pypi: CellProfiler | Projects | Ecosyste.ms: Papers

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

10.15252/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

10.1038/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

10.1371/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

10.3390/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/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

10.1186/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

10.1083/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

10.3390/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

10.1172/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.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

10.1038/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

10.1371/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

10.3390/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: about 6 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.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

10.1186/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.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: about 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: about 5 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

10.1093/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

10.1186/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

10.1186/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: about 5 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

10.1038/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

10.1007/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: over 9 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: about 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

10.1002/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

10.3390/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

10.1186/1741-7007-10-1

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

10.3390/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/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/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/s41598-018-28482-y

Environmental properties of cells improve machine learning-based phenotype recognition accuracy
Cited by: 12
Author(s): Tímea Tóth, Tamás Balassa, Norbert Bara, Ferenc Kovács, András Kriston, Csaba Molnár, Lajos Haracska, Farkas Sükösd, Péter Horváth
Software Mentions: 2
Published: about 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.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

10.1186/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: about 7 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

10.1186/s40425-018-0406-y

Ibuprofen supports macrophage differentiation, T cell recruitment, and tumor suppression in a model of postpartum breast cancer
Cited by: 39
Author(s): Nathan D. Pennock, Holly A. Martinson, Qiuchen Guo, Courtney B. Betts, Sonali Jindal, Takahiro Tsujikawa, Lisa M. Coussens, Virginia F. Borges, Pepper Schedin
Software Mentions: 2
Published: almost 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

10.1042/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

10.1002/sctm.16-0343

Microfluidic Screening Reveals Heparan Sulfate Enhances Human Mesenchymal Stem Cell Growth by Modulating Fibroblast Growth Factor-2 Transport
Cited by: 24
Author(s): Drew M. Titmarsh, Clarissa Tan, Nick Glass, Victor Nurcombe, Justin J. Cooper-White, Simon M. Cool
Software Mentions: 2
Published: over 9 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: almost 5 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

10.1016/j.stemcr.2016.11.014

Cytosine-5 RNA Methylation Regulates Neural Stem Cell Differentiation and Motility
Cited by: 118
Author(s): Joana V. Flores, Lucía Cordero-Espinoza, Feride Oeztuerk-Winder, Amanda Andersson-Rolf, Tommaso Selmi, Sandra Blanco, Jignesh Tailor, Sabine Dietmann, Michaela Frye
Software Mentions: 2
Published: over 9 years ago

10.18632/oncotarget.20833

STK38L kinase ablation promotes loss of cell viability in a subset of KRAS-dependent pancreatic cancer cell lines
Cited by: 6
Author(s): Trevor J. Grant, Anita K. Mehta, Anamika Gupta, Ahmad A.D. Sharif, Kshitij S. Arora, Vikram Deshpande, David T. Ting, Nabeel Bardeesy, Neil J. Ganem, Alexander Hergovich, Anurag Singh
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-019-47521-w

A principled strategy for mapping enhancers to genes
Cited by: 13
Author(s): Dongkyeong Kim, Hongjoo An, Randall S. Shearer, Mohamed Sharif, Chuandong Fan, Jinok Choi, Sun Hwa Ryu, Yungki Park
Software Mentions: 2
Published: about 7 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

10.18632/oncotarget.23639

Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma
Cited by: 13
Author(s): John A. Smestad, Oksana Hamidi, Lin Wang, Molly Nelson Holte, Fatimah Al Khazal, Luke Erber, Yue Chen, L. James Maher
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.25433

BCL2 and BCL(X)L selective inhibitors decrease mitochondrial ATP production in breast cancer cells and are synthetically lethal when combined with 2-deoxy-D-glucose
Cited by: 36
Author(s): Federico Lucantoni, Heiko Düßmann, Irene Llorente‐Folch, Jochen H M Prehn
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-021-88382-6

Aggressive and recurrent ovarian cancers upregulate ephrinA5, a non-canonical effector of EphA2 signaling duality
Cited by: 10
Author(s): Joonas Jukonen, Lidia Moyano‐Galceran, Katrin Höpfner, Elina Pietilä, Laura Lehtinen, Kaisa Huhtinen, Erika Gucciardo, Johanna Hynninen, Sakari Hietanen, Seija Grénman, Päivi M. Ojala, Olli Carpén, Kaisa Lehti
Software Mentions: 2
Published: over 5 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: about 5 years ago

10.1038/s41598-020-75835-7

A versatile toolbox for semi-automatic cell-by-cell object-based colocalization analysis
Cited by: 19
Author(s): Anders Lunde, Joel C. Glover
Software Mentions: 2
Published: almost 6 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: over 9 years ago

