bioconductor: GENIE3 | Projects | Ecosyste.ms: Papers

10.1186/s12870-018-1589-6

Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis
Cited by: 15
Author(s): Fuping Zhang, Xiaoping Li, Aidi Zhang, Zhenfei Jiang, Luonan Chen, Xiujun Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1186/1752-0509-8-5

Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment
Cited by: 33
Author(s): Wei‐Po Lee, Yu‐Ting Hsiao, Wei-Che Hwang
Software Mentions: 2
Published: almost 11 years ago

10.1186/1752-0509-7-87

Modularity and evolutionary constraints in a baculovirus gene regulatory network
Cited by: 12
Author(s): Juliana Velasco de Castro Oliveira, Anderson F. Brito, Carla Torres Braconi, Caio César de Melo Freire, Atila Iamarino, Paolo Marinho de Andrade Zanotto
Software Mentions: 2
Published: about 11 years ago

10.1186/s12918-018-0635-1

MICRAT: a novel algorithm for inferring gene regulatory networks using time series gene expression data
Cited by: 16
Author(s): Beifang Yang, Yaohui Xu, Andrew S. Maxwell, Wonryull Koh, Ping Gong, Chaoyang Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1093/bioinformatics/btx194

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
Cited by: 275
Author(s): Hirotaka Matsumoto, Hisanori Kiryu, Chikara Furusawa, Minoru S.H. Ko, Shigeru B. H. Ko, Norio Gouda, Tetsutaro Hayashi, Itoshi Nikaido
Software Mentions: 2
Published: over 7 years ago

10.1093/bioinformatics/btx575

SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles
Cited by: 129
Author(s): Nan Gao, S. M. Minhaz Ud-Dean, Olivier Gandrillon, Rudiyanto Gunawan
Software Mentions: 2
Published: about 7 years ago

10.1093/bioinformatics/btab295

A novel constrained genetic algorithm-based Boolean network inference method from steady-state gene expression data
Cited by: 5
Author(s): Hung-Cuong Trinh, Yung-Keun Kwon
Software Mentions: 2
Published: over 3 years ago

10.1093/bioinformatics/btab269

Bayesian information sharing enhances detection of regulatory associations in rare cell types
Cited by: 1
Author(s): Alexander P. Wu, Jian Peng, Bonnie Berger, Hyunghoon Cho
Software Mentions: 2
Published: over 3 years ago

10.1038/s41413-021-00163-z

Spatially defined single-cell transcriptional profiling characterizes diverse chondrocyte subtypes and nucleus pulposus progenitors in human intervertebral discs
Cited by: 57
Author(s): Gan Ye, Jian He, Jun Zhu, Zhengyang Xu, Zhong Wang, Yan Jing, Ou Hu, Zhijie Bai, Lin Chen, Yangli Xie, Min Jin, Shuo Huang, Bing Liu, Peng Liu
Software Mentions: 2
Published: over 3 years ago

10.15252/msb.20209506

Integrated regulatory models for inference of subtype‐specific susceptibilities in glioblastoma
Cited by: 3
Author(s): Yunpeng Liu, Ning Shi, Aviv Regev, Shan He, Michael T. Hemann
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1004590

Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models
Cited by: 20
Author(s): Dmitry Svetlichnyy, Hana Imrichová, Mark Fiers, Zeynep Kalender Atak, Stein Aerts
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pcbi.1007435

Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data
Cited by: 18
Author(s): Jiajun Zhang, Wenbo Zhu, Qianliang Wang, Jiayu Gu, Lei Huang, Xiaoqiang Sun
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0185475

Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae
Cited by: 7
Author(s): Maria Simak, Chen Hsiang Yeang, Henry Horng Shing Lu
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0226190

Shannon entropy approach reveals relevant genes in Alzheimer’s disease
Cited by: 18
Author(s): A. Monaco, Nicola Amoroso, Loredana Bellantuono, Eufemia Lella, Angela Lombardi, Anna Monda, Andrea Tateo, R. Bellotti, Sabina Tangaro
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0170340

