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Adam P. Arkin - Publications

University of California, Berkeley, Berkeley, CA 
cellular regulatory networks

335 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Kosina SM, Rademacher P, Wetmore KM, de Raad M, Zemla M, Zane GM, Zulovich JJ, Chakraborty R, Bowen BP, Wall JD, Auer M, Arkin AP, Deutschbauer AM, Northen TR. Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Co-culture Biofilms. Frontiers in Microbiology. 12: 757856. PMID 34956122 DOI: 10.3389/fmicb.2021.757856  1
2021 Adler BA, Kazakov AE, Zhong C, Liu H, Kutter E, Lui LM, Nielsen TN, Carion H, Deutschbauer AM, Mutalik VK, Arkin AP. The genetic basis of phage susceptibility, cross-resistance and host-range in . Microbiology (Reading, England). 167. PMID 34910616 DOI: 10.1099/mic.0.001126  1
2021 Skerker JM, Pianalto KM, Mondo SJ, Yang K, Arkin AP, Keller NP, Grigoriev IV, Louise Glass NL. Chromosome assembled and annotated genome sequence of Aspergillus flavus NRRL 3357. G3 (Bethesda, Md.). 11. PMID 34849826 DOI: 10.1093/g3journal/jkab213  1
2021 McNulty MJ, Berliner AJ, Negulescu PG, McKee L, Hart O, Yates K, Arkin AP, Nandi S, McDonald KA. Evaluating the Cost of Pharmaceutical Purification for a Long-Duration Space Exploration Medical Foundry. Frontiers in Microbiology. 12: 700863. PMID 34707576 DOI: 10.3389/fmicb.2021.700863  1
2021 Song F, Kuehl JV, Chandran A, Arkin AP. A Simple, Cost-Effective, and Automation-Friendly Direct PCR Approach for Bacterial Community Analysis. Msystems. e0022421. PMID 34581599 DOI: 10.1128/mSystems.00224-21  1
2021 Paradis CJ, Miller JI, Moon JW, Spencer SJ, Lui LM, Van Nostrand JD, Ning D, Steen AD, McKay LD, Arkin AP, Zhou J, Alm EJ, Hazen TC. Sustained ability of a natural microbial community to remove nitrate from groundwater. Ground Water. PMID 34490626 DOI: 10.1111/gwat.13132  1
2021 Thorgersen MP, Xue J, Majumder ELW, Trotter VV, Ge X, Poole FL, Owens TK, Lui LM, Nielsen TN, Arkin AP, Deutschbauer AM, Siuzdak G, Adams MWW. Deciphering Microbial Metal Toxicity Responses using RB-TnSeq and Activity-Based Metabolomics. Applied and Environmental Microbiology. AEM0103721. PMID 34432491 DOI: 10.1128/AEM.01037-21  1
2021 Cestellos-Blanco S, Friedline S, Sander KB, Abel AJ, Kim JM, Clark DS, Arkin AP, Yang P. Production of PHB From CO-Derived Acetate With Minimal Processing Assessed for Space Biomanufacturing. Frontiers in Microbiology. 12: 700010. PMID 34394044 DOI: 10.3389/fmicb.2021.700010  0.04
2021 Kothari A, Roux S, Zhang H, Prieto A, Soneja D, Chandonia JM, Spencer S, Wu X, Altenburg S, Fields MW, Deutschbauer AM, Arkin AP, Alm EJ, Chakraborty R, Mukhopadhyay A. Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance. Msystems. e0053721. PMID 34184913 DOI: 10.1128/mSystems.00537-21  1
2021 Lui LM, Nielsen TN, Arkin AP. A method for achieving complete microbial genomes and improving bins from metagenomics data. Plos Computational Biology. 17: e1008972. PMID 33961626 DOI: 10.1371/journal.pcbi.1008972  1
2021 Lui LM, Majumder EL, Smith HJ, Carlson HK, von Netzer F, Fields MW, Stahl DA, Zhou J, Hazen TC, Baliga NS, Adams PD, Arkin AP. Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. Frontiers in Microbiology. 12: 642422. PMID 33841364 DOI: 10.3389/fmicb.2021.642422  1
2021 Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, ... ... Arkin AP, et al. Author Correction: A genomic catalog of Earth's microbiomes. Nature Biotechnology. PMID 33795890 DOI: 10.1038/s41587-021-00898-4  1
2021 Wall JD, Zane GM, Juba TR, Kuehl JV, Ray J, Chhabra SR, Trotter VV, Shatsky M, De León KB, Keller KL, Bender KS, Butland G, Arkin AP, Deutschbauer AM. Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. Microbiology Resource Announcements. 10. PMID 33737356 DOI: 10.1128/MRA.00072-21  1
2021 McNulty MJ, Xiong YM, Yates K, Karuppanan K, Hilzinger JM, Berliner AJ, Delzio J, Arkin AP, Lane NE, Nandi S, McDonald KA. Molecular pharming to support human life on the moon, mars, and beyond. Critical Reviews in Biotechnology. 1-16. PMID 33715563 DOI: 10.1080/07388551.2021.1888070  0.12
2021 Liu H, Shiver AL, Price MN, Carlson HK, Trotter VV, Chen Y, Escalante V, Ray J, Hern KE, Petzold CJ, Turnbaugh PJ, Huang KC, Arkin AP, Deutschbauer AM. Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments. Cell Reports. 34: 108789. PMID 33657378 DOI: 10.1016/j.celrep.2021.108789  1
2021 Carim S, Azadeh AL, Kazakov AE, Price MN, Walian PJ, Lui LM, Nielsen TN, Chakraborty R, Deutschbauer AM, Mutalik VK, Arkin AP. Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins. The Isme Journal. PMID 33649553 DOI: 10.1038/s41396-021-00921-1  1
2021 Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 184: 844. PMID 33545038 DOI: 10.1016/j.cell.2021.01.019  1
2021 Price MN, Deutschbauer AM, Arkin AP. Four families of folate-independent methionine synthases. Plos Genetics. 17: e1009342. PMID 33534785 DOI: 10.1371/journal.pgen.1009342  1
2020 do Amaral FP, Tuleski TR, Pankievicz VCS, Melnyk RA, Arkin AP, Griffitts J, Tadra-Sfeir MZ, Maltempi de Souza E, Deutschbauer A, Monteiro RA, Stacey G. Diverse Bacterial Genes Modulate Plant Root Association by Beneficial Bacteria. Mbio. 11. PMID 33323518 DOI: 10.1128/mBio.03078-20  1
2020 Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, ... ... Arkin AP, et al. Publisher Correction: A genomic catalog of Earth's microbiomes. Nature Biotechnology. PMID 33208936 DOI: 10.1038/s41587-020-00769-4  1
2020 Ge X, Thorgersen MP, Poole FL, Deutschbauer AM, Chandonia JM, Novichkov PS, Gushgari-Doyle S, Lui LM, Nielsen T, Chakraborty R, Adams PD, Arkin AP, Hazen TC, Adams MWW. Characterization of a Metal-Resistant Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation. Frontiers in Microbiology. 11: 587127. PMID 33193240 DOI: 10.3389/fmicb.2020.587127  1
2020 Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber ME, Best AA, DeJongh M, Kimbrel JA, D'haeseleer P, McCorkle SR, ... ... Arkin AP, et al. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Research. PMID 33179751 DOI: 10.1093/nar/gkaa1143  1
2020 Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, ... ... Arkin AP, et al. A genomic catalog of Earth's microbiomes. Nature Biotechnology. PMID 33169036 DOI: 10.1038/s41587-020-0718-6  1
2020 Ge X, Thorgersen MP, Poole FL, Deutschbauer AM, Chandonia JM, Novichkov PS, Adams PD, Arkin AP, Hazen TC, Adams MWW. Draft Genome Sequence of sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment. Microbiology Resource Announcements. 9. PMID 33122416 DOI: 10.1128/MRA.01149-20  1
2020 Mutalik VK, Adler BA, Rishi HS, Piya D, Zhong C, Koskella B, Kutter EM, Calendar R, Novichkov PS, Price MN, Deutschbauer AM, Arkin AP. High-throughput mapping of the phage resistance landscape in E. coli. Plos Biology. 18: e3000877. PMID 33048924 DOI: 10.1371/journal.pbio.3000877  1
2020 Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber ME, Best AA, DeJongh M, Kimbrel JA, D'haeseleer P, McCorkle SR, ... ... Arkin AP, et al. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Research. PMID 32986834 DOI: 10.1093/nar/gkaa746  1
2020 Wilpiszeski RL, Gionfriddo CM, Wymore AM, Moon JW, Lowe KA, Podar M, Rafie S, Fields MW, Hazen TC, Ge X, Poole F, Adams MWW, Chakraborty R, Fan Y, Van Nostrand JD, ... ... Arkin AP, et al. In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations. Plos One. 15: e0232437. PMID 32986713 DOI: 10.1371/journal.pone.0232437  1
2020 Ning D, Yuan M, Wu L, Zhang Y, Guo X, Zhou X, Yang Y, Arkin AP, Firestone MK, Zhou J. A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming. Nature Communications. 11: 4717. PMID 32948774 DOI: 10.1038/S41467-020-18560-Z  1
2020 Kempher ML, Tao X, Song R, Wu B, Stahl DA, Wall JD, Arkin AP, Zhou A, Zhou J. Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature. Mbio. 11. PMID 32817099 DOI: 10.1128/Mbio.00569-20  1
2020 Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Redefining fundamental concepts of transcription initiation in bacteria. Nature Reviews. Genetics. PMID 32665585 DOI: 10.1038/S41576-020-0254-8  0.04
2020 Price MN, Deutschbauer AM, Arkin AP. GapMind: Automated Annotation of Amino Acid Biosynthesis. Msystems. 5. PMID 32576650 DOI: 10.1128/mSystems.00291-20  1
2020 Moon JW, Paradis CJ, Joyner DC, von Netzer F, Majumder EL, Dixon ER, Podar M, Ge X, Walian PJ, Smith HJ, Wu X, Zane GM, Walker KF, Thorgersen MP, Poole Ii FL, ... ... Arkin AP, et al. Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer. Chemosphere. 255: 126951. PMID 32417512 DOI: 10.1016/J.Chemosphere.2020.126951  1
2020 Carlson HK, Lui LM, Price MN, Kazakov AE, Carr AV, Kuehl JV, Owens TK, Nielsen T, Arkin AP, Deutschbauer AM. Selective carbon sources influence the end products of microbial nitrate respiration. The Isme Journal. PMID 32372050 DOI: 10.1038/S41396-020-0666-7  1
2020 Tian R, Ning D, He Z, Zhang P, Spencer SJ, Gao S, Shi W, Wu L, Zhang Y, Yang Y, Adams BG, Rocha AM, Detienne BL, Lowe KA, Joyner DC, ... ... Arkin AP, et al. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Microbiome. 8: 51. PMID 32252814 DOI: 10.1186/S40168-020-00825-W  1
2019 Anderson DA, Jones RD, Arkin AP, Weiss R. Principles of synthetic biology: a MOOC for an emerging field. Synthetic Biology (Oxford, England). 4: ysz010. PMID 32995535 DOI: 10.1093/Synbio/Ysz010  0.01
2019 Protzko RJ, Hach CA, Coradetti ST, Hackhofer MA, Magosch S, Thieme N, Geiselman GM, Arkin AP, Skerker JM, Dueber JE, Benz JP. Genomewide and Enzymatic Analysis Reveals Efficient d-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides. Msystems. 4. PMID 31848309 DOI: 10.1128/mSystems.00389-19  1
