pypi: CellProfiler | Projects | Ecosyste.ms: Papers

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

10.1245/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/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

10.12688/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

10.1002/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.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

10.1186/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

10.1186/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

10.15252/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

10.1038/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

10.1186/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

10.1242/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

10.15252/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: almost 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

10.1038/s41598-019-45284-y

Dynamic adaptation of mesenchymal stem cell physiology upon exposure to surface micropatterns
Cited by: 31
Author(s): Nick R. M. Beijer, Zarina Nauryzgaliyeva, Estela M. Arteaga, Laurent Pieuchot, Karine Anselme, Jeroen van de Peppel, Aliaksei Vasilevich, Nathalie Gröen, Nadia Roumans, Dennie G. A. J. Hebels, Jan de Boer
Software Mentions: 2
Published: about 7 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: about 5 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

10.15252/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: almost 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: almost 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: over 5 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/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

10.15252/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

10.1371/journal.pone.0200027

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

10.3390/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/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

10.1016/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

10.3390/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

10.1371/journal.pone.0239047

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

10.1371/journal.pone.0078320

Mice Deficient in Sfrp1 Exhibit Increased Adiposity, Dysregulated Glucose Metabolism, and Enhanced Macrophage Infiltration
Cited by: 39
Author(s): Kelly J Gauger, Lotfi M. Bassa, Elizabeth Henchey, Josephine Wyman, Brooke Bentley, Melissa Brown, Akihiko Shimono, Sallie S. Schneider
Software Mentions: 2
Published: over 12 years ago

10.1186/s12885-017-3453-8

CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer
Cited by: 30
Author(s): Olafur A. Stefansson, Stefan Hermanowicz, Jasper van der Horst, Hólmfríður Hilmarsdóttir, Zuzanna Staszczak, Jón G. Jonasson, Laufey Tryggvadóttír, Thorkell Gudjonsson, Stefan Sigurdsson
Software Mentions: 2
Published: about 9 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/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: about 6 years ago

10.1186/s12885-019-5813-z

Master regulator analysis of paragangliomas carrying SDHx, VHL, or MAML3 genetic alterations
Cited by: 6
Author(s): John A. Smestad, Jim Maher
Software Mentions: 2
Published: about 7 years ago

10.1155/2019/7232781

Automated and Reproducible Detection of Vascular Endothelial Growth Factor (VEGF) in Renal Tissue Sections
Cited by: 1
Author(s): Nayana Damiani Macedo, Aline Rodrigues Buzin, Isabela Bastos de Araujo, Breno Valentim Nogueira, Tadeu Uggere de Andrade, Denise Coutinho Endringer, Dominik Lenz
Software Mentions: 2
Published: over 7 years ago

10.1016/j.ymeth.2016.08.018

An open-source solution for advanced imaging flow cytometry data analysis using machine learning
Cited by: 77
Author(s): Holger Hennig, Paul Rees, Thomas Blasi, Lee Kamentsky, Jia‐Jang Hung, David Dao, Anne E. Carpenter, Andrew Filby
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0153022

SAMA: A Method for 3D Morphological Analysis
Cited by: 11
Author(s): Tessie Paulose, Maël Montévil, Lucía Speroni, F. Cerruti, Carlos Sonnenschein, Ana M. Soto
Software Mentions: 2
Published: over 10 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

10.1186/1471-2105-11-30

Enhanced CellClassifier: a multi-class classification tool for microscopy images
Cited by: 80
Author(s): Benjamin Misselwitz, Gerhard Strittmatter, Balamurugan Periaswamy, Markus C. Schlumberger, Rout Samuel, Péter Horváth, Karol Kozak, Wolf‐Dietrich Hardt
Software Mentions: 2
Published: over 16 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

10.7554/eLife.24060

Systematic morphological profiling of human gene and allele function via Cell Painting
Cited by: 110
Author(s): Mohammad Hossein Rohban, Shantanu Singh, Xiaoyun Wu, Julia B Berthet, Mark-Anthony Bray, Yashaswi Shrestha, Xaralabos Varelas, Jesse S. Boehm, Anne E. Carpenter
Software Mentions: 2
Published: over 9 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

10.15252/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

10.1371/journal.pone.0020148

Simultaneous Visualization of Both Signaling Cascade Activity and End-Point Gene Expression in Single Cells
Cited by: 14
Author(s): Irene Weibrecht, Ida Grundberg, Mats Nilsson, Ola Söderberg
Software Mentions: 2
Published: about 15 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

10.1186/s12860-018-0166-z

Novel roles for scleraxis in regulating adult tenocyte function
Cited by: 35
Author(s): Anne E. C. Nichols, Robert E. Settlage, Stephen R. Werre, Linda A. Dahlgren
Software Mentions: 2
Published: about 8 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

10.3390/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

10.1371/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

10.1371/journal.pone.0015535

Quantitative High-Throughput Screening Identifies 8-Hydroxyquinolines as Cell-Active Histone Demethylase Inhibitors
Cited by: 195
Author(s): Oliver N. King, Xuan Shirley Li, Masaaki Sakurai, Akane Kawamura, Nathan R. Rose, Stanley S. Ng, Amy Quinn, Ganesha Rai, Bryan T. Mott, Paul J. Beswick, Robert J. Klose, U. Oppermann, Ajit Jadhav, Tom D. Heightman, David J. Maloney, Christopher J. Schofield, Anton Simeonov
Software Mentions: 2
Published: over 15 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

10.1007/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.0255096

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

10.1016/j.molcel.2019.08.005

Polyamines Control eIF5A Hypusination, TFEB Translation, and Autophagy to Reverse B Cell Senescence
Cited by: 189
Author(s): Hanlin Zhang, Ghada Alsaleh, Jack Feltham, Yizhe Sun, Gennaro Napolitano, Thomas Riffelmacher, P. David Charles, Lisa Frau, Philip Hublitz, Zhanru Yu, Shabaz Mohammed, Andrea Ballabio, Stefan Balabanov, Jane Mellor, Anna Katharina Simon
Software Mentions: 2
Published: almost 7 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.0245653

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

10.1016/j.molcel.2018.02.023

Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability
Cited by: 130
Author(s): Dominika Kwaśna, S.A. Abdul Rehman, N. Jayaprakash, S. Matthews, Ross Madden, Virginia De Cesare, Simone Weidlich, Satpal Virdee, Ivan Ahel, Ian Gibbs-Seymour, Yogesh Kulathu
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

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Papers Mentioning CellProfiler 1,504