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: bioconductor: GENIE3
https://packages.ecosyste.ms/registries/bioconductor.org/packages/GENIE3
GEne Network Inference with Ensemble of trees
1 version
Latest release: about 1 year ago
2 dependent packages
60,884 downloads total
Papers Mentioning GENIE3 172
10.3389/fgene.2021.652189
Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought ResistanceCited by: 11
Author(s): Chirag Gupta, Venkategowda Ramegowda, Supratim Basu, Andy Pereira
Software Mentions: 13
Published: over 3 years ago
10.1038/s41422-020-00453-x
Establishment of intestinal organoid cultures modeling injury-associated epithelial regenerationCited by: 39
Author(s): Molong Qu, Liang Xiong, Yulin Lyu, Xiannian Zhang, Jie Shen, Jingyang Guan, Peiyuan Chai, Lin Zheng, Boyao Nie, Cheng Li, Jun Xu, Hongkui Deng
Software Mentions: 13
Published: almost 4 years ago
10.7554/eLife.58993
Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patternsCited by: 23
Author(s): Kathleen Greenham, Ryan C. Sartor, Stevan Zorich, Ping Lou, Todd C. Mockler, C. Robertson McClung
Software Mentions: 12
Published: about 4 years ago
10.3389/fgene.2021.655536
Machine Intelligence in Single-Cell Data Analysis: Advances and New ChallengesCited by: 30
Author(s): Jiajia Li, Zusen Fan, Weiling Zhao, Xiaobo Zhou
Software Mentions: 12
Published: over 3 years ago
10.1186/s12915-019-0709-6
Single-cell reconstruction of differentiation trajectory reveals a critical role of ETS1 in human cardiac lineage commitmentCited by: 31
Author(s): Hang Ruan, Yingnan Liao, Zongna Ren, Lin Mao, Fang Yao, Yu Peng, Youqiong Ye, Zhao Zhang, Shengli Li, Hanshi Xu, Jiewei Liu, Lixia Diao, Bingying Zhou, Leng Han, Li Wang
Software Mentions: 10
Published: almost 5 years ago
10.1038/s41422-021-00467-z
Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analysesCited by: 44
Author(s): Jian He, Yan Jing, Jianfang Wang, Liangyu Zhao, Xin Qian, Yang Zeng, Yuxi Sun, Han Zhang, Zhijie Bai, Zongcheng Li, Yanli Ni, Yandong Gong, Yunqiao Li, Han He, Zhilei Bian, Yu Lan, Chunyu Ma, Lihong Bian, Heng Zhu, Bing Liu, Rui Yue
Software Mentions: 10
Published: almost 4 years ago
10.1126/sciadv.abc3781
Extensive tissue-specific expression variation and novel regulators underlying circadian behaviorCited by: 21
Author(s): Maria Litovchenko, Antonio C. A. Meireles-Filho, Michael Frochaux, R. Bevers, Alessio Prunotto, Ane Martín Anduaga, Brian Hollis, Vincent Gardeux, Virginie Braman, Julie Russeil, Sebastián Kadener, Matteo Dal Peraro, Bart Deplancke
Software Mentions: 10
Published: almost 4 years ago
10.1534/g3.120.401436
The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid WheatCited by: 18
Author(s): Sophie A Harrington, Anna E Backhaus, Ajit Singh, Keywan Hassani‐Pak, Cristóbal Uauy
Software Mentions: 9
Published: about 4 years ago
10.26508/lsa.202000658
Predicting gene regulatory networks from cell atlasesCited by: 7
Author(s): Andreas Fønss Møller, Kedar Nath Natarajan
Software Mentions: 9
Published: about 4 years ago
10.1371/journal.pcbi.1008223
Causal network inference from gene transcriptional time-series response to glucocorticoidsCited by: 15
Author(s): Jonathan Lu, Bianca Dumitrascu, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt
Software Mentions: 9
Published: almost 4 years ago
10.1371/journal.pcbi.1009029
G2S3: A gene graph-based imputation method for single-cell RNA sequencing dataCited by: 7
Author(s): Weimiao Wu, Yunqing Liu, Qile Dai, Xiting Yan, Zuoheng Wang
Software Mentions: 9
Published: over 3 years ago
10.1186/s12864-021-07659-2
Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suiteCited by: 15
Author(s): Océane Cassan, Sophie Lèbre, Antoine Martin
Software Mentions: 8
Published: over 3 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
10.1093/database/baz046
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing dataCited by: 621
Author(s): Oscar Franzén, Li‐Ming Gan, Johan Björkegren
Software Mentions: 8
Published: almost 6 years ago
10.3233/JAD-170011
Analytical Strategy to Prioritize Alzheimer’s Disease Candidate Genes in Gene Regulatory Networks Using Public Expression DataCited by: 17
Author(s): Shweta Bagewadi Kawalia, Tamara Raschka, Mufassra Naz, Ricardo de Matos Simoes, Philipp Senger, Martin Hofmann-Apitius
Software Mentions: 8
Published: about 7 years ago
10.1038/s41422-018-0053-3
Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysisCited by: 162
Author(s): Xiaoying Fan, Ji Dong, Shaobo Zhong, Wei Yuan, Qian Wu, Liying Yan, Jun Yong, Le Sun, Xiaoye Wang, Yangyu Zhao, Wei Wang, Jie Yan, Xiaoqun Wang, Jie Qiao, Fuchou Tang
Software Mentions: 8
Published: over 6 years ago
10.1186/s12859-016-1235-y
BTR: training asynchronous Boolean models using single-cell expression dataCited 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
10.1038/s41422-020-00412-6
Single-cell transcriptomic atlas of primate cardiopulmonary agingCited by: 76
Author(s): Shuai Ma, Shuhui Sun, Jiaming Li, Yanling Fan, Jing Qu, Liang Sun, Si Wang, Yiyuan Zhang, Shanshan Yang, Zunpeng Liu, Zeming Wu, Sheng Zhang, Qiaoran Wang, Ai Zheng, Shuguang Duo, Yang Yu, Juan Carlos Izpisúa Belmonte, Piu Chan, Qi Zhou, Moshi Song, Weiqi Zhang, Guang Hui Liu
Software Mentions: 7
Published: about 4 years ago
10.1186/s12864-020-07338-8
Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteriaCited by: 10
Author(s): Ilhan Cem Duru, Anne Ylinen, Sergei Belanov, Alan Avila Pulido, Lars Paulín, Petri Auvinen
Software Mentions: 7
Published: almost 4 years ago
10.3389/fpls.2021.661361
Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory NetworksCited by: 2
Author(s): Laura Serrano-Ron, Javier Cabrera, Pablo Pérez-García, Miguel A. Moreno-Risueño
Software Mentions: 7
Published: over 3 years ago
10.1038/s41598-021-87234-7
Discovering key transcriptomic regulators in pancreatic ductal adenocarcinoma using Dirichlet process Gaussian mixture modelCited 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
10.1016/j.ccell.2020.06.004
Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric EpendymomaCited by: 86
Author(s): Johannes Gojo, Bernhard Englinger, Li Jiang, Jens Martin Hübner, McKenzie Shaw, Olivia A. Hack, Sibylle Madlener, Dominik Kirchhofer, Ilon Liu, Jason W. Pyrdol, Volker Hovestadt, Emanuele Mazzola, Nathan D. Mathewson, Maria Trissal, Daniela Lötsch, Christian Dorfer, Christine Haberler, Angela Halfmann, Lisa Mayr, Andreas Peyrl, René Geyeregger, Benjamin Schwalm, Monica Mauermann, Kristian W. Pajtler, Till Milde, Marni E. Shore, Jack Geduldig, Kristine Pelton, Thomas Czech, Orr Ashenberg, Kai W. Wucherpfennig, Orit Rozenblatt-Rosen, Sanda Alexandrescu, Keith L. Ligon, Stefan M. Pfister, Aviv Regev, Irene Slavc, Walter Berger, Mario L. Suvà, Marcel Kool, Mariella G. Filbin
Software Mentions: 7
Published: over 4 years ago
10.18632/oncotarget.27808
Identification of novel prognostic markers of survival time in high-risk neuroblastoma using gene expression profilesCited by: 6
Author(s): Abdulazeez Giwa, Azeez Ayomide Fatai, Junaid Gamieldien, Alan Christoffels, Hocine Bendou
Software Mentions: 7
Published: almost 4 years ago
10.7150/thno.44306
Single-cell Transcriptome Profiling reveals Dermal and Epithelial cell fate decisions during Embryonic Hair Follicle DevelopmentCited by: 39
Author(s): Wei Ge, Shao-Jing Tan, Shan-He Wang, Lan Li, Xiaowen Sun, Wei Shen, Xin Wang
Software Mentions: 7
Published: almost 5 years ago
10.1186/s13073-021-00908-9
scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networksCited by: 16
Author(s): Ting Jin, Peter Rehani, Mufang Ying, Jiawei Huang, Shuang Liu, Panagiotis Roussos, Daifeng Wang
Software Mentions: 7
Published: over 3 years ago
10.1186/s12864-016-3317-7
A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic dataCited by: 32
Author(s): Yongli Hu, Takeshi Hase, Hui Peng Li, Shyam Prabhakar, Hiroaki Kitano, See Ket Ng, Samik Ghosh, Lionel Wee
Software Mentions: 7
Published: almost 8 years ago
10.1371/journal.pone.0111661
How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks?Cited by: 18
Author(s): Djordje Djordjevic, Andrian Yang, Armella Zadoorian, Kevin Rungrugeecharoen, Joshua W. K. Ho
Software Mentions: 6
Published: about 10 years ago
10.1038/s42003-020-01476-1
Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancerCited by: 58
Author(s): Baijun Dong, Juju Miao, Yanqing Wang, Wenqin Luo, Zhongzhong Ji, Huadong Lai, Man Zhang, Xiaomu Cheng, Jinming Wang, Yuxiang Fang, Helen He Zhu, Chee Wai Chua, Liancheng Fan, Yao Zhu, Jiahua Pan, Jia Wang, Wei Xue, Wei‐Qiang Gao
Software Mentions: 6
Published: almost 4 years ago
10.3389/fpls.2019.00698
PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network PropagationCited by: 5
Author(s): Hongryul Ahn, Kyuri Jo, Dabin Jeong, Minwoo Pak, Jihye Hur, Wi Hoon Jung, Sun Kim
Software Mentions: 6
Published: over 5 years ago
10.18632/aging.202718
TMBIM6, a potential virus target protein identified by integrated multiomics data analysis in SARS-CoV-2-infected host cellsCited by: 4
Author(s): Qizheng Han, Junhao Wang, Haihua Luo, Lei Li, Xinya Lu, Aihua Liu, Yongqiang Deng, Yong Jiang
Software Mentions: 6
Published: over 3 years ago
10.3389/fpls.2021.619062
Genome-Wide Identification and Characterization of Potato Long Non-coding RNAs Associated With Phytophthora infestans ResistanceCited by: 5
Author(s): Weilin Cao, Li‐Ming Gan, Chenchen Wang, Xuan Zhao, Mingyu Zhang, Jinyan Du, Shumei Zhou, Changxiang Zhu
Software Mentions: 6
Published: over 3 years ago
10.3389/fnmol.2019.00316
Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria VascularisCited by: 62
Author(s): Soumya Korrapati, Ian Taukulis, Rafal T. Olszewski, Madeline Pyle, Shoujun Gu, Riya Singh, C. M. Griffiths, Daniel Martin, Erich T. Boger, Robert J. Morell, Michael Hoa
Software Mentions: 6
Published: almost 5 years ago
10.1186/s12920-018-0413-3
Genomic analyses based on pulmonary adenocarcinoma in situ reveal early lung cancer signatureCited by: 20
Author(s): Dan Li, William Yang, Yifan Zhang, Jack Yang, Renchu Guan, Dong Xu, Mary Qu Yang
Software Mentions: 6
Published: about 6 years ago
10.1186/s12859-020-03707-y
A sparse Bayesian factor model for the construction of gene co-expression networks from single-cell RNA sequencing count dataCited by: 11
Author(s): Michael Sekula, Jeremy Gaskins, Susmita Datta
Software Mentions: 6
Published: about 4 years ago
10.1002/pld3.279
Gene expression changes occurring at bolting time are associated with leaf senescence in ArabidopsisCited by: 12
Author(s): Will E. Hinckley, Judy A. Brusslan
Software Mentions: 6
Published: about 4 years ago
10.7150/thno.58433
Single-cell transcriptomic profiling provides insights into the toxic effects of Zearalenone exposure on primordial follicle assemblyCited by: 20
