Publications

2023

31. Droplet-based forward genetic screening of astrocyte–microglia cross-talk

Wheeler* MA, Clark* IC, Lee* H-G, Li Z, Linnerbauer M, Rone JM, Blain M, Akl CF, Piester G, Giovannoni F, Charabati M, Lee J-H, Kye Y-C, Choi J, Sanmarco LM, Srun L, Chung EN, Flausino LE, Andersen BM, Rothhammer V, Yano H, Illouz T, Zandee SEJ, Daniel C, Artis D, Prinz M, Abate AR, Kuchroo VK, Antel JP, Prat A, Quintana FJ. Science (2023).

30. Microfluidics-free single-cell genomics with templated emulsification

Clark, I. C., K. M. Fontanez, R. H. Meltzer, Y. Xue, C. Hayford, A. May-Zhang, C. D’Amato, A. Osman, J. Q. Zhang, P. Hettige, J. S. A. Ishibashi, C. L. Delley, D. W. Weisgerber, J. M. Replogle, M. Jost, K. T. Phong, V. E. Kennedy, C. A. C. Peretz, E. A. Kim, S. Song, W. Karlon, J. S. Weissman, C. C. Smith, Z. J. Gartner, and A. R. Abate. Nat Biotechnol (2023).

29. HIV silencing and cell survival signatures in infected T cell reservoirs

Clark, I. C., P. Mudvari, S. Thaploo, S. Smith, M. Abu-Laban, M. Hamouda, M. Theberge, S. Shah, S. H. Ko, L. Pérez, D. G. Bunis, J. S. Lee, D. Kilam, S. Zakaria, S. Choi, S. Darko, A. R. Henry, M. A. Wheeler, R. Hoh, S. Butrus, S. G. Deeks, F. J. Quintana, D. C. Douek, A. R. Abate and E. A. Boritz. Nature (2023).

28. Identification of astrocyte regulators by nucleic acid cytometry

Clark, I. C.*, M. A. Wheeler*, H.-G. Lee, Z. Li, L. M. Sanmarco, S. Thaploo, C. M. Polonio, S. W. Shin, G. Scalisi, A. R. Henry, J. M. Rone, F. Giovannoni, M. Charabati, C. F. Akl, D. M. Aleman, S. E. J. Zandee, A. Prat, D. C. Douek, E. A. Boritz, F. J. Quintana and A. R. Abate. Nature (2023).

2022

27. Microfluidics-free single-cell genomics with templated emulsification

2021

26. Barcoded viral tracing of single-cell interactions in central nervous system inflammation

Clark, I. C.*, Gutierrez-Vazquez*, C., Wheeler, M. A.*, Li, Z., Rothhammer, V., Linnerbauer, M., Sanmarco, L. M., Guo, L., Blain, M., Zandee, S. E. J., Chao, C. C., Batterman, K. V., Schwabenland, M., Lotfy, P., Tejeda-Velarde, A., Hewson, P., Manganeli Polonio, C., Shultis, M. W., Salem, Y., Tjon, E. C., Fonseca-Castro, P. H., Borucki, D. M., Alves de Lima, K., Plasencia, A., Abate, A. R., Rosene, D. L., Hodgetts, K. J., Prinz, M., Antel, J. P., Prat, A. & Quintana, F. J. Science 372, doi:10.1126/science.abf1230 (2021).

25. Protein design-scapes generated by microfluidic DNA assembly elucidate domain coupling in the bacterial histidine kinase CpxA.

Clark IC, Mensa B, Ochs CJ, Schmidt NW, Mravic M, Quintana FJ, DeGrado WF, and Abate AR. Proceedings of the National Academy of Sciences. 2021 March 118 (12) e2017719118. doi.org/10.1073/pnas.2017719118

2020

24. Targeted Single-Cell RNA and DNA Sequencing With Fluorescence-Activated Droplet Merger.

Clark IC, Delley CL, Sun C, Thakur R, Stott SL, Thaploo S, Li Z, Quintana FJ, Abate AR. Analytical Chemistry. 2020 Nov 3;92(21):14616-14623. doi: 10.1021/acs.analchem.0c03059.PMID: 33049138.

