pypi: CellProfiler | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1008680

Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids
Cited 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: over 5 years ago

10.1007/s00204-016-1781-0

High-content imaging-based BAC-GFP toxicity pathway reporters to assess chemical adversity liabilities
Cited by: 50
Author(s): Steven Wink, Steven Hiemstra, Bram Herpers, Bob van de Water
Software Mentions: 4
Published: over 9 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 lineages
Cited 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: about 4 years ago

10.1093/gigascience/giab018

Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit
Cited by: 2
Author(s): Ben Blamey, Salman Toor, Martin Dahlö, Håkan Wieslander, Philip J. Harrison, Ida‐Maria Sintorn, Alan Sabirsh, Carolina Wählby, Ola Spjuth, Andreas Hellander
Software Mentions: 4
Published: over 4 years ago

10.1534/genetics.117.300077

RNA Interference (RNAi) Screening inDrosophila
Cited by: 86
Author(s): Florian Heigwer, Fillip Port, Michael Boutros
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-14-S16-S4

cellXpress: a fast and user-friendly software platform for profiling cellular phenotypes
Cited by: 25
Author(s): Danai Laksameethanasan, Rui Zhen Tan, Geraldine Wei-Ling Toh, Lit‐Hsin Loo
Software Mentions: 4
Published: about 12 years ago

10.3390/app10186187

ACDC: Automated Cell Detection and Counting for Time-Lapse Fluorescence Microscopy
Cited 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: about 5 years ago

10.1093/gigascience/giaa041

Community standards for open cell migration data
Cited by: 11
Author(s): Alejandra González-Beltrán, Paola Masuzzo, Christophe Ampè, Gert-Jan Bakker, Sébastien Besson, Robert H. Eibl, Peter Friedl, Matthias Gunzer, Mark Kittisopikul, Sylvia E. Le Dévédec, Simone Leo, Josh Moore, Yael Paran, Jaime Prilusky, Philippe Rocca-Serra, Philippe Roudot, Marc Schuster, Gwendolien Sergeant, Staffan Strömblad, Jason R. Swedlow, Merijn van Erp, Marleen Van Troys, Assaf Zaritsky, Susanna Assunta Sansone, Lennart Martens
Software Mentions: 4
Published: over 5 years ago

10.1172/jci.insight.146883

Highly multiplexed 2-dimensional imaging mass cytometry analysis of HBV-infected liver
Cited by: 14
Author(s): Daniel Traum, Yue J. Wang, Kathleen B. Schwarz, Jonathan Schug, David Wong, Harry L.A. Janssen, Norah A. Terrault, Mandana Khalili, Abdus S. Wahed, Karen F. Murray, Phillip Rosenthal, Simon C. Ling, Norberto Rodriguez‐Baez, Richard K. Sterling, Daryl Lau, Timothy M. Block, Michael D. Feldman, Elizabeth E. Furth, William M. Lee, David E. Kleiner, Anna S. Lok, Klaus H. Kaestner, Kyong Mi Chang
Software Mentions: 4
Published: over 4 years ago

10.3389/fonc.2021.636451

Integrative Analysis of Histopathological Images and Genomic Data in Colon Adenocarcinoma
Cited by: 7
Author(s): Hui Li, Linyan Chen, Hao Zeng, Qimeng Liao, Jianrui Ji, Xuelei Ma
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pcbi.1007348

Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting
Cited by: 64
Author(s): Alex X. Lu, Oren Kraus, Sam Cooper, Alan M. Moses
Software Mentions: 4
Published: about 6 years ago

10.12688/wellcomeopenres.15232.2

Genome-wide CRISPR screening identifies new regulators of glycoprotein secretion
Cited by: 2
Author(s): Stephanie Popa, Julien Villeneuve, Sarah E. Stewart, Esther Perez Garcia, Anna Petrunkina Harrison, Kévin Moreau
Software Mentions: 4
Published: almost 6 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 burden
Cited 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: over 4 years ago

10.3389/fcimb.2021.678482

Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells
Cited 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: over 4 years ago

10.1371/journal.pone.0218230

Atoh8 acts as a regulator of chondrocyte proliferation and differentiation in endochondral bones
Cited by: 10
Author(s): Nadine Schroeder, Manuela Wuelling, Daniel Hoffmann, Beate Brand‐Saberi, Andrea Vortkamp
Software Mentions: 4
Published: about 6 years ago

