pypi: CellProfiler | Projects | Ecosyste.ms: Papers

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 6 years ago

5-aminoimidazole-4-carboxamide ribonucleoside induces differentiation in a subset of primary acute myeloid leukemia blasts
Cited by: 4
Author(s): Vilma Dembitz, Hrvoje Lalić, Ivan Kodvanj, Barbara Tomić, Josip Batinić, Klara Dubravčić, Drago Batinić, Antonio Bedalov, Dora Višnjić
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.55585

A whole-brain connectivity map of mouse insular cortex
Cited by: 129
Author(s): Daniel August Gehrlach, Caroline Weiand, Thomas N. Gaitanos, Eunjae Cho, Alexandra S. Klein, Alexandru A Hennrich, Karl-Klaus Conzelmann, Nadine Gogolla
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.17290

Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62
Cited by: 114
Author(s): Rowena DeJesus, Francesca Moretti, Gregory McAllister, Zuncai Wang, Philip S. Bergman, Shanming Liu, Elizabeth Frias, John Alford, John S. Reece‐Hoyes, Alicia Lindeman, Jennifer Kelliher, Carsten Russ, Judith Knehr, Walter Carbone, Martin Beibel, Guglielmo Roma, Aylwin Ng, John A. Tallarico, Jeffery A. Porter, Ramnik J. Xavier, Craig Mickanin, Leon O. Murphy, Gregory R. Hoffman, Beat Nyfeler
Software Mentions: 2
Published: about 9 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 8 years ago

10.7554/eLife.59384

Toxoplasma TgATG9 is critical for autophagy and long-term persistence in tissue cysts
Cited by: 21
Author(s): David W. Smith, Geetha Kannan, Isabelle Coppens, Feng-Rong Wang, Hoa Mai Nguyen, Aude Cerutti, Einar B. Ólafsson, Patrick A Rimple, Tracey L. Schultz, Nayanna M Mercado Soto, Manlio Di Cristina, Sébastien Besteiro, Vern B. Carruthers
Software Mentions: 2
Published: over 4 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 8 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 15 years ago

10.1093/jmcb/mju026

The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells
Cited by: 30
Author(s): Tim Ammon, Sudhish Mishra, Kaja Kowalska, Grzegorz M. Popowicz, Tad A. Holak, Stefan Jentsch
Software Mentions: 2
Published: about 11 years ago

10.1186/s40168-020-00818-9

Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts
Cited by: 26
Author(s): Alba Cortés, John W. Wills, Xiaopei Su, Rachel E. Hewitt, Jack Robertson, Riccardo Scotti, Daniel D. Price, Yvonne Bartley, Tom N. McNeilly, Lutz Krause, Jonathan J. Powell, Alasdair J. Nisbet, Cinzia Cantacessi
Software Mentions: 2
Published: about 5 years ago

10.1016/j.jmb.2015.03.004

Genome-Wide Localization Study of Yeast Pex11 Identifies Peroxisome–Mitochondria Interactions through the ERMES Complex
Cited by: 123
Author(s): Matej Ušaj, Mojca Brložnik, Petra Kaferle, Marinka Žitnik, Heimo Wolinski, Florian Leitner, Sepp D. Kohlwein, Blaž Zupan, Uroš Petrovič
Software Mentions: 2
Published: about 10 years ago

10.7554/eLife.40560

Defining host–pathogen interactions employing an artificial intelligence workflow
Cited by: 62
Author(s): Daniel Fisch, Artur Yakimovich, Barbara Clough, J. D. Wright, Monique Bunyan, Michael Howell, Jason Mercer, Eva Frickel
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.202755

Aging and pathological aging signatures of the brain: through the focusing lens of SIRT6
Cited by: 10
Author(s): Daniel Stein, Amir Mizrahi, Anastasia V. Golova, Adam Saretzky, Alfredo Garcia Venzor, Zeev Slobodnik, Shai Kaluski, Monica Einav, Ekaterina E. Khrameeva, Debra Toiber
Software Mentions: 2
Published: over 4 years ago

