Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: CellProfiler
https://packages.ecosyste.ms/registries/pypi.org/packages/CellProfiler
17 versions
Latest release: 9 months ago
534 downloads last month
Papers Mentioning CellProfiler 1,504
10.3390/ijms21197069
Human Fibroblasts In Vitro Exposed to 2.45 GHz Continuous and Pulsed Wave Signals: Evaluation of Biological Effects with a Multimethodological ApproachCited by: 7
Author(s): Elisa Regalbuto, Anna Anselmo, Stefania De Sanctis, Valeria Franchini, Florigio Lista, Monica Benvenuto, Roberto Bei, Laura Masuelli, G. D’Inzeo, Alessandra Paffi, Eugenio Trodella, Antonella Sgura
Software Mentions: 4
Published: over 3 years ago
10.7554/eLife.35786
Human axial progenitors generate trunk neural crest cells in vitroCited by: 70
Author(s): Thomas J.R. Frith, Ilaria Granata, Matthew Wind, Erin Stout, Oliver Thompson, Katrin Neumann, Dylan Stavish, Paul R. Heath, Daniel Ortmann, James Hackland, Konstantinos Anastassiadis, Mina Gouti, James Briscoe, Valerie Wilson, Stuart L. Johnson, Marysia Placzek, Mario Rosario Guarracino, Peter W. Andrews, Anestis Tsakiridis
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pone.0110289
SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide ImagesCited by: 23
Author(s): Bastiaan G. L. Nelissen, Joost A. van Herwaarden, Frans L. Moll, Paul J. van Diest, Gérard Pasterkamp
Software Mentions: 4
Published: over 9 years ago
10.7554/eLife.40162
Motion sensing superpixels (MOSES) is a systematic computational framework to quantify and discover cellular motion phenotypesCited by: 8
Author(s): Felix Zhou, Carlos Ruiz‐Puig, Richard Owen, Michael J. White, Jens Rittscher, Xin Lü
Software Mentions: 4
Published: about 5 years ago
10.1007/s00204-018-2178-z
Dynamic imaging of adaptive stress response pathway activation for prediction of drug induced liver injuryCited by: 45
Author(s): Steven Wink, Steven Hiemstra, Suzanna Huppelschoten, Janna E. Klip, Bob van de Water
Software Mentions: 4
Published: about 6 years ago
10.1371/journal.pone.0218230
Atoh8 acts as a regulator of chondrocyte proliferation and differentiation in endochondral bonesCited by: 10
Author(s): Nadine Schroeder, Manuela Wuelling, Daniel Hoffmann, Beate Brand‐Saberi, Andrea Vortkamp
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0242677
Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeatsCited by: 16
Author(s): Sara Sajko, Irina Grishkovskaya, Július Košťan, Melissa A. Graewert, Kim Setiawan, Linda Trübestein, Korbinian Niedermüller, Charlotte Gehin, Antonio Sponga, Martin Puchinger, Anne‐Claude Gavin, Thomas A. Leonard, D. I. Svergun, Terry Smith, Brooke Morriswood, Kristina Djinović-Carugo
Software Mentions: 4
Published: over 3 years ago
10.1186/s12915-020-00874-5
Automated identification of the mouse brain’s spatial compartments from in situ sequencing dataCited by: 16
Author(s): Gabriele Partel, Markus M. Hilscher, Milli Giorgia, Leslie Solorzano, Anna H. Klemm, Mats Nilsson, Carolina Wählby
Software Mentions: 4
Published: over 3 years ago
10.1093/molbev/msaa172
Gene Loss Predictably Drives Evolutionary AdaptationCited by: 49
Author(s): Jana Helsen, Karin Voordeckers, Laura Vanderwaeren, Toon Santermans, Maria Tsontaki, Kevin J. Verstrepen, Rob Jelier
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41598-020-64623-y
Comparative analysis of MACROD1, MACROD2 and TARG1 expression, localisation and interactomeCited by: 20
Author(s): Roko Žaja, Gülcan Aydin, Barbara E. Lippok, Regina Feederle, Bernhard Lüscher, Karla L. H. Feijs
Software Mentions: 4
Published: about 4 years ago
10.1007/s00204-021-03127-8
Fluorescent tagging of endogenous Heme oxygenase-1 in human induced pluripotent stem cells for high content imaging of oxidative stress in various differentiated lineagesCited by: 11
Author(s): Kirsten E. Snijders, András Fehér, Zsuzsanna Táncos, István Bock, Annamária Téglási, Linda van den Berk, Marije Niemeijer, Peter Bouwman, Sylvia E. Le Dévédec, Martijn J. Moné, Rob Van Rossom, Manoj Kumar, Anja Wilmes, Paul Jennings, Cathérine Verfaillie, Julianna Kobolák, Bas ter Braak, András Dinnyés, Bob van de Water
Software Mentions: 4
Published: over 2 years ago
10.3390/app10186187
ACDC: Automated Cell Detection and Counting for Time-Lapse Fluorescence MicroscopyCited by: 7
