pypi: CellProfiler | Projects | Ecosyste.ms: Papers

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

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.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

10.1016/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

10.1371/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

10.1186/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

10.1172/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

10.1172/jci.insight.139445

Smooth muscle–derived progenitor cell myofibroblast differentiation through KLF4 downregulation promotes arterial remodeling and fibrosis
Cited by: 30
Author(s): Sizhao Lu, Austin Jolly, Keith A. Strand, Allison Dubner, Marie Mutryn, Karen S. Moulton, Raphael A. Nemenoff, Mark W. Majesky, Mary C.M. Weiser‐Evans
Software Mentions: 2
Published: almost 6 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

10.1177/1087057116652064

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

10.1371/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

10.1093/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

10.1245/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

10.1038/s41398-020-01175-9

A cortical immune network map identifies distinct microglial transcriptional programs associated with β-amyloid and Tau pathologies
Cited by: 16
Author(s): Ellis Patrick, Marta Olah, Mariko Taga, Hans-Ulrich Klein, Jishu Xu, Charles C. White, Daniel Felsky, Shweta Agrawal, Chris Gaiteri, Lori B. Chibnik, Sara Mostafavi, Julie A. Schneider, David A. Bennett, Elizabeth M. Bradshaw, Philip L. De Jager
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: over 6 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

10.3389/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

10.1242/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: 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

10.15252/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

10.15252/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

10.7717/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

10.1242/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.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

10.1093/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

10.1002/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

10.1038/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

10.1242/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

10.1038/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/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

10.1007/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/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

10.1242/bio.045906

Heterogeneous response of endothelial cells to insulin like growth factor 1 treatment is explained by spatially clustered subpopulations
Cited by: 4
Author(s): Christina Kim, Gregory J. Seedorf, Steven H. Abman, Douglas P. Shepherd
Software Mentions: 2
Published: over 7 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

10.3390/v13010091

Zika Virus Infection Leads to Demyelination and Axonal Injury in Mature CNS Cultures
Cited by: 15
Author(s): Verena Schultz, Stephanie L. Cumberworth, Quan Gu, Natasha Johnson, Claire L. Donald, George A. McCanney, Jennifer A. Barrie, Ana da Silva Filipe, Christopher Linington, Hugh J. Willison, Julia M. Edgar, Susan C. Barnett, Alain Kohl
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

10.1186/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/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

10.3390/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

10.1186/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

10.1038/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

10.1016/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

10.3390/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: 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/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

10.1186/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

10.1016/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

10.1371/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

10.1016/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

10.1074/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

10.1186/s40478-016-0306-7

C9orf72 is differentially expressed in the central nervous system and myeloid cells and consistently reduced in C9orf72, MAPT and GRN mutation carriers
Cited by: 54
Author(s): Patrizia Rizzu, Cornelis Blauwendraat, Sasja Heetveld, Emily M. Lynes, Melissa Castillo-Lizardo, Ashutosh Dhingra, Elwira Pyż, Markus A. Hobert, Matthis Synofzik, Javier Simón‐Sánchez, Margherita Francescatto, Peter Heutink
Software Mentions: 2
Published: over 10 years ago

10.1016/j.jbc.2021.101003

Development of a specific live-cell assay for native autophagic flux
Cited by: 7
Author(s): Nathaniel Safren, Elizabeth M.H. Tank, Aatika Malik, Jason P. Chua, Nicholas Santoro, Sami J. Barmada
Software Mentions: 2
Published: about 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

10.1016/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

10.1083/jcb.201908132

LUZP1 and the tumor suppressor EPLIN modulate actin stability to restrict primary cilia formation
Cited by: 22
Author(s): João Gonçalves, Amit Sharma, Étienne Coyaud, Estelle Laurent, Brian Raught, Laurence Pelletier
Software Mentions: 2
Published: over 6 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

10.1186/s13059-014-0442-y

GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images
Cited by: 9
Author(s): Anne Trinh, Inga Hansine Rye, Vanessa Almendro, Åslaug Helland, Hege G. Russnes, Florian Markowetz
Software Mentions: 2
Published: about 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: over 10 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

10.1186/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: almost 5 years ago

10.1016/j.cmet.2019.12.012

Calcitonin Receptor Neurons in the Mouse Nucleus Tractus Solitarius Control Energy Balance via the Non-aversive Suppression of Feeding
Cited by: 63
Author(s): Wenwen Cheng, Ian E. Gonzalez, Warren Pan, Anthony H. Tsang, Jeffrey Adams, Ermelinda Ndoka, Desiree Gordian, Basma Khoury, Karen J. Roelofs, Simon S. Evers, Andrew MacKinnon, Shuangcheng Wu, Henriette Frikke-Schmidt, Jonathan N. Flak, James L. Trevaskis, Christopher J. Rhodes, So‐ichiro Fukada, Randy J. Seeley, Darleen A. Sandoval, David P. Olson, Clémence Blouet, Martin G. Myers
Software Mentions: 2
Published: over 6 years ago

