Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: beeswarm
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/beeswarm
The Bee Swarm Plot, an Alternative to Stripchart
9 versions
Latest release: over 3 years ago
8 dependent packages
21,396 downloads last month
Papers Mentioning beeswarm 52
10.1371/journal.pone.0253950
Registered Report Protocol: Survey on attitudes and experiences regarding preregistration in psychological researchCited by: 2
Author(s): Lisa Spitzer, Stefanie Mueller
Software Mentions: 21
Published: over 3 years ago
10.3389/fcell.2021.671736
Identification of a Novel Immune Landscape Signature for Predicting Prognosis and Response of Endometrial Carcinoma to Immunotherapy and ChemotherapyCited by: 6
Author(s): Jinhui Liu, Yichun Wang, Jie Mei, Song Nie, Yan Zhang
Software Mentions: 15
Published: over 3 years ago
10.3389/fcell.2020.00790
The Construction of Bone Metastasis-Specific Prognostic Model and Co-expressed Network of Alternative Splicing in Breast CancerCited by: 4
Author(s): Runzhi Huang, Jian Guo, Penghui Yan, Suna Zhai, Peng Hu, Xiaolong Zhu, Jiayao Zhang, Yannan Qiao, Yu Zhang, Hui Liu, Ling Huang, Jie Zhang, Daoke Yang, Zongqiang Huang
Software Mentions: 15
Published: about 4 years ago
10.3389/fonc.2020.573295
Differential Expression Analysis Revealing CLCA1 to Be a Prognostic and Diagnostic Biomarker for Colorectal CancerCited by: 11
Author(s): Fang-Ze Wei, Shiwen Mei, Zhijie Wang, Jianan Chen, Huan Shen, Fen Zhao, Juan Li, Zheng Liu, Qian Liu
Software Mentions: 14
Published: about 4 years ago
10.3389/fmolb.2021.611508
CXCL10 is a Tumor Microenvironment and Immune Infiltration Related Prognostic Biomarker in Pancreatic AdenocarcinomaCited by: 17
Author(s): Huimin Huang, Wangxiao Zhou, Renpin Chen, Bingfeng Xiang, Shipeng Zhou, Linhua Lan
Software Mentions: 11
Published: over 3 years ago
10.3389/fimmu.2021.664845
CD2 Is a Novel Immune-Related Prognostic Biomarker of Invasive Breast Carcinoma That Modulates the Tumor MicroenvironmentCited by: 24
Author(s): Yanzhu Chen, Zhishang Meng, Lin Zhang, Feng Liu
Software Mentions: 11
Published: over 3 years ago
10.3389/fpsyg.2021.620307
No Evidence for a Decrease in Physical Activity Among Swiss Office Workers During COVID-19: A Longitudinal StudyCited by: 19
Author(s): Andrea Martina Aegerter, Manja Deforth, Gisela Sjøgaard, Venerina Johnston, Thomas Volken, Hannu Luomajoki, Julia Dratva, Holger Dressel, Oliver Distler, Markus Melloh, Achim Elfering
Software Mentions: 10
Published: over 3 years ago
10.3389/fmolb.2020.604252
Prognostic Model of Colorectal Cancer Constructed by Eight Immune-Related GenesCited by: 14
Author(s): Shuting Wen, Lina He, Zhuotai Zhong, Hong Mi, Fengbin Liu
Software Mentions: 9
Published: almost 4 years ago
10.3389/fneur.2021.615790
Retinal Thickness Analysis in Progressive Multiple Sclerosis Patients Treated With Epigallocatechin Gallate: Optical Coherence Tomography Results From the SUPREMES StudyCited by: 7
Author(s): Katharina Klumbies, Rebekka Rust, Jan Dörr, Frank Konietschke, Friedemann Paul, Judith Bellmann‐Strobl, Alexander U. Brandt, Hanna Zimmermann
Software Mentions: 8
Published: over 3 years ago
10.1016/j.molcel.2019.01.009
Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA SequencingCited by: 195
Author(s): Alba Rodríguez-Meira, Gemma Buck, Sally-Ann Clark, Benjamin Povinelli, Verónica Alcolea, Eleni Louka, Simon J. McGowan, Angela Hamblin, Nikolaos Sousos, Nikolaos Barkas, Alice Giustacchini, Bethan Psaila, Sten Eirik W. Jacobsen, Supat Thongjuea, Adam J. Mead
