Loading...

Adam Abate, PhD

TitleAssociate Professor
InstitutionUniversity of California San Francisco
DepartmentBioengineering
Address1700 4th Street
San Francisco CA 94158
Phone415-476-9819
vCardDownload vCard

    Collapse Biography 
    Collapse Awards and Honors
    Harvard University2000  - 2002Stanley A. Marks Scholar
    NSF2013  - 2018CAREER Award
    NSF, NIMS2013  - 2014US-Japan Young Scientist Exchange Program
    NIH2014  - 2019New Innovator Award

    Collapse Overview 
    Collapse Overview
    Dr. Adam Abate is a physicist who brings a unique research program to the campus. His research employs microfluidics for high-throughput biological applications. He has developed microfluidic methods to create emulsions that consist of droplets of very precise and consistent sizes and to manipulate the processing and contents of individual droplets in different ways. The droplets are used to create micro-compartments, which can be loaded with single cells and other active materials, such as drugs, nutrients, and assay reagents. By chaining together different microdevice components, the droplets can be used as tiny "test tubes" for performing chemical and biological reactions. This allows multiple, independent reactions to take place at the rate of thousands per second, while using minuscule amounts of total reagent. Adam is using this approach for directed evolution, genetic sequencing, and cell sorting.


    Collapse Research 
    Collapse Research Activities and Funding
    SINGLE-CELL TRANSCRIPTOMIC ANALYSIS OF HIV-INFECTED CD4 T CELLS IN BLOOD AND LYMPHOID TISSUE USING PCR-ACTIVATED CELL SORTING
    NIH/NIAID U01AI129206Aug 17, 2017 - Jul 31, 2021
    Role: Principal Investigator
    Accurate and unbiased single cell sequencing with digital droplet MDA
    NIH/NHGRI R01HG008978Sep 9, 2016 - Jun 30, 2019
    Role: Principal Investigator
    Microfluidic immunoprofiling for biomarker discovery in rheumatoid arthritis
    NIH/NIAMS DP2AR068129Sep 30, 2014 - Jun 30, 2019
    Role: Principal Investigator
    Gigapixel digital PCR in Giant Unilamellar Vesicles
    NIH/NIBIB R01EB019453Sep 30, 2014 - May 31, 2018
    Role: Principal Investigator
    Accurate, long-read sequencing with droplet-microfluidic barcoding
    NIH/NHGRI R21HG007233Aug 1, 2013 - Jun 30, 2015
    Role: Principal Investigator
    Advancing Whole-Organism Screening for Chemical Modifiers of the Brain
    NIH/NINDS R21NS082938Feb 1, 2013 - Jan 31, 2015
    Role: Co-Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News
    Collapse Featured Videos

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Demaree B, Weisgerber D, Dolatmoradi A, Hatori M, Abate AR. Direct quantification of EGFR variant allele frequency in cell-free DNA using a microfluidic-free digital droplet PCR assay. Methods Cell Biol. 2018; 148:119-131. PMID: 30473066.
      View in: PubMed
    2. Clark IC, Abate AR. Microfluidic bead encapsulation above 20 kHz with triggered drop formation. Lab Chip. 2018 Oct 26. PMID: 30362490.
      View in: PubMed
    3. Hatori MN, Kim SC, Abate AR. Particle-Templated Emulsification for Microfluidics-Free Digital Biology. Anal Chem. 2018 Aug 01. PMID: 30033717.
      View in: PubMed
    4. Demaree B, Weisgerber D, Lan F, Abate AR. An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing. J Vis Exp. 2018 05 23; (135). PMID: 29889211.
      View in: PubMed
    5. Siltanen CA, Cole RH, Poust S, Chao L, Tyerman J, Kaufmann-Malaga B, Ubersax J, Gartner ZJ, Abate AR. An Oil-Free Picodrop Bioassay Platform for Synthetic Biology. Sci Rep. 2018 May 21; 8(1):7913. PMID: 29784937.
