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: DEP
https://packages.ecosyste.ms/registries/bioconductor.org/packages/DEP
Differential Enrichment analysis of Proteomics data
1 version
Latest release: 12 months ago
1 dependent package
39,223 downloads total
Papers Mentioning DEP 35
10.3389/fimmu.2021.616967
A Multi-Omics Analysis of Mucosal-Associated-Invariant T Cells Reveals Key Drivers of Distinct Modes of ActivationCited by: 12
Author(s): Kristin Schubert, Isabel Karkossa, Jana Schor, Beatrice Engelmann, Lisa Maria Steinheuer, Tony Bruns, Ulrike Rolle-Kampczyk, Jörg Hackermüller, Martin von Bergen
Software Mentions: 24
Published: over 3 years ago
10.3389/fimmu.2021.620270
Non-Genomic AhR-Signaling Modulates the Immune Response in Endotoxin-Activated Macrophages After Activation by the Environmental Stressor BaPCited by: 18
Author(s): Henning Großkopf, Katharina Walter, Isabel Karkossa, Martin von Bergen, Kristin Schubert
Software Mentions: 18
Published: over 3 years ago
10.3390/cancers12030692
Hypoxia-Induced Adaptations of miRNomes and Proteomes in Melanoma Cells and Their Secreted Extracellular VesiclesCited by: 29
Author(s): Geoffroy Walbrecq, Odile Lecha, Anthoula Gaigneaux, Miriam Rebecca Fougeras, Demetra Philippidou, Christiane Margue, Miléne Tetsi Nomigni, François Bernardin, Gunnar Dittmar, Iris Behrmann, Stephanie Kreis
Software Mentions: 11
Published: over 4 years ago
10.3389/fnins.2021.621121
Analysis of the Neuroproteome Associated With Cell Therapy After Intranigral Grafting in a Mouse Model of Parkinson DiseaseCited by: 1
Author(s): Hassan Dakik, Sarah Mantash, Ali Nehme, Firas Kobeissy, Masoud Zabet-Moghaddam, Parvin Mirzaei, Yehia Mechref, Afsaneh Gaillard, Laetitia Prestoz, Kazem Zibara
Software Mentions: 7
Published: over 3 years ago
10.1242/dev.178590
Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body planCited by: 13
Author(s): Julien Rougeot, Naomi D. Chrispijn, Marco Aben, Dei M. Elurbe, Karolina M. Andralojc, Patrick J. Murphy, Pascal W.T.C. Jansen, Michiel Vermeulen, Bradley R. Cairns, Leonie M. Kamminga
Software Mentions: 7
Published: almost 6 years ago
10.1084/jem.20192275
<i>NCKAP1L</i> defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammationCited by: 44
Author(s): Carla Castro, Michelle Rosenzwajg, Raphaël Carapito, Mohammad Shahrooei, Martina Konantz, Amjad Khan, Zhichao Miao, Miriam Groß, Thibaud Tranchant, Mirjana Radosavljevic, Nicodème Paul, Tristan Stemmelen, Fabien Pitoiset, Aurélie Hirschler, Benoît Nespola, Anne Molitor, Véronique Rolli, Angélique Pichot, Laura Faletti, Bruno Rinaldi, Sylvie Friant, Mark Mednikov, Hatice Karaüzüm, M. Javad Aman, Christine Carapito, Claudia Lengerke, Vahid Ziaee, Wafaa Eyaid, Stephan Ehl, Fayhan Alroqi, Nima Parvaneh, Seiamak Bahram
Software Mentions: 6
Published: about 4 years ago
10.18632/aging.202978
Dietary-challenged mice with Alzheimer-like pathology show increased energy expenditure and reduced adipocyte hypertrophy and steatosisCited by: 2
Author(s): Stefanie Schreyer, Nikolaus Berndt, Johannes Eckstein, Michael Mülleder, Shabnam Hemmati‐Sadeghi, Charlotte Klein, Basim Abuelnor, Alina Elisabeth Catharina Panzel, David Meierhofer, Joachim Spranger, Barbara Steiner, Sebastian Brachs
Software Mentions: 6
Published: over 3 years ago
10.1186/s41512-018-0036-3
Methods for Evaluation of medical prediction Models, Tests And Biomarkers (MEMTAB) 2018 SymposiumCited by: 3
Author(s):
Software Mentions: 6
Published: over 6 years ago
10.3390/antiox10030498
Characterization of NADPH Oxidase Expression and Activity in Acute Myeloid Leukemia Cell Lines: A Correlation with the Differentiation StatusCited by: 10
Author(s): Hassan Dakik, Maya El Dor, Joan Leclerc, Farah Kouzi, Ali Nehme, Margaux Deynoux, Christelle Debeissat, Georges Khamis, Elfi Ducrocq, Aida Ibrik, Marie‐José Stasia, Houssam Raad, Hamid Reza Rezvani, Fabrice Gouilleux, Kazem Zibara, Olivier Hérault, Frédéric Mazurier
Software Mentions: 4
Published: over 3 years ago
10.1016/j.cell.2021.03.012
Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactionsCited by: 126
Author(s): Ryan A. Flynn, Julia A. Belk, Yanyan Qi, Yuki Yasumoto, Wei Jin, Mia Madel Alfajaro, Quanming Shi, Maxwell R. Mumbach, Aditi Limaye, Peter C DeWeirdt, Cameron O. Schmitz, Kevin R. Parker, Elizabeth Woo, Howard Y. Chang, Tamás L. Horváth, Jan E. Carette, Carolyn R. Bertozzi, Craig B. Wilen, Ansuman T. Satpathy
Software Mentions: 3
Published: over 3 years ago
10.3390/genes11101128
Proteomics Reveals Distinct Changes Associated with Increased Gamma Radiation Resistance in the Black Yeast Exophiala dermatitidisCited by: 7
Author(s): Zachary Schultzhaus, Janna N. Schultzhaus, Jillian Romsdahl, Amy Chen, W. Judson Hervey, Dagmar H. Leary, Zheng Wang
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pgen.1008681
The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)Cited by: 20
Author(s): Christos N. Velanis, Pumi Perera, Bennett Thomson, Erica de Leau, Shih Chieh Liang, Ben Hartwig, Alexander Förderer, Harry Thornton, Pedro Arêde, Jiawen Chen, Kimberly M. Webb, Serin Gümüs, Geert De Jaeger, Clinton A. Page, C. Nathan Hancock, Christos Spanos, Juri Rappsilber, Philipp Voigt, Franziska Turck, Frank Wellmer, Justin Goodrich
Software Mentions: 3
Published: over 4 years ago
10.1186/s12918-016-0311-2
Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literatureCited by: 19
Author(s): Yaoyun Zhang, Hui Wu, Jun Xu, Jingqi Wang, Ergin Soysal, Lang Li, Hua Xu
Software Mentions: 2
Published: about 8 years ago
10.3390/cancers13164157
The Fatty Acid and Protein Profiles of Circulating CD81-Positive Small Extracellular Vesicles Are Associated with Disease Stage in Melanoma PatientsCited by: 14
Author(s): Giovanni Paolino, Veronica Huber, Serena Camerini, Marialuisa Casella, Alberto Macone, Lucia Bertuccini, Francesca Iosi, Elisa Moliterni, Serena Cecchetti, Irene Ruspantini, Flavia Chiarotti, Elisabetta Vergani, Luca Lalli, Carla Raggi, Antonella Di Biase, Stefano Calvieri, Santo Raffaele Mercuri, Luana Lugini, Cristina Federici
Software Mentions: 2
Published: about 3 years ago
10.3389/fimmu.2021.599530
Dietary Inclusion of Black Soldier Fly (Hermetia Illucens) Larvae Meal and Paste Improved Gut Health but Had Minor Effects on Skin Mucus Proteome and Immune Response in Atlantic Salmon (Salmo Salar)Cited by: 30
