pypi: CellProfiler | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0201507

Head-to-head comparison of three experimental methods of quantifying competitive fitness in C. elegans
Cited by: 5
Author(s): Timothy A. Crombie, Sayran Saber, Ayush Shekhar Saxena, Robyn Egan, Charles F. Baer
Software Mentions: 2
Published: almost 8 years ago

10.3390/jpm11060515

Accurate Segmentation of Nuclear Regions with Multi-Organ Histopathology Images Using Artificial Intelligence for Cancer Diagnosis in Personalized Medicine
Cited by: 15
Author(s): Tahir Mahmood, Muhammad Owais, Kyoung Jun Noh, Hyo Sik Yoon, Ja Hyung Koo, Adnan Haider, Haseeb Sultan, Kang Ryoung Park
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0215267

Muscle fiber hypertrophy in response to 6 weeks of high-volume resistance training in trained young men is largely attributed to sarcoplasmic hypertrophy
Cited by: 52
Author(s): Cody T. Haun, Christopher G. Vann, Shelby C. Osburn, Petey W. Mumford, Paul A. Roberson, Matthew A. Romero, Carlton D. Fox, Christopher Johnson, Hailey A. Parry, Andreas N. Kavazis, Jordan R. Moon, Veera L.D. Badisa, Benjamin M. Mwashote, Victor Ibeanusi, Kaelin C. Young, Michael D. Roberts
Software Mentions: 2
Published: over 7 years ago

10.1242/bio.055228

Quantitative analysis of subcellular distributions with an open-source, object-based tool
Cited by: 7
Author(s): Pearl V. Ryder, Dorothy A. Lerit
Software Mentions: 2
Published: almost 7 years ago

10.1186/1478-811X-11-24

Light microscopy applications in systems biology: opportunities and challenges
Cited by: 35
Author(s): Paul Paul Michel Aloyse Antony, Christophe Trefois, Aleksandar Stojanović, Aidos Baumuratov, Karol Kozak
Software Mentions: 2
Published: almost 14 years ago

10.7554/eLife.51678

High-dimensional analysis of intestinal immune cells during helminth infection
Cited by: 21
Author(s): Laura Ferrer‐Font, Palak Mehta, Phoebe Harmos, Alfonso Schmidt, Sally Claire Chappell, Kylie M. Price, Ian F. Hermans, Franca Ronchese, Graham Le Gros, Johannes U Mayer
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-021-04334-x

A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells
Cited by: 2
Author(s): M. Elena Garcia-Pardo, Jeremy C. Simpson, Niamh C. O’Sullivan
Software Mentions: 2
Published: about 5 years ago

10.1038/micronano.2016.79

Subcellular western blotting of single cells
Cited by: 46
Author(s): Kevin A. Yamauchi, Amy E. Herr
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms140815810

Highly Sensitive Automated Method for DNA Damage Assessment: Gamma-H2AX Foci Counting and Cell Cycle Sorting
Cited by: 34
Author(s): Laia Hernández, Mariona Terradas, Marga Martı́n, Laura Tusell, Anna Genescà
Software Mentions: 2
Published: about 13 years ago

10.1098/rsob.150262

Primate-specific oestrogen-responsive long non-coding RNAs regulate proliferation and viability of human breast cancer cells
Cited by: 10
Author(s): Chin-Yo Lin, Erica L. Kleinbrink, Fabien Dachet, Juan Cai, Donghong Ju, Amanda Goldstone, Emily J. Wood, Liu Ka, Hui Jia, Anton Scott Goustin, Mary A. Kosir, Pattaraporn Thepsuwan, Leonard Lipovich
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13578-021-00618-0

A ribonucleoprotein transfection strategy for CRISPR/Cas9‐mediated gene editing and single cell cloning in rainbow trout cells
Cited by: 5
Author(s): Marina Zoppo, Nicole Okoniewski, Stanislav Pantelyushin, Johannes vom Berg, Kristin Schirmer
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0138760

Plaque2.0—A High-Throughput Analysis Framework to Score Virus-Cell Transmission and Clonal Cell Expansion
Cited by: 43
Author(s): Artur Yakimovich, Vardan Andriasyan, Robert Witte, I-Hsuan Wang, Ralf Bartenschlager, Maarit Suomalainen, Urs F. Greber
Software Mentions: 2
Published: about 11 years ago

10.1186/s40478-020-01011-7

Lipid-specific IgMs induce antiviral responses in the CNS: implications for progressive multifocal leukoencephalopathy in multiple sclerosis
Cited by: 5
Author(s): Lorna Hayden, Tiia Semenoff, Verena Schultz, Simon F. Merz, Katie J. Chapple, Moses Rodriguez, Arthur E. Warrington, Xia Shi, Clive S. McKimmie, Julia M. Edgar, Katja Thümmler, Christopher Linington, Marieke Pingen
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2105-15-342

A comparative study of cell classifiers for image-based high-throughput screening
Cited by: 12
Author(s): Syed Saiden Abbas, Tjeerd M. H. Dijkstra, Tom Heskes
Software Mentions: 2
Published: almost 12 years ago

