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: parmigene

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

Parallel Mutual Information Estimation for Gene Network Reconstruction
4 versions
Latest release: over 4 years ago
4 dependent packages
464 downloads last month

Papers Mentioning parmigene 16

10.1371/journal.pcbi.1004765

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers
Cited by: 29
Author(s): Yasin Şenbabaoğlu, S. Onur Sumer, Francisco Sánchez-Vega, Debra L. Bemis, Giovanni Ciriello, Nikolaus Schultz, Chris Sander
Software Mentions: 7
Published: almost 9 years ago

10.1371/journal.pone.0035077

Hub-Centered Gene Network Reconstruction Using Automatic Relevance Determination
Cited by: 20
Author(s): M. Bock, Soichi Ogishima, Hiroshi Tanaka, Stefan Krämer, Lars Kaderali
Software Mentions: 6
Published: over 12 years ago

10.1038/srep29647

Tracking Cancer Genetic Evolution using OncoTrack
Cited by: 4
Author(s): Asoke K. Talukder, Mahima Agarwal, Kenneth H. Buetow, Patrice Denèfle
Software Mentions: 5
Published: over 8 years ago

10.1093/bib/bbaa072

Scoring functions for drug-effect similarity
Cited by: 13
Author(s): Stephan Struckmann, Markus Ernst, Sarah Fischer, Nancy Mah, Georg Fuellen, Steffen Möller
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0105942

Inference of Gene Regulatory Networks Incorporating Multi-Source Biological Knowledge via a State Space Model with L1 Regularization
Cited by: 18
Author(s): Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano, Seiya Imoto
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0158247

Nonlinear Network Reconstruction from Gene Expression Data Using Marginal Dependencies Measured by DCOL
Cited by: 10
Author(s): Haodong Liu, Peng Li, Mengyao Zhu, Xiaofei Wang, Jianwei Lu, Tianwei Yu
Software Mentions: 4
Published: over 8 years ago

10.3390/biom10040557

Deciphering Master Gene Regulators and Associated Networks of Human Mesenchymal Stromal Cells
Cited by: 6
Author(s): Elena Sánchez-Luis, Andrea Joaquín-García, Francisco J. Campos‐Laborie, Fermín Sánchez‐Guijo, Javier De Las Rivas
Software Mentions: 4
Published: over 4 years ago

10.1007/s00204-015-1573-y

A transcriptome-based classifier to identify developmental toxicants by stem cell testing: design, validation and optimization for histone deacetylase inhibitors
Cited by: 79
Author(s): Eugen Rempel, Lisa Hoelting, Tanja Waldmann, Nina V. Balmer, Stefan Schildknecht, Marianna Grinberg, John Antonydas Gaspar, Vaibhav Shinde, Regina Stöber, Rosemarie Marchan, Christoph van Thriel, Julia Liebing, Johannes Meisig, Nils Blüthgen, Agapios Sachinidis, Jörg Rahnenführer, Jan G. Hengstler, Marcel Leist
Software Mentions: 3
Published: over 9 years ago

10.3390/e21070645

Context Based Predictive Information
Cited by: 0
Author(s): Yuval Shalev, Irad Ben‐Gal
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms141123160

Systems Biology Approach to the Dissection of the Complexity of Regulatory Networks in the S. scrofa Cardiocirculatory System
Cited by: 4
Author(s): Paolo Martini, Gabriele Sales, Enrica Calura, Mattia Brugiolo, Gerolamo Lanfranchi, Chiara Romualdi, Stefano Cagnin
Software Mentions: 2
Published: about 11 years ago

10.1186/s12967-015-0492-2

Systems biology analysis reveals NFAT5 as a novel biomarker and master regulator of inflammatory breast cancer
Cited by: 36
Author(s): Andrea Remo, Ines Simeone, Massimo Pancione, Pietro Parcesepe, Pascal Finetti, Luigi Cerulo, Halima Bensmail, Daniel Birnbaum, Steven J. Van Laere, Vittorio Colantuoni, Franco Bonetti, François Bertucci, Erminia Manfrin, Michele Ceccarelli
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-15-421

Expression-based network biology identifies immune-related functional modules involved in plant defense
Cited by: 36
Author(s): Joel P. Tully, Aubrey E. Hill, Hadia Ahmed, Ryan Whitley, Anthony Skjellum, M. Shahid Mukhtar
Software Mentions: 2
Published: over 10 years ago

10.1007/s00204-016-1741-8

Definition of transcriptome-based indices for quantitative characterization of chemically disturbed stem cell development: introduction of the STOP-Toxukn and STOP-Toxukk tests
Cited by: 47
Author(s): Vaibhav Shinde, Lisa Hoelting, Sureshkumar Perumal Srinivasan, Johannes Meisig, Kesavan Meganathan, Smita Jagtap, Marianna Grinberg, Julia Liebing, Nils Bluethgen, Jörg Rahnenführer, Eugen Rempel, Regina Stoeber, Stefan Schildknecht, Sunniva Förster, Patrício Godoy, Christoph van Thriel, John Antonydas Gaspar, Jürgen Hescheler, Tanja Waldmann, Jan G. Hengstler, Marcel Leist, Agapios Sachinidis
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-16-S7-S10

BMRF-MI: integrative identification of protein interaction network by modeling the gene dependency
Cited by: 4
Author(s): Xu Shi, Xiao Wang, Ayesha N. Shajahan, Leena Hilakivi‐Clarke, Robert Clarke, Jianhua Xuan
Software Mentions: 1
Published: over 9 years ago

10.1155/2013/798912

Identifying Breast Cancer Subtype Related miRNAs from Two Constructed miRNAs Interaction Networks in Silico Method
Cited by: 7
Author(s): Lin Hua, Lin Li, Ping Zhou
Software Mentions: 1
Published: almost 12 years ago