pypi: CellProfiler | Projects | Ecosyste.ms: Papers

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: almost 5 years ago

10.1038/srep13113

Human cell dedifferentiation in mesenchymal condensates through controlled autophagy
Cited by: 34
Author(s): Rebecca Rose Pennock, Elen Bray, Paul R. Pryor, Sally James, Paul J. McKeegan, Roger G. Sturmey, Paul G. Genever
Software Mentions: 2
Published: about 11 years ago

10.1038/s41598-017-07599-6

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation
Cited by: 109
Author(s): Sajith Kecheril Sadanandan, Petter Ranefall, Sylvie Le Guyader, Carolina Wählby
Software Mentions: 2
Published: about 9 years ago

10.1177/2472555218824280

The Academic Pill: How Academia Contributes to Curing Diseases
Cited by: 3
Author(s): Marc Bickle
Software Mentions: 2
Published: over 7 years ago

10.1126/sciadv.aba4526

Esophageal extracellular matrix hydrogel mitigates metaplastic change in a dog model of Barrett’s esophagus
Cited by: 24
Author(s): Juan Diego Naranjo, Lindsey T. Saldin, Eric Sobieski, Lina M. Quijano, Ryan C. Hill, Patrick Chan, Crisanto M Torres, Jenna L. Dziki, Madeline C. Cramer, Yoojin C. Lee, Rohit Das, Anant K. Bajwa, Rania Nossair, Molly Klimak, Lucile Marchal, Shil Patel, Sachin Velankar, Kirk C. Hansen, Kevin McGrath, Stephen F. Badylak
Software Mentions: 2
Published: about 6 years ago

10.1038/sdata.2018.81

A multi-phenotypic imaging screen to identify bacterial effectors by exogenous expression in a HeLa cell line
Cited by: 3
Author(s): Adam Collins, Alan Huett
Software Mentions: 2
Published: over 8 years ago

10.1073/pnas.2021450118

Targeting transcriptional regulation of SARS-CoV-2 entry factors ACE2 and TMPRSS2
Cited by: 133
Author(s): Yuanyuan Qiao, Xiaoming Wang, Rahul Mannan, Sethuramasundaram Pitchiaya, Yuping Zhang, Jesse W Wotring, Lanbo Xiao, Dan R. Robinson, Yi-Mi Wu, Jean C. Tien, Xuhong Cao, Stephanie A. Simko, Ingrid J. Apel, Pushpinder Bawa, Steven Kregel, Sathiya Pandi Narayanan, Gregory Raskind, Stephanie J. Ellison, Abhijit Parolia, Sylvia Zelenka-Wang, Lisa McMurry, Fengyun Su, Rui Wang, Yunhui Cheng, Andrew Delekta, Zejie Mei, Carla D. Pretto, Shaomeng Wang, Rohit Mehra, Jonathan Z. Sexton, Arul M. Chinnaiyan
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1008690

Inhibition of anti-viral stress granule formation by coronavirus endoribonuclease nsp15 ensures efficient virus replication
Cited by: 68
Author(s): Bo Gao, Xiaoyi Gong, Shouguo Fang, Wenlian Weng, Huan Wang, Hongyan Chu, Yingjie Sun, Meng Chen, Lei Tan, Song Chen, Xusheng Qiu, Weiwei Liu, Maria Forlenza, Chan Ding, Ying Liao
Software Mentions: 2
Published: over 5 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

10.1371/journal.ppat.1009580

A Ran-binding protein facilitates nuclear import of human papillomavirus type 16
Cited by: 10
Author(s): Kun-Yi Lai, Matteo Rizzato, Inci Aydin, Ruth Villalonga-Planells, Hannes C.A. Drexler, Mario Schelhaas
Software Mentions: 2
Published: over 5 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: over 14 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.ppat.1008554

The ATGL lipase cooperates with ABHD5 to mobilize lipids for hepatitis C virus assembly
Cited by: 21
Author(s): Gabrielle Vièyres, I. Reichert, Arnaud Carpentier, Florian W. R. Vondran, Thomas Pietschmann
Software Mentions: 2
Published: about 6 years ago

10.1186/1741-7007-11-114

The p53 response in single cells is linearly correlated to the number of DNA breaks without a distinct threshold
Cited by: 65
Author(s): Alexander Loewer, Ketki Karanam, Charles Mock, Galit Lahav
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.ppat.1007698

