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: COCONUT

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

COmbat CO-Normalization Using conTrols (COCONUT)
3 versions
Latest release: about 7 years ago
1 dependent package
566 downloads last month

Papers Mentioning COCONUT 20

Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses
Cited by: 40
Author(s): Hong Zheng, A. Koneti Rao, Denis Đermadi, Jiaying Toh, Lara Jones, Michèle Donato, Yiran E. Liu, Yapeng Su, Dai Cl, Sergey A. Kornilov, Minas Karagiannis, Theodoros Marantos, Yehudit Hasin-Brumshtein, Yudong He, Evangelos J. Giamarellos‐Bourboulis, James R. Heath, Purvesh Khatri
Software Mentions: 4
Published: over 3 years ago

10.1186/s12906-019-2634-1

ETM-DB: integrated Ethiopian traditional herbal medicine and phytochemicals database
Cited by: 22
Author(s): Lemessa Etana Bultum, Assefa Mussa Woyessa, Doheon Lee
Software Mentions: 3
Published: about 5 years ago

10.3390/molecules26144323

Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT
Cited by: 1
Author(s): Ozren Jović, Tomislav Šmuc
Software Mentions: 3
Published: over 3 years ago

10.3390/molecules25081967

A Systems Biological Approach to Understanding the Mechanisms Underlying the Therapeutic Potential of Red Ginseng Supplements against Metabolic Diseases
Cited by: 4
Author(s): Eunseon Jeong, Yeni Lim, Kyeong Jin Kim, Hyeon Hui Ki, Doheon Lee, Jae-Hyun Suh, Seung Ho So, Oran Kwon, Ji Yeon Kim
Software Mentions: 2
Published: over 4 years ago

10.1016/j.isci.2020.101947

Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections
Cited by: 54
Author(s): Simone A. Thair, Yudong He, Yehudit Hasin-Brumshtein, Suraj Sakaram, Rushika Pandya, Jiaying Toh, David Rawling, Melissa Remmel, Sabrina Coyle, Georgios N. Dalekos, Ioannis Koutsodimitropoulos, Glykeria Vlachogianni, Eleni Gkeka, Eleni Karakike, Georgia Damoraki, Nikolaos Antonakos, Purvesh Khatri, Evangelos J. Giamarellos‐Bourboulis, Timothy E. Sweeney
Software Mentions: 2
Published: almost 4 years ago

10.3390/biom10111518

Fragment Library of Natural Products and Compound Databases for Drug Discovery
Cited by: 19
Author(s): Ana L. Chávez-Hernández, Norberto Sánchez-Cruz, José L. Medina-Franco
Software Mentions: 2
Published: about 4 years ago

10.3390/metabo11010048

Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB
Cited by: 3
Author(s): Marc Feuermann, Emmanuel Boutet, Anne Morgat, Kristian B. Axelsen, Parit Bansal, Jerven Bolleman, Edouard de Castro, Elisabeth Coudert, Elisabeth Gasteiger, Sébastien Géhant, Damien Lieberherr, Thierry Lombardot, Teresa Batista Neto, Ivo Pedruzzi, Sylvain Poux, Monica Pozzato, Nicole Redaschi, Alan Bridge
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms22063148

Identification of a Minimal 3-Transcript Signature to Differentiate Viral from Bacterial Infection from Best Genome-Wide Host RNA Biomarkers: A Multi-Cohort Analysis
Cited by: 5
Author(s): Alberto Gómez‐Carballa, Ruth Barral-Arca, Miriam Cebey-López, Xabier Bello, Jacobo Pardo‐Seco, Federico Martinón‐Torres, Antonio Salas
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms22094632

Target Prediction Model for Natural Products Using Transfer Learning
Cited by: 8
Author(s): Bo Qiang, Junyong Lai, Hongwei Jin, Liangren Zhang, Zhenming Liu
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms22115655

