bioconductor: flowCore | Projects

10.1186/s12859-019-3152-3

flowEMMi: an automated model-based clustering tool for microbial cytometric data
Cited by: 16
Author(s): Joachim Ludwig, Christian Höner zu Siederdissen, Zishu Liu, Peter F. Stadler, Susann Müller
Software Mentions: 18
Published: almost 5 years ago

10.1186/s12859-021-04054-2

CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data
Cited by: 13
Author(s): Yuting Dai, Aining Xu, Jianfeng Li, Liang Wu, Shanhe Yu, Jun Chen, Wei‐Li Zhao, Xiao Jian Sun, Jinyan Huang
Software Mentions: 17
Published: over 3 years ago

10.12688/f1000research.11622.3

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
Cited by: 205
Author(s): Małgorzata Nowicka, Carsten Krieg, Helena L. Crowell, Lukas M. Weber, Felix J. Hartmann, Silvia Guglietta, Burkhard Becher, Mitchell P. Levesque, Mark D. Robinson
Software Mentions: 15
Published: over 5 years ago

10.1038/s42003-020-01625-6

Mapping the immune environment in clear cell renal carcinoma by single-cell genomics
Cited by: 103
Author(s): Nicholas Borcherding, Ajaykumar Vishwakarma, Andrew P. Voigt, Andrew M. Bellizzi, Jacob Kaplan, Kenneth G. Nepple, Aliasger K. Salem, Russell W. Jenkins, Yousef Zakharia, Weizhou Zhang
Software Mentions: 14
Published: almost 4 years ago

10.1186/s12859-019-2787-4

flowDiv: a new pipeline for analyzing flow cytometric diversity
Cited by: 9
Author(s): Bruno Wanderley, Daniel Araújo, María Victoria Quiroga, André Megali Amado, Adrião Duarte Dória Neto, Hugo Sarmento, Sebastián Metz, Fernando Unrein
Software Mentions: 13
Published: over 5 years ago

10.1186/s40425-019-0764-0

34th Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2019): part 2
Cited by: 28
Author(s):
Software Mentions: 12
Published: about 5 years ago

10.3389/fcell.2020.618552

A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation
Cited by: 12
Author(s): Jenny Ostrop, Rosalie T. Zwiggelaar, Marianne Terndrup Pedersen, François Gerbe, Korbinian Bösl, Håvard T. Lindholm, Alberto Díez-Sánchez, Naveen Parmar, Silke Radetzki, Jens Peter von Kries, Philippe Jay, Kim B. Jensen, C.H. Arrowsmith, Menno J. Oudhoff
Software Mentions: 12
Published: almost 4 years ago

10.3390/cancers13081788

Analysis of Intra-Tumoral Macrophages and T Cells in Non-Small Cell Lung Cancer (NSCLC) Indicates a Role for Immune Checkpoint and CD200-CD200R Interactions
Cited by: 7
Author(s): Anders Tøndell, Yashwanth Subbannayya, Sissel Gyrid Freim Wahl, Arnar Flatberg, Sveinung Sørhaug, Magne Børset, Markus Haug
Software Mentions: 12
Published: over 3 years ago

10.7554/eLife.65372

Image3C, a multimodal image-based and label-independent integrative method for single-cell analysis
Cited by: 6
Author(s): Alice Accorsi, Andrew Box, Robert Peuß, Christopher J. Wood, Alejandro Sánchez Alvarado, Nicolas Rohner
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pgen.1008458

Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations
Cited by: 23
Author(s): Jessica A. Lee, Siavash Riazi, Shahla Nemati, Jannell V. Bazurto, Andreas E. Vasdekis, Benjamin J. Ridenhour, Christopher H. Remien, Christopher J. Marx
Software Mentions: 10
Published: about 5 years ago

10.3389/fonc.2016.00188

Immunophenotype Discovery, Hierarchical Organization, and Template-Based Classification of Flow Cytometry Samples
Cited by: 12
Author(s): Ariful Azad, Bartek Rajwa, Alex Pothen
Software Mentions: 10
Published: about 8 years ago

10.1128/mSystems.00895-20

Computational Analysis of Microbial Flow Cytometry Data
Cited by: 16
Author(s): Peter Rubbens, Ruben Props
Software Mentions: 9
Published: almost 4 years ago

10.1371/journal.pcbi.1003806

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis
Cited by: 171
Author(s): Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W. Newell, John Ramey, Mark M. Davis, Spyros A. Kalams, Stephen C. De Rosa, Raphaël Gottardo
Software Mentions: 8
Published: over 10 years ago