2019 Knott GJ, Cress BF, Liu JJ, Thornton BW, Lew RJ, Al-Shayeb B, Rosenberg DJ, Hammel M, Adler BA, Lobba MJ, Xu M, Arkin AP, Fellmann C, Doudna JA. Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a. Elife. 8. PMID 31397669 DOI: 10.7554/Elife.49110  1
2019 Zelaya AJ, Parker AE, Bailey KL, Zhang P, Van Nostrand J, Ning D, Elias DA, Zhou J, Hazen TC, Arkin AP, Fields MW. High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer. Water Research. 164: 114917. PMID 31387058 DOI: 10.1016/J.Watres.2019.114917  1
2019 Thorgersen MP, Ge X, Poole FL, Price MN, Arkin AP, Adams MWW. Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation. Applied and Environmental Microbiology. PMID 31253673 DOI: 10.1128/Aem.00896-19  1
2019 Thompson MG, Blake-Hedges JM, Cruz-Morales P, Barajas JF, Curran SC, Eiben CB, Harris NC, Benites VT, Gin JW, Sharpless WA, Twigg FF, Skyrud W, Krishna RN, Henrique Pereira J, Baidoo EEK, ... ... Arkin AP, et al. Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Lysine Metabolism. Mbio. 10. PMID 31064836 DOI: 10.1128/Mbio.02577-18  1
2019 Savitskaya J, Protzko RJ, Li FZ, Arkin AP, Dueber JE. Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production. Scientific Reports. 9: 5815. PMID 30967567 DOI: 10.1038/S41598-019-41759-0  1
2019 Price MN, Arkin AP. Curated BLAST for Genomes. Msystems. 4. PMID 30944879 DOI: 10.1128/mSystems.00072-19  1
2019 Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, Arkin AP. Correction: Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. Plos Genetics. 15: e1008106. PMID 30943208 DOI: 10.1371/Journal.Pgen.1008106  1
2019 Otoupal PB, Ito M, Arkin AP, Magnuson JK, Gladden JM, Skerker JM. Multiplexed CRISPR-Cas9-Based Genome Editing of . Msphere. 4. PMID 30894433 DOI: 10.1128/mSphere.00099-19  1
2019 Egbert RG, Rishi HS, Adler BA, McCormick DM, Toro E, Gill RT, Arkin AP. A versatile platform strain for high-fidelity multiplex genome editing. Nucleic Acids Research. PMID 30788501 DOI: 10.1093/Nar/Gkz085  1
2019 Price MN, Ray J, Iavarone AT, Carlson HK, Ryan EM, Malmstrom RR, Arkin AP, Deutschbauer AM. Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. Msystems. 4. PMID 30746495 DOI: 10.1128/mSystems.00297-18  1
2019 Mutalik VK, Novichkov PS, Price MN, Owens TK, Callaghan M, Carim S, Deutschbauer AM, Arkin AP. Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria. Nature Communications. 10: 308. PMID 30659179 DOI: 10.1038/S41467-018-08177-8  1
2019 Sanchez MR, Payen C, Cheong F, Hovde BT, Bissonnette S, Arkin AP, Skerker JM, Brem RB, Caudy AA, Dunham MJ. Transposon insertional mutagenesis in reveals trans-acting effects influencing species-dependent essential genes. Genome Research. PMID 30635343 DOI: 10.1101/Gr.232330.117  1
2019 Oakes BL, Fellmann C, Rishi H, Taylor KL, Ren SM, Nadler DC, Yokoo R, Arkin AP, Doudna JA, Savage DF. CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. Cell. 176: 254-267.e16. PMID 30633905 DOI: 10.1016/J.Cell.2018.11.052  1
2019 Knott GJ, Cress BF, Liu J, Thornton BW, Lew RJ, Al-Shayeb B, Rosenberg DJ, Hammel M, Adler BA, Lobba MJ, Xu M, Arkin AP, Fellmann C, Doudna JA. Author response: Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a Elife. DOI: 10.7554/Elife.49110.037  1
2018 Tei M, Perkins ML, Hsia J, Arcak M, Arkin AP. Designing spatially distributed gene regulatory networks to elicit contrasting patterns. Acs Synthetic Biology. PMID 30540439 DOI: 10.1021/Acssynbio.8B00377  1
2018 Carlson HK, Price MN, Callaghan M, Aaring A, Chakraborty R, Liu H, Kuehl JV, Arkin AP, Deutschbauer AM. The selective pressures on the microbial community in a metal-contaminated aquifer. The Isme Journal. PMID 30523276 DOI: 10.1038/S41396-018-0328-1  1
2018 Weiss CV, Roop JI, Hackley RK, Chuong JN, Grigoriev IV, Arkin AP, Skerker JM, Brem RB. Genetic dissection of interspecific differences in yeast thermotolerance. Nature Genetics. PMID 30297967 DOI: 10.1038/S41588-018-0243-4  1
2018 Ge X, Vaccaro BJ, Thorgersen MP, Poole FL, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, et al. Iron- and Aluminum-Induced Depletion of Molybdenum in Acidic Environments Impedes the Nitrogen Cycle. Environmental Microbiology. PMID 30289197 DOI: 10.1111/1462-2920.14435  1
2018 Smith HJ, Zelaya AJ, De León KB, Chakraborty R, Elias DA, Hazen TC, Arkin AP, Cunningham AB, Fields MW. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. Fems Microbiology Ecology. PMID 30265315 DOI: 10.1093/Femsec/Fiy191  1
2018 Cernak P, Estrela R, Poddar S, Skerker JM, Cheng YF, Carlson AK, Chen B, Glynn VM, Furlan M, Ryan OW, Donnelly MK, Arkin AP, Taylor JW, Cate JHD. Engineering Kluyveromyces marxianus as a Robust Synthetic Biology Platform Host. Mbio. 9. PMID 30254120 DOI: 10.1128/Mbio.01410-18  1
2018 Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 36: 566-569. PMID 29979655 DOI: 10.1038/Nbt.4163  1
2018 Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, Hromada S, Northen T, Arkin AP. Deciphering microbial interactions in synthetic human gut microbiome communities. Molecular Systems Biology. 14: e8157. PMID 29930200 DOI: 10.15252/Msb.20178157  1
2018 Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, ... ... Arkin AP, et al. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature. PMID 29769716 DOI: 10.1038/S41586-018-0124-0  1
2018 Paradis CJ, Dixon ER, Lui LM, Arkin AP, Parker JC, Istok JD, Perfect E, McKay LD, Hazen TC. Improved method for estimating reaction rates during push-pull tests. Ground Water. PMID 29656383 DOI: 10.1111/Gwat.12770  1
2018 Christensen GA, Moon J, Veach AM, Mosher JJ, Wymore AM, van Nostrand JD, Zhou J, Hazen TC, Arkin AP, Elias DA. Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition. Plos One. 13: e0194663. PMID 29558522 DOI: 10.1371/Journal.Pone.0194663  1
2018 Coradetti ST, Pinel D, Geiselman G, Ito M, Mondo S, Reilly MC, Cheng YF, Bauer S, Grigoriev I, Gladden JM, Simmons BA, Brem R, Arkin AP, Skerker JM. Functional genomics of lipid metabolism in the oleaginous yeast. Elife. 7. PMID 29521624 DOI: 10.7554/Elife.32110  1
2018 He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, ... ... Arkin AP, et al. Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning. Mbio. 9. PMID 29463661 DOI: 10.1128/Mbio.02435-17  1
2018 Liu H, Price MN, Waters RJ, Ray J, Carlson HK, Lamson JS, Chakraborty R, Arkin AP, Deutschbauer AM. Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria. Msystems. 3. PMID 29359196 DOI: 10.1128/mSystems.00143-17  1
2018 Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, Arkin AP. Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. Plos Genetics. 14: e1007147. PMID 29324779 DOI: 10.1371/Journal.Pgen.1007147  1
2018 Coradetti ST, Pinel D, Geiselman GM, Ito M, Mondo SJ, Reilly MC, Cheng Y, Bauer S, Grigoriev IV, Gladden JM, Simmons BA, Brem RB, Arkin AP, Skerker JM. Author response: Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides Elife. DOI: 10.7554/Elife.32110.041  1
2017 Zhou A, Lau R, Baran R, Ma J, von Netzer F, Shi W, Gorman-Lewis D, Kempher ML, He Z, Qin Y, Shi Z, Zane GM, Wu L, Bowen BP, Northen TR, ... ... Arkin AP, et al. Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris. Mbio. 8. PMID 29138306 DOI: 10.1128/Mbio.01780-17  1
2017 Yaegashi J, Kirby J, Ito M, Sun J, Dutta T, Mirsiaghi M, Sundstrom ER, Rodriguez A, Baidoo E, Tanjore D, Pray T, Sale K, Singh S, Keasling JD, Simmons BA, ... ... Arkin AP, et al. Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts. Biotechnology For Biofuels. 10: 241. PMID 29075325 DOI: 10.1186/S13068-017-0927-5  1
2017 De León KB, Zane GM, Trotter VV, Krantz GP, Arkin AP, Butland GP, Walian PJ, Fields MW, Wall JD. Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough. Mbio. 8. PMID 29042504 DOI: 10.1128/Mbio.01696-17  1
2017 Rand JM, Pisithkul T, Clark RL, Thiede JM, Mehrer CR, Agnew DE, Campbell CE, Markley AL, Price MN, Ray J, Wetmore KM, Suh Y, Arkin AP, Deutschbauer AM, Amador-Noguez D, et al. A metabolic pathway for catabolizing levulinic acid in bacteria. Nature Microbiology. PMID 28947739 DOI: 10.1038/S41564-017-0028-Z  1
2017 Thorgersen MP, Lancaster WA, Ge X, Zane GM, Wetmore KM, Vaccaro BJ, Poole FL, Younkin AD, Deutschbauer AM, Arkin AP, Wall JD, Adams MWW. Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions. Frontiers in Microbiology. 8: 1529. PMID 28848534 DOI: 10.3389/Fmicb.2017.01529  1
2017 Price MN, Arkin AP. PaperBLAST: Text Mining Papers for Information about Homologs. Msystems. 2. PMID 28845458 DOI: 10.1128/mSystems.00039-17  1
2017 Wu X, Deutschbauer AM, Kazakov AE, Wetmore KM, Cwick BA, Walker RM, Novichkov PS, Arkin AP, Chakraborty R. Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center. Genome Announcements. 5. PMID 28663297 DOI: 10.1128/Genomea.00582-17  1
2017 Sagawa S, Price MN, Deutschbauer AM, Arkin AP. Validating regulatory predictions from diverse bacteria with mutant fitness data. Plos One. 12: e0178258. PMID 28542589 DOI: 10.1371/Journal.Pone.0178258  1
2017 Venturelli OS, Tei M, Bauer S, Chan LJG, Petzold CJ, Arkin AP. Programming mRNA decay to modulate synthetic circuit resource allocation. Nature Communications. 8: 15128. PMID 28443619 DOI: 10.1038/Ncomms15128  1
2017 Birkel GW, Ghosh A, Kumar VS, Weaver D, Ando D, Backman TWH, Arkin AP, Keasling JD, Martín HG. Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. Bmc Bioinformatics. 18: 219. PMID 28420344 DOI: 10.1186/s12859-017-1631-y  1
2017 Birkel GW, Ghosh A, Kumar VS, Weaver D, Ando D, Backman TW, Arkin AP, Keasling JD, Martín HG. The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. Bmc Bioinformatics. 18: 205. PMID 28381205 DOI: 10.1186/S12859-017-1615-Y  1
2017 Zhang P, He Z, Van Nostrand JD, Qin Y, Deng Y, Wu L, Tu Q, Wang J, Schadt CW, W Fields M, Hazen TC, Arkin AP, Stahl DA, Zhou J. Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer. Environmental Science & Technology. PMID 28300407 DOI: 10.1021/Acs.Est.6B02980  1
