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Sebastian Maerkl

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Related publications (71)

Single Molecule Localization and Discrimination of DNA–Protein Complexes by Controlled Translocation Through Nanocapillaries

Aleksandra Radenovic, Sebastian Maerkl, Sebastian James Davis, Roman Bulushev, Ekaterina Emilova Petrova, Sanjin Marion

Through the use of optical tweezers we performed controlled translocations of DNA-protein complexes through nanocapillaries. We used RNA polymerase (RNAP) with two binding sites on a 7.2 kbp DNA fragment and a dCas9 protein tailored to have five binding si ...

American Chemical Society (ACS)2016

GreA and GreB Enhance Expression of Escherichia coil RNA Polymerase Promoters in a Reconstituted Transcription-Translation System

Sebastian Maerkl, Henrike Marie Niederholtmeyer, Zoe Newell Swank

Cell-free environments are becoming viable alternatives for implementing biological networks in synthetic biology. The reconstituted cell-free expression system (PURE) allows characterization of genetic networks under defined conditions but its applicabili ...

Amer Chemical Soc2016

A Digital-Analog Microfluidic Platform for Patient-Centric Multiplexed Biomarker Diagnostics of Ultralow Volume Samples

Sebastian Maerkl, Francesca Volpetti, Francesco Piraino

Microfluidic diagnostic devices have the potential to transform the practice of medicine. We engineered a multiplexed digital-analog microfluidic platform for the rapid and highly sensitive detection of 3-4 biomarkers in quadruplicate in 16 independent and ...

Amer Chemical Soc2016

Rapid cell-free forward engineering of novel genetic ring oscillators

Amanda Verpoorte, Sebastian Maerkl, Henrike Marie Niederholtmeyer

2015

High-throughput nanoimmunoassay chip

Sebastian Maerkl, Jose Luis Garcia Cordero

The nanoimmunoassay chip comprises at least flow and control layers, divided into several rows, each row containing a plurality of single assay units, each assay unit contains two spotting chambers (1) and an assay chamber in the middle, wherein neck valve ...

2015

A microfluidic platform for high-throughput multiplexed protein quantitation

Sebastian Maerkl, Jose Luis Garcia Cordero, Francesca Volpetti

We present a high-throughput microfluidic platform capable of quantitating up to 384 biomarkers in 4 distinct samples by immunoassay. The microfluidic device contains 384 unit cells, which can be individually programmed with pairs of capture and detection ...

Public Library of Science2015

A 1024-sample serum analyzer chip for cancer diagnostics

Sebastian Maerkl, Jose Luis Garcia Cordero

We present a platform that combines microarrays and microfluidic techniques to measure four protein biomarkers in 1024 serum samples for a total of 4096 assays per device. Detection is based on a surface fluorescence sandwich immunoassay with a limit of de ...

Royal Society of Chemistry2014

Long-Term Single Cell Analysis of S. pombe on a Microfluidic Microchemostat Array

Jean-Bernard Nobs, Sebastian Maerkl

Although Schyzosaccharomyces pombe is one of the principal model organisms for studying the cell cycle, surprisingly few methods have characterized S. pombe growth on the single cell level, and no methods exist capable of analyzing thousands of cells and t ...

Public Library of Science2014

LSPR Chip for Parallel, Rapid, and Sensitive Detection of Cancer Markers in Serum

Sebastian Maerkl, Jose Luis Garcia Cordero

Label-free biosensing based on metallic nano-particles supporting localized surface plasmon resonances (LSPR) has recently received growing interest (Anker, J. N., et al. Nat. Mater. 2008, 7, 442-453). Besides its competitive sensitivity (Yonzon, C. R., et ...

Amer Chemical Soc2014

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

Felix Naef, Philippe Jacquet, Nicolas Dénervaud, Sebastian Maerkl, Jacques Rougemont, Marcel Geertz

In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we ...