23. MAFG-driven astrocytes promote CNS inflammation.

Wheeler MA, Clark IC, Tjon EC, Li Z, Zandee SEJ, Couturier CP, Watson BR, Scalisi G, Alkwai S, Rothhammer V, Rotem A, Heyman JA, Thaploo S, Sanmarco LM, Ragoussis J, Weitz DA, Petrecca K, Moffitt JR, Becher B, Antel JP, Prat A, Quintana FJ. Nature. 2020 Feb;578(7796):593-599. doi: 10.1038/s41586-020-1999-0.PMID: 32051591

2019

22. Microfluidic bead encapsulation above 20 kHz with triggered drop formation.

Clark IC, Abate AR. Lab Chip. 2018 Dec 7;18(23):3598-3605. doi: 10.1039/c8lc00514a. PMID: 30362490.

2018

21. Concentric electrodes improve microfluidic droplet sorting.

Clark IC, Thakur R, Abate AR. Lab Chip. 2018 Feb 27;18(5):710-713. doi: 10.1039/c7lc01242j.PMID: 29383336.

20. Single-Cell RT-PCR in Microfluidic Droplets with Integrated Chemical Lysis.

Kim SC, Clark IC, Shahi P, Abate AR. Analytical Chemistry. 2018 Jan 16;90(2):1273-1279. doi: 10.1021/acs.analchem.7b04050.PMID: 29256243.

2017

19. Finding a helix in a haystack: nucleic acid cytometry with droplet microfluidics.

Clark IC, Abate AR. Lab Chip. 2017 Jun 13;17(12):2032-2045. doi: 10.1039/c7lc00241f.PMID: 28540956.

18. Efficient extraction of oil from droplet microfluidic emulsions.

Haliburton JR, Kim SC, Clark IC, Sperling RA, Weitz DA, Abate AR. Biomicrofluidics. 2017 May 19;11(3):034111. doi: 10.1063/1.4984035.PMID: 28611871

17. Measurement of copy number variation in single cancer cells using rapid-emulsification digital droplet MDA.

Kim SC, Premasekharan G, Clark IC, Gemeda HB, Paris PL, Abate AR. Microsyst Nanoeng. 2017;3:17018. doi: 10.1038/micronano.2017.18. PMID: 30147985.

16. Rapid encapsulation of cell and polymer solutions with bubble-triggered droplet generation.

Y Zihao*, IC Clark*, and AR Abate. Macromolecular Chemistry and Physics. 2017, 218: 1600297.

2016

15. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

Youngblut MD, Tsai CL, Clark IC, Carlson HK, Maglaqui AP, Gau-Pan PS, Redford SA, Wong A, Tainer JA, Coates JD. J Biol Chem. 2016 Apr 22;291(17):9190-202. doi: 10.1074/jbc. M116.714618. PMID: 26940877.

14. Genetic dissection of chlorate respiration in Pseudomonas stutzeri PDA reveals syntrophic (per)chlorate reduction.

Clark IC, Youngblut M, Jacobsen G, Wetmore KM, Deutschbauer A, Lucas L, Coates JD. Environ Microbiol. 2016 Oct;18(10):3342-3354. doi: 10.1111/1462-2920.13068.PMID: 26411776.

2015

13. Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1.

Clark IC, Melnyk RA, Youngblut MD, Carlson HK, Iavarone AT, Coates JD. mBio. 2015 May 19;6(3):e00282-15. doi: 10.1128/mBio.00282-15.PMID: 25991681.

12. Phenotypic and genotypic description of Sedimenticola selenatireducens strain CUZ, a marine (per)chlorate-respiring gammaproteobacterium, and its close relative the chlorate-respiring Sedimenticola strain NSS.

