Search Results - "Logan, David J"

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software by KAMENTSKY, Lee, JONAS, Thouis R, FRAMER, Adam, BRAY, Mark-Anthony, LOGAN, David J, MADDEN, Katherine L, LJOSA, Vebjorn, RUEDEN, Curtis, ELICEIRI, Kevin W, CARPENTER, Anne E

“…There is a strong and growing need in the biology research community for accurate, automated image analysis. Here, we describe CellProfiler 2.0, which has been…”
Get full text

Identification of small molecules for human hepatocyte expansion and iPS differentiation by Shan, Jing, Schwartz, Robert E, Ross, Nathan T, Logan, David J, Thomas, David, Duncan, Stephen A, North, Trista E, Goessling, Wolfram, Carpenter, Anne E, Bhatia, Sangeeta N

“…A high-throughput chemical screen of primary human hepatocytes in combination with machine-learning algorithms for evaluation of imaging data identifies…”
Get full text

A Microscale Human Liver Platform that Supports the Hepatic Stages of Plasmodium falciparum and vivax by March, Sandra, Ng, Shengyong, Velmurugan, Soundarapandian, Galstian, Ani, Shan, Jing, Logan, David J., Carpenter, Anne E., Thomas, David, Sim, B. Kim Lee, Mota, Maria M., Hoffman, Stephen L., Bhatia, Sangeeta N.

“…The Plasmodium liver stage is an attractive target for the development of antimalarial drugs and vaccines, as it provides an opportunity to interrupt the life…”
Get full text

A chemical screen probing the relationship between mitochondrial content and cell size by Kitami, Toshimori, Logan, David J, Negri, Joseph, Hasaka, Thomas, Tolliday, Nicola J, Carpenter, Anne E, Spiegelman, Bruce M, Mootha, Vamsi K

“…The cellular content of mitochondria changes dynamically during development and in response to external stimuli, but the underlying mechanisms remain obscure…”
Get full text

High content image analysis identifies novel regulators of synaptogenesis in a high-throughput RNAi screen of primary neurons by Nieland, Thomas J F, Logan, David J, Saulnier, Jessica, Lam, Daniel, Johnson, Caroline, Root, David E, Carpenter, Anne E, Sabatini, Bernardo L

“…The formation of synapses, the specialized points of chemical communication between neurons, is a highly regulated developmental process fundamental to…”
Get full text

A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells by Jolly, Amber L., Luan, Chi-Hao, Dusel, Brendon E., Dunne, Sara F., Winding, Michael, Dixit, Vishrut J., Robins, Chloe, Saluk, Jennifer L., Logan, David J., Carpenter, Anne E., Sharma, Manu, Dean, Deborah, Cohen, Andrew R., Gelfand, Vladimir I.

“…Long-distance intracellular transport of organelles, mRNA, and proteins (“cargo”) occurs along the microtubule cytoskeleton by the action of kinesin and dynein…”
Get full text

Effects of temperature variation on TSD in turtle ( C. picta) populations by Parrott, Amy, David Logan, J.

“…We formulate a two-sex model of temperature-dependent sex determination (TSD) for a freshwater turtle ( C. picta) population. The aim is to understand how…”
Get full text

Aldehyde dehydrogenase 3a2 protects AML cells from oxidative death and the synthetic lethality of ferroptosis inducers by Yusuf, Rushdia Zareen, Saez, Borja, Sharda, Azeem, van Gastel, Nick, Yu, Vionnie W.C., Baryawno, Ninib, Scadden, Elizabeth W., Acharya, Sanket, Chattophadhyay, Shrikanta, Huang, Cherrie, Viswanathan, Vasanthi, S'aulis, Dana, Cobert, Julien, Sykes, David B., Keibler, Mark A., Das, Sudeshna, Hutchinson, John N., Churchill, Michael, Mukherjee, Siddhartha, Lee, Dongjun, Mercier, Francois, Doench, John, Bullinger, Lars, Logan, David J., Schreiber, Stuart, Stephanopoulos, Gregory, Rizzo, William B., Scadden, David T.

“…Metabolic alterations in cancer represent convergent effects of oncogenic mutations. We hypothesized that a metabolism-restricted genetic screen, comparing…”
Get full text

Optimizing the Cell Painting assay for image-based profiling by Cimini, Beth A., Chandrasekaran, Srinivas Niranj, Kost-Alimova, Maria, Miller, Lisa, Goodale, Amy, Fritchman, Briana, Byrne, Patrick, Garg, Sakshi, Jamali, Nasim, Logan, David J., Concannon, John B., Lardeau, Charles-Hugues, Mouchet, Elizabeth, Singh, Shantanu, Shafqat Abbasi, Hamdah, Aspesi, Peter, Boyd, Justin D., Gilbert, Tamara, Gnutt, David, Hariharan, Santosh, Hernandez, Desiree, Hormel, Gisela, Juhani, Karolina, Melanson, Michelle, Mervin, Lewis H., Monteverde, Tiziana, Pilling, James E., Skepner, Adam, Swalley, Susanne E., Vrcic, Anita, Weisbart, Erin, Williams, Guy, Yu, Shan, Zapiec, Bolek, Carpenter, Anne E.