Prophetic Granger Causality to infer gene regulatory networks
Cited by: 9
Author(s): Daniel E. Carlin, Evan O. Paull, Kiley Graim, Christopher Wong, Adrian Bivol, Peter Ryabinin, Kyle Ellrott, Artem Sokolov, Joshua M. Stuart
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0092709

NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms
Cited by: 54
Author(s): Joeri Ruyssinck, Vân Anh Huynh-Thu, Pierre Geurts, Tom Dhaene, Piet Demeester, Yvan Saeys
Software Mentions: 2
Published: over 10 years ago

10.1242/dev.174441

BNC1 regulates cell heterogeneity in human pluripotent stem cell derived-epicardium
Cited by: 22
Author(s): Laure Gambardella, Sophie A. McManus, Victoria Moignard, Derya Sebukhan, Agathe Delaune, Simon Andrews, William G. Bernard, Maura A. Morrison, Paul R. Riley, Berthold Göttgens, Nicolas Gambardella Le Novère, Sanjay Sinha
Software Mentions: 2
Published: almost 6 years ago

10.15252/embj.2020106785

Employing core regulatory circuits to define cell identity
Cited by: 15
Author(s): Nathália Alves Araújo de Almeida, Matthew Wai Heng Chung, Elena M Drudi, Elise N. Engquist, Eva Hamrud, Abigail Isaacson, Victoria Tsang, Fiona M. Watt, Francesca M. Spagnoli
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2021.649764

Filtering of Data-Driven Gene Regulatory Networks Using Drosophila melanogaster as a Case Study
Cited by: 1
Author(s): Yesid Cuesta-Astroz, Guilherme Gischkow Rucatti, Leandro Murgas, Carol D. SanMartín, Mario Sanhueza, Alberto J. M. Martin
Software Mentions: 2
Published: over 3 years ago

10.3389/fphys.2020.00081

Editorial: Integrated Omics for Defining Interactomes
Cited by: 0
Author(s): Sudipto Saha, Rob M. Ewing
Software Mentions: 2
Published: almost 5 years ago

10.3390/genes12091351

Identification of Key Transcription Factors Related to Bacterial Spot Resistance in Pepper through Regulatory Network Analyses
Cited by: 6
Author(s): Qingquan Zhu, Shenghua Gao, Wenli Zhang
Software Mentions: 2
Published: about 3 years ago

10.1186/s13059-021-02366-3

Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf
Cited by: 22
Author(s): Naresh Loudya, Pravas Mishra, Kotaro Takahagi, Yukiko Uehara‐Yamaguchi, Komaki Inoue, László Bögre, Keiichi Mochida, Enrique López‐Juez
Software Mentions: 2
Published: over 3 years ago

10.1111/jcmm.15607

Systematic profiling of ACE2 expression in diverse physiological and pathological conditions for COVID‐19/SARS‐CoV‐2
Cited by: 39
Author(s): Yunjin Li, Qiyue Xu, Lu Ma, Duojiao Wu, Jie Gao, Geng Chen, Hua Li
Software Mentions: 2
Published: over 4 years ago

10.1038/srep11432

TRRUST: a reference database of human transcriptional regulatory interactions
Cited by: 289
Author(s): Heonjong Han, Hongseok Shim, Donghyun Shin, Jung Eun Shim, Yun-Hee Ko, Junha Shin, Hanhae Kim, Ara Cho, Eiru Kim, Tak H. Lee, Hyojin Kim, Kyung-Soo Kim, Sunmo Yang, Dasom Bae, Ayoung Yun, Sunphil Kim, Chan Yeong Kim, Hyeon Jin Cho, Byung Ha Kang, Seunghwan Shin, Insuk Lee
Software Mentions: 2
Published: over 9 years ago

10.1038/srep41174

Enhancing gene regulatory network inference through data integration with markov random fields
Cited by: 31
Author(s): Michael Banf, Seung Y. Rhee
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-019-49498-y

NeTFactor, a framework for identifying transcriptional regulators of gene expression-based biomarkers
Cited by: 12
Author(s): Mehmet Eren Ahsen, Yoojin Chun, Alexander Grishin, Galina Grishina, Gustavo Stolovitzky, Gaurav Pandey, Supinda Bunyavanich
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-61758-w

Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress
Cited by: 17
Author(s): Tim S. Crawford, Fazeelat Karamat, Nóra Lehotai, Matilda Rentoft, Jeanette Blomberg, Åsa Strand, Stefan Björklund
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-63043-2

BICORN: An R package for integrative inference of de novo cis-regulatory modules
Cited by: 2
Author(s): Xi Chen, Jin Gu, Andrew F. Neuwald, Leena Hilakivi‐Clarke, Robert Clarke, Jianhua Xuan
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-94919-6

KBoost: a new method to infer gene regulatory networks from gene expression data
Cited by: 5
Author(s): Luis F. Iglesias-Martinez, Barbara De Kegel, Walter Kölch
Software Mentions: 2
Published: over 3 years ago

10.3390/genes10100754

Coordinated Activity of Transcriptional Networks Responding to the Pattern of Action Potential Firing in Neurons
Cited by: 22
Author(s): Dumitru A. Iacobaş, Sanda Iacobaş, Philip R. Lee, Jeffrey K. Cohen, R. Douglas Fields
Software Mentions: 1
Published: about 5 years ago

10.1186/s12859-015-0754-2

BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference
Cited by: 14
Author(s): Aurélie Pirayre, Camille Couprie, Frédérique Bidard, Laurent Duval, Jean‐Christophe Pesquet
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0103812

Ensemble Inference and Inferability of Gene Regulatory Networks
Cited by: 28
Author(s): S. M. Minhaz Ud-Dean, Rudiyanto Gunawan
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0195997

IncGraph: Incremental graphlet counting for topology optimisation
Cited by: 3
Author(s): Robrecht Cannoodt, Joeri Ruyssinck, Jana Ramon, Katleen De Preter, Yvan Saeys
Software Mentions: 1
Published: over 6 years ago

10.1155/2017/8514071

Module Anchored Network Inference: A Sequential Module-Based Approach to Novel Gene Network Construction from Genomic Expression Data on Human Disease Mechanism
Cited by: 2
Author(s): Annamalai Muthiah, Susanna R. Keller, Jae K. Lee
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0110094

Expression Profiling of Mitochondrial Voltage-Dependent Anion Channel-1 Associated Genes Predicts Recurrence-Free Survival in Human Carcinomas
Cited by: 28
Author(s): Jae Hong Ko, Wanjun Gu, Inja Lim, Tong Zhou, Hyoweon Bang
Software Mentions: 1
Published: about 10 years ago

10.1016/j.gpb.2016.02.005

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients
Cited by: 14
Author(s): Lianshuo Li, Zicheng Wang, Huan Peng, Shuping Ma, Jie Du, Rui Jiang
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0043819

Gene Regulatory Network Inference from Multifactorial Perturbation Data Using both Regression and Correlation Analyses
Cited by: 25
Author(s): Jie Xiong, Tong Zhou
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pcbi.1003252

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks
Cited by: 67
Author(s): Sushmita Roy, Stephen Lagree, Zhonggang Hou, James A. Thomson, Ron Stewart, Audrey P. Gasch
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pcbi.1006674

Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator
Cited by: 15
Author(s): Laurent Mombaerts, Alberto Carignano, Fiona C. Robertson, Timothy J. Hearn, Junyang Jin, David Hayden, Zoe Rutterford, Carlos Takeshi Hotta, Katherine E Hubbard, Maria C. Marti Ruiz, Ye Yuan, Matthew A. Hannah, Jorge Gonçalves, Alex Webb
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12859-018-2402-0

Improving network inference algorithms using resampling methods
Cited by: 5
Author(s): Sean Colby, Ryan McClure, Christopher C. Overall, Ryan Renslow, Jason McDermott
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pcbi.1005024

Inference of Gene Regulatory Network Based on Local Bayesian Networks
Cited by: 102
Author(s): Fei Liu, Shaowu Zhang, Weifeng Guo, Ze-Gang Wei, Luonan Chen
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.7211

