cran: GeneNet | Projects | Ecosyste.ms: Papers

10.1186/s13059-019-1851-8

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer
Cited by: 44
Author(s): Dharmesh D. Bhuva, Joseph Cursons, Gordon K. Smyth, Melissa J. Davis
Software Mentions: 14
Published: about 5 years ago

10.3390/ijerph17197127

Relationship between Quality of Life and the Complexity of Default Mode Network in Resting State Functional Magnetic Resonance Image in Down Syndrome
Cited by: 6
Author(s): María Carbó‐Carreté, Cristina Cañete‐Massé, María Dolores Figueroa-Jiménez, Maribel Peró‐Cebollero, Joan Guàrdia‐Olmos
Software Mentions: 9
Published: about 4 years ago

10.3389/fpls.2015.01172

The Potential of the MAGIC TOM Parental Accessions to Explore the Genetic Variability in Tomato Acclimation to Repeated Cycles of Water Deficit and Recovery
Cited by: 23
Author(s): Julie Ripoll, Laurent Urban, Nadia Bertin
Software Mentions: 9
Published: almost 9 years ago

10.1186/s12859-016-1235-y

BTR: training asynchronous Boolean models using single-cell expression data
Cited by: 62
Author(s): Chee Lim, Huange Wang, Steven Woodhouse, Nir Piterman, Lorenz Wernisch, Jasmin Fisher, Berthold Göttgens
Software Mentions: 8
Published: about 8 years ago

10.17179/excli2015-168

Data- and knowledge-based modeling of gene regulatory networks: an update.
Cited by: 24
Author(s): Jörg Linde, Sylvie Schulze, Sebastian Henkel, Reinhard Guthke
Software Mentions: 8
Published: almost 10 years ago

10.1038/s41598-021-87234-7

Discovering key transcriptomic regulators in pancreatic ductal adenocarcinoma using Dirichlet process Gaussian mixture model
Cited by: 9
Author(s): Sk Md Mosaddek Hossain, Aanzil Akram Halsana, Lutfunnesa Khatun, Sumanta Ray, Anirban Mukhopadhyay
Software Mentions: 7
Published: over 3 years ago

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: over 8 years ago

10.1371/journal.pone.0060045

The Structure of a Gene Co-Expression Network Reveals Biological Functions Underlying eQTLs
Cited by: 37
Author(s): Nathalie Villa-Vialaneix, Laurence Liaubet, Thibault Laurent, Pierre Chérel, Adrien Gamot, Magali SanCristobal
Software Mentions: 6
Published: over 11 years ago

10.3389/fgene.2013.00303

Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data
Cited by: 18
Author(s): Mário Lopes, Gianluca Bontempi
Software Mentions: 6
Published: almost 12 years ago

10.1155/2013/203681

Time Series Expression Analyses Using RNA-seq: A Statistical Approach
Cited by: 23
Author(s): Sangwon Oh, Seongho Song, Gregory A. Grabowski, Hongyu Zhao, James P. Noonan
Software Mentions: 6
Published: almost 12 years ago

10.1093/bib/bbw102

A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles
Cited by: 1
Author(s): Felicia Ng, David Ruau, Lorenz Wernisch, Berthold Göttgens
Software Mentions: 6
Published: about 8 years ago

10.1186/1752-0509-8-47

Fast Bayesian inference for gene regulatory networks using ScanBMA
Cited by: 78
Author(s): William Chad Young, Adrian E. Raftery, Ka Yee Yeung
Software Mentions: 6
Published: over 10 years ago

10.3390/metabo11050326

Exploration of Blood Lipoprotein and Lipid Fraction Profiles in Healthy Subjects through Integrated Univariate, Multivariate, and Network Analysis Reveals Association of Lipase Activity and Cholesterol Esterification with Sex and Age
Cited by: 4
Author(s): Yasmijn Balder, Alessia Vignoli, Leonardo Tenori, Claudio Luchinat, Edoardo Saccenti
Software Mentions: 6
Published: over 3 years ago

10.1186/1471-2105-11-311

FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases
Cited by: 25
Author(s): Stephen J. Goodswen, Cedric Gondro, Nathan S. Watson-Haigh, Haja N. Kadarmideen
Software Mentions: 5
Published: over 14 years ago

10.1371/journal.pone.0184515

Unraveling the human salivary microbiome diversity in Indian populations
Cited by: 19
Author(s): Anujit Sarkar, Mark Stoneking, Madhusudan R. Nandineni
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0060536