10.1136/jitc-2020-000588

Monocyte-derived APCs are central to the response of PD1 checkpoint blockade and provide a therapeutic target for combination therapy
Cited by: 30
Author(s): Sjoerd Schetters, Elizabeth Rodríguez, Laura Kruijssen, Matheus H.W. Crommentuijn, Louis Boon, Jan Van den Bossche, Joke M. M. den Haan, Yvette van Kooyk
Software Mentions: 8
Published: over 4 years ago

10.1186/1471-2105-13-252

QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data
Cited by: 17
Author(s): Greg Finak, Wenxin Jiang, Jorge Pardo, Adam Asare, Raphaël Gottardo
Software Mentions: 8
Published: about 12 years ago

10.15252/msb.20209442

High‐throughput, microscope‐based sorting to dissect cellular heterogeneity
Cited by: 40
Author(s): Nicholas Hasle, Anthony Cooke, Sanjay Srivatsan, Heather Z Huang, Jason J. Stephany, Zachary Krieger, Dana L. Jackson, Weiliang Tang, Sriram Pendyala, Raymond J. Monnat, Cole Trapnell, Emily M. Hatch, Douglas M. Fowler
Software Mentions: 7
Published: over 4 years ago

10.3389/fimmu.2020.01166

Non-sterilizing, Infection-Permissive Vaccination With Inactivated Influenza Virus Vaccine Reshapes Subsequent Virus Infection-Induced Protective Heterosubtypic Immunity From Cellular to Humoral Cross-Reactive Immune Responses
Cited by: 6
Author(s): Angela Choi, Lorena Itatí Ibáñez, Shirin Strohmeier, Florian Krammer, Adolfo Garcı́a-Sastre, Michael Schotsaert
Software Mentions: 7
Published: over 4 years ago

10.7554/eLife.31867

Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry
Cited by: 16
Author(s): Peter L. Freddolino, Jiping Yang, Amir Momen-Roknabadi, Saeed Tavazoie
Software Mentions: 7
Published: over 6 years ago

10.3390/vaccines7030113

TIV Vaccination Modulates Host Responses to Influenza Virus Infection that Correlate with Protection against Bacterial Superinfection
Cited by: 5
Author(s): Angela Choi, Ioanna Christopoulou, Xavier Saelens, Adolfo Garcı́a-Sastre, Michael Schotsaert
Software Mentions: 7
Published: about 5 years ago

10.1186/1471-2105-11-44

The curvHDR method for gating flow cytometry samples
Cited by: 29
Author(s): Ulrike Naumann, George Luta, M. P. Wand
Software Mentions: 7
Published: almost 15 years ago

10.3389/fimmu.2021.632667

PD-1 Blockade Modulates Functional Activities of Exhausted-Like T Cell in Patients With Cutaneous Leishmaniasis
Cited by: 16
Author(s): Renan Garcia de Moura, Luciana Polaco Covre, Carlos Henrique Fantecelle, Vitor Alejandro Torres Gajardo, Carla Baroni Cunha, Lorenzzo Lyrio Stringari, Ashton T. Belew, Camila Batista Daniel, Sandra Ventorin von Zeidler, Carlos E. Tadokoro, Herbert Leonel de Matos Guedes, Raphael Lubiana Zanotti, David M. Mosser, Aloísio Falqueto, Arne N. Akbar, Daniel Cláudio Oliveira Gomes
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2018.02137

Traditional Norwegian Kveik Are a Genetically Distinct Group of Domesticated Saccharomyces cerevisiae Brewing Yeasts
Cited by: 36
Author(s): Richard Preiss, Caroline Tyrawa, Kristoffer Krogerus, Lars Marius Garshol, George van der Merwe
Software Mentions: 6
Published: about 6 years ago

10.1186/1471-2105-10-145

flowClust: a Bioconductor package for automated gating of flow cytometry data
Cited by: 165
Author(s): Kenneth Lo, Florian Hahne, Ryan R. Brinkman, Raphaël Gottardo
Software Mentions: 6
Published: over 15 years ago

10.1186/s12870-017-1103-6

Avocado fruit maturation and ripening: dynamics of aliphatic acetogenins and lipidomic profiles from mesocarp, idioblasts and seed
Cited by: 32
Author(s): Carlos E. Rodríguez López, Carmen Hernández-Brenes, Víctor Treviño, Rocío I. Díaz de la Garza
Software Mentions: 6
Published: about 7 years ago

10.1186/s12859-016-1083-9

flowVS: channel-specific variance stabilization in flow cytometry
Cited by: 15
Author(s): Ariful Azad, Bartek Rajwa, Alex Pothen
Software Mentions: 6
Published: over 8 years ago

10.1128/mBio.02399-20

Hemozoin Promotes Lung Inflammation via Host Epithelial Activation
Cited by: 1
Author(s): Shivang S. Shah, David A. Fidock, Alice Prince
Software Mentions: 6
Published: almost 4 years ago

10.1186/1751-0473-3-10

Flow: Statistics, visualization and informatics for flow cytometry
Cited by: 11
Author(s): Jacob Frelinger, Thomas B. Kepler, Cliburn Chan
Software Mentions: 6
Published: over 16 years ago

10.1371/journal.pone.0205291

CytoBinning: Immunological insights from multi-dimensional data
Cited by: 1
Author(s): Yang Shen, Benjamin Chaigne-Delalande, Richard W. Lee, Wolfgang Losert
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0243746

Image-based screen capturing misfolding status of Niemann-Pick type C1 identifies potential candidates for chaperone drugs
Cited by: 7
Author(s): Ryuta Shioi, Fumika Karaki, Hirosuke Yoshioka, Tomomi Noguchi‐Yachide, Minoru Ishikawa, Kosuke Dodo, Yuichi Hashimoto, Mikiko Sodeoka, Kenji Ohgane
Software Mentions: 6
Published: almost 4 years ago

10.1002/cyto.a.23775

Automating the Shared Resource Laboratory Using Computer Scripts: A Case Report
Cited by: 0
Author(s): Christopher Hall, Laura Brown, Jennifer Graham, Sam Thompson, Bee Ling Ng
Software Mentions: 6
Published: over 5 years ago

10.1534/g3.112.004283

Transcriptional Networks Controlling the Cell Cycle
Cited by: 24
Author(s): Martin Bonke, Mikko Turunen, Maria Sokolova, Anna Vähärautio, Teemu Kivioja, Minna Taipale, Mikael Björklund, Jussi Taipale
Software Mentions: 6
Published: almost 12 years ago

10.3389/fmicb.2018.02253

A Unique Saccharomyces cerevisiae × Saccharomyces uvarum Hybrid Isolated From Norwegian Farmhouse Beer: Characterization and Reconstruction
Cited by: 38
Author(s): Kristoffer Krogerus, Richard Preiss, Brian Gibson
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-021-92838-0

Light intensity and spectral composition drive reproductive success in the marine benthic diatom Seminavis robusta
Cited by: 4
Author(s): Gust Bilcke, Lore Van Craenenbroeck, Alexandre Castagna, Cristina Maria Osuna-Cruz, Klaas Vandepoele, Koen Sabbe, Lieven De Veylder, Wim Vyverman
Software Mentions: 5
Published: about 3 years ago

10.7554/eLife.51739

A phenotypic screening platform utilising human spermatozoa identifies compounds with contraceptive activity
Cited by: 14
Author(s): Franz S Gruber, Zoe C Johnston, Christopher L.R. Barratt, Paul D. Andrews
Software Mentions: 5
Published: almost 5 years ago

10.1172/jci.insight.142680

Exhausted-like CD8+ T cell phenotypes linked to C-peptide preservation in alefacept-treated T1D subjects
Cited by: 33
Author(s): Kirsten E. Diggins, Elisavet Serti, Virginia S. Muir, Mario G. Rosasco, Tingting Lü, Elisa Balmas, Gerald T. Nepom, S. Alice Long, Peter S. Linsley
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.isci.2021.102402

Absence of Batf3 reveals a new dimension of cell state heterogeneity within conventional dendritic cells
Cited by: 14
Author(s): Samuel W. Lukowski, Inga Rødahl, S. Thomas Kelly, Meihua Yu, James Gotley, Chenhao Zhou, Susan Millard, Stacey Andersen, Angelika N. Christ, Gabrielle T. Belz, Ian H. Frazer, Janin Chandra
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-98176-5

Flow cytometry method for absolute counting and single-cell phenotyping of mycobacteria
Cited by: 5
Author(s): David Barr, Charles Onyango Omollo, Mandy K. Mason, Anastasia Koch, Robert J. Wilkinson, David G. Lalloo, Graeme Meintjes, Valerie Mizrahi, Digby F. Warner, Gerry Davies
Software Mentions: 5
Published: about 3 years ago

10.1016/j.xcrm.2020.100039

Human Tumor-Infiltrating MAIT Cells Display Hallmarks of Bacterial Antigen Recognition in Colorectal Cancer
Cited by: 27
Author(s): Shamin Li, Yannick Simoni, Étienne Becht, Chiew Yee Loh, Naisi Li, Daniel M. Lachance, Si-Lin Koo, Teck Por Lim, Emile Tan, Ronnie Mathew, Andrew Nguyen, Justin Golovato, Julia D. Berkson, Martin Prlic, Bernett Lee, Samuel S. Minot, Niranjan Nagarajan, Neelendu Dey, Daniel S.W. Tan, Iain Bee Huat Tan, Evan W. Newell
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.53948

