Embedded Files
Denish Piya, Nicholas Nolan, Madeline L Moore, Luis A Ramirez Hernandez, Brady F Cress, Ry Young, Adam P Arkin*, Vivek K Mutalik*. “Genome-wide CRISPRi knockdown to map gene essentiality landscape in coliphages lambda and P1” PLoS Biology, Dec 4, 2023 https://doi.org/10.1371/journal.pbio.3002416
(*corresponding authors)
Hans K Carlson*, Denish Piya, Madeline L Moore, Roniya T Magar, Nathalie H Elisabeth, Adam M Deutschbauer, Adam P Arkin, Vivek K Mutalik*. "Geochemical constraints on bacteriophage infectivity in terrestrial environments”. ISME communications, 3, p78, 2023
(*corresponding authors)
Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. “Phage therapy: From biological mechanisms to future directions”. Cell. 2023 Jan 5;186(1):17-31. PubMed Central PMCID: PMC9827498.
Benjamin A. Adler, Karthik Chamakura, Heloise Carion, Jonathan Krog, Adam M Deutschbauer, Ryland F Young, Vivek K. Mutalik*, Adam P. Arkin*. ”Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins” Nature Chemical Biology, 1-8, 2023
(*corresponding authors)
News from Berkeley Lab :A quick new way to screen virus proteins for antibiotic properties
and Innovative Genomics Institute news: Secrets of smallest phages
Adler B, Hessler T, Cress B, Lahiri A, Mutalik V, Barrangou R, Banfield J, Doudna J. “Broadspectrum CRISPR-Cas13a enables efficient phage genome editing”. Nature Microbiology. 2022 October 31; 7(12):1967-1979.
News from Berkeley lab: Broad spectrum crispr-cas13a enables efficient phage genome engineering
Vivek K. Mutalik*, Adam P. Arkin*. “A phage foundry framework to systematically develop viral countermeasures to combat antibiotic-resistant bacterial pathogens” iScience 25, 104121, April 15, 2022
(*corresponding authors)
Vivek K. Mutalik*, Benjamin A. Adler, Harneet S. Rishi, Denish Piya, Crystal Zhong, Britt Koskella, Elizabeth Kutter, Richard Calendar, Pavel Novichkov, Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin*. “High-throughput mapping of the phage resistance landscape in E. coli”. PLoS Biology 2021, 18(10): e3000877 https://doi.org/10.1371/journal.pbio.3000877
(*corresponding authors)
(work highlighted in Phage registry, Mammoth Biosciences news letter, LBNL News, Capsid & Tails newsletter, Finding Genius podcast, Nature Biotech 2019)
Sean Carim, Ashley L. Azadeh, Alexey E. Kazakov, Morgan N. Price, Peter J. Walian, Romy Chakraborty, Adam M. Deutschbauer, Vivek K. Mutalik*, Adam P. Arkin*. “Systematic discovery of Pseudomonad genetic factors involved in sensitivity to tailocins”. ISME Journal 2021 Mar 1. doi: 10.1038/s41396-021-00921-1 (work highlighted in LBNL News, Bio-IT World)
(*corresponding authors)
Sean Carim and Vivek Mutalik, A tale of tailocins bacterial stabbing tools
LBNL News: Bacterial Homing missiles
Benjamin A. Adler, Crystal Zhong, Hualan Liu, Elizabeth Kutter, Adam M. Deutschbauer, Vivek K. Mutalik* and Adam P. Arkin*. “The Genetic Basis of phage susceptibility, cross-resistance and host-range in Salmonella”. Microbiology, 2021, 167 (12) 001126,
(*corresponding authors)
(work highlighted in Phage registry, Mammoth Biosciences news letter, LBNL News, Capsid & Tails newsletter, Finding Genius podcast, Nature Biotech 2019)
Vivek K. Mutalik*, Pavel S. Novichkov, Morgan N. Price, Trenton K. Owens, Mark Callaghan, Sean Carim, Adam M. Deutschbauer and Adam P. Arkin*, “Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria”. Nature Communication. 2019 Jan 18;10(1):308.
