bioconductor: graph | Projects | Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited 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 Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: about 16 years ago

10.1186/s13321-020-00455-2

spyrmsd: symmetry-corrected RMSD calculations in Python
Cited by: 23
Author(s): Rocco Meli, Philip C. Biggin
Software Mentions: 13
Published: over 4 years ago

Self-assembling manifolds in single-cell RNA sequencing data
Cited by: 48
Author(s): Alexander J. Tarashansky, Yuan Xue, Pengyang Li, Stephen R. Quake, Bo Wang
Software Mentions: 12
Published: over 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 data
Cited 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 data
Cited 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 Patients
Cited 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: almost 4 years ago

10.1093/bioinformatics/btw763

ontologyX: a suite of R packages for working with ontological data
Cited 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 Media
Cited 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 structure
Cited 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 transcriptomes
Cited by: 17
Author(s): Sergio Castillo-Lara, Josep F. Abril
Software Mentions: 8
Published: about 7 years ago

10.2196/jmir.5461

What Are We Looking for in Computer-Based Learning Interventions in Medical Education? A Systematic Review
Cited 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 Analysis
Cited 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 Data
Cited by: 11
Author(s): Filippo Valle, Matteo Osella, Michele Caselle
Software Mentions: 8
Published: about 4 years ago

10.1186/1471-2105-8-S6-S8

Graphs in molecular biology
Cited by: 108
Author(s): Wolfgang Huber, Vincent J. Carey, Long Li, Seth Falcon, Robert Gentleman
Software Mentions: 7
Published: over 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 database
Cited by: 62
Author(s): Antonio M. Mora, Ian Donaldson
Software Mentions: 6
Published: about 13 years ago

10.1186/s12864-019-5933-5

Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thaliana
Cited 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 services
Cited by: 11
Author(s): Tobias Kuhn, Ruben Taelman, Vincent Emonet, Haris Antonatos, Stian Soiland‐Reyes, Michel Dumontier
Software Mentions: 6
Published: almost 4 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 disorder
Cited 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 subtypes
Cited 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 approach
Cited 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 Germany
Cited 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: over 3 years ago

10.1371/journal.pone.0123082

Genomic Heterogeneity of Osteosarcoma - Shift from Single Candidates to Functional Modules
Cited 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 Analysis
Cited 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 meshes
Cited 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 graphs
Cited 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 Blocks
Cited 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 architecture
Cited 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 model
Cited by: 6
Author(s): M Köhler, Philipp Stratmann, Florian Röhrbein, Alois Knoll, Alin Albu‐Schäffer, Henrik Jörntell
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.ppat.1006476

Innate immunity restricts Citrobacter rodentium A/E pathogenesis initiation to an early window of opportunity
Cited 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 Validation
Cited by: 5
Author(s): Daniel J. Hicks
Software Mentions: 3
Published: about 8 years ago

10.3390/ma10020169

A Bio-Electro-Fenton System Employing the Composite FePc/CNT/SS316 Cathode
Cited 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 Molluscs
Cited 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 indexes
Cited 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 leukemia
Cited 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 genome
Cited 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 padi
Cited 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 Cells
Cited 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 Degeneracy
Cited 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 functions
Cited by: 1
Author(s): Marnix Van Soom, Milan van den Heuvel, Jan Ryckebusch, Koen Schoors
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1005968

Reactome graph database: Efficient access to complex pathway data
Cited 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 Algorithms
Cited by: 0
Author(s): Haihe Shi, Jun Wang
Software Mentions: 2
Published: almost 4 years ago

Projects: bioconductor: graph

Papers Mentioning graph 45