2017 Rin Kim S, Skerker JM, Iok Kong I, Kim H, Maurer MJ, Zhang GC, Peng D, Wei N, Arkin AP, Jin YS. Metabolic engineering of a haploid strain derived from a triploid industrial yeast for producing cellulosic ethanol. Metabolic Engineering. PMID 28216106 DOI: 10.1016/J.Ymben.2017.02.006  1
2017 Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, Goodwin LA, Kazakov A, Novichkov P, Arkin AP, Hazen TC. Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Standards in Genomic Sciences. 12: 23. PMID 28194258 DOI: 10.1186/S40793-017-0233-7  1
2017 Haliburton JR, Shao W, Deutschbauer A, Arkin A, Abate AR. Genetic interaction mapping with microfluidic-based single cell sequencing. Plos One. 12: e0171302. PMID 28170417 DOI: 10.1371/Journal.Pone.0171302  1
2017 King AJ, Preheim SP, Bailey KL, Robeson MS, Roy Chowdhury T, Crable BR, Hurt RA, Mehlhorn TL, Lowe KA, Phelps TJ, Palumbo AV, Brandt CC, Brown SD, Podar M, Zhang P, ... ... Arkin AP, et al. Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. Environmental Science & Technology. PMID 28112946 DOI: 10.1021/Acs.Est.6B04751  1
2017 Menezes AA, Vilardi RF, Arkin AP, Cohen MJ. Targeted clinical control of trauma patient coagulation through a thrombin dynamics model. Science Translational Medicine. 9. PMID 28053156 DOI: 10.1126/Scitranslmed.Aaf5045  1
2016 Bosak T, Schubotz F, de Santiago-Torio A, Kuehl JV, Carlson HK, Watson N, Daye M, Summons RE, Arkin AP, Deutschbauer AM. System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions. Plos One. 11: e0168719. PMID 28030630 DOI: 10.1371/Journal.Pone.0168719  1
2016 Maurer MJ, Sutardja L, Pinel D, Bauer S, Muehlbauer AL, Ames TD, Skerker JM, Arkin AP. QTL-guided metabolic engineering of a complex trait. Acs Synthetic Biology. PMID 27936603 DOI: 10.1021/Acssynbio.6B00264  1
2016 Thorgersen MP, Lancaster WA, Rajeev L, Ge X, Vaccaro BJ, Poole FL, Arkin AP, Mukhopadhyay A, Adams MW. A Highly Expressed High Molecular Weight S-Layer Complex of Pelosinus Strain UFO1 Binds Uranium. Applied and Environmental Microbiology. PMID 27913415 DOI: 10.1128/Aem.03044-16  1
2016 Price MN, Wetmore KM, Deutschbauer AM, Arkin AP. A Comparison of the Costs and Benefits of Bacterial Gene Expression. Plos One. 11: e0164314. PMID 27711251 DOI: 10.1371/Journal.Pone.0164314  1
2016 Zhang S, Ito M, Skerker JM, Arkin AP, Rao CV. Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation. Applied Microbiology and Biotechnology. PMID 27678117 DOI: 10.1007/S00253-016-7815-Y  1
2016 Vaccaro BJ, Lancaster WA, Thorgersen MP, Zane GM, Younkin AD, Kazakov AE, Wetmore KM, Deutschbauer A, Arkin AP, Novichkov PS, Wall JD, Adams MW. Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri. Applied and Environmental Microbiology. PMID 27474723 DOI: 10.1128/Aem.01845-16  1
2016 Price MN, Arkin AP. A Theoretical Lower Bound for Selection on the Expression Levels of Proteins. Genome Biology and Evolution. PMID 27289091 DOI: 10.1093/Gbe/Evw126  1
2016 Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, et al. The Genome Project-Write. Science (New York, N.Y.). PMID 27256881 DOI: 10.1126/Science.Aaf6850  1
2016 Quarterman J, Skerker JM, Feng X, Liu IY, Zhao H, Arkin AP, Jin YS. Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae. Journal of Biotechnology. PMID 27140870 DOI: 10.1016/J.Jbiotec.2016.04.041  1
2016 Cambray G, Guimaraes JC, Mutalik VK, Lam C, Mai QA, Thimmaiah T, Carothers JM, Arkin AP, Endy D. Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Research. PMID 27131373 DOI: 10.1093/nar/gkw379  1
2016 Oh EJ, Skerker JM, Kim SR, Wei N, Turner TL, Maurer MJ, Arkin AP, Jin YS. Gene amplification on demand accelerates cellobiose utilization in engineered Saccharomyces cerevisiae. Applied and Environmental Microbiology. PMID 27084006 DOI: 10.1128/Aem.00410-16  1
2016 Bassalo MC, Garst AD, Halweg-Edwards AL, Grau WC, Domaille DW, Mutalik V, Arkin AP, Gill RT. Rapid and efficient one-step metabolic pathway integration in E. coli. Acs Synthetic Biology. PMID 27072506 DOI: 10.1021/Acssynbio.5B00187  1
2016 Hemme CL, Green SJ, Rishishwar L, Prakash O, Pettenato A, Chakraborty R, Deutschbauer AM, Van Nostrand JD, Wu L, He Z, Jordan IK, Hazen TC, Arkin AP, Kostka JE, Zhou J. Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community. Mbio. 7. PMID 27048805 DOI: 10.1128/Mbio.02234-15  1
2016 Kosina SM, Danielewicz MA, Mohammed M, Ray J, Suh Y, Yilmaz S, Singh AK, Arkin AP, Deutschbauer AM, Northen TR. Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism. Acs Synthetic Biology. PMID 26885935 DOI: 10.1021/Acssynbio.5B00236  1
2015 Price MN, Arkin AP. Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes. Mbio. 6. PMID 26670382 DOI: 10.1128/Mbio.01302-15  1
2015 Menezes AA, Montague MG, Cumbers J, Hogan JA, Arkin AP. Grand challenges in space synthetic biology. Journal of the Royal Society, Interface / the Royal Society. 12. PMID 26631337 DOI: 10.1098/Rsif.2015.0803  1
2015 Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JD, Wu L, He Z, Chain PS, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, ... Arkin AP, et al. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Frontiers in Microbiology. 6: 1205. PMID 26583008 DOI: 10.3389/Fmicb.2015.01205  1
2015 Venturelli OS, Egbert RG, Arkin AP. Towards engineering biological systems in a broader context. Journal of Molecular Biology. PMID 26546279 DOI: 10.1016/J.Jmb.2015.10.025  1
2015 Stephens CM, Skerker JM, Sekhon MS, Arkin AP, Riley LW. Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections. Genome Announcements. 3. PMID 26543109 DOI: 10.1128/Genomea.01241-15  1
2015 Rubin BE, Wetmore KM, Price MN, Diamond S, Shultzaberger RK, Lowe LC, Curtin G, Arkin AP, Deutschbauer A, Golden SS. The essential gene set of a photosynthetic organism. Proceedings of the National Academy of Sciences of the United States of America. PMID 26508635 DOI: 10.1073/Pnas.1519220112  1
2015 Zhang S, Skerker JM, Rutter CD, Maurer MJ, Arkin AP, Rao CV. Engineering Rhodosporidium toruloides for increased lipid production. Biotechnology and Bioengineering. PMID 26479039 DOI: 10.1002/Bit.25864  1
2015 Freed EF, Winkler JD, Weiss SJ, Garst AD, Mutalik VK, Arkin AP, Knight R, Gill RT. Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits. Acs Synthetic Biology. PMID 26478262 DOI: 10.1021/Acssynbio.5B00133  1
2015 Vaccaro BJ, Thorgersen MP, Lancaster WA, Price MN, Wetmore KM, Poole FL, Deutschbauer A, Arkin AP, Adams MW. Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses. Applied and Environmental Microbiology. PMID 26452555 DOI: 10.1128/Aem.02602-15  1
2015 De León KB, Utturkar SM, Camilleri LB, Elias DA, Arkin AP, Fields MW, Brown SD, Wall JD. Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum. Genome Announcements. 3. PMID 26404608 DOI: 10.1128/Genomea.01090-15  1
2015 García Martín H, Kumar VS, Weaver D, Ghosh A, Chubukov V, Mukhopadhyay A, Arkin A, Keasling JD. A Method to Constrain Genome-Scale Models with 13C Labeling Data. Plos Computational Biology. 11: e1004363. PMID 26379153 DOI: 10.1371/Journal.Pcbi.1004363  1
2015 Thorgersen MP, Lancaster WA, Vaccaro BJ, Poole FL, Rocha AM, Mehlhorn T, Pettenato A, Ray J, Waters RJ, Melnyk RA, Chakraborty R, Hazen TC, Deutschbauer AM, Arkin AP, Adams MW. Molybdenum Availability is Key to Nitrate Removal in Contaminated Groundwater Environments. Applied and Environmental Microbiology. PMID 25979890 DOI: 10.1128/Aem.00917-15  1
2015 Ray J, Waters RJ, Skerker JM, Kuehl JV, Price MN, Huang J, Chakraborty R, Arkin AP, Deutschbauer A. Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site. Genome Announcements. 3. PMID 25977418 DOI: 10.1128/Genomea.00322-15  1
2015 Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, ... ... Arkin AP, et al. Natural bacterial communities serve as quantitative geochemical biosensors. Mbio. 6: e00326-15. PMID 25968645 DOI: 10.1128/Mbio.00326-15  1
2015 Wetmore KM, Price MN, Waters RJ, Lamson JS, He J, Hoover CA, Blow MJ, Bristow J, Butland G, Arkin AP, Deutschbauer A. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. Mbio. 6: e00306-15. PMID 25968644 DOI: 10.1128/Mbio.00306-15  1
2015 Melnyk RA, Youngblut MD, Clark IC, Carlson HK, Wetmore KM, Price MN, Iavarone AT, Deutschbauer AM, Arkin AP, Coates JD. Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich Peptide and methionine sulfoxide reductase. Mbio. 6: e00233-15. PMID 25968643 DOI: 10.1128/Mbio.00233-15  1
2015 Dey SS, Foley JE, Limsirichai P, Schaffer DV, Arkin AP. Orthogonal control of expression mean and variance by epigenetic features at different genomic loci. Molecular Systems Biology. 11: 806. PMID 25943345 DOI: 10.15252/Msb.20145704  1
2015 Zhang P, Wu WM, Van Nostrand JD, Deng Y, He Z, Gihring T, Zhang G, Schadt CW, Watson D, Jardine P, Criddle CS, Brooks S, Marsh TL, Tiedje JM, Arkin AP, et al. Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction. Applied and Environmental Microbiology. 81: 4164-72. PMID 25862231 DOI: 10.1128/Aem.00043-15  1
2015 Zhou A, Hillesland KL, He Z, Schackwitz W, Tu Q, Zane GM, Ma Q, Qu Y, Stahl DA, Wall JD, Hazen TC, Fields MW, Arkin AP, Zhou J. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. The Isme Journal. PMID 25848870 DOI: 10.1038/Ismej.2015.45  1
2015 Zhang P, Van Nostrand JD, He Z, Chakraborty R, Deng Y, Curtis D, Fields M, Hazen TC, Arkin AP, Zhou J. A slow-release substrate stimulates groundwater microbial communities for long-term in-situ Cr(VI) reduction. Environmental Science & Technology. PMID 25835088 DOI: 10.1021/Acs.Est.5B00024  1