10.1093/bioinformatics/btw013

Collaborative analysis of multi-gigapixel imaging data using Cytomine
Cited by: 138
Author(s): Raphaël Marée, Loïc Rollus, Benjamin H. Stevens, Renaud Hoyoux, Gilles Louppe, Rémy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts, Louis Wehenkel
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12859-016-0895-y

CP-CHARM: segmentation-free image classification made accessible
Cited by: 53
Author(s): Virginie Uhlmann, Shantanu Singh, Anne E. Carpenter
Software Mentions: 2
Published: over 10 years ago

10.1016/j.cell.2018.02.030

Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis
Cited by: 174
Author(s): Mikhail M. Savitski, Nico Zinn, Maria Faelth-Savitski, Daniel Poeckel, Stephan Gade, Isabelle Becher, Marcel Muelbaier, Anne J. Wagner, Katrin Strohmer, Thilo Werner, Stephanie Melchert, Massimo Petretich, Anna Rutkowska, Johanna Vappiani, Holger Franken, Michael Steidel, Gavain Sweetman, Omer Gilan, Enid Y.N. Lam, Mark A. Dawson, Rab K. Prinjha, Paola Grandi, Giovanna Bergamini, Marcus Bantscheff
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms21072323

Detection of Rare Objects by Flow Cytometry: Imaging, Cell Sorting, and Deep Learning Approaches
Cited by: 27
Author(s): Denis V. Voronin, Anastasiia Kozlova, Roman A. Verkhovskii, А. V. Ermakov, Mikhail A. Makarkin, Olga A. Inozemtseva, Daniil N. Bratashov
Software Mentions: 2
Published: over 6 years ago

10.1186/s13058-021-01418-7

High IRF8 expression correlates with CD8 T cell infiltration and is a predictive biomarker of therapy response in ER-negative breast cancer
Cited by: 16
Author(s): Gerardo Gatti, Courtney B. Betts, Darío Rocha, Maribel Nicola, Verónica Grupe, Cecilia Ditada, Nicolás Núñez, Emiliano Roselli, Paula Araya, Jeremías Dutto, Lucia Boffelli, Elmer Fernández, Lisa M. Coussens, Mariana Maccioni
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.11875

Importance of experimental information (metadata) for archived sequence data: case of specific gene bias due to lag time between sample harvest and RNA protection in RNA sequencing
Cited by: 1
Author(s): Tomoko Matsuda
Software Mentions: 2
Published: about 5 years ago

10.1098/rsif.2016.0705

Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform
Cited by: 52
Author(s): Cristian Versari, Szymon Stoma, Kirill Batmanov, Artémis Llamosi, Filip Mroz, Adam Kaczmarek, Matt Deyell, Cédric Lhoussaine, Pascal Hersen, Grégory Batt
Software Mentions: 2
Published: over 9 years ago

10.1063/1.5143779

Cell shape, and not 2D migration, predicts extracellular matrix-driven 3D cell invasion in breast cancer
Cited by: 35
Author(s): Janani P. Baskaran, Anna Weldy, Justinne R. Guarin, Gabrielle Munoz, Polina Shpilker, Michael Kotlik, Nandita Subbiah, Andrew Wishart, Yifan Peng, Miles A. Miller, Lenore Cowen, Madeleine J. Oudin
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0177408

Ubiquitylation of the acetyltransferase MOF in Drosophila melanogaster
Cited by: 10
Author(s): Sarah Schunter, Raffaella Villa, Victoria K. Flynn, Jan B. Heidelberger, Anne-Kathrin Classen, Petra Beli, Peter B. Becker
Software Mentions: 2
Published: over 9 years ago

10.1186/s13058-021-01416-9

Cellular dormancy in minimal residual disease following targeted therapy
Cited by: 13
Author(s): Jason R. Ruth, Dhruv K. Pant, Tien-Chi Pan, Hans E. Seidel, Sanjeethan C. Baksh, Blaine A. Keister, Rita Singh, Christopher J. Sterner, Suzanne J. Bakewell, Susan E. Moody, George K. Belka, Lewis A. Chodosh
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1008967

Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development
Cited by: 8
Author(s): Katherine I Farley-Barnes, Engin Deniz, Maya M Overton, Mustafa K. Khokha, Susan J. Baserga
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0216251

A 61% lighter cell culture dish to reduce plastic waste
Cited by: 4
Author(s): Pedro Réu, Gustav Svedberg, Lars Hässler, Bjørn Møller, Helene Andersson Svahn, Jesper Gantelius
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms21239332

Genomic Instability Is an Early Event in Aluminium-Induced Tumorigenesis
Cited by: 8
Author(s): Stefano J. Mandriota, Mirna Tenan, Adeline Nicolle, Julia Jankowska, Paolo Ferrari, Jean-Christophe Tille, Mary-Anne Durin, Catherine Green, Sébastien P. Tabruyn, Daniela Moralli, André‐Pascal Sappino
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1007688