Stimulation strength controls the rate of initiation but not the molecular organisation of TCR-induced signalling
Cited by: 14
Author(s): Y. Claire, John C. Marioni, Gillian M. Griffiths, Alison F. Richard
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2105-10-106

flowCore: a Bioconductor package for high throughput flow cytometry
Cited by: 421
Author(s): Florian Hahne, Nolwenn Le Meur, Ryan R. Brinkman, Byron Ellis, Perry D. Haaland, Deepayan Sarkar, Josef Špidlen, Errol Strain, Robert Gentleman
Software Mentions: 5
Published: over 15 years ago

10.7554/eLife.60645

Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation
Cited by: 28
Author(s): Christian Brion, Sheila Lutz, Frank W. Albert
Software Mentions: 4
Published: about 4 years ago

10.1016/j.celrep.2019.06.049

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy
Cited by: 81
Author(s): Felix J. Hartmann, Joël Babdor, Pier Federico Gherardini, El-ad David Amir, Kyle Jones, Bita Sahaf, Diana M. Márquez, Peter O. Krutzik, Erika O’Donnell, Natalia Sigal, Holden T. Maecker, Everett Meyer, Matthew H. Spitzer, Sean C. Bendall
Software Mentions: 4
Published: over 5 years ago

10.1155/2009/809469

Bridging the Divide between Manual Gating and Bioinformatics with the Bioconductor Package flowFlowJo
Cited by: 4
Author(s): John J. Gosink, Gary Means, William Rees, Cheng Su, Hugh Rand
Software Mentions: 4
Published: about 15 years ago

10.3389/fimmu.2019.02403

Adaptive Features of Natural Killer Cells in Multiple Sclerosis
Cited by: 15
Author(s): Antía Moreira, Elisenda Alari-Pahissa, Elvira Munteis, Antonio Vera, Ana Zabalza, Mireia Llop, Noelia Villarrubia, Marcel Costa‐García, Roberto Álvarez‐Lafuente, Luisa María Villar, Miguel López‐Botet, José Enrique Martínez-Rodríguez
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2017.01786

Isolation and Characterization of Bacteria That Degrade Phosphonates in Marine Dissolved Organic Matter
Cited by: 31
Author(s): Oscar A. Sosa, Daniel J. Repeta, Sara Ferrón, Jessica A. Bryant, Daniel R. Mende, David M. Karl, Edward F. DeLong
Software Mentions: 4
Published: about 7 years ago

10.1186/1471-2105-11-546

Optimizing transformations for automated, high throughput analysis of flow cytometry data
Cited by: 71
Author(s): Greg Finak, Juan-Manuel Perez, Andrew P. Weng, Raphaël Gottardo
Software Mentions: 4
Published: about 14 years ago

10.3389/fimmu.2016.00603

TGF-β Affects the Differentiation of Human GM-CSF+ CD4+ T Cells in an Activation- and Sodium-Dependent Manner
Cited by: 5
Author(s): Szabolcs Éliás, Angelika Schmidt, Venkateshan Kannan, John Andersson, Jesper Tegnér
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-020-68693-w

Inhibition of indole production increases the activity of quinolone antibiotics against E. coli persisters
Cited by: 13
Author(s): Ashraf Zarkan, Marta Matuszewska, Stephen Trigg, Meng Zhang, Daaniyah Belgami, Cameron Croft, Junyan Liu, Sawssen El-Ouisi, Jack Greenhalgh, James S. Duboff, Taufiq Rahman, David Summers
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pgen.1008686

Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels
Cited by: 6
Author(s): Michael D. Morgan, Étienne Patin, Bernd Jabla, Milena Hasan, Lluís Quintana‐Murci, John C. Marioni
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers12071913

The LIM Protein Ajuba Augments Tumor Metastasis in Colon Cancer
Cited by: 10
Author(s): Noëlle Dommann, Daniel Sánchez-Taltavull, Linda Eggs, Fabienne Esther Birrer, Tess M. Brodie, Lilian Salm, Felix Alexander Baier, Michaela Medová, Magali Humbert, Mario P. Tschan, Guido Beldi, Daniel Candinas, Deborah Stroka
Software Mentions: 4
Published: over 4 years ago

10.1083/jcb.201711048

A timer for analyzing temporally dynamic changes in transcription during differentiation in vivo
Cited by: 54
Author(s): David Bending, Paz Prieto Martín, Alina Paduraru, Catherine Ducker, Erik Marzaganov, Marie Laviron, Satsuki Kitano, Hitoshi Miyachi, Tessa Crompton, M. Ono
Software Mentions: 4
Published: over 6 years ago