2015 Ramsay BD, Hwang C, Woo HL, Carroll SL, Lucas S, Han J, Lapidus AL, Cheng JF, Goodwin LA, Pitluck S, Peters L, Chertkov O, Held B, Detter JC, Han CS, ... ... Arkin AP, et al. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater. Genome Announcements. 3. PMID 25767232 DOI: 10.1128/Genomea.00092-15  1
2015 Carlson HK, Stoeva MK, Justice NB, Sczesnak A, Mullan MR, Mosqueda LA, Kuehl JV, Deutschbauer AM, Arkin AP, Coates JD. Monofluorophosphate is a selective inhibitor of respiratory sulfate-reducing microorganisms. Environmental Science & Technology. 49: 3727-36. PMID 25698072 DOI: 10.1021/Es505843Z  1
2015 Korte HL, Saini A, Trotter VV, Butland GP, Arkin AP, Wall JD. Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth. Environmental Science & Technology. 49: 924-31. PMID 25534748 DOI: 10.1021/Es504484M  1
2015 Carlson HK, Kuehl JV, Hazra AB, Justice NB, Stoeva MK, Sczesnak A, Mullan MR, Iavarone AT, Engelbrektson A, Price MN, Deutschbauer AM, Arkin AP, Coates JD. Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate. The Isme Journal. 9: 1295-305. PMID 25405978 DOI: 10.1038/Ismej.2014.216  1
2015 Menezes AA, Cumbers J, Hogan JA, Arkin AP. Towards synthetic biological approaches to resource utilization on space missions. Journal of the Royal Society, Interface / the Royal Society. 12: 20140715. PMID 25376875 DOI: 10.1098/Rsif.2014.0715  1
2015 Christensen GA, Zane GM, Kazakov AE, Li X, Rodionov DA, Novichkov PS, Dubchak I, Arkin AP, Wall JD. Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH. Journal of Bacteriology. 197: 29-39. PMID 25313388 DOI: 10.1128/Jb.02083-14  1
2015 Whitaker WR, Lee H, Arkin AP, Dueber JE. Avoidance of truncated proteins from unintended ribosome binding sites within heterologous protein coding sequences. Acs Synthetic Biology. 4: 249-57. PMID 24931615 DOI: 10.1021/Sb500003X  1
2014 Price MN, Ray J, Wetmore KM, Kuehl JV, Bauer S, Deutschbauer AM, Arkin AP. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Frontiers in Microbiology. 5: 577. PMID 25400629 DOI: 10.3389/Fmicb.2014.00577  1
2014 Lee S, Geller JT, Torok T, Wu CH, Singer M, Reid FC, Tarjan DR, Hazen TC, Arkin AP, Hillson NJ. Characterization of wastewater treatment plant microbial communities and the effects of carbon sources on diversity in laboratory models. Plos One. 9: e105689. PMID 25148472 DOI: 10.1371/Journal.Pone.0105689  1
2014 Ryan OW, Skerker JM, Maurer MJ, Li X, Tsai JC, Poddar S, Lee ME, DeLoache W, Dueber JE, Arkin AP, Cate JH. Selection of chromosomal DNA libraries using a multiplex CRISPR system. Elife. 3. PMID 25139909 DOI: 10.7554/Elife.03703  1
2014 Deutschbauer A, Price MN, Wetmore KM, Tarjan DR, Xu Z, Shao W, Leon D, Arkin AP, Skerker JM. Towards an informative mutant phenotype for every bacterial gene. Journal of Bacteriology. 196: 3643-55. PMID 25112473 DOI: 10.1128/Jb.01836-14  1
2014 Shao W, Price MN, Deutschbauer AM, Romine MF, Arkin AP. Conservation of transcription start sites within genes across a bacterial genus. Mbio. 5: e01398-14. PMID 24987095 DOI: 10.1128/Mbio.01398-14  1
2014 Gowda H, Ivanisevic J, Johnson CH, Kurczy ME, Benton HP, Rinehart D, Nguyen T, Ray J, Kuehl J, Arevalo B, Westenskow PD, Wang J, Arkin AP, Deutschbauer AM, Patti GJ, et al. Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses. Analytical Chemistry. 86: 6931-9. PMID 24934772 DOI: 10.1021/Ac500734C  1
2014 Rinehart D, Johnson CH, Nguyen T, Ivanisevic J, Benton HP, Lloyd J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G. Metabolomic data streaming for biology-dependent data acquisition. Nature Biotechnology. 32: 524-7. PMID 24911492 DOI: 10.1038/Nbt.2927  1
2014 Kuehl JV, Price MN, Ray J, Wetmore KM, Esquivel Z, Kazakov AE, Nguyen M, Kuehn R, Davis RW, Hazen TC, Arkin AP, Deutschbauer A. Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Mbio. 5: e01041-14. PMID 24865553 DOI: 10.1128/Mbio.01041-14  1
2014 Korte HL, Fels SR, Christensen GA, Price MN, Kuehl JV, Zane GM, Deutschbauer AM, Arkin AP, Wall JD. Genetic basis for nitrate resistance in Desulfovibrio strains. Frontiers in Microbiology. 5: 153. PMID 24795702 DOI: 10.3389/Fmicb.2014.00153  1
2014 Qi LS, Arkin AP. A versatile framework for microbial engineering using synthetic non-coding RNAs. Nature Reviews. Microbiology. 12: 341-54. PMID 24736794 DOI: 10.1038/Nrmicro3244  1
2014 Zhou J, Deng Y, Zhang P, Xue K, Liang Y, Van Nostrand JD, Yang Y, He Z, Wu L, Stahl DA, Hazen TC, Tiedje JM, Arkin AP. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proceedings of the National Academy of Sciences of the United States of America. 111: E836-45. PMID 24550501 DOI: 10.1073/Pnas.1324044111  1
2014 Guimaraes JC, Rocha M, Arkin AP. Transcript level and sequence determinants of protein abundance and noise in Escherichia coli. Nucleic Acids Research. 42: 4791-9. PMID 24510099 DOI: 10.1093/Nar/Gku126  1
2014 Meyer B, Kuehl JV, Price MN, Ray J, Deutschbauer AM, Arkin AP, Stahl DA. The energy-conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf. Environmental Microbiology. 16: 3463-86. PMID 24447568 DOI: 10.1111/1462-2920.12405  1
2014 Guimaraes JC, Rocha M, Arkin AP, Cambray G. D-Tailor: automated analysis and design of DNA sequences. Bioinformatics (Oxford, England). PMID 24398007 DOI: 10.1093/Bioinformatics/Btt742  1
2014 Novichkov PS, Li X, Kuehl JV, Deutschbauer AM, Arkin AP, Price MN, Rodionov DA. Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Environmental Microbiology. 16: 1-8. PMID 24118949 DOI: 10.1111/1462-2920.12273  1
2014 Ryan OW, Skerker JM, Maurer MJ, Li X, Tsai JC, Poddar S, Lee ME, DeLoache W, Dueber JE, Arkin AP, Cate JH. Author response: Selection of chromosomal DNA libraries using a multiplex CRISPR system Elife. DOI: 10.7554/Elife.03703.012  1
2014 Rufino Ferreira AS, Hsia J, Arcak M, Maharbiz M, Arkin A. Pattern formation with a compartmental lateral inhibition system Proceedings of the Ieee Conference On Decision and Control. 2015: 5413-5418. DOI: 10.1109/CDC.2014.7040235  1
2014 Greer DR, Basso TP, Ibanez AB, Bauer S, Skerker JM, Ozcam AE, Leon D, Shin C, Arkin AP, Balsara NP. Fermentation of hydrolysate detoxified by pervaporation through block copolymer membranes Green Chemistry. 16: 4206-4213. DOI: 10.1039/C4Gc00756E  1
2013 Somenahally AC, Mosher JJ, Yuan T, Podar M, Phelps TJ, Brown SD, Yang ZK, Hazen TC, Arkin AP, Palumbo AV, Van Nostrand JD, Zhou J, Elias DA. Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities. Plos One. 8: e83909. PMID 24376771 DOI: 10.1371/Journal.Pone.0083909  1
2013 Arkin AP. A wise consistency: engineering biology for conformity, reliability, predictability. Current Opinion in Chemical Biology. 17: 893-901. PMID 24268562 DOI: 10.1016/J.Cbpa.2013.09.012  1
2013 Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA. RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. Bmc Genomics. 14: 745. PMID 24175918 DOI: 10.1186/1471-2164-14-745  1
2013 Louie KB, Bowen BP, Cheng X, Berleman JE, Chakraborty R, Deutschbauer A, Arkin A, Northen TR. "Replica-extraction-transfer" nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria. Analytical Chemistry. 85: 10856-62. PMID 24111681 DOI: 10.1021/Ac402240Q  1
2013 Deangelis KM, D'Haeseleer P, Chivian D, Simmons B, Arkin AP, Mavromatis K, Malfatti S, Tringe S, Hazen TC. Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. Standards in Genomic Sciences. 7: 382-98. PMID 24019987 DOI: 10.4056/Sigs.3377516  1
2013 Meyer B, Kuehl JV, Deutschbauer AM, Arkin AP, Stahl DA. Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. Journal of Bacteriology. 195: 4900-14. PMID 23974031 DOI: 10.1128/Jb.00504-13  1
2013 Kosuri S, Goodman DB, Cambray G, Mutalik VK, Gao Y, Arkin AP, Endy D, Church GM. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 110: 14024-9. PMID 23924614 DOI: 10.1073/Pnas.1301301110  1
2013 Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, Wall JD, Mukhopadhyay A, Novichkov PS. New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. Journal of Bacteriology. 195: 4466-75. PMID 23913324 DOI: 10.1128/Jb.00679-13  1
2013 Zhou A, He Z, Qin Y, Lu Z, Deng Y, Tu Q, Hemme CL, Van Nostrand JD, Wu L, Hazen TC, Arkin AP, Zhou J. StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses. Environmental Science & Technology. 47: 9841-9. PMID 23889170 DOI: 10.1021/Es4018656  1
2013 Miller-Jensen K, Skupsky R, Shah PS, Arkin AP, Schaffer DV. Genetic selection for context-dependent stochastic phenotypes: Sp1 and TATA mutations increase phenotypic noise in HIV-1 gene expression. Plos Computational Biology. 9: e1003135. PMID 23874178 DOI: 10.1371/Journal.Pcbi.1003135  1
2013 Cardinale S, Joachimiak MP, Arkin AP. Effects of genetic variation on the E. coli host-circuit interface. Cell Reports. 4: 231-7. PMID 23871664 DOI: 10.1016/J.Celrep.2013.06.023  1
2013 Skerker JM, Leon D, Price MN, Mar JS, Tarjan DR, Wetmore KM, Deutschbauer AM, Baumohl JK, Bauer S, Ibáñez AB, Mitchell VD, Wu CH, Hu P, Hazen T, Arkin AP. Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates. Molecular Systems Biology. 9: 674. PMID 23774757 DOI: 10.1038/Msb.2013.30  1
2013 Huh JH, Kittleson JT, Arkin AP, Anderson JC. Modular design of a synthetic payload delivery device. Acs Synthetic Biology. 2: 418-24. PMID 23654275 DOI: 10.1021/Sb300107H  1
2013 Price MN, Deutschbauer AM, Skerker JM, Wetmore KM, Ruths T, Mar JS, Kuehl JV, Shao W, Arkin AP. Indirect and suboptimal control of gene expression is widespread in bacteria. Molecular Systems Biology. 9: 660. PMID 23591776 DOI: 10.1038/Msb.2013.16  1
2013 Brown SD, Utturkar SM, Arkin AP, Deutschbauer AM, Elias DA, Hazen TC, Chakraborty R. Draft Genome Sequence for Desulfovibrio africanus Strain PCS. Genome Announcements. 1: e0014413. PMID 23580709 DOI: 10.1128/Genomea.00144-13  1