Author(s): Leonardo Rundo, Andrea Tangherloni, Darren R. Tyson, Riccardo Betta, Carmelo Militello, Simone Spolaor, Marco S. Nobile, Daniela Besozzi, Alexander L R Lubbock, Vito Quaranta, Giancarlo Mauri, Carlos F. López, Paolo Cazzaniga
Software Mentions: 4
Published: over 3 years ago
10.1186/1471-2105-14-S16-S4
cellXpress: a fast and user-friendly software platform for profiling cellular phenotypesCited by: 25
Author(s): Danai Laksameethanasan, Rui Zhen Tan, Geraldine Wei-Ling Toh, Lit‐Hsin Loo
Software Mentions: 4
Published: over 10 years ago
10.12688/wellcomeopenres.15232.2
Genome-wide CRISPR screening identifies new regulators of glycoprotein secretionCited by: 2
Author(s): Stephanie Popa, Julien Villeneuve, Sarah E. Stewart, Esther Perez Garcia, Anna Petrunkina Harrison, Kévin Moreau
Software Mentions: 4
Published: over 4 years ago
10.1038/s41597-021-00933-8
Cric searchable image database as a public platform for conventional pap smear cytology dataCited by: 19
Author(s): Mariana T. Rezende, Raniere Silva, Fagner de O. Bernardo, Alessandra Hermógenes Gomes Tobias, Paulo H. C. Oliveira, Tales Mota Machado, Caio S. Costa, Fátima N. S. de Medeiros, Daniela Ushizima, Cláudia Martins Carneiro, Andrea Gomes Campos Bianchi
Software Mentions: 4
Published: almost 3 years ago
10.1038/s42003-021-02166-2
Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and diseaseCited by: 5
Author(s): Mayar Allam, Thomas Hu, Shuangyi Cai, Krishnan Laxminarayanan, Robert B. Hughley, Ahmet F. Coşkun
Software Mentions: 4
Published: almost 3 years ago
10.3389/fcimb.2021.678482
Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic CellsCited by: 38
Author(s): Syairah Hanan Shaharuddin, Victoria Wang, Reginaldo da Silva Santos, Andrew Gross, Yizhou Wang, Harneet Jawanda, Yi Zhang, Wohaib Hasan, Gustavo García, Vaithilingaraja Arumugaswami, Dhruv Sareen
Software Mentions: 4
Published: almost 3 years ago
10.1038/s41597-019-0051-4
Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological mediaCited by: 14
Author(s): Saugat Poudel, Hannah Tsunemoto, Michael J. Meehan, Richard Szubin, Connor A. Olson, Anne Lamsa, Yara Seif, Nicholas Dillon, Alison Vrbanac, Joseph Sugie, Samira Dahesh, Jonathan M. Monk, Pieter C. Dorrestein, Joseph Pogliano, Rob Knight, Victor Nizet, Bernhard Ø. Palsson, Adam M. Feist
Software Mentions: 4
Published: about 5 years ago
10.1242/bio.052936
A fully automated deep learning pipeline for high-throughput colony segmentation and classificationCited by: 4
Author(s): Sarah H. Carl, Lea Duempelmann, Yukiko Shimada, Marc Bühler
Software Mentions: 4
Published: almost 4 years ago
10.3389/fgene.2019.00308
661W Photoreceptor Cell Line as a Cell Model for Studying Retinal CiliopathiesCited by: 37
Author(s): Gabrielle Wheway, Liliya Nazlamova, Dann Turner, Stephen Cross
Software Mentions: 4
Published: about 5 years ago
10.1186/s13014-021-01853-y
Complete response to neoadjuvant chemoradiotherapy in rectal cancer is associated with RAS/AKT mutations and high tumour mutational burdenCited by: 4
Author(s): Joanne Stockton, Louise Tee, Celina M. Whalley, Jonathan James, Mark Dilworth, Rachel Wheat, Thomas Nieto, Ian Geh, João D. Barros-Silva, Andrew D Beggs
Software Mentions: 4
Published: almost 3 years ago
10.1186/s12859-021-04117-4
MAPS: machine-assisted phenotype scoring enables rapid functional assessment of genetic variants by high-content microscopyCited by: 3
Author(s): Jesse T. Chao, Calvin D. Roskelley, Christopher Loewen
Software Mentions: 4
Published: about 3 years ago
10.1093/bioinformatics/btab178
PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samplesCited by: 13
Author(s): Antti Häkkinen, Kaiyang Zhang, Amjad Alkodsi, Noora Andersson, Erdoğan Pekcan Erkan, Jun Dai, Katja Kaipio, Tarja Lamminen, Naziha Mansuri, Kaisa Huhtinen, Anna Vähärautio, Olli Carpén, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 4
Published: about 3 years ago
10.1093/bioinformatics/btw390
CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image setsCited by: 106
Author(s): David Dao, Adam Fraser, Jia‐Jang Hung, Vebjorn Ljosa, Shantanu Singh, Anne E. Carpenter
Software Mentions: 4
Published: almost 8 years ago
10.3389/frai.2021.754641
Deep Learning of Histopathology Images at the Single Cell LevelCited by: 19
Author(s): Kyubum Lee, John H. Lockhart, Mengyu Xie, Ritu Chaudhary, Robbert J.C. Slebos, Elsa R. Flores, Christine H. Chung, Aik Choon Tan