Proximity-dependent proteomics of the Chlamydia trachomatis inclusion membrane reveals functional interactions with endoplasmic reticulum exit sites
Cited by: 24
Author(s): Mary S Dickinson, Lindsey Anderson, Bobbie-Jo M. Webb-Robertson, Joshua Hansen, Richard Smith, Aaron Wright, Kevin Hybiske
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1008656

Influenza A viruses use multivalent sialic acid clusters for cell binding and receptor activation
Cited by: 34
Author(s): Christian Sieben, Erdinç Sezgin, Christian Eggeling, Suliana Manley
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.ppat.1003640

A Structural Basis for BRD2/4-Mediated Host Chromatin Interaction and Oligomer Assembly of Kaposi Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus LANA Proteins
Cited by: 75
Author(s): Jan Hellert, Magdalena Weidner-Glunde, J. Krausze, Ulrike Richter, Heiko Adler, Roman Fedorov, Marcel Pietrek, Jessica Rückert, Christiane Ritter, Thomas F. Schulz, Thorsten Lührs
Software Mentions: 2
Published: almost 13 years ago

10.1172/JCI132987

3D model of harlequin ichthyosis reveals inflammatory therapeutic targets
Cited by: 28
Author(s): Florence Enjalbert, P. Dewan, Matthew Caley, Erica Jones, Mary A. Morse, David P. Kelsell, Anton J. Enright, Edel A. O’Toole
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.ppat.1005263

Interferon-γ Inhibits Ebola Virus Infection
Cited by: 69
Author(s): Bethany A. Rhein, Linda S. Powers, Kai J. Rogers, Manu Anantpadma, Brajesh K. Singh, Yoshio Sakurai, Thomas B. Bair, Catherine L. Miller-Hunt, Patrick L. Sinn, Robert A. Davey, Martha M. Monick, Wendy Maury
Software Mentions: 2
Published: almost 11 years ago

10.1083/jcb.202012114

CYRI-A limits invasive migration through macropinosome formation and integrin uptake regulation
Cited by: 14
Author(s): Anh Hoang Le, Tamas Yelland, Nikki R. Paul, Loïc Fort, Savvas Nikolaou, Shehab Ismail, Laura M. Machesky
Software Mentions: 2
Published: about 5 years ago

10.1083/jcb.201904113

ALIX- and ESCRT-III–dependent sorting of tetraspanins to exosomes
Cited by: 188
Author(s): Jorge Larios, Vincent Mercier, Aurélien Roux, Jean Grüenberg
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1006354

A second wave of Salmonella T3SS1 activity prolongs the lifespan of infected epithelial cells
Cited by: 42
Author(s): Ciaran E. Finn, Audrey Chong, Kendal G. Cooper, Tregei Starr, Olivia Steele‐Mortimer
Software Mentions: 2
Published: over 9 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

10.1016/j.jbc.2021.100633

Early nucleolar responses differentiate mechanisms of cell death induced by oxaliplatin and cisplatin
Cited by: 26
Author(s): Emily Sutton, Victoria J. DeRose
Software Mentions: 2
Published: over 5 years ago

10.1186/s13036-019-0161-8

Tools to reverse-engineer multicellular systems: case studies using the fruit fly
Cited by: 9
Author(s): Qinfeng Wu, Nilay Kumar, Vijay Velagala, Jeremiah J. Zartman
Software Mentions: 2
Published: over 7 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: almost 11 years ago

10.1128/JB.00460-18

Connecting the Dots between Mechanosensitive Channel Abundance, Osmotic Shock, and Survival at Single-Cell Resolution
Cited by: 11
Author(s): Griffin Chure, Heun Jin Lee, Akiko Rasmussen, Rob Phillips
Software Mentions: 2
Published: almost 8 years ago

10.1172/jci.insight.141486

CD109-GP130 interaction drives glioblastoma stem cell plasticity and chemoresistance through STAT3 activity
Cited by: 21
Author(s): Pauliina Filppu, Jayendrakishore Tanjore Ramanathan, Kirsi J. Granberg, Erika Gucciardo, Hannu Haapasalo, Kaisa Lehti, Matti Nykter, Vadim Le Joncour, Pirjo Laakkonen
Software Mentions: 2
Published: over 5 years ago

10.1074/jbc.RA120.015398

AggreCount: an unbiased image analysis tool for identifying and quantifying cellular aggregates in a spatially defined manner
Cited by: 28
Author(s): Jacob Klickstein, Sirisha Mukkavalli, Malavika Raman
Software Mentions: 2
Published: almost 6 years ago