10.1242/bio.052936

A fully automated deep learning pipeline for high-throughput colony segmentation and classification
Cited by: 4
Author(s): Sarah H. Carl, Lea Duempelmann, Yukiko Shimada, Marc Bühler
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2019.00308

661W Photoreceptor Cell Line as a Cell Model for Studying Retinal Ciliopathies
Cited by: 37
Author(s): Gabrielle Wheway, Liliya Nazlamova, Dann Turner, Stephen Cross
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-021-04117-4

MAPS: machine-assisted phenotype scoring enables rapid functional assessment of genetic variants by high-content microscopy
Cited by: 3
Author(s): Jesse T. Chao, Calvin D. Roskelley, Christopher Loewen
Software Mentions: 4
Published: over 4 years ago

10.1093/bioinformatics/btab178

PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples
Cited 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: over 4 years ago

10.1093/bioinformatics/btw390

CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets
Cited by: 106
Author(s): David Dao, Adam Fraser, Jia‐Jang Hung, Vebjorn Ljosa, Shantanu Singh, Anne E. Carpenter
Software Mentions: 4
Published: over 9 years ago

10.3389/frai.2021.754641

Deep Learning of Histopathology Images at the Single Cell Level
Cited 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: about 4 years ago

10.7554/eLife.55911

Histone deacetylase knockouts modify transcription, CAG instability and nuclear pathology in Huntington disease mice
Cited by: 4
Author(s): Marina Kovalenko, Serkan Erdin, Marissa A Andrew, Jason St. Claire, Melissa Shaughnessey, Leroy Hubert, João Luís Neto, Alexei Stortchevoi, Daniel M. Fass, Ricardo Mouro Pinto, Stephen J. Haggarty, John H. Wilson, Michael E. Talkowski, Vanessa C. Wheeler
Software Mentions: 4
Published: about 5 years ago

10.1016/j.molcel.2021.04.028

Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human disease
Cited 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: over 4 years ago

10.1186/s12859-019-2880-8

Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison
Cited by: 126
Author(s): Pavel Kopel, Jan Balvan, Josef Jaroš, Florian Jug, Radim Kolář, Michal Masařík, Jaromír Gumulec
Software Mentions: 4
Published: over 6 years ago

10.1111/mmi.14417

BactMAP: An R package for integrating, analyzing and visualizing bacterial microscopy data
Cited by: 23
Author(s): Renske van Raaphorst, Morten Kjos, Jan‐Willem Veening
Software Mentions: 4
Published: almost 6 years ago

10.1007/s00018-017-2695-6

Downregulation of p53 drives autophagy during human trophoblast differentiation
Cited 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: about 8 years ago

10.7554/eLife.56969

Drosophila PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity
Cited by: 22
Author(s): Arpan C. Ghosh, Sudhir Gopal Tattikota, Yifang Liu, Aram Comjean, Yanhui Hu, Víctor Barrera, Shannan Ho Sui, Norbert Perrimon
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.59780

On the objectivity, reliability, and validity of deep learning enabled bioimage analyses
Cited by: 25
Author(s): Dennis Segebarth, Matthias Griebel, Nikolai Stein, Cora R. von Collenberg, Corinna Martin, Dominik Fiedler, Lucas B. Comeras, Anupam Sah, Victoria Schoeffler, Teresa M. Lüffe, Alexander Dürr, Rohini Gupta, Manju Sasi, Christina Lillesaar, Maren D. Lange, Ramon Tasan, Nicolas Singewald, Hans‐Christian Pape, Christoph M. Flath, Robert Blum
Software Mentions: 4
Published: about 5 years ago

10.1186/s40170-021-00257-6

High-resolution spatiotemporal pHe and pO2 imaging in head and neck and oesophageal carcinoma cells
Cited 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: over 4 years ago

10.1186/1746-1596-8-34

CognitionMaster: an object-based image analysis framework
Cited 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: over 12 years ago

10.1016/j.jbc.2021.101049

Fused in sarcoma regulates DNA replication timing and kinetics
Cited by: 5
Author(s): Weiyan Jia, Sang Hwa Kim, Mark Scalf, Peter Tonzi, Robert Millikin, William Guns, Lu Liu, Adam S. Mastrocola, Lloyd M. Smith, Tony T. Huang, Randal S. Tibbetts
Software Mentions: 4
Published: about 4 years ago