Software Mentions: 4
Published: over 2 years ago
10.1038/s41598-020-78081-z
Adaptive selection drives TRPP3 loss-of-function in an Ethiopian populationCited by: 0
Author(s): Sandra M. Walsh, Mercè Izquierdo-Serra, Sandra Acosta, Albert Edo, María C. Estévez Lloret, Roser Moret, Elena Bosch, Baldo Oliva, Jaume Bertranpetit, José M. Fernández-Fernández
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1007348
Learning unsupervised feature representations for single cell microscopy images with paired cell inpaintingCited by: 64
Author(s): Alex X. Lu, Oren Kraus, Sam Cooper, Alan M. Moses
Software Mentions: 4
Published: over 4 years ago
10.1016/j.molcel.2021.04.028
Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human diseaseCited by: 46
Author(s): Evgeniia Prokhorova, Thomas Agnew, Anne R. Wondisford, Michael Tellier, Nicole Kaminski, Danique Beijer, James Holder, Joséphine Groslambert, Marcin Suskiewicz, Kang Zhu, Julia M Reber, Sarah C. Krassnig, Luca Palazzo, Shona Murphy, Michael L. Nielsen, Aswin Mangerich, Dragana Ahel, Jonathan Baets, Roderick J. O’Sullivan, Ivan Ahel
Software Mentions: 4
Published: almost 3 years ago
10.1186/s12859-019-2880-8
Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparisonCited by: 126
Author(s): Pavel Kopel, Jan Balvan, Josef Jaroš, Florian Jug, Radim Kolář, Michal Masařík, Jaromír Gumulec
Software Mentions: 4
Published: almost 5 years ago
10.1111/mmi.14417
BactMAP: An R package for integrating, analyzing and visualizing bacterial microscopy dataCited by: 23
Author(s): Renske van Raaphorst, Morten Kjos, Jan‐Willem Veening
Software Mentions: 4
Published: over 4 years ago
10.1007/s00018-017-2695-6
Downregulation of p53 drives autophagy during human trophoblast differentiationCited by: 23
Author(s): Martin Gauster, Sabine Maninger, Monika Siwetz, Alexander Deutsch, Amin El‐Heliebi, Dagmar Kolb-Lenz, Ursula Hiden, Gernot Desoyé, Florian Herse, Andreas Prokesch
Software Mentions: 4
Published: over 6 years ago
10.1038/s41598-018-20856-6
A cleavage product of Polycystin-1 is a mitochondrial matrix protein that affects mitochondria morphology and function when heterologously expressedCited by: 68
Author(s): Cheng-Chao Lin, Mahiro Kurashige, Yi Liu, Takeshi Terabayashi, Yu Ishimoto, Tanchun Wang, Vineet Choudhary, Ryan P. Hobbs, Li-Ka Liu, Ping-Hsien Lee, Patricia Outeda, Fang Zhou, Nicholas P. Restifo, Terry Watnick, Haruna Kawano, Shigeo Horie, William A. Prinz, Hong Xu, Luís F. Menezes, Gregory G. Germino
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pgen.1008680
Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybridsCited by: 24
Author(s): Quinn K. Langdon, David Peris, Juan Ignacio Eizaguirre, Dana A. Opulente, Kelly V. Buh, Kayla Sylvester, Martin Jarzyna, María Esther Rodríguez, Christian A. Lopes, Diego Libkind, Chris Todd Hittinger
Software Mentions: 4
Published: about 4 years ago
10.1007/s00204-016-1781-0
High-content imaging-based BAC-GFP toxicity pathway reporters to assess chemical adversity liabilitiesCited by: 50
Author(s): Steven Wink, Steven Hiemstra, Bram Herpers, Bob van de Water
Software Mentions: 4
Published: almost 8 years ago
10.1186/s40170-021-00257-6
High-resolution spatiotemporal pHe and pO2 imaging in head and neck and oesophageal carcinoma cellsCited by: 2
Author(s): Alexandra Blancke Soares, Robert J. Meier, Gregor Liebsch, Sabina Schwenk‐Zieger, Martin E. Kirmaier, Sebastian Theurich, Magdalena Widmann, Martin Canis, Olivier Gires, Frank Haubner
Software Mentions: 4
Published: about 3 years ago
10.1186/1746-1596-8-34
CognitionMaster: an object-based image analysis frameworkCited by: 41
Author(s): Stephan Wienert, Daniel Heim, Manato Kotani, Bjoern Lindequist, Albrecht Stenzinger, Masaru Ishii, Peter Hufnagl, Michael Beil, Manfred Dietel, Carsten Denkert, Frederick Klauschen
Software Mentions: 4
Published: about 11 years ago
10.3389/fonc.2021.636451
Integrative Analysis of Histopathological Images and Genomic Data in Colon AdenocarcinomaCited by: 7
Author(s): Hui Li, Linyan Chen, Hao Zeng, Qimeng Liao, Jianrui Ji, Xuelei Ma
Software Mentions: 4
Published: over 2 years ago
10.1186/1471-2105-12-126
STSE: Spatio-Temporal Simulation Environment Dedicated to BiologyCited by: 9
Author(s): Szymon Stoma, Martina Fröhlich, Susanne Gerber, Edda Klipp
Software Mentions: 3
Published: about 13 years ago