(*corresponding authors)
(Work highlighted in Nature Methods, LBNL News, Winner of 2017 R & D 100 award)
Thomas L Ruegg, Jose H Pereira, Joseph C Chen, Andy DeGiovanni, Pavel Novichkov, Vivek K Mutalik, Giovani P Tomaleri, Steven W Singer, Nathan J Hillson, Blake A Simmons, Paul D Adams, Michael P Thelen, “Jungle Express is a versatile repressor system for tight transcriptional control”, Nature Communication, 9, 3617, 2018
Marcelo C Bassalo, Andrew D Garst, Andrea L Halweg-Edwards, William C Grau, Dylan W Domaille, Vivek K Mutalik, Adam P Arkin, Ryan T Gill, “Rapid and efficient one-step metabolic pathway integration in E. coli”, ACS Synthetic Biology, 5 (7), 561-568, 2016
Pouya Javidpour, Samuel Deutsch, Vivek K Mutalik, Nathan J Hillson, Christopher J Petzold, Jay D Keasling, Harry R Beller, “Investigation of proposed Ladderane biosynthetic genes from Anammox bacteria by heterologous expression in E. coli”, PLOS one, 11 (3), e0151087, 2016
Emily Freed, James Winkler, Sophie Weiss, Andrew Garst, Vivek Mutalik, Adam Arkin, Rob Knight and Ryan Gill, “Genome-wide tuning of protein expression levels to rapidly engineer microbial traits” ACS Synthetic Biology, 4 (11), 1244-1253, 2015.
Gregory Linshiz, Nina Stawski, Garima Goyal, Changhao Bi, Sean Poust, Monica Sharma, Vivek Mutalik, Jay D Keasling, Nathan J Hillson, “PR-PR: Cross-Platform Laboratory Automation System” ACS Synthetic Biology, 3 (8) 515-524, 2014
Vivek Mutalik, Joao Guimaraes, Guillaume Cambray, Colin Lam, Marc Juul Christoffersen, Quynh-Anh Mai, Andrew Tran, Paull Morgan, Adam Arkin and Drew Endy, “Precise and reliable gene expression via standard transcription and translation initiation elements”, Nature Methods, 10 (4), 354-360, 2013.
(Predictability the brass ring for synthetic biology in Nature, Nature Methods, Nature Reviews Genetics, Bioengineered, New Scientist, various Science news agencies).
Vivek Mutalik, Joao Guimaraes, Guillaume Cambray, Quynh-Anh Mai, Marc Juul Christoffersen, Lance Martin, Ayumi Yu, Colin Lam, Cesar Rodriguez, Gaymon Bennett, Drew Endy and Adam Arkin, “Quantitative Estimation of Activity and Quality for Collections of Functional Genetic Elements”, Nature Methods, 10 (4), 354-360, 2013.
(Predictability the brass ring for synthetic biology in Nature, Nature Methods, Nature Reviews Genetics, Bioengineered, New Scientist, various Science news agencies).
Sriram Kosuri, Daniel B. Goodman, Guillaume Cambray, Vivek K. Mutalik, Yuan Gao, Adam P. Arkin, Drew Endy, George M. Church “Composability of regulatory sequences controlling transcription and translation in E. coli” Proceedings of the National Academy of Science, USA 110 (34), 14024-14029, 2013
Cambray, G., Guimaraes, J., Mutalik, Vivek, Lam, C., Mai, Quynh-Anh, Thimmaiah, T., Carothers, J., Arkin, A., Endy, D., “Measurement and Modeling of Intrinsic Transcription Terminators”, Nucleic Acid Research, 41 (9), 5139-5148, 2013.
(Predictability the brass ring for synthetic biology in Nature, Nature Methods, Nature Reviews Genetics, Bioengineered, New Scientist, various Science news agencies).
Goldbeck C. P., Jensen H. M., TerAvest M. A., Beedle N., Appling Y., Hepler M., Cambray G., Vivek Mutalik., Angenent L. T. and Ajo-Franklin C. M. (2013). Tuning promoter strengths for improved synthesis and function of electron conduits in Escherichia coli. ACS Synthetic Biology, 2(3), 150-159, 2013.