2013 Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, Joachimiak MP, Xie M, Song R, Arkin AP, Hazen TC, Keasling JD, Wall JD, Stahl DA, Zhou J. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. The Isme Journal. 7: 1790-802. PMID 23575373 DOI: 10.1038/Ismej.2013.60  1
2013 Cipriano MJ, Novichkov PN, Kazakov AE, Rodionov DA, Arkin AP, Gelfand MS, Dubchak I. RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. Bmc Genomics. 14: 213. PMID 23547897 DOI: 10.1186/1471-2164-14-213  1
2013 Cambray G, Guimaraes JC, Mutalik VK, Lam C, Mai QA, Thimmaiah T, Carothers JM, Arkin AP, Endy D. Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Research. 41: 5139-48. PMID 23511967 DOI: 10.1093/Nar/Gkt163  1
2013 Mutalik VK, Guimaraes JC, Cambray G, Mai QA, Christoffersen MJ, Martin L, Yu A, Lam C, Rodriguez C, Bennett G, Keasling JD, Endy D, Arkin AP. Quantitative estimation of activity and quality for collections of functional genetic elements. Nature Methods. 10: 347-53. PMID 23474467 DOI: 10.1038/Nmeth.2403  1
2013 Mutalik VK, Guimaraes JC, Cambray G, Lam C, Christoffersen MJ, Mai QA, Tran AB, Paull M, Keasling JD, Arkin AP, Endy D. Precise and reliable gene expression via standard transcription and translation initiation elements. Nature Methods. 10: 354-60. PMID 23474465 DOI: 10.1038/Nmeth.2404  1
2013 Kim SR, Skerker JM, Kang W, Lesmana A, Wei N, Arkin AP, Jin YS. Rational and evolutionary engineering approaches uncover a small set of genetic changes efficient for rapid xylose fermentation in Saccharomyces cerevisiae. Plos One. 8: e57048. PMID 23468911 DOI: 10.1371/Journal.Pone.0057048  1
2013 Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 152: 1173-83. PMID 23452860 DOI: 10.1016/J.Cell.2013.02.022  1
2013 Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin AP, Aitchison JD, Adams MW, Baliga NS. Metallochaperones regulate intracellular copper levels. Plos Computational Biology. 9: e1002880. PMID 23349626 DOI: 10.1371/Journal.Pcbi.1002880  1
2013 Wang L, Wang X, Arkin AP, Samoilov MS. Inference of gene regulatory networks from genome-wide knockout fitness data. Bioinformatics (Oxford, England). 29: 338-46. PMID 23271269 DOI: 10.1093/Bioinformatics/Bts634  1
2013 Meyer B, Kuehl J, Deutschbauer AM, Price MN, Arkin AP, Stahl DA. Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. Journal of Bacteriology. 195: 990-1004. PMID 23264581 DOI: 10.1128/Jb.01959-12  1
2013 Chivian D, Dehal PS, Keller K, Arkin AP. MetaMicrobesOnline: phylogenomic analysis of microbial communities. Nucleic Acids Research. 41: D648-54. PMID 23203984 DOI: 10.1093/Nar/Gks1202  1
2013 Kazakov AE, Rodionov DA, Price MN, Arkin AP, Dubchak I, Novichkov PS. Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. Journal of Bacteriology. 195: 29-38. PMID 23086211 DOI: 10.1128/Jb.01977-12  1
2013 Baran R, Bowen BP, Price MN, Arkin AP, Deutschbauer AM, Northen TR. Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. Acs Chemical Biology. 8: 189-99. PMID 23082955 DOI: 10.1021/Cb300477W  1
2013 DeAngelis KM, Chivian D, Fortney JL, Arkin AP, Simmons B, Hazen TC, Silver WL. Changes in microbial dynamics during long-term decomposition in tropical forests Soil Biology and Biochemistry. 66: 60-68. DOI: 10.1016/J.Soilbio.2013.06.010  1
2013 Arkin AP, Fussenegger M. Synthetic biology Current Opinion in Chemical Biology. 17: 869-870. DOI: 10.1016/j.cbpa.2013.11.005  1
2013 Guimaraes JC, Liu CC, Arkin AP. From biological parts to circuit design Synthetic Biology. 63-78. DOI: 10.1016/B978-0-12-394430-6.00004-2  1
2012 Chen D, Arkin AP. Sequestration-based bistability enables tuning of the switching boundaries and design of a latch. Molecular Systems Biology. 8: 620. PMID 23089683 DOI: 10.1038/Msb.2012.52  1
2012 Whitaker WR, Davis SA, Arkin AP, Dueber JE. Engineering robust control of two-component system phosphotransfer using modular scaffolds. Proceedings of the National Academy of Sciences of the United States of America. 109: 18090-5. PMID 23071327 DOI: 10.1073/Pnas.1209230109  1
2012 Liu CC, Qi L, Lucks JB, Segall-Shapiro TH, Wang D, Mutalik VK, Arkin AP. An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Nature Methods. 9: 1088-94. PMID 23023598 DOI: 10.1038/Nmeth.2184  1
2012 Qi L, Haurwitz RE, Shao W, Doudna JA, Arkin AP. RNA processing enables predictable programming of gene expression. Nature Biotechnology. 30: 1002-6. PMID 22983090 DOI: 10.1038/Nbt.2355  1
2012 Bowen De León K, Young ML, Camilleri LB, Brown SD, Skerker JM, Deutschbauer AM, Arkin AP, Fields MW. Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction. Journal of Bacteriology. 194: 5456-7. PMID 22965085 DOI: 10.1128/Jb.01224-12  1
2012 Brown SD, Podar M, Klingeman DM, Johnson CM, Yang ZK, Utturkar SM, Land ML, Mosher JJ, Hurt RA, Phelps TJ, Palumbo AV, Arkin AP, Hazen TC, Elias DA. Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7. Journal of Bacteriology. 194: 5147-8. PMID 22933770 DOI: 10.1128/Jb.01174-12  1
2012 Rajeev L, Hillesland KL, Zane GM, Zhou A, Joachimiak MP, He Z, Zhou J, Arkin AP, Wall JD, Stahl DA. Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. Journal of Bacteriology. 194: 5783-93. PMID 22904289 DOI: 10.1128/Jb.00749-12  1
2012 Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A, Stahl DA. Functional responses of methanogenic archaea to syntrophic growth. The Isme Journal. 6: 2045-55. PMID 22739494 DOI: 10.1038/Ismej.2012.60  1
2012 Novichkov PS, Brettin TS, Novichkova ES, Dehal PS, Arkin AP, Dubchak I, Rodionov DA. RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Research. 40: W604-8. PMID 22700702 DOI: 10.1093/nar/gks562  1
2012 McKee AE, Rutherford BJ, Chivian DC, Baidoo EK, Juminaga D, Kuo D, Benke PI, Dietrich JA, Ma SM, Arkin AP, Petzold CJ, Adams PD, Keasling JD, Chhabra SR. Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli. Microbial Cell Factories. 11: 79. PMID 22694848 DOI: 10.1186/1475-2859-11-79  1
2012 Cardinale S, Arkin AP. Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems. Biotechnology Journal. 7: 856-66. PMID 22649052 DOI: 10.1002/Biot.201200085  1
2012 Chen Z, Friedland GD, Pereira JH, Reveco SA, Chan R, Park JI, Thelen MP, Adams PD, Arkin AP, Keasling JD, Blanch HW, Simmons BA, Sale KL, Chivian D, Chhabra SR. Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. The Journal of Biological Chemistry. 287: 25335-43. PMID 22645145 DOI: 10.1074/Jbc.M112.362640  1
2012 Miller-Jensen K, Dey SS, Pham N, Foley JE, Arkin AP, Schaffer DV. Chromatin accessibility at the HIV LTR promoter sets a threshold for NF-κB mediated viral gene expression. Integrative Biology : Quantitative Biosciences From Nano to Macro. 4: 661-71. PMID 22555315 DOI: 10.1039/C2Ib20009K  1
2012 Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou JZ, Arkin AP, Mukhopadhyay A, Fields MW. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state. Bmc Genomics. 13: 138. PMID 22507456 DOI: 10.1186/1471-2164-13-138  1
2012 Mutalik VK, Qi L, Guimaraes JC, Lucks JB, Arkin AP. Rationally designed families of orthogonal RNA regulators of translation. Nature Chemical Biology. 8: 447-54. PMID 22446835 DOI: 10.1038/Nchembio.919  1
2012 Qi L, Lucks JB, Liu CC, Mutalik VK, Arkin AP. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Research. 40: 5775-86. PMID 22383579 DOI: 10.1093/Nar/Gks168  1
2012 Mosher JJ, Phelps TJ, Podar M, Hurt RA, Campbell JH, Drake MM, Moberly JG, Schadt CW, Brown SD, Hazen TC, Arkin AP, Palumbo AV, Faybishenko BA, Elias DA. Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp. Applied and Environmental Microbiology. 78: 2082-91. PMID 22267668 DOI: 10.1128/Aem.07165-11  1
2012 Dey SS, Xue Y, Joachimiak MP, Friedland GD, Burnett JC, Zhou Q, Arkin AP, Schaffer DV. Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression. The Journal of Biological Chemistry. 287: 7945-55. PMID 22253435 DOI: 10.1074/Jbc.M111.302653  1
2012 Zhou A, Chen YI, Zane GM, He Z, Hemme CL, Joachimiak MP, Baumohl JK, He Q, Fields MW, Arkin AP, Wall JD, Hazen TC, Zhou J. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Applied and Environmental Microbiology. 78: 1168-77. PMID 22156435 DOI: 10.1128/Aem.05666-11  1
2012 Arkin AP. Abstract IA21: Changing chasses and inventing elements: Developing a combined systems biology and engineering approach to designing complex function in cells Cancer Research. 72. DOI: 10.1158/1538-7445.Csb12-Ia21  0.01
2011 Deangelis KM, D'Haeseleer P, Chivian D, Fortney JL, Khudyakov J, Simmons B, Woo H, Arkin AP, Davenport KW, Goodwin L, Chen A, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, et al. Complete genome sequence of "Enterobacter lignolyticus" SCF1. Standards in Genomic Sciences. 5: 69-85. PMID 22180812 DOI: 10.4056/Sigs.2104875  1
2011 Deutschbauer A, Price MN, Wetmore KM, Shao W, Baumohl JK, Xu Z, Nguyen M, Tamse R, Davis RW, Arkin AP. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. Plos Genetics. 7: e1002385. PMID 22125499 DOI: 10.1371/Journal.Pgen.1002385  1
2011 Rajeev L, Luning EG, Dehal PS, Price MN, Arkin AP, Mukhopadhyay A. Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. Genome Biology. 12: R99. PMID 21992415 DOI: 10.1186/Gb-2011-12-10-R99  1
2011 Jajamovich GH, Wang X, Arkin AP, Samoilov MS. Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites. Nucleic Acids Research. 39: e146. PMID 21948794 DOI: 10.1093/Nar/Gkr745  1
2011 Chhabra SR, Butland G, Elias DA, Chandonia JM, Fok OY, Juba TR, Gorur A, Allen S, Leung CM, Keller KL, Reveco S, Zane GM, Semkiw E, Prathapam R, Gold B, ... ... Arkin AP, et al. Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome. Applied and Environmental Microbiology. 77: 7595-604. PMID 21908633 DOI: 10.1128/Aem.05495-11  1
2011 Cambray G, Mutalik VK, Arkin AP. Toward rational design of bacterial genomes. Current Opinion in Microbiology. 14: 624-30. PMID 21865081 DOI: 10.1016/J.Mib.2011.08.001  1