10.1186/s12951-020-0576-x

Core–shell nanoparticles suppress metastasis and modify the tumour-supportive activity of cancer-associated fibroblasts
Cited by: 33
Author(s): Dóra Kovács, Nóra Igaz, Annamária Marton, Andrea Rónavári, Péter Bélteky, László Bodai, Gabriella Spengler, László Tiszlavicz, Zsolt Rázga, Péter Hegyi, Csaba Vízler, Imre Boros, Zoltán Kónya, Mónika Kiricsi
Software Mentions: 4
Published: almost 6 years ago

10.18632/oncotarget.8412

miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer
Cited by: 49
Author(s): Yinghong Pan, Gordon Robertson, Lykke Pedersen, Emilia L. Lim, Anadulce Hernández-Herrera, Amy C. Rowat, Sagar L. Patil, CY Chan, Yunfei Wen, Xinna Zhang, Upal Basu-Roy, Alka Mansukhani, Andy Chu, Payal Sipahimalani, Reanne Bowlby, Denise Brooks, Nina Thiessen, Cristian Coarfa, Yussanne Ma, Richard A. Moore, Jacquie Schein, Andrew J. Mungall, Jinsong Liu, Chad V. Pecot, Anil K. Sood, Steven J.M. Jones, Marco A. Marra, Preethi H. Gunaratne
Software Mentions: 4
Published: over 9 years ago

10.18632/oncotarget.11038

Role of the immune system in the peritoneal tumor spread of high grade serous ovarian cancer
Cited by: 33
Author(s): Katharina Auer, Anna Bachmayr-Heyda, Nyamdelger Sukhbaatar, Stefanie Aust, Klaus G. Schmetterer, Samuel M. Meier, Christopher Gerner, Christoph Grimm, Reinhard Horvat, Dietmar Pils
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.35786

Human axial progenitors generate trunk neural crest cells in vitro
Cited 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: about 7 years ago

10.7554/eLife.40162

Motion sensing superpixels (MOSES) is a systematic computational framework to quantify and discover cellular motion phenotypes
Cited by: 8
Author(s): Felix Zhou, Carlos Ruiz‐Puig, Richard Owen, Michael J. White, Jens Rittscher, Xin Lü
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21197069

Human Fibroblasts In Vitro Exposed to 2.45 GHz Continuous and Pulsed Wave Signals: Evaluation of Biological Effects with a Multimethodological Approach
Cited 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: about 5 years ago

10.18632/oncotarget.12298

Case-specific potentiation of glioblastoma drugs by pterostilbene
Cited 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: about 9 years ago

10.7554/eLife.36330

TFAP2 transcription factors are regulators of lipid droplet biogenesis
Cited by: 31
Author(s): Cameron C. Scott, Stefania Vossio, Jacques Rougemont, Jean Grüenberg
Software Mentions: 3
Published: about 7 years ago

10.3390/ijms22179595

Regulation of the Golgi Apparatus by p38 and JNK Kinases during Cellular Stress Responses
Cited 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: about 4 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 methylation
Cited 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: about 8 years ago

10.21307/jofnem-2020-108

Competitive fitness analysis using Convolutional Neural Network
Cited by: 1
Author(s): Joanna Palka, Krzysztof Fiok, Weronika Antoł, Zofia M. Prokop
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms22031167

Glutamine Uptake via SNAT6 and Caveolin Regulates Glutamine–Glutamate Cycle
Cited 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: almost 5 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 Behavior
Cited 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: about 5 years ago

10.3390/ijms21103672

Sonic Hedgehog and Triiodothyronine Pathway Interact in Mouse Embryonic Neural Stem Cells
Cited 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: over 5 years ago

10.3390/nu12030624

Alliin, An Allium sativum Nutraceutical, Reduces Metaflammation Markers in DIO Mice
Cited 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: over 5 years ago

10.1186/1471-2105-12-126

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology
Cited by: 9
Author(s): Szymon Stoma, Martina Fröhlich, Susanne Gerber, Edda Klipp
Software Mentions: 3
Published: over 14 years ago

10.1128/mBio.01569-16

The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment
Cited by: 24
Author(s): Leo Hanke, Kevin E. Knockenhauer, R. Camille Brewer, Eline van Diest, Florian I. Schmidt, Thomas Schwartz, Hidde L. Ploegh
Software Mentions: 3
Published: almost 9 years ago

