@article{Weber2009,
title = {A synthetic mammalian electro-genetic transcription circuit},
author = {Wilfried Weber and Stefan Luzi and Maria Karlsson and Carlota Diaz Sanchez-Bustamante and Urs Frey and Andreas Hierlemann and Martin Fussenegger},
url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp014},
doi = {10.1093/nar/gkp014},
issn = {03051048},
year = {2009},
date = {2009-02-03},
journal = {Nucleic Acids Research},
volume = {37},
number = {4},
pages = {1-8},
abstract = {Electric signal processing has evolved to manage rapid information transfer in neuronal networks and muscular contraction in multicellular organisms and controls the most sophisticated man-built devices. Using a synthetic biology approach to assemble electronic parts with genetic control units engineered into mammalian cells, we designed an electric power-adjustable transcription control circuit able to integrate the intensity of a direct current over time, to translate the amplitude or frequency of an alternating current into an adjustable genetic readout or to modulate the beating frequency of primary heart cells. Successful miniaturization of the electro-genetic devices may pave the way for the design of novel hybrid electrogenetic implants assembled from electronic and genetic parts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Sanchez-Bustamante2008,
title = {Modulation of cardiomyocyte electrical properties using regulated bone morphogenetic protein-2 expression.},
author = {Carlota Diaz Sanchez-Bustamante and Urs Frey and Jens M Kelm and Andreas Hierlemann and Martin Fussenegger},
url = {http://online.liebertpub.com/doi/abs/10.1089/ten.tea.2007.0302?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed},
doi = {10.1089/ten.tea.2007.0302},
issn = {1937-3341},
year = {2008},
date = {2008-11-19},
journal = {Tissue Engineering. Part A},
volume = {14},
number = {12},
pages = {1969-1988},
abstract = {Because cardiomyocytes lose their ability to divide after birth, any subsequent cell loss or dysfunction results in pathologic cardiac rhythm initiation or impulse conduction. Strategies to restore and control the electrophysiological activity of the heart may, therefore, greatly affect the regeneration of cardiac tissue functionality. Using lentivirus-derived particles to regulate the bone morphogenetic protein-2 (BMP-2) gene expression in a pristinamycin- or gaseous acetaldehyde-inducible manner, we demonstrated the adjustment of cardiomyocyte electrophysiological characteristics. Complementary metal oxide semiconductor-based high-density microelectrode arrays (HD-MEAs) were used to monitor the electrophysiological activity of neonatal rat cardiomyocytes (NRCs) cultured as monolayers (NRCml) or as microtissues (NRCmt). NRCmt more closely resembled heart tissue physiology than did NRCml and could be conveniently monitored using HD-MEAs because of their ability to detect low-signal events and to sub-select the region of interest, namely, areas where the microtissues were placed. Cardiomyocyte-forming microtissues, transduced using lentiviral vectors encoding BMP-2, were capable of restoring myocardial microtissue electrical activity. We also engineered NRCmt to functionally couple within a cardiomyocyte monolayer, thus showing pacemaker-like activity upon local regulation of transgenic BMP-2 expression. The controlled expression of therapeutic transgenes represents a crucial advance for clinical interventions and gene-function analysis.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Hierlemann2007,
title = {A CMOS-based microelectrode array for interaction with neuronal cultures},
author = {Flavio Heer and Sadik Hafizovic and T Ugniwenko and Urs Frey and Axel Blau and Christiane Ziegler and Andreas Hierlemann},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0165027007001781},
doi = {10.1016/j.jneumeth.2007.04.006},
issn = {0165-0270},
year = {2007},
date = {2007-04-19},
journal = {Journal of Neuroscience Methods},
volume = {164},
number = {1},
pages = {93-106},
abstract = {We report on the system integration of a CMOS chip that is capable of bidirectionally communicating (stimulation and recording) with electrogenic cells such as neurons or cardiomyocytes and that is targeted at investigating electrical signal propagation within cellular networks in vitro. The overall system consists of three major subunits: first, the core component is a 6.5 mm × 6.5 mm CMOS chip, on top of which the cells are cultured. It features 128 bidirectional electrodes, each equipped with dedicated analog filters and amplification stages and a stimulation buffer. The electrodes are sampled at 20 kHz with 8-bit resolution. The measured input-referred circuitry noise is 5.9 muV root mean square (10 Hz to 100 kHz), which allows to reliably detect the cell signals ranging from 1 mVpp down to 40 muVpp. Additionally, temperature sensors, a digital-to-analog converter for stimulation, and a