Software Mentions: 8
Published: over 5 years ago
10.1186/s12935-020-01560-w
Identification of an immune gene signature for predicting the prognosis of patients with uterine corpus endometrial carcinomaCited by: 19
Author(s): Cankun Zhou, Chaomei Li, Fangli Yan, Yuhua Zheng
Software Mentions: 8
Published: almost 4 years ago
10.1002/1878-0261.12139
Transcription instability in high-risk neuroblastoma is associated with a global perturbation of chromatin domainsCited by: 4
Author(s): Carlo Zanon, Gian Paolo Tonini
Software Mentions: 8
Published: about 7 years ago
10.1038/srep46658
Metabolism dysregulation induces a specific lipid signature of nonalcoholic steatohepatitis in patientsCited by: 148
Author(s): Franck Chiappini, Audrey Coilly, Hanane Kadar, Philippe Gual, Albert Tran, Christophe Desterke, Didier Samuel, Jean‐Charles Duclos‐Vallée, David Touboul, Justine Bertrand‐Michel, Alain Brunelle, Catherine Guettier, François Le Naour
Software Mentions: 8
Published: over 7 years ago
10.3389/fmolb.2021.651525
Potential Role of NEU1 in Hepatocellular Carcinoma: A Study Based on Comprehensive Bioinformatical AnalysisCited by: 5
Author(s): Zhulin Wu, Li He, Lina Yang, Xuehong Fang, Lisheng Peng
Software Mentions: 7
Published: about 3 years ago
10.3389/fmolb.2021.656145
Identification and Exploration of Novel Macrophage M2-Related Biomarkers and Potential Therapeutic Agents in EndometriosisCited by: 10
Author(s): Zhongqi Cui, Ramesh Singh Bhandari, Lei Qin, Mingzhi Lu, Lei Zhang, Mengmei Zhang, Fenyong Sun, Lijin Feng, Shasha Zhao
Software Mentions: 7
Published: over 3 years ago
10.7717/peerj.11430
Identification of Vitamin D-related gene signature to predict colorectal cancer prognosisCited by: 1
Author(s): Luping Bu, Fengxing Huang, Mengting Li, Yanan Peng, Haizhou Wang, Meng Zhang, Linfa Peng, Lan Liu, Qiu Zhao
Software Mentions: 7
Published: over 3 years ago
10.1186/s13568-016-0191-2
Automation of antimicrobial activity screeningCited by: 8
Author(s): Samuel P. Forry, Meggan C. Madonna, Daneli López-Pérez, Nancy J. Lin, Madeleine D. Pasco
Software Mentions: 6
Published: over 8 years ago
10.1371/journal.pone.0099926
Insights from Computational Modeling in Inflammation and Acute Rejection in Limb TransplantationCited by: 23
Author(s): Dolores Wolfram, Ravi Starzl, Hubert Hackl, Derek Barclay, Theresa Hautz, Bettina Zelger, Gerald Brandacher, W. P. Andrew Lee, Nadine Eberhart, Yoram Vodovotz, Johann Pratschke, Gerhard Pierer, Stefan Schneeberger
Software Mentions: 6
Published: over 10 years ago
10.1371/journal.pone.0132932
Spatiotemporal Patterns of Tumor Occurrence in Children with Intraocular RetinoblastomaCited by: 13
Author(s): Benjamin King, Carlos Parra, Yimei Li, Kathleen J. Helton, Ibrahim Qaddoumi, Matthew W. Wilson, Robert J. Ogg
Software Mentions: 6
Published: over 9 years ago
10.3389/fmicb.2021.701796
L-Canavanine, a Root Exudate From Hairy Vetch (Vicia villosa) Drastically Affecting the Soil Microbial Community and Metabolite PathwaysCited by: 7
Author(s): Hossein Mardani-Korrani, Masaru Nakayasu, Shinichi Yamazaki, Yosuke Aoki, Rumi Kaida, Takashi Motobayashi, Masaru Kobayashi, Naoko Ohkama‐Ohtsu, Yosei Oikawa, Akifumi Sugiyama, Yoshiharu Fujii
Software Mentions: 6
Published: about 3 years ago
10.1038/s41598-020-58493-7
VGLL3 is a prognostic biomarker and correlated with clinical pathologic features and immune infiltrates in stomach adenocarcinomaCited by: 13
Author(s): Lihua Zhang, Longhai Li, Yong Mao, Hua Dong
Software Mentions: 6
Published: almost 5 years ago
10.1038/s41598-021-87384-8
Field multi-omics analysis reveals a close association between bacterial communities and mineral properties in the soybean rhizosphereCited by: 11
Author(s): Shinichi Yamazaki, Hossein Mardani-Korrani, Rumi Kaida, Kumiko Ochiai, Masaru Kobayashi, Atsushi J. Nagano, Yoshiharu Fujii, Akifumi Sugiyama, Yosuke Aoki
Software Mentions: 6
Published: over 3 years ago
10.1264/jsme2.ME17160
Chitin Increases <i>Mycobacterium ulcerans</i> Growth in Acidic EnvironmentsCited by: 6
Author(s): Daniel Sanhueza, Christine Chevillon, Nicolas Bouzinbi, Sylvain Godreuil, Jean‐François Guégan
Software Mentions: 5
Published: almost 7 years ago
10.1186/s13046-020-01823-4
The EGFR-HSF1 axis accelerates the tumorigenesis of pancreatic cancerCited by: 9
Author(s): Weikun Qian, Ke Chen, Tao Qin, Ying Xiao, Jie Li, Yangyang Yue, Cancan Zhou, Jiguang Ma, Wanxing Duan, Jing Liu, Liang Han, Li Li, Xin Shen, Zheng Wu, Qingyong Ma, Zheng Wang
Software Mentions: 5
Published: almost 4 years ago
10.3390/diagnostics11030476
Association of Circulating miRNA Expression with Preeclampsia, Its Onset, and SeverityCited by: 8
Author(s): Zuzana Kolková, Veronika Holubeková, Marián Grendár, Marcela Ňachajová, Pavol Žúbor, Terézia Pribulová, Dušan Loderer, Imrich Zigo, Kamil Biringer, Andrea Horňáková
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-017-4100-0
Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolatesCited by: 61
Author(s): Lee M. Yeoh, Christopher D. Goodman, Vanessa Mollard, Geoffrey I. McFadden, Stuart A. Ralph
Software Mentions: 5
Published: about 7 years ago
10.1038/s41598-020-76991-6
Salivary microbiome composition changes after bariatric surgeryCited by: 11
Author(s): Mária Džunková, Róbert Lipták, Barbora Vlková, Roman Gardlík, M Cierny, Andrés Moya, Peter Celec
Software Mentions: 5
Published: almost 4 years ago
10.2196/27633
Web-Based Survival Analysis Tool Tailored for Medical Research (KMplot): Development and ImplementationCited by: 716
Author(s): András Lánczky, Balázs Győrffy
Software Mentions: 5
Published: over 3 years ago
10.3389/fncel.2018.00106
Automated Morphological Analysis of Microglia After StrokeCited by: 155
Author(s): Steffanie Heindl, Benno Gesierich, Corinne Benakis, Gemma Llovera, Marco Duering, Arthur Liesz
Software Mentions: 5
Published: over 6 years ago
10.18632/aging.102841
Identification of biomarkers related to CD8+ T cell infiltration with gene co-expression network in clear cell renal cell carcinomaCited by: 47
Author(s): Jiaxing Lin, Meng Yu, Xiao Xu, Yutao Wang, Haotian Xing, Jing An, Jieping Yang, Chaozhi Tang, Dan Sun, Yuyan Zhu
Software Mentions: 5
Published: over 4 years ago
10.1038/srep29971
The impact of preconceptional obesity on trajectories of maternal lipids during gestationCited by: 26
Author(s): Latife Bozkurt, Christian Göbl, Anna-Theresa Hörmayer, Anton Luger, Giovanni Pacini, Alexandra Kautzky‐Willer
Software Mentions: 5
Published: over 8 years ago
10.18632/aging.202281
Integrated bioinformatic analysis of RNA binding proteins in hepatocellular carcinomaCited by: 16
Author(s): Ling Wang, Zhen Zhang, Yuan Li, Yanyan Wan, Baocai Xing
Software Mentions: 5
Published: almost 4 years ago
10.3390/ijms21197288
Pathway Analysis of Selected Circulating miRNAs in Plasma of Breast Cancer Patients: A Preliminary StudyCited by: 13
Author(s): Veronika Holubeková, Zuzana Kolková, Marián Grendár, Dušan Braný, Dana Dvorská, Igor Stastny, Marianna Jagelková, Katarína Zelinová, Marek Samec, Alena Líšková, Zuzana Laučeková, Erik Kúdela, Martina Bobrovská, Michal Kalman, Pavol Žúbor, Zuzana Daňková
Software Mentions: 5
Published: about 4 years ago
10.3389/fneur.2020.00316
Observational Study of Pulse Transit Time in Children With Sleep Disordered BreathingCited by: 1
Author(s): Michael Yanney, Andrew Prayle, Nicola J. Rowbotham, Miguel Kurc, Sean Tilbrook, Nabeel Ali
Software Mentions: 4
Published: over 4 years ago
10.1080/15592294.2016.1182272
Bisphenol A causes reproductive toxicity, decreases <i>dnmt1</i> transcription, and reduces global DNA methylation in breeding zebrafish <i>(Danio rerio)</i>Cited by: 138
Author(s): Lauren V. Laing, Joana Viana, Emma Dempster, Maciej Trznadel, L. A. Trunkfield, Tamsyn M. Uren Webster, Ronny van Aerle, Gregory C. Paull, Robert J. Wilson, Jonathan Mill, Eduarda M. Santos
Software Mentions: 4
Published: over 8 years ago
10.12688/f1000research.4856.2
Thrombocytosis portends adverse prognostic significance in patients with stage II colorectal carcinomaCited by: 12
Author(s): Tianhua Guo, Marcin Krzystanek, Zoltán Szállási, A Szállaśi
Software Mentions: 4
Published: about 10 years ago
10.1042/BSR20201491
Exploration of immune-related genes in high and low tumor mutation burden groups of chromophobe renal cell carcinomaCited by: 9
Author(s): Lei Li, Xi Chen, Lu Hao, Qiuyan Chen, Haosheng Liu, Qing Zhou
Software Mentions: 4
Published: over 4 years ago
10.18632/aging.203049
Construction of a novel mRNA-miRNA-lncRNA network and identification of potential regulatory axis associated with prognosis in colorectal cancer liver metastasesCited by: 8
Author(s): Lu Chen, Xiaochun Luo, Xing Cheng, Yonghuan Mao, Yuting Xu, Wenjie Gao, Wulin Wang, Tian Zhan, Guoguang Wang, Zhengxia Liu, Chang-Feng Yu
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0129350
Multiplexing of ChIP-Seq Samples in an Optimized Experimental Condition Has Minimal Impact on Peak DetectionCited by: 0
Author(s): Thadeous J. Kacmarczyk, Caitlin Bourque, Xihui Zhang, Yanwen Jiang, Yariv Houvras, Alicia Alonso, Doron Betel
Software Mentions: 4
Published: over 9 years ago
10.3390/ijerph18137158
A Possible Preventive Role of Physically Active Lifestyle during the SARS-CoV-2 Pandemic; Might Regular Cold-Water Swimming and Exercise Reduce the Symptom Severity of COVID-19?Cited by: 3
Author(s): Viktor Bielik, Marián Grendár, Martin Kolísek
Software Mentions: 3
Published: over 3 years ago
10.1186/s40168-016-0182-1
The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynxCited by: 139
Author(s): Robyn L. Marsh, Mirjam Kaestli, Anne B. Chang, Michael J. Binks, Charles E. Pope, Lucas R. Hoffman, Heidi Smith‐Vaughan
Software Mentions: 3
Published: over 8 years ago
10.3390/jcm10112297
Complex Interplay of Genes Underlies Invasiveness in Fibrosarcoma Progression ModelCited by: 0
Author(s): Michaela Kripnerová, Hamendra Singh Parmar, Jiří Šána, Alena Kopková, Lenka Radová, Sieghart Sopper, Krzysztof Biernacki, Jan Jedlička, M Kohoutová, Jitka Kuncová, Jan Peychl, Emil Rudolf, Miroslav Červinka, Zbyněk Houdek, Pavel Dvořák, Kateřina Houfková, Martin Pešta, Zdeněk Tůma, M. Dolejšová, Filip Tichánek, Václav Babuška, Martin Leba, Ondřej Slabý, Jiřı́ Hatina
Software Mentions: 3
Published: over 3 years ago
10.3389/fimmu.2017.00221
Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire SequencingCited by: 14
Author(s): Polina Reshetova, Barbera D. C. van Schaik, Paul L. Klarenbeek, Marieke E. Doorenspleet, Rebecca E. E. Esveldt, Paul‐Peter Tak, Jeroen E. J. Guikema, Niek de Vries, Antoine H. C. van Kampen
Software Mentions: 3
Published: over 7 years ago
10.7717/peerj.450
Local norms of cheating and the cultural evolution of crime and punishment: a study of two urban neighborhoodsCited by: 22
Author(s): Kari Britt Schroeder, Gillian Pepper, Daniel Nettle
Software Mentions: 3
Published: over 10 years ago
10.18632/oncotarget.7451
Ioncopy: a novel method for calling copy number alterations in amplicon sequencing data including significance assessmentCited by: 21
Author(s): Jan Budczies, Nicole Pfarr, Albrecht Stenzinger, Denise Treue, Volker Endris, Fakher Ismaéel, Nikola Bangemann, Jens-Uwe Blohmer, Manfred Dietel, Sibylle Loibl, Frederick Klauschen, Wilko Weichert, Carsten Denkert
Software Mentions: 3
Published: over 8 years ago
10.1186/s12885-020-07529-2
Increased E2F2 predicts poor prognosis in patients with HCC based on TCGA dataCited by: 12
Author(s): Zhili Zeng, Zebiao Cao, Ying Tang
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pgen.1009674
An auxin signaling network translates low-sugar-state input into compensated cell enlargement in the fugu5 cotyledonCited by: 11
Author(s): Hiromitsu Tabeta, S. Watanabe, Koichiro Fukuda, Shizuka Gunji, Mariko Asaoka, Masami Yokota Hirai, Mitsunori Seo, Hirokazu Tsukaya, Ali Ferjani
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pone.0150852
Spontaneous 8bp Deletion in Nbeal2 Recapitulates the Gray Platelet Syndrome in MiceCited by: 12
Author(s): Kärt Tomberg, Rami Khoriaty, Randal J. Westrick, Heather Fairfield, Laura G. Reinholdt, Gary Brodsky, Pavel Davizon‐Castillo, David Ginsburg, Jorge Di Paola
Software Mentions: 2
Published: over 8 years ago
10.1093/femsec/fiw096
Formation of lipid bodies and changes in fatty acid composition upon pre-akinete formation in Arctic and Antarctic<i>Zygnema</i>(Zygnematophyceae, Streptophyta) strainsCited by: 54
Author(s): Martina Pichrtová, Erwann Arc, Wolfgang Stöggl, Ilse Kranner, Tomáš Hájek, Hubert Hackl, Andreas Holzinger
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pbio.2001867
Integrated time-lapse and single-cell transcription studies highlight the variable and dynamic nature of human hematopoietic cell fate commitmentCited by: 48
Author(s): Alice Moussy, Jérémie Cosette, Romuald Parmentier, Cindy da Silva, Guillaume Corre, Richard Angélique, Olivier Gandrillon, Daniel Stockholm, Andràs Páldi
Software Mentions: 2
Published: over 7 years ago
10.1242/bio.030015
Distribution of PEG-coated hollow polyelectrolyte microcapsules after introduction into the circulatory system and muscles of zebrafishCited by: 8
Author(s): Ekaterina Borvinskaya, Anton Gurkov, Ekaterina Shchapova, Boris Baduev, Igor Meglinski, Maxim A. Timofeyev
Software Mentions: 1
Published: almost 7 years ago
10.3389/fimmu.2018.00428
Autoantibodies in Serum of Systemic Scleroderma Patients: Peptide-Based Epitope Mapping Indicates Increased Binding to Cytoplasmic Domains of CXCR3Cited by: 13
Author(s): Andreas Recke, Ann-Katrin Regensburger, Florian Weigold, Antje Müller, Harald Heidecke, G Marschner, Christoph M Hammers, Ralf J. Ludwig, Gabriela Riemekasten
Software Mentions: 1
Published: over 6 years ago