10.1155/2021/9975423

Hyperion Image Analysis Depicts a Preliminary Landscape of Tumor Immune Microenvironment in OSCC with Lymph Node Metastasis
Cited by: 7
Author(s): Shang Xie, Mengjie Zhang, Xiaofeng Shan, Vicky Yau, Jianyun Zhang, Wei Wang, Yongpan Yan, Zhigang Cai
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-15-1162

Simultaneous analysis of large-scale RNAi screens for pathogen entry
Cited 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: almost 11 years ago

10.3390/cancers13184600

Role of Artificial Intelligence in the Early Diagnosis of Oral Cancer. A Scoping Review
Cited 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: about 4 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 accumulation
Cited 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: about 6 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)/GPC6
Cited 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: over 4 years ago

10.7554/eLife.07759

Progerin reduces LAP2α-telomere association in Hutchinson-Gilford progeria
Cited by: 89
Author(s): Alexandre Chojnowski, P.P. Ong, Esther Wong, John Lim, Rafidah Mutalif, Raju Navasankari, Bamaprasad Dutta, Henry Yang, Yi Y. Liow, Siu Kwan Sze, Thomas Boudier, Alan Colman, Brian Burke, Colin L. Stewart, Oliver Dreesen
Software Mentions: 3
Published: about 10 years ago

10.1186/1751-0473-8-16

CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation
Cited by: 76
Author(s): Erlend Hodneland, Tanja Kögel, Dominik Frei, Hans‐Hermann Gerdes, Arvid Lundervold
Software Mentions: 3
Published: about 12 years ago

10.1016/j.stemcr.2021.01.013

Unraveling the Developmental Roadmap toward Human Brown Adipose Tissue
Cited 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: over 4 years ago

10.1371/journal.pone.0027886

Extracting Fluorescent Reporter Time Courses of Cell Lineages from High-Throughput Microscopy at Low Temporal Resolution
Cited 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: almost 14 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 detection
Cited 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: over 4 years ago

10.1371/journal.pone.0115907

High Reproducibility of Histological Characterization by Whole Virtual Slide Quantification; An Example Using Carotid Plaque Specimens
Cited 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: almost 11 years ago

10.1038/s41598-021-91846-4

High-resolution transcriptional landscape of xeno-free human induced pluripotent stem cell-derived cerebellar organoids
Cited by: 28
Author(s): Samuel Nayler, Devika Agarwal, Fabiola Curion, Rory Bowden, Esther B. E. Becker
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0237972

Interactive machine learning for fast and robust cell profiling
Cited by: 1
Author(s): Lisa Laux, Marie F.A. Cutiongco, Nikolaj Gadegaard, Bjørn Sand Jensen
Software Mentions: 3
Published: about 5 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 background
Cited by: 9
Author(s): Lech Kaczmarczyk, Nicole Reichenbach, Nelli Blank, Maria Jonson, Lars Dittrich, Gabor C. Petzold, Walker S. Jackson
Software Mentions: 3
Published: over 4 years ago

10.1101/2021.08.11.455959

Multiplexed detection of SARS-CoV-2 genomic and subgenomic RNA using in situ hybridization
Cited by: 3
Author(s): Kofi Acheampong, Dylan L. Schaff, Benjamin Emert, Jonathan I. Lake, Sam Reffsin, Emily Shea, Courtney E Comar, Leslie A. Litzky, Nigar Khurram, Rebecca L. Linn, Michael D. Feldman, Susan R. Weiss, Kathleen T. Montone, Sara Cherry, Sydney M. Shaffer
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-59988-z

A salivary metabolite signature that reflects gingival host-microbe interactions: instability predicts gingivitis susceptibility
Cited 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: over 5 years ago

10.1371/journal.pone.0116329

IQM: An Extensible and Portable Open Source Application for Image and Signal Analysis in Java
Cited by: 28
Author(s): Philipp Kainz, Michael Mayrhofer-Reinhartshuber, Helmut Ahammer
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0215337

FluoroCellTrack: An algorithm for automated analysis of high-throughput droplet microfluidic data
Cited by: 22
Author(s): Manibarathi Vaithiyanathan, Nora Safa, Adam T. Melvin
Software Mentions: 3
Published: over 6 years ago

