Rafael Gómez-Sjöberg

Principal Engineer at Quanticel Pharmaceuticals

Location
San Francisco Bay Area
Industry
Biotechnology

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Rafael Gómez-Sjöberg's Overview

Current
  • Principal Engineer at Quanticel Pharmaceuticals
Past
Education
  • Gimnasio de los Cerros
Connections

206 connections

Websites

Rafael Gómez-Sjöberg's Experience

Principal Engineer

Quanticel Pharmaceuticals

October 2012Present (2 years) San Francisco Bay Area

Designing, building and maintaining custom robotic instrumentation for biomedical research.
Overseeing the development and quality control of the company's gene expression analysis platform.
Managing the design and implementation of a database for organizing the experimental data generated by the platform.
Managing RNA-sequencing projects.

Assistant Adjunct Professor, Dept. of Biochemistry & Biophysics

UCSF

February 2012September 2013 (1 year 8 months) San Francisco, CA

Scientist, Engineering Division

Lawrence Berkeley National Laboratory

May 2008October 2012 (4 years 6 months) Berkeley, CA

Postdoctoral Scholar

Stanford University

January 2005May 2008 (3 years 5 months)

Postdoctoral Research Scholar

California Institute of Technology

March 2004December 2004 (10 months)

May 1998August 1998 (4 months)

February 1995July 1997 (2 years 6 months)

March 1994August 1994 (6 months)

Rafael Gómez-Sjöberg's Languages

  • English

    (Native or bilingual proficiency)
  • Spanish

    (Native or bilingual proficiency)
  • French

    (Limited working proficiency)

Rafael Gómez-Sjöberg's Publications

  • Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices

    • Biosensors and Bioelectronics
    • July 18, 2014
    Authors: Skarphedinn Halldorsson, Edinson Lucumi, Rafael Gómez-Sjöberg, Ronan M.T. Fleming

    Culture of cells using various microfluidic devices is becoming more common within experimental cell biology. At the same time, a technological radiation of microfluidic cell culture device designs is currently in progress. Ultimately, the utility of microfluidic cell culture will be determined by its capacity to permit new insights into cellular function. Especially insights that would otherwise be difficult or impossible to obtain with macroscopic cell culture in traditional polystyrene dishes, flasks or well-plates. Many decades of heuristic optimisation have gone into perfecting conventional cell culture devices and protocols. In comparison, even for the most commonly used microfluidic cell culture devices, such as those fabricated from polydimethylsiloxane (PDMS), collective understanding of the differences in cellular behaviour between microfluidic and macroscopic culture is still developing. Moving in vitro culture from macroscopic culture to PDMS based devices can come with unforeseen challenges. Changes in device material, surface coating, cell number per unit surface area or per unit media volume may all affect the outcome of otherwise standard protocols. In this review, we outline some of the advantages and challenges that may accompany a transition from macroscopic to microfluidic cell culture. We focus on decisive factors that distinguish macroscopic from microfluidic cell culture to encourage a reconsideration of how macroscopic cell culture principles might apply to microfluidic cell culture.

  • High-throughput microfluidic single-cell analysis pipeline for studies of signaling dynamics

    • Nature Protocols
    • June 26, 2014
    Authors: Ryan A. Kellogg, Rafael Gómez-Sjöberg, Anne Leyrat, Savas Tay

    Time-dependent analysis of dynamic processes in single live cells is a revolutionary technique for the quantitative studies of signaling networks. Here we describe an experimental pipeline and associated protocol that incorporate microfluidic cell culture, precise stimulation of cells with signaling molecules or drugs, live-cell microscopy, computerized cell tracking, on-chip staining of key proteins and subsequent retrieval of cells for high-throughput gene expression analysis using microfluidic quantitative PCR (qPCR). Compared with traditional culture dish approaches, this pipeline enhances experimental precision and throughput by orders of magnitude and introduces much-desired new capabilities in cell and fluid handling, thus representing a major step forward in dynamic single-cell analysis. A combination of microfluidic membrane valves, automation and a streamlined protocol now enables a single researcher to generate 1 million data points on single-cell protein localization within 1 week, in various cell types and densities, under 48 predesigned experimental conditions selected from different signaling molecules or drugs, their doses, timings and combinations.

  • Integrated microfluidic test-bed for energy conversion devices

    • Physical Chemistry - Chemical Physics
    • March 28, 2013
    Authors: Miguel Modestino, Camilo A. Diaz-Botia, Sophia Haussener, Rafael Gómez-Sjöberg, Joel W. Ager, Rachel A. Segalman

    Energy conversion devices require the parallel functionality of a variety of components for efficient operation. We present a versatile microfluidic test-bed for facile testing of integrated catalysis and mass transport components for energy conversion via water electrolysis. This system can be readily extended to solar-fuels generators and fuel-cell devices.