10.1177/1087057116652064

A Novel Automated High-Content Analysis Workflow Capturing Cell Population Dynamics from Induced Pluripotent Stem Cell Live Imaging Data
Cited by: 16
Author(s): Maximilian Kerz, Amos Folarin, Ruta Meleckyte, Fiona M. Watt, Richard Dobson, Davide Danovi
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-017-12608-9

Nucleosome stability measured in situ by automated quantitative imaging
Cited by: 16
Author(s): László Imre, Zoltán Simándi, Attila Horváth, György Fenyőfalvi, Péter P. Nánási, Erfaneh Firouzi Niaki, Éva Hegedüs, Zsolt Bacsó, Urbain Weyemi, Rebekka Mauser, Juan Ausió, Albert Jeltsch, William M. Bonner, László Nagy, Hiroshi Kimurâ, Gábor Szabó
Software Mentions: 2
Published: almost 9 years ago

10.1093/gigascience/giw014

A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay
Cited by: 84
Author(s): Mark-Anthony Bray, Sigrún M. Gústafsdóttir, Mohammad Hossein Rohban, Shantanu Singh, Vebjorn Ljosa, Katherine L Sokolnicki, Joshua A. Bittker, Nicole E. Bodycombe, Vlado Dančík, Thomas Hasaka, C. Suk-Yee Hon, Melissa M. Kemp, Kejie Li, Deepika Walpita, Mathias Wawer, Todd R. Golub, Stuart L. Schreiber, Paul A. Clemons, Alykhan F. Shamji, Anne E. Carpenter
Software Mentions: 2
Published: over 9 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

10.1186/1471-2105-15-S16-S6

FMAj: a tool for high content analysis of muscle dynamics in Drosophila metamorphosis
Cited by: 9
Author(s): Yadav Kuleesha, Wee Choo Puah, Feng Lin, Martin Wasser
Software Mentions: 2
Published: almost 12 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

10.1186/s13059-021-02301-6

Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity
Cited by: 5
Author(s): Matan Sorek, Walaa Oweis, Malka Nissim-Rafinia, Moria Maman, Shahar Simon, Cynthia C. Hession, Xian Adiconis, Sean Simmons, Neville E. Sanjana, Xi Shi, Congyi Lu, Jen Q. Pan, Xiaohong Xu, Mahmoud A. Pouladi, Lisa M. Ellerby, Feng Zhang, Joshua Z. Levin, Eran Meshorer
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2020.01275

Volumetric Segmentation of Cell Cycle Markers in Confocal Images Using Machine Learning and Deep Learning
Cited by: 3
Author(s): Faraz Ahmad Khan, Ute Voß, Michael P. Pound, A. P. French
Software Mentions: 2
Published: about 6 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: almost 5 years ago

10.3389/fpls.2015.01187

Developmental Nuclear Localization and Quantification of GFP-Tagged EB1c in Arabidopsis Root Using Light-Sheet Microscopy
Cited by: 15
Author(s): Dominik Novák, Anna Kuchařová, Miroslav Ovečka, George Komis, Jozef Šamaj
Software Mentions: 2
Published: over 10 years ago

10.1186/s13068-016-0687-7

A molecular genetic toolbox for Yarrowia lipolytica
Cited by: 52
Author(s): Erin L. Bredeweg, Kyle R. Pomraning, Ziyu Dai, Jens Nielsen, Eduard J. Kerkhoven, Scott E. Baker
Software Mentions: 2
Published: over 9 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: almost 10 years ago

10.3389/fonc.2020.00292

Transcriptomic and Functional Screens Reveal MicroRNAs That Modulate Prostate Cancer Metastasis
Cited by: 6
Author(s): S. Madhusudana Rao, Alison Howarth, Patrick Krätschmer, Ann Snaith, Clarence Yapp, Daniel Ebner, Freddie C. Hamdy, Claire Edwards
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2017.00627

Measuring Leukocyte Adhesion to (Primary) Endothelial Cells after Photon and Charged Particle Exposure with a Dedicated Laminar Flow Chamber
Cited by: 11
Author(s): N. Erbeldinger, Felicitas Rapp, Svetlana Ktitareva, Philipp Wendel, Anna S. Bothe, Till Dettmering, Marco Durante, Thomas Friedrich, Bianca Bertulat, Steven De Meyer, M. C. Cardoso, Stephanie Hehlgans, Franz Rödel, Claudia Fournier
Software Mentions: 2
Published: over 9 years ago