Author(s): Pabodha Weththasinghe, Leidy Lagos, Marcos Cortés, Jon Øvrum Hansen, Margareth Øverland
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2019.01305
A Pretraining-Retraining Strategy of Deep Learning Improves Cell-Specific Enhancer PredictionsCited by: 11
Author(s): Xiaohui Niu, Kun Yang, Ge Zhang, Zhiquan Yang, Xuehai Hu
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-021-84274-x
Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birdsCited by: 1
Author(s): Eleni Voukali, Nithya Kuttiyarthu Veetil, Pavel Němec, Pavel Stopka, Michal Vinkler
Software Mentions: 2
Published: over 3 years ago
10.1155/2016/7357123
Multiphase Simulated Annealing Based on Boltzmann and Bose-Einstein Distribution Applied to Protein Folding ProblemCited by: 3
Author(s): Juan Frausto–Solís, Ernesto Liñán-García, Juan Paulo Sánchez-Hernández, Juan J. González-Barbosa, Carlos González-Flores, Guadalupe Castilla-Valdez
Software Mentions: 1
Published: over 8 years ago
10.3390/ijms21103501
Physical Activity Dynamically Regulates the Hippocampal Proteome along the Dorso-Ventral AxisCited by: 2
Author(s): Surina Frey, Rico Schieweck, Ignasi Forné, Axel Imhof, Tobias Straub, Bastian Popper, Michael A. Kiebler
Software Mentions: 1
Published: over 4 years ago
10.1186/s12889-021-11632-9
Effectiveness and economic impact of a diabetes education program among adults with type 2 diabetes in South TexasCited by: 6
Author(s): Matthew Lee Smith, Lixian Zhong, Shinduk Lee, Samuel D. Towne, Marcia G. Ory
Software Mentions: 1
Published: about 3 years ago
10.1016/j.media.2020.101712
Automatic spatial estimation of white matter hyperintensities evolution in brain MRI using disease evolution predictor deep neural networksCited by: 13
Author(s): Muhammad Febrian Rachmadi, Maria del C. Valdés-Hernández, Stephen Makin, Joanna M. Wardlaw, Taku Komura
Software Mentions: 1
Published: over 4 years ago
10.3390/mi11110990
A Prominent Cell Manipulation Technique in BioMEMS: DielectrophoresisCited by: 17
Author(s): Zeynep Çağlayan, Yağmur Demircan Yalçın, Haluk Külah
Software Mentions: 1
Published: almost 4 years ago
10.1186/s13578-021-00659-5
SNX27-driven membrane localisation of OTULIN antagonises linear ubiquitination and NF-κB signalling activationCited by: 4
Author(s): Ruona Shi, Xue Shi, Dajiang Qin, Shibing Tang, Michiel Vermeulen, Xiaofei Zhang
Software Mentions: 1
Published: about 3 years ago
10.1016/j.ebiom.2016.03.046
Climate Change and Aedes Vectors: 21st Century Projections for Dengue Transmission in EuropeCited by: 132
Author(s): Jing Liu-Helmersson, Mikkel Quam, Annelies Wilder‐Smith, Hans Stenlund, Kristie L. Ebi, Eduardo Massad, Joacim Rocklöv
Software Mentions: 1
Published: over 8 years ago
10.1186/s13637-016-0040-2
Inference of protein-protein interaction networks from multiple heterogeneous dataCited by: 14
Author(s): Lei Huang, Li Liao, Cathy H. Wu
Software Mentions: 1
Published: over 8 years ago
10.1002/elps.202000156
Dielectrophoresis: Developments and applications from 2010 to 2020Cited by: 41
Author(s): Benjamin Sarno, Daniel Heineck, Michael Heller, Stuart Ibsen
Software Mentions: 1
Published: almost 4 years ago
10.1038/s12276-019-0242-2
Phosphoregulation of the oncogenic protein regulator of cytokinesis 1 (PRC1) by the atypical CDK16/CCNY complexCited by: 18
Author(s): Sara Hernández-Ortega, Abril Sánchez-Botet, Eva Quandt, Núria Masip, Laura Gasa, Gaetano Verde, Javier Jiménez, Rebecca S. Levin, Florentine U. Rutaganira, Alma L. Burlingame, Don Wolfgeher, Mariana P.C. Ribeiro, Stephen J. Kron, Kevan M. Shokat, Josep Clotet
Software Mentions: 1
Published: over 5 years ago
10.3389/fimmu.2021.644700
The Contact Allergen NiSO4 Triggers a Distinct Molecular Response in Primary Human Dendritic Cells Compared to Bacterial LPSCited by: 9
Author(s): Tessa Höper, Katherina Siewert, Verónica I. Dumit, Martin von Bergen, Kristin Schubert, Andrea Haase
Software Mentions: 1
Published: over 3 years ago
10.1093/jxb/ery389
Profiling of advanced glycation end products uncovers abiotic stress-specific target proteins in ArabidopsisCited by: 17
Author(s): Amanda K. Chaplin, Igor Chernukhin, Ulrike Bechtold
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.ppat.1001329
Dissection of the Influenza A Virus Endocytic Routes Reveals Macropinocytosis as an Alternative Entry PathwayCited by: 264
Author(s): Erik de Vries, Donna M. Tscherne, Marleen J. Wienholts, Viviana Cobos-Jiménez, Florine E. M. Scholte, Adolfo Garcı́a-Sastre, Peter J. M. Rottier, Cornelis A. M. de Haan
Software Mentions: 1
Published: over 13 years ago
10.1038/s41598-019-46311-8
A Pilot Proof-Of-Principle Analysis Demonstrating Dielectrophoresis (DEP) as a Glioblastoma Biomarker PlatformCited by: 23
Author(s): Jeffrey Lewis, Ali Al-Attar, Johnny Akers, Bob S. Carter, Michael Heller, Clark C. Chen
Software Mentions: 1
Published: about 5 years ago
10.1038/s41598-020-69865-4
Proteomic analysis identifies plasma correlates of remote ischemic conditioning in the context of experimental traumatic brain injuryCited by: 2
Author(s): Maha Saber, Khyatiben V. Pathak, Marissa McGilvrey, Krystine Garcia-Mansfield, Jordan L. Harrison, Rachel K. Rowe, Jonathan Lifshitz, Patrick Pirrotte
Software Mentions: 1
Published: about 4 years ago
10.1155/2015/940243
A Review of the Effects of Major Atmospheric Pollutants on Pollen Grains, Pollen Content, and AllergenicityCited by: 127
Author(s): Hélène Sénéchal, Nicolas Visez, D. Charpin, Youcef Shahali, Gabriel Peltre, Jean-Philippe Biolley, F. Lhuissier, Rémy Couderc, Ohri Yamada, Audrey Malrat-Domenge, N. Pham‐Thi, Pascal Poncet, Jean-Pierre Sutra
Software Mentions: 1
Published: almost 10 years ago
10.3390/s17010045
DEP-On-Go for Simultaneous Sensing of Multiple Heavy Metals Pollutants in Environmental SamplesCited by: 18
Author(s): Madhu Biyani, Radhika Biyani, Tomoko Tsuchihashi, Yuzuru Takamura, Hiromi Ushijima, Eiichi Tamiya, Manish Biyani
Software Mentions: 1
Published: almost 8 years ago
10.2196/16391
Strategies for the Successful Implementation of a Novel iPhone Loaner System (iShare) in mHealth Interventions: Prospective StudyCited by: 17
Author(s): William Yang, Erin M Spaulding, David Lumelsky, George Hung, Pauline P. Huynh, Kellen Knowles, Francoise A Marvel, Valerie Vilarino, Jane Wang, Lochan M. Shah, Helen Xun, Rongzi Shan, Shannon Wongvibulsin, Seth S. Martin
Software Mentions: 1
Published: almost 5 years ago