10.15252/msb.20199243

Systematic genetics and single‐cell imaging reveal widespread morphological pleiotropy and cell‐to‐cell variability
Cited by: 32
Author(s): Mojca Mattiazzi Ušaj, Nil Sahin, Helena Friesen, Carles Pons, Matej Ušaj, Myra Paz David Masinas, Ermira Shuteriqi, Aleksei Shkurin, Patrick Aloy, Quaid Morris, Charles Boone, Brenda Andrews
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-14-297

An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy
Cited by: 120
Author(s): Felix Buggenthin, Carsten Marr, Michael Schwarzfischer, Philipp S. Hoppe, Oliver Hilsenbeck, Timm Schroeder, Fabian J. Theis
Software Mentions: 2
Published: almost 13 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

10.1038/s41419-020-2704-9

Reduced replication origin licensing selectively kills KRAS-mutant colorectal cancer cells via mitotic catastrophe
Cited by: 4
Author(s): Bastian Gastl, Kathleen Klotz-Noack, Bertram Klinger, Sylvia Ispasanie, Krenoula Hani Fouad Salib, Johannes Zuber, Soulafa Mamlouk, Natalie Bublitz, Nils Blüthgen, David Horst, Markus Morkel, Reinhold Schäfer, Christine Sers
Software Mentions: 2
Published: about 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

10.1371/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.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

10.1007/s00018-020-03467-1

The Rab5 activator RME-6 is required for amyloid precursor protein endocytosis depending on the YTSI motif
Cited by: 7
Author(s): Simone Eggert, Tomas Gruebl, Ritu Rajender, Carsten Rupp, Bianca Sander, Amelie Heesch, Marius Zimmermann, Sebastian Hoepfner, Hanswalter Zentgraf, Stefan Kins
Software Mentions: 2
Published: over 6 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: over 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

10.1038/s41419-017-0039-y

Systems modeling accurately predicts responses to genotoxic agents and their synergism with BCL-2 inhibitors in triple negative breast cancer cells
Cited by: 37
Author(s): Federico Lucantoni, Andreas U. Lindner, Norma O’Donovan, Heiko Düßmann, Jochen H M Prehn
Software Mentions: 2
Published: over 8 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

10.1186/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

10.1042/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: almost 13 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

10.3390/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

10.3390/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/s12859-021-04344-9

CellProfiler 4: improvements in speed, utility and usability
Cited by: 388
Author(s): David R. Stirling, Madison J. Swain-Bowden, Alice M. Lucas, Anne E. Carpenter, Beth A. Cimini, Allen Goodman
Software Mentions: 2
Published: almost 5 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

10.1371/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

10.1002/1878-0261.12876

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: over 5 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

10.1186/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

10.1186/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: 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

10.1371/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

10.1186/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.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: over 7 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

10.1371/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

10.1186/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: about 6 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

10.1371/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

10.1371/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

10.1038/s41598-018-25571-w

Propyl-5-hydroxy-3-methyl-1-phenyl-1H-pyrazole-4-carbodithioate (HMPC): a new bacteriostatic agent against methicillin—resistant Staphylococcus aureus
Cited by: 6
Author(s): Tatiana Johnston, Daria Van Tyne, Roy Fangxing Chen, Nicolas L. Fawzi, Bumsup Kwon, Michael J. Kelso, Michael S. Gilmore, Eleftherios Mylonakis
Software Mentions: 2
Published: over 8 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

10.1016/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

10.1038/s41598-018-31726-6

High-Reynolds Microfluidic Sorting of Large Yeast Populations
Cited by: 7
Author(s): Eliezer Keinan, Ayelet Chen Abraham, Anna Cohen, Alexander I. Alexandrov, Reshef Mintz, Merav Cohen, Dana Reichmann, Daniel Kaganovich, Yaakov Nahmias
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-018-32364-8

Cell-based RNAi screening and high-content analysis in primary calvarian osteoblasts applied to identification of osteoblast differentiation regulators
Cited by: 7
Author(s): Mubashir Ahmad, Torsten Kroll, Jeanette Jakob, Alexander Rauch, Aspasia Ploubidou, Jan Tuckermann
Software Mentions: 2
Published: almost 8 years ago

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Papers Mentioning CellProfiler 1,504