Transcription factors involved in abiotic stress responses in Maize (Zea maysL.) and their roles in enhanced productivity in the post genomics era
Cited by: 53
Author(s): Roy Njoroge Kimotho, Elamin Hafiz Baillo, Zhang Zhengbin
Software Mentions: 1
Published: over 5 years ago

10.15252/msb.20145108

An integrative, multi‐scale, genome‐wide model reveals the phenotypic landscape of <scp>E</scp> scherichia coli 
Cited by: 73
Author(s): Javier Carrera, Raíssa Estrela, Jing Luo, Navneet Rai, Αθανάσιος Τσουκαλάς, Ilias Tagkopoulos
Software Mentions: 1
Published: over 10 years ago

10.1186/s12859-021-04074-y

ModularBoost: an efficient network inference algorithm based on module decomposition
Cited by: 0
Author(s): Xinyu Li, Wei Zhang, Jianming Zhang, Guang Li
Software Mentions: 1
Published: over 3 years ago

10.1038/srep17617

An integrated network of Arabidopsis growth regulators and its use for gene prioritization
Cited by: 7
Author(s): Ehsan Sabaghian, Zuzanna Drebert, Dirk Inzé, Yvan Saeys
Software Mentions: 1
Published: almost 9 years ago

10.1093/bioinformatics/btt099

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks
Cited by: 141
Author(s): Alex Greenfield, Christoph Hafemeister, Richard Bonneau
Software Mentions: 1
Published: over 11 years ago

10.1186/1752-0509-6-145

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection
Cited by: 339
Author(s): Anne-Claire Haury, Fantine Mordelet, Paola Vera-Licona, Jean-Philippe Vert
Software Mentions: 1
Published: about 12 years ago

10.1038/srep39684

miRsig: a consensus-based network inference methodology to identify pan-cancer miRNA-miRNA interaction signatures
Cited by: 24
Author(s): Joseph J. Nalluri, Debmalya Barh, Vasco Azevedo, Preetam Ghosh
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-017-1489-z

A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data
Cited by: 7
Author(s): Shupeng Gui, Andrew P. Rice, Rui Chen, Liang Wu, Ji Liu, Hongyu Miao
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-05472-0

A gene network regulated by FGF signalling during ear development
Cited by: 23
Author(s): Maryam Anwar, Monica Tambalo, Ramya Ranganathan, Timothy Grocott, Andrea Streit
Software Mentions: 1
Published: over 7 years ago

10.1186/1752-0509-7-106

ENNET: inferring large gene regulatory networks from expression data using gradient boosting
Cited by: 32
Author(s): Janusz Sławek, Tomasz Arodź
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41598-018-21715-0

dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data
Cited by: 115
Author(s): Vân Anh Huynh-Thu, Pierre Geurts
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms20153730

Evaluation of the Common Molecular Basis in Alzheimer’s and Parkinson’s Diseases
Cited by: 12
Author(s): Pratip Rana, Edian F. Franco, Yug Rao, Khajamoinuddin Syed, Debmalya Barh, Vasco Azevedo, Rommel Thiago Jucá Ramos, Preetam Ghosh
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-016-1398-6

Gene regulatory network inference using PLS-based methods
Cited by: 45
Author(s): Shun Guo, Qingshan Jiang, Lifei Chen, Donghui Guo
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.21268

Inference of time-delayed gene regulatory networks based on dynamic Bayesian network hybrid learning method
Cited by: 13
Author(s): Bin Yu, Jiameng Xu, Shan Li, Cheng Chen, Ruixin Chen, Lei Wang, Yan Zhang, Minghui Wang
Software Mentions: 1
Published: about 7 years ago

10.1186/1752-0509-7-118

Identification of direction in gene networks from expression and methylation
Cited by: 5
Author(s): David Simcha, Laurent Younes, Martin J. Aryee, Donald Geman
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13015-017-0100-5

The feasibility of genome-scale biological network inference using Graphics Processing Units
Cited by: 5
Author(s): Thiagarajan Raghuram, Amir Alavi, Jagdeep T. Podichetty, Jason N. Bazil, Daniel A. Beard
Software Mentions: 1
Published: over 7 years ago