Carlström CI, Loutey DE, Wang O, Engelbrektson A, Clark I, Lucas LN, Somasekhar PY, Coates JD. Appl Environ Microbiol. 2015 Apr;81(8):2717-26. doi: 10.1128/AEM.03606-14. PMID: 25662971

11. Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich Peptide and methionine sulfoxide reductase

Melnyk RA, Youngblut MD, Clark IC, Carlson HK, Wetmore KM, Price MN, Iavarone AT, Deutschbauer AM, Arkin AP, Coates JD. mBio. 2015 May 12;6(3):e00233-15. doi: 10.1128/mBio.00233-15. PMID: 25968643; PMCID: PMC4436054.

10. (Per)chlorate-reducing bacteria can utilize aerobic and anaerobic pathways of aromatic degradation with (per)chlorate as an electron acceptor.

Carlström CI, Loutey D, Bauer S, Clark IC, Rohde RA, Iavarone AT, Lucas L, Coates JD. mBio. 2015 Mar 24;6(2):e02287-14. doi: 10.1128/mBio.02287-14.PMID: 25805732.

2014

9.Chlorate reduction in Shewanella algae ACDC is a recently acquired metabolism characterized by gene loss, suboptimal regulation and oxidative stress.

Clark IC, Melnyk RA, Iavarone AT, Novichkov PS, Coates JD. Mol Microbiol. 2014 Oct;94(1):107-25. doi: 10.1111/mmi.12746. Epub 2014 Sep 5.PMID: 25099177

2013

8.Transposon and deletion mutagenesis of genes involved in perchlorate reduction in Azospira suillum PS.

Melnyk RA, Clark IC, Liao A, Coates JD. mBio. 2013 Dec 31;5(1):e00769-13. doi: 10.1128/mBio.00769-13.PMID: 24381299.

7. Structure and evolution of chlorate reduction composite transposons.

Clark IC, Melnyk RA, Engelbrektson A, Coates JD. mBio. 2013 Aug 6;4(4):e00379-13. doi: 10.1128/mBio.00379-13.PMID: 23919996.

6. Fe(II) oxidation is an innate capability of nitrate-reducing bacteria that involves abiotic and biotic reactions.

Carlson HK, Clark IC, Blazewicz SJ, Iavarone AT, Coates JD. J Bacteriol. 2013 Jul;195(14):3260-8. doi: 10.1128/JB.00058-13. Epub 2013 May 17.PMID: 23687275.

2012

5. Bioelectrical redox cycling of anthraquinone-2, 6-disulfonate coupled to perchlorate reduction.

Clark IC, Carlson HK, Iavarone AT, and Coates JD. Energy Environ Sci 2012 5: 7970–7978.

4. Toward a mechanistic understanding of anaerobic nitrate-dependent iron oxidation: balancing electron uptake and detoxification.

Carlson HK, Clark IC, Melnyk RA, Coates JD. Front Microbiol. 2012 Feb 20;3:57. doi: 10.3389/fmicb.2012.00057. PMID: 22363331.

3. The effect of low pressure and mixing on biological hydrogen production via anaerobic fermentation.

Clark IC, Zhang, R.H., and Upadhyaya, S.K. International Journal of Hydrogen Energy 2012 37: 11504–11513.

2011

2. Identification of a perchlorate reduction genomic island with novel regulatory and metabolic genes.

Melnyk RA, Engelbrektson A, Clark IC, Carlson HK, Byrne-Bailey K, Coates JD. Appl Environ Microbiol. 2011 Oct;77(20):7401-4. doi: 10.1128/AEM.05758-11. Epub 2011 Aug 19.PMID: 21856823.

1. Development of a low-flow meter for measuring gas production in bioreactors.

Clark IC, Zhang R, Pan Z, Brown BR, Ambuel J, and Delwiche M. Transactions of the ASABE. 2011 54: 1959–1964.