Lam KN, Spanogiannopoulos P, Soto-Perez P, Alexander M, Nalley MJ, Bisanz JE, Nayak RR, Weakley AM, Yu FB, Turnbaugh PJ, "Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome," Cell Reports November 2, 2021

Vasquez KS, Willis L, Cira NJ, Ng KM, Pedro MF, Aranda-Diaz A, Rajendram M, Yu FB, Higginbottom SK, Neff N, Sherlock G, Xavier KB, Quake SR, Sonnenburg JL, Good BH, Huang KC, "Quantifying rapid bacterial evolution and transmission within the mouse intestine," Cell Host & Microbe September 8, 2021

Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Yu FB, Topf M, Gonzales CG, Van Treuren W, Han S, Robinson JL, Elias JE, Sonnenburg ED, Gardner CD, Sonnenburg JL, "Gut-microbiota-targeted diets modulate human immune status," Cell August 5, 2021

Speth DR, Yu FB, Lim S, Magyar JS, Pena ME, Quake SR, Orphan VJ, "Microbial community of recently discovered Auka vent field sheds light on vent biogeography and evolutionary history of thermophily," bioRxiv August 2, 2021

West PT, Peters SL, Olm MR, Yu FB, Gause H, Lou YC, Firek BA, Baker R, Johnson AD, Morowitz MJ, Hettich RL, Banfield JF, "Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics," Microbiome June 21,2021

Cesar S, Anjur-Dietrich M, Yu FB, Li E, Rojas E, Neff N, Cooper TF, Huang KC, "Bacterial evolution in high-osmolarity environments," mBio August 4, 2020

Bisanz JE, Soto-Perez P, Noecker C, Aksenov AA, Lam KN, Kenney GE, Bess EN, Haiser HJ, Kyaw TS, Yu FB, Rekdal VM, Ha CWY, Devkota S, Balskus E, Dorrestein PC, Allen-Vercoe E, Turnbaugh PJ, "A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria," Cell Host & Microbe June 10, 2020

Gulati GS, Sikandar SS, Wesche DJ, Manjunath A, Bharadwaj A, Berger MJ, Ilagan F, Kuo AH, Hsieh RW, Cai S, Zabala M, Scheeren FA, Lobo NA, Qian D, Yu FB, Dirbas FM, Clarke MF, Newman AM, "Single-cell transcriptional diversity is a hallmark of developmental potential," Science January 24, 2020

Pre-print is available on bioRxiv here

Ng KM, Aranda-Diaz A, Tropini C, Frankel MR, Van Treuren WW, O'Laughlin C, Merrill BD, Yu FB, Pruss KM, Oliveira RA, Higginbottom SK, Neff NF, Fischbach MA, Xavier KB, Sonnenburg JL, Huang KC, "Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs," Cell Host & Microbe November 13, 2019

Pre-print is available on bioRxiv here

Schmidt ST, Yu FB, Blainey PC, May AP, Quake SR, "Nucleic Acid Cleavage with a Hyperthermophilic Cas9 from an Unculturable Ignavibacterium," PNAS October 28, 2019

Pre-print is available on bioRxiv here

Deaton J, Yu FB, Quake SR, "Mini-Metagenomics and Nucleotide Composition Aid the Identification and Host Association of Novel Bacteriophage Sequences," Advanced Biosystems August 16, 2019

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Pre-print is available on bioRxiv here

Berghuis BA, Yu FB, Schulz F, Blainey PC, Woyke T, Quake SR, "Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens," PNAS March 12, 2019

Pre-print is available on bioRxiv here

Schulz F, Alteio L, Goudeau D, Ryan EM, Yu FB, Malmstrom RR, Blanchard J, Woyke T, "Hidden diversity of soil giant viruses," Nature Communications November 19, 2018

Gasch AP*, Yu FB*, Hose J, Escalante E, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriev I, Kendziorski C, Quake SR, McClean MN, "Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress," Plos Biology December 14, 2017

Pre-print is available on bioRxiv here

Yu FB, Blainey PC, Schulz F, Woyke T, Horowitz MA, Quake SR, "Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples," eLife 6:e26580, July 5 2017

Pre-print is available on bioRxiv here

Details of the Fluidigm C1 IFC with associated custom scripts and protocols can be found here

Raw sequencing data associated with this publication is deposited on NCBI under BioProject PRJNA378813.

