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: bioconductor: oposSOM
https://packages.ecosyste.ms/registries/bioconductor.org/packages/oposSOM
Comprehensive analysis of transcriptome data
1 version
Latest release: 10 months ago
16,063 downloads total
Papers Mentioning oposSOM 27
10.3390/cells9030779
Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea (Pisum sativum L.)Cited by: 12
Author(s): Yury V. Malovichko, O. Y. Shtark, Ekaterina N. Vasileva, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 10
Published: over 4 years ago
10.3390/cancers11081057
Mining of Self-Organizing Map Gene-Expression Portraits Reveals Prognostic Stratification of HPV-Positive Head and Neck Squamous Cell CarcinomaCited by: 21
Author(s): Laura D. Locati, Mara Serena Serafini, Maria Federica Iannò, Andrea Carenzo, Ester Orlandi, Carlo Resteghin, Stefano Cavalieri, Paolo Bossi, Silvana Canevari, Lisa Licitra, Loris De Cecco
Software Mentions: 9
Published: about 5 years ago
10.3390/genes10110875
The Role of Plasticity and Adaptation in the Incipient Speciation of a Fire Salamander PopulationCited by: 6
Author(s): Joana Sabino‐Pinto, Daniel J. Goedbloed, Eugenia Sanchez, Thomas Czypionka, Arne W. Nolte, Sebastian Steinfartz
Software Mentions: 8
Published: over 4 years ago
10.1371/journal.pgen.1009201
Genomic and transcriptomic landscape of conjunctival melanomaCited by: 14
Author(s): Katarina Cisarova, Marc Folcher, Ikram El Zaoui, Rosanna Pescini Gobert, Virginie G. Peter, Béryl Royer‐Bertrand, Léonidas Zografos, Ann Schalenbourg, Michaël Nicolas, Donata Rimoldi, Serge Leyvraz, Nicolò Riggi, Alexandre Moulin, Carlo Rivolta
Software Mentions: 7
Published: over 3 years ago
10.1186/1471-2105-12-306
Expression cartography of human tissues using self organizing mapsCited by: 71
Author(s): Henry Wirth, Markus Löffler, Martin von Bergen, Hans Binder
Software Mentions: 5
Published: about 13 years ago
10.1371/journal.pone.0187572
Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profilesCited by: 56
Author(s): Arsen Arakelyan, Lilit Nersisyan, David Poghosyan, Lusine Khondkaryan, Աննա Հակոբյան, Henry Löffler-Wirth, Evie Melanitou, Hans Binder
Software Mentions: 4
Published: over 6 years ago
10.3390/genes11070817
SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural NetworksCited by: 5
Author(s): Maria Nikoghosyan, Maria Schmidt, K. Margaryan, Henry Loeffler‐Wirth, Arsen Arakelyan, Hans Binder
Software Mentions: 3
Published: about 4 years ago
10.3390/cells10071718
Epigenetic Drifts during Long-Term Intestinal Organoid CultureCited by: 5
Author(s): Torsten Thalheim, Susann Siebert, Marianne Quaas, Maria Herberg, Michal R. Schweiger, Gabriela Aust, Joerg Galle
Software Mentions: 3
Published: about 3 years ago
10.1186/s12864-021-08016-z
Transcriptome profile of the sinoatrial ring reveals conserved and novel genetic programs of the zebrafish pacemakerCited by: 13
Author(s): Rashid Minhas, Henry Loeffler‐Wirth, Yusra Siddiqui, Tomasz Obrębski, Shikha Vashisht, Karim Abu Nahia, Aleksandra Paterek, Angelika Brzozowska, Łukasz Bugajski, Katarzyna Piwocka, Vladimir Korzh, Hans Binder, Cecilia Lanny Winata
Software Mentions: 3
Published: almost 3 years ago
10.3389/fgene.2016.00079
Cartography of Pathway Signal Perturbations Identifies Distinct Molecular Pathomechanisms in Malignant and Chronic Lung DiseasesCited by: 6
Author(s): Arsen Arakelyan, Lilit Nersisyan, Martin Petřek, Henry Löffler-Wirth, Hans Binder
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pbio.2003389
Aging alters the epigenetic asymmetry of HSC divisionCited by: 94
Author(s): Maria Carolina Florian, Markus Klose, Mehmet Saçma, Jelena Jablanovic, Luke Knudson, Kalpana Nattamai, Gina Marka, Angelika Vollmer, Karin Soller, Vadim Sakk, Nina Cabezas-Wallscheid, Yi Zheng, Medhanie Mulaw, Ingmar Glauche, Hartmut Geiger
Software Mentions: 3
Published: almost 6 years ago
10.3390/cells8080870
Teratogenic Rubella Virus Alters the Endodermal Differentiation Capacity of Human Induced Pluripotent Stem CellsCited by: 14
Author(s): Nicole C. Bilz, Edith Willscher, Hans Binder, Janik Böhnke, Megan L. Stanifer, Denise Hübner, Steeve Boulant, Uwe G. Liebert, Claudia Claus
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12859-020-03806-w
oposSOM-Browser: an interactive tool to explore omics data landscapes in health scienceCited by: 10
Author(s): Henry Loeffler‐Wirth, Jasmin Reikowski, Siras Hakobyan, Jonas Wagner, Hans Binder
Software Mentions: 2
Published: almost 4 years ago
10.1186/1756-0381-5-18