      View in: PubMed
    6. Wagner JM, Liu L, Yuan SF, Venkataraman MV, Abate AR, Alper HS. A comparative analysis of single cell and droplet-based FACS for improving production phenotypes: Riboflavin overproduction in Yarrowia lipolytica. Metab Eng. 2018 Apr 23; 47:346-356. PMID: 29698778.
      View in: PubMed
    7. Clark IC, Thakur R, Abate AR. Concentric electrodes improve microfluidic droplet sorting. Lab Chip. 2018 Feb 27; 18(5):710-713. PMID: 29383336.
      View in: PubMed
    8. Delley CL, Liu L, Sarhan MF, Abate AR. Combined aptamer and transcriptome sequencing of single cells. Sci Rep. 2018 Feb 13; 8(1):2919. PMID: 29440771.
      View in: PubMed
    9. Kim SC, Clark IC, Shahi P, Abate AR. Single-Cell RT-PCR in Microfluidic Droplets with Integrated Chemical Lysis. Anal Chem. 2018 Jan 16; 90(2):1273-1279. PMID: 29256243.
      View in: PubMed
    10. Sukovich DJ, Kim SC, Ahmed N, Abate AR. Bulk double emulsification for flow cytometric analysis of microfluidic droplets. Analyst. 2017 Dec 04; 142(24):4618-4622. PMID: 29131209.
      View in: PubMed
    11. Hori Y, Kantak C, Murray RM, Abate AR. Cell-free extract based optimization of biomolecular circuits with droplet microfluidics. Lab Chip. 2017 09 12; 17(18):3037-3042. PMID: 28770936.
      View in: PubMed
    12. Abatemarco J, Sarhan MF, Wagner JM, Lin JL, Liu L, Hassouneh W, Yuan SF, Alper HS, Abate AR. RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes. Nat Commun. 2017 08 23; 8(1):332. PMID: 28835641.
      View in: PubMed
    13. Cole RH, Tang SY, Siltanen CA, Shahi P, Zhang JQ, Poust S, Gartner ZJ, Abate AR. Printed droplet microfluidics for on demand dispensing of picoliter droplets and cells. Proc Natl Acad Sci U S A. 2017 Aug 15; 114(33):8728-8733. PMID: 28760972.
      View in: PubMed
    14. Karbaschi M, Shahi P, Abate AR. Rapid, chemical-free breaking of microfluidic emulsions with a hand-held antistatic gun. Biomicrofluidics. 2017 Jul; 11(4):044107. PMID: 28794817.
      View in: PubMed
    15. Kim SC, Premasekharan G, Clark IC, Gemeda HB, Paris PL, Abate AR. Measurement of copy number variation in single cancer cells using rapid-emulsification digital droplet MDA. Microsyst Nanoeng. 2017; 3. PMID: 30147985.
      View in: PubMed
    16. Clark IC, Abate AR. Finding a helix in a haystack: nucleic acid cytometry with droplet microfluidics. Lab Chip. 2017 06 13; 17(12):2032-2045. PMID: 28540956.
      View in: PubMed
    17. Lan F, Demaree B, Ahmed N, Abate AR. Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding. Nat Biotechnol. 2017 Jul; 35(7):640-646. PMID: 28553940.
      View in: PubMed
    18. Shahi P, Kim SC, Haliburton JR, Gartner ZJ, Abate AR. Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding. Sci Rep. 2017 Mar 14; 7:44447. PMID: 28290550.
      View in: PubMed
    19. Haliburton JR, Shao W, Deutschbauer A, Arkin A, Abate AR. Genetic interaction mapping with microfluidic-based single cell sequencing. PLoS One. 2017; 12(2):e0171302. PMID: 28170417.
      View in: PubMed
    20. Sukovich DJ, Lance ST, Abate AR. Sequence specific sorting of DNA molecules with FACS using 3dPCR. Sci Rep. 2017 Jan 04; 7:39385. PMID: 28051104.
      View in: PubMed
    21. Lim SW, Lance ST, Stedman KM, Abate AR. PCR-activated cell sorting as a general, cultivation-free method for high-throughput identification and enrichment of virus hosts. J Virol Methods. 2017 04; 242:14-21. PMID: 28042018.
