pypi: CellProfiler | Projects | Ecosyste.ms: Papers

10.7554/eLife.70560

Processing of the ribosomal ubiquitin-like fusion protein FUBI-eS30/FAU is required for 40S maturation and depends on USP36
Cited by: 5
Author(s): Jasmin van den Heuvel, Caroline Ashiono, Ludovic Gillet, Kerstin Dörner, Emanuel Wyler, Ivo Zemp, Ulrike Kutay
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.22693

The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels
Cited by: 77
Author(s): A. J. Miles, Stephen P. Burr, GL Grice, James A. Nathan
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.52370

Cortical RORβ is required for layer 4 transcriptional identity and barrel integrity
Cited by: 14
Author(s): Erin Clark, Michael Rutlin, Lucia Capano, Samuel Aviles, Jordan R Saadon, Praveen Taneja, Qiyu Zhang, James B. Bullis, Timothy Lauer, Emma Myers, Anton Schulmann, Douglas Forrest, Sacha B. Nelson
Software Mentions: 3
Published: almost 5 years ago

10.15252/msb.20178064

Large‐scale image‐based profiling of single‐cell phenotypes in arrayed CRISPR‐Cas9 gene perturbation screens
Cited by: 55
Author(s): Reinoud E. A. de Groot, Joel Lüthi, Helen Lindsay, René Holtackers, Lucas Pelkmans
Software Mentions: 3
Published: over 7 years ago

10.15252/msb.20178007

Antisense transcription‐dependent chromatin signature modulates sense transcript dynamics
Cited 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 7 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: over 5 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: about 7 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: almost 4 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: over 8 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: about 4 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: almost 12 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: about 4 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: almost 9 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

10.7717/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: about 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

10.1007/s00497-020-00398-6

Quantitative methods in microscopy to assess pollen viability in different plant taxa
Cited by: 9
Author(s): Lorenzo Ascari, Cristina Novara, Virginia Dusio, Ludovica Oddi, Consolata Siniscalco
Software Mentions: 3
Published: almost 5 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: almost 10 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: 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: about 4 years ago

10.15252/embj.201489282

Aberrant methylation of t<scp>RNA</scp>s links cellular stress to neuro‐developmental disorders
Cited 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: about 11 years ago

10.1007/s00018-020-03682-w

Semaphorin 7A restricts serotonergic innervation and ensures recovery after spinal cord injury
Cited by: 10
Author(s): Kristina Loy, Julie Fourneau, Ning Meng, Carmen K. Denecke, Giuseppe Locatelli, Florence M. Bareyre
Software Mentions: 3
Published: almost 5 years ago

10.1242/dev.199616

Deep learning for bioimage analysis in developmental biology
Cited by: 24
Author(s): Adrien Hallou, Hannah Yevick, Bianca Dumitrascu, Virginie Uhlmann
Software Mentions: 3
Published: almost 4 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: about 4 years ago

10.1186/s12964-019-0336-4

Autocrine motility factor promotes endometrial cancer progression by targeting GPER-1
Cited by: 22
Author(s): Yiran Li, Yuanhui Jia, Yiding Bian, Huan Tong, Junjie Qu, Kai Wang, Xiaoping Wan
Software Mentions: 3
Published: over 6 years ago

10.1038/s42003-021-02517-z

Comprehensive in situ mapping of human cortical transcriptomic cell types
Cited 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: almost 4 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: over 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

10.1371/journal.ppat.1002957

De novo GTP Biosynthesis Is Critical for Virulence of the Fungal Pathogen Cryptococcus neoformans
Cited by: 53
Author(s): Carl A. Morrow, Eugene Valkov, Anna Stamp, Eve W. L. Chow, I. Russel Lee, Ania Wronski, Simon J. Williams, Jennifer Hill, Julianne T. Djordjevic, Ulrike Kappler, Boštjan Kobe, James S. Fraser
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41419-021-03408-1

SCA-1 micro-heterogeneity in the fate decision of dystrophic fibro/adipogenic progenitors
Cited by: 13
Author(s): Giulio Giuliani, Simone Vumbaca, Claudia Fuoco, Cesare Gargioli, Ezio Giorda, Giorgia Massacci, Alessandro Palma, Alessio Reggio, Federica Riccio, Marco Rosina, Maria Vinci, Luisa Castagnoli, Gianni Cesareni
Software Mentions: 3
Published: over 4 years ago

10.1016/j.celrep.2019.03.108

PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination
Cited by: 53
Author(s): Ana Mendanha Falcão, Mandy Meijer, Antonella Scaglione, Puneet Rinwa, Eneritz Agirre, Jialiang Liang, Sara C. Buch-Larsen, Abeer Heskol, Rebecca Frawley, Michael Klingener, Manuel Varas-Godoy, Alexandre A.S.F. Raposo, Patrik Ernfors, Diogo S. Castro, Michael L. Nielsen, Patrizia Casaccia, Gonçalo Castelo‐Branco
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giaa156

Identifying the effect of vancomycin on health care–associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media
Cited by: 4
Author(s): Abhishek Rajput, Saugat Poudel, Hannah Tsunemoto, Michael J. Meehan, Richard Szubin, Connor A. Olson, Yara Seif, Anne Lamsa, Nicholas Dillon, Alison Vrbanac, Joseph Sugie, Samira Dahesh, Jonathan M. Monk, Pieter C. Dorrestein, Rob Knight, Joe Pogliano, Victor Nizet, Adam M. Feist, Bernhard Ø. Palsson
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.ppat.1009687

The endogenous cellular protease inhibitor SPINT2 controls SARS-CoV-2 viral infection and is associated to disease severity
Cited by: 4
Author(s): Carlos Ramirez Alvarez, Carmon Kee, Ashwini Kumar Sharma, Leonie Thomas, Florian I. Schmidt, Megan L. Stanifer, Steeve Boulant, Carl Herrmann
Software Mentions: 3
Published: about 4 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: almost 4 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: over 4 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: over 4 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: about 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: about 8 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

10.1007/s00018-020-03467-1

The Rab5 activator RME-6 is required for amyloid precursor protein endocytosis depending on the YTSI motif
Cited by: 7
Author(s): Simone Eggert, Tomas Gruebl, Ritu Rajender, Carsten Rupp, Bianca Sander, Amelie Heesch, Marius Zimmermann, Sebastian Hoepfner, Hanswalter Zentgraf, Stefan Kins
Software Mentions: 2
Published: over 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: about 11 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

10.1186/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

10.1038/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.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

10.1093/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.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

10.1371/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.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

10.1172/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

10.1073/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

10.1038/s41419-017-0039-y

Systems modeling accurately predicts responses to genotoxic agents and their synergism with BCL-2 inhibitors in triple negative breast cancer cells
Cited by: 37
Author(s): Federico Lucantoni, Andreas U. Lindner, Norma O’Donovan, Heiko Düßmann, Jochen H M Prehn
Software Mentions: 2
Published: over 7 years ago

10.1002/cyto.a.23794

Label‐Free Identification of White Blood Cells Using Machine Learning
Cited by: 62
Author(s): Mariam Nassar, Minh Doan, Andrew Filby, Olaf Wolkenhauer, Darin K. Fogg, Justyna Piasecka, Catherine A. Thornton, Anne E. Carpenter, Huw D. Summers, Paul Rees, Holger Hennig
Software Mentions: 2
Published: about 6 years ago

10.1016/j.celrep.2018.03.021

Extracellular Monomeric and Aggregated Tau Efficiently Enter Human Neurons through Overlapping but Distinct Pathways
Cited by: 143
Author(s): Lewis Evans, Thomas Wassmer, Graham Fraser, James Smith, Michael S. Perkinton, Andrew Billinton, Frederick J. Livesey
Software Mentions: 2
Published: over 7 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

10.1186/1478-811X-11-24

Light microscopy applications in systems biology: opportunities and challenges
Cited by: 35
Author(s): Paul Paul Michel Aloyse Antony, Christophe Trefois, Aleksandar Stojanović, Aidos Baumuratov, Karol Kozak
Software Mentions: 2
Published: over 12 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

10.1016/j.celrep.2021.109280

Positive feedback between the T cell kinase Zap70 and its substrate LAT acts as a clustering-dependent signaling switch
Cited by: 6
Author(s): Elliot Dine, Ellen H. Reed, Jared E. Toettcher
Software Mentions: 2
Published: about 4 years ago

10.1016/j.celrep.2018.04.044

mTOR Senses Environmental Cues to Shape the Fibroblast-like Synoviocyte Response to Inflammation
Cited by: 46
Author(s): Thomas Karonitsch, Richard K. Kandasamy, Felix Kartnig, Barbara Herdy, K Dalwigk, Birgit Niederreiter, Johannes Holinka, Florian Sevelda, Reinhard Windhager, Martin Bilban, Thomas Weichhart, Marcus D. Säemann, Thomas Pap, Günter Steiner, Josef S Smolen, Hans P. Kiener, Giulio Superti‐Furga
Software Mentions: 2
Published: over 7 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

10.1128/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

10.1242/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

10.1074/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

10.1016/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

10.1016/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

10.3390/cells9030673

Cyclin-Dependent Kinase 18 Controls Trafficking of Aquaporin-2 and Its Abundance through Ubiquitin Ligase STUB1, Which Functions as an AKAP
Cited by: 18
Author(s): Alessandro Dema, Dörte Faust, Katina Lazarow, Marc Wippich, Martin Neuenschwander, Kerstin Zühlke, Andrea Geelhaar, Tamara Pallien, Eileen Hallscheidt, Jenny Eichhorst, Burkhard Wiesner, Hana Černecká, Oliver Popp, Philipp Mertins, Gunnar Dittmar, Jens Peter von Kries, Jens Peter Klußmann
Software Mentions: 2
Published: over 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

10.1177/1087057116652064

A Novel Automated High-Content Analysis Workflow Capturing Cell Population Dynamics from Induced Pluripotent Stem Cell Live Imaging Data
Cited by: 16
Author(s): Maximilian Kerz, Amos Folarin, Ruta Meleckyte, Fiona M. Watt, Richard Dobson, Davide Danovi
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.cmet.2019.12.012

Calcitonin Receptor Neurons in the Mouse Nucleus Tractus Solitarius Control Energy Balance via the Non-aversive Suppression of Feeding
Cited by: 63
Author(s): Wenwen Cheng, Ian E. Gonzalez, Warren Pan, Anthony H. Tsang, Jeffrey Adams, Ermelinda Ndoka, Desiree Gordian, Basma Khoury, Karen J. Roelofs, Simon S. Evers, Andrew MacKinnon, Shuangcheng Wu, Henriette Frikke-Schmidt, Jonathan N. Flak, James L. Trevaskis, Christopher J. Rhodes, So‐ichiro Fukada, Randy J. Seeley, Darleen A. Sandoval, David P. Olson, Clémence Blouet, Martin G. Myers
Software Mentions: 2
Published: over 5 years ago

10.3390/cells10040838

Aquaglyceroporin-3’s Expression and Cellular Localization Is Differentially Modulated by Hypoxia in Prostate Cancer Cell Lines
Cited by: 5
Author(s): Andreia de Almeida, Dimitris Parthimos, Holly Dew, Oliver S. Smart, Marie Wiltshire, Rachel J. Errington
Software Mentions: 2
Published: over 4 years ago

10.1083/jcb.201904113

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

10.1083/jcb.201908132

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

10.1016/j.stem.2021.03.022

Commitment and oncogene-induced plasticity of human stem cell-derived pancreatic acinar and ductal organoids
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Author(s): Ling Huang, Ridhdhi Desai, Daniel N. Conrad, Nayara C. Leite, Dipikaa Akshinthala, Christine Lim, Raúl González, Lakshmi Muthuswamy, Zev J. Gartner, Senthil K. Muthuswamy
Software Mentions: 2
Published: about 4 years ago

10.1016/j.cels.2020.04.003

nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer
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Author(s): Réka Hollandi, Ábel Szkalisity, Tímea Tóth, Ervin Tasnádi, Csaba Molnár, Botond Mathe, István Grexa, J. Molnár, Árpád Bálind, Mate Gorbe, Mária Kovács, Ede Migh, Allen Goodman, Tamás Balassa, Krisztián Koós, Wenyu Wang, Juan C. Caicedo, Norbert Bara, Ferenc Kovács, Lassi Paavolainen, Tivadar Danka, András Kriston, Anne E. Carpenter, Kevin Smith, Péter Horváth
Software Mentions: 2
Published: over 5 years ago

10.1186/s13630-019-0061-z

New software for automated cilia detection in cells (ACDC)
Cited by: 16
Author(s): Max C. Lauring, Tianqi Zhu, Wei Luo, Wenqi Wu, Feng Yu, Derek Toomre
Software Mentions: 2
Published: about 6 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

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

10.1016/j.cels.2018.02.001

Microenvironment-Mediated Mechanisms of Resistance to HER2 Inhibitors Differ between HER2+ Breast Cancer Subtypes
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Author(s): Spencer S. Watson, Mark Dane, Koei Chin, Zuzana Tatárová, Moqing Liu, Tiera Liby, Wallace Thompson, Rebecca Smith, Michel Nederlof, Elmar Bucher, David Kilburn, Matthew A. Whitman, Damir Sudar, Gordon B. Mills, Laura M. Heiser, Oliver Jonas, Joe W. Gray, James E. Korkola
Software Mentions: 2
Published: over 7 years ago

10.15252/embj.201798714

Evidence for the nuclear import of histones H3.1 and H4 as monomers
Cited by: 39
Author(s): Michael James Apta‐Smith, Juan R. Hernández-Fernaud, Andrew Bowman
Software Mentions: 2
Published: almost 7 years ago

10.1242/jcs.249706

DROSHA is recruited to DNA damage sites by the MRN complex to promote non-homologous end joining
Cited by: 9
Author(s): Matteo Cabrini, Marco Roncador, Alessandro Galbiati, Lina Cipolla, Antonio Maffia, Fabio Iannelli, Simone Sabbioneda, Fabrizio d’Adda di Fagagna, Sofia Francia
Software Mentions: 2
Published: over 4 years ago

10.1172/JCI132987

3D model of harlequin ichthyosis reveals inflammatory therapeutic targets
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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

10.15252/embj.2020104948

Receptor‐mediated clustering of FIP200 bypasses the role of LC3 lipidation in autophagy
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Author(s): Amelia E Ohnstad, José A. Delgado Delgado, Brian J. North, Isha Nasa, Arminja N. Kettenbach, Sebastian W. Schultz, Christopher J. Shoemaker
Software Mentions: 2
Published: over 4 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

10.15252/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/s42003-019-0626-9

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

10.15252/embj.2020107182

Reciprocal priming between receptor tyrosine kinases at recycling endosomes orchestrates cellular signalling outputs
Cited by: 9
Author(s): Michael P. Smith, Harriet R. Ferguson, Jennifer Ferguson, Egor Zindy, Katarzyna M. Kowalczyk, Thomas Kedward, Christian Bates, Joseph Parsons, Joanne Watson, Sarah Chandler, Paul Fullwood, Stacey Warwood, David Knight, Robert B. Clarke, Chiara Francavilla
Software Mentions: 2
Published: about 4 years ago

10.1016/j.cell.2018.02.030

Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis
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Author(s): Mikhail M. Savitski, Nico Zinn, Maria Faelth-Savitski, Daniel Poeckel, Stephan Gade, Isabelle Becher, Marcel Muelbaier, Anne J. Wagner, Katrin Strohmer, Thilo Werner, Stephanie Melchert, Massimo Petretich, Anna Rutkowska, Johanna Vappiani, Holger Franken, Michael Steidel, Gavain Sweetman, Omer Gilan, Enid Y.N. Lam, Mark A. Dawson, Rab K. Prinjha, Paola Grandi, Giovanna Bergamini, Marcus Bantscheff
Software Mentions: 2
Published: over 7 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
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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

10.1186/s13578-021-00618-0

A ribonucleoprotein transfection strategy for CRISPR/Cas9‐mediated gene editing and single cell cloning in rainbow trout cells
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Author(s): Marina Zoppo, Nicole Okoniewski, Stanislav Pantelyushin, Johannes vom Berg, Kristin Schirmer
Software Mentions: 2
Published: about 4 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

10.3389/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

10.1038/s41419-020-2704-9

Reduced replication origin licensing selectively kills KRAS-mutant colorectal cancer cells via mitotic catastrophe
Cited by: 4
Author(s): Bastian Gastl, Kathleen Klotz-Noack, Bertram Klinger, Sylvia Ispasanie, Krenoula Hani Fouad Salib, Johannes Zuber, Soulafa Mamlouk, Natalie Bublitz, Nils Blüthgen, David Horst, Markus Morkel, Reinhold Schäfer, Christine Sers
Software Mentions: 2
Published: about 5 years ago

10.1038/s42003-021-01708-y

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

10.3390/cells9061423

Chromatin Trapping of Factors Involved in DNA Replication and Repair Underlies Heat-Induced Radio- and Chemosensitization
Cited by: 3
Author(s): Artem V. Luzhin, Bogdan Avanesyan, Artem K. Velichko, Victoria О. Shender, Natalia Ovsyannikova, Georgij Arapidi, Polina V. Shnaider, Nadezhda V. Petrova, Igor I. Kireev, Sergey V. Razin, Omar L. Kantidze
Software Mentions: 2
Published: about 5 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

10.1038/s41598-020-78764-7

Leaf proteome modulation and cytological features of seagrass Cymodocea nodosa in response to long-term high CO2 exposure in volcanic vents
Cited by: 2
Author(s): Amalia Piro, Letizia Bernardo, Ilia Anna Serra, Isabel Barrote, Irene Olivé, Monya M. Costa, Luigi Lucini, Rui Santos, Silvia Mazzuca, João Silva
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-75835-7

A versatile toolbox for semi-automatic cell-by-cell object-based colocalization analysis
Cited by: 19
Author(s): Anders Lunde, Joel C. Glover
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-82752-w

Integrins mediate placental extracellular vesicle trafficking to lung and liver in vivo
Cited by: 27
Author(s): Sean L. Nguyen, Soo Hyun Ahn, Jacob W. Greenberg, Benjamin W. Collaer, Dalen Agnew, Ritu Arora, Margaret G. Petroff
Software Mentions: 2
Published: over 4 years ago

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