2011 Price MN, Deutschbauer AM, Kuehl JV, Liu H, Witkowska HE, Arkin AP. Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. 193: 5716-27. PMID 21840973 DOI: 10.1128/Jb.05563-11  1
2011 Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, ... Arkin AP, et al. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. Bmc Genomics. 12: S3. PMID 21810205 DOI: 10.1186/1471-2164-12-S1-S3  1
2011 Liu P, Meagher RJ, Light YK, Yilmaz S, Chakraborty R, Arkin AP, Hazen TC, Singh AK. Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH). Lab On a Chip. 11: 2673-9. PMID 21755095 DOI: 10.1039/C1Lc20151D  1
2011 Chhabra SR, Joachimiak MP, Petzold CJ, Zane GM, Price MN, Reveco SA, Fok V, Johanson AR, Batth TS, Singer M, Chandonia JM, Joyner D, Hazen TC, Arkin AP, Wall JD, et al. Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. Plos One. 6: e21470. PMID 21738675 DOI: 10.1371/Journal.Pone.0021470  1
2011 Miller-Jensen K, Dey SS, Schaffer DV, Arkin AP. Varying virulence: epigenetic control of expression noise and disease processes. Trends in Biotechnology. 29: 517-25. PMID 21700350 DOI: 10.1016/J.Tibtech.2011.05.004  1
2011 Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure. Proceedings of the National Academy of Sciences of the United States of America. 108: 11069-74. PMID 21642536 DOI: 10.1073/Pnas.1106541108  1
2011 Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proceedings of the National Academy of Sciences of the United States of America. 108: 11063-8. PMID 21642531 DOI: 10.1073/Pnas.1106501108  1
2011 Bates JT, Chivian D, Arkin AP. GLAMM: Genome-Linked Application for Metabolic Maps. Nucleic Acids Research. 39: W400-5. PMID 21624891 DOI: 10.1093/Nar/Gkr433  1
2011 Gerasimova A, Kazakov AE, Arkin AP, Dubchak I, Gelfand MS. Comparative genomics of the dormancy regulons in mycobacteria. Journal of Bacteriology. 193: 3446-52. PMID 21602344 DOI: 10.1128/Jb.00179-11  1
2011 Zhou J, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, Arkin AP. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nature Reviews. Microbiology. 9: 452-66. PMID 21572460 DOI: 10.1038/Nrmicro2575  1
2011 Lucks JB, Qi L, Mutalik VK, Wang D, Arkin AP. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proceedings of the National Academy of Sciences of the United States of America. 108: 8617-22. PMID 21555549 DOI: 10.1073/Pnas.1015741108  1
2011 Arkin AP, Schaffer DV. Network news: innovations in 21st century systems biology. Cell. 144: 844-9. PMID 21414475 DOI: 10.1016/J.Cell.2011.03.008  1
2011 Huang YW, Arkin AP, Chandonia JM. WIST: toolkit for rapid, customized LIMS development. Bioinformatics (Oxford, England). 27: 437-8. PMID 21258060 DOI: 10.1093/Bioinformatics/Btq676  1
2011 Liu CC, Qi L, Yanofsky C, Arkin AP. Regulation of transcription by unnatural amino acids. Nature Biotechnology. 29: 164-8. PMID 21240267 DOI: 10.1038/Nbt.1741  1
2011 Patti GJ, Tautenhahn R, Fonslow BR, Cho Y, Deutschbauer A, Arkin A, Northen T, Siuzdak G. Meta-analysis of global metabolomics and proteomics data to link alterations with phenotype Spectroscopy. 26: 151-154. DOI: 10.3233/Spe-2011-0534  1
2011 Lucks J, Arkin A. The hunt for the biological transistor Ieee Spectrum. 48: 38-43. DOI: 10.1109/Mspec.2011.5719724  1
2011 Morimoto M, Arkin A, Poolla K. Modeling sporulation decisions in Bacillus subtilis as optimal evolutionary decision-making Proceedings of the American Control Conference. 3508-3513.  1
2011 Densmore D, Horowitz M, Krishnaswamy S, Shen X, Arkin A, Winfree E, Voigt C. Joint DAC/IWBDA special session design and synthesis of biological circuits Proceedings - Design Automation Conference. 114-115.  1
2010 Liu CC, Arkin AP. Cell biology. The case for RNA. Science (New York, N.Y.). 330: 1185-6. PMID 21109657 DOI: 10.1126/Science.1199495  1
2010 Willerth SM, Pedro HA, Pachter L, Humeau LM, Arkin AP, Schaffer DV. Development of a low bias method for characterizing viral populations using next generation sequencing technology. Plos One. 5: e13564. PMID 21042592 DOI: 10.1371/Journal.Pone.0013564  1
2010 Skupsky R, Burnett JC, Foley JE, Schaffer DV, Arkin AP. HIV promoter integration site primarily modulates transcriptional burst size rather than frequency. Plos Computational Biology. 6. PMID 20941390 DOI: 10.1371/Journal.Pcbi.1000952  1
2010 Hemme CL, Mouttaki H, Lee YJ, Zhang G, Goodwin L, Lucas S, Copeland A, Lapidus A, Glavina del Rio T, Tice H, Saunders E, Brettin T, Detter JC, Han CS, Pitluck S, ... ... Arkin AP, et al. Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. Journal of Bacteriology. 192: 6494-6. PMID 20889752 DOI: 10.1128/Jb.01064-10  1
2010 Aviran S, Shah PS, Schaffer DV, Arkin AP. Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles. Plos Computational Biology. 6. PMID 20711350 DOI: 10.1371/Journal.Pcbi.1000883  1
2010 Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Research. 38: W299-307. PMID 20542910 DOI: 10.1093/Nar/Gkq531  1
2010 Oh J, Fung E, Price MN, Dehal PS, Davis RW, Giaever G, Nislow C, Arkin AP, Deutschbauer A. A universal TagModule collection for parallel genetic analysis of microorganisms. Nucleic Acids Research. 38: e146. PMID 20494978 DOI: 10.1093/Nar/Gkq419  1
2010 Zhou A, He Z, Redding-Johanson AM, Mukhopadhyay A, Hemme CL, Joachimiak MP, Luo F, Deng Y, Bender KS, He Q, Keasling JD, Stahl DA, Fields MW, Hazen TC, Arkin AP, et al. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environmental Microbiology. 12: 2645-57. PMID 20482586 DOI: 10.1111/J.1462-2920.2010.02234.X  1
2010 He Q, He Z, Joyner DC, Joachimiak M, Price MN, Yang ZK, Yen HC, Hemme CL, Chen W, Fields MM, Stahl DA, Keasling JD, Keller M, Arkin AP, Hazen TC, et al. Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris. The Isme Journal. 4: 1386-97. PMID 20445634 DOI: 10.1038/Ismej.2010.59  1
2010 Burnett JC, Lim KI, Calafi A, Rossi JJ, Schaffer DV, Arkin AP. Combinatorial latency reactivation for HIV-1 subtypes and variants. Journal of Virology. 84: 5958-74. PMID 20357084 DOI: 10.1128/Jvi.00161-10  1
2010 Andrews SS, Addy NJ, Brent R, Arkin AP. Detailed simulations of cell biology with Smoldyn 2.1. Plos Computational Biology. 6: e1000705. PMID 20300644 DOI: 10.1371/Journal.Pcbi.1000705  1
2010 Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. Plos One. 5: e9490. PMID 20224823 DOI: 10.1371/Journal.Pone.0009490  1
2010 Anderson JC, Dueber JE, Leguia M, Wu GC, Goler JA, Arkin AP, Keasling JD. BglBricks: A flexible standard for biological part assembly. Journal of Biological Engineering. 4: 1. PMID 20205762 DOI: 10.1186/1754-1611-4-1  1
2010 He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, Phan R, Mukhopadhyay A, Hemme CL, Huang K, Alm EJ, Fields MW, Wall J, Stahl D, Hazen TC, ... ... Arkin AP, et al. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation. Applied and Environmental Microbiology. 76: 1574-86. PMID 20038696 DOI: 10.1128/Aem.02141-09  1
2010 Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Research. 38: D396-400. PMID 19906701 DOI: 10.1093/Nar/Gkp919  1
2010 Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA. RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Research. 38: D111-8. PMID 19884135 DOI: 10.1093/Nar/Gkp894  1
2010 Mosher JJ, Drake MM, Carroll SL, Yang ZK, Schadt CW, Brown SD, Podar M, Hazen TC, Arkin AP, Phelps TJ, Palumbo AV, Faybishenko BA, Elias DA. Microbial Community Dynamics of Lactate Enriched Hanford Groundwaters Lawrence Berkeley National Laboratory. DOI: 10.2172/986244  1
2010 Zhou A, Hillesland K, He Z, Joachimiak M, Zane G, Dehal P, Arkin A, Stahl D, Wall J, Hazen T, Zhou J, Baidoo E, Benke P, Mukhopadhyay A. Genetic Adaptation to Salt Stress in Experimental Evolution of Desulfovibrio vulgaris Hildenborough Lawrence Berkeley National Laboratory. DOI: 10.2172/985929  1
2010 Burns A, Joachimiak M, Deutschbauer A, Arkin A, Bender K. Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough Lawrence Berkeley National Laboratory. DOI: 10.2172/985922  1
2010 Timberlake S, Joachimiak M, Joyner D, Chakraborty R, Baumohl J, Dehal P, Arkin A, Hazen T, Alm E. Conservation of Modules but not Phenotype in Bacterial Response to Environmental Stress Lawrence Berkeley National Laboratory. DOI: 10.2172/985921  1
2010 Jajamovich GH, Samoilov MS, Wang X, Arkin AP. Inference of binding sites with a Bayesian multiple-instance motif discovery method 2010 48th Annual Allerton Conference On Communication, Control, and Computing, Allerton 2010. 487-494. DOI: 10.1109/ALLERTON.2010.5706946  1
2009 Skerker JM, Lucks JB, Arkin AP. Evolution, ecology and the engineered organism: lessons for synthetic biology. Genome Biology. 10: 114. PMID 19941672 DOI: 10.1186/Gb-2009-10-11-114  1
2009 Walker CB, Stolyar S, Chivian D, Pinel N, Gabster JA, Dehal PS, He Z, Yang ZK, Yen HC, Zhou J, Wall JD, Hazen TC, Arkin AP, Stahl DA. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity. Environmental Microbiology. 11: 2244-52. PMID 19737303 DOI: 10.1111/J.1462-2920.2009.01946.X  1
2009 Tang YJ, Martin HG, Deutschbauer A, Feng X, Huang R, Llora X, Arkin A, Keasling JD. Invariability of central metabolic flux distribution in Shewanella oneidensis MR-1 under environmental or genetic perturbations. Biotechnology Progress. 25: 1254-9. PMID 19610125 DOI: 10.1002/Btpr.227  1
2009 Walker CB, He Z, Yang ZK, Ringbauer JA, He Q, Zhou J, Voordouw G, Wall JD, Arkin AP, Hazen TC, Stolyar S, Stahl DA. The electron transfer system of syntrophically grown Desulfovibrio vulgaris. Journal of Bacteriology. 191: 5793-801. PMID 19581361 DOI: 10.1128/Jb.00356-09  1
2009 Bischofs IB, Hug JA, Liu AW, Wolf DM, Arkin AP. Complexity in bacterial cell-cell communication: quorum signal integration and subpopulation signaling in the Bacillus subtilis phosphorelay. Proceedings of the National Academy of Sciences of the United States of America. 106: 6459-64. PMID 19380751 DOI: 10.1073/Pnas.0810878106  1