Iterative Reconstruction of High-Dimensional Gaussian Graphical Models Based on a New Method to Estimate Partial Correlations under Constraints
Cited by: 0
Author(s): Vincent Guillemot, Andreas Bender, Anne‐Laure Boulesteix
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0068551

A Systems-Genetics Approach and Data Mining Tool to Assist in the Discovery of Genes Underlying Complex Traits in Oryza sativa
Cited by: 17
Author(s): Stephen P. Ficklin, F. Alex Feltus
Software Mentions: 4
Published: over 11 years ago

10.3390/metabo9060117

Integration of Metabolomic and Other Omics Data in Population-Based Study Designs: An Epidemiological Perspective
Cited by: 42
Author(s): Su H. Chu, Mengna Huang, Rachel S. Kelly, Elisa Benedetti, Jalal K. Siddiqui, Oana A. Zeleznik, Alexandre Pereira, David M. Herrington, Craig E. Wheelock, Jan Krumsiek, Michael J. McGeachie, Steven C. Moore, Peter Kraft, Ewy A. Mathé, Jessica Lasky‐Su
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms8040513

Relationships between Gut Microbiota, Metabolome, Body Weight, and Glucose Homeostasis of Obese Dogs Fed with Diets Differing in Prebiotic and Protein Content
Cited by: 15
Author(s): Emmanuelle Apper, Lisa Privet, Bernard Taminiau, Cindy Le Bourgot, Ljubica Svilar, Jean‐Charles Martin, Marianne Diez
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.2478

Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells
Cited by: 13
Author(s): Chien-Hung Huang, Jin-Shuei Ciou, Shun-Tsung Chen, Victor C. Kok, Yuan‐Chiang Chung, Jeffrey J. P. Tsai, Nilubon Kurubanjerdjit, Chi-Ying F. Huang, Ka-Lok Ng
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0122309

Module-Based Association Analysis for Omics Data with Network Structure
Cited by: 5
Author(s): Zhi Wang, Arnab Maity, Chuhsing Kate Hsiao, Deepak Voora, Rima Kaddurah‐Daouk, Jung Ying Tzeng
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pcbi.1001034

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells
Cited by: 21
Author(s): Florian Markowetz, Klaas W. Mulder, Edoardo M. Airoldi, Ihor R. Lemischka, Olga G. Troyanskaya
Software Mentions: 4
Published: almost 14 years ago

10.1038/s41598-019-46737-0

Dynamic Bayesian network in infectious diseases surveillance: a simulation study
Cited by: 8
Author(s): Tao Zhang, Yue Ma, Xiong Xiao, Yun Lin, Xingyu Zhang, Fei Yin, Xiaosong Li
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-017-1731-8

sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters
Cited by: 9
Author(s): Shailesh Tripathi, Jason Lloyd-Price, André S. Ribeiro, Olli Yli‐Harja, Matthias Dehmer, Frank Emmert‐Streib
Software Mentions: 4
Published: over 7 years ago

10.1038/srep20518

Discovering gene re-ranking efficiency and conserved gene-gene relationships derived from gene co-expression network analysis on breast cancer data
Cited by: 27
Author(s): Marilena M. Bourdakou, Emmanouil Athanasiadis, George M. Spyrou
Software Mentions: 4
Published: almost 9 years ago

10.3389/fpls.2017.01725

Combined Effects of Irrigation Regime, Genotype, and Harvest Stage Determine Tomato Fruit Quality and Aptitude for Processing into Puree
Cited by: 20
Author(s): Alexandre Arbex de Castro Vilas Boas, David L. Page, Robert Giovinazzo, Nadia Bertin, Anne-Laure Fanciullino
Software Mentions: 4
Published: about 7 years ago

10.1186/s12879-020-05135-y

The correlations between Th1 and Th2 cytokines in human alveolar echinococcosis
Cited by: 7
Author(s): Xingming Ma, Xuefei Zhang, Jia Liu, Yufang Liu, Cunzhe Zhao, Huixia Cai, Lei Wen, Jun Ma, Haining Fan, Jianye Zhou, Na Liu, Jingxiao Zhang, Yongshun Wang, Wei Wang, Peizhen Zhan, Xiongying Zhang, Qing Zhang, Kemei Shi, Peiyun Liu
Software Mentions: 4
Published: over 4 years ago

10.1186/s12870-017-1077-4

Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response
Cited by: 23
Author(s): Shisong Ma, Zehong Ding, Pinghua Li
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0214868

Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network
Cited by: 5
Author(s): Jimmy Omony, Anne de Jong, Jan Kok, Sacha A. F. T. van Hijum
Software Mentions: 4
Published: over 5 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: about 10 years ago

10.1186/1752-0509-4-159

Deducing corticotropin-releasing hormone receptor type 1 signaling networks from gene expression data by usage of genetic algorithms and graphical Gaussian models
Cited by: 6
Author(s): Dietrich Trümbach, Cornelia Graf, Benno Pütz, Claudia Kühne, Marcus Panhuysen, Peter Weber, Florian Holsboer, Wolfgang Wurst, Gerhard Welzl, Jan M. Deussing
Software Mentions: 4
Published: about 14 years ago

10.1371/journal.pone.0160791

Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data
Cited by: 31
Author(s): Agata Michna, Herbert Braselmann, Martin Selmansberger, Anne Dietz, Julia Heß, Maria Gomolka, Sabine Hornhardt, Nils Blüthgen, Horst Zitzelsberger, Kristian Unger
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0192613

NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples
Cited by: 17
Author(s): Hua Yu, Bingke Jiao, Lu Lu, Pengfei Wang, Shuangcheng Chen, Chengzhi Liang, Wei Liu
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41389-020-00245-3

Histoepigenetic analysis of the mesothelin network within pancreatic ductal adenocarcinoma cells reveals regulation of retinoic acid receptor gamma and AKT by mesothelin
Cited by: 6
Author(s): Eugene Lurie, Dongliang Liu, Emily L. LaPlante, Lillian R Thistlethwaite, Qizhi Yao, Aleksandar Milosavljevic
Software Mentions: 4
Published: over 4 years ago

10.1186/s12918-017-0440-2

Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size
Cited by: 14
Author(s): Wenbin Guo, Cristiane P. G. Calixto, Nikoleta A. Τzioutziou, Ping Lin, Robbie Waugh, John W. Brown, Runxuan Zhang
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2021.617282

Evaluating the Reproducibility of Single-Cell Gene Regulatory Network Inference Algorithms
Cited by: 19
Author(s): Yoonjee Kang, Denis Thieffry, Laura Cantini
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-015-0710-1

Prior knowledge driven Granger causality analysis on gene regulatory network discovery
Cited by: 16
Author(s): Shun Yao, Shinjae Yoo, D. Yu
Software Mentions: 3
Published: about 9 years ago

10.1186/s12859-017-1576-1

Enhanced construction of gene regulatory networks using hub gene information
Cited by: 62
Author(s): Daren Yu, Jong-Tae Lim, Xinlei Wang, Faming Liang, Guanghua Xiao
Software Mentions: 3
Published: over 7 years ago

10.1186/s12918-017-0419-z

Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization
Cited by: 14
Author(s): Saskia Trescher, Jannes Münchmeyer, Ulf Leser
Software Mentions: 3
Published: over 7 years ago

10.1155/2020/6867081

Soil Water Contents Control the Responses of Dissolved Nitrogen Pools and Bacterial Communities to Freeze-Thaw in Temperate Soils
Cited by: 5
Author(s): Nan Jiang, Juan Yang, Lulu Tian, Xiao Chen, Wei Sun, Lijun Chen
Software Mentions: 3
Published: over 4 years ago

10.1002/pld3.99

Field‐grown soybean transcriptome shows diurnal patterns in photosynthesis‐related processes
Cited by: 10
Author(s): Anna M. Locke, Rebecca Slattery, Donald R. Ort
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1003840

Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways
Cited by: 66
Author(s): Shisong Ma, Smit Shah, Hans J. Bohnert, M Snyder, Savithramma P. Dinesh‐Kumar
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pgen.1009190