10.3390/cancers13184600
Role of Artificial Intelligence in the Early Diagnosis of Oral Cancer. A Scoping ReviewCited by: 37
Author(s): María García-Pola, Eduardo Pons-Fuster, Carlota Suárez-Fernández, Juan M. Seoane-Romero, Amparo Romero-Méndez, Pı́a López-Jornet
Software Mentions: 3
Published: over 2 years ago
10.1186/s12902-019-0442-8
CRISPR-Cas9-mediated knockout of SPRY2 in human hepatocytes leads to increased glucose uptake and lipid droplet accumulationCited by: 5
Author(s): Naomi L. Cook, Milos Pjanic, Andrew Emmerich, Abhiram Rao, Susanne Hetty, Joshua Knowles, Thomas Quertermous, Casimiro Castillejo-López, Erik Ingelsson
Software Mentions: 3
Published: over 4 years ago
10.1186/s40478-021-01148-z
TDP-43 proteinopathy alters the ribosome association of multiple mRNAs including the glypican Dally-like protein (Dlp)/GPC6Cited by: 10
Author(s): Erik M. Lehmkuhl, Suvithanandhini Loganathan, Eric Alsop, Alexander D. Blythe, Tina Kovalik, Nicholas P. Mortimore, Dianne Barrameda, Chuol Kueth, Randall J. Eck, Bhavani Bagevalu Siddegowda, Archi Joardar, Hannah E. Ball, Maria E. Macias, Robert Bowser, Kendall Van Keuren‐Jensen, Daniela C. Zarnescu
Software Mentions: 3
Published: about 3 years ago
10.3390/nu12030624
Alliin, An Allium sativum Nutraceutical, Reduces Metaflammation Markers in DIO MiceCited by: 17
Author(s): Marina A. Sánchez-Sánchez, Adelaida Sara Minia Zepeda-Morales, Lucrecia Carrera-Quintanar, Juan Manuel Viveros–Paredes, Noel N Franco-Arroyo, Marisol Godínez-Rubí, Daniel Ortuño-Sahagún, Rocío Ivette López-Roa
Software Mentions: 3
Published: about 4 years ago
10.1523/ENEURO.0202-20.2020
Sex-Specific Role for Dopamine Receptor D2 in Dorsal Raphe Serotonergic Neuron Modulation of Defensive Acoustic Startle and Dominance BehaviorCited by: 6
Author(s): Krissy A Lyon, Benjamin D. Rood, Lorna Wu, Rebecca A. Senft, Lisa V. Goodrich, Susan M. Dymecki
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0027886
Extracting Fluorescent Reporter Time Courses of Cell Lineages from High-Throughput Microscopy at Low Temporal ResolutionCited by: 28
Author(s): Michael Downey, Danuta M. Jeziorska, Sascha Ott, T. Katherine Tamai, Georgy Koentges, Keith W. Vance, Till Bretschneider
Software Mentions: 3
Published: over 12 years ago
10.1371/journal.pone.0115907
High Reproducibility of Histological Characterization by Whole Virtual Slide Quantification; An Example Using Carotid Plaque SpecimensCited by: 11
Author(s): Joyce E. P. Vrijenhoek, Bastiaan G. L. Nelissen, Evelyn Velema, Kristy Vons, Jean‐Paul P.M. de Vries, Marinus J.C. Eijkemans, Hester M. den Ruijter, Gert J. de Borst, Frans L. Moll, Gérard Pasterkamp
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0237972
Interactive machine learning for fast and robust cell profilingCited by: 1
Author(s): Lisa Laux, Marie F.A. Cutiongco, Nikolaj Gadegaard, Bjørn Sand Jensen
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2164-15-1162
Simultaneous analysis of large-scale RNAi screens for pathogen entryCited by: 37
Author(s): Pauli Rämö, Anna Drewek, Cécile Arrieumerlou, Niko Beerenwinkel, Houchaïma Ben-Tekaya, Bettina Cardel, Alain Casanova, Raquel Conde-Álvarez, Pascale Cossart, Gábor Csúcs, Simone Eicher, Mario Emmenlauer, Urs F. Greber, Wolf‐Dietrich Hardt, Ari Helenius, Christoph Kasper, Andreas M. Kaufmann, Saskia Kreibich, Andreas Kühbacher, Péter Z. Kunszt, Shyan Huey Low, Jason Mercer, Daria Mudrak, Simone Muntwiler, Lucas Pelkmans, Javier Pizarro‐Cerdá, Michael Podvinec, Eva Pujadas, Bernd Rinn, Vincent Rouilly, Fabian Schmich, Juliane Siebourg‐Polster, Berend Snijder, Michael Stebler, Gabriel Studer, Ewa Szczurek, Matthias C. Truttmann, Christian von Mering, Andreas Vonderheit, Artur Yakimovich, Peter Bühlmann, Christoph Dehio
Software Mentions: 3
Published: over 9 years ago
10.21307/jofnem-2020-108
Competitive fitness analysis using Convolutional Neural NetworkCited by: 1
Author(s): Joanna Palka, Krzysztof Fiok, Weronika Antoł, Zofia M. Prokop
Software Mentions: 3
Published: over 4 years ago
10.18632/oncotarget.12298
Case-specific potentiation of glioblastoma drugs by pterostilbeneCited by: 16
Author(s): Linnéa Schmidt, Sathishkumar Baskaran, Patrik Johansson, Narendra Padhan, Damian J. Matuszewski, Lydia C. Green, Ludmila Elfineh, Shimei Wee, Maria Häggblad, Ulf Märtens, Bengt Westermark, Karin Forsberg-Nilsson, Lene Uhrbom, Lena Claesson‐Welsh, Michael Andäng, Ida‐Maria Sintorn, Bo Lundgren, Ingrid Lönnstedt, Cecilia Krona, Sven Nelander