10.1172/jci.insight.146883

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

10.1002/yea.3246

Alternative<i>Saccharomyces</i>interspecies hybrid combinations and their potential for low-temperature wort fermentation
Cited by: 54
Author(s): Jarkko Nikulin, Kristoffer Krogerus, Brian Gibson
Software Mentions: 3
Published: about 7 years ago

10.1155/2009/356141

Analysis of High-Throughput Flow Cytometry Data Using plateCore
Cited by: 7
Author(s): Errol Strain, Florian Hahne, Ryan R. Brinkman, Perry D. Haaland
Software Mentions: 3
Published: about 15 years ago

10.1002/aps3.1164

flowPloidy: An R package for genome size and ploidy assessment of flow cytometry data
Cited by: 15
Author(s): Tyler Smith, Paul Kron, Sara L. Martin
Software Mentions: 3
Published: over 6 years ago

10.1186/1756-0500-4-50

Flow cytometry data standards
Cited by: 12
Author(s): Josef Špidlen, Parisa Shooshtari, Tobias R. Kollmann, Ryan R. Brinkman
Software Mentions: 3
Published: over 13 years ago

10.1093/bioinformatics/btaa946

Agile workflow for interactive analysis of mass cytometry data
Cited by: 6
Author(s): Julia Casado, Oskari Lehtonen, Ville Rantanen, Katja Kaipio, Luca Pasquini, Antti Häkkinen, Eleonora Petrucci, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Mauro Biffoni, Anniina Färkkilä, Sampsa Hautaniemi
Software Mentions: 3
Published: almost 4 years ago

10.1155/2009/193947

FlowFP: A Bioconductor Package for Fingerprinting Flow Cytometric Data
Cited by: 39
Author(s): Wade T. Rogers, Herbert A. Holyst
Software Mentions: 3
Published: about 15 years ago

10.1371/journal.pone.0188853

Indole at low concentration helps exponentially growing Escherichia coli survive at high temperature
Cited by: 7
Author(s): Junyan Liu, David Summers
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0197902

DNA immunization site determines the level of gene expression and the magnitude, but not the type of the induced immune response
Cited by: 16
Author(s): Stefan Petkov, Elizaveta Starodubova, Anastasia Latanova, Athina Kilpeläinen, Oleg Latyshev, Šimons Svirskis, Britta Wahrén, Francesca Chiodi, Ilya Gordeychuk, Maria Isaguliants
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0035693

A Computational Framework to Emulate the Human Perspective in Flow Cytometric Data Analysis
Cited by: 16
Author(s): Surajit Ray, Saumyadipta Pyne
Software Mentions: 3
Published: over 12 years ago

10.1038/s42003-020-1075-1

Cell-to-cell expression dispersion of B-cell surface proteins is linked to genetic variants in humans
Cited by: 2
Author(s): Gérard Triqueneaux, Claire Burny, Orsolya Symmons, Stéphane Janczarski, Henri Gruffat, Gaël Yvert
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2019.01194

Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses
Cited by: 39
Author(s): Shadi Toghi Eshghi, Amelia Au-Yeung, Chikara Takahashi, Christopher R. Bolen, Maclean N. Nyachienga, Sean Lear, Cherie Green, W. Rodney Mathews, William O’Gorman
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2019.02009

A Computational Pipeline for the Diagnosis of CVID Patients
Cited by: 11
Author(s): Annelies Emmaneel, Debby Bogaert, Sofie Van Gassen, Simon Tavernier, Mélissa Dullaers, Filomeen Haerynck, Yvan Saeys
Software Mentions: 3
Published: about 5 years ago

10.1016/j.xpro.2020.100092

AbSeq Protocol Using the Nano-Well Cartridge-Based Rhapsody Platform to Generate Protein and Transcript Expression Data on the Single-Cell Level
Cited by: 11
Author(s): Jami R. Erickson, Florian Mair, Grace Bugos, Jody Martin, Aaron J. Tyznik, Margaret Nakamoto, Stefanie Mortimer, Martin Prlic
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-018-31181-3

Characterization and induction of prophages in human gut-associated Bifidobacterium hosts
Cited by: 23
Author(s): Travis N. Mavrich, Eoghan Casey, Joana Oliveira, Francesca Bottacini, Kieran James, Charles M. A. P. Franz, Gabriele Andrea Lugli, Horst Neve, Marco Ventura, Graham F. Hatfull, Jennifer Mahony, Douwe van Sinderen
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-72610-6

Ontogeny of different subsets of yellow fever virus-specific circulatory CXCR5+ CD4+ T cells after yellow fever vaccination
Cited by: 6
Author(s): Quinn DeGottardi, Theresa J. Gates, Junbao Yang, Eddie A. James, Uma Malhotra, I-Ting Chow, Yannick Simoni, Michael G. Fehlings, Evan W. Newell, Hannah A. DeBerg, William W. Kwok
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-75417-7