10.26508/lsa.202101084

Quantitative proteomics identifies PTP1B as modulator of B cell antigen receptor signaling
Cited by: 0
Author(s): Jennifer Schwarz, Lorenz Grundmann, Thomas Kokot, Kathrin Kläsener, Sandra Fotteler, Dávid Medgyesi, Maja Köhn, Michael Reth, Bettina Warscheid
Software Mentions: 2
Published: almost 4 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 6 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: almost 7 years ago

10.7554/eLife.50416

PPM1H phosphatase counteracts LRRK2 signaling by selectively dephosphorylating Rab proteins
Cited by: 85
Author(s): Kerryn Berndsen, Paweł Lis, Wondwossen M Yeshaw, Paulina S. Wawro, Raja Sekhar Nirujogi, Melanie Wightman, Thomas Macartney, Mark Dorward, Axel Knebel, Francesca Tonelli, Suzanne R Pfeffer, Dario R. Alessi
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.53072

Defining the role of pulmonary endothelial cell heterogeneity in the response to acute lung injury
Cited by: 128
Author(s): Terren K. Niethamer, Collin T. Stabler, John P. Leach, Jarod A. Zepp, Michael Morley, Apoorva Babu, Shanshan Zhou, Edward E Morrisey
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.00028-21

High-Content Imaging to Phenotype Antimicrobial Effects on Individual Bacteria at Scale
Cited by: 14
Author(s): Sushmita Sridhar, Sally Forrest, Ben Warne, Mailis Maes, Stephen Baker, Gordon Dougan, Josefin Bartholdson Scott
Software Mentions: 2
Published: about 4 years ago

10.1186/s40425-018-0406-y

Ibuprofen supports macrophage differentiation, T cell recruitment, and tumor suppression in a model of postpartum breast cancer
Cited by: 39
Author(s): Nathan D. Pennock, Holly A. Martinson, Qiuchen Guo, Courtney B. Betts, Sonali Jindal, Takahiro Tsujikawa, Lisa M. Coussens, Virginia F. Borges, Pepper Schedin
Software Mentions: 2
Published: almost 7 years ago

10.1128/mBio.01393-18

NADPH Oxidase and Guanylate Binding Protein 5 Restrict Survival of Avirulent Type III Strains of Toxoplasma gondii in Naive Macrophages
Cited by: 29
Author(s): Sumit Kumar Matta, Kelley T. Patten, Quiling Wang, Bae-Hoon Kim, John D. MacMicking, L. David Sibley
Software Mentions: 2
Published: almost 7 years ago

10.1128/mBio.00640-18

Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells
Cited by: 144
Author(s): Frédéric Goormaghtigh, Nathan Fraikin, Marta Putrinš, Thibaut Hallaert, Vasili Hauryliuk, Abel García-Pino, Andreas Sjödin, Sergo Kasvandik, Klas I. Udekwu, Tanel Tenson, Niilo Kaldalu, Laurence Van Melderen
Software Mentions: 2
Published: about 7 years ago

10.1128/mSphere.00380-19

A Role for the VPS Retromer in Brucella Intracellular Replication Revealed by Genomewide siRNA Screening
Cited by: 9
Author(s): Alain Casanova, Shyan Huey Low, Maxime Québatte, Jarosław Sędzicki, Therese Tschon, Maren Ketterer, Kevin Smith, Mario Emmenlauer, Houchaïma Ben-Tekaya, Christoph Dehio
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.35907

A Rho signaling network links microtubules to PKD controlled carrier transport to focal adhesions
Cited by: 29
Author(s): Stephan A. Eisler, Filipa Curado, Gisela Link, Sarah Schulz, Melanie Noack, Maren Steinke, Monilola A. Olayioye, Angelika Haußer
Software Mentions: 2
Published: about 7 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 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: almost 5 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 4 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 13 years ago

10.1038/s41398-021-01319-5

Depression patient-derived cortical neurons reveal potential biomarkers for antidepressant response
Cited by: 5
Author(s): Yishai Avior, Shiri Ron, Dana Kroitorou, Claudia Albeldas, Vitaly Lerner, Barbara Corneo, Erez Nitzan, Daphna Laifenfeld, Talia Cohen Solal
Software Mentions: 2
Published: over 4 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: about 4 years ago

10.1186/1741-7007-11-114

The p53 response in single cells is linearly correlated to the number of DNA breaks without a distinct threshold
Cited by: 65
Author(s): Alexander Loewer, Ketki Karanam, Charles Mock, Galit Lahav
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-019-39854-3