Phenotype-based probabilistic analysis of heterogeneous responses to cancer drugs and their combination efficacy
Cited by: 10
Author(s): Natacha Comandante-Lou, Mehwish Khaliq, Divya Venkat, Mohan Manikkam, Mohammad Fallahi-Sichani
Software Mentions: 2
Published: over 6 years ago

10.3390/nu11102439

High Dose of Dietary Nicotinamide Riboside Induces Glucose Intolerance and White Adipose Tissue Dysfunction in Mice Fed a Mildly Obesogenic Diet
Cited by: 25
Author(s): Wenbiao Shi, Maria A. Hegeman, Atanaska Doncheva, Melissa Bekkenkamp‐Grovenstein, Vincent C.J. de Boer, Jaap Keijer
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0015535

Quantitative High-Throughput Screening Identifies 8-Hydroxyquinolines as Cell-Active Histone Demethylase Inhibitors
Cited by: 195
Author(s): Oliver N. King, Xuan Shirley Li, Masaaki Sakurai, Akane Kawamura, Nathan R. Rose, Stanley S. Ng, Amy Quinn, Ganesha Rai, Bryan T. Mott, Paul J. Beswick, Robert J. Klose, U. Oppermann, Ajit Jadhav, Tom D. Heightman, David J. Maloney, Christopher J. Schofield, Anton Simeonov
Software Mentions: 2
Published: almost 16 years ago

10.1186/s13058-021-01457-0

Sensitivity to targeted therapy differs between HER2-amplified breast cancer cells harboring kinase and helical domain mutations in PIK3CA
Cited by: 5
Author(s): Joseph P. Garay, Rebecca Smith, Kaylyn L. Devlin, Daniel P. Hollern, Tiera Liby, Moqing Liu, Shanta Boddapati, Spencer S. Watson, Amanda Esch, Ting Zheng, Wallace Thompson, Darcie Babcock, Sunjong Kwon, Koei Chin, Laura M. Heiser, Joe W. Gray, James E. Korkola
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22073740

RAD51 Inhibition Induces R-Loop Formation in Early G1 Phase of the Cell Cycle
Cited by: 5
Author(s): Zuzana Naščáková, Barbora Boleslavska, Václav Urban, Anna Oravetzova, Edita Vlachova, Pavel Janscak, Jana Dobrovolná
Software Mentions: 2
Published: over 5 years ago

10.1186/s13104-019-4866-z

CACTUS: cancer image annotating, calibrating, testing, understanding and sharing in breast cancer histopathology
Cited by: 3
Author(s): Alper Aksaç, Tansel Özyer, Douglas J. Demetrick, Reda Alhajj
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0221245

Predicting the future direction of cell movement with convolutional neural networks
Cited by: 11
Author(s): S. Nishimoto, Yuta Tokuoka, Takahiro Yamada, Noriko Hiroi, Akira Funahashi
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0255096

Unified platform for genetic and serological detection of COVID-19 with single-molecule technology
Cited by: 4
Author(s): Noa Furth, Shay Shilo, Niv Cohen, Nir Erez, Vadim Fedyuk, Alexander M. Schrager, Adina Weinberger, Amiel A. Dror, Asaf Zigron, Mona Shehadeh, Eyal Sela, Samer Srouji, Sharon Amit, Itzchak Levy, Eran Segal, Rony Dahan, Dan Jones, Daniel C. Douek, Efrat Shema
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1007673

DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning
Cited by: 125
Author(s): Jean-Baptiste Lugagne, Haonan Lin, Mary J. Dunlop
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms22126323

Proteome Profiling of PMJ2-R and Primary Peritoneal Macrophages
Cited by: 5
Author(s): А. Л. Русанов, П. М. Кожин, Olga V. Tikhonova, Victor G. Zgoda, Dmitry S. Loginov, Adéla Chlastáková, Martin Selinger, Ján Štěrba, Libor Grubhoffer, Н. Г. Лузгина
Software Mentions: 2
Published: over 5 years ago

10.1186/s13007-021-00749-y

High-throughput soybean seeds phenotyping with convolutional neural networks and transfer learning
Cited by: 23
Author(s): Shuanying Yang, Lihua Zheng, Peng He, Tingting Wu, Shi Sun, Minjuan Wang
Software Mentions: 2
Published: over 5 years ago

10.1186/s13007-019-0549-y

Phenotyping analysis of maize stem using micro-computed tomography at the elongation and tasseling stages
Cited by: 7
Author(s): Ying Zhang, Liming Ma, Jinglu Wang, Xiaodong Wang, Xinyu Guo, Jianjun Du
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0245653

Pten regulates collagen fibrillogenesis by fibroblasts through SPARC
Cited by: 7
Author(s): Caitlin E. Jones, Joe T. Sharick, Sheila E. Colbert, Vasudha Shukla, Joshua Zent, Michael C. Ostrowski, Samir N. Ghadiali, Steven T. Sizemore, Jennifer L. Leight
Software Mentions: 2
Published: over 5 years ago