Software Mentions: 3
Published: over 7 years ago
10.3390/ijms21103672
Sonic Hedgehog and Triiodothyronine Pathway Interact in Mouse Embryonic Neural Stem CellsCited by: 1
Author(s): Pavel Ostašov, Jan Tůma, Pavel Pitule, Jiřı́ Moravec, Zbyněk Houdek, F Vožeh, Milena Králíčková, Jan Cendelín, Václav Babuška
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0116329
IQM: An Extensible and Portable Open Source Application for Image and Signal Analysis in JavaCited by: 28
Author(s): Philipp Kainz, Michael Mayrhofer-Reinhartshuber, Helmut Ahammer
Software Mentions: 3
Published: over 9 years ago
10.3390/ijms22031167
Glutamine Uptake via SNAT6 and Caveolin Regulates Glutamine–Glutamate CycleCited by: 14
Author(s): Nikhil R. Gandasi, Vasiliki Arapi, Michel‐Edwar Mickael, Prajakta A. Belekar, Louise Granlund, Lakshmi Kothegala, Robert Fredriksson, Sonchita Bagchi
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0215337
FluoroCellTrack: An algorithm for automated analysis of high-throughput droplet microfluidic dataCited by: 22
Author(s): Manibarathi Vaithiyanathan, Nora Safa, Adam T. Melvin
Software Mentions: 3
Published: about 5 years ago
10.1186/1472-6750-7-66
High content image analysis for human H4 neuroglioma cells exposed to CuO nanoparticlesCited by: 44
Author(s): Fuhai Li, Xiaobo Zhou, Jinmin Zhu, Jinwen Ma, Xudong Huang, Stephen T.C. Wong
Software Mentions: 3
Published: over 16 years ago
10.7554/eLife.23468
A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylationCited by: 29
Author(s): Meng Amy Li, Paulo Amaral, Priscilla Cheung, Jan H. Bergmann, Masaki Kinoshita, Tüzer Kalkan, Markus Ralser, Sam Robson, Ferdinand von Meyenn, Maike Paramor, Fengtang Yang, Caifu Chen, Jennifer Nichols, David L. Spector, Tony Kouzarides, Lin He, Austin Smith
Software Mentions: 3
Published: almost 7 years ago
10.1371/journal.pone.0163453
Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine ExperimentsCited by: 31
Author(s): Christian Carsten Sachs, Alexander Grünberger, Stefan Helfrich, Christopher Probst, Wolfgang Wiechert, Dietrich Kohlheyer, Katharina Nöh
Software Mentions: 3
Published: over 7 years ago
10.3390/ijms22179595
Regulation of the Golgi Apparatus by p38 and JNK Kinases during Cellular Stress ResponsesCited by: 6
Author(s): Cathrine Nordgaard, Maxim A. X. Tollenaere, Ana Martinez Del Val, Dorte B. Bekker-Jensen, Melanie Blasius, Jesper V. Olsen, Simon Bekker‐Jensen
Software Mentions: 3
Published: over 2 years ago
10.1186/1751-0473-8-16
CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentationCited by: 76
Author(s): Erlend Hodneland, Tanja Kögel, Dominik Frei, Hans‐Hermann Gerdes, Arvid Lundervold
Software Mentions: 3
Published: almost 11 years ago
10.1016/j.stemcr.2021.01.013
Unraveling the Developmental Roadmap toward Human Brown Adipose TissueCited by: 9
Author(s): Stefania Carobbio, Anne Claire Guenantin, Myriam Bahri, Sonia Rodríguez-Fdez, Floris Honig, Ioannis Kamzolas, Isabella Samuelson, Kathleen Long, Sherine Awad, Dunja Lukovic, Slaven Erceg, Andrew Bassett, Sasha Mendjan, Ludovic Vallier, Barry Rosen, Davide Chiarugi, António Vidal-Puig
Software Mentions: 3
Published: about 3 years ago
10.1038/s41598-021-91846-4
High-resolution transcriptional landscape of xeno-free human induced pluripotent stem cell-derived cerebellar organoidsCited by: 28
Author(s): Samuel Nayler, Devika Agarwal, Fabiola Curion, Rory Bowden, Esther B. E. Becker
Software Mentions: 3
Published: almost 3 years ago
10.1038/s41598-021-86087-4
Microdroplet-based one-step RT-PCR for ultrahigh throughput single-cell multiplex gene expression analysis and rare cell detectionCited by: 13
Author(s): Jennifer Ma, Gary Tran, Alwin M. D. Wan, Elton T. Young, Eugenia Kumacheva, Norman N. Iscove, Peter W. Zandstra
Software Mentions: 3
Published: about 3 years ago
10.1007/s00204-020-02792-5
Multiparametric assessment of mitochondrial respiratory inhibition in HepG2 and RPTEC/TERT1 cells using a panel of mitochondrial targeting agrochemicalsCited by: 26
Author(s): Wanda van der Stel, Giada Carta, Julie Eakins, Salihanur Darici, Johannes Delp, Anna Forsby, Susanne Hougaard Bennekou, Iain Gardner, Marcel Leist, Erik H.J. Danen, Paul Walker, Bob van de Water, Paul Jennings