Kawasaki Disease Patient Stratification and Pathway Analysis Based on Host Transcriptomic and Proteomic Profiles
Cited by: 3
Author(s): Heather Jackson, Stephanie Menikou, Shea Hamilton, Andrew McArdle, Chisato Shimizu, Rachel Galassini, Hongtai Huang, J Kim, Adriana H. Tremoulet, Adam M Thorne, Román Fischer, M.I. de Jonge, Taco W. Kuijpers, Victoria J. Wright, Jane C. Burns, Climent Casals-Pascual, Jethro Herberg, Michael Levin, Myrsini Kaforou
Software Mentions: 2
Published: over 3 years ago

10.2144/fsoa-2020-0068

Towards a unified Latin American Natural Products Database: LANaPD
Cited by: 16
Author(s): José L. Medina-Franco
Software Mentions: 1
Published: about 4 years ago

10.3390/biom10111566

Cheminformatics to Characterize Pharmacologically Active Natural Products
Cited by: 29
Author(s): José L. Medina-Franco, Fernanda I. Saldívar-González
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13321-020-00424-9

Review on natural products databases: where to find data in 2020
Cited by: 223
Author(s): Maria Sorokina, Christoph Steinbeck
Software Mentions: 1
Published: over 4 years ago

10.1186/s13321-020-00478-9

COCONUT online: Collection of Open Natural Products database
Cited by: 180
Author(s): Maria Sorokina, Peter Merseburger, Kohulan Rajan, Mehmet Aziz Yirik, Christoph Steinbeck
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13321-021-00530-2

MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis
Cited by: 5
Author(s): Jan Přívratský, Jiří Novák
Software Mentions: 1
Published: over 3 years ago

10.1186/s13321-021-00546-8

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop
Cited by: 3
Author(s): Fidele Ntie‐Kang, Kiran K. Telukunta, Serge Alain Tanemossu Fobofou, Victor Chukwudi Osamor, Samuel Egieyeh, Marília Valli, Yannick Djoumbou-Feunang, Maria Sorokina, Conrad Stork, Neann Mathai, Paul Zierep, Ana L. Chávez-Hernández, Miquel Duran‐Frigola, Smith B. Babiaka, Romuald Tématio Fouedjou, Donatus B. Eni, Simeon Akame, Augustine B. Arreyetta-Bawak, Oyere Tanyi Ebob, Jonathan Alunge Metuge, Boris D. Bekono, Mustafa Alhaji Isa, Raphael Onuku, Daniel M. Shadrack, Thommas M. Musyoka, Vaishali M. Patil, Justin J. J. van der Hooft, Vanderlan da Silva Bolzani, José L. Medina‐Franco, Johannes Kirchmair, Tilmann Weber, Özlem Taştan Bishop, Marnix H. Medema, Ludger A. Wessjohann, Jutta Ludwig‐Müller
Software Mentions: 1
Published: about 3 years ago

10.3390/biom11040486

Description and Analysis of Glycosidic Residues in the Largest Open Natural Products Database
Cited by: 4
Author(s): Jonas Schaub, Achim Zielesny, Christoph Steinbeck, Maria Sorokina
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules26030637

The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of Urceolina peruviana (C. Presl) J.F. Macbr. as a Preliminary Test Case
Cited by: 14
Author(s): Mariacaterina Lianza, Ritchy Leroy, Carine Machado Rodrigues, Nicolas Borie, Charlotte Sayagh, Simon Rémy, Stefan Kühn, Jean‐Hugues Renault, Jean‐Marc Nuzillard
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0184159

Unique transcriptomic response to sepsis is observed among patients of different age groups
Cited by: 36
Author(s): Steven L. Raymond, María Cecilia López, Henry V. Baker, Shawn D. Larson, Philip A. Efron, Timothy E. Sweeney, Purvesh Khatri, Lyle L. Moldawer, James L. Wynn
Software Mentions: 1
Published: about 7 years ago

10.1155/2021/9990020

The Combination of Tradition and Future: Data-Driven Natural-Product-Based Treatments for Parkinson’s Disease
Cited by: 5
Author(s): Zhijun Miao, Jinwei Bai, Li Shen, Rajeev K. Singla
Software Mentions: 1
Published: over 3 years ago