10.1186/s13007-018-0278-7

Citizen crowds and experts: observer variability in image-based plant phenotyping
Cited by: 35
Author(s): Mario Valerio Giuffrida, Feng Chen, Hanno Scharr, Sotirios A. Tsaftaris
Software Mentions: 2
Published: over 8 years ago

10.26508/lsa.202101084

Quantitative proteomics identifies PTP1B as modulator of B cell antigen receptor signaling
Cited by: 0
Author(s): Jennifer Schwarz, Lorenz Grundmann, Thomas Kokot, Kathrin Kläsener, Sandra Fotteler, Dávid Medgyesi, Maja Köhn, Michael Reth, Bettina Warscheid
Software Mentions: 2
Published: about 5 years ago

10.1186/s12859-020-03603-5

A cell-level quality control workflow for high-throughput image analysis
Cited by: 3
Author(s): Minhua Qiu, Bin Zhou, Frederick Lo, Steven C. Cook, Jason Chyba, Doug Quackenbush, Jason Matzen, Zhizhong Li, Puiying A. Mak, Kaisheng Chen, Yingyao Zhou
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms22189758

Perturbation of TM6SF2 Expression Alters Lipid Metabolism in a Human Liver Cell Line
Cited by: 2
Author(s): Asmita Pant, Yue Chen, Annapurna Kuppa, Xiaomeng Du, Brian D. Halligan, Elizabeth K. Speliotes
Software Mentions: 2
Published: about 5 years ago

10.3390/cancers13153801

Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development
Cited by: 3
Author(s): Tabea L. Bauer, Katrin Collmar, Till Kaltofen, Ann-Katrin Loeffler, Lorena Decker, Jan Mueller, Sabine Pinter, Stephan A. Eisler, Sven Mahner, Patricia Fraungruber, Stefan Kommoss, Annette Staebler, Lewis Francis, R. Steven Conlan, Johannes Zuber, Udo Jeschke, Fabian Trillsch, Philipp Rathert
Software Mentions: 2
Published: about 5 years ago

10.1186/s40168-020-00818-9

Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts
Cited by: 26
Author(s): Alba Cortés, John W. Wills, Xiaopei Su, Rachel E. Hewitt, Jack Robertson, Riccardo Scotti, Daniel D. Price, Yvonne Bartley, Tom N. McNeilly, Lutz Krause, Jonathan J. Powell, Alasdair J. Nisbet, Cinzia Cantacessi
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1007744

Control of nongenetic heterogeneity in growth rate and stress tolerance of Saccharomyces cerevisiae by cyclic AMP-regulated transcription factors
Cited by: 30
Author(s): Shuang Li, Daniella M. Giardina, Mark L. Siegal
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pcbi.1004078

NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation
Cited by: 16
Author(s): Juliane Siebourg‐Polster, Daria Mudrak, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Urs F. Greber, Holger Fröhlich, Niko Beerenwinkel
Software Mentions: 2
Published: over 11 years ago

10.1002/cam4.3965

Histopathological image and gene expression pattern analysis for predicting molecular features and prognosis of head and neck squamous cell carcinoma
Cited by: 8
Author(s): Linyan Chen, Hao Zeng, Mingxuan Zhang, Yuling Luo, Xuelei Ma
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0095124

A Module of Human Peripheral Blood Mononuclear Cell Transcriptional Network Containing Primitive and Differentiation Markers Is Related to Specific Cardiovascular Health Variables
Cited by: 6
Author(s): Leni Moldovan, Mirela Anghelina, Taylor Kantor, Desirée Jones, Enass Ramadan, Yang Xiang, Kun Huang, Arunark Kolipaka, William B. Malarkey, Nima Ghasemzadeh, Peter J. Mohler, Arshed A. Quyyumi, Nicanor I. Moldovan
Software Mentions: 2
Published: over 12 years ago

10.1186/s12974-021-02194-z

Phloretin suppresses neuroinflammation by autophagy-mediated Nrf2 activation in macrophages
Cited by: 22
Author(s): Tess Dierckx, Mansour Haidar, Elien Grajchen, Elien Wouters, Sam Vanherle, Melanie Loix, Annick Boeykens, D. Bylemans, Kévin Hardonnière, Saadia Kerdine-Römer, Jeroen F. J. Bogie, Jerome J. A. Hendriks
Software Mentions: 2
Published: over 5 years ago

10.1111/acel.13468

Inhibition of the cGAS‐STING pathway ameliorates the premature senescence hallmarks of Ataxia‐Telangiectasia brain organoids
Cited by: 28
Author(s): Julio Aguado, Harman Chaggar, Cecilia Gómez-Inclán, Mohammed R. Shaker, Hannah C Leeson, Alan Mackay‐Sim, Ernst J. Wolvetang
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pbio.3000297

Cytosine-5 RNA methylation links protein synthesis to cell metabolism
Cited by: 79
Author(s): Nikoletta A. Gkatza, Cecilia Castro, R Harvey, MM Heiss, Martyna Popis, Sandra Blanco, Susanne Bornelöv, Abdulrahim A. Sajini, Joseph G. Gleeson, Julian L. Griffin, James A. West, Stefanie Kellner, Anne E. Willis, Sabine Dietmann, Michaela Frye
Software Mentions: 2
Published: over 7 years ago