digital interface for data transmission are integrated. Second, there is a reconfigurable logic device, which provides chip control, event detection, data buffering and an USB interface, capable of processing the 2.56 million samples per second. The third element includes software that is running on a standard PC performing data capturing, processing, and visualization. Experiments involving the stimulation of neurons with two different spatio-temporal patterns and the recording of the triggered spiking activity have been carried out. The response patterns have been successfully classified (83% correct) with respect to the different stimulation patterns. The advantages over current microelectrode arrays, as has been demonstrated in the experiments, include the capability to stimulate (voltage stimulation, 8 bit, 60 kHz) spatio-temporal patterns on arbitrary sets of electrodes and the fast stimulation reset mechanism that allows to record neuronal signals on a stimulating electrode 5 ms after stimulation (instantaneously on all other electrodes). Other advantages of the overall system include the small number of needed electrical connections due to the digital interface and the short latency time that allows to initiate a stimulation less than 2 ms after the detection of an action potential in closed-loop configurations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Greve2007,
title = {A perforated CMOS microchip platform for immobilization and activity monitoring of electrogenic cells},
author = {Frauke Greve and Jan Lichtenberg and Kay Uwe Kirstein and Urs Frey and Jean Claude Perriard and Andreas Hierlemann},
url = {http://iopscience.iop.org/article/10.1088/0960-1317/17/3/007/},
doi = {10.1088/0960-1317/17/3/007},
issn = {0960-1317},
year = {2007},
date = {2007-01-30},
journal = {Journal of Micromechanics and Microengineering},
volume = {17},
number = {3},
pages = {462-471},
abstract = {CMOS-based microelectrode systems offer decisive advantages over conventional micro-electrode arrays, which include the possibility to perform on-chip signal conditioning or to efficiently use larger numbers of electrodes to obtain statistically relevant data, e.g., in pharmacological drug screening. A larger number of electrodes can only be realized with the help of on-chip multiplexing and readout schemes, which require integrated electronics. Another fundamental issue in performing high-fidelity recordings from electrogenic cells is a good electrical coupling between the cells and the microelectrodes, in particular, since the recorded extracellular signals are in the range of only 10–1000 µV. In this paper we present the first CMOS microelectrode system with integrated micromechanical cell-placement features fabricated in a commercial CMOS process with subsequent post-CMOS bulk micromachining. This new microdevice aims at enabling the precise placement of single cells in the center of the electrodes to ensure an efficient use of the available electrodes, even for low-density cell cultures. Small through-chip holes have been generated at the metal-electrode sites by using a combination of bulk micromachining and reactive-ion etching. These holes act as orifices so that cell immobilization can be achieved by means of pneumatic anchoring. The chip additionally hosts integrated circuitry, i.e., multiplexers to select the respective readout electrodes, an amplifier with selectable gain (2×, 10×, 100×), and a high-pass filter (100 Hz cut-off). In this paper we show that electrical signals from most of the electrodes can be recorded, even in low-density cultures of neonatal rat cardiomyocytes, by using perforated metal electrodes and by applying a small underpressure from the backside of the chip. The measurements evidenced that, in most cases, about 90% of the electrodes were covered with single cells, approximately 4% were covered with more than one cell due to clustering and approximately 6% were not covered with any cell, mostly as a consequence of orifice clogging. After 4 days of culturing, the cells were still in place on the electrodes so that the cell electrical activity could be measured using the on-chip circuitry. Measured signal amplitudes were in the range of 500–700 µV, while the input-referred noise of the readout was below 15 µVrms (100 Hz–4 kHz bandwidth). We report on the development and fabrication of this new cell-biological tool and present first results collected during the characterization and evaluation of the chip. The recordings of electrical potentials of neonatal rat cardiomyocytes after several days in vitro, which, on the one hand, were conventionally cultured (no pneumatic anchoring) and, on the other hand, were anchored and immobilized, will be detailed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Hierlemann2006,
title = {Single-chip microelectronic system to interface with living cells},