Genetic parameters and associated genomic regions for global immunocompetence and other health-related traits in pigs
Cited by: 19
Author(s): María Ballester, Yuliaxis Ramayo-Caldas, Olga González‐Rodríguez, M. Pascual, Josep Peñuelas i Reixach, Marta Díaz, Fany Blanc, Sergi López-Serrano, J. Tibau, Raquel Quintanilla
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.67806

Mutational sources of trans-regulatory variation affecting gene expression in Saccharomyces cerevisiae
Cited by: 10
Author(s): Fabien Duveau, Petra Vande Zande, Brian P. H. Metzger, Crisandra J. Diaz, Elizabeth A. Walker, Stephen Tryban, Mohammad A. Siddiq, Bing Yang, Patricia J. Wittkopp
Software Mentions: 3
Published: about 3 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 6 years ago

10.1371/journal.pone.0182532

Proliferative capacity exhibited by human liver-resident CD49a+CD25+ NK cells
Cited by: 21
Author(s): Glòria Martrus, Tobias Kautz, Sebastian Lunemann, Laura Richert, Laura Glau, Wilhelm Salzberger, Hanna Goebels, Annika E. Langeneckert, Leonard U. Hess, T Poch, Christoph Schramm, Karl J. Oldhafer, Martina Koch, Eva Tolosa, Björn Nashan, Marcus Altfeld
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1006213

Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects
Cited by: 11
Author(s): Florent Chuffart, Magali Richard, Daniel Jost, Claire Burny, Hélène Duplus-Bottin, Yoshikazu Ohya, Gaël Yvert
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2020.02059

Changes in Population Age-Structure Obscure the Temperature-Size Rule in Marine Cyanobacteria
Cited by: 4
Author(s): Antonio S Palacio, Ana María Cabello, Francisca C. García, Abbrar Labban, Xosé Anxelu G. Morán, Laurence Garczarek, Laura Alonso‐Sáez, Ángel López‐Urrutia
Software Mentions: 2
Published: over 4 years ago

10.15252/emmm.202013549

Flow cytometry multiplexed method for the detection of neutralizing human antibodies to the native SARS‐CoV‐2 spike protein
Cited by: 26
Author(s): Lydia Horndler, Pilar Delgado, David Abia, Ivaylo Balabanov, Pedro Martínez‐Fleta, Georgina H. Cornish, Miguel Ángel Llamas, Sergio Serrano‐Villar, Francisco Sánchez-Madrid, Manuel Fresno, Hisse M. van Santen, Balbino Alarcón
Software Mentions: 2
Published: almost 4 years ago

10.1038/cddiscovery.2016.22

Hypoxia and classical activation limits Mycobacterium tuberculosis survival by Akt-dependent glycolytic shift in macrophages
Cited by: 28
Author(s): Sumit Kumar Matta, Sumit Kumar Matta
Software Mentions: 2
Published: over 8 years ago

10.1186/s40425-019-0695-9

Late-differentiated effector neoantigen-specific CD8+ T cells are enriched in peripheral blood of non-small cell lung carcinoma patients responding to atezolizumab treatment
Cited by: 45
Author(s): Michael G. Fehlings, Suchit Jhunjhunwala, Marcin Kowanetz, William O’Gorman, Priti S. Hegde, Hermi Sumatoh, Boon Heng Lee, Alessandra Nardin, Étienne Becht, Shannon L. Flynn, Marcus Ballinger, Evan W. Newell, Mahesh Yadav
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.37272

Fitness effects of altering gene expression noise in Saccharomyces cerevisiae
Cited by: 55
Author(s): Fabien Duveau, Andrea Hodgins‐Davis, Brian P. H. Metzger, Bing Yang, Stephen Tryban, Elizabeth A. Walker, Tricia Lybrook, Patricia J. Wittkopp
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-017-07851-z

Luciferase Expression Allows Bioluminescence Imaging But Imposes Limitations on the Orthotopic Mouse (4T1) Model of Breast Cancer
Cited by: 86
Author(s): V. P. Baklaushev, Athina Kilpeläinen, Stefan Petkov, Maxim A. Abakumov, N. F. Grinenko, Gaukhar M. Yusubalieva, Anastasia Latanova, Ilya Gubskiy, Ф Г Забозлаев, Elizaveta Starodubova, Tatiana O. Abakumova, Maria Isaguliants, V. P. Chekhonin
Software Mentions: 2
Published: over 7 years ago

10.15252/msb.20177823

Genomics of cellular proliferation in periodic environmental fluctuations
Cited by: 12
Author(s): Jérôme Salignon, Magali Richard, Etienne Fulcrand, Hélène Duplus-Bottin, Gaël Yvert
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms8121980

