bioconductor: KEGGgraph | Projects

10.3390/metabo9100200

The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago

10.3390/biology3010085

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: almost 11 years ago

10.1186/s12859-016-0884-1

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
Cited by: 62
Author(s): Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Software Mentions: 14
Published: almost 9 years ago

10.1371/journal.pone.0131656

iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data
Cited by: 1
Author(s): Ashis Saha, Minji Jeon, Aik Choon Tan, Jaewoo Kang
Software Mentions: 10
Published: over 9 years ago

10.18632/oncotarget.16664

MiRNA profiling of gastrointestinal stromal tumors by next-generation sequencing
Cited by: 31
Author(s): Ugnė Gyvytė, Simonas Juzėnas, Violeta Šaltenienė, Juozas Kupčinskas, Lina Poškienė, Laimutis Kučinskas, Sonata Jarmalaitė, Kristina Stuopelytė, Rūta Steponaitienė, Georg Hemmrich-Stanisak, Matthias Hübenthal, Alexander Link, Sabine Franke, André Franke, Dalia Pangonytė, Vaiva Lesauskaitė, Limas Kupčinskas, Jurgita Skiecevičienė
Software Mentions: 8
Published: over 7 years ago

10.3389/fgene.2021.664654

Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in Cancer
Cited by: 0
Author(s): Qi Wang, Yonghe Wu, Tim Vorberg, Roland Eils, Carl Herrmann
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-020-60998-0

Temporal changes in the gene expression heterogeneity during brain development and aging
Cited by: 28
Author(s): Ulas Işıldak, Mehmet Somel, Janet M. Thornton, Handan Melike Dönertaş
Software Mentions: 8
Published: over 4 years ago

10.1186/1471-2105-13-20

graphite - a Bioconductor package to convert pathway topology to gene network
Cited by: 157
Author(s): Gabriele Sales, Enrica Calura, Duccio Cavalieri, Chiara Romualdi
Software Mentions: 7
Published: almost 13 years ago

10.3390/metabo11050269

Influence of Extraction Solvent on Nontargeted Metabolomics Analysis of Enrichment Reactor Cultures Performing Enhanced Biological Phosphorus Removal (EBPR)
Cited by: 4
Author(s): Nay Min Min Thaw Saw, Pipob Suwanchaikasem, Rogelio Zuniga-Montanez, Guanglei Qiu, Ezequiel M. Marzinelli, Stefan Wuertz, Rohan B.H. Williams
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0026146

Graph Constrained Discriminant Analysis: A New Method for the Integration of a Graph into a Classification Process
Cited by: 5
Author(s): Vincent Guillemot, Arthur Tenenhaus, Laurent Le Brusquet, Vincent Frouin
Software Mentions: 6
Published: about 13 years ago

10.1038/s41598-017-14650-z

Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females
Cited by: 18
Author(s): Louise Pease, Peter Clegg, Carole J. Proctor, Daryl P. Shanley, Simon Cockell, Mandy J. Peffers
Software Mentions: 5
Published: about 7 years ago

10.1093/bioinformatics/btx651

A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease
Cited by: 23
Author(s): Lei Han, Mateusz Maciejewski, Christoph Brockel, William Gordon, Scott B. Snapper, Joshua R. Korzenik, Lovisa Afzelius, Russ B. Altman
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-018-31882-9

Investigating the genetic profile of dopaminergic neurons in the VTA in response to perinatal nicotine exposure using mRNA-miRNA analyses
Cited by: 14
Author(s): Renee F. Keller, Andrei Dragomir, Yonggang Fan, Yasemin M. Akay, Metin Akay
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0022176

Time-Resolved Human Kinome RNAi Screen Identifies a Network Regulating Mitotic-Events as Early Regulators of Cell Proliferation
Cited by: 9
Author(s): Jitao David Zhang, Cindy Körner, Stephanie Bechtel, Christian Bender, Ioanna Keklikoglou, Christian Schmidt, Anja Irsigler, Ute Ernst, Özgür Şahin, Stefan Wiemann, Ulrich Tschulena
Software Mentions: 5
Published: over 13 years ago

