pypi: CellProfiler | Projects | Ecosyste.ms: Papers

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: about 4 years ago

Analyzing microtomography data with Python and the scikit-image library
Cited by: 22
Author(s): Emmanuelle Gouillart, Juan Nunez-Iglesias, Stéfan van der Walt
Software Mentions: 14
Published: over 7 years ago

10.1038/s41375-018-0360-1

Immune cell constitution in bone marrow microenvironment predicts outcome in adult ALL
Cited by: 39
Author(s): Helena Hohtari, Oscar Brück, Sami Blom, Riku Turkki, Marjatta Sinisalo, Panu E. Kovanen, Olli Kallioniemi, Teijo Pellinen, Kimmo Porkka, Satu Mustjoki
Software Mentions: 14
Published: over 5 years ago

10.7554/eLife.62915

ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data
Cited by: 9
Author(s): James W. Opzoomer, Jessica A Timms, Kevin Blighe, Thanos P. Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan G. Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca D. Ciccarelli, Peter J. Parker, Michaéla Fontenay, Paul R. Barber, James N. Arnold, Shahram Kordasti
Software Mentions: 13
Published: about 3 years ago

10.7554/eLife.50087

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle
Cited by: 58
Author(s): Elias T Friman, Cédric Deluz, Antonio C. A. Meireles-Filho, Subashika Govindan, Vincent Gardeux, Bart Deplancke, David M. Suter
Software Mentions: 13
Published: over 4 years ago

10.1371/journal.pcbi.1006207

Network supporting contextual fear learning after dorsal hippocampal damage has increased dependence on retrosplenial cortex
Cited by: 18
Author(s): Cesar A.O. Coelho, Tatiana Lima Ferreira, Juliana Carlota Kramer Soares, João Ricardo Sato, Maria Gabriela Menezes Oliveira
Software Mentions: 11
Published: almost 6 years ago

10.15252/msb.20209522

Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma
Cited by: 19
Author(s): Samantha O'Connor, Heather Feldman, Sonali Arora, Pia Hoellerbauer, Chad M. Toledo, Philip Corrin, Lucas Carter, Megan Kufeld, Hamid Bolouri, Ryan Basom, Jeffrey J. Delrow, José L. McFaline-Figueroa, Cole Trapnell, Steven M. Pollard, Anoop P. Patel, Patrick J. Paddison, Christopher Plaisier
Software Mentions: 10
Published: almost 3 years ago

10.1371/journal.pone.0114749

FindFoci: A Focus Detection Algorithm with Automated Parameter Training That Closely Matches Human Assignments, Reduces Human Inconsistencies and Increases Speed of Analysis
Cited by: 88
Author(s): Alex Herbert, Antony Carr, Eva R. Hoffmann
Software Mentions: 10
Published: over 9 years ago

10.12688/f1000research.27062.2

SAPHIR: a Shiny application to analyze tissue section images
Cited by: 0
Author(s): Elodie Germani, Hugues Lelouard, Mathieu Fallet
Software Mentions: 9
Published: about 3 years ago

10.1128/mBio.00399-21

Salmonella enterica Serovar Typhimurium SPI-1 and SPI-2 Shape the Global Transcriptional Landscape in a Human Intestinal Organoid Model System
Cited by: 12
Author(s): Anna-Lisa E. Lawrence, Basel H. Abuaita, Ryan P. Berger, David R. Hill, Sha Huang, Veda K. Yadagiri, Brooke Bons, Courtney Fields, Christiane E. Wobus, Jason R. Spence, Vincent B. Young, Mary X. O’Riordan
Software Mentions: 9
Published: almost 3 years ago

10.3390/cancers13102498

Comparative Transcriptomics of Immune Checkpoint Inhibitor Myocarditis Identifies Guanylate Binding Protein 5 and 6 Dysregulation
Cited by: 16
Author(s): Daniel Finke, Markus Heckmann, Janek Salatzki, Johannes Riffel, Esther Herpel, Lucie Heinzerling, Benjamin Meder, Mirko Völkers, Oliver Müller, Norbert Frey, Hugo A. Katus, Florian Leuschner, Ziya Kaya, Lorenz Lehmann
Software Mentions: 9
Published: almost 3 years ago

10.1371/journal.pone.0177276

Succinct workflows for circulating tumor cells after enrichment: From systematic counting to mutational profiling
Cited by: 11
Author(s): Vernon G. Wong, Josephine Mun Yee Ko, Chi-Tat Lam, Maria Li Lung
Software Mentions: 9
Published: about 7 years ago

10.15252/msb.20199002

Endogenous fluctuations of <scp>OCT</scp> 4 and <scp>SOX</scp> 2 bias pluripotent cell fate decisions
Cited by: 35
Author(s): Daniel Strebinger, Cédric Deluz, Elias T Friman, Subashika Govindan, Andrea Brigitta Alber, David M. Suter
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.42448

Respiratory syncytial virus co-opts host mitochondrial function to favour infectious virus production
Cited by: 40
Author(s): Mengjie Hu, Keith E. Schulze, Reena Ghildyal, Darren C. Henstridge, Jacek L. Kolanowski, Elizabeth J. New, Yuning Hong, Alan Hsu, Philip M. Hansbro, Peter Wark, Marie A. Bogoyevitch, David A. Jans
Software Mentions: 8
Published: almost 5 years ago