Annotated contigs and genomes are deposited in the Integrated Microbial Genomes database maintained by Department of Energy Joint Genome Institute under Genome IDs 3300006068, 3300006065, and 2630969008.

This work was featured on The Scientist Magazine.

Yu FB, Willis L, Chau R, Zambon A, Horowitz MA, Bhaya D, Huang KC, Quake SR, "Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing," BMC Biology, vol 15, issue 1, pp. 11, February 2017.
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Hu K, Yu FB, Ho TY, Chakrabarty K, "Testing of Flow-Based Microfluidic Biochips: Fault Modeling, Test Generation, and Experimental Demonstration," IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol 33, issue 10, pp. 1463-1475, October 2014.
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Yu FB, Horowitz MA, Quake SR, "Microfluidic serial digital to analog pressure converter for arbitrary pressure generation and contamination-free flow control," Lab on a Chip, vol. 13, pp. 1911-8, May 21 2013.
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Cerny R, Cattell M, Sauka-Spengler R, Bronner-Fraser M, Yu F, Medeiros DM, "Evidence for the prepattern/cooption model of vertebrate jaw evolution," Proceedings of the National Academy of Sciences of the United States of America, vol. 107, pp. 17262-17267, Oct 5 2010.
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Yu F, Horowitz MA, Quake SR, "High throughput microfluidic sample preparation for metagenomic analysis," Proceedings of the 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2014), San Antonio, U.S.A., October 2014, pp. 129-131.

Yu F, Horowitz MA, Quake SR, "Robust Layout Techniques Decrease Volume Injection and Capacitive Mismatch due to Alignment Errors," Proceedings of the 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2013), Freiburg, Germany, November 2013, pp. 940-942.
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Yu F, Song K, Horowitz MA, Quake SR, "Single Cell Tracking of Synechocystis Growth in a Microfluidic Culture Device Using a Probablistic Automated Image Analysis Technique," Proceedings of the 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2013), Freiburg, Germany, November 2013, pp. 1689-1691.
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Yu F, Kibardin V, Horowitz MA, Quake SR, "Microfluidic Serial DAC for Analog Pressure Generation," Proceedings of the 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2012), Okinawa, Japan, November 2012, pp. 70-72.

Lin JCH, Yu F, Tai YC, "Integration of slanted tether check-valves for high pressure applications," Proceedings of 6th IEEE International Conference on Nano/Micro Engineered and Molecular Systems (NEMS 2011), Kaohsiung, Taiwan, February 2011, pp. 715-718.
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Lin JCH, Yu F, Tai YC, "Cracking pressure control of parylene check valve using slanted tensile tethers," Proceedings of 23rd IEEE International Conference on Micro Electro Mechanical Systems (MEMS 2010), Hong Kong, China, January 2010.
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Yu F, Lin JCH, Chen PJ, Tai YC, "Parylene stiction," Proceedings of 23rd IEEE International Conference on Micro Electro Mechanical Systems (MEMS 2010), Hong Kong, China, January 2010.
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Lin JCH, Yu F, Saati S, Varma R, Humayun MS, Tai YC, "Ex vivo implantation study of minimally invasive glaucoma drainage device," Proceedings of the 5th IEEE International Conference on Nano/Micro Engineered and Molecular Systems (NEMS 2010), Xiamen, China, January 2010.
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Yu F, Lin JCH, Chen PJ, Tai YC, "Stiction of parylene C to silicon surface measured using blister tests," Proceedings of the 5th IEEE International Conference on Nano/Micro Engineered and Molecular Systems (NEMS 2010), Xiamen, China, January 2010.
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Lin YCH, Chen PJ, Yu B, Humayun M, Tai YC, "Minimally Invasive Parylene Dual-Valved Flow Drainage Shunt for Glaucoma Implant," Proceedings of 22nd IEEE International Conference on Micro Electro Mechanical Systems (MEMS 2009), Sorrento, Italy, January 2009, pp. 196-199.
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