10.3390/biom10060850

Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity?
Cited by: 8
Author(s): Mehran Piran, Reza Karbalaei, Mehrdad Piran, Jehad Aldahdooh, Mehdi Mirzaie, Naser Ansari-Pour, Jing Tang, Mohieddin Jafari
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0107629

Tracking Difference in Gene Expression in a Time-Course Experiment Using Gene Set Enrichment Analysis
Cited by: 4
Author(s): Pui Shan Wong, Michihiro Tanaka, Yoshihiko Sunaga, Masayoshi Tanaka, Tadatsugu Taniguchi, Tomoko Yoshino, Tsuyoshi Tanaka, Wataru Fujibuchi, Sachiyo Aburatani
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pcbi.1004088

Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms
Cited by: 28
Author(s): Vesna Memišević, Nela Zavaljevski, Seesandra V. Rajagopala, Ki-Ryong Kwon, Rembert Pieper, David DeShazer, Jaques Reifman, Anders Wallqvist
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0144398

The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington’s Disease
Cited by: 47
Author(s): Xianjun Dong, Junko Tsuji, Adam Labadorf, Panos Roussos, Jiang‐Fan Chen, Richard H. Myers, Schahram Akbarian, Zhiping Weng
Software Mentions: 3
Published: almost 9 years ago

10.14806/ej.26.0.949

KEGG2Net: Deducing gene interaction networks and acyclic graphs from KEGG pathways
Cited by: 6
Author(s): Sree Krishna Chanumolu, Mustafa Albahrani, Handan Can, Hasan H. Otu
Software Mentions: 3
Published: over 3 years ago

10.1186/s12885-021-08777-6

ER expression associates with poor prognosis in male lung squamous carcinoma after radical resection
Cited by: 2
Author(s): Xue Yang, Xiangfeng Jin, Rongjian Xu, Zhuang Yu, Ning An
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0186004

Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks
Cited by: 11
Author(s): Anthony Deeter, Mark Dalman, Joseph Haddad, Zhong-Hui Duan
Software Mentions: 3
Published: about 7 years ago

10.1200/CCI.19.00097

Evidence-Based Network Approach to Recommending Targeted Cancer Therapies
Cited by: 7
Author(s): Jayaram Kancherla, Shruti Rao, Krithika Bhuvaneshwar, Rebecca B. Riggins, Robert A. Beckman, Subha Madhavan, Héctor Corrada Bravo, Simina M. Boca
Software Mentions: 3
Published: about 4 years ago

10.1186/1477-5956-10-S1-S15

Identifying transcription factors and microRNAs as key regulators of pathways using Bayesian inference on known pathway structures
Cited by: 9
Author(s): Damian Roqueiro, Lei Huang, Yang Dai
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-020-71875-1

Investigating the influence of perinatal nicotine and alcohol exposure on the genetic profiles of dopaminergic neurons in the VTA using miRNA–mRNA analysis
Cited by: 15
Author(s): Tina Kazemi, Shuyan Huang, Naze G. Avci, Charlotte Mae K. Waits, Yasemin M. Akay, Metin Akay
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2164-13-S8-S14

Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma
Cited by: 38
Author(s): Lingyao Zeng, Jian Yu, Tao Huang, Hongyan Jia, Qiongzhu Dong, Fei He, Weilan Yuan, Lun–Xiu Qin, Yixue Li, Lu Xie
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12918-015-0243-2

Prediction of drugs having opposite effects on disease genes in a directed network
Cited by: 18
Author(s): Hasun Yu, Sungji Choo, Junseok Park, Jin‐Myung Jung, Yeeok Kang, Doheon Lee
Software Mentions: 2
Published: almost 9 years ago

10.1093/bioinformatics/btw697

MetaboSignal: a network-based approach for topological analysis of metabotype regulation <i>via</i> metabolic and signaling pathways
Cited by: 15
Author(s): Andrea Rodriguez-Martinez, Rafael Ayala, Joram M. Posma, Ana Luísa Neves, Dominique Guyader, Jeremy K. Nicholson, Marc Dumas
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13062-015-0058-5