A novel mutation tolerant padlock probe design for multiplexed detection of hypervariable RNA viruses
Cited by: 21
Author(s): Sibel Ciftci, Felix Neumann, Iván Hernandez-Neuta, Mikhayil Hakhverdyan, Ádám Bálint, David Holzmann, Narayanan Madaboosi, Mats Nilsson
Software Mentions: 2
Published: over 6 years ago

10.1186/s13058-021-01457-0

Sensitivity to targeted therapy differs between HER2-amplified breast cancer cells harboring kinase and helical domain mutations in PIK3CA
Cited by: 5
Author(s): Joseph P. Garay, Rebecca Smith, Kaylyn L. Devlin, Daniel P. Hollern, Tiera Liby, Moqing Liu, Shanta Boddapati, Spencer S. Watson, Amanda Esch, Ting Zheng, Wallace Thompson, Darcie Babcock, Sunjong Kwon, Koei Chin, Laura M. Heiser, Joe W. Gray, James E. Korkola
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-018-25571-w

Propyl-5-hydroxy-3-methyl-1-phenyl-1H-pyrazole-4-carbodithioate (HMPC): a new bacteriostatic agent against methicillin—resistant Staphylococcus aureus
Cited by: 6
Author(s): Tatiana Johnston, Daria Van Tyne, Roy Fangxing Chen, Nicolas L. Fawzi, Bumsup Kwon, Michael J. Kelso, Michael S. Gilmore, Eleftherios Mylonakis
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-31726-6

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

10.1038/s41598-017-18815-8

Automated brightfield morphometry of 3D organoid populations by OrganoSeg
Cited by: 84
Author(s): Michael A. Borten, Sameer S. Bajikar, Nobuo Sasaki, Hans Clevers, Kevin A. Janes
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-19024-z

Scaffold-free generation of uniform adipose spheroids for metabolism research and drug discovery
Cited by: 85
Author(s): Aloysius J. Klingelhutz, Françoise A. Gourronc, Anna L Chaly, David Wadkins, Anthony J. Burand, Kathleen R. Markan, Sharon O. Idiga, Meng Wu, Matthew J. Potthoff, James A. Ankrum
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-23582-1

Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes
Cited by: 27
Author(s): Axel Klaesson, Karin Grannas, Tonge Ebai, Johan Heldin, Björn Koos, Mattias Leino, Doroteya Raykova, Johan Oelrich, Linda Arngården, Ola Söderberg, Ulf Landegren
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-32364-8

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

10.1038/s41598-017-07599-6

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation
Cited by: 109
Author(s): Sajith Kecheril Sadanandan, Petter Ranefall, Sylvie Le Guyader, Carolina Wählby
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep34785

Single cell dynamic phenotyping
Cited by: 16
Author(s): Katherin Patsch, Charles B. Chiu, Mark Engeln, David B. Agus, Parag Mallick, Shannon M. Mumenthaler, Daniel Ruderman
Software Mentions: 2
Published: almost 9 years ago

10.1038/srep46571

Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells
Cited by: 33
Author(s): Gregor Mönke, Elena Cristiano, Ana Finzel, Dhana Friedrich, Hanspeter Herzel, Martin Falcke, Alexander Loewer
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0138760

Plaque2.0—A High-Throughput Analysis Framework to Score Virus-Cell Transmission and Clonal Cell Expansion
Cited by: 43
Author(s): Artur Yakimovich, Vardan Andriasyan, Robert Witte, I-Hsuan Wang, Ralf Bartenschlager, Maarit Suomalainen, Urs F. Greber
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep13113

Human cell dedifferentiation in mesenchymal condensates through controlled autophagy
Cited by: 34
Author(s): Rebecca Rose Pennock, Elen Bray, Paul R. Pryor, Sally James, Paul J. McKeegan, Roger G. Sturmey, Paul G. Genever
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep29752

A high-content image-based method for quantitatively studying context-dependent cell population dynamics
Cited by: 48
Author(s): Colleen M. Garvey, Erin Spiller, Danika Lindsay, Chun-Te Chiang, Nathan C. Choi, David B. Agus, Parag Mallick, Jasmine Foo, Shannon M. Mumenthaler
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-12608-9