  • Multinozzle Emitter Array Chips for Small-Volume Proteomics

    • Analytical Chemistry
    • January 15, 2013
    Authors: Pan Mao, Rafael Gómez-Sjöberg, Daojing Wang

    High-throughput multiplexed proteomics of small-volume biospecimens will generate new opportunities in theranostics. Achieving parallel top-down and bottom-up mass spectrometry analyses of target proteins using a unified apparatus will improve proteome characterization. We have developed a novel silicon-based microfluidic device, multinozzle emitter array chip (MEA chip), as a new platform for small-volume proteomics using liquid chromatography-nanoelectrospray ionization mass spectrometry (LC-nanoESI-MS). We demonstrate parallel, on-chip, and online LC-MS analysis of hemoglobin and its tryptic digests directly from microliters of blood, achieving a detection limit of less than 5 red blood cells. Our MEA chip will enable clinical proteomics of small-volume samples.

  • Programmable Microfluidic Synthesis of Spectrally Encoded Microspheres

    • Lab on a Chip
    • November 21, 2012
    Authors: Rafael Gómez-Sjöberg, Rachel E. Gerver, Brian Baxter, Kurt Thorn, Polly Fordyce, Joseph DeRisi, Camilo Diaz-Botia, Brett Helms

    Spectrally encoded fluorescent beads are an attractive platform for assay miniaturization and multiplexing in the biological sciences. Here, we synthesize hydrophilic PEG–acrylate polymer beads encoded with lanthanide nanophosphors using a fully automated microfluidic synthesis device. These beads are encoded by including varying amounts of two lanthanide nanophosphors relative to a third reference nanophosphor to generate 24 distinct ratios. These codes differ by less than 3% from their target values and can be distinguished from each other with an error rate of <0.1%. The encoded bead synthesis strategy we have used is readily extensible to larger numbers of codes, potentially up to millions, providing a new platform technology for assay multiplexing.

  • Systematic characterization of feature dimensions and closing pressures for microfluidic valves produced via phototresist reflow

    • Lab on a Chip
    • July 11, 2012
    Authors: Rafael Gómez-Sjöberg, Polly Fordyce, Camilo Diaz-Botia, Joseph DeRisi

    Multilayer soft lithography (MSL) provides a convenient and low-cost method for fabricating poly(dimethyl siloxane) (PDMS) microfluidic devices with on-chip valves for automated and precise control of fluid flow. MSL casting molds for flow channels typically incorporate small patches of rounded positive photoresist at valve locations to achieve the rounded cross-sectional profile required for these valves to function properly. Despite the importance of these rounded features for device performance, a comprehensive characterization of how the rounding process affects feature dimensions and closing pressures has been lacking. Here, we measure valve dimensions both before and after rounding and closing pressures for 120 different valve widths and lengths at post-rounding heights between 15 and 84 μm, for a total of 1200 different geometries spanning a wide range of useful sizes. We find that valve height and width after rounding depend strongly on valve aspect ratios, with these effects becoming more pronounced for taller and narrower features. Based on the measured data, we provide a simple fitted model and an online tool for estimating the pre-rounding dimensions needed to achieve desired post-rounding dimensions. We also find that valve closing pressures are well explained by modelling valve membranes in a manner analogous to a suspension bridge, shedding new light on device physics and providing a practical model for estimating closing pressures during device design.

  • Biocompatibility and reduced drug absorption of sol-gel-treated poly(dimethyl siloxane) for microfluidic cell culture applications

    • Analytical Chemistry
    • November 11, 2010
    Authors: Rafael Gómez-Sjöberg, Anne Leyrat, Stephen R. Quake, Benjamin T. Houseman, Kevan Shokat

    Poly(dimethyl siloxane) (PDMS)-based microfluidic devices are now commonly used for a wide variety of biological experiments, including cell culture assays. However, the porous, hydrophobic polymer matrix of PDMS rapidly absorbs small hydrophobic molecules, including hormones and most small-molecule drugs. This makes it challenging to perform experiments that require such substances in PDMS microfluidic devices. This study presents evidence that a sol−gel treatment of PDMS that fills the polymer matrix with silica nanoparticles is effective at reducing the absorption of drugs into the material while preserving its biocompatibility, transparency, and oxygen permeability. We show that the absorption of two anticancer drugs, camptothecin and a kinase inhibitor, is reduced to such an extent that on-chip microfluidic cell culture experiments can recapitulate the results obtained off-chip.