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-021-84887-2
Slc1a3-2A-CreERT2 mice reveal unique features of Bergmann glia and augment a growing collection of Cre drivers and effectors in the 129S4 genetic backgroundCited by: 9
Author(s): Lech Kaczmarczyk, Nicole Reichenbach, Nelli Blank, Maria Jonson, Lars Dittrich, Gabor C. Petzold, Walker S. Jackson
Software Mentions: 3
Published: about 3 years ago
10.7554/eLife.36330
TFAP2 transcription factors are regulators of lipid droplet biogenesisCited by: 31
Author(s): Cameron C. Scott, Stefania Vossio, Jacques Rougemont, Jean Grüenberg
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-019-53428-3
Immune cell type, cell activation, and single cell heterogeneity revealed by label-free optical methodsCited by: 10
Author(s): Nicolas Pavillon, Nicholas I. Smith
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-019-50010-9
Cell Type Classification and Unsupervised Morphological Phenotyping From Low-Resolution Images Using Deep LearningCited by: 30
Author(s): Kai Yao, Nash D. Rochman, Sean X. Sun
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-020-59988-z
A salivary metabolite signature that reflects gingival host-microbe interactions: instability predicts gingivitis susceptibilityCited by: 0
Author(s): Marcela M. Fernandez-Gutierrez, Sultan Imangaliyev, Andrei Prodan, Bruno G. Loos, Bart J. F. Keijser, Michiel Kleerebezem
Software Mentions: 3
Published: about 4 years ago
10.1038/s41598-018-31924-2
3D Shape Modeling for Cell Nuclear Morphological Analysis and ClassificationCited by: 21
Author(s): Alexandr A. Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, David S. Dilworth, Syed Sameed Husain, Jeffrey R. de Wet, Gerald A. Higgins, Gen Zheng, Amy L. Creekmore, John W. Wiley, James E. Verdone, Robert W. Veltri, Kenneth J. Pienta, Donald S. Coffey, Brian D. Athey, Ivo D. Dinov
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pgen.1008083
The dPix-Git complex is essential to coordinate epithelial morphogenesis and regulate myosin during Drosophila egg chamber developmentCited by: 6
Author(s): Lucas Dent, Samuel A. Manning, Benjamin Kroeger, Audrey Miller Williams, Abdul Jabbar Saiful Hilmi, Luke Crea, Shu Kondo, Sally Horne‐Badovinac, Kieran F. Harvey
Software Mentions: 3
Published: almost 5 years ago
10.1038/s41598-018-35383-7
Vasoinhibin comprises a three-helix bundle and its antiangiogenic domain is located within the first 79 residuesCited by: 13
Author(s): Juan Pablo Robles, Magdalena Zamora, José Luis Velasco-Bolom, Miriam Tovar, Ramón Garduño‐Juárez, Thomas Bertsch, Gonzalo Martı́nez de la Escalera, Jakob Triebel, Carmen Clapp
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pcbi.1008630
Rapid 3D phenotypic analysis of neurons and organoids using data-driven cell segmentation-free machine learningCited by: 11
Author(s): Philipp Mergenthaler, Santosh Hariharan, James M Pemberton, Corey Lourenco, Linda Z. Penn, David W. Andrews
Software Mentions: 3
Published: about 3 years ago
10.1038/s41598-017-12747-z
Role of autophagy in cell-penetrating peptide transfection modelCited by: 23
Author(s): Moataz Dowaidar, Maxime Gestin, Carmine Pasquale Cerrato, Mohammed Hakim Jafferali, Helerin Margus, Paula Ann Kivistik, Kariem Ezzat, Einar Hallberg, Margus Pooga, Mattias Hällbrink, Ülo Langel
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pcbi.1005075
Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection EfficiencyCited by: 22
Author(s): Max Schelker, Caroline Mair, Fabian Jolmes, Robert-William Welke, Edda Klipp, Andreas Herrmann, Max Flöttmann, Christian Sieben
Software Mentions: 3
Published: over 7 years ago
10.1038/s41598-018-19871-4
Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasionCited by: 29
Author(s): Heather Armstrong, Joanna L. Gillis, I. R. Johnson, Zeyad D. Nassar, Max Moldovan, Claire Levrier, Martin C. Sadowski, Mei Yieng Chin, Emma S. Tomlinson Guns, Gerard A. Tarulli, David J. Lynn, Doug A. Brooks, Luke A. Selth, Margaret M. Centenera, Lisa M. Butler
Software Mentions: 3
Published: over 6 years ago
10.1177/2472555218820805
Evaluation of Machine Learning Classifiers to Predict Compound Mechanism of Action When Transferred across Distinct Cell LinesCited by: 12
Author(s): Scott J. Warchal, John C. Dawson, Neil O. Carragher
Software Mentions: 3
Published: about 5 years ago
10.1177/2472555218818053