“…In image-based profiling, software extracts thousands of morphological features of cells from multi-channel fluorescence microscopy images, yielding…”
Get full text

Mining for osteogenic surface topographies: In silico design to in vivo osseo-integration by Hulshof, Frits F.B, Papenburg, Bernke, Vasilevich, Aliaksei, Hulsman, Marc, Zhao, Yiping, Levers, Marloes, Fekete, Natalie, de Boer, Meint, Yuan, Huipin, Singh, Shantanu, Beijer, Nick, Bray, Mark-Anthony, Logan, David J, Reinders, Marcel, Carpenter, Anne E, van Blitterswijk, Clemens, Stamatialis, Dimitrios, de Boer, Jan

“…Abstract Stem cells respond to the physicochemical parameters of the substrate on which they grow. Quantitative material activity relationships – the…”
Get full text

Morphology and gene expression profiling provide complementary information for mapping cell state by Way, Gregory P, Natoli, Ted, Adeboye, Adeniyi, Litichevskiy, Lev, Yang, Andrew, Lu, Xiaodong, Caicedo, Juan C, Cimini, Beth A, Karhohs, Kyle, Logan, David J, Rohban, Mohammad H, Kost-Alimova, Maria, Hartland, Kate, Bornholdt, Michael, Chandrasekaran, Srinivas Niranj, Haghighi, Marzieh, Weisbart, Erin, Singh, Shantanu, Subramanian, Aravind, Carpenter, Anne E

“…Morphological and gene expression profiling can cost-effectively capture thousands of features in thousands of samples across perturbations by disease,…”
Get more information

Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification by Logan, David J., Shan, Jing, Bhatia, Sangeeta N., Carpenter, Anne E.

“…[Display omitted] •We present an improved image analysis approach to identify co-cultured cells.•Analysis combines user-friendly pixel-based classification and…”
Get full text

Abnormalities in Mitochondrial Structure in Cells from Patients with Bipolar Disorder by Cataldo, Anne M, McPhie, Donna L, Lange, Nicholas T, Punzell, Steven, Elmiligy, Sarah, Ye, Nancy Z, Froimowitz, Michael P, Hassinger, Linda C, Menesale, Emily B, Sargent, Laura W, Logan, David J, Carpenter, Anne E, Cohen, Bruce M

“…Postmortem, genetic, brain imaging, and peripheral cell studies all support decreased mitochondrial activity as a factor in the manifestation of Bipolar…”
Get full text

Deep representation learning determines drug mechanism of action from cell painting images by Wong, Daniel R, Logan, David J, Hariharan, Santosh, Stanton, Robert, Clevert, Djork-Arné, Kiruluta, Andrew

“…Fluorescent-based microscopy screens carry a broad range of phenotypic information about how compounds affect cellular biology. From changes in cellular…”
Get full text

Niche-based screening identifies small-molecule inhibitors of leukemia stem cells by Hartwell, Kimberly A, Miller, Peter G, Mukherjee, Siddhartha, Kahn, Alissa R, Stewart, Alison L, Logan, David J, Negri, Joseph M, Duvet, Mildred, Järås, Marcus, Puram, Rishi, Dancik, Vlado, Al-Shahrour, Fatima, Kindler, Thomas, Tothova, Zuzana, Chattopadhyay, Shrikanta, Hasaka, Thomas, Narayan, Rajiv, Dai, Mingji, Huang, Christina, Shterental, Sebastian, Chu, Lisa P, Haydu, J Erika, Shieh, Jae Hung, Steensma, David P, Munoz, Benito, Bittker, Joshua A, Shamji, Alykhan F, Clemons, Paul A, Tolliday, Nicola J, Carpenter, Anne E, Gilliland, D Gary, Stern, Andrew M, Moore, Malcolm A S, Scadden, David T, Schreiber, Stuart L, Ebert, Benjamin L, Golub, Todd R

“…High-throughput screening systems that better mimic the physiological complexity of diseased tissues may aid the discovery of more efficacious compounds. A…”
Get full text

Location, Time, and Temperature Dependence of Digestion in Simple Animal Tracts by DAVID LOGAN, J., JOERN, ANTHONY, WOLESENSKY, WILLIAM

“…In this paper, we develop plug flow reactor models that simultaneously investigate how reaction and absorption, morphological differences, and temperature…”
Get full text

An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells by Dordea, Ana C., Bray, Mark-Anthony, Allen, Kaitlin, Logan, David J., Fei, Fei, Malhotra, Rajeev, Gregory, Meredith S., Carpenter, Anne E., Buys, Emmanuel S.

“…A fully automated and robust method was developed to quantify β-III-tubulin-stained retinal ganglion cells, combining computational recognition of individual…”
Get full text

High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro by Shan, Jing, Logan, David J, Root, David E, Carpenter, Anne E, Bhatia, Sangeeta N

“…Liver disease is a leading cause of morbidity worldwide and treatment options are limited, with organ transplantation being the only form of definitive…”
Get more information

Cortical Area MSTd Combines Visual Cues to Represent 3-D Self-Movement by Logan, David J., Duffy, Charles J.

“…As arboreal primates move through the jungle, they are immersed in visual motion that they must distinguish from the movement of predators and prey. We…”
Get full text

Macroparasite Population Dynamics Among Geographical Localities and Host Life Cycle Stages: Eugregarines in Ischnura verticalis by Bunker, Brittany E, Janovy, John, Tracey, Elisabeth, Barnes, Austin, Duba, Ayla, Shuman, Matthew, Logan, J. David

“…Populations of several species of gregarine parasites within a single host species, the damselfly Ischnura verticalis, were examined over the course of 1…”
Get full text