2009 Ross J, Arkin AP. Complex systems: from chemistry to systems biology. Proceedings of the National Academy of Sciences of the United States of America. 106: 6433-4. PMID 19380716 DOI: 10.1073/Pnas.0903406106  1
2009 Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution. 26: 1641-50. PMID 19377059 DOI: 10.1093/Molbev/Msp077  1
2009 Yang Y, Harris DP, Luo F, Xiong W, Joachimiak M, Wu L, Dehal P, Jacobsen J, Yang Z, Palumbo AV, Arkin AP, Zhou J. Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. Bmc Genomics. 10: 131. PMID 19321007 DOI: 10.1186/1471-2164-10-131  1
2009 Jo WJ, Kim JH, Oh E, Jaramillo D, Holman P, Loguinov AV, Arkin AP, Nislow C, Giaever G, Vulpe CD. Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae. Bmc Genomics. 10: 130. PMID 19321002 DOI: 10.1186/1471-2164-10-130  1
2009 Elias DA, Mukhopadhyay A, Joachimiak MP, Drury EC, Redding AM, Yen HC, Fields MW, Hazen TC, Arkin AP, Keasling JD, Wall JD. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation. Nucleic Acids Research. 37: 2926-39. PMID 19293273 DOI: 10.1093/Nar/Gkp164  1
2009 Burnett JC, Miller-Jensen K, Shah PS, Arkin AP, Schaffer DV. Control of stochastic gene expression by host factors at the HIV promoter. Plos Pathogens. 5: e1000260. PMID 19132086 DOI: 10.1371/Journal.Ppat.1000260  1
2009 Tang YJ, Martin HG, Dehal PS, Deutschbauer A, Llora X, Meadows A, Arkin A, Keasling JD. Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism. Biotechnology and Bioengineering. 102: 1161-9. PMID 19031428 DOI: 10.1002/Bit.22129  1
2009 Kazakov AE, Rodionov DA, Alm E, Arkin AP, Dubchak I, Gelfand MS. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria Journal of Bacteriology. 91: 52-64. PMID 18820024 DOI: 10.1128/Jb.01175-08  1
2008 Lucks JB, Qi L, Whitaker WR, Arkin AP. Toward scalable parts families for predictable design of biological circuits. Current Opinion in Microbiology. 11: 567-73. PMID 18983935 DOI: 10.1016/J.Mib.2008.10.002  1
2008 Price MN, Dehal PS, Arkin AP. FastBLAST: homology relationships for millions of proteins. Plos One. 3: e3589. PMID 18974889 DOI: 10.1371/Journal.Pone.0003589  1
2008 Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, DeSantis TZ, Gihring TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richardson PM, Southam G, Wanger G, Pratt LM, ... ... Arkin AP, et al. Environmental genomics reveals a single-species ecosystem deep within Earth. Science (New York, N.Y.). 322: 275-8. PMID 18845759 DOI: 10.1126/Science.1155495  1
2008 Flaherty P, Radhakrishnan ML, Dinh T, Rebres RA, Roach TI, Jordan MI, Arkin AP. A dual receptor crosstalk model of G-protein-coupled signal transduction. Plos Computational Biology. 4: e1000185. PMID 18818727 DOI: 10.1371/Journal.Pcbi.1000185  1
2008 Ham TS, Lee SK, Keasling JD, Arkin AP. Design and construction of a double inversion recombination switch for heritable sequential genetic memory. Plos One. 3: e2815. PMID 18665232 DOI: 10.1371/Journal.Pone.0002815  1
2008 Singh AH, Wolf DM, Wang P, Arkin AP. Modularity of stress response evolution. Proceedings of the National Academy of Sciences of the United States of America. 105: 7500-5. PMID 18495925 DOI: 10.1073/Pnas.0709764105  1
2008 Wolf DM, Fontaine-Bodin L, Bischofs I, Price G, Keasling J, Arkin AP. Memory in microbes: Quantifying history-dependent behavior in a bacterium Plos One. 3. PMID 18324309 DOI: 10.1371/Journal.Pone.0001700  1
2008 Price MN, Dehal PS, Arkin AP. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biology. 9: R4. PMID 18179685 DOI: 10.1186/Gb-2008-9-1-R4  1
2008 Jo WJ, Loguinov A, Chang M, Wintz H, Nislow C, Arkin AP, Giaever G, Vulpe CD. Identification of genes involved in the toxic response of saccharomyces cerevisiae against iron and copper overload by parallel analysis of deletion mutants Toxicological Sciences. 101: 140-151. PMID 17785683 DOI: 10.1093/Toxsci/Kfm226  1
2008 Andrews SS, Arkin AP. A mechanical explanation for cytoskeletal rings and helices in bacteria (Biophysical Journal (2007) 93, (1872-1884)) Biophysical Journal. 95: 6081. DOI: 10.1529/biophysj.108.0900195  1
2007 Stolyar S, He Q, Joachimiak MP, He Z, Yang ZK, Borglin SE, Joyner DC, Huang K, Alm E, Hazen TC, Zhou J, Wall JD, Arkin AP, Stahl DA. Response of Desulfovibrio vulgaris to alkaline stress. Journal of Bacteriology. 189: 8944-52. PMID 17921288 DOI: 10.1128/Jb.00284-07  1
2007 Price MN, Dehal PS, Arkin AP. Orthologous transcription factors in bacteria have different functions and regulate different genes. Plos Computational Biology. 3: 1739-50. PMID 17845071 DOI: 10.1371/Journal.Pcbi.0030175  1
2007 Osterhout RE, Figueroa IA, Keasling JD, Arkin AP. Global analysis of host response to induction of a latent bacteriophage. Bmc Microbiology. 7: 82. PMID 17764558 DOI: 10.1186/1471-2180-7-82  1
2007 Anderson JC, Voigt CA, Arkin AP. Environmental signal integration by a modular AND gate. Molecular Systems Biology. 3: 133. PMID 17700541 DOI: 10.1038/Msb4100173  1
2007 Bender KS, Yen HC, Hemme CL, Yang Z, He Z, He Q, Zhou J, Huang KH, Alm EJ, Hazen TC, Arkin AP, Wall JD. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Applied and Environmental Microbiology. 73: 5389-400. PMID 17630305 DOI: 10.1128/Aem.00276-07  1
2007 Andrews SS, Arkin AP. Systems biology: a switch for sex. Current Biology : Cb. 17: R410-2. PMID 17550765 DOI: 10.1016/J.Cub.2007.03.060  1
2007 Mukhopadhyay A, Redding AM, Joachimiak MP, Arkin AP, Borglin SE, Dehal PS, Chakraborty R, Geller JT, Hazen TC, He Q, Joyner DC, Martin VJ, Wall JD, Yang ZK, Zhou J, et al. Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. 189: 5996-6010. PMID 17545284 DOI: 10.1128/Jb.00368-07  1
2007 Andrews SS, Arkin AP. A mechanical explanation for cytoskeletal rings and helices in bacteria. Biophysical Journal. 93: 1872-84. PMID 17513368 DOI: 10.1529/Biophysj.106.102343  1
2007 Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I. RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Research. 35: D407-12. PMID 17142223 DOI: 10.1093/Nar/Gkl865  1
2007 Jacobsen JS, Joyner DC, Borglin SE, Hazen TC, Arkin AP, Bethel EW. Visualization of growth curve data from phenotype microarray experiments Proceedings of the International Conference On Information Visualisation. 535-544. DOI: 10.1109/IV.2007.131  1
2007 Plyasunov S, Arkin AP. Efficient stochastic sensitivity analysis of discrete event systems Journal of Computational Physics. 221: 724-738. DOI: 10.1016/J.Jcp.2006.06.047  1
2007 Cassman M, Arkin A, Doyle F, Katagiri F, Lauffenburger D, Stokes C. Systems biology: International research and development Systems Biology: International Research and Development. 1-262. DOI: 10.1007/978-1-4020-5468-6  1
2006 Samoilov MS, Price G, Arkin AP. From fluctuations to phenotypes: the physiology of noise Science's Stke : Signal Transduction Knowledge Environment. 2006: re17. PMID 17179490 DOI: 10.1126/Stke.3662006Re17  1
2006 Alm E, Huang K, Arkin A. The evolution of two-component systems in bacteria reveals different strategies for niche adaptation Plos Computational Biology. 2: 1329-1342. PMID 17083272 DOI: 10.1371/Journal.Pcbi.0020143  1
2006 Samoilov MS, Arkin AP. Deviant effects in molecular reaction pathways Nature Biotechnology. 24: 1235-1240. PMID 17033664 DOI: 10.1038/Nbt1253  1
2006 Onsum MD, Wong K, Herzmark P, Bourne HR, Arkin AP. Morphology matters in immune cell chemotaxis: membrane asymmetry affects amplification. Physical Biology. 3: 190-9. PMID 17021383 DOI: 10.1088/1478-3975/3/3/004  1
2006 Arkin AP, Fletcher DA. Fast, cheap and somewhat in control. Genome Biology. 7: 114. PMID 16942631 DOI: 10.1186/Gb-2006-7-8-114  1
2006 Clark ME, He Q, He Z, Huang KH, Alm EJ, Wan XF, Hazen TC, Arkin AP, Wall JD, Zhou JZ, Fields MW. Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion. Applied and Environmental Microbiology. 72: 5578-88. PMID 16885312 DOI: 10.1128/Aem.00284-06  1
2006 Andrews SS, Arkin AP. Simulating cell biology. Current Biology : Cb. 16: R523-7. PMID 16860723 DOI: 10.1016/J.Cub.2006.06.048  1
2006 Price MN, Arkin AP, Alm EJ. The life-cycle of operons. Plos Genetics. 2: e96. PMID 16789824 DOI: 10.1371/Journal.Pgen.0020096  1
2006 He Q, Huang KH, He Z, Alm EJ, Fields MW, Hazen TC, Arkin AP, Wall JD, Zhou J. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. Applied and Environmental Microbiology. 72: 4370-81. PMID 16751553 DOI: 10.1128/Aem.02609-05  1
2006 Feeley R, Frenklach M, Onsum M, Russi T, Arkin A, Packard A. Model discrimination using data collaboration. The Journal of Physical Chemistry. A. 110: 6803-13. PMID 16722696 DOI: 10.1021/Jp056309S  1
2006 Mukhopadhyay A, He Z, Alm EJ, Arkin AP, Baidoo EE, Borglin SC, Chen W, Hazen TC, He Q, Holman HY, Huang K, Huang R, Joyner DC, Katz N, Keller M, et al. Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. Journal of Bacteriology. 188: 4068-78. PMID 16707698 DOI: 10.1128/Jb.01921-05  1
2006 Deutschbauer AM, Chivian D, Arkin AP. Genomics for environmental microbiology. Current Opinion in Biotechnology. 17: 229-35. PMID 16650754 DOI: 10.1016/J.Copbio.2006.04.003  1
2006 Price MN, Alm EJ, Arkin AP. The histidine operon is ancient. Journal of Molecular Evolution. 62: 807-8. PMID 16612542 DOI: 10.1007/S00239-005-0191-3  1
2006 Ham TS, Lee SK, Keasling JD, Arkin AP. A tightly regulated inducible expression system utilizing the fim inversion recombination switch. Biotechnology and Bioengineering. 94: 1-4. PMID 16534780 DOI: 10.1002/Bit.20916  1
2006 Chhabra SR, He Q, Huang KH, Gaucher SP, Alm EJ, He Z, Hadi MZ, Hazen TC, Wall JD, Zhou J, Arkin AP, Singh AK. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. 188: 1817-28. PMID 16484192 DOI: 10.1128/Jb.188.5.1817-1828.2006  1