10.1093/bioinformatics/btz403

MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures
Cited by: 27
Author(s): Michael J. Whitehead, George A. McCanney, Hugh J. Willison, Susan C. Barnett
Software Mentions: 2
Published: over 7 years ago

10.1186/s12974-016-0602-y

Reduction of cytosolic phospholipase A2α upregulation delays the onset of symptoms in SOD1G93A mouse model of amyotrophic lateral sclerosis
Cited by: 22
Author(s): Yulia Solomonov, Nurit Hadad, Rachel Lévy
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1009736

Genes in human obesity loci are causal obesity genes in C. elegans
Cited by: 14
Author(s): Wenfan Ke, Jordan N. Reed, Clayton S.-C. Yang, Noel Higgason, Leila Rayyan, Carolina Wählby, Anne E. Carpenter, Mete Civelek, Eyleen J. O’Rourke
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0209648

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types
Cited by: 367
Author(s): Trygve E. Bakken, Rebecca D. Hodge, Jeremy A. Miller, Zizhen Yao, Thuc Nghi Nguyen, Brian D. Aevermann, Eliza Barkan, Darren Bertagnolli, Tamara Casper, Nick Dee, Emma Garren, Jeff Goldy, Lucas T. Graybuck, Matthew Kroll, Roger S. Lasken, Kanan Lathia, Sheana Parry, Christine Rimorin, Richard H. Scheuermann, Nicholas J. Schork, Soraya I. Shehata, Michael Tieu, John W. Phillips, Amy Bernard, Kimberly A. Smith, Hongkui Zeng, Ed Lein, Bosiljka Tasic
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.ymeth.2020.05.017

An integrated pipeline for high-throughput screening and profiling of spheroids using simple live image analysis of frame to frame variations
Cited by: 12
Author(s): Haneen Alsehli, Fuad Mosis, Christopher Thompson, Eva Hamrud, Erika Wiseman, Eileen Gentleman, Davide Danovi
Software Mentions: 2
Published: over 5 years ago

10.1016/j.isci.2020.101601

MitoSegNet: Easy-to-use Deep Learning Segmentation for Analyzing Mitochondrial Morphology
Cited by: 31
Author(s): Christian Fischer, Laura Besora-Casals, Stéphane G. Rolland, Simon Haeussler, Kritarth Singh, Michael R. Duchen, Barbara Conradt, Carsten Marr
Software Mentions: 2
Published: about 6 years ago

10.3390/cancers12082047

The Tumor Suppressor CYLD Inhibits Mammary Epithelial to Mesenchymal Transition by the Coordinated Inhibition of YAP/TAZ and TGFβ Signaling
Cited by: 9
Author(s): Athanasios Pseftogas, Konstantinos Xanthopoulos, Theofilos Poutahidis, Chrysanthi Ainali, Dimitra Dafou, Emmanuel Panteris, Joseph G. Kern, Xaralabos Varelas, Alexandros Hardas, Christos Gonidas, Anastasia Tsingotjidou, Eudoxia Hatzivassiliou, George Mosialos
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1003670

A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis
Cited by: 25
Author(s): Carlos Castro-González, Miguel Luengo-Oroz, Louise Duloquin, Thierry Savy, B Rizzi, Sophie Desnoulez, René Doursat, Yannick Kergosien, María J. Ledesma-Carbayo, Paul Bourgine, Nadine Peyriéras, A. Santos
Software Mentions: 2
Published: over 12 years ago

10.1016/j.ymeth.2016.08.018

An open-source solution for advanced imaging flow cytometry data analysis using machine learning
Cited by: 77
Author(s): Holger Hennig, Paul Rees, Thomas Blasi, Lee Kamentsky, Jia‐Jang Hung, David Dao, Anne E. Carpenter, Andrew Filby
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pbio.3000457

Cell confinement reveals a branched-actin independent circuit for neutrophil polarity
Cited by: 50
Author(s): Brian R. Graziano, Jason P. Town, E Sitarska, Tamas L. Nagy, Miha Fošnarič, Samo Penič, Aleš Iglič, Veronika Kralj‐Iglič, Nir S. Gov, Alba Diz-Muñoz, Orion D. Weiner
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pbio.2005970

CellProfiler 3.0: Next-generation image processing for biology
Cited by: 1,445
Author(s): Claire McQuin, Allen Goodman, Vasiliy S. Chernyshev, Lee Kamentsky, Beth A. Cimini, Kyle W. Karhohs, Minh Doan, Liya Ding, Susanne M. Rafelski, Derek Thirstrup, Winfried Wiegraebe, Shantanu Singh, Tim Becker, Juan C. Caicedo, Anne E. Carpenter
Software Mentions: 2
Published: over 8 years ago