      View in: PubMed
    22. Lance ST, Sukovich DJ, Stedman KM, Abate AR. Peering below the diffraction limit: robust and specific sorting of viruses with flow cytometry. Virol J. 2016 12 01; 13(1):201. PMID: 27906039.
      View in: PubMed
    23. Ahmed N, Sukovich D, Abate AR. Operation of Droplet-Microfluidic Devices with a Lab Centrifuge. Micromachines (Basel). 2016 Sep 06; 7(9). PMID: 30404331.
      View in: PubMed
    24. Lan F, Haliburton JR, Yuan A, Abate AR. Droplet barcoding for massively parallel single-molecule deep sequencing. Nat Commun. 2016 Jun 29; 7:11784. PMID: 27353563; PMCID: PMC4931254.
      View in: PubMed, PubMed Central
    25. Cole RH, Gartner ZJ, Abate AR. Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers. J Vis Exp. 2016 05 05; (111). PMID: 27214249.
      View in: PubMed
    26. Cole RH, Tran TM, Abate AR. Double Emulsion Generation Using a Polydimethylsiloxane (PDMS) Co-axial Flow Focus Device. J Vis Exp. 2015 Dec 25; (106):e53516. PMID: 26780079.
      View in: PubMed
    27. Sidore AM, Lan F, Lim SW, Abate AR. Enhanced sequencing coverage with digital droplet multiple displacement amplification. Nucleic Acids Res. 2016 Apr 20; 44(7):e66. PMID: 26704978; PMCID: PMC4838355.
      View in: PubMed, PubMed Central
    28. Kim SC, Sukovich DJ, Abate AR. Patterning microfluidic device wettability with spatially-controlled plasma oxidation. Lab Chip. 2015 Aug 07; 15(15):3163-9. PMID: 26105774.
      View in: PubMed
    29. Cole RH, de Lange N, Gartner ZJ, Abate AR. Compact and modular multicolour fluorescence detector for droplet microfluidics. Lab Chip. 2015 Jul 07; 15(13):2754-8. PMID: 26032595; PMCID: PMC4505729.
      View in: PubMed, PubMed Central
    30. Romero PA, Tran TM, Abate AR. Dissecting enzyme function with microfluidic-based deep mutational scanning. Proc Natl Acad Sci U S A. 2015 Jun 09; 112(23):7159-64. PMID: 26040002; PMCID: PMC4466731.
      View in: PubMed, PubMed Central
    31. Eastburn DJ, Huang Y, Pellegrino M, Sciambi A, Ptácek LJ, Abate AR. Microfluidic droplet enrichment for targeted sequencing. Nucleic Acids Res. 2015 Jul 27; 43(13):e86. PMID: 25873629; PMCID: PMC4513844.
      View in: PubMed, PubMed Central
    32. Lim SW, Tran TM, Abate AR. PCR-activated cell sorting for cultivation-free enrichment and sequencing of rare microbes. PLoS One. 2015; 10(1):e0113549. PMID: 25629401; PMCID: PMC4309575.
      View in: PubMed, PubMed Central
    33. Ochs CJ, Abate AR. Rapid modulation of droplet composition with pincer microvalves. Lab Chip. 2015 Jan 07; 15(1):52-6. PMID: 25385230.
      View in: PubMed
    34. Sciambi A, Abate AR. Accurate microfluidic sorting of droplets at 30 kHz. Lab Chip. 2015 Jan 07; 15(1):47-51. PMID: 25352174; PMCID: PMC4256106.
      View in: PubMed, PubMed Central
    35. Stieglitz E, Troup CB, Gelston LC, Haliburton J, Chow ED, Yu KB, Akutagawa J, Taylor-Weiner AN, Liu YL, Wang YD, Beckman K, Emanuel PD, Braun BS, Abate A, Gerbing RB, Alonzo TA, Loh ML. Subclonal mutations in SETBP1 confer a poor prognosis in juvenile myelomonocytic leukemia. Blood. 2015 Jan 15; 125(3):516-24. PMID: 25395418; PMCID: PMC4296011.