  • Versatile, Fully Automated, Microfluidic Cell Culture System

    • Analytical Chemistry
    • October 23, 2007
    Authors: Rafael Gómez-Sjöberg, Anne Leyrat, Dana M. Pirone, Christopher S. Chen, Stephen R. Quake

    There is increasing demand for automated and quantitative cell culture technology, driven both by the intense activity in stem cell biology and by the emergence of systems biology. We built a fully automated cell culture screening system based on a microfluidic chip that creates arbitrary culture media formulations in 96 independent culture chambers and maintains cell viability for weeks. Individual culture conditions are customized in terms of cell seeding density, composition of culture medium, and feeding schedule, and each chamber is imaged with time-lapse microscopy. Using this device, we perform the first quantitative measurements of the influence of transient stimulation schedules on the proliferation, osteogenic differentiation, and motility of human primary mesenchymal stem cells.

  • Impedance Microbiology-on-a-Chip: Microfluidic Bioprocessor for Rapid Detection of Bacterial Metabolism

    • Journal of Microelectromechanical Systems
    • August 2005
    Authors: Rafael Gómez-Sjöberg, Dallas Morisette, Rashid Bashir

    Detection of a few live bacterial cells in many industrial or clinical samples is a very important technological problem. We have developed a microscale technique for concentrating bacterial cells from a dilute sample, by factors on the order of 10,000 to 100,000, and detecting their metabolic activity by purely electrical means. The technique was implemented on a silicon-based microfluidic chip where the cells are concentrated and incubated in a chamber with a volume of 400 pL. Concentration and capture are obtained by the use of dielectrophoresis on the bacterial cells, and metabolism detection is achieved by means of impedance measurements of the medium in which the bacteria are incubated. Performing impedance-based detection at the microscale results in drastically reduced detection times for dilute bacterial samples, thanks to the ability to efficiently concentrate and capture the cells in an extremely small volume. Such concentration eliminates the need to amplify the bacterial population by long culture steps. This detection technique can be used for a wide variety of applications.

  • Measurements of Radiation Characteristics of Fused Quartz Containing Bubbles

    • Journal of the Optical Society of America A
    • January 1, 2004
    Authors: Rafael Gómez-Sjöberg, Laurent Pilon, Dominique Baillis, Harifidy Randrianalisoa, Raymond Viskanta

    We report experimental measurement of radiation characteristics of fused quartz containing bubbles over the spectral region from 1.67 to 3.5 micrometers. The radiation characteristics were retrieved by an inverse method that minimizes the quadratic difference between the measured and the calculated spectral bidirectional transmittance and reflectance for different sample thicknesses. The theoretical spectral transmittances and reflectances were computed by solving the one-dimensional radiative transfer equation by the discrete-ordinates method for a nonemitting, homogeneous, and scattering medium. The results of the inversion were shown to be independent of the sample thickness for samples thicker than 3 mm and clearly demonstrate that bubbles have an effect on the radiation characteristics of fused quartz.

Rafael Gómez-Sjöberg's Skills & Expertise

  1. Cell Culture
  2. Microfluidics
  3. Experimentation
  4. MEMS
  5. Cell Based Assays
  6. Laboratory Automation
  7. Matlab
  8. NI LabVIEW
  9. Pro Engineer
  10. Microscopy
  11. Microfabrication
  12. Photolithography
  13. Semiconductors
  14. Soft Lithography
  15. Cell
  16. Nanotechnology
  17. Sensors
  18. Fluorescence Microscopy
  19. Image Processing
  20. Solidworks
  21. Simulations
  22. Biotechnology
  23. Electronics
  24. Biochemistry
  25. Characterization

View All (25) Skills View Fewer Skills

Rafael Gómez-Sjöberg's Education

Purdue University

PhD, Electrical Engineering / MEMS / Microfabrication / Microfluidics

19992003

Grade: 3.93

Developed a microfabricated device for impedance-based electronic detection of bacterial metabolism

Activities and Societies: Purdue Argentinean Tango Club, Outing Club

Purdue University

MS, Electrical Engineering / Microelectronics

19971999

Grade: 4.0

Developed a novel lateral bipolar transistor compatible with deep-submicron CMOS technology.

Universidad de Los Andes

B.S., Electrical Engineering

19891993

Gimnasio de los Cerros

International Baccalaureate

19781988

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