10.3389/fmicb.2020.578669

Environmental Factors Driving Spatial Heterogeneity in Desert Halophile Microbial Communities
Cited by: 9
Author(s): Gherman Uritskiy, Adam Munn, Micah Dailey, Diego Rivera Gelsinger, Samantha Getsin, Alfonso F. Dávila, Peter McCullough, James Taylor, Jocelyne DiRuggiero
Software Mentions: 2
Published: almost 6 years ago

10.3389/fchem.2019.00791

Neuraminidase-3 Is a Negative Regulator of LFA-1 Adhesion
Cited by: 13
Author(s): Md. Amran Howlader, Caishun Li, Chunxia Zou, Radhika Chakraberty, Njuacha Ebesoh, Christopher W. Cairo
Software Mentions: 2
Published: almost 7 years ago

10.3389/fncel.2019.00535

Live-Cell Assays for Cell Stress Responses Reveal New Patterns of Cell Signaling Caused by Mutations in Rhodopsin, α-Synuclein and TDP-43
Cited by: 6
Author(s): Kevin Harlen, Elizabeth C. Roush, Joseph E. Clayton, Scott Martinka, Thom Hughes
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2021.671756

The 5-Phosphatase SHIP2 Promotes Neutrophil Chemotaxis and Recruitment
Cited by: 3
Author(s): Melina Michael, Barrett L. McCormick, Karen E. Anderson, Utsa Karmakar, Matthieu Vermeren, Stéphane Schurmans, Augustin Amour, Sonja Vermeren
Software Mentions: 2
Published: over 5 years ago

10.3389/fnana.2015.00142

Crowdsourcing the creation of image segmentation algorithms for connectomics
Cited by: 273
Author(s): Ignacio Arganda‐Carreras, Srinivas C. Turaga, Daniel R. Berger, Dan Cireşan, Alessandro Giusti, Luca Maria Gambardella, Juergen Schmidhuber, Dmitry Laptev, Sarvesh Dwivedi, Joachim M. Buhmann, Ting Liu, Mojtaba Seyedhosseini, Tolga Taşdizen, Lee Kamentsky, Radim Bürget, Václav Uher, Xiao Tan, Changming Sun, Tuan D. Pham, Erhan Bas, Mustafa Gökhan Uzunbaş, Albert Cardona, Johannes Schindelin, H. Sebastian Seung
Software Mentions: 2
Published: almost 11 years ago

10.3389/fcimb.2017.00475

Predictable, Tunable Protein Production in Salmonella for Studying Host-Pathogen Interactions
Cited by: 14
Author(s): Kendal G. Cooper, Audrey Chong, Tregei Starr, Ciaran E. Finn, Olivia Steele‐Mortimer
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pcbi.1008974

The hierarchical packing of euchromatin domains can be described as multiplicative cascades
Cited by: 3
Author(s): Amra Noa, Hui-Shun Kuan, Vera Aschmann, Vasily Zaburdaev, Lennart Hilbert
Software Mentions: 2
Published: over 5 years ago

10.3389/fcell.2020.00579

Glucose Availability Alters Gene and Protein Expression of Several Newly Classified and Putative Solute Carriers in Mice Cortex Cell Culture and D. melanogaster
Cited by: 6
Author(s): Mikaela M. Ceder, Emilia Lekholm, Axel Klaesson, Rekha Tripathi, Nadine Schweizer, Lydia Weldai, Sourabh Patil, Robert Fredriksson
Software Mentions: 2
Published: about 6 years ago

10.3389/fcell.2020.584314

Transcriptome Response and Spatial Pattern of Gene Expression in the Primate Subventricular Zone Neurogenic Niche After Cerebral Ischemia
Cited by: 6
Author(s): Monika C Chongtham, Haifang Wang, Christina Thaller, Nai–Hua Hsiao, Ivan H. Vachkov, Stoyan Pavlov, Lorenz H Williamson, Tetsumori Yamashima, Anastassia Stoykova, Jun Yan, Gregor Eichele, Anton B. Tonchev
Software Mentions: 2
Published: almost 6 years ago

