monica R; Payen, Celia; Cheong, Frances; Hovde, Blake T; Bissonnette, Sarah; Arkin, Adam P; Skerker, Jeffrey M; Brem, Rachel B; Caudy, Amy A; Dunham, Maitreya J.

Genome Res ; 29(3): 396-406, 2019 03.

Article in English | MEDLINE | ID: mdl-30635343

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CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification.

Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages.

Redefining fundamental concepts of transcription initiation in bacteria.

Network news: innovations in 21st century systems biology.

Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins.

Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics.

Evaluating E. coli genome-scale metabolic model accuracy with high-throughput mutant fitness data.

Eliminating genes for a two-component system increases PHB productivity in Cupriavidus basilensis 4G11 under PHB suppressing, nonstress conditions.

Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide.

Mutant phenotypes for thousands of bacterial genes of unknown function.

Four families of folate-independent methionine synthases.

Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone.

Data-driven flow-map models for data-efficient discovery of dynamics and fast uncertainty quantification of biological and biochemical systems.

High-throughput mapping of the phage resistance landscape in E. coli.

Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products.

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.

Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments.

Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes.