pypi: CellProfiler | Projects | Ecosyste.ms: Papers

10.1186/1471-2105-8-117

Colony size measurement of the yeast gene deletion strains for functional genomics
Cited by: 51
Author(s): Negar Memarian, Matthew Jessulat, Javad Alirezaie, Nadereh Mir-Rashed, Jianhua Xu, Mehri Zareie, Myron L. Smith, Ashkan Golshani
Software Mentions: 3
Published: over 18 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

10.7554/eLife.39234

Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources
Cited by: 38
Author(s): Bram Cerulus, Abbas Jariani, Gemma Perez-Samper, Lieselotte Vermeersch, Julian Pietsch, Matthew M. Crane, Aaron M. New, Brigida Gallone, Miguel Roncoroni, Maria C. Dzialo, Sander K. Govers, Jhana O. Hendrickx, Eva Galle, Maarten Coomans, Pieter Berden, Sara Verbandt, Peter S. Swain, Kevin J. Verstrepen
Software Mentions: 3
Published: about 7 years ago

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: over 4 years ago

10.1093/bioinformatics/btab185

GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction
Cited by: 24
Author(s): Zhiqin Wang, Ruiqing Li, Minghui Wang, Ao Li
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

10.1093/bioinformatics/btaa1061

cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data
Cited by: 31
Author(s): Nils Eling, Nicolas Damond, Tobias Hoch, Bernd Bodenmiller
Software Mentions: 3
Published: almost 5 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

10.1038/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

10.1186/1751-0473-8-16

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

10.1371/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

10.1016/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

10.1155/2021/9975423

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

10.1038/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

10.15252/msb.202010188

SARS‐CoV‐2 infection remodels the host protein thermal stability landscape
Cited by: 15
Author(s): Joel Selkrig, Megan L. Stanifer, André Mateus, Karin Mitosch, Iñigo Barrio-Hernandez, Mandy Rettel, Heeyoung Kim, Carlos G.P. Voogdt, Philipp Walch, Carmon Kee, Nils Kurzawa, Frank Stein, Clement M Potel, Anna Jarząb, Bernhard Küster, Ralf Bartenschlager, Steeve Boulant, Pedro Beltrão, Athanasios Typas, Mikhail M. Savitski
Software Mentions: 3
Published: almost 5 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

10.1038/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

10.1073/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

10.15252/msb.202010135

The circadian oscillator analysed at the single‐transcript level
Cited by: 6
Author(s): Nicholas E. Phillips, Alice Hugues, Jake Yeung, Eric Durandau, Damien Nicolas, Félix Naef
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

10.1371/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

10.1038/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

10.1038/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

10.1083/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

10.1371/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.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: about 13 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

10.1016/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

10.1016/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

10.1371/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

10.1111/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.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

10.1093/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: almost 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

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: about 5 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: over 4 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

10.7554/eLife.69795

A zebrafish screen reveals Renin-angiotensin system inhibitors as neuroprotective via mitochondrial restoration in dopamine neurons
Cited by: 18
Author(s): Ghahyun J. Kim, Han Mo, Harrison Liu, Zhihao Wu, Steven Chen, Jiashun Zheng, Xiang Zhao, Daryl Nucum, James Shortland, Longping Peng, Mannuel Elepano, Benjamin C. Tang, Steven H. Olson, Nick A. Paras, Hao Li, Adam R. Renslo, Michelle R. Arkin, Bo Huang, Bingwei Lu, Marina Sirota, Su Guo
Software Mentions: 3
Published: about 4 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: over 11 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: 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

10.1016/j.molcel.2017.04.027

Bromodomain Protein BRD4 Is a Transcriptional Repressor of Autophagy and Lysosomal Function
Cited by: 170
Author(s): Jun-Ichi Sakamaki, Simon Wilkinson, Marcel Hahn, Nilgun Tasdemir, Jim O’Prey, William Clark, Ann Hedley, Colin Nixon, Jaclyn Long, Maria I. New, Tim Van Acker, Sharon A. Tooze, Scott W. Lowe, Ivan Đikić, Kevin M. Ryan
Software Mentions: 2
Published: over 8 years ago

10.1016/j.molcel.2018.02.023

Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability
Cited by: 130
Author(s): Dominika Kwaśna, S.A. Abdul Rehman, N. Jayaprakash, S. Matthews, Ross Madden, Virginia De Cesare, Simone Weidlich, Satpal Virdee, Ivan Ahel, Ian Gibbs-Seymour, Yogesh Kulathu
Software Mentions: 2
Published: over 7 years ago

10.1111/acel.13468

Inhibition of the cGAS‐STING pathway ameliorates the premature senescence hallmarks of Ataxia‐Telangiectasia brain organoids
Cited by: 28
Author(s): Julio Aguado, Harman Chaggar, Cecilia Gómez-Inclán, Mohammed R. Shaker, Hannah C Leeson, Alan Mackay‐Sim, Ernst J. Wolvetang
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: almost 10 years ago

10.1016/j.molcel.2019.08.005

Polyamines Control eIF5A Hypusination, TFEB Translation, and Autophagy to Reverse B Cell Senescence
Cited by: 189
Author(s): Hanlin Zhang, Ghada Alsaleh, Jack Feltham, Yizhe Sun, Gennaro Napolitano, Thomas Riffelmacher, P. David Charles, Lisa Frau, Philip Hublitz, Zhanru Yu, Shabaz Mohammed, Andrea Ballabio, Stefan Balabanov, Jane Mellor, Anna Katharina Simon
Software Mentions: 2
Published: about 6 years ago

10.3389/fonc.2020.00292

Transcriptomic and Functional Screens Reveal MicroRNAs That Modulate Prostate Cancer Metastasis
Cited by: 6
Author(s): S. Madhusudana Rao, Alison Howarth, Patrick Krätschmer, Ann Snaith, Clarence Yapp, Daniel Ebner, Freddie C. Hamdy, Claire Edwards
Software Mentions: 2
Published: over 5 years ago

10.3389/fnana.2015.00142

Crowdsourcing the creation of image segmentation algorithms for connectomics
Cited by: 273
Author(s): Ignacio Arganda‐Carreras, Srinivas C. Turaga, Daniel R. Berger, Dan Cireşan, Alessandro Giusti, Luca Maria Gambardella, Juergen Schmidhuber, Dmitry Laptev, Sarvesh Dwivedi, Joachim M. Buhmann, Ting Liu, Mojtaba Seyedhosseini, Tolga Taşdizen, Lee Kamentsky, Radim Bürget, Václav Uher, Xiao Tan, Changming Sun, Tuan D. Pham, Erhan Bas, Mustafa Gökhan Uzunbaş, Albert Cardona, Johannes Schindelin, H. Sebastian Seung
Software Mentions: 2
Published: almost 10 years ago

10.3389/fnins.2021.629067

Recent Trends and Perspectives in Cerebral Organoids Imaging and Analysis
Cited by: 11
Author(s): Clara Brémond Martin, Camille Simon Chane, Cédric Clouchoux, Aymeric Histace
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2017.00627

Measuring Leukocyte Adhesion to (Primary) Endothelial Cells after Photon and Charged Particle Exposure with a Dedicated Laminar Flow Chamber
Cited by: 11
Author(s): N. Erbeldinger, Felicitas Rapp, Svetlana Ktitareva, Philipp Wendel, Anna S. Bothe, Till Dettmering, Marco Durante, Thomas Friedrich, Bianca Bertulat, Steven De Meyer, M. C. Cardoso, Stephanie Hehlgans, Franz Rödel, Claudia Fournier
Software Mentions: 2
Published: over 8 years ago

10.1038/micronano.2016.79

Subcellular western blotting of single cells
Cited by: 46
Author(s): Kevin A. Yamauchi, Amy E. Herr
Software Mentions: 2
Published: over 8 years ago

10.3389/fimmu.2021.671756

The 5-Phosphatase SHIP2 Promotes Neutrophil Chemotaxis and Recruitment
Cited by: 3
Author(s): Melina Michael, Barrett L. McCormick, Karen E. Anderson, Utsa Karmakar, Matthieu Vermeren, Stéphane Schurmans, Augustin Amour, Sonja Vermeren
Software Mentions: 2
Published: over 4 years ago

10.3389/fchem.2019.00791

Neuraminidase-3 Is a Negative Regulator of LFA-1 Adhesion
Cited by: 13
Author(s): Md. Amran Howlader, Caishun Li, Chunxia Zou, Radhika Chakraberty, Njuacha Ebesoh, Christopher W. Cairo
Software Mentions: 2
Published: almost 6 years ago

10.3389/fncel.2019.00535

Live-Cell Assays for Cell Stress Responses Reveal New Patterns of Cell Signaling Caused by Mutations in Rhodopsin, α-Synuclein and TDP-43
Cited by: 6
Author(s): Kevin Harlen, Elizabeth C. Roush, Joseph E. Clayton, Scott Martinka, Thom Hughes
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2020.578669

Environmental Factors Driving Spatial Heterogeneity in Desert Halophile Microbial Communities
Cited by: 9
Author(s): Gherman Uritskiy, Adam Munn, Micah Dailey, Diego Rivera Gelsinger, Samantha Getsin, Alfonso F. Dávila, Peter McCullough, James Taylor, Jocelyne DiRuggiero
Software Mentions: 2
Published: about 5 years ago

10.3389/fcell.2020.00579

Glucose Availability Alters Gene and Protein Expression of Several Newly Classified and Putative Solute Carriers in Mice Cortex Cell Culture and D. melanogaster
Cited by: 6
Author(s): Mikaela M. Ceder, Emilia Lekholm, Axel Klaesson, Rekha Tripathi, Nadine Schweizer, Lydia Weldai, Sourabh Patil, Robert Fredriksson
Software Mentions: 2
Published: over 5 years ago

10.3389/fcell.2020.584314

Transcriptome Response and Spatial Pattern of Gene Expression in the Primate Subventricular Zone Neurogenic Niche After Cerebral Ischemia
Cited by: 6
Author(s): Monika C Chongtham, Haifang Wang, Christina Thaller, Nai–Hua Hsiao, Ivan H. Vachkov, Stoyan Pavlov, Lorenz H Williamson, Tetsumori Yamashima, Anastassia Stoykova, Jun Yan, Gregor Eichele, Anton B. Tonchev
Software Mentions: 2
Published: almost 5 years ago

10.3389/fcell.2021.657192

Loss of stra8 Increases Germ Cell Apoptosis but Is Still Compatible With Sperm Production in Atlantic Salmon (Salmo salar)
Cited by: 5
Author(s): Kai Ove Skaftnesmo, Diego Crespo, Lene Kleppe, Eva Andersson, Rolf B. Edvardsen, Birgitta Norberg, Per Gunnar Fjelldal, Tom Hansen, Rüdiger Schulz, Anna Wargelius
Software Mentions: 2
Published: over 4 years ago

10.1016/j.ymeth.2016.08.018

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

10.1186/s12885-019-5813-z

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

10.1186/s12885-020-07533-6

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: almost 5 years ago

10.3389/fnagi.2021.704041

Poly (ADP-ribose) Interacts With Phosphorylated α-Synuclein in Post Mortem PD Samples
Cited by: 13
Author(s): Laura Puentes, Zsofia Lengyel‐Zhand, Ji Youn Lee, Chia-Ju Hsieh, Mark E. Schneider, Kimberly J. Edwards, Kelvin C. Luk, Virginia M.‐Y. Lee, John Q. Trojanowski, Robert H. Mach
Software Mentions: 2
Published: over 4 years ago

10.3389/fcell.2020.00570

ABHD11 Is Critical for Embryonic Stem Cell Expansion, Differentiation and Lipid Metabolic Homeostasis
Cited by: 4
Author(s): Gaoke Liu, Yan Ruan, Junlei Zhang, Xueyue Wang, Wei Wu, Ping He, Jiali Wang, Jiaxiang Xiong, Yuda Cheng, Lianlian Liu, Yi Yang, Yanping Tian, Rui Jian
Software Mentions: 2
Published: over 5 years ago

10.1016/j.ymeth.2020.05.017

An integrated pipeline for high-throughput screening and profiling of spheroids using simple live image analysis of frame to frame variations
Cited by: 12
Author(s): Haneen Alsehli, Fuad Mosis, Christopher Thompson, Eva Hamrud, Erika Wiseman, Eileen Gentleman, Davide Danovi
Software Mentions: 2
Published: over 4 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: almost 16 years ago

10.3389/fcell.2020.00493

Telomere Length Measurement by Molecular Combing
Cited by: 34
Author(s): Vívian Francília Silva Kahl, Joshua A. M. Allen, Christopher B. Nelson, Alexander P. Sobinoff, Michael Lee, Tatjana Kilo, Raja S. Vasireddy, Hilda A. Pickett
Software Mentions: 2
Published: over 5 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: over 5 years ago

10.3389/fcimb.2017.00475

Predictable, Tunable Protein Production in Salmonella for Studying Host-Pathogen Interactions
Cited by: 14
Author(s): Kendal G. Cooper, Audrey Chong, Tregei Starr, Ciaran E. Finn, Olivia Steele‐Mortimer
Software Mentions: 2
Published: almost 8 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: almost 9 years ago

10.12688/f1000research.16802.1

An in vitro model for studying CNS white matter: functional properties and experimental approaches
Cited by: 12
Author(s): Silvia Bijland, Gemma Thomson, Matthew Euston, Kyriakos Michail, Katja Thümmler, Steve Mücklisch, Colin L. Crawford, Susan C. Barnett, Marκ McLaughlin, Thomas Anderson, Christopher Linington, Euan R. Brown, Eric R. Kalkman, Julia M. Edgar
Software Mentions: 2
Published: almost 7 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: over 8 years ago

10.12688/f1000research.52531.1

Developing open-source software for bioimage analysis: opportunities and challenges
Cited by: 20
Author(s): Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
Software Mentions: 2
Published: over 4 years ago

10.1186/s12860-018-0166-z

Novel roles for scleraxis in regulating adult tenocyte function
Cited by: 35
Author(s): Anne E. C. Nichols, Robert E. Settlage, Stephen R. Werre, Linda A. Dahlgren
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2105-11-248

Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images
Cited by: 73
Author(s): Pekka Ruusuvuori, Tarmo Äijö, Sharif Chowdhury, Cecilia Garmendia-Torres, Jyrki Selinummi, Mirko Birbaumer, Andrew T. Dudley, Lucas Pelkmans, Olli Yli‐Harja
Software Mentions: 2
Published: over 15 years ago

10.1186/s13072-017-0157-x

H2A O-GlcNAcylation at serine 40 functions genomic protection in association with acetylated H2AZ or γH2AX
Cited by: 12
Author(s): Koji Hayakawa, Mitsuko Hirosawa, Ruiko Tani, Chikako Yoneda, Satoshi Tanaka, Kunio Shiota
Software Mentions: 2
Published: about 8 years ago

10.1042/ETLS20160025

Computational biology: deep learning
Cited by: 60
Author(s): William Jones, Kaur Alasoo, Dmytro Fishman, Leopold Parts
Software Mentions: 2
Published: almost 8 years ago

10.12688/f1000research.52569.1

Bioimage analysis workflows: community resources to navigate through a complex ecosystem
Cited by: 8
Author(s): Perrine Paul‐Gilloteaux, Sébastien Tosi, Jean-Karim Hèriché, Alban Gaignard, Hervé Ménager, Raphaël Marée, Volker Baecker, Anna H. Klemm, Matúš Kalaš, Chong Zhang, Kota Miura, Julien Colombelli
Software Mentions: 2
Published: over 4 years ago

10.15252/embr.201947845

Myc‐dependent endothelial proliferation is controlled by phosphotyrosine 1212 in <scp>VEGF</scp> receptor‐2
Cited by: 23
Author(s): Chiara Testini, Ross O Smith, Yi Jin, Pernilla Martinsson, Ying Sun, Mattias Hedlund, Miguel Sáinz‐Jaspeado, Masabumi Shibuya, Mats Hellström, Lena Claesson‐Welsh
Software Mentions: 2
Published: about 6 years ago

10.15252/embr.201744837

<scp>SNX</scp> 18 regulates <scp>ATG</scp> 9A trafficking from recycling endosomes by recruiting Dynamin‐2
Cited by: 66
Author(s): Kristiane Søreng, Michael J. Munson, Christopher R. Lamb, Gunnveig Toft Bjørndal, Serhiy Pankiv, Sven R. Carlsson, Sharon A. Tooze, Anne Simonsen
Software Mentions: 2
Published: over 7 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: about 4 years ago

10.15252/emmm.201910852

A thiol‐bound drug reservoir enhances APR‐246‐induced mutant p53 tumor cell death
Cited by: 20
Author(s): Sophia Ceder, Sofi Eriksson, Emarndeena H Cheteh, Swati Dawar, Mariana Corrales Benitez, Vladimir J. N. Bykov, Kenji M. Fujihara, Mélodie Grandin, Xiaodun Li, Susanne Ramm, Corina Behrenbruch, Kaylene J. Simpson, Frédéric Hollande, Lars Abrahmsén, Nicholas J. Clemons, Klas G. Wiman
Software Mentions: 2
Published: almost 5 years ago

10.1111/febs.14857

Two Nimrod receptors, NimC1 and Eater, synergistically contribute to bacterial phagocytosis in Drosophila melanogaster
Cited by: 32
Author(s): Claudia Melcarne, Elodie Ramond, Jan Paul Dudzic, Andrew J. Bretscher, Éva Kurucz, István Andó, Bruno Lemaître
Software Mentions: 2
Published: over 6 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: about 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: about 5 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: 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: about 7 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: almost 6 years ago

10.15252/embj.2020104948

Receptor‐mediated clustering of FIP200 bypasses the role of LC3 lipidation in autophagy
Cited by: 61
Author(s): Amelia E Ohnstad, José A. Delgado Delgado, Brian J. North, Isha Nasa, Arminja N. Kettenbach, Sebastian W. Schultz, Christopher J. Shoemaker
Software Mentions: 2
Published: almost 5 years ago

10.1186/s40478-020-01011-7

Lipid-specific IgMs induce antiviral responses in the CNS: implications for progressive multifocal leukoencephalopathy in multiple sclerosis
Cited by: 5
Author(s): Lorna Hayden, Tiia Semenoff, Verena Schultz, Simon F. Merz, Katie J. Chapple, Moses Rodriguez, Arthur E. Warrington, Xia Shi, Clive S. McKimmie, Julia M. Edgar, Katja Thümmler, Christopher Linington, Marieke Pingen
Software Mentions: 2
Published: about 5 years ago

10.1002/cyto.a.23794

Label‐Free Identification of White Blood Cells Using Machine Learning
Cited by: 62
Author(s): Mariam Nassar, Minh Doan, Andrew Filby, Olaf Wolkenhauer, Darin K. Fogg, Justyna Piasecka, Catherine A. Thornton, Anne E. Carpenter, Huw D. Summers, Paul Rees, Holger Hennig
Software Mentions: 2
Published: over 6 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: almost 14 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: almost 10 years ago

10.1002/cam4.3965

Histopathological image and gene expression pattern analysis for predicting molecular features and prognosis of head and neck squamous cell carcinoma
Cited by: 8
Author(s): Linyan Chen, Hao Zeng, Mingxuan Zhang, Yuling Luo, Xuelei Ma
Software Mentions: 2
Published: over 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: almost 12 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: over 4 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: over 4 years ago

10.1186/s13058-021-01416-9

Cellular dormancy in minimal residual disease following targeted therapy
Cited by: 13
Author(s): Jason R. Ruth, Dhruv K. Pant, Tien-Chi Pan, Hans E. Seidel, Sanjeethan C. Baksh, Blaine A. Keister, Rita Singh, Christopher J. Sterner, Suzanne J. Bakewell, Susan E. Moody, George K. Belka, Lewis A. Chodosh
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: about 6 years ago

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