10.3389/fcell.2020.00493

Telomere Length Measurement by Molecular Combing
Cited by: 34
Author(s): Vívian Francília Silva Kahl, Joshua A. M. Allen, Christopher B. Nelson, Alexander P. Sobinoff, Michael Lee, Tatjana Kilo, Raja S. Vasireddy, Hilda A. Pickett
Software Mentions: 2
Published: about 6 years ago

10.3389/fcell.2021.657192

Loss of stra8 Increases Germ Cell Apoptosis but Is Still Compatible With Sperm Production in Atlantic Salmon (Salmo salar)
Cited by: 5
Author(s): Kai Ove Skaftnesmo, Diego Crespo, Lene Kleppe, Eva Andersson, Rolf B. Edvardsen, Birgitta Norberg, Per Gunnar Fjelldal, Tom Hansen, Rüdiger Schulz, Anna Wargelius
Software Mentions: 2
Published: over 5 years ago

10.3389/fnins.2021.629067

Recent Trends and Perspectives in Cerebral Organoids Imaging and Analysis
Cited by: 11
Author(s): Clara Brémond Martin, Camille Simon Chane, Cédric Clouchoux, Aymeric Histace
Software Mentions: 2
Published: about 5 years ago

10.12688/f1000research.52569.1

Bioimage analysis workflows: community resources to navigate through a complex ecosystem
Cited by: 8
Author(s): Perrine Paul‐Gilloteaux, Sébastien Tosi, Jean-Karim Hèriché, Alban Gaignard, Hervé Ménager, Raphaël Marée, Volker Baecker, Anna H. Klemm, Matúš Kalaš, Chong Zhang, Kota Miura, Julien Colombelli
Software Mentions: 2
Published: over 5 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: about 12 years ago

10.1002/2211-5463.13036

Spatiotemporal immunolocalisation of REST in the brain of healthy ageing and Alzheimer’s disease rats
Cited by: 3
Author(s): Myrthe Mampay, María Velasco-Estévez, Sara O. Rolle, Aisling M. Chaney, Hervé Boutin, Kumlesh K. Dev, Emad Moeendarbary, Graham K. Sheridan
Software Mentions: 2
Published: almost 6 years ago

10.12688/f1000research.16802.1

An in vitro model for studying CNS white matter: functional properties and experimental approaches
Cited by: 12
Author(s): Silvia Bijland, Gemma Thomson, Matthew Euston, Kyriakos Michail, Katja Thümmler, Steve Mücklisch, Colin L. Crawford, Susan C. Barnett, Marκ McLaughlin, Thomas Anderson, Christopher Linington, Euan R. Brown, Eric R. Kalkman, Julia M. Edgar
Software Mentions: 2
Published: over 7 years ago

10.1128/AAC.01002-20

The FDA-Approved Drug Nelfinavir Inhibits Lytic Cell-Free but Not Cell-Associated Nonlytic Transmission of Human Adenovirus
Cited by: 16
Author(s): Fanny Georgi, Vardan Andriasyan, Robert Witte, Luca Murer, Silvio Hemmi, Lisa Yu, Melanie Grove, Nicole Meili, Fabien Kuttler, Artur Yakimovich, Gerardo Turcatti, Urs F. Greber
Software Mentions: 2
Published: about 6 years ago

10.12688/f1000research.52531.1

Developing open-source software for bioimage analysis: opportunities and challenges
Cited by: 20
Author(s): Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
Software Mentions: 2
Published: over 5 years ago

10.3389/fnagi.2021.704041

Poly (ADP-ribose) Interacts With Phosphorylated α-Synuclein in Post Mortem PD Samples
Cited by: 13
Author(s): Laura Puentes, Zsofia Lengyel‐Zhand, Ji Youn Lee, Chia-Ju Hsieh, Mark E. Schneider, Kimberly J. Edwards, Kelvin C. Luk, Virginia M.‐Y. Lee, John Q. Trojanowski, Robert H. Mach
Software Mentions: 2
Published: about 5 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

10.15252/embr.201744837

<scp>SNX</scp> 18 regulates <scp>ATG</scp> 9A trafficking from recycling endosomes by recruiting Dynamin‐2
Cited by: 66
Author(s): Kristiane Søreng, Michael J. Munson, Christopher R. Lamb, Gunnveig Toft Bjørndal, Serhiy Pankiv, Sven R. Carlsson, Sharon A. Tooze, Anne Simonsen
Software Mentions: 2
Published: over 8 years ago

