Publications by Hüseyin Baris Atakan

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Bart Deplancke, Daniel Migliozzi, Hüseyin Baris Atakan, Mustafa Demir, Riccardo Dainese, Daniel Alpern, Dariia Gudkova, Gilles Weder

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Springer2024

Study of Thin Film LiNbO3 Laterally Excited Bulk Acoustic Resonators

Victor Plessky, Luis Guillermo Villanueva Torrijo, Hüseyin Baris Atakan, Soumya Yandrapalli

This work presents an in-depth study of simulation and measurement results of laterally excited shear bulk acoustic resonators (XBAR) in Lithium Niobate, at 5 GHz with high electromechanical coupling factor (k(t)(2)) as high as 25%, and with impedances at ...

Institute of Electrical and Electronics Engineers2022

Automated phenotyping of Caenorhabditis elegans embryos with a high-throughput-screening microfluidic platform

Martinus Gijs, Matteo Cornaglia, Hüseyin Baris Atakan, Tunç Alkanat, Raphaël Etienne Jean Trouillon

The nematode Caenorhabditis elegans has been extensively used as a model multicellular organism to study the influence of osmotic stress conditions and the toxicity of chemical compounds on developmental and motility-associated phenotypes. However, the sev ...

2020

Anin vivomicrofluidic study of bacterial transit inC. elegansnematodes

Thomas Lehnert, Martinus Gijs, Matteo Cornaglia, Hüseyin Baris Atakan, Vittorio Viri

Caenorhabditis elegans(C. elegans) constitutes an important model organism for use in nutrition and aging studies. We report a novel method for studying the dynamics ofEscherichia coli(E. coli) bacterial transit through the worms' intestine. A microfluidic ...

2020

PDMS filter structures for size-dependent larval sorting and on-chip egg extraction of C. elegans

Martinus Gijs, Hüseyin Baris Atakan, Furkan Ayhan

C. elegans-based assays require age-synchronized populations prior to experimentation to achieve standardized sets of worm populations, due to which age-induced heterogeneous phenotyping effects can be avoided. There have been several approaches to synchro ...

ROYAL SOC CHEMISTRY2020

Automated Platform for Long-Term Culture and High-Content Phenotyping of Single C. elegans Worms

Martinus Gijs, Elena Katsyuba, Johan Auwerx, Matteo Cornaglia, Laurent Mouchiroud, Hüseyin Baris Atakan, Rongrong Xiang

The nematode Caenorhabditis elegans is a suitable model organism in drug screening. Traditionally worms are grown on agar plates, posing many challenges for long-term culture and phenotyping of animals under identical conditions. Microfluidics allows for ' ...

Nature Research2019

The Detection of Early Epigenetic Inheritance of Mitochondrial Stress in C. Elegans with a Microfluidic Phenotyping Platform

Martinus Gijs, Johan Auwerx, Matteo Cornaglia, Hüseyin Baris Atakan

Fluctuations and deterioration in environmental conditions potentially have a phenotypic impact that extends over generations. Transgenerational epigenetics is the defined term for such intergenerational transient inheritance without an alteration in the D ...

Nature Research2019

Long-term imaging, automated high-content phenotyping and sorting of C. elegans larvae and embryos using microfluidic platforms

Hüseyin Baris Atakan

C. elegans is frequently studied to address fundamental biological questions motivated by its short life cycle, small size, hermaphrodite behavior and well-annotated genome. In this work, we present novel microfluidic platforms that support long-term cultu ...

EPFL2019

Automated High-Content Phenotyping Of The Nematode C. Elegans At Single Animal Resolution With A Microfluidic Platform

Martinus Gijs, Johan Auwerx, Matteo Cornaglia, Laurent Mouchiroud, Hüseyin Baris Atakan, Rongrong Xiang

In this work, we present a novel microfluidic approach to culture the nematode C. elegans from the onset of embryogenesis to the adult stage at single animal resolution. Our device allows high-throughput experimentation, high-resolution imaging, thereby pr ...

IEEE2019

Automated high-content phenotyping from the first larval stage till the onset of adulthood of the nematode Caenorhabditis elegans

Martinus Gijs, Johan Auwerx, Matteo Cornaglia, Laurent Mouchiroud, Hüseyin Baris Atakan

The nematode Caenorhabditis elegans is increasingly used as a model for human biology. However, in vivo culturing platforms for C. elegans allowing high-content phenotyping during their life cycle in an automated fashion are lacking so far. Here, a multipl ...

ROYAL SOC CHEMISTRY2019

Variable-height microfluidic channels for accurate immobilization of C. elegans worms by using a single dry etching step

Martinus Gijs, Hüseyin Baris Atakan, Rongrong Xiang

We present an aspect ratio dependent etching (ARDE) method, utilizing the Bosch dry etching process of silicon, to create the optimal silicon master microstructures for replication of polydimethylsiloxane (PDMS) microchannels that allow immobilizing C. ele ...

2018

A microfluidic platform for automated phenotyping during full lifespan of Caenorhabditis elegans at high-throughput

Martinus Gijs, Johan Auwerx, Matteo Cornaglia, Laurent Mouchiroud, Hüseyin Baris Atakan

We present a multiplexed and automated microfluidic platform for phenotyping of C. elegans during their full lifespan and at high-throughput. We used the fluorescent hsp-6::gfp strain of worms and performed experiments to observe the effect of four differe ...

2017

Hardware-Oriented Dynamically Adaptive Disparity Estimation Algorithm and its Real-Time Hardware

Alexandre Schmid, Yusuf Leblebici, Abdulkadir Akin, Ipek Baz, Irem Boybat Kara, Hüseyin Baris Atakan

A real-time stereo camera disparity estimation device comprises input means arranged to input measured data corresponding to rows of left and right images; a plurality of on-chip memories arranged to buffer the input measured data; a vertical rotator hardw ...

2015

A Hardware-Oriented Dynamically Adaptive Disparity Estimation Algorithm and its Real-Time Hardware

Alexandre Schmid, Yusuf Leblebici, Abdulkadir Akin, Ipek Baz, Irem Boybat Kara, Hüseyin Baris Atakan

The computational complexity of disparity estimation algorithms and the need of large size and bandwidth for the external and internal memory make the real-time processing of disparity estimation challenging, especially for High Resolution (HR) images. Thi ...

2013