10.1186/s13024-020-00387-3

BIN1 protein isoforms are differentially expressed in astrocytes, neurons, and microglia: neuronal and astrocyte BIN1 are implicated in tau pathology
Cited by: 24
Author(s): Mariko Taga, Vladislav Petyuk, Charles C. White, Graham Marsh, Yiyi Ma, Hans‐Ulrich Klein, Sarah M. Connor, Alexandra Kroshilina, Christina J. Yung, Anthony Khairallah, Marta Olah, Julie A. Schneider, Kyle W. Karhohs, Anne E. Carpenter, Richard M. Ransohoff, David A. Bennett, Andrea Crotti, Elizabeth M. Bradshaw, Philip L. De Jager
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0217346

TISMorph: A tool to quantify texture, irregularity and spreading of single cells
Cited by: 17
Author(s): Elaheh Alizadeh, Wenlong Xu, Jordan Castle, Jacqueline Foss, Ashok Prasad
Software Mentions: 2
Published: over 7 years ago

10.3390/cells9061423

Chromatin Trapping of Factors Involved in DNA Replication and Repair Underlies Heat-Induced Radio- and Chemosensitization
Cited by: 3
Author(s): Artem V. Luzhin, Bogdan Avanesyan, Artem K. Velichko, Victoria О. Shender, Natalia Ovsyannikova, Georgij Arapidi, Polina V. Shnaider, Nadezhda V. Petrova, Igor I. Kireev, Sergey V. Razin, Omar L. Kantidze
Software Mentions: 2
Published: over 6 years ago

10.1007/s12035-020-01907-4

Human Pluripotent Stem Cell-Derived Neurons Are Functionally Mature In Vitro and Integrate into the Mouse Striatum Following Transplantation
Cited by: 17
Author(s): Andrea Comella-Bolla, Javier G. Orlandi, Andrés Miguez, Marco Straccia, María García‐Bravo, Georgina Bombau, Mireia Galofré, Phil Sanders, Jordi Carrère, José C. Segovia, Joan Blasi, Nicholas Denby Allen, Jordi Alberch, Jordi Soriano, Josep M. Canals
Software Mentions: 2
Published: over 6 years ago

10.1002/1878-0261.12876

Circulating tumor cell detection and single‐cell analysis using an integrated workflow based on ChimeraX<sup>®</sup>‐i120 Platform: A prospective study
Cited by: 9
Author(s): Pengxiang Wang, Yun-Fan Sun, Weixiang Jin, Jian‐Wen Cheng, Hai-Xiang Peng, Yang Xu, Kaiyu Zhou, Li-Meng Chen, Kai Huang, Sui-Yi Wu, Bo Hu, Zefan Zhang, Wei Guo, Yang Cao, Jian Zhou, Jia Fan, Xin‐Rong Yang
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.cels.2018.02.001

Microenvironment-Mediated Mechanisms of Resistance to HER2 Inhibitors Differ between HER2+ Breast Cancer Subtypes
Cited by: 64
Author(s): Spencer S. Watson, Mark Dane, Koei Chin, Zuzana Tatárová, Moqing Liu, Tiera Liby, Wallace Thompson, Rebecca Smith, Michel Nederlof, Elmar Bucher, David Kilburn, Matthew A. Whitman, Damir Sudar, Gordon B. Mills, Laura M. Heiser, Oliver Jonas, Joe W. Gray, James E. Korkola
Software Mentions: 2
Published: over 8 years ago

10.1016/j.cels.2020.04.003

nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer
Cited by: 137
Author(s): Réka Hollandi, Ábel Szkalisity, Tímea Tóth, Ervin Tasnádi, Csaba Molnár, Botond Mathe, István Grexa, J. Molnár, Árpád Bálind, Mate Gorbe, Mária Kovács, Ede Migh, Allen Goodman, Tamás Balassa, Krisztián Koós, Wenyu Wang, Juan C. Caicedo, Norbert Bara, Ferenc Kovács, Lassi Paavolainen, Tivadar Danka, András Kriston, Anne E. Carpenter, Kevin Smith, Péter Horváth
Software Mentions: 2
Published: over 6 years ago

10.1016/j.stem.2021.03.022

Commitment and oncogene-induced plasticity of human stem cell-derived pancreatic acinar and ductal organoids
Cited by: 51
Author(s): Ling Huang, Ridhdhi Desai, Daniel N. Conrad, Nayara C. Leite, Dipikaa Akshinthala, Christine Lim, Raúl González, Lakshmi Muthuswamy, Zev J. Gartner, Senthil K. Muthuswamy
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-11-248

Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images
Cited by: 73
Author(s): Pekka Ruusuvuori, Tarmo Äijö, Sharif Chowdhury, Cecilia Garmendia-Torres, Jyrki Selinummi, Mirko Birbaumer, Andrew T. Dudley, Lucas Pelkmans, Olli Yli‐Harja
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0102284

Neutrophils Contribute to Excess Serum BAFF Levels and Promote CD4+ T Cell and B Cell Responses in Lupus-Prone Mice
Cited by: 44
Author(s): Christine M. Coquery, Nekeithia S. Wade, William Loo, Jason M. Kinchen, Kimberly Cox, Chao Jiang, Kenneth S. K. Tung, Loren D. Erickson
Software Mentions: 2
Published: over 12 years ago

