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: CIDER

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/CIDER

Meta-Clustering for Single-Cell Data Integration and Evaluation
2 versions
Latest release: about 2 years ago
242 downloads last month

Papers Mentioning CIDER 18

Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein
Cited by: 11
Author(s): Ruchi Lohia, Reza Salari, Grace Brannigan
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijms21082794

Similar Yet Different–Structural and Functional Diversity among Arabidopsis thaliana LEA_4 Proteins
Cited by: 10
Author(s): Patrick Knox-Brown, Tobias Rindfleisch, Anne Günther, Kim Balow, Anne Bremer, Dirk Walther, Markus S. Miettinen, Dirk K. Hincha, Anja Thalhammer
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0152860

Predicting miRNA Targets by Integrating Gene Regulatory Knowledge with Expression Profiles
Cited by: 14
Author(s): Weijia Zhang, Thuc Duy Le, Lin Liu, Zhi‐Hua Zhou, Jiuyong Li
Software Mentions: 2
Published: over 8 years ago

10.1186/s12964-020-00626-6

Orchestration of signaling by structural disorder in class 1 cytokine receptors
Cited by: 19
Author(s): Pernille Seiffert, Katrine Bugge, Mads Nygaard, Gitte W. Haxholm, Jacob H. Martinsen, Martin Nors Pedersen, Lise Arleth, Wouter Boomsma, Birthe B. Kragelund
Software Mentions: 2
Published: about 4 years ago

10.3389/fcell.2021.674203

A Hypothesis: Linking Phase Separation to Meiotic Sex Chromosome Inactivation and Sex-Body Formation
Cited by: 6
Author(s): Yiding Xu, Huanyu Qiao
Software Mentions: 1
Published: about 3 years ago

10.3389/fmolb.2019.00064

Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins
Cited by: 22
Author(s): Omar Demerdash, Utsab R. Shrestha, Loukas Petridis, Jeremy C. Smith, Julie C. Mitchell, Arvind Ramanathan
Software Mentions: 1
Published: about 5 years ago

10.1074/jbc.AC119.009198

Liquid–liquid phase separation of tau protein: The crucial role of electrostatic interactions
Cited by: 136
Author(s): Solomiia Boyko, Qi Xu, Tien‐Hao Chen, Krystyna Surewicz, Witold K. Surewicz
Software Mentions: 1
Published: about 5 years ago

10.1038/srep11999

Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells
Cited by: 31
Author(s): Marco Mina, Shigeyuki Magi, Giuseppe Jurman, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Peter Arner, Alistair R.R. Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O. Daub, Mariko Okada‐Hatakeyama, Cesare Furlanello
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-019-49745-2

Role of protein conformation and weak interactions on γ-gliadin liquid-liquid phase separation
Cited by: 17
Author(s): Line Sahli, Denis Renard, Véronique Solé-Jamault, Alexandre Giuliani, Adeline Boire
Software Mentions: 1
Published: about 5 years ago

10.1186/s13643-021-01787-2

CogTale: an online platform for the evaluation, synthesis, and dissemination of evidence from cognitive interventions studies
Cited by: 2
Author(s): Julieta Sabatés, Sylvie Belleville, Mary Castellani, Tzvi Dwolatzky, Benjamin M. Hampstead, Amit Lampit, Sharon Sanz Simon, Kaarin J. Anstey, Belinda Goodenough, Serafino G. Mancuso, Davis Marques, Richard Sinnott, Alex Bahar‐Fuchs
Software Mentions: 1
Published: about 3 years ago

10.3390/ijms21176208

Relevance of Electrostatic Charges in Compactness, Aggregation, and Phase Separation of Intrinsically Disordered Proteins
Cited by: 50
Author(s): Greta Bianchi, Sonia Longhi, Rita Grandori, Stefania Brocca
Software Mentions: 1
Published: about 4 years ago

10.3390/ijms21186796

Protein Databases Related to Liquid–Liquid Phase Separation
Cited by: 26
Author(s): Qian Li, Xi Wang, Zhihui Dou, Weishan Yang, Beifang Huang, Jizhong Lou, Zhuqing Zhang
Software Mentions: 1
Published: about 4 years ago

10.3390/ijms22157912

Seeing Keratinocyte Proteins through the Looking Glass of Intrinsic Disorder
Cited by: 8
Author(s): Rambon Shamilov, Victoria Robinson, Brian J. Aneskievich
Software Mentions: 1
Published: about 3 years ago

10.3390/biom11081173

Insight into Calcium-Binding Motifs of Intrinsically Disordered Proteins
Cited by: 11
Author(s): Estella A. Newcombe, Catarina B. Fernandes, Jeppe E. Lundsgaard, Inna Brakti, Kresten Lindorff‐Larsen, Annette Eva Langkilde, Karen Skriver, Birthe B. Kragelund
Software Mentions: 1
Published: about 3 years ago

10.3390/ijms221810174

Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: A Force Field Comparison
Cited by: 11
Author(s): Ellen Rieloff, Marie Skepö
Software Mentions: 1
Published: almost 3 years ago

10.1016/j.bpj.2020.02.015

Molecular Dynamics Ensemble Refinement of Intrinsically Disordered Peptides According to Deconvoluted Spectra from Circular Dichroism
Cited by: 17
Author(s): Jacob C. Ezerski, Pengzhi Zhang, Nathaniel C. Jennings, M. Neal Waxham, Margaret S. Cheung
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.4930

Metal-binding polymorphism in late embryogenesis abundant protein AtLEA4-5, an intrinsically disordered protein
Cited by: 9
Author(s): Leidys French-Pacheco, Cesar L. Cuevas-Velazquez, Lina Rivillas‐Acevedo, Alejandra A. Covarrubias, Carlos Amero
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1008474

Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2
Cited by: 1
Author(s): N. Suhas Jagannathan, Christopher W. V. Hogue, Lisa Tucker-Kellogg
Software Mentions: 1
Published: over 3 years ago