      View in: PubMed, PubMed Central
    36. Eastburn DJ, Sciambi A, Abate AR. Identification and genetic analysis of cancer cells with PCR-activated cell sorting. Nucleic Acids Res. 2014; 42(16):e128. PMID: 25030902; PMCID: PMC4176366.
      View in: PubMed, PubMed Central
    37. O'Donovan B, Tran T, Sciambi A, Abate A. Picoinjection of microfluidic drops without metal electrodes. J Vis Exp. 2014 Apr 18; (86). PMID: 24797680; PMCID: PMC4172202.
      View in: PubMed, PubMed Central
    38. Sciambi A, Abate AR. Generating electric fields in PDMS microfluidic devices with salt water electrodes. Lab Chip. 2014 Aug 07; 14(15):2605-9. PMID: 24671446; PMCID: PMC4079735.
      View in: PubMed, PubMed Central
    39. Tran TM, Cater S, Abate AR. Coaxial flow focusing in poly(dimethylsiloxane) microfluidic devices. Biomicrofluidics. 2014 Jan; 8(1):016502. PMID: 24753732; PMCID: PMC3977865.
      View in: PubMed, PubMed Central
    40. Abate AR, Hung T, Sperling RA, Mary P, Rotem A, Agresti JJ, Weiner MA, Weitz DA. DNA sequence analysis with droplet-based microfluidics. Lab Chip. 2013 Dec 21; 13(24):4864-9. PMID: 24185402; PMCID: PMC4090915.
      View in: PubMed, PubMed Central
    41. Lim SW, Abate AR. Ultrahigh-throughput sorting of microfluidic drops with flow cytometry. Lab Chip. 2013 Dec 07; 13(23):4563-72. PMID: 24146020.
      View in: PubMed
    42. Eastburn DJ, Sciambi A, Abate AR. Ultrahigh-throughput Mammalian single-cell reverse-transcriptase polymerase chain reaction in microfluidic drops. Anal Chem. 2013 Aug 20; 85(16):8016-21. PMID: 23885761.
      View in: PubMed
    43. Sciambi A, Abate AR. Adding reagent to droplets with controlled rupture of encapsulated double emulsions. Biomicrofluidics. 2013; 7(4):44112. PMID: 24404045; PMCID: PMC3751951.
      View in: PubMed, PubMed Central
    44. Eastburn DJ, Sciambi A, Abate AR. Picoinjection enables digital detection of RNA with droplet rt-PCR. PLoS One. 2013; 8(4):e62961. PMID: 23658657; PMCID: PMC3637249.
      View in: PubMed, PubMed Central
    45. van Steijn V, Korczyk PM, Derzsi L, Abate AR, Weitz DA, Garstecki P. Block-and-break generation of microdroplets with fixed volume. Biomicrofluidics. 2013; 7(2):24108. PMID: 24404013; PMCID: PMC3637280.
      View in: PubMed, PubMed Central
    46. Thompson CS, Abate AR. Adhesive-based bonding technique for PDMS microfluidic devices. Lab Chip. 2013 Feb 21; 13(4):632-5. PMID: 23282717.
      View in: PubMed
    47. Romero PA, Abate AR. Flow focusing geometry generates droplets through a plug and squeeze mechanism. Lab Chip. 2012 Dec 21; 12(24):5130-2. PMID: 23117576.
      View in: PubMed
    48. Rotem A, Abate AR, Utada AS, Van Steijn V, Weitz DA. Drop formation in non-planar microfluidic devices. Lab Chip. 2012 Nov 07; 12(21):4263-8. PMID: 22864475.
      View in: PubMed
    49. O'Donovan B, Eastburn DJ, Abate AR. Electrode-free picoinjection of microfluidic drops. Lab Chip. 2012 Oct 21; 12(20):4029-32. PMID: 22930333.
      View in: PubMed
    50. Duncanson WJ, Lin T, Abate AR, Seiffert S, Shah RK, Weitz DA. Microfluidic synthesis of advanced microparticles for encapsulation and controlled release. Lab Chip. 2012 Jun 21; 12(12):2135-45. PMID: 22510961.
      View in: PubMed
    51. Abate AR, Mary P, van Steijn V, Weitz DA. Experimental validation of plugging during drop formation in a T-junction. Lab Chip. 2012 Apr 21; 12(8):1516-21. PMID: 22402628.