10.3389/fonc.2020.01254

Unraveling the Complexity of the Cancer Microenvironment With Multidimensional Genomic and Cytometric Technologies
Cited by: 39
Author(s): Natasja L. de Vries, Ahmed Mahfouz, Frits Koning, Noel F.C.C. de Miranda
Software Mentions: 8
Published: almost 4 years ago

10.15252/msb.202110232

Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut
Cited by: 64
Author(s): Sergio Triana, Camila Metz-Zumaran, C. Ramı́rez, Carmon Kee, Patricio Doldan, Mohammed Shahraz, Daniel Schraivogel, Andreas R. Gschwind, Ashwini Kumar Sharma, Lars M. Steinmetz, Carl Herrmann, Theodore Alexandrov, Steeve Boulant, Megan L. Stanifer
Software Mentions: 8
Published: about 3 years ago

10.1038/s41419-020-03356-2

PU.1 drives specification of pluripotent stem cell-derived endothelial cells to LSEC-like cells
Cited by: 20
Author(s): Jonathan De Smedt, Elise Anne van Os, Irene Talón, Syamal K. Ghosh, Burak Toprakhisar, Rosa Maria Esteves Moreira da Costa, Samantha Zaunz, Marta Aguirre Vazquez, Ruben Boon, Pieter Baatsen, Ayla Smout, Stefaan Verhulst, Leo A. van Grunsven, Cathérine Verfaillie
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.65228

Egr2 induction in spiny projection neurons of the ventrolateral striatum contributes to cocaine place preference in mice
Cited by: 8
Author(s): Diptendu Mukherjee, Ben J. Gonzales, Reut Ashwal-Fluss, Hagit Turm, Maya Groysman, Ami Citri
Software Mentions: 8
Published: about 3 years ago

10.3390/vaccines9030217

HIV-Exposed Seronegative Sex Workers Express Low T-Cell Activation and an Intact Ectocervical Tissue Microenvironment
Cited by: 2
Author(s): Maria Röhl, Annelie Tjernlund, Julie Lajoie, Gabriella Edfeldt, Frideborg Bradley, Sofia Bergström, Vilde Kaldhusdal, Alexandra Åhlberg, Anna Månberg, Kenneth Omollo, Geneviève Boily-Larouche, Muhammad Asghar, Douglas S. Kwon, Julius Oyugi, Joshua Kimani, Peter Nilsson, Keith R. Fowke, Kristina Broliden
Software Mentions: 8
Published: about 3 years ago

10.1038/s41598-021-95068-6

CENPL, ISG20L2, LSM4, MRPL3 are four novel hub genes and may serve as diagnostic and prognostic markers in breast cancer
Cited by: 17
Author(s): Jun Yin, Chen Lin, Meng Jiang, Xuhai Tang, Danlin Xie, Jingwen Chen, Rongqin Ke
Software Mentions: 8
Published: almost 3 years ago

10.1038/s41598-021-94732-1

A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes
Cited by: 22
Author(s): Tanya Grancharova, Kaytlyn A. Gerbin, Alexander Rosenberg, Charles M. Roco, Joy Arakaki, Colette M DeLizo, Stephanie Q. Dinh, Rory Donovan-Maiye, Matthew Hirano, Angelique M. Nelson, Joyce Tang, Julie A. Theriot, Calysta Yan, Vilas Menon, Sean P. Palecek, Georg Seelig, Ruwanthi N. Gunawardane
Software Mentions: 8
Published: almost 3 years ago

10.1038/s41598-020-67324-8

Venom alkaloids against Chagas disease parasite: search for effective therapies
Cited by: 10
Author(s): Rafael Cardoso Maciel Costa Silva, Eduardo Gonçalves Paterson Fox, Fabio M. Gomes, Daniel F. Feijó, Isabela Ramos, Carolina M. Koeller, Tatiana F. R. Costa, Nathalia S. Rodrigues, Ana Paula Lima, Geórgia C. Atella, Kildare Miranda, Alejandra Cecilia Schoijet, Guillermo D. Alonso, Ednildo A. Machado, Norton Heise
Software Mentions: 7
Published: almost 4 years ago

10.7554/eLife.69975

Notch-induced endoplasmic reticulum-associated degradation governs mouse thymocyte β−selection
Cited by: 8
Author(s): Xia Liu, Jingjing Yu, Longyong Xu, Katharine Umphred-Wilson, Fanglue Peng, Yao Ding, Brendan M Barton, Xiangdong Lv, Michael Y Zhao, Shengyi Sun, Yuning Hong, Ling Qi, Stanley Adoro, Xi Chen
Software Mentions: 7
Published: almost 3 years ago

10.1186/s12859-021-03984-1

PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies
Cited by: 6
Author(s): Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal K. Das, Paweł Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska, Dariusz Plewczynski
Software Mentions: 7
Published: about 3 years ago

10.1172/jci.insight.139930

Contribution of plasma cells and B cells to hidradenitis suppurativa pathogenesis
Cited by: 88
Author(s): Johann E. Gudjonsson, Lam C. Tsoi, Feiyang Ma, Allison C. Billi, Kelsey R. van Straalen, Allard R. J. V. Vossen, Hessel H. van der Zee, Paul W. Harms, Rachael Wasikowski, Christopher Yee, Syed Monem Rizvi, Xianying Xing, Enze Xing, Olesya Plazyo, Chang Zeng, Matthew Patrick, Margaret M. Lowe, Richard E. Burney, Jeffrey H. Kozlow, Jill R. Cherry-Bukowiec, Yanyun Jiang, Joseph Kirma, Stephan Weidinger, Kelly C. Cushing, Michael D. Rosenblum, Céline C. Berthier, Amanda S. MacLeod, John J. Voorhees, Fei Wen, J. Michelle Kahlenberg, Emanual Maverakis, Robert L. Modlin, Errol P. Prens
Software Mentions: 7
Published: over 3 years ago

10.1186/s13195-020-00709-z

TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages
Cited by: 25
Author(s): Hazel Hall‐Roberts, Devika Agarwal, Juliane Obst, Thomas B. Smith, Jimena Monzón‐Sandoval, Elena Di Daniel, Caleb Webber, William James, Emma Mead, John B. Davis, Sally A. Cowley
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pcbi.1006269

Evaluating reproducibility of AI algorithms in digital pathology with DAPPER
Cited by: 43
Author(s): Andrea Bizzego, Nicole Bussola, Marco Chierici, Valerio Maggio, Margherita Francescatto, Luca Cima, Marco Cristoforetti, Giuseppe Jurman, Cesare Furlanello
Software Mentions: 7
Published: about 5 years ago

10.7554/eLife.56523

DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors
Cited by: 25
Author(s): Maria M. Mikedis, Yuting Fan, Peter K. Nicholls, Toshihiko Endo, Emily Jackson, Sarah A. Cobb, Dirk G. de Rooij, David C. Page
Software Mentions: 7
Published: almost 4 years ago

10.1016/j.cmet.2018.04.013

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes
Cited by: 104
Author(s): Tess Tsai-Hsiu Lu, Steffen Heyne, Erez Dror, Eduard Casas, Laura Leonhardt, Thorina Boenke, Ching‐Yao Yang, Sagar, Laura Arrigoni, Kevin Dalgaard, Raffaele Teperino, Lennart Enders, Madhan Selvaraj, Marius Ruf, Sunil Jayaramaiah Raja, Huafeng Xie, Ulrike Boenisch, Stuart H. Orkin, Francis C. Lynn, Brad G. Hoffman, Dominic Grün, Tanya Vavouri, Adelheid Lempradl, J. Andrew Pospisilik
Software Mentions: 7
Published: almost 6 years ago

10.7554/eLife.61408

Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain
Cited by: 13
Author(s): David M. Young, Siavash Fazel Darbandi, Grace B. Schwartz, Zachary Bonzell, Deniz Yuruk, Mai Nojima, Leena Gole, John L.R. Rubenstein, Weimiao Yu, Stephan Sanders
Software Mentions: 7
Published: about 3 years ago

10.7554/eLife.29312

Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis
Cited by: 35
Author(s): Isabelle Bergiers, Tallulah Andrews, Özge Vargel Bölükbaşı, Andreas Buneß, Ewa Janosz, Natalia López-Anguita, Kerstin Ganter, Kinga Kosim, Cemre Celen, Gülce Itır Perçin, Paul Collier, Bianka Baying, Vladimı́r Beneš, Martin Hemberg, Christophe Lancrin
Software Mentions: 7
Published: about 6 years ago

10.1126/sciimmunol.abg0833

SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation
Cited by: 127
Author(s): Bingyu Yan, Tilo Freiwald, Daniel Chauss, Luopin Wang, Erin E. West, Carmen Mirabelli, Zhang Cj, Eva-Maria Nichols, Nazish T. Malik, Richard I. Gregory, Marcus Bantscheff, Sonja Ghidelli-Disse, Martin Kolev, Tristan Frum, Jason R. Spence, Jonathan Z. Sexton, Konstantinos D. Alysandratos, Darrell N. Kotton, Stefania Pittaluga, Jack Bibby, Nathalie Niyonzima, Matthew R. Olson, Shahram Kordasti, Didier Portilla, Christiane E. Wobus, Arian Laurence, Michail S Lionakis, Claudia Kemper, Behdad Afzali, Majid Kazemian
Software Mentions: 7
Published: about 3 years ago

10.1038/srep21518

Activation of the TGFβ pathway impairs endothelial to haematopoietic transition
Cited by: 32
Author(s): Özge Vargel, Yang Zhang, Kinga Kosim, Kerstin Ganter, Sophia Föehr, Yannicka Mardenborough, Maya Shvartsman, Anton J. Enright, Jeroen Krijgsveld, Christophe Lancrin
Software Mentions: 6
Published: about 8 years ago

10.1002/1878-0261.12829

Identification of RUNX1T1 as a potential epigenetic modifier in small‐cell lung cancer
Cited by: 10
Author(s): He Tian, Gary Wildey, Karen McColl, Alyssa Savadelis, Kyle B. Spainhower, Cassidy McColl, Adam Kresak, Aik Choon Tan, Michael Yang, Ata Abbas, Afshin Dowlati
Software Mentions: 6
Published: over 3 years ago

10.1186/s12859-015-0759-x

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data
Cited by: 36
Author(s): Mark‐Anthony Bray, Anne E. Carpenter
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pgen.1007276

Argonaute2 and LaminB modulate gene expression by controlling chromatin topology
Cited by: 19
Author(s): Ezequiel Názer, Ryan Dale, Madoka Chinen, Behram Radmanesh, Elissa P. Lei
Software Mentions: 6
Published: about 6 years ago

10.1186/s40170-020-00217-6

Therapy-induced lipid uptake and remodeling underpin ferroptosis hypersensitivity in prostate cancer
Cited by: 56
Author(s): Kaylyn D. Tousignant, Anja Rockstroh, Berwyck L. J. Poad, Ali Talebi, Reuben S. E. Young, Atefeh Taherian Fard, Rajesh Gupta, Tuo Zang, Chenwei Wang, Melanie Lehman, Johan Swinnen, Stephen J. Blanksby, Colleen C. Nelson, Martin C. Sadowski
Software Mentions: 6
Published: almost 4 years ago

10.1523/ENEURO.0286-20.2020

Molecular Diversity of Glutamatergic and GABAergic Synapses from Multiplexed Fluorescence Imaging
Cited by: 7
Author(s): Eric Danielson, Karen Perez de Arce, Beth A. Cimini, Eike‐Christian Wamhoff, Shantanu Singh, Jeffrey R. Cottrell, Anne E. Carpenter, Mark Bathe
Software Mentions: 6
Published: over 3 years ago

10.1186/s12915-021-01086-1

A phenomics approach for antiviral drug discovery
Cited by: 10
Author(s): Jonne Rietdijk, Marianna Tampere, Aleksandra Pettke, Polina Georgiev, Maris Lapins, Ulrika Warpman Berglund, Ola Spjuth, Marjo-Riitta Puumalainen, Jordi Carreras-Puigvert
Software Mentions: 6
Published: almost 3 years ago

10.1186/gm549

A genome scale overexpression screen to reveal drug activity in human cells
Cited by: 30
Author(s): Anthony Arnoldo, Saranya Kittanakom, Lawrence E. Heisler, Anthony B. Mak, Andrey I. Shukalyuk, Dax Torti, Jason Moffat, Guri Giaever, Corey Nislow
Software Mentions: 6
Published: over 10 years ago

10.7554/eLife.46464

Molecular and anatomical organization of the dorsal raphe nucleus
Cited by: 120
Author(s): Kee Wui Huang, Nicole Ochandarena, Adrienne C. Philson, Minsuk Hyun, Jaclyn E Birnbaum, Marcelo Cicconet, Bernardo L. Sabatini
Software Mentions: 6
Published: over 4 years ago

10.15252/msb.202110272

RNA polymerase II clusters form in line with surface condensation on regulatory chromatin
Cited by: 32
Author(s): Agnieszka Pancholi, Tim Klingberg, Weichun Zhang, Roshan Prizak, Irina Mamontova, Amra Noa, Marcel Sobucki, Andrei Yu Kobitski, G. Ulrich Nienhaus, Vasily Zaburdaev, Lennart Hilbert
Software Mentions: 6
Published: over 2 years ago

10.1371/journal.pcbi.1008044

Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits
Cited by: 15
Author(s): Craig A. Glastonbury, Sara L. Pulit, Julius Honecker, Jenny C Censin, Samantha Laber, Hanieh Yaghootkar, Nilüfer Rahmioğlu, Emilie Pastel, Katarina Kos, Andrew M. Pitt, Michelle Hudson, Christoffer Nellåker, Nicola L. Beer, Hans Hauner, Christian M. Becker, Krina T. Zondervan, Timothy M. Frayling, Melina Claussnitzer, Cecilia M. Lindgren
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.51085

CytoCensus, mapping cell identity and division in tissues and organs using machine learning
Cited by: 12
Author(s): Martin Hailstone, Dominic Waithe, Tamsin J Samuels, Yang Lu, Ita Costello, Yoav Arava, Elizabeth J. Robertson, Richard M. Parton, Ilan Davis
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pbio.3000675

SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution
Cited by: 35
Author(s): Alexandros Sountoulidis, Andreas Liontos, Hong Phuong Nguyen, Alexandra B. Firsova, Athanasios Fysikopoulos, Xiaoyan Qian, Werner Seeger, Erik Sundström, Mats Nilsson, Christos Samakovlis
Software Mentions: 6
Published: over 3 years ago

10.1038/s42003-021-02397-3

Three-dimensional CRISPR screening reveals epigenetic interaction with anti-angiogenic therapy
Cited by: 4
Author(s): Michael Y. He, Michael M. Halford, Ruofei Liu, James P Roy, Zoe L. Grant, Leigh Coultas, Niko Thio, Omer Gilan, Yih Chih Chan, Mark A. Dawson, Marc G. Achen, Steven A. Stacker
Software Mentions: 6
Published: almost 3 years ago

10.1016/j.stem.2019.07.009

Distinct Molecular Trajectories Converge to Induce Naive Pluripotency
Cited by: 27
Author(s): Hannah Stuart, Giuliano Giuseppe Stirparo, Tim Lohoff, Lawrence E. Bates, Masaki Kinoshita, Chee Lim, Elsa Joana Sousa, Katsiaryna Maskalenka, Aliaksandra Radzisheuskaya, Andrew A. Malcolm, Mariana R. P. Alves, Rebecca L. Lloyd, Sonia Nestorowa, Peter Humphreys, William Mansfield, Wolf Reik, Paul Bertone, Jennifer Nichols, Berthold Göttgens, José C.R. Silva
Software Mentions: 6
Published: over 4 years ago

10.1002/2211-5463.12692

Multidimensional profiling of drug‐treated cells by Imaging Mass Cytometry
Cited by: 33
Author(s): Alexandre Bouzekri, Amanda Esch, Olga Ornatsky
Software Mentions: 6
Published: almost 5 years ago

10.7554/eLife.59733

Activation of a neural stem cell transcriptional program in parenchymal astrocytes
Cited by: 41
Author(s): Jens P Magnusson, Margherita Zamboni, Giuseppe Santopolo, Jeff E. Mold, Mauricio Barrientos‐Somarribas, Carlos Talavera-López, Björn Andersson, Jonas Frisén
Software Mentions: 6
Published: almost 4 years ago

10.15252/msb.20209833

Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection
Cited by: 17
Author(s): Sergio Triana, Megan L. Stanifer, Camila Metz-Zumaran, Mohammed Shahraz, Markus Mukenhirn, Carmon Kee, Clara Serger, Ronald Koschny, Diana Ordoñez-Rueda, Malte Paulsen, Vladimı́r Beneš, Steeve Boulant, Theodore Alexandrov
Software Mentions: 6
Published: almost 3 years ago

10.1002/jev2.12022

Microglial derived extracellular vesicles activate autophagy and mediate multi‐target signaling to maintain cellular homeostasis
Cited by: 22
Author(s): Bram Van den Broek, Isabel Pintelon, Ibrahim Hamad, Sofie Kessels, Mansour Haidar, Niels Hellings, Jerome J. A. Hendriks, Markus Kleinewietfeld, Bert Brône, Vincent Timmerman, Jean‐Pierre Timmermans, Veerle Somers, Luc Michiels, Joy Irobi
Software Mentions: 6
Published: over 3 years ago

10.1038/s41419-021-03738-0

A KDM4A-PAF1-mediated epigenomic network is essential for acute myeloid leukemia cell self-renewal and survival
Cited by: 18
Author(s): Matthew E. Massett, Laura Monaghan, Shaun Patterson, Niamh Mannion, Roderick P Bunschoten, Alex Hoose, Sandra Marmiroli, Rob M. J. Liskamp, Heather G. Jørgensen, David Vetrie, Alison M. Michie, Xu Huang
Software Mentions: 6
Published: almost 3 years ago

10.1186/s12915-021-01043-y

MATISSE: a method for improved single cell segmentation in imaging mass cytometry
Cited by: 16
Author(s): Matthijs J.D. Baars, Neeraj Sinha, Mojtaba Amini, Annelies Pieterman-Bos, Stephanie van Dam, Maroussia M. P. Ganpat, Miangela M. Laclé, Bas Oldenburg, Yvonne Vercoulen
Software Mentions: 6
Published: almost 3 years ago

10.1007/s00439-020-02228-1

A CRISPR and high-content imaging assay compliant with ACMG/AMP guidelines for clinical variant interpretation in ciliopathies
Cited by: 5
Author(s): Liliya Nazlamova, N. Simon Thomas, Man‐Kim Cheung, Jelmer Legebeke, Jenny Lord, Reuben J. Pengelly, William Tapper, Gabrielle Wheway
Software Mentions: 6
Published: over 3 years ago

10.1126/sciimmunol.abc3582

TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes
Cited by: 754
Author(s): Ruochen Zang, María Florencia Gómez Castro, Broc T. McCune, Qiru Zeng, Paul W. Rothlauf, Naomi Sonnek, Zhuoming Liu, Kevin Brulois, Xin Wang, Harry B. Greenberg, Michael S. Diamond, Matthew A. Ciorba, Sean P. J. Whelan, Siyuan Ding
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pcbi.1006384

Context-explorer: Analysis of spatially organized protein expression in high-throughput screens
Cited by: 9
Author(s): Joel Östblom, Emanuel Joseph Paul Nazareth, Mukul Tewary
Software Mentions: 5
Published: over 5 years ago

10.15252/msb.20177608

Landscape of nuclear transport receptor cargo specificity
Cited by: 79
Author(s): Marie‐Therese Mackmull, Bernd Klaus, Ivonne Heinze, Manopriya Chokkalingam, Andreas Beyer, Robert B. Russell, Alessandro Ori, Martin Beck
Software Mentions: 5
Published: over 6 years ago

10.1038/srep23490

Combinatorial microenvironmental regulation of liver progenitor differentiation by Notch ligands, TGFβ and extracellular matrix
Cited by: 33
Author(s): Kerim B. Kaylan, Viktoriya Ermilova, Ravi Chandra Yada, Gregory H. Underhill
Software Mentions: 5
Published: about 8 years ago

10.1073/pnas.2100920118

Single-cell sequencing reveals suppressive transcriptional programs regulated by MIS/AMH in neonatal ovaries
Cited by: 23
Author(s): Marie-Charlotte Meinsohn, Hatice D. Saatcioglu, Lina Wei, Yang Li, Heiko Horn, Maëva Chauvin, Mariko Kano, Ngoc Minh Nguyen, Nicholas Nagykery, A Kashiwagi, Wesley Samore, Dan Wang, Esther Oliva, Guangping Gao, Mary E. Morris, Patricia K. Donahoe, David Pépin
Software Mentions: 5
Published: almost 3 years ago

10.1186/s12859-019-3055-3

Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging
Cited by: 38
Author(s): Eric Czech, Bülent Arman Aksoy, Pınar Aksoy, Jeff Hammerbacher
Software Mentions: 5
Published: over 4 years ago

10.1186/s40478-020-01010-8

Single-cell mass cytometry reveals complex myeloid cell composition in active lesions of progressive multiple sclerosis
Cited by: 34
Author(s): Chotima Böttcher, Marlijn van der Poel, Camila Fernández-Zapata, Stephan Schlickeiser, Julia Koehler Leman, Cheng-Chih Hsiao, Mark R. Mizee, Adelia, Maria C. J. Vincenten, Désirée Kunkel, Inge Huitinga, Jörg Hamann, Josef Priller
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.60579

SON and SRRM2 are essential for nuclear speckle formation
Cited by: 94
Author(s): İbrahim Avşar Ilık, Michal Malszycki, Anna Katharina Lübke, Claudia Schade, David Meierhofer, Tuğçe Aktaş
Software Mentions: 5
Published: over 3 years ago

10.1186/s13293-015-0056-4

Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development
Cited by: 24
Author(s): Martin M. Johansson, E. Lundin, Xiaoyan Qian, Mohammadreza Mirzazadeh, Jonatan Halvardson, Elisabeth Darj, Lars Feuk, Mats Nilsson, Elena Jazin
Software Mentions: 5
Published: over 8 years ago

10.3389/fimmu.2019.02657

Mass Cytometry Imaging for the Study of Human Diseases—Applications and Data Analysis Strategies
Cited by: 128
Author(s): Heeva Baharlou, Nicolas P Canete, Anthony L. Cunningham, Andrew N. Harman, Ellis Patrick
Software Mentions: 5
Published: over 4 years ago

10.15252/msb.202010138

Natural variants suppress mutations in hundreds of essential genes
Cited by: 10
Author(s): Leopold Parts, Amandine Batté, Maykel Lopes, Michael Wai-Keong Yuen, Meredith Laver, Bryan-Joseph San Luis, Jia-Xing Yue, Carles Pons, Elise Eray, Patrick Aloy, Gianni Liti, Jolanda van Leeuwen
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0185376

Cellular heterogeneity contributes to subtype-specific expression of ZEB1 in human glioblastoma
Cited by: 10
Author(s): Philipp Euskirchen, Josefine Radke, Marc Soeren Schmidt, Eva Schulze Heuling, Eric Kadikowski, Meron Maricos, Felix Knab, Ulrike Grittner, Norman Zerbe, Marcus Czabanka, Christoph Dieterich, Hrvoje Miletić, Sverre Mørk, Arend Koch, Matthias Endres, Christoph Harms
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0188772

Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells
Cited by: 21
Author(s): Johan Boström, Zuzana Šrámková, Alena Salašová, Helena A.D. Johard, Diana Mahdessian, Radek Fedr, Carolyn Marks, Jiřina Medalová, Karel Souček, Emma Lundberg, Sten Linnarsson, Vı́tězslav Bryja, Petra Sekyrová, Mikael Altun, Michael Andäng
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1007559

Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression
Cited by: 141
Author(s): Rachel Kaletsky, Victoria Yao, April Williams, Alexi Runnels, Alicja Tadych, Shaoqiang Zhou, Olga G. Troyanskaya, Coleen T. Murphy
Software Mentions: 5
Published: over 5 years ago

10.3389/fendo.2021.736286

Gene Signatures of NEUROGENIN3+ Endocrine Progenitor Cells in the Human Pancreas
Cited by: 2
Author(s): Hyo Jeong Yong, Gengqiang Xie, Chengyang Liu, Wei Wang, Ali Naji, Jerome Irianto, Yue J. Wang
Software Mentions: 5
Published: over 2 years ago

10.1002/advs.201903392

Immune Modulation by Design: Using Topography to Control Human Monocyte Attachment and Macrophage Differentiation
Cited by: 85
Author(s): Matthew Vassey, Grazziela P. Figueredo, David J. Scurr, Aliaksei Vasilevich, Steven Vermeulen, Aurélie Carlier, Jeni Luckett, Nick R. M. Beijer, Paul Williams, David A. Winkler, Jan de Boer, Amir M. Ghaemmaghami, Morgan R. Alexander
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pgen.1007828

The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea
Cited by: 13
Author(s): David Schmidt, Hanna Reuter, Katja Hüttner, Larissa Ruhe, Franziska Rabert, Florian Seebeck, Manuel Irimia, Jordi Solana, Kerstin Bartscherer
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.33402

Rev7 and 53BP1/Crb2 prevent RecQ helicase-dependent hyper-resection of DNA double-strand breaks
Cited by: 20
Author(s): Bryan A. Leland, Angela C Chen, Amy Zhao, Robert Wharton, Megan C. King
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0214878

Statistical models discriminating between complex samples measured with microfluidic receptor-cell arrays
Cited by: 2
Author(s): Ron Wehrens, Margriet Roelse, Maurice Henquet, Marco van Lenthe, P.W. Goedhart, M.A. Jongsma
Software Mentions: 5
Published: about 5 years ago

10.3389/fcimb.2021.667327

Development and Characterization of High-Throughput Caenorhabditis elegans – Enterococcus faecium Infection Model
Cited by: 4
Author(s): Alexey V. Revtovich, Elissa Tjahjono, Kavindra V. Singh, Blake Hanson, Barbara E. Murray, Natalia V. Kirienko
Software Mentions: 5
Published: about 3 years ago

10.7554/eLife.53008

Functional heterogeneity of lymphocytic patterns in primary melanoma dissected through single-cell multiplexing
Cited by: 39
Author(s): Francesca Maria Bosisio, Asier Antoranz, Yannick Van Herck, Maddalena M. Bolognesi, Lukas Marcelis, Clizia Chinello, Jasper Wouters, Fulvio Magni, Leonidas G. Alexopoulos, Marguerite Stas, Veerle Boecxstaens, Oliver Bechter, Giorgio Cattoretti, Joost van den Oord
Software Mentions: 5
Published: about 4 years ago

10.1186/s12859-017-1934-z

ImageJ2: ImageJ for the next generation of scientific image data
Cited by: 4,051
Author(s): Curtis Rueden, Johannes Schindelin, Mark Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena, Kevin W. Eliceiri
Software Mentions: 5
Published: over 6 years ago

10.1016/j.devcel.2021.07.019

Genetically variant human pluripotent stem cells selectively eliminate wild-type counterparts through YAP-mediated cell competition
Cited by: 25
Author(s): Christopher J. Price, Dylan Stavish, Paul J. Gokhale, Ben A. Stevenson, Samantha Sargeant, Joanne Lacey, Tristan A. Rodríguez, Ivana Barbaric
Software Mentions: 5
Published: over 2 years ago

10.3390/cells8121510

A New Sensitive Method for the Detection of Mycoplasmas Using Fluorescence Microscopy
Cited by: 10
Author(s): Anna Ligasová, Markéta Vydržalová, Renata Buriánová, Lenka Brůčková, Renata Večeřová, Anna Janošťáková, Karel Koberna
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.60326

Antagonistic roles for Ataxin-2 structured and disordered domains in RNP condensation
Cited by: 15
Author(s): Amanjot Singh, Joern Hulsmeier, Arvind Reddy Kandi, Sai Shruti Pothapragada, Jens Hillebrand, Arnas Petrauskas, Khushboo Agrawal, Krishnan Rt, Devasena Thiagarajan, Deepa Jayaprakashappa, K. VijayRaghavan, Mani Ramaswami, Baskar Bakthavachalu
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0188415

Physiological effects of a novel artificially synthesized antimalarial cyclic peptide: Mahafacyclin B
Cited by: 2
Author(s): Yūkō Fujita, Panpaki Seekaki, Naoya Ogata, Kazuhiro Chiba
Software Mentions: 5
Published: over 6 years ago

10.1002/ece3.7684

Expansion of rDNA and pericentromere satellite repeats in the genomes of bank voles <i>Myodes glareolus</i> exposed to environmental radionuclides
Cited by: 4
Author(s): Toni Jernfors, John M Danforth, Jenni Kesäniemi, Anton Lavrinienko, Eugene Tukalenko, Jiřı́ Fajkus, Martina Dvořáčková, Johanna Mappes, Phillip C. Watts
Software Mentions: 5
Published: almost 3 years ago

10.1038/s41598-021-84667-y

Neuron-specific spinal cord translatomes reveal a neuropeptide code for mouse dorsal horn excitatory neurons
Cited by: 15
Author(s): Rebecca R Das Gupta, Louis Scheurer, Paweł Pelczar, Hendrik Wildner, Hanns Ulrich Zeilhofer
Software Mentions: 5
Published: about 3 years ago

10.1038/s41598-021-81472-5

Drosophila Hox genes induce melanized pseudo-tumors when misexpressed in hemocytes
Cited by: 6
Author(s): Titus Ponrathnam, Ravina Saini, Sofia Banu, Rakesh Mishra
Software Mentions: 5
Published: over 3 years ago

10.1186/1751-0473-3-13

Wndchrm – an open source utility for biological image analysis
Cited by: 193
Author(s): Lior Shamir, Nikita Orlov, D. Mark Eckley, Tomasz Macura, Josiah Johnston, Ilya G. Goldberg
Software Mentions: 5
Published: almost 16 years ago

10.1038/s41598-020-78081-z

Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population
Cited by: 0
Author(s): Sandra M. Walsh, Mercè Izquierdo-Serra, Sandra Acosta, Albert Edo, María C. Estévez Lloret, Roser Moret, Elena Bosch, Baldo Oliva, Jaume Bertranpetit, José M. Fernández-Fernández
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-64623-y

Comparative analysis of MACROD1, MACROD2 and TARG1 expression, localisation and interactome
Cited by: 20
Author(s): Roko Žaja, Gülcan Aydin, Barbara E. Lippok, Regina Feederle, Bernhard Lüscher, Karla L. H. Feijs
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-019-54493-4

Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa
Cited by: 17
Author(s): Gökçe Günaydın, Gabriella Edfeldt, David Garber, Muhammad Asghar, Laura Noël‐Romas, Adam Burgener, Carolina Wählby, Lin Wang, Lisa C. Rohan, Patricia C. Guenthner, James Mitchell, Nobuyuki Matoba, Janet M. McNicholl, Kenneth E. Palmer, Annelie Tjernlund, Kristina Broliden
Software Mentions: 4
Published: over 4 years ago