author = {Flavio Heer and Sadik Hafizovic and T Ugniwenko and Urs Frey and Wendy Franks and Evelyne Perriard and Jean Claude Perriard and Axel Blau and Christiane Ziegler and Andreas Hierlemann},
url = {http://www.sciencedirect.com/science/article/pii/S0956566306004891?via%3Dihub},
doi = {10.1016/j.bios.2006.10.003},
issn = {0956-5663},
year = {2006},
date = {2006-11-13},
journal = {Biosensors & Bioelectronics},
volume = {22},
number = {11},
pages = {2546-2553},
abstract = {A high degree of connectivity and the coordinated electrical activity of neural cells or networks are believed to be the reason that the brain is capable of highly sophisticated information processing. Likewise, the effectiveness of an animal heart largely depends on such coordinated cell activity. To advance our understanding of these complex biological systems, high spatiotemporal-resolution techniques to monitor the cell electrical activity and an ideally seamless interaction between cells and recording devices are desired. Here we present a monolithic microsystem in complementary metal oxide semiconductor (CMOS) technology that provides bidirectional communication (stimulation and recording) between standard electronics technology and cultured electrogenic cells. The microchip can be directly used as a substrate for cell culturing, it features circuitry units per electrode for stimulation and immediate cell signal treatment, and it provides on-chip signal transformation as well as a digital interface so that a very fast, almost real-time interaction (2ms loop time from event recognition to, e.g., a defined stimulation) is possible at remarkable signal quality. The corresponding spontaneous and stimulated electrical activity recordings with neuronal and cardiac cell cultures will be presented. The system can be used to, e.g., study the development of neural networks, reveal the effects of neuronal plasticity and study cellular or network activity in response to pharmacological treatments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Hierlemann2006b,
title = {Patterned cell adhesion by self-assembled structures for use with a CMOS cell-based biosensor},
author = {Wendy Franks and Samuele Tosatti and Flavio Heer and Philipp Seif and Marcus Textor and Andreas Hierlemann},
url = {http://www.sciencedirect.com/science/article/pii/S095656630600282X?via%3Dihub},
doi = {10.1016/j.bios.2006.06.031},
issn = {0956-5663},
year = {2006},
date = {2006-10-19},
journal = {Biosensors & Bioelectronics},
volume = {22},
number = {7},
pages = {1426-1433},
abstract = {A strategy for patterned cell adhesion based on chemical surface modification is presented. To confine cell adhesion to specific locations, an engineered surface for high-contrast protein adsorption and, hence, cell attachment has been developed. Surface functionalization is based on selective molecular-assembly patterning (SMAP). An amine-terminated self-assembled monolayer is used to define areas of cell adhesion. A protein-repellent grafted copolymer, poly(l-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG), is used to render the surrounding silicon dioxide resistant to protein adsorption. X-ray photoelectron spectroscopy, scanning ellipsometry and fluorescence microscopy techniques were used to monitor the individual steps of the patterning process. Successful guided growth using these layers is demonstrated with primary neonatal rat cardiomyocytes, up to 4 days in vitro, and with the HL-1 cardiomyocyte cell line, up to 7 days in vitro. The advantage of the presented method is that high-resolution engineered surfaces can be realized using a simple, cost-effective, dip-and-rinse process. The technique has been developed for application on a CMOS cell-based biosensor, which comprises an array of microelectrodes to extracellularly record electrical activity from cardiomyocytes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Heer2006,
title = {CMOS microelectrode array for bidirectional interaction with neuronal networks},
author = {Flavio Heer and Sadik Hafizovic and Wendy Franks and Axel Blau and Christiane Ziegler and Andreas Hierlemann},
url = {http://ieeexplore.ieee.org/document/1644873/},
doi = {10.1109/JSSC.2006.873677},
issn = {0018-9200},
year = {2006},
date = {2006-07-07},
journal = {IEEE Journal of Solid-State Circuits},
volume = {41},
number = {7},
pages = {1620-1629},