      View in: PubMed
    52. Romanowsky MB, Abate AR, Rotem A, Holtze C, Weitz DA. High throughput production of single core double emulsions in a parallelized microfluidic device. Lab Chip. 2012 Feb 21; 12(4):802-7. PMID: 22222423.
      View in: PubMed
    53. Liu T, Seiffert S, Thiele J, Abate AR, Weitz DA, Richtering W. Non-coalescence of oppositely charged droplets in pH-sensitive emulsions. Proc Natl Acad Sci U S A. 2012 Jan 10; 109(2):384-9. PMID: 22203968; PMCID: PMC3258642.
      View in: PubMed, PubMed Central
    54. Abate AR, Rotem A, Thiele J, Weitz DA. Efficient encapsulation with plug-triggered drop formation. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Sep; 84(3 Pt 1):031502. PMID: 22060374.
      View in: PubMed
    55. Knowles TP, White DA, Abate AR, Agresti JJ, Cohen SI, Sperling RA, De Genst EJ, Dobson CM, Weitz DA. Observation of spatial propagation of amyloid assembly from single nuclei. Proc Natl Acad Sci U S A. 2011 Sep 06; 108(36):14746-51. PMID: 21876182.
      View in: PubMed
    56. Thiele J, Windbergs M, Abate AR, Trebbin M, Shum HC, Förster S, Weitz DA. Early development drug formulation on a chip: fabrication of nanoparticles using a microfluidic spray dryer. Lab Chip. 2011 Jul 21; 11(14):2362-8. PMID: 21617823.
      View in: PubMed
    57. Mary P, Chen A, Chen I, Abate AR, Weitz DA. On-chip background noise reduction for cell-based assays in droplets. Lab Chip. 2011 Jun 21; 11(12):2066-70. PMID: 21541376.
      View in: PubMed
    58. Abate AR, Weitz DA. Faster multiple emulsification with drop splitting. Lab Chip. 2011 Jun 07; 11(11):1911-5. PMID: 21505660.
      View in: PubMed
    59. Mary P, Abate AR, Agresti JJ, Weitz DA. Controlling droplet incubation using close-packed plug flow. Biomicrofluidics. 2011 Apr 04; 5(2):24101. PMID: 21544238; PMCID: PMC3085533.
      View in: PubMed, PubMed Central
    60. Abate AR, Weitz DA. Air-bubble-triggered drop formation in microfluidics. Lab Chip. 2011 May 21; 11(10):1713-6. PMID: 21448493.
      View in: PubMed
    61. Abate AR, Weitz DA. Syringe-vacuum microfluidics: A portable technique to create monodisperse emulsions. Biomicrofluidics. 2011 Mar 16; 5:14107. PMID: 21483661; PMCID: PMC3073010.
      View in: PubMed, PubMed Central
    62. Abate AR, Kutsovsky M, Seiffert S, Windbergs M, Pinto LF, Rotem A, Utada AS, Weitz DA. Synthesis of monodisperse microparticles from non-Newtonian polymer solutions with microfluidic devices. Adv Mater. 2011 Apr 19; 23(15):1757-60. PMID: 21394794.
      View in: PubMed
    63. Abate AR, Thiele J, Weitz DA. One-step formation of multiple emulsions in microfluidics. Lab Chip. 2011 Jan 21; 11(2):253-8. PMID: 20967395.
      View in: PubMed
    64. Abate AR, Hung T, Mary P, Agresti JJ, Weitz DA. High-throughput injection with microfluidics using picoinjectors. Proc Natl Acad Sci U S A. 2010 Nov 09; 107(45):19163-6. PMID: 20962271; PMCID: PMC2984161.
      View in: PubMed, PubMed Central
    65. Thiele J, Abate AR, Shum HC, Bachtler S, Förster S, Weitz DA. Fabrication of polymersomes using double-emulsion templates in glass-coated stamped microfluidic devices. Small. 2010 Aug 16; 6(16):1723-7. PMID: 20665757.