Cold Spring Harbor Laboratory Press2014

iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks

Bart Deplancke, Sebastian Maerkl, Sylvie Rockel, Marcel Geertz

Mapping gene regulatory networks is a significant challenge in systems biology, yet only a few methods are currently capable of systems-level identification of transcription factors (TFs) that bind a specific regulatory element. We developed a microfluidic ...

Oxford University Press2013

A high-throughput nanoimmunoassay chip applied to large-scale vaccine adjuvant screening

Jeffrey Alan Hubbell, Sebastian Maerkl, Armando Stano, Jose Luis Garcia Cordero

Large-scale experimentation is becoming instrumental in enabling new discoveries in systems biology and personalized medicine. We developed a multiplexed high-throughput nanoimmunoassay chip capable of quantifying four biomarkers in 384 5 nL samples, for a ...

Royal Soc Chemistry2013

Mapping the fine structure of a eukaryotic promoter input-output function

Nicolas Dénervaud, Sebastian Maerkl, Arun Stephen Rajkumar

The precise tuning of gene expression levels is essential for the optimal performance of transcriptional regulatory networks. We created 209 variants of the Saccharomyces cerevisiae PHO5 promoter to quantify how different binding sites for the transcriptio ...

Nature Publishing Group2013

A chemostat array enables the spatio-temporal analysis of the yeast proteome

Felix Naef, Michaël Unser, Nicolas Dénervaud, Sebastian Maerkl, Ricard Delgado Gonzalo, Arun Stephen Rajkumar, Johannes Becker

Observing cellular responses to perturbations is central to generating and testing hypotheses in biology. We developed a massively parallel microchemostat array capable of growing and observing 1,152 yeast-GFP strains on the single-cell level with 20 min t ...

National Academy of Sciences2013

Implementation of cell-free biological networks at steady state

Viktoria Stepanova, Sebastian Maerkl, Henrike Marie Niederholtmeyer

Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely cons ...

National Academy of Sciences2013

Live mammalian cell arrays

Matthias Lütolf, Sebastian Maerkl, Samy Gobaa, Luis Miguel Fidalgo Rabanera, Kristina Pan Woodruff

High-content assays have the potential to drastically increase throughput in cell biology and drug discovery, but handling and culturing large libraries of cells such as primary tumor or cancer cell lines requires expensive, dedicated robotic equipment. We ...

Nature Publishing Group2013

Multiplexed surface micropatterning of proteins with a pressure-modulated microfluidic button-membrane

Sebastian Maerkl, Jose Luis Garcia Cordero

We report the flow-based in situ patterning of multiple proteins in microfluidic channels by simply tuning the actuation pressure of a microfluidic button-membrane. We show that a single button-membrane can pattern several concentric protein annuli, and we ...

Royal Society of Chemistry2013

Topology and dynamics of the zebrafish segmentation clock core circuit

Bart Deplancke, Sebastian Maerkl, Alina Isakova, Andrew Charles Oates, Daniele Soroldoni

During vertebrate embryogenesis, the rhythmic and sequential segmentation of the body axis is regulated by an oscillating genetic network termed the segmentation clock. We describe a new dynamic model for the core pace-making circuit of the zebrafish segme ...

2012

Massively parallel measurements of molecular interaction kinetics on a microfluidic platform

Sebastian Maerkl, Marcel Geertz

Quantitative biology requires quantitative data. No high-throughput technologies exist capable of obtaining several hundred independent kinetic binding measurements in a single experiment. We present an integrated microfluidic device (k-MITOMI) for the sim ...

National Academy of Sciences2012

Real-Time mRNA Measurement during an

Sebastian Maerkl, Henrike Marie Niederholtmeyer

In vitro transcription and translation reactions have become popular for a bottom-up approach to synthetic biology. Concentrations of the mRNA intermediate are rarely determined, although knowledge of synthesis and degradation rates could facilitate ration ...

Amer Chemical Soc2012

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