abstract = {A CMOS metal-electrode-based micro system for bidirectional communication (stimulation and recording) with neuronal cells in vitro is presented. The chip overcomes the interconnect challenge that limits today's bidirectional microelectrode arrays. The microsystem has been fabricated in an industrial CMOS technology with several post-CMOS processing steps to realize 128 biocompatible electrodes and to ensure chip stability in physiological saline. The system comprises all necessary control circuitry and on-chip A/D and D/A conversion. A modular design has been implemented, where individual stimulation- and signal-conditioning circuitry units are associated with each electrode. Stimulation signals with a resolution of 8 bits can be sent to any subset of electrodes at a rate of 60 kHz, while all electrodes of the chip are continuously sampled at a rate of 20 kHz. The circuitry at each electrode can be individually reset to its operating point in order to suppress artifacts evoked by the stimulation pulses. Biological measurements from cultured neuronal networks originating from dissociated cortical tissue of fertilized chicken eggs with amplitudes of up to 500 muVpp are presented.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Linder2006,
title = {Microfluidics/CMOS orthogonal capabilities for cell biology},
author = {Vincent Linder and Sander Koster and Wendy Franks and Tobias Kraus and Elisabeth Verpoorte and Flavio Heer and Andreas Hierlemann and Nico F de Rooij},
url = {https://link.springer.com/article/10.1007%2Fs10544-006-7711-9},
doi = {10.1007/s10544-006-7711-9},
issn = {1572-8781},
year = {2006},
date = {2006-06-01},
journal = {Biomedical Microdevices},
volume = {8},
number = {2},
pages = {159-166},
abstract = {The study of individual cells and cellular networks can greatly benefit from the capabilities of microfabricated devices for the stimulation and the recording of electrical cellular events. In this contribution, we describe the development of a device, which combines capabilities for both electrical and pharmacological cell stimulation, and the subsequent recording of electrical cellular activity. The device combines the unique advantages of integrated circuitry (CMOS technology) for signal processing and microfluidics for drug delivery. Both techniques are ideally suited to study electrogenic mammalian cells, because feature sizes are of the same order as the cell diameter, ∼50 mum. Despite these attractive features, we observe a size mismatch between microfluidic devices, with bulky fluidic connections to the outside world, and highly miniaturized CMOS chips. To overcome this problem, we developed a microfluidic flow cell that accommodates a small CMOS chip. We simulated the performances of a flow cell based on a 3-D microfluidic system, and then fabricated the device to experimentally verify the nutrient delivery and localized drug delivery performance. The flow-cell has a constant nutrient flow, and six drug inlets that can individually deliver a drug to the cells. The experimental analysis of the nutrient and drug flow mass transfer properties in the flowcell are in good agreement with our simulations. For an experimental proof-of-principle, we successfully delivered, in a spatially resolved manner, a `drug' to a culture of HL-1 cardiac myocytes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Koster2006,
title = {Characterization of a microfluidic dispensing system for localised stimulation of cellular networks},
author = {Tobias Kraus and Elisabeth Verpoorte and Vincent Linder and Wendy Franks and Andreas Hierlemann and Flavio Heer and Sadik Hafizovic and Teruo Fujii and Nico F de Rooij and Sander Koster},
url = {http://pubs.rsc.org/en/Content/ArticleLanding/2006/LC/b511768b#!divAbstract},
doi = {10.1039/B511768B},
year = {2006},
date = {2006-01-04},
journal = {Lab Chip},
volume = {6},
number = {2},
pages = {218-229},
publisher = {The Royal Society of Chemistry},
abstract = {We present a 3-D microfluidic device designed for localized drug delivery to cellular networks. The device features a flow cell comprising a main channel for nutrient delivery as well as multiple channels for drug delivery. This device is one key component of a larger, fully integrated system now under development, based upon a microelectrode array (MEA) with on-chip CMOS circuitry for recording and stimulation of electrogenic cells (e.g. neurons, cardiomyocytes). As a critical system unit, the microfluidics must be carefully designed and characterized to ensure that candidate drugs are delivered to specific regions of the culture at known concentrations. Furthermore, microfluidic design and functionality is dictated by the size, geometry, and material/electrical characteristics of the CMOS MEA. Therefore, this paper reports on the design considerations and fabrication of the flow cell, including theoretical and experimental analysis of the mass transfer properties of the nutrient and drug flows, which are in good agreement with one another. To demonstrate proof of concept, the flow cell was mounted on a dummy CMOS chip, which had been plated with HL-1 cardiomyocytes. A test chemical compound was delivered to the cell culture in a spatially resolved manner. Envisioned applications of this stand-alone system include simultaneous toxicological testing of multiple compounds and chemical stimulation of natural neural networks for neuroscience investigations},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Franks2005,