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density
Cited by: 17
Author(s): Anna L Swan, Christine Schütt, Jan Rozman, Maria del Mar Muñiz Moreno, Stefan Brandmaier, Michelle Simon, Stefanie Leuchtenberger, Mark Griffiths, Robert Brommage, Piia Keskivali-Bond, Harald Grallert, Thomás Werner, Raffaele Teperino, Lore Becker, Gregor Miller, Ala Moshiri, John R. Seavitt, Derek D. Cissell, Fabio Mammano, Elif F. Acar, Christopher J. Lelliott, Ann M. Flenniken, Marie‐France Champy, Tania Sorg, Abdel Ayadi, Robert E. Braun, Heather Cater, Mary E. Dickinson, Paul Flicek, Juan Gallegos, Elena J. Ghirardello, Jason D. Heaney, Sylvie Jacquot, Connor Lally, John G. Logan, Lydia Teboul, Jeremy Mason, Nadine Spielmann, Colin McKerlie, Stephen A. Murray, Lauryl M. J. Nutter, Kristian F. Odfalk, Helen Parkinson, Jan Procházka, Corey Reynolds, Mohammed Selloum, František Špoutil, Karen L. Svenson, Taylor S. Vales, Sara Wells, Jacqueline K. White, Radislav Sedláček, Wolfgang Wurst, Kevin C K Lloyd, Peter I. Croucher, Helmut Fuchs, Graham R. Williams, J. H. Duncan Bassett, Valérie Gailus‐Durner, Yann Hérault, Ann‐Marie Mallon, Steve Brown, Philipp Mayer‐Kuckuk, Martin Hrabě de Angelis
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0031194

A Relative Variation-Based Method to Unraveling Gene Regulatory Networks
Cited by: 12
Author(s): Yali Wang, Tong Zhou
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0152648

DTW-MIC Coexpression Networks from Time-Course Data
Cited by: 9
Author(s): Samantha Riccadonna, Giuseppe Jurman, Roberto Visintainer, Michele Filosi, Cesare Furlanello
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0053085

The Transcriptional and Gene Regulatory Network of Lactococcus lactis MG1363 during Growth in Milk
Cited by: 23
Author(s): Anne de Jong, Morten Ejby, Oscar P. Kuipers, Mogens Kilstrup, Jan Kok
Software Mentions: 3
Published: almost 12 years ago

10.3389/fgene.2013.00291

Network statistics of genetically-driven gene co-expression modules in mouse crosses
Cited by: 4
Author(s): Marie Pier Scott-Boyer, Benjamin Haibe‐Kains, Christian F. Deschepper
Software Mentions: 3
Published: almost 12 years ago

10.3389/fgene.2019.00535

Inferring Interaction Networks From Multi-Omics Data
Cited by: 95
Author(s): Johann S. Hawe, Fabian J. Theis, Matthias Heinig
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2020.00853

Use of Dual RNA-seq for Systems Biology Analysis of Zea mays and Aspergillus flavus Interaction
Cited by: 10
Author(s): Bryan Musungu, Deepak Bhatnagar, Sylvie Quiniou, Robert L. Brown, Gary A. Payne, Greg O'Brian, Ahmad M. Fakhoury, Matt Geisler
Software Mentions: 3
Published: over 4 years ago

10.1155/2008/893941

Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data II: Analysis Beyond Single Gene
Cited by: 11
Author(s): Issa Coulibaly, Grier P. Page
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pbio.2002176

Dynamic transcriptome changes during adipose tissue energy expenditure reveal critical roles for long noncoding RNA regulators
Cited by: 67
Author(s): Zhiqiang Bai, Xiaoran Chai, Myeong Jin Yoon, Hye-Jin Kim, Kinyui Alice Lo, Zhichun Zhang, Dan Xu, Diana Teh Chee Siang, Arcinas Camille Esther Walet, Shaohai Xu, Sook-Yoong Chia, Peng Chen, Hongyuan Yang, Sujoy Ghosh, Li Sun
Software Mentions: 2
Published: over 7 years ago

10.1002/pld3.167

SoyCSN: Soybean context‐specific network analysis and prediction based on tissue‐specific transcriptome data
Cited by: 12
Author(s): Juexin Wang, Shakhawat Hossain, Zhen Lyu, Jeremy Schmutz, Gary Stacey, Dong Xu, Trupti Joshi
Software Mentions: 2
Published: about 5 years ago

10.1186/s12918-015-0154-2

Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks
Cited by: 2
Author(s): Takanori Hasegawa, Takahide Mori, Rui Yamaguchi, Teppei Shimamura, Satoru Miyano, Seiya Imoto, Tatsuya Akutsu
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0047350

Comparative Expression Profiles of Midgut Genes in Dengue Virus Refractory and Susceptible Aedes aegypti across Critical Period for Virus Infection
Cited by: 56
Author(s): Chitra Chauhan, Susanta K. Behura, Becky deBruyn, Diane D. Lovin, Brent W. Harker, Consuelo Gomez-Machorro, Akio Mori, Jeanne Romero‐Severson, David W. Severson
Software Mentions: 2
Published: about 12 years ago