10.1186/1472-6750-7-66

High content image analysis for human H4 neuroglioma cells exposed to CuO nanoparticles
Cited by: 44
Author(s): Fuhai Li, Xiaobo Zhou, Jinmin Zhu, Jinwen Ma, Xudong Huang, Stephen T.C. Wong
Software Mentions: 3
Published: about 18 years ago

10.1038/s41598-019-50010-9

Cell Type Classification and Unsupervised Morphological Phenotyping From Low-Resolution Images Using Deep Learning
Cited by: 30
Author(s): Kai Yao, Nash D. Rochman, Sean X. Sun
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0163453

Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine Experiments
Cited by: 31
Author(s): Christian Carsten Sachs, Alexander Grünberger, Stefan Helfrich, Christopher Probst, Wolfgang Wiechert, Dietrich Kohlheyer, Katharina Nöh
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-019-53428-3

Immune cell type, cell activation, and single cell heterogeneity revealed by label-free optical methods
Cited by: 10
Author(s): Nicolas Pavillon, Nicholas I. Smith
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-19871-4

Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasion
Cited 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: almost 8 years ago

10.1038/s41598-018-31924-2

3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification
Cited 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: about 7 years ago

10.1038/s41598-017-12747-z

Role of autophagy in cell-penetrating peptide transfection model
Cited 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: about 8 years ago

10.1038/s41598-018-35383-7

Vasoinhibin comprises a three-helix bundle and its antiangiogenic domain is located within the first 79 residues
Cited 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: almost 7 years ago

10.1038/s41597-019-0331-z

Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media
Cited 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: almost 6 years ago

10.1177/2472555218818053

Unbiased Phenotype Detection Using Negative Controls
Cited by: 2
Author(s): Antje Janosch, Carolin Kaffka, Marc Bickle
Software Mentions: 3
Published: over 6 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 agrochemicals
Cited 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: over 5 years ago

10.1038/s41598-018-37522-6

MITF has a central role in regulating starvation-induced autophagy in melanoma
Cited by: 60
Author(s): Katrín Möller, Sara Sigurbjörnsdóttir, Asgeir Ö. Arnthórsson, Vivian Pogenberg, Ramile Dilshat, Valerie Fock, Sólveig Hlín Brynjólfsdóttir, Christian Bindesbøll, M. Bessadóttir, Helga M. Ögmundsdóttir, Anne Simonsen, Lionel Larue, Matthias Wilmanns, Vésteinn Thórsson, Eiríkur Steingrimsson, Margrét H. Ögmundsdóttir
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.ppat.1009838

Probing the spatiotemporal patterns of HBV multiplication reveals novel features of its subcellular processes
Cited by: 10
Author(s): Lei Yue, Chang Li, Mingzhu Xu, Min Wu, Jiahui Ding, Jiangxia Liu, Xiaonan Zhang, Zhenghong Yuan
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.ppat.1007601

RNAi-based small molecule repositioning reveals clinically approved urea-based kinase inhibitors as broadly active antivirals
Cited by: 25
Author(s): Markus Lesch, Madlen Luckner, Michaël Meyer, Friderike Weege, Isabella Gravenstein, Martin Raftery, Christian Sieben, Laura Martin-Sancho, Aki Imai-Matsushima, Robert-William Welke, Rebecca Frise, William Barclay, Günther Schönrich, Andreas Herrmann, Thomas Meyer, Alexander Karlas
Software Mentions: 3
Published: over 6 years ago

10.1073/pnas.1921055117

ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in Arabidopsis
Cited by: 54
Author(s): Christophe Lambing, Pallas Kuo, Andrew J. Tock, Stephanie D. Topp, Ian Henderson
Software Mentions: 3
Published: over 5 years ago

10.1083/jcb.201702099

BAIAP3, a C2 domain–containing Munc13 protein, controls the fate of dense-core vesicles in neuroendocrine cells
Cited by: 44
Author(s): Xingmin Zhang, Shan Jiang, Kelly A. Mitok, Lingjun Li, Alan D. Attie, Thomas F.J. Martin
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1008083

The dPix-Git complex is essential to coordinate epithelial morphogenesis and regulate myosin during Drosophila egg chamber development
Cited 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: over 6 years ago

10.1083/jcb.202011078

Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1
Cited by: 6
Author(s): Kristina Väth, Carsten Mattes, John F. Reinhard, Roberto Covino, Heike Stumpf, Gerhard Hummer, Robert Ernst
Software Mentions: 3
Published: over 4 years ago