10.1186/s12918-019-0695-x

Fusing gene expressions and transitive protein-protein interactions for inference of gene regulatory networks
Cited by: 7
Author(s): Wenting Liu, Jagath C. Rajapakse
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-97207-5

Spatiotemporal tracing of pandemic spread from infection data
Cited by: 3
Author(s): Samit Roy, Preetom Biswas, Preetam Ghosh
Software Mentions: 1
Published: about 3 years ago

10.1186/s12920-017-0312-z

Reverse-engineering of gene networks for regulating early blood development from single-cell measurements
Cited by: 15
Author(s): Jiangyong Wei, Xiaohua Hu, Xiufen Zou, Tianhai Tian
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-019-6298-5

D3GRN: a data driven dynamic network construction method to infer gene regulatory networks
Cited by: 7
Author(s): Xiang Chen, Min Li, Ruiqing Zheng, Fang‐Xiang Wu, Jianxin Wang
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-016-2791-2

Reconstructing directed gene regulatory network by only gene expression data
Cited by: 11
Author(s): Lu Zhang, Xikang Feng, Yen Kaow Ng, Shuai Cheng Li
Software Mentions: 1
Published: over 8 years ago

10.3389/fimmu.2019.01283

Combining Mathematical Models With Experimentation to Drive Novel Mechanistic Insights Into Macrophage Function
Cited by: 9
Author(s): Joanneke E. Jansen, Eamonn A. Gaffney, Jonathan Wagg, Mark Coles
Software Mentions: 1
Published: over 5 years ago

10.1128/mSystems.00114-19

Toward a Better Understanding of Species Interactions through Network Biology
Cited by: 3
Author(s): Ryan McClure
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2019.01280

Revealing Dynamic Mechanisms of Cell Fate Decisions From Single-Cell Transcriptomic Data
Cited by: 19
Author(s): Jiajun Zhang, Qing Nie, Tianshou Zhou
Software Mentions: 1
Published: almost 5 years ago

10.1242/dev.159707

GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis
Cited by: 59
Author(s): Michitaro Shibata, Christian Breuer, Ayako Kawamura, Natalie M Clark, Bart Rymen, Luke Braidwood, Kengo Morohashi, Wolfgang Busch, Philip N. Benfey, Rosangela Sozzani, Keiko Sugimoto
Software Mentions: 1
Published: almost 7 years ago

10.1002/cso2.1021

Computational systems‐biology approaches for modeling gene networks driving epithelial–mesenchymal transitions
Cited by: 9
Author(s): Ataur Katebi, Daniel C. Ramirez, Mingyang Lu
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0012776

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
Cited by: 1,319
Author(s): Vân Anh Huynh-Thu, Alexandre Irrthum, Louis Wehenkel, Pierre Geurts
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0171532

Recursive random forest algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways
Cited by: 25
Author(s): Wenping Deng, Kui Zhang, Victor Busov, Hairong Wei
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0033624

Bagging Statistical Network Inference from Large-Scale Gene Expression Data
Cited by: 111
Author(s): Ricardo de Matos Simoes, Frank Emmert‐Streib
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0067434

LegumeGRN: A Gene Regulatory Network Prediction Server for Functional and Comparative Studies
Cited by: 39
Author(s): Mingyi Wang, Jérôme Verdier, Vagner A. Benedito, Yuhong Tang, Jeremy D. Murray, Yinbing Ge, Jörg Becker, Helena Carvalho, Christian Rogers, Michael K. Udvardi, Ji He
Software Mentions: 1
Published: over 11 years ago

10.3390/genes10070502

Global Dynamics in Protein Disorder during Maize Seed Development
Cited by: 4
Author(s): Jesús Alejandro Zamora‐Briseño, Alejandro Pereira-Santana, Sandi Julissa Reyes-Hernández, Enrique Castaño, Luis Carlos Rodríguez-Zapata
Software Mentions: 1
Published: over 5 years ago

Projects: bioconductor: GENIE3

Papers Mentioning GENIE3 172