Nucleosome stability measured in situ by automated quantitative imaging
Cited by: 16
Author(s): László Imre, Zoltán Simándi, Attila Horváth, György Fenyőfalvi, Péter P. Nánási, Erfaneh Firouzi Niaki, Éva Hegedüs, Zsolt Bacsó, Urbain Weyemi, Rebekka Mauser, Juan Ausió, Albert Jeltsch, William M. Bonner, László Nagy, Hiroshi Kimurâ, Gábor Szabó
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-018-35001-6

Expression profiling and in situ screening of circular RNAs in human tissues
Cited by: 20
Author(s): Ammar Zaghlool, Adam Ameur, Chenglin Wu, Jakub Orzechowski Westholm, Adnan Niazi, Manimozhi Manivannan, Kelli Bramlett, Mats Nilsson, Lars Feuk
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.44353

Phosphorylation-mediated interactions with TOPBP1 couple 53BP1 and 9-1-1 to control the G1 DNA damage checkpoint
Cited by: 33
Author(s): Nicolas Bigot, Matthew Day, Robert A. Baldock, Felicity Z. Watts, Antony W. Oliver, Laurence H. Pearl
Software Mentions: 2
Published: about 6 years ago

10.1126/sciadv.aba4526

Esophageal extracellular matrix hydrogel mitigates metaplastic change in a dog model of Barrett’s esophagus
Cited by: 24
Author(s): Juan Diego Naranjo, Lindsey T. Saldin, Eric Sobieski, Lina M. Quijano, Ryan C. Hill, Patrick Chan, Crisanto M Torres, Jenna L. Dziki, Madeline C. Cramer, Yoojin C. Lee, Rohit Das, Anant K. Bajwa, Rania Nossair, Molly Klimak, Lucile Marchal, Shil Patel, Sachin Velankar, Kirk C. Hansen, Kevin McGrath, Stephen F. Badylak
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2105-15-S16-S6

FMAj: a tool for high content analysis of muscle dynamics in Drosophila metamorphosis
Cited by: 9
Author(s): Yadav Kuleesha, Wee Choo Puah, Feng Lin, Martin Wasser
Software Mentions: 2
Published: over 10 years ago

10.1038/sdata.2018.81

A multi-phenotypic imaging screen to identify bacterial effectors by exogenous expression in a HeLa cell line
Cited by: 3
Author(s): Adam Collins, Alan Huett
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1007744

Control of nongenetic heterogeneity in growth rate and stress tolerance of Saccharomyces cerevisiae by cyclic AMP-regulated transcription factors
Cited by: 30
Author(s): Shuang Li, Daniella M. Giardina, Mark L. Siegal
Software Mentions: 2
Published: over 6 years ago

10.1073/pnas.2021450118

Targeting transcriptional regulation of SARS-CoV-2 entry factors ACE2 and TMPRSS2
Cited by: 133
Author(s): Yuanyuan Qiao, Xiaoming Wang, Rahul Mannan, Sethuramasundaram Pitchiaya, Yuping Zhang, Jesse W Wotring, Lanbo Xiao, Dan R. Robinson, Yi-Mi Wu, Jean C. Tien, Xuhong Cao, Stephanie A. Simko, Ingrid J. Apel, Pushpinder Bawa, Steven Kregel, Sathiya Pandi Narayanan, Gregory Raskind, Stephanie J. Ellison, Abhijit Parolia, Sylvia Zelenka-Wang, Lisa McMurry, Fengyun Su, Rui Wang, Yunhui Cheng, Andrew Delekta, Zejie Mei, Carla D. Pretto, Shaomeng Wang, Rohit Mehra, Jonathan Z. Sexton, Arul M. Chinnaiyan
Software Mentions: 2
Published: over 4 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: about 4 years ago

10.1371/journal.ppat.1008656

Influenza A viruses use multivalent sialic acid clusters for cell binding and receptor activation
Cited by: 34
Author(s): Christian Sieben, Erdinç Sezgin, Christian Eggeling, Suliana Manley
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.ppat.1008690