10.1186/1741-7007-10-1

Detailed interrogation of trypanosome cell biology via differential organelle staining and automated image analysis
Cited by: 45
Author(s): Richard J. Wheeler, Keith Gull, Eva Gluenz
Software Mentions: 2
Published: almost 15 years ago

10.1186/s40478-019-0779-2

The landscape of myeloid and astrocyte phenotypes in acute multiple sclerosis lesions
Cited by: 38
Author(s): Calvin Park, Gerald Ponath, Maya Levine-Ritterman, Edward Bull, Eric Swanson, Philip L. De Jager, Benjamin M. Segal, David Pitt
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1006353

A Multistate Toggle Switch Defines Fungal Cell Fates and Is Regulated by Synergistic Genetic Cues
Cited by: 24
Author(s): Matthew Anderson, Allison M. Porman, Na Wang, Eugenio Mancera, Denis Huang, Christina A. Cuomo, Richard J. Bennett
Software Mentions: 2
Published: about 10 years ago

10.3390/cells9030673

Cyclin-Dependent Kinase 18 Controls Trafficking of Aquaporin-2 and Its Abundance through Ubiquitin Ligase STUB1, Which Functions as an AKAP
Cited by: 18
Author(s): Alessandro Dema, Dörte Faust, Katina Lazarow, Marc Wippich, Martin Neuenschwander, Kerstin Zühlke, Andrea Geelhaar, Tamara Pallien, Eileen Hallscheidt, Jenny Eichhorst, Burkhard Wiesner, Hana Černecká, Oliver Popp, Philipp Mertins, Gunnar Dittmar, Jens Peter von Kries, Jens Peter Klußmann
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1005177

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments
Cited by: 425
Author(s): David Ashley Van Valen, Tetsuichi Kudo, Keara Lane, Derek N. Macklin, Nicolas Quach, Mialy M. DeFelice, Inbal Maayan, Tao Yu, Euan A. Ashley, Markus W. Covert
Software Mentions: 2
Published: almost 10 years ago

10.3390/cancers12020346

WNT5A-Induced Activation of the Protein Kinase C Substrate MARCKS Is Required for Melanoma Cell Invasion
Cited by: 15
Author(s): Purusottam Mohapatra, Vikas Yadav, Maren Toftdahl, Tommy Andersson
Software Mentions: 2
Published: over 6 years ago

10.1016/j.celrep.2018.04.044

mTOR Senses Environmental Cues to Shape the Fibroblast-like Synoviocyte Response to Inflammation
Cited by: 46
Author(s): Thomas Karonitsch, Richard K. Kandasamy, Felix Kartnig, Barbara Herdy, K Dalwigk, Birgit Niederreiter, Johannes Holinka, Florian Sevelda, Reinhard Windhager, Martin Bilban, Thomas Weichhart, Marcus D. Säemann, Thomas Pap, Günter Steiner, Josef S Smolen, Hans P. Kiener, Giulio Superti‐Furga
Software Mentions: 2
Published: over 8 years ago

10.3390/cells10040838

Aquaglyceroporin-3’s Expression and Cellular Localization Is Differentially Modulated by Hypoxia in Prostate Cancer Cell Lines
Cited by: 5
Author(s): Andreia de Almeida, Dimitris Parthimos, Holly Dew, Oliver S. Smart, Marie Wiltshire, Rachel J. Errington
Software Mentions: 2
Published: over 5 years ago

10.1016/j.celrep.2021.109280

Positive feedback between the T cell kinase Zap70 and its substrate LAT acts as a clustering-dependent signaling switch
Cited by: 6
Author(s): Elliot Dine, Ellen H. Reed, Jared E. Toettcher
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0200027

Reproductive strategy and gamete development of an invasive fanworm, Sabella spallanzanii (Polychaeta: Sabellidae), a field study in Gulf St Vincent, South Australia
Cited by: 4
Author(s): Aria L. Lee, Katherine A. Dafforn, Pat Hutchings, Emma L. Johnston
Software Mentions: 2
Published: over 8 years ago

10.1016/j.celrep.2018.03.021

Extracellular Monomeric and Aggregated Tau Efficiently Enter Human Neurons through Overlapping but Distinct Pathways
Cited by: 143
Author(s): Lewis Evans, Thomas Wassmer, Graham Fraser, James Smith, Michael S. Perkinton, Andrew Billinton, Frederick J. Livesey
Software Mentions: 2
Published: over 8 years ago

10.1186/s13630-019-0061-z

New software for automated cilia detection in cells (ACDC)
Cited by: 16
Author(s): Max C. Lauring, Tianqi Zhu, Wei Luo, Wenqi Wu, Feng Yu, Derek Toomre
Software Mentions: 2
Published: about 7 years ago

