Search Results - "Kraus, Oren"

Classifying and segmenting microscopy images with deep multiple instance learning by Kraus, Oren Z, Ba, Jimmy Lei, Frey, Brendan J

“…High-content screening (HCS) technologies have enabled large scale imaging experiments for studying cell biology and for drug screening. These systems produce…”
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Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting by Lu, Alex X, Kraus, Oren Z, Cooper, Sam, Moses, Alan M

“…Cellular microscopy images contain rich insights about biology. To extract this information, researchers use features, or measurements of the patterns of…”
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Automated analysis of high‐content microscopy data with deep learning by Kraus, Oren Z, Grys, Ben T, Ba, Jimmy, Chong, Yolanda, Frey, Brendan J, Boone, Charles, Andrews, Brenda J

“…Existing computational pipelines for quantitative analysis of high‐content microscopy data rely on traditional machine learning approaches that fail to…”
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Machine learning and computer vision approaches for phenotypic profiling by Grys, Ben T, Lo, Dara S, Sahin, Nil, Kraus, Oren Z, Morris, Quaid, Boone, Charles, Andrews, Brenda J

“…With recent advances in high-throughput, automated microscopy, there has been an increased demand for effective computational strategies to analyze…”
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Computer vision for high content screening by Kraus, Oren Z, Frey, Brendan J

“…High Content Screening (HCS) technologies that combine automated fluorescence microscopy with high throughput biotechnology have become powerful systems for…”
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Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle by Litsios, Athanasios, Grys, Benjamin T, Kraus, Oren Z, Friesen, Helena, Ross, Catherine, Masinas, Myra Paz David, Forster, Duncan T, Couvillion, Mary T, Timmermann, Stefanie, Billmann, Maximilian, Myers, Chad, Johnsson, Nils, Churchman, L Stirling, Boone, Charles, Andrews, Brenda J

“…Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional…”
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Integrating images from multiple microscopy screens reveals diverse patterns of change in the subcellular localization of proteins by Lu, Alex X, Chong, Yolanda T, Hsu, Ian Shen, Strome, Bob, Handfield, Louis-Francois, Kraus, Oren, Andrews, Brenda J, Moses, Alan M

“…The evaluation of protein localization changes on a systematic level is a powerful tool for understanding how cells respond to environmental, chemical, or…”
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Data-analysis strategies for image-based cell profiling by Caicedo, Juan C, Cooper, Sam, Heigwer, Florian, Warchal, Scott, Qiu, Peng, Molnar, Csaba, Vasilevich, Aliaksei S, Barry, Joseph D, Bansal, Harmanjit Singh, Kraus, Oren, Wawer, Mathias, Paavolainen, Lassi, Herrmann, Markus D, Rohban, Mohammad, Hung, Jane, Hennig, Holger, Concannon, John, Smith, Ian, Clemons, Paul A, Singh, Shantanu, Rees, Paul, Horvath, Peter, Linington, Roger G, Carpenter, Anne E

“…This Review covers the steps required to create high-quality image-based profiles from high-throughput microscopy images. Image-based cell profiling is a…”
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Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer by Ehteshami Bejnordi, Babak, Veta, Mitko, Johannes van Diest, Paul, van Ginneken, Bram, Karssemeijer, Nico, Litjens, Geert, van der Laak, Jeroen A. W. M, Hermsen, Meyke, Manson, Quirine F, Balkenhol, Maschenka, Geessink, Oscar, Stathonikos, Nikolaos, van Dijk, Marcory CRF, Bult, Peter, Beca, Francisco, Beck, Andrew H, Wang, Dayong, Khosla, Aditya, Gargeya, Rishab, Irshad, Humayun, Zhong, Aoxiao, Dou, Qi, Li, Quanzheng, Chen, Hao, Lin, Huang-Jing, Heng, Pheng-Ann, Haß, Christian, Bruni, Elia, Wong, Quincy, Halici, Ugur, Öner, Mustafa Ümit, Cetin-Atalay, Rengul, Berseth, Matt, Khvatkov, Vitali, Vylegzhanin, Alexei, Kraus, Oren, Shaban, Muhammad, Rajpoot, Nasir, Awan, Ruqayya, Sirinukunwattana, Korsuk, Qaiser, Talha, Tsang, Yee-Wah, Tellez, David, Annuscheit, Jonas, Hufnagl, Peter, Valkonen, Mira, Kartasalo, Kimmo, Latonen, Leena, Ruusuvuori, Pekka, Liimatainen, Kaisa, Albarqouni, Shadi, Mungal, Bharti, George, Ami, Demirci, Stefanie, Navab, Nassir, Watanabe, Seiryo, Seno, Shigeto, Takenaka, Yoichi, Matsuda, Hideo, Ahmady Phoulady, Hady, Kovalev, Vassili, Kalinovsky, Alexander, Liauchuk, Vitali, Bueno, Gloria, Fernandez-Carrobles, M. Milagro, Serrano, Ismael, Deniz, Oscar, Racoceanu, Daniel, Venâncio, Rui