Inhibition of anti-viral stress granule formation by coronavirus endoribonuclease nsp15 ensures efficient virus replication
Cited by: 68
Author(s): Bo Gao, Xiaoyi Gong, Shouguo Fang, Wenlian Weng, Huan Wang, Hongyan Chu, Yingjie Sun, Meng Chen, Lei Tan, Song Chen, Xusheng Qiu, Weiwei Liu, Maria Forlenza, Chan Ding, Ying Liao
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1006353

A Multistate Toggle Switch Defines Fungal Cell Fates and Is Regulated by Synergistic Genetic Cues
Cited by: 24
Author(s): Matthew Anderson, Allison M. Porman, Na Wang, Eugenio Mancera, Denis Huang, Christina A. Cuomo, Richard J. Bennett
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.ppat.1007698

Proximity-dependent proteomics of the Chlamydia trachomatis inclusion membrane reveals functional interactions with endoplasmic reticulum exit sites
Cited by: 24
Author(s): Mary S Dickinson, Lindsey Anderson, Bobbie-Jo M. Webb-Robertson, Joshua Hansen, Richard Smith, Aaron Wright, Kevin Hybiske
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1006354

A second wave of Salmonella T3SS1 activity prolongs the lifespan of infected epithelial cells
Cited by: 42
Author(s): Ciaran E. Finn, Audrey Chong, Kendal G. Cooper, Tregei Starr, Olivia Steele‐Mortimer
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.ppat.1008554

The ATGL lipase cooperates with ABHD5 to mobilize lipids for hepatitis C virus assembly
Cited by: 21
Author(s): Gabrielle Vièyres, I. Reichert, Arnaud Carpentier, Florian W. R. Vondran, Thomas Pietschmann
Software Mentions: 2
Published: about 5 years ago

10.1172/JCI132987

3D model of harlequin ichthyosis reveals inflammatory therapeutic targets
Cited by: 28
Author(s): Florence Enjalbert, P. Dewan, Matthew Caley, Erica Jones, Mary A. Morse, David P. Kelsell, Anton J. Enright, Edel A. O’Toole
Software Mentions: 2
Published: almost 5 years ago

10.1083/jcb.202012114

CYRI-A limits invasive migration through macropinosome formation and integrin uptake regulation
Cited by: 14
Author(s): Anh Hoang Le, Tamas Yelland, Nikki R. Paul, Loïc Fort, Savvas Nikolaou, Shehab Ismail, Laura M. Machesky
Software Mentions: 2
Published: about 4 years ago

10.1083/jcb.201904113

ALIX- and ESCRT-III–dependent sorting of tetraspanins to exosomes
Cited by: 188
Author(s): Jorge Larios, Vincent Mercier, Aurélien Roux, Jean Grüenberg
Software Mentions: 2
Published: over 5 years ago

10.1186/s13036-019-0161-8

Tools to reverse-engineer multicellular systems: case studies using the fruit fly
Cited by: 9
Author(s): Qinfeng Wu, Nilay Kumar, Vijay Velagala, Jeremiah J. Zartman
Software Mentions: 2
Published: over 6 years ago

10.1083/jcb.201908132

LUZP1 and the tumor suppressor EPLIN modulate actin stability to restrict primary cilia formation
Cited by: 22
Author(s): João Gonçalves, Amit Sharma, Étienne Coyaud, Estelle Laurent, Brian Raught, Laurence Pelletier
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.ppat.1003640

A Structural Basis for BRD2/4-Mediated Host Chromatin Interaction and Oligomer Assembly of Kaposi Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus LANA Proteins
Cited by: 75
Author(s): Jan Hellert, Magdalena Weidner-Glunde, J. Krausze, Ulrike Richter, Heiko Adler, Roman Fedorov, Marcel Pietrek, Jessica Rückert, Christiane Ritter, Thomas F. Schulz, Thorsten Lührs
Software Mentions: 2
Published: almost 12 years ago

10.1016/j.jbc.2021.100633

Early nucleolar responses differentiate mechanisms of cell death induced by oxaliplatin and cisplatin
Cited by: 26
Author(s): Emily Sutton, Victoria J. DeRose
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pcbi.1008974

The hierarchical packing of euchromatin domains can be described as multiplicative cascades
Cited by: 3
Author(s): Amra Noa, Hui-Shun Kuan, Vera Aschmann, Vasily Zaburdaev, Lennart Hilbert
Software Mentions: 2
Published: about 4 years ago