      View in: PubMed
    66. Abate AR, Thiele J, Weinhart M, Weitz DA. Patterning microfluidic device wettability using flow confinement. Lab Chip. 2010 Jul 21; 10(14):1774-6. PMID: 20490412.
      View in: PubMed
    67. Seiffert S, Thiele J, Abate AR, Weitz DA. Smart microgel capsules from macromolecular precursors. J Am Chem Soc. 2010 May 12; 132(18):6606-9. PMID: 20397695.
      View in: PubMed
    68. Romanowsky MB, Heymann M, Abate AR, Krummel AT, Fraden S, Weitz DA. Functional patterning of PDMS microfluidic devices using integrated chemo-masks. Lab Chip. 2010 Jun 21; 10(12):1521-4. PMID: 20454730.
      View in: PubMed
    69. Agresti JJ, Antipov E, Abate AR, Ahn K, Rowat AC, Baret JC, Marquez M, Klibanov AM, Griffiths AD, Weitz DA. Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc Natl Acad Sci U S A. 2010 Mar 02; 107(9):4004-9. PMID: 20142500; PMCID: PMC2840095.
      View in: PubMed, PubMed Central
    70. Schonbrun E, Abate AR, Steinvurzel PE, Weitz DA, Crozier KB. High-throughput fluorescence detection using an integrated zone-plate array. Lab Chip. 2010 Apr 07; 10(7):852-6. PMID: 20300671.
      View in: PubMed
    71. Shum HC, Abate AR, Lee D, Studart AR, Wang B, Chen CH, Thiele J, Shah RK, Krummel A, Weitz DA. Droplet microfluidics for fabrication of non-spherical particles. Macromol Rapid Commun. 2010 Jan 18; 31(2):108-18. PMID: 21590882.
      View in: PubMed
    72. Tang SK, Li Z, Abate AR, Agresti JJ, Weitz DA, Psaltis D, Whitesides GM. A multi-color fast-switching microfluidic droplet dye laser. Lab Chip. 2009 Oct 07; 9(19):2767-71. PMID: 19967111.
      View in: PubMed
    73. Abate AR, Chen CH, Agresti JJ, Weitz DA. Beating Poisson encapsulation statistics using close-packed ordering. Lab Chip. 2009 Sep 21; 9(18):2628-31. PMID: 19704976.
      View in: PubMed
    74. Franke T, Abate AR, Weitz DA, Wixforth A. Surface acoustic wave (SAW) directed droplet flow in microfluidics for PDMS devices. Lab Chip. 2009 Sep 21; 9(18):2625-7. PMID: 19704975.
      View in: PubMed
    75. Chen CH, Shah RK, Abate AR, Weitz DA. Janus particles templated from double emulsion droplets generated using microfluidics. Langmuir. 2009 Apr 21; 25(8):4320-3. PMID: 19366216.
      View in: PubMed
    76. Abate AR, Durian DJ. Effective temperatures and activated dynamics for a two-dimensional air-driven granular system on two approaches to jamming. Phys Rev Lett. 2008 Dec 12; 101(24):245701. PMID: 19113632.
      View in: PubMed
    77. Abate AR, Krummel AT, Lee D, Marquez M, Holtze C, Weitz DA. Photoreactive coating for high-contrast spatial patterning of microfluidic device wettability. Lab Chip. 2008 Dec; 8(12):2157-60. PMID: 19023480.
      View in: PubMed
    78. Abate AR, Lee D, Do T, Holtze C, Weitz DA. Glass coating for PDMS microfluidic channels by sol-gel methods. Lab Chip. 2008 Apr; 8(4):516-8. PMID: 18369504.
      View in: PubMed
    79. Abate AR, Durian DJ. Spatially heterogeneous dynamics in a granular system near jamming. Chaos. 2007 Dec; 17(4):041107. PMID: 18163762.
      View in: PubMed
    Adam's Networks
    Concepts
    Derived automatically from this person's publications.
    See all (146) concept(s)
    _
    Co-Authors
    People in Profiles who have published with this person.
    See all (12) people
    _
    Related Authors
    People who share related concepts with this person.
    See all (60) people
    _
    ↑