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: pypi: graph
https://packages.ecosyste.ms/registries/pypi.org/packages/graph
Directed and undirected graph data structures and algorithms.
4 versions
Latest release: over 1 year ago
Papers Mentioning graph 45
10.1002/pmic.201400392
Visualization of proteomics data using R and BioconductorCited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago
10.1371/journal.pcbi.1000227
Analyzing ChIP-chip Data Using BioconductorCited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: almost 16 years ago
10.1186/s13321-020-00455-2
spyrmsd: symmetry-corrected RMSD calculations in PythonCited by: 23
Author(s): Rocco Meli, Philip C. Biggin
Software Mentions: 13
Published: about 4 years ago
10.7554/eLife.48994
Self-assembling manifolds in single-cell RNA sequencing dataCited by: 48
Author(s): Alexander J. Tarashansky, Yuan Xue, Pengyang Li, Stephen R. Quake, Bo Wang
Software Mentions: 12
Published: about 5 years ago
10.1007/s12032-017-0963-9
The identification of key genes and pathways in hepatocellular carcinoma by bioinformatics analysis of high-throughput dataCited by: 107
Author(s): Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Software Mentions: 12
Published: over 7 years ago
10.1186/s12859-015-0763-1
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq dataCited by: 29
Author(s): Ivana Ihnatová, Eva Budínská
Software Mentions: 12
Published: about 9 years ago
10.3390/metabo11030133
Correlation of Metabolic Profiles of Plasma and Cerebrospinal Fluid of High-Grade Glioma PatientsCited by: 9
Author(s): Artem D. Rogachev, Н. А. Алемасов, В. А. Иванисенко, Nikita V. Ivanisenko, E. V. Gaisler, Olga Oleshko, С. В. Чересиз, С. В. Мишинов, В. В. Ступак, Andrey G. Pokrovsky
Software Mentions: 9
Published: over 3 years ago
10.1093/bioinformatics/btw763
ontologyX: a suite of R packages for working with ontological dataCited by: 66
Author(s): Daniel Greene, Sylvia Richardson, Ernest Turro
Software Mentions: 9
Published: almost 8 years ago
10.3390/e23020160
Influence Cascades: Entropy-Based Characterization of Behavioral Influence Patterns in Social MediaCited by: 5
Author(s): Chathurani Senevirathna, Chathika Gunaratne, William Rand, Chathura Jayalath, Iván Garibay
Software Mentions: 8
Published: almost 4 years ago
10.1186/1471-2105-14-179
Modelling and visualizing fine-scale linkage disequilibrium structureCited by: 3
Author(s): D.J. Edwards
Software Mentions: 8
Published: over 11 years ago
10.1093/bioinformatics/btx738
PlanNET: homology-based predicted interactome for multiple planarian transcriptomesCited by: 17
Author(s): Sergio Castillo-Lara, Josep F. Abril
Software Mentions: 8
Published: almost 7 years ago
10.2196/jmir.5461
What Are We Looking for in Computer-Based Learning Interventions in Medical Education? A Systematic ReviewCited by: 60
Author(s): Tiago Taveira-Gomes, Patrícia Ferreira, Isabel Taveira-Gomes, Mílton Severo, Manuela Ferreira
Software Mentions: 8
Published: over 8 years ago
10.7150/ijms.48244
Identification of Key Genes and Pathways in Myeloma side population cells by Bioinformatics AnalysisCited by: 21
Author(s): Yang Qin, Kaihu Li, Xin Li, Jing Liu
Software Mentions: 8
Published: almost 5 years ago
10.3390/cancers12123799
A Topic Modeling Analysis of TCGA Breast and Lung Cancer Transcriptomic DataCited by: 11
Author(s): Filippo Valle, Matteo Osella, Michele Caselle
Software Mentions: 8
Published: almost 4 years ago
10.1186/1471-2105-8-S6-S8
Graphs in molecular biologyCited by: 108
Author(s): Wolfgang Huber, Vincent J. Carey, Long Li, Seth Falcon, Robert Gentleman
Software Mentions: 7
Published: about 17 years ago
10.1186/gb-2012-13-4-r29
RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.Cited by: 84
Author(s): Mauro A. A. Castro, Xin Wang, Michael Fletcher, Kerstin B. Meyer, Florian Markowetz
Software Mentions: 7
Published: almost 13 years ago
10.1186/1471-2105-12-455
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction databaseCited by: 62
Author(s): Antonio M. Mora, Ian Donaldson
Software Mentions: 6
Published: almost 13 years ago
10.1186/s12864-019-5933-5
Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thalianaCited by: 13
Author(s): Sony Kumari, Sneha Yadav, Debadutta Patra, Sharmila Singh, Ananda K. Sarkar, Kishore C. S. Panigrahi
Software Mentions: 6
Published: over 5 years ago
10.7717/peerj-cs.387
Semantic micro-contributions with decentralized nanopublication servicesCited by: 11
Author(s): Tobias Kuhn, Ruben Taelman, Vincent Emonet, Haris Antonatos, Stian Soiland‐Reyes, Michel Dumontier
Software Mentions: 6
Published: over 3 years ago
10.1186/s40246-020-00291-3
Aldh1l2 knockout mouse metabolomics links the loss of the mitochondrial folate enzyme to deregulation of a lipid metabolism observed in rare human disorderCited by: 9
Author(s): Natalia I. Krupenko, Jaspreet Sharma, Peter Pediaditakis, Kristi L. Helke, Madeline S. Hall, Xiuxia Du, Susan Sumner, Sergey A. Krupenko
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pone.0234752
Bayesian networks established functional differences between breast cancer subtypesCited by: 5
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Jorge M. Arevalillo, Rocío López-Vacas, Elena López-Camacho, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, María Ferrer-Gómez, Hilario Navarro, Paolo Nanni, Pilar Zamora, Enrique Espinosa, Paloma Maı́n, Juan Ángel Fresno Vara
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.pone.0223745
Measuring the complexity of directed graphs: A polynomial-based approachCited by: 7
Author(s): Matthias Dehmer, Zengqiang Chen, Frank Emmert‐Streib, Shailesh Tripathi, Abbe Mowshowitz, Alexei Leviţchi, Lihua Feng, Yongtang Shi, Tao Jin
Software Mentions: 5
Published: about 5 years ago
10.1038/s41598-021-98249-5
Psychological factors shaping public responses to COVID-19 digital contact tracing technologies in GermanyCited by: 14
Author(s): Anastasia Kozyreva, Philipp Lorenz-Spreen, Stephan Lewandowsky, Paul Michael Garrett, Stefan M. Herzog, Thorsten Pachur, Ralph Hertwig
Software Mentions: 4
Published: about 3 years ago
10.1371/journal.pone.0123082
Genomic Heterogeneity of Osteosarcoma - Shift from Single Candidates to Functional ModulesCited by: 27
Author(s): Kathrin Poos, Jan Smida, Doris Maugg, Gertrud Eckstein, Daniel Baumhoer, Michaela Nathrath, Eberhard Korsching
Software Mentions: 4
Published: over 9 years ago
10.3389/fimmu.2019.02186
Common Nodes of Virus–Host Interaction Revealed Through an Integrated Network AnalysisCited by: 65
Author(s): Korbinian Bösl, Aleksandr Ianevski, Thoa Thi Than, Petter I. Andersen, Suvi Kuivanen, Mona Teppor, Eva Žusinaite, Uga Dumpis, Astra Vitkauskienė, Rebecca Jane Cox, Hannimari Kallio‐Kokko, Anders Bergqvist, Tanel Tenson, Andres Merits, Valentyn Oksenych, Magnar Bjørås, Marit W. Anthonsen, David Shum, Mari Kaarbø, Olli Vapalahti, Marc P. Windisch, Giulio Superti‐Furga, Berend Snijder, Denis E. Kainov, Richard K. Kandasamy
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pone.0197883
The regulatory ancestral network of surgical meshesCited by: 21
Author(s): Nasim Zargar, Andrew Carr
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pone.0232384
Socio-ecological network structures from process graphsCited by: 11
Author(s): Angelyn R. Lao, Heriberto Cabezas, Ákos Orosz, Ferenc Friedler, Raymond R. Tan
Software Mentions: 4
Published: over 4 years ago
10.3389/fmolb.2021.715972
Fuzzle 2.0: Ligand Binding in Natural Protein Building BlocksCited by: 5
Author(s): Noelia Ferruz, Florian Michel, Francisco Lobos, Steffen Schmidt, Birte Höcker
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1005388
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architectureCited by: 12
Author(s): Dongjun Chung, Hang J. Kim, Hongyu Zhao