Unbiased Phenotype Detection Using Negative ControlsCited by: 2
Author(s): Antje Janosch, Carolin Kaffka, Marc Bickle
Software Mentions: 3
Published: about 5 years ago
10.1371/journal.pbio.3000580
12-h clock regulation of genetic information flow by XBP1sCited by: 34
Author(s): Yinghong Pan, Heather Ballance, Huan Meng, Naomi Gonzalez, Sam-Moon Kim, Leymaan Abdurehman, Brian York, Xi Chen, Yisrael Schnytzer, Oren Levy, Clifford C. Dacso, Colleen A. McClung, Bert W. O’Malley, Silvia Liu, Bokai Zhu
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pcbi.1005746
A deep convolutional neural network for classification of red blood cells in sickle cell anemiaCited by: 149
Author(s): Mengjia Xu, Dimitrios Papageorgiou, Sabia Z. Abidi, Ming Dao, Hong Zhao, George Em Karniadakis
Software Mentions: 3
Published: over 6 years ago
10.1186/s13014-015-0453-1
The Focinator - a new open-source tool for high-throughput foci evaluation of DNA damageCited by: 44
Author(s): Sebastian Oeck, Nathalie M. Malewicz, Sebastian Hurst, Justine Rudner, Verena Jendrossek
Software Mentions: 3
Published: almost 9 years ago
10.1038/s41597-019-0331-z
Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological mediaCited by: 7
Author(s): Abhishek Rajput, Saugat Poudel, Hannah Tsunemoto, Michael J. Meehan, Richard Szubin, Connor A. Olson, Anne Lamsa, Yara Seif, Nicholas Dillon, Alison Vrbanac, Joseph Sugie, Samira Dahesh, Jonathan M. Monk, Pieter C. Dorrestein, Rob Knight, Victor Nizet, Bernhard Ø. Palsson, Adam M. Feist, Joe Pogliano
Software Mentions: 3
Published: over 4 years ago
10.3390/ph14030195
Inhibition of Intercellular Cytosolic Traffic via Gap Junctions Reinforces Lomustine-Induced Toxicity in Glioblastoma Independent of MGMT Promoter Methylation StatusCited by: 7
Author(s): Matthias Schneider, Anna-Laura Potthoff, Bernd O. Evert, Marius Dicks, Denise Ehrentraut, Andreas Dolf, Elena N. C. Schmidt, Niklas Schäfer, Valeri Borger, Torsten Pietsch, Mike‐Andrew Westhoff, Erdem Güresir, Andreas Waha, Hartmut Vatter, Dieter Henrik Heiland, Patrick Schuss, Ulrich Herrlinger
Software Mentions: 3
Published: about 3 years ago
10.3389/fmicb.2020.00548
Genomic and Phenotypic Analyses of Acinetobacter baumannii Isolates From Three Tertiary Care Hospitals in ThailandCited by: 24
Author(s): Jessica Loraine, Eva Heinz, Rosesathorn Soontarach, Grace A. Blackwell, Richard A. Stabler, Supayang Piyawan Voravuthikunchai, Potjanee Srimanote, Pattarachai Kiratisin, Nicholas R. Thomson, Peter W. Taylor
Software Mentions: 3
Published: about 4 years ago
10.7717/peerj-cs.584
Machine learning analysis of TCGA cancer dataCited by: 9
Author(s): José Liñares-Blanco, Alejandro Pazos, Carlos Fernández-Lozano
Software Mentions: 3
Published: almost 3 years ago
10.3389/fonc.2021.636057
A Multi-Omics Analysis of Metastatic Melanoma Identifies a Germinal Center-Like Tumor Microenvironment in HLA-DR-Positive Tumor AreasCited by: 6
Author(s): Laura Gadeyne, Yannick Van Herck, Giorgia Milli, Zeynep Kalender Atak, Maddalena M. Bolognesi, Jasper Wouters, Lukas Marcelis, Angeliki Minia, Vaia Pliaka, Jan Roznac, Leonidas G. Alexopoulos, Giorgio Cattoretti, Oliver Bechter, Joost van den Oord, Frederik De Smet, Asier Antoranz, Francesca Maria Bosisio
Software Mentions: 3
Published: about 3 years ago
10.1007/s00497-020-00398-6
Quantitative methods in microscopy to assess pollen viability in different plant taxaCited by: 9
Author(s): Lorenzo Ascari, Cristina Novara, Virginia Dusio, Ludovica Oddi, Consolata Siniscalco
Software Mentions: 3
Published: over 3 years ago
10.3389/fonc.2019.01144
Quantitative Spatial Analysis of Metabolic Heterogeneity Across in vivo and in vitro Tumor ModelsCited by: 18
Author(s): Tiffany M. Heaster, Bennett A. Landman, Melissa C. Skala
Software Mentions: 3
Published: over 4 years ago
10.15252/msb.202010135
The circadian oscillator analysed at the single‐transcript levelCited by: 6
Author(s): Nicholas E. Phillips, Alice Hugues, Jake Yeung, Eric Durandau, Damien Nicolas, Félix Naef
Software Mentions: 3
Published: about 3 years ago
10.15252/msb.20209798
A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroidsCited by: 15
Author(s): Vito Riccardo Tomaso Zanotelli, Matthias Leutenegger, Xiao-Kang Lun, Fanny Georgi, Natalie de Souza, Bernd Bodenmiller
Software Mentions: 3
Published: over 3 years ago
10.15252/msb.202010188