10.1016/j.jbc.2021.101003

Development of a specific live-cell assay for native autophagic flux
Cited by: 7
Author(s): Nathaniel Safren, Elizabeth M.H. Tank, Aatika Malik, Jason P. Chua, Nicholas Santoro, Sami J. Barmada
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2105-11-287

Colonyzer: automated quantification of micro-organism growth characteristics on solid agar
Cited by: 63
Author(s): Conor Lawless, Darren J. Wilkinson, A. E. Young, Stephen G. Addinall, David Lydall
Software Mentions: 2
Published: about 15 years ago

10.1074/jbc.RA120.015398

AggreCount: an unbiased image analysis tool for identifying and quantifying cellular aggregates in a spatially defined manner
Cited by: 28
Author(s): Jacob Klickstein, Sirisha Mukkavalli, Malavika Raman
Software Mentions: 2
Published: over 4 years ago

10.1172/jci.insight.141486

CD109-GP130 interaction drives glioblastoma stem cell plasticity and chemoresistance through STAT3 activity
Cited by: 21
Author(s): Pauliina Filppu, Jayendrakishore Tanjore Ramanathan, Kirsi J. Granberg, Erika Gucciardo, Hannu Haapasalo, Kaisa Lehti, Matti Nykter, Vadim Le Joncour, Pirjo Laakkonen
Software Mentions: 2
Published: about 4 years ago

10.1128/JB.00460-18

Connecting the Dots between Mechanosensitive Channel Abundance, Osmotic Shock, and Survival at Single-Cell Resolution
Cited by: 11
Author(s): Griffin Chure, Heun Jin Lee, Akiko Rasmussen, Rob Phillips
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1005263

Interferon-γ Inhibits Ebola Virus Infection
Cited by: 69
Author(s): Bethany A. Rhein, Linda S. Powers, Kai J. Rogers, Manu Anantpadma, Brajesh K. Singh, Yoshio Sakurai, Thomas B. Bair, Catherine L. Miller-Hunt, Patrick L. Sinn, Robert A. Davey, Martha M. Monick, Wendy Maury
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pcbi.1005177

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments
Cited by: 425
Author(s): David Ashley Van Valen, Tetsuichi Kudo, Keara Lane, Derek N. Macklin, Nicolas Quach, Mialy M. DeFelice, Inbal Maayan, Tao Yu, Euan A. Ashley, Markus W. Covert
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pcbi.1003670

A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis
Cited by: 25
Author(s): Carlos Castro-González, Miguel Luengo-Oroz, Louise Duloquin, Thierry Savy, B Rizzi, Sophie Desnoulez, René Doursat, Yannick Kergosien, María J. Ledesma-Carbayo, Paul Bourgine, Nadine Peyriéras, A. Santos
Software Mentions: 2
Published: about 11 years ago

10.1093/gigascience/giw014

A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay
Cited by: 84
Author(s): Mark-Anthony Bray, Sigrún M. Gústafsdóttir, Mohammad Hossein Rohban, Shantanu Singh, Vebjorn Ljosa, Katherine L Sokolnicki, Joshua A. Bittker, Nicole E. Bodycombe, Vlado Dančík, Thomas Hasaka, C. Suk-Yee Hon, Melissa M. Kemp, Kejie Li, Deepika Walpita, Mathias Wawer, Todd R. Golub, Stuart L. Schreiber, Paul A. Clemons, Alykhan F. Shamji, Anne E. Carpenter
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pcbi.1007673

DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning
Cited by: 125
Author(s): Jean-Baptiste Lugagne, Haonan Lin, Mary J. Dunlop
Software Mentions: 2
Published: over 5 years ago

10.1128/AAC.01002-20

The FDA-Approved Drug Nelfinavir Inhibits Lytic Cell-Free but Not Cell-Associated Nonlytic Transmission of Human Adenovirus
Cited by: 16
Author(s): Fanny Georgi, Vardan Andriasyan, Robert Witte, Luca Murer, Silvio Hemmi, Lisa Yu, Melanie Grove, Nicole Meili, Fabien Kuttler, Artur Yakimovich, Gerardo Turcatti, Urs F. Greber
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13059-014-0442-y

GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images
Cited by: 9
Author(s): Anne Trinh, Inga Hansine Rye, Vanessa Almendro, Åslaug Helland, Hege G. Russnes, Florian Markowetz
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12859-020-03603-5

A cell-level quality control workflow for high-throughput image analysis
Cited by: 3
Author(s): Minhua Qiu, Bin Zhou, Frederick Lo, Steven C. Cook, Jason Chyba, Doug Quackenbush, Jason Matzen, Zhizhong Li, Puiying A. Mak, Kaisheng Chen, Yingyao Zhou
Software Mentions: 2
Published: about 5 years ago

10.1186/s13059-021-02301-6

Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity
Cited by: 5
Author(s): Matan Sorek, Walaa Oweis, Malka Nissim-Rafinia, Moria Maman, Shahar Simon, Cynthia C. Hession, Xian Adiconis, Sean Simmons, Neville E. Sanjana, Xi Shi, Congyi Lu, Jen Q. Pan, Xiaohong Xu, Mahmoud A. Pouladi, Lisa M. Ellerby, Feng Zhang, Joshua Z. Levin, Eran Meshorer
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2020.01275

Volumetric Segmentation of Cell Cycle Markers in Confocal Images Using Machine Learning and Deep Learning
Cited by: 3
Author(s): Faraz Ahmad Khan, Ute Voß, Michael P. Pound, A. P. French
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pbio.2003998

Stable centrosomal roots disentangle to allow interphase centriole independence
Cited by: 13
Author(s): Robert Mahen
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2015.01187

Developmental Nuclear Localization and Quantification of GFP-Tagged EB1c in Arabidopsis Root Using Light-Sheet Microscopy
Cited by: 15
Author(s): Dominik Novák, Anna Kuchařová, Miroslav Ovečka, George Komis, Jozef Šamaj
Software Mentions: 2
Published: over 9 years ago

10.1172/jci.insight.139445

Smooth muscle–derived progenitor cell myofibroblast differentiation through KLF4 downregulation promotes arterial remodeling and fibrosis
Cited by: 30
Author(s): Sizhao Lu, Austin Jolly, Keith A. Strand, Allison Dubner, Marie Mutryn, Karen S. Moulton, Raphael A. Nemenoff, Mark W. Majesky, Mary C.M. Weiser‐Evans
Software Mentions: 2
Published: over 4 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 7 years ago

10.1371/journal.pbio.2005970

CellProfiler 3.0: Next-generation image processing for biology
Cited by: 1,445
Author(s): Claire McQuin, Allen Goodman, Vasiliy S. Chernyshev, Lee Kamentsky, Beth A. Cimini, Kyle W. Karhohs, Minh Doan, Liya Ding, Susanne M. Rafelski, Derek Thirstrup, Winfried Wiegraebe, Shantanu Singh, Tim Becker, Juan C. Caicedo, Anne E. Carpenter
Software Mentions: 2
Published: about 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 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 4 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 9 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 5 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 5 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 4 years ago

10.1371/journal.pbio.3000297

Cytosine-5 RNA methylation links protein synthesis to cell metabolism
Cited by: 79
Author(s): Nikoletta A. Gkatza, Cecilia Castro, R Harvey, MM Heiss, Martyna Popis, Sandra Blanco, Susanne Bornelöv, Abdulrahim A. Sajini, Joseph G. Gleeson, Julian L. Griffin, James A. West, Stefanie Kellner, Anne E. Willis, Sabine Dietmann, Michaela Frye
Software Mentions: 2
Published: about 6 years ago

10.1038/s42003-021-01708-y

Insulin-like 3 affects zebrafish spermatogenic cells directly and via Sertoli cells
Cited by: 8
Author(s): Diego Crespo, Luiz H. C. Assis, Yu Ting Zhang, Diego Safian, Tomasz Furmanek, Kai Ove Skaftnesmo, Birgitta Norberg, Wei Ge, Yung Ching Choi, Marjo J. den Broeder, Juliette Legler, Jan Bogerd, Rüdiger Schulz
Software Mentions: 2
Published: over 4 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 4 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 6 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: almost 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 4 years ago

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Papers Mentioning CellProfiler 1,504