Exopolymeric Substances Control Microbial Community Structure and Function by Contributing to both C and Fe Nutrition in Fe-Limited Southern Ocean Provinces
Cited by: 5
Author(s): Sonia Blanco‐Ameijeiras, Damien Cabanes, Rachel N. Cable, Scarlett Trimborn, Stéphan Jacquet, Sonja Wiegmann, Christian Völkner, Florian Lelchat, Astrid Bracher, Melissa B. Duhaime, Christel Hassler
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.meteno.2016.06.003

The impact of respiration and oxidative stress response on recombinant α-amylase production by Saccharomyces cerevisiae
Cited by: 23
Author(s): José Luis Martínez, Eugenio Meza, Dina Petranović, Jens Nielsen
Software Mentions: 2
Published: almost 8 years ago

10.3389/fimmu.2015.00564

Increased NK Cell Maturation in Patients with Acute Myeloid Leukemia
Cited by: 20
Author(s): Anne-Sophie Chrétien, Samuel Granjeaud, Françoise Gondois-Rey, Samia Harbi, Florence Orlanducci, Didier Blaise, Norbert Vey, Christine Arnoulet, Cyril Fauriat, Daniel Olive
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-018-26281-z

Codon optimization and improved delivery/immunization regimen enhance the immune response against wild-type and drug-resistant HIV-1 reverse transcriptase, preserving its Th2-polarity
Cited by: 19
Author(s): Anastasia Latanova, Stefan Petkov, Athina Kilpeläinen, Juris Jansons, Oleg Latyshev, Yulia Kuzmenko, Jorma Hinkula, Maxim Abakumov, Vladimir T. Valuev-Elliston, Mark Gomelsky, В.Л. Карпов, Francesca Chiodi, Britta Wahrén, Denis Y. Logunov, Elizaveta Starodubova, Maria Isaguliants
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.31989

Efficient termination of nuclear lncRNA transcription promotes mitochondrial genome maintenance
Cited by: 25
Author(s): Dorine Jeanne Mariëtte du Mee, Maxim Ivanov, Joseph Paul Parker, Stephen Buratowski, Sebastian Marquardt
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-56279-0

Rheumatoid arthritis patients display B-cell dysregulation already in the naïve repertoire consistent with defects in B-cell tolerance
Cited by: 35
Author(s): Yan Wang, Katy A. Lloyd, Ioannis N. Melas, Diana Zhou, Radha Thyagarajan, Joakim Lindqvist, Monika Hansson, Anna Svärd, Linda Mathsson‐Alm, Alf Kastbom, Karin Lundberg, Lars Klareskog, Anca I. Catrina, Stephen Rapecki, Vivianne Malmström, Caroline Grönwall
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41375-020-0855-4

Deep immune profiling of patients treated with lenalidomide and dexamethasone with or without daratumumab
Cited by: 59
Author(s): Tineke Casneuf, Homer Adams, Niels W.C.J. van de Donk, Yann Abraham, Jaime Bald, Greet Vanhoof, Koen Van der Borght, Tina Smets, Brad Foulk, Karl Nielsen, Joshua Rusbuldt, Amy Axel, Andrew C. Lysaght, Hugo Ceulemans, Frederik Stevenaert, Saad Z. Usmani, Torben Plesner, Hervé Avet‐Loiseau, Inger S. Nijhof, Tuna Mutis, Jordan M. Schecter, Christopher Chiu, Nizar J. Bahlis
Software Mentions: 2
Published: over 4 years ago

10.1111/ejh.13013

Cytochemical flow analysis of intracellular G6PD and aggregate analysis of mosaic G6PD expression
Cited by: 11
Author(s): Michael Kalnoky, Germana Bancone, Maria Kahn, Cindy S. Chu, Nongnud Chowwiwat, Pornpimon Wilaisrisak, Sampa Pal, Nicole LaRue, Brandon T. Leader, François Nosten, Gonzalo J. Domingo
Software Mentions: 2
Published: almost 7 years ago

10.15252/emmm.201810092

Mutating chikungunya virus non‐structural protein produces potent live‐attenuated vaccine candidate
Cited by: 15
Author(s): Yi‐Hao Chan, Teck‐Hui Teo, Age Utt, Jeslin J. L. Tan, Siti Naqiah Amrun, Farhana Abu Bakar, Wearn‐Xin Yee, Étienne Becht, Cheryl Yi‐Pin Lee, Bernett Lee, Ravisankar Rajarethinam, Evan W. Newell, Andres Merits, Guillaume Carissimo, Fok‐Moon Lum, Lisa F. P. Ng
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-015-0602-4