10.1038/s41598-020-58397-6

Active nuclear import of the deacetylase Sirtuin-2 is controlled by its C-terminus and importins
Cited by: 19
Author(s): Matthew J. G. Eldridge, Jorge A. Pereira, Francis Impens, Mélanie Hamon
Software Mentions: 2
Published: over 6 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

10.1038/s41598-019-50334-6

The human long non-coding RNA gene RMRP has pleiotropic effects and regulates cell-cycle progression at G2
Cited by: 20
Author(s): Svetlana Vakkilainen, Tiina Skoog, Elisabet Einarsdottir, Anna Middleton, Minna Pekkinen, Tiina Öhman, Shintaro Katayama, Kaarel Krjutškov, Panu E. Kovanen, Markku Varjosalo, Arne Lindqvist, Juha Kere, Outi Mäkitie
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-68567-1

Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach
Cited by: 12
Author(s): Benedikt von der Heyde, Anastasia Emmanouilidou, Eugenia Mazzaferro, Silvia Vicenzi, Ida Höijer, Tiffany Klingström, Sitaf Jumaa, Olga Dethlefsen, Harold Snieder, Eco J. C. de Geus, Adam Ameur, Erik Ingelsson, Amin Allalou, Hannah L. Brooke, Marcel den Hoed
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-021-82752-w

Integrins mediate placental extracellular vesicle trafficking to lung and liver in vivo
Cited by: 27
Author(s): Sean L. Nguyen, Soo Hyun Ahn, Jacob W. Greenberg, Benjamin W. Collaer, Dalen Agnew, Ritu Arora, Margaret G. Petroff
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-90569-w

Gene expression alterations in salivary gland epithelia of Sjögren’s syndrome patients are associated with clinical and histopathological manifestations
Cited by: 8
Author(s): Ariana Dela Cruz, Vinay K. Kartha, Andrew Tilston-Lünel, Ruifa Mi, Taylor L. Reynolds, Michaël Mingueneau, Stefano Monti, Janicke Liaaen Jensen, Kathrine Skarstein, Xaralabos Varelas, Maria A. Kukuruzinska
Software Mentions: 2
Published: about 5 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: almost 7 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

10.3390/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

10.1038/s41598-021-92830-8

Serine residues 726 and 780 have nonredundant roles regulating STAT5a activity in luminal breast cancer
Cited by: 6
Author(s): Alicia E. Woock, Jacqueline M Grible, Amy L. Olex, J. Chuck Harrell, Patricija Zot, Michael O. Idowu, Charles V. Clevenger
Software Mentions: 2
Published: about 5 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: over 5 years ago

10.1038/s41598-020-78764-7

Leaf proteome modulation and cytological features of seagrass Cymodocea nodosa in response to long-term high CO2 exposure in volcanic vents
Cited by: 2
Author(s): Amalia Piro, Letizia Bernardo, Ilia Anna Serra, Isabel Barrote, Irene Olivé, Monya M. Costa, Luigi Lucini, Rui Santos, Silvia Mazzuca, João Silva
Software Mentions: 2
Published: over 5 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: about 5 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: about 10 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: almost 6 years ago

10.1038/s41598-019-48929-0

A high-throughput screen to identify novel synthetic lethal compounds for the treatment of E-cadherin-deficient cells
Cited by: 13
Author(s): Henry Beetham, Augustine Chen, Bryony J. Telford, Andrew Single, Kate E. Jarman, Kurt Lackovic, Andreas Luxenburger, Parry Guilford
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-47659-7

Colorectal cancer cells respond differentially to autophagy inhibition in vivo
Cited by: 42
Author(s): Annie Lauzier, Josiann Normandeau-Guimond, Vanessa Vaillancourt-Lavigueur, Vincent Boivin, Martine Charbonneau, Nathalie Rivard, Michelle S. Scott, Claire M. Dubois, Steve Jean
Software Mentions: 2
Published: about 7 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: about 5 years ago

10.1038/s41598-021-87494-3

Lymphedema alters lipolytic, lipogenic, immune and angiogenic properties of adipose tissue: a hypothesis-generating study in breast cancer survivors
Cited by: 12
Author(s): Michal Koc, Martin Wald, Zuzana Varaliová, Barbora Ondrůjová, Terezie Čížková, Milan Brychta, Jana Kračmerová, Lenka Beranová, Jan Pala, Veronika Šrámková, Michaela Šiklová, Jan Gojda, Lenka Rossmeislová
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-57691-7

A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules
Cited by: 26
Author(s): Natasha L. Patel-Murray, Miriam Adam, Nhan Huynh, Brook T. Wassie, Pamela Milani, Ernest Fraenkel
Software Mentions: 2
Published: over 6 years ago

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