Chang Liu, Lei Qi, Julius Lucks, Thomas Segall-Shapiro, Denise Wang, Vivek Mutalik, and Adam Arkin, “An adapter from translational to transcriptional control yields composable regulators of gene expression”, Nature Methods, 9 (11),1088-1094, 2012.
Vivek K Mutalik, L. Qi, J. C. Guimaraes, J.B. Lucks and A. P. Arkin, “Rationally designed families of orthogonal RNA regulators of translation”, Nature Chemical Biology, 8(5):447-54, 2012.
News & Views
Automated design of RNA devices
L. Qi, J.B. Lucks, L.C. Chang, Vivek K Mutalik and A. P. Arkin, “Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals”, Nucleic Acid Research, 40(12):5775-86, 2012
V. A. Rhodius, Vivek K Mutalik and C. A. Gross, “Predicting the strength of UP-elements and full-length E coli σE promoters”, Nucleic Acid Research, 40(7):2907-24, 2012
G. Cambray, Vivek K Mutalik and A. P. Arkin, “Towards rational design of bacterial genomes”, Current Opinion in Microbiology, 14 (5), 624-630, 2011
J. B Lucks, L. Qi, Vivek K Mutalik, D, Wang and A. P. Arkin, “Versatile RNA-sensing transcriptional regulators for engineering genetic networks” Proceedings of the National Academy of Sciences,USA 108 (21), 8617-8622, 2011
Vivek K Mutalik, G. Nonaka, S. Ades, V. A. Rhodius and C. A. Gross, “Promoter strength properties of the complete sigma-E regulon of E coli and Salmonella”, J. Bacteriology, 191(23), 7279-7287, 2009
I. L. Grigorova, N. J. Phleger, Vivek. K. Mutalik, and C. A. Gross, “Insights into transcriptional regulation and sigma competition from an equilibrium model of RNA polymerase binding to DNA”, Proceedings of the National Academy of Sciences, USA [103] (14), 5332–5337, 2006
Prior 2007
Vivek. K. Mutalik and K.V. Venkatesh, “A theoretical steady state analysis indicates that induction of Escherichia coli glnALG operon can display all-or-none behavior”, BioSystems, 90: 1-19, 2007
Vivek. K. Mutalik and K V. Venkatesh, “Effect of the MAPK cascade structure, nuclear translocation and regulation of transcription factors on gene expression”, BioSystems, 85(2):144-57, 2006
Vivek. K. Mutalik and K V Venkatesh, “Quantification of glycogen cascade system: A highly ultrasensitive response of Glycogen Synthase in the liver and Phosphorylase in the muscle is due to distinctive regulatory design”, Theoretical Biology and Medical Modelling 2005, 2:19
Vivek. K. Mutalik, A. P. Singh, J. S. Edwards and K. V. Venkatesh, “Equilibrium analysis of allosteric interactions shows zero order effects”, Cell Biochemistry and Biophysics Cell Biochemistry and Biophysics [41] (2), 179-192, 2004.
Vivek. K. Mutalik, A. P. Singh, J. S. Edwards and K. V. Venkatesh, “Robust global sensitivity in multiple enzyme cascade system explains how the downstream cascade structure may remain unaffected by cross-talk”, FEBS Letters, [558] (1-3), 79-84, 2004.
L. Giri*, Vivek. K. Mutalik* and K.V. Venkatesh, “A steady state analysis indicates that negative feedback regulation of PTP1B by Akt elicits bistability in insulin-stimulated GLUT4 translocation”, Theoretical Biology and Medical Modelling 2004, 1:2 (3 August 2004), *Equal Contribution
Vivek. K. Mutalik, P. Shah and K V Venkatesh, “Allosteric Interactions and Bifunctionality Make the Response of Glutamine Synthetase Cascade System of Escherichia coli Robust and Ultrasensitive”, The Journal of Biological chemistry, [278] (29), 26327-26332, 2003.
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