10.1016/j.cub.2020.10.030

Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria
Cited by: 18
Author(s): Stephan Köstlbacher, Astrid Collingro, Tamara Halter, Daryl Domman, Matthias Horn
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12866-014-0316-1

Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa
Cited by: 119
Author(s): Jing Li, Dominique Quinque, Hans-Peter Horz, Mingkun Li, Margarita Rzhetskaya, Jennifer Raff, M. Geoffrey Hayes, Mark Stoneking
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2105-11-517

Inferring gene regression networks with model trees
Cited by: 27
Author(s): Isabel A. Nepomuceno-Chamorro, Jesús S. Aguilar–Ruiz, José C. Riquelme
Software Mentions: 2
Published: about 14 years ago

10.3390/ijms20102463

Transcriptome and Proteome Profiling of Different Colored Rice Reveals Physiological Dynamics Involved in the Flavonoid Pathway
Cited by: 25
Author(s): Xiaoqiong Chen, Tao Yu, Asif Ali, Zhenhua Zhuang, Daiming Guo, Qiaoling Guo, Asad Riaz, Hongyu Zhang, Peizhou Xu, Yongxiang Liao, Jing Wang, Changhui Sun, Quanju Xiang
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-16-S6-S5

Inferring slowly-changing dynamic gene-regulatory networks
Cited by: 12
Author(s): Ernst Wit, Antonino Abbruzzo
Software Mentions: 2
Published: over 9 years ago

10.3389/fpls.2020.00524

Centralization Within Sub-Experiments Enhances the Biological Relevance of Gene Co-expression Networks: A Plant Mitochondrial Case Study
Cited by: 1
Author(s): Simon R. Law, Therese G. Kellgren, Rafael Björk, Patrik Rydén, Olivier Keech
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-015-0728-4

NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference
Cited by: 43
Author(s): Pau Bellot, Catharina Olsen, Philippe Salembier, Albert Oliveras-Vergés, Patrick Meyer
Software Mentions: 2
Published: about 9 years ago

10.1186/s13014-020-01620-5

Transcriptome network of the papillary thyroid carcinoma radiation marker CLIP2
Cited by: 1
Author(s): Martin Selmansberger, Agata Michna, Herbert Braselmann, Ines Höfig, Kenji Schorpp, Peter Weber, Nataša Anastasov, Horst Zitzelsberger, Julia Heß, Kristian Unger
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2105-10-262

Integrative modeling of transcriptional regulation in response to antirheumatic therapy
Cited by: 36
Author(s): Michael Hecker, Robert Goertsches, Robby Engelmann, Hans‐Juergen Thiesen, Reinhard Guthke
Software Mentions: 2
Published: about 15 years ago

10.1186/s12859-019-2788-3

Adapting machine-learning algorithms to design gene circuits
Cited by: 23
Author(s): Tom W. Hiscock
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0001385

Global Cross-Talk of Genes of the Mosquito Aedes aegypti in Response to Dengue Virus Infection
Cited by: 116
Author(s): Susanta K. Behura, Consuelo Gomez-Machorro, Brent W. Harker, Becky deBruyn, Diane D. Lovin, Ryan R. Hemme, Akio Mori, Jeanne Romero‐Severson, David W. Severson
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0106319

Ensemble-Based Network Aggregation Improves the Accuracy of Gene Network Reconstruction
Cited by: 25
Author(s): Rui Zhong, Jeffrey D. Allen, Guanghua Xiao, Yang Xie
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pcbi.1004791

Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering
Cited by: 45
Author(s): Chuan Gao, Ian C. McDowell, Shuaiguo Zhao, Christopher D. Brown, Barbara E. Engelhardt
Software Mentions: 2
Published: over 8 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.0029348

Comparing Statistical Methods for Constructing Large Scale Gene Networks
Cited by: 170
Author(s): Jeffrey D. Allen, Yang Xie, Min Chen, Luc Girard, Guanghua Xiao
Software Mentions: 2
Published: almost 13 years ago

10.1186/1748-7188-6-22

Multi-membership gene regulation in pathway based microarray analysis
Cited by: 7
Author(s): Stelios Pavlidis, Annette Payne, Stephen Swift
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0252901

Revealing nuclear receptor hub modules from Basal-like breast cancer expression networks
Cited by: 0
Author(s): Sharon Hsu, Erika Wong En Hui, Mengzhen Liu, Di Wu, Tom Hughes, James M. Smith
Software Mentions: 1
Published: over 3 years ago