NetworkPainter: dynamic intracellular pathway animation in Cytobank
Cited by: 3
Author(s): Jonathan R. Karr, Harendra Guturu, Edward Y. Chen, Stuart L Blair, Jonathan M. Irish, Nikesh Kotecha, Markus W. Covert
Software Mentions: 2
Published: over 9 years ago

10.1002/cti2.1175

Partial absence of PD‐1 expression by tumor‐infiltrating EBV‐specific CD8<sup>+</sup> T cells in EBV‐driven lymphoepithelioma‐like carcinoma
Cited by: 7
Author(s): Yannick Simoni, Étienne Becht, Shamin Li, Chiew Yee Loh, Joe Yeong, Tony Kiat Hon Lim, Angela Takano, Daniel S.W. Tan, Evan W. Newell
Software Mentions: 2
Published: almost 5 years ago

10.3389/fbioe.2021.642671

Automated Online Flow Cytometry Advances Microalgal Ecosystem Management as in situ, High-Temporal Resolution Monitoring Tool
Cited by: 8
Author(s): Iris Haberkorn, Cosima L. Off, Michael D. Besmer, Leandro Buchmann, Alexander Mathys
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2016.00742

Gene Flow Across Genus Barriers – Conjugation of Dinoroseobacter shibae’s 191-kb Killer Plasmid into Phaeobacter inhibens and AHL-mediated Expression of Type IV Secretion Systems
Cited by: 16
Author(s): Diana Patzelt, Victoria Michael, Orsola Päuker, Matthias Ebert, Petra Tielen, Dieter Jahn, Jürgen Tomasch, Jörn Petersen, Irene Wagner‐Döbler
Software Mentions: 1
Published: over 8 years ago

10.3389/fonc.2019.01214

The Tumor Suppressor Role of Zinc Finger Protein 671 (ZNF671) in Multiple Tumors Based on Cancer Single-Cell Sequencing
Cited by: 9
Author(s): Jian Zhang, Jianbin Luo, Huali Jiang, Tao Xie, Juanjuan Zheng, Yunhong Tian, Rong Li, Baiyao Wang, Jie Lin, Anan Xu, Xiaoting Huang, Yawei Yuan
Software Mentions: 1
Published: about 5 years ago

10.1016/j.celrep.2016.05.043

Protein Abundance Control by Non-coding Antisense Transcription
Cited by: 50
Author(s): Florian Huber, Daria Bunina, Ishaan Gupta, Anton Khmelinskii, Matthias Meurer, Patrick Theer, Lars M. Steinmetz, Michael Knop
Software Mentions: 1
Published: over 8 years ago

10.1074/jbc.M116.734020

The Coronary Artery Disease-associated Coding Variant in Zinc Finger C3HC-type Containing 1 (ZC3HC1) Affects Cell Cycle Regulation
Cited by: 14
Author(s): Peter D. Jones, Michael Kaiser, Maryam Ghaderi Najafabadi, David G. McVey, Allan Beveridge, Christine Schofield, Nilesh J. Samani, Tom R. Webb
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0169754

Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities
Cited by: 31
Author(s): Peter Rubbens, Ruben Props, Nico Boon, Willem Waegeman
Software Mentions: 1
Published: almost 8 years ago

10.7554/eLife.53226

Identification of a super-functional Tfh-like subpopulation in murine lupus by pattern perception
Cited by: 5
Author(s): Stefanie Gryzik, Yen Hoang, Timo Lischke, Elodie Mohr, Melanie Venzke, Isabelle Kadner, Josephine Poetzsch, Detlef Groth, Andreas Radbruch, Andreas Hutloff, Ria Baumgrass
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-88411-4

Circulating endothelial cells transiently increase in peripheral blood after kidney transplantation
Cited by: 3
Author(s): Héctor Tejeda Mora, Jeroen G H P Verhoeven, Wenda Verschoor, Karin Boer, Dennis A. Hesselink, Martijn W.F. van den Hoogen, Luc J. W. van der Laan, Carla C. Baan, Robert C. Minnee, Martin J. Hoogduijn
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1002443

A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli
Cited by: 149
Author(s): Olin K. Silander, Nela Nikolić, Alon Zaslaver, Anat Bren, Ilya Kikoin, Uri Alon, Martin Ackermann
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pbio.1001764

Different Levels of Catabolite Repression Optimize Growth in Stable and Variable Environments
Cited by: 171
Author(s): Aaron M. New, Bram Cerulus, Sander K. Govers, Gemma Perez-Samper, Bo Zhu, Sarah Boogmans, João B. Xavier, Kevin J. Verstrepen
Software Mentions: 1
Published: almost 11 years ago

Projects: bioconductor: flowCore

Papers Mentioning flowCore 109