2006 Leaphart AB, Thompson DK, Huang K, Alm E, Wan XF, Arkin A, Brown SD, Wu L, Yan T, Liu X, Wickham GS, Zhou J. Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH. Journal of Bacteriology. 188: 1633-42. PMID 16452448 DOI: 10.1128/Jb.188.4.1633-1642.2006  1
2006 Price MN, Arkin AP, Alm EJ. OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments. Bmc Bioinformatics. 7: 19. PMID 16412220 DOI: 10.1186/1471-2105-7-19  1
2006 Brown SD, Martin M, Deshpande S, Seal S, Huang K, Alm E, Yang Y, Wu L, Yan T, Liu X, Arkin A, Chourey K, Zhou J, Thompson DK. Cellular response of Shewanella oneidensis to strontium stress Applied and Environmental Microbiology. 72: 890-900. PMID 16391131 DOI: 10.1128/Aem.72.1.890-900.2006  1
2006 Anderson JC, Clarke EJ, Arkin AP, Voigt CA. Environmentally controlled invasion of cancer cells by engineered bacteria. Journal of Molecular Biology. 355: 619-27. PMID 16330045 DOI: 10.1016/J.Jmb.2005.10.076  1
2006 Plyasunov S, Arkin AP. Averaging methods for stochastic dynamics of complex reaction networks: Description of multiscale couplings Multiscale Modeling and Simulation. 5: 497-513. DOI: 10.1137/050633822  1
2006 Kuwahara H, Myers CJ, Samoilov MS, Barker NA, Arkin AP. Automated abstraction methodology for genetic regulatory networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4220: 150-175.  1
2005 Rodionov DA, Dubchak IL, Arkin AP, Alm EJ, Gelfand MS. Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. Plos Computational Biology. 1: e55. PMID 16261196 DOI: 10.1371/Journal.Pcbi.0010055  1
2005 Rao CV, Kirby JR, Arkin AP. Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles. Physical Biology. 2: 148-58. PMID 16224120 DOI: 10.1088/1478-3975/2/3/002  1
2005 Lee W, St Onge RP, Proctor M, Flaherty P, Jordan MI, Arkin AP, Davis RW, Nislow C, Giaever G. Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. Plos Genetics. 1: e24. PMID 16121259 DOI: 10.1371/Journal.Pgen.0010024  1
2005 Schwartz P, Adalsteinsson D, Colella P, Arkin AP, Onsum M. Numerical computation of diffusion on a surface. Proceedings of the National Academy of Sciences of the United States of America. 102: 11151-6. PMID 16076952 DOI: 10.1073/Pnas.0504953102  1
2005 Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell. 122: 169-82. PMID 16051143 DOI: 10.1016/J.Cell.2005.06.006  1
2005 Alm EJ, Huang KH, Price MN, Koche RP, Keller K, Dubchak IL, Arkin AP. The MicrobesOnline Web site for comparative genomics. Genome Research. 15: 1015-22. PMID 15998914 DOI: 10.1101/Gr.3844805  1
2005 Price MN, Alm EJ, Arkin AP. Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. Nucleic Acids Research. 33: 3224-34. PMID 15942025 DOI: 10.1093/Nar/Gki638  1
2005 Price MN, Huang KH, Arkin AP, Alm EJ. Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Research. 15: 809-19. PMID 15930492 DOI: 10.1101/Gr.3368805  1
2005 Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin AP. A latent variable model for chemogenomic profiling. Bioinformatics (Oxford, England). 21: 3286-93. PMID 15919724 DOI: 10.1093/Bioinformatics/Bti515  1
2005 Liu Y, Gao W, Wang Y, Wu L, Liu X, Yan T, Alm E, Arkin A, Thompson DK, Fields MW, Zhou J. Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions Journal of Bacteriology. 187: 2501-2507. PMID 15774893 DOI: 10.1128/Jb.187.7.2501-2507.2005  1
2005 Wolf DM, Vazirani VV, Arkin AP. A microbial modified prisoner's dilemma game: how frequency-dependent selection can lead to random phase variation. Journal of Theoretical Biology. 234: 255-62. PMID 15757682 DOI: 10.1016/J.Jtbi.2004.11.021  1
2005 Wolf DM, Vazirani VV, Arkin AP. Diversity in times of adversity: probabilistic strategies in microbial survival games. Journal of Theoretical Biology. 234: 227-53. PMID 15757681 DOI: 10.1016/J.Jtbi.2004.11.020  1
2005 Price MN, Huang KH, Alm EJ, Arkin AP. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Research. 33: 880-92. PMID 15701760 DOI: 10.1093/Nar/Gki232  1
2005 Voigt CA, Wolf DM, Arkin AP. The Bacillus subtilis sin operon: an evolvable network motif. Genetics. 169: 1187-202. PMID 15466432 DOI: 10.1534/Genetics.104.031955  1
2005 Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV. Stochastic gene expression in a lentiviral positive feedback loop: HIV-1 tat fluctuations drive phenotypic diversity Aiche Annual Meeting, Conference Proceedings. 10416.  1
2005 Flaherty P, Jordan MI, Arkin AP. Robust design of biological experiments Advances in Neural Information Processing Systems. 363-370.  1
2004 Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS. Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria Genome Biology. 5: R90. PMID 15535866 DOI: 10.1186/Gb-2004-5-11-R90  1
2004 Gao H, Wang Y, Liu X, Yan T, Wu L, Alm E, Arkin A, Thompson DK, Zhou J. Global transcriptome analysis of the heat shock response of Shewanella oneidensis. Journal of Bacteriology. 186: 7796-803. PMID 15516594 DOI: 10.1128/Jb.186.22.7796-7803.2004  1
2004 Rao CV, Frenklach M, Arkin AP. An allosteric model for transmembrane signaling in bacterial chemotaxis. Journal of Molecular Biology. 343: 291-303. PMID 15451661 DOI: 10.1016/J.Jmb.2004.08.046  1
2004 Vlad MO, Arkin A, Ross J. Response experiments for nonlinear systems with application to reaction kinetics and genetics. Proceedings of the National Academy of Sciences of the United States of America. 101: 7223-8. PMID 15123834 DOI: 10.1073/Pnas.0402049101  0.36
2004 McAdams HH, Srinivasan B, Arkin AP. The evolution of genetic regulatory systems in bacteria. Nature Reviews. Genetics. 5: 169-78. PMID 14970819 DOI: 10.1038/Nrg1292  1
2004 Rao CV, Kirby JR, Arkin AP. Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. Plos Biology. 2: E49. PMID 14966542 DOI: 10.1371/Journal.Pbio.0020049  1
2004 Giaever G, Flaherty P, Kumm J, Proctor M, Nislow C, Jaramillo DF, Chu AM, Jordan MI, Arkin AP, Davis RW. Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proceedings of the National Academy of Sciences of the United States of America. 101: 793-8. PMID 14718668 DOI: 10.1073/Pnas.0307490100  1
2003 Weinberger LS, Schaffer DV, Arkin AP. Theoretical design of a gene therapy to prevent AIDS but not human immunodeficiency virus type 1 infection. Journal of Virology. 77: 10028-36. PMID 12941913 DOI: 10.1128/Jvi.77.18.10028-10036.2003  1
2003 Alm E, Arkin AP. Biological networks Current Opinion in Structural Biology. 13: 193-202. PMID 12727512 DOI: 10.1016/S0959-440X(03)00031-9  1
2003 Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (Oxford, England). 19: 524-31. PMID 12611808 DOI: 10.1093/Bioinformatics/Btg015  1
2003 Rao CV, Arkin AP. Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm Journal of Chemical Physics. 118: 4999-5010. DOI: 10.1063/1.1545446  1
2002 Gilman AG, Simon MI, Bourne HR, Harris BA, Long R, Ross EM, Stull JT, Taussig R, Bourne HR, Arkin AP, Cobb MH, Cyster JG, Devreotes PN, Ferrell JE, Fruman D, ... ... Arkin AP, et al. Overview of the Alliance for Cellular Signaling. Nature. 420: 703-6. PMID 12478301 DOI: 10.1038/Nature01304  1
2002 Rao CV, Wolf DM, Arkin AP. Control, exploitation and tolerance of intracellular noise. Nature. 420: 231-7. PMID 12432408 DOI: 10.1038/Nature01258  1
2002 Gilman A, Arkin AP. Genetic "code": representations and dynamical models of genetic components and networks. Annual Review of Genomics and Human Genetics. 3: 341-69. PMID 12142360 DOI: 10.1146/Annurev.Genom.3.030502.111004  1
2002 Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418: 387-91. PMID 12140549 DOI: 10.1038/Nature00935  1
2001 Rao CV, Arkin AP. Control motifs for intracellular regulatory networks Annual Review of Biomedical Engineering. 3: 391-419. PMID 11447069 DOI: 10.1146/Annurev.Bioeng.3.1.391  1
2000 McAdams HH, Arkin A. Towards a circuit engineering discipline. Current Biology : Cb. 10: R318-20. PMID 10801411 DOI: 10.1016/S0960-9822(00)00440-1  1
1999 McAdams HH, Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends in Genetics : Tig. 15: 65-9. PMID 10098409 DOI: 10.1016/S0168-9525(98)01659-X  1
1998 McAdams HH, Arkin A. Simulation of prokaryotic genetic circuits. Annual Review of Biophysics and Biomolecular Structure. 27: 199-224. PMID 9646867 DOI: 10.1146/Annurev.Biophys.27.1.199  1
1997 Swanson CA, Arkin AP, Ross J. An endogenous calcium oscillator may control early embryonic division. Proceedings of the National Academy of Sciences of the United States of America. 94: 1194-9. PMID 9037029 DOI: 10.1073/Pnas.94.4.1194  1
1997 McAdams HH, Arkin A. Stochastic mechanisms in gene expression. Proceedings of the National Academy of Sciences of the United States of America. 94: 814-9. PMID 9023339 DOI: 10.1073/Pnas.94.3.814  1
1994 Arkin A, Ross J. Computational functions in biochemical reaction networks. Biophysical Journal. 67: 560-78. PMID 7948674 DOI: 10.1016/S0006-3495(94)80516-8  0.4
1992 Arkin AP, Youvan DC. An algorithm for protein engineering: simulations of recursive ensemble mutagenesis. Proceedings of the National Academy of Sciences of the United States of America. 89: 7811-5. PMID 1502200 DOI: 10.1073/Pnas.89.16.7811  1
1992 Arkin AP, Youvan DC. Optimizing nucleotide mixtures to encode specific subsets of amino acids for semi-random mutagenesis. Bio/Technology (Nature Publishing Company). 10: 297-300. PMID 1368102 DOI: 10.1038/Nbt0392-297  1
1990 Arkin AP, Goldman ER, Robles SJ, Goddard CA, Coleman WJ, Yang MM, Youvan DC. Applications of imaging spectroscopy in molecular biology. II. Colony screening based on absorption spectra. Bio/Technology (Nature Publishing Company). 8: 746-9. PMID 1366901 DOI: 10.1038/Nbt0890-746  1
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