10.1111/imm.13341

Modified recombinant human IgG1‐Fc is superior to natural intravenous immunoglobulin at inhibiting immune‐mediated demyelination
Cited by: 1
Author(s): Christine Baksmeier, Patricia A. Blundell, Julia Steckel, Verena Schultz, Quan Gu, Ana da Silva Filipe, Alain Kohl, Chris Linnington, Dongli Lu, Anne Dell, Stuart M. Haslam, Jiabin Wang, Dan Czajkowsky, Norbert Goebels, Richard J. Pleass
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1008630

Rapid 3D phenotypic analysis of neurons and organoids using data-driven cell segmentation-free machine learning
Cited by: 11
Author(s): Philipp Mergenthaler, Santosh Hariharan, James M Pemberton, Corey Lourenco, Linda Z. Penn, David W. Andrews
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1005075

Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency
Cited 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: about 9 years ago

10.1080/19490976.2021.1911534

Intestinal microbiota drives cholestasis-induced specific hepatic gene expression patterns
Cited by: 13
Author(s): Oriol Juanola, Mohsin Hassan, Pranav Kumar, Bahtiyar Yılmaz, Irene Keller, Cédric Simillion, Cornelius Engelmann, Frank Tacke, Jean‐François Dufour, Andrea De Gottardi, Sheida Moghadamrad
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.jbc.2021.100295

The cytoprotective protein MANF promotes neuronal survival independently from its role as a GRP78 cofactor
Cited by: 27
Author(s): Ave Eesmaa, Li-Ying Yu, Helka Göös, Kristofer Nõges, Vera Kovaleva, Maarit Hellman, Richard Zimmermann, Martin Jung, Perttu Permi, Markku Varjosalo, Päivi Lindholm, Märt Saarma
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13014-015-0453-1

The Focinator - a new open-source tool for high-throughput foci evaluation of DNA damage
Cited by: 44
Author(s): Sebastian Oeck, Nathalie M. Malewicz, Sebastian Hurst, Justine Rudner, Verena Jendrossek
Software Mentions: 3
Published: over 10 years ago

10.1534/g3.116.033654

Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning
Cited by: 112
Author(s): Tanel Pärnamaa, Leopold Parts
Software Mentions: 3
Published: over 8 years ago

10.1016/j.gpb.2020.11.003

Computational Screening of Phase-separating Proteins
Cited by: 27
Author(s): Boyan Shen, Zhaoming Chen, Chunyu Yu, Taoyu Chen, Minglei Shi, Tingting Li
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pbio.3000580

12-h clock regulation of genetic information flow by XBP1s
Cited 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: almost 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 mice
Cited by: 35
Author(s): Alberto Roselló-Díez, Linda Madisen, Sébastien Bastide, Hongkui Zeng, Alexandra L. Joyner
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1005746

A deep convolutional neural network for classification of red blood cells in sickle cell anemia
Cited by: 149
Author(s): Mengjia Xu, Dimitrios Papageorgiou, Sabia Z. Abidi, Ming Dao, Hong Zhao, George Em Karniadakis
Software Mentions: 3
Published: about 8 years ago

10.3389/fpls.2020.615922

Hazelnut Pollen Phenotyping Using Label-Free Impedance Flow Cytometry
Cited by: 9
Author(s): Lorenzo Ascari, V. Cristofori, Federico Macrì, Roberto Botta, Cristian Silvestri, Tommaso De Gregorio, Eloy Suarez Huerta, Marco Di Berardino, Silvan Kaufmann, Consolata Siniscalco
Software Mentions: 3
Published: almost 5 years ago

10.3389/fonc.2021.620989

Characterization of the Tumor Immune Microenvironment in Lung Squamous Cell Carcinoma Using Imaging Mass Cytometry
Cited 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: 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 Status
Cited 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: over 4 years ago

10.3389/fmicb.2020.00548

Genomic and Phenotypic Analyses of Acinetobacter baumannii Isolates From Three Tertiary Care Hospitals in Thailand
Cited 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: over 5 years ago

10.7717/peerj-cs.584

Machine learning analysis of TCGA cancer data
Cited by: 9
Author(s): José Liñares-Blanco, Alejandro Pazos, Carlos Fernández-Lozano
Software Mentions: 3
Published: over 4 years ago

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