title = {Impedance characterization and modeling of electrodes for biomedical applications},
author = {Wendy Franks and Iwan Schenker and Patrik Schmutz and Andreas Hierlemann},
url = {http://ieeexplore.ieee.org/document/1440608/},
doi = {10.1109/TBME.2005.847523},
issn = {00189294},
year = {2005},
date = {2005-06-13},
journal = {IEEE Transactions on Biomedical Engineering},
volume = {52},
number = {7},
pages = {1295-1302},
abstract = {A low electrode-electrolyte impedance interface is critical in the design of electrodes for biomedical applications. To design low-impedance interfaces a complete understanding of the physical processes contributing to the impedance is required. In this work a model describing these physical processes is validated and extended to quantify the effect of organic coatings and incubation time. Electrochemical impedance spectroscopy has been used to electrically characterize the interface for various electrode materials: platinum, platinum black, and titanium nitride; and varying electrode sizes: 1 cm2, and 900 mu m2. An equivalent circuit model comprising an interface capacitance, shunted by a charge transfer resistance, in series with the solution resistance has been fitted to the experimental results. Theoretical equations have been used to calculate the interface capacitance impedance and the solution resistance, yielding results that correspond well with the fitted parameter values, thereby confirming the validity of the equations. The effect of incubation time, and two organic cell-adhesion promoting coatings, poly-L-lysine and laminin, on the interface impedance has been quantified using the model. This demonstrates the benefits of using this model in developing better understanding of the physical processes occurring at the interface in more complex, biomedically relevant situations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Jenkner2004,
title = {Cell-based CMOS sensor and actuator arrays},
author = {Martin Jenkner and Marco Tartagni and Andreas Hierlemann and Roland Thewes},
url = {http://ieeexplore.ieee.org/document/1362853/},
doi = {10.1109/JSSC.2004.837082},
issn = {00189200},
year = {2004},
date = {2004-11-30},
journal = {IEEE Journal of Solid-State Circuits},
volume = {39},
number = {12},
pages = {2431-2437},
abstract = {In recent years, increasing knowledge about in vitro cell handling and culturing has encouraged a variety of CMOS-based approaches to stimulate and detect electrical activity of biological cells. This paper outlines in a topical review the scope of cell-based biosensors and actuators for in vitro applications ranging from single-cell detection to multisite probing of complex neural tissue. Recent examples are selected to demonstrate how standard CMOS processes have been used to engineer arrays with different functionality.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Baltes2004,
title = {CMOS microelectrode array for the monitoring of electrogenic cells},
author = {Flavio Heer and Wendy Franks and Axel Blau and S Taschini and Christiane Ziegler and Andreas Hierlemann and Henry Baltes},
url = {http://www.sciencedirect.com/science/article/pii/S0956566304000806?via%3Dihub},
doi = {10.1016/j.bios.2004.02.006},
issn = {0956-5663},
year = {2004},
date = {2004-03-19},
journal = {Biosensors & Bioelectronics},
volume = {20},
number = {2},
pages = {358-366},
abstract = {Signal degradation and an array size dictated by the number of available interconnects are the two main limitations inherent to standalone microelectrode arrays (MEAs). A new biochip consisting of an array of microelectrodes with fully-integrated analog and digital circuitry realized in an industrial CMOS process addresses these issues. The device is capable of on-chip signal filtering for improved signal-to-noise ratio (SNR), on-chip analog and digital conversion, and multiplexing, thereby facilitating simultaneous stimulation and recording of electrogenic cell activity. The designed electrode pitch of 250 mu m significantly limits the space available for circuitry: a repeated unit of circuitry associated with each electrode comprises a stimulation buffer and a bandpass filter for readout. The bandpass filter has corner frequencies of 100 Hz and 50 kHz, and a gain of 1000. Stimulation voltages are generated from an 8-bit digital signal and converted to an analog signal at a frequency of 120 kHz. Functionality of the read-out circuitry is demonstrated by the measurement of cardiomyocyte activity. The microelectrode is realized in a shifted design for flexibility and biocompatibility. Several microelectrode materials (platinum, platinum black and titanium nitride) have been electrically characterized. An equivalent circuit model, where each parameter represents a macroscopic physical quantity contributing to the interface impedance, has been successfully fitted to experimental results.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}