Software Mentions: 3
Published: almost 8 years ago
10.1371/journal.pone.0238586
Biological data questions the support of the self inhibition required for pattern generation in the half center modelCited by: 6
Author(s): M Köhler, Philipp Stratmann, Florian Röhrbein, Alois Knoll, Alin Albu‐Schäffer, Henrik Jörntell
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.ppat.1006476
Innate immunity restricts Citrobacter rodentium A/E pathogenesis initiation to an early window of opportunityCited by: 14
Author(s): Stefanie Buschor, Miguelangel Cuenca, Stephanie S. Uster, Olivier P. Schären, Maria L. Balmer, Miguel A. Terrazos, Christian M. Schürch, Siegfried Hapfelmeier
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0168597
Bibliometrics for Social ValidationCited by: 5
Author(s): Daniel J. Hicks
Software Mentions: 3
Published: almost 8 years ago
10.3390/ma10020169
A Bio-Electro-Fenton System Employing the Composite FePc/CNT/SS316 CathodeCited by: 14
Author(s): Yi-Ta Wang, Ruei-Shiang Wang
Software Mentions: 2
Published: almost 8 years ago
10.3390/ijms140611842
Peptide Induced Crystallization of Calcium Carbonate on Wrinkle Patterned Substrate: Implications for Chitin Formation in MolluscsCited by: 15
Author(s): Anindita Sengupta Ghatak, Marcus Koch, Christina Guth, Ingrid M. Weiss
Software Mentions: 2
Published: over 11 years ago
10.1093/bioinformatics/btz575
Haplotype-aware graph indexesCited by: 47
Author(s): Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
Software Mentions: 2
Published: over 5 years ago
10.1186/1746-1596-7-75
Molecular characteristics and chromatin texture features in acute promyelocytic leukemiaCited by: 10
Author(s): Mariana R. B. Mello, Dulcinéia Martins Albuquerque, F.G. Pereira-Cunha, Krizzia Borges Albanez, Kátia Bórgia Barbosa Pagnano, Fernando Ferreira Costa, Konradin Metze, Irene Lorand-Metze
Software Mentions: 2
Published: over 12 years ago
10.1002/ece3.6587
EXFI: Exon and splice graph prediction without a reference genomeCited by: 0
Author(s): Jorge Langa, Andone Estonba, Darrell Conklin
Software Mentions: 2
Published: over 4 years ago
10.3389/fpls.2021.710268
Effects of Methyl Salicylate on Host Plant Acceptance and Feeding by the Aphid Rhopalosiphum padiCited by: 11
Author(s): Velemir Ninkovic, Robert Glinwood, Ayse Gül Ünlü, Suresh Ganji, C. Rikard Unelius
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0135420
Melatonin Cytotoxicity Is Associated to Warburg Effect Inhibition in Ewing Sarcoma CellsCited by: 55
Author(s): Ana M. Sánchez‐Sánchez, Isaac Antolı́n, Noelia Puente‐Moncada, S. Suárez, Marina Gomez-Lobo, Carmen Rodríguez, Vanesa Martı́n
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0011393
New Polynomial-Based Molecular Descriptors with Low DegeneracyCited by: 16
Author(s): Matthias Dehmer, Laurin A. J. Mueller, Armin Graber
Software Mentions: 2
Published: over 14 years ago
10.1111/jeb.13731
Speciation‐by‐depth on coral reefs: Sympatric divergence with gene flow or cryptic transient isolation?Cited by: 24
Author(s): Carlos Prada, Michael E. Hellberg
Software Mentions: 2
Published: about 4 years ago
10.1038/s41598-019-48924-5
Loan maturity aggregation in interbank lending networks obscures mesoscale structure and economic functionsCited by: 1
Author(s): Marnix Van Soom, Milan van den Heuvel, Jan Ryckebusch, Koen Schoors
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pcbi.1005968
Reactome graph database: Efficient access to complex pathway dataCited by: 181
Author(s): Antonio Fabregat, Florian Korninger, Guilherme Viteri, Konstantinos Sidiropoulos, Pablo Marín-García, Peipei Ping, Guanming Wu, Lincoln Stein, P D'Eustachio, Henning Hermjakob
Software Mentions: 2
Published: almost 7 years ago
10.1155/2021/6636710
New Construction of Family of MLCS AlgorithmsCited by: 0
Author(s): Haihe Shi, Jun Wang
Software Mentions: 2
Published: almost 4 years ago