10.1186/s13148-021-01160-z

Targeting the methyltransferase SETD8 impairs tumor cell survival and overcomes drug resistance independently of p53 status in multiple myeloma
Cited by: 8
Author(s): Laurie Herviou, Sara Ovejero, Fanny Izard, Ouissem Karmous-Gadacha, Claire Gourzonès, Céline Bellanger, Eva De Smedt, Anqi Ma, Laure Vincent, Guillaume Cartron, Jian Jin, Elke De Bruyne, Charlotte Grimaud, Éric Julien, Jérôme Moreaux
Software Mentions: 2
Published: about 5 years ago

10.1007/s00392-020-01801-y

Impaired in vitro growth response of plasma-treated cardiomyocytes predicts poor outcome in patients with transthyretin amyloidosis
Cited by: 3
Author(s): Selina Hein, Jennifer Furkel, Maximilian Knoll, Fabian aus dem Siepen, Stefan Schönland, Ute Hegenbart, Hugo A. Katus, Arnt V. Kristen, Mathias Konstandin
Software Mentions: 2
Published: over 5 years ago

10.15252/msb.20199083

<scp>KCML</scp> : a machine‐learning framework for inference of multi‐scale gene functions from genetic perturbation screens
Cited by: 9
Author(s): Heba Sailem, Jens Rittscher, Lucas Pelkmans
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-019-0626-9

Ribosomal mistranslation leads to silencing of the unfolded protein response and increased mitochondrial biogenesis
Cited by: 32
Author(s): Dmitry Shcherbakov, Youjin Teo, Heithem Boukari, Adrian Cortes-Sanchon, Matilde Mantovani, Ivan Osinnii, James M. Moore, Reda Juskeviciene, Margarita Brilkova, Stefan Duscha, Harshitha Santhosh Kumar, Endre Laczkó, Hubert Rehrauer, Éric Westhof, Rashid Akbergenov, Erik C. Böttger
Software Mentions: 2
Published: almost 7 years ago

10.1093/bioinformatics/btaa541

TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data
Cited by: 28
Author(s): Leslie Solorzano, Gabriele Partel, Carolina Wählby
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0141365

Lentivirus Live Cell Array for Quantitative Assessment of Gene and Pathway Activation during Myogenic Differentiation of Mesenchymal Stem Cells
Cited by: 5
Author(s): Janhavi Moharil, Pedro Lei, Jun Tian, Daniel P. Gaile, Stelios T. Andreadis
Software Mentions: 2
Published: almost 11 years ago

10.1042/BJ20130579

Nogo-A couples with Apg-1 through interaction and co-ordinate expression under hypoxic and oxidative stress
Cited by: 13
Author(s): Florian Kern, Ruslan I. Stanika, Bettina Sarg, Martin Offterdinger, Daniel Heß, Gerald J. Obermair, Herbert Lindner, Christine E. Bandtlow, Ludger Hengst, Rüdiger Schweigreiter
Software Mentions: 2
Published: about 13 years ago

10.15252/msb.20167295

An atlas of human kinase regulation
Cited by: 87
Author(s): David Ochoa, Mindaugas Jonikas, Robert Lawrence, Bachir El Debs, Joel Selkrig, Athanasios Typas, Judit Villén, Silvia Santos, Pedro Beltrão
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12859-020-03635-x

Keras R-CNN: library for cell detection in biological images using deep neural networks
Cited by: 40
Author(s): Jia‐Jang Hung, Allen Goodman, Deepali Ravel, Stefanie Costa Pinto Lopes, Gabriel W. Rangel, Odailton Amaral Nery, Benoît Malleret, François Nosten, Marcus Lacerda, Marcelo U. Ferreira, Laurent Rénia, Manoj T. Duraisingh, Fabio T. M. Costa, Matthias Marti, Anne E. Carpenter
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-021-01708-y

Insulin-like 3 affects zebrafish spermatogenic cells directly and via Sertoli cells
Cited by: 8
Author(s): Diego Crespo, Luiz H. C. Assis, Yu Ting Zhang, Diego Safian, Tomasz Furmanek, Kai Ove Skaftnesmo, Birgitta Norberg, Wei Ge, Yung Ching Choi, Marjo J. den Broeder, Juliette Legler, Jan Bogerd, Rüdiger Schulz
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0252000

easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler
Cited by: 7
Author(s): Joy Nyaanga, Timothy A. Crombie, Samuel J. Widmayer, Erik C. Andersen
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0239047

The calmodulin redox sensor controls myogenesis
Cited by: 2
Author(s): Alex W Steil, Jacob W Kailing, Cade J Armstrong, Daniel G. Walgenbach, Jennifer C. Klein
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0078320

Mice Deficient in Sfrp1 Exhibit Increased Adiposity, Dysregulated Glucose Metabolism, and Enhanced Macrophage Infiltration
Cited by: 39
Author(s): Kelly J Gauger, Lotfi M. Bassa, Elizabeth Henchey, Josephine Wyman, Brooke Bentley, Melissa Brown, Akihiko Shimono, Sallie S. Schneider
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2105-11-287

Colonyzer: automated quantification of micro-organism growth characteristics on solid agar
Cited by: 63
Author(s): Conor Lawless, Darren J. Wilkinson, A. E. Young, Stephen G. Addinall, David Lydall
Software Mentions: 2
Published: over 16 years ago

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