“…IMPORTANCE: Application of deep learning algorithms to whole-slide pathology images can potentially improve diagnostic accuracy and efficiency. OBJECTIVE:…”
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Exploring whole-genome duplicate gene retention with complex genetic interaction analysis by Kuzmin, Elena, VanderSluis, Benjamin, Nguyen Ba, Alex N, Wang, Wen, Koch, Elizabeth N, Usaj, Matej, Khmelinskii, Anton, Usaj, Mojca Mattiazzi, van Leeuwen, Jolanda, Kraus, Oren, Tresenrider, Amy, Pryszlak, Michael, Hu, Ming-Che, Varriano, Brenda, Costanzo, Michael, Knop, Michael, Moses, Alan, Myers, Chad L, Andrews, Brenda J, Boone, Charles

“…Whole-genome duplication has played a central role in the genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated,…”
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Automating High Content Screening with Deep Learning by Kraus, Oren Zeev

“…High-content screening (HCS) combines automated microscopy with high throughput technologies for assaying genetic or environmental perturbations. HCS systems…”
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Development of a Microfluidic Platform to Investigate Effect of Dissolved Gases on Small Blood Vessel Function by Kraus, Oren Zeev

“…In this thesis I present a microfluidic platform developed to control dissolved gases and monitor dissolved oxygen concentrations within the microenvironment…”
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ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy by Kenyon-Dean, Kian, Wang, Zitong Jerry, Urbanik, John, Donhauser, Konstantin, Hartford, Jason, Saberian, Saber, Sahin, Nil, Bendidi, Ihab, Celik, Safiye, Fay, Marta, Vera, Juan Sebastian Rodriguez, Haque, Imran S, Kraus, Oren

“…Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic…”
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Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology by Kraus, Oren, Kenyon-Dean, Kian, Saberian, Saber, Fallah, Maryam, McLean, Peter, Leung, Jess, Sharma, Vasudev, Khan, Ayla, Balakrishnan, Jia, Celik, Safiye, Beaini, Dominique, Sypetkowski, Maciej, Cheng, Chi Vicky, Morse, Kristen, Makes, Maureen, Mabey, Ben, Earnshaw, Berton

“…Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spanning millions of…”
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RxRx1: A Dataset for Evaluating Experimental Batch Correction Methods by Sypetkowski, Maciej, Rezanejad, Morteza, Saberian, Saber, Kraus, Oren, Urbanik, John, Taylor, James, Mabey, Ben, Victors, Mason, Yosinski, Jason, Sereshkeh, Alborz Rezazadeh, Haque, Imran, Earnshaw, Berton

“…High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising…”
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Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology by Kraus, Oren, Kenyon-Dean, Kian, Saberian, Saber, Fallah, Maryam, McLean, Peter, Leung, Jess, Sharma, Vasudev, Khan, Ayla, Balakrishnan, Jia, Celik, Safiye, Beaini, Dominique, Sypetkowski, Maciej, Cheng, Chi Vicky, Morse, Kristen, Makes, Maureen, Mabey, Ben, Earnshaw, Berton

“…Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spanning millions of…”
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RxRx1: A Dataset for Evaluating Experimental Batch Correction Methods by Sypetkowski, Maciej, Rezanejad, Morteza, Saberian, Saber, Kraus, Oren, Urbanik, John, Taylor, James, Mabey, Ben, Victors, Mason, Yosinski, Jason, Sereshkeh, Alborz Rezazadeh, Haque, Imran, Earnshaw, Berton

“…High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising…”
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Masked Autoencoders are Scalable Learners of Cellular Morphology by Kraus, Oren, Kenyon-Dean, Kian, Saberian, Saber, Fallah, Maryam, McLean, Peter, Leung, Jess, Sharma, Vasudev, Khan, Ayla, Balakrishnan, Jia, Celik, Safiye, Sypetkowski, Maciej, Cheng, Chi Vicky, Morse, Kristen, Makes, Maureen, Mabey, Ben, Earnshaw, Berton

“…Inferring biological relationships from cellular phenotypes in high-content microscopy screens provides significant opportunity and challenge in biological…”
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Classifying and Segmenting Microscopy Images Using Convolutional Multiple Instance Learning by Kraus, Oren Z, Ba, Lei Jimmy, Frey, Brendan

“…Bioinformatics (2016) 32 (12): i52-i59 Convolutional neural networks (CNN) have achieved state of the art performance on both classification and segmentation…”
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