Mining SOM expression portraits: feature selection and integrating concepts of molecular functionCited by: 51
Author(s): Henry Wirth, Martin von Bergen, Hans Binder
Software Mentions: 2
Published: almost 12 years ago
10.3390/v13091764
The Evolving Faces of the SARS-CoV-2 GenomeCited by: 14
Author(s): Maria Schmidt, Mamoona Arshad, Stephan H. Bernhart, Siras Hakobyan, Arsen Arakelyan, Henry Loeffler‐Wirth, Hans Binder
Software Mentions: 2
Published: almost 3 years ago
10.3390/pharmaceutics11120677
Transcriptome-Guided Drug RepositioningCited by: 11
Author(s): Arsen Arakelyan, Lilit Nersisyan, Maria Nikoghosyan, Siras Hakobyan, Arman Simonyan, Lydia Hopp, Henry Loeffler‐Wirth, Hans Binder
Software Mentions: 2
Published: over 4 years ago
10.1093/dnares/dsv014
Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in<i>Paramecium tetraurelia</i>Cited by: 18
Author(s): Miriam Cheaib, Azim Dehghani Amirabad, Karl Nordström, Marcel H. Schulz, Martín Simón
Software Mentions: 2
Published: almost 9 years ago
10.3389/fphys.2018.01180
The Diurnal Timing of Starvation Differently Impacts Murine Hepatic Gene Expression and Lipid Metabolism – A Systems Biology Analysis Using Self-Organizing MapsCited by: 10
Author(s): Christiane Rennert, Sebastian Vlaic, Eugenia Marbach-Breitrück, Carlo Thiel, Susanne Sales, Andrej Shevchenko, Rolf Gebhardt, Madlen Matz‐Soja
Software Mentions: 2
Published: almost 6 years ago
10.3389/fsurg.2021.663377
Long Non-coding RNAs in Traumatic Brain Injury Accelerated Fracture HealingCited by: 2
Author(s): Guoning Guo, Yajun Gou, Xingyu Jiang, Shuhong Wang, Ruilie Wang, Changqiang Liang, Guang Yang, Tinggang Wang, Anyong Yu, Guofu Zhu
Software Mentions: 2
Published: about 3 years ago
10.3390/genes6041076
Epigenetic Heterogeneity of B-Cell Lymphoma: Chromatin ModifiersCited by: 14
Author(s): Lydia Hopp, Lilit Nersisyan, Henry Löffler-Wirth, Arsen Arakelyan, Hans Binder
Software Mentions: 2
Published: almost 9 years ago
10.3390/genes6030812
Epigenetic Heterogeneity of B-Cell Lymphoma: DNA Methylation, Gene Expression and Chromatin StatesCited by: 28
Author(s): Lydia Hopp, Henry Löffler-Wirth, Hans Binder
Software Mentions: 1
Published: almost 9 years ago
10.3390/ijms22052551
Deciphering the Transcriptomic Heterogeneity of Duodenal Coeliac Disease BiopsiesCited by: 9
Author(s): Johannes Wolf, Edith Willscher, Henry Loeffler‐Wirth, Maria Schmidt, Gunter Flemming, Marlen Zurek, Holm H. Uhlig, Norman Händel, Hans Binder
Software Mentions: 1
Published: over 3 years ago
10.3389/fdata.2020.548873
The Human Blood Transcriptome in a Large Population Cohort and Its Relation to Aging and HealthCited by: 20
Author(s): Michael Schmidt, Lydia Hopp, Arsen Arakelyan, Holger Kirsten, Christoph Engel, Kerstin Wirkner, Knut Krohn, Ralph Burkhardt, Joachim Thiery, Markus Loeffler, Henry Loeffler‐Wirth, Hans Binder
Software Mentions: 1
Published: over 3 years ago
10.3390/cancers13133198
High-Resolution Cartography of the Transcriptome and Methylome Landscapes of Diffuse GliomasCited by: 5
Author(s): Edith Willscher, Lydia Hopp, Markus Kreuz, Maria Schmidt, Siras Hakobyan, Arsen Arakelyan, Bettina Hentschel, David Jones, Stefan M. Pfister, Markus Loeffler, Henry Loeffler‐Wirth, Hans Binder
Software Mentions: 1
Published: about 3 years ago
10.3389/fgene.2019.00394
Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians – A Machine Learning ApproachCited by: 9
Author(s): Maria Nikoghosyan, Siras Hakobyan, Անահիտ Հովհաննիսյան, Henry Loeffler‐Wirth, Hans Binder, Arsen Arakelyan
Software Mentions: 1
Published: over 5 years ago
10.1186/s13073-019-0637-7
A modular transcriptome map of mature B cell lymphomasCited by: 31
Author(s): Henry Loeffler‐Wirth, Markus Kreuz, Lydia Hopp, Arsen Arakelyan, Andrea Haake, Sergio Cogliatti, Alfred C. Feller, Martin‐Leo Hansmann, Dido Lenze, Peter Möller, Hans Konrad Müller‐Hermelink, Erik Fortenbacher, Edith Willscher, German Ott, Andreas Rosenwald, Christiane Pott, Carsten Schwäenen, Heiko Trautmann, Swen Weßendorf, Harald Stein, Monika Szczepanowski, Lorenz Trümper, Michael Hummel, Wolfram Klapper, Reiner Siebert, Markus Loeffler, Hans Binder
Software Mentions: 1
Published: about 5 years ago
10.3390/ijms22031220
Coxsackievirus B3 Infection of Human iPSC Lines and Derived Primary Germ-Layer Cells Regarding Receptor ExpressionCited by: 2
Author(s): Janik Böhnke, Sandra Pinkert, Maria Schmidt, Hans Binder, Nicole C. Bilz, Matthias Jung, Uta Reibetanz, Antje Beling, Dan Rujescu, Claudia Claus
Software Mentions: 1
Published: over 3 years ago