SARS‐CoV‐2 infection remodels the host protein thermal stability landscapeCited by: 15
Author(s): Joel Selkrig, Megan L. Stanifer, André Mateus, Karin Mitosch, Iñigo Barrio-Hernandez, Mandy Rettel, Heeyoung Kim, Carlos G.P. Voogdt, Philipp Walch, Carmon Kee, Nils Kurzawa, Frank Stein, Clement M Potel, Anna Jarząb, Bernhard Küster, Ralf Bartenschlager, Steeve Boulant, Pedro Beltrão, Athanasios Typas, Mikhail M. Savitski
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2105-8-117
Colony size measurement of the yeast gene deletion strains for functional genomicsCited by: 51
Author(s): Negar Memarian, Matthew Jessulat, Javad Alirezaie, Nadereh Mir-Rashed, Jianhua Xu, Mehri Zareie, Myron L. Smith, Ashkan Golshani
Software Mentions: 3
Published: about 17 years ago
10.3389/fonc.2021.620989
Characterization of the Tumor Immune Microenvironment in Lung Squamous Cell Carcinoma Using Imaging Mass CytometryCited by: 17
Author(s): Ran Li, Ying Lin, Yu Wang, Shaoyuan Wang, Yang Yang, Xinlin Mu, Yu‐Sheng Chen, Zhancheng Gao
Software Mentions: 3
Published: about 3 years ago
10.15252/msb.20178007
Antisense transcription‐dependent chromatin signature modulates sense transcript dynamicsCited by: 38
Author(s): Tom Brown, Françoise S. Howe, Struan C. Murray, M Wouters, P. Lorenz, Emily A. Seward, Scott Rata, Andrew Angel, Jane Mellor
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pbio.2005086
Cell-nonautonomous local and systemic responses to cell arrest enable long-bone catch-up growth in developing miceCited by: 35
Author(s): Alberto Roselló-Díez, Linda Madisen, Sébastien Bastide, Hongkui Zeng, Alexandra L. Joyner
Software Mentions: 3
Published: almost 6 years ago
10.15252/msb.20178064
Large‐scale image‐based profiling of single‐cell phenotypes in arrayed CRISPR‐Cas9 gene perturbation screensCited by: 55
Author(s): Reinoud E. A. de Groot, Joel Lüthi, Helen Lindsay, René Holtackers, Lucas Pelkmans
Software Mentions: 3
Published: over 6 years ago
10.1093/bioinformatics/btab185
GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis predictionCited by: 24
Author(s): Zhiqin Wang, Ruiqing Li, Minghui Wang, Ao Li
Software Mentions: 3
Published: about 3 years ago
10.1093/bioinformatics/btaa1061
<i>cytomapper</i>: an R/Bioconductor package for visualization of highly multiplexed imaging dataCited by: 31
Author(s): Nils Eling, Nicolas Damond, Tobias Hoch, Bernd Bodenmiller
Software Mentions: 3
Published: over 3 years ago
10.15252/emmm.202012574
Cooperation of LIM domain‐binding 2 (LDB2) with EGR in the pathogenesis of schizophreniaCited by: 2
Author(s): Tetsuo Ohnishi, Yuji Kiyama, Fumiko Arima-Yoshida, Mitsutaka Kadota, Tomoe Ichikawa, Kazuyuki Yamada, Akïharu Watanabe, Hideki Ohba, Kaori Tanaka, Akihiro Nakaya, Yasue Horiuchi, Yoshimi Iwayama, Manabu Toyoshima, Itone Ogawa, Chie Shimamoto-Mitsuyama, Motoko Maekawa, Shabeesh Balan, Makoto Arai, Mitsuhiro Miyashita, Kazuya Toriumi, Yayoi Nozaki, Rumi Kurokawa, Kazuhiro Suzuki, Akane Yoshikawa, Tomoko Toyota, Toshihiko Hosoya, Hiroyuki Okuno, Haruhiko Bito, Masanari Itokawa, Shigehiro Kuraku, Toshiya Manabe, Takeo Yoshikawa
Software Mentions: 3
Published: about 3 years ago
10.15252/embr.201745642
Negative feedback via <scp>RSK</scp> modulates Erk‐dependent progression from naïve pluripotencyCited by: 25
Author(s): Isabelle Nett, Carla Mulas, Laurent Guy, Kathryn S. Lilley, Austin Smith
Software Mentions: 3
Published: almost 6 years ago
10.15252/embj.201489282
Aberrant methylation of t<scp>RNA</scp>s links cellular stress to neuro‐developmental disordersCited by: 426
Author(s): Sandra Blanco, Sabine Dietmann, Joana V. Flores, Shobbir Hussain, Claudia Kutter, Peter Humphreys, Margus Lukk, Patrick Lombard, Lucas Treps, Martyna Popis, Stefanie Kellner, Sabine M. Hölter, Lillian Garrett, Wolfgang Wurst, Lore Becker, Thomas Klopstock, Helmut Fuchs, Valérie Gailus‐Durner, Martin Hrabé de Angelis, Ragnhildur Thóra Káradóttir, Mark Helm, Jernej Ule, Joseph G. Gleeson, Duncan T. Odom, Michaela Frye
Software Mentions: 3
Published: almost 10 years ago
10.1038/s42003-021-02517-z
Comprehensive in situ mapping of human cortical transcriptomic cell typesCited by: 11
Author(s): Christoffer Mattsson Langseth, Daniel Gyllborg, Jeremy A. Miller, Jennie Close, Brian Long, Ed Lein, Markus M. Hilscher, Mats Nilsson
Software Mentions: 3
Published: over 2 years ago