Design principles for cancer therapy guided by changes in complexity of protein-protein interaction networks
Cited by: 25
Author(s): Sébastien Benzekry, Jack A. Tuszyński, Edward A. Rietman, Giannoula Klement
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-10-324

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database
Cited by: 34
Author(s): Κωνσταντίνος Μούτσελος, Ioannis Kanaris, Aristotelis Chatziioannou, Ilias Maglogiannis, Fragiskos N. Kolisis
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0048472

Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis)
Cited by: 64
Author(s): Timothy I. Shaw, Anuj Srivastava, Wen‐Chi Chou, Liang Liu, Ann Hawkinson, Travis C. Glenn, Robert M. Adams, Tony Schountz
Software Mentions: 2
Published: about 12 years ago

10.1016/j.csbj.2015.03.009

KENeV : A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments
Cited by: 10
Author(s): Eleftherios Pilalis, Θεόδωρος Κουτσανδρέας, Ioannis Valavanis, Emmanouil Athanasiadis, George M. Spyrou, Aristotelis Chatziioannou
Software Mentions: 2
Published: almost 10 years ago

10.3389/fgene.2019.01401

Evaluation of Pathway Activation for a Single Sample Toward Inflammatory Bowel Disease Classification
Cited by: 8
Author(s): Xingyi Li, Min Li, Ruiqing Zheng, Xiang Chen, Xu Ju, Fang‐Xiang Wu, Jianxin Wang
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13073-016-0352-6

Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in type 2 diabetic rat congenic series
Cited by: 19
Author(s): Marc Dumas, Céline Domange, Sophie Caldérari, Andrea Rodríguez Martínez, Rafael Ayala, Steven P. Wilder, Nicolas Suárez-Zamorano, Stephan C. Collins, Robert H. Wallis, Quan Gu, Yulan Wang, Christophe Hue, G. Otto, Karène Argoud, Vincent Navratil, S.C. Mitchell, John C. Lindon, Elaine Holmes, Jean‐Baptiste Cazier, Jeremy K. Nicholson, Dominique Guyader
Software Mentions: 1
Published: about 8 years ago

10.1038/srep39279

A pathway-centric view of spatial proximity in the 3D nucleome across cell lines
Cited by: 7
Author(s): Hiren Karathia, Carl Kingsford, Michelle Girvan, Sridhar Hannenhalli
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0188071

Mechanisms of action of Coxiella burnetii effectors inferred from host-pathogen protein interactions
Cited by: 11
Author(s): Anders Wallqvist, Hao Wang, Nela Zavaljevski, Vesna Memišević, Ki-Ryong Kwon, Rembert Pieper, Seesandra V. Rajagopala, Jaques Reifman
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0196351

Core signaling pathways in ovarian cancer stem cell revealed by integrative analysis of multi-marker genomics data
Cited by: 18
Author(s): Tianyu Zhang, Jielin Xu, Siyuan Deng, Fengqi Zhao, Jin Li, Liwei Zhang, Lang Li, Qi En Wang, Fuhai Li
Software Mentions: 1
Published: over 6 years ago

10.3390/molecules15118177

Analysis of Protein Pathway Networks Using Hybrid Properties
Cited by: 30
Author(s): Lei Chen, Tao Huang, Xiaohe Shi, Yu-Dong Cai, Kuo‐Chen Chou
Software Mentions: 1
Published: about 14 years ago

10.1155/2015/358125

Novel Candidate Key Drivers in the Integrative Network of Genes, MicroRNAs, Methylations, and Copy Number Variations in Squamous Cell Lung Carcinoma
Cited by: 19
Author(s): Tao Huang, Yang Jing, Yu-Dong Cai
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12920-020-00773-2

Integrative network analysis identifies potential targets and drugs for ovarian cancer
Cited by: 5
Author(s): Tianyu Zhang, Liwei Zhang, Fuhai Li
Software Mentions: 1
Published: about 4 years ago

Projects: bioconductor: KEGGgraph

Papers Mentioning KEGGgraph 39