Author(s): Yu Tian, Mingyu Zhang, Ai-Hong Zhao, Li Kong, Junjie Wang, Wei Shen, Lan Li
Software Mentions: 6
Published: almost 4 years ago
10.1186/s13059-020-1949-z
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq dataCited by: 173
Author(s): Christian H. Holland, Jovan Tanevski, Javier Perales-Patón, Jan Gleixner, Manu P. Kumar, Elisabetta Mereu, Brian A. Joughin, Oliver Stegle, Douglas A. Lauffenburger, Holger Heyn, Bence Szalai, Julio Sáez-Rodríguez
Software Mentions: 6
Published: over 4 years ago
10.1038/s41422-020-0374-x
Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinomaCited by: 155
Author(s): Yu-Pei Chen, Jianhua Yin, Wenfei Li, Han-Jie Li, Dongping Chen, Cuijuan Zhang, Jiawei Lv, Yaqin Wang, Xiaomin Li, Junyan Li, Panpan Zhang, Ying‐Qin Li, Qing‐Mei He, Xiaojing Yang, Yuan Liu, Ling‐Long Tang, Guan-Qun Zhou, Yan‐Ping Mao, Wei Chen, Ke Xiong, Hongbo Zhang, Shida Zhu, Yong Hou, Ying Sun, Michael Dean, Ido Amit, Kui Wu, Dong-Ming Kuang, Guibo Li, Na Liu
Software Mentions: 6
Published: over 4 years ago
10.1016/j.csbj.2020.06.033
Integration of single-cell multi-omics for gene regulatory network inferenceCited by: 37
Author(s): Xinlin Hu, Yaohua Hu, Fanjie Wu, Ricky Wai Tak Leung, Jing Qin
Software Mentions: 5
Published: almost 5 years ago
10.1038/srep20533
Gene regulatory network inference using fused LASSO on multiple data setsCited by: 114
Author(s): Nooshin Omranian, Jeanne M. O. Eloundou-Mbebi, Bernd Mueller‐Roeber, Zoran Nikoloski
Software Mentions: 5
Published: over 8 years ago
10.1186/s12976-019-0103-7
Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestansCited by: 19
Author(s): Juan Castro, Iván Valdés, Laura González-García, Giovanna Danies, Silvia Cañas, Flávia Vischi Winck, Carlos Eduardo Ñústez, Silvia Restrepo, Diego Mauricio Riaño‐Pachón
Software Mentions: 5
Published: over 5 years ago
10.1186/s12920-016-0202-9
Integrative approach for inference of gene regulatory networks using lasso-based random featuring and application to psychiatric disordersCited by: 5
Author(s): Dongchul Kim, Min-Hee Kang, Ashis Kumer Biswas, Chun Yu Liu, Jean Gao
Software Mentions: 5
Published: over 8 years ago
10.3389/fimmu.2021.670574
Single-Cell Transcriptional Heterogeneity of Neutrophils During Acute Pulmonary Cryptococcus neoformans InfectionCited by: 14
Author(s): M. Elizabeth Deerhake, Estefany Y. Reyes, Shengjie Xu-Vanpala, Mari L. Shinohara
Software Mentions: 5
Published: over 3 years ago
10.1242/dev.184143
A single cell transcriptome atlas of the developing zebrafish hindbrainCited by: 33
Author(s): Monica Tambalo, Richard Mitter, David Wilkinson
Software Mentions: 5
Published: almost 5 years ago
10.1093/jxb/eraa108
Crosstalk between heterotrimeric G protein-coupled signaling pathways and WRKY transcription factors modulating plant responses to suboptimal micronutrient conditionsCited by: 16
Author(s): Tai‐Hsi Wu, Shalini Krishnamoorthi, Honzhen Goh, Richalynn Leong, Amy Catherine Sanson, Daisuke Urano
Software Mentions: 5
Published: over 4 years ago
10.3389/fgene.2021.652623
Construction of Condition-Specific Gene Regulatory Network Using Kernel Canonical Correlation AnalysisCited by: 2
Author(s): Dabin Jeong, Sangsoo Lim, Sangseon Lee, Minsik Oh, Changyun Cho, Hyeju Seong, Wi Hoon Jung, Sun Kim
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pgen.1008156
Transcriptomic basis and evolution of the ant nurse-larval social interactomeCited by: 14
Author(s): Michael Warner, Alexander S. Mikheyev, Timothy A. Linksvayer
Software Mentions: 5
Published: over 5 years ago
10.3389/fcvm.2020.615161
Comprehensive Integration of Single-Cell Transcriptional Profiling Reveals the Heterogeneities of Non-cardiomyocytes in Healthy and Ischemic HeartsCited by: 21
Author(s): Lingfang Zhuang, Lin Lü, Ruiyan Zhang, Kang Chen, Xiaoxiang Yan
Software Mentions: 5
Published: almost 4 years ago
10.1186/s13059-020-02210-0
Single-cell transcriptome profiling of an adult human cell atlas of 15 major organsCited by: 98
Author(s): Shuai He, Lin He Wang, Yang Liu, Yi Qi Li, Hai Tian Chen, Jing Xu, Peng Wan, Guo Wang Lin, Pan Wei, Bo Li, Xiaojun Xia, Dan Wang, Jin Xin Bei, Xiaoshun He, Zhiyong Guo
Software Mentions: 5
Published: almost 4 years ago
10.1186/s12918-018-0547-0
BTNET : boosted tree based gene regulatory network inference algorithm using time-course measurement dataCited by: 30
Author(s): Sungjoon Park, Jung Min Kim, Weon Ho Shin, Sung Won Han, Minji Jeon, Hyun Jin Jang, Ik Soon Jang, Jaewoo Kang
Software Mentions: 5
Published: over 6 years ago
10.3390/cells10082143
Single-Cell Transcriptomics Reveals Core Regulatory Programs That Determine the Heterogeneity of Circulating and Tissue-Resident Memory CD8+ T CellsCited by: 12
Author(s): Yao Chen, Jian Shen, Moujtaba Y. Kasmani, Paytsar Topchyan, Weiguo Cui
Software Mentions: 5
Published: about 3 years ago
10.1371/journal.pone.0251666
PEPN-GRN: A Petri net-based approach for the inference of gene regulatory networks from noisy gene expression dataCited by: 4
Author(s): Deepika Vatsa, Sumeet Agarwal
Software Mentions: 5
Published: over 3 years ago
10.1186/s12859-019-2749-x
Efficient proximal gradient algorithm for inference of differential gene networksCited by: 3
Author(s): Chen Wang, Feng Gao, Georgios B. Giannakis, Gennaro D’Urso, Xiaodong Cai
Software Mentions: 5
Published: over 5 years ago
10.1186/s12870-018-1329-y
Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maizeCited by: 39
Author(s): Ji Huang, Jue-Fei Zheng, Hui Yuan, Karen M. McGinnis
Software Mentions: 5
Published: over 6 years ago
10.1038/s41598-021-96837-z
Partitioning of gene expression among zebrafish photoreceptor subtypesCited by: 20
Author(s): Yohsuke Ogawa, Joseph C. Corbo
Software Mentions: 4
Published: about 3 years ago
10.3389/fimmu.2021.739605
Prednisone Reprograms the Transcriptional Immune Cell Landscape in CNS Autoimmune DiseaseCited by: 3
Author(s): Lin He, Yuehan Gao, Lihui Xie, Rong Wang, Runping Duan, Zhaohuai Li, Binyao Chen, Lei Zhu, Xianggui Wang, Wenru Su
Software Mentions: 4
Published: about 3 years ago
10.1007/s13238-019-0648-6
Core transcriptional signatures of phase change in the migratory locustCited by: 26
Author(s): Pengcheng Yang, Hou Li, Xianhui Wang, Le Kang
Software Mentions: 4
Published: over 5 years ago
10.7717/peerj.6694
Integrated analysis reveals five potential ceRNA biomarkers in human lung adenocarcinomaCited by: 14
Author(s): Yu Liu, Deyao Xie, Zuhua He, Liangcheng Zheng
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pone.0110134
Integrated Exon Level Expression Analysis of Driver Genes Explain Their Role in Colorectal CancerCited by: 20
Author(s): Mohammad Azhar Aziz, Sathish Periyasamy, Zeyad Yousef, Ibrahim AlAbdulkarim, Majed Al Otaibi, Abdulaziz Alfahed, Glowi Alasiri
Software Mentions: 4
Published: about 10 years ago
10.3390/plants10020364
A Systems Biology Approach to Identify Essential Epigenetic Regulators for Specific Biological Processes in PlantsCited by: 5
Author(s): Rachel M. McCoy, Russell Julian, Shoban R V Kumar, Rajeev Ranjan, Kranthi Varala, Ying Liu
Software Mentions: 4
Published: over 3 years ago
10.18632/oncotarget.14286
Comprehensive tissue-specific gene set enrichment analysis and transcription factor analysis of breast cancer by integrating 14 gene expression datasetsCited by: 23
Author(s): Wen‐Xing Li, Kan He, Ling Tang, Shao‐Xing Dai, Gong‐Hua Li, Wen Lv, Yicheng Guo, Sanqi An, Guoying Wu, Dahai Liu, Jing‐Fei Huang
Software Mentions: 4
Published: almost 8 years ago
10.1371/journal.pcbi.1003361
Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory NetworksCited by: 33
Author(s): Takeshi Hase, Samik Ghosh, Ryota Yamanaka, Hiroaki Kitano
Software Mentions: 4
Published: almost 11 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 dataCited by: 27
Author(s): Marilena M. Bourdakou, Emmanouil Athanasiadis, George M. Spyrou
Software Mentions: 4
Published: over 8 years ago
10.1172/jci.insight.141024
Single-cell omics analysis reveals functional diversification of hepatocytes during liver regenerationCited by: 34
Author(s): Tianyi Chen, Seh–Hoon Oh, Simon Gregory, Xiling Shen, Anna Mae Diehl
Software Mentions: 4
Published: almost 4 years ago
10.1002/ece3.6691
Leaf shape in <i>Populus tremula</i> is a complex, omnigenic traitCited by: 17
Author(s): Niklas Mähler, Bastian Schiffthaler, Kathryn M. Robinson, Barbara K Terebieniec, Matej Vučak, Chanaka Mannapperuma, Mark E.S. Bailey, Stefan Jansson, Torgeir R. Hvidsten, Nathaniel R. Street
Software Mentions: 4
Published: about 4 years ago
10.1093/gigascience/gix078
fastBMA: scalable network inference and transitive reductionCited by: 6
Author(s): Ling‐Hong Hung, Kaiyuan Shi, Migao Wu, William Chad Young, Adrian E. Raftery, Ka Yee Yeung
Software Mentions: 4
Published: about 7 years ago
10.7554/eLife.67436
Single-cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenesisCited by: 48
Author(s): Arantxa Cebrián-Silla, Marcos Assis Nascimento, Stephanie Redmond, Benjamin Mansky, David Wu, Kirsten Obernier, Ricardo Romero Rodriguez, Susana González-Granero, José Manuel García‐Verdugo, Daniel A. Lim, Arturo Álvarez-Buylla
Software Mentions: 4
Published: over 3 years ago
10.1186/s12918-017-0440-2
Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample sizeCited 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
10.1128/mSystems.00729-19
Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human InfectionCited by: 7
Author(s): Ryan McClure, Ashwini Sunkavalli, Phillip M. Balzano, Paola Massi, Christine Cho, William M. Nauseef, Michael A. Apicella, Caroline A. Genco
Software Mentions: 4
Published: over 4 years ago
10.1038/s41598-017-17143-1
Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional ChangesCited by: 16
Author(s): Jigar Desai, Ryan C. Sartor, Lovely Mae F Lawas, S. V. Krishna Jagadish, Colleen J. Doherty
Software Mentions: 4
Published: almost 7 years ago
10.15252/embj.2019104159
Deciphering the regulatory landscape of fetal and adult γδ T‐cell development at single‐cell resolutionCited by: 38
Author(s): Sagar, Maria Pokrovskii, Josip Stefan Herman, Shruti Naik, Elisabeth Sock, Patrice Zeis, Ute Lausch, Michael Wegner, Yakup Tanriver, Dan R. Littman, Dominic Grün
Software Mentions: 4
Published: over 4 years ago
10.1186/s12859-018-2217-z
Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression dataCited by: 175
Author(s): Shuonan Chen, Jessica C. Mar
Software Mentions: 4
Published: over 6 years ago
10.3390/biomedicines9010034
Shared Blood Transcriptomic Signatures between Alzheimer’s Disease and Diabetes MellitusCited by: 14
Author(s): Taesic Lee, Hyunju Lee
Software Mentions: 4
Published: almost 4 years ago
10.1186/s12936-021-03848-2
MALBoost: a web-based application for gene regulatory network analysis in Plasmodium falciparumCited by: 0
Author(s): Roelof van Wyk, Riëtte van Biljon, Lyn-Marié Birkholtz
Software Mentions: 4
Published: over 3 years ago
10.1093/bib/bbw139
Gene co-expression analysis for functional classification and gene–disease predictionsCited by: 511
Author(s): Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
Software Mentions: 3
Published: almost 8 years ago
10.1093/bfgp/elx046
Mapping gene regulatory networks from single-cell omics dataCited by: 165
Author(s): Mark Fiers, Liesbeth Minnoye, Sara Aibar, Carmen Bravo González-Blas, Zeynep Kalender Atak, Stein Aerts
Software Mentions: 3
Published: almost 7 years ago
10.3389/fgene.2021.617282
Evaluating the Reproducibility of Single-Cell Gene Regulatory Network Inference AlgorithmsCited by: 19
Author(s): Yoonjee Kang, Denis Thieffry, Laura Cantini
Software Mentions: 3
Published: over 3 years ago
10.7717/peerj-cs.363
MKL-GRNI: A parallel multiple kernel learning approach for supervised inference of large-scale gene regulatory networksCited by: 4
Author(s): Nisar Ahmad Wani, Khalid Raza
Software Mentions: 3
Published: almost 4 years ago
10.3389/fpls.2018.01770
Statistical and Machine Learning Approaches to Predict Gene Regulatory Networks From Transcriptome DatasetsCited by: 45
Author(s): Keiichi Mochida, Satoru Koda, Komaki Inoue, Ryuei Nishii
Software Mentions: 3
Published: almost 6 years ago
10.1186/s12918-017-0419-z
Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimizationCited by: 14
Author(s): Saskia Trescher, Jannes Münchmeyer, Ulf Leser
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pbio.3001025
Single-cell transcriptome landscape of ovarian cells during primordial follicle assembly in miceCited by: 55
Author(s): Jun-Jie Wang, Wei Ge, Qiu-Yue Zhai, Jing-Cai Liu, Xiaowen Sun, Wen-Xiang Liu, Lan Li, Chuzhao Lei, Paul W. Dyce, Massimo De Felici, Wei Shen
Software Mentions: 3
Published: almost 4 years ago
10.3389/fpls.2021.687652
Overcoming the Challenges to Enhancing Experimental Plant Biology With Computational ModelingCited by: 4
Author(s): Renee Dale, S. Oswald, Amogh Prabhav Jalihal, Mary-Francis LaPorte, Daniel McKay Fletcher, Allen Hubbard, Shin-Han Shiu, Andrew D. L. Nelson, Alexander Bucksch
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1007241
Unified feature association networks through integration of transcriptomic and proteomic dataCited by: 6
Author(s): Ryan McClure, Jason P. Wendler, Joshua N. Adkins, Jesica Swanstrom, Ralph S. Baric, Brooke L. Deatherage Kaiser, Kristie Oxford, Katrina M. Waters, Jason McDermott
Software Mentions: 3
Published: about 5 years ago
10.3389/fgene.2019.00535
Inferring Interaction Networks From Multi-Omics DataCited by: 95
Author(s): Johann S. Hawe, Fabian J. Theis, Matthias Heinig
Software Mentions: 3
Published: over 5 years ago
10.1186/s12864-020-07003-0
Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicityCited by: 28
Author(s): Maria Lytrivi, Kassem Ghaddar, Miguel Lopes, Victoria Rosengren, Anthony Piron, Xiaoyan Yi, Henrik J. Johansson, Janne Lehtiö, Mariana Igoillo-Esteve, Daniel Andrade Da Cunha, Lorella Marselli, Piero Marchetti, Henrik Ortsäter, Décio L. Eizirik, Miriam Cnop
Software Mentions: 3
Published: about 4 years ago
10.1186/s12864-021-07940-4
Gene co-expression network analysis in zebrafish reveals chemical class specific modulesCited by: 6
Author(s): Prarthana Shankar, Ryan McClure, Katrina M. Waters, Robyn L Tanguay
Software Mentions: 3
Published: about 3 years ago
10.1371/journal.pcbi.1004103
An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory NetworksCited by: 23
Author(s): Saheed Imam, Daniel R. Noguera, Timothy J. Donohue
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pcbi.1008379
Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samplesCited by: 12
Author(s): Xiaoqiang Sun, Ji Zhang, Qing Nie
Software Mentions: 3
Published: over 3 years ago
10.1186/s12918-018-0637-z
Systems biology analysis reveals new insights into invasive lung cancerCited by: 2
Author(s): Dan Li, William Yang, Carolyn Arthur, Jun S. Liu, Carolina Cruz-Niera, Mary Qu Yang
Software Mentions: 3
Published: almost 6 years ago
10.1534/g3.120.401477
Network Analysis Prioritizes <i>DEWAX</i> and <i>ICE1</i> as the Candidate Genes for Major eQTL Hotspots in Seed Germination of <i>Arabidopsis thaliana</i>Cited by: 5
Author(s): Margi Hartanto, Ronny V.L. Joosen, L. Basten Snoek, Leo A.J. Willems, Mark G. Sterken, Dick de Ridder, Henk W. M. Hilhorst, Wilco Ligterink, Harm Nijveen
Software Mentions: 3
Published: about 4 years ago
10.1093/jmcb/mjy089
Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellumCited by: 34
Author(s): Jian Peng, Ai-Li Sheng, Qi Xiao, Libing Shen, Xiang-Chun Ju, Min Zhang, Siting He, Chao Wu, Zhen-Ge Luo
Software Mentions: 3
Published: almost 6 years ago
10.1111/acel.13428
Single‐oocyte transcriptome analysis reveals aging‐associated effects influenced by life stage and calorie restrictionCited by: 13
Author(s): Tomobumi Mishina, Namine Tabata, Tetsutaro Hayashi, Mika Yoshimura, Mana Umeda, Midori Mori, Yayoi Ikawa, Hiroshi Hamada, Itoshi Nikaido, Tomoya S. Kitajima
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1005703
Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation dataCited by: 32
Author(s): Lingfei Wang, Tom Michoel
Software Mentions: 3
Published: about 7 years ago
10.1038/s12276-020-00528-0
Single-cell network biology for resolving cellular heterogeneity in human diseasesCited by: 66
Author(s): Junha Cha, Insuk Lee
Software Mentions: 2
Published: about 4 years ago
10.1186/s12859-019-2695-7
VIGLA-M: visual gene expression data analyticsCited by: 8
Author(s): Ismael Navas‐Delgado, José García-Nieto, Esteban López-Camacho, Maciej Rybiński, Rocío Lavado, Miguel‐Ángel Berciano‐Guerrero, José F. Aldana‐Montes
Software Mentions: 2
Published: over 5 years ago
10.1186/s12859-019-3042-8
BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessusCited by: 5
Author(s): Patrick M. Staunton, Aleksandra A. Miranda-CasoLuengo, Brendan J. Loftus, Isobel Claire Gormley
Software Mentions: 2
Published: about 5 years ago
10.1186/1471-2105-15-336
Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infectionCited by: 34
Author(s): Zhi Ping Liu, Hulin Wu, Jian Zhu, Hongyu Miao
Software Mentions: 2
Published: about 10 years ago
10.1186/s12859-016-0913-0
Netter: re-ranking gene network inference predictions using structural network propertiesCited by: 8
Author(s): Joeri Ruyssinck, Piet Demeester, Tom Dhaene, Yvan Saeys
Software Mentions: 2
Published: over 8 years ago
10.1186/s12885-015-1884-7
Network analysis of an in vitro model of androgen-resistance in prostate cancerCited by: 2
Author(s): Sujitra Detchokul, Aparna Elangovan, Edmund J. Crampin, Melissa J. Davis, Albert G Frauman
Software Mentions: 2
Published: almost 9 years ago
10.1186/s12864-020-07079-8
Globally learning gene regulatory networks based on hidden atomic regulators from transcriptomic big dataCited by: 1
Author(s): Ming Shi, Sheng Tan, Xueping Xie, Ao Li, Wulin Yang, Tao Zhu, Hongqiang Wang
Software Mentions: 2
Published: about 4 years ago