10.3390/metabo10070271

Systematic Evaluation of Normalization Methods for Glycomics Data Based on Performance of Network Inference
Cited by: 10
Author(s): Elisa Benedetti, Nathalie Gerstner, Maja Pučić‐Baković, Toma Keser, Karli R. Reiding, L. Renee Ruhaak, Tamara Štambuk, Maurice H. J. Selman, Igor Rudan, Ozren Polašek, Caroline Hayward, Marian Beekman, Eline Slagboom, Manfred Wuhrer, Malcolm Dunlop, Gordan Lauc, Jan Krumsiek
Software Mentions: 1
Published: over 4 years ago

10.1155/2013/350358

Computational Systems Biology
Cited by: 2
Author(s): Xing Zhao, Weidong Tian, Rui Jiang, Jun Wan
Software Mentions: 1
Published: almost 12 years ago

10.3390/ijms21082955

The Sodium Channel B4-Subunits are Dysregulated in Temporal Lobe Epilepsy Drug-Resistant Patients
Cited by: 11
Author(s): Mariam A Sheilabi, Louise Y. C. Takeshita, Edward J Sims, Francesco Falciani, Alessandra Princivalle
Software Mentions: 1
Published: over 4 years ago

10.1186/1752-0509-7-S3-S9

A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks
Cited by: 32
Author(s): Zuoshuang Xiang, Tingting Qin, Zhaohui Qin, Yongqun He
Software Mentions: 1
Published: about 11 years ago

10.1186/s12918-015-0200-0

The wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy in drosophila melanogaster
Cited by: 14
Author(s): Justin M. Fear, Michelle N. Arbeitman, Matthew P. Salomon, Justin E. Dalton, John Tower, Sergey V. Nuzhdin, Lauren M. McIntyre
Software Mentions: 1
Published: about 9 years ago

10.1186/1752-0509-3-85

From gene expression to gene regulatory networks in Arabidopsis thaliana
Cited by: 43
Author(s): Chris J. Needham, Iain W. Manfield, Andrew J. Bulpitt, Philip M. Gilmartin, David R. Westhead
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0107193

Connecting Prognostic Ligand Receptor Signaling Loops in Advanced Ovarian Cancer
Cited by: 5
Author(s): Kevin H. Eng, Christina Ruggeri
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2105-14-94

An inferential framework for biological network hypothesis tests
Cited by: 20
Author(s): Phillip D. Yates, Nitai D. Mukhopadhyay
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0255940

Character matters: The network structure of leader character and its relation to follower positive outcomes
Cited by: 6
Author(s): Lucas Monzani, Gerard Seijts, Mary Crossan
Software Mentions: 1
Published: about 3 years ago

10.1186/1753-6561-3-S4-S12

Gene network reconstruction from microarray data
Cited by: 7
Author(s): Florence Jaffrézic, Gwenola Tosser‐Klopp
Software Mentions: 1
Published: over 15 years ago

10.3390/cancers13030393

Cancers in Agreement? Exploring the Cross-Talk of Cancer Metabolomic and Transcriptomic Landscapes Using Publicly Available Data
Cited by: 3
Author(s): Derek van Tilborg, Edoardo Saccenti
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12859-018-2560-0

GeNeCK: a web server for gene network construction and visualization
Cited by: 24
Author(s): Minzhe Zhang, Qiwei Li, Daren Yu, Bo Yao, Wenfei Guo, Yang Xie, Guanghua Xiao
Software Mentions: 1
Published: almost 6 years ago

10.1038/srep39224

NetDiff – Bayesian model selection for differential gene regulatory network inference
Cited by: 8
Author(s): Thomas Thorne
Software Mentions: 1
Published: almost 8 years ago

10.1155/2014/382452

Network Completion for Static Gene Expression Data
Cited by: 3
Author(s): N. Nakajima, Tatsuya Akutsu
Software Mentions: 1
Published: over 10 years ago

10.1100/2012/957620

Network Completion Using Dynamic Programming and Least-Squares Fitting
Cited by: 12
Author(s): N. Nakajima, Takeyuki Tamura, Yoshihiro Yamanishi, Katsuhisa Horimoto, Tatsuya Akutsu
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-12-608

Defense mechanisms against herbivory in Picea: sequence evolution and expression regulation of gene family members in the phenylpropanoid pathway
Cited by: 38
Author(s): Ilga Porth, Björn Hamberger, Richard Allen White, Kermit Ritland
Software Mentions: 1
Published: almost 13 years ago

Projects: cran: GeneNet

Papers Mentioning GeneNet 87