10.1038/s41597-021-00933-8

Cric searchable image database as a public platform for conventional pap smear cytology data
Cited by: 19
Author(s): Mariana T. Rezende, Raniere Silva, Fagner de O. Bernardo, Alessandra Hermógenes Gomes Tobias, Paulo H. C. Oliveira, Tales Mota Machado, Caio S. Costa, Fátima N. S. de Medeiros, Daniela Ushizima, Cláudia Martins Carneiro, Andrea Gomes Campos Bianchi
Software Mentions: 4
Published: almost 3 years ago

10.1016/j.cell.2013.03.012

Exit from Pluripotency Is Gated by Intracellular Redistribution of the bHLH Transcription Factor Tfe3
Cited by: 288
Author(s): Joerg Betschinger, Jennifer Nichols, Sabine Dietmann, Philip Corrin, Patrick J. Paddison, Austin Smith
Software Mentions: 4
Published: about 11 years ago

10.1007/s00401-020-02176-0

Congenic expression of poly-GA but not poly-PR in mice triggers selective neuron loss and interferon responses found in C9orf72 ALS
Cited by: 36
Author(s): Katherine D. LaClair, Qihui Zhou, Meike Michaelsen, Benedikt Wefers, Monika S. Brill, Aleksandar Janjic, Birgit Rathkolb, Daniel Farny, Mikolaj Cygan, Martin Hrabě de Angelis, Wolfgang Wurst, Manuela Neumann, Wolfgang Enard, Thomas Misgeld, Thomas Arzberger, Dieter Edbauer
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41597-019-0051-4

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media
Cited by: 14
Author(s): Saugat Poudel, Hannah Tsunemoto, Michael J. Meehan, Richard Szubin, Connor A. Olson, Anne Lamsa, Yara Seif, Nicholas Dillon, Alison Vrbanac, Joseph Sugie, Samira Dahesh, Jonathan M. Monk, Pieter C. Dorrestein, Joseph Pogliano, Rob Knight, Victor Nizet, Bernhard Ø. Palsson, Adam M. Feist
Software Mentions: 4
Published: about 5 years ago

10.1172/jci.insight.146883

Highly multiplexed 2-dimensional imaging mass cytometry analysis of HBV-infected liver
Cited by: 14
Author(s): Daniel Traum, Yue J. Wang, Kathleen B. Schwarz, Jonathan Schug, David Wong, Harry L.A. Janssen, Norah A. Terrault, Mandana Khalili, Abdus S. Wahed, Karen F. Murray, Phillip Rosenthal, Simon C. Ling, Norberto Rodriguez‐Baez, Richard K. Sterling, Daryl Lau, Timothy M. Block, Michael D. Feldman, Elizabeth E. Furth, William M. Lee, David E. Kleiner, Anna S. Lok, Klaus H. Kaestner, Kyong Mi Chang
Software Mentions: 4
Published: about 3 years ago

10.1111/mmi.14417

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

10.1016/j.jbc.2021.101049

Fused in sarcoma regulates DNA replication timing and kinetics
Cited by: 5
Author(s): Weiyan Jia, Sang Hwa Kim, Mark Scalf, Peter Tonzi, Robert Millikin, William Guns, Lu Liu, Adam S. Mastrocola, Lloyd M. Smith, Tony T. Huang, Randal S. Tibbetts
Software Mentions: 4
Published: over 2 years ago

10.1371/journal.pone.0110289

SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images
Cited by: 23
Author(s): Bastiaan G. L. Nelissen, Joost A. van Herwaarden, Frans L. Moll, Paul J. van Diest, Gérard Pasterkamp
Software Mentions: 4
Published: over 9 years ago

10.1007/s00204-018-2178-z

Dynamic imaging of adaptive stress response pathway activation for prediction of drug induced liver injury
Cited by: 45
Author(s): Steven Wink, Steven Hiemstra, Suzanna Huppelschoten, Janna E. Klip, Bob van de Water
Software Mentions: 4
Published: about 6 years ago

10.1093/gigascience/giaa041

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

10.1016/j.molcel.2021.04.028

Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human disease
Cited by: 46
Author(s): Evgeniia Prokhorova, Thomas Agnew, Anne R. Wondisford, Michael Tellier, Nicole Kaminski, Danique Beijer, James Holder, Joséphine Groslambert, Marcin Suskiewicz, Kang Zhu, Julia M Reber, Sarah C. Krassnig, Luca Palazzo, Shona Murphy, Michael L. Nielsen, Aswin Mangerich, Dragana Ahel, Jonathan Baets, Roderick J. O’Sullivan, Ivan Ahel
Software Mentions: 4
Published: almost 3 years ago

10.1186/s12915-020-00874-5

Automated identification of the mouse brain’s spatial compartments from in situ sequencing data
Cited by: 16
Author(s): Gabriele Partel, Markus M. Hilscher, Milli Giorgia, Leslie Solorzano, Anna H. Klemm, Mats Nilsson, Carolina Wählby
Software Mentions: 4
Published: over 3 years ago

10.1093/gigascience/giab018

Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit
Cited by: 2
Author(s): Ben Blamey, Salman Toor, Martin Dahlö, Håkan Wieslander, Philip J. Harrison, Ida‐Maria Sintorn, Alan Sabirsh, Carolina Wählby, Ola Spjuth, Andreas Hellander
Software Mentions: 4
Published: about 3 years ago

Projects: pypi: CellProfiler

Papers Mentioning CellProfiler 1,504