10.1042/ETLS20160025

Computational biology: deep learning
Cited by: 60
Author(s): William Jones, Kaur Alasoo, Dmytro Fishman, Leopold Parts
Software Mentions: 2
Published: almost 9 years ago

10.15252/emmm.201910852

A thiol‐bound drug reservoir enhances APR‐246‐induced mutant p53 tumor cell death
Cited by: 20
Author(s): Sophia Ceder, Sofi Eriksson, Emarndeena H Cheteh, Swati Dawar, Mariana Corrales Benitez, Vladimir J. N. Bykov, Kenji M. Fujihara, Mélodie Grandin, Xiaodun Li, Susanne Ramm, Corina Behrenbruch, Kaylene J. Simpson, Frédéric Hollande, Lars Abrahmsén, Nicholas J. Clemons, Klas G. Wiman
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.2003998

Stable centrosomal roots disentangle to allow interphase centriole independence
Cited by: 13
Author(s): Robert Mahen
Software Mentions: 2
Published: over 8 years ago

10.15252/embr.201947845

Myc‐dependent endothelial proliferation is controlled by phosphotyrosine 1212 in <scp>VEGF</scp> receptor‐2
Cited by: 23
Author(s): Chiara Testini, Ross O Smith, Yi Jin, Pernilla Martinsson, Ying Sun, Mattias Hedlund, Miguel Sáinz‐Jaspeado, Masabumi Shibuya, Mats Hellström, Lena Claesson‐Welsh
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13072-017-0157-x

H2A O-GlcNAcylation at serine 40 functions genomic protection in association with acetylated H2AZ or γH2AX
Cited by: 12
Author(s): Koji Hayakawa, Mitsuko Hirosawa, Ruiko Tani, Chikako Yoneda, Satoshi Tanaka, Kunio Shiota
Software Mentions: 2
Published: almost 9 years ago

10.15252/embj.2020104948

Receptor‐mediated clustering of FIP200 bypasses the role of LC3 lipidation in autophagy
Cited by: 61
Author(s): Amelia E Ohnstad, José A. Delgado Delgado, Brian J. North, Isha Nasa, Arminja N. Kettenbach, Sebastian W. Schultz, Christopher J. Shoemaker
Software Mentions: 2
Published: almost 6 years ago

10.15252/embj.201798714

Evidence for the nuclear import of histones H3.1 and H4 as monomers
Cited by: 39
Author(s): Michael James Apta‐Smith, Juan R. Hernández-Fernaud, Andrew Bowman
Software Mentions: 2
Published: about 8 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: about 8 years ago

10.15252/embj.2019103889

Proteasomal degradation induced by DPP9‐mediated processing competes with mitochondrial protein import
Cited by: 21
Author(s): Yannik Finger, Markus Habich, Sarah Gerlich, Sophia Urbanczyk, Erik van de Logt, Julian Koch, Laura Schu, Kim Jasmin Lapacz, Muna Ali, Carmelina Petrungaro, Silja Lucia Salscheider, C. Pichlo, Ulrich Baumann, Dirk Mielenz, Jörn Dengjel, Bent Brachvogel, Kay Hofmann, Jan Riemer
Software Mentions: 2
Published: about 6 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: almost 7 years ago

10.1242/dev.199611

MOrgAna: accessible quantitative analysis of organoids with machine learning
Cited by: 19
Author(s): Nicola Gritti, Jia Le Lim, Kerim Anlaş, Mallica Pandya, Germaine Aalderink, Guillermo Martínez-Ara, Vikas Trivedi
Software Mentions: 2
Published: almost 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: about 6 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

10.1093/database/baw118

Mining biomedical images towards valuable information retrieval in biomedical and life sciences
Cited by: 20
Author(s): Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar
Software Mentions: 2
Published: over 10 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

10.1242/dev.187187

Control of skeletal morphogenesis by the Hippo-YAP/TAZ pathway
Cited by: 17
Author(s): Hannah K. Vanyai, Fabrice Prin, Oriane Guillermin, N. Bishara Marzook, Stefan Boeing, Alexander Howson, Rebecca E. Saunders, T Snoeks, Michael Howell, Timothy J. Mohun, Barry Thompson
Software Mentions: 2
Published: over 6 years ago

10.15252/embj.2020104858

<scp>MSH</scp> 2 shapes the meiotic crossover landscape in relation to interhomolog polymorphism in Arabidopsis
Cited by: 33
Author(s): Alexander R. Blackwell, Julia Dluzewska, Maja Szymańska-Lejman, Stuart D. Desjardins, Andrew J. Tock, Nadia Kbiri, Christophe Lambing, Emma Lawrence, Tomasz Bieluszewski, Beth A. Rowan, James D. Higgins, Piotr A Ziolkowski, Ian Henderson
Software Mentions: 2
Published: almost 6 years ago

10.1038/s42003-021-02272-1

Genome-wide CRISPR screen identifies protein pathways modulating tau protein levels in neurons
Cited by: 12
Author(s): Carlos Sanchez, Christopher M. Acker, Audrey Gray, Malini Varadarajan, Chun-Yan Song, Nadire Cochran, Steven Paula, Alicia Lindeman, Shaojian An, Gregory McAllister, John Alford, John S. Reece‐Hoyes, Carsten Russ, Lucas Craig, Ketthsy Capre, Christian Doherty, Gregory R. Hoffman, Sarah J. Luchansky, Manuela Polydoro, Ricardo E. Dolmetsch, Fiona Elwood
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: about 7 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

10.1038/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

10.1111/febs.14857

Two Nimrod receptors, NimC1 and Eater, synergistically contribute to bacterial phagocytosis in Drosophila melanogaster
Cited by: 32
Author(s): Claudia Melcarne, Elodie Ramond, Jan Paul Dudzic, Andrew J. Bretscher, Éva Kurucz, István Andó, Bruno Lemaître
Software Mentions: 2
Published: over 7 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

10.1038/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

10.1186/1471-2105-11-287

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

10.1245/s10434-020-08659-4

Multiparametric MRI and Whole Slide Image-Based Pretreatment Prediction of Pathological Response to Neoadjuvant Chemoradiotherapy in Rectal Cancer: A Multicenter Radiopathomic Study
Cited by: 32
Author(s): Lizhi Shao, Zhenyu Liu, Lili Feng, Xiaoying Lou, Zhenhui Li, Xiao Yan Zhang, Xiang-Bo Wan, Xuezhi Zhou, Kai Sun, Da Fu Zhang, Lin Wu, Guanyu Yang, Ying Sun, Rui‐hua Xu, Xinjuan Fan, Jie Tian
Software Mentions: 2
Published: about 6 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: almost 5 years ago

10.1002/cyto.a.23794

Label‐Free Identification of White Blood Cells Using Machine Learning
Cited by: 62
Author(s): Mariam Nassar, Minh Doan, Andrew Filby, Olaf Wolkenhauer, Darin K. Fogg, Justyna Piasecka, Catherine A. Thornton, Anne E. Carpenter, Huw D. Summers, Paul Rees, Holger Hennig
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1009193

Machine learning reveals mesenchymal breast carcinoma cell adaptation in response to matrix stiffness
Cited by: 8
Author(s): Vlada S. Rozova, Ayad G. Anwer, Anna Guller, Hamidreza Aboulkheyr Es, Zahra Khabir, Anastasiya I. Sokolova, Maxim U. Gavrilov, Ewa M. Goldys, Majid Ebrahimi Warkiani, Jean Paul Thiery, Andrei V. Zvyagin
Software Mentions: 2
Published: about 5 years ago

10.15252/embj.2020107182

Reciprocal priming between receptor tyrosine kinases at recycling endosomes orchestrates cellular signalling outputs
Cited by: 9
Author(s): Michael P. Smith, Harriet R. Ferguson, Jennifer Ferguson, Egor Zindy, Katarzyna M. Kowalczyk, Thomas Kedward, Christian Bates, Joseph Parsons, Joanne Watson, Sarah Chandler, Paul Fullwood, Stacey Warwood, David Knight, Robert B. Clarke, Chiara Francavilla
Software Mentions: 2
Published: over 5 years ago

10.3389/fcell.2020.00570

ABHD11 Is Critical for Embryonic Stem Cell Expansion, Differentiation and Lipid Metabolic Homeostasis
Cited by: 4
Author(s): Gaoke Liu, Yan Ruan, Junlei Zhang, Xueyue Wang, Wei Wu, Ping He, Jiali Wang, Jiaxiang Xiong, Yuda Cheng, Lianlian Liu, Yi Yang, Yanping Tian, Rui Jian
Software Mentions: 2
Published: about 6 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

10.1186/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

10.1186/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: over 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

10.1186/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

Projects